What Is Bioremediation?

Bioremediation can be defined as any process that uses microorganisms or their enzymes to return the environment altered by contaminants to its original condition. Bioremediation may be employed in order to attack specific contaminants, such as chlorinated pesticides that are degraded by bacteria, or a more general approach may be taken, such as oil spills that are broken down using multiple techniques including the addition of fertilizer to facilitate the decomposition of crude oil by bacteria.

Not all contaminants are readily treated through the use of bioremediation; for example, heavy metals such as cadmium and lead are not readily absorbed or captured by organisms. The integration of metals such as mercury into the food chain may make things worse as organisms bioaccumulate these metals.

However, there are a number of advantages to bioremediation, which may be employed in areas which cannot be reached easily without excavation. For example, hydrocarbon spills (or more specific: gasoline) may contaminate groundwater well below the surface of the ground; injecting the right organisms, in conjunction with oxygen-forming compounds, may significantly reduce concentrations after a period of time. This is much less expensive than excavation followed by burial elsewhere or incineration, and reduces or eliminates the need for pumping and treatment, which is a common practice at sites where hydrocarbons have contaminated groundwater.

Generally, bioremediation technologies can be classified as in situ or ex situ. In situ bioremediation involves treating the contaminated material at the site while ex situ involves the removal of the contaminated material to be treated elsewhere. Some examples of bioremediation technologies are bioventing, land farming, bioreactor, composting, bioaugmentation and biostimulation.

Compost is the decomposed remnants of organic materials (those with plant and animal origins). Compost is used in gardening and agriculture, mixed in with the soil. It improves soil structure, increases the amount of organic matter, and provides nutrients.

Compost is a common name for humus, which is the result of the decomposition of organic matter. Decomposition is performed primarily by microbes, although larger creatures such as worms and ants contribute to the process. Decomposition occurs naturally in all but the most hostile environments, such as buried in landfills or in extremely arid deserts, which prevent the microbes and other decomposers from thriving.

Composting is the controlled decomposition of organic matter. Rather than allowing nature to take its slow course, a composter provides an optimal environment in which decomposers can thrive. To encourage the most active microbes, the compost pile needs the proper mix of the following ingredients:

Carbon Nitrogen Oxygen (air) Water Decomposition happens even in the absence of some of these ingredients, but not nearly as quickly and not nearly as pleasantly (for example, the plastic bag of vegetables in your refrigerator is decomposed by microbes, but the absence of air encourages anaerobic microbes that produce disagreeable odors).

All guidelines for building compost piles have the goal of creating the proper environment for a decomposing ecosystem. The ecosystem in a compost pile is a microcosm of larger ecosystems. The correct environment must be maintained for a healthy and vigorous community of decomposers. In addition to the decomposers that work directly on the organic content of the pile, compost piles provide habitat for those that prey upon direct decomposers. Their waste also becomes part of the process.

The most effective decomposers are bacteria and other microorganisms. Also important are fungi, molds, protozoa, and actinomycetes--which is something between a fungus and a mold and is often seen as white filaments in decomposing organic matter. At a macroscopic level, earthworms, ants, snails, slugs, millipedes, sow bugs, springtails, and others work on consuming and breaking down the organic matter. Centipedes and other predators feed upon these decomposers.

Compost ingredients The goal in a compost pile is to provide a healthy environment--and nutrition--for the rapid decomposers, the bacteria.

The most rapid composting occurs with the ideal ratio--by dry chemical weight--of carbon to nitrogen, from 25-to-1 to 30-to-1. In other words, the ingredients placed in the pile should contain 30 times as much carbon as nitrogen. For example, grass clippings average about 19-to-1 and dry autumn leaves average about 55-to-1. Mixing equal parts by volume approximates the ideal range. Commercial-grade composting operations pay strict attention to this ratio. For backyard composters, however, the charts of carbon and nitrogen ratios in various ingredients and the calculations required to get the ideal mixture can be intimidating, so many rules of thumb exist to guide composters in approximating this mixture.

High-carbon sources provide the cellulose needed by the composting bacteria for conversion to sugars and heat.

High-nitrogen sources provide the most concentrated protein, which allow the compost bacteria to thrive.

Some ingredients with higher carbon content:

Dry, straw-type material, such as cereal straws Autumn leaves Sawdust and wood chips Some paper and cardboard (such as corrugated cardboard or newsprint with soy-based inks) Some ingredients with higher nitrogen content:

Green plant material (fresh or wilted,) such as crop residues, hay, grass clippings, weeds Animal manures (vegetarian, not carnivore) Fruit and vegetable trimmings Seaweeds Poultry manure provides lots of nitrogen but little carbon. Horse manure provides both. Sheep and cattle manure don't drive the compost heap to as high a temperature as poultry or horse manure, so the heap takes longer to produce the finished product.

In an attempt to judge the proper mix of materials, different rules of thumb are available. Some prefer to add one basket full of nitrogen source followed by one basket of carbon source. Mixing the materials as they are added increases the rate of decomposition, but some people prefer to place the materials in alternating layers, approximately 15 cm (6 inches) thick, to help estimate the quantities. Keeping carbon and nitrogen sources separated in the pile can slow down the process but decomposition will occur in any event.

Composting techniques There are two primary methods of aerobic composting:

Active (or hot) composting, which allows the most effective decomposing bacteria to thrive, kills most pathogens and seeds, and rapidly produces usable compost Passive (or cold) composting, which lets nature take its course in a more leisurely manner and leaves many pathogens and seeds dormant in the pile Most commercial and industrial composting operations use active composting techniques. This ensures a higher quality product and produces results in the shortest time (SEE compost windrow turner).

Home composters use a range of techniques varying from extremely passive composting (throw everything in a pile in a corner and leave it alone for a year or two) to extremely active (monitoring the temperature, turning the pile regularly, and adjusting the ingredients over time) and combinations of both.

Some composters use mineral powders to absorb smells, although a well-maintained pile seldom has bad odors.

Microbes and heating the pile An effective compost pile is kept about as damp as a well wrung-out sponge. This provides the moisture that all life needs to survive; in a compost pile, it provides an environment in which microbes can begin to do their work. Bacteria and other microorganisms fall into a variety of groups in terms of what their ideal temperature is and how much heat they generate as they do their work. Mesophilic bacteria enjoy midrange temperatures, from about 20 to 40 °C (70 to 110 °F). As they decompose the organic matter, they generate heat, and the inner part of a compost pile heats up the most.

The heap should be about 1 m (3 ft) wide, 1 m (3 ft) tall, and as long as is practicable – the advantage to making the heap at least 1 mł (1 ydł) is that it provides suitable insulating mass to allow a good heat build-up as the material decays. The ideal temperature range hovers around 60 °C (140 °F), which kills most pathogens and weed seeds and also provides a suitable environment for thermophilic (heat-loving) bacteria, which are the fastest acting decomposers. The centre of the heap should get quite warm, possibly hot enough to burn a bare hand. If this fails to happen, common reasons include the following:

The heap is too wet, thus excluding the oxygen required by the compost bacteria The heap is too dry, so that the bacteria do not have the moisture needed to survive and reproduce There is insufficient protein (nitrogen rich material) The solution is to add material, if necessary, and/or to turn the pile to aerate it.

Depending on how quickly the compost is required, the heap can be turned one or more times to bring the outer layers to the inside of the heap and vice versa, as well as to aerate the mixture. Adding water at this time keeps the pile as damp as a wrung-out sponge. One guideline is to turn the pile when the high temperature has begun to drop, indicating that the food source for the fastest-acting bacteria (in the center of the pile) has been largely consumed. After the temperature stops rising after the pile has been turned, there is no further advantage in turning the pile. When all the material has become barely recognisable from the original ingredients, turning into dark brown or nearly black crumbly matter, it's ready to use. Some practitioners like to leave the compost to mature further for up to a year as this seems to make the benefits of compost last longer.

Bioaugmentation refers to the introduction of a group of natural microbial strain or a genetically engineered variant so as to achive bioremediation.

Usually the step involves studying the indigenous varieties present in the location. If the indigenous variety do not have the metabolic machinery that can do the remediation process, exogenous varieties with such sophisticated pathways are introduced.

Remediation is the removal of pollution or contaminants from land (including sediments in waterways) for the general protection of the environment or, quite commonly, from a brownfield site so that it can be reused. The reuse of brownfield sites is part of the urban consolidation movement and allows the regeneration of decaying former industrial areas, sometimes for industry, but often for high density housing, particulalry in areas of scenic beauty (along Harbours and rivers) and close to the CBD of a city or major transport infrastructure such as railway stations.

Remediation is generally subject to an array of legislation, and is based on assessments of health and ecological risks where there are no legislated standards or where standards are advisory (often called preliminary remediation goals (PRG)s).

Remediation in terms of new media, is the representation of one medium in another. (Jay David Bolter and Richard Grusin 1999)

In the USA the most comprehensive set of PRG's is from the EPA Region 9, although the Canadian EPA also has a comprehensive spreadsheet of PRG's. There is also a set of standard used in Europe commonly called the Dutch standards. The EU is rapidly moving towards European wide standards, although most of the industrialised nations in Europe have their own standards at present

Site assessment Once a site is suspected of being seriously contaminated there is a need to assess it. The historical use of the site and the materials used and produced on site will guide the assessment strategy and nature of sampling and chemical testing to be done. Often nearby sites owned by the same company or which are nearby and have been reclaimed, levelled or filled are also contaminated even where the current land use seems innocuous. For example, the car park may have been levelled by using contaminated waste in the fill. It is also important to consider off site contamination or nearby sites often through decades of emissions to soil, water, and air. Ceiling dust, topsoil, surface and groundwater of nearby properties should be tested both before and after the remediation. This is a controversial step as:

No one wants to have to pay for the clean up of the site; If nearby properties are found to be contaminated it may have to be noted on their property title, potentially affecting saleability or value; No one wants to pay for the cost of assessment. Often corporations which do voluntary testing of their sites are protected from the reports to environmental agencies becoming public under Freedom of Information Acts, however a Freedom Of Information inquiry will often produce other documents that are not protected or will produce references to the reports.

Funding remediation In the US there has been a mechanism for taxing polluting industries to form a Superfund to remediate abandoned sites, or to litigate to force corporations to remediate their contaminated sites. Other countries have other mechanisms and commonly sites are rezoned to "higher" uses such as high density housing, to give the land a higher value so that after deducting clean up costs there is still an incentive for a developer to purchase the land, clean it up, redevelop it and sell it on, often as apartments (home units).

Remediation technologies Remediation technologies are many and varied. The best source of information is probably http://www.clu-in.org/

Some technologies are controversial, particularly anything involving relative low temperature incineration because of the risks of dioxins released in the atmosphere through the exhaust gases. For this reason remediation proponents often use terminolgy like thermal oxidiser and direct thermal desorption to minimise the risk of the community thinking about incineration risks. However, controlled, high temperature incineration with filtering of exhaust gases should not pose any risks.

The treatment of environmental problems through biological means is known as bioremediation and the specific use of plants is known as phytoremediation.

For an example of a complete rezoning by a state government over the opposition of local government and local communities of former chemical plants to fund remediation to allow for redevelopment for high density residential, retail and office development in Australia see http://rhodesnsw.org

In this case the proposed rezoning, remediation and redevelopment has a wealth of material available through the internet from:

List of sources of publicly available material, most accessible through the internet and from http://rhodesnsw.org: Numerous investigations and reports by Australian and International consultants For the former Union Carbide site, a previous remediation by excavation and containment in a clay capped sarcophagus, separated from the Bay by a bentonite wall. A Parliamentary Inquiry by the Upper House of the Parliament of New South Wales, a state of Australia; Two Commissions of Inquiry, one for each of the major dioxin contaminated sites, both contaminated by the operations of Union Carbide; Resolutions by the relevant local government bodies (originally Concord council and after the Municipality of Concord was merged with Drummoyne Council to form the City of Canada Bay, by that Council); Campaigns by local residents' groups, Greenpeace Australia, Nature Conservation Council of NSW, and Inner West (of Sydney branch of the) Greens published submissions by Planning NSW and Environmental Protection Agency of NSW; Comprehensive Environmental Impact studies published in digital format and available on CD from Planning NSW. This rezoning, remediation and redevelopment of land contaminated by Union Carbide, ICI and others also involves the remediation of a strip of dioxin contaminated sediments in Homebush Bay, New South Wales. The Homebush Bay area was home to the main events of the Sydney 2000 Summer Olympics. The sediments were dealt with in the Commission of Inquiry into the Lednez site formerly owned by Union Carbide, but not to the satisfaction of local community activists.

The remediation of Homebush Bay is important because of its impact on the food chain which extends through benthos not only to local protected and threatened species of birds, but also to JAMBA and CAMBA protected species and species which use other RAMSAR protected wetlands. Ultimately human health is impacted through the food chain. Homebush Bay has a complete fishing ban, there is a commercial fin fishing ban west of the Gladesville Bridge, and based on submissions of the remediator and NSW Waterways and EPA the complete fishing ban ought be extended to the whole of the Parramatta River west of Homebush Bay and at least as far East as the Ryde Traffic Bridge.

Phytoremediation is the technical term used to describe the treatment of environmental problems through the use of plants.

Certain plants are able to extract hazardous substances such as arsenic, lead and uranium from soil and water. One example is alpine pennycress, a plant which naturally accumulates high levels of cadmium and zinc from the environment. Alpine pennycress is therefore known as a hyperaccumulator of these metals, which in unnaturally high levels would be poisonous to many plants. Another example of a hyperaccumulator is the bracken fern. This fern extracts arsenic from the soil at a much greater rate than other plants. This arsenic is stored in the fern's leaves at as much as 200 times that present in the soil, thus enabling effective and practical clean-up programs. Sunflowers were also used to clean up uranium near Chernobyl.

Breeding programs and genetic engineering are powerful methods for enhancing natural tendencies of plant, or for introducing these tendencies into alternative types of plant which might be more suitable for the environmental conditions.

The range of biological treatments for environmental problems, as described by the term phytoremediation, actually consists of several specific processes:

Phytoextraction - Uptake of substances from the environment, with storage in the plant (phytoaccumulation). Phytostabilisation - Reducing the movement or transfer of substances in the environment. For example, limiting the leaching of substances contaminating soil. Phytostimulation - Enhancement of microbial activity for the degradation of contaminants, typically around plant roots. Phytotransformation - Uptake of substances from the environment, with degradation occurring within the plant (phytodegradation). Phytovolatilization - Removal of substances from the soil or water with release into the air, possibly after degradation. Rhizofiltration - The removal of toxic metals from ground water.

Chemosphere, 2004 Dec, 57(10), 1439 - 47
Study on the possibility of hydrogen peroxide pretreatment and plant system to remediate soil pollution; Lin Q et al.; Hydrogen peroxide was widely selected as the chemical oxidant in chemical remediation or as the donor of oxygen in in situ aerobic bioremediation of organic pollutants . In this paper, hydrogen peroxide pretreatment and plant system was done to examine its possibility to remediate the heavy metal contaminated soil or heavy metal-organic combined contaminated soil . Heavy metal contaminated soil was collected from the heavily industrialized area, in Fuyang county, Zhejiang province, China . And heavy metal-organic combined contaminated soil was prepared from the same contaminated soil by spiking 100 microg g(-1) 2,4-dichlorophenol (2,4-DCP) . Results showed that H2O2 could improve the dissipation of 2,4-DCP and enhance the availability of Cu and Zn in soil . The greatly increased DOC (dissolved organic carbon) in the oxidation process was probably the main reason for the greatly increased water soluble Cu in higher pH condition . Water soluble Zn, however, easily rebound to soil components with the time being and had no positive relation with dissolved organic carbon . Planting with ryegrass influenced the behavior of pollutants in soil . It was observed that the dissipation of 2,4-DCP could be enhanced by the presence of plant roots and the availability of Cu and Zn in the planted soil was changed due to the mobilization and rebound mechanisms in the rhizosphere . Co-contamination of 2,4-DCP caused the greater availability of Cu and Zn in H2O2 pretreatment . But with the ryegrass planting, it was easier to rebound to the less available phase in the rhizosphere . Both Cu and Zn concentration in shoots increased with the H2O2 treatment . Therefore our results suggested that H2O2 pretreatment was probably a promising way for promoting the dissipation of persistent organic pollutants and enhancing the solubility of Cu and Zn in soil . A combination of H2O2 pretreatment and suitable plant might be an efficient alternative for remedying heavy metal or heavy metal-organic contaminated soil.

Adv Microb Physiol, 2004, 49, 219 - 86
Dissimilatory Fe(III) and Mn(IV) reduction; Lovley DR et al.; Dissimilatory Fe(III) and Mn(IV) reduction has an important influence on the geochemistry of modern environments, and Fe(III)-reducing microorganisms, most notably those in the Geobacteraceae family, can play an important role in the bioremediation of subsurface environments contaminated with organic or metal contaminants . Microorganisms with the capacity to conserve energy from Fe(III) and Mn(IV) reduction are phylogenetically dispersed throughout the Bacteria and Archaea . The ability to oxidize hydrogen with the reduction of Fe(III) is a highly conserved characteristic of hyperthermophilic microorganisms and one Fe(III)-reducing Archaea grows at the highest temperature yet recorded for any organism . Fe(III)- and Mn(IV)-reducing microorganisms have the ability to oxidize a wide variety of organic compounds, often completely to carbon dioxide . Typical alternative electron acceptors for Fe(III) reducers include oxygen, nitrate, U(VI) and electrodes . Unlike other commonly considered electron acceptors, Fe(III) and Mn(IV) oxides, the most prevalent form of Fe(III) and Mn(IV) in most environments, are insoluble . Thus, Fe(III)- and Mn(IV)-reducing microorganisms face the dilemma of how to transfer electrons derived from central metabolism onto an insoluble, extracellular electron acceptor . Although microbiological and geochemical evidence suggests that Fe(III) reduction may have been the first form of microbial respiration, the capacity for Fe(III) reduction appears to have evolved several times as phylogenetically distinct Fe(III) reducers have different mechanisms for Fe(III) reduction . Geobacter species, which are representative of the family of Fe(III) reducers that predominate in a wide diversity of sedimentary environments, require direct contact with Fe(III) oxides in order to reduce them . In contrast, Shewanella and Geothrix species produce chelators that solubilize Fe(III) and release electron-shuttling compounds that transfer electrons from the cell surface to the surface of Fe(III) oxides not in direct contact with the cells . Electron transfer from the inner membrane to the outer membrane in Geobacter and Shewanella species appears to involve an electron transport chain of inner-membrane, periplasmic, and outer-membrane c-type cytochromes, but the cytochromes involved in these processes in the two organisms are different . In addition, Geobacter species specifically express flagella and pili during growth on Fe(III) and Mn(IV) oxides and are chemotactic to Fe(II) and Mn(II), which may lead Geobacter species to the oxides under anoxic conditions . The physiological characteristics of Geobacter species appear to explain why they have consistently been found to be the predominant Fe(III)- and Mn(IV)-reducing microorganisms in a variety of sedimentary environments . In comparison with other respiratory processes, the study of Fe(III) and Mn(IV) reduction is in its infancy, but genome-enabled approaches are rapidly advancing our understanding of this environmentally significant physiology.

J Bacteriol, 2004 Nov, 186(22), 7796 - 803
Global transcriptome analysis of the heat shock response of Shewanella oneidensis; Gao H et al.; Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities . However, the genetic basis and regulatory mechanisms underlying the ability of S . oneidensis to survive and adapt to various environmentally relevant stresses is poorly understood . To define this organism's molecular response to elevated growth temperatures, temporal gene expression profiles were examined in cells subjected to heat stress by using whole-genome DNA microarrays for S . oneidensis . Approximately 15% (n = 711) of the total predicted S . oneidensis genes (n = 4,648) represented on the microarray were significantly up- or downregulated (P < 0.05) over a 25-min period after shift to the heat shock temperature . As expected, the majority of the genes that showed homology to known chaperones and heat shock proteins in other organisms were highly induced . In addition, a number of predicted genes, including those encoding enzymes in glycolysis and the pentose cycle, serine proteases, transcriptional regulators (MerR, LysR, and TetR families), histidine kinases, and hypothetical proteins were induced . Genes encoding membrane proteins were differentially expressed, suggesting that cells possibly alter their membrane composition or structure in response to variations in growth temperature . A substantial number of the genes encoding ribosomal proteins displayed downregulated coexpression patterns in response to heat stress, as did genes encoding prophage and flagellar proteins . Finally, a putative regulatory site with high conservation to the Escherichia coli sigma32-binding consensus sequence was identified upstream of a number of heat-inducible genes.

Environ Sci Pollut Res Int, 2004, 11(5), 340 - 6
Phytoremediation of petroleum hydrocarbons in tropical coastal soils . II . Microbial response to plant roots and contaminant; Jones RK et al.; GOAL, SCOPE AND BACKGROUND: The goal of this study was to understand the interaction between plants and microorganisms during petroleum-hydrocarbon bioremediation in Pacific Islands coastal soils . Total bacteria and hydrocarbon-degrading microorganisms population dyanamics were examined in the rhizospheres of tropical trees and shrubs, which were evaluated for their phytoremediation potential in a greenhouse experiment . The respective and combined effects of plant roots and diesel contaminant on the microbial populations were determined in relation to diesel fuel depletion . An increase in the grading populations size of the hydrocarbon-degrading populations of microbes, elicited by rhizodeposition, is generally regarded as conducive to an enhanced degradation of petroleum hydrocarbon pollutants in vegetated soil . METHODS: The soil was a coastal sandy loam (pH 7.8) which was artificially contaminated with 10 g of No . 2 diesel fuel/kg soil or left uncontaminated . The pots were irrigated with fertilizer and 1% NaCl . The enumerations were carried out in the contaminated and uncontaminated rhizospheres of three trees, kiawe (Prosopis pallida), milo (Thespesia populnea), and kou (Cordia subcordata) and three shrubs, beach naupaka (Scaevola sericea), false sandalwood (Myoporum sandwicense), and oleander (Nerium oleander) . Unplanted control soils were included in the experiment . Total bacteria and phenanthrene-degrading bacteria were enumerated on plates . Diesel- and pristane-degrading microorganisms were enumerated by the most-probable-number technique in tissue-culture plates . RESULTS AND DISCUSSION: All four types of microorganisms responded to the rhizosphere of the 6 plants in uncontaminated soil and to the diesel contaminant in unplanted soil . In contaminated rhizospheres, no effect of the plant on the hydrocarbon-degrader numbers was visible . Total bacteria responded more to the plant roots than to the contaminant . The phenanthrene-degrading bacteria and pristane-degrading microorganisms were more influenced by the contaminant than by the plants . The diesel-degrading microorganisms were equally stimulated by the plants and the contaminant . The numbers of hydrocarbon degraders were similar in the contaminated rhizospheres of the three effective plants (kiawe, kou, and milo) and in those of the three ineffective shrubs . CONCLUSION: The results suggest the quality of the rhizodeposition is plant-dependent and governs the type of diesel-degrader populations that will be enhanced by a given plant . RECOMMENDATIONS AND OUTLOOK: In the proposed phytoremediation-benefit model plant roots maintain high levels of hydrocaron degraders in uncontaminated soil . When the root enters a contaminated zone of soil, those hydrocarbon degraders that prefer the contaminant would switch to the contaminant as a carbon source, effectively removing the hydrocarbons . If the root exudates and the contaminant are equally attractive to the hydrocarbon degraders, the contaminant degradaton would be less effective.

Chemosphere, 2004 Dec, 57(9), 1079 - 89
An evaluation of surfactant foam technology in remediation of contaminated soil; Wang S et al.; Soil contamination is notoriously difficult to treat because the contaminants are often tightly bound to the soil particles . Conventional remediation technologies are becoming less popular due to the high treatment costs . This paper gives a comprehensive overview and evaluation of an emerging promising alternative, surfactant foam technology . Different from other approaches, surfactant foam technology may be designed either to remove contaminants or/and simultaneously act as an augmentation for the existing technologies such as pump-and-treat systems and bioremediation processes to improve the contaminant removal efficiency and cost effectiveness . Encouraging results were achieved from laboratory and field demonstrations . However, as an innovative technology, there are many factors to be investigated with the future development . Special attention is paid to the selection of the most appropriate foaming surfactant and surfactant concentration, which are critical to the success of the implementation of the remediation process and have significant effects on the treatment costs . Moreover, development of predictive mathematical models in for future research is helpful to optimize the remediation process.

FEMS Microbiol Lett, 2004 Nov 1, 240(1), 49 - 53
Microbial degradation of the organophosphate pesticide, Ethion; Foster LJ et al.; The organophosphate pesticide, Ethion, remains a major environmental contaminant in rural Australia and poses a significant threat to environmental and public health . The aerobic degradation of Ethion by mesophilic bacteria isolated from contaminated soils surrounding disused cattle dip sites was investigated . Two isolates, identified as Pseudomonas and Azospirillum species, were capable of biodegrading Ethion when cultivated in minimal salts medium . The abiotic hydrolytic degradation products of Ethion such as Ethion Dioxon and O,O-diethylthiosphosphate were not detected . The data suggest the rapid degradation of Ethion to support microbial growth . The results have implications for the development of a bioremediation strategy.

Crit Rev Biotechnol, 2004, 24(2-3), 85 - 95
Mechanisms prevalent during bioremediation of wastewaters from the pulp and paper industry; van Driesser B et al.; Bioremediation of wastewaters represents an important treatment methodology, especially when examined against the backdrop of ever-stricter legislation that is evolving in order to regulate effluent release into the environment . It has been reported that bioremediation specifically holds promise in solving environmental problems . Crucial questions surrounding the treatment of effluents include: efficiency of the process, economic feasibility, legal requirements, and the mechanisms involved in the remediation process . Of all these issues mentioned, the last requires special attention . This paper investigates these matters and focuses on techniques that are currently employed to determine the efficiency of bioremediation and mechanisms involved therein . The physiological significance of biosorption is also examined, as this subject has not been fully addressed in previous publications.

Int Microbiol, 2004 Sep, 7(3), 173 - 80
Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility; Diaz E; Although most organisms have detoxification abilities (i.e mineralization, transformation and/or immobilization of pollutants), microorganisms, particularly bacteria, play a crucial role in biogeochemical cycles and in sustainable development of the biosphere . Next to glucosyl residues, the benzene ring is the most widely distributed unit of chemical structure in nature, and many of the aromatic compounds are major environmental pollutants . Bacteria have developed strategies for obtaining energy from virtually every compound under oxic or anoxic conditions (using alternative final electron acceptors such as nitrate, sulfate, and ferric ions) . Clusters of genes coding for the catabolism of aromatic compounds are usually found in mobile genetic elements, such as transposons and plasmids, which facilitate their horizontal gene transfer and, therefore, the rapid adaptation of microorganisms to new pollutants . A successful strategy for in situ bioremediation has been the combination, in a single bacterial strain or in a syntrophic bacterial consortium, of different degrading abilities with genetic traits that provide selective advantages in a given environment . The advent of high-throughput methods for DNA sequencing and analysis of gene expression (genomics) and function (proteomics), as well as advances in modelling microbial metabolism in silico, provide a global, rational approach to unravel the largely unexplored potentials of microorganisms in biotechnological processes thereby facilitating sustainable development.

Curr Microbiol, 2004 Nov, 49(5), 321 - 6
Effect of chromium(VI) action on Arthrobacter oxydans; Asatiani NV et al.; Arthrobacter species is of interest because of its high potential for bioremediation . Bacteria can detoxify chromium, by either reduction or accumulation inside the bacteria and/or absorption of chromium(VI) (CrVI) on their surface, and efflux pump . The possible pathway of Cr(VI) reduction by Arthrobacter oxydans isolated from Columbia basalt rocks at a US DOE highly contaminated site (USA) has been considered in the present study . FTIR absorption spectroscopy showed that these bacteria reduce Cr(VI) . In the present study the threshold Cr(VI) nontoxic concentration (35 microg/mL) for A . oxydans growing in liquid medium was estimated . Complete uptake of this concentration was achieved in about 10 days after chromium addition into the medium . At this concentration an increase in the protein isolated from the cell wall of A . oxydans was observed . This increased protein predominated independently of the growth phase at which Cr(VI) was added . Thermal analysis was used to identify any influence of Cr(VI) on the DNP complex of A . oxydans . According to the data obtained it can be supposed that Cr(VI) reduction predominantly occurs on the bacterial surface and that cell wall represents a permeable barrier for these bacteria at the non-toxic chromium action.

J Environ Sci Health A Tox Hazard Subst Environ Eng, 2004 Aug, 39(9), 2465 - 72
Effects of crude oil, oil components, and bioremediation on plant growth; Baek KH et al.; The phytotoxic effects of crude oil and oil components on the growth of red beans (Phaseolus nipponesis OWH1) and corn (Zea mays) was investigated . In addition, the beneficial effects of bioremediation with the oil-degrading microorganism, Nocardia sp . H17-1, on corn and red bean growth in oil-contaminated soil was also determined . It was found that crude oil-contaminated soil (10,000mg/kg) was phytotoxic to corn and red beans . In contrast, obvious phytotoxicity was not observed in soils contaminated with 0-1000 mg/kg of aliphatic hydrocarbons such as decane (C10) and eicosane (C20) . Phytotoxicity was observed in soils contaminated with 10-1000mg/kg of the poly aromatic hydrocarbons (PAHs) naphthalene, phenanthrene, and pyrene . It was observed that phytotoxicity increased with the number of aromatic rings, and that corn was more sensitive than red beans to PAH-contaminated soil . Bioremediation with Nocardia sp . H17-1 reduced phytotoxicity more in corn than in red bean, suggesting that this microbial species might degrade PAHs to some degree.

Biodegradation, 2004 Aug, 15(4), 261 - 74
Does bioavailability limit biodegradation? A comparison of hydrocarbon biodegradation and desorption rates in aged soils; Huesemann MH et al.; In order to determine whether bioavailability limits the biodegradability of petroleum hydrocarbons in aged soils, both the biodegradation and abiotic desorption rates of PAHs and n-alkanes were measured at various time points in six different aged soils undergoing slurry bioremediation treatment . Alkane biodegradation rates were always much greater than the respective desorption rates, indicating that these saturated hydrocarbons apparently do not need to be dissolved into the aqueous phase prior to metabolism by soil microorganisms . The biodegradation of PAHs was generally not mass-transfer rate limited during the initial phase, while it often became so at the end of the treatment period when biodegradation rates equaled abiotic desorption rates . However, in all cases where PAH biodegradation was not observed or PAH removal temporarily stalled, bioavailability limitations were not deemed responsible for this recalcitrance since these PAHs desorbed rapidly from the soil into the aqueous phase . Consequently, aged PAHs that are often thought to be recalcitrant due to bioavailability limitations may not be so and therefore may pose a greater risk to environmental receptors than previously thought.

Biotechnol Prog, 2004 Sep-Oct, 20(5), 1567 - 71
Bioremediation of organophosphorus pesticides by surface-expressed carboxylesterase from mosquito on Escherichia coli; Zhang J et al.; The insecticide resistance-associated esterase, carboxylesterase B1 (CaE B1), from mosquito was used to degrade the organophosphorus compounds . To eradicate the need for enzyme purification and minimize the resistance to mass transport of the substrate and product across the cell membranes, the CaE B1 was displayed on the cell surface of Escherichia coli fused to the C-terminus of the ice nucleation protein (INP) . The presence of CaE B1 on the bacterial cell surface was verified by SDS-PAGE, Western blotting analysis, and immunofluorescence microscopy . More than 50% of active CaE B1 is exported across the membrane and anchored onto the cell surface as determined by proteinase accessibility and cell fractionation experiments . In contrast, only a 6% drop in activity for proteinase K-treated cells was detected from E.coli cells containing pET-B1 . From the degradation experiment, more than 80% of the malathion was degraded by whole cells containing plasmid pUC-NC-B1 . Constitutive expression of CaE B1 on the surface using INPNC resulted in no cell lysis, and the suspended cultures also exhibited good stability . Because of their high biodegradation activity and superior stability, these "live biocatalysts" are promising for detoxification of organophosphorus pesticides.

Biotechnol Bioeng, 2004 Oct 20, 88(2), 214 - 23
Effects of humic substances and soya lecithin on the aerobic bioremediation of a soil historically contaminated by polycyclic aromatic hydrocarbons (PAHs); Fava F et al.; The high hydrophobicity of polycyclic aromatic hydrocarbons (PAHs) strongly reduces their bioavailability in aged contaminated soils, thus limiting their bioremediation . The biodegradation of PAHs in soils can be enhanced by employing surface-active agents . However, chemical surfactants are often recalcitrant and exert toxic effects in the amended soils . The effects of two biogenic materials as pollutant-mobilizing agents on the aerobic bioremediation of an aged-contaminated soil were investigated here . A soil historically contaminated by about 13 g kg(-1) of a large variety of PAHs, was amended with soya lecithin (SL) or humic substances (HS) at 1.5% w/w and incubated in aerobic solid-phase and slurry-phase reactors for 150 days . A slow and only partial biodegradation of low-molecular weight PAHs, along with a moderate depletion of the initial soil ecotoxicity, was observed in the control reactors . The overall removal of PAHs in the presence of SL or HS was faster and more extensive and accompanied by a larger soil detoxification, especially under slurry-phase conditions . The SL and HS could be metabolized by soil aerobic microorganisms and enhanced the occurrence of both soil PAHs and indigenous aerobic PAH-degrading bacteria in the reactor water phase . These results indicate that SL and HS are biodegradable and efficiently enhance PAH bioavailability in soil . These natural surfactants significantly intensified the aerobic bioremediation of a historically PAH-contaminated soil under treatment conditions similar to those commonly employed in large-scale soil bioremediation.

Biotechnol Bioeng, 2004 Oct 5, 88(1), 111 - 20
Effects of cyclodextrins, humic substances, and rhamnolipids on the washing of a historically contaminated soil and on the aerobic bioremediation of the resulting effluents; Berselli S et al.; Nontoxic and biodegradable pollutant-mobilizing agents, instead of chemical surfactants, were tested in the washing of an actual-site chloroaromatic-contaminated soil . A soil historically contaminated by chlorinated anilines and benzenes, thiophenes and several polycyclic aromatic hydrocarbons was subjected to washing by suspending it (15% w/v) in water or in water with 1.0% (w/v) beta-clodextrin (beta-CD), hydroxypropyl-beta-cyclodextrin (HP-beta-CD), rhamnolipid (RL), dissolved humic substances (HS), or Triton X-100 (TX) in shaken batch reactors for 24 hr . The resulting wastewaters were amended with nutrients and treated aerobically in shaken reactors for 65 days . The biogenic agents markedly enhanced (by 237%, beta-CD; 265%, HP-beta-CD; 400%, RL; 566%, HS) the capability of water of eluting organic pollutants from the soil . TX enhanced the overall pollutant removal by about 660%; however, a lower depletion of the initial soil ecotoxicity, along with a more extensive impact on the soil organic matter, was observed . Furthermore, TX adversely affected the bioremediation of the resulting effluent by apparently inducing a premature decrease of specialized bacterial biomass . By contrast, the biogenic agents, and in particular HS and RL, sustained the biodegradation and dechlorination of pollutants by apparently enhancing the availability of specialized bacteria in the reactors . Thus, the biogenic agents proposed here seem to be promising nontoxic and nonaggressive soil washing agents for the integrated physicochemical (washing) and biological (aerobic posttreatment) restoration of poorly bioremediable (chloro) organics-contaminated soils.

Water Res, 2004 Nov, 38(18), 3869 - 80
A reactor model for pulsed pumping groundwater remediation; Tenney CM et al.; A hybrid in situ bioremediation/pulsed pumping strategy has been developed to cost effectively remediate a carbon tetrachloride plume in Schoolcraft, Michigan . The pulsed pumping system uses a line of alternating injection and extraction wells perpendicular to the direction of natural groundwater flow . The wells pump periodically to clean the recirculation zone between adjacent wells . During the pump-off phase, natural groundwater flow brings new contaminant into the recirculation zone . The wells are pumped again prior to breakthrough of contaminant from the recirculation zone . A computationally efficient reactor model has been developed, which conceptually divides the aquifer into injection, extraction, and recirculation zones, which are represented by a network of chemical reactors . Solute concentration histories from three-dimensional finite difference simulations and from field data confirm the reactor model predictions . The reactor model is used to investigate the optimal well configuration, pumping rate, and pumping schedule for achieving maximum pollutant degradation.

J Mol Biol, 2004 Oct 1, 342(5), 1519 - 31
The structure of Rigidoporus lignosus Laccase containing a full complement of copper ions, reveals an asymmetrical arrangement for the T3 copper pair; Garavaglia S et al.; Laccase is a multicopper blue oxidase that couples the four-electron reduction of oxygen with the oxidation of a broad range of organic substrates, including phenols and arylamines . The enzyme is the object of intense biotechnological research, due to its employment in bioremediation of soils and water as well as in other biotechnological applications . We report here the cDNA and protein sequences, the post-translational modifications, the crystallization and X-ray structure determination of a laccase from the white-rot fungus Rigidoporus lignosus . The amino acid residues sequence deduced from cDNA clearly identified a pre-sequence of 21 residues representing the signal for extra-cellular localization . Mass spectrometry analysis performed on the salvage enzyme, confirmed the deduced sequence and precisely mapped two glycosylation sites at Asn337 and Asn435, determining the nature of the bound glycosidic moieties . The crystal structure was determined at 1.7A resolution from perfectly hemihedrally twinned crystals, by molecular replacement technique . While the overall structure closely resembled those reported for other fungal laccases, the analysis of the T2/T3 trinuclear cluster revealed an unprecedented coordination sphere for the T3 copper pair . No bridging oxygen ligand was present between the two T3 copper ions, which were no longer symmetrically coordinated . The observed structure could represent an intermediate along the process of four-electron reduction of oxygen to water taking place at the trinuclear copper cluster.

Microbiol Mol Biol Rev, 2004 Sep, 68(3), 474 - 500, table of contents
Bacterial transcriptional regulators for degradation pathways of aromatic compounds; Tropel D et al.; Human activities have resulted in the release and introduction into the environment of a plethora of aromatic chemicals . The interest in discovering how bacteria are dealing with hazardous environmental pollutants has driven a large research community and has resulted in important biochemical, genetic, and physiological knowledge about the degradation capacities of microorganisms and their application in bioremediation, green chemistry, or production of pharmacy synthons . In addition, regulation of catabolic pathway expression has attracted the interest of numerous different groups, and several catabolic pathway regulators have been exemplary for understanding transcription control mechanisms . More recently, information about regulatory systems has been used to construct whole-cell living bioreporters that are used to measure the quality of the aqueous, soil, and air environment . The topic of biodegradation is relatively coherent, and this review presents a coherent overview of the regulatory systems involved in the transcriptional control of catabolic pathways . This review summarizes the different regulatory systems involved in biodegradation pathways of aromatic compounds linking them to other known protein families . Specific attention has been paid to describing the genetic organization of the regulatory genes, promoters, and target operon(s) and to discussing present knowledge about signaling molecules, DNA binding properties, and operator characteristics, and evidence from regulatory mutants . For each regulator family, this information is combined with recently obtained protein structural information to arrive at a possible mechanism of transcription activation . This demonstrates the diversity of control mechanisms existing in catabolic pathways.

Environ Toxicol Chem, 2004 Aug, 23(8), 1861 - 6
Assessment of the availability of polycyclic aromatic hydrocarbons from gasworks soil using different extraction solvents and techniques; Bergknut M et al.; This study was designed to assess the availability of polycyclic aromatic hydrocarbons (PAHs) present at a gasworks site to different soil remediation techniques . The study examined the effect on PAH availability of using different organic solvents, the degree of pretreatment, and the extraction time . In total, 25 PAHs (with two to six fused rings) and five carbonyl derivatives were measured . The results indicated that the PAHs and their derivatives were bound loosely to the surface of the studied soil and that there were no significant kinetic boundaries associated with the extraction of the PAHs . Furthermore, it was concluded that the studied soil was not suitable for bioremediation, as the concentration of PAHs with low molecular weight were limited . However, pressurized liquid extraction (PLE) with methanol as the solvent extracted 97% of all PAHs and PAH-derivatives, indicating that extraction may be effective as part of a soil remediation technique for old gasworks soils.

Appl Microbiol Biotechnol, 2005 Jan, 66(4), 450 - 6 Epub 2004 Sep 02.
Expression of laccase IIIb from the white-rot fungus Trametes versicolor in the yeast Yarrowia lipolytica for environmental applications; Jolivalt C et al.; Improvement of the catalytic properties of fungal laccases is a current challenge for the efficient bioremediation of natural media polluted by xenobiotics . We developed the heterologous expression of a laccase from the white-rot fungus Trametes versicolor in the yeast Yarrowia lipolytica as a first step for enzyme evolution . The full-length cDNA consisted of a 1,561-bp open reading frame encoding lacIIIb, a 499-amino-acid protein and a 21-amino-acid signal peptide . Native and yeast secretion signals were used to direct the secretion of the enzyme, with the native signal yielding higher enzyme activity in the culture medium . The level of laccase activity secreted by the transformed yeast was similar to that observed for the non-induced wild-type strain of T . versicolor . The identity of the recombinant enzyme was checked by Western blot and matrix-assisted laser desorption/ionization time-of-flight analysis . Electrophoresis separation in native conditions indicated a molecular mass of the recombinant protein slightly higher (5 kDa) than that of the mature T . versicolor laccase IIIb, suggesting a limited excess of glycosylation . The laccase production level reached 2.5 mg/l (0.23 units/ml), which is suitable for engineering purpose.

Environ Sci Pollut Res Int, 2004, 11(4), 260 - 6
Phytoremediation of petroleum hydrocarbons in tropical coastal soils . I . Selection of promising woody plants; Sun WH et al.; GOAL, SCOPE AND BACKGROUND: This glasshouse study is aimed at evaluating tropical plants for phytoremediation of petroleum hydrocarbon-contaminated saline sandy subsurface soils . Tropical plants were selected for their ability to tolerate high salinity and remove No . 2 diesel fuel in coastal topsoil prior to further investigation of the phytoremediation feasibility in deep contaminated soils . The residual petroleum-hydrocarbon contaminant at the John Rogers Tank Farm site, a former petroleum storage facility, at Hickam Air Force Base, Honolulu, Hawaii, is located in a coastal area . It lies below a layer of silt in the subsurface, in loamy sand characterized by moderate salinity and high pH . Little is known regarding the ability of tropical plants to remediate petroleum hydrocarbon-contaminated subsurface soil in Hawaiian and other Pacific Island ecosystems although suitable plants have been identified and utilized for bioremediation in surface soil or marine sediments . METHODS: The experiments were conducted in long narrow pots under glasshouse conditions in two phases . A preliminary experiment was done with nine tropical plants: kiawe (Prosopis pallida), milo (Thespesia populnea), common ironwood (Casuarina equisetifolia), kou (Cordia subcordata), tropical coral tree (Erythrina variegata), false sandalwood (Myoporum sandwicense), beach naupaka (Scaevola sericea), oleander (Nerium oleander), and buffelgrass (Cenchrus ciliaris) . These plants were screened for resistance to high salinity treatment (2% NaCl) and two diesel fuel levels (5 and 10 g No . 2 diesel fuel/kg soil) in separate treatments . Plants that showed good tolerance of both factors were further evaluated in a second phase for their efficacy in the phytoremediation of diesel-fuel petroleum hydrocarbons under moderate salinity treatment (1% NaCl) . RESULTS: Tropical coral tree and buffelgrass were susceptible to either 2% NaCl or diesel fuel at 10 g/kg soil, but tolerant of diesel fuel at 5 g/kg soil . Kiawe, milo, kou, common ironwood, N . oleander, beach naupaka and false sandalwood were tolerant of high salinity (2% NaCl) or high diesel fuel level (10 g/kg soil) . These seven plants were also tolerant of the combined adverse effects of a moderate salinity (1% NaCl) and 10 g diesel fuel/kg soil . Three trees, kiawe, milo and kou significantly accelerated the degradation of petroleum hydrocarbons in the soil spiked with 10 g diesel fuel/kg soil under a moderate salinity treatment (1% NaCl). , . CONCLUSION: Thus the tropical woody plants, kiawe, milo and kou showed potential for use in phytoremediation of petroleum hydrocarbons in coastal tropical soils . RECOMMENDATIONS AND OUTLOOK: Two fast growing trees, milo and kou, appeared promising for further phytoremediation evaluation in experiments that simulate the soil profile at the field site.

J Contam Hydrol, 2004 Sep, 73(1-4), 65 - 98
Plant aided bioremediation in the vadose zone: model development and applications; Sung K et al.; Phytoremediation has the potential to enhance clean up of land contaminated by various pollutants . A mathematical model that includes a two-fluid phase flow model of water flow as well as a two-region soil model of contaminant reactions was developed and applied to various bioremediation scenarios in the unsaturated zone, especially to plant-aided bioremediation . To investigate model behavior and determine the main parameters and mechanisms that affect bioremediation in unplanted and planted soils, numerical simulations of theoretical scenarios were conducted before applying the model to field data . It is observed from the results that parameters affecting the contaminant concentration in the water phase, such as aqueous solubility, the octanol-water partition coefficient, and organic carbon content of the soil controlled the contaminant fate in the vadose zone . Simulation using the developed model also characterized the fate and transport of the contaminants both in planted and unplanted soils satisfactorily for field applications . Although phytoremediation has the potential for remediation of contaminated soils, results from both modeling and field studies suggested that plants may not always enhance the remediation efficiency when the soil already has a high microbial concentration, when the contaminant bioavailability is low, or when the overall reaction is mass transfer-limited . Therefore, other steps to increase contaminant bioavailability are needed in phytoremediation applications; natural purification mechanisms such as aging, volatilization, and natural bioremediation should be considered to maximize the plant effect and minimize the cost .

J Contam Hydrol, 2004 Sep, 73(1-4), 3 - 14
Impact of transverse and longitudinal dispersion on first-order degradation rate constant estimation; Stenback GA et al.; A two-dimensional analytical model is employed for estimating the first-order degradation rate constant of hydrophobic organic compounds (HOCs) in contaminated groundwater under steady-state conditions . The model may utilize all aqueous concentration data collected downgradient of a source area, but does not require that any data be collected along the plume centerline . Using a least squares fit of the model to aqueous concentrations measured in monitoring wells, degradation rate constants were estimated at a former manufactured gas plant (FMGP) site in the Midwest U.S . The estimated degradation rate constants are 0.0014, 0.0034, 0.0031, 0.0019, and 0.0053 day(-1) for acenaphthene, naphthalene, benzene, ethylbenzene, and toluene, respectively . These estimated rate constants were as low as one-half those estimated with the one-dimensional (centerline) approach of Buscheck and Alcantar {Buscheck, T.E., Alcantar, C.M., 1995 . Regression techniques and analytical solutions to demonstrate intrinsic bioremediation . In: Hinchee, R.E., Wilson, J.T., Downey, D.C . (Eds.), Intrinsic Bioremediation, Battelle Press, Columbus, OH, pp . 109-116} which does not account for transverse dispersivity . Varying the transverse and longitudinal dispersivity values over one order of magnitude for toluene data obtained from the FMGP site resulted in nearly a threefold variation in the estimated degradation rate constant-highlighting the importance of reliable estimates of the dispersion coefficients for obtaining reasonable estimates of the degradation rate constants . These results have significant implications for decision making and site management where overestimation of a degradation rate may result in remediation times and bioconversion factors that exceed expectations . For a complex source area or non-steady-state plume, a superposition of analytical models that incorporate longitudinal and transverse dispersion and time may be used at sites where the centerline method would not be applicable .

Indian J Exp Biol, 2003 Nov, 41(11), 1239 - 48
Bioremediation of paper and pulp mill effluents; Murugesan K; Pulp and paper mill effluents pollute water, air and soil, causing a major threat to the environment . Several methods have been attempted by various researchers throughout the world for the removal of colour from pulp and paper mill effluents . The biological colour removal process uses several classes of microorganisms--bacteria, algae and fungi--to degrade the polymeric lignin derived chromophoric material . White rot fungi such as Phanerochaete chrysosporium, Corius versicolor, Trametes versicolor etc., are efficient in decolourizing paper and pulp mill effluents . Gliocladium virens, a saprophytic soil fungus decolourised paper and pulp mill effluents by 42% due to the production of hemicellulase, lignin peroxidase, manganese peroxidase and laccase.

Huan Jing Ke Xue, 2004 Jan, 25(1), 91 - 4
{Nutrient balance and mechanism of biological degradation of oil}; He LJ et al.; This paper studied the nutrient balance and mechanism for enhancing the bioremediation of petroleum contaminated soils by the bio-slurry method . Oil degrading strains isolated and screened from Liaohe oil field was used . The results show that the suitable weight ratio of N and P element in the nutrient is 5.67:1, which is similar to their proportion in the microbial cells . It was found that the degradation of oil was significantly enhanced by adding nutriment and about 30% oil was decreased in the 14,000 mg/kg-15,000 mg/kg samples during 16 days . Using (NH4)2SO4, NH4NO3, NaNO3, CO(NH2)2 as the nitrogen source respectively, it shows that the inorganic nitrogen is better than the organic one, and the nitrogen in nitrate is more effective than that in ammonia . Adding nutrient salt can change the system's pH and promote the growing of the microbes.

Huan Jing Ke Xue, 2004 May, 25(3), 110 - 4
{The relationship between abiotic factors and microbial activities of microbial eco-system in contaminated soil with petroleum hydrocarbons}; Jia JL et al.; By means of the biostimulation and bioaugmentation in the micro-ecological environment of contaminated soil with petrochemical hydrocarbons, the biodegradation rates and mode of the contaminants were significantly improved . Based on the investigations carried out in some oilfields and petrochemical industrial area of Northern China, the relationship between the abiotic factors such as nutrient, pH, contaminants, water content, alkalinity, etc., and microbial activities was interpreted and identified in this paper . The results from the investigations and indoor and in-situ experiments conducted recent years indicated that the soils in the areas, to the extent, have been polluted by the different kinds of organic compounds composed of monoaromatic benzene, PAHs, chlorinated solvent, and alkanes, and the concentrations of the compounds mostly were elevated as compared to the background, with the highest 34,000 mg/kg dry soil . The column chromatography analysis results showed that the alkyl and aromatic compounds were accounted for more than 50% of the total hydrocarbon contents, which was readily degraded by degrading bacteria and improved the degrading microbe activities . The effective nitrogen and phosphorus encountered in the soil was less than 30 mg/kg dry soil and 10 mg/kg dry soil, only about 5% of total contents of them respectively. , . Based on the stoichiometric calculation and reasonable ratio of carbon to nutrient content regarding the biodegradation of organic compounds, the nutrient levels mainly composed of nitrogen and phosphorus in polluted soil as importantly limiting factors to degrading bacterial growth and activity were insufficient to the biodegradation of petrochemicals, and it is needed to add the nutrient for the bioremediation of contaminated soil . It is undoubted that the optimization of abiotic factors play significant role in increasing the microbial activity and improving the biodegradation rates.

Mar Pollut Bull, 2004 Sep, 49(5-6), 425 - 35
Evaluation of bioremediation strategies of a controlled oil release in a wetland; Mills MA et al.; A controlled petroleum release was conducted to evaluate bioremediation in a wetland near Houston, Texas . The 140-day study was conducted using a randomized, complete block design to test three treatments with six replicates per treatment . The three treatment strategies were inorganic nutrients, inorganic nutrients with an alternative electron acceptor, and a no-action oiled control . Samples were analyzed for petroleum chemistry and inorganic nutrients . These results are discussed in the context of our related research involving toxicology and microbiology at the site during the experiment . To evaluate biodegradation, the targeted compounds were normalized to the conservative compound C3017alpha, 21beta-{H}hopane, thus reducing the effects of spatial heterogeneity and physical transport . The two biostimulation treatments demonstrated statistically-higher rates of biodegradation than the oiled no-action control . For the majority of the experiment, target nutrient levels were maintained . Further research may be warranted to optimize these bioremediation strategies as well as evaluating additional treatment strategies for wetlands and other shoreline systems .

FEMS Microbiol Lett, 2004 Aug 15, 237(2), 249 - 53
Microplate screening assay for the detection of arsenite-oxidizing and arsenate-reducing bacteria; Simeonova DD et al.; An efficient, inexpensive microplate colorimetric assay for screening of bacteria which can be used in bioremediation of arsenic was developed . The assay is based on the colorimetric analysis of the precipitates formed upon reaction of silver nitrate with arsenic . The method proved reliable and sensitive for the detection of As{III} oxidizers and As{V} reducers and can be used over a large pH range (5.8-8.4) . Seventy-eight bacterial strains isolated from different environments were tested by this method . It also showed agreement with results obtained by high-performance liquid chromatography coupled with inductively coupled plasma atomic emission spectrometry.

Appl Microbiol Biotechnol, 2004 Dec, 66(2), 123 - 30 Epub 2004 Dec.
Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics; Eyers L et al.; Increasing pollution of water and soils by xenobiotic compounds has led in the last few decades to an acute need for understanding the impact of toxic compounds on microbial populations, the catabolic degradation pathways of xenobiotics and the set-up and improvement of bioremediation processes . Recent advances in molecular techniques, including high-throughput approaches such as microarrays and metagenomics, have opened up new perspectives and pointed towards new opportunities in pollution abatement and environmental management . Compared with traditional molecular techniques dependent on the isolation of pure cultures in the laboratory, microarrays and metagenomics allow specific environmental questions to be answered by exploring and using the phenomenal resources of uncultivable and uncharacterized micro-organisms . This paper reviews the current potential of microarrays and metagenomics to investigate the genetic diversity of environmentally relevant micro-organisms and identify new functional genes involved in the catabolism of xenobiotics.

Philos Trans R Soc Lond B Biol Sci, 2004 Jun 29, 359(1446), 907 - 18
Plant perceptions of plant growth-promoting Pseudomonas; Preston GM; Plant-associated Pseudomonas live as saprophytes and parasites on plant surfaces and inside plant tissues . Many plant-associated Pseudomonas promote plant growth by suppressing pathogenic micro-organisms, synthesizing growth-stimulating plant hormones and promoting increased plant disease resistance . Others inhibit plant growth and cause disease symptoms ranging from rot and necrosis through to developmental dystrophies such as galls . It is not easy to draw a clear distinction between pathogenic and plant growth-promoting Pseudomonas . They colonize the same ecological niches and possess similar mechanisms for plant colonization . Pathogenic, saprophytic and plant growth-promoting strains are often found within the same species, and the incidence and severity of Pseudomonas diseases are affected by environmental factors and host-specific interactions . Plants are faced with the challenge of how to recognize and exclude pathogens that pose a genuine threat, while tolerating more benign organisms . This review examines Pseudomonas from a plant perspective, focusing in particular on the question of how plants perceive and are affected by saprophytic and plant growth-promoting Pseudomonas (PGPP), in contrast to their interactions with plant pathogenic Pseudomonas . A better understanding of the molecular basis of plant-PGPP interactions and of the key differences between pathogens and PGPP will enable researchers to make more informed decisions in designing integrated disease-control strategies and in selecting, modifying and using PGPP for plant growth promotion, bioremediation and biocontrol.

Environ Sci Technol, 2004 Jul 15, 38(14), 3958 - 64
Optimizing detection limits for the analysis of petroleum hydrocarbons in complex environmental samples; Douglas GS et al.; To evaluate the sources, transport, bioremediation, fate, and effects of spilled petroleum and petroleum products, environmental studies often measure parent and alkylated polycyclic aromatic hydrocarbons (PAH), alkanes, and chemical biomarkers (e.g., triterpanes) . Accurate data for low analyte concentrations are required when environmental samples contain hydrocarbons from multiple sources that need to be resolved and quantified . The accuracy and usefulness of the analyses can be improved by lowering the method detection limits (MDLs) for these compounds . Misidentification of hydrocarbon source can result when the MDLs are too high . Modifications to standard analytical methods (i.e., U.S . Environmental Protection Agency Method 8270) can lower MDLs by factors ranging from 10 to 1000 . This reduction has important implications for ecological-risk assessments . Modifications having the greatest impact on the MDL include GCMS analysis in the selected-ion-monitoring mode (SIM), increased sample size, column cleanup of the extract, and decreased preinjection volume (volume of final extract prior to injection into instrument) . In one study in which a benthic sediment sample was spiked with low levels of topped (heated to remove more volatile PAH that are naturally enriched in crude oil) Alaska North Slope crude, MDLs for individual PAH analytes and biomarkers were determined to be less than 0.5 ng/g (ppb) dry weight and less than 5 ppb dry weightfor individual alkanes . Similar results were obtained when the sediment was spiked with the 16 EPA priority pollutants . In addition, a method has been developed to estimate MDLs for source-specific alkylated PAH analytes and chemical biomarker compounds for which standards are not commercially available or are prohibitively expensive . These improved analytical techniques have been used to identify and quantify low levels of hydrocarbons, derived from both natural and anthropogenic sources, found in the benthic sediments of Prince William Sound, AK.

Curr Opin Biotechnol, 2004 Aug, 15(4), 374 - 9
Biocatalytic degradation of pollutants; Parales RE et al.; Microbial reactions play key roles in biocatalysis and biodegradation . The recent genome sequencing of environmentally relevant bacteria has revealed previously unsuspected metabolic potential that could be exploited for useful purposes . For example, oxygenases and other biodegradative enzymes are benign catalysts that can be used for the production of industrially useful compounds . In conjunction with their biodegradative capacities, bacterial chemotaxis towards pollutants might contribute to the ability of bacteria to compete with other organisms in the environment and to be efficient agents for bioremediation . In addition to the bacterial biomineralization of organic pollutants, certain bacteria are also capable of immobilizing toxic heavy metals in contaminated aquifers, further illustrating the potential of microorganisms for the removal of pollutants.

J Chromatogr A, 2004 Jul 9, 1042(1-2), 89 - 97
Determination of alkylbenzene metabolites in groundwater by solid-phase extraction and liquid chromatography-tandem mass spectrometry; Alumbaugh RE et al.; Benzylsuccinate (BSA), methylbenzylsuccinate (methylBSA), and ethylbenzylsuccinate (ethylBSA) are unambiguous anaerobic biotransformation products from toluene, xylenes, and ethylbenzene decay, respectively, and may be used to indicate intrinsic bioremediation is occurring at hydrocarbon-contaminated sites . In order to improve upon current methods that detect and quantify anaerobic hydrocarbon metabolites in field samples, solid-phase extraction (SPE) and direct sample injection methods coupled with liquid chromatography-tandem mass spectrometry (LC-MS-MS) were evaluated . In laboratory studies, recoveries of authentic standards of non-deuterated or deuterated benzylsuccinates and toluates ranged from 80 to 106% with relative standard errors ranging from 2 to 4% . The method detection limits for these analytes using SPE-LC-MS-MS ranged from 0.006 to 0.029 microg/L whereas those for direct injection-LC-MS-MS ranged from 0.61 to 1.5 microg/L . Given the increased sensitivity of using SPE coupled with LC-MS-MS, this technique was then used to analyze for the presence of putative anaerobic alkylbenzene metabolites in groundwater from a hydrocarbon-contaminated site where single-well push-pull tests were conducted using deuterated aromatic hydrocarbons . Both deuterated and non-deuterated benzylsuccinates and toluates were successfully detected and quantified in field samples using this method.

Environ Sci Technol, 2004 Jul 1, 38(13), 3689 - 97
Compound-specific carbon and hydrogen isotope analysis of sub-parts per billion level waterborne petroleum hydrocarbons; Wang Y et al.; Compound-specific carbon and hydrogen isotope analysis (CSCIA and CSHIA) has been increasingly used to study the source, transport, and bioremediation of organic contaminants such as petroleum hydrocarbons . In natural aquatic systems, dissolved contaminants represent the bioavailable fraction that generally is of the greatest toxicological significance . However, determining the isotopic ratios of waterborne hydrophobic contaminants in natural waters is very challenging because of their extremely low concentrations (often at sub-parts ber billion, or even lower) . To acquire sufficient quantities of polycyclic aromatic hydrocarbons with 10 ng/L concentration for CSHIA, more than 1000 L of water must be extracted . Conventional liquid/liquid or solid-phase extraction is not suitable for such large volume extractions . We have developed a new approach that is capable of efficiently sampling sub-parts per billion level waterborne petroleum hydrocarbons for CSIA . We use semipermeable membrane devices (SPMDs) to accumulate hydrophobic contaminants from polluted waters and then recover the compounds in the laboratory for CSIA . In this study, we demonstrate, under a variety of experimental conditions (different concentrations, temperatures, and turbulence levels), that SPMD-associated processes do not induce C and H isotopic fractionations. , . The applicability of SPMD-CSIA technology to natural systems is further demonstrated by determining the delta13C and deltaD values of petroleum hydrocarbons present in the Pawtuxet River, RI . Our results show that the combined SPMD-CSIA is an effective tool to investigate the source and fate of hydrophobic contaminants in the aquatic environments.

Commun Agric Appl Biol Sci, 2003, 68(2 Pt A), 59 - 66
Use of biolog methodology for optimizing the degradation of hydrocarbons by bacterial consortia; Ambrosoli R et al.; Biolog methodology was used for the preliminary screening of different cultural conditions in order to detect the best combination/s of factors influencing the metabolic performance of bacterial consortia active in the degradation of hydrocarbons . Two microbial consortia were tested for their activity on 2 hydrocarbons (nonadecane and eicosane) in presence of the following cultural coadjuvants: vegetal oil, beta-cyclodextrine, sodium acetate, mineral solution . Tests were conducted in Biolog MT plates, where only the redox indicator of microbial growth (tetrazolium violet) and no carbon sources are provided . The microwells were filled with various combinations of hydrocarbons, microbial inoculum and coadjuvants . Blanks were prepared with the same combinations but without hydrocarbons . The results obtained show the suitability of the methodology developed to identify the most active consortium and the conditions for its best degradation performance . The efficacy of Biolog methodology (Biolog Inc., USA) for the characterization of microbial communities on the basis of the metabolic profiles obtained on specific carbon sources in the microwells of Elisa-type plates, is widely acknowledged (Garland, 1997; Pietikainen et al., 2000; Dauber and Wolters, 2000) . Due to its aptitude to simultaneously evaluate multiple microbial responses and directly organize the results, it can be adapted to meet specific study purposes (Gamo and Shji, 1999) . In the present research Biolog methodology was fitted for the preliminary screening of different cultural conditions, in order to detect the best combination/s of factors influencing the metabolic performance of bacterial consortia active in the degradation of aliphatic hydrocarbons, in view of their utilization for the bioremediation of polluted sites.

Appl Environ Microbiol, 2004 Aug, 70(8), 4911 - 20
Change in bacterial community structure during in situ biostimulation of subsurface sediment cocontaminated with uranium and nitrate; North NN et al.; Previous studies have demonstrated that metal-reducing microorganisms can effectively promote the precipitation and removal of uranium from contaminated groundwater . Microbial communities were stimulated in the acidic subsurface by pH neutralization and addition of an electron donor to wells . In single-well push-pull tests at a number of treated sites, nitrate, Fe(III), and uranium were extensively reduced and electron donors (glucose, ethanol) were consumed . Examination of sediment chemistry in cores sampled immediately adjacent to treated wells 3.5 months after treatment revealed that sediment pH increased substantially (by 1 to 2 pH units) while nitrate was largely depleted . A large diversity of 16S rRNA gene sequences were retrieved from subsurface sediments, including species from the alpha, beta, delta, and gamma subdivisions of the class Proteobacteria, as well as low- and high-G+C gram-positive species . Following in situ biostimulation of microbial communities within contaminated sediments, sequences related to previously cultured metal-reducing delta-Proteobacteria increased from 5% to nearly 40% of the clone libraries . Quantitative PCR revealed that Geobacter-type 16S rRNA gene sequences increased in biostimulated sediments by 1 to 2 orders of magnitude at two of the four sites tested . Evidence from the quantitative PCR analysis corroborated information obtained from 16S rRNA gene clone libraries, indicating that members of the delta-Proteobacteria subdivision, including Anaeromyxobacter dehalogenans-related and Geobacter-related sequences, are important metal-reducing organisms in acidic subsurface sediments . This study provides the first cultivation-independent analysis of the change in metal-reducing microbial communities in subsurface sediments during an in situ bioremediation experiment.

Appl Environ Microbiol, 2004 Aug, 70(8), 4720 - 6
Enhanced anaerobic biodegradation of benzene-toluene-ethylbenzene-xylene-ethanol mixtures in bioaugmented aquifer columns; Da Silva ML et al.; Methanogenic flowthrough aquifer columns were used to investigate the potential of bioaugmentation to enhance anaerobic benzene-toluene-ethylbenzene-xylene (BTEX) degradation in groundwater contaminated with ethanol-blended gasoline . Two different methanogenic consortia (enriched with benzene or toluene and o-xylene) were used as inocula . Toluene was the only hydrocarbon degraded within 3 years in columns that were not bioaugmented, although anaerobic toluene degradation was observed after only 2 years of acclimation . Significant benzene biodegradation (up to 88%) was observed only in a column bioaugmented with the benzene-enriched methanogenic consortium, and this removal efficiency was sustained for 1 year with no significant decrease in permeability due to bioaugmentation . Benzene removal was hindered by the presence of toluene, which is a more labile substrate under anaerobic conditions . Real-time quantitative PCR analysis showed that the highest numbers of bssA gene copies (coding for benzylsuccinate synthase) occurred in aquifer samples exhibiting the highest rate of toluene degradation, which suggests that this gene could be a useful biomarker for environmental forensic analysis of anaerobic toluene bioremediation potential . bssA continued to be detected in the columns 1 year after column feeding ceased, indicating the robustness of the added catabolic potential . Overall, these results suggest that anaerobic bioaugmentation might enhance the natural attenuation of BTEX in groundwater contaminated with ethanol-blended gasoline, although field trials would be needed to demonstrate its feasibility . This approach may be especially attractive for removing benzene, which is the most toxic and commonly the most persistent BTEX compound under anaerobic conditions.

Appl Microbiol Biotechnol, 2004 Oct, 65(5), 627 - 34 Epub 2004 Aug 04.
Evaluation of chemical pretreatment of contaminated soil for improved PAH bioremediation; Piskonen R et al.; The efficiency of several chemical treatments as potential enhancers of the biodegradation of polycyclic aromatic hydrocarbons (PAHs) in contaminated soil was evaluated by analyzing the mineralization of 14C-labeled phenanthrene, pyrene, and benzo(a)pyrene . The effect of nonionic surfactants with Fenton oxidation and combinations of surfactants with the Fenton oxidation was evaluated in a microtiter plate assay . The surfactants selected for the study were Tween 80, Brij 35, Tergitol NP-10, and Triton X-100 . The addition of Fenton's reagent significantly enhanced the mineralization of pyrene at the two concentrations studied: 2.8 M H2O2 with 0.1 M FeSO4 and 0.7 M H2O2 with 0.025 M FeSO4 . Phenanthrene mineralization was also positively induced by the Fenton treatments . However, none of the treatments had a significant effect on benzo(a)pyrene mineralization . Surfactant additions at concentrations of 20% and 80% of the aqueous critical micelle concentration did not significantly affect the mineralization rates . When surfactant addition was combined with the Fenton oxidation, reduced mineralization rates were obtained when compared with mineralization after Fenton's treatment alone . The results indicate that the addition of Fenton's reagent may enhance the mineralization of PAHs in contaminated soil, whereas the addition of surfactants has no significant beneficial effect . The efficiency of the Fenton oxidation may decrease when surfactants are added simultaneously with Fenton's reagent to contaminated soil.

J Environ Monit, 2004 Aug, 6(8), 713 - 8 Epub 2004 Jun 11.
Characterisation of weathered hydrocarbon wastes at contaminated sites by GC-simulated distillation and nitrous oxide chemical ionisation GC-MS, with implications for bioremediation; Pollard SJ et al.; An extended analytical characterisation of weathered hydrocarbons isolated from historically contaminated sites in Alberta is presented . The characterisation of soil extracts, chromatographically separated into component classes, by GC-simulated distillation and nitrous oxide (N2O) chemical ionisation (CI) GC-MS provides new insights into the composition of the residual oil at these sites, the principal partition medium for risk critical components . The combined polar and asphaltene content of representative soil extracts ranged from 40% w/w to 70% w/w of the oils encountered . An abundance of C14-C22 2-4 ring alicyclics, alkylbenzenes and benzocycloparaffins is prevalent within the saturate fractions of site soils . Implications for the partitioning of risk critical compounds at sites with weathered hydrocarbons and the practical application of bioremediation technologies are discussed.

Chemosphere, 2004 Sep, 56(11), 1021 - 32
Environmental impact of diuron transformation: a review; Giacomazzi S et al.; Diuron is a biologically active pollutant present in soil, water and sediments . A synthesis of literature data on its physicochemical properties, partitioning behaviour, abiotic and biotic transformations, toxicological and ecotoxicological impacts has been here performed . Data have shown that diuron is generally persistent in soil, water and groundwater . It is also slightly toxic to mammals and birds as well as moderately toxic to aquatic invertebrates . However, its principal product of biodegradation, 3,4-dichloroaniline exhibits a higher toxicity and is also persistent in soil, water and groundwater . Thus, diuron indirectly possesses a significant amount of toxicity and could be a potential poisoning pesticide contaminant of groundwater . Unfortunately, groundwater contamination will still persist despite the progressive suppression of diuron (Directive 200/60/CE) . Therefore, determining the main factors influencing its degradation and its ecotoxicological effects on the environment and health could provide a basis for further development of bioremediation processes.

Environ Toxicol, 2004 Aug, 19(4), 267 - 73
Toxicity assessment of oil-contaminated freshwater sediments; Blaise C et al.; The performance of four microscale toxicity bioassays conducted on whole sediments was evaluated during a bioremediation project undertaken in 1999-2000 on a crude oil-contaminated freshwater shoreline of the St . Lawrence River, Quebec, Canada . The toxicity tests assessed included: (1) the Microtox solid-phase assay (MSPT), (2) the Biotox Flash solid-phase test (Flash), (3) the algal solid-phase assay (ASPA), and 4) the Ostracodtoxkit solid-phase assay . Data generated with these assays were compared with those obtained using the standard endobenthic amphipod (Hyalella azteca) bioassay . Bioanalytical comparisons indicated that all five solid-phase tests were useful in detecting the toxicity of oiled sediments; however, statistical analyses distinguished a difference in response between the invertebrate (amphipod and Ostracodtoxkit) and bacterial luminescence tests (MSPT and Flash) . Based on these results, it is recommended that careful selection of biotests be made in the design of the test battery for assessment of residual oil sediment toxicity. , , . Time-series toxicity data generated with ASPA indicated that oiled sediments in the freshwater wetlands of the St . Lawrence River remained toxic to phytoplankton for at least 65 weeks and that remediation treatment was able to accelerate detoxification by 16 weeks .

J Environ Qual, 2004 Jul-Aug, 33(4), 1210 - 6
Application of a slow-release fertilizer for oil bioremediation in beach sediment; Xu R et al.; A 105-d field experiment was conducted to determine the potential of the slow-release fertilizer, Osmocote (Scotts, Marysville, OH), to stimulate the indigenous microbial biodegradation of petroleum hydrocarbons in an oil-spiked beach sediment on an intertidal foreshore in Singapore . Triplicate microcosms containing 80 kg of weathered sediment, spiked with 5% (w/w) Arabian light crude oil and 1.2% (w/w) Osmocote pellets, were established, together with control microcosms minus Osmocote . Relative to the control, the presence of the Osmocote sustained a significantly higher level of nutrients (NH(4)(+)-N, NO(3)(-)-N, and PO(4)(3-)-P) in the sediment pore water over the duration of the experiment . The metabolic activity of the indigenous microbial biomass, as measured using an intracellular dehydrogenase enzyme assay, was also significantly enhanced over the duration of the experiment in amended sediments . The loss of total recoverable petroleum hydrocarbons (TRPH) and biodegradation of total n-alkanes (C(10)-C(33)), branched alkanes (pristane and phytane), as well as total target polycyclic aromatic hydrocarbons (PAHs) (two- to six-ring), in both the control and Osmocote-amended sediments, followed a first-order biodegradation model . The first-order loss rate of total recoverable petroleum hydrocarbons was 2.57 times greater than that of the control . The hopane-normalized rate constants for total n-alkane, branched alkane, and total target PAH biodegradation in the Osmocote-treated sediments were 3.95-, 5.50-, and 2.45-fold higher than the control, respectively . Overall, the presence of Osmocote was able to significantly enhance and accelerate the biodegradation of aliphatics and PAHs in oil-contaminated sediments under natural field conditions in an intertidal foreshore environment.

Chemosphere, 2004 Aug, 56(8), 803 - 11
Bioremediation of HCH-contaminated soil: elimination of inhibitory effects of the insecticide on radish and green gram seed germination; Bidlan R et al.; The effects of technical grade hexachlorocyclohexane (tech-HCH) on the germination of different seeds were tested . Two types of seeds, radish and green gram showed marked reduction in germination percentage and seeding vigour index . The abnormalities and reduction in germination increased with increasing concentration of tech-HCH . At 100 microg HCH level the germination of radish and green gram seeds was inhibited almost completely on moist filter paper and soil . Protease and amylase activities were reduced in seeds grown in soil spiked with tech-HCH . Bioremediation of HCH-spiked soils with a HCH-degrading microbial consortium helped in eliminating the toxic effects of tech-HCH towards seed germination . The degradation of 25 microg tech-HCH g(-1) soil was complete by 120 h . The seed germination and the activities of the assayed enzymes, amylase and protease, were same as before or better in bioremediated soils.

Appl Microbiol Biotechnol, 2004 Aug, 65(3), 250 - 8 Epub 2004 Jul 10.
Strategies for bioremediation of polychlorinated biphenyls; Ohtsubo Y et al.; Polychlorinated biphenyls (PCBs) are serious environmental pollutants that threaten both the natural ecosystem and human health . For remediation of environments contaminated with PCBs, several approaches that exploit the potential of microbes to degrade PCBs have been developed . These approaches include improvement of PCB solubilization and entry into the cell, pathway and enzyme engineering, and control of enzyme expression . In this mini-review, we briefly summarize these strategies and provide potentially useful knowledge for the further improvement of the bacterial breakdown of PCBs.

J Environ Sci Health A Tox Hazard Subst Environ Eng, 2004 Jun, 39(6), 1399 - 414
Reductive dechlorination of tetrachloroethene by a mixed bacterial culture growing on ethyl lactate; Jayaraj J et al.; Chloroethenes like tetrachloroethene (PCE) are the most prevalent groundwater contaminants in the USA . Their presence as nonaqueous phase liquids (NAPLs) makes remediation difficult . Among options for NAPL cleanup, co-solvent injection has demonstrated success . However, the process has the potential to leave considerable residue of the co-solvent as well as residual chloroethene . Our rationale in this study was to examine whether this residual solvent could be a potential electron donor for the remediation of the residual chloroethene . We hypothesized that ethyl lactate, a "green" solvent, could serve both as a NAPL extraction solvent and an electron donor for reductive dechlorination of residual chloroethene . We examined whether a mixed culture known to degrade PCE with lactate could also grow on ethyl lactate and whether it could stimulate PCE dechlorination . Biomass growth and PCE dechlorination were observed by protein and chloride production, respectively, in the culture; with a specific dechlorination rate of 50 150 microg (mg cell d)(-1) . Ethyl lactate abiotically breaks down to ethanol and lactate, the latter being a rich source of hydrogen fo reductive dechlorination . The results demonstrate that ethyl lactate may be promising for in situ bioremediation following NAPL extraction.

Indian J Exp Biol, 2003 Sep, 41(9), 1068 - 75
Bioremediation concepts for treatment of dye containing wastewater: a review; Keharia H et al.; Synthetic dyes are extensively used in wide range of industries amongst which textile processing industries are the major consumers . Large amounts of dyes are lost in wastewaters of these industries during dyeing and subsequent washing steps of textiles . These dyes are resistant to de gradation by conventional wastewater treatment plants and are released into environment untreated thus causing pollution of surface and ground waters in the areas of the world harboring such industries . Presence of color in wastewaters has become major environmental concern and stringent discharge standards are being enforced on release of colored wastewaters in environment . The seriousness of the problem is apparent from the magnitude of the research done in this field in last decade . Increasing number of microorganisms are being described for their ability to decolorize and degrade artificial dyes and novel bioremediation approaches for treatment dye bearing wastewaters are being worked out . In this review we have investigated potential microbial processes for developing feasible remediation technology to combat environmental pollution due to dye bearing wastewaters.

Indian J Exp Biol, 2003 Sep, 41(9), 1046 - 67
Anaerobic biodegradation of aromatic compounds; Jothimani P et al.; Many aromatic compounds and their monomers are existing in nature . Besides they are introduced into the environment by human activity . The conversion of these aromatic compounds is mainly an aerobic process because of the involvement of molecular oxygen in ring fission and as an electron acceptor . Recent literatures indicated that ring fission of monomers and obligomers mainly occurs in anaerobic environments through anaerobic respiration with nitrate, sulphate, carbon dioxide or carbonate as electron acceptors . These anaerobic processes will help to work out the better situation for bioremediation of contaminated environments . While there are plenty of efforts to reduce the release of these chemicals to the environment, already contaminated sites need to be remediated not only to restore the sites but to prevent the leachates spreading to nearby environment . Basically microorganisms are better candidates for breakdown of these compounds because of their wider catalytic mechanisms and the ability to act even in the absence of oxygen . These microbes can be grouped based on their energy mechanisms . Normally, the aerobic counterparts employ the enzymes like mono-and-dioxygenases . The end product is basically catechol, which further may be metabolised to CO2 by means of quinones reductases cycles . In the absense of reductases compounds, the reduced catechols tend to become oxidised to form many quinone compounds . The quinone products are more recalcitrant and lead to other aesthetic problems like colour in water, unpleasant odour, etc . On the contrary, in the reducing environment this process is prevented and in a cascade of pathways, the cleaved products are converted to acetyl co-A to be integrated into other central metabolite paths . The central metabolite of anaerobic degradation is invariably co-A thio-esters of benzoic acid or hydroxy benzoic acid . The benzene ring undergoes various substitution and addition reactions to form chloro-, nitro-, methyl- compounds . For complete degradation the side chains must be removed first and then the benzene ring is activated by carboxylation or hydroxylation or co-A thioester formation . In the next step the activated ring is converted to a form that can be collected in the central pool of metabolism . The third step is the channeling reaction in which the products of the catalysis are directed into central metabolite pool . The enzymes involved in these mechanisms are mostly benzyl co-A ligase, benzyl alcohol dehydrogenase . Other enzymes involved in this path are yet to be purified though many of the reactions products that have been theoretically postulated have been identified . This is mainly due to the instability of intermediate compounds as well as the association of the enzyme substrate is femoral and experimental conditions need to be sophisticated further for isolation of these enzymes . The first structural genes of benzoate and hydroxy benzoate ligases were isolated from Rhodopseudomonas palustris. , , . This gene cluster of 30 kb size found in Rhodopseudomonas palustris coded for the Bad A protein . Similarly, some of the bph A,B,C and D cluster of genes coding for the degradation of pentachlorobenzenes were located in Pseudomonas pseudoalgaligenesKF 707.

Indian J Exp Biol, 2003 Sep, 41(9), 1030 - 45
Bioremediation: an important alternative for soil and industrial wastes clean-up; Soccol CR et al.; Industrial and environmental biotechnology are going to new paths, resulting in processes with "clean technologies", with the maximum production and the less residues . Technologies of remediation and bioremediation are continuously being improved using genetically modified microorganisms or those naturally occurring, to clean residues and contaminated areas from toxic organics . Bioremediation of soils, water and marine environments has many advantages but at the same time it is a challenge for the researchers and engineers . Consequently, it is extremely important to carry out feasibility study based on pilot-testing before starting a remediation project in order to determine the best conditions for the process . The article presents a brief review of bioremediation including the description of the different methods applied to soil and industrial wastes, and, finally, some experiences of solid-state fermentation in relation to bioremediation.

Indian J Exp Biol, 2003 Sep, 41(9), 935 - 44
Microbes in heavy metal remediation; Rajendran P et al.; Heavy metal contamination due to natural and anthropogenic sources is a global environmental concern . Release of heavy metal without proper treatment poses a significant threat to public health because of its persistence, biomagnification and accumulation in food chain . Non-biodegradability and sludge production are the two major constraints of metal treatment . Microbial metal bioremediation is an efficient strategy due to its low cost, high efficiency and ecofriendly nature . Recent advances have been made in understanding metal--microbe interaction and their application for metal accumulation/detoxification . This article summarizes the potentials of microbes in metal remediation.

J Environ Qual, 2004 May-Jun, 33(3), 861 - 7
Biodegradation of polycyclic aromatic hydrocarbons in oil-contaminated beach sediments treated with nutrient amendments; Xu R et al.; Microbial biodegradation of polycyclic aromatic hydrocarbons (PAHs) during the process of bioremediation can be constrained by lack of nutrients, low bioavailability of the contaminants, or scarcity of PAH-biodegrading microorganisms . This study focused on addressing the limitation of nutrient availability for PAH biodegradation in oil-contaminated beach sediments . In our previous study, three nutrient sources including inorganic soluble nutrients, the slow-release fertilizer Osmocote (Os; Scotts, Marysville, OH) and Inipol EAP-22 (Ip; ATOFINA Chemicals, Philadelphia, PA), as well as their combinations, were applied to beach sediments contaminated with an Arabian light crude oil . Osmocote was the most effective nutrient source for aliphatic biodegradation . This study presents data on PAH biodegradation in the oil-spiked beach sediments amended with the three nutrients . Biodegradation of total target PAHs (two- to six-ring) in all treatments followed a first-order biodegradation model . The biodegradation rates of total target PAHs in the sediments treated with Os were significantly higher than those without . On Day 45, approximately 9.3% of total target PAHs remained in the sediments amended with Os alone, significantly lower than the 54.2 to 58.0% remaining in sediment treatments without Os . Amendment with Inipol or soluble nutrients alone, or in combination, did not stimulate biodegradation rates of PAHs with a ring number higher than 2 . The slow-release fertilizer (Os) is therefore recommended as an effective nutrient amendment for intrinsic biodegradation of PAHs in oil-contaminated beach sediments.

Environ Sci Technol, 2004 Jun 1, 38(11), 3126 - 30
Stable carbon isotope fractionation during aerobic biodegradation of chlorinated ethenes; Chu KH et al.; Stable isotope analysis is recognized as a powerful tool for monitoring, assessing, and validating in-situ bioremediation processes . In this study, kinetic carbon isotope fractionation factors (epsilon) associated with the aerobic biodegradation of vinyl chloride (VC), cis-1,2-dichloroethylene (cDCE), and trichloroethylene (TCE) were examined . Of the three solvents, the largest fractionation effects were observed for biodegradation of VC . Both metabolic and cometabolic VC degradation were studied using Mycobacterium aurum L1 (grown on VC), Methylosinus trichosporium OB3b (grown on methane), Mycobacterium vaccae JOB5 (grown on propane), and two VC enrichment cultures seeded from contaminated soils of Alameda Point and Travis Air Force Base, CA . M . aurum L1 caused the greatest fractionation (epsilon = -5.7) while for the cometabolic cultures, epsilon values ranged from -3.2 to -4.8 . VC fractionation patterns for the enrichment cultures were within the range of those observed for the metabolic and cometabolic cultures (epsilon = -4.5 to -5.5) . The fractionation for cometabolic degradation of TCE by Me . trichosporium OB3b was low (epsilon = -1.1), while no quantifiable carbon isotopic fractionation was observed during the cometabolic degradation of cDCE . For all three of the tested chlorinated ethenes, isotopic fractionation measured during aerobic degradation was significantly smaller than that reported for anaerobic reductive dechlorination . This study suggests that analysis of compound-specific isotopic fractionation could assist in determining whether aerobic or anaerobic degradation of VC and cDCE predominates in field applications of in-situ bioremediation . In contrast, isotopic fractionation effects associated with metabolic and cometabolic reactions are not sufficiently dissimilar to distinguish these processes in the field.

J Ind Microbiol Biotechnol, 2004 Jun, 31(5), 216 - 22 Epub 2004 Jun 18.
Mineralization of hexachlorocyclohexane in soil during solid-phase bioremediation; Phillips TM et al.; Soil containing hexachlorocyclohexane (HCH) was spiked with (14)C-gamma-HCH and then subjected to bioremediation in bench-scale microcosms to determine the rate and extent of mineralization of the (14)C-labeled HCH to (14)CO(2) . The soil was treated using two different DARAMEND amendments, D6386 and D6390 . The amendments were previously found to enhance natural HCH bioremediation as determined by measuring the disappearance of parent compounds under either strictly oxic conditions (D6386), or cycled anoxic/oxic conditions (D6390) . Within 80 days of the initiation of treatment, mineralization was observed in all of the strictly oxic microcosms . However, mineralization was negligible in the cycled anoxic/oxic microcosms throughout the 275-day study, even after cycling was ceased at 84 days and although significant removal (up to 51%) of indigenous gamma-HCH (146 mg/kg) was detected by GC with electron capture detector . Of the amended, strictly oxic treatments, only one, in which 47% of the spiked (14)C-HCH was recovered as (14)CO(2), enhanced mineralization compared with an unamended treatment (in which 34% recovery was measured) . Other oxic treatments involving higher amendment application rates or auxiliary carbon sources were inhibitory to mineralization . Thus, although HCH degradation occurs during the application of either oxic or cycled anoxic/oxic DARAMEND treatments, mineralization of gamma-HCH may be inhibited depending on the amendment and treatment protocol.

J Environ Manage, 2004 Jul, 71(4), 361 - 9
Growth substrate selection and biodegradation of PCP by New Zealand white-rot fungi; Walter M et al.; Nine New Zealand native white-rot fungi were studied for their ability to grow and survive on different substrates formulated from bark, wheat straw, sawdust, apple pomace and maize products in order to identify their pentachlorophenol (PCP) biodegradation potential and to select a fungal carrier for bioaugmentation of polluted soils . Isolates were also evaluated to mineralize (14)C-PCP in liquid culture and in soil . The American fungus Phanerochaete chrysosporium outgrew the native fungi on the substrates tested, but the high colonisation did not result in superior PCP dechlorination as measured by chloride release . Whilst Trametes versicolor inocula produced on wheat straw and SCS (sawdust-corn meal-starch-mix) gave the highest chloride release, colonization of these two substrates as measured by biological potential was lower compared to the pomace and pomace-sawdust-mix . Neither lignin peroxidase nor manganese peroxidase production were measured for New Zealand white-rot fungi during the experiments . Laccase was the only enzyme detected . In liquid culture, the mineralisation rate was higher for T . versicolor isolates compared to P . chyrysoporium . Very little to no pentachloroanisole (PCA) was captured in the volatile fraction of T . versicolor isolates, whereas 75% of the volatile fraction of P . chrysosporium consisted of PCA . The soil microcosms studies, using contaminated soil from a timber treatment site, clearly showed that the New Zealand T . versicolor isolates mineralized PCP . Degradation of PCP in non-sterile soil was higher in the presence of white-rot fungi than in soil without white-rot fungus . This demonstrates that viable white-rot fungus is necessary for significant PCP degradation and that T . versicolor isolates showed PCP remediation potential . Wheat straw and SCS could be suitable carriers for New Zealand native T . versicolor isolates for bioremediation of PCP polluted soil sites.

Sci Total Environ, 2004 Jul 26, 328(1-3), 1 - 14
Bioremediation of 60Co from simulated spent decontamination solutions; Rashmi K et al.; Bioremediation of 60Co from simulated spent decontamination solutions by utilizing different biomass of (Neurospora crassa, Trichoderma viridae, Mucor recemosus, Rhizopus chinensis, Penicillium citrinum, Aspergillus niger and, Aspergillus flavus) fungi is reported . Various fungal species were screened to evaluate their potential for removing cobalt from very low concentrations (0.03-0.16 microM) in presence of a high background of iron (9.33 mM) and nickel (0.93 mM) complexed with EDTA (10.3 mM) . The different fungal isolates employed in this study showed a pickup of cobalt in the range 8-500 ng/g of dry biomass . The {Fe}/{Co} and {Ni}/{Co} ratios in the solutions before and after exposure to the fungi were also determined . At micromolar level the cobalt pickup by many fungi especially the mutants of N . crassa is seen to be proportional to the initial cobalt concentration taken in the solution . However, R . chinensis exhibits a low but iron concentration dependent cobalt pickup . Prior saturating the fungi with excess of iron during their growth showed the presence of selective cobalt pickup sites . The existence of cobalt specific sorption sites is shown by a model experiment with R . chinensis wherein at a constant cobalt concentration (0.034 microM) and varying iron concentrations so as to yield {Fe/Co}initial ratios in solution of 10, 100, 1000 and 287000 have all yielded a definite Co pickup capacity in the range 8-47 ng/g . The presence of Cr(III)EDTA (3 mM) in solution along with complexed Fe and Ni has not influenced the cobalt removal . The significant feature of this study is that even when cobalt is present in trace level (sub-micromolar) in a matrix of high concentration (millimolar levels) of iron, nickel and chromium, a situation typically encountered in spent decontamination solutions arising from stainless steel based primary systems of nuclear reactors, a number of fungi studied in this work showed a good sensitivity for cobalt pickup .

Huan Jing Ke Xue, 2004 Mar, 25(2), 129 - 33
{Issues concerned with the bioremediation of contaminated soils}; Song YF et al.; Several issues faced in the process of bioremediation were discussed in this paper, which are included as below: The principal and condition for the introducing of foreigner microbial; Mechanisms of suitability for microorganisms in the bioremediation process and the factors that influenced the degradation of pollutants; The correlations between the concentration of pollutants and their bioremediation; The secondary pollutants in the process of degradation of organic chemicals; The technology amplification of bioremediation technique on situ or/and in situ; the leaching process of contaminants; The Eco-toxicological diagnosis and evaluation for bioremediation technology and so on in order to enhance the realization for problems existed in the process of bioremediation and make it possible for more effective application of the bioremediation technology.

Huan Jing Ke Xue, 2004 Mar, 25(2), 98 - 103
{Movement and transformation of nitrate in soil by non-uniform electrokinetics}; Luo QS et al.; Movement and accumulation of nitrate in soil and groundwater has become a serious threat in many cities and agricultural areas . At the same time, application of nitrate as bacterial nitrogenous nutrient in the in-situ bioremediation of some organics-polluted sites is often required . Laboratory experiments were conducted to examine the feasibility of using non-uniform electrokinetics (NUEK) to control the movement of nitrate in unsaturated soil-water system . A natural soil taken from woodland was used as experimental soil . Three electrokinetic processes were tested in bench-scale cells at a constant potential gradient of 1.0 V/cm: unidirectional NUEK, NUEK with periodic polarity-reversal, and conventional uniform electrokinetic (UEK) . The tests showed that NUEK drove NO3- through the experimental soil at a rate of 13.5-20 cm/d depending upon the concentration of NO3- and the distribution of electric field density . Compared with UEK, NUEK process more effectively concentrated and retained NO3- close to the anode . Moreover, NUEK process maintained soil characteristics and consumed much less electric energy. , . Reversal the polarity of NUEK weakened the concentration of NO3- to electrodes, but it stimulated the transformation of NO3- to NO2- and further lowered the electric energy consumption.

Environ Int, 2004 Sep, 30(7), 949 - 51
Plants against the global epidemic of arsenic poisoning; Alkorta I et al.; Due to the growing current trend around the world of drinking water from underground sources, in an attempt to replace heavily polluted surface water supplies, arsenic is causing a global epidemic of poisoning with hundreds of millions of people now being thought at serious risk in many countries . Phytoremediation (bioremediation mediated by plants) has been proposed as an effective tool in arsenic cleanup . Actually, some plants (most notably, the Chinese brake fern Pteris vittata) have been reported to be suitable for arsenic phytoremediation . In this respect, transgenic plants are being developed to improve their capacity to accumulate arsenic . Most interestingly, rhizofiltration (use of plants to absorb or adsorb pollutants from water) is being considered for the ex situ and in situ remediation of arsenic-contaminated water . Similarly, some plants show great potential to remove arsenic from polluted soil.

Biotechnol Prog, 2004 May-Jun, 20(3), 655 - 60
Industrial potential of organic solvent tolerant bacteria; Sardessai YN et al.; Most bacteria and their enzymes are destroyed or inactivated in the presence of organic solvents . Organic solvent tolerant bacteria are a relatively novel group of extremophilic microorganisms that combat these destructive effects and thrive in the presence of high concentrations of organic solvents as a result of various adaptations . These bacteria are being explored for their potential in industrial and environmental biotechnology, since their enzymes retain activity in the presence of toxic solvents . This property could be exploited to carry out bioremediation and biocatalysis in the presence of an organic phase . Because a large number of substrates used in industrial chemistry, such as steroids, are water-insoluble, their bioconversion rates are affected by poor dissolution in water . This problem can be overcome by carrying out the process in a biphasic organic-aqueous fermentation system, wherein the substrate is dissolved in the organic phase and provided to cells present in the aqueous phase . In bioprocessing of fine chemicals such as cis-diols and epoxides using such cultures, organic solvents can be used to extract a toxic product from the aqueous phase, thereby improving the efficiency of the process . Bacterial strains reported to grow on and utilize saturated concentrations of organic solvents such as toluene can revolutionize the removal of such pollutants . It is now known that enzymes display striking new properties in the presence of organic solvents . The role of solvent-stable enzymes in nonaqueous biocatalysis needs to be explored and could result in novel applications.

J Biotechnol, 2004 Jun 10, 110(3), 235 - 50
Biodegradation of phenanthrene in soil-slurry systems with different mass transfer regimes and soil contents; Woo SH et al.; The effect of soil contents and mass transfer rates on soil bioremediation was investigated . Phenanthrene, a 3-ring polycyclic aromatic hydrocarbon (PAH), was chosen as a model target compound . The biodegradation tests were performed in soil-slurry systems at two distinct mass transfer rates: fast in flasks tests at 150 rpm and slow in roller-bottle tests at 2 rpm . The rate of phenanthrene biodegradation was similar at low soil content (2 wt.%) in both slurry systems, but the rates at high soil contents (6 and 18 wt.%) were higher in the roller-bottle tests . The maximum utilization rate constant for sorbed-phase biodegradation obtained from curve fitting using a mathematical model was decreased in the flask tests with increasing soil content, while not decreased in the roller-bottle tests .

Bioresour Technol, 2004 Sep, 94(2), 143 - 51
Anaerobic biodegradation of no . 2 diesel fuel in soil: a soil column study; Boopathy R; Soil and sediments are contaminated with petroleum hydrocarbons in many parts of the world . Anaerobic degradation of petroleum hydrocarbon is very relevant in removing oil spills in the anaerobic zones of soil and sediments . This research investigates the possibility of degrading no . diesel fuel under anaerobic conditions . Anaerobic packed soil columns were used to simulate and study in situ bioremediation of soil contaminated with diesel fuel . Several anaerobic conditions were evaluated in soil columns, including sulfate reducing, nitrate reducing, methanogenic, and mixed electron acceptor conditions . The objectives were to determine the extent of diesel fuel degradation in soil columns under various anaerobic conditions and identify the best conditions for efficient removal of diesel fuel . Diesel fuels were degraded significantly under all conditions compared to no electron supplemented soil column (natural attenuation) . However, the rate of diesel degradation was the highest under mixed electron acceptor conditions followed in order by sulfate reducing, nitrate reducing, and methanogenic conditions . Under mixed electron acceptor condition 81% of diesel fuel was degraded within 310 days . While under sulfate reducing condition 54.5% degradation of diesel fuel was observed for the same period . This study showed evidence for diesel fuel metabolism in a mixed microbial population system similar to any contaminated field sites, where heterogeneous microbial population exists .

Commun Agric Appl Biol Sci, 2003, 68(4 Pt A), 409 - 13
Biodegradation of simazine in olive fields; Santiago R et al.; Simazine (2-chloro-4, bis ethylamino-1,3,5-triazine) is a herbicide of the s-triazine group used mainly to control broad-leaved weeds in different crops . Several papers report about simazine and other s-triazine derivates as being actual polluting agents . In fact, simazine has been detected in groundwater and soil . Since this herbicide has been extensively used in Andalusia (south of Spain), we are analyzing the levels of simazine residues found in the soil of olive fields . We are also simazine could be detected isolating live micro organisms able to degrade this compound, and are characterizing the metabolic pathways leading to this degradation and the fate of this compound in nature . With all these data in mind, we will try to develop a strategy for the bioremediation of contaminated soils . We have taken samples of soil from many olive orchards of Andalusia that have been treated with simazine . These samples were located with the help of a handheld GPS . The presence of simazine of these samples was detected by HPLC . In most of the samples taken no, and those where it could be, contained very low levels of this herbicide (lower than 0.5 ppm) . Soil samples are being characterized to determine their physicochemical characteristics {pH, organic matter, texture, etc), and we are attempting to correlate all these parameters with the presence or absence of simazine . From some of the soils, we have isolated a group of micro organisms that can grow using simazine as the sole carbon and nitrogen sources . We are analyzing how the addition of carbon or nitrogen can influence the rate of the simazine degradation.

Environ Microbiol, 2004 Jun, 6(6), 596 - 604
Graphite electrodes as electron donors for anaerobic respiration; Gregory KB et al.; It has been demonstrated previously that Geobacter species can transfer electrons directly to electrodes . In order to determine whether electrodes could serve as electron donors for microbial respiration, enrichment cultures were established from a sediment inoculum with a potentiostat-poised graphite electrode as the sole electron donor and nitrate as the electron acceptor . Nitrate was reduced to nitrite with the consumption of electrical current . The stoichiometry of electron and nitrate consumption and nitrite accumulation were consistent with the electrode serving as the sole electron donor for nitrate reduction . Analysis of 16 rRNA gene sequences demonstrated that the electrodes supplied with current were specifically enriched in microorganisms with sequences most closely related to the sequences of known Geobacter species . A pure culture of Geobacter metallireducens was shown to reduce nitrate to nitrite with the electrode as the sole electron donor with the expected stoichiometry of electron consumption . Cells attached to the electrode appeared to be responsible for the nitrate reduction . Attached cells of Geobacter sulfurreducens reduced fumarate to succinate with the electrode as an electron donor . These results demonstrate for the first time that electrodes may serve as a direct electron donor for anaerobic respiration . This finding has implications for the harvesting of electricity from anaerobic sediments and the bioremediation of oxidized contaminants.

J Agric Food Chem, 2004 May 19, 52(10), 3030 - 5
Algal degradation of a known endocrine disrupting insecticide, alpha-endosulfan, and its metabolite, endosulfan sulfate, in liquid medium and soil; Sethunathan N et al.; The role of algae in the persistence, transformation, and bioremediation of two endocrine disrupting chemicals, alpha-endosulfan (a cyclodiene insecticide) and its oxidation product endosulfan sulfate, in soil (incubated under light or in darkness) and a liquid medium was examined . Incubation of soil under light dramatically decreased the persistence of alpha-endosulfan and enhanced its transformation to endosulfan sulfate, over that of dark-incubated soil samples, under both nonflooded and flooded conditions . This enhanced degradation of soil-applied alpha-endosulfan was associated with profuse growth of indigenous phototrophic organisms such as algae in soil incubated under light . Inoculation of soil with green algae, Chlorococcum sp . or Scenedesmus sp., further enhanced the degradation of alpha-endosulfan . The role of algae in alpha-endosulfan degradation was convincingly demonstrated when these algae degraded alpha-endosulfan to endosulfan sulfate, the major metabolite, and endosulfan ether, a minor metabolite, in a defined liquid medium . When a high density of the algal inoculum was used, both metabolites appeared to undergo further degradation as evident from their accumulation only in small amounts and the appearance of an endosulfan-derived aldehyde . Interestingly, beta-endosulfan was detected during degradation of alpha-endosulfan by high density algal cultures . These algae were also capable of degrading endosulfan sulfate but to a lesser extent than alpha-endosulfan . Evidence suggested that both alpha-endosulfan and endosulfan sulfate were immediately sorbed by the algae from the medium, which then effected their degradation. , . Biosorption, coupled with their biotransformation ability, especially at a high inoculum density, makes algae effective candidates for remediation of alpha-endosulfan-polluted environments.

Appl Environ Microbiol, 2004 May, 70(5), 2952 - 8
Impact of temperature on the physiological status of a potential bioremediation inoculant, Arthrobacter chlorophenolicus A6; Backman A et al.; Arthrobacter chlorophenolicus A6 (A6) can degrade large amounts of 4-chlorophenol in soil at 5 and 28 degrees C . In this study, we investigated the effects of temperature on the physiological status of this bacterium in pure culture and in soil . A derivative of A6 tagged with the gfp gene (encoding green fluorescent protein {GFP}) was used to specifically quantify A6 cells in soil . In addition, cyano-ditolyl-tetrazoliumchloride was used to stain GFP-fluorescent cells with an active electron transfer system ("viable cells") whereas propidium iodide (PI) was used to stain cells with damaged membranes ("dead cells") . Another derivative of the strain (tagged with the firefly luciferase gene {luc}) was used to monitor the metabolic activity of the cell population, since the bioluminescence phenotype is dependent on cellular energy reserves . When the cells were incubated in soil at 28 degrees C, the majority were stained with PI, indicating that they had lost their cell integrity . In addition, there was a corresponding decline in metabolic activity and in the ability to be grown in cultures on agar plates after incubation in soil at 28 degrees C, indicating that the cells were dying under those conditions . When the cells were incubated in soil at 5 degrees C, by contrast, the majority of the cells remained intact and a large fraction of the population remained metabolically active . A similar trend towards better cell survival at lower temperatures was found in pure-culture experiments . These results make A . chlorophenolicus A6 a good candidate for the treatment of chlorophenol-contaminated soil in cold climates.

Appl Environ Microbiol, 2004 May, 70(5), 2935 - 40
Stable isotope fractionation caused by glycyl radical enzymes during bacterial degradation of aromatic compounds; Morasch B et al.; Stable isotope fractionation was studied during the degradation of m-xylene, o-xylene, m-cresol, and p-cresol with two pure cultures of sulfate-reducing bacteria . Degradation of all four compounds is initiated by a fumarate addition reaction by a glycyl radical enzyme, analogous to the well-studied benzylsuccinate synthase reaction in toluene degradation . The extent of stable carbon isotope fractionation caused by these radical-type reactions was between enrichment factors (epsilon) of -1.5 and -3.9, which is in the same order of magnitude as data provided before for anaerobic toluene degradation . Based on our results, an analysis of isotope fractionation should be applicable for the evaluation of in situ bioremediation of all contaminants degraded by glycyl radical enzyme mechanisms that are smaller than 14 carbon atoms . In order to compare carbon isotope fractionations upon the degradation of various substrates whose numbers of carbon atoms differ, intrinsic epsilon (epsilon(intrinsic)) were calculated . A comparison of epsilon(intrinsic) at the single carbon atoms of the molecule where the benzylsuccinate synthase reaction took place with compound-specific epsilon elucidated that both varied on average to the same extent . Despite variations during the degradation of different substrates, the range of epsilon found for glycyl radical reactions was reasonably narrow to propose that rough estimates of biodegradation in situ might be given by using an average epsilon if no fractionation factor is available for single compounds.

Appl Environ Microbiol, 2004 May, 70(5), 2614 - 20
Response of Archaeal communities in beach sediments to spilled oil and bioremediation; Roling WF et al.; While the contribution of Bacteria to bioremediation of oil-contaminated shorelines is well established, the response of Archaea to spilled oil and bioremediation treatments is unknown . The relationship between archaeal community structure and oil spill bioremediation was examined in laboratory microcosms and in a bioremediation field trial . 16S rRNA gene-based PCR and denaturing gradient gel analysis revealed that the archaeal community in oil-free laboratory microcosms was stable for 26 days . In contrast, in oil-polluted microcosms a dramatic decrease in the ability to detect Archaea was observed, and it was not possible to amplify fragments of archaeal 16S rRNA genes from samples taken from microcosms treated with oil . This was the case irrespective of whether a bioremediation treatment (addition of inorganic nutrients) was applied . Since rapid oil biodegradation occurred in nutrient-treated microcosms, we concluded that Archaea are unlikely to play a role in oil degradation in beach ecosystems . A clear-cut relationship between the presence of oil and the absence of Archaea was not apparent in the field experiment . This may have been related to continuous inoculation of beach sediments in the field with Archaea from seawater or invertebrates and shows that the reestablishment of Archaea following bioremediation cannot be used as a determinant of ecosystem recovery following bioremediation . Comparative 16S rRNA sequence analysis showed that the majority of the Archaea detected (94%) belonged to a novel, distinct cluster of group II uncultured Euryarchaeota, which exhibited less than 87% identity to previously described sequences . A minor contribution of group I uncultured Crenarchaeota was observed.

Appl Environ Microbiol, 2004 May, 70(5), 2603 - 13
Bacterial community dynamics and hydrocarbon degradation during a field-scale evaluation of bioremediation on a mudflat beach contaminated with buried oil; Roling WF et al.; A field-scale experiment with a complete randomized block design was performed to study the degradation of buried oil on a shoreline over a period of almost 1 year . The following four treatments were examined in three replicate blocks: two levels of fertilizer treatment of oil-treated plots, one receiving a weekly application of liquid fertilizer and the other treated with a slow-release fertilizer; and two controls, one not treated with oil and the other treated with oil but not with fertilizer . Oil degradation was monitored by measuring carbon dioxide evolution and by chemical analysis of the oil . Buried oil was degraded to a significantly greater extent in fertilized plots, but no differences in oil chemistry were observed between the two different fertilizer treatments, although carbon dioxide production was significantly higher in the oil-treated plots that were treated with slow-release fertilizer during the first 14 days of the experiment . Bacterial communities present in the beach sediments were profiled by denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA gene fragments and 16S rRNA amplified by reverse transcriptase PCR . Similarities between the DGGE profiles were calculated, and similarity matrices were subjected to statistical analysis . These analyses showed that although significant hydrocarbon degradation occurred both in plots treated with oil alone and in the plots treated with oil and liquid fertilizer, the bacterial community structure in these plots was, in general, not significantly different from that in the control plots that were not treated with oil and did not change over time . In contrast, the bacterial community structure in the plots treated with oil and slow-release fertilizer changed rapidly, and there were significant differences over time, as well as between blocks and even within plots . The differences were probably related to the higher concentrations of nutrients measured in interstitial water from the plots treated with slow-release fertilizer . Bacteria with 16S rRNA sequences closely related (>99.7% identity) to Alcanivorax borkumensis and Pseudomonas stutzeri sequences dominated during the initial phase of oil degradation in the plots treated with slow-release fertilizer . Field data were compared to the results of previous laboratory microcosm experiments, which revealed significant differences.

Chemosphere, 2004 Jul, 56(2), 159 - 66
Enhanced degradation of fluorene in soil slurry by Absidia cylindrospora and maltosyl-cyclodextrin; Garon D et al.; This study investigates the fungal biodegradation of fluorene, a polycyclic aromatic hydrocarbon, in liquid medium and soil slurry . Fungal strains and cyclodextrins were used in order to degrade fluorene and optimize fluorene bioavailability and degradation in soil slurries . After a procedure of selection in solid and liquid media, maltosyl-cyclodextrin, a branched cyclodextrin was chosen . 47 fungal strains isolated from a contaminated site were tested for biodegradation . Results showed the greater efficiency of "adapted" fungi isolated from contaminated soil vs reference strains belonging to the collection of the laboratory . These assays allowed us to select the most efficient strain, Absidia cylindrospora, which was used in a bioaugmentation process . Bioaugmentation tests were performed in an artificially contaminated non-sterile soil . In the presence of A . cylindrospora, more than 90% of the fluorene was degraded within 288 h, while 576 h were necessary in the absence of fungal bioremediation . It also appeared that biodegradation was enhanced by amendment with previously selected maltosyl-cyclodextrin . The results of this study indicate that A . cylindrospora and maltosyl-cyclodextrin could be used successfully in fluorene bioremediation systems.

Environ Technol, 2004 Feb, 25(2), 201 - 10
Aerobic biotransformation of octylphenol polyethoxylate surfactant in soil microcosms; Chen HJ et al.; The biotransformation of octylphenol polyethoxylate surfactant (Triton X-100) and bacterial communities in soil microcosms was investigated . The soil microcosms were designed to simulate real sites of bioremediation . The soil used in this study was contaminated with pesticides and alkylphenol polyethoxylate surfactants over a long period of time . The nitrogen source, (NH4)2SO4 and the mineral salt basal solution were added to the microcosm and the water content was adjusted to 50% with distilled water . The microcosms were aerated using an aeration system with an air flow rate of 0.3 l min(-1) . The exogenous bacterial strain Pseudomonas sp . SH4 was added to the microcosms to increase the rate of biotransformation of the Triton X-100 . The number of microorganisms and the theoretical extent of formation of carbon dioxide were estimated to evaluate the biotransformation of Triton X-100 in the microcosms . The analytical results revealed that the exogenous bacteria could increase the rate of transformation of Triton X-100 by approximately 50% . Aeration of the microcosm increased the biotransformation of Triton X-100 by 45% . Bacterial count of 6.8x10(10) MPN g(-1) of soil was achieved in the M5 microcosm . Analysis of the bacterial community by 16S rDNA sequences revealed that Pseudomonas sp . SH4 could dominate all the microcosms to which it was added as an exogenous bacteria. , , . The quantity of the indigenous bacterial strains Stenotrophomonas maltophilia, Stenotrophomonas sp . and clone 4-70 were also enhanced in the microcosms by the aeration, and the addition of carbon and nitrogen source.

Mar Pollut Bull, 2004 May, 48(9-10), 983 - 5
Tolerance and accumulation of hexavalent chromium by two seaweed associated aspergilli; Vala AK et al.; Marine seaweed (Eucheuma sp.) associated strains of Aspergillus flavus and Aspergillus niger were tested for their Cr(VI) tolerance . Both the isolates showed luxuriant growth in different concentrations of Cr(VI), i.e., 25, 50 and 100 ppm . There was no marked variation in the dry weight of control and test isolates, which indicated that both the isolates can tolerate a wide range of hexavalent chromium and their application for bioremediation purpose can be envisaged as XRF data revealed both the isolates accumulated more than 25% of the chromium supplied . A . flavus invariably exhibited higher accumulation potential.

FEMS Microbiol Lett, 2004 May 1, 234(1), 75 - 80
Novel pollutant-resistant methylotrophic bacteria for use in bioremediation; De Marco P et al.; Thirty one novel methylotrophic bacterial strains were isolated from a range of soil and sediment sources (both pristine and polluted) under different enrichment regimes . They were characterised physiologically and classified by their 16S rRNA gene sequence . A great taxonomical and phenotypical variety was recovered . Some of the isolates display interesting features of resistance to heavy metals, arsenate or organic pollution and four can be considered real 'super-bugs' for their ability to withstand extremely high concentrations of a variety of pollutants . A description of the 31 strains is presented in this work.

Environ Sci Pollut Res Int, 2004, 11(2), 98 - 106
Effects of lindane on the photosynthetic apparatus of the cyanobacterium Anabaena: fluorescence induction studies and immunolocalization of ferredoxin-NADP+ reductase; Bueno M et al.; INTENTION, GOAL, SCOPE, BACKGROUND: Cyanobacteria have the natural ability to degrade moderate amounts of organic pollutants . However, when pollutant concentration exceeds the level of tolerance, bleaching of the cells and death occur within 24 hours . Under stress conditions, cyanobacterial response includes the short-term adaptation of the photosynthetic apparatus to light quality, named state transitions . Moreover, prolonged stresses produce changes in the functional organization of phycobilisomes and in the core-complexes of both photosystems, which can result in large changes in the PS II fluorescence yield . The localization of ferredoxin-NADP+ reductase (FNR) at the ends of some peripheral rods of the cyanobacterial phycobilisomes, makes this protein a useful marker to check phycobilisome integrity . OBJECTIVE: The goal of this work is to improve the knowledge of the mechanism of action of a very potent pesticide, lindane (gamma-hexaclorociclohexane), in the cyanobacterium Anabaena sp., which can be considered a potential candidate for bioremediation of pesticides . We have studied the effect of lindane on the photosynthetic apparatus of Anabaena using fluorescence induction studies . As ferredoxin-NADP+ reductase plays a key role in the response to oxidative stress in several systems, changes in synthesis, degradation and activity of FNR were analyzed . Immunolocalization of this enzyme was used as a marker of phycobilisome integrity . The knowledge of the changes caused by lindane in the photosynthetic apparatus is essential for rational further design of genetically-modified cyanobacteria with improved biorremediation abilities . METHODS: Polyphasic chlorophyll a fluorescence rise measurements (OJIP) have been used to evaluate the vitality and stress adaptation of the nitrogen-fixing cyanobacterium Anabaena PCC 7119 in the presence of increasing concentrations of lindane . Effects of the pesticide on the ultrastructure have been investigated by electron microscopy, and FNR has been used as a marker of phycobilisome integrity . RESULTS AND DISCUSSION: Cultures of Anabaena sp . treated with moderate amounts of lindane showed a decrease in growth rate followed by a recovery after 72 hours of pesticide treatment . Concentrations of lindane below 5 ppm increased the photosynthetic performance and activity of the cells . Higher amounts of pesticide caused a decrease in these activities which seems to be due to a non-competitive inhibition of PS II . Active PS II units are converted into non-QA reducing, so called heat sink centers . Specific activity and amount of FNR in lindane-treated cells were similar to the values measured in control cultures . Release of FNR from the thylakoid after 48 hours of exposure to 5 ppm of lindane towards the cytoplasm was detected by immunogold labeling and electron microscopy . CONCLUSIONS: From these results, we conclude that the photosynthetic performance and activity of the cells are slightly increased in the presence of lindane up to 5 ppm . Moreover, in those conditions, lindane did not produce significant changes in the synthesis, degradation or activity of FNR . The high capability of Anabaena to tolerate lindane makes this cyanobacterium a good candidate for phytoremediation of polluted areas . RECOMMENDATION AND OUTLOOK: The results of this study show that cultures of Anabaena PCC 7119 tolerate lindane up to 5 ppm, without significant changes in the photosynthetic vitality index of the cells . However, a slight increase in phycobiliprotein synthesis is observed, which is related to total protein content . This change might be due to degradation of proteins less stable than phycobiliproteins . An identification of the proteins with altered expression pattern in the presence of the pesticide remains the subject of further work and will provide valuable information for the preparation of strains which are highly tolerant to lindane.

Microb Ecol, 2004 Aug, 48(2), 230 - 8 Epub 2004 May 06.
Isolation and characterization of polycyclic aromatic hydrocarbon-degrading Mycobacterium isolates from soil; Miller CD et al.; Bioremediation of soils contaminated with wood preservatives containing polycyclic aromatic hydrocarbons (PAHs) is desired because of their toxic, mutagenic, and carcinogenic properties . Creosote wood preservative-contaminated soils at the Champion International Superfund Site in Libby, Montana currently undergo bioremediation in a prepared-bed land treatment unit (LTU) process . Microbes isolated from these LTU soils rapidly mineralized the (14)C-labeled PAH pyrene in the LTU soil . Gram staining, electron microscopy, and 16S rDNA-sequencing revealed that three of these bacteria, JLS, KMS, and MCS, were Mycobacterium strains . The phylogeny of the 16S rDNA showed that they were distinct from other Mycobacterium isolates with PAH-degrading activities . Catalase and superoxide dismutase (SOD) isozyme profiles confirmed that each isolate was distinct from each other and from the PAH-degrading mycobacterium, Mycobacterium vanbaalenii sp . nov, isolated from a petroleum-contaminated soil . We find that dioxygenase genes nidA and nidB are present in each of the Libby Mycobacterium isolates and are adjacent to each other in the sequence nidB-nidA, an order that is unique to the PAH-degrading mycobacteria.

Genet Mol Res, 2004 Mar 31, 3(1), 117 - 33
Transport genes of Chromobacterium violaceum: an overview; Grangeiro TB et al.; The complete genome sequence of the free-living bacterium Chromobacterium violaceum has been determined by a consortium of laboratories in Brazil . Almost 500 open reading frames (ORFs) coding for transport-related membrane proteins were identified in C . violaceum, which represents 11% of all genes found . The main class of transporter proteins is the primary active transporters (212 ORFs), followed by electrochemical potential-driven transporters (154 ORFs) and channels/pores (62 ORFs) . Other classes (61 ORFs) include group translocators, transport electron carriers, accessory factors, and incompletely characterized systems . Therefore, all major categories of transport-related membrane proteins currently recognized in the Transport Protein Database are present in C . violaceum . The complex apparatus of transporters of C . violaceum is certainly an important factor that makes this bacterium a dominant microorganism in a variety of ecosystems in tropical and subtropical regions . From a biotechnological point of view, the most important finding is the transporters of heavy metals, which could lead to the exploitation of C . violaceum for bioremediation.

J Biol Chem, 2004 Jul 16, 279(29), 30600 - 10 Epub 2004 Apr 19.
Crystal structure of the toluene/o-xylene monooxygenase hydroxylase from Pseudomonas stutzeri OX1 . Insight into the substrate specificity, substrate channeling, and active site tuning of multicomponent monooxygenases; Sazinsky MH et al.; The four-component toluene/o-xylene monooxygenase (ToMO) from Pseudomonas stutzeri OX1 is capable of oxidizing arenes, alkenes, and haloalkanes at a carboxylate-bridged diiron center similar to that of soluble methane monooxygenase (sMMO) . The remarkable variety of substrates accommodated by ToMO invites applications ranging from bioremediation to the regio- and enantiospecific oxidation of hydrocarbons on an industrial scale . We report here the crystal structures of the ToMO hydroxylase (ToMOH), azido ToMOH, and ToMOH containing the product analogue 4-bromophenol to 2.3 A or greater resolution . The catalytic diiron(III) core resembles that of the sMMO hydroxylase, but aspects of the alpha2beta2gamma2 tertiary structure are notably different . Of particular interest is a 6-10 A-wide channel of approximately 35 A in length extending from the active site to the protein surface . The presence of three bromophenol molecules in this space confirms this route as a pathway for substrate entrance and product egress., , , . An analysis of the ToMOH active site cavity offers insights into the different substrate specificities of multicomponent monooxygenases and explains the behavior of mutant forms of homologous enzymes described in the literature.

Acta Microbiol Pol, 2003, 52(4), 405 - 17
Hydrocarbon bioremediation potential of an unimpacted Kuwaiti oil-field environment; Obuekwe C et al.; Seasonal variations in the hydrocarbon-degrading potential of soil samples from an unimpacted site in the Kuwaiti Burgan oil field environment were studied under mesophilic conditions . Hydrocarbon-degrading microorganisms occurred but varied all-year-round, and their numbers ranged from 1.3 x 10(7) to 9.3 x 10(7) CFU g(-1) dry soil, while hydrocarbon-degrading fungi ranged from 3.0 x 10(4) - 3.8 x 10(5) CFU g(-1) dry soil, depending on the sampling period . These hydrocarbon-degraders also comprised variable but generally high proportions of the total aerobic heterotrophic organisms (2 to > 98%) for bacteria and lower levels (7-9%) for fungi . The crude oil-degrading capacity of the oil-degrading populations (bacteria and fungi) ranged from 80-95% of the hexane-extractable fractions . Differential inhibition studies carried out on soil samples showed that bacteria were the greater contributors to hydrocarbon degradation (79-92%) than fungi . Pure hydrocarbon substrates, hexadecane and phenanthrene, were degraded to near completion after a 28-day incubation by both the bacterial and fungal portions of the soil flora.

Environ Toxicol Chem, 2004 Apr, 23(4), 938 - 44
Physical and biochemical interactions of soil fungi with asbestos fibers; Martino E et al.; Iron, a structural component of most asbestos, is thought to play a crucial role in asbestos toxicity . Surface iron favors fiber uptake by mammalian cells and promotes the generation of free radicals with consequent DNA and lipid damage . In some cases, chemical removal of iron from asbestos fibers has reduced several cellular responses to asbestos . Since iron represents an essential element for soil microorganisms, many of them have developed mechanisms to scavenge this element from poorly soluble forms . We have investigated the ability of some soil fungi to produce iron chelators capable of extracting iron from crocidolite (blue asbestos) . Many of the species/isolates investigated could remove significant amounts of iron from crocidolite fibers, Fusarium oxysporum being the most effective . The fungal responses following exposure to asbestos fibers also have been investigated with morphological and biochemical approaches . In liquid cultures, the fibers were visibly cleared from the suspension because they were tightly bound to the fungal hyphae . Modifications in the fungal protein profiles were observed following exposure to asbestos fibers . By binding the fibers and depriving them of iron, selected species/strains of soil fungi might represent interesting tools for the bioremediation of asbestos-contaminated soils.

Appl Environ Microbiol, 2000 Nov, 66(11), 4935 - 9
Monitoring bacterial transport by stable isotope enrichment of cells; Holben WE et al.; Understanding the transport and behavior of bacteria in the environment has broad implications in diverse areas, ranging from agriculture to groundwater quality, risk assessment, and bioremediation . The ability to reliably track and enumerate specific bacterial populations in the context of native communities and environments is key to developing this understanding . We report a novel bacterial tracking approach, based on altering the stable carbon isotope value (delta(13)C) of bacterial cells, which provides specific and sensitive detection and quantification of those cells in environmental samples . This approach was applied to the study of bacterial transport in saturated porous media . The transport of introduced organisms was indicated by mass spectrometric analysis of groundwater samples, where the presence of (13)C-enriched bacteria resulted in increased delta(13)C values of the samples, allowing specific and sensitive detection and enumeration of the bacteria of interest . We demonstrate the ability to produce highly (13)C-enriched bacteria, present data indicating that results obtained with this approach accurately represent intact introduced bacteria, and include field data on the use of this stable isotope approach to monitor in situ bacterial transport . This detection strategy allows sensitive detection of an introduced, unmodified bacterial strain in the presence of the indigenous bacterial community, including itself in its unenriched form.

Crit Rev Microbiol, 2000, 26(3), 163 - 78
Biodegradation of methyl tertiary-butyl ether (MTBE) and other fuel oxygenates; Prince RC; Methyl tertiary-butyl ether (MTBE) has been added to gasoline in the U.S . for the last decade in order to meet the mandates of the 1990 Clean Air Act . This law decreed that gasoline sold in many locations must contain oxygenates to improve combustion and minimize air pollution . Unfortunately, this widespread use has led to the contamination of some soils and aquifers, and remediation is now required . Bioremediation has proven to be an environmentally responsible and cost-effective approach to remediating petroleum spills; this article reviews the potential that bioremediation may also be appropriate for remediating MTBE contamination . There is now good evidence that MTBE can be degraded by bacteria and fungi under aerobic conditions, and promising indications that the process also occurs under methanogenic and ferric iron-reducing conditions . Yet, apparently it is not a widespread phenomenon . The challenge is to find effective bioremediation strategies that maximize this biodegradation so that it can be used reliably in cleaning contaminated sites . Both simple biostimulation and more complex bioaugmentation protocols are being developed to meet this pressing need.

J Chromatogr A, 2000 Sep 15, 892(1-2), 421 - 33
Comparisons of soxhlet extraction, pressurized liquid extraction, supercritical fluid extraction and subcritical water extraction for environmental solids: recovery, selectivity and effects on sample matrix; Hawthorne SB et al.; Extractions of a polycyclic aromatic hydrocarbon (PAH)-contaminated soil from a former manufactured gas plant site were performed with a Soxhlet apparatus (18 h), by pressurized liquid extraction (PLE) (50 min at 100 degrees C), supercritical fluid extraction (SFE) (1 h at 150 degrees C with pure CO2), and subcritical water (1 h at 250 degrees C, or 30 min at 300 degrees C) . Although minor differences in recoveries for some PAHs resulted from the different methods, quantitative agreement between all of the methods was generally good . However, the extract quality differed greatly . The organic solvent extracts (Soxhlet and PLE) were much darker, while the extracts from subcritical water (collected in toluene) were orange, and the extracts from SFE (collected in CH2Cl2) were light yellow . The organic solvent extracts also yielded more artifact peaks in the gas chromatography (GC)-mass spectrometry and GC-flame ionization detection chromatograms, especially compared to supercritical CO2 . Based on elemental analysis (carbon and nitrogen) of the soil residues after each extraction, subcritical water, PLE, and Soxhlet extraction had poor selectivity for PAHs versus bulk soil organic matter (approximately 1/4 to 1/3 of the bulk soil organic matter was extracted along with the PAHs), while SFE with pure CO2 removed only 8% of the bulk organic matrix . Selectivities for different compound classes also vary with extraction method . Extraction of urban air particulate matter with organic solvents yields very high concentrations of n- and branched alkanes (approximately C18 to C30) from diesel exhaust as well as lower levels of PAHs, and no selectivity between the bulk alkanes and PAHs is obtained during organic solvent extraction . Some moderate selectivity with supercritical CO2 can be achieved by first extracting the bulk alkanes at mild conditions, followed by stronger conditions to extract the remaining PAHs, i.e., the least polar organics are the easiest organics to extract with pure CO2 . In direct contrast, subcritical water prefers the more polar analytes, i.e., PAHs were efficiently extracted from urban air particulates at 250 degrees C, with little or no extraction of the alkanes . Finally, recent work has demonstrated that many pollutant molecules become "sequestered" as they age for decades in the environment (i.e., more tightly bound to soil particles and less available to organisms or transport) . Therefore, it may be more important for an extraction method to only recover pollutant molecules that are environmentally-relevant, rather than the conventional attempts to extract all pollutant molecules regardless of how tightly bound they are to the soil or sediment matrix . Initial work comparing SFE extraction behavior using mild to strong conditions with bioremediation behavior of PAHs shows great promise to develop extraction methodology to measure environmentally-relevant concentrations of pollutants in addition to their total concentrations.

Sci Total Environ, 2000 Oct 16, 261(1-3), 109 - 13
Capacity of mercury volatilization by mer (from Escherichia coli) and glutathione S-transferase (from Schistosoma mansoni) genes cloned in Escherichia coli; Cursino L et al.; A study was carried out to evaluate the capacity for mercury volatilization by genetically engineered strains that express the mer and glutathione S-transferase genes from Escherichia coli and Schistosoma mansoni, respectively . This method enabled strains containing simultaneously mer and glutathione S-transferase genes to grow in high concentrations of mercuric chloride (30 microg/ml) and to volatilize part of the mercury (248 microg/g cell dry wt.) present in the culture medium, while strains bearing only a single gene, did not have the same behavior . Up to 70% of the total mercury of bacterial volatilization occurred in the first 4 h . Although the findings were preliminary, the genetically engineered strain containing simultaneously the mer and glutathione S-transferase genes show a great potential for bioremediation . It may be used in a closed system to remove by volatilization, and recover mercury (Hg0) from contaminated effluents, such as industrial effluent, for instance.

Appl Microbiol Biotechnol, 2000 Sep, 54(3), 424 - 31
Biodegradation of propanol and isopropanol by a mixed microbial consortium; Bustard MT et al.; The aerobic biodegradation of high concentrations of 1-propanol and 2-propanol (IPA) by a mixed microbial consortium was investigated . Solvent concentrations were one order of magnitude greater than any previously reported in the literature . The consortium utilized these solvents as their sole carbon source to a maximum cell density of 2.4 x 10(9) cells ml(-1) . Enrichment experiments with propanol or IPA as carbon sources were carried out in batch culture and maximum specific growth rates (mumax) calculated . At 20 degrees C, mumax values were calculated to be 0.0305 h(-1) and 0.1093 h(-1) on 1% (v/v) IPA and 1-propanol, respectively . Growth on propanol and IPA was carried out between temperatures of 10 degrees C and 45 degrees C . Temperature shock responses by the microbial consortium at temperatures above 45 degrees C were demonstrated by considerable cell flocculation . An increase in propanol substrate concentration from 1% (v/v) to 2% (v/v) decreased the mumax from 0.1093 h(-1) to 0.0715 h(-1) . Maximum achievable biodegradation rates of propanol and IPA were 6.11 x 10(-3)% (v/v) h(-1) and 2.72 x 10(-3)% (v/v) h(-1), respectively. , , . Generation of acetone during IPA biodegradation commenced at 264 h and reached a maximum concentration of 0.4% (v/v) . The results demonstrate the potential of mixed microbial consortia in the bioremediation of solvent-containing waste streams.

Appl Microbiol Biotechnol, 2000 Sep, 54(3), 418 - 23
Use of microorganism-immobilized polyurethane foams to absorb and degrade oil on water surface; Oh YS et al.; Highly oil-absorbent polyurethane foam (PUF) materials were obtained by polymerizing polyether polyol mixture and carbodiimide-modified D-methyl diisocyanate in a weight ratio of 10:2 . The foam materials were prepared to contain inorganic nutrients (slow-release fertilizer; SRF) and oil-degrading yeast cells, Yarrowia lipolytica 180, to be applied for removal of oil films on surface waters through absorption and biodegradation after oil spills . PUFs absorbed 7-9 times their own weight of Arabian light crude oil and the oil absorbency appeared to improve as the ratio of surface area to foam weight increased . PUFs showed excellent floatability which was maintained for more than 6 months in sea water, and less than 5% of the absorbed oil was released when the foams were left on water for more than 10 days . For immobilization of yeast cells into PUFs, various immobilization techniques were tested to compare their oil degrading ability and the maintenance thereof . All immobilized cells showed oil degrading abilities as good as those of free cells immediately after the preparation of PUFs, however, the activity of chitin-immobilized cells remained at a high level for the longest period of preservation . The high efficiency of oil absorption and oil degradation by PUF-immobilized yeast cells suggested that PUF-immobilized cells have a high potential as a bioremediation technique for the treatment of oil films on surface waters.

Curr Opin Biotechnol, 2000 Oct, 11(5), 450 - 4
Expressing genes in different Escherichia coli compartments; Cornelis P; Production of heterologous proteins or parts thereof in different extra-cytoplasmic compartments (in the periplasm, outer membrane or extracellularly) of Escherichia coli offers multiple applications, for example, in vaccine development, immobilised enzymes and bioremediation . Nowadays, not only surface display of short peptides, but also cell-surface anchoring or secretion of functional proteins is possible . Factors influencing folding, stability and export of extra-cytoplasmic proteins are also better understood.

Trends Biotechnol, 2000 Oct, 18(10), 408 - 12
Emerging techniques for anaerobic bioremediation of contaminated environments; Coates JD et al.; Over the past decade, it has been recognized that the diversity of anaerobic microbial metabolism is far greater than was previously assumed, and that many contaminants previously considered to be recalcitrant under anoxic conditions can in fact be biotransformed in the absence of molecular oxygen . Here, we summarize recent advances in the understanding of novel forms of anaerobic microbial metabolism and their potential application to bioremediative technologies.

Math Biosci, 2000 Oct, 167(2), 177 - 99
Competition in the presence of a lethal external inhibitor; Hsu SB et al.; The study considers two organisms competing for a nutrient in an open system in the presence of an inhibitor (or toxicant) . The inhibitor is input at a constant rate and is lethal to one competitor while being taken up by the other without harm . This is in contrast to previous studies, where the inhibitor decreases the reproductive rate of one of the organisms . The mathematical result of the lethal effect, modeled by a mass action term, is that the system cannot be reduced to a monotone dynamical system of one order lower as is common with chemostat-like problems . The model is described by four non-linear, ordinary differential equations and we seek to describe the asymptotic behavior as a function of the parameters of the system . Several global exclusion results are presented with mathematical proofs . However, in the case of coexistence, oscillatory behavior is possible and the study proceeds with numerical examples . The model is relevant to bioremediation problems in nature and to laboratory bio-reactors.

Mol Microbiol, 2000 Sep, 37(5), 989 - 94
The evolution of secondary metabolism - a unifying model; Firn RD et al.; Why do microbes make secondary products? That question has been the subject of intense debate for many decades . There are two extreme opinions . Some argue that most secondary metabolites play no role in increasing the fitness of an organism . The opposite view, now widely held, is that every secondary metabolite is made because it possesses (or did possess at some stage in evolution) a biological activity that endows the producer with increased fitness . These opposing views can be reconciled by recognizing that, because of the principles governing molecular interactions, potent biological activity is a rare property for any molecule to possess . Consequently, in order for an organism to evolve the rare potent, biologically active molecule, a great many chemical structures have to be generated, most of which will possess no useful biological activity . Thus, the two sides of the debate about the role and evolution of secondary metabolism can be accommodated within the view that the possession of secondary metabolism can enhance fitness, but that many products of secondary metabolism will not enhance the fitness of the producer . It is proposed that secondary metabolism will have evolved such that traits that optimize the production and retention of chemical diversity at minimum cost will have been selected . Evidence exists for some of these predicted traits . Opportunities now exist to exploit these unique properties of secondary metabolism to enhance secondary product diversity and to devise new strategies for biotransformation and bioremediation.

Appl Microbiol Biotechnol, 2000 Aug, 54(2), 255 - 61
Estimating the availability of polycyclic aromatic hydrocarbons for bioremediation of creosote contaminated soils; Breedveld GD et al.; Bioremediation of soil contaminated by organic compounds can remove the contaminants to a large extent, but residual contamination levels may remain which are not or only slowly biodegraded . Residual levels often exceed existing clean-up guidelines and thereby limit the use of bioremediation in site clean-up . A method for estimating the expected residual levels would be a useful tool in the assessment of the feasibility of bioremediation . In this study, three soil types from a creosote-contaminated field site, which had been subjected to 6 months of bioremediation in laboratory column studies, were used to characterize the residual contamination levels and assess their availability for biodegradation . The soils covered a wide range of organic carbon levels and particle size distributions . Results from the biodegradation studies were compared with desorption rate measurements and selective extractability using butanol . Residual levels of polycyclic aromatic hydrocarbons after bioremediation were found to be strongly dependent on soil type . The presence of both soil organic matter and asphaltic compounds in the soil was found to be associated with higher residual levels . Good agreement was found between the biodegradable fraction and the rapidly desorbable fraction in two of the three soils studied . Butanol extraction was found to be a useful method for roughly estimating the biodegradable fraction in the soil samples . The results indicate that both desorption and selective extraction measurements could aid the assessment of the feasibility for bioremediation and identifying acceptable end-points.

Biochem Biophys Res Commun, 2000 Aug 18, 275(1), 129 - 33
Chemotaxis and biodegradation of 3-methyl- 4-nitrophenol by Ralstonia sp . SJ98; Bhushan B et al.; 3-Methyl-4-nitrophenol is one of the major breakdown products of fenitrothion {O,O-dimethyl O-(3-methyl-4-nitrophenyl) thiophosphate}, a recalcitrant organophosphate insecticide used in agriculture . Being the non-polar methylated aromatic compound, 3-methyl-4-nitrophenol is highly toxic and, therefore, a complete degradation of this compound is important for environmental decontamination/bioremediation purposes . A gram negative, motile Ralstonia sp . SJ98 was isolated by selective screening from a soil sample contaminated with pesticides . The microorganism was capable of utilizing 3-methyl-4-nitrophenol as the sole source of carbon and energy . Thin layer chromatography (TLC), gas chromatography (GC), gas chromatography-mass spectrometry (GC-MS), and high performance liquid chromatography (HPLC) were performed to determine the possible intermediates in the degradative pathway of this compound . Taken together, catechol was found to be one of the major intermediate of the pathway . Furthermore, the chemotactic behavior of Ralstonia sp . SJ98 towards 3-methyl-4-nitrophenol was tested using three different methods i.e., drop assay, swarm plate assay and capillary assay, which were found to be positive towards this compound . This is the first report clearly indicating the involvement of a microorganism in the chemotaxis and biodegradation of methyl-4-nitrophenol and formation of catechol as an intermediate in the degradative pathway .

J Mol Microbiol Biotechnol, 1999 Aug, 1(1), 63 - 70
Petroleum biodegradation in marine environments; Harayama S et al.; Petroleum-based products are the major source of energy for industry and daily life . Petroleum is also the raw material for many chemical products such as plastics, paints, and cosmetics . The transport of petroleum across the world is frequent, and the amounts of petroleum stocks in developed countries are enormous . Consequently, the potential for oil spills is significant, and research on the fate of petroleum in a marine environment is important to evaluate the environmental threat of oil spills, and to develop biotechnology to cope with them . Crude oil is constituted from thousands of components which are separated into saturates, aromatics, resins and asphaltenes . Upon discharge into the sea, crude oil is subjected to weathering, the process caused by the combined effects of physical, chemical and biological modification . Saturates, especially those of smaller molecular weight, are readily biodegraded in marine environments . Aromatics with one, two or three aromatic rings are also efficiently biodegraded; however, those with four or more aromatic ring are quite resistant to biodegradation . The asphaltene and resin fractions contain higher molecular weight compounds whose chemical structures have not yet been resolved . The biodegradability of these compounds is not yet known . It is known that the concentrations of available nitrogen and phosphorus in seawater limit the growth and activities of hydrocarbon-degrading microorganisms in a marine environment . In other words, the addition of nitrogen and phosphorus fertilizers to an oil-contaminated marine environment can stimulate the biodegradation of spilled oil . This notion was confirmed in the large-scale operation for bioremediation after the oil spill from the Exxon Valdez in Alaska . Many microorganisms capable of degrading petroleum components have been isolated . However, few of them seem to be important for petroleum biodegradation in natural environments., , , , . One group of bacteria belonging to the genus Alcanivorax does become predominant in an oil-contaminated marine environment, especially when nitrogen and phosphorus fertilizers are added to stimulate the growth of endogenous microorganisms.

Can J Microbiol, 2000 Jun, 46(6), 525 - 31
Enzymatic degradation of nitriles by a Candida guilliermondii UFMG-Y65; Dias JC et al.; Candida guilliermondii UFMG-Y65, isolated from a gold mine, was able to utilize different nitriles and the corresponding amides as sole source of nitrogen, at concentrations up to 2 M . Resting cells cultivated on YCB-acetonitrile medium showed nitrile hydrolyzing enzyme activities against acrylonitrile and benzonitrile . These enzymes were inducible and intracellular; the optimum pH was 7.0-8.0, and the optimum temperature 25 degrees C-30 degrees C . Liquid chromatographic analysis indicated that C . guilliermondii UFMG-Y65 metabolized 12 mM benzonitrile to 11 mM benzoic acid and 10 mM acrylonitrile to 7.9 mM acrylic acid . The results suggest that C . guilliermondii UFMG-Y65 may be useful for the bioproduction of amides and acids, and for the bioremediation of environments contaminated with nitriles.

Can J Microbiol, 1999 Oct, 45(10), 840 - 8
Degradation of 2,4-dinitrophenol and selected nitroaromatic compounds by Sphingomonas sp . UG30; Zablotowicz RM et al.; Sphingomonas strain UG30 mineralizes both p-nitrophenol (PNP) and pentachlorophenol (PCP) . Our current studies showed that UG30 oxidatively metabolized certain other p-substituted nitrophenols, i.e., p-nitrocatechol, 2,4-dinitrophenol (2,4-DNP), and 4,6-dinitrocresol with liberation of nitrite . 2,6-DNP, o- or m-nitrophenol, picric acid, or the herbicide dinoseb were not metabolized . Studies using 14C-labelled 2,4-DNP indicated that in glucose-glutamate broth cultures of UG30, greater than 90% of 103 microM 2,4-DNP was transformed to other compounds, while 8-19% of the 2,4-DNP was mineralized within 5 days . A significant portion (20-50%) of the 2,4-DNP was metabolized to highly polar metabolite(s) with one major unidentified metabolite accumulating from 5 to 25% of the initial radioactivity . The amounts of 2,4-DNP mineralized and converted to polar metabolites was affected by glutamate concentration in the medium . Nitrophenolic compounds metabolized by UG30 were also suitable substrates for the UG30 PCP-4-monooxygenase (pcpB gene expressed in Escherichia coli) which is likely central to degradation of these compounds . The wide substrate range of UG30 could render this strain useful in bioremediation of some chemically contaminated soils.

Chemosphere, 2000 Oct, 41(8), 1115 - 23
Bioremediation of a soil contaminated by hydrocarbon mixtures: the residual concentration problem; Nocentini M et al.; The phenomenon of residual concentration was investigated in the aerobic biodegradation of three different petroleum commercial products (i.e., kerosene, diesel fuel and a lubricating mineral oil) in static microcosms . Two different soils exhibiting different physical-chemical characteristics were used (i.e., a biologically treated hydrocarbon-contaminated soil and a pristine soil) . Residual concentrations were observed and a simple way to take this phenomenon into account was proposed.

Arch Microbiol, 2000 May-Jun, 173(5-6), 325 - 32
Molecular biology and regulation of methane monooxygenase; Murrell JC et al.; Methanotrophs are ubiquitous in the environment and play an important role in mitigating global warming due to methane . They are also potentially interesting for industrial applications such as production of bulk chemicals or bioremediation . The first step in the oxidation of methane is the conversion to methanol by methane monooxygenase, the key enzyme, which exists in two forms: the cytoplasmic, soluble methane monooxygenase (sMMO) and the membrane-bound, particulate methane monooxygenase (pMMO) . This paper reviews the biochemistry and molecular biology of both forms of MMO . In the past few years there have been many exciting new findings . sMMO components have been expressed in heterologous and homologous hosts . The pMMO has been purified and biochemically studied in some detail and the genes encoding the pMMO have been sequenced . Copper ions have been shown to play a key role in regulating the expression of both MMO enzyme complexes . We also present a model for copper regulation based on results from Northern analysis, primer-extensions and new sequence data, and raise a number of unanswered questions for future studies.

Appl Environ Microbiol, 2000 Jul, 66(7), 2822 - 8
Enrichment of an endosulfan-degrading mixed bacterial culture; Sutherland TD et al.; An endosulfan-degrading mixed bacterial culture was enriched from soil with a history of endosulfan exposure . Enrichment was obtained by using the insecticide as the sole source of sulfur . Chemical hydrolysis was minimized by using strongly buffered culture medium (pH 6.6), and the detergent Tween 80 was included to emulsify the insecticide, thereby increasing the amount of endosulfan in contact with the bacteria . No growth occurred in control cultures in the absence of endosulfan . Degradation of the insecticide occurred concomitant with bacterial growth . The compound was both oxidized and hydrolyzed . The oxidation reaction favored the alpha isomer and produced endosulfate, a terminal pathway product . Hydrolysis involved a novel intermediate, tentatively identified as endosulfan monoaldehyde on the basis of gas chromatography-mass spectrometry and chemical derivatization results . The accumulation and decline of metabolites suggest that the parent compound was hydrolyzed to the putative monoaldehyde, thereby releasing the sulfite moiety required for growth . The monoaldehyde was then oxidized to endosulfan hydroxyether and further metabolized to (a) polar product(s) . The cytochrome P450 inhibitor, piperonyl butoxide, did not prevent endosulfan oxidation or the formation of other metabolites . These results suggest that this mixed culture is worth investigating as a source of endosulfan-hydrolyzing enzymes for use in enzymatic bioremediation of endosulfan residues.

Biodegradation, 1999, 10(5), 341 - 52
Biodegradation of gasoline and BTEX in a microaerophilic biobarrier; Yerushalmi L et al.; Continuous bioremediation of gasoline-contaminated water in a packed-bed biobarrier system under oxygen-limited conditions is discussed . This study was part of an extensive effort to develop an alternative technology for the in situ bioremediation of hydrocarbons where there is a limited supply of oxygen . Protruded stainless steel pieces and granulated peat moss were used as packing material to support microbial growth in two biobarriers . The inoculum was an enrichment culture of an indigenous microbial population from a soil sample . The biobarriers' inlet gasoline concentrations and the linear liquid velocities were similar to those commonly found at in situ conditions . Gasoline removal efficiencies ranged from 94% to 99.9% in the stainless steel-packed biobarrier, and from 86.6% to 99.6% in the peat moss-packed biobarrier . Effluent gasoline concentrations below 0.03 mg/l were obtained at gasoline loading rates less than 27.5 mg/l.d in the stainless steel-packed biobarrier . The remaining fraction of gasoline in the effluent consisted mainly of three aliphatic compounds and not the aromatic compounds . Both biobarrier packings supported near complete removal of the most soluble aromatic hydrocarbons of gasoline (BTEX) under all the conditions examined . The consumption of sulfate and the presence of sulfate-reducing microorganisms suggested the presence of anaerobic metabolism during the degradation of gasoline . Up to 92% gasoline was removed during the first 3 cm of the biobarriers' length.

J Theor Biol, 2000 Jul 7, 205(1), 73 - 84
Translocation induced outgrowth of fungi in nutrient-free environments; Davidson FA et al.; The study of alternatives to chemical methods of nematode control in agriculture has received significant recent interest . One such method is biological control using nematode trapping fungi such as Arthrobotrys superba . To understand how these fungi can be implemented as effective nematicides, it is essential to study their outgrowth into soil from localized nutrient resources . In this paper, we use a mathematical model to investigate the outgrowth of fungi into an environment essentially without available nutrients capable of supporting net growth . By comparing model solutions with experimental results, we show that in such circumstances, continual mycelial expansion can only be obtained if internal metabolites are actively translocated through the mycelium . Predictions are made concerning the maximal extension possible from a given quantity of nutrients and a testable functional relationship between the two is derived . Using this modelling technique we are able to map not only biomass extent but also biomass distribution at each stage . The type of environmental heterogeneity investigated here is encountered by many species of fungi in nature and is of relevance for the introduction of specific fungi into soil for biological control or bioremediation purposes .

Appl Microbiol Biotechnol, 2000 May, 53(5), 495 - 508
Potential commercial applications of microbial surfactants; Banat IM et al.; Surfactants are surface-active compounds capable of reducing surface and interfacial tension at the interfaces between liquids, solids and gases, thereby allowing them to mix or disperse readily as emulsions in water or other liquids . The enormous market demand for surfactants is currently met by numerous synthetic, mainly petroleum-based, chemical surfactants . These compounds are usually toxic to the environment and non-biodegradable . They may bio-accumulate and their production, processes and by-products can be environmentally hazardous . Tightening environmental regulations and increasing awareness for the need to protect the ecosystem have effectively resulted in an increasing interest in biosurfactants as possible alternatives to chemical surfactants . Biosurfactants are amphiphilic compounds of microbial origin with considerable potential in commercial applications within various industries . They have advantages over their chemical counterparts in biodegradability and effectiveness at extreme temperature or pH and in having lower toxicity . Biosurfactants are beginning to acquire a status as potential performance-effective molecules in various fields . At present biosurfactants are mainly used in studies on enhanced oil recovery and hydrocarbon bioremediation . The solubilization and emulsification of toxic chemicals by biosurfactants have also been reported . Biosurfactants also have potential applications in agriculture, cosmetics, pharmaceuticals, detergents, personal care products, food processing, textile manufacturing, laundry supplies, metal treatment and processing, pulp and paper processing and paint industries . Their uses and potential commercial applications in these fields are reviewed.

Curr Opin Biotechnol, 2000 Jun, 11(3), 262 - 70
Engineering bacteria for bioremediation; Pieper DH et al.; The treatment of environmental pollution by microorganisms is a promising technology . Various genetic approaches have been developed and used to optimize the enzymes, metabolic pathways and organisms relevant for biodegradation . New information on the metabolic routes and bottlenecks of degradation is still accumulating, enlarging the available toolbox . With molecular methods allowing the characterization of microbial community structure and activities, the performance of microorganisms under in situ conditions and in concert with the indigenous microflora will become predictable.

Curr Opin Biotechnol, 2000 Jun, 11(3), 236 - 43
Aromatic hydrocarbon dioxygenases in environmental biotechnology; Gibson DT et al.; Aromatic hydrocarbon dioxygenases belong to a large family of Rieske non-heme iron oxygenases . The dioxygenases have a broad substrate specificity and catalyze enantiospecific reactions with a wide range of substrates . These characteristics make them attractive synthons for the production of industrially and medically important chiral chemicals and also provide essential information for the development of bioremediation technology.

Appl Environ Microbiol, 2000 Jun, 66(6), 2620 - 6
Physiologic determinants of radiation resistance in Deinococcus radiodurans; Venkateswaran A et al.; Immense volumes of radioactive wastes, which were generated during nuclear weapons production, were disposed of directly in the ground during the Cold War, a period when national security priorities often surmounted concerns over the environment . The bacterium Deinococcus radiodurans is the most radiation-resistant organism known and is currently being engineered for remediation of the toxic metal and organic components of these environmental wastes . Understanding the biotic potential of D . radiodurans and its global physiological integrity in nutritionally restricted radioactive environments is important in development of this organism for in situ bioremediation . We have previously shown that D . radiodurans can grow on rich medium in the presence of continuous radiation (6,000 rads/h) without lethality . In this study we developed a chemically defined minimal medium that can be used to analyze growth of this organism in the presence and in the absence of continuous radiation; whereas cell growth was not affected in the absence of radiation, cells did not grow and were killed in the presence of continuous radiation . Under nutrient-limiting conditions, DNA repair was found to be limited by the metabolic capabilities of D . radiodurans and not by any nutritionally induced defect in genetic repair . The results of our growth studies and analysis of the complete D . radiodurans genomic sequence support the hypothesis that there are several defects in D . radiodurans global metabolic regulation that limit carbon, nitrogen, and DNA metabolism . We identified key nutritional constituents that restore growth of D . radiodurans in nutritionally limiting radioactive environments.

Rapid Commun Mass Spectrom, 2000, 14(10), 905 - 10
Biotreatment of tannin-rich beer-factory wastewater with white-rot basidiomycete Coriolopsis gallica monitored by pyrolysis/gas chromatography/mass spectrometry; Yague S et al.; Some fractions of beer-factory wastewaters represent an important environmental concern owing to their high content of polyphenols and dark-brown color . The capacity of Coriolopsis gallica to preferentially degrade lignin has been successfully applied in our laboratory to the biotreatment and decolorization of paper-industry effluents . In this work, the ability of this white-rot fungus to degrade high-tannin-containing wastewaters is evaluated . Under all the conditions studied, effluent decolorization and chemical oxygen demand reduction achieved by C . gallica at day 12 of incubation were close to 50 and 65%, respectively . No adhesion of dark color to the fungal mycelium was observed suggesting that decolorization could be ascribed to C . gallica degradation systems . Mycelium dry-weight values showed that C . gallica is tolerant to relatively high tannin content present in the effluent samples . In the sample containing the highest effluent concentration (60% v/v), dry-weight values suggested an inhibition of fungal growth at day 6 of incubation and a further adaptation of the fungus to the stressing tannin effect at day 12 of fungal treatment . Pyrolysis/gas chromatography/mass spectrometry results showed a decrease of polyphenols pyrolysis products, mainly phenol and guaiacol, with the incubation time . All these results indicate the potential use of C . gallica in bioremediation of tannin-containing industrial wastewaters and in other applications where a reduction in polyphenols content is required .

J Agric Food Chem, 2000 May, 48(5), 1941 - 8
Bioremediation of olive oil mill wastewater: chemical alterations induced by Azotobacter vinelandii; Piperidou CI et al.; An environmentally friendly bioremediation system of olive oil mill wastewater (OMWW) is studied with respect to its physicochemical characteristics and degradation efficiency on major characteristic constituents . The method exploits the biochemical versatility of the dinitrogen fixing bacterium Azotobacter vinelandii (strain A) to grow in OMWW at the expense of its constituents and to transform it into an organic liquid fertilizer . The system eliminates the phytotoxic principles from OMWW and concomitantly enriches it with an agriculturally beneficial microbial consortium along with useful metabolites of the latter . The end product, branded "biofertilizer", is used as soil conditioner and liquid organic fertilizer . Growth of A . vinelandii in OMWW results in the decline of content of most of the compounds associated with phytotoxicity, and this is confirmed by the assessment of degradation yields . In parallel, during the process several other compounds noncommittally undergo degradation and biotransformation . More specifically, the biofertilization system is capable of achieving removal yields as high as 90 and 96% after 3 and 7 days of treatment, respectively . Statistical analysis of the results showed that between the periods of operation no significant difference occurs with respect to the degradation yield . Moreover, the degradation yield from 3 to 7 days of continuous operation of the system remains almost unaltered during 2 consecutive years.

Chemosphere, 2000 Jun, 40(12), 1427 - 33
Relationship between electron donor and microorganism on the dechlorination of carbon tetrachloride by an anaerobic enrichment culture; Doong RA et al.; An investigation involving the supplement of different concentrations of substrates and microorganisms was carried out under anaerobic condition to assess the feasibility of bioremediation of carbon tetrachloride (CCl4) with the amendment of low concentrations of auxiliary substrate and microorganisms . The concentrations of substrate and microorganisms ranged from 10 to 100 mg/l and from 3.7 x 10(4) to 3.7 x 10(6) cell/ml, respectively . The biotransformation rate of CCl4 increased progressively with the increase in the concentrations of the substrate and microorganisms . In the low biomass-amended system (3.7 x 10(4) cells/ml), 28-71% and 57-96% of CCl4 removals were exhibited when 10-100 mg/l of acetate or glucose was supplemented, respectively, whereas nearly complete degradation of CCl4 was observed in the heavily inoculated systems (3.7 x 10(6) cells/ml) . An addition of electron donor in the low microbial activity batches enhanced greater efficiency in dechlorination than in the high microbial activity batches . The second-order rate constants ranged from 0.0059 to 0.0092 l/mg/day in high biomass input system, while a two- to four-fold increase in rate constant was obtained in the low microbial activity system . This study indicates that biomass was the more important environmental parameter than substrate affecting the fate of CCl4 . The addition of auxiliary substrates was effective only in low biomass-amended batches (0.56 mg-VSS/l) and diminished inversely with the increase of microbial concentration.

Can J Microbiol, 2000 Mar, 46(3), 269 - 77
Biodegradation of carbazole by Ralstonia sp . RJGII.123 isolated from a hydrocarbon contaminated soil; Schneider J et al.; The use of microorganisms for bioremediation of contaminated soils may be enhanced with an understanding of the pathways involved in their degradation of hazardous compounds . Ralstonia sp . strain RJGII.123 was isolated from soil located at a former coal gasification plant, based on its ability to mineralize carbazole, a three-ring N-heterocyclic pollutant . Experiments were carried out with strain RJGHII.123 and 14C-carbazole (2 mg/L and 500 mg/L) as the sole organic carbon source . At 15 days, 80% of the 2 mg/L carbazole was recovered as CO2, and <1% remained as undegraded carbazole, while 24% of the 500 mg/L carbazole was recovered as CO2 and approximately 70% remained as undegraded carbazole . Several stable intermediates were formed during this time . These intermediates were separated by high performance liquid chromatography (HPLC) and were characterized using high resolution mass spectroscopy (HR-MS) and gas chromatography - mass spectroscopy (GC-MS) . At least 10 ring cleavage products of carbazole degradation were identified; four of these were confirmed as anthranilic acid, indole-2-carboxylic acid, indole-3-carboxylic acid, and (1H)-4-quinolinone by comparison with standards . These data indicate that strain RJGII.123 shares aspects of carbazole degradation with previously described Pseudomonas spp., and may be useful in facilitating the bioremediation of NHA from contaminated soils.

Lett Appl Microbiol, 2000 Feb, 30(2), 161 - 6
Construction and expression of functional multi-domain polypeptides in Escherichia coli: expression of the Neurospora crassa metallothionein gene; Mauro JM et al.; A system for the construction of polymeric peptides in Escherichia coli was utilized to prepare a library of plasmids coding for tandem repeats of the Neurospora crassa metallothionein gene . Selected oligomeric metallothionein clones were expressed and targeted to the periplasm as a fusion with the maltose-binding protein . Bacterial cells harbouring the expressed oligopeptides were characterized for their ability to bind 109Cd2+ . The metal-binding ability was enhanced for all the oligomeric constructs tested and, in the best case, a 6.5-fold increased capacity for metal uptake was achieved with cells expressing a tandem 9-mer in comparison with cells expressing a monomer . Plateauing of the metal uptake ability occurred at between six and nine tandem repeats, possibly due to a combination of lowered translation levels, inefficient export and prematurely terminated translation products . The overall enhancement of the heavy metal removal capacity was approximately 65-fold relative to non-recombinant cells., , , . The use of this strategy for the design and expression of de novo polypeptides containing multiple functional domains for use in bioremediation is discussed.

Essays Biochem, 1999, 34, 173 - 89
Catechol dioxygenases; Broderick JB; Catechol dioxygenases are key enzymes in the metabolism of aromatic rings by soil bacteria . Catechol dioxygenases have been found that participate in the metabolism of halogenated aromatic compounds and, in doing so, play a key role in bioremediation of halogenated pollutants . The catechol dioxygenases can be divided into two major groups: those that cleave the aromatic ring between the vicinal diols (the intradiol enzymes) and those that cleave the ring to one side of the vicinal diols (the extradiol enzymes) . Whereas both types of catechol dioxygenase contain an active-site iron that is required absolutely for enzymic activity, the intradiol enzymes contain Fe(III), while the extradiol enzymes contain Fe(II) . The nature of the protein ligands determines this specificity . The differences in oxidation state of the active-site iron appear to result in mechanistic differences that lead to the differing regioselectivity of the two groups of catechol dioxygenase . Mechanistic proposals based on available evidence suggest a substrate-activation mechanism for the intradiol enzymes and an oxygen-activation mechanism for the extradiol enzymes.

Gene, 2000 Mar 7, 245(1), 65 - 74
Complete nucleotide sequence and evolutionary significance of a chromosomally encoded naphthalene-degradation lower pathway from Pseudomonas stutzeri AN10; Bosch R et al.; Pseudomonas stutzeri strain AN10 is a naphthalene-degrading strain whose dissimilatory genes are chromosomally encoded . We sequenced the entire naphthalene-degradation lower pathway of P . stutzeri AN10, this being, together with the upper-pathway reported previously (Bosch R . et al., 1999a . Gene 236, 149-157) the first complete DNA sequence for an entire naphthalene-catabolic pathway . Eleven open reading frames were identified . The nahGTHINLOMKJ genes encode enzymes for the metabolism of salicylate to pyruvate and acetyl-CoA, and nahR encodes the NahR regulatory protein . Our findings suggest that catabolic modules were recruited through transposition events and recombination among tnpA-like genes, and subsequent rearrangements and deletions of non-essential DNA fragments allowed the formation of the actual catabolic pathway . Our results also suggest that the genes encoding the xylene/toluene-degradation enzymes of P . putida mt-2 (pWW0) have coexisted with the nah genes of the P . stutzeri AN10 ancestral genome . This could allow the selection, via recombination events among homologous genes, for a combination of genes enabling the metabolism of a given aromatic compound in the ancestral host strain . Such events accelerate the evolution of modern catabolic pathways and provide new genetic material to the environment, ultimately resulting in improved, natural, bioremediation potential.

Trends Plant Sci, 2000 Mar, 5(3), 116 - 23
Cytochromes P450 for engineering herbicide tolerance; Werck-Reichhart D et al.; In recent years, genome sequencing has revealed that cytochromes P450 (P450s) constitute the largest family of enzymatic proteins in higher plants . P450s are mono-oxygenases that insert one atom of oxygen into inert hydrophobic molecules to make them more reactive and hydrosoluble . Besides their physiological functions in the biosynthesis of hormones, lipids and secondary metabolites, P450s help plants to cope with harmful exogenous chemicals including pesticides and industrial pollutants, making them less phytotoxic . The recovery of an increasing number of plant P450 genes in recombinant form has enabled their use in experimentation, which has revealed their extraordinary potential for engineering herbicide tolerance, biosafening, bioremediation and green chemistry.

Chemosphere, 2000 Apr, 40(7), 741 - 50
Phytotoxicity to and uptake of flumequine used in intensive aquaculture on the aquatic weed, Lythrum salicaria L; Migliore L et al.; Phytotoxicity of Flumequine on the aquatic weed Lythrum salicaria L . was determined by two laboratory models: a single concentration test, by which the effects of 100 mg l-1 were evaluated after 10, 20, 30 days and a multiple concentration test, by which the effects of 5000-1000-500-100-50 micrograms l-1 were evaluated after 35-day exposure . 100 mg l-1 are highly toxic and significantly decrease the growth of plants; this effect increases with time . Concentrations between 5000 and 50 micrograms l-1 induced hormesis in plants, by significantly increasing mean number and dimension of leaves and secondary roots . The effect is the highest at 50 micrograms l-1 and decreases with increase in concentration . Both toxic effect and hormesis can be related to plant drug uptake, quite high, in the order of micrograms g-1 . The ecological implication of Flumequine contamination in aquatic environments and the possible use of Lythrum salicaria for bioremediation and/or monitoring technique are discussed.

Trends Biotechnol, 2000 Mar, 18(3), 103 - 7
Cold-adapted enzymes: from fundamentals to biotechnology; Gerday C et al.; Psychrophilic enzymes produced by cold-adapted microorganisms display a high catalytic efficiency and are most often, if not always, associated with high thermosensitivity . Using X-ray crystallography, these properties are beginning to become understood, and the rules governing their adaptation to cold appear to be relatively diverse . The application of these enzymes offers considerable potential to the biotechnology industry, for example, in the detergent and food industries, for the production of fine chemicals and in bioremediation processes.

Chemosphere, 2000 Feb, 40(4), 419 - 26
Temporal ecological assessment of oil contaminated soils before and after bioremediation; Dorn PB et al.; Ecotoxicity methods were used to assess different soil and oil combinations before, during and after laboratory bioremediation with associated hydrocarbon analysis . Heavy, medium and light crude oil (API gravity 14, 30, and 55) was spiked (ca . 5% w/w) into two sandy soils in the laboratory having organic carbon concentrations of 0.3 (Norwood) and 4.7% (Norwood/Baccto) . The earthworm (Eisenia fetida) 14-d lethality assay, the modified Microbics Microtox Solid-Phase assay, and the 14-d plant seed germination and growth assays using corn, wheat and oats, were spiked and tested during a 360-d laboratory remediation . Eisenia was the most sensitive of the three methods utilized with survival increasing throughout bioremediation with fastest toxicity reduction in the high carbon Norwood/Baccto soils where LC50's were 100% or greater at the end of 90-d whereas, > 150-d were required to achieve a similar result in the low carbon soil . Analysis of the undiluted treatments with oily soil alone showed that earthworm survival was high after 90-d in all high organic carbon soils, and after eight months in the low carbon soils, except for the Norwood soil-light oil treatment, which required 360-d to achieve 100% survival . The Microtox assay was less sensitive with EC50's 100% or greater observed after 90-d in high carbon soils and after 240-d for all low carbon soils . After bioremediation, no effects on seed germination were observed, although some plant growth inhibition effects remained . There was no direct correlation between total petroleum hydrocarbon concentrations and toxicity.

Chemosphere, 2000 Feb, 40(4), 339 - 46
Monitoring of bioremediation by soil biological activities; Margesin R et al.; An evaluation of soil biological activities as a monitoring instrument for the decontamination process of a mineral-oil-contaminated soil was made using measurements of microbial counts, soil respiration, soil biomass and several enzyme activities . The correlations between these parameters and with the levels of hydrocarbon residues were investigated; the effects of different N- and P-sources on hydrocarbon decontamination and soil biological activities were determined . Inorganic nutrients stimulated hydrocarbon biodegradation but not all biological activities to a significant extent . Biodegradation could be monitored well by soil biological parameters: the residual hydrocarbon content correlated positively with soil respiration, biomass-C (substrate-induced respiration), and with activities of soil dehydrogenase, urease and catalase . Soil lipase activity and the number of hydrocarbon utilizers correlated negatively (P < 0.0001) with the remaining hydrocarbon content.

Naturwissenschaften, 2000 Feb, 87(2), 59 - 69
Enzymes involved in the aerobic bacterial degradation of N-heteroaromatic compounds: molybdenum hydroxylases and ring-opening 2,4-dioxygenases; Fetzner S; Many N-heteroaromatic compounds are utilized by micro-organisms as a source of carbon (and nitrogen) and energy . The aerobic bacterial degradation of these growth substrates frequently involves several hydroxylation steps and subsequent dioxygenolytic cleavage of (di)hydroxy-substituted heteroaromatic intermediates to aliphatic metabolites which finally are channeled into central metabolic pathways . As a rule, the initial bacterial hydroxylation of a N-heteroaromatic compound is catalyzed by a molybdenum hydroxylase, which uses a water molecule as source of the incorporated oxygen . The enzyme's redox-active centers - the active site molybdenum ion coordinated to a distinct pyranopterin cofactor, two different {2Fe2S} centers, and in most cases, flavin adenine dinucleotide - transfer electrons from the N-heterocyclic substrate to an electron acceptor, which for many molybdenum hydroxylases is still unknown . Ring-opening 2,4-dioxygenases involved in the bacterial degradation of quinaldine and 1H-4-oxoquinoline catalyze the cleavage of two carbon-carbon bonds with concomitant formation of carbon monoxide . Since they contain neither a metal center nor an organic cofactor, and since they do not show any sequence similarity to known oxygenases, these unique dioxygenases form a separate enzyme family . Quite surprisingly, however, they appear to be structurally and mechanistically related to enzymes of the alpha/beta hydrolase fold superfamily . Microbial enzymes are a great resource for biotechnological applications . Microbial strains or their enzymes may be used for degradative (bioremediation) or synthetic (biotransformation) purposes . Modern bioremediation or biotransformation strategies may even involve microbial catalysts or strains designed by protein engineering or pathway engineering . Prerequisite for developing such modern tools of biotechnology is a comprehensive understanding of microbial metabolic pathways, of the structure and function of enzymes, and of the molecular mechanisms of biocatalysis.

Appl Environ Microbiol, 2000 Feb, 66(2), 678 - 83
Development of catechol 2,3-dioxygenase-specific primers for monitoring bioremediation by competitive quantitative PCR; Mesarch MB et al.; Benzene, toluene, xylenes, phenol, naphthalene, and biphenyl are among a group of compounds that have at least one reported pathway for biodegradation involving catechol 2,3-dioxygenase enzymes . Thus, detection of the corresponding catechol 2,3-dioxygenase genes can serve as a basis for identifying and quantifying bacteria that have these catabolic abilities . Primers that can successfully amplify a 238-bp catechol 2,3-dioxygenase gene fragment from eight different bacteria are described . The identities of the amplicons were confirmed by hybridization with a 238-bp catechol 2,3-dioxygenase probe . The detection limit was 10(2) to 10(3) gene copies, which was lowered to 10(0) to 10(1) gene copies by hybridization . Using the dioxygenase-specific primers, an increase in catechol 2, 3-dioxygenase genes was detected in petroleum-amended soils . The dioxygenase genes were enumerated by competitive quantitative PCR with a 163-bp competitor that was amplified using the same primers . Target and competitor sequences had identical amplification kinetics . Potential PCR inhibitors that could coextract with DNA, nonamplifying DNA, soil factors (humics), and soil pollutants (toluene) did not impact enumeration . Therefore, this technique can be used to accurately and reproducibly quantify catechol 2, 3-dioxygenase genes in complex environments such as petroleum-contaminated soil . Direct, non-cultivation-based molecular techniques for detecting and enumerating microbial pollutant-biodegrading genes in environmental samples are powerful tools for monitoring bioremediation and developing field evidence in support of natural attenuation.

Nat Biotechnol, 2000 Jan, 18(1), 85 - 90
Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments; Brim H et al.; We have developed a radiation resistant bacterium for the treatment of mixed radioactive wastes containing ionic mercury . The high cost of remediating radioactive waste sites from nuclear weapons production has stimulated the development of bioremediation strategies using Deinococcus radiodurans, the most radiation resistant organism known . As a frequent constituent of these sites is the highly toxic ionic mercury (Hg) (II), we have generated several D . radiodurans strains expressing the cloned Hg (II) resistance gene (merA) from Escherichia coli strain BL308 . We designed four different expression vectors for this purpose, and compared the relative advantages of each . The strains were shown to grow in the presence of both radiation and ionic mercury at concentrations well above those found in radioactive waste sites, and to effectively reduce Hg (II) to the less toxic volatile elemental mercury . We also demonstrated that different gene clusters could be used to engineer D . radiodurans for treatment of mixed radioactive wastes by developing a strain to detoxify both mercury and toluene . These expression systems could provide models to guide future D . radiodurans engineering efforts aimed at integrating several remediation functions into a single host.

Biodegradation, 1999, 10(4), 251 - 60
Radiotoxicity of plutonium in NTA-degrading Chelatobacter heintzii cell suspensions; Reed DT et al.; The radiotoxicity of plutonium in NTA-degrading Chelatobacter heintzii cell suspensions was investigated as part of a more general study to establish the key interactions between actinide-organic complexes and microorganisms in the subsurface . The radiation tolerance of C . heintzii, based on 60Co gamma irradiation experiments, was 165 +/- 30 Gy . No bacteria survived irradiation doses greater than 500 Gy . In the presence of plutonium, where alpha particle decay was the primary source of ionizing radiation, the observed toxicity was predominantly radiolytic rather than chemical . This was evident by the greater effect of activity, rather than concentration, on the toxicity noted . Bioassociation of plutonium with C . heintzii was postulated to be an important and necessary step in the observed loss of cell viability since this was the best way to account for the observed death rate . The radiotoxicity of plutonium towards bacteria is a potentially important consideration in the bioremediation of sites contaminated with radionuclide-organic mixtures and the bioprocessing of nuclear waste.

Microb Ecol, 1999 Oct, 38(3), 191 - 200
Application of Traditional and Phylogenetically Based Comparative Methods to Test for a Trade-off in Bacterial Growth Rate at Low versus High Substrate Concentration; Velicer GJ et al.; Abstract It is often hypothesized that those organisms that are superior competitors for sparse resources fare poorly in competition for abundant resources, and vice versa . If there is indeed such a systematic trade-off, then this has important implications for the choice of bacterial strains in bioremediation and other applications . We studied seven bacterial strains that can grow on either 2,4-dichlorophenoxyacetate (2,4-D) or succinate as a sole source of carbon . Growth rates were measured on each substrate at both low (5 microg/ml) and high (500 microg/ml) concentrations . We used two different methods to test the significance of correlations among growth rates, a traditional method that treats each strain as an independent observation and a newer method that takes into account phylogenetic relationships between strains, thereby avoiding spurious correlations caused by a lack of statistical independence of strains . In both 2,4-D and succinate, we observed significant positive correlations between growth rates measured at high and low substrate concentrations by the traditional comparative method . No significant correlations were detected after adjusting for the phylogenetic relationships among the strains . In neither case did we observe the negative correlation expected from a trade-off between growth rates at high and low substrate levels.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p191.html</hea

Appl Environ Microbiol, 1999 Dec, 65(12), 5198 - 206
Soluble methane monooxygenase gene clusters from trichloroethylene-degrading Methylomonas sp . strains and detection of methanotrophs during in situ bioremediation; Shigematsu T et al.; The soluble MMO (sMMO) gene clusters from group I methanotrophs were characterized . An 8.1-kb KpnI fragment from Methylomonas sp . strain KSWIII and a 7.5-kb SalI fragment from Methylomonas sp . strain KSPIII which contained the sMMO gene clusters were cloned and sequenced . The sequences of these two fragments were almost identical . The sMMO gene clusters in the fragment consisted of six open reading frames which were 52 to 79% similar to the corresponding genes of previously described sMMO gene clusters of the group II and group X methanotrophs . The phylogenetic analysis of the predicted amino acid sequences of sMMO demonstrated that the sMMOs from these strains were closer to that from M . capsulatus Bath in the group X methanotrophs than to those from Methylosinus trichosporium OB3b and Methylocystis sp . strain M in the group II methanotrophs . Based on the sequence data of sMMO genes of our strains and other methanotrophs, we designed a new PCR primer to amplify sMMO gene fragments of all the known methanotrophs harboring the mmoX gene . The primer set was successfully used for detecting methanotrophs in the groundwater of trichloroethylene-contaminated sites during in situ-biostimulation treatments.

Acta Microbiol Pol, 1999, 48(2), 185 - 96
Biodegradation of engine oil in soil; Sztompka E; Laboratory experiments were conducted with the aim of bioremediation of sandy soil from engine oil in 5% concentration . Bacterial strains, active in degrading oil hydrocarbons as a sole source of carbon and energy were selected and identified . Optimal parameters, such as concentration of inorganic nutrients (expressed as C:N and C:P ratio) and the size of inoculum were established in experiments on 1% engine oil biodegradation . Process enhancing role of surfactants addition, the application of immobilized biomass and reinoculations was also evaluated.

Bioorg Med Chem, 1999 Oct, 7(10), 2175 - 81
In vivo screening of haloalkane dehalogenase mutants; Chang CH et al.; Haloalkane dehalogenase (Dh1A) from Xanthobacter autotrophicus GJ10 catalyzes the dehalogenation of short chain primary alkyl halides . Due to the high Km and low turnover, wild type Dh1A is not optimal for applications in bioremediation . We have developed an in vivo screen, based on a colorimetric pH indicator, to identify Dh1A mutant with improved catalytic activity . After screening 50,000 colonies, we identified a Dh1A mutant with a lower pH optimum . Sequence analysis of the mutant revealed a single substitution, alanine 149 to threonine, which is located close to the active site of Dh1A . Replacement of alanine 149 via site-directed mutagenesis with threonine, serine or cysteine retained the mutant phenotype . Other substitutions at position 149 show little or no activity.

J Biochem Mol Toxicol, 2000, 14(1), 20 - 5
Metabolism of phenanthrene by house fly CYP6D1 and dog liver cytochrome P450; Korytko PJ et al.; Polycyclic aromatic hydrocarbons (PAHs) are a ubiquitous class of environmental contaminants . The compound phenanthrene is a model PAH . A novel fluorometric method for measuring phenanthrene metabolism in vitro was developed and verified with direct measurement of {14C}phenanthrene using dog liver microsomes . The fluorometric assay and direct measurement of {14C}phenanthrene metabolism were used to show that CYP6D1, a house fly cytochrome P450, is the major house fly P450 involved in phenanthrene metabolism . Phenanthrene was metabolized by microsomes from the LPR strain of house fly that overexpresses CYP6D1, but metabolism was not observed in the CS strain that has a lower level of CYP6D1 . Furthermore, the majority of phenanthrene metabolism was inhibited by a CYP6D1-specific antibody . This study increases the number of known substrates of CYP6D1 and identifies polyaromatic hydrocarbons as potential substrates of CYP6D1 . The utility of CYP6D1 as an agent in bioremediation and the utility of the new fluorometric assay for understanding PAH metabolism in insects and mammals are discussed.

Appl Environ Microbiol, 1999 Nov, 65(11), 4781 - 7
Characterization of an operon encoding two c-type cytochromes, an aa(3)-type cytochrome oxidase, and rusticyanin in Thiobacillus ferrooxidans ATCC 33020; Appia-Ayme C et al.; Despite the importance of Thiobacillus ferrooxidans in bioremediation and bioleaching, little is known about the genes encoding electron transfer proteins implicated in its energetic metabolism . This paper reports the sequences of the four cox genes encoding the subunits of an aa(3)-type cytochrome c oxidase . These genes are in a locus containing four other genes: cyc2, which encodes a high-molecular-weight cytochrome c; cyc1, which encodes a c(4)-type cytochrome (c(552)); open reading frame 1, which encodes a putative periplasmic protein of unknown function; and rus, which encodes rusticyanin . The results of Northern and reverse transcription-PCR analyses indicated that these eight genes are cotranscribed . Two transcriptional start sites were identified for this operon . Upstream from each of the start sites was a sigma70-type promoter recognized in Escherichia coli . While transcription in sulfur-grown T . ferrooxidans cells was detected from the two promoters, transcription in ferrous-iron-grown T . ferrooxidans cells was detected only from the downstream promoter . The cotranscription of seven genes encoding redox proteins suggests that all these proteins are involved in the same electron transfer chain; a model taking into account the biochemistry and the genetic data is discussed.

J Hazard Mater, 1999 Oct 29, 69(2), 229 - 43
Hydrogen peroxide decomposition in model subsurface systems; Watts RJ et al.; Rates of hydrogen peroxide decomposition, hydroxyl radical production, and oxygen evolution were investigated in silica sand-goethite slurries using unstabilized and stabilized hydrogen peroxide formulations . The goethite-catalyzed decomposition of unstabilized hydrogen peroxide formulations resulted in more rapid hydrogen peroxide loss and oxygen evolution relative to systems containing a highly stabilized hydrogen peroxide formulation . Systems at neutral pH and those containing higher goethite concentrations were characterized by higher rates of hydrogen peroxide decomposition and by more oxygen evolution . The stabilized hydrogen peroxide formulation showed greater hydroxyl radical production relative to the unstabilized formulations . Furthermore, hydroxyl radical production rates were greater at neutral pH than at the acidic pH regimes . The results suggest that when stabilized hydrogen peroxide is injected into the subsurface during in situ bioremediation, naturally occurring minerals such as goethite may initiate Fenton-like reactions . While these reactions may prove to be toxic to microorganisms, they have the potential to chemically oxidize contaminants in soils and groundwater.

FEMS Microbiol Ecol, 1999 Nov 1, 30(3), 229 - 236
Bacterial survival and mineralization of p-nitrophenol in soil by green fluorescent protein-marked Moraxella sp . G21 encapsulated cells; Errampalli D et al.; Moraxella sp . G21 cells marked with the green fluorescent protein (gfp) survived in kappa-carrageenan beads and as free cells for a month after inoculation into autoclaved soil and non-sterile soil contaminated with p-nitrophenol (PNP) . Similar {U-(14)C}PNP mineralization values were produced by encapsulated Moraxella sp . G21 cells and as free cells (53 and 60% mineralization) . There was no significant difference between cell survival and {U-(14)C}PNP mineralization activity in soil by the rifampicin-resistant Moraxella sp . mental strain and Moraxella sp . G21 . The ability of encapsulated Moraxella sp . G21 cells to survive, retain their green fluorescence and mineralize {U-(14)C}PNP suggests that the GFP-marked strain encapsulated in kappa-carrageenan may be useful for bioremediation of toxic chemicals in soil.

J Clin Microbiol, 1999 Nov, 37(11), 3594 - 600
Genotypic and phenotypic relationships between clinical and environmental isolates of Stenotrophomonas maltophilia; Berg G et al.; While the gram-negative bacterium Stenotrophomonas maltophilia is used in biotechnology (e.g., for biological control of plant pathogens and for bioremediation), the number of S . maltophilia diseases in humans has dramatically increased in recent years . A total of 40 S . maltophilia isolates from clinical and environmental sources (plant associated and water) was investigated to determine the intraspecies diversity of the group and to determine whether or not the strains could be grouped based on the source of isolation . The isolates were investigated by phenotypic profiling (enzymatic and metabolic activity and antibiotic resistance patterns) and by molecular methods such as temperature-gradient gel electrophoresis of the 16S rRNA gene fragment, PCR fingerprinting with BOX primers, and pulsed-field gel electrophoresis (PFGE) after digestion with DraI . Results of the various methods revealed high intraspecies diversity . PFGE was the most discriminatory method for typing S . maltophilia when compared to the other molecular methods . The environmental strains of S . maltophilia were highly resistant to antibiotics, and the resistance profile pattern of the strains was not dependent on their source of isolation . Computer-assisted cluster analysis of the phenotypic and genotypic features did not reveal any clustering patterns for either clinical or environmental isolates.

J Hazard Mater, 1999 Oct 1, 69(1), 67 - 79
Intrinsic bioremediation of trichloroethylene and chlorobenzene: field and laboratory studies; Kao CM et al.; Activities at a former fire training area at Robins Air Force Base in Georgia, USA resulted in contamination of groundwater with a mixture of trichloroethylene (TCE) and chlorobenzene (CB) . Results from the field investigation suggest that intrinsic bioremediation process is occurring, which caused the decrease in TCE and CB concentrations, and increase in TCE degradation byproducts {e.g., dichloroethylene isomers (DCEs), vinyl chloride (VC)} concentrations . Contaminated groundwater samples collected from this site were used to conduct microbial enumeration tests, and used as the inocula for microcosm establishment . Results from the microbial enumeration study indicate that methanogenesis was the dominant biodegradation pattern within the source and mid-plume areas, and the aerobic biodegradation process dominated the downgradient area . Laboratory microcosm experiments were conducted to evaluate the feasibility of using CB as the primary substrate to enhance the intrinsic biodegradation of TCE . Microcosm results suggest that CB can serve as the primary substrate (electron donor), and enhance TCE biodegradation to less-chlorinated compounds under both aerobic cometabolism and reductive dechlorination conditions.

J Hazard Mater, 1999 Oct 1, 69(1), 25 - 39
Use of calcium peroxide to provide oxygen for contaminant biodegradation in a saturated soil; Cassidy DP et al.; Laboratory studies were conducted in solid-phase reactors on a silty loam contaminated with bis-(2-ethylhexyl) phthalate (BEHP) to determine the conditions under which calcium peroxide (CaO(2)) would promote the aerobic bioremediation of water-saturated soil . Closed 500 ml solid-phase reactors were operated to determine whether CaO(2) stimulated the biodegradation of BEHP in saturated soil . Ex situ bioremediation conditions were then simulated by mixing water-saturated soil for 6 h before placing the soil in three vented, 2 l solid-phase reactors for 50 days . Biodegradation of BEHP was quantified using four different measurements of microbial activity: (1) oxygen concentrations in the reactor gas; (2) bacterial colony-forming units (CFU); (3) fungal CFU; and (4) 2-(p-iodophenyl)-3-(p-nitrophenyl)-5-phenyl tetrazolium chloride dehydrogenase activity (INT-DHA) . CaO(2) released molecular O(2), which retarded dewatering but substantially enhanced BEHP biodegradation . After 20 days, BEHP in the amended reactor was reduced from 20.3 to roughly 5 g kg(-1) vs . 15 g kg(-1) in the reactor without CaO(2) . Bacterial growth was favored over fungal growth at elevated moisture and BEHP levels.

Appl Microbiol Biotechnol, 1999 Aug, 52(2), 154 - 62
High- and low-molecular-mass microbial surfactants; Rosenberg E et al.; Microorganisms synthesize a wide variety of high- and low-molecular-mass bioemulsifiers . The low-molecular-mass bioemulsifiers are generally glycolipids, such as trehalose lipids, sophorolipids and rhamnolipids, or lipopeptides, such as surfactin, gramicidin S and polymyxin . The high-molecular-mass bioemulsifiers are amphipathic polysaccharides, proteins, lipopolysaccharides, lipoproteins or complex mixtures of these biopolymers . The low-molecular-mass bioemulsifiers lower surface and interfacial tensions, whereas the higher-molecular-mass bioemulsifiers are more effective at stabilizing oil-in-water emulsions . Three natural roles for bioemulsifiers have been proposed: (i) increasing the surface area of hydrophobic water-insoluble growth substrates; (ii) increasing the bioavailability of hydrophobic substrates by increasing their apparent solubility or desorbing them from surfaces; (iii) regulating the attachment and detachment of microorganisms to and from surfaces . Bioemulsifiers have several important advantages over chemical surfactants, which should allow them to become prominent in industrial and environmental applications . The potential commercial applications of bioemulsifiers include bioremediation of oil-polluted soil and water, enhanced oil recovery, replacement of chlorinated solvents used in cleaning-up oil-contaminated pipes, vessels and machinery, use in the detergent industry, formulations of herbicides and pesticides and formation of stable oil-in-water emulsions for the food and cosmetic industries.

The bioremediation technology most suitable for a specific site is determined by several factors, such as site conditions, indigenous microorganism population, and the type, quantity, and toxicity of contaminant chemicals present. Some treatment technologies involve the addition of nutrients to stimulate or accelerate the activity of indigenous microbes. Optimizing environmental conditions enhance the growth of microorganisms and increase microbial population resulting in improved degradation of hazardous substances. However, if the biological activity needed to degrade a particular contaminant is not present at the site, suitable microbes from other locations, called exogenous microorganisms, can be introduced and nurtured. Other technologies being demonstrated are phytoremediation, or the use of plants to clean up contaminated soils and ground water, and fungal remediation, which employs white-rot fungus to degrade contaminants.

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