Biosynthesis of the iron-molybdenum cofactor of nitrogenase

Investigation of the Cyanothece nitrogenase cluster in Synechocystis: a blueprint for engineering nitrogen-fixing photoautotrophs

The nitrogenase gene cluster of unicellular diazotrophic cyanobacteria, such as Cyanothece, is frequently selected by nature for nitrogen-fixing partnerships with eukaryotic phototrophs. The essential cluster components that confer an advantage in such partnerships remain underexplored. To use this cluster for the development of synthetic, phototrophic nitrogen-fixing systems, a thorough and systematic analysis of its constituent genes is necessary. An initial effort to assess the possibility of engineering this cluster into non-diazotrophic phototrophs led to the generation of a Synechocystis 6803 strain with significant nitrogenase activity. In the current study, a refactoring approach was taken to determine the dispensability of the non-structural genes in the cluster and define a minimal gene set for constructing a functional nitrogenase for phototrophs. Using a bottom-up strategy, the nif genes from Cyanothece 51142 were re-organized to form new operons. The genes were then seamlessly removed to determine their essentiality in the nitrogen fixation process. We demonstrate that besides the structural genes nifHDK, nifBSUENPVZTXW, as well as hesAB, are important for optimal nitrogenase function in a phototroph. We also show that optimal expression of these genes is crucial for efficient nitrogenase activity. Our findings provide a solid foundation for generating synthetic systems that will facilitate solar-powered conversion of atmospheric nitrogen into nitrogen-rich compounds, a stride toward a greener world.IMPORTANCEIntegrating nitrogen fixation genes into various photosynthetic organisms is an exciting strategy for converting atmospheric nitrogen into nitrogen-rich products in a green and energy-efficient way. In order to facilitate this process, it is essential that we understand the fundamentals of the functioning of a prokaryotic nitrogen-fixing machinery in a non-diazotrophic, photoautotrophic cell. This study examines a nitrogenase gene cluster that has been naturally selected on multiple occasions for a nitrogen-fixing partnership by eukaryotic photoautotrophs and provides a basic blueprint for designing a photosynthetic organism with nitrogen-fixing ability.

Using synthetic biology to express nitrogenase biosynthesis pathway in rice and to overcome barriers of nitrogenase instability in plant cytosol

Engineering nitrogen fixation in cereals could reduce usage of chemical nitrogen fertilizers. Here, a nitrogenase biosynthesis pathway comprising 13 genes (nifB nifH nifD nifK nifE nifN nifX hesA nifV nifS nifU groES groEL) was introduced into rice by transforming multigene vectors and subsequently by sexual crossing between transgenic rice plants. Genome sequencing analysis revealed that 13 nif genes in F4 hybrid rice lines L12-13 and L8-17 were inserted at two loci on rice chromosome 1. Eleven nitrogen fixation (Nif) proteins were produced and stable NifDK tetramer was formed in rice cytosol. NifH in rice cytosol was unstable and NifH-S18 was found to be a key residue that conferred susceptibility to proteinase degradation. NifH variants with Fe protein activity and resistance to plant endoproteinase cleavage were obtained. This study provides an efficient approach for introducing multiple nif genes into plants and also helps to pre-evaluate the stability of prokaryotic proteins in plant cytosol.

Targeted genome mining with GATOR-GC maps the evolutionary landscape of biosynthetic diversity

Gene clusters, groups of physically adjacent genes that work collectively, are pivotal to bacterial fitness and valuable in biotechnology and medicine. While various genome mining tools can identify and characterize gene clusters, they often overlook their evolutionary diversity, a crucial factor in revealing novel cluster functions and applications. To address this gap, we developed GATOR-GC, a targeted genome mining tool that enables comprehensive and flexible exploration of gene clusters in a single execution. We show that GATOR-GC identified a diversity of over 4 million gene clusters similar to experimentally validated biosynthetic gene clusters (BGCs) that other tools fail to detect. To highlight the utility of GATOR-GC, we identified previously uncharacterized co-occurring conserved genes potentially involved in mycosporine-like amino acid biosynthesis and mapped the taxonomic and evolutionary patterns of genomic islands that modify DNA with 7-deazapurines. Additionally, with its proximity-weighted similarity scoring, GATOR-GC successfully differentiated BGCs of the FK-family of metabolites (e.g., rapamycin, FK506/520) according to their chemistries. We anticipate GATOR-GC will be a valuable tool to assess gene cluster diversity for targeted, exploratory, and flexible genome mining. GATOR-GC is available at https://github.com/chevrettelab/gator-gc.

Role of Environmental Factors in Legume-Rhizobium Symbiosis: A Review

Legumes play a pivotal role in addressing global challenges of food and nutrition security by offering a sustainable source of protein and bioactive compounds. The capacity of legumes to establish symbiotic relationships with rhizobia bacteria enables biological nitrogen fixation (BNF), reducing the dependence on chemical fertilizers while enhancing soil health. However, the efficiency of this symbiosis is significantly influenced by environmental factors, such as soil acidity, salinity, temperature, moisture content, light intensity, and nutrient availability. These factors affect key processes, including rhizobia survival, nodule formation, and nitrogenase activity, ultimately determining the growth and productivity of legumes. This review summarizes current knowledge on legume-rhizobia interactions under varying abiotic conditions. It highlights the impact of salinity and acidity in limiting nodule development, soil temperature in regulating microbial community dynamics, and moisture availability in modulating metabolic and hormonal responses during drought and waterlogging. Moreover, the role of essential nutrients, including nitrogen, phosphorus, potassium, and trace elements such as iron, molybdenum, and boron, in optimizing symbiosis is critically analyzed.

Structural basis for the conformational protection of nitrogenase from O2

The low reduction potentials required for the reduction of dinitrogen (N2) render metal-based nitrogen-fixation catalysts vulnerable to irreversible damage by dioxygen (O2)1-3. Such O2 sensitivity represents a major conundrum for the enzyme nitrogenase, as a large fraction of nitrogen-fixing organisms are either obligate aerobes or closely associated with O2-respiring organisms to support the high energy demand of catalytic N2 reduction4. To counter O2 damage to nitrogenase, diazotrophs use O2 scavengers, exploit compartmentalization or maintain high respiration rates to minimize intracellular O2 concentrations4-8. A last line of damage control is provided by the 'conformational protection' mechanism9, in which a [2Fe:2S] ferredoxin-family protein termed FeSII (ref. 10) is activated under O2 stress to form an O2-resistant complex with the nitrogenase component proteins11,12. Despite previous insights, the molecular basis for the conformational O2 protection of nitrogenase and the mechanism of FeSII activation are not understood. Here we report the structural characterization of the Azotobacter vinelandii FeSII-nitrogenase complex by cryo-electron microscopy. Our studies reveal a core complex consisting of two molybdenum-iron proteins (MoFePs), two iron proteins (FePs) and one FeSII homodimer, which polymerize into extended filaments. In this three-protein complex, FeSII mediates an extensive network of interactions with MoFeP and FeP to position their iron-sulphur clusters in catalytically inactive but O2-protected states. The architecture of the FeSII-nitrogenase complex is confirmed by solution studies, which further indicate that the activation of FeSII involves an oxidation-induced conformational change.

Dickeya ananae sp. nov., pectinolytic bacterium isolated from pineapple (Ananas comosus)

Recently, species clustering within Dickeya zeae has been identified as complex, encompassing validly published names, including D. oryzae and D. parazeae, with some strains potentially delineating new species. In this study, genomes of strains isolated from a bacterial heart rot outbreak in pineapple (Ananas comosus var. comosus) on Oahu, Hawaii, along with two strains from pineapple in Malaysia, were sequenced. Orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the sequenced genomes ranged from 98.93-99.9% and 91.8-99.9%, respectively, supporting the classification of seven strains within the same species. Comparisons of ANI and dDDH values between these seven strains and type strains of D. zeae, D. parazeae, and D. oryzae ranged from 94.4-95.9% and 57.2-66.5%, respectively. These values fall below the proposed boundaries for new species designation, supporting the delineation of a novel species. Phylogenetic analyses, including 16S rRNA, gapA, multi-locus sequence analysis (MLSA) of 10 housekeeping genes, whole-genome, and pangenome analyses, were concordant and revealed a distinct monophyletic clade, separating these strains from other members of the D. zeae complex, with D. oryzae as the closest relative. Notably, a nitrogen fixation gene cluster comprising 28 genes, similar to the Klebsiella spp. nitrogenase gene cluster, was found in the genome of the seven pineapple strains. Based on polyphasic approaches, including ANI, dDDH, biochemical, physiological, and phylogenomic analyses, we propose the reclassification in a new species of the five pineapple strains from Hawaii A5391, A5410T, A5611, A6136, and A6137, together with the two pineapple strains from Malaysia CFBP 1272 and CFBP 1278, previously classified as D. zeae. We propose the name Dickeya ananae sp. nov. for this taxon, represented by the type strain A5410T (= ICMP 25020T = LMG 33197T).

Nitrogen-Fixing Gamma Proteobacteria Azotobacter vinelandii-A Blueprint for Nitrogen-Fixing Plants?

The availability of fixed nitrogen limits overall agricultural crop production worldwide. The so-called modern "green revolution" catalyzed by the widespread application of nitrogenous fertilizer has propelled global population growth. It has led to imbalances in global biogeochemical nitrogen cycling, resulting in a "nitrogen problem" that is growing at a similar trajectory to the "carbon problem". As a result of the increasing imbalances in nitrogen cycling and additional environmental problems such as soil acidification, there is renewed and increasing interest in increasing the contributions of biological nitrogen fixation to reduce the inputs of nitrogenous fertilizers in agriculture. Interestingly, biological nitrogen fixation, or life's ability to convert atmospheric dinitrogen to ammonia, is restricted to microbial life and not associated with any known eukaryotes. It is not clear why plants never evolved the ability to fix nitrogen and rather form associations with nitrogen-fixing microorganisms. Perhaps it is because of the large energy demand of the process, the oxygen sensitivity of the enzymatic apparatus, or simply failure to encounter the appropriate selective pressure. Whatever the reason, it is clear that this ability of crop plants, especially cereals, would transform modern agriculture once again. Successfully engineering plants will require creating an oxygen-free niche that can supply ample energy in a tightly regulated manner to minimize energy waste and ensure the ammonia produced is assimilated. Nitrogen-fixing aerobic bacteria can perhaps provide a blueprint for engineering nitrogen-fixing plants. This short review discusses the key features of robust nitrogen fixation in the model nitrogen-fixing aerobe, gamma proteobacteria Azotobacter vinelandii, in the context of the basic requirements for engineering nitrogen-fixing plants.

Alternative sources of molybdenum for Methanococcus maripaludis and their implication for the evolution of molybdoenzymes

Molybdoenzymes are essential in global nitrogen, carbon, and sulfur cycling. To date, the only known bioavailable source of molybdenum (Mo) is molybdate. However, in the sulfidic and anoxic (euxinic) habitats that predominate in modern subsurface environments and that were pervasive prior to Earth's widespread oxygenation, Mo occurs as soluble tetrathiomolybdate ion and molybdenite mineral that is not known to be bioavailable. This presents a paradox for how organisms obtain Mo to support molybdoenzymes in these environments. Here, we show that tetrathiomolybdate and molybdenite sustain the high Mo demand of a model anaerobic methanogen, Methanococcus maripaludis, grown via Mo-dependent formate dehydrogenase, formylmethanofuran dehydrogenase, and nitrogenase. Cells grown with tetrathiomolybdate and molybdenite have similar growth kinetics, Mo content, and transcript levels of proteins involved in Mo transport and cofactor biosynthesis when compared to those grown with molybdate, implying similar mechanisms of transport and cofactor biosynthesis. These results help to reconcile the paradox of how Mo is acquired in modern and ancient anaerobes and provide new insight into how molybdoenzymes could have evolved prior to Earth's oxygenation.

Chemosynthetic alphaproteobacterial diazotrophs reside in deep-sea cold-seep bottom waters

Nitrogen (N)-fixing organisms, also known as diazotrophs, play a crucial role in N-limited ecosystems by controlling the production of bioavailable N. The carbon-dominated cold-seep ecosystems are inherently N-limited, making them hotspots of N fixation. However, the knowledge of diazotrophs in cold-seep ecosystems is limited compared to other marine ecosystems. In this study, we used multi-omics to investigate the diversity and catabolism of diazotrophs in deep-sea cold-seep bottom waters. Our findings showed that the relative abundance of diazotrophs in the bacterial community reached its highest level in the cold-seep bottom waters compared to the cold-seep upper waters and non-seep bottom waters. Remarkably, more than 98% of metatranscriptomic reads aligned on diazotrophs in cold-seep bottom waters belonged to the genus Sagittula, an alphaproteobacterium. Its metagenome-assembled genome, named Seep-BW-D1, contained catalytic genes (nifHDK) for nitrogen fixation, and the nifH gene was actively transcribed in situ. Seep-BW-D1 also exhibited chemosynthetic capability to oxidize C1 compounds (methanol, formaldehyde, and formate) and thiosulfate (S2O32-). In addition, we observed abundant transcripts mapped to genes involved in the transport systems for acetate, spermidine/putrescine, and pectin oligomers, suggesting that Seep-BW-D1 can utilize organics from the intermediates synthesized by methane-oxidizing microorganisms, decaying tissues from cold-seep benthic animals, and refractory pectin derived from upper photosynthetic ecosystems. Overall, our study corroborates that carbon-dominated cold-seep bottom waters select for diazotrophs and reveals the catabolism of a novel chemosynthetic alphaproteobacterial diazotroph in cold-seep bottom waters.

IMPORTANCE

Bioavailable nitrogen (N) is a crucial element for cellular growth and division, and its production is controlled by diazotrophs. Marine diazotrophs contribute to nearly half of the global fixed N and perform N fixation in various marine ecosystems. While previous studies mainly focused on diazotrophs in the sunlit ocean and oxygen minimum zones, recent research has recognized cold-seep ecosystems as overlooked N-fixing hotspots because the seeping fluids in cold-seep ecosystems introduce abundant bioavailable carbon but little bioavailable N, making most cold seeps inherently N-limited. With thousands of cold-seep ecosystems detected at continental margins worldwide in the past decades, the significant role of cold seeps in marine N biogeochemical cycling is emphasized. However, the diazotrophs in cold-seep bottom waters remain poorly understood. Through multi-omics, this study identified a novel alphaproteobacterial chemoheterotroph belonging to Sagittula as one of the most active diazotrophs residing in cold-seep bottom waters and revealed its catabolism.

An overview of Parafrankia (Nod+/Fix+) and Pseudofrankia (Nod+/Fix-) interactions through genome mining and experimental modeling in co-culture and co-inoculation of Elaeagnus angustifolia

In many frankia, the ability to nodulate host plants (Nod+) and fix nitrogen (Fix+) is a common strategy. However, some frankia within the Pseudofrankia genus lack one or two of these traits. This phenomenon has been consistently observed across various actinorhizal nodule isolates, displaying Nod- and/or Fix- phenotypes. Yet, the mechanisms supporting the colonization and persistence of these inefficient frankia within nodules, both with and without symbiotic strains (Nod+/Fix+), remain unclear. It is also uncertain whether these associations burden or benefit host plants. This study delves into the ecological interactions between Parafrankia EUN1f and Pseudofrankia inefficax EuI1c, isolated from Elaeagnus umbellata nodules. EUN1f (Nod+/Fix+) and EuI1c (Nod+/Fix-) display contrasting symbiotic traits. While the prediction suggests a competitive scenario, the absence of direct interaction evidence implies that the competitive advantage of EUN1f and EuI1c is likely contingent on contextual factors such as substrate availability and the specific nature of stressors in their respective habitats. In co-culture, EUN1f outperforms EuI1c, especially under specific conditions, driven by its nitrogenase activity. Iron-depleted conditions favor EUN1f, emphasizing iron's role in microbial competition. Both strains benefit from host root exudates in pure culture, but EUN1f dominates in co-culture, enhancing its competitive traits. Nodulation experiments show that host plant preferences align with inoculum strain abundance under nitrogen-depleted conditions, while consistently favoring EUN1f in nitrogen-supplied media. This study unveils competitive dynamics and niche exclusion between EUN1f and EuI1c, suggesting that host plant may penalize less effective strains and even all strains. These findings highlight the complex interplay between strain competition and host selective pressure, warranting further research into the underlying mechanisms shaping plant-microbe-microbe interactions in diverse ecosystems.

IMPORTANCE

While Pseudofrankia strains typically lack the common traits of ability to nodulate the host plant (Nod-) and/or fix nitrogen (Fix-), they are still recovered from actinorhizal nodules. The enigmatic question of how and why these unconventional strains establish themselves within nodule tissue, thriving either alongside symbiotic strains (Nod+/Fix+) or independently, while considering potential metabolic costs to the host plant, remains a perplexing puzzle. This study endeavors to unravel the competitive dynamics between Pseudofrankia inefficax strain EuI1c (Nod+/Fix-) and Parafrankia strain EU1Nf (Nod+/Fix+) through a comprehensive exploration of genomic data and empirical modeling, conducted both in controlled laboratory settings and within the host plant environment.

Analyses of the electronic structures of FeFe-cofactors compared with those of FeMo- and FeV-cofactors and their P-clusters

The electronic structures of FeFe-cofactors (FeFe-cos) in resting and turnover states, together with their PN clusters from iron-only nitrogenases, have been calculated using the bond valence method, and their crystallographic data were reported recently and deposited in the Protein Data Bank (PDB codes: 8BOQ and 8OIE). The calculated results have also been compared with those of their homologous Mo- and V-nitrogenases. For FeFe-cos in the resting state, Fe1/2/4/5/6/7/8 atoms are prone to Fe3+, while the Fe3 atom shows different degrees of mixed valences. The results support that the Fe8 atom at the terminal positions of FeFe-cos possesses the same oxidation states as the Mo3+/V3+ atoms of FeMo-/FeV-cos. In the turnover state, the overall oxidation state of FeFe-co is slightly reduced than those in the resting species, and its electronic configuration is rearranged after the substitution of S2B with OH, compatible with those found in CO-bound FeV-co. Moreover, the calculations give the formal oxidation states of 6Fe2+-2Fe3+ for the electronic structures of PN clusters in Fe-nitrogenases. By the comparison of Mo-, V- and Fe-nitrogenases, the overall oxidation levels of 7Fe atoms (Fe1-Fe7) for both FeFe- and FeMo-cos in resting states are found to be higher than that of FeV-co. For the PN clusters in MoFe-, VFe- and FeFe-proteins, they all exhibit a strong reductive character.

Metal nutrition and transport in the process of symbiotic nitrogen fixation

Symbiotic nitrogen fixation (SNF) facilitated by the interaction between legumes and rhizobia is a well-documented and eco-friendly alternative to chemical nitrogen fertilizers. Host plants obtain fixed nitrogen from rhizobia by providing carbon and mineral nutrients. These mineral nutrients, which are mostly in the form of metal ions, are implicated in various stages of the SNF process. This review describes the functional roles played by metal ions in nodule formation and nitrogen fixation and specifically addresses their transport mechanisms and associated transporters within root nodules. Future research directions and potential strategies for enhancing SNF efficiency are also discussed.

Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere

BACKGROUND

Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted.

RESULTS

Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera.

CONCLUSIONS

The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture.

Phylogenetic analysis of Nostocales (Cyanobacteria) based on two novel molecular markers, implicated in the nitrogenase biosynthesis

The characterization of cyanobacteria communities remains challenging, as taxonomy of several cyanobacterial genera is still unresolved, especially within Nostocales taxa. Nostocales cyanobacteria are capable of nitrogen fixation; nitrogenase genes are grouped into operons and are located in the same genetic locus. Structural nitrogenase genes (nifH, nifK and nifD) as well as 16S rRNA have been shown to be adequate genetic markers for distinguishing cyanobacterial genera. However, there is no available information regarding the phylogeny of regulatory genes of the nitrogenase cluster. Aiming to provide a more accurate overview of the evolution of nitrogen fixation, this study analyzed for the first time nifE and nifN genes, which regulate the production of nitrogenase, alongside nifH. Specific primers were designed to amplify nifE and nifN genes, previously not available in literature and phylogenetic analysis was carried out in 13 and 14 TAU-MAC culture collection strains, respectively, of ten Nostocales genera along with other sequences retrieved from cyanobacteria genomes. Phylogenetic analysis showed that these genes seem to follow a common evolutionary pattern with nitrogenase structural genes and 16S rRNA. The classification of cyanobacteria based on these molecular markers seems to distinguish Nostocales strains with common morphological, ecological, and physiological characteristics.

Genome-based analyses to learn from and about Paenibacillus sonchi genomovar Riograndensis SBR5T

Paenibacillus sonchi genomovar Riograndensis SBR5T is a plant growth-promoting rhizobacterium (PGPR) isolated in the Brazilian state of Rio Grande do Sul from the rhizosphere of Triticum aestivum. It fixes nitrogen, produces siderophores as well as the phytohormone indole-3-acetic acid, solubilizes phosphate and displays antagonist activity against Listeria monocytogenes and Pectobacterium carotovorum. Comprehensive omics analysis and the development of genetic tools are key to characterizing and engineering such non-model microorganisms. Therefore, the complete genome of SBR5T was sequenced, and shown to encode 6,705 proteins, 87 tRNAs, and 27 rRNAs and it enabled a landscape transcriptome analysis that unveiled conserved transcriptional and translational patterns and characterized operon structures and riboswitches. The pangenome of P. sonchi species is open with a stable core pangenome. At the same time, the analysis of genes coding for nitrogenases revealed that the trait of nitrogen fixation is sparse within the Paenibacillaceae family and the presence of Fe-only nitrogenase in the P. sonchi group was exclusive to SBR5T. The development of genetic tools for SBR5T enabled genetic transformation, plasmid construction for constitutive and inducible gene expression, and gene repression using the CRISPRi system. Altogether, the work with P. sonchi can guide the study of non-model bacteria with economic potential.

The RND efflux system ParXY affects siderophore secretion in Pseudomonas putida KT2440

IMPORTANCE

Gram-negative bacteria from the Pseudomonas group are survivors in various environmental niches. For example, the bacteria secrete siderophores to capture ferric ions under deficiency conditions. Tripartite efflux systems are involved in the secretion of siderophores, which are also important for antibiotic resistance. For one of these efflux systems, the resistance-nodulation-cell division transporter ParXY from the model organism Pseudomonas putida KT2440, we show that it influences the secretion of the siderophore pyoverdine in addition to its already known involvement in antibiotic resistance. Phenotypically, its role in pyoverdine secretion is only apparent when other pyoverdine secretion systems are inactive. The results confirm that the different tripartite efflux systems have overlapping substrate specificities and can at least partially functionally substitute for each other, especially in important physiological activities such as supplying the cell with iron ions. This fact must be taken into account when developing specific inhibitors for tripartite efflux systems.

Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential

Glacier retreat is a visible consequence of climate change worldwide. Although taxonomic change of the soil microbiomes in glacier forefields have been widely documented, how microbial genetic potential changes along succession is little known. Here, we used shotgun metagenomics to analyse whether the soil microbial genetic potential differed between four stages of soil development (SSD) sampled along three transects in the Damma glacier forefield (Switzerland). The SSDs were characterized by an increasing vegetation cover, from barren soil, to biological soil crust, to sparsely vegetated soil and finally to vegetated soil. Results suggested that SSD significantly influenced microbial genetic potential, with the lowest functional diversity surprisingly occurring in the vegetated soils. Overall, carbohydrate metabolism and secondary metabolite biosynthesis genes overrepresented in vegetated soils, which could be partly attributed to plant-soil feedbacks. For C degradation, glycoside hydrolase genes enriched in vegetated soils, while auxiliary activity and carbohydrate esterases genes overrepresented in barren soils, suggested high labile C degradation potential in vegetated, and high recalcitrant C degradation potential in barren soils. For N-cycling, organic N degradation and synthesis genes dominated along succession, and gene families involved in nitrification were overrepresented in barren soils. Our study provides new insights into how the microbial genetic potential changes during soil formation along the Damma glacier forefield.

MtESN2 is a subgroup II sulphate transporter required for symbiotic nitrogen fixation and prevention of nodule early senescence in Medicago truncatula

Adequate distribution of mineral sulphur (S) nutrition to nodules mediated by sulphate transporters is crucial for nitrogen fixation in symbiosis establishment process. However, the molecular mechanisms underlying this process remain largely unknown. In this study, we characterized the function of Early Senescent Nodule 2 (MtESN2), a gene crucial to nitrogen fixation in Medicago truncatula. Mutations in MtESN2 resulted in severe developmental and functional defects including dwarf shoots, early senescent nodules, and lower nitrogenase activity under symbiotic conditions compared to wild-type plants. MtESN2 encodes an M. truncatula sulphate transporter that is expressed only in roots and nodules, with the highest expression levels in the transition zone and nitrogen-fixing zone of nodules. MtESN2 exhibited sulphate transport activity when expressed in yeast. Immunolocalization analysis showed that MtESN2-yellow fluorescent protein fusion protein was localized to the plasma membranes of both uninfected and infected cells of nodules, where it might transport sulphate into both rhizobia-infected and uninfected cells within the nodules. Our results reveal an unreported sulphate transporter that contributes to effective symbiosis and prevents nodule early senescence in M. truncatula.

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.

Whole-genome assembly of A02 bacteria involved in nitrogen fixation within cassava leaves

The endophytic nitrogen (N)-fixing bacterium A02 belongs to the genus Curtobacterium (Curtobacterium sp.) and is crucial for the N metabolism of cassava ( Manihot esculenta Crantz). We isolated the A02 strain from cassava cultivar SC205 and used the 15N isotope dilution method to study the impacts of A02 on growth and accumulation of N in cassava seedlings. Furthermore, the whole genome was sequenced to determine the N-fixation mechanism of A02. Compared with low N control (T1), inoculation with the A02 strain (T2) showed the highest increase in leaf and root dry weight of cassava seedlings, and 120.3 nmol/(mL·h) was the highest nitrogenase activity recorded in leaves, which were considered the main site for colonization and N-fixation. The genome of A02 was 3,555,568 bp in size and contained a circular chromosome and a plasmid. Comparison with the genomes of other short bacilli revealed that strain A02 showed evolutionary proximity to the endophytic bacterium NS330 (Curtobacterium citreum) isolated from rice (Oryza sativa) in India. The genome of A02 contained 13 nitrogen fixation (nif) genes, including 4 nifB, 1 nifR3, 2 nifH, 1 nifU, 1 nifD, 1 nifK, 1 nifE, 1 nifN, and 1 nifC, and formed a relatively complete N fixation gene cluster 8-kb long that accounted for 0.22% of the whole genome length. The nifHDK of strain A02 (Curtobacterium sp.) is identical to the Frankia alignment. Function prediction showed high copy number of the nifB gene was related to the oxygen protection mechanism. Our findings provide exciting information about the bacterial genome in relation to N support for transcriptomic and functional studies for increasing N use efficiency in cassava.

Exploring the cellular surface polysaccharide and root nodule symbiosis characteristics of the rpoN mutants of Bradyrhizobium sp. DOA9 using synchrotron-based Fourier transform infrared microspectroscopy in conjunction with X-ray absorption spectroscopy

The functional significance of rpoN genes that encode two sigma factors in the Bradyrhizobium sp. strain DOA9 has been reported to affect colony formation, root nodulation characteristics, and symbiotic interactions with Aeschynomene americana. rpoN mutant strains are defective in cellular surface polysaccharide (CSP) production compared with the wild-type (WT) strain, and they accordingly exhibit smaller colonies and diminished symbiotic effectiveness. To gain deeper insights into the changes in CSP composition and the nodules of rpoN mutants, we employed synchrotron-based Fourier transform infrared (SR-FTIR) microspectroscopy and X-ray absorption spectroscopy. FTIR analysis of the CSP revealed the absence of specific components in the rpoN mutants, including lipids, carboxylic groups, polysaccharide-pyranose rings, and β-galactopyranosyl residues. Nodules formed by DOA9WT exhibited a uniform distribution of lipids, proteins, and carbohydrates; mutant strains, particularly DOA9∆rpoNp:ΩrpoNc, exhibited decreased distribution uniformity and a lower concentration of C=O groups. Furthermore, Fe K-edge X-ray absorption near-edge structure and extended X-ray absorption fine structure analyses revealed deficiencies in the nitrogenase enzyme in the nodules of DOA9∆rpoNc and DOA9∆rpoNp:ΩrpoNc mutants; nodules from DOA9WT and DOA9∆rpoNp exhibited both leghemoglobin and the nitrogenase enzyme. IMPORTANCE This work provides valuable insights into how two rpoN genes affect the composition of cellular surface polysaccharides (CSPs) in Bradyrhizobium sp., which subsequently dictates root nodule chemical characteristics and nitrogenase production. We used advanced synchrotron methods, including synchrotron-based Fourier transform infrared (SR-FTIR) microspectroscopy and X-ray absorption spectroscopy (XAS), for the first time in this field to analyze CSP components and reveal the biochemical changes occurring within nodules. These cutting-edge techniques confer significant advantages by providing detailed molecular information, enabling the identification of specific functional groups, chemical bonds, and biomolecule changes. This research not only contributes to our understanding of plant-microbe interactions but also establishes a foundation for future investigations and potential applications in this field. The combined use of the synchrotron-based FTIR and XAS techniques represents a significant advancement in facilitating a comprehensive exploration of bacterial CSPs and their implications in plant-microbe interactions.

Molecular Mechanisms of Pseudomonas-Assisted Plant Nitrogen Uptake: Opportunities for Modern Agriculture

Pseudomonas spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the plant. Several species in the family Pseudomonadaceae, including Azotobacter vinelandii AvOP, Pseudomonas stutzeri A1501, Pseudomonas stutzeri DSM4166, Pseudomonas szotifigens 6HT33bT, and Pseudomonas sp. strain K1 can fix nitrogen from the air. The genes required for these reactions are organized in a nitrogen fixation island, obtained via horizontal gene transfer from Klebsiella pneumoniae, Pseudomonas stutzeri, and Azotobacter vinelandii. Today, this island is conserved in Pseudomonas spp. from different geographical locations, which, in turn, have evolved to deal with different geo-climatic conditions. Here, we summarize the molecular mechanisms behind Pseudomonas-driven plant growth promotion, with particular focus on improving plant performance at limiting nitrogen (N) and improving plant N content. We describe Pseudomonas-plant interaction strategies in the soil, noting that the mechanisms of denitrification, ammonification, and secondary metabolite signaling are only marginally explored. Plant growth promotion is dependent on the abiotic conditions and differs at sufficient and deficient N. The molecular controls behind different plant responses are not fully elucidated. We suggest that superposition of transcriptome, proteome, and metabolome data and their integration with plant phenotype development through time will help fill these gaps. The aim of this review is to summarize the knowledge behind Pseudomonas-driven nitrogen fixation and to point to possible agricultural solutions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Co-expression of nitrogenase proteins in cotton (Gossypium hirsutum L.)

Chemical nitrogen fertilizer can maintain crop productivity, but overuse of chemical nitrogen fertilizers leads to economic costs and environmental pollution. One approach to reduce use of nitrogen fertilizers is to transfer nitrogenase biosynthetic pathway to non-legume plants. Fe protein encoded by nifH and MoFe protein encoded by nifD and nifK are two structural components of nitrogenase. NifB encoded by nifB is a critical maturase that catalyzes the first committed step in the biosynthesis of nitrogenase FeMo-cofactor that binds and reduces N2. Expression of the nifB, nifH, nifD and nifK is essential to generate plants that are able to fix atmospheric N2. In this study, the four genes (nifB, nifH, nifD and nifK) from Paenibacillu polymyxaWLY78 were assembled in plant expression vector pCAMBIA1301 via Cre/LoxP recombination system, yielding the recombinant expression vector pCAMBIA1301-nifBHDK. Then, the four nif genes carried in the expression vector were co-introduced into upland cotton R15 using Agrobacterium tumefaciens-mediated transformation. Homozygous transgenic cotton lines B2, B5 and B17 of T3 generation were selected by PCR and RT-PCR. qRT-PCR showed that nifB, nifH, nifD and nifK were co-expressed in the transgenic cottons at similar levels. Western blotting analysis demonstrated that NifB, NifH, NifD and NifK were co-produced in the transgenic cottons. Co-expression of the four critical Nif proteins (NifB, NifH, NifD and NifK) in cottons represents an important step in engineering nitrogenase biosynthetic pathway to non-legume plants.

Influence of sulfide on diazotrophic growth of the methanogen Methanococcus maripaludis and its implications for the origin of nitrogenase

Methanogens inhabit euxinic (sulfide-rich) or ferruginous (iron-rich) environments that promote the precipitation of transition metals as metal sulfides, such as pyrite, reducing metal or sulfur availability. Such environments have been common throughout Earth's history raising the question as to how anaerobes obtain(ed) these elements for the synthesis of enzyme cofactors. Here, we show a methanogen can synthesize molybdenum nitrogenase metallocofactors from pyrite as the source of iron and sulfur, enabling nitrogen fixation. Pyrite-grown, nitrogen-fixing cells grow faster and require 25-fold less molybdenum than cells grown under euxinic conditions. Growth yields are 3 to 8 times higher in cultures grown under ferruginous relative to euxinic conditions. Physiological, transcriptomic, and geochemical data indicate these observations are due to sulfide-promoted metal limitation, in particular molybdenum. These findings suggest that molybdenum nitrogenase may have originated in a ferruginous environment that titrated sulfide to form pyrite, facilitating the availability of sufficient iron, sulfur, and molybdenum for cofactor biosynthesis.

Rhizobial nitrogen fixation efficiency shapes endosphere bacterial communities and Medicago truncatula host growth

BACKGROUND

Despite the knowledge that the soil-plant-microbiome nexus is shaped by interactions amongst its members, very little is known about how individual symbioses regulate this shaping. Even less is known about how the agriculturally important symbiosis of nitrogen-fixing rhizobia with legumes is impacted according to soil type, yet this knowledge is crucial if we are to harness or improve it. We asked how the plant, soil and microbiome are modulated by symbiosis between the model legume Medicago truncatula and different strains of Sinorhizobium meliloti or Sinorhizobium medicae whose nitrogen-fixing efficiency varies, in three distinct soil types that differ in nutrient fertility, to examine the role of the soil environment upon the plant-microbe interaction during nodulation.

RESULTS

The outcome of symbiosis results in installment of a potentially beneficial microbiome that leads to increased nutrient uptake that is not simply proportional to soil nutrient abundance. A number of soil edaphic factors including Zn and Mo, and not just the classical N/P/K nutrients, group with microbial community changes, and alterations in the microbiome can be seen across different soil fertility types. Root endosphere emerged as the plant microhabitat more affected by this rhizobial efficiency-driven community reshaping, manifested by the accumulation of members of the phylum Actinobacteria. The plant in turn plays an active role in regulating its root community, including sanctioning low nitrogen efficiency rhizobial strains, leading to nodule senescence in particular plant-soil-rhizobia strain combinations.

CONCLUSIONS

The microbiome-soil-rhizobial dynamic strongly influences plant nutrient uptake and growth, with the endosphere and rhizosphere shaped differentially according to plant-rhizobial interactions with strains that vary in nitrogen-fixing efficiency levels. These results open up the possibility to select inoculation partners best suited for plant, soil type and microbial community. Video Abstract.

Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii

Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic catalysts based on the biological mechanism. Over the past 30 years, the free-living nitrogen-fixing bacterium Azotobacter vinelandii emerged as a preferred model organism for mechanistic, structural, genetic, and physiological studies aimed at understanding biological nitrogen fixation. This review provides a contemporary overview of these studies and places them within the context of their historical development.

Holistic view of biological nitrogen fixation and phosphorus mobilization in Azotobacter chroococcum NCIMB 8003

Nitrogen (N) and phosphorus (P) deficiencies are two of the most agronomic problems that cause significant decrease in crop yield and quality. N and P chemical fertilizers are widely used in current agriculture, causing environmental problems and increasing production costs. Therefore, the development of alternative strategies to reduce the use of chemical fertilizers while maintaining N and P inputs are being investigated. Although dinitrogen is an abundant gas in the atmosphere, it requires biological nitrogen fixation (BNF) to be transformed into ammonium, a nitrogen source assimilable by living organisms. This process is bioenergetically expensive and, therefore, highly regulated. Factors like availability of other essential elements, as phosphorus, strongly influence BNF. However, the molecular mechanisms of these interactions are unclear. In this work, a physiological characterization of BNF and phosphorus mobilization (PM) from an insoluble form (Ca₃(PO₄)₂) in Azotobacter chroococcum NCIMB 8003 was carried out. These processes were analyzed by quantitative proteomics in order to detect their molecular requirements and interactions. BNF led to a metabolic change beyond the proteins strictly necessary to carry out the process, including the metabolism related to other elements, like phosphorus. Also, changes in cell mobility, heme group synthesis and oxidative stress responses were observed. This study also revealed two phosphatases that seem to have the main role in PM, an exopolyphosphatase and a non-specific alkaline phosphatase PhoX. When both BNF and PM processes take place simultaneously, the synthesis of nitrogenous bases and L-methionine were also affected. Thus, although the interdependence is still unknown, possible biotechnological applications of these processes should take into account the indicated factors.

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.

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.

Assembly of nitrogenase biosynthetic pathway in Saccharomyces cerevisiae by using polyprotein strategy

Nitrogenase in some bacteria and archaea catalyzes conversion of N₂ to ammonia. To reconstitute a nitrogenase biosynthetic pathway in a eukaryotic host is still a challenge, since synthesis of nitrogenase requires a large number of nif (nitrogen fixation) genes. Viral 2A peptide mediated "cleavage" of polyprotein is one of strategies for multigene co-expression. Here, we show that cleavage efficiency of NifB-2A-NifH polyprotein linked by four different 2A peptides (P2A, T2A, E2A, and F2A) in Saccharomyces cerevisiae ranges from ~50% to ~90%. The presence of a 2A tail in NifB, NifH, and NifD does not affect their activity. Western blotting shows that 9 Nif proteins (NifB, NifH, NifD, NifK, NifE, NifN, NifX, HesA, and NifV) from Paenibacillus polymyxa that are fused into two polyproteins via 2A peptides are co-expressed in S. cerevisiae. Expressed NifH from Klebsiella oxytoca NifU and NifS and P. polymyxa NifH fusion linked via 2A in S. cerevisiae exhibits Fe protein activity.

Reactive Sulfur Species Produced by Cystathionine γ-lyase Function in the Establishment of Mesorhizobium loti-Lotus japonicus Symbiosis

Reactive sulfur species (RSS) are present in root nodules; however, their role in symbiosis and the mechanisms underlying their production remain unclear. We herein investigated whether RSS produced by the cystathionine γ-lyase (CSE) of microsymbionts are involved in root nodule symbiosis. A cse mutant of Mesorhizobium loti exhibited the decreased production of hydrogen sulfide and other RSS. Although the CSE mutation of M. loti did not affect the early stages of symbiosis, i.e., infection and nodulation, with Lotus japonicus, it reduced the nitrogenase activity of nodules and induced their early senescence. Additionally, changes in the production of sulfur compounds and an increase in reactive oxygen species (ROS) were observed in the infected cells of nodules induced by the cse mutants. The effects of CSE inhibitors in the L. japonicus rhizosphere on symbiosis with M. loti were also investigated. All three CSE inhibitors suppressed infection and nodulation by M. loti concomitant with decreased RSS levels and increased ROS and nitric oxide levels. Therefore, RSS derived from the CSE activity of both the microsymbiont and host plant are required for symbiosis, but function at different stages of symbiosis, possibly with crosstalk with other reactive mole-cular species.

A naturalist perspective of microbiology: Examples from methanogenic archaea

Storytelling has been the primary means of knowledge transfer over human history. The effectiveness and reach of stories are improved when the message is appropriate for the target audience. Oftentimes, the stories that are most well received and recounted are those that have a clear purpose and that are told from a variety of perspectives that touch on the varied interests of the target audience. Whether scientists realize or not, they are accustomed to telling stories of their own scientific discoveries through the preparation of manuscripts, presentations, and lectures. Perhaps less frequently, scientists prepare review articles or book chapters that summarize a body of knowledge on a given subject matter, meant to be more holistic recounts of a body of literature. Yet, by necessity, such summaries are often still narrow in their scope and are told from the perspective of a particular discipline. In other words, interdisciplinary reviews or book chapters tend to be the rarity rather than the norm. Here, we advocate for and highlight the benefits of interdisciplinary perspectives on microbiological subjects.

Reductive biomining of pyrite by methanogens

Pyrite (FeS₂) is the most abundant iron sulfide mineral in Earth's crust. Until recently, FeS₂ has been considered a sink for iron (Fe) and sulfur (S) at low temperature in the absence of oxygen or oxidative weathering, making these elements unavailable to biology. However, anaerobic methanogens can transfer electrons extracellularly to reduce FeS₂ via direct contact with the mineral. Reduction of FeS₂ occurs through a multistep process that generates aqueous sulfide (HS^-) and FeS₂-associated pyrrhotite (Fe_1-xS). Subsequent dissolution of Fe_1-xS provides Fe(II)_(aq), but not HS^-, that rapidly complexes with HS^-_(aq) generated from FeS₂ reduction to form soluble iron sulfur clusters [nFeS_(aq)]. Cells assimilate nFeS_(aq) to meet Fe/S nutritional demands by mobilizing and hyperaccumulating Fe and S from FeS₂. As such, reductive dissolution of FeS₂ by methanogens has important implications for element cycling in anoxic habitats, both today and in the geologic past.

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.

Phylogenomics uncovers evolutionary trajectory of nitrogen fixation in Cyanobacteria

Biological nitrogen fixation (BNF) by cyanobacteria is of significant importance for the Earth’s biogeochemical nitrogen cycle but is restricted to a few genera that do not form monophyletic group. To explore the evolutionary trajectory of BNF and investigate the driving forces of its evolution, we analyze 650 cyanobacterial genomes and compile the database of diazotrophic cyanobacteria based on the presence of nitrogen fixation gene clusters (NFGCs). We report that 266 of 650 examined genomes are NFGC-carrying members, and these potentially diazotrophic cyanobacteria are unevenly distributed across the phylogeny of Cyanobacteria, that multiple independent losses shaped the scattered distribution. Among the diazotrophic cyanobacteria, two types of NFGC exist, with one being ancestral and abundant, which have descended from diazotrophic ancestors, and the other being anaerobe-like and sparse, possibly being acquired from anaerobic microbes through horizontal gene transfer. Interestingly, we illustrate that the origin of BNF in Cyanobacteria coincide with two major evolutionary events. One is the origin of multicellularity of cyanobacteria, and the other is concurrent genetic innovations with massive gene gains and expansions, implicating their key roles in triggering the evolutionary transition from nondiazotrophic to diazotrophic cyanobacteria. Additionally, we reveal that genes involved in accelerating respiratory electron transport (coxABC), anoxygenic photosynthetic electron transport (sqr), as well as anaerobic metabolisms (pfor, hemN, nrdG, adhE) are enriched in diazotrophic cyanobacteria, representing adaptive genetic signatures that underpin the diazotrophic lifestyle. Collectively, our study suggests that multicellularity, together with concurrent genetic adaptations contribute to the evolution of diazotrophic cyanobacteria.

Biological nitrogen fixation and prospects for ecological intensification in cereal-based cropping systems

The demand for nitrogen (N) for crop production increased rapidly from the middle of the twentieth century and is predicted to at least double by 2050 to satisfy the on-going improvements in productivity of major food crops such as wheat, rice and maize that underpin the staple diet of most of the world's population. The increased demand will need to be fulfilled by the two main sources of N supply - biological nitrogen (gas) (N2) fixation (BNF) and fertilizer N supplied through the Haber-Bosch processes. BNF provides many functional benefits for agroecosystems. It is a vital mechanism for replenishing the reservoirs of soil organic N and improving the availability of soil N to support crop growth while also assisting in efforts to lower negative environmental externalities than fertilizer N. In cereal-based cropping systems, legumes in symbiosis with rhizobia contribute the largest BNF input; however, diazotrophs involved in non-symbiotic associations with plants or present as free-living N2-fixers are ubiquitous and also provide an additional source of fixed N. This review presents the current knowledge of BNF by free-living, non-symbiotic and symbiotic diazotrophs in the global N cycle, examines global and regional estimates of contributions of BNF, and discusses possible strategies to enhance BNF for the prospective benefit of cereal N nutrition. We conclude by considering the challenges of introducing in planta BNF into cereals and reflect on the potential for BNF in both conventional and alternative crop management systems to encourage the ecological intensification of cereal and legume production.

Comparisons of bond valences and distances for CO- and N2-bound clusters of FeMo-cofactors

By comparisons of N2 and isoelectronic substrate CO bound FeMo-cofactors (FeMo-cos) in nitrogenases, we have used a classical bond valence method to calculate the oxidation states of the iron and molybdenum atoms in FeMo-cos.

Metabolic Remodeling during Nitrogen Fixation in Zymomonas mobilis

Zymomonas mobilis is an ethanologenic bacterium currently being developed for production of advanced biofuels. Recent studies have shown that Z. mobilis can fix dinitrogen gas (N2) as a sole nitrogen source. During N2 fixation, Z. mobilis exhibits increased biomass-specific rates of ethanol production. In order to better understand the physiology of Z. mobilis during N2 fixation and during changes in ammonium (NH4+) availability, we performed liquid chromatography-mass spectrometry (LC-MS)-based targeted metabolomics and shotgun proteomics under three regimes of nitrogen availability: continuous N2 fixation, gradual NH4+ depletion, and acute NH4+ addition to N2-fixing cells. We report dynamic changes in abundance of proteins and metabolites related to nitrogen fixation, motility, ammonium assimilation, amino acid biosynthesis, nucleotide biosynthesis, isoprenoid biosynthesis, and Entner-Doudoroff (ED) glycolysis, providing insight into the regulatory mechanisms that control these processes in Z. mobilis. Our analysis identified potential physiological mechanisms that may contribute to increased specific ethanol production during N2 fixation, including decreased activity of biosynthetic pathways, increased protein abundance of alcohol dehydrogenase (ADHI), and increased thermodynamic favorability of the ED pathway. Of particular relevance to advanced biofuel production, we found that intermediates in the methylerythritol phosphate (MEP) pathway for isoprenoid biosynthesis were depleted during N2 fixation, coinciding with decreased protein abundance of deoxyxylulose 5-phosphate synthase (DXS), the first enzyme in the pathway. This implies that DXS protein abundance serves as a native control point in regulating MEP pathway activity in Z. mobilis. The results of this study will inform metabolic engineering to further develop Z. mobilis as a platform organism for biofuel production. IMPORTANCE Biofuels and bioproducts have the potential to serve as environmentally sustainable replacements for petroleum-derived fuels and commodity molecules. Advanced fuels such as higher alcohols and isoprenoids are more suitable gasoline replacements than bioethanol. Developing microbial systems to generate advanced biofuels requires metabolic engineering to reroute carbon away from ethanol and other native products and toward desired pathways, such as the MEP pathway for isoprenoid biosynthesis. However, rational engineering of microbial metabolism relies on understanding metabolic control points, in terms of both enzyme activity and thermodynamic favorability. In Z. mobilis, the factors that control glycolytic rates, ethanol production, and isoprenoid production are still not fully understood. In this study, we performed metabolomic, proteomic, and thermodynamic analysis of Z. mobilis during N2 fixation. This analysis identified key changes in metabolite levels, enzyme abundance, and glycolytic thermodynamic favorability that occurred during changes in NH4+ availability, helping to inform future efforts in metabolic engineering.

Construction of recombinant Escherichia coli producing nitrogenase-related proteins from Azotobacter vinelandii

Biological nitrogen fixation by nitrogenase has attracted attention as an alternative method to chemical nitrogen fixation, which requires large amounts of fossil fuels. Azotobacter vinelandii, which produces an oxygen-sensitive nitrogenase, can fix nitrogen even under aerobic conditions; therefore, the heterologous expression of nif-related genes from A. vinelandii is a promising strategy for developing a biological nitrogen fixation method. We assembled 17 nif-related genes, which are scattered throughout the genome of A. vinelandii, into synthetic gene clusters by overlap-extension-PCR and seamless cloning and expressed them in Escherichia coli. The transcription and translation of the 17 nif-related genes were evaluated by RT-qPCR and LC-MS/MS, respectively. The constructed E. coli showed nitrogenase activity under anaerobic and microaerobic conditions. This strain would be a useful model for examining the effect of other genes from A. vinelandii on nitrogen fixation by expressing them in addition to the minimal set of nif-related genes.

A Taxon-Wise Insight Into Rock Weathering and Nitrogen Fixation Functional Profiles of Proglacial Systems

The Arctic environment is particularly affected by global warming, and a clear trend of the ice retreat is observed worldwide. In proglacial systems, the newly exposed terrain represents different environmental and nutrient conditions compared to later soil stages. Therefore, proglacial systems show several environmental gradients along the soil succession where microorganisms are active protagonists of the soil and carbon pool formation through nitrogen fixation and rock weathering. We studied the microbial succession of three Arctic proglacial systems located in Svalbard (Midtre Lovénbreen), Sweden (Storglaciären), and Greenland (foreland close to Kangerlussuaq). We analyzed 65 whole shotgun metagenomic soil samples for a total of more than 400 Gb of sequencing data. Microbial succession showed common trends typical of proglacial systems with increasing diversity observed along the forefield chronosequence. Microbial trends were explained by the distance from the ice edge in the Midtre Lovénbreen and Storglaciären forefields and by total nitrogen (TN) and total organic carbon (TOC) in the Greenland proglacial system. Furthermore, we focused specifically on genes associated with nitrogen fixation and biotic rock weathering processes, such as nitrogenase genes, obcA genes, and genes involved in cyanide and siderophore synthesis and transport. Whereas we confirmed the presence of these genes in known nitrogen-fixing and/or rock weathering organisms (e.g., Nostoc, Burkholderia), in this study, we also detected organisms that, even if often found in soil and proglacial systems, have never been related to nitrogen-fixing or rock weathering processes before (e.g., Fimbriiglobus, Streptomyces). The different genera showed different gene trends within and among the studied systems, indicating a community constituted by a plurality of organisms involved in nitrogen fixation and biotic rock weathering, and where the latter were driven by different organisms at different soil succession stages.

Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea

The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico prediction of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocumented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes are currently supported by biochemical evidence of diazotrophy. In addition, this work provides reference for any inter-phyla comparison of Nif sequences and a quality database of Nif proteins that can be used for identifying new Nif sequences.

Structure, reactivity, and spectroscopy of nitrogenase-related synthetic and biological clusters

The reduction of dinitrogen (N2) is essential for its incorporation into nucleic acids and amino acids, which are vital to life on earth. Nitrogenases convert atmospheric dinitrogen to two ammonia molecules (NH3) under ambient conditions. The catalytic active sites of these enzymes (known as FeM-cofactor clusters, where M = Mo, V, Fe) are the sites of N2 binding and activation and have been a source of great interest for chemists for decades. In this review, recent studies on nitrogenase-related synthetic molecular complexes and biological clusters are discussed, with a focus on their reactivity and spectroscopic characterization. The molecular models that are discussed span from simple mononuclear iron complexes to multinuclear iron complexes and heterometallic iron complexes. In addition, recent work on the extracted biological cofactors is discussed. An emphasis is placed on how these studies have contributed towards our understanding of the electronic structure and mechanism of nitrogenases.

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.

Bacterial nitric oxide metabolism: Recent insights in rhizobia

Nitric oxide (NO) is a reactive gaseous molecule that has several functions in biological systems depending on its concentration. At low concentrations, NO acts as a signaling molecule, while at high concentrations, it becomes very toxic due to its ability to react with multiple cellular targets. Soil bacteria, commonly known as rhizobia, have the capacity to establish a N₂-fixing symbiosis with legumes inducing the formation of nodules in their roots. Several reports have shown NO production in the nodules where this gas acts either as a signaling molecule which regulates gene expression, or as a potent inhibitor of nitrogenase and other plant and bacteria enzymes. A better understanding of the sinks and sources of NO in rhizobia is essential to protect symbiotic nitrogen fixation from nitrosative stress. In nodules, both the plant and the microsymbiont contribute to the production of NO. From the bacterial perspective, the main source of NO reported in rhizobia is the denitrification pathway that varies significantly depending on the species. In addition to denitrification, nitrate assimilation is emerging as a new source of NO in rhizobia. To control NO accumulation in the nodules, in addition to plant haemoglobins, bacteroids also contribute to NO detoxification through the expression of a NorBC-type nitric oxide reductase as well as rhizobial haemoglobins. In the present review, updated knowledge about the NO metabolism in legume-associated endosymbiotic bacteria is summarized.

A Research Road Map for Responsible Use of Agricultural Nitrogen

Nitrogen (N) is an essential but generally limiting nutrient for biological systems. Development of the Haber-Bosch industrial process for ammonia synthesis helped to relieve N limitation of agricultural production, fueling the Green Revolution and reducing hunger. However, the massive use of industrial N fertilizer has doubled the N moving through the global N cycle with dramatic environmental consequences that threaten planetary health. Thus, there is an urgent need to reduce losses of reactive N from agriculture, while ensuring sufficient N inputs for food security. Here we review current knowledge related to N use efficiency (NUE) in agriculture and identify research opportunities in the areas of agronomy, plant breeding, biological N fixation (BNF), soil N cycling, and modeling to achieve responsible, sustainable use of N in agriculture. Amongst these opportunities, improved agricultural practices that synchronize crop N demand with soil N availability are low-hanging fruit. Crop breeding that targets root and shoot physiological processes will likely increase N uptake and utilization of soil N, while breeding for BNF effectiveness in legumes will enhance overall system NUE. Likewise, engineering of novel N-fixing symbioses in non-legumes could reduce the need for chemical fertilizers in agroecosystems but is a much longer-term goal. The use of simulation modeling to conceptualize the complex, interwoven processes that affect agroecosystem NUE, along with multi-objective optimization, will also accelerate NUE gains.

Nitrogen fixation in maize: breeding opportunities

Maize (Zea mays L.) is a highly versatile crop with huge demand of nitrogen (N) for its growth and development. N is the most essential macronutrient for crop production. Despite being the highest abundant element in the atmosphere (~ 78%), it is scarcely available for plant growth. To fulfil the N demand, commercial agriculture is largely dependent on synthetic fertilizers. Excessive dependence on inorganic fertilizers has created extensive ecological as well as economic problems worldwide. Hence, for a sustainable solution to nitrogenous fertilizer use, development of biological nitrogen fixation (BNF) in cereals will be the best alternative. BNF is a well-known mechanism in legumes where diazotrophs convert atmospheric nitrogen (N≡N) to plant-available form, ammonium (NH₄⁺). From many decades, researchers have dreamt to develop a similar symbiotic partnership as in legumes to the cereal crops. A large number of endophytic diazotrophs have been found associated with maize. Elucidation of the genetic and molecular aspects of their interaction will open up new avenues to introgress BNF in maize breeding. With the advanced understanding of N-fixation process, researchers are at a juncture of breeding and engineering this symbiotic relationships in cereals. Different breeding, genetic engineering, omics, gene editing, and synthetic biology approaches will be discussed in this review to make BNF a reality in cereals. It will help to provide a road map to develop/improve the BNF in maize to an advance step for the sustainable production system to achieve the food and nutritional security.

β-N-Methylamino-L-Alanine (BMAA) Causes Severe Stress in Nostoc sp. PCC 7120 Cells under Diazotrophic Conditions: A Proteomic Study

Non-proteinogenic neurotoxic amino acid β-N-methylamino-L-alanine (BMAA) is synthesized by cyanobacteria, diatoms, and dinoflagellates, and is known to be a causative agent of human neurodegenerative diseases. Different phytoplankton organisms' ability to synthesize BMAA could indicate the importance of this molecule in the interactions between microalgae in nature. We were interested in the following: what kinds of mechanisms underline BMAA's action on cyanobacterial cells in different nitrogen supply conditions. Herein, we present a proteomic analysis of filamentous cyanobacteria Nostoc sp. PCC 7120 cells that underwent BMAA treatment in diazotrophic conditions. In diazotrophic growth conditions, to survive, cyanobacteria can use only biological nitrogen fixation to obtain nitrogen for life. Note that nitrogen fixation is an energy-consuming process. In total, 1567 different proteins of Nostoc sp. PCC 7120 were identified by using LC-MS/MS spectrometry. Among them, 123 proteins belonging to different functional categories were selected-due to their notable expression differences-for further functional analysis and discussion. The presented proteomic data evidences that BMAA treatment leads to very strong (up to 80%) downregulation of α (NifD) and β (NifK) subunits of molybdenum-iron protein, which is known to be a part of nitrogenase. This enzyme is responsible for catalyzing nitrogen fixation. The genes nifD and nifK are under transcriptional control of a global nitrogen regulator NtcA. In this study, we have found that BMAA impacts in a total of 22 proteins that are under the control of NtcA. Moreover, BMAA downregulates 18 proteins that belong to photosystems I or II and light-harvesting complexes; BMAA treatment under diazotrophic conditions also downregulates five subunits of ATP synthase and enzyme NAD(P)H-quinone oxidoreductase. Therefore, we can conclude that the disbalance in energy and metabolite amounts leads to severe intracellular stress that induces the upregulation of stress-activated proteins, such as starvation-inducible DNA-binding protein, four SOS-response enzymes, and DNA repair enzymes, nine stress-response enzymes, and four proteases. The presented data provide new leads into the ecological impact of BMAA on microalgal communities that can be used in future investigations.

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

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

Identification of Genes Involved in Fe-S Cluster Biosynthesis of Nitrogenase in Paenibacillus polymyxa WLY78

NifS and NifU (encoded by nifS and nifU) are generally dedicated to biogenesis of the nitrogenase Fe–S cluster in diazotrophs. However, nifS and nifU are not found in N₂-fixing Paenibacillus strains, and the mechanisms involved in Fe–S cluster biosynthesis of nitrogenase is not clear. Here, we found that the genome of Paenibacillus polymyxa WLY78 contains the complete sufCDSUB operon, a partial sufC2D2B2 operon, a nifS-like gene, two nifU-like genes (nfuA-like and yutI), and two iscS genes. Deletion and complementation studies showed that the sufC, sufD, and sufB genes of the sufCDSUB operon, and nifS-like and yutI genes were involved in the Fe–S cluster biosynthesis of nitrogenase. Heterologous complementation studies demonstrated that the nifS-like gene of P. polymyxa WLY78 is interchangeable with Klebsiella oxytoca nifS, but P. polymyxa WLY78 SufCDB cannot be functionally replaced by K. oxytoca NifU. In addition, K. oxytoca nifU and Escherichia coli nfuA are able to complement the P. polymyxa WLY78 yutI mutant. Our findings thus indicate that the NifS-like and SufCDB proteins are the specific sulfur donor and the molecular scaffold, respectively, for the Fe–S cluster formation of nitrogenase in P. polymyxa WLY78. YutI can be an Fe–S cluster carrier involved in nitrogenase maturation in P. polymyxa WLY78.