Coordinated regulation of nitrogen fixation and molybdate transport by molybdenum

The molybdate transport protein ModA regulates nitrate reductase activity to increase the intestinal colonization and extraintestinal dissemination of Klebsiella pneumoniae in the inflamed gut

The mammalian intestine is a major site of colonization and a starting point of severe infections by Klebsiella pneumoniae. Inflammatory bowel disease (IBD) is an inflammatory disorder of the gut, and host-derived nitrate in IBD confers a luminal growth advantage upon Escherichia coli and Salmonella typhimurium through nitrate respiration in the inflamed gut. However, the impact of nitrate on the growth and pathogenicity of K. pneumoniae in this microenvironment is poorly understood. In this study, we used oral administration of dextran sodium sulphate to induce IBD in mouse models. We then analysed the colonization levels of K. pneumoniae wild-type (WT), the nitrate reductase gene mutant strains (ΔnarG, ΔnarZ and ΔnarGΔnarZ), and the molybdate uptake gene mutant strain (ΔmodA) in the inflamed intestinal tract. Results showed that the growth, intestinal colonization, and extraintestinal dissemination of K. pneumoniae were increased in the intestines of dextran sulphate sodium (DSS)-treated mice. Nitrate in the inflamed bowel conferred a growth advantage to K. pneumoniae through nitrate respiration. The molybdate transport protein ModA regulated nitrate reductase activity to increase the growth, intestinal colonization, and extraintestinal dissemination of K. pneumoniae. Tungstate will be a promising antibacterial agent to tackle K. pneumoniae infections in IBD patients.

ModE Regulates Alternative Nitrogenase Expression in the Methanogen Methanosarcina acetivorans

All methanogens that can fix nitrogen use molybdenum (Mo) nitrogenase. Some methanogens, including Methanosarcina acetivorans, also contain alternative vanadium- and iron-nitrogenases, encoded by the vnf and anf operons, respectively. These nitrogenases are produced when there is insufficient Mo to support Mo-nitrogenase activity. The factors that control the expression of the alternative nitrogenases in response to Mo availability are unknown in methanogens. Here we show that ModE is the regulator that represses transcription of the vnf and anf operons in M. acetivorans when cells are grown with Mo. CRISPRi repression of modE results in a significant increase in the transcription of the vnf and anf operons as well as the detection of Fe-nitrogenase during nitrogen fixation in the presence of Mo. Gel shift assays with recombinant ModE demonstrated that ModE binds a specific sequence motif upstream of the vnf and anf operons, as well as other genes and operons related to nitrogen fixation and Mo transport. However, purified ModE does not contain Mo, and the addition of Mo does not alter the affinity of ModE for DNA, indicating M. acetivorans ModE may not directly bind Mo. This study shows that ModE is the primary Mo-responsive regulator of alternative nitrogenase expression in M. acetivorans, but other factor(s) are likely involved in directly sensing Mo.

Storage of the vital metal tungsten in a dominant SCFA-producing human gut microbe Eubacterium limosum and implications for other gut microbes

Enzymes containing tungsten rather than the ubiquitous and analogous element molybdenum are prevalent in the human gut microbiome, especifically in microbes that contribute to overall gut health. Eubacterium limosum is a dominant human gut organism whose production of beneficial short-chain fatty acids (SCFAs) from lactate involves tungstoenzymes. Here, we characterized E. limosum Tub, a tungsten storage protein. Tub has a sub-nanomolar affinity for tungstate and contains a single TOBE domain first characterized in a molybdate storage protein. Crystal structures revealed Tub assembles as a hexamer composed of a trimer of dimers, capable of binding eight tungstate oxyanions at two distinct binding sites located at inter-subunit interfaces. Tungstate-saturated Tub exhibited unusually high thermal and chemical stability. Glucose-grown E. limosum accumulates tungsten in Tub and has low levels of two tungstoenzymes, termed WOR1 and FDH, which oxidize aldehydes and formate, respectively. Lactate-grown cells contain high concentrations of these two tungstoenzymes where WOR1 and FDH are involved in converting lactate to SCFAs. Glucose-grown cells appear to accumulate tungstate in Tub in preparation for lactate availability in the human gut. Tub and other TOBE-containing proteins are widespread in the human gut microbiome, and gene co-occurrence analysis predicts that there are comparable numbers of TOBE-containing proteins involved in the storage of tungstate as there are that bind molybdate. The results with E. limosum represent an important step for understanding tungsten storage mechanisms for tungstoenzymes within human gut microbes in general.IMPORTANCETungsten metabolism was found to be prevalent in the human gut microbiome, which is involved in the detoxification of food and antimicrobial aldehydes, as well as in the production of beneficial SCFAs. In this study, we characterized a protein in the human gut microbe, Eubacterium limosum, that stores tungstate in preparation for its use in enzymes involved in SCFA generation. This revealed several families of tungstate binding proteins that are also involved in tungstate transport and tungstate-dependent regulation and are widely distributed in the human gut microbiome. Elucidating how tungsten is stored and transported in the human gut microbes contributes to our understanding of the human gut microbiome and its impact on human health.

Kineothrix sedimenti sp. nov., a 3-hydroxybutyrate-producing bacterium isolated from sediment of the meromictic Lake Pavin

An anaerobic, spore-forming, 3-hydroxybutyrate (3-HB)-producing bacterium, strain IPX_CKT, was isolated from sediment of a meromictic lake located in Massif Central (France). Cells were rods, forming filamentous chains which were observed moving under the microscope. Strain IPX_CKT utilized a wide variety of carbohydrates, but not raffinose, rhamnose and starch. Hydrogen (H2), 3-HB, acetate and ethanol were the main fermentative end-products from growth in medium containing glucose. Strain IPX_CKT grew optimally at 37 °C and pH 7. Its closest phylogenetic relative was Kineothrix alysoides (16S rRNA gene sequence identity 98.7%, isDDH 34.6%, ANIb 87.4%). The genomic DNA G+C content was 43.0 mol%. As for K. alysoides, whole-genome sequencing suggested that strain IPX_CKT is capable of fixing nitrogen (N2). However, strain IPX_CKT carried a five-nif-gene-set (nifHDKEB), not present in K. alysoides. Genome sequence also showed a high number of encoded chemotaxis receptors (42 genes, the second highest in the family Lachnospiraceae after K. alysoides). Based on phenotypic, genomic, phylogenetic and chemotaxonomic analyses, it is proposed that a novel species, Kineothrix sedimenti sp. nov., be created, with strain IPX_CKT (DSM 118044T, CIP 112511T) as the type strain.

Hindguts of Kyphosus sydneyanus harbor phylogenetically and genomically distinct Alistipes capable of degrading algal polysaccharides and diazotrophy

The genus Alistipes (Bacteroidota) is most often associated with human clinical samples and livestock. However, Alistipes are also prevalent in the hindgut of the marine herbivorous fish Kyphosus sydneyanus (Silver Drummer), and analysis of their carbohydrate-active enzyme (CAZyme) encoding gene repertoires suggests Alistipes degrade macroalgal biomass to support fish nutrition. To further explore host-associated traits unique to K. sydneyanus-derived Alistipes, we compared 445 high-quality genomes of Alistipes available in public databases (e.g., human and ruminant associated) with 99 metagenome-assembled genomes (MAGs) from the K. sydneyanus gut. Analyses showed that Alistipes from K. sydneyanus are phylogenetically distinct from other hosts and comprise 26 species based on genomic average nucleotide identity (ANI) analyses. Ruminant- and fish-derived Alistipes had significantly smaller genomes than human-derived strains, and lower GC contents, possibly reflecting a symbiotic relationship with their hosts. The fish-derived Alistipes were further delineated by their genetic capacity to fix nitrogen, biosynthesize cobalamin (vitamin B12), and utilize marine polysaccharides (e.g., alginate and carrageenan). The distribution of CAZymes encoded by Alistipes from K. sydneyanus was not phylogenetically conserved. Distinct CAZyme gene compositions were observed between closely related species. Conversely, CAZyme gene clusters (operons) targeting the same substrates were found across diverse species. Nonetheless, transcriptional data suggest that closely related Alistipes target specific groups of substrates within the fish hindgut. Results highlight host-specific adaptations among Alistipes in the fish hindgut that likely contribute to K. sydneyanus digesting their seaweed diet, and diverse and redundant carbohydrate-degrading capabilities across these Alistipes species.IMPORTANCEDespite numerous reports of the Alistipes genus in humans and ruminants, its diversity and function remain understudied, and there is no clear consensus on whether it positively or negatively impacts host health. Given the symbiotic role of gut communities in the Kyphosus sydneyanus hindgut, where Alistipes are prevalent, and the diversity of carbohydrate-active enzymes (CAZymes) encoded that likely contribute to the breakdown of important substrates in the host diet, it is likely that this genus provides essential services to the fish host. Therefore, considering its metabolism in various contexts and hosts is crucial for understanding the ecology of the genus. Our study highlights the distinct genetic traits of Alistipes based on host association, and the potential of fish-associated Alistipes to transform macroalgae biomass into nutraceuticals (alginate oligosaccharides, β-glucans, sulfated galactans, and sulfated fucans).

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.

Combined dynamic transcriptome and flavonoid metabolome reveal the role of Mo nanoparticles in the nodulation process in soybean

Symbiotic nitrogen fixation can reduce the impact of agriculture on the environment by reducing fertilizer input. The rapid development of nanomaterials in agriculture provides a new prospect for us to improve the biological nitrogen fixation ability of leguminous crops. Molybdenum is an important component of nitrogenase, and the potential application of MoO3NPs in agriculture is largely unexplored. In this study, on the basis of verifying that MoO3NPs can improve the nitrogen fixation ability of soybean, the effects of MoO3NPs on the symbiotic nitrogen fixation process of soybean were investigated by using dynamic transcriptome and targeted metabolome techniques. Here we showed that compared with conventional molybdenum fertilizer, minute concentrations of MoO3NPs (0.01-0.1 mg kg-1) could promote soybean growth and nitrogen fixation efficiency. The nodules number, fresh nodule weight and nitrogenase activity of 0.1 mg kg-1 were increased by 17 %, 14 % and 27 %, and plant nitrogen accumulation increased by 17 %. Compared with conventional molybdenum fertilizer, MoO3NPs had a greater effect on apigenin, kaempferol and other flavonoid, and the expression of nodulation related genes such as ENOD93, F3'H. Based on WGCNA analysis, we identified a core gene GmCHS9 that was positively responsive to molybdenum and was highly expressed during MoO3NPs induced nodulation. MoO3NPs could improve the nitrogen fixation ability of soybean by promoting the secretion of flavonoids and the expression of key genes. This study provided a new perspective for the nano-strengthening strategy of nodules development and flavonoid biosynthesis by molybdenum.

Promoting agricultural waste-driven denitrification and nitrogen sequestration with nano-enabled strategy

Nanotechnology and biotechnology offer promising avenues for bolstering food security through the facilitation of soil nitrogen (N) sequestration and the reduction of nitrate leaching. Nonetheless, a comprehensive and mechanistic evaluation of their effectiveness and safety remains unclear. In this study, a soil remediation strategy employing nano-Fe3O4 and straw in N-contaminated soil was developed to elucidate N retention mechanisms via diverse metagenomics techniques. The findings revealed that subsoil amended with straw, particularly in conjunction with nano-Fe3O4, significantly increased subsoil N content (53.2%) and decreased nitrate concentration (74.6%) in leachate. Furthermore, the enrichment of functional genes associated with N-cycling, sulfate, nitrate, and iron uptake, along with chemotaxis, and responses to environmental stimuli or microbial collaboration, effectively mitigates nitrate leaching while enhancing soil N sequestration. This study introduces a pioneering approach utilizing nanomaterials in soil remediation, thereby offering the potential for the cultivation of safe vegetables in high N input greenhouse agriculture.

Bioaccumulation of molybdate ions by alkanotrophic Rhodococcus leads to significant alterations in cellular ultrastructure and physiology

Alkanotrophic Rhodococcus strains from the Regional Specialised Collection of Alkanotrophic Microorganisms (acronym IEGM, www.iegmcol.ru) were screened for accumulation and sorption of MoO42- ions. Morphological and ultrastructural changes observed in bacterial cells during their cultivation in the molybdenum-containing medium are described. The species peculiarities, growth substrate preferences, and other physiological features allowing for the efficient removal of molybdate ions from the culture medium are discussed. Bioinformatics analysis of genes and proteins responsible for resistance to and accumulation of molybdenum was carried out using the sequenced R. ruber IEGM 231 and other published Rhodococcus genomes. n-Hexadecane growing strains with high (up to 85 %) accumulative activity and resistance to elevated (up to 20.0 mM) molybdenum concentrations were selected, which can be used for bioremediation of environments co-contaminated with heavy metals and hydrocarbons. Transmission electron microscopy and energy dispersive X-ray spectroscopy (TEM-EDX) revealed the ability of Rhodococcus not only to accumulate, but also to chemically convert soluble toxic molybdenum into insoluble compounds detected in the form of electron-dense nanoparticles.

Proteome profiling of Paenibacillus sonchi genomovar Riograndensis SBR5T under conventional and alternative nitrogen fixation

Paenibacillus sonchi SBR5T is a Gram-positive, endospore-forming facultative aerobic diazotrophic bacterium that can fix nitrogen via an alternative Fe-only nitrogenase (AnfHDGK). In several bacteria, this alternative system is expressed under molybdenum (Mo)-limiting conditions when the conventional Mo-dependent nitrogenase (NifHDK) production is impaired. The regulatory mechanisms, metabolic processes, and cellular functions of N2 fixation by alternative and/or conventional systems are poorly understood in the Paenibacillus genus. We conducted a comparative proteomic profiling study of P. sonchi SBR5T grown under N2-fixing conditions with and without Mo supply through an LC-MS/MS and label-free quantification analysis to address this gap. Protein abundances revealed overrepresented processes related to anaerobiosis growth adaption, Fe-S cluster biosynthesis, ammonia assimilation, electron transfer, and sporulation under N2-fixing conditions compared to non-fixing control. Under Mo limitation, the Fe-only nitrogenase components were overrepresented together with the Mo-transporter system, while the dinitrogenase component (NifDK) of Mo‑nitrogenase was underrepresented. The dinitrogenase reductase component (NifH) and accessory proteins encoded by the nif operon had no significant differential expression, suggesting post-transcriptional regulation of nif gene products in this strain. Overall, this was the first comprehensive proteomic analysis of a diazotrophic strain from the Paenibacillaceae family, and it provided insights related to alternative N2-fixation by Fe-only nitrogenase. SIGNIFICANCE: In this work, we try to understand how the alternative nitrogen fixation system, presented by some diazotrophic bacteria, works. For this, we used the SBR5 lineage of P. sonchi, which presents the alternative system in which the nitrogenase cofactor is composed only of iron. In addition, we tried to unravel the proteome of this strain in different situations of nitrogen fixation, since, for Gram-positive bacteria, these systems are little known. The results achieved, through LC-MS/MS and label-free quantitative analysis, showed an overrepresentation of proteins related to different processes involved with growth under stressful conditions in situations of nitrogen deficiency, in addition to suggesting that some encoded proteins by the nif operon may be regulated at post-transcriptional levels. Our findings represent important steps toward the elucidation of nitrogen fixation systems in Gram-positive diazotrophic bacteria.

Environmental stress mediates groundwater microbial community assembly

Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.

The Mechanisms of Molybdate Distribution and Homeostasis with Special Focus on the Model Plant Arabidopsis thaliana

This review article deals with the pathways of cellular and global molybdate distribution in plants, especially with a full overview for the model plant Arabidopsis thaliana. In its oxidized state as bioavailable molybdate, molybdenum can be absorbed from the environment. Especially in higher plants, molybdenum is indispensable as part of the molybdenum cofactor (Moco), which is responsible for functionality as a prosthetic group in a variety of essential enzymes like nitrate reductase and sulfite oxidase. Therefore, plants need mechanisms for molybdate import and transport within the organism, which are accomplished via high-affinity molybdate transporter (MOT) localized in different cells and membranes. Two different MOT families were identified. Legumes like Glycine max or Medicago truncatula have an especially increased number of MOT1 family members for supplying their symbionts with molybdate for nitrogenase activity. In Arabidopsis thaliana especially, the complete pathway followed by molybdate through the plant is traceable. Not only the uptake from soil by MOT1.1 and its distribution to leaves, flowers, and seeds by MOT2-family members was identified, but also that inside the cell. the transport trough the cytoplasm and the vacuolar storage mechanisms depending on glutathione were described. Finally, supplying the Moco biosynthesis complex by MOT1.2 and MOT2.1 was demonstrated.

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.

Regulatory response to a hybrid ancestral nitrogenase in Azotobacter vinelandii

Biological nitrogen fixation, the microbial reduction of atmospheric nitrogen to bioavailable ammonia, represents both a major limitation on biological productivity and a highly desirable engineering target for synthetic biology. However, the engineering of nitrogen fixation requires an integrated understanding of how the gene regulatory dynamics of host diazotrophs respond across sequence-function space of its central catalytic metalloenzyme, nitrogenase. Here, we interrogate this relationship by analyzing the transcriptome of Azotobacter vinelandii engineered with a phylogenetically inferred ancestral nitrogenase protein variant. The engineered strain exhibits reduced cellular nitrogenase activity but recovers wild-type growth rates following an extended lag period. We find that expression of genes within the immediate nitrogen fixation network is resilient to the introduced nitrogenase sequence-level perturbations. Rather the sustained physiological compatibility with the ancestral nitrogenase variant is accompanied by reduced expression of genes that support trace metal and electron resource allocation to nitrogenase. Our results spotlight gene expression changes in cellular processes adjacent to nitrogen fixation as productive engineering considerations to improve compatibility between remodeled nitrogenase proteins and engineered host diazotrophs. IMPORTANCE Azotobacter vinelandii is a key model bacterium for the study of biological nitrogen fixation, an important metabolic process catalyzed by nitrogenase enzymes. Here, we demonstrate that compatibilities between engineered A. vinelandii strains and nitrogenase variants can be modulated at the regulatory level. The engineered strain studied here responds by adjusting the expression of proteins involved in cellular processes adjacent to nitrogen fixation, rather than that of nitrogenase proteins themselves. These insights can inform future strategies to transfer nitrogenase variants to non-native hosts.

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.

The molybdate-binding protein ModA is required for Proteus mirabilis-induced UTI

Background

Proteus mirabilis is one of the pathogens commonly causing urinary tract infections (UTIs). The molybdate-binding protein ModA encoded by modA binds molybdate with high affinity and transports it. Increasing evidence shows that ModA promotes the survival of bacteria in anaerobic environments and participates in bacterial virulence by obtaining molybdenum. However, the role of ModA in the pathogenesis of P. mirabilis remains unknown.

Results

In this study, a series of phenotypic assays and transcriptomic analyses were used to study the role of ModA in the UTIs induced by P. mirabilis. Our data showed that ModA absorbed molybdate with high affinity and incorporated it into molybdopterin, thus affecting the anaerobic growth of P. mirabilis. Loss of ModA enhanced bacterial swarming and swimming and up-regulated the expression of multiple genes in flagellar assembly pathway. The loss of ModA also resulted in decreased biofilm formation under anaerobic growth conditions. The modA mutant significantly inhibited bacterial adhesion and invasion to urinary tract epithelial cells and down-regulated the expression of multiple genes associated with pilus assembly. Those alterations were not due to anaerobic growth defects. In addition, the decreased bacteria in the bladder tissue, the weakened inflammatory damage, the low level of IL-6, and minor weight change was observed in the UTI mouse model infected with modA mutant.

Conclusion

Here, we reported that in P. mirabilis, ModA mediated the transport of molybdate, thereby affecting the activity of nitrate reductase and thus affecting the growth of bacteria under anaerobic conditions. Overall, this study clarified the indirect role of ModA in the anaerobic growth, motility, biofilm formation, and pathogenicity of P. mirabilis and its possible pathway, and emphasized the importance of the molybdate-binding protein ModA to P. mirabilis in mediating molybdate uptake, allowing the bacterium to adapt to complex environmental conditions and cause UTIs. Our results provided valuable information on the pathogenesis of ModA-induced P. mirabilis UTIs and may facilitate the development of new treatment strategies.

An Important Role of the Type VI Secretion System of Pseudomonas aeruginosa Regulated by Dnr in Response to Anaerobic Environments

The type VI secretion system (T6SS) is capable of secreting a variety of metal-binding proteins involved in metal ion uptake, and it mediates an active metal ion transport system that contributes to competition between bacteria. Pseudomonas aeruginosa H2-T6SS can increase molybdenum ion acquisition and enhance bacterial survival advantage by promoting the secretion of the molybdate-binding protein ModA, in which the expression of H2-T6SS core genes hcp2, hsiA2, and clpV2 is activated by anaerobic conditions and are all regulated by the global regulator Anr. Here, we report the regulation of T6SS by Dnr, a dedicated dissimilatory nitrate respiration regulator in P. aeruginosa. Of the three distinct T6SS loci carried by P. aeruginosa, only the anaerobic expression of H2-T6SS was activated by Dnr; H1-T6SS or H3-T6SS did not respond to anaerobically induced activation. We also demonstrated that Dnr promotes the anaerobic secretion of ModA, which acts as a potential substrate for H2-T6SS, providing an advantage not only for the anaerobic growth of bacteria but also for functional competition. Overall, this study elucidates the important role played by Dnr in mediating the anaerobic expression of T6SS in P. aeruginosa, indicating that the functional advantage of H2-T6SS in response to anaerobic induction may be a conditional environmental adaptation. It also extends our understanding of the function of Dnr as a specific regulator of dissimilatory nitrate respiration. IMPORTANCE The type VI secretion system (T6SS) plays an important role in bacterial competition by mediating the transport of active metal ions. Pseudomonas aeruginosa carries three distinct T6SS loci (H1-, H2-, and H3-T6SS). The H2-T6SS promotes the secretion of the molybdate-binding protein ModA for the acquisition of molybdenum ions to adapt to anaerobic survival. Here, we report that the specialized dissimilatory nitrate respiration regulator Dnr in P. aeruginosa controls the anaerobic expression of H2-T6SS and that this regulation is essential for ModA protein secretion, anaerobic growth, and bacterial competition. This study elucidates the regulatory mechanism of Dnr on H2-T6SS in P. aeruginosa, revealing an important role played by H2-T6SS in adapting to an anaerobic environment.

Gluconacetobacter diazotrophicus Gene Fitness during Diazotrophic Growth

Plant growth-promoting (PGP) bacteria are important to the development of sustainable agricultural systems. PGP microbes that fix atmospheric nitrogen (diazotrophs) could minimize the application of industrially derived fertilizers and function as a biofertilizer. The bacterium Gluconacetobacter diazotrophicus is a nitrogen-fixing PGP microbe originally discovered in association with sugarcane plants, where it functions as an endophyte. It also forms endophyte associations with a range of other agriculturally relevant crop plants. G. diazotrophicus requires microaerobic conditions for diazotrophic growth. We generated a transposon library for G. diazotrophicus and cultured the library under various growth conditions and culture medium compositions to measure fitness defects associated with individual transposon inserts (transposon insertion sequencing [Tn-seq]). Using this library, we probed more than 3,200 genes and ascertained the importance of various genes for diazotrophic growth of this microaerobic endophyte. We also identified a set of essential genes. IMPORTANCE Our results demonstrate a succinct set of genes involved in diazotrophic growth for G. diazotrophicus, with a lower degree of redundancy than what is found in other model diazotrophs. The results will serve as a valuable resource for those interested in biological nitrogen fixation and will establish a baseline data set for plant free growth, which could complement future studies related to the endophyte relationship.

Origin and evolution of nitrogen fixation in prokaryotes

The origin of nitrogen fixation is an important issue in evolutionary biology. While nitrogen is required by all living organisms, only a small fraction of bacteria and archaea can fix nitrogen. The prevailing view is that nitrogen fixation first evolved in archaea and was later transferred to bacteria. However, nitrogen-fixing (Nif) bacteria are far larger in number and far more diverse in ecological niches than Nif archaea. We, therefore, propose the bacteria-first hypothesis, which postulates that nitrogen fixation first evolved in bacteria and was later transferred to archaea. As >30,000 prokaryotic genomes have been sequenced, we conduct an in-depth comparison of the two hypotheses. We first identify the six genes involved in nitrogen fixation in all sequenced prokaryotic genomes and then reconstruct phylogenetic trees using the six Nif proteins individually or in combination. In each of these trees, the earliest lineages are bacterial Nif protein sequences and in the oldest clade (group) the archaeal sequences are all nested inside bacterial sequences, suggesting that the Nif proteins first evolved in bacteria. The bacteria-first hypothesis is further supported by the observation that the majority of Nif archaea carry the major bacterial Mo (molybdenum) transporter (ModABC) rather than the archaeal Mo transporter (WtpABC). Moreover, in our phylogeny of all available ModA and WtpA protein sequences, the earliest lineages are bacterial sequences while archaeal sequences are nested inside bacterial sequences. Furthermore, the bacteria-first hypothesis is supported by available isotopic data. In conclusion, our study strongly supports the bacteria-first hypothesis.

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.

Current and future threats to human health in the Anthropocene

It has been widely recognised that the threats to human health from global environmental changes (GECs) are increasing in the Anthropocene epoch, and urgent actions are required to tackle these pressing challenges. A scoping review was conducted to provide an overview of the nine planetary boundaries and the threats to population health posed by human activities that are exceeding these boundaries in the Anthropocene. The research progress and key knowledge gaps were identified in this emerging field. Over the past three decades, there has been a great deal of research progress on health risks from climate change, land-use change and urbanisation, biodiversity loss and other GECs. However, several significant challenges remain, including the misperception of the relationship between human and nature; assessment of the compounding risks of GECs; strategies to reduce and prevent the potential health impacts of GECs; and uncertainties in fulfilling the commitments to the Paris Agreement. Confronting these challenges will require rigorous scientific research that is well-coordinated across different disciplines and various sectors. It is imperative for the international community to work together to develop informed policies to avert crises and ensure a safe and sustainable planet for the present and future generations.

Specificity of NifEN and VnfEN for the Assembly of Nitrogenase Active Site Cofactors in Azotobacter vinelandii

The nitrogen-fixing microbe Azotobacter vinelandii has the ability to produce three genetically distinct, but mechanistically similar, components that catalyze nitrogen fixation. For two of these components, the Mo-dependent and V-dependent components, their corresponding metal-containing active site cofactors, designated FeMo-cofactor and FeV-cofactor, respectively, are preformed on separate molecular scaffolds designated NifEN and VnfEN, respectively. From prior studies, and the present work, it is now established that neither of these scaffolds can replace the other with respect to their in vivo cofactor assembly functions. Namely, a strain inactivated for NifEN cannot produce active Mo-dependent nitrogenase nor can a strain inactivated for VnfEN produce an active V-dependent nitrogenase. It is therefore proposed that metal specificities for FeMo-cofactor and FeV-cofactor formation are supplied by their respective assembly scaffolds. In the case of the third, Fe-only component, its associated active site cofactor, designated FeFe-cofactor, requires neither the NifEN nor VnfEN assembly scaffold for its formation. Furthermore, there are no other genes present in A. vinelandii that encode proteins having primary structure similarity to either NifEN or VnfEN. It is therefore concluded that FeFe-cofactor assembly is completed within its cognate catalytic protein partner without the aid of an intermediate assembly site. IMPORTANCE Biological nitrogen fixation is a complex process involving the nitrogenases. The biosynthesis of an active nitrogenase involves a large number of genes and the coordinated function of their products. Understanding the details of the assembly and activation of the different nitrogen fixation components, in particular the simplest one known so far, the Fe-only nitrogenase, would contribute to the goal of transferring the necessary genetic elements of bacterial nitrogen fixation to cereal crops to endow them with the capacity for self-fertilization. In this work, we show that there is no need for a scaffold complex for the assembly of the FeFe-cofactor, which provides the active site for Fe-only nitrogenase. These results are in agreement with previously reported genetic reconstruction experiments using a non-nitrogen-fixing microbe. In aggregate, these findings provide a high degree of confidence that the Fe-only system represents the simplest and, therefore, most attractive target for mobilizing nitrogen fixation into plants.

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.

Effectiveness of nitrogen fixation in rhizobia

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

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

The enzyme molybdenum nitrogenase converts atmospheric nitrogen gas to ammonia and is of critical importance for the cycling of nitrogen in the biosphere and for the sustainability of life. Alternative vanadium and iron-only nitrogenases that are homologous to molybdenum nitrogenases are also found in archaea and bacteria, but they have a different transition metal, either vanadium or iron, at their active sites. So far alternative nitrogenases have only been found in microbes that also have molybdenum nitrogenase. They are less widespread than molybdenum nitrogenase in bacteria and archaea, and they are less efficient. The presumption has been that alternative nitrogenases are fail-safe enzymes that are used in situations where molybdenum is limiting. Recent work indicates that vanadium nitrogenase may play a role in the global biological nitrogen cycle and iron-only nitrogenase may contribute products that shape microbial community interactions in nature.

Contribution of autochthonous diazotrophs to polycyclic aromatic hydrocarbon dissipation in contaminated soils

Understanding the role played by autochthonous functional microbes involved in the biotransformation of pollutants would help optimize bioremediation performance at contaminated sites. However, our knowledge of the remediation potential of indigenous diazotrophs in contaminated soils remains inadequate. Using a microcosm experiment, soil nitrogen fixation activity was manipulated by molybdenum (Mo) and tungsten (W), and their effect on the removal of polycyclic aromatic hydrocarbons (PAHs) was determined in agricultural and industrial soils. Results showed that after 42 days of incubation, PAH dissipation efficiency was significantly enhanced by 1.06-fold in 600 μg kg^-1 Mo-treated agricultural soil, compared with that in the control. For the industrial soil, 1200 μg kg^-1 Mo treatment significantly promoted PAH removal by 90.76% in 21 days, whereas no significant change was observed between treatments and control at the end of the incubation period. W also exerted a similar effect on PAH dissipation. The activity and gene abundance of nitrogenase were also increased under Mo/W treatments in the two soils. Spearman's correlation analysis further indicated that removal of PAHs was positively correlated with nitrogenase activity in soil, which could be due to the elevated abundances of PAH-degrading genes (PAH-RHDα) in these treatments. Our results suggest the importance of autochthonous diazotrophs in PAH-contaminated soils, which indicates a feasible and environmentally friendly biostimulation strategy of manipulating nitrogen fixation capacity.

Transition metal transporters in rhizobia: tuning the inorganic micronutrient requirements to different living styles

A group of bacteria known as rhizobia are key players in symbiotic nitrogen fixation (SNF) in partnership with legumes. After a molecular exchange, the bacteria end surrounded by a plant membrane forming symbiosomes, organelle-like structures, where they differentiate to bacteroids and fix nitrogen. This symbiotic process is highly dependent on dynamic nutrient exchanges between the partners. Among these are transition metals (TM) participating as inorganic and organic cofactors of fundamental enzymes. While the understanding of how plant transporters facilitate TMs to the very near environment of the bacteroid is expanding, our knowledge on how bacteroid transporters integrate to TM homeostasis mechanisms in the plant host is still limited. This is significantly relevant considering the low solubility and scarcity of TMs in soils, and the in crescendo gradient of TM bioavailability rhizobia faces during the infection and bacteroid differentiation processes. In the present work, we review the main metal transporter families found in rhizobia, their role in free-living conditions and, when known, in symbiosis. We focus on discussing those transporters which could play a significant role in TM-dependent biochemical and physiological processes in the bacteroid, thus paving the way towards an optimized SNF.

Rhodobacter capsulatus AnfA is essential for production of Fe-nitrogenase proteins but dispensable for cofactor biosynthesis and electron supply

The photosynthetic α‐proteobacterium Rhodobacter capsulatus reduces and thereby fixes atmospheric dinitrogen (N₂) by a molybdenum (Mo)‐nitrogenase and an iron‐only (Fe)‐nitrogenase. Differential expression of the structural genes of Mo‐nitrogenase (nifHDK) and Fe‐nitrogenase (anfHDGK) is strictly controlled and activated by NifA and AnfA, respectively. In contrast to NifA‐binding sites, AnfA‐binding sites are poorly defined. Here, we identified two highly similar AnfA‐binding sites in the R. capsulatus anfH promoter by studying the effects of promoter mutations on in vivo anfH expression and in vitro promoter binding by AnfA. Comparison of the experimentally determined R. capsulatus AnfA‐binding sites and presumed AnfA‐binding sites from other α‐proteobacteria revealed a consensus sequence of dyad symmetry, TAC–N₆–GTA, suggesting that AnfA proteins bind their target promoters as dimers. Chromosomal replacement of the anfH promoter by the nifH promoter restored anfHDGK expression and Fe‐nitrogenase activity in an R. capsulatus strain lacking AnfA suggesting that AnfA is required for AnfHDGK production, but dispensable for biosynthesis of the iron‐only cofactor and electron delivery to Fe‐nitrogenase, pathways activated by NifA. These observations strengthen our model, in which the Fe‐nitrogenase system in R. capsulatus is largely integrated into the Mo‐nitrogenase system.

Bioreactor performance using biochar and its effect on aerobic granulation

The effects that rice husk (biochar-rh), rice bran (biochar-rb) and walnut shell (biochar-ws) biochar had on aerobic granulation and reactor performance during the treatment of petroleum wastewater have been investigated. The different biochars reduced aerobic granulation time by 15 days compared with the control and also increased resistance to shock loading. The average COD and TN removal increased by 3.2%-5.1% and 10%-13%, respectively. Bacteria having functional metabolisms associated with the treatment of petroleum wastewaters were enriched in granular sludge that contained biochars. The reactor containing biochar-rb was the most stable and removed the most nutrients. The reactor containing biochar-rh had the largest initial granule size. This study provides insights into how the physicochemical properties of different biochars influence aerobic granular sludge systems.

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

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

Microbiological strategies for enhancing biological nitrogen fixation in nonlegumes

In an agro-ecosystem, industrially produced nitrogenous fertilizers are the principal sources of nitrogen for plant growth; unfortunately these also serve as the leading sources of pollution. Hence, it becomes imperative to find pollution-free methods of providing nitrogen to crop plants. A diverse group of free-living, plant associative and symbiotic prokaryotes are able to perform biological nitrogen fixation (BNF). BNF is a two component process involving the nitrogen fixing diazotrophs and the host plant. Symbiotic nitrogen fixation is most efficient as it can fix nitrogen inside the nodule formed on the roots of the plant; delivering nitrogen directly to the host. However, most of the important crop plants are nonleguminous and are unable to form symbiotic associations. In this context, the plant associative and endophytic diazotrophs assume importance. BNF in nonlegumes can be encouraged either through the transfer of BNF traits from legumes or by elevating the nitrogen fixing capacity of the associative and endophytic diazotrophs. In this review we discuss mainly the microbiological strategies which may be used in nonleguminous crops for enhancement of BNF.

NifA is the master regulator of both nitrogenase systems in Rhodobacter capsulatus

Rhodobacter capsulatus fixes atmospheric nitrogen (N₂) by a molybdenum (Mo)‐nitrogenase and a Mo‐free iron (Fe)‐nitrogenase, whose production is induced or repressed by Mo, respectively. At low nanomolar Mo concentrations, both isoenzymes are synthesized and contribute to nitrogen fixation. Here we examined the regulatory interplay of the central transcriptional activators NifA and AnfA by proteome profiling. As expected from earlier studies, synthesis of the structural proteins of Mo‐nitrogenase (NifHDK) and Fe‐nitrogenase (AnfHDGK) required NifA and AnfA, respectively, both of which depend on the alternative sigma factor RpoN to activate expression of their target genes. Unexpectedly, NifA was found to be essential for the synthesis of Fe‐nitrogenase, electron supply to both nitrogenases, biosynthesis of their cofactors, and production of RpoN. Apparently, RpoN is the only NifA‐dependent factor required for target gene activation by AnfA, since plasmid‐borne rpoN restored anfH transcription in a NifA‐deficient strain. However, plasmid‐borne rpoN did not restore Fe‐nitrogenase activity in this strain. Taken together, NifA requirement for synthesis and activity of both nitrogenases suggests that Fe‐nitrogenase functions as a complementary nitrogenase rather than an alternative isoenzyme in R. capsulatus.

The regulation of Moco biosynthesis and molybdoenzyme gene expression by molybdenum and iron in bacteria

The regulation of the operons involved in Moco biosynthesis is dependent on the availability of Fe–S clusters in the cell.