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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 (S 2 O 3 ). 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.2- ). 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., Competing Interests: The authors declare no conflict of interest.

Abstract Free‐living nitrogen fixation (FLNF) represents an important terrestrial N source and is gaining interest for its potential to contribute plant available N to bioenergy cropping systems. Switchgrass, a cellulosic bioenergy crop, may be particularly reliant on FLNF when grown on low N systems, like marginal lands. However, the potential contributions of FLNF to switchgrass as well as the controls on this process are not well understood. In this study, we evaluated drivers of FLNF rates and N‐fixing microbial (diazotrophic) community composition in field‐grown switchgrass systems over two growing seasons with high temporal sampling. We found that climate variables are strong drivers of FLNF rates in switchgrass systems, compared to other environmental and biological factors including soil nutrients and diazotrophic community composition. Increased soil moisture availability generally promoted FLNF rates, but extreme rainfall events were detrimental. These climate‐related responses suggest a potential for loss of FLNF‐derived N contributions under projected climate shifts. We found a significant, but weak correlation between diazotrophic community composition and FLNF rates. We also observed a significant shift in the diazotrophic community composition between 2017 and 2018 and similarly measured a significant difference in FLNF rates between growing seasons. Lastly, we found that seasonal FLNF N contributions, based on measurement with high temporal resolution, has the potential to meet up to 80% of switchgrass N demands suggesting that FLNF measurements extrapolated from fewer time points or locations may underestimate these potential N contributions.

Abstract Background Nitrogen-fixing prokaryotes (diazotrophs) contribute substantially to nitrogen input in mangrove sediments, and their structure and nitrogen fixation rate (NFR) are significantly controlled by environmental conditions. Despite the well-known studies on diazotrophs in surficial sediments, the diversity, structure, and ecological functions of diazotrophic communities along environmental gradients of mangrove sediment across different depths are largely unknown. Here, we investigated how biological nitrogen fixation varied with the depth of mangrove sediments from the perspectives of both NFR and diazotrophic communities. Results Through acetylene reduction assay, nifH gene amplicon and metagenomic sequencing, we found that the NFR increased but the diversity of diazotrophic communities decreased with the depth of mangrove sediments. The structure of diazotrophic communities at different depths was largely driven by salinity and exhibited a clear divergence at the partitioning depth of 50 cm. Among diazotrophic genera correlated with NFR, Agrobacterium and Azotobacter were specifically enriched at 50–100 cm sediments, while Anaeromyxobacter, Rubrivivax, Methylocystis, Dickeya, and Methylomonas were more abundant at 0–50 cm. Consistent with the higher NFR, metagenomic analysis demonstrated the elevated abundance of nitrogen fixation genes (nifH/D/K) in deep sediments, where nitrification genes (amoA/B/C) and denitrification genes (nirK and norB) became less abundant. Three metagenome-assembled genomes (MAGs) of diazotrophs from deep mangrove sediments indicated their facultatively anaerobic and mixotrophic lifestyles as they contained genes for low-oxygen-dependent metabolism, hydrogenotrophic respiration, carbon fixation, and pyruvate fermentation. Conclusions This study demonstrates the depth-dependent variability of biological nitrogen fixation in terms of NFR and diazotrophic communities, which to a certain extent relieves the degree of nitrogen limitation in deep mangrove sediments. Video Abstract

The apparently obligate symbiosis between the diazotroph Candidatus Atelocyanobacterium thalassa (UCYN-A) and its haptophyte host, Braarudosphaera bigelowii, has recently been found to fix dinitrogen (N2) in polar waters at rates (per cell) comparable to those observed in the tropical/subtropical oligotrophic ocean basins. This study presents the novel observation that this symbiosis increased in abundance during a wind-driven upwelling event along the Alaskan Beaufort shelfbreak. As upwelling relaxed, the relative abundance of B. bigelowii among eukaryotic phytoplankton increased most significantly in waters over the upper slope. As the host’s nitrogen demands are believed to be supplied primarily by UCYN-A, this response suggests that upwelling may enhance N2 fixation as displaced coastal waters are advected offshore, potentially extending the duration of upwelling-induced phytoplankton blooms. Given that such events are projected to increase in intensity and number with ocean warming, upwelling-driven N2 fixation as a feedback on climate merits investigation.

Microalgae are used in various biotechnological processes, such as biofuel production due to their high biomass yields, agriculture as biofertilizers, production of high-value-added products, decontamination of wastewater, or as biological models for carbon sequestration. The number of these biotechnological applications is increasing, and as such, any advances that contribute to reducing costs and increasing economic profitability can have a significant impact. Nitrogen fixing organisms, often called diazotroph, also have great biotechnological potential, mainly in agriculture as an alternative to chemical fertilizers. Microbial consortia typically perform more complex tasks than monocultures and can execute functions that are challenging or even impossible for individual strains or species. Interestingly, microalgae and diazotrophic organisms are capable to embrace different types of symbiotic associations. Certain corals and lichens exhibit this symbiotic relationship in nature, which enhances their fitness. However, this relationship can also be artificially created in laboratory conditions with the objective of enhancing some of the biotechnological processes that each organism carries out independently. As a result, the utilization of microalgae and diazotrophic organisms in consortia is garnering significant interest as a potential alternative for reducing production costs and increasing yields of microalgae biomass, as well as for producing derived products and serving biotechnological purposes. This review makes an effort to examine the associations of microalgae and diazotrophic organisms, with the aim of highlighting the potential of these associations in improving various biotechnological processes.

The excessive usage of nitrogen (N) fertilizers can accelerate the tendency of global climate change. Biological N fixation by diazotrophs contributes substantially to N input and is a viable solution to sustainable agriculture via reducing inorganic N fertilization. However, how manure application influences the abundance, community structure and assembly process of diazotrophs in soil aggregates is not fully understood. Here, we investigated the effect of manure amendment on diazotrophic communities in soil aggregates of an arable soil. Manure application increased soil aggregation, crop yield and the abundance of nifH genes. The abundance of nifH genes increased with aggregate sizes, indicating that diazotrophs prefer to live in larger aggregates. The abundance of nifH genes in large macroaggregates, rather than in microaggregates and silt and clay, was positively associated with plant biomass and crop yield. Both manure application and aggregate size did not alter the Shannon diversity of diazotrophs but significantly changed the diazotrophic community structure. The variation of diazotrophic community structure explained by manure application was greater than that by aggregate size. Manure application promoted the relative abundance of Firmicutes but reduced that of a-Proteobacteria. Stochastic processes played a dominant role in the assembly of diazotrophs in the control treatment. Low-rate manure (9Mg ha-1) application, rather than medium-rate (18Mg ha-1) and high-rate (27Mg ha-1) manure, significantly increased the relative importance of deterministic processes in diazotrophic community assembly. Taken together, our findings demonstrated that long-term manure application increased nifH gene abundance and altered the community structure and assembly process of diazotrophs in soil aggregates, which advanced our understanding of the ecophysiology and functionality of diazotrophs in acidic Ultisols. [ABSTRACT FROM AUTHOR]

The genome of the moderately haloalkaliphilic diazotrophic anoxygenic phototrophic bacterium Rhodovulum tesquicola A-36sT isolated from an alkaline lake was analyzed and compared to the genomes of the closest species Rhodovulum steppense A-20sT and Rhodovulum strictum DSM 11289T. The genomic features of three organisms are quite similar, reflecting their ecological and physiological role of facultative photoheterotrophs. Nevertheless, the nitrogenase activity of the pure cultures of the studied bacteria differed significantly: the highest rate (4066 nmoles C2H2/mg of dry weight per hour) was demonstrated by Rhodovulum strictum while the rates in Rhodovulum tesquicola and Rhodovulum steppense were an order of magnitude lower (278 and 523 nmoles C2H2/mg of dry weight per hour, respectively). This difference can be attributed to the presence of an additional nitrogenase operon found exclusively in R. strictum and to the structural variation in nitrogenase operon in R. tesquicola. [ABSTRACT FROM AUTHOR]

Background: The importance of symbiosis has long been recognized on coral reefs, where the photosynthetic dinoflagellates of corals (Symbiodiniaceae) are the primary symbiont. Numerous studies have now shown that a diverse assemblage of prokaryotes also make-up part of the microbiome of corals. A subset of these prokaryotes is capable of fixing nitrogen, known as diazotrophs, and is also present in the microbiome of scleractinian corals where they have been shown to supplement the holobiont nitrogen budget. Here, an analysis of the microbiomes of 16 coral species collected from Australia, Curaçao, and Hawai'i using three different marker genes (16S rRNA, nifH, and ITS2) is presented. These data were used to examine the effects of biogeography, coral traits, and ecological life history characteristics on the composition and diversity of the microbiome in corals and their diazotrophic communities. Results: The prokaryotic microbiome community composition (i.e., beta diversity) based on the 16S rRNA gene varied between sites and ecological life history characteristics, but coral morphology was the most significant factor affecting the microbiome of the corals studied. For 15 of the corals studied, only two species Pocillopora acuta and Seriotopora hystrix, both brooders, showed a weak relationship between the 16S rRNA gene community structure and the diazotrophic members of the microbiome using the nifH marker gene, suggesting that many corals support a microbiome with diazotrophic capabilities. The order Rhizobiales, a taxon that contains primarily diazotrophs, are common members of the coral microbiome and were eight times greater in relative abundances in Hawai'i compared to corals from either Curacao or Australia. However, for the diazotrophic component of the coral microbiome, only host species significantly influenced the composition and diversity of the community. Conclusions: The roles and interactions between members of the coral holobiont are still not well understood, especially critical functions provided by the coral microbiome (e.g., nitrogen fixation), and the variation of these functions across species. The findings presented here show the significant effect of morphology, a coral "super trait," on the overall community structure of the microbiome in corals and that there is a strong association of the diazotrophic community within the microbiome of corals. However, the underlying coral traits linking the effects of host species on diazotrophic communities remain unknown. 2iUFYDy-sBVn2WqgoVCqfb Video Abstract [ABSTRACT FROM AUTHOR]

Nitrogen (N) shortage poses a great challenge to the implementation of in situ bioremediation practices in mining-contaminated sites. Diazotrophs can fix atmospheric N2 into a bioavailable form to plants and microorganisms inhabiting adverse habitats. Increasing numbers of studies mainly focused on the diazotrophic communities in the agroecosystems, while those communities in mining areas are still not well understood. This study compared the variations of diazotrophic communities in composition and interactions in the mining areas with different extents of arsenic (As) and antimony (Sb) contamination. As and Sb co-contamination increased alpha diversities and the abundance of nifH encoding the dinitrogenase reductase, while inhibited the diazotrophic interactions and substantially changed the composition of communities. Based on the multiple lines of evidence (e.g., the enrichment analysis of diazotrophs, microbe-microbe network, and random forest regression), six diazotrophs (e.g., Sinorhizobium, Dechloromonas, Trichormus, Herbaspirillum, Desmonostoc, and Klebsiella) were identified as keystone taxa. Environment-microbe network and random forest prediction demonstrated that these keystone taxa were highly correlated with the As and Sb contamination fractions. All these results imply that the above-mentioned diazotrophs may be resistant to metal(loid)s. [ABSTRACT FROM AUTHOR]

The nitrogen‐fixing, non‐heterocystous cyanobacterium Hydrocoleum sp. (Oscillatoriales) is a common epiphytic and benthic bloom‐former in tropical and subtropical shallow water systems but shares high phylogenetic similarity with the planktonic, globally important diazotroph Trichodesmium. Multiphasic observations in this study resulted in unexpected identification of Hydrocoleum sp. in mass accumulations in a coastal lagoon in the Western temperate North Atlantic Ocean. Hydrocoleum physiology was examined in situ through measurements of N2 and CO2 fixation rates and expression of genes involved with N2 fixation, CO2 fixation, and phosphorus (P) stress. Bulk N2 fixation rates and Hydrocoleum nifH expression peaked at night and were strongly suppressed by dissolved inorganic nitrogen (DIN). The expression of high affinity phosphate transporter (pstS) and alkaline phosphatase (phoA) genes of Hydrocoleum was elevated during the night and negatively responded to phosphate amendments, as evidence that these mechanisms contribute to P acquisition during diazotrophic growth of Hydrocoleum in situ. This discovery at the edge of the previously known Hydrocoleum habitat range in the warming oceans raises intriguing questions about diazotrophic cyanobacterial adaptations and transitions on the benthic‐pelagic continuum. [ABSTRACT FROM AUTHOR]

Biological nitrogen fixation catalyzed by nitrogenase contributes greatly to the global nitrogen cycle. Nitrogenase expression is subject to regulation in response to nitrogen availability. However, the mechanism through which the transcriptional activator NifA regulates nitrogenase expression by interacting with P II nitrogen regulatory proteins remains unclear in diazotrophic proteobacteria lacking NifL. Here, we demonstrate that in Rhodopseudomonas palustris grown with ammonium, NifA bound deuridylylated P II proteins to form an inactive NifA-P II complex, thereby inhibiting the expression of nitrogenase. Upon nitrogen limitation, the dissociation of uridylylated P II proteins from NifA resulted in the full restoration of NifA activity, and, simultaneously, uridylylation of the significantly up-regulated P II protein GlnK2 led to the increased expression of NifA in R. palustris. This insight into how NifA interacts with P II proteins and controls nitrogenase expression sets the stage for creating highly efficient diazotrophs, reducing the need for energy-intensive chemical fertilizers and helping to diminish carbon emissions. [Display omitted] • NifA is subject to transcriptional and posttranslational regulation in diazotrophs • The increased expression of fully active NifA is primarily stimulated by uridylylated GlnK2 • Deuridylylated P II proteins inhibit NifA activity by forming NifA-P II complex • Deuridylylated P II proteins interact with both GAF and AAA+ domains of NifA protein Zeng et al. report that the formation of an inactive NifA-P II complex inhibits the biological nitrogen fixation in diazotrophs grown with ammonium, paving the way for creating highly efficient artificial biofertilizers that contribute substantially to the reduction of carbon emissions by cutting dependence on energy-intensive chemical fertilizers. [ABSTRACT FROM AUTHOR]

Considering the crucial role of soil diazotrophs and root arbuscular mycorrhizal fungi (AMF) in soil nutrient cycling during ecosystem restoration, diazotroph and AMF communities may be determined by slope position. However, the effect of slope position on diazotroph and AMF abundance, diversity, and community composition of karst ecosystems remains unknown. In this study, soil diazotrophs and root AMF characteristics on varying slope positions were assessed in a karst shrub ecosystem. The results displayed that the abundance of soil diazotrophs and root AMF diversity were significantly affected by slope position. Diazotroph abundance accompanied by soil nutrient and plant richness was higher on the lower slopes than the upper slopes, whereas root AMF diversity displayed the opposite trend. The soil diazotroph and root AMF community composition differed among the upper, middle, and lower slopes. The dominant taxa of soil diazotrophs and root AMF at the order level were Rhizobiales and Glomerales, respectively. Moreover, the diazotroph order of Nostocales and the AMF order of Paraglomerales were richer on the upper slopes than on the lower slopes. The slope position directly affected the plant diversity and soil nutrient distribution, indirectly affecting the diazotroph and AMF communities. Increased available nitrogen on the lower slope caused great diazotroph abundance by stimulating plant growth with sufficient carbohydrates. However, low soil nutrients and plant diversity but high plant root biomass induced more root AMF diversity on the upper slope than on the lower slope. Therefore, this study expands the knowledge of soil diazotroph and root AMF ecological functions along different slope positions during vegetation recovery for the successive stages of grass and shrub in the karst region.

Aims: Most studies focus on the effects of biofertilizer on the bacterial and fungal communities, and we still lack an understanding of biofertilizer on the protistan community. Here, the effects of biofertilizer containing Paenibacillus triticisoli BJ‐18 on composition and interaction of the protistan community in the wheat rhizosphere were investigated. Methods and Results: Biofertilizer application altered soil physicochemical properties and the protistan community composition, and significantly induced an alpha diversity decline. Random forecast and redundancy analysis demonstrated that nitrogenase activity and available phosphorus were the main drivers. Trichomonas classified to the phylum Metamonada was enriched by biofertilizer, and was significantly positive connected with soil nitrogenase activity and some function genes involved in nitrogen‐fixation and nitrogen‐dissimilation. Biofertilization loosely connected biotic interactions, while it did not affect the stability of the protistan community. Besides, biofertilizer promoted the connections of protists with fungi, bacteria, and archaea. Combined with biotic networks (protists, fungi, bacteria, and archaea) and interactions between protists and soil physicochemical properties/function genes, protists may act as keystone taxa potentially driving soil microbiome composition and function. Significance and Impact of the Study: Overall, these results suggest that the biofertilizer is a driver of the soil protistan community, contributing to ecosystem functioning. [ABSTRACT FROM AUTHOR]

Trichodesmium spp. is a colonial diazotrophic cyanobacterium found in the oligotrophic (sub)tropical oceans, where dissolved inorganic phosphorus (DIP) can be depleted. To cope with low P concentrations, P can be scavenged from the dissolved organic P (DOP) pool. This requires the deployment of multiple enzymes activated by trace metals, potentially enhancing metal requirements under stronger P limitations. To test this, we grew Trichodesmium under trace-metal-controlled conditions, where P was supplied as either DIP or DOP (methylphosphonic acid). Mean steady-state biomass under the DOP treatment was only 40% of that grown under equivalent DIP supply, carbon normalized alkaline phosphorus activity was elevated 4-fold, and the zinc (Zn)–carbon ratio was elevated 3.5-fold. Our finding matches the known, dominant Zn requirement across a diversity of enzymes involved in P stress responses and supports an important interaction in the oceanic cycles of these two nutrients. [ABSTRACT FROM AUTHOR]

Inputs of new nitrogen by cyanobacterial diazotrophs are critical to ocean ecosystem structure and function. Relative to other ocean regions, there is a lack of data on the distribution of these microbes in the western South Atlantic. Here, the abundance of six diazotroph phylotypes: Trichodesmium, Crocosphaera, UCYN-A, Richelia associated with Rhizosolenia (Het-1) or Hemiaulus (Het-2), and Calothrix associated with Chaetoceros (Het-3) was measured by quantitative PCR (qPCR) of the nifH gene along a transect extending from the shelf-break to the open ocean along the Vitória-Trindade seamount chain (1200 km). Using nifH gene copies as a proxy for phylotype abundance, Crocosphaera signals were the most abundant, with a broad distribution throughout the study region. Trichodesmium signals were the second most abundant, with the greatest numbers confined to the warmer waters closer to the coast, and a significant positive correlation with temperature. The average signals for the host-associated diazotrophs (UCYN-A, Het-1, and Het-2) were consistently lower than for the other phylotypes. These findings expand measurements of cyanobacterial diazotroph distribution in the western South Atlantic, and provide a new resource to enhance modeling studies focused on patterns of nitrogen fixation in the global ocean.

Since nitrogen (N) is often limiting in permafrost soils, we investigated the N2-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlated to differences in the NifH sequence classes with those most closely related to group I nifH-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III nifH-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N2-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites.

This study addresses the plant beneficial enterobacteria present in rice rhizosphere and their efficiency for enhancing nitrogen uptake in rice plant. Using culturable approaches, the population of total diazotrophs present in rhizosphere samples collected from different organic rice fields of Sikkim were studied and recorded in the range between 4.62 to 4.97 log10 CFU/g soil. All the isolated commonly occurred diazotrophic bacterial isolates were screened based on their ability to fix nitrogen in milligram per gram of sugar consumed under in-vitro condition with the reference check. In addition to nitrogen fixation, plant growth promoting traits such as production of indole-3-acetic acid and gibberellic acid were estimated using spectrophotometric approaches and compared against Bacillus subtilis as reference multi-potent plant growth promoting strain. In-vivo evaluation of these diazotrophic species in rice found improvement in both above and below ground responses in rice plant evaluated by estimating changes in chlorophyll concentration, plant biomass, root architecture, nitrogen uptake, microbial biomass and associated biochemical activity of soil. Further, the selected isolates were identified through DNA targeted analysis of 16S rRNA gene present in diazotrophs and which identified that the isolates belonged to the Enterobacter genus. Statistical models were prepared for deciphering the dynamics of plant growth improvement due to selective enrichment of rhizosphere bacteria and found significant (p

Soil nitrogen (N) fixation, driven by microbial reactions, is critical to support the entrance of nitrogen in nutrient poor and pioneer ecosystems. However, how and why N fixation and soil diazotrophs evolve as forests develop remain poorly understood. Here, we used a 60-year forest rewilding chronosequence and found that soil N fixation activity gradually decreased with increasing forest age, experiencing dramatic drops of 64.8% in intermediate stages and 93.0% in the oldest forests. Further analyses revealed loses in diazotrophic diversity and a significant reduction in the abundance of important diazotrophs (e.g., Desulfovibrio and Pseudomonas) as forest develops. This reduction in N fixation, and associated shifts in soil microbes, was driven by acidification and increases in N content during forest succession. Our results provide new insights on the life history of one of the most important groups of soil organisms in terrestrial ecosystems, with consequences for understanding the buildup of nutrients as forest soil develops., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

Biological nitrogen fixation catalyzed by nitrogenase contributes greatly to the global nitrogen cycle. Nitrogenase expression is subject to regulation in response to nitrogen availability. However, the mechanism through which the transcriptional activator NifA regulates nitrogenase expression by interacting with P II nitrogen regulatory proteins remains unclear in diazotrophic proteobacteria lacking NifL. Here, we demonstrate that in Rhodopseudomonas palustris grown with ammonium, NifA bound deuridylylated P II proteins to form an inactive NifA-P II complex, thereby inhibiting the expression of nitrogenase. Upon nitrogen limitation, the dissociation of uridylylated P II proteins from NifA resulted in the full restoration of NifA activity, and, simultaneously, uridylylation of the significantly up-regulated P II protein GlnK2 led to the increased expression of NifA in R. palustris. This insight into how NifA interacts with P II proteins and controls nitrogenase expression sets the stage for creating highly efficient diazotrophs, reducing the need for energy-intensive chemical fertilizers and helping to diminish carbon emissions., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Diazotrophic bacteria isolated from the rhizosphere of a wild wheat ancestor, grown from its refuge area in the Fertile Crescent, were found to be efficient Plant Growth-Promoting Rhizobacteria (PGPR), upon interaction with an elite wheat cultivar. In nitrogen-starved plants, they increased the amount of nitrogen in the seed crop (per plant) by about twofold. A bacterial growth medium was developed to investigate the effects of bacterial exudates on root development in the elite cultivar, and to analyze the exo-metabolomes and exo-proteomes. Altered root development was observed, with distinct responses depending on the strain, for instance, with respect to root hair development. A first conclusion from these results is that the ability of wheat to establish effective beneficial interactions with PGPRs does not appear to have undergone systematic deep reprogramming during domestication. Exo-metabolome analysis revealed a complex set of secondary metabolites, including nutrient ion chelators, cyclopeptides that could act as phytohormone mimetics, and quorum sensing molecules having inter-kingdom signaling properties. The exo-proteome-comprised strain-specific enzymes, and structural proteins belonging to outer-membrane vesicles, are likely to sequester metabolites in their lumen. Thus, the methodological processes we have developed to collect and analyze bacterial exudates have revealed that PGPRs constitutively exude a highly complex set of metabolites; this is likely to allow numerous mechanisms to simultaneously contribute to plant growth promotion, and thereby to also broaden the spectra of plant genotypes (species and accessions/cultivars) with which beneficial interactions can occur.

The diazotrophic cyanobacterium Trichodesmium has been recognized as a potentially significant contributor to aerobic methane generation via several mechanisms including the utilization of methylphophonate (MPn) as a source of phosphorus. Currently, there is no information about how environmental factors regulate methane production by Trichodesmium . Here, we grew Trichodesmium IMS101 at five temperatures ranging from 16 to 31°C, and found that its methane production rates increased with rising temperatures to peak (1.028 ± 0.040 nmol CH 4 μmol POC -1  day -1 ) at 27°C, and then declined. Its specific growth rate changed from 0.03 ± 0.01 d -1 to 0.34 ± 0.02 d -1 , with the optimal growth temperature identified between 27 and 31°C. Within the tested temperature range the Q 10 for the methane production rate was 4.6 ± 0.7, indicating a high sensitivity to thermal changes. In parallel, the methane production rates showed robust positive correlations with the assimilation rates of carbon, nitrogen, and phosphorus, resulting in the methane production quotients (molar ratio of carbon, nitrogen, or phosphorus assimilated to methane produced) of 227-494 for carbon, 40-128 for nitrogen, and 1.8-3.4 for phosphorus within the tested temperature range. Based on the experimental data, we estimated that the methane released from Trichodesmium can offset about 1% of its CO 2 mitigation effects., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Zou, Yi, Li, Bizic, Berman-Frank and Gao.)

Rhizosphere is a vital area for substance exchange and energy transfer between roots and soil microorganisms. Therefore, diazotrophs in the rhizosphere play a pivotal role in facilitating plant nitrogen acquisition. We investigated the variability in the abundance and community structure of soil diazotrophs and the influencing factors across rhizosphere soils of Cunninghamia lanceolata in three locations: Baisha State-owned Forest Farm in Longyan City (BS), Sanming Forest Ecosystem and Global Change Research Station (SM), and Wuyishan National Forest Park in Nanping City (WYS), located in the western region of Fujian Province, quantified the diazotrophic abundance by using real-time quantitative PCR, and assessed the community structure by high-throughput sequencing. The results showed that soil pH, C:N ratio, and C:(N:P) stoichiometry in SM were notably lower compared to those in BS and WYS. In SM, the abundance of the nifH gene was 6.38×10 8 copies·g -1 , significantly lower than 1.35×10 9 copies·g -1 in BS and 1.10×10 9 copies·g -1 in WYS. Additionally, α diversity index of diazotrophs was lower in SM compared to BS and WYS, while the community structure of diazotrophs in rhizosphere soils of BS and WYS was similar, which differed significantly from that in SM. The diazotrophic sequences in the three forest farms could be divided into 5 phylum, 8 classes, 15 orders, 23 families and 33 genera, with Proteobacteria, α-proteobacteria, and Bradyrhizobium as the dominant phylotypes. Soil pH, available phosphorus, NO 3 - -N and C:(N:P) ratio were identified as significant factors influencing both the abundance and community structure of nifH genes, with soil pH performing the greatest. Taken together, there were spatial variations in the distribution of diazotrophic abundance and community structure in C. lanceolata rhizosphere soils, with soil pH as the primary driving factor.

The impacts of global environmental change on productivity in northern latitudes will be contingent on nitrogen (N) availability. In circumpolar boreal ecosystems, nonvascular plants (i.e., bryophytes) and associated N2‐fixing diazotrophs provide one of the largest known N inputs but are rarely accounted for in Earth system models. Instead, most models link N2‐fixation with the functioning of vascular plants. Neglecting nonvascular N2‐fixation may be contributing toward high uncertainty that currently hinders model predictions in northern latitudes, where nonvascular N2‐fixing plants are more common. Adequately accounting for nonvascular N2‐fixation and its drivers could subsequently improve predictions of future N availability and ultimately, productivity, in northern latitudes. Here, we review empirical evidence of boreal nonvascular N2‐fixation responses to global change factors (elevated CO2, N deposition, warming, precipitation, and shading by vascular plants), and compare empirical findings with model predictions of N2‐fixation using nine Earth system models. The majority of empirical studies found positive effects of CO2, warming, precipitation, or light on nonvascular N2‐fixation, but N deposition strongly downregulated N2‐fixation in most empirical studies. Furthermore, we found that the responses of N2‐fixation to elevated CO2 were generally consistent between models and very limited empirical data. In contrast, empirical‐model comparisons suggest that all models we assessed, and particularly those that scale N2‐fixation with net primary productivity or evapotranspiration, may be overestimating N2‐fixation under increasing N deposition. Overestimations could generate erroneous predictions of future N stocks in boreal ecosystems unless models adequately account for the drivers of nonvascular N2‐fixation. Based on our comparisons, we recommend that models explicitly treat nonvascular N2‐fixation and that field studies include more targeted measurements to improve model structures and parameterization. [ABSTRACT FROM AUTHOR]

Free‐living nitrogen fixation (FLNF) represents an important terrestrial N source and is gaining interest for its potential to contribute plant available N to bioenergy cropping systems. Switchgrass, a cellulosic bioenergy crop, may be particularly reliant on FLNF when grown on low N systems, like marginal lands. However, the potential contributions of FLNF to switchgrass as well as the controls on this process are not well understood. In this study, we evaluated drivers of FLNF rates and N‐fixing microbial (diazotrophic) community composition in field‐grown switchgrass systems over two growing seasons with high temporal sampling. We found that climate variables are strong drivers of FLNF rates in switchgrass systems, compared to other environmental and biological factors including soil nutrients and diazotrophic community composition. Increased soil moisture availability generally promoted FLNF rates, but extreme rainfall events were detrimental. These climate‐related responses suggest a potential for loss of FLNF‐derived N contributions under projected climate shifts. We found a significant, but weak correlation between diazotrophic community composition and FLNF rates. We also observed a significant shift in the diazotrophic community composition between 2017 and 2018 and similarly measured a significant difference in FLNF rates between growing seasons. Lastly, we found that seasonal FLNF N contributions, based on measurement with high temporal resolution, has the potential to meet up to 80% of switchgrass N demands suggesting that FLNF measurements extrapolated from fewer time points or locations may underestimate these potential N contributions. [ABSTRACT FROM AUTHOR]

Background: Nitrogen-fixing prokaryotes (diazotrophs) contribute substantially to nitrogen input in mangrove sediments, and their structure and nitrogen fixation rate (NFR) are significantly controlled by environmental conditions. Despite the well-known studies on diazotrophs in surficial sediments, the diversity, structure, and ecological functions of diazotrophic communities along environmental gradients of mangrove sediment across different depths are largely unknown. Here, we investigated how biological nitrogen fixation varied with the depth of mangrove sediments from the perspectives of both NFR and diazotrophic communities. Results: Through acetylene reduction assay, nifH gene amplicon and metagenomic sequencing, we found that the NFR increased but the diversity of diazotrophic communities decreased with the depth of mangrove sediments. The structure of diazotrophic communities at different depths was largely driven by salinity and exhibited a clear divergence at the partitioning depth of 50 cm. Among diazotrophic genera correlated with NFR, Agrobacterium and Azotobacter were specifically enriched at 50–100 cm sediments, while Anaeromyxobacter, Rubrivivax, Methylocystis, Dickeya, and Methylomonas were more abundant at 0–50 cm. Consistent with the higher NFR, metagenomic analysis demonstrated the elevated abundance of nitrogen fixation genes (nifH/D/K) in deep sediments, where nitrification genes (amoA/B/C) and denitrification genes (nirK and norB) became less abundant. Three metagenome-assembled genomes (MAGs) of diazotrophs from deep mangrove sediments indicated their facultatively anaerobic and mixotrophic lifestyles as they contained genes for low-oxygen-dependent metabolism, hydrogenotrophic respiration, carbon fixation, and pyruvate fermentation. Conclusions: This study demonstrates the depth-dependent variability of biological nitrogen fixation in terms of NFR and diazotrophic communities, which to a certain extent relieves the degree of nitrogen limitation in deep mangrove sediments. BxKuS27-gQH4xs4TJqgBb7 Video Abstract [ABSTRACT FROM AUTHOR]

Plants can adapt to their surroundings by hosting beneficial bacteria that confer a selective advantage in stressful conditions. Endophytes are a class of beneficial bacteria that exist within the internal spaces of plants and many species can improve plant nitrogen use efficiency. Nitrogen is an essential plant macronutrient, and is often a limiting factor to plant growth, especially in cereal crops such as maize. Every year farmers apply over 100 million metric tonnes of synthetic nitrogen fertilizer to meet the growing demand for stable food crops. Breeding efforts in maize over the past several decades has focused heavily on yield in response to nitrogen inputs, and so may have selected against adaptations that allow plants to survive in nitrogen stressed conditions. Data suggests that our heavy dependence on synthetic nitrogen fertilizer is not sustainable in the long term, and so there is on-going research efforts to reduce and replace this currently essential part of modern agriculture. Bacteria that improve plant tolerance to nitrogen stressed environments would allow farmers to reduce the amount of fertilizer they apply. The selection of maize under high nitrogen conditions to create modern varieties may have caused the plant to lose these beneficial bacteria that allowed wild maize ancestors to thrive in low nitrogen soil. Here in this study, we examine the root and shoot microbiomes of the wild ancestor of all maize, Parviglumis, and an ancient Mexican landrace (Mixteco) from Oaxaca, the area of early maize diversification. Both of these maize genotypes have thrived for thousands of years with little to no nitrogen inputs and so we hypothesized that they host beneficial bacteria that allow them to thrive in nitrogen stressed conditions. We identified multiple root endophyte species from each ancient maize relative that increased the growth of annual ryegrass (model maize relative) under nitrogen starvation. Furthermore, research infers these strains were vertically transmitted to new generations of plants, potentially through seed, indicating selection pressure for Parviglumis and Mixteco to maintain them in their microbiome. [ABSTRACT FROM AUTHOR]

One challenge in field-based marine microbial ecology is to achieve sufficient spatial resolution to obtain representative information about microbial distributions and biogeochemical processes. The challenges are exacerbated when conducting rate measurements of biological processes due to potential perturbations during sampling and incubation. Here we present the first application of a robotic microlaboratory, the 4 L-submersible incubation device (SID), for conducting in situ measurements of the rates of biological nitrogen (N2) fixation (BNF). The free-drifting autonomous instrument obtains samples from the water column that are incubated in situ after the addition of 15N2 tracer. After each of up to four consecutive incubation experiments, the 4-L sample is filtered and chemically preserved. Measured BNF rates from two deployments of the SID in the oligotrophic North Pacific ranged from 0.8 to 2.8 nmol N L-1 day-1, values comparable with simultaneous rate measurements obtained using traditional conductivity-temperature-depth (CTD)-rosette sampling followed by on-deck or in situ incubation. Future deployments of the SID will help to better resolve spatial variability of oceanic BNF, particularly in areas where recovery of seawater samples by CTD compromises their integrity, e.g. anoxic habitats.

Endophytic nitrogen-fixing (diazotrophic) bacteria are essential members of the microbiome of switchgrass (Panicum virgatum), considered to be an important commodity crop in bioenergy production. While endophytic diazotrophs are known to provide fixed atmospheric nitrogen to their host plant, there are many other plant growth-promoting (PGP) capabilities of these organisms to be demonstrated. The diversity of PGP traits across different taxa of switchgrass-colonizing endophytes is understudied, yet critical for understanding endophytic function and improving cultivation methods of important commodity crops. Here, we present the isolation and characterization of three diazotrophic endophytes: Azospirillum agricola R1C, Klebsiella variicola F10Cl, and Raoultella terrigena R1Gly. Strains R1C and F10Cl were isolated from switchgrass and strain R1Gly, while isolated from tobacco, is demonstrated herein to colonize switchgrass. Each strain exhibited highly diverse genomic and phenotypic PGP capabilities. Strain F10Cl and R1Gly demonstrated the highest functional similarity, suggesting that, while endophyte community structure may vary widely based on host species, differences in functional diversity are not a clearly delineated. The results of this study advance our understanding of diazotrophic endophyte diversity, which will allow us to design robust strategies to improve cultivation methods of many economically important commodity crops.

Plants can adapt to their surroundings by hosting beneficial bacteria that confer a selective advantage in stressful conditions. Endophytes are a class of beneficial bacteria that exist within the internal spaces of plants and many species can improve plant nitrogen use efficiency. Nitrogen is an essential plant macronutrient, and is often a limiting factor to plant growth, especially in cereal crops such as maize. Every year farmers apply over 100 million metric tonnes of synthetic nitrogen fertilizer to meet the growing demand for stable food crops. Breeding efforts in maize over the past several decades has focused heavily on yield in response to nitrogen inputs, and so may have selected against adaptations that allow plants to survive in nitrogen stressed conditions. Data suggests that our heavy dependence on synthetic nitrogen fertilizer is not sustainable in the long term, and so there is on-going research efforts to reduce and replace this currently essential part of modern agriculture. Bacteria that improve plant tolerance to nitrogen stressed environments would allow farmers to reduce the amount of fertilizer they apply. The selection of maize under high nitrogen conditions to create modern varieties may have caused the plant to lose these beneficial bacteria that allowed wild maize ancestors to thrive in low nitrogen soil. Here in this study, we examine the root and shoot microbiomes of the wild ancestor of all maize, Parviglumis, and an ancient Mexican landrace (Mixteco) from Oaxaca, the area of early maize diversification. Both of these maize genotypes have thrived for thousands of years with little to no nitrogen inputs and so we hypothesized that they host beneficial bacteria that allow them to thrive in nitrogen stressed conditions. We identified multiple root endophyte species from each ancient maize relative that increased the growth of annual ryegrass (model maize relative) under nitrogen starvation. Furthermore, research infers these strains were vertically transmitted to new generations of plants, potentially through seed, indicating selection pressure for Parviglumis and Mixteco to maintain them in their microbiome.

Assessment of plant-associative bacterial nitrogen (N) fixation is crucial for selection and development of elite diazotrophic inoculants that could be used to supply cereal crops with nitrogen in a sustainable manner. Although diazotrophic bacteria possess diverse oxygen tolerance mechanisms, most require a sub 21% oxygen environment to achieve optimal stability and function of the N-fixing catalyst nitrogenase. Consequently, assessment of N fixation is routinely carried out on “free-living” bacteria grown in the absence of a host plant and such experiments may not accurately divulge activity in the rhizosphere where the availability and forms of nutrients such as carbon and N, which are key regulators of N fixation, may vary widely. Here, we present a modified in situ acetylene reduction assay (ARA), utilizing the model cereal barley as a host to comparatively assess nitrogenase activity in diazotrophic bacteria. The assay is rapid, highly reproducible, applicable to a broad range of diazotrophs, and can be performed with simple equipment commonly found in most laboratories that investigate plant-microbe interactions. Thus, the assay could serve as a first point of order for high-throughput identification of elite plant-associative diazotrophs.

There is an increasing interest in understanding the structure and function of the microbiota associated with marine and terrestrial organisms, because it can play a major role in host nutrition and resistance to environmental stress. Reef-building corals live in association with diazotrophs, which are microbes able to fix dinitrogen. Corals are known to assimilate diazotrophically-derived nitrogen (DDN), but it is still not clear whether this nitrogen source is derived from coral-associated diazotrophs and whether it substantially contributes to the coral's nitrogen budget. In this study, we aimed to provide a better understanding of the importance of DDN for corals using a holistic approach by simultaneously assessing DDN assimilation rates (using 15N2 tracer technique), the diazotrophic bacterial community (using nifH gene amplicon sequencing) and the natural δ15N signature in Stylophora pistillata corals from the Northern Red Sea along a depth gradient in winter and summer. Overall, our results show a discrepancy between the three parameters. DDN was assimilated by the coral holobiont during winter only, with an increased assimilation with depth. Assimilation rates were, however, not linked to the presence of coral-associated diazotrophs, suggesting that the presence of nifH genes does not necessarily imply functionality. It also suggests that DDN assimilation was independent from coral-associated diazotrophs and may instead result from nitrogen derived from planktonic diazotrophs. In addition, the δ15N signature presented negative values in almost all coral samples in both seasons, suggesting that nitrogen sources other than DDN contribute to the nitrogen budget of corals from this region. This study yields novel insight into the origin and importance of diazotrophy for scleractinian corals from the Northern Red Sea using multiple proxies. [ABSTRACT FROM AUTHOR]

Assessment of plant-associative bacterial nitrogen (N) fixation is crucial for selection and development of elite diazotrophic inoculants that could be used to supply cereal crops with nitrogen in a sustainable manner. Although diazotrophic bacteria possess diverse oxygen tolerance mechanisms, most require a sub 21% oxygen environment to achieve optimal stability and function of the N-fixing catalyst nitrogenase. Consequently, assessment of N fixation is routinely carried out on "free-living" bacteria grown in the absence of a host plant and such experiments may not accurately divulge activity in the rhizosphere where the availability and forms of nutrients such as carbon and N, which are key regulators of N fixation, may vary widely. Here, we present a modified in situ acetylene reduction assay (ARA), utilizing the model cereal barley as a host to comparatively assess nitrogenase activity in diazotrophic bacteria. The assay is rapid, highly reproducible, applicable to a broad range of diazotrophs, and can be performed with simple equipment commonly found in most laboratories that investigate plant-microbe interactions. Thus, the assay could serve as a first point of order for high-throughput identification of elite plant-associative diazotrophs. [ABSTRACT FROM AUTHOR]

Aim: Microbial diversity is one of the most important factors for maintaining the performance of multiple functions in soils (multifunctionality). However, existing studies typically consider the taxonomic richness or Shannon diversity of the entire community. We know little about the connection network of taxonomic and phylogenetic facets of diversity and their collective impact on multifunctionality. In this study, the linkages of effects of diversity within functional groups were disentangled in drylands. Location: The central Tibetan Plateau. Time period: Present. Major taxa studied: Phototrophs and diazotrophs (mainly cyanobacteria). Methods: Given the carbon‐ and nitrogen‐limited nature of drylands, we conducted a high‐throughput sequencing of C/N‐fixing functional groups from biocrusts and evaluated multiple facets of diversity (i.e., richness, evenness and phylogeny‐related trait dissimilarity), together with seven crucial variables of soil functioning to calculate multifunctionality. The relationships between multifaceted diversity and abundance with individual functions and multifunctionality were validated by a set of solid statistical analyses. Results: We found that the integrated biodiversity index was a stronger predictor of multifunctionality than richness. The divergent performance of different facets of diversity determined the idiosyncratic effect of each functional group on soil multifunctionality. Moreover, the evaluation of functional significance at the species level gave important clues on the trade‐offs and redundancy in each functional group, explaining the distinct patterns of effects of diversity. Richness was the dominant factor for diazotrophs to maximize multifunctionality, whereas phylogenetic dissimilarity was the essential one for phototrophs. Main conclusions: Our study demonstrated that multiple facets of diversity should be considered when assessing the effects of biodiversity. In contrast to the community level, within‐functional group measures might adequately capture the features of diversity that are most correlated with soil multifunctionality. Our results provide a perspective to bridge the gap between taxonomic and trait‐based approaches for elucidating the biodiversity–ecosystem function relationship. [ABSTRACT FROM AUTHOR]

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 N 2 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 N 2 -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 N 2 -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 N 2 -fixation by Fe-only nitrogenase. 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. [Display omitted] • A proteomic analysis of a diazotrophic strain from the Paenibacillaceae family is presented. • NifDK proteins exhibit differential expression under Mo scarcity. • NifH shows no significant changes under Mo scarcity. • Expression of the alternative nitrogenase is coordinated with Mo transport and metabolism. • Paenibacillus ' adaptation to nitrogen fixation is associated with multiple processes. [ABSTRACT FROM AUTHOR]

Abstract The perennial energy crop Miscanthus × giganteus is recognized for its extraordinary nitrogen‐use efficiency. While the remobilization of nitrogen (N) to the rhizome after the growth phase contributes to this efficiency, the plant‐associated microbiome might also contribute, as N‐fixing bacterial species had been isolated from this grass. Here, we studied established Miscanthus × giganteus plots in southern Germany that either received 80 kg N ha−1 a−1 or that were not N‐fertilized for 14 years. The bacterial communities of the bulk soil, rhizosphere, roots and rhizomes were analysed. Major differences were encountered between plant‐associated fractions. Nitrogen had little effect on soil communities. The roots and rhizomes showed less microbial diversity than soil fractions. In these compartments, Actinobacteria and N‐fixing symbiosis‐associated Proteobacteria depended on N. Intriguingly, N2‐fixing‐related bacterial families were enriched in the rhizomes in long‐term zero N plots, while denitrifier‐related families were depleted. These findings point to the rhizome as a potentially interesting plant organ for N fixation and demonstrate long‐term differences in the organ‐specific bacterial communities associated with different N supply, which are mainly shaped by the plant.

Abstract Different types of steppes could provide heterogeneous habitat environments for underground microorganisms, but much less is known about how soil microbes fit the distinct habitats and what are the underlying mechanisms in shaping their community patterns. We simultaneously examined the community compositions and structures of soil bacteria, fungi, and diazotrophs across desert, typical, and meadow steppes in Inner Mongolia using high‐throughput sequencing. The results showed that soil bacteria, fungi, and diazotrophs exhibited different distribution patterns across steppe types. Although different steppes displayed obvious differences in climate conditions, plant traits, and soil properties, most of bacterial species were shared by all the steppes while only a few species were unique, indicating that the soil bacterial compositions were hardly influenced by the steppe types. Nevertheless, the habitat heterogeneity could cause shifts in the relative abundance of some bacterial groups, which resulted in significant changes in the community structure of soil bacteria across steppes. However, the fungal community compositions and structures were similar in typical and meadow steppes but that in desert steppe were significantly different. Whereas, the community compositions and structures of diazotrophs were strongly related to the steppe types. In this study, the similar parent material backgrounds of the steppe soils might be the important factor in shaping the homologous bacterial compositions. However, the variations in soil fertility, soil water repellency, and plant species across steppes would be the major driving forces in regulating the compositions and structures of fungal communities, while the diazotrophic communities would be more closely related to the changes in plant traits and soil fertility among steppes. Our results provided evidence of habitat specificity for different microbial groups and their underlying drivers.

The genome of the moderately haloalkaliphilic diazotrophic anoxygenic phototrophic bacterium Rhodovulum tesquicola A-36sT isolated from an alkaline lake was analyzed and compared to the genomes of the closest species Rhodovulum steppense A-20sT and Rhodovulum strictum DSM 11289T. The genomic features of three organisms are quite similar, reflecting their ecological and physiological role of facultative photoheterotrophs. Nevertheless, the nitrogenase activity of the pure cultures of the studied bacteria differed significantly: the highest rate (4066 nmoles C2H2/mg of dry weight per hour) was demonstrated by Rhodovulum strictum while the rates in Rhodovulum tesquicola and Rhodovulum steppense were an order of magnitude lower (278 and 523 nmoles C2H2/mg of dry weight per hour, respectively). This difference can be attributed to the presence of an additional nitrogenase operon found exclusively in R. strictum and to the structural variation in nitrogenase operon in R. tesquicola.

Aims: Free-living diazotrophs play a critical role in nitrogen (N) supply to ecosystems. Land-use change and plant rhizosphere are two important factors influencing diazotroph populations, but their relative strength in determining the soil diazotrophic community is still unclear, especially in acidic soils. Methods: One natural vegetation (the dominant species is green foxtail) and three agricultural land-uses (maize, peanut and soybean, respectively) widely distributed in the acidic soil region of southern China were selected. Bulk and rhizosphere soils were collected from every land-use, and their properties were determined. Quantitative PCR and high-throughput sequencing were applied to investigate soil diazotrophic abundance, diversity and community composition. Results: Land use conversion from natural vegetation to different agricultural land-uses significantly reduced diazotroph abundances in bulk soils, however, the rhizosphere had a positive effect on the abundances in agricultural land-uses. Statistical analysis showed that the rhizosphere exerted a stronger effect on diazotroph abundance than land-use change. Converting natural vegetation to agricultural land-uses also decreased diazotroph richness and land-use types differed significantly in community composition, but plant rhizosphere did not cause these effects. In particular, the community variations in leguminous plants were more distinct than maize. Land-use change also influenced some topological properties of the community network. Conclusions: In acidic soil, land-use change has noticeable effects on the richness and composition of diazotrophic community than the rhizosphere. The rhizosphere, however, has a more obvious effect in increasing the abundance of the diazotrophs. These results highlight the critical role of land-use change in manipulating soil diazotrophic community composition. [ABSTRACT FROM AUTHOR]

The Arctic Ocean is the smallest ocean on Earth, yet estimated to play a substantial role as a global carbon sink. As climate change is rapidly changing fundamental components of the Arctic, it is of local and global importance to understand and predict consequences for its carbon dynamics. Primary production in the Arctic Ocean is often nitrogen-limited, and this is predicted to increase in some regions. It is therefore of critical interest that biological nitrogen fixation, a process where some bacteria and archaea termed diazotrophs convert nitrogen gas to bioavailable ammonia, has now been detected in the Arctic Ocean. Several studies report diverse and active diazotrophs on various temporal and spatial scales across the Arctic Ocean. Their ecology and biogeochemical impact remain poorly known, and nitrogen fixation is so far absent from models of primary production in the Arctic Ocean. The composition of the diazotroph community appears distinct from other oceans – challenging paradigms of function and regulation of nitrogen fixation. There is evidence of both symbiotic cyanobacterial nitrogen fixation and heterotrophic diazotrophy, but large regions are not yet sampled, and the sparse quantitative data hamper conclusive insights. Hence, it remains to be determined to what extent nitrogen fixation represents a hitherto overlooked source of new nitrogen to consider when predicting future productivity of the Arctic Ocean. Here, we discuss current knowledge on diazotroph distribution, composition, and activity in pelagic and sea ice-associated environments of the Arctic Ocean. Based on this, we identify gaps and outline pertinent research questions in the context of a climate change-influenced Arctic Ocean – with the aim of guiding and encouraging future research on nitrogen fixation in this region.

Nitrogen fixation and methane production in surface sediments of a long bioturbated beach at the northeast coast of Bay of Bengal were quantified in vitro through gas chromatography. The beach was selected because it serves as a primary tourist destination and no prior data of it existed. The beach was segmented in littoral zones. Microbial assay was performed for all the sediment samples of the littoral subsection. The influence of the presence and absence of bioturbation on nitrogen fixation and methane production was investigated. One-way ANOVA revealed the statistical significance of the datasets through the rejection of null hypothesis. [ABSTRACT FROM AUTHOR]

Although diazotrophs are major participants in biological nitrogen fixation (BNF) processes, the variations in community structure and assembly processes in response to long‐term fertilization with different fertilizer application are still ambiguous, especially under various doses with balance or not. Using nifH amplicon sequencing, we investigated the soil diazotrophic communities in a paddy field which received 20‐year fertilization including control (CK), balanced fertilization (three doses of nitrogen (N), phosphorus (P), and potassium (K) at same ratio (NPK, 2(NPK), and 3(NPK)), unbalanced fertilization (three ratios, (2 N)PK, N(2P)K, and NP(2K)), and manure (M). Our results showed that the diazotrophic diversity increased with the long‐term fertilization, but it was tapering‐off with doses increment. However, the community dissimilarities increased with fertilizer doses. These variations were attributed to the trade‐off between the variation of soil pH and nutrients. The increasing of fertilizer doses induced the transformation of community assembly processes, which changed from mainly dominated by deterministic processes in CK, NPK, NP(2K) and M to stochastic processes in the other treatments. Our findings suggest that the long‐term fertilization, especially different fertilizer doses, strongly affect soil diazotrophic diversity, community structure, and assembly processes, which could help to improve the sustainable agricultural management in the future. [ABSTRACT FROM AUTHOR]

The Arctic Ocean is the smallest ocean on Earth, yet estimated to play a substantial role as a global carbon sink. As climate change is rapidly changing fundamental components of the Arctic, it is of local and global importance to understand and predict consequences for its carbon dynamics. Primary production in the Arctic Ocean is often nitrogen-limited, and this is predicted to increase in some regions. It is therefore of critical interest that biological nitrogen fixation, a process where some bacteria and archaea termed diazotrophs convert nitrogen gas to bioavailable ammonia, has now been detected in the Arctic Ocean. Several studies report diverse and active diazotrophs on various temporal and spatial scales across the Arctic Ocean. Their ecology and biogeochemical impact remain poorly known, and nitrogen fixation is so far absent from models of primary production in the Arctic Ocean. The composition of the diazotroph community appears distinct from other oceans – challenging paradigms of function and regulation of nitrogen fixation. There is evidence of both symbiotic cyanobacterial nitrogen fixation and heterotrophic diazotrophy, but large regions are not yet sampled, and the sparse quantitative data hamper conclusive insights. Hence, it remains to be determined to what extent nitrogen fixation represents a hitherto overlooked source of new nitrogen to consider when predicting future productivity of the Arctic Ocean. Here, we discuss current knowledge on diazotroph distribution, composition, and activity in pelagic and sea ice-associated environments of the Arctic Ocean. Based on this, we identify gaps and outline pertinent research questions in the context of a climate change-influenced Arctic Ocean – with the aim of guiding and encouraging future research on nitrogen fixation in this region. [ABSTRACT FROM AUTHOR]

Cellulosic bioenergy crops, like switchgrass (Panicum virgatum), have potential for growth on lands unsuitable for food production coupled with potential for climate mitigation. Sustainability of these systems lies in identifying conditions that promote high biomass yields on marginal lands under low-input agricultural practices. Associative nitrogen fixation (ANF) is a potentially important nitrogen (N) source for these crops, yet ANF contributions to plant N, especially under fertilizer N addition are unclear. In this study, we assess structure (nifH) and function (ANF) of switchgrass root-associated diazotrophic communities to long-term and short-term N additions using soil from three marginal land sites. ANF rates were variable and often unexpectedly high, sometimes 10× greater than reported in the literature, and did not respond in repeatable ways to long-term or short-term N. We found few impacts of N addition on root-associated diazotrophic community structure or membership. Instead, we found a very consistent root-associated diazotrophic community even though switchgrass seeds were germinated in soil from field sites with distinct diazotrophic communities. Ultimately, this work demonstrates that root-associated diazotrophic communities have the potential to contribute to switchgrass N demands, independent of N addition, and this may be driven by selection of the diazotrophic community by switchgrass roots. [ABSTRACT FROM AUTHOR]

Bacterial wilt caused by Ralstonia solanacearum (RS) has become one of the most destructive plant diseases in agricultural crops. Obtaining effective strains with disease control activity is an urgent prerequisite for biological control efficiency. This study was performed to explore if the root-associated diazotrophic rhizobacteria in ginger plants have any potential to induce resistance to RS. Three bacterial strains named N10, SJN3 and SJN5 were obtained from the rhizosphere soil of ginger root and were further evaluated regarding their high inhibitory activity in the preliminary screening and in vitro antagonistic activity against RS. Inoculation with N10, SJN3 and SJN5 showed 47.61%, 49.33% and 43.15% relative disease incidence, respectively. N10 and SJN5 showed the most successful biocontrol efficacy and reduced disease incidence by 39.98% and 45.61%, respectively. Moreover, N10 and SJN5 promoted root length by 25.5% and 26.6%, shoot dry weight by 12.5% and 20.1% and root dry weight by 15.4% and 17.9%, respectively. According to the 16S rDNA partial sequence, N10, SJN3 and SJN5 belonged to the genus Pantoea, Burkholderia and Arthrobacter, respectively. Fluorescent in situ hybridization assay revealed that SJN5 cells were distributed on the root surface and formed a condensed biofilm. This result suggests that this strain, which shows nitrogen fixation and antagonism toward RS, not only can increase plant growth, but can also inhibit plant diseases. The findings of the present study expand our current understanding on the application of diazotrophs as a bacterial biocontrol agent, especially for Arthrobacter sp.

Oil palm is a leading commodity of the plantation sector in Indonesia. Improving the quality of oil palm still be carried out to increase production. Seed technology can be used as an effort to improve the quality of oil palm seeds. The aim of this experiment was to determine the effect of seed enrichment with consortium of three microbes to increase vigor of oil palm seedling in pre nursery stage. The experiment design of this reseach was using completely randomize block design consisted of two factors. The first was seed coating consist of two factors, ie: coated seed and uncoated seed. Second was seed enrichment consist of eight factors, ie: control, enrichment with E. sacchari, abruscular mycorrhizal fungi (AMF), T. asperellum, E. sacchari+ AMF, E. sacchari+ T. asperellum, AMF + T. asperellum, E. sacchari+ AMF + T. asperellum. The result showed that enrichment with consortium of three microbes could increase vigor of oil palm seedling based on seedling germination, rate of germination, palm height, and numbers of survival seedling.