Nitrogen fixation by Rhizobium cultured on a defined medium

Variation in Bacterial Community Structure Under Long-Term Fertilization, Tillage, and Cover Cropping in Continuous Cotton Production

Agricultural practices alter the structure and functions of soil microbial community. However, few studies have documented the alterations of bacterial communities in soils under long-term conservation management practices for continuous crop production. In this study, we evaluated soil bacterial diversity using 16S rRNA gene sequencing and soil physical and chemical properties within 12 combinations of inorganic N fertilization, cover cropping, and tillage throughout a cotton production cycle. Soil was collected from field plots of the West Tennessee Agriculture Research and Education Center in Jackson, TN, United States. The site has been under continuous cotton production for 38 years. A total of 38,038 OTUs were detected across 171 soil samples. The dominant bacterial phyla were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi, accounting for ∼70% of the total bacterial community membership. Conventional tillage increased alpha diversity in soil samples collected in different stages of cotton production. The effects of inorganic N fertilization and conventional tillage on the structure of bacterial communities were significant at all four sampling dates (p < 0.01). However, cover cropping (p < 0.05) and soil moisture content (p < 0.05) only showed significant influence on the bacterial community structure after burn-down of the cover crops and before planting of cotton (May). Nitrate-N appeared to have a significant effect on the structure of bacterial communities after inorganic fertilization and at the peak of cotton growth (p < 0.01). Structural equation modeling revealed that the relative abundances of denitrifying and nitrifying bacteria were higher when conventional tillage and vetch cover crop practices were applied, respectively. Our results indicate that long-term tillage and fertilization are key factors increasing the diversity and restructuring the composition of bacterial communities, whereas cover cropping may have shorter-term effects on soil bacteria community structure. In this study, management practices might positively influence relative abundances of bacterial functional groups associated with N cycling. The bacteria functional groups may build a network for providing N and meet microbial N needs in the long term.

Microbiome Profiles of Nebulizers in Hospital Use

Background: Nebulizers are used to provide treatment to respiratory patients. Concerns over nosocomial infection risks from contaminated nebulizers raise the critical need to identify all microbial populations in nebulizers used by patients. However, conventional culture-dependent techniques are inadequate with the ability to identify specific microbial populations only. Therefore, the aims of this study were to acquire complete profiles of microbiomes in nebulizers used by in-patients with culture-independent high-throughput sequencing and identify sources of microbial contaminants for the development of effective practices to reduce microbial contamination in nebulizer devices. Methods: This study was conducted at the University of Tennessee Medical Center in Knoxville, TN. Nebulizers were collected between May 2018 and October 2018 from inpatients admitted to the floors for pneumonia or chronic obstructive pulmonary disease exacerbations. Nebulizers were sampled for 16S rRNA gene-based amplicon sequencing to profile nebulizer microbiomes and perform phylogenetic analysis. A Bayesian community-wide culture-independent microbial source tracking technique was used to quantify the contribution of human-associated microbiota as potential sources of nebulizer contamination. Results: Culture-independent sequencing detected diverse microbial populations in nebulizers, represented by 18 abundant genera. Stenotrophomonas was identified as the most abundant genus, accounting for 12.4% of the nebulizer microbiome, followed by Rhizobium, Staphylococcus, Streptococcus, and Ralstonia. Phylogenetic analysis revealed the presence of multiple phylotypes with close relationship to potential pathogens. Contributing up to 15% to nebulizer microbiomes, human-associated microbiota was not identified as the primary sources of nebulizer contamination. Conclusion: Culture-independent sequencing was demonstrated to be capable of acquiring comprehensive profiles of microbiomes in nebulizers used by in-patients. Phylogenetic analysis identified differences in pathogenicity between closely related phylotypes. Microbiome profile-enabled community-wide culture-independent microbial source tracking suggested greater importance of environmental sources than human sources as contributors to nebulizer microbiomes, providing important insight for the development of effective strategies for the monitoring and control of nebulizer devices to mitigate infection risks in the hospital.

Interaction of the novel bacterium Brachybacterium saurashtrense JG06 with Arachis hypogaea leads to changes in physio-biochemical activity of plants to cope with nitrogen starvation conditions

Plant-microbe interactions are widely accepted, steady, and native methods used against different environmental stress conditions. In this study, peanut plants grown under control (with N₂) and stressed (N₂ deficit) conditions with or without the bacterium Brachybacterium saurashtrense were assessed for different physio-biochemical activities and differential gene expression. Higher shoot (24-25 cm) and root length (12-15 cm), and fresh (7-9 g) and dry weight (1-1.5 g) were observed in the treated plants compared to untreated plants under stress conditions. Similarly, high total chlorophyll (0.5-0.7 mg.g^-1Fw), chlorophyll b (0.2-0.4 mg.g^-1Fw), and carotenoid (12-13 mg.g^-1Fw), whereas low electrolyte leakage and lipid peroxidation, and high membrane stability were observed in the treated plants. Interestingly, low proline content (20-21 μg.g^-1Fw) and total soluble sugar (0.2 mg.g^-1Fw) were observed in the treated plants. In contrast, a higher total amino acid content (1.0 mg.g^-1Fw) was estimated in the treated plants. Enhanced antioxidant and scavenging activities of treated plants were observed compared to untreated plants under N₂ stress conditions. A total of 263 genes were differentially expressed; the majority (93%) of which belonged to unknown/uncharacterized/hypothetical categories, followed by metabolism (1.8%) and photosynthesis (1.3%) in the treated peanut plants. Overall, the diazotrophic plant growth promoting novel bacterium B. saurashtrense JG06 provides endurance to peanut plants by modulating physio-biochemical activity and host-gene expression under nitrogen starvation conditions. Plant metabolites, including flavonoids and phenolics, also play a protective role in abiotic stress by scavenging free radicles. This study provides new insight into plant-microbe interactions in the host plant.

Evolution and function of nitrogen fixation gene clusters in sugarcane associated Bradyrhizobium strains

Bradyrhizobium spp. are well known to mediate biological nitrogen fixation (BNF) as microsymbionts inhabiting nodules on leguminous plants. However, they may also contribute to plant growth via free-living N₂ fixation (FLNF) in association with non-legumes. Notably, several Bradyrhizobium strains from sugarcane roots display FLNF activity. Among them, Bradyrhizobium sacchari is a legume symbiotic species, whereas strains AG48 and M12 are non-symbiotic. In the present study, a phylogenomic approach was applied to study peculiarities of these and other Bradyrhizobium strains with respect to N fixation (nif) gene content in order to reveal genetic features that enable FNLF in Bradyrhizobium spp. All FLNF strains carry an ancestral 'non-symbiotic' nif-gene cluster (NSC). B. sacchari also contains a second 'symbiotic' nif-gene cluster (SC), a characteristic observed in only three of 156 evaluated genomes. B. sacchari stood out and presented a high level of sequence divergence between individual nif-gene homologues and we discuss scenarios for the evolutionary origin of these clusters. The transcript level of NSC nifH gene increased during FLNF, when compared to symbiotic conditions. The data suggest that sugarcane roots harbor diverse Bradyrhizobium spp. that are genetically adapted to a dynamic environment where leguminous and non-leguminous host plants are alternately available.

Mechanisms of Rice Endophytic Bradyrhizobial Cell Differentiation and Its Role in Nitrogen Fixation

Bradyrhizobium sp. strain SUTN9-2 is a symbiotic and endophytic diazotrophic bacterium found in legume and rice plants and has the potential to promote growth. The present results revealed that SUTN9-2 underwent cell enlargement, increased its DNA content, and efficiently performed nitrogen fixation in response to rice extract. Some factors in rice extract induced the expression of cell cycle and nitrogen fixation genes. According to differentially expressed genes (DEGs) from the transcriptomic analysis, SUTN9-2 was affected by rice extract and the deletion of the bclA gene. The up-regulated DEGs encoding a class of oxidoreductases, which act with oxygen atoms and may have a role in controlling oxygen at an appropriate level for nitrogenase activity, followed by GroESL chaperonins are required for the function of nitrogenase. These results indicate that following its exposure to rice extract, nitrogen fixation by SUTN9-2 is induced by the collective effects of GroESL and oxidoreductases. The expression of the sensitivity to antimicrobial peptides transporter (sapDF) was also up-regulated, resulting in cell differentiation, even when bclA (sapDF) was mutated. This result implies similarities in the production of defensin-like antimicrobial peptides (DEFs) by rice and nodule-specific cysteine-rich (NCR) peptides in legume plants, which affect bacterial cell differentiation.

Molecular Analyses of the Distribution and Function of Diazotrophic Rhizobia and Methanotrophs in the Tissues and Rhizosphere of Non-Leguminous Plants

Biological nitrogen fixation (BNF) by plants and its bacterial associations represent an important natural system for capturing atmospheric dinitrogen (N₂) and processing it into a reactive form of nitrogen through enzymatic reduction. The study of BNF in non-leguminous plants has been difficult compared to nodule-localized BNF in leguminous plants because of the diverse sites of N₂ fixation in non-leguminous plants. Identification of the involved N₂-fixing bacteria has also been difficult because the major nitrogen fixers were often lost during isolation attempts. The past 20 years of molecular analyses has led to the identification of N₂ fixation sites and active nitrogen fixers in tissues and the rhizosphere of non-leguminous plants. Here, we examined BNF hotspots in six reported non-leguminous plants. Novel rhizobia and methanotrophs were found to be abundantly present in the free-living state at sites where carbon and energy sources were predominantly available. In the carbon-rich apoplasts of plant tissues, rhizobia such as Bradyrhizobium spp. microaerobically fix N₂. In paddy rice fields, methane molecules generated under anoxia are oxidized by xylem aerenchyma-transported oxygen with the simultaneous fixation of N₂ by methane-oxidizing methanotrophs. We discuss the effective functions of the rhizobia and methanotrophs in non-legumes for the acquisition of fixed nitrogen in addition to research perspectives.

Isolation and characterization of N2 -fixing bacteria from giant reed and switchgrass for plant growth promotion and nutrient uptake

The aims of this study were to isolate and characterize N₂ -fixing bacteria from giant reed and switchgrass and evaluate their plant growth promotion and nutrient uptake potential for use as biofertilizers. A total of 190 bacteria were obtained from rhizosphere soil and inside stems and roots of giant reed and switchgrass. All the isolates were confirmed to have nitrogenase activity, 96.9% produced auxin, and 85% produced siderophores. Then the top six strains, including Sphingomonas trueperi NNA-14, Sphingomonas trueperi NNA-19, Sphingomonas trueperi NNA-17, Sphingomonas trueperi NNA-20, Psychrobacillus psychrodurans NP-3, and Enterobacter oryzae NXU-38, based on nitrogenase activity, were inoculated on maize and wheat seeds in greenhouse tests to assess their potential benefits to plants. All the selected strains promoted plant growth by increasing at least one plant growth parameter or increasing the nutrient concentration of maize or wheat plants. NNA-14 outperformed others in promoting early growth and nutrient uptake by maize. Specifically, NNA-14 significantly increased root length, surface area, and fine roots of maize by 14%, 12%, and 17%, respectively, and enhanced N, Ca, S, B, Cu, and Zn in maize. NNA-19 and NXU-38 outperformed others in promoting both early growth and nutrient uptake by wheat. Specifically, NNA-19 significantly increased root dry weight and number of root tips of wheat by 25% and 96%, respectively, and enhanced Ca in wheat. NXU-38 significantly increased root length, surface area, and fine roots of wheat by 21%, 13%, and 26%, respectively, and enhanced levels of Ca and Mg in wheat. It is concluded that switchgrass and giant reed are colonized by N₂ -fixing bacteria that have the potential to contribute to plant growth and nutrient uptake by agricultural crops.

Bacteria as Emerging Indicators of Soil Condition

Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon-to-nitrogen ratios, members of Bradyrhizobium and the levels of Olsen P (a measure of plant available phosphorus), and members of Chitinophagaceae and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition.

IMPORTANCE

The impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and soil condition. We provide evidence of strong relationships between individual taxa and specific soil attributes even across large spatial scales and soil and land use types. Collectively, we were able to demonstrate the largely untapped potential of microorganisms to indicate the condition of soil and thereby influence the way that we monitor the effects of anthropogenic activity on soil ecosystems into the future.

Bacteria as Emerging Indicators of Soil Condition

Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon-to-nitrogen ratios, members of Bradyrhizobium and the levels of Olsen P (a measure of plant available phosphorus), and members of Chitinophagaceae and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition.

IMPORTANCE

The impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and soil condition. We provide evidence of strong relationships between individual taxa and specific soil attributes even across large spatial scales and soil and land use types. Collectively, we were able to demonstrate the largely untapped potential of microorganisms to indicate the condition of soil and thereby influence the way that we monitor the effects of anthropogenic activity on soil ecosystems into the future.

Rhizobium oryzicola sp. nov., potential plant-growth-promoting endophytic bacteria isolated from rice roots

Bacterial strains ZYY136(T) and ZYY9 were isolated from surface-sterilized rice roots from a long-term experiment of rice-rice--Astragalus sinicus rotation. The 16S rRNA gene sequences of strains ZYY136(T) and ZYY9 showed the highest similarity, of 97.0%, to Rhizobium tarimense PL-41(T). Sequence analysis of the housekeeping genes recA, thrC and atpD clearly differentiated the isolates from currently described species of the genus Rhizobium. The DNA-DNA relatedness value between ZYY136(T) and ZYY9 was 82.3%, and ZYY136(T) showed 34.0% DNA-DNA relatedness with the most closely related type strain, R. tarimense PL-41(T). The DNA G+C content of strain ZYY136(T) was 58.1 mol%. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C16 : 0 3-OH. Strains ZYY136(T) and ZYY9 could be differentiated from the previously defined species of the genus Rhizobium by several phenotypic characteristics. Therefore, we conclude that strains ZYY136(T) and ZYY9 represent a novel species of the genus Rhizobium, for which the name Rhizobium oryzicola sp. nov. is proposed (type strain ZYY136(T) = ACCC 05753(T) = KCTC 32088(T)).

Production and Metabolism of Indole Acetic Acid in Root Nodules and Symbiont (Rhizobium undicola) Isolated from Root Nodule of Aquatic Medicinal Legume Neptunia oleracea Lour

Indole acetic acid is a phytohormone which plays a vital role in plant growth and development. The purpose of this study was to shed some light on the production of IAA in roots, nodules, and symbionts of an aquatic legume Neptunia oleracea and its possible role in nodular symbiosis. The symbiont (N37) was isolated from nodules of this plant and identified as Rhizobium undicola based on biochemical characteristics, 16S rDNA sequence homology, and DNA-DNA hybridization results. The root nodules were found to contain more IAA and tryptophan than root; however, no detectable amount of IAA was found in root. The IAA metabolizing enzymes IAA oxidase, IAA peroxidase (E.C.1.11.1.7), and polyphenol oxidase (E.C.1.14.18.1) were higher in root than nodule but total phenol and IAA content were reversed. The strain N37 was found to produce copious amount of IAA in YEM broth medium with tryptophan and reached its stationary phase at 20 h. An enrichment of the medium with mannitol, ammonium sulphate, B12, and 4-hydroxybenzaldehyde was found to promote the IAA production. The presence of IAA metabolizing enzymes and IAA production with PGPR traits including ACC deaminase activity of the symbionts was essential for plant microbe interaction and nodule function.

Endophytic Bradyrhizobium spp. isolates from sugarcane obtained through different culture strategies

Brazilian sugarcane has been shown to obtain part of its nitrogen via biological nitrogen fixation (BNF). Recent reports, based on the culture independent sequencing of bacterial nifH complementary DNA (cDNA) from sugarcane tissues, have suggested that members of the Bradyrhizobium genus could play a role in sugarcane-associated BNF. Here we report on the isolation of Bradyrhizobium spp. isolates and a few other species from roots of sugarcane cultivar RB867515 by two cultivation strategies: direct isolation on culture media and capture of Bradyrhizobium spp. using the promiscuous legume Vigna unguiculata as trap-plant. Both strategies permitted the isolation of genetically diverse Bradyrhizobium spp. isolates, as concluded from enterobacterial repetitive intergenic consensus polymerase chain reaction (PCR) fingerprinting and 16S ribosomal RNA, nifH and nodC sequence analyses. Several isolates presented nifH phylotypes highly similar to nifH cDNA phylotypes detected in field-grown sugarcane by a culture-independent approach. Four isolates obtained by direct plate cultivation were unable to nodulate V. unguiculata and, based on PCR analysis, lacked a nodC gene homologue. Acetylene reduction assay showed in vitro nitrogenase activity for some Bradyrhizobium spp. isolates, suggesting that these bacteria do not require a nodule environment for BNF. Therefore, this study brings further evidence that Bradyrhizobium spp. may play a role in sugarcane-associated BNF under field conditions.

Distinctive bacterial communities in the rhizoplane of four tropical tree species

It is known that the microbial community of the rhizosphere is not only influenced by factors such as root exudates, phenology, and nutrient uptake but also by the plant species. However, studies of bacterial communities associated with tropical rainforest tree root surfaces, or rhizoplane, are lacking. Here, we analyzed the bacterial community of root surfaces of four species of native trees, Agathis borneensis, Dipterocarpus kerrii, Dyera costulata, and Gnetum gnemon, and nearby bulk soils, in a rainforest arboretum in Malaysia, using 454 pyrosequencing of the 16S rRNA gene. The rhizoplane bacterial communities for each of the four tree species sampled clustered separately from one another on an ordination, suggesting that these assemblages are linked to chemical and biological characteristics of the host or possibly to the mycorrhizal fungi present. Bacterial communities of the rhizoplane had various similarities to surrounding bulk soils. Acidobacteria, Alphaproteobacteria, and Betaproteobacteria were dominant in rhizoplane communities and in bulk soils from the same depth (0-10 cm). In contrast, the relative abundance of certain bacterial lineages on the rhizoplane was different from that in bulk soils: Bacteroidetes and Betaproteobacteria, which are known as copiotrophs, were much more abundant in the rhizoplane in comparison to bulk soil. At the genus level, Burkholderia, Acidobacterium, Dyella, and Edaphobacter were more abundant in the rhizoplane. Burkholderia, which are known as both pathogens and mutualists of plants, were especially abundant on the rhizoplane of all tree species sampled. The Burkholderia species present included known mutualists of tropical crops and also known N fixers. The host-specific character of tropical tree rhizoplane bacterial communities may have implications for understanding nutrient cycling, recruitment, and structuring of tree species diversity in tropical forests. Such understanding may prove to be useful in both tropical forestry and conservation.

Genotypic characterization of phage-typed indigenous soybean bradyrhizobia and their host range symbiotic effectiveness

Analysis of genetic diversity among indigenous rhizobia and its symbiotic effectiveness with soybean cultivar is important for development of knowledge about rhizobial ecology. In India, little is known about the genetic resources and diversity of rhizobia nodulating soybean. Indigenous bradyrhizobia isolated from root nodules of soybean plants, collected from traditional cultivating regions of two states (Madhya Pradesh and Uttar Pradesh) of India, were screened for bacteriophage sensitivity to identify successful broad host range symbiotic effectivity. Of 172 rhizobial isolates, 91 showed sensitivities to eight lytic phages and form ten groups on the basis of sensitivity patterns. The genetic diversity of 23 isolates belonging to different phage groups was assessed along with that of strains USDA123 and USDA94 by the restriction fragment length polymorphism (RFLP) analysis of 16S rDNA, intergenic spacer (IGS) (16S-23S rDNA), and DnaK regions. RFLP analysis of 16S rDNA formed 5 groups, whereas 19 and 9 groups were revealed by IGS and the DnaK genes, respectively. The IGS regions showed many amplified polymorphic bands. Nine isolates which revealed high RFLP polymorphism in the abovementioned regions (16S rRNA, IGS, DnaK) were used for 16S rRNA sequence analyses. The results indicate that taxonomically, all isolates were related to Rhizobium etli, Bradyrhizobium spp., and Bradyrhizobium yuanmingense. The doubling time of isolates varied from 9 h (MPSR155) to 16.2 h (MPSR068) in YM broth. Five isolates which did not show cross infectivity with isolated phage strains were studied for symbiotic efficiency. All isolates showed broad host range symbiotic effectiveness forming effective nodules on Vigna mungo, Vigna radiata, Vigna unguiculata, and Cajanus cajan. The present study provides information on genetic diversity and host range symbiosis of indigenous soybean rhizobia typed by different phages.

Transformation of pWWO in Rhizobium leguminosarum DPT to Engineer Toluene Degrading Ability for Rhizoremediation

Rhizoremediation of organic xenobiotics is based on interactions between plants and their associated micro-organisms. The present work was designed to engineer a bacterial system having toluene degradation ability along with plant growth promoting characteristics for effective rhizoremediation. pWWO harboring the genes responsible for toluene breakdown was isolated from Pseudomonas putida MTCC 979 and successfully transformed in Rhizobium DPT. This resulted in a bacterial strain (DPT(T)) which had the ability to degrade toluene as well as enhance growth of host plant. The frequency of transformation was recorded 5.7 × 10(-6). DPT produced IAA, siderophore, chitinase, HCN, ACC deaminase, solubilized inorganic phosphate, fixed atmospheric nitrogen and inhibited the growth of Fusarium oxysporum and Macrophomina phaseolina in vitro. During pot assay, 50 ppm toluene in soil was found to inhibit the germination of Cajanus cajan seeds. However when the seeds bacterized with toluene degrading P. putida or R. leguminosarum DPT were sown in pots, again no germination was observed. Non-bacterized as well as bacterized seeds germinated successfully in toluene free soil as control. The results forced for an alternative mode of application of bacteria for rhizoremediation purpose. Hence bacterial suspension was mixed with soil having 50 ppm of toluene. Germination index in DPT treated soil was 100% while in P. putida it was 50%. Untreated soil with toluene restricted the seeds to germinate.

Host plant genome overcomes the lack of a bacterial gene for symbiotic nitrogen fixation

Homocitrate is a component of the iron-molybdenum cofactor in nitrogenase, where nitrogen fixation occurs. NifV, which encodes homocitrate synthase (HCS), has been identified from various diazotrophs but is not present in most rhizobial species that perform efficient nitrogen fixation only in symbiotic association with legumes. Here we show that the FEN1 gene of a model legume, Lotus japonicus, overcomes the lack of NifV in rhizobia for symbiotic nitrogen fixation. A Fix(-) (non-fixing) plant mutant, fen1, forms morphologically normal but ineffective nodules. The causal gene, FEN1, was shown to encode HCS by its ability to complement a HCS-defective mutant of Saccharomyces cerevisiae. Homocitrate was present abundantly in wild-type nodules but was absent from ineffective fen1 nodules. Inoculation with Mesorhizobium loti carrying FEN1 or Azotobacter vinelandii NifV rescued the defect in nitrogen-fixing activity of the fen1 nodules. Exogenous supply of homocitrate also recovered the nitrogen-fixing activity of the fen1 nodules through de novo nitrogenase synthesis in the rhizobial bacteroids. These results indicate that homocitrate derived from the host plant cells is essential for the efficient and continuing synthesis of the nitrogenase system in endosymbionts, and thus provide a molecular basis for the complementary and indispensable partnership between legumes and rhizobia in symbiotic nitrogen fixation.

Bioformulation of Burkholderia sp. MSSP with a multispecies consortium for growth promotion of Cajanus cajan

The present work was undertaken to formulate an effective bioformulation using Burkholderia sp. strain MSSP, a known plant-growth-promoting rhizobacterium. MSSP was tagged with the reporter gene of green fluorescent protein (gfp) to monitor its population in cost-effective solid carriers, including sugarcane-bagasse, sawdust, cocoa peat, rice husk, wheat bran, charcoal, and rock phosphate, and paneer-whey as liquid carrier. Physical and chemical properties of different low-cost carrier materials were studied. The viability of the green fluorescent tagged variant of MSSP was estimated in different sterile carrier materials. Whey and wheat bran proved to be efficient carrier materials for the bioformulation. Sawdust, rock phosphate, rice husk, and cocoa peat were average, while charcoal and sugarcane-bagasse proved to be inferior carriers. The viability of strain MSSP was also assessed in wheat bran and whey-based consortium, having three other bacterial strains, namely Sinorhizobium meliloti PP3, Rhizobium leguminosarum Pcc, and Bacillus sp. strain B1. Presence of other plant-growth-promoting bacteria did not have any detrimental effect on the viability of MSSP. Efficiency of the wheat-bran-based multispecies consortium was studied on the growth of pigeonpea in field conditions. A considerable increase in plant biomass, nodule number and weight, and number of pods was recorded as compared with individual trials and with the control.

Occurrence of rhizobia in the gut of the higher termite Nasutitermes nigriceps

Wood-eating termites feed on a diet highly deficient in nitrogen. They must complement their diet with the aid of nitrogen-fixing bacteria. Nitrogen fixation in the gut has been demonstrated, but information about nitrogen-fixing bacteria in pure culture is scarce. From the higher termite Nasutitermes nigriceps the symbiotic bacterial strain M3A was isolated, which thrives in the hindgut contents. The Gram-negative strain exhibited similarities to the species of the genus Ensifer (including Sinorhizobium) on the basis of morphological and physiological/biochemical features. The 16S rRNA gene analysis showed the highest sequence similarity of the isolate M3A to Ensifer adhaerens (>99%; ATCC 33499). The DNA-DNA hybridization revealed a similarity of 66% with E. adhaerens (NCIMB12342(T)). In contrast to the type strain the isolate M3A possesses the capacity to nodulate plant roots. This is the first report on the detailed identification of a rhizobia-related strain from the intestinal tract of animals. Strain M3A has been deposited with two culture collections (DSM10169; ATCC BAA-396).

Nitrogen fixation

The International Biological Programme served as a focal point for studies on biological nitrogen fixation during the 1960s. The introduction of the acetylene reduction technique for measuring nitrogenase activity in the field led to estimates becoming available of the contribution of lichens, blue-green algae, nodulated non-legumes and bacterial-grass associations, as well as of legumes. Other studies carried out on the physiology and biochemistry of the process led to the eventual purification and characterization of the nitrogenase enzyme. These studies, collectively, provided the springboard for current work, so essential in view of the present energy crisis, on how to increase the use and efficiency of nitrogen-fixing plants, on the metabolic regulation of the nitrogenase enzyme and on the genetics of the nitrogen-fixing process, both in higher plants and in free-living micro-organisms.

Isolation and characterization of symbiotic mutants of bradyrhizobium sp. (Arachis) strain NC92: mutants with host-specific defects in nodulation and nitrogen fixation

Random transposon Tn5 mutagenesis of Bradyrhizobium sp. (Arachis) strain NC92, a member of the cowpea cross-inoculation group, was carried out, and kanamycin-resistant transconjugants were tested for their symbiotic phenotype on three host plants: groundnut, siratro, and pigeonpea. Two nodulation (Nod- phenotype) mutants were isolated. One is unable to nodulate all three hosts and appears to contain an insertion in one of the common nodulation genes (nodABCD); the other is a host-specific nodulation mutant that fails to nodulate pigeonpea, elicits uninvaded nodules on siratro, and elicits normal, nitrogen-fixing nodules on groundnut. In addition, nine mutants defective in nitrogen fixation (Fix- phenotype) were isolated. Three fail to supply symbiotically fixed nitrogen to all three host plants. Surprisingly, nodules elicited by one of these mutants exhibit high levels of acetylene reduction activity, demonstrating the presence of the enzyme nitrogenase. Three more mutants have partially effective phenotypes (Fix +/-) in symbiosis with all three host plants. The remaining three mutants fail to supply fixed nitrogen to one of the host plants tested while remaining partially or fully effective on the other two hosts; two of these mutants are Fix- in pigeonpea and Fix +/- on groundnut and on siratro, whereas the other one is Fix- on groundnut but Fix+ on siratro and on pigeonpea. These latter mutants also retain significant nodule acetylene reduction activity, even in the ineffective symbioses. Such bacterial host-specific fixation (Hsf) mutants have not previously been reported.

Rhizobium trifolii 0403 Is Capable of Growth in the Absence of Combined Nitrogen

Rhizobium trifolii 0403 was treated with 16.6 mM succinate and other nutrients and thereby induced to grow in nitrogen-free medium. The organism grew microaerophilically on either semisolid or liquid medium, fixing atmospheric nitrogen to meet metabolic needs. Nitrogen fixation was measured via 15 N incorporation (18% 15 N enrichment in 1.5 doublings) and acetylene reduction. Nitrogen-fixing cells had a K m for acetylene of 0.07 atm (ca. 7.09 kPa), required about 3% oxygen for optimum growth in liquid medium, and showed a maximal specific activity of 5 nmol of acetylene reduced per min per mg of protein at 0.04 atm (ca. 4.05 kPa) of acetylene. The doubling time on N-free liquid medium ranged from 1 to 5 days, depending on oxygen tension, with an optimum temperature for growth of about 30°C. Nodulation of white clover by the cultures showing in vitro nitrogenase activity indicates that at least part of the population maintained identity with wild-type strain 0403.

Asymbiotic Acetylene Reduction by a Fast-Growing Cowpea Rhizobium Strain with Nitrogenase Structural Genes Located on a Symbiotic Plasmid

A procedure was designed which enabled the detection of ex planta nitrogenase activity in the fast-growing cowpea Rhizobium strain IHP100. Nitrogenase activity in agar culture under air occurred at a rate similar to that found for Bradyrhizobium strain CB756 but lower than that for Rhizobium strain ORS571. Hybridization studies showed that both nod and nif genes were located on a 410-kilobase Sym plasmid in strain IHP100.

Physiology of Ex Planta Nitrogenase Activity in Rhizobium japonicum

Thirty-nine wild-type strains of Rhizobium japonicum have been studied for their ability to synthesize nitrogenase ex planta in defined liquid media under microaerobic conditions. Twenty-one produced more than trace amounts of acetylene reduction activity, but only a few of these yielded high activity. The oxygen response curves were similar for most of the nitrogenase-positive strains. The strains derepressible for activity had several phenotypic characteristics different from non-derepressible strains. These included slower growth and lower oxygen consumption under microaerobic conditions and lower extracellular polysaccharide production. Extracellular polysaccharide production during growth on gluconate in every nitrogenase-positive strain assayed was lower under both aerobic and microaerobic conditions than the non-derepressible strains. These phenotypic characteristics may be representative of a genotype of a subspecies of R. japonicum. These studies were done in part to enlarge the base number of strains available for studies on the physiology, biochemistry, and genetics of nitrogen fixation.

Free-Living Rhizobium Strain Able To Grow on N 2 as the Sole Nitrogen Source

A Rhizobium strain isolated from stem nodules of the legume Sesbania rostrata was shown to grow on atmospheric nitrogen (N 2 ) as the sole nitrogen source. Non-N 2 -fixing mutants isolated directly on agar plates formed nodules that did not fix N 2 when inoculated into the host plant.

Parasitic origins of nitrogen-mixing Rhizobium-legume symbioses. A review of the evidence

This paper is divided into two sections. The first part (I) reviews the literature on the legume-Rhizobium association with emphasis on the processes leading to the establishment of the association. In the second part (II) it is proposed that the legume-Rhizobium association was originally necrotrophic , beginning when the free-living, nitrogen-fixing, saprotrophic Rhizobium developed the ability to infect the plant. The pre-infection events, infection processes and nodulation in the colonization of the legumes by the Rhizobium are similar to those of other parasitic associations. Likewise, the host responses to the Rhizobium entry, infection thread synthesis and bacteroid formation are comparable to those of other plants when they encounter phytopathogens . Evolutionary processes acted in the selection of biotrophy , the fine control and regulation of the extracellular enzymes of the necrotrophic Rhizobium converted the association into biotrophy . The nutritional dependence of the Rhizobium on the legume, the requirement of the plant for combined nitrogen and the Rhizobium potential to meet this requirement drove the biotrophic association into mutualism . This became possible when regulation of the nitrogen-fixing system of the Rhizobium was modified and the oxygen carrying protein leghemoglobin was acquired or evolved by the legume to enhance nitrogen fixation.

In vitro expression of nitrogenase activity in Parasponia-Rhizobium strain ANU 289

Rhizobium strain ANU 289 derepressed nitrogenase activity under defined in vitro conditions. Acetylene reduction was detected both in agar and liquid stationary culture. The strain is capable of nitrogen-fixing nodulation of legumes [such as siratro (Macroptilium atropurpureum Urb] as well as the non-legumes Parasponia andersonii and P. rugosa. Nitrogenase activity as high as 40-70 nmol C2H4 per mg protein after 7 days of incubation was detected. Strain ANU 289 was similar to Rhizobium strains 32 H1 and CB 756 with regard to oxygen requirement in the gas phase for development of nitrogenase activity between 0 and 10% O2, but showed increased sensitivity to oxygen repression at 20% O2. Strain ANU 289 also showed pronounced sensitivity to exogenous glutamine compared to strains 32 H1 and CB 756.

Requirement for carbon dioxide for nonsymbiotic expression of Rhizobium japonicum nitrogenase activity

The expression and maintenance of nitrogenase (C(2)H(2)) activity in growing, microaerobic liquid cultures of Rhizobium japonicum 3I1b110 was found to be stringently dependent on the sustained supply of CO(2). This requirement for CO(2) appeared to exceed the basal requirement for growth and was not related to effects on pH.