Folia Microbiol (Praha), 2003, 48(4), 510 - 20 Polyphasic taxonomy of symbiotic rhizobia from wild leguminous plants growing in Egypt; Zahran HH et al.; About 20 strains of rhizobia from wild legumes were characterized based on numerical analysis of phenotypic characteristics, nodulating ability, fatty acid methyl esters (FAME) and SDS-PAGE profiles of whole cell proteins . FAME analysis revealed that palmitic (16:0), stearic (18:0) and arachidonic (20:0) were detected in most of wild-legume rhizobia, the latter being uncommon in fatty acid profiles of Rhizobium and Sinorhizobium . Numerical analysis of FAME classified strains of wild-legume rhizobia into 9 clusters and one heterogeneous group . There was both agreement and disagreement with the clustering data based on phenotypic analysis and FAME analysis . Four strains were grouped together in the same cluster based on both methods . However, 4 another strains, which were placed in one cluster of phenotypic analysis, were distributed in several clusters after FAME analysis . SDS-PAGE of whole-cell proteins revealed that the rhizobial strains exhibited protein profiles with peptide bands ranging from 5-19 band per profile and showed molar mass of 110-183 kDa . As in the case of FAME analysis, numerical analysis of protein bands was compared with clustering of phenotypic analysis . Agreement of the two methods was obvious when clustering some strains but conflicted in the classification of some other strains . However, integration of the three methods could be the basis of a polyphasic taxonomy . The twenty strains of wild-legume rhizobia were finally classified as follows: 12 strains related to Rhizobium leguminosarum, 5 strains related to Sinorhizobium meliloti and 3 strains to Rhizobium spp . Rhizobia nodulating wild herb legumes are among indigenous strains nodulating crop legumes in cultivated as well as noncultivated lands. Syst Appl Microbiol, 2003 Sep, 26(3), 453 - 65 A catalogue of molecular, physiological and symbiotic properties of soybean-nodulating rhizobial strains from different soybean cropping areas of China; Thomas-Oates J et al.; We have analysed 198 fast-growing soybean-nodulating rhizobial strains from four different regions of China for the following characteristics: generation time; number of plasmids; lipopolysaccharide (LPS), nodulation factors (LCOs) and PCR profiles; acidification of growth medium; capacity to grow at acid, neutral, and alkaline pH; growth on LC medium; growth at 28 and 37 degrees C; melanin production capacity; Congo red absorption and symbiotic characteristics . These unbiased analyses of a total subset of strains isolated from specific soybean-cropping areas (an approach which could be called "strainomics") can be used to answer various biological questions . We illustrate this by a comparison of the molecular characteristics of five strains with interesting symbiotic properties . From this comparison we conclude, for instance, that differences in the efficiency of nitrogen fixation or competitiveness for nodulation of these strains are not apparently related to differences in Nod factor structure. Microbiol Res, 2003, 158(3), 243 - 8 Growth promoting influence of siderophore-producing Pseudomonas strains GRP3A and PRS9 in maize (Zea mays L.) under iron limiting conditions; Sharma A et al.; Maize seeds were bacterized with siderophore-producing pseudomonads with the goal to develop a system suitable for better iron uptake under iron-stressed conditions . Siderophore production was compared in fluorescent Pseudomonas spp . GRP3A, PRS9 and P . chlororaphis ATCC 9446 in standard succinate (SSM) and citrate (SCM) media . Succinate was better suited for siderophore production, however, deferration of media resulted in increased siderophore production in all the strains . Maximum siderophore level (216.23 microg/ml) was observed in strain PRS9 in deferrated SSM after 72 h of incubation . Strains GRP3A and PRS9 were used for plant growth promotion experiments . Strains GRP3A and PRS9 were also antagonistic against the phytopathogens, Colletotrichum dematium, Rhizoctonia solani and Sclerotium rolfsii . Bacterization of maize seeds with strains GRP3A and PRS9 showed significant increase in germination percentage and plant growth . Maximum shoot and root length and dry weight were observed with 10 microM Fe3+ along with bacterial inoculants suggesting application of siderophore producing plant growth promoting rhizobacterial strains in crop productivity in calcareous soil system. Biotechnol Lett, 2003 Aug, 25(15), 1267 - 70 Anions effects on biosorption of Mn(II) by extracellular polymeric substance (EPS) from Rhizobium etli; Pulsawat W et al.; Microbial extracellular polymeric substances (EPS) are potential biosorbents for metal remediation and recovery . The Langmuir and Freundlich kinetics of Mn(II) binding by the EPS from a novel Mn(II) oxidising strain of Rhizobium etli were determined . Maximum manganese specific adsorptions (q(max)) decreased in the sequence: sulphate (62 mg Mn per g EPS) > nitrate (53 mg g(-1)) > chloride (21 mg g(-1)) . Consideration of the anion during kinetic studies is usually neglected but is important in providing more practical and comparable data between different biosorbent systems. Biotechnol Lett, 2003 Sep, 25(17), 1407 - 13 Screening, identification and kinetic characterization of a bacterium for Mn(II) uptake and oxidation; Moy YP et al.; Following sample collection and screening at a number of Mn-associated mine sites in Northern Australia, a microbial strain was selected for its enhanced rate of Mn uptake . The strain was identified by phylogenetic analysis as a Rhizobium sp . Kinetic studies of Mn(II) uptake and oxidation by this strain in glucose-based media established that the uptake of Mn(II) was much greater than the conversion of Mn(II) to Mn oxide . Chemical analysis and scanning electron microscopy confirmed the production of significant amounts of polysaccharides by this strain . These polysaccharides may play a role both in enhancing Mn(II) accumulation and in minimizing Mn oxide production. Environ Microbiol, 2003 Oct, 5(10), 916 - 24 Effect of thorium on the growth and capsule morphology of Bradyrhizobium; Santamaria M et al.; The thorium effect on Bradyrhizobium growth was assayed in liquid media . Th4+ inhibited the growth of Bradyrhizobium (Chamaecytisus) BGA-1, but this effect decreased in the presence of suspensions of live or dead bacterial cells . Th4+ induced the formation of a gel-like precipitate when added to a dense suspension of B . (Chamaecytisus) BGA-1 cells . Viable Bradyrhizobium cells remained in suspension after precipitate formation . Thorium was recovered in the precipitate, in which polysaccharide, lipopolysaccharide and proteins were also found . After Th4+ addition, the morphology of B . (Chamaecytisus) BGA-1 or Bradyrhizobium japonicum USDA 110 sedimented cells studied by scanning electron microscopy changed from an entangled network of capsulated bacteria to uncapsulated individual cells and an amorphous precipitate . Energy-dispersive X-ray spectroscopy showed that thorium was mainly in the amorphous fraction . Precipitate was also formed between B . (Chamaecytisus) BGA-1 and Al3+, which was also toxic to this bacterium . Precipitate induced by Th4+ or Al3+ was found in all Bradyrhizobium and Sinorhizobium strains tested, but not in Rhizobium, Salmonella typhimurium, Aerobacter aerogenes or Escherichia coli . These results suggest a specific defence mechanism based on metal precipitation by extracellular polymers. Environ Microbiol, 2003 Oct, 5(10), 888 - 95 Temporal change in culturable phenanthrene degraders in response to long-term exposure to phenanthrene in a soil column system; Bodour AA et al.; Widespread environmental contamination by polycyclic aromatic hydrocarbons (PAH) has led to increased interest in the use of natural attenuation as a clean-up strategy . However, few bioremediation studies have investigated the behaviour of the indigenous PAH-degrading community after long-term exposure to a PAH . In this study, a column packed with sandy loam soil was exposed to a solution saturated with phenanthrene ( approximately 1.2 mg l-1) for a 6-month period to examine the temporal response of the indigenous phenanthrene-degrading community . Initial soil, effluent, and final soil samples were collected and analysed for phenanthrene concentration and culturable phenanthrene degraders . Phenanthrene-degrading isolates were grouped by colony morphology . For each unique group, 16S rDNA polymerase chain reaction was performed, and then sequencing analysis was used to identify the isolate at the genus level . Twenty-five phenanthrene-degrading isolates, potentially representing 19 genera, were obtained from this analysis . Of these, eight genera have not been reported previously to degrade phenanthrene, including Afipia, Janthinobacterium, Leptothrix, Massilia, Methylobacterium, Rhizobium, Sinorhizobium and Thiobacillus . Results indicate that the dominant phenanthrene-degrading population changed over the course of this 6-month experiment . Specifically, the isolates obtained initially from the soil were not subsequently found in either effluent samples or the soil at the end of the experiment . Furthermore, several isolates that were found in the soil at the end of the experiment were not observed in the soil initially or in the effluent samples . This study confirms earlier findings indicating that a diverse community participates in phenanthrene degradation in the environment, and also suggests that the composition of this community is temporally variable. Planta, 2003 Nov, 218(1), 42 - 9 Epub 2003 Sep 24. Expression of ENOD40 during tomato plant development; Vleghels I et al.; In legumes, ENOD40 expression is increased upon interaction of plants with rhizobia . Little is known of the expression pattern of ENOD40 during other stages of the plant life cycle . Studies of ENOD40 expression in non-legume development may give an indication of the function of the gene . To investigate the ENOD40 expression pattern during plant development, a fusion between the beta-glucuronidase (GUS) reporter gene and 150 bp of the 5' untranslated region plus 3,000 bp of 5' untranscribed tomato ENOD40 sequence was constructed and introduced into Lycopersicon esculentum Miller . Based on the observed GUS expression patterns in transgenic tomato we speculate that ENOD40 in tomato has a role in counteracting ethylene-provoked responses. Curr Microbiol, 2003 Aug, 47(2), 134 - 7 nodD alleles of Sinorhizobium fredii USDA191 differentially influence soybean nodulation, nodC expression, and production of exopolysaccharides; Machado D et al.; All Rhizobium strains examined to date have one or multiple alleles of nodD . At least one copy of nodD and the presence of flavonoid exudates are required for nod gene induction and nodulation . Sinorhizobium fredii USDA191 has two copies of nodD . In this study, we demonstrate that inactivation of either copy of nodD caused a reduction in basal levels of expression of nodC . Extra copies of nodD1 had no effect on the expression of nodC when compared with the wild type, but extra copies of nodD2 abolished the inducer requirement, thereby rendering nodC constitutive . A nodD1 mutant was unable to nodulate soybean cultivars 'Peking' and 'McCall' . Inactivation of nodD2 or addition of extra copies of nodD1 or nodD2 caused delayed nodulation on Peking, and reduced the number of nodules on McCall . Both nodD alleles of S . fredii USDA191 appear to be involved in regulation of exopolysaccharide production; however, nodD2 appears to be more important in this respect than nodD1. Microb Ecol, 2003 Oct, 46(3), 302 - 11 Epub 2003 Sep 17. Microbial processes associated with roots of bulbous rush coated with iron plaques; Kusel K et al.; Bulbous rush (Juncus bulbosus) is a pioneer species in acidic, iron-rich, coal mining lakes in the eastern part of Germany . Juncus roots are coated with iron plaques, and it has been suggested that microbial processes under the iron plaques might be supportive for Juncus plant growth . The objectives of this work were to enumerate the microbes involved in the turnover of iron and organic root exudates in the rhizoplane, to investigate the effect of oxygen and pH on the utilization of these exudates by the rhizobacteria, and to study the ability of the root-colonizing microbiota to reduce sulfate . Enumeration studies done at pH 3 demonstrated that 10(6) Fe(III) reducers and 10(7) Fe(II) oxidizers g (fresh wt root)(-1) were associated with Juncus roots . When roots were incubated in goethite-containing medium without and with supplemental glucose, Fe(II) was formed at rates approximating 1.1 mmol g (fresh wt root) (-1) d(-1) and 3.6 mmol g (fresh wt root)(-1) d(-1) under anoxic conditions, respectively . These results suggest that a rapid microbially mediated cycling of iron occurs in the rhizosphere of Juncus roots under changing redox conditions . Most-probable-number estimates of aerobes and anaerobes capable of consuming root exudates at pH 3 were similar in the rhizosphere sediment and in Juncus roots, but numbers of aerobes were significantly higher than those of anaerobes . At pH 3, supplemental organic exudates were primarily subject to aerobic oxidation to CO2 and not subject to fermentation . However, at pH 4.5, root exudates were also rapidly utilized under anoxic conditions . Root-associated sulfate reduction was not observed at pH 3 to 4.5 but was observed at pH 4.9 . The pH increased during all root-incubation studies both under oxic and anoxic conditions . Thus, as result of the microbial turnover of organic root exudates, pH and CO2 levels might be elevated at the root surface and favor Juncus plants to colonize acidic habitats. Int J Parasitol, 2003 Sep 30, 33(11), 1269 - 76 Interactions between bacteria and plant-parasitic nematodes: now and then; Bird DM et al.; Based on genome-to-genome analyses of gene sequences obtained from plant-parasitic, root-knot nematodes (Meloidogyne spp.), it seems likely that certain genes have been derived from bacteria by horizontal gene transfer . Strikingly, a common theme underpinning the function of these genes is their apparent direct relationship to the nematodes' parasitic lifestyle . Phylogenetic analyses implicate rhizobacteria as the predominant group of 'gene donor' bacteria . Root-knot nematodes and rhizobia occupy similar niches in the soil and in roots, and thus the opportunity for genetic exchange may be omnipresent . Further, both organisms establish intimate developmental interactions with host plants, and mounting evidence suggests that the mechanisms for these interactions are shared too . We propose that the origin of parasitism in Meloidogyne may have been facilitated by acquisition of genetic material from soil bacteria through horizontal transfer, and that such events represented key steps in speciation of plant-parasitic nematodes . To further understand the mechanisms of horizontal gene transfer, and also to provide experimental tools to manipulate this promising bio-control agent, we have initiated a genomic sequence of the bacterial hyper-parasite of plant parasitic nematodes, Pasteuria penetrans . Initial data have established that P . penetrans is closely related to Bacillus spp., to the extent that considerable genome synteny is apparent . Hence, Bacillus serves as a model for Pasteuria, and vice versa. Indian J Environ Health, 2002 Oct, 44(4), 282 - 9 Mechanical, physico-chemical and microbial analysis of oil refinery waste receiving agricultural soil; Ashok BT et al.; The mechanical, physico-chemical characteristics of soil and the activity of indigenous microflora were studied in the agricultural soil steadily receiving petroleum refinery effluent at Mathura, U.P, India The data on the soil grain size and texture revealed that the soil in the test region was basically loam or silty loam . Physic-chemical analysis showed considerable variability in the soil pH, temperature, moisture content and water holding capacity (WHC) . A substantially higher microbial activity was noticed at the test sites as evident from the total variable (10(5) to 10(9) CFU g-1 soil) bacterial population . In addition, a significant population of proteolytic and cellulolytic bacteria, rhizobium and actinomycetes was detected . Oligotrophs were isolated and characterized into four types (I-IV) . A fraction of oligotrophic bacteria, particularly those belonging to type II and type IV exhibited appreciable in distilled water . Invariably higher microbial biomass ranging from 366 to 1604 mg CO2 . 100 g-1 soil, clearly implied that the soil in the test region was very well nourished and the refinery waste was providing enough nitrites to support the growth of soil microflora. Int J Syst Evol Microbiol, 2003 Sep, 53(Pt 5), 1575 - 83 Characterization of rhizobia isolated from legume species within the genera Astragalus and Lespedeza grown in the Loess Plateau of China and description of Rhizobium loessense sp . nov; Wei GH et al.; Twenty-nine rhizobial isolates from root nodules of Astragalus and Lespedeza spp . growing in the Loess Plateau of China were characterized by numerical taxonomy, RFLP and sequencing of PCR-amplified 16S rRNA genes, measurement of DNA G+C content, DNA-DNA relatedness and cross-nodulation with selected legume species . Based on the results of numerical taxonomy, the isolates formed two clusters (1 and 2) with some single isolates at a similarity level of 82 % . Cluster 1 contained six isolates from Astragalus and Lespedeza spp . Cluster 2 consisted of nine isolates from Astragalus spp . DNA relatedness was greater than 80 % among isolates within cluster 2 . Phylogenetic analysis based on 16S rRNA gene sequences showed that CCBAU 7190B(T), representing cluster 2, was closely related to Rhizobium galegae and Rhizobium huautlense . DNA-DNA relatedness between CCBAU 7190B(T) and reference strains of R . galegae, R . huautlense and other related species ranged from 0 to 48.6 % . The cluster 2 isolates could also be differentiated phenotypically from related species . Based on these data, a novel species, Rhizobium loessense sp . nov., is proposed for cluster 2, with the type strain CCBAU 7190B(T) (=AS1.3401(T)=LMG 21975(T)). Mol Cell Biol, 2003 Oct, 23(19), 6780 - 9 Targeted disruption of the mouse PAS domain serine/threonine kinase PASKIN; Katschinski DM et al.; PASKIN is a novel mammalian serine/threonine kinase containing two PAS (Per-Arnt-Sim) domains . PASKIN is related to the Rhizobium oxygen sensor protein FixL and to AMP-regulated kinases . Like FixL, the sensory PAS domain of PASKIN controls the kinase activity by autophosphorylation in a (unknown) ligand-dependent manner . In Saccharomyces cerevisiae, the two PASKIN orthologues PSK1 and PSK2 phosphorylate three translation factors and two enzymes involved in glycogen synthesis, thereby coordinately regulating protein synthesis and glycolytic flux . To elucidate the function of mammalian PASKIN, we inactivated the mouse Paskin gene by homologous recombination in embryonic stem cells . Paskin(-/-) mice showed normal development, growth, and reproduction . The targeted integration of a lacZ reporter gene allowed the identification of the cell types expressing mouse PASKIN . Surprisingly, PASKIN expression is strongly upregulated in postmeiotic germ cells during spermatogenesis . However, fertility and sperm production and motility were not affected by the PASKIN knockout . The Ppp1r7 gene encoding Sds22, a regulatory subunit of protein phosphatase 1, shares the promoter region with the Paskin gene, pointing towards a common transcriptional regulation . Indeed, Sds22 colocalized with the cell types expressing PASKIN in vivo, suggesting a functional role of protein phosphatase-1 in the regulation of PASKIN autophosphorylation. Mol Plant Microbe Interact, 2003 Sep, 16(9), 796 - 807 Distinct patterns of symbiosis-related gene expression in actinorhizal nodules from different plant families; Pawlowski K et al.; Phylogenetic analyses suggest that, among the members of the Eurosid I clade, nitrogen-fixing root nodule symbioses developed multiple times independently, four times with rhizobia and four times with the genus Frankia . In order to understand the degree of similarity between symbiotic systems of different phylogenetic subgroups, gene expression patterns were analyzed in root nodules of Datisca glomerata and compared with those in nodules of another actinorhizal plant, Alnus glutinosa, and with the expression patterns of homologous genes in legumes . In parallel, the phylogeny of actinorhizal plants was examined more closely . The results suggest that, although relationships between major groups are difficult to resolve using molecular phylogenetic analysis, the comparison of gene expression patterns can be used to inform evolutionary relationships . In this case, stronger similarities were found between legumes and intracellularly infected actinorhizal plants (Alnus) than between actinorhizal plants of two different phylogenetic subgroups (Alnus/Datisca). Mol Plant Microbe Interact, 2003 Sep, 16(9), 743 - 51 Characterization of Nops, nodulation outer proteins, secreted via the type III secretion system of NGR234; Marie C et al.; The nitrogen-fixing symbiotic bacterium Rhizobium species NGR234 secretes, via a type III secretion system (TTSS), proteins called Nops (nodulation outer proteins) . Abolition of TTSS-dependent protein secretion has either no effect or leads to a change in the number of nodules on selected plants . More dramatically, Nops impair nodule development on Crotalaria juncea roots, resulting in the formation of nonfixing pseudonodules . A double mutation of nopX and nopL, which code for two previously identified secreted proteins, leads to a phenotype on Pachyrhizus tuberosus differing from that of a mutant in which the TTSS is not functional . Use of antibodies and a modification of the purification protocol revealed that NGR234 secretes additional proteins in a TTSS-dependent manner . One of them was identified as NopA, a small 7-kDa protein . Single mutations in nopX and nopL were also generated to assess the involvement of each Nop in protein secretion and nodule formation . Mutation of nopX had little effect on NopL and NopA secretion but greatly affected the interaction of NGR234 with many plant hosts tested . NopL was not necessary for the secretion of any Nops but was required for efficient nodulation of some plant species . NopL may thus act as an effector protein whose recognition is dependent upon the hosts' genetic background. J Appl Microbiol, 2003, 95(4), 832 - 8 Effect of Azospirillum-mediated plant growth promotion on the development of bacterial diseases on fresh-market and cherry tomato; Romero AM et al.; AIMS: Plant growth-promoting (PGP) activity of two Azospirillum strains and their effects on foliar and vascular bacterial diseases were evaluated on fresh market and cherry tomato . METHODS AND RESULTS: Tomato seeds were inoculated with A . brasilense Sp7 or Azospirillum sp . BNM-65 . Four-week-old plants were challenge-inoculated with Clavibacter michiganensis subsp . michiganensis (bacterial canker) or with Xanthomonas campestris pv . vesicatoria (bacterial spot) . Azospirillum-induced PGP was greater on cherry than on fresh-market tomato . Cherry tomato was more resistant to bacterial canker but more susceptible to bacterial spot than the fresh-market tomato . Canker severity was not affected by Azospirillum seed treatments . However, leaf- and plant-death were delayed on Azospirillum-treated plants compared with nontreated controls . Azospirillum increased the bacterial spot severity on cherry but not on fresh-market tomato . CONCLUSIONS: PGP was observed on both tomato genotypes, although growth effects were larger on cherry tomato . Also, Azospirillum treatments may alter tomato susceptibility to bacterial diseases . SIGNIFICANCE AND IMPACT OF THE STUDY: The interaction between PGP rhizobacteria like Azospirillum spp., not known to induce systemic resistance, with plant pathogens distantly located is frequently overlooked . This work demonstrates the importance of this kind of evaluation. Environ Manage . 2003 Sep 11; {Epub ahead of print} Comparison of Four Sesbania Species to Remediate Pb/Zn and Cu Mine Tailings; Chan GY et al.; A 6-month greenhouse pot trial was performed, aimed at screening appropriate Sesbania species for remediation of Pb/Zn and Cu mine tailings . Performances of young seedlings of four Sesbania species ( S . cannabina, S . grandiflora, S . rostrata, and S . sesban) were compared with and without inoculation of rhizobia . Seedlings were planted in two types of tailings amended with garden soil or garden soil mixed with river sediment . The results indicated that inoculated plants generally produced a higher biomass than samples without inoculation . Pb/Zn mine tailings containing rather high concentrations of total and water-soluble Cu, Pb, and Zn were toxic to plant growth compared with Cu mine tailings, according to the growth performance of the four species . Sesbania sesban and S . rostrata showed superior growth performance, compared to the other two species . Thus, they can serve as pioneer species to modify the barren environment, by providing organic matter and essential nutrients such as nitrogen, upon decomposition, in a relatively short period of time . This is especially true for S . rostrata, which is an annual plant that forms both stem and root nodules . However, a longer-term field trial should be conducted to investigate if superior species can beneficially modify the habitat for the growth of subsequent plant communities. J Biol Chem, 2003 Nov 28, 278(48), 47915 - 21 Epub 2003 Sep 08. Temperature-controlled structural alterations of an RNA thermometer; Chowdhury S et al.; Thermoresponsive structures in the 5'-untranslated region of mRNA are known to control translation of heat shock and virulence genes . Expression of many rhizobial heat shock genes is regulated by a conserved sequence element called ROSE for repression of heat shock gene expression . This cis-acting, untranslated mRNA is thought to prevent ribosome access at low temperature through an extended secondary structure, which partially melts when the temperature rises . We show here by a series of in vivo and in vitro approaches that ROSE is a sensitive thermometer responding in the physiologically relevant temperature range between 30 and 40 degrees C . Point mutations predicted to disrupt base pairing enhanced expression at 30 degrees C . Compensatory mutations restored repression, emphasizing the importance of secondary structures in the sensory RNA . Only moderate inducibility of a 5'-truncated ROSE variant suggests that interactions between individual stem loops coordinate temperature sensing . In the presence of a complementary oligonucleotide, the functionally important stem loop of ROSE was rendered susceptible to RNase H treatment at heat shock temperatures . Since major structural rearrangements were not observed during UV and CD spectroscopy, subtle structural changes involving the Shine-Dalgarno sequence are proposed to mediate translational control . Temperature perception by the sensory RNA is an ordered process that most likely occurs without the aid of accessory factors. Nature, 2003 Sep 4, 425(6953), 78 - 81 Host sanctions and the legume-rhizobium mutualism; Kiers ET et al.; Explaining mutualistic cooperation between species remains one of the greatest problems for evolutionary biology . Why do symbionts provide costly services to a host, indirectly benefiting competitors sharing the same individual host? Host monitoring of symbiont performance and the imposition of sanctions on 'cheats' could stabilize mutualism . Here we show that soybeans penalize rhizobia that fail to fix N(2) inside their root nodules . We prevented a normally mutualistic rhizobium strain from cooperating (fixing N(2)) by replacing air with an N(2)-free atmosphere (Ar:O(2)) . A series of experiments at three spatial scales (whole plants, half root systems and individual nodules) demonstrated that forcing non-cooperation (analogous to cheating) decreased the reproductive success of rhizobia by about 50% . Non-invasive monitoring implicated decreased O(2) supply as a possible mechanism for sanctions against cheating rhizobia . More generally, such sanctions by one or both partners may be important in stabilizing a wide range of mutualistic symbioses. FEMS Microbiol Lett, 2003 Aug 29, 225(2), 227 - 33 Nematode-enhanced microbial colonization of the wheat rhizosphere; Knox OG et al.; The mechanisms by which seed-applied bacteria colonize the rhizosphere in the absence of percolating water are poorly understood . Without mass flow, transport of bacteria by growing roots or soil animals, particularly nematodes may be important . We used a sand-based microcosm system to investigate the ability of three species of nematodes (Caenorhabditis elegans, Acrobeloides thornei and a Cruznema sp.) to promote rhizosphere colonization by four strains of beneficial rhizobacteria . In nearly all cases, rhizosphere colonization was substantially increased by the presence of nematodes, irrespective of bacterial or nematode species . Our results suggest that nematodes are important vectors for bacteria rhizosphere colonization in the absence of percolating water. Science, 2003 Oct 24, 302(5645), 630 - 3 Epub 2003 Aug 28. LysM domain receptor kinases regulating rhizobial Nod factor-induced infection; Limpens E et al.; The rhizobial infection of legumes has the most stringent demand toward Nod factor structure of all host responses, and therefore a specific Nod factor entry receptor has been proposed . The SYM2 gene identified in certain ecotypes of pea (Pisum sativum) is a good candidate for such an entry receptor . We exploited the close phylogenetic relationship of pea and the model legume Medicago truncatula to identify genes specifically involved in rhizobial infection . The SYM2 orthologous region of M . truncatula contains 15 putative receptor-like genes, of which 7 are LysM domain-containing receptor-like kinases (LYKs) . Using reverse genetics in M . truncatula, we show that two LYK genes are specifically involved in infection thread formation . This, as well as the properties of the LysM domains, strongly suggests that they are Nod factor entry receptors. Biophys J, 2003 Sep, 85(3), 1345 - 57 Bacterial flagellar microhydrodynamics: Laminar flow over complex flagellar filaments, analog archimedean screws and cylinders, and its perturbations; Trachtenberg S et al.; The flagellar filament, the bacterial organelle of motility, is the smallest rotary propeller known . It consists of 1), a basal body (part of which is the proton driven rotary motor), 2), a hook (universal joint-allowing for off-axial transmission of rotary motion), and 3), a filament (propeller-a long, rigid, supercoiled helical assembly allowing for the conversion of rotary motion into linear thrust) . Helically perturbed (so-called "complex") filaments have a coarse surface composed of deep grooves and ridges following the three-start helical lines . These surface structures, reminiscent of a turbine or Archimedean screw, originate from symmetry reduction along the six-start helical lines due to dimerization of the flagellin monomers from which the filament self assembles . Using high-resolution electron microscopy and helical image reconstruction methods, we calculated three-dimensional density maps of the complex filament of Rhizobium lupini H13-3 and determined its surface pattern and boundaries . The helical symmetry of the filament allows viewing it as a stack of identical slices spaced axially and rotated by constant increments . Here we use the closed outlines of these slices to explore, in two dimensions, the hydrodynamic effect of the turbine-like boundaries of the flagellar filament . In particular, we try to determine if, and under what conditions, transitions from laminar to turbulent flow (or perturbations of the laminar flow) may occur on or near the surface of the bacterial propeller . To address these questions, we apply the boundary element method in a manner allowing the handling of convoluted boundaries . We tested the method on several simple, well-characterized cylindrical structures before applying it to real, highly convoluted biological surfaces and to simplified mechanical analogs . Our results indicate that under extreme structural and functional conditions, and at low Reynolds numbers, a deviation from laminar flow might occur on the flagellar surface . These transitions, and the conditions enabling them, may affect flagellar polymorphism and the formation and dispersion of flagellar bundles-factors important in the chemotactic response. Adv Biochem Eng Biotechnol, 2003, 84, 49 - 89 Rhizobacterial diversity in India and its influence on soil and plant health; Johri BN et al.; The rhizosphere or the zone of influence around roots harbors a multitude of microorganisms that are affected by both abiotic and biotic stresses . Among these are the dominant rhizobacteria that prefer living in close vicinity to the root or on its surface and play a crucial role in soil health and plant growth . Both free-living and symbiotic bacteria are involved in such specific ecological niches and help in plant matter degradation, nutrient mobilization and biocontrol of plant disease . While the rhizosphere as a domain of fierce microbial activity has been studied for over a century, the availability of modern tools in microbial ecology has now permitted the study of microbial communities associated with plant growth and development, in situ localization of important forms, as well as the monitoring of introduced bacteria as they spread in the soil and root environment . This interest is linked to environmental concerns for reduced use of chemicals for disease control as well as an appreciation for utilization of biologicals and organics in agriculture . Indian researchers have studied the diversity of rhizobacteria in a variety of plants, cereals, legumes and others along with assessment of their functionality based on the release of enzymes (soil dehydrogenase, phosphatase, nitrogenase, etc.), metabolites (siderophores, antifungals, HCN, etc.), growth promoters (IAA, ethylene) and as inducers of systemic disease resistance (ISR) . Based on such primary screening protocols, effective rhizobacteria have been field tested with success stories from various agroecological zones of the country, as reflected in the control of root- and soil-borne diseases, improved soil health and increased crop yields . Several commercial formulations, mostly based on dry powder (charcoal, lignite, farmyard manure, etc.) have been prepared and field tested, however, problems of appropriate shelf-life and cell viability are still to be solved . Also, inherent in such low cost technologies are the problems of variability in field performance and successful establishment of introduced inoculants in the root zone . In addition, most products available in the market are not properly monitored for quality before they reach the farmer . As a consequence, the acceptance of rhizobacterial formulations in the country is limited . However, several laboratories have now developed protocols for the rapid characterization of effective isolates based on molecular fingerprinting and other similar tools . Also, the use of molecular markers (gus, lux, gfp, etc.) makes it easy to monitor introduced inoculants in situ in soil and rhizosphere environments . The government initiative in integrated nutrient management and pest management systems has provided additional incentives to relate rhizobacterial science to other ongoing activities so that the benefit of this research leads to technologies that are environmentally and socially acceptable. Nucleic Acids Res, 2003 Sep 1, 31(17), 5003 - 15 Structural motifs in the RNA encoded by the early nodulation gene enod40 of soybean; Girard G et al.; The plant gene enod40 is highly conserved among legumes and also present in various non-legume species . It is presumed to play a central regulatory role in the Rhizobium-legume interaction, being expressed well before the initiation of cortical cell divisions resulting in nodule formation . Two small peptides encoded by enod40 mRNA as well as its secondary structure have been shown to be key elements in the signalling processes underlying nodule organogenesis . Here results concerning the secondary structure of mRNA of enod40 in soybean are presented . This study combined a theoretical approach, involving structure prediction and comparison, as well as structure probing . Our study indicates five conserved domains in enod40 mRNA among numerous leguminous species . Structure comparison suggests that some domains are also conserved in non-leguminous species and that an additional domain exists that was found only in leguminous species developing indeterminate nodules . Enzymatic and chemical probing data support the structure for three of the domains, and partially for the remaining two . The rest of the molecule appears to be less structured . Some of the domains include motifs, such as U-containing internal loops and bulges, which seem to be conserved . Therefore, they might be involved in the regulatory role of enod40 RNA. J Mol Biol, 2003 Aug 29, 331(5), 1093 - 108 The axial alpha-helices and radial spokes in the core of the cryo-negatively stained complex flagellar filament of Pseudomonas rhodos: recovering high-resolution details from a flexible helical assembly; Cohen-Krausz S et al.; Of the two known "complex" flagellar filaments, those of Pseudomonas are far more flexible than those of Rhizobium . Their diameter is larger and their outer three-start ridges and grooves are more prominent . Although the symmetry of both complex filaments is similar, the polymer's linear mass density and the flagellin molecular mass of the latter are lower . A recent comparison of a three-dimensional reconstruction of the filament of Pseudomonas rhodos to that of Rhizobium lupini indicates that the outer flagellin domain (D3) is missing in R.lupini . Here, we concentrate on the structure of the inner core of the filament of P.rhodos using field emission cryo-negative staining electron microscopy and a hybrid helical/single particle reconstruction technique . Averaging 158 filaments caused the density band corresponding to the radial spokes to nearly average out due to their variability and inferred flexibility . Treating the Z=0 cross-sections through the aligned individual three-dimensional density maps as images, classifying them by correspondence analysis (using a mask containing the radial spokes domain) and re-averaging the subclasses (using helical reconstruction techniques) allowed a recovery of the radial spokes and resolved the alpha-helices in domain D0 and the triple alpha-helical bundles in domain D1 at a resolution of 1/7A(-1) . Although the perturbed components of the helical lattice are present along the entire filament's radius, the interior of the complex filament is similar to that of the plain one, whereas it's exterior is altered . Reconstructions of vitrified and cryo-negatively stained plain, right-handed filaments of Salmonella typhimurium SJW1655 prepared and imaged under conditions identical with those used for P.rhodos confirm the similarity of their inner cores and that the secondary structures in the interior of the flagellar filament can, under critical conditions of image recording and correction, be resolved in negative stain. Plant Physiol, 2003 Aug, 132(4), 1982 - 8 Nod factor-induced root hair curling: continuous polar growth towards the point of nod factor application; Esseling JJ et al.; A critical step in establishing a successful nitrogen-fixing symbiosis between rhizobia and legume plants is the entrapment of the bacteria between root hair cell walls, usually in characteristic 180 degrees to 360 degrees curls, shepherd's crooks, which are formed by the host's root hairs . Purified bacterial signal molecules, the nodulation factors (NFs), which are lipochitooligosaccharides, induce root hair deformation in the appropriate host legume and have been proposed to be a key player in eliciting root hair curling . However, for curling to occur, the presence of intact bacteria is thought to be essential . Here, we show that, when spot applied to one side of the growing Medicago truncatula root hair tip, purified NF alone is sufficient to induce reorientation of the root hair growth direction, or a full curl . Using wild-type M . truncatula containing the pMtENOD11::GUS construct, we demonstrate that MtENOD11::GUS is expressed after spot application . The data have been incorporated into a cell biological model, which explains the formation of shepherd's crook curls around NF-secreting rhizobia by continuous tip growth reorientation. J Appl Microbiol, 2003, 95(3), 484 - 91 Effect of trehalose on survival of Bradyrhizobium japonicum during desiccation; Streeter JG; AIMS: A major reason for the ineffectiveness of legume inoculants in the field is the rapid death of rhizobia because of desiccation . The major purpose of this study was to identify conditions under which alpha,alpha-trehalose would improve survival of Bradyrhizobium japonicum during desiccation . METHODS AND RESULTS: Trehalose was added to cultures just prior to desiccation or was supplied to bacteria during the 6-day growth period . A wide variety of trehalose concentrations was tested . Trehalose added to cultures at the time of desiccation improved survival slightly, but trehalose loading during growth was much more effective in protection against desiccation . Growth of bacteria with 3 mmol l-1 trehalose increased trehalose concentration in cells by about threefold and increased survival of cells placed on soya bean {Glycine max (L.) Merr.} seeds by two- to four-fold after 2 or 24 h . Average of overall results indicate that growth of bacteria with trehalose in the medium resulted in a 294% increase in survival after 24 h of desiccation . The concentration of trehalose in cells was very highly correlated with survival of bacteria . When trehalose-loaded cells were suspended in buffer or water, 60-85% of cellular trehalose was lost in about 1 h and, in spite of these losses, survival during desiccation was not reduced . CONCLUSIONS: Accumulation of trehalose in the cytoplasm is critical to the survival of B . japonicum during desiccation . Increasing the periplasmic concentration of trehalose is also beneficial but is not so critical as the concentration of trehalose in the cytoplasm . Because B . japonicum cannot utilize trehalose as a carbon source, cells can be loaded with trehalose by providing the disaccharide during the growth period . SIGNIFICANCE AND IMPACT OF THE STUDY: Although it may not be practical to use trehalose as a carbon source in inoculant production, it may be possible to engineer greater trehalose accumulation in rhizobia . Trehalose concentration in cells should be a useful predictor of survival during desiccation. Appl Environ Microbiol, 2003 Aug, 69(8), 4396 - 402 Rhizobium leguminosarum biovar viciae 1-aminocyclopropane-1-carboxylate deaminase promotes nodulation of pea plants; Ma W et al.; Ethylene inhibits nodulation in various legumes . In order to investigate strategies employed by Rhizobium to regulate nodulation, the 1-aminocyclopropane-1-carboxylate (ACC) deaminase gene was isolated and characterized from one of the ACC deaminase-producing rhizobia, Rhizobium leguminosarum bv . viciae 128C53K . ACC deaminase degrades ACC, the immediate precursor of ethylene in higher plants . Through the action of this enzyme, ACC deaminase-containing bacteria can reduce ethylene biosynthesis in plants . Insertion mutants with mutations in the rhizobial ACC deaminase gene (acdS) and its regulatory gene, a leucine-responsive regulatory protein-like gene (lrpL), were constructed and tested to determine their abilities to nodulate Pisum sativum L . cv . Sparkle (pea) . Both mutants, neither of which synthesized ACC deaminase, showed decreased nodulation efficiency compared to that of the parental strain . Our results suggest that ACC deaminase in R . leguminosarum bv . viciae 128C53K enhances the nodulation of P . sativum L . cv . Sparkle, likely by modulating ethylene levels in the plant roots during the early stages of nodule development . ACC deaminase might be the second described strategy utilized by Rhizobium to promote nodulation by adjusting ethylene levels in legumes. Arch Microbiol, 2003 Nov, 180(5), 309 - 18 Epub 2003 Aug 01. Poly beta-hydroxybutyrate depolymerase (PhaZ) in Azospirillum brasilense and characterization of a phaZ mutant; Kadouri D et al.; Like many other prokaryotes, rhizobacteria of the genus Azospirillum produce high levels of poly-beta-hydroxybutyrate (PHB) under sub-optimal growth conditions . Utilization of PHB by bacteria under stress has been proposed as a mechanism that favors their compatible establishment in competitive environments . PHB depolymerase (PhaZ) is an essential enzyme in PHB degradation . The phaZ gene was identified in Azospirillum brasilense, cloned, sequenced, and shown to be located on the chromosome . Insertion of a kanamycin-resistant cassette within phaZ of A . brasilense resulted in a phaZ mutant that was unable to degrade PHB; however, carbon source utilization was similar in both the wild-type and the mutant strain . The ability of the wild-type to endure starvation conditions, ultraviolet irradiation, heat, and osmotic shock, and to grow in the presence of hydrogen peroxide was higher than that of the mutant strain . By contrast, the ability of the phaZ mutant strain to endure desiccation was higher than that of the wild-type strain . No differences between the strains were seen in their ability to endure sonication, or to survive in carrier materials used for soil inoculants . In addition, motility was the same between the two strains, whereas cell aggregation and exopolysaccharide production were higher in the wild-type than in the phaZ mutant strain. Can J Microbiol, 2003 Apr, 49(4), 237 - 43 Comparative analysis of the Bradyrhizobium japonicum sucA region; Green LS et al.; To study the adjustments made to the tricarboxylic acid cycle during symbiosis of nitrogen-fixing rhizobia with their host legumes, we have characterized the genes encoding the alpha-ketoglutarate dehydrogenase enzyme complex in Bradyrhizobium japonicum . The genes were arranged in the order sucA-sucB-scdA-lpdA, where scdArepresents a short-chain dehydrogenase gene (GenBank accession No . AY049030) . All four genes appeared to be co-transcribed, an arrangement that is so far unique to B . japonicum . The mdh gene, encoding malate dehydrogenase, was located upstream of the sucA operon, and its primary transcript appeared to be monocistronic . Primer extension indicated that the sucA operon and mdh were transcribed from typical housekeeping promoters. Res Microbiol, 2003 Jul-Aug, 154(6), 433 - 42 Exopolysaccharide synthesis in Rhizobium leguminosarum bv . trifolii is related to various metabolic pathways; Janczarek M et al.; Rhizobium leguminosarum bv . trifolii synthesizes extracellular polysaccharide (EPS) that is postulated to be a biologically active signalling molecule in clover symbiosis . A group of seven exopolysaccharide-deficient (Exo), non-nitrogen-fixing mutants of R . leguminosarum bv . trifolii strain 24.1 isolated by transposon mutagenesis were complemented to mucoid phenotype by a low-copy plasmid carrying the pssA gene encoding the first glucosyl-IP-transferase . Some of these mutants were not corrected in their symbiotic defect by the pssA gene . Precise localization of Tn5 insertion sites by subcloning and sequencing the adjacent genomic DNA in the Exo mutants identified the disrupted genes and their possible functions . Only one mutant (Rt74) was mutated in pssA gene; others were mutated in diverse genes that were not directly involved in EPS biosynthesis . The suppression of EPS deficiency in these mutants by additional copies of pssA indicated a possible connection between exopolysaccharide biosynthesis and various metabolic pathways. Int J Syst Evol Microbiol, 2003 Jul, 53(Pt 4), 1207 - 17 Description of new Ensifer strains from nodules and proposal to transfer Ensifer adhaerens Casida 1982 to Sinorhizobium as Sinorhizobium adhaerens comb . nov . Request for an opinion; Willems A et al.; A group of four diverse rhizobial isolates and two soil isolates that are highly related to Ensifer adhaerens were characterized by a polyphasic approach . On the basis of DNA-DNA hybridizations and phenotypic features, these strains cannot be distinguished clearly form Ensifer adhaerens, a soil bacterium that was described in 1982, mainly on the basis of phenotypic characteristics . Phylogenetically, Ensifer and Sinorhizobium form a single group in the 16S rDNA dendrogram of the alpha-Proteobacteria, as well as in an analysis of partial recA gene sequences . They may therefore be regarded as a single genus . Because Sinorhizobium was proposed in 1988, according to the Bacteriological Code (1990 Revision) the older name, Ensifer, has priority . However, there are several reasons why a change from Sinorhizobium to Ensifer may not be the best solution and making an exception to Rule 38 may be more appropriate . We therefore propose the species Sinorhizobium adhaerens comb . nov . and put forward a Request for an Opinion to the Judicial Commission regarding the conservation of Sinorhizobium adhaerens over Ensifer adhaerens. Biotechnol Lett, 2003 Jan, 25(2), 115 - 9 Enhanced biosynthesis of polyhydroxyalkanoates in a mutant strain of Rhizobium meliloti; Lakshman K et al.; Strains of Rhizobium spp . isolated from leguminous plants and standard strains accumulated 27% to 57% polyhydroxyalkanoate (PHA) of their cell biomass . Among these cultures, one strain of Rhizobium meliloti synthesized 10-30% more PHA than others and contained 3% hydroxyvalerate (HV) when grown on sucrose as carbon substrate . The occurrence of hydroxybutyrate (HB) and HV was confirmed by GC and 1H NMR analysis . Treatment of the culture with 4'-N-piperidinobutyl-2-chlorophenoxazine resulted in a mutant which synthesized up to 69%, PHA of the cell biomass with an improved yield of 11 to 47% under different carbon and nitrogen ratios, compared to the parent strain. Ann Bot (Lond), 2003 Aug, 92(2), 247 - 58 Morphological compatibility of white clover and perennial ryegrass cultivars grown under two nitrate levels in flowing solution culture; Collins RP et al.; The effects of nitrate (NO3-) supply on shoot morphology, vertical distribution of shoot and root biomass and total nitrogen (N) acquisition by two perennial ryegrass (Lolium perenne L.) cultivars (AberElan and Preference) and two white clover (Trifolium repens L.) cultivars (Grasslands Huia and AberHerald) were studied in flowing nutrient culture . Cultivars were grown from seed as monocultures and the clovers inoculated with Rhizobium . The 6-week measurement period began on day 34 (grasses) and day 56 (clovers) when the NO3- supply was adjusted to either 2 mmol m-3 (low nitrogen, LN) or 50 mmol m-3 (high nitrogen, HN) . These treatments were subsequently maintained automatically . Plants were harvested at intervals to measure their morphology and N content . Cultivars of both species differed significantly in several aspects of their response to NO3- supply . In the grasses, the LN treatment increased the root : shoot ratio of AberElan but did not affect the distribution of root length in the root profile . In contrast, this treatment changed the root distribution of Preference compared with HN, resulting in a larger proportion of root length being distributed further down the root profile . The morphology of white clover Grasslands Huia was for the most part unaffected by the level of NO3- supply . In contrast, AberHerald exhibited different growth strategies, with LN plants increasing their stolon weight per unit length at the expense of leaf production, leaf area and stolon length, whereas HN plants showed reduced stolon thickness, greater leaf area production and stolon length per plant . Cultivars with different morphological/physiological strategies in response to NO3- supply may be of value in the construction of 'compatible mixtures' aimed at reducing oscillations in sward clover content by extending the range of conditions that allow balanced coexistence of species to occur. J Biol Chem, 2003 Oct 10, 278(41), 39269 - 79 Epub 2003 Jul 16. Expression cloning and biochemical characterization of a Rhizobium leguminosarum lipid A 1-phosphatase; Karbarz MJ et al.; Lipid A of Rhizobium leguminosarum, a nitrogen-fixing plant endosymbiont, displays several significant structural differences when compared with Escherichia coli . An especially striking feature of R . leguminosarum lipid A is that it lacks both the 1- and 4'-phosphate groups . Distinct lipid A phosphatases that attack either the 1 or the 4' positions have previously been identified in extracts of R . leguminosarum and Rhizobium etli but not Sinorhizobium meliloti or E . coli . Here we describe the identification of a hybrid cosmid (pMJK-1) containing a 25-kb R . leguminosarum 3841 DNA insert that directs the overexpression of the lipid A 1-phosphatase . Transfer of pMJK-1 into S . meliloti 1021 results in heterologous expression of 1-phosphatase activity, which is normally absent in extracts of strain 1021, and confers resistance to polymyxin . Sequencing of a 7-kb DNA fragment derived from the insert of pMJK-1 revealed the presence of a lipid phosphatase ortholog (designated LpxE) . Expression of lpxE in E . coli behind the T7lac promoter results in the appearance of robust 1-phosphatase activity, which is normally absent in E . coli membranes . Matrix-assisted laser-desorption/time of flight and radiochemical analysis of the product generated in vitro from the model substrate lipid IVA confirms the selective removal of the 1-phosphate group . These findings show that lpxE is the structural gene for the 1-phosphatase . The availability of lpxE may facilitate the re-engineering of lipid A structures in diverse Gram-negative bacteria and allow assessment of the role of the 1-phosphatase in R . leguminosarum symbiosis with plants . Possible orthologs of LpxE are present in some intracellular human pathogens, including Francisella tularensis, Brucella melitensis, and Legionella pneumophila. J Bacteriol, 2003 Aug, 185(15), 4382 - 92 immX immunity region of rhizobium phage 16-3: two overlapping cistrons of repressor function; Csiszovszki Z et al.; 16-3 is a temperate phage of the symbiotic nitrogen-fixing bacterium Rhizobium meliloti 41 . Its prophage state and immunity against superinfection by homoimmune phages are governed by a complex set of controls: the immC and immX repressor systems and the avirT element are all located in well-separated, distinct regions which span 25 kb on the bacteriophage chromosome . The anatomy and function of the immC region are well documented; however, fewer analyses have addressed the immX and avirT regions . We focused in this paper on the immX region and dissected it into two major parts: X(U/L) and X(V) . The X(U/L) part (0.6 kb) contained two overlapping cistrons, X(U) and X(L), coding for proteins pXU and pXL, respectively . Inactivation of either gene inactivated the repressor function of the immX region . Loss-of-function mutants of X(U) and X(L) complemented each other in trans in double lysogens . The X(V) part (1 kb) contained a target for X(U/L) repressor action . Mutations at three sites in X(V) led to various degree of ImmX insensitivity in a hierarchic manner . Two sites (X(V1) and X(V3)) exhibited the inverted-repeat structures characteristic of many repressor binding sites . However, X(V1) could also be folded into a transcription terminator . Of the two immunity regions of 16-3, immX seems to be unique both in its complex genetic anatomy and in its sequence . To date, no DNA or peptide sequence homologous to that of ImmX has been found in the data banks . In contrast, immC shares properties of a number of immunity systems commonly found in temperate phages. Plant Mol Biol, 2003 May, 52(2), 303 - 16 The Lotus japonicus ndx gene family is involved in nodule function and maintenance; Gronlund M et al.; To elucidate the function of the ndx homeobox genes during the Rhizobium-legume symbiosis, two Lotus japonicus ndr genes were expressed in the antisense orientation under the control of the nodule-expressed promoter Psenod12 in transgenic Lotus japonicus plants . Many of the transformants obtained segregated into plants that failed to sustain proper development and maintenance of root nodules concomitant with down-regulation of the two ndx genes . The root nodules were actively fixing nitrogen 3 weeks after inoculation, but the plants exhibited a stunted growth phenotype . The nodules on such antisense plants had under-developed vasculature and lenticels when grown on medium lacking nitrogen sources . These nodules furthermore entered senescence earlier than the wild-type nodules . Normal plant growth was resumed upon external addition of nitrogen . This suggests that assimilated nitrogen is not properly supplied to the plants in which the two ndx genes are down-regulated . The results presented here, indicate that the ndx genes play a role in the development of structural nodule features, required for proper gas diffusion into the nodule and/or transport of the assimilated nitrogen to the plant. Mol Plant Microbe Interact, 2003 Jul, 16(7), 617 - 25 Extracellular proteins involved in soybean cultivar-specific nodulation are associated with pilus-like surface appendages and exported by a type III protein secretion system in Sinorhizobium fredii USDA257; Krishnan HB et al.; Several gram-negative plant and animal pathogenic bacteria have evolved a type III secretion system (TTSS) to deliver effector proteins directly into the host cell cytosol . Sinorhizobium fredii USDA257, a symbiont of soybean and many other legumes, secretes proteins called Nops (nodulation outer proteins) into the extracellular environment upon flavonoid induction . Mutation analysis and the nucleotide sequence of a 31.2-kb symbiosis (sym) plasmid DNA region of USDA257 revealed the existence of a TTSS locus in this symbiotic bacterium . This locus includes rhc (rhizobia conserved) genes that encode components of a TTSS and proteins that are secreted into the environment (Nops) . The genomic organization of the TTSS locus of USDA257 is remarkably similar to that of another broad-host range symbiont, Rhizobium sp . strain NGR234 . Flavonoids that activate the transcription of the nod genes of USDA257 also stimulate the production of novel filamentous appendages known as pili . Electron microscope examination of isolated pili reveals needle-like filaments of 6 to 8 nm in diameter . The production of the pili is dependent on a functional nodD1 and the presence of a nod gene-inducing compound . Mutations in several of the TTSS genes negate the ability of USDA257 to elaborate pili . Western blot analysis using antibodies raised against purified NopX, Nop38, and Nop7 reveals that these proteins were associated with the pili . Mutations in rhcN, rhcJ, rhcC, and ttsI alter the ability of USDA257 to form nodules on Glycine max and Macroptilium atropurpureum. Pest Manag Sci, 2003 Jun-Jul, 59(6-7), 665 - 70 United States Department of Agriculture-Agricultural Research Service research programs on microbes for management of plant-parasitic nematodes; Meyer SL; Restrictions on the use of conventional nematicides have increased the need for new methods of managing plant-parasitic nematodes . Consequently, nematode-antagonistic microbes, and active compounds produced by such organisms, are being explored as potential additions to management practices . Programs in this area at the USDA Agricultural Research Service investigate applied biocontrol agents, naturally occurring beneficial soil microbes and natural compounds . Specific research topics include use of plant growth-promoting rhizobacteria and cultural practices for management of root-knot and ring nematodes, determination of management strategies that enhance activity of naturally occurring Pasteuria species (bacterial obligate parasites of nematodes), studies on interactions between biocontrol bacteria and bacterial-feeding nematodes, and screening of microbes for compounds active against plant-parasitic nematodes . Some studies involve biocontrol agents that are active against nematodes and soil-borne plant-pathogenic fungi, or combinations of beneficial bacteria and fungi, to manage a spectrum of plant diseases or to increase efficacy over a broader range of environmental conditions . Effective methods or agents identified in the research programs are investigated as additions to existing management systems for plant-parasitic nematodes. Biosci Biotechnol Biochem, 2003 May, 67(5), 1144 - 8 Rhizoremediation of dioxin-like compounds by a recombinant Rhizobium tropici strain expressing carbazole 1,9a-dioxygenase constitutively; Saiki Y et al.; A recombinant Rhizobium strain, PBK3-IS, that constitutively expressed the oxygenase component of carbazole 1,9a-dioxygenase from Sphingomonas sp . strain KA1, was constructed . In the water-cultured siratro rhizospheres inoculated with strain PBK3-IS, 48% of the dibenzofuran was removed within 3 days (initial substrate, 25 microg) . Similar results were obtained in soil-cultured siratro rhizospheres using sterile vermiculite . When non-sterile field soils were used instead of sterile vermiculite, the inoculated recombinant strain could grow on the siratro root in all soils tested, except for wet paddy field. Proteomics, 2003 Jun, 3(6), 1077 - 85 Proteome analysis of aerobic and fermentative metabolism in Rhizobium etli CE3; Encarnacion S et al.; Rhizobium etli undergoes a transition from an aerobic to a fermentative metabolism during successive subcultures in minimal medium . This metabolic transition does not occur in cells subcultured in rich medium, or in minimal medium containing either biotin or thiamine . In this report, we characterize the aerobic and fermentative metabolism of R . etli using proteome analysis . According to their synthesis patterns in response to aerobic (rich medium, minimal medium with biotin or minimal medium with thiamine) or fermentative (minimal medium without supplements) growth conditions, proteins were assigned to five different classes: (i) proteins produced only in aerobic conditions (e.g., catalase-peroxidase KatG and the E2 component of pyruvate dehydrogenase); (ii) protein produced under both conditions but strongly induced in aerobic metabolism (e.g., malate dehydrogenase and the succinyl-CoA synthetase beta subunit); (iii) proteins that were induced equally under all conditions tested (e.g., AniA, DnaK, and GroEL); (iv) proteins downregulated during aerobic metabolism, and (v) proteins specific to only one of the conditions analyzed . Northern blotting studies of katG expression confirmed the proteome data for this protein . The negative regulation of carbon metabolism proteins observed in fermentative metabolism is consistent with the drastic physiological changes which occur during this process. FEMS Microbiol Lett, 2003 Jun 27, 223(2), 239 - 44 The ECF sigma factor RpoI of R . leguminosarum initiates transcription of the vbsGSO and vbsADL siderophore biosynthetic genes in vitro; Yeoman KH et al.; When complexed with Escherichia coli RNA polymerase core enzyme, purified RpoI protein of Rhizobium leguminosarum initiated transcription in vitro from promoters of the vbsADL and vbsGSO operons, which are needed to synthesise the siderophore vicibactin . There is a single transcription initiation site for rpoI, regardless of whether the cells are grown in Fe-replete or Fe-depleted media, but levels of rpoI mRNA were reduced, though not abolished, in the presence of Fe . Unlike PvdS, a similar Pseudomonas sigma factor needed to transcribe genes involved in pyoverdine synthesis, RpoI transcribes vbsADL and vbsGSO in the absence of the cognate siderophore . The RpoI sigma factor is not required for transcription of rpoI. Ying Yong Sheng Tai Xue Bao, 2003 Feb, 14(2), 187 - 90 {Role of Rhizobium in wheat-astragalus mixed cropping system}; Zhong Z et al.; Inoculation experiments were carried out in wheat-astragalus mixed cropping system to study the changes of plant biomass, nitrogen content in plants and soil, and enzyme activity of Rhizobium . The results showed that in the mixed cropping system inoculated with Rhizobium, the growth of plants was stimulated, total nitrogen of plants and soil was increased significantly, and the increment of enzyme activity of Rhizobium was also found. Arch Microbiol, 2003 Aug, 180(2), 118 - 26 Epub 2003 Jun 19. IS Rm31, a new insertion sequence of the IS 66 family in Sinorhizobium meliloti; Biondi EG et al.; Sinorhizobium meliloti natural populations show a high level of genetic polymorphism possibly due to the presence of mobile genetic elements such as insertion sequences (IS), transposons, and bacterial mobile introns . The analysis of the DNA sequence polymorphism of the nod region of S . meliloti p SymA megaplasmid in an Italian isolate led to the discovery of a new insertion sequence, IS Rm31 . IS Rm31 is 2,803 bp long and has 22-bp-long terminal inverted repeat sequences, 8-bp direct repeat sequences generated by transposition, and three ORFs (A, B, C) coding for proteins of 124, 115, and 541 amino acids, respectively . ORF A and ORF C are significantly similar to members of the transposase family . Amino acid and nucleotide sequences indicate that IS Rm31 is a member of the IS 66 family . IS Rm31 sequences were found in 30.5% of the Italian strains analyzed, and were also present in several collection strains of the Rhizobiaceae family, including S . meliloti strain 1021 . Alignment of targets sites in the genome of strains carrying IS Rm31 suggested that IS Rm31 inserts randomly into S . meliloti genomes . Moreover, analysis of IS Rm31 insertion sites revealed DNA sequences not present in the recently sequenced S . meliloti strain 1021 genome . In fact, IS Rm31 was in some cases linked to DNA fragments homologous to sequences found in other rhizobia species. ScientificWorldJournal, 2001 Nov 10, 1 Suppl 2, 17 - 21 Symbiotic performance of herbaceous legumes in tropical cover cropping systems; Ibewiro B et al.; Increasing use of herbaceous legumes such as mucuna ( Mucuna pruriens var . utilis {Wright} Bruck) and lablab ( Lablab purpureus {L.} Sweet) in the derived savannas of West Africa can be attributed to their potential to fix atmospheric nitrogen (N2) . The effects of management practices on N2 fixation in mucuna and lablab were examined using 15N isotope dilution technique . Dry matter yield of both legumes at 12 weeks was two to five times more in in situ mulch (IM) than live mulch (LM) systems . Land Equivalent Ratios, however, showed 8 to 30% more efficient utilization of resources required for biomass production under LM than IM systems . Live mulching reduced nodule numbers in the legumes by one third compared to values in the IM systems . Similarly, nodule mass was reduced by 34 to 58% under LM compared to the IM systems . The proportion of fixed N2 in the legumes was 18% higher in LM than IM systems . Except for inoculated mucuna, the amounts of N fixed by both legumes were greater in IM than LM systems . Rhizobia inoculation of the legumes did not significantly increase N2 fixation compared to uninoculated plots . Application of N fertilizer reduced N2 fixed in the legumes by 36 to 51% compared to inoculated or uninoculated systems . The implications of cover cropping, N fertilization, and rhizobia inoculation on N contributions of legumes into tropical low-input systems were discussed. ScientificWorldJournal, 2001 Dec 11, 1 Suppl 2, 722 - 7 Economy of fertilizer nitrogen through organic sources in rain-fed rice-legume cropping systems in West Bengal, India; Puste AM et al.; Field experiments were conducted at a farmers" plot adjacent to the Regional Research Station, red and laterite zone, Sub-center Sekhampur (Birbhum district) of West Bengal, India, situated 23 degrees 24' N latitude, 87 degrees 24' E longitude, to study the effect of different bio- and organic sources of nutrients instead of total fertilizer N in terms of crop productivity in the sequence and building up of soil fertility . During the wet seasons of 1997 and 1998, 12 combinations of bio- and organic sources (crop residues, well decomposed cow dung, dhanicha as green manure) were substituted for 25-50% of N fertilizer applied on transplanted rice (Cv . IR 36) . Subsequently, during the winters of 1997-1998 and 1998-1999, leguminous pulse crops like lentil (Lens culinaris {L.} Medic.), gram ( Cicer arietinum L.) and lathyrus (Lathyrus sativus L.) were grown with and without inoculation of Rhizobium . Results revealed that the application of inorganic N in combination with organic sources exhibited a significant increase in rice yield (3.60-3.84 t ha(-1) ) compared to the yield from sole application of N (3.19-3.26 t ha(-1) ) . The study showed that about 25% of total applied N was saved without significant yield reduction with simultaneous improvement of soil physical properties (pH, organic matter, available N, P, K, and CEC) . Seed yield of pulses (lentil, gram, and lathyrus) were more pronounced in the treatment inoculated with Rhizobium, with a saving of 42.6-48.4 kg N ha(-1) . Therefore, the results suggest that the combined application of inorganic and organic N sources in a 75:25 ratio is a superior N-management practice with regards to crop yields as well as improvement of soil fertility. Arch Microbiol, 2003 Jul, 180(1), 45 - 52 Epub 2003 Jun 07. Genetic diversity of fast-growing rhizobia that nodulate soybean ( Glycine max L . Merr); Saldana G et al.; The fast-growing Rhizobium sp . strain NGR234, isolated from Papua New Guinea, and 13 strains of Sinorhizobium fredii, isolated from China and Vietnam, were fingerprinted by means of RAPD, REP, ERIC and ARDRA . ERIC, REP and RAPD markers revealed a considerable genetic diversity among fast-growing rhizobia . Chinese isolates showed higher levels of diversity than those strains isolated from Vietnam . ARDRA analysis revealed three different genotypes among fast-growing rhizobia that nodulate soybean, even though all belonged to a subcluster that included Sinorhizobium saheli and Sinorhizobium meliloti . Among S . fredii rhizobia, two strains, SMH13 and HH303, might be representatives of other species of nitrogen-fixing organisms . Although restriction analysis of the nifD- nifK intergenic DNA fragment confirmed the unique nature of Rhizobium sp . strain NGR234, several similarities between Rhizobium sp . strain NGR234 and S . fredii USDA257, the ARDRA analysis and the full sequence of the 16S rDNA confirmed that NGR234 is a S . fredii strain . In addition, ARDRA analysis and the full sequence of the 16S rDNA suggested that two strains of rhizobia might be representatives of other species of rhizobia. Genome Biol . 2003;4(6):R39 . Epub 2003 May 19. Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach; Scholl EH et al.; BACKGROUND: Published accounts of horizontally acquired genes in plant-parasitic nematodes have not been the result of a specific search for gene transfer per se, but rather have emerged from characterization of individual genes . We present a method for a high-throughput genome screen for horizontally acquired genes, illustrated using expressed sequence tag (EST) data from three species of root-knot nematode, Meloidogyne species . RESULTS: Our approach identified the previously postulated horizontally transferred genes and revealed six new candidates . Screening was partially dependent on sequence quality, with more candidates identified from clustered sequences than from raw EST data . Computational and experimental methods verified the horizontal gene transfer candidates as bona fide nematode genes . Phylogenetic analysis implicated rhizobial ancestors as donors of horizontally acquired genes in Meloidogyne . CONCLUSIONS: High-throughput genomic screening is an effective way to identify horizontal gene transfer candidates . Transferred genes that have undergone amelioration of nucleotide composition and codon bias have been identified using this approach . Analysis of these horizontally transferred gene candidates suggests a link between horizontally transferred genes in Meloidogyne and parasitism. Genome Biol . 2003;4(6):R36 . Epub 2003 May 13. The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments; Gonzalez V et al.; BACKGROUND: Symbiotic bacteria known as rhizobia interact with the roots of legumes and induce the formation of nitrogen-fixing nodules . In rhizobia, essential genes for symbiosis are compartmentalized either in symbiotic plasmids or in chromosomal symbiotic islands . To understand the structure and evolution of the symbiotic genome compartments (SGCs), it is necessary to analyze their common genetic content and organization as well as to study their differences . To date, five SGCs belonging to distinct species of rhizobia have been entirely sequenced . We report the complete sequence of the symbiotic plasmid of Rhizobium etli CFN42, a microsymbiont of beans, and a comparison with other SGC sequences available . RESULTS: The symbiotic plasmid is a circular molecule of 371,255 base-pairs containing 359 coding sequences . Nodulation and nitrogen-fixation genes common to other rhizobia are clustered in a region of 125 kilobases . Numerous sequences related to mobile elements are scattered throughout . In some cases the mobile elements flank blocks of functionally related sequences, thereby suggesting a role in transposition . The plasmid contains 12 reiterated DNA families that are likely to participate in genomic rearrangements . Comparisons between this plasmid and complete rhizobial genomes and symbiotic compartments already sequenced show a general lack of synteny and colinearity, with the exception of some transcriptional units . There are only 20 symbiotic genes that are shared by all SGCs . CONCLUSIONS: Our data support the notion that the symbiotic compartments of rhizobia genomes are mosaic structures that have been frequently tailored by recombination, horizontal transfer and transposition. Nucleic Acids Res, 2003 Jun 15, 31(12), 3143 - 56 Inactivation of the nod box distal half-site allows tetrameric NodD to activate nodA transcription in an inducer-independent manner; Feng J et al.; In Rhizobium leguminosarum, NodD can activate nodA transcription in response to inducer flavonoids . Here, we show that the inducible nodA promoter contains an intrinsic part through which NodD can activate nodA transcription in an inducer-independent manner . Evidence was provided that NodD binds to target DNA through anchoring the two half-sites of the nod box as a tetramer . An imperfect inverted repeat AT-N10-GAT was found in each half-site and is critical for NodD binding . Mutation of the inverted repeat of the nod box distal half-site allowed NodD to activate nodA transcription in an inducer-independent manner in vivo, and to modulate the DNA bending of the NodD-nod box complex in the absence of inducer in vitro. Biotechnol Prog, 2003 May-Jun, 19(3), 714 - 9 Metabolite profiles and growth characteristics of Rhizobium meliloti cultivated at different specific growth rates; Ong LC et al.; Rhizobium meliloti (ATCC 55340) was grown at different specific growth rates in a chemostat apparatus . Metabolic products, relating to the Embden-Meyerhof-Parnas (EMP) pathway and the tricarboxylic acid (TCA) cycle, were measured and quantified to probe the influence of specific growth rate on the distribution of important metabolites . The detection of propionate in the fermentation broth implies that the imbalance of reducing equivalents of FADH(2) and NADH + H(+) resulted in a partially reductive operation of the TCA cycle . Additionally, experimental results show that the specific growth rate plays an essential role in modulating the biomass concentration, the specific substrate uptake rate, the cell length, the specific exopolysaccharide (EPS) production rate, the distribution of EPS molecular weight, and the profiles of carbohydrate and organic acid . The specific EPS production rate (varying from 13.3 to 111 mg EPS/g-DW/h) follows a growth-associated pattern at the specific growth rate ranging from 0.06 to 0.20 h(-1) and switches into non-growth-associated mode when the specific growth rate is over 0.20 h(-1). Appl Environ Microbiol, 2003 Jun, 69(6), 3561 - 8 Citrate synthase mutants of Sinorhizobium fredii USDA257 form ineffective nodules with aberrant ultrastructure; Krishnan HB et al.; The tricarboxylic acid (TCA) cycle plays an important role in generating the energy required by bacteroids to fix atmospheric nitrogen . Citrate synthase is the first enzyme that controls the entry of carbon into the TCA cycle . We cloned and determined the nucleotide sequence of the gltA gene that encodes citrate synthase in Sinorhizobium fredii USDA257, a symbiont of soybeans (Glycine max {L.} Merr.) and several other legumes . The deduced citrate synthase protein has a molecular weight of 48,198 and exhibits sequence similarity to citrate synthases from several bacterial species, including Sinorhizobium meliloti and Rhizobium tropici . Southern blot analysis revealed that the fast-growing S . fredii strains and Rhizobium sp . strain NGR234 contained a single copy of the gene located in the bacterial chromosome . S . fredii USDA257 gltA mutant HBK-CS1, which had no detectable citrate synthase activity, had diminished nodulation capacity and produced ineffective nodules on soybean . Light and electron microscopy observations revealed that the nodules initiated by HBK-CS1 contained very few bacteroids . The infected cells contained large vacuoles and prominent starch grains . Within the vacuoles, membrane structures that appeared to be reminiscent of disintegrating bacteroids were detected . The citrate synthase mutant had altered cell surface characteristics and produced three times more exopolysaccarides than the wild type produced . A plasmid carrying the USDA257 gltA gene, when introduced into HBK-CS1, was able to restore all of the defects mentioned above . Our results demonstrate that a functional citrate synthase gene of S . fredii USDA257 is essential for efficient soybean nodulation and nitrogen fixation. Appl Environ Microbiol, 2003 Jun, 69(6), 3244 - 50 Involvement of the reserve material poly-beta-hydroxybutyrate in Azospirillum brasilense stress endurance and root colonization; Kadouri D et al.; When grown under suboptimal conditions, rhizobacteria of the genus Azospirillum produce high levels of poly-beta-hydroxybutyrate (PHB) . Azospirillum brasilense strain Sp7 and a phbC (PHB synthase) mutant strain in which PHB production is impaired were evaluated for metabolic versatility, for the ability to endure various stress conditions, for survival in soil inoculants, and for the potential to promote plant growth . The carbon source utilization data were similar for the wild-type and mutant strains, but the generation time of the wild-type strain was shorter than that of the mutant strain with all carbon sources tested . The ability of the wild type to endure UV irradiation, heat, osmotic pressure, osmotic shock, and desiccation and to grow in the presence of hydrogen peroxide was greater than that of the mutant strain . The motility and cell aggregation of the mutant strain were greater than the motility and cell aggregation of the wild type . However, the wild type exhibited greater chemotactic responses towards attractants than the mutant strain exhibited . The wild-type strain exhibited better survival than the mutant strain in carrier materials used for soil inoculants, but no difference in the ability to promote plant growth was detected between the strains . In soil, the two strains colonized roots to the same extent . It appears that synthesis and utilization of PHB as a carbon and energy source by A . brasilense under stress conditions favor establishment of this bacterium and its survival in competitive environments . However, in A . brasilense, PHB production does not seem to provide an advantage in root colonization under the conditions tested. Mol Microbiol, 2003 Jun, 48(5), 1305 - 16 The structure of the helically perturbed flagellar filament of Pseudomonas rhodos: implications for the absence of the outer domain in other complex flagellins and for the flexibility of the radial spokes; Cohen-Krausz S et al.; Bacterial flagella, the organelles of motility, are commonly divided into two classes: 'plain' and 'complex' . The complex filaments are pairwise, helically perturbed forms of the plain filaments and have been reported to occur only in Rhizobium and Pseudomonas . Previously, we reconstructed and analysed the structure of the complex filaments of Rhizobium lupini H13-3 and determined their unique symmetry and origin of the perturbations (Trachtenberg et al., 1986, J Mol Biol 190: 569-576; 1987, 195: 603-620; 1998, 276: 759-773; Cohen-Krausz and Trachtenberg, 1998, J Struct Biol 122: 267-282) . Here, we analyse the structure of the flagellar filament of the other known complex filament, that of Pseudomonas rhodos, as reconstructed from electron microscope images . Compared with the filament of R . lupini, the filament of P . rhodos is more flexible, as implied from high-intensity darkfield light microscopy and, although constructed from flagellins of higher molecular weights (59 versus 41 kDa), has similar symmetry . Using cryonegative stained specimens and low-dose, field emission electron microscopy, we reconstructed and averaged 158 filaments each containing 170 statistically significant layer lines . The three-dimensional density maps of P . rhodos clearly suggest, when compared with those of R . lupini and the right-handed Salmonella typhimurium SJW1655, that R . lupini is missing the outer flagellin domain (D3), that the interior of the complex filament is rather similar to that of the plain filament and that the radial spokes (connecting domains D0 and D1), present in individual density maps, average out because of their variability and implied flexibility . Extending the three-start grooves and ridges on the propeller's surface, in the form of an Archimedean screw, may further improve the motility of the cell in viscous environments. Mol Microbiol, 2003 Jun, 48(5), 1195 - 207 The twin-arginine translocation (Tat) system is essential for Rhizobium-legume symbiosis; Meloni S et al.; The Tat (twin-arginine translocation) system mediates export of periplasmic proteins in folded conformation . Proteins transported via Tat contain a characteristic twin-arginine motif in their signal peptide . Genetic determinants (tatABC genes) of the Tat system from Rhizobium leguminosarum bv . viciae were cloned and characterized, and a tatBC deletion mutant was constructed . The mutant lacked the ability for membrane targeting of hydrogenase, a known Tat substrate, and was impaired in hydrogenase activity . Interestingly, in the absence of a functional Tat system, only small, white nodules unable to fix nitrogen were induced in symbiosis with pea plants . Analysis of nodule structure and location of green fluorescent protein (GFP)-tagged bacteria within nodules indicated that the symbiotic process was blocked in the tat mutant at a stage previous to bacteria release into cortical cells . The R . leguminosarum Tat-deficient mutant lacked a functional cytochrome bc1 complex . This was consistent with the fact that R . leguminosarum Rieske protein, a key component of the symbiosis-essential cytochrome bc1 complex, contained a typical twin-arginine signal peptide . However, comparative analyses of nodule structure indicated that nodule development in the tat mutant was arrested at an earlier step than in a cytochrome bc1 mutant . These data indicate that the Tat pathway is also critical for proteins relevant to the initial stages of the symbiotic process. J Am Chem Soc, 2003 May 21, 125(20), 6103 - 12 Synthesis and biological evaluation of Rhizobium sin-1 lipid A derivatives; Demchenko AV et al.; A highly convergent strategy for the synthesis of several derivatives of the lipid A of Rhizobium sin-1 has been developed . The approach employed the advanced intermediate 3-O-acetyl-6-O-(3-O-acetyl-4,6-O-benzylidene-2-deoxy-2-phthalimido-beta-d-glucopyrano-syl)-2-azido-4-O-benzyl-2-deoxy-1-thio-alpha-d-glucopyranoside (5), which is protected in such a way that the anomeric center, the C-2 and C-2' amino groups, and the C-3 and C-3' hydroxyls can be selectively functionalized . The synthetic strategy was used for the preparation of 2-deoxy-6-O-{2-deoxy-3-O-{(R)-3-hydroxy-hexadecanoyl}-2-{(R)-3-octacosanoyloxy-hexadecan}amido-beta-d-glucopyranosyl}-2-{(R)-3-hydroxy-hexadecan}amido-3-O-{(R)-3-hydroxy-hexadecanoyl}-alpha-d-glucopyranose (11) and 2-deoxy-6-O-{2-deoxy-3-O-{(R)-3-hydroxy-hexadecanoyl}-2-{(R)-3-octacosanoyloxy-hexadecan}amido-beta-d-glucopyranosyl}-2-{(R)-3-hydroxy-hexadecan}amido-3-O-{(R)-3-hydroxy-hexadecanoyl}-d-glucono-1,5-lactone (13), which contain an unusual octacosanoic acid moiety and differ in the oxidation state of the anomeric center . The results of biological studies indicate that 11 and 13 lack the proinflammatory effects of Escherichia coli lipopolysaccharides (LPS) . Furthermore, 13 emulated the ability of heterogeneous R . sin-1 LPS to antagonize enteric LPS, providing evidence for the critical role of the gluconolactone moiety of R . sin-1 LPS in mediating this antagonistic effect . Compound 13 is the first example of a lipid A derivative that is devoid of phosphate but possesses antagonistic properties, making it an attractive lead compound for development of a drug to use in the treatment of Gram-negative septicemia. Antonie Van Leeuwenhoek, 2003, 83(3), 285 - 91 Prevalence of 1-aminocyclopropane-1-carboxylate deaminase in Rhizobium spp; Ma W et al.; This is the first report documenting the presence of 1-aminocyclopropane-1-carboxylate (ACC) deaminase in Rhizobium . This enzyme, previously found in free-living bacteria, yeast and fungi, degrades ACC, the immediate precursor of ethylene in higher plants . Thirteen different rhizobial strains were examined by Southern hybridization, Western blots and ACC deaminase enzyme assay . Five of them tested positive for ACC deaminase . Induction of the expression of ACC deaminase was examined in one of the positively tested strains, Rhizobium leguminosarum bv . viciae 128C53K . This rhizobial ACC deaminase had a trace basal level of expression without ACC, but could be induced by a concentration of ACC as low as 1 microM . The more ACC added to this Rhizobium the higher the expression level of the ACC deaminase. J Exp Bot, 2003 Jul, 54(388), 1691 - 700 Epub 2003 May 28. Sugar uptake and proton release by protoplasts from the infected zone of Vicia faba L . nodules: evidence against apoplastic sugar supply of infected cells; Peiter E et al.; Symbiotic dinitrogen fixation of legume nodules is fuelled by phloem-imported carbohydrates . These have to pass several cell layers to reach cells infected with Rhizobium bacteroids . It is unclear whether apoplastic steps are involved in carbohyd-rate translocation within the nodule . Protoplasts were isolated from the infected and uninfected cells of the central tissue of Vicia faba nodules using a recently developed protocol . These protoplasts were used to elucidate pathways for sugar transport in this tissue . Both types of protoplasts released protons into the medium . Acidification was inhibited by vanadate and erythrosin B . However, it was stimulated by fusicoccin only in uninfected cells . A symport of sugars with protons can therefore be energized in both cell types . Uptake of 14C-labelled sugars was determined using a phthalate centrifugation technique . Uninfected protoplasts accumulated glucose through high-affinity H+/glucose-symport that was not competitively inhibited by fructose or sucrose . Uninfected protoplasts also absorbed sucrose with biphasic kinetics . At 0.1, 1, and 10 mM sucrose, uptake was inhibited by CCCP . Fusicoccin did not stimulate the linear phase of sucrose uptake . Glucose inhibited sucrose uptake nearly completely . This was not related to sucrose cleavage in the medium because sucrose was absorbed at a much higher rate than glucose, and glucose concentration did not increase in sucrose-containing protoplast suspensions . By contrast with uninfected protoplasts, infected cells did not show transporter-mediated glucose or sucrose uptake . The findings underline a role of uninfected cells in sugar translocation . Infected cells are not apoplastically supplied with sugars and possibly depend on uninfected cells for carbon supply. Plant J, 2003 May, 34(4), 495 - 506 The NFP locus of Medicago truncatula controls an early step of Nod factor signal transduction upstream of a rapid calcium flux and root hair deformation; Amor BB et al.; Establishment of the Rhizobium-legume symbiosis depends on a molecular dialogue, in which rhizobial nodulation (Nod) factors act as symbiotic signals, playing a key role in the control of specificity of infection and nodule formation . Using nodulation-defective (Nod-) mutants of Medicago truncatula to study the mechanisms controlling Nod factor perception and signalling, we have previously identified five genes that control components of a Nod factor-activated signal transduction pathway . Characterisation of a new M . truncatula Nod- mutant led to the identification of the Nod Factor Perception (NFP) locus . The nfp mutant has a novel phenotype among Nod- mutants of M . truncatula, as it does not respond to Nod factors by any of the responses tested . The nfp mutant thus shows no rapid calcium flux, the earliest detectable Nod factor response of wild-type plants, and no root hair deformation . The nfp mutant is also deficient in Nod factor-induced calcium spiking and early nodulin gene expression . While certain genes controlling Nod factor signal transduction also control the establishment of an arbuscular mycorrhizal symbiosis, the nfp mutant shows a wild-type mycorrhizal phenotype . These data indicate that the NFP locus controls an early step of Nod factor signal transduction, upstream of previously identified genes and specific to nodulation. Lett Appl Microbiol, 2003, 36(6), 349 - 53 Isolation and characterization of phorate degrading soil bacteria of environmental and agronomic significance; Bano N et al.; Phorate {O,O-diethyl-S-(ethylthio)methyl phosphoradiothioate} degrading bacteria were isolated from agricultural soil and characterized based on their morphological and biochemical characteristics . The selected isolates PS-1, PS-2 and PS-3 were presumptively identified as Rhizobium, Pseudomonas and Proteous species, respectively . The HPLC analysis of phorate in bioaugmented soil revealed its complete disappearance within 40 days . The degradation isotherms of the isolates PS-1, PS-2 and PS-3 suggested time-dependent disappearance of phorate following the first order rate kinetics at the corresponding rate constants of 0.04, 0.05 and 0.04 days-1 . Besides, the isolates concurrently exhibited substantial phosphate solubilization, indole acetic acid, and siderophore production . The isolate PS-3 also showed anti-fungal activity against a phytopathogen Fusarium oxysporum . As a result of the multifarious biological properties, the isolates have been suggested to be important bioresource for efficient bioinoculant development. Syst Appl Microbiol, 2003 Mar, 26(1), 47 - 53 Description of Devosia neptuniae sp . nov . that nodulates and fixes nitrogen in symbiosis with Neptunia natans, an aquatic legume from India; Rivas R et al.; Neptunia natans is a unique aquatic legume indigenous to tropical and sub-tropical regions and is nodulated symbiotically by rhizobia using an unusual infection process unlike any previously described . Previously, isolates of neptunia-nodulating rhizobia from Senegal were characterized as Allorhizobium undicola . Here we report on a different group of neptunia-nodulating rhizobia isolated from India . Sequencing of the 16S rDNA gene from two of these Indian isolates (strains J1T and J2) show that they belong in the genus Devosia rather than Allorhizobium . Currently, the only described Devosia species is D . riboflavina (family Hyphomicrobiaceae, order Rhizobiales) . The complete 16S rDNA sequences of strains J1T and J2 are 95.9% homologous to the type strain, D . riboflavina LMG 2277T, suggesting that these neptunia-nodulating strains from India belong to a new Devosia species . This hypothesis was confirmed by further studies of polyphasic taxonomy (DNA-DNA hybridisation, TP-RAPD patterns, SDS-PAGE of cellular proteins, 16S rDNA RFLP patterns, carbon source utilisation, cellular fatty acid analysis and other phenotypic characterisations), all of which support the proposal that these neptunia-nodulating strains constitute a new Devosia species, which we name Devosia neptuniae sp . nov . These gram negative, strictly aerobic short rods are motile by a subpolar flagellum, positive for catalase, oxidase, urease and beta-galactosidase, can utilise several carbohydrates (but not organic acids) as carbon sources and contain C18:0 3-OH, cis-7 C18:1 11-methyl and cis-7 C18:1 as their major cellular fatty acids . Unlike D . riboflavina, the longer-chain C24:1 3-OH and C26:1 3-OH hydroxy fatty acids are not detected . The type strain of D . neptuniae is LMG 21357T (CECT 5650T) . Assignment of this new taxon represents the fourth example in the literature of a non-rhizobial genus of bacteria capable of forming a bonafide dinitrogen-fixing root-nodule symbiosis with legume plants. Plant Physiol, 2003 May, 132(1), 311 - 7 Nod factor and elicitors activate different phospholipid signaling pathways in suspension-cultured alfalfa cells; den Hartog M et al.; Lipo-chitooligosaccharides (Nod factors) are produced by symbiotic Rhizobium sp . bacteria to elicit Nod responses on their legume hosts . One of the earliest responses is the formation of phosphatidic acid (PA), a novel second messenger in plant cells . Remarkably, pathogens have also been reported to trigger the formation of PA in nonlegume plants . To investigate how host plants can distinguish between symbionts and pathogens, the effects of Nod factor and elicitors (chitotetraose and xylanase) on the formation of PA were investigated in suspension-cultured alfalfa (Medicago sativa) cells . Theoretically, PA can be synthesized via two signaling pathways, i.e . via phospholipase D (PLD) and via phospholipase C in combination with diacylglycerol (DAG) kinase . Therefore, a strategy involving differential radiolabeling with {(32)P}orthophosphate was used to determine the contribution of each pathway to PA formation . In support, PLD activity was specifically measured by using the ability of the enzyme to transfer the phosphatidyl group of its substrate to a primary alcohol . In practice, Nod factor, chitotetraose, and xylanase induced the formation of PA and its phosphorylated product DAG pyrophosphate within 2 min of treatment . However, whereas phospholipase C and DAG kinase were activated during treatment with all three different compounds, PLD was only activated by Nod factor . No evidence was obtained for the activation of phospholipase A(2). Mol Plant Microbe Interact, 2003 May, 16(5), 371 - 5 Nitrogen comes down to earth: report from the 5th European Nitrogen Fixation Conference; De Hoff P et al.; For four days and four nights, with almost 50 presentations and more than 175 posters, the 5th European Nitrogen Fixation Conference continued a tradition of excellence, bringing scientists from diverse fields such as microbiology, biochemistry, computational genomics, and plant physiology together to address the complex problems associated with biological nitrogen fixation (BNF) . The conference was hosted by the John Innes Center and the University of East Anglia in Norwich, England and took place from September 6 through 10, 2002 . A diverse range of topics was presented, from the evolution of rhizobial genomes to the plant genes involved in bacterial and fungal symbiosis, to the structure of nitrogenase, and to the means by which nitrogen is shuttled between the symbiotic bacteria and the plant . Additionally, sessions involving broader issues, such as nitrogen fertilizer use and work being done in developing countries, brought home the importance of the research being carried out in BNF around the world. Mol Plant Microbe Interact, 2003 Apr, 16(4), 335 - 41 Rhizobium-lnduced calcium spiking in Lotus japonicus; Harris JM et al.; Legumes and rhizobium bacteria form a symbiosis that results in the development of nitrogen-fixing nodules on the root of the host plant . The earliest plant developmental changes are triggered by bacterially produced nodulation (Nod) factors . Within minutes of exposure to Nod factors, sharp oscillations in cytoplasmic calcium levels (calcium spiking) occur in epidermal cells of several closely related legumes . We found that Lotus japonicus, a legume that follows an alternate developmental pathway, responds to both its bacterial partner and to the purified bacterial signal with calcium spiking . Thus, calcium spiking is not restricted to a particular pathway of nodule development and may be a general component of the response of host legumes to their bacterial partner . Using Nod factor-induced calcium spiking as a tool to identify mutants blocked early in the response to Nod factor, we show that the L . japonicus Ljsym22-1 mutant but not the Ljsym30 mutant fails to respond to Nod factor with calcium spiking. Mol Plant Microbe Interact, 2003 Apr, 16(4), 326 - 34 The role of nod factor substituents in actin cytoskeleton rearrangements in Phaseolus vulgaris; Cardenas L et al.; In order to define the symbiotic role of some of the chemical substituents in the Rhizobium etli Nod factors (NFs), we purified Nod metabolites secreted by the SM25 strain, which carries most of the nodulation genes, and SM17 with an insertion in nodS . These NFs were analyzed for their capabilities to induce root hair curling and cytoskeletal rearrangements . The NFs secreted by strain SM17 lack the carbamoyl and methyl substituents on the nonreducing terminal residue and an acetyl moiety on the fucosyl residue on the reducing-terminal residue as determined by mass spectrometry . We have reported previously that the root hair cell actin cytoskeleton from bean responds with a rapid fragmentation of the actin bundles within 5 min of NF exposure, and also is accompanied by increases in the apical influxes and intracellular calcium levels . In this article, we report that methyl-bearing NFs are more active in inducing root hair curling and actin cytoskeleton rearrangements than nonmethylated NFs . However, the carbamoyl residue on the nonreducing terminal residue and the acetyl group at the fucosyl residue on the reducing terminal residue do not seem to have any effect on root hair curling induction or in actin cytoskeleton rearrangement. Curr Opin Biotechnol, 2003 Apr, 14(2), 200 - 5 Genomics insights into symbiotic nitrogen fixation; Weidner S et al.; Following an interaction with rhizobial soil bacteria, legume plants are able to form a novel organ, termed the root nodule . This organ houses the rhizobial microsymbionts, which perform the biological nitrogen fixation process resulting in the incorporation of ammonia into plant organic molecules . Recent advances in genomics have opened exciting new perspectives in this field by providing the complete gene inventory of two rhizobial microsymbionts . The complete genome sequences of Mesorhizobium loti, the symbiont of several Lotus species, and Sinorhizobium meliloti, the symbiont of alfalfa, were determined and annotated in detail . For legume macrosymbionts, expressed sequence tag projects and expression analyses using DNA arrays in conjunction with proteomics approaches have identified numerous genes involved in root nodule formation and nitrogen fixation . The isolation of legume genes by tagging or positional cloning recently allowed the identification of genes that control the very early steps of root nodule organogenesis. J Bacteriol, 2003 May, 185(10), 2988 - 98 Discordant phylogenies within the rrn loci of Rhizobia; van Berkum P et al.; It is evident from complete genome sequencing results that lateral gene transfer and recombination are essential components in the evolutionary process of bacterial genomes . Since this has important implications for bacterial systematics, the primary objective of this study was to compare estimated evolutionary relationships among a representative set of alpha-Proteobacteria by sequencing analysis of three loci within their rrn operons . Tree topologies generated with 16S rRNA gene sequences were significantly different from corresponding trees assembled with 23S rRNA gene and internally transcribed space region sequences . Besides the incongruence in tree topologies, evidence that distinct segments along the 16S rRNA gene sequences of bacteria currently classified within the genera Bradyrhizobium, Mesorhizobium and Sinorhizobium have a reticulate evolutionary history was also obtained . Our data have important implications for bacterial taxonomy, because currently most taxonomic decisions are based on comparative 16S rRNA gene sequence analysis . Since phylogenetic placement based on 16S rRNA gene sequence divergence perhaps is questionable, we suggest that the proposals of bacterial nomenclature or changes in their taxonomy that have been made may not necessarily be warranted . Accordingly, a more conservative approach should be taken in the future, in which taxonomic decisions are based on the analysis of a wider variety of loci and comparative analytical methods are used to estimate phylogenetic relationships among the genomes under consideration. Microbiology, 2003 May, 149(Pt 5), 1357 - 65 Fur is not the global regulator of iron uptake genes in Rhizobium leguminosarum; Wexler M et al.; Rhizobium leguminosarum fur mutants were unaffected in Fe-dependent regulation of several operons that specify different Fe uptake systems, yet cloned R . leguminosarum fur partially corrected an Escherichia coli fur mutant and R . leguminosarum Fur protein bound to canonical fur boxes . The lack of a phenotype in fur mutants is not due to functional redundancy with Irr, another member of the Fur superfamily found in the rhizobia, since irr fur double mutants are also unaffected in Fe-responsive regulation of several operons involved in Fe uptake . Neither Irr nor Fur is needed for symbiotic N(2) fixation on peas . As in Bradyrhizobium japonicum, irr mutants accumulated protoporphyrin IX . R . leguminosarum irr is not regulated by Fur and its Irr protein lacks the motif needed for haem-dependent post-translational modification that occurs in B . japonicum Irr . The similarities and differences in the Fur superfamily in the rhizobia and other Gram-negative bacteria are discussed. Microbiology, 2003 May, 149(Pt 5), 1165 - 76 Only one catalase, katG, is detectable in Rhizobium etli, and is encoded along with the regulator OxyR on a plasmid replicon; Vargas Mdel C et al.; The plasmid-borne Rhizobium etli katG gene encodes a dual-function catalase-peroxidase (KatG) (EC 1.11.1.7) that is inducible and heat-labile . In contrast to other rhizobia, katG was shown to be solely responsible for catalase and peroxidase activity in R . etli . An R . etli mutant that did not express catalase activity exhibited increased sensitivity to hydrogen peroxide (H(2)O(2)) . Pre-exposure to a sublethal concentration of H(2)O(2) allowed R . etli to adapt and survive subsequent exposure to higher concentrations of H(2)O(2) . Based on a multiple sequence alignment with other catalase-peroxidases, it was found that the catalytic domains of the R . etli KatG protein had three large insertions, two of which were typical of KatG proteins . Like the katG gene of Escherichia coli, the R . etli katG gene was induced by H(2)O(2) and was important in sustaining the exponential growth rate . In R . etli, KatG catalase-peroxidase activity is induced eightfold in minimal medium during stationary phase . It was shown that KatG catalase-peroxidase is not essential for nodulation and nitrogen fixation in symbiosis with Phaseolus vulgaris, although bacteroid proteome analysis indicated an alternative compensatory mechanism for the oxidative protection of R . etli in symbiosis . Next to, and divergently transcribed from the catalase promoter, an ORF encoding the regulator OxyR was found; this is the first plasmid-encoded oxyR gene described so far . Additionally, the katG promoter region contained sequence motifs characteristic of OxyR binding sites, suggesting a possible regulatory mechanism for katG expression. Ying Yong Sheng Tai Xue Bao, 2003 Jan, 14(1), 143 - 7 {Roles of rhizosphere in remediation of contaminated soils and its mechanisms}; Wei S et al.; Rhizosphere is a special 'ecological remediation unit' to treat contaminated soils, which contains a great quantity of microorganisms such as fungi and rhizobacteria living with plant roots . Thus, physiological and ecological roles of plant roots to remedy contaminated soils, to accumulate and to solidify heavy metals, to absorb and degrade organic pollutants in rhizosphere were illustrated, and the function of mycorrhizospheric fungi to absorb, barrier and chelate heavy metals, to degrade organic pollutants through their metabolism activities, the action of rhizobacteria to absorb and solidify heavy metals, to degrade organic pollutants in rhizosphere through their active living activities, and the combined remediation of fungi and bacteria to pollutants in rhizosphere and their relevant mechanisms were explained . It was suggested that the remediation role of rhizosphere was the main part of phytoremediation, and one of the main basic theories to remedy contaminated soils by the activity of green plants and other organisms . The use of hyperaccumulative plants in remedying soils contaminated by some heavy metals would be prospective . It would be one of the important approach to contaminated soils remediation by organic pollutants through the mechanism of screening some special plants whose roots had strong secreting ability to absorb and accumulate dissolvent organic pollutants on the basis of inoculating specific or non-specific fungi and bacteria from the rhizosphere . This will be a developing trend of research on the remediation of contaminated soils by organic pollutants. J Hered, 2003 Mar-Apr, 94(2), 191 - 3 Allelic relationships of pea nodulation mutants; Novak K; Thirteen stable nonnodulating mutant lines of pea (Pisum sativum L.) originating from cv . Finale were tested for allelism in pairwise crosses . The F(1) plants were evaluated for the symbiotic phenotype under controlled growth conditions against the nodule bacterium Rhizobium leguminosarum bv . viciae strain 248 . All mutations were found to be recessive and the lines were classified into eight complementation groups comprising Risnod1-Risnod23, Risnod8, Risnod9-Risnod22, Risnod14, Risnod19-Risnod25, Risnod20, Risnod24-Risnod26, and Risnod32 . Position of Risnod21 was not firmly established, leaving the possibility of allelism both with Risnod19-Risnod25 and Risnod20 . The results were partially consistent with the previous reports on the allelism of these lines . Additional crosses confirmed the correspondence of Risnod14 with the locus sym7 and of Risnod19-Risnod25 with sym8 . The high number of eight complementation groups formed by 13 mutants provides an indication of additional nodulation loci in pea to those already reported and confirms the complexity of the genetic control of the early stages of nodulation. J Exp Bot, 2003 May, 54(386), 1481 - 7 Suppression of arbuscular mycorrhizal colonization and nodulation in split-root systems of alfalfa after pre-inoculation and treatment with Nod factors; Catford JG et al.; Roots of legumes establish symbiosis with arbuscular mycorrhizal fungi (AMF) and nodule-inducing rhizobia . The existing nodules systemically suppress subsequent nodule formation in other parts of the root, a phenomenon termed autoregulation . Similarly, mycorrhizal roots reduce further AMF colonization on other parts of the root system . In this work, split- root systems of alfalfa (Medicago sativa) were used to study the autoregulation of symbiosis with Sinorhizobium meliloti and the mycorrhizal fungus Glomus mosseae . It is shown that nodulation systemically influences AMF root colonization and vice versa . Nodules on one half of the split-root system suppressed subsequent AMF colonization on the other half . Conversely, root systems pre-colonized on one side by AMF exhibited reduced nodule formation on the other side . An inhibition effect was also observed with Nod factors (lipo-chito-oligosaccharides) . NodSm-IV(C16:2, S) purified from S . meliloti systemically suppressed both nodule formation and AMF colonization . The application of Nod factors, however, did not influence the allocation of (14)C within the split-root system, excluding competition for carbohydrates as the regulatory mechanism . These results indicate a systemic regulatory mechanism in the rhizobial and the arbuscular mycorrhizal association, which is similar in both symbioses. Carbohydr Res, 2003 May 1, 338(10), 1143 - 6 Enantioseparation using cyclosophoraoses as a novel chiral additive in capillary electrophoresis; Lee S et al.; Cyclosophoraoses, cyclic beta-(1-->2)-D-glucans produced by Rhizobium meliloti 2011, were used as a novel chiral additive for the separation of terbutaline, amethopterin, thyroxine and N-acetylphenylalanine enantiomers in aqueous capillary electrophoresis (CE) . Enantioseparation took place in the normal- or reversed-polarity mode when a high concentration of neutral (60 mM) or anionic (40 mM) cyclosophoraoses was added to the background electrolyte (BGE). Biochem Biophys Res Commun, 2003 Apr 25, 304(1), 136 - 42 O2-specific regulation of the ferrous heme-based sensor kinase FixL from Sinorhizobium meliloti and its aberrant inactivation in the ferric form; Akimoto S et al.; FixL, a rhizobial heme-based O2-sensing histidine kinase, catalyzes autophosphorylation in the deoxy form at low O2 tension, while the kinase activity is inhibited in the case of the O2-bound form . The present study unambiguously shows that the binding of CO and NO does not significantly inhibit the kinase activity of dithiothreitol (DTT)-reduced ferrous FixL from Sinorhizobium meliloti, which is inconsistent with the spin state mechanism previously reported . Kinase inactivation is caused by aberrant disulfide (S-S) bond formation at Cys301 in the ferric homodimer, which explains these contradictory observations . The addition of DTT cleaved the S-S bond, leading to restoration of kinase activity in the ferric form as well as heme reduction, but, sodium hydrosulfite treatment produced the kinase-inactive deoxy form without S-S cleavage . On the basis of these experimental results, it can be concluded that ferrous FixL discriminates O2 from CO and NO, and signals the O2-bound state by downregulating the phosphoryl transfer reaction. Genome Biol . 2003;4(4):R26 . Epub 2003 Mar 31. Analysis and functional classification of transcripts from the nematode Meloidogyne incognita; McCarter JP et al.; BACKGROUND: Plant parasitic nematodes are major pathogens of most crops . Molecular characterization of these species as well as the development of new techniques for control can benefit from genomic approaches . As an entree to characterizing plant parasitic nematode genomes, we analyzed 5,700 expressed sequence tags (ESTs) from second-stage larvae (L2) of the root-knot nematode Meloidogyne incognita . RESULTS: From these, 1,625 EST clusters were formed and classified by function using the Gene Ontology (GO) hierarchy and the Kyoto KEGG database . L2 larvae, which represent the infective stage of the life cycle before plant invasion, express a diverse array of ligand-binding proteins and abundant cytoskeletal proteins . L2 are structurally similar to Caenorhabditis elegans dauer larva and the presence of transcripts encoding glyoxylate pathway enzymes in the M . incognita clusters suggests that root-knot nematode larvae metabolize lipid stores while in search of a host . Homology to other species was observed in 79% of translated cluster sequences, with the C . elegans genome providing more information than any other source . In addition to identifying putative nematode-specific and Tylenchida-specific genes, sequencing revealed previously uncharacterized horizontal gene transfer candidates in Meloidogyne with high identity to rhizobacterial genes including homologs of nodL acetyltransferase and novel cellulases . CONCLUSIONS: With sequencing from plant parasitic nematodes accelerating, the approaches to transcript characterization described here can be applied to more extensive datasets and also provide a foundation for more complex genome analyses. Physiol Plant, 2003 May, 118(1), 10 - 15 Methods for isolating and characterizing ACC deaminase-containing plant growth-promoting rhizobacteria; Penrose DM et al.; One of the major mechanisms utilized by plant growth-promoting rhizobacteria (PGPR) to facilitate plant growth and development is the lowering of ethylene levels by deamination of 1-aminocyclopropane-1-carboxylic acid (ACC) the immediate precursor of ethylene in plants . The enzyme catalysing this reaction, ACC deaminase, hydrolyses ACC to alpha-ketobutyrate and ammonia . Several bacterial strains that can utilize ACC as a sole source of nitrogen have been isolated from rhizosphere soil samples . All of these strains are considered to be PGPR based on the ability to promote canola seedling root elongation under gnotobiotic conditions . The treatment of plant seeds or roots with these bacteria reduces the amount of ACC in plants, thereby lowering the concentration of ethylene . Here, a rapid procedure for the isolation of ACC deaminase-containing bacteria, a root elongation assay for evaluating the effects of selected bacteria on root growth, and a method of assessing bacterial ACC deaminase activity are described in detail . This should allow researchers to readily isolate new PGPR strains adapted to specific environments. Meded Rijksuniv Gent Fak Landbouwkd Toegep Biol Wet, 2002, 67(2), 377 - 80 Biological control of soybean damping-off by antagonistic rhizobacteria; Sharifi Tehrani A et al.; Experiments were carried out with 133 bacterial isolates t