Hydrogen evolution: A major factor affecting the efficiency of nitrogen fixation in nodulated symbionts

Growth and Phytochemistry of Cymbopogon citratus Stapf Inoculated with Plant Growth-Promoting Bacteria under Different Lead Levels

This study aimed to investigate the phytochemistry of lemongrass (Cymbopogon citratus) inoculated with Azospirillum brasilense and grown in lead (Pb)-contaminated soil to assess its responses to inoculation under different Pb levels. The experimental design was completely randomized in a 2 × 5 factorial scheme: two levels of A. brasilense (absence or presence) and five Pb levels. After four months of treatment, the following were analyzed: total and reducing sugars, total phenolic content, flavonoids, antioxidant activity, antioxidant enzymes, proline, and essential oil (EO) content and composition. Soil Pb levels and A. brasilense inoculation affected phytochemicals in lemongrass plants. Azospirillum inoculation reduced total sugars in the roots at all soil Pb levels, while increasing Pb levels favored a rise in sugar contents. There was an increase in flavonoid content in treatments associated with Pb and inoculated with A. brasilense. Antioxidant capacity was lower at lower Pb levels, regardless of bacterial inoculation. Enzymatic response was mainly affected by Pb concentrations between 50 and 100 mg kg-1 soil. EO content was influenced by soil Pb levels, with higher EO production at 500 mg Pb kg-1 soil and without A. brasilense inoculation. Overall, lemongrass cultivation in Pb-contaminated areas can be an alternative to phytoremediation and EO production for the industry.

Phytomelatonin and gasotransmitters: a crucial combination for plant physiological functions

Melatonin, a molecule that was first identified in animal tissues, has been confirmed to be involved as a potential phytohormone in a variety of plant physiological responses. It is considered primarily as an antioxidant with important actions in controlling reactive oxygen and reactive nitrogen species. In addition to its role in regulating plant growth and development, phytomelatonin is involved in protection against abiotic and biotic stresses. The 'gasotransmitter'-that is, a gaseous signaling molecule-is a new concept that has been advanced in the past two decades, with functions in animal and plant physiological regulation. Gasotransmitters including nitric oxide, carbon monoxide, hydrogen sulfide, methane, and, more recently identified, hydrogen gas are critical and indispensable in a wide range of biological processes. This review investigates the interrelationship between phytomelatonin and the above-mentioned gasotransmitters from the perspective of biosynthetic origin and functions. Moreover, the potential future research directions for phytomelatonin and gasotransmitters interactions are discussed.

A directed genome evolution method to enhance hydrogen production in Rhodobacter capsulatus

Nitrogenase-dependent H2 production by photosynthetic bacteria, such as Rhodobacter capsulatus, has been extensively investigated. An important limitation to increase H2 production using genetic manipulation is the scarcity of high-throughput screening methods to detect possible overproducing mutants. Previously, we engineered R. capsulatus strains that emitted fluorescence in response to H2 and used them to identify mutations in the nitrogenase Fe protein leading to H2 overproduction. Here, we used ultraviolet light to induce random mutations in the genome of the engineered H2-sensing strain, and fluorescent-activated cell sorting to detect and isolate the H2-overproducing cells from libraries containing 5 × 105 mutants. Three rounds of mutagenesis and strain selection gradually increased H2 production up to 3-fold. The whole genomes of five H2 overproducing strains were sequenced and compared to that of the parental sensor strain to determine the basis for H2 overproduction. No mutations were present in well-characterized functions related to nitrogen fixation, except for the transcriptional activator nifA2. However, several mutations mapped to energy-generating systems and to carbon metabolism-related functions, which could feed reducing power or ATP to nitrogenase. Time-course experiments of nitrogenase depression in batch cultures exposed mismatches between nitrogenase protein levels and their H2 and ethylene production activities that suggested energy limitation. Consistently, cultivating in a chemostat produced up to 19-fold more H2 than the corresponding batch cultures, revealing the potential of selected H2 overproducing strains.

Legume-rhizobium dance: an agricultural tool that could be improved?

The specific interaction between rhizobia and legume roots leads to the development of a highly regulated process called nodulation, by which the atmospheric nitrogen is converted into an assimilable plant nutrient. This capacity is the basis for the use of bacterial inoculants for field crop cultivation. Legume plants have acquired tools that allow the entry of compatible bacteria. Likewise, plants can impose sanctions against the maintenance of nodules occupied by rhizobia with low nitrogen-fixing capacity. At the same time, bacteria must overcome different obstacles posed first by the environment and then by the legume. The present review describes the mechanisms involved in the regulation of the entire legume-rhizobium symbiotic process and the strategies and tools of bacteria for reaching the nitrogen-fixing state inside the nodule. Also, we revised different approaches to improve the nodulation process for a better crop yield.

Hydrogen agronomy: research progress and prospects

Agriculture is the foundation of social development. Under the pressure of population growth, natural disasters, environmental pollution, climate change, and food safety, the interdisciplinary "new agriculture" is becoming an important trend of modern agriculture. In fact, new agriculture is not only the foundation of great health and new energy sources, but is also the cornerstone of national food security, energy security, and biosafety. Hydrogen agronomy focuses mainly on the mechanism of hydrogen gas (H₂) biology effects in agriculture, and provides a theoretical foundation for the practice of hydrogen agriculture, a component of the new agriculture. Previous research on the biological effects of H₂ focused chiefly on medicine. The mechanism of selective antioxidant is the main theoretical basis of hydrogen medicine. Subsequent experiments have demonstrated that H₂ can regulate the growth and development of plant crops, edible fungus, and livestock, and enhance the tolerance of these agriculturally important organisms against abiotic and biotic stresses. Even more importantly, H₂ can regulate the growth and development of crops by changing the soil microbial community composition and structure. Use of H₂ can also improve the nutritional value and postharvest quality of agricultural products. Researchers have also shown that the biological functions of molecular hydrogen are mediated by modulating reactive oxygen species (ROS), nitric oxide (NO), and carbon monoxide (CO) signaling cascades in plants and microbes. This review summarizes and clarifies the history of hydrogen agronomy and describes recent progress in the field. We also argue that emerging hydrogen agriculture will be an important direction in the new agriculture. Further, we discuss several scientific problems in hydrogen agronomy, and suggest that the future of hydrogen agronomy depends on contributions by multiple disciplines. Important future research directions of hydrogen agronomy include hydrogen agriculture in special environments, such as islands, reefs, aircraft, and outer space.

Evaluation of argon-induced hydrogen production as a method to measure nitrogen fixation by cyanobacteria

The production of dihydrogen (H₂ ) is an enigmatic yet obligate component of biological dinitrogen (N₂ ) fixation. This study investigates the effect on H₂ production by N₂ fixing cyanobacteria when they are exposed to either air or a gas mixture consisting of argon, oxygen, and carbon dioxide (Ar:O₂ :CO₂ ). In the absence of N₂ , nitrogenase diverts the flow of electrons to the production of H₂ , which becomes a measure of Total Nitrogenase Activity (TNA). This method of argon-induced hydrogen production (AIHP) is much less commonly used to infer rates of N₂ fixation than the acetylene reduction (AR) assay. We provide here a full evaluation of the AIHP method and demonstrate its ability to achieve high-resolution measurements of TNA in a gas exchange flow-through system. Complete diel profiles of H₂ production were obtained for N₂ fixing cyanobacteria despite the absence of N₂ that broadly reproduced the temporal patterns observed by the AR assay. Comparison of H₂ production under air versus Ar:O₂ :CO₂ revealed the efficiency of electron usage during N₂ fixation and place these findings in the broader context of cell metabolism. Ultimately, AIHP is demonstrated to be a viable alternative to the AR assay with several additional merits that provide an insight into cell physiology and promise for successful field application.

Hydrogen Commonly Applicable from Medicine to Agriculture: From Molecular Mechanisms to the Field

The emerging field of hydrogen biology has to date mainly been applied in medicine. However, hydrogen biology can also enable positive outcomes in agriculture. Agriculture faces significant challenges resulting from a growing population, climate change, natural disasters, environmental pollution, and food safety issues. In fact, hydrogen agriculture is a practical application of hydrogen biology, which may assist in addressing many of these challenges. It has been demonstrated that hydrogen gas (H₂) may enhance plant tolerance towards abiotic and biotic stresses, regulate plant growth and development, increase nutritional values, prolong the shelf life, and decrease the nitrite accumulation during the storage of vegetables, as well as increase the resilience of livestock to pathogens. Our field trials show that H₂ may have a promising potential to increase yield and improve the quality of agricultural products. This review aims to elucidate mechanisms for a novel agricultural application of H₂ in China. Future development of hydrogen agriculture is proposed as well. Obviously, hydrogen agriculture belongs to a low carbon economy, and has great potential to provide "safe, tasty, healthy, and high-yield" agricultural products so that it may improve the sustainability of agriculture.

Downstream Signalling from Molecular Hydrogen

Molecular hydrogen (H2) is now considered part of the suite of small molecules that can control cellular activity. As such, H2 has been suggested to be used in the therapy of diseases in humans and in plant science to enhance the growth and productivity of plants. Treatments of plants may involve the creation of hydrogen-rich water (HRW), which can then be applied to the foliage or roots systems of the plants. However, the molecular action of H2 remains elusive. It has been suggested that the presence of H2 may act as an antioxidant or on the antioxidant capacity of cells, perhaps through the scavenging of hydroxyl radicals. H2 may act through influencing heme oxygenase activity or through the interaction with reactive nitrogen species. However, controversy exists around all the mechanisms suggested. Here, the downstream mechanisms in which H2 may be involved are critically reviewed, with a particular emphasis on the H2 mitigation of stress responses. Hopefully, this review will provide insight that may inform future research in this area.

Candidatus Frankia nodulisporulans sp. nov., an Alnus glutinosa-infective Frankia species unable to grow in pure culture and able to sporulate in-planta

We describe a new Frankia species, for three non-isolated strains obtained from Alnus glutinosa in France and Sweden, respectively. These strains can nodulate several Alnus species (A. glutinosa, A. incana, A. alnobetula), they form hyphae, vesicles and sporangia in the root nodule cortex but have resisted all attempts at isolation in pure culture. Their genomes have been sequenced, they are significantly smaller than those of other Alnus-infective species (5Mb instead of 7.5Mb) and are very closely related to one another (ANI of 100%). The name Candidatus Frankia nodulisporulans is proposed. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and draft genome sequences reported in this study for AgTrS, AgUmASt1 and AgUmASH1 are MT023539/LR778176/LR778180 and NZ_CADCWS000000000.1/CADDZU010000001/CADDZW010000001, respectively.

Hydrogenases and the Role of Molecular Hydrogen in Plants

Molecular hydrogen (H2) has been suggested to be a beneficial treatment for a range of species, from humans to plants. Hydrogenases catalyze the reversible oxidation of H2, and are found in many organisms, including plants. One of the cellular effects of H2 is the selective removal of reactive oxygen species (ROS) and reactive nitrogen species (RNS), specifically hydroxyl radicals and peroxynitrite. Therefore, the function of hydrogenases and the action of H2 needs to be reviewed in the context of the signalling roles of a range of redox active compounds. Enzymes can be controlled by the covalent modification of thiol groups, and although motifs targeted by nitric oxide (NO) can be predicted in hydrogenases sequences it is likely that the metal prosthetic groups are the target of inhibition. Here, a selection of hydrogenases, and the possibility of their control by molecules involved in redox signalling are investigated using a bioinformatics approach. Methods of treating plants with H2 along with the role of H2 in plants is also briefly reviewed. It is clear that studies report significant effects of H2 on plants, improving growth and stress responses, and therefore future work needs to focus on the molecular mechanisms involved.

Effectiveness of nitrogen fixation in rhizobia

Biological nitrogen fixation in rhizobia occurs primarily in root or stem nodules and is induced by the bacteria present in legume plants. This symbiotic process has fascinated researchers for over a century, and the positive effects of legumes on soils and their food and feed value have been recognized for thousands of years. Symbiotic nitrogen fixation uses solar energy to reduce the inert N2 gas to ammonia at normal temperature and pressure, and is thus today, especially, important for sustainable food production. Increased productivity through improved effectiveness of the process is seen as a major research and development goal. The interaction between rhizobia and their legume hosts has thus been dissected at agronomic, plant physiological, microbiological and molecular levels to produce ample information about processes involved, but identification of major bottlenecks regarding efficiency of nitrogen fixation has proven to be complex. We review processes and results that contributed to the current understanding of this fascinating system, with focus on effectiveness of nitrogen fixation in rhizobia.

Carbon substrate re-orders relative growth of a bacterium using Mo-, V-, or Fe-nitrogenase for nitrogen fixation

Biological nitrogen fixation is catalyzed by the molybdenum (Mo), vanadium (V) and iron (Fe)‐only nitrogenase metalloenzymes. Studies with purified enzymes have found that the ‘alternative’ V‐ and Fe‐nitrogenases generally reduce N₂ more slowly and produce more byproduct H₂ than the Mo‐nitrogenase, leading to an assumption that their usage results in slower growth. Here we show that, in the metabolically versatile photoheterotroph Rhodopseudomonas palustris, the type of carbon substrate influences the relative rates of diazotrophic growth based on different nitrogenase isoforms. The V‐nitrogenase supports growth as fast as the Mo‐nitrogenase on acetate but not on the more oxidized substrate succinate. Our data suggest that this is due to insufficient electron flux to the V‐nitrogenase isoform on succinate compared with acetate. Despite slightly faster growth based on the V‐nitrogenase on acetate, the wild‐type strain uses exclusively the Mo‐nitrogenase on both carbon substrates. Notably, the differences in H₂:N₂ stoichiometry by alternative nitrogenases (~1.5 for V‐nitrogenase, ~4–7 for Fe‐nitrogenase) and Mo‐nitrogenase (~1) measured here are lower than prior in vitro estimates. These results indicate that the metabolic costs of V‐based nitrogen fixation could be less significant for growth than previously assumed, helping explain why alternative nitrogenase genes persist in diverse diazotroph lineages and are broadly distributed in the environment.

Oxygen regulatory mechanisms of nitrogen fixation in rhizobia

Rhizobia are α- and β-proteobacteria that form a symbiotic partnership with legumes, fixing atmospheric dinitrogen to ammonia and providing it to the plant. Oxygen regulation is key in this symbiosis. Fixation is performed by an oxygen-intolerant nitrogenase enzyme but requires respiration to meet its high energy demands. To satisfy these opposing constraints the symbiotic partners cooperate intimately, employing a variety of mechanisms to regulate and respond to oxygen concentration. During symbiosis rhizobia undergo significant changes in gene expression to differentiate into nitrogen-fixing bacteroids. Legumes host these bacteroids in specialized root organs called nodules. These generate a near-anoxic environment using an oxygen diffusion barrier, oxygen-binding leghemoglobin and control of mitochondria localization. Rhizobia sense oxygen using multiple interconnected systems which enable a finely-tuned response to the wide range of oxygen concentrations they experience when transitioning from soil to nodules. The oxygen-sensing FixL-FixJ and hybrid FixL-FxkR two-component systems activate at relatively high oxygen concentration and regulate fixK transcription. FixK activates the fixNOQP and fixGHIS operons producing a high-affinity terminal oxidase required for bacterial respiration in the microaerobic nodule. Additionally or alternatively, some rhizobia regulate expression of these operons by FnrN, an FNR-like oxygen-sensing protein. The final stage of symbiotic establishment is activated by the NifA protein, regulated by oxygen at both the transcriptional and protein level. A cross-species comparison of these systems highlights differences in their roles and interconnections but reveals common regulatory patterns and themes. Future work is needed to establish the complete regulon of these systems and identify other regulatory signals.

Light Enhanced Fe-Mediated Nitrogen Fixation: Mechanistic Insights Regarding H2 Elimination, HER, and NH3 Generation

Despite their proposed accumulation at the Fe sites of the FeMo-cofactor of MoFe-nitrogenase, the presence of hydride ligands in molecular model systems capable of the nitrogen reduction reaction (N₂RR) appears to diminish the catalytic N₂-to-NH₃ conversion. We find that for an iron-based system bearing the trisphosphine ligand P₂P^Ph, a dramatic difference in yields is observed for N₂RR catalyzed by precatalysts with zero, one, or two hydride ligands; however, irradiating the three different catalysts with a mercury lamp results in similar yields. Although the efficacy for N₂RR versus the hydrogen evolution reaction (HER) is modest for this system by comparison to certain iron (and other metal) catalysts, the system provides an opportunity to study the role of hydrides in the selectivity for N₂RR versus HER, which is a central issue in catalyst design. Stochiometric reactions with hydride containing precatalysts reveal a hydrogen evolution cycle in which no nitrogen fixation occurs. Irradiation of the dihydride precatalysts, observed during turnover, results in H₂ elimination and formation of (P₂P^Ph)Fe(N₂)₂, which itself is unreactive with acids at low temperature. N₂ functionalization does occur with acids and silyl electrophiles for the reduced species [(P₂P^Ph)Fe(N₂)]^- and [(P₂P^Ph)Fe(N₂)]^2-, which have been characterized independently. The requirement of accessing such low formal oxidation states explains the need for strong reductants. The low selectivity of the system for functionalization at N_β versus Fe creates off-path hydride species that participate in unproductive HER, helping to explain the low selectivity for N₂RR over HER. The data presented here hence lends further insight into the growing understanding of the selectivity, activity, and required driving force relevant to iron (and other) N₂RR catalysts.

Azotobacter vinelandii Nitrogenase Activity, Hydrogen Production, and Response to Oxygen Exposure

Azotobacter vinelandii selectively utilizes three types of nitrogenase (molybdenum, vanadium, and iron only) to fix N₂, with their expression regulated by the presence or absence of different metal cofactors in its environment. Each alternative nitrogenase isoenzyme is predicted to have different electron flux requirements based on in vitro measurements, with the molybdenum nitrogenase requiring the lowest flux and the iron-only nitrogenase requiring the highest. Here, prior characterized strains, derepressed in nitrogenase synthesis and also deficient in uptake hydrogenase, were further modified to generate new mutants lacking the ability to produce poly-β-hydroxybutyrate (PHB). PHB is a storage polymer generated under oxygen-limiting conditions and can represent up to 70% of the cells' dry weight. The absence of such granules facilitated the study of relationships between catalytic biomass and product molar yields across different adaptive respiration conditions. The released hydrogen gas observed during growth, due to the inability of the mutants to recapture hydrogen, allowed for direct monitoring of in vivo nitrogenase activity for each isoenzyme. The data presented here show that increasing oxygen exposure limits equally the in vivo activities of all nitrogenase isoenzymes, while under comparative conditions, the Mo nitrogenase enzyme evolves more hydrogen per unit of biomass than the alternative isoenzymes.IMPORTANCEA. vinelandii has been a focus of intense research for over 100 years. It has been investigated for a variety of functions, including agricultural fertilization and hydrogen production. All of these endeavors are centered around A. vinelandii's ability to fix nitrogen aerobically using three nitrogenase isoenzymes. The majority of research up to this point has targeted in vitro measurements of the molybdenum nitrogenase, and robust data contrasting how oxygen impacts the in vivo activity of each nitrogenase isoenzyme are lacking. This article aims to provide in vivo nitrogenase activity data using a real-time evaluation of hydrogen gas released by derepressed nitrogenase mutants lacking an uptake hydrogenase and PHB accumulation.

Evolutionarily Conserved nodE, nodO, T1SS, and Hydrogenase System in Rhizobia of Astragalus membranaceus and Caragana intermedia

Mesorhizobium species are the main microsymbionts associated with the medicinal or sand-fixation plants Astragalus membranaceus and Caragana intermedia (AC) in temperate regions of China, while all the Mesorhizobium strains isolated from each of these plants could nodulate both of them. However, Rhizobium yanglingense strain CCBAU01603 could nodulate AC plants and it's a high efficiency symbiotic and competitive strain with Caragana. Therefore, the common features shared by these symbiotic rhizobia in genera of Mesorhizobium and Rhizobium still remained undiscovered. In order to study the genomic background influencing the host preference of these AC symbiotic strains, the whole genomes of two (M. silamurunense CCBAU01550, M. silamurunense CCBAU45272) and five representative strains (M. septentrionale CCBAU01583, M. amorphae CCBAU01570, M. caraganae CCBAU01502, M. temperatum CCBAU01399, and R. yanglingense CCBAU01603) originally isolated from AC plants were sequenced, respectively. As results, type III secretion systems (T3SS) of AC rhizobia evolved in an irregular pattern, while an evolutionarily specific region including nodE, nodO, T1SS, and a hydrogenase system was detected to be conserved in all these AC rhizobia. Moreover, nodO was verified to be prevalently distributed in other AC rhizobia and was presumed as a factor affecting the nodule formation process. In conclusion, this research interpreted the multifactorial features of the AC rhizobia that may be associated with their host specificity at cross-nodulation group, including nodE, nodZ, T1SS as the possible main determinants; and nodO, hydrogenase system, and T3SS as factors regulating the bacteroid formation or nitrogen fixation efficiency.

Unraveling the presence of multi-class toxins from Trichodesmium bloom in the Gulf of Mannar region of the Bay of Bengal

Trichodesmium is an enigmatic bloom forming, non-heterocystous cyanobacterium reported most frequently in the coastal waters of India. However, the toxigenic potential of this globally significant N₂ fixing cyanobacterium has not been characterized. In this study, we report for the first time the presence of potent multi-class neurotoxins such as Anatoxin-a, Saxitoxins, Gonyautoxin and hepatotoxins like MC-LR, MC-YA from a bloom material of Trichodesmium sp. MBDU 524 collected at the Gulf of Mannar region. Toxins were determined using liquid chromatography-electrospray ionization mass spectrometry (LC-ESI-MS) analysis of HPLC purified aqueous and solvent fractions. Molecular phylogenetic analysis through 16S rRNA gene sequencing showed the close relationship with Trichodesmium erythraeum clade. The toxigenic potential was validated through brine shrimp toxicity assay and showed 100% mortality after 48 h of incubation. The results suggest the potential toxigenic and environmental impacts of Trichodesmium bloom sample from the Gulf of Mannar region.

Direct Raman Spectroscopic Measurements of Biological Nitrogen Fixation under Natural Conditions: An Analytical Approach for Studying Nitrogenase Activity

Biological N₂ fixation is a major input of bioavailable nitrogen, which represents the most frequent factor limiting the agricultural production throughout the world. Especially, the symbiotic association between legumes and Rhizobium bacteria can provide substantial amounts of nitrogen (N) and reduce the need for industrial fertilizers. Despite its importance in the global N cycle, rates of biological nitrogen fixation have proven difficult to quantify. In this work, we propose and demonstrate a simple analytical approach to measure biological N₂ fixation rates directly without a proxy or isotopic labeling. We determined a mean N₂ fixation rate of 78 ± 5 μmol N₂ (g dry weight nodule)^-1 h^-1 of a Medicago sativa-Rhizobium consortium by continuously analyzing the amount of atmospheric N₂ in static environmental chambers with Raman gas spectroscopy. By simultaneously analyzing the CO₂ uptake and photosynthetic plant activity, we think that a minimum CO₂ mixing ratio might be needed for natural N₂ fixation and only used the time interval above this minimum CO₂ mixing ratio for N₂ fixation rate calculations. The proposed approach relies only on noninvasive measurements of the gas phase and, given its simplicity, indicates the potential to estimate biological nitrogen fixation of legume symbioses not only in laboratory experiments. The same methods can presumably also be used to detect N₂ fluxes by denitrification from ecosystems to the atmosphere.

Inorganic clusters with a [Fe2MoOS3] core—a functional model for acetylene reduction by nitrogenases

We report the first example of a wholly inorganic mimic of a part of the FeMoco active centre of nitrogenases.

Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean

BACKGROUND

The soybean-Bradyrhizobium symbiosis can be highly efficient in fixing nitrogen, but few genomic sequences of elite inoculant strains are available. Here we contribute with information on the genomes of two commercial strains that are broadly applied to soybean crops in the tropics. B. japonicum CPAC 15 (=SEMIA 5079) is outstanding in its saprophytic capacity and competitiveness, whereas B. diazoefficiens CPAC 7 (=SEMIA 5080) is known for its high efficiency in fixing nitrogen. Both are well adapted to tropical soils. The genomes of CPAC 15 and CPAC 7 were compared to each other and also to those of B. japonicum USDA 6T and B. diazoefficiens USDA 110T.

RESULTS

Differences in genome size were found between species, with B. japonicum having larger genomes than B. diazoefficiens. Although most of the four genomes were syntenic, genome rearrangements within and between species were observed, including events in the symbiosis island. In addition to the symbiotic region, several genomic islands were identified. Altogether, these features must confer high genomic plasticity that might explain adaptation and differences in symbiotic performance. It was not possible to attribute known functions to half of the predicted genes. About 10% of the genomes was composed of exclusive genes of each strain, but up to 98% of them were of unknown function or coded for mobile genetic elements. In CPAC 15, more genes were associated with secondary metabolites, nutrient transport, iron-acquisition and IAA metabolism, potentially correlated with higher saprophytic capacity and competitiveness than seen with CPAC 7. In CPAC 7, more genes were related to the metabolism of amino acids and hydrogen uptake, potentially correlated with higher efficiency of nitrogen fixation than seen with CPAC 15.

CONCLUSIONS

Several differences and similarities detected between the two elite soybean-inoculant strains and between the two species of Bradyrhizobium provide new insights into adaptation to tropical soils, efficiency of N2 fixation, nodulation and competitiveness.

A proteomic approach of bradyrhizobium/aeschynomene root and stem symbioses reveals the importance of the fixA locus for symbiosis

Rhizobia are soil bacteria that are able to form symbiosis with plant hosts of the legume family. These associations result in the formation of organs, called nodules in which bacteria fix atmospheric nitrogen to the benefit of the plant. Most of our knowledge on the metabolism and the physiology of the bacteria during symbiosis derives from studying roots nodules of terrestrial plants. Here we used a proteomics approach to investigate the bacterial physiology of photosynthetic Bradyrhizobium sp. ORS278 during the symbiotic process with the semi aquatical plant Aeschynomene indica that forms root and stem nodules. We analyzed the proteomes of bacteria extracted from each type of nodule. First, we analyzed the bacteroid proteome at two different time points and found only minor variation between the bacterial proteomes of 2-week- and 3-week-old nodules. High conservation of the bacteroid proteome was also found when comparing stem nodules and root nodules. Among the stem nodule specific proteins were those related to the phototrophic ability of Bradyrhizobium sp. ORS278. Furthermore, we compared our data with those obtained during an extensive genetic screen previously published. The symbiotic role of four candidate genes which corresponding proteins were found massively produced in the nodules but not identified during this screening was examined. Mutant analysis suggested that in addition to the EtfAB system, the fixA locus is required for symbiotic efficiency.

Ammonium induces differential expression of methane and nitrogen metabolism-related genes in Methylocystis sp. strain SC2

Nitrogen source and concentration are major determinants of methanotrophic activity, but their effect on global gene expression is poorly studied. Methylocystis sp. strain SC2 produces two isozymes of particulate methane monooxygenase. These are encoded by pmoCAB1 (low-affinity pMMO1) and pmoCAB2 (high-affinity pMMO2). We used RNA-Seq to identify strain SC2 genes that respond to standard (10 mM) and high (30 mM) NH4(+) concentrations in the medium, compared with 10 mM NO3(-). While the expression of pmoCAB1 was unaffected, pmoCAB2 was significantly downregulated (log2 fold changes of -5.0 to -6.0). Among nitrogen metabolism-related processes, genes involved in hydroxylamine detoxification (haoAB) were highly upregulated, while those for assimilatory nitrate/nitrite reduction, high-affinity ammonium uptake and nitrogen regulatory protein PII were downregulated. Differential expression of pmoCAB2 and haoAB was independently validated by end-point reverse transcription polymerase chain reaction. Methane oxidation by SC2 cells exposed to 30 mM NH4(+) was inhibited at ≤ 400 ppmv CH4 , where pMMO2 but not pMMO1 is functional. When transferred back to standard nitrogen concentration, methane oxidation capability and pmoCAB2 expression were restored. Given that Methylocystis contributes to atmospheric methane oxidation in upland soils, differential expression of pmoCAB2 explains, at least to some extent, the strong inhibitory effect of ammonium fertilizers on this activity.

Dissolved hydrogen and nitrogen fixation in the oligotrophic North Pacific Subtropical Gyre

The production of hydrogen (H2) is an inherent component of biological dinitrogen (N2) fixation, and there have been several studies quantifying H2 production relative to N2 fixation in cultures of diazotrophs. However, conducting the relevant measurements for a field population is more complex as shown by this study of N2 fixation, H2 consumption and dissolved H2 concentrations in the oligotrophic North Pacific Ocean. Measurements of H2 oxidation revealed microbial consumption of H2 was equivalent to 1-7% of ethylene produced during the acetylene reduction assay and 11-63% of (15)N2 assimilation on a molar scale. Varying abundances of Crocosphaera and Trichodesmium as revealed by nifH gene abundances broadly corresponded with diel changes observed in both N2 fixation and H2 oxidation. However, no corresponding changes were observed in the dissolved H2 concentrations which remained consistently supersaturated (147-560%) relative to atmospheric equilibrium. The results from this field study allow the efficiency of H2 cycling by natural populations of diazotrophs to be compared to cultured representatives. The findings indicate that dissolved H2 concentrations may depend not only on the community composition of diazotrophs but also upon relevant environmental parameters such as light intensity or the presence of other H2-metabolizing microorganisms.

Genomic basis of broad host range and environmental adaptability of Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 which are used in inoculants for common bean (Phaseolus vulgaris L.)

BACKGROUND

Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 are α-Proteobacteria that establish nitrogen-fixing symbioses with a range of legume hosts. These strains are broadly used in commercial inoculants for application to common bean (Phaseolus vulgaris) in South America and Africa. Both strains display intrinsic resistance to several abiotic stressful conditions such as low soil pH and high temperatures, which are common in tropical environments, and to several antimicrobials, including pesticides. The genetic determinants of these interesting characteristics remain largely unknown.

RESULTS

Genome sequencing revealed that CIAT 899 and PRF 81 share a highly-conserved symbiotic plasmid (pSym) that is present also in Rhizobium leucaenae CFN 299, a rhizobium displaying a similar host range. This pSym seems to have arisen by a co-integration event between two replicons. Remarkably, three distinct nodA genes were found in the pSym, a characteristic that may contribute to the broad host range of these rhizobia. Genes for biosynthesis and modulation of plant-hormone levels were also identified in the pSym. Analysis of genes involved in stress response showed that CIAT 899 and PRF 81 are well equipped to cope with low pH, high temperatures and also with oxidative and osmotic stresses. Interestingly, the genomes of CIAT 899 and PRF 81 had large numbers of genes encoding drug-efflux systems, which may explain their high resistance to antimicrobials. Genome analysis also revealed a wide array of traits that may allow these strains to be successful rhizosphere colonizers, including surface polysaccharides, uptake transporters and catabolic enzymes for nutrients, diverse iron-acquisition systems, cell wall-degrading enzymes, type I and IV pili, and novel T1SS and T5SS secreted adhesins.

CONCLUSIONS

Availability of the complete genome sequences of CIAT 899 and PRF 81 may be exploited in further efforts to understand the interaction of tropical rhizobia with common bean and other legume hosts.

Ocean acidification slows nitrogen fixation and growth in the dominant diazotroph Trichodesmium under low-iron conditions

Dissolution of anthropogenic CO(2) increases the partial pressure of CO(2) (pCO(2)) and decreases the pH of seawater. The rate of Fe uptake by the dominant N(2)-fixing cyanobacterium Trichodesmium declines as pH decreases in metal-buffered medium. The slower Fe-uptake rate at low pH results from changes in Fe chemistry and not from a physiological response of the organism. Contrary to previous observations in nutrient-replete media, increasing pCO(2)/decreasing pH causes a decrease in the rates of N(2) fixation and growth in Trichodesmium under low-Fe conditions. This result was obtained even though the bioavailability of Fe was maintained at a constant level by increasing the total Fe concentration at low pH. Short-term experiments in which pCO(2) and pH were varied independently showed that the decrease in N(2) fixation is caused by decreasing pH rather than by increasing pCO(2) and corresponds to a lower efficiency of the nitrogenase enzyme. To compensate partially for the loss of N(2) fixation efficiency at low pH, Trichodesmium synthesizes additional nitrogenase. This increase comes partly at the cost of down-regulation of Fe-containing photosynthetic proteins. Our results show that although increasing pCO(2) often is beneficial to photosynthetic marine organisms, the concurrent decreasing pH can affect primary producers negatively. Such negative effects can occur both through chemical mechanisms, such as the bioavailability of key nutrients like Fe, and through biological mechanisms, as shown by the decrease in N(2) fixation in Fe-limited Trichodesmium.

Choice of hydrogen uptake (Hup) status in legume-rhizobia symbioses

The H₂ is an obligate by-product of N-fixation. Recycling of H₂ through uptake hydrogenase (Hup) inside the root nodules of leguminous plants is often considered an advantage for plants. However, many of the rhizobium-legume symbioses found in nature, especially those used in agriculture are shown to be Hup⁻, with the plants releasing H₂ produced by nitrogenase activity from root nodules into the surrounding rhizosphere. Recent studies have suggested that, H₂ induces plant-growth-promoting rhizobacteria, which may explain the widespread of Hup⁻ symbioses in spite of the low energy efficiency of such associations. Wild legumes grown in Nova Scotia, Canada, were surveyed to determine if any plant-growth characteristics could give an indication of Hup choice in leguminous plants. Out of the plants sampled, two legumes, Securigera varia and Vicia cracca, showed Hup⁺ associations. Securigera varia exhibited robust root structure as compared with the other plants surveyed. Data from the literature and the results from this study suggested that plants with established root systems are more likely to form the energy-efficient Hup⁺ symbiotic relationships with rhizobia. Conversely, Hup⁻ associations could be beneficial to leguminous plants due to H₂-oxidizing plant-growth-promoting rhizobacteria that allow plants to compete successfully, early in the growing season. However, some nodules from V. cracca tested Hup⁺, while others were Hup⁻. This was similar to that observed in Glycine max and Pisum sativum, giving reason to believe that Hup choice might be affected by various internal and environmental factors.

NITROGEN FIXATION, HYDROGEN CYCLING, AND ELECTRON TRANSPORT KINETICS IN TRICHODESMIUM ERYTHRAEUM (CYANOBACTERIA) STRAIN IMS101(1)

This study describes the relationships between dinitrogen (N2 ) fixation, dihydrogen (H2 ) production, and electron transport associated with photosynthesis and respiration in the marine cyanobacterium Trichodesmium erythraeum Ehrenb. strain IMS101. The ratio of H2 produced:N2 fixed (H2 :N2 ) was controlled by the light intensity and by the light spectral composition and was affected by the growth irradiance level. For Trichodesmium cells grown at 50 μmol photons · m(-2)  · s(-1) , the rate of N2 fixation, as measured by acetylene reduction, saturated at light intensities of 200 μmol photons · m(-2)  · s(-1) . In contrast, net H2 production continued to increase with light levels up to 1,000 μmol photons · m(-2)  · s(-1) . The H2 :N2 ratios increased monotonically with irradiance, and the variable fluorescence measured using a fast repetition rate fluorometer (FRRF) revealed that this increase was accompanied by a progressive reduction of the plastoquinone (PQ) pool. Additions of 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB), an inhibitor of electron transport from PQ pool to PSI, diminished both N2 fixation and net H2 production, while the H2 :N2 ratio increased with increasing level of PQ pool reduction. In the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), nitrogenase activity declined but could be prolonged by increasing the light intensity and by removing the oxygen supply. These results on the coupling of N2 fixation and H2 cycling in Trichodesmium indicate how light intensity and light spectral quality of the open ocean can influence the H2 :N2 ratio and modulate net H2 production.

Cultivation-independent detection of autotrophic hydrogen-oxidizing bacteria by DNA stable-isotope probing

Knallgas bacteria are a physiologically defined group that is primarily studied using cultivation-dependent techniques. Given that current cultivation techniques fail to grow most bacteria, cultivation-independent techniques that selectively detect and identify knallgas bacteria will improve our ability to study their diversity and distribution. We used stable-isotope probing (SIP) to identify knallgas bacteria in rhizosphere soil of legumes and in a microbial mat from Obsidian Pool in Yellowstone National Park. When samples were incubated in the dark, incorporation of (13)CO(2) was H(2) dependent. SIP enabled the detection of knallgas bacteria that were not detected by cultivation, and the majority of bacteria identified in the rhizosphere soils were betaproteobacteria predominantly related to genera previously known to oxidize hydrogen. Bacteria in soil grew on hydrogen at concentrations as low as 100 ppm. A hydB homolog encoding a putative high-affinity NiFe hydrogenase was amplified from (13)C-labeled DNA from both vetch and clover rhizosphere soil. The results indicate that knallgas bacteria can be detected by SIP and populations that respond to different H(2) concentrations can be distinguished. The methods described here should be applicable to a variety of ecosystems and will enable the discovery of additional knallgas bacteria that are resistant to cultivation.

Response of archaeal communities in the rhizosphere of maize and soybean to elevated atmospheric CO2 concentrations

BACKGROUND

Archaea are important to the carbon and nitrogen cycles, but it remains uncertain how rising atmospheric carbon dioxide concentrations ([CO(2)]) will influence the structure and function of soil archaeal communities.

METHODOLOGY/PRINCIPAL FINDINGS

We measured abundances of archaeal and bacterial 16S rRNA and amoA genes, phylogenies of archaeal 16S rRNA and amoA genes, concentrations of KCl-extractable soil ammonium and nitrite, and potential ammonia oxidation rates in rhizosphere soil samples from maize and soybean exposed to ambient (∼385 ppm) and elevated (550 ppm) [CO(2)] in a replicated and field-based study. There was no influence of elevated [CO(2)] on copy numbers of archaeal or bacterial 16S rRNA or amoA genes, archaeal community composition, KCl-extractable soil ammonium or nitrite, or potential ammonia oxidation rates for samples from maize, a model C(4) plant. Phylogenetic evidence indicated decreased relative abundance of crenarchaeal sequences in the rhizosphere of soybean, a model leguminous-C(3) plant, at elevated [CO(2)], whereas quantitative PCR data indicated no changes in the absolute abundance of archaea. There were no changes in potential ammonia oxidation rates at elevated [CO(2)] for soybean. Ammonia oxidation rates were lower in the rhizosphere of maize than soybean, likely because of lower soil pH and/or abundance of archaea. KCl-extractable ammonium and nitrite concentrations were lower at elevated than ambient [CO(2)] for soybean.

CONCLUSION

Plant-driven shifts in soil biogeochemical processes in response to elevated [CO(2)] affected archaeal community composition, but not copy numbers of archaeal genes, in the rhizosphere of soybean. The lack of a treatment effect for maize is consistent with the fact that the photosynthesis and productivity of maize are not stimulated by elevated [CO(2)] in the absence of drought.

Comparing symbiotic efficiency between swollen versus nonswollen rhizobial bacteroids

Symbiotic rhizobia differentiate physiologically and morphologically into nitrogen-fixing bacteroids inside legume host nodules. The differentiation is apparently terminal in some legume species, such as peas (Pisum sativum) and peanuts (Arachis hypogaea), likely due to extreme cell swelling induced by the host. In other legume species, such as beans (Phaseolus vulgaris) and cowpeas (Vigna unguiculata), differentiation into bacteroids, which are similar in size and shape to free-living rhizobia, is reversible. Bacteroid modification by plants may affect the effectiveness of the symbiosis. Here, we compare symbiotic efficiency of rhizobia in two different hosts where the rhizobia differentiate into swollen nonreproductive bacteroids in one host and remain nonswollen and reproductive in the other. Two such dual-host strains were tested: Rhizobium leguminosarum A34 in peas and beans and Bradyrhizobium sp. 32H1 in peanuts and cowpeas. In both comparisons, swollen bacteroids conferred more net host benefit by two measures: return on nodule construction cost (plant growth per gram nodule growth) and nitrogen fixation efficiency (H(2) production by nitrogenase per CO(2) respired). Terminal bacteroid differentiation among legume species has evolved independently multiple times, perhaps due to the increased host fitness benefits observed in this study.

Symbiotic legume nodules employ both rhizobial exo- and endo-hydrogenases to recycle hydrogen produced by nitrogen fixation

Background

In symbiotic legume nodules, endosymbiotic rhizobia (bacteroids) fix atmospheric N₂, an ATP-dependent catalytic process yielding stoichiometric ammonium and hydrogen gas (H₂). While in most legume nodules this H₂ is quantitatively evolved, which loss drains metabolic energy, certain bacteroid strains employ uptake hydrogenase activity and thus evolve little or no H₂. Rather, endogenous H₂ is efficiently respired at the expense of O₂, driving oxidative phosphorylation, recouping ATP used for H₂ production, and increasing the efficiency of symbiotic nodule N₂ fixation. In many ensuing investigations since its discovery as a physiological process, bacteroid uptake hydrogenase activity has been presumed a single entity.

Methodology/Principal Findings

Azorhizobium caulinodans, the nodule endosymbiont of Sesbania rostrata stems and roots, possesses both orthodox respiratory (exo-)hydrogenase and novel (endo-)hydrogenase activities. These two respiratory hydrogenases are structurally quite distinct and encoded by disparate, unlinked gene-sets. As shown here, in S. rostrata symbiotic nodules, haploid A. caulinodans bacteroids carrying single knockout alleles in either exo- or-endo-hydrogenase structural genes, like the wild-type parent, evolve no detectable H₂ and thus are fully competent for endogenous H₂ recycling. Whereas, nodules formed with A. caulinodans exo-, endo-hydrogenase double-mutants evolve endogenous H₂ quantitatively and thus suffer complete loss of H₂ recycling capability. More generally, from bioinformatic analyses, diazotrophic microaerophiles, including rhizobia, which respire H₂ may carry both exo- and endo-hydrogenase gene-sets.

Conclusions/Significance

In symbiotic S. rostrata nodules, A. caulinodans bacteroids can use either respiratory hydrogenase to recycle endogenous H₂ produced by N₂ fixation. Thus, H₂ recycling by symbiotic legume nodules may involve multiple respiratory hydrogenases.

Mutant Strains of Rhizobium japonicum with Increased Ability to Fix Nitrogen for Soybean

A strain of Rhizobium japonicum used in commercial inoculants was mutagenized and screened by a rapid effectiveness assay with soybean plants. Two mutant strains nodulated the roots earlier than the wild type and also expressed greater symbiotic nitrogen-fixing activity than the wild type in the presence and absence of fixed nitrogen. In addition, one of the mutants formed more root nodules than the wild type. Plants inoculated with these strains had increased dry weights ( approximately 60 percent) and nitrogen content ( approximately 100 percent) when grown in growth chambers.

Distribution of hydrogen-metabolizing bacteria in alfalfa field soil

H(2) evolved by alfalfa root nodules during the process of N(2) fixation may be an important factor influencing the distribution of soil bacteria. To test this hypothesis under field conditions, over 700 bacterial isolates were obtained from fallow soil or from the 3-mm layer of soil surrounding alfalfa (Medicago sativa L.) root nodules, alfalfa roots, or bindweed (Convolvulus arvensis L.) roots. Bacteria were isolated under either aerobic or microaerophilic conditions and were tested for their capacity to metabolize H(2). Isolates showing net H(2) uptake and H(2) incorporation activity under laboratory conditions were assigned a Hup phenotype, whereas organisms with significant H(2) output capacity were designated as a Hout phenotype. Under aerobic isolation conditions two Hup isolates were obtained, whereas under microaerophilic conditions five Hup and two Hout isolates were found. The nine isolates differed on the basis of 24 standard bacteriological characteristics or fatty acid composition. Five of the nine organisms were isolated from soil around root nodules, whereas the other four were found distributed among the other three soil environments. On the basis of the microaerophilic isolations, 4.8% of the total procaryotic isolates from soil around root nodules were capable of oxidizing H(2), and 1.2% could produce H(2). Two of the Hup isolates were identified as Rhizobium meliloti by root nodulation tests, but the fact that none of the isolates reduced C(2)H(2) under the assay conditions suggested that the H(2) metabolism traits were associated with various hydrogenase systems rather than with nitrogenase activity. Results from this study support the concept that H(2) evolution by alfalfa root nodules has a significant effect on the surrounding microenvironment and influences the number and diversity of bacteria occupying that region.

Mutant strains of clover rhizobium (Rhizobium trifolii) that form nodules on soybean (Glycine max)

Mutant strains of Rhizobium trifolii that induce nitrogenase activity in the free-living state were isolated. These strains, unlike the wild type, nodulated soybean and mungbean plants, producing effective nodules. One of the strains, strain DT72, also nodulated clover but the nodules were ineffective. Strain DT125 consumed hydrogen gas from the gas phase, which can be coupled to nitrogenase activity under appropriate conditions.

Uptake Hydrogenase (Hup) in Common Bean (Phaseolus vulgaris) Symbioses

Strains of Rhizobium forming nitrogen-fixing symbioses with common bean were systematically examined for the presence of the uptake hydrogenase (hup) structural genes and expression of uptake hydrogenase (Hup) activity. DNA with homology to the hup structural genes of Bradyrhizobium japonicum was present in 100 of 248 strains examined. EcoRI fragments with molecular sizes of approximately 20.0 and 2.2 kb hybridized with an internal SacI fragment, which contains part of both bradyrhizobial hup structural genes. The DNA with homology to the hup genes was located on pSym of one of the bean rhizobia. Hup activity was observed in bean symbioses with 13 of 30 strains containing DNA homologous with the hup structural genes. However, the Hup activity was not sufficient to eliminate hydrogen evolution from the nodules. Varying the host plant with two of the Hup strains indicated that expression of Hup activity was host regulated, as has been reported with soybean, pea, and cowpea strains.

Transposon Tn5-Generated Bradyrhizobium japonicum Mutants Unable To Grow Chemoautotrophically with H(2)

Twelve Tn5-induced mutants of Bradyrhizobium japonicum unable to grow chemoautotrophically with CO(2) and H(2) (Aut) were isolated. Five Aut mutants lacked hydrogen uptake activity (Hup). The other seven Aut mutants possessed wild-type levels of hydrogen uptake activity (Hup), both in free-living culture and symbiotically. Three of the Hup mutants lacked hydrogenase activity both in free-living culture and as nodule bacteroids. The other two mutants were Hup only in free-living culture. The latter two mutants appeared to be hypersensitive to repression by oxygen, since Hup activity could be derepressed under 0.4% O(2). All five Hup mutants expressed both ex planta and symbiotic nitrogenase activities. Two of the seven Aut Hup mutants expressed no free-living nitrogenase activity, but they did express it symbiotically. These two strains, plus one other Aut Hup mutant, had CO(2) fixation activities 20 to 32% of the wild-type level. The cosmid pSH22, which was shown previously to contain hydrogenase-related genes of B. japonicum, was conjugated into each Aut mutant. The Aut Hup mutants that were Hup both in free-living culture and symbiotically were complemented by the cosmid. None of the other mutants was complemented by pSH22. Individual subcloned fragments of pSH22 were used to complement two of the Hup mutants.

Nitrogen Fixation in an Establishing Alfalfa (Medicago sativa L.) Ley in Sweden, Estimated by Three Different Methods

In an investigation of the ability of alfalfa to fix nitrogen under field conditions in Scandinavia, N(2) fixation during the establishment year ranged between 7.85 and 10.37 g of N m, depending on the method used. The methods used were an in situ acetylene reduction method, a N isotope dilution method using two reference crops, and a total-N difference method. The dynamics of nitrogenase activity in relation to plant development was studied by using the acetylene reduction method. Also, the diurnal variation in N(2) fixation at the field site was studied with the acetylene reduction method; no diurnal change was detected, which is explained by the fact that the nodules within the soil were protected against short-term fluctuations in temperature. The significant amount of nitrogen fixed by alfalfa during its first year even at northern latitudes suggests that this crop offers an alternative to conventional field management of heavily fertilized nonlegume leys.

Rhizobial Ecology of the Woody Legume Mesquite (Prosopis glandulosa) in the Sonoran Desert

Soil samples were collected from the surface (0 to 0.6 m) and phreatic (3.9 to 4.5 m) root systems of a Prosopis glandulosa woodland in the Sonoran Desert of southern California. P. glandulosa seedlings were inoculated with these soils, and rhizobia were isolated from nodules. The phreatic soil, characterized by constant moisture and temperature but low nutrient availability, favored slow-growing (SG) isolates as nodule occupants (85%). SG isolates from the surface and phreatic soil were distinct based on differences in colony morphology. Isolates from the surface soil, characterized by high nutrient availability and widely fluctuating water content and temperature, were equally represented by fast-growing and SG rhizobia. Most SG isolates (83%) had nodule relative efficiencies of <0.80, whereas 54% of the fast-growing isolates had relative efficiency values of >0.80.

Symbiotic Expression of Cosmid-Borne Bradyrhizobium japonicum Hydrogenase Genes

The expression of cosmid-borne Bradyrhizobium japonicum hydrogenase genes in alfalfa, clover, and soybean nodules harboring Rhizobium transconjugants was studied. Cosmid pHU52 conferred hydrogen uptake (Hup) activity in both free-living bacteria and in nodules on the different plant hosts, although in nodules the instability of the cosmid resulted in low levels of Hup activity. In contrast, cosmid pHU1, which does not confer Hup activity on free-living bacteria, gave a Hup phenotype in nodules on alfalfa and soybean. Nodules formed by B. japonicum USDA 123Spc(pHU1) recycled about 90% of nitrogenase-mediated hydrogen evolution. Both subunits of hydrogenase (30- and 60-kilodalton polypeptides) were detected in enzyme-linked immunosorbent assays of bacteroid preparations from nodules harboring B. japonicum strains with pHU1 or pHU52. Neither pHU53 nor pLAFR1 conferred detectable Hup activity in either nodules or free-living bacteria. Based on the physical maps of pHU1 and pHU52, it is suggested that a 5.5-kilobase EcoRI fragment unique to pHU52 contains a gene or part of a gene required for Hup activity in free-living bacteria but not in nodules. This conclusion is supported by the observation that two Tn5 insertions in the chromosome of B. japonicum USDA 122DES obtained by marker exchange with Tn5-mutagenized pHU1 abolished Hup activity in free-living bacteria but not in nodules.

Influence of the Bradyrhizobium japonicum Hydrogenase on the Growth of Glycine and Vigna Species

The effect of the Bradyrhizobium japonicum hydrogenase on nitrogen fixation was evaluated by comparing the growth of Vigna and Glycine species inoculated with a Hup mutant and its Hup revertant. In all experiments, the growth of plants inoculated with the strain without hydrogenase was at least equal to the growth of the strain with hydrogenase. For Glycine usuriensis and Glycine max cv. Hodgson in liquid culture, the growth was higher with the Hup strain. It is possible that reduced rates of nitrogen fixation in the presence of hydrogenase are due to O(2) depletion caused by the hydrogen oxidizing, since the oxygen pressure in the air appears to be a limiting factor of symbiotic nitrogen fixation in the soybean.

Uptake Hydrogenase Activity Determined by Plasmid pRL6JI in Rhizobium leguminosarum Does Not Increase Symbiotic Nitrogen Fixation

Six mutants of Rhizobium leguminosarum 3855 lacking uptake hydrogenase activity (Hup phenotype) as a result of Tn5-mob mutagenesis of the hup-containing plasmid pRL6JI were tested for symbiotic performance on Pisum sativum L. and Vicia benghalensis L. Three pea cultivars and one vetch line, which induce four different levels of Hup activity in strain 3855, were grown to flowering under microbiologically controlled conditions in the absence of combined N. Direct Kjeldahl N measurements showed that in every case at least one Hup mutant fixed as much N(2) as the isogenic Hup strain. Measures of C(2)H(2) reduction, H(2) evolution, H(2) incorporation, and plant dry weight were consistent with the interpretation that the oxidation of H(2) produced by the nitrogenase enzyme complex was not necessarily associated with increased N(2) fixation in these symbiotic associations. Tests with a smaller subset of the Hup strains under four different root environments ranging from pH 5.0 to 8.2 likewise showed no significant advantage for the isogenic Hup strain. It was concluded that the improvements in symbiotic N(2) fixation produced by pRL6JI are associated with some trait other than the Hup phenotype.