Iron-Only and Vanadium Nitrogenases: Fail-Safe Enzymes or Something More?

Deciphering the Nitrogen Fixation Gene Cluster in Vibrio natriegens: A Study on Optimized Expression and Application of Nitrogenase

Microbial nitrogen fixation presents a viable alternative to chemical fertilizers, yet the limited colonization and specificity of naturally occurring nitrogen-fixing microorganisms present significant challenges to their widespread application. In this study, we identified a nitrogen fixation gene cluster (VNnif) in Vibrio natriegens (VN) and tested its nitrogenase activity through the acetylene reduction assay. We investigated the potential utilization of nitrogenase by incorporating the nitrogenase gene cluster from VN into plant growth-promoting rhizosphere bacteria Pseudomonas protegens CHA0 and enhancing its activity to 48.16 nmol C2H2/mg/h through promoter replacement and cluster rearrangement. The engineered strain CHA0-PVNnif was found to positively impact the growth of Arabidopsis thaliana col-0 and Triticum aestivum L. (wheat). This study expanded the role of plant growth-promoting rhizobacteria (PGPR) and provided a research foundation for enhancing nitrogenase activity.

Organic amendments increased Chinese milk vetch symbiotic nitrogen fixation by enriching Mesorhizobium in rhizosphere

Symbiotic nitrogen fixation of Chinese milk vetch (Astragalus sinicus L.) can fix nitrogen from the atmosphere and serve as an organic nitrogen source in agricultural ecosystems. Exogenous organic material application is a common practice of affecting symbiotic nitrogen fixation; however, the results of the regulation activities remain under discussion. Studies on the impact of organic amendments on symbiotic nitrogen fixation have focused on dissolved organic carbon content changes, whereas the impact on dissolved organic carbon composition and the underlying mechanism remain unclear. In situ pot experiments were carried out using soils from a 40-year-old field experiment platform to investigate symbiotic nitrogen fixation rate trends, dissolved organic carbon concentration and component, and diazotroph community structure in roots and in rhizosphere soils following long-term application of different exogenous organic substrates, i.e., green manure, green manure and pig manure, and green manure and rice straw. Remarkable increases in rate were observed in and when compared with that in green manure treatment, with the greatest enhancement observed in the treatment. Moreover, organic amendments, particularly pig manure application, altered diazotroph community composition in rhizosphere soils, therefore increasing the abundance of the host-specific genus Mesorhizobium. Furthermore, organic amendments influence the diazotroph communities through two primary mechanisms. Firstly, the components of dissolved organic carbon promote an increase in available iron, facilitated by the presence of humus substrates. Secondly, the elevated content of dissolved organic carbon and available iron expands the niche breadth of Mesorhizobium within the rhizosphere. Consequently, these alterations result in a modified diazotroph community within the rhizosphere, which in turn influences Mesorhizobium nodulation in the root and symbiotic nitrogen fixation rate. The results of the present study enhance our understanding of the impact of organic amendments on symbiotic nitrogen fixation and the underlying mechanism, highlighting the key role of dissolved organic carbon composition on diazotroph community composition in the rhizosphere.

Strategies to enhance biohydrogen production from microalgae: A comprehensive review

Microalgae represent a promising renewable feedstock for the sustainable production of biohydrogen. Their high growth rates and ability to fix carbon utilizing just sunlight, water, and nutrients make them well-suited for this application. Recent advancements have focused on improving microalgal hydrogen yields and cultivation methods. This review aims to summarize recent developments in microalgal cultivation techniques and genetic engineering strategies for enhanced biohydrogen production. Specific areas of focus include novel microalgal species selection, immobilization methods, integrated hybrid systems, and metabolic engineering. Studies related to microalgal strain selection, cultivation methods, metabolic engineering, and genetic manipulations were compiled and analyzed. Promising microalgal species with high hydrogen production capabilities such as Synechocystis sp., Anabaena variabilis, and Chlamydomonas reinhardtii have been identified. Immobilization techniques like encapsulation in alginate and integration with dark fermentation have led to improved hydrogen yields. Metabolic engineering through modulation of hydrogenase activity and photosynthetic pathways shows potential for enhanced biohydrogen productivity. Considerable progress has been made in developing microalgal systems for biohydrogen. However, challenges around process optimization and scale-up remain. Future work involving metabolic modeling, photobioreactor design, and genetic engineering of electron transfer pathways could help realize the full potential of this renewable technology.

Rice N-biofertilization by inoculation with an engineered photosynthetic diazotroph

Photosynthetic diazotrophs expressing iron-only (Fe-only) nitrogenase can be developed into a promising biofertilizer, as it is independent on the molybdenum availability in the soil. However, the expression of Fe-only nitrogenase in diazotrophs is repressed by the fixed nitrogen of the soil, limiting the efficiency of nitrogen fixation in farmland with low ammonium concentrations that are inadequate for sustainable crop growth. Here, we succeeded in constitutively expressing the Fe-only nitrogenase even in the presence of ammonium by controlling the transcription of Fe-only nitrogenase gene cluster (anfHDGK) with the transcriptional activator of Mo nitrogenase (NifA*) in several different ways, indicating that the engineered NifA* strains can be used as promising chassis cells for efficient expression of different types of nitrogenases. When applied as a biofertilizer, the engineered Rhodopseudomonas palustris effectively stimulated rice growth, contributing to the reduced use of chemical fertilizer and the development of sustainable agriculture.

Toxicity of VO2 micro/nanoparticles to nitrogen-fixing bacterium Azotobacter vinelandii

Vanadium dioxide (VO2) has been used in a variety of products due to its outstanding phase transition properties. However, as potential heavy metal contaminants, the environmental hazards and risks of VO2 should be systematically investigated. Biological nitrogen fixation is one of the most dominant processes in biogeochemical cycle, which is associated with nitrogen-fixing bacteria. In this study, we reported the environmental bio-effects of VO2 micro/nanoparticles on the nitrogen-fixing bacterium Azotobacter vinelandii. VO2 at 10 and 30 mg/L caused severe hazards to A. vinelandii, such as cell apoptosis, oxidative damage, physical damage, genotoxicity, and the loss of nitrogen fixation activity. The up-regulated differentially expressed genes of A. vinelandii were related to stress response, and the down-regulated genes were mainly related to energy metabolism. Surprisingly, VO2 of 10 mg/L decreased the nif gene expression but elevated the vnf gene expression, which enhanced the ability of A. vinelandii to reduce acetylene in anaerobic environment. In addition, under tested conditions, VO2 nanoparticles exhibited insignificantly higher toxicity than VO2 microparticles.

Asymmetric dinuclear, hexanuclear and octanuclear oxovanadium citrates with triazolates: novel mixed-ligands and mixed-valence complexes

The triazolate-assisted asymmetric dinuclear oxovanadium(IV) citrate [V2O2(cit)(Hdatrz)3]·5H2O (1, H4cit = citric acid, Hdatrz = 1H-1,2,4-triazole-3,5-diamine) and its additive salt [V2O2(cit)(Hdatrz)3][V2O2(cit)2]½·2H2datrz·9.5H2O (2) and the polymerized hexanuclear product [V6O6(μ3-O)2(cit)2(Hdatrz)4]·4H2O (3) have been isolated at different temperatures, respectively. Adduct 2 shows strong evidence for the conversion of a symmetric dinuclear oxovanadium(IV) citrate to a mixed-ligand asymmetric oxovanadium(IV) citrate. Moreover, a fully oxidized trinuclear vanadium(V) species [V3O6(μ2-OH)(μ3-O)(Hdatrz)2]·4.5H2O (4) has also been isolated as a quasi-intermediate product of 3 without the coordination of citrate. Intriguingly, an octanuclear mixed-valence oxovanadium(V/IV) citrate K2{[VIV/V2O2(cit)(Hdatrz)(datrz)]2[VIV2O2(cit)(Hdatrz)(datrz)]2}·27.5H2O (5) has been obtained with different vanadium units, where dinuclear mixed-ligands and mixed-valence oxovanadium(IV/V) citrates [VIV/V2O2(cit)(Hdatrz)(datrz)] (5a) and [VIV2O2(cit)(Hdatrz)(datrz)] (5b) have been trapped. Citrate adopts a μ2-η1:η1:η1:η2 coordination mode in 1, 2 and 5, while a μ3-η1:η1:η1:η2 fashion has been observed in 3. Unlike 1-4, complex 5 contains both protonated and deprotonated triazolates simultaneously, where four triazolates further coordinate in a μ3-η1:η1:η1 manner to construct an octanuclear unit. These different structural features in 1-5 are dominated by flexible multidentate citrates and protonated/deprotonated triazolates, showing their synergistic effects. Furthermore, 1 exhibits a rectangular channel, showing preferential adsorption of O2 and CO2 over gases N2, H2, and CH4.

Molecular hydrogen positively regulates nitrate uptake and seed size by targeting nitrate reductase

Although the sources of molecular hydrogen (H2) synthesis in plants remain to be fully elucidated, ample evidence shows that plant-based H2 can regulate development and stress responses. Here, we present genetic and molecular evidence indicating that nitrate reductase (NR) might be a target of H2 sensing that positively regulates nitrogen use efficiency (NUE) and seed size in Arabidopsis (Arabidopsis thaliana). The expression level of NR and changes of NUE under control and, in particular, low nitrogen supply were positively associated with H2 addition supplied exogenously or through genetic manipulation. The improvement in nitrate assimilation achieved by H2 was also mediated via NR dephosphorylation. H2 control of seed size was impaired by NR mutation. Further genetic evidence revealed that H2, NR, and nitric oxide can synergistically regulate nitrate assimilation in response to N starvation conditions. Collectively, our data indicate that NR might be a target for H2 sensing, ultimately positively regulating nitrate uptake and seed size. These results provide insights into H2 signaling and its functions in plant metabolism.

Expression of V-nitrogenase and Fe-nitrogenase in Methanosarcina acetivorans is controlled by molybdenum, fixed nitrogen, and the expression of Mo-nitrogenase

All nitrogen-fixing bacteria and archaea (diazotrophs) use molybdenum (Mo) nitrogenase to reduce dinitrogen (N2) to ammonia, with some also containing vanadium (V) and iron-only (Fe) nitrogenases that lack Mo. Among diazotrophs, the regulation and usage of the alternative V-nitrogenase and Fe-nitrogenase in methanogens are largely unknown. Methanosarcina acetivorans contains nif, vnf, and anf gene clusters encoding putative Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase, respectively. This study investigated nitrogenase expression and growth by M. acetivorans in response to fixed nitrogen, Mo/V availability, and CRISPRi repression of the nif, vnf, and/or anf gene clusters. The availability of Mo and V significantly affected growth of M. acetivorans with N2 but not with NH4Cl. M. acetivorans exhibited the fastest growth rate and highest cell yield during growth with N2 in medium containing Mo, and the slowest growth in medium lacking Mo and V. qPCR analysis revealed the transcription of the nif operon is only moderately affected by depletion of fixed nitrogen and Mo, whereas vnf and anf transcription increased significantly when fixed nitrogen and Mo were depleted, with removal of Mo being key. Immunoblot analysis revealed Mo-nitrogenase is detected when fixed nitrogen is depleted regardless of Mo availability, while V-nitrogenase and Fe-nitrogenase are detected only in the absence of fixed nitrogen and Mo. CRISPRi repression studies revealed that V-nitrogenase and/or Fe-nitrogenase are required for Mo-independent diazotrophy, and unexpectedly that the expression of Mo-nitrogenase is also required. These results reveal that alternative nitrogenase production in M. acetivorans is tightly controlled and dependent on Mo-nitrogenase expression. IMPORTANCE Methanogens and closely related methanotrophs are the only archaea known or predicted to possess nitrogenase. Methanogens play critical roles in both the global biological nitrogen and carbon cycles. Moreover, methanogens are an ancient microbial lineage and nitrogenase likely originated in methanogens. An understanding of the usage and properties of nitrogenases in methanogens can provide new insight into the evolution of nitrogen fixation and aid in the development nitrogenase-based biotechnology. This study provides the first evidence that a methanogen can produce all three forms of nitrogenases, including simultaneously. The results reveal components of Mo-nitrogenase regulate or are needed to produce V-nitrogenase and Fe-nitrogenase in methanogens, a result not seen in bacteria. Overall, this study provides a foundation to understand the assembly, regulation, and activity of the alternative nitrogenases in methanogens.

Vanadium as Auxiliary for Fe-V Dual-Atom Electrocatalyst in Lithium-Sulfur Batteries: "3D in 2D" Morphology Inducer and Coordination Structure Regulator

The undesirable shuttling behavior, the sluggish redox kinetics of liquid-solid transformation, and the large energy barrier for decomposition of Li2S have been the recognized problems impeding the practical application of lithium-sulfur batteries. Herein, inspired by the spectacular catalytic activity of the Fe/V center in bioenzyme for nitrogen/sulfur fixation, we design an integrated electrocatalyst comprising N-bridged Fe-V dual-atom active sites (Fe/V-N7) dispersed on ingenious "3D in 2D" carbon nanosheets (denoted as DAC), in which vanadium induces the laminar structure and regulates the coordination configuration of active centers simultaneously, realizing the redistribution of the 3d-orbital electrons of Fe centers. The high coupling/conjunction between Fe/V 3d electrons and S 2p electrons shows strong affinity and enhanced reactivity of DAC-Li2Sn (1 ≤ n ≤ 8) systems. Thus, DAC presents strengthened chemisorption ability toward polysulfides and significantly boosts bidirectional sulfur redox reaction kinetics, which have been evidenced theoretically and experimentally. Besides, the well-designed "3D in 2D" morphology of DAC enables uniform sulfur distribution, facilitated electron transfer, and abundant active sites exposure. Therefore, the assembled Li-S cells present outstanding cycling stability (637.3 mAh g-1 after 1000 cycles at 1 C) and high rate capability (711 mAh g-1 at 4 C) under high sulfur content (70 wt %).

Enzymatic Fischer-Tropsch-Type Reactions

The Fischer-Tropsch (FT) process converts a mixture of CO and H2 into liquid hydrocarbons as a major component of the gas-to-liquid technology for the production of synthetic fuels. Contrary to the energy-demanding chemical FT process, the enzymatic FT-type reactions catalyzed by nitrogenase enzymes, their metalloclusters, and synthetic mimics utilize H+ and e- as the reducing equivalents to reduce CO, CO2, and CN- into hydrocarbons under ambient conditions. The C1 chemistry exemplified by these FT-type reactions is underscored by the structural and electronic properties of the nitrogenase-associated metallocenters, and recent studies have pointed to the potential relevance of this reactivity to nitrogenase mechanism, prebiotic chemistry, and biotechnological applications. This review will provide an overview of the features of nitrogenase enzymes and associated metalloclusters, followed by a detailed discussion of the activities of various nitrogenase-derived FT systems and plausible mechanisms of the enzymatic FT reactions, highlighting the versatility of this unique reactivity while providing perspectives onto its mechanistic, evolutionary, and biotechnological implications.

Mineral-Bound Trace Metals as Cofactors for Anaerobic Biological Nitrogen Fixation

Nitrogenase is the only known biological enzyme capable of reducing N₂ to bioavailable NH₃. Most nitrogenases use Mo as a metallocofactor, while alternative cofactors V and Fe are also viable. Both geological and bioinformatic evidence suggest an ancient origin of Mo-based nitrogenase in the Archean, despite the low concentration of dissolved Mo in the Archean oceans. This apparent paradox would be resolvable if mineral-bound Mo were bioavailable for nitrogen fixation by ancient diazotrophs. In this study, the bioavailability of mineral-bound Mo, V, and Fe was determined by incubating an obligately anaerobic diazotroph Clostridium kluyveri with Mo-, V-, and Fe-bearing minerals (molybdenite, cavansite, and ferrihydrite, respectively) and basalt under diazotrophic conditions. The results showed that C. kluyveri utilized mineral-associated metals to express nitrogenase genes and fix nitrogen, as measured by the reverse transcription quantitative polymerase chain reaction and acetylene reduction assay, respectively. C. kluyveri secreted chelating molecules to extract metals from the minerals. As a result of microbial weathering, mineral surface chemistry significantly changed, likely due to surface coating by microbial exudates for metal extraction. These results provide important support for the ancient origin of Mo-based nitrogenase, with profound implications for coevolution of the biosphere and geosphere.

Enigmatic evolution of microbial nitrogen fixation: insights from Earth's past

The evolution of nitrogen fixation undoubtedly altered nearly all corners of the biosphere, given the essential role of nitrogen in the synthesis of biomass. To date, there is no unified view on what planetary conditions gave rise to nitrogen fixation or how these conditions have sustained it evolutionarily. Intriguingly, the concentrations of metals that nitrogenases require to function have changed throughout Earth's history. In this review, we describe the interconnection of the metal and nitrogen cycles with nitrogenase evolution and the importance of ancient ecology in the formation of the modern nitrogen cycle. We argue that exploration of the nitrogen cycle's deep past will provide insights into humanity's immediate environmental challenges centered on nitrogen availability.

Engineering Nitrogenases for Synthetic Nitrogen Fixation: From Pathway Engineering to Directed Evolution

Globally, agriculture depends on industrial nitrogen fertilizer to improve crop growth. Fertilizer production consumes fossil fuels and contributes to environmental nitrogen pollution. A potential solution would be to harness nitrogenases-enzymes capable of converting atmospheric nitrogen N2 to NH3 in ambient conditions. It is therefore a major goal of synthetic biology to engineer functional nitrogenases into crop plants, or bacteria that form symbiotic relationships with crops, to support growth and reduce dependence on industrially produced fertilizer. This review paper highlights recent work toward understanding the functional requirements for nitrogenase expression and manipulating nitrogenase gene expression in heterologous hosts to improve activity and oxygen tolerance and potentially to engineer synthetic symbiotic relationships with plants.

The elements of life: A biocentric tour of the periodic table

Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.

Molecular Mechanism and Agricultural Application of the NifA-NifL System for Nitrogen Fixation

Nitrogen-fixing bacteria execute biological nitrogen fixation through nitrogenase, converting inert dinitrogen (N₂) in the atmosphere into bioavailable nitrogen. Elaborating the molecular mechanisms of orderly and efficient biological nitrogen fixation and applying them to agricultural production can alleviate the "nitrogen problem". Azotobacter vinelandii is a well-established model bacterium for studying nitrogen fixation, utilizing nitrogenase encoded by the nif gene cluster to fix nitrogen. In Azotobacter vinelandii, the NifA-NifL system fine-tunes the nif gene cluster transcription by sensing the redox signals and energy status, then modulating nitrogen fixation. In this manuscript, we investigate the transcriptional regulation mechanism of the nif gene in autogenous nitrogen-fixing bacteria. We discuss how autogenous nitrogen fixation can better be integrated into agriculture, providing preliminary comprehensive data for the study of autogenous nitrogen-fixing regulation.

Quantification of biological nitrogen fixation by Mo-independent complementary nitrogenases in environmental samples with low nitrogen fixation activity

Biological nitrogen fixation (BNF) by canonical molybdenum and complementary vanadium and iron-only nitrogenase isoforms is the primary natural source of newly fixed nitrogen. Understanding controls on global nitrogen cycling requires knowledge of the isoform responsible for environmental BNF. The isotopic acetylene reduction assay (ISARA), which measures carbon stable isotope (¹³C/¹²C) fractionation between ethylene and acetylene in acetylene reduction assays, is one of the few methods that can quantify isoform-specific BNF fluxes. Application of classical ISARA has been challenging because environmental BNF activity is often too low to generate sufficient ethylene for isotopic analyses. Here we describe a high sensitivity method to measure ethylene δ¹³C by in-line coupling of ethylene preconcentration to gas chromatography-combustion-isotope ratio mass spectrometry (EPCon-GC-C-IRMS). Ethylene requirements in samples with 10% v/v acetylene are reduced from > 500 to ~ 20 ppmv (~ 2 ppmv with prior offline acetylene removal). To increase robustness by reducing calibration error, single nitrogenase-isoform Azotobacter vinelandii mutants and environmental sample assays rely on a common acetylene source for ethylene production. Application of the Low BNF activity ISARA (LISARA) method to low nitrogen-fixing activity soils, leaf litter, decayed wood, cryptogams, and termites indicates complementary BNF in most sample types, calling for additional studies of isoform-specific BNF.

Alternative nitrogenase of Paenibacillus sonchi genomovar Riograndensis: An insight in the origin of Fe-nitrogenase in the Paenibacillaceae family

Paenibacillus sonchi genomovar Riograndensis is a nitrogen-fixing bacteria isolated from wheat that displays diverse plant growth-promoting abilities. Beyond conventional Mo-nitrogenase, this organism also harbors an alternative Fe-nitrogenase, whose many aspects related to regulation, physiology, and evolution remain to be elucidated. In this work, the origins of this alternative system were investigated, exploring the distribution and diversification of nitrogenases in the Panibacillaceae family. Our analysis showed that diazotrophs represent 17% of Paenibacillaceae genomes, of these, only 14.4% (2.5% of all Paenibacillaceae genomes) also contained Fe or V- nitrogenases. Diverse nif-like sequences were also described, occurring mainly in genomes that also harbor the alternative systems. The analysis of genomes containing Fe-nitrogenase showed a conserved cluster of nifEN anfHDGK across three genera: Gorillibacterium, Fontibacillus, and Paenibacillus. A phylogeny of anfHDGK separated the Fe-nitrogenases into three main groups. Our analysis suggested that Fe-nitrogenase was acquired by the ancestral lineage of Fontibacillus, Gorillibacterium, and Paenibacillus genera via horizontal gene transfer (HGT), and further events of transfer and gene loss marked the evolution of this alternative nitrogenase in these groups. The species phylogeny of N-fixing Paenibacillaceae separated the diazotrophs into five clades, one of these containing all occurrences of strains harboring alternative nitrogenases in the Paenibacillus genus. The pangenome of this clade is open and composed of more than 96% of accessory genes. Diverse functional categories were enriched in the flexible genome, including functions related to replication and repair. The latter involved diverse genes related to HGT, suggesting that such events may have an important role in the evolution of diazotrophic Paenibacillus. This study provided an insight into the organization, distribution, and evolution of alternative nitrogenase genes in Paenibacillaceae, considering different genomic aspects.

Genome-Resolved Metagenomics Informs the Functional Ecology of Uncultured Acidobacteria in Redox Oscillated Sphagnum Peat

Understanding microbial niche differentiation along ecological and geochemical gradients is critical for assessing the mechanisms of ecosystem response to hydrologic variation and other aspects of global change. The lineage-specific biogeochemical roles of the widespread phylum Acidobacteria in hydrologically sensitive ecosystems, such as peatlands, are poorly understood. Here, we demonstrate that Acidobacteria sublineages in Sphagnum peat respond differentially to redox fluctuations due to variable oxygen (O₂) availability, a typical feature of hydrologic variation. Our genome-centric approach disentangles the mechanisms of niche differentiation between the Acidobacteria genera Holophaga and Terracidiphilus in response to the transient O₂ exposure of peat in laboratory incubations. Interlineage functional diversification explains the enrichment of the otherwise rare Holophaga in anoxic peat after transient O₂ exposure in comparison to Terracidiphilus dominance in continuously anoxic peat. The observed niche differentiation of the two lineages is linked to differences in their carbon degradation potential. Holophaga appear to be primarily reliant on carbohydrate oligomers and amino acids, produced during the prior period of O₂ exposure via the O₂-stimulated breakdown of peat carbon, rich in complex aromatics and carbohydrate polymers. In contrast, Terracidiphilus genomes are enriched in diverse respiratory hydrogenases and carbohydrate active enzymes, enabling the degradation of complex plant polysaccharides into monomers and oligomers for fermentation. We also present the first evidence for the potential contribution of Acidobacteria in peat nitrogen fixation. In addition to canonical molybdenum-based diazotrophy, the Acidobacteria genomes harbor vanadium and iron-only alternative nitrogenases. Together, the results better inform the different functional roles of Acidobacteria in peat biogeochemistry under global change. IMPORTANCE Acidobacteria are among the most widespread and abundant members of the soil bacterial community, yet their ecophysiology remains largely underexplored. In acidic peat systems, Acidobacteria are thought to perform key biogeochemical functions, yet the mechanistic links between the phylogenetic and metabolic diversity within this phylum and peat carbon transformations remain unclear. Here, we employ genomic comparisons of Acidobacteria subgroups enriched in laboratory incubations of peat under variable O₂ availability to disentangle the lineage-specific functional roles of these microorganisms in peat carbon transformations. Our genome-centric approach reveals that the diversification of Acidobacteria subpopulations across transient O₂ exposure is linked to differences in their carbon substrate preferences. We also identify a previously unknown functional potential for biological nitrogen fixation in these organisms. This has important implications for carbon, nitrogen, and trace metal cycling in peat systems.

Nitrogenase Cofactor Maturase NifB Isolated from Transgenic Rice is Active in FeMo-co Synthesis

The engineering of nitrogen fixation in plants requires assembly of an active prokaryotic nitrogenase complex, which is yet to be achieved. Nitrogenase biogenesis relies on NifB, which catalyzes the formation of the [8Fe-9S-C] metal cluster NifB-co. This is the first committed step in the biosynthesis of the iron-molybdenum cofactor (FeMo-co) found at the nitrogenase active site. The production of NifB in plants is challenging because this protein is often insoluble in eukaryotic cells, and its [Fe-S] clusters are extremely unstable and sensitive to O₂. As a first step to address this challenge, we generated transgenic rice plants expressing NifB from the Archaea Methanocaldococcus infernus and Methanothermobacter thermautotrophicus. The recombinant proteins were targeted to the mitochondria to limit exposure to O₂ and to have access to essential [4Fe-4S] clusters required for NifB-co biosynthesis. M. infernus and M. thermautotrophicus NifB accumulated as soluble proteins in planta, and the purified proteins were functional in the in vitro FeMo-co synthesis assay. We thus report NifB protein expression and purification from an engineered staple crop, representing a first step in the biosynthesis of a functional NifDK complex, as required for independent biological nitrogen fixation in cereals.

Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments

Microbially mediated nitrogen cycling in carbon-dominated cold seep environments remains poorly understood. So far anaerobic methanotrophic archaea (ANME-2) and their sulfate-reducing bacterial partners (SEEP-SRB1 clade) have been identified as diazotrophs in deep sea cold seep sediments. However, it is unclear whether other microbial groups can perform nitrogen fixation in such ecosystems. To fill this gap, we analyzed 61 metagenomes, 1428 metagenome-assembled genomes, and six metatranscriptomes derived from 11 globally distributed cold seeps. These sediments contain phylogenetically diverse nitrogenase genes corresponding to an expanded diversity of diazotrophic lineages. Diverse catabolic pathways were predicted to provide ATP for nitrogen fixation, suggesting diazotrophy in cold seeps is not necessarily associated with sulfate-dependent anaerobic oxidation of methane. Nitrogen fixation genes among various diazotrophic groups in cold seeps were inferred to be genetically mobile and subject to purifying selection. Our findings extend the capacity for diazotrophy to five candidate phyla (Altarchaeia, Omnitrophota, FCPU426, Caldatribacteriota and UBA6262), and suggest that cold seep diazotrophs might contribute substantially to the global nitrogen balance.

Microbial nitrogen fixation could be important in the deep sea. Here the authors investigate metagenomes and metatranscriptomes of diazotrophs from deep sea cold seep sediments, reveal greater phylogenetic and functional diversity than hitherto known.

Nitrogen fixation and other biogeochemically important features of Atacama Desert giant horsetail plant microbiomes inferred from metagenomic contig analysis

BACKGROUND AND AIMS

Canyon stream beds in the hyperarid Atacama Desert surprisingly harbour magnificent groves of endemic giant horsetail wetland plants, Equisetum xylochaetum. Our previous metagenomic study of eukaryotes closely associated with this plant indicated that the microbiome included prokaryotes that might likewise influence host success and environment. We explored this possibility by using the metagenomic sequence to characterize prokaryote taxa and functional genes present in the microbiome of E. xylochaetum sampled from remote sites differing in the degree of anthropogenic disturbance. We focused on biogeochemical functions known to be important in wetland ecosystems.

METHODS

To ensure that analyses were conducted on microbes most closely associated with plants, we extracted DNA from well-washed plant organs whose microbial biofilms were revealed with scanning electron microscopy. To assess the benefits of longer sequences for taxonomic and gene classifications, results of analyses performed using contigs were compared with those obtained with unassembled reads. We employed methods widely used to estimate genomic coverage of single taxa for genomic analysis to infer relative abundances of taxa and functional genes.

KEY RESULTS

Key functional bacterial genera (e.g. Hydrogenophaga, Sulfuritalea and Rhodoferax) inferred from taxonomic and functional gene analysis of contigs - but not unassembled reads - to occur on surfaces of (or within) plants at relatively high abundance (>50× genomic coverage) indicated roles in nitrogen, sulfur and other mineral cycling processes. Comparison between sites revealed impacts on biogeochemical functions, e.g. reduced levels of the nifH gene marker under disturbance. Vanadium nitrogenases were more important than molybdenum nitrogenases, indicated by both functional genes and taxa such as Rhodomicrobium and Phaeospirillum inferred from contigs but not unassembled reads.

CONCLUSIONS

Our contig-based metagenomic analyses revealed that microbes performing key wetland biogeochemical functions occur as tightly adherent biofilms on the plant body, not just in water or sediments, and that disturbance reduces such functions, providing arguments for conservation efforts.

Functional Nitrogenase Cofactor Maturase NifB in Mitochondria and Chloroplasts of Nicotiana benthamiana

Engineering plants to synthesize nitrogenase and assimilate atmospheric N2 will reduce crop dependency on industrial N fertilizers. This technology can be achieved by expressing prokaryotic nitrogen fixation gene products for the assembly of a functional nitrogenase in plants. NifB is a critical nitrogenase component since it catalyzes the first committed step in the biosynthesis of all types of nitrogenase active-site cofactors. Here, we used a library of 30 distinct nifB sequences originating from different phyla and ecological niches to restore diazotrophic growth of an Azotobacter vinelandii nifB mutant. Twenty of these variants rescued the nifB mutant phenotype despite their phylogenetic distance to A. vinelandii. Because multiple protein interactions are required in the iron-molybdenum cofactor (FeMo-co) biosynthetic pathway, the maturation of nitrogenase in a heterologous host can be divided in independent modules containing interacting proteins that function together to produce a specific intermediate. Therefore, nifB functional modules composed of a nifB variant, together with the A. vinelandii NifS and NifU proteins (for biosynthesis of NifB [Fe4S4] clusters) and the FdxN ferredoxin (for NifB function), were expressed in Nicotiana benthamiana chloroplasts and mitochondria. Three archaeal NifB proteins accumulated at high levels in soluble fractions of chloroplasts (Methanosarcina acetivorans and Methanocaldococcus infernus) or mitochondria (M. infernus and Methanothermobacter thermautotrophicus). These NifB proteins were shown to accept [Fe4S4] clusters from NifU and were functional in FeMo-co synthesis in vitro. The accumulation of significant levels of soluble and functional NifB proteins in chloroplasts and mitochondria is critical to engineering biological nitrogen fixation in plants. IMPORTANCE Biological nitrogen fixation is the conversion of inert atmospheric dinitrogen gas into nitrogen-reactive ammonia, a reaction catalyzed by the nitrogenase enzyme of diazotrophic bacteria and archaea. Because plants cannot fix their own nitrogen, introducing functional nitrogenase in cereals and other crop plants would reduce our strong dependency on N fertilizers. NifB is required for the biosynthesis of the active site cofactors of all nitrogenases, which arguably makes it the most important protein in global nitrogen fixation. NifB functionality is therefore a requisite to engineer a plant nitrogenase. The expression of nifB genes from a wide range of prokaryotes into the model diazotroph Azotobacter vinelandii shows a surprising level of genetic complementation suggestive of plasticity in the nitrogenase biosynthetic pathway. In addition, we obtained NifB proteins from both mitochondria and chloroplasts of tobacco that are functional in vitro after reconstitution by providing [Fe4S4] clusters from NifU, paving the way to nitrogenase cofactor biosynthesis in plants.

Characteristics and Application of Rhodopseudomonas palustris as a Microbial Cell Factory

Rhodopseudomonas palustris, a purple nonsulfur bacterium, is a bacterium with the properties of extraordinary metabolic versatility, carbon source diversity and metabolite diversity. Due to its biodetoxification and biodegradation properties, R. palustris has been traditionally applied in wastewater treatment and bioremediation. R. palustris is rich in various metabolites, contributing to its application in agriculture, aquaculture and livestock breeding as additives. In recent years, R. palustris has been engineered as a microbial cell factory to produce valuable chemicals, especially photofermentation of hydrogen. The outstanding property of R. palustris as a microbial cell factory is its ability to use a diversity of carbon sources. R. palustris is capable of CO₂ fixation, contributing to photoautotrophic conversion of CO₂ into valuable chemicals. R. palustris can assimilate short-chain organic acids and crude glycerol from industrial and agricultural wastewater. Lignocellulosic biomass hydrolysates can also be degraded by R. palustris. Utilization of these feedstocks can reduce the industry cost and is beneficial for environment. Applications of R. palustris for biopolymers and their building blocks production, and biofuels production are discussed. Afterward, some novel applications in microbial fuel cells, microbial electrosynthesis and photocatalytic synthesis are summarized. The challenges of the application of R. palustris are analyzed, and possible solutions are suggested.

Genomic Features of the Bundle-Forming Heliobacterium Heliophilum fasciatum

Eight species of heliobacteria have had their genomes sequenced. However, only two of these genomes have been analyzed in detail, those from the thermophilic Heliomicrobium (Hmi.) modesticaldum and the alkaliphilic Heliorestis (Hrs.) convoluta. Here we present analyses of the draft genome sequence of a species of heliobacterium that grows optimally at a moderate temperature and neutral pH. The organism, Heliophilum (Hph.) fasciatum, is phylogenetically unique among cultured heliobacteria and was isolated from rice soil, a common habitat for heliobacteria. The Hph. fasciatum genome contains 3.14 Mbp—similar to that of other reported heliobacteria—but has a G+C base ratio that lies between that of Hmi. modesticaldum and Hrs. convoluta. Many of the genomic features of Hmi. modesticaldum and Hrs. convoluta, such as the absence of genes encoding autotrophic pathways, the presence of a superoperonal cluster of photosynthesis-related genes, and genes encoding endospore-specific proteins, are also characteristic of the Hph. fasciatum genome. However, despite the fact that Hph. fasciatum is diazotrophic, classical nif genes encoding the alpha and beta subunits of dinitrogenase (nifDK) present in other heliobacteria could not be identified. Instead, genes encoding several highly divergent NifDK homologs were present, at least one of which likely encodes a functional dinitrogenase and another a methylthio-alkane reductase (MarDK) for sulfur assimilation. A classical NifH (dinitrogenase reductase) homolog was also absent in Hph. fasciatum, but a related protein was identified that likely carries out this function as well as electron delivery to MarDK. The N₂-fixing system of Hph. fasciatum is therefore distinct from that of other heliobacteria and may have unusual properties.

Potential of Phototrophic Purple Nonsulfur Bacteria to Fix Nitrogen in Rice Fields

Biological nitrogen fixation catalyzed by Mo-nitrogenase of symbiotic diazotrophs has attracted interest because its potential to supply plant-available nitrogen offers an alternative way of using chemical fertilizers for sustainable agriculture. Phototrophic purple nonsulfur bacteria (PNSB) diazotrophically grow under light anaerobic conditions and can be isolated from photic and microaerobic zones of rice fields. Therefore, PNSB as asymbiotic diazotrophs contribute to nitrogen fixation in rice fields. An attempt to measure nitrogen in the oxidized surface layer of paddy soil estimates that approximately 6–8 kg N/ha/year might be accumulated by phototrophic microorganisms. Species of PNSB possess one of or both alternative nitrogenases, V-nitrogenase and Fe-nitrogenase, which are found in asymbiotic diazotrophs, in addition to Mo-nitrogenase. The regulatory networks control nitrogenase activity in response to ammonium, molecular oxygen, and light irradiation. Laboratory and field studies have revealed effectiveness of PNSB inoculation to rice cultures on increases of nitrogen gain, plant growth, and/or grain yield. In this review, properties of the nitrogenase isozymes and regulation of nitrogenase activities in PNSB are described, and research challenges and potential of PNSB inoculation to rice cultures are discussed from a viewpoint of their applications as nitrogen biofertilizer.

Mechanisms underlying Clostridium pasteurianum's metabolic shift when grown with Geobacter sulfurreducens

Recently, a study showed that glycerol fermentation by Clostridium pasteurianum could be metabolically redirected when the electroactive bacterium Geobacter sulfurreducens was added in the culture. It was assumed that this metabolic shift of the fermentative species resulted from an interspecies electron transfer. The aim of this study was to find out the mechanisms used for this interaction and how they affect the metabolism of C. pasteurianum. To get insights into the mechanisms involved, several coculture setups and RNA sequencing with differential expression analysis were performed. As a result, a putative interaction model was proposed: G. sulfurreducens produces cobamide molecules that possibly modify C. pasteurianum metabolic pathway at the key enzyme glycerol dehydratase, and affect its vanadium nitrogenase expression. In addition, the results suggested that G. sulfurreducens' electrons could enter C. pasteurianum through its transmembrane flavin-bound polyferredoxin and cellular cytochrome b5-rubredoxin interplay, putatively reinforcing the metabolic shift. Unravelling the mechanisms behind the interaction between fermentative and electroactive bacteria helps to better understand the role of bacterial interactions in fermentation setups. KEY POINTS: • C. pasteurianum-G. sulfurreducens interaction inducing a metabolic shift is mediated • C. pasteurianum's metabolic shift in coculture might be induced by cobamides • Electrons possibly enter C. pasteurianum through a multiflavin polyferredoxin.

The Conversion of Carbon Monoxide and Carbon Dioxide by Nitrogenases

Nitrogenases are the only known family of enzymes that catalyze the reduction of molecular nitrogen (N₂) to ammonia (NH₃). The N₂ reduction drives biological nitrogen fixation and the global nitrogen cycle. Besides the conversion of N₂, nitrogenases catalyze a whole range of other reductions, including the reduction of the small gaseous substrates carbon monoxide (CO) and carbon dioxide (CO₂) to hydrocarbons. However, it remains an open question whether these ‘side reactivities’ play a role under environmental conditions. Nonetheless, these reactivities and particularly the formation of hydrocarbons have spurred the interest in nitrogenases for biotechnological applications. There are three different isozymes of nitrogenase: the molybdenum and the alternative vanadium and iron‐only nitrogenase. The isozymes differ in their metal content, structure, and substrate‐dependent activity, despite their homology. This minireview focuses on the conversion of CO and CO₂ to methane and higher hydrocarbons and aims to specify the differences in activity between the three nitrogenase isozymes.

Vanadium(V) Complexes with Siderophore Vitamin E-Hydroxylamino-Triazine Ligands

Novel vitamin E chelate siderophore derivatives and their VV and FeIII complexes have been synthesised and the chemical and biological properties have been evaluated. In particular, the α- and δ-tocopherol derivatives with bis-methyldroxylamino triazine (α-tocTHMA) and (δ-tocDPA) as well their VV complexes, [V2VO3(α-tocTHMA)2] and [V2IVO3(δ-tocTHMA)2], have been synthesised and characterised by infrared (IR), nuclear magnetic resonance (NMR), electron paramagnetic resonance (EPR) and ultra violet-visible (UV-Vis) spectroscopies. The dimeric vanadium complexes in solution are in equilibrium with their respefrctive monomers, H2O + [V2VO2(μ-O)]4+ = 2 [VVO(OH)]2+. The two amphiphilic vanadium complexes exhibit enhanced hydrolytic stability. EPR shows that the complexes in lipophilic matrix are mild radical initiators. Evaluation of their biological activity shows that the compounds do not exhibit any significant cytotoxicity to cells.

Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue

Biological N₂ fixation was key to the expansion of life on early Earth. The N₂-fixing microorganisms and the nitrogenase type used in the Proterozoic are unknown, although it has been proposed that the canonical molybdenum-nitrogenase was not used due to low molybdenum availability. We investigate N₂ fixation in Lake Cadagno, an analogue system to the sulfidic Proterozoic continental margins, using a combination of biogeochemical, molecular and single cell techniques. In Lake Cadagno, purple sulfur bacteria (PSB) are responsible for high N₂ fixation rates, to our knowledge providing the first direct evidence for PSB in situ N₂ fixation. Surprisingly, no alternative nitrogenases are detectable, and N₂ fixation is exclusively catalyzed by molybdenum-nitrogenase. Our results show that molybdenum-nitrogenase is functional at low molybdenum conditions in situ and that in contrast to previous beliefs, PSB may have driven N₂ fixation in the Proterozoic ocean.

Functional analysis of multiple nifB genes of Paenibacillus strains in synthesis of Mo-, Fe- and V-nitrogenases

Background

Biological nitrogen fixation is catalyzed by Mo-, V- and Fe-nitrogenases that are encoded by nif, vnf and anf genes, respectively. NifB is the key protein in synthesis of the cofactors of all nitrogenases. Most diazotrophic Paenibacillus strains have only one nifB gene located in a compact nif gene cluster (nifBHDKENX(orf1)hesAnifV). But some Paenibacillus strains have multiple nifB genes and their functions are not known.

Results

A total of 138 nifB genes are found in the 116 diazotrophic Paenibacillus strains. Phylogeny analysis shows that these nifB genes fall into 4 classes: nifBI class including the genes (named as nifB1 genes) that are the first gene within the compact nif gene cluster, nifBII class including the genes (named as nifB2 genes) that are adjacent to anf or vnf genes, nifBIII class whose members are designated as nifB3 genes and nifBIV class whose members are named as nifB4 genes are scattered on genomes. Functional analysis by complementation of the ∆nifB mutant of P. polymyxa which has only one nifB gene has shown that both nifB1 and nifB2 are active in synthesis of Mo-nitrogenase, while nifB3 and nifB4 genes are not. Deletion analysis also has revealed that nifB1 of Paenibacillus sabinae T27 is involved in synthesis of Mo-nitrogenase, while nifB3 and nifB4 genes are not. Complementation of the P. polymyxa ∆nifBHDK mutant with the four reconstituted operons: nifB1anfHDGK, nifB2anfHDGK, nifB1vnfHDGK and nifB2vnfHDGK, has shown both that nifB1 and nifB2 were able to support synthesis of Fe- or V-nitrogenases. Transcriptional results obtained in the original Paenibacillus strains are consistent with the complementation results.

Conclusions

The multiple nifB genes of the diazotrophic Paenibacillus strains are divided into 4 classes. The nifB1 located in a compact nif gene cluster (nifBHDKENX(orf1)hesAnifV) and the nifB2 genes being adjacent to nif or anf or vnf genes are active in synthesis of Mo-, Fe and V-nitrogenases, but nifB3 and nifB4 are not. The reconstituted anf system comprising 8 genes (nifBanfHDGK and nifXhesAnifV) and vnf system comprising 10 genes (nifBvnfHDGKEN and nifXhesAnifV) support synthesis of Fe-nitrogenase and V-nitrogenase in Paenibacillus background, respectively.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01629-9.

Exploring the Role of the Central Carbide of the Nitrogenase Active-Site FeMo-cofactor through Targeted 13C Labeling and ENDOR Spectroscopy

Mo-dependent nitrogenase is a major contributor to global biological N₂ reduction, which sustains life on Earth. Its multi-metallic active-site FeMo-cofactor (Fe₇MoS₉C-homocitrate) contains a carbide (C^4-) centered within a trigonal prismatic CFe₆ core resembling the structural motif of the iron carbide, cementite. The role of the carbide in FeMo-cofactor binding and activation of substrates and inhibitors is unknown. To explore this role, the carbide has been in effect selectively enriched with ¹³C, which enables its detailed examination by ENDOR/ESEEM spectroscopies. ¹³C-carbide ENDOR of the S = 3/2 resting state (E₀) is remarkable, with an extremely small isotropic hyperfine coupling constant, ^Ca = +0.86 MHz. Turnover under high CO partial pressure generates the S = 1/2 hi-CO state, with two CO molecules bound to FeMo-cofactor. This conversion surprisingly leaves the small magnitude of the ¹³C carbide isotropic hyperfine-coupling constant essentially unchanged, ^Ca = -1.30 MHz. This indicates that both the E₀ and hi-CO states exhibit an exchange-coupling scheme with nearly cancelling contributions to ^Ca from three spin-up and three spin-down carbide-bound Fe ions. In contrast, the anisotropic hyperfine coupling constant undergoes a symmetry change upon conversion of E₀ to hi-CO that may be associated with bonding and coordination changes at Fe ions. In combination with the negligible difference between CFe₆ core structures of E₀ and hi-CO, these results suggest that in CO-inhibited hi-CO the dominant role of the FeMo-cofactor carbide is to maintain the core structure, rather than to facilitate inhibitor binding through changes in Fe-carbide covalency or stretching/breaking of carbide-Fe bonds.

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.

Ferric iron reductases and their contribution to unicellular ferrous iron uptake

Iron is a necessary element for nearly all forms of life, and the ability to acquire this trace nutrient has been identified as a key virulence factor for the establishment of infection by unicellular pathogens. In the presence of O2, iron typically exists in the ferric (Fe3+) oxidation state, which is highly unstable in aqueous conditions, necessitating its sequestration into cofactors and/or host proteins to remain soluble. To counter this insolubility, and to compete with host sequestration mechanisms, many unicellular pathogens will secrete low molecular weight, high-affinity Fe3+ chelators known as siderophores. Once acquired, unicellular pathogens must liberate the siderophore-bound Fe3+ in order to assimilate this nutrient into metabolic pathways. While these organisms may hydrolyze the siderophore backbone to release the chelated Fe3+, this approach is energetically costly. Instead, iron may be liberated from the Fe3+-siderophore complex through reduction to Fe2+, which produces a lower-affinity form of iron that is highly soluble. This reduction is performed by a class of enzymes known as ferric reductases. Ferric reductases are broadly-distributed electron-transport proteins that are expressed by numerous infectious organisms and are connected to the virulence of unicellular pathogens. Despite this importance, ferric reductases remain poorly understood. This review provides an overview of our current understanding of unicellular ferric reductases (both soluble and membrane-bound), with an emphasis on the important but underappreciated connection between ferric-reductase mediated Fe3+ reduction and the transport of Fe2+ via ferrous iron transporters.

The electronic structure of FeV-cofactor in vanadium-dependent nitrogenase

The electronic structure of the active-site metal cofactor (FeV-cofactor) of resting-state V-dependent nitrogenase has been an open question, with earlier studies indicating that it exhibits a broad S = 3/2 EPR signal (Kramers state) having g values of ∼4.3 and 3.8, along with suggestions that it contains metal-ions with valencies [1V3+, 3Fe3+, 4Fe2+]. In the present work, genetic, biochemical, and spectroscopic approaches were combined to reveal that the EPR signals previously assigned to FeV-cofactor do not correlate with active VFe-protein, and thus cannot arise from the resting-state of catalytically relevant FeV-cofactor. It, instead, appears resting-state FeV-cofactor is either diamagnetic, S = 0, or non-Kramers, integer-spin (S = 1, 2 etc.). When VFe-protein is freeze-trapped during high-flux turnover with its natural electron-donating partner Fe protein, conditions which populate reduced states of the FeV-cofactor, a new rhombic S = 1/2 EPR signal from such a reduced state is observed, with g = [2.18, 2.12, 2.09] and showing well-defined 51V (I = 7/2) hyperfine splitting, a iso = 110 MHz. These findings indicate a different assignment for the electronic structure of the resting state of FeV-cofactor: S = 0 (or integer-spin non-Kramers state) with metal-ion valencies, [1V3+, 4Fe3+, 3Fe2+]. Our findings suggest that the V3+ does not change valency throughout the catalytic cycle.

Large Hydrogen Isotope Fractionation Distinguishes Nitrogenase-Derived Methane from Other Methane Sources

Biological nitrogen fixation is catalyzed by the enzyme nitrogenase. Two forms of this metalloenzyme, the vanadium (V)- and iron (Fe)-only nitrogenases, were recently found to reduce small amounts of carbon dioxide (CO2) into the potent greenhouse gas methane (CH4). Here, we report carbon (13C/12C) and hydrogen (2H/1H) stable isotopic compositions and fractionations of methane generated by V- and Fe-only nitrogenases in the metabolically versatile nitrogen fixer Rhodopseudomonas palustris The stable carbon isotope fractionation imparted by both forms of alternative nitrogenase are within the range observed for hydrogenotrophic methanogenesis (13αCO2/CH4 = 1.051 ± 0.002 for V-nitrogenase and 1.055 ± 0.001 for Fe-only nitrogenase; values are means ± standard errors). In contrast, the hydrogen isotope fractionations (2αH2O/CH4 = 2.071 ± 0.014 for V-nitrogenase and 2.078 ± 0.018 for Fe-only nitrogenase) are the largest of any known biogenic or geogenic pathway. The large 2αH2O/CH4 shows that the reaction pathway nitrogenases use to form methane strongly discriminates against 2H, and that 2αH2O/CH4 distinguishes nitrogenase-derived methane from all other known biotic and abiotic sources. These findings on nitrogenase-derived methane will help constrain carbon and nitrogen flows in microbial communities and the role of the alternative nitrogenases in global biogeochemical cycles.IMPORTANCE All forms of life require nitrogen for growth. Many different kinds of microbes living in diverse environments make inert nitrogen gas from the atmosphere bioavailable using a special enzyme, nitrogenase. Nitrogenase has a wide substrate range, and, in addition to producing bioavailable nitrogen, some forms of nitrogenase also produce small amounts of the greenhouse gas methane. This is different from other microbes that produce methane to generate energy. Until now, there was no good way to determine when microbes with nitrogenases are making methane in nature. Here, we present an isotopic fingerprint that allows scientists to distinguish methane from microbes making it for energy versus those making it as a by-product of nitrogen acquisition. With this new fingerprint, it will be possible to improve our understanding of the relationship between methane production and nitrogen acquisition in nature.