ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank

Intensification of harmful cyanobacterial blooms in a eutrophic, temperate lake caused by nitrogen, temperature, and CO2

Warmer temperatures can significantly increase the intensity of cyanobacterial harmful algal blooms (CHABs) in eutrophic freshwater ecosystems. However, few studies have examined the effects of CO2 enrichment in tandem with elevated temperature and/or nutrients on cyanobacterial taxa in freshwater ecosystems. Here, we observed changes in the biomass of cyanobacteria, nutrients, pH, and carbonate chemistry over a two-year period in a shallow, eutrophic freshwater lake and performed experiments to examine the effects and co-effects of CO2, temperature, and nutrient enrichment on cyanobacterial and N2-fixing (diazotrophic) communities assessed via high throughput sequencing of the 16S rRNA and nifH genes, respectively. During both years, there were significant CHABs (50-500 μg cyanobacterial chlorophyll-a L-1) and lake CO2 levels were undersaturated (≤300 μatm pCO2). NH4+ significantly increased the net growth rates of cyanobacteria as well as the biomass of the diazotrophic cyanobacterial order Nostocales under elevated and ambient CO2 conditions. In a fall experiment, the N2 fixation rates of Nostocales were significantly higher when populations were enriched with CO2 and P, relative to CO2-enriched populations that were not amended with P. During a summer experiment, N2 fixation rates increased significantly under N and CO2 - enriched conditions relative to N-enriched and ambient CO2 conditions. Nostocales dominated the diazotrophic communities of both experiments, achieving the highest relative abundance under CO2-enriched conditions when N was added in the first experiment and when CO2 and temperature were elevated in the second experiment, when N2 fixation rates also increased significantly. Collectively, this study indicates that N promotes cyanobacterial blooms including those formed by Dolichospermum and that the biomass and N2 fixation rates of diazotrophic cyanobacterial taxa may benefit from enhanced CO2 levels in eutrophic lakes.

A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization

BACKGROUND

Plant microbiomes play crucial roles in nutrient cycling and plant growth, and are shaped by a complex interplay between plants, microbes, and the environment. The role of bacteria as mediators of the 400-million-year-old partnership between the majority of land plants and, arbuscular mycorrhizal (AM) fungi is still poorly understood. Here, we test whether AM hyphae-associated bacteria influence the success of the AM symbiosis.

RESULTS

Using partitioned microcosms containing field soil, we discovered that AM hyphae and roots selectively assemble their own microbiome from the surrounding soil. In two independent experiments, we identified several bacterial genera, including Devosia, that are consistently enriched on AM hyphae. Subsequently, we isolated 144 pure bacterial isolates from a mycorrhiza-rich sample of extraradical hyphae and isolated Devosia sp. ZB163 as root and hyphal colonizer. We show that this AM-associated bacterium synergistically acts with mycorrhiza on the plant root to strongly promote plant growth, nitrogen uptake, and mycorrhization.

CONCLUSIONS

Our results highlight that AM fungi do not function in  isolation and that the plant-mycorrhiza symbiont can recruit beneficial bacteria that support the symbiosis. Video Abstract.

Predominant heterotrophic diazotrophic bacteria are involved in Sargassum proliferation in the Great Atlantic Sargassum Belt

Since 2011, the Caribbean coasts have been subject to episodic influxes of floating Sargassum seaweed of unprecedented magnitude originating from a new area "the Great Atlantic Sargassum Belt" (GASB), leading in episodic influxes and mass strandings of floating Sargassum. For the biofilm of both holopelagic and benthic Sargassum as well as in the surrounding waters, we characterized the main functional groups involved in the microbial nitrogen cycle. The abundance of genes representing nitrogen fixation (nifH), nitrification (amoA), and denitrification (nosZ) showed the predominance of diazotrophs, particularly within the GASB and the Sargasso Sea. In both location, the biofilm associated with holopelagic Sargassum harboured a more abundant proportion of diazotrophs than the surrounding water. The mean δ15N value of the GASB seaweed was very negative (-2.04‰), and lower than previously reported, reinforcing the hypothesis that the source of nitrogen comes from the nitrogen-fixing activity of diazotrophs within this new area of proliferation. Analysis of the diversity of diazotrophic communities revealed for the first time the predominance of heterotrophic diazotrophic bacteria belonging to the phylum Proteobacteria in holopelagic Sargassum biofilms. The nifH sequences belonging to Vibrio genus (Gammaproteobacteria) and Filomicrobium sp. (Alphaproteobacteria) were the most abundant and reached, respectively, up to 46.0% and 33.2% of the community. We highlighted the atmospheric origin of the nitrogen used during the growth of holopelagic Sargassum within the GASB and a contribution of heterotrophic nitrogen-fixing bacteria to a part of the Sargassum proliferation.

Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters

Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.

Glacial meltwater and seasonality influence community composition of diazotrophs in Arctic coastal and open waters

The Arctic Ocean is particularly affected by climate change with unknown consequences for primary productivity. Diazotrophs-prokaryotes capable of converting atmospheric nitrogen to ammonia-have been detected in the often nitrogen-limited Arctic Ocean but distribution and community composition dynamics are largely unknown. We performed amplicon sequencing of the diazotroph marker gene nifH from glacial rivers, coastal, and open ocean regions and identified regionally distinct Arctic communities. Proteobacterial diazotrophs dominated all seasons, epi- to mesopelagic depths and rivers to open waters and, surprisingly, Cyanobacteria were only sporadically identified in coastal and freshwaters. The upstream environment of glacial rivers influenced diazotroph diversity, and in marine samples putative anaerobic sulphate-reducers showed seasonal succession with highest prevalence in summer to polar night. Betaproteobacteria (Burkholderiales, Nitrosomonadales, and Rhodocyclales) were typically found in rivers and freshwater-influenced waters, and Delta- (Desulfuromonadales, Desulfobacterales, and Desulfovibrionales) and Gammaproteobacteria in marine waters. The identified community composition dynamics, likely driven by runoff, inorganic nutrients, particulate organic carbon, and seasonality, imply diazotrophy a phenotype of ecological relevance with expected responsiveness to ongoing climate change. Our study largely expands baseline knowledge of Arctic diazotrophs-a prerequisite to understand underpinning of nitrogen fixation-and supports nitrogen fixation as a contributor of new nitrogen in the rapidly changing Arctic Ocean.

Partners to survive: Hoffmannseggia doellii root-associated microbiome at the Atacama Desert

The discovery and characterization of plant species adapted to extreme environmental conditions have become increasingly important. Hoffmannseggia doellii is a perennial herb endemic to the Chilean Atacama Desert that grows in the western Andes between 2800 and 3600 m above sea level. Its growing habitat is characterized by high radiation and low water and nutrient availability. Under these conditions, H. doellii can grow, reproduce, and develop an edible tuberous root. We characterized the H. doellii soil-associated microbiomes to understand the biotic factors that could influence their surprising ability to survive. We found an increased number of observed species and higher phylogenetic diversity of bacteria and fungi on H. doellii root soils compared with bare soil (BS) along different sites and to soil microbiomes of other plant species. Also, the H. doellii-associated microbiome had a higher incidence of overall positive interactions and fungal within-kingdom interactions than their corresponding BS network. These findings suggest a microbial diversity soil modulation mechanism that may be a characteristic of highly tolerant plants to diverse and extreme environments. Furthermore, since H. doellii is related to important cultivated crops, our results create an opportunity for future studies on climate change adaptation of crop plants.

Contribution of Heterotrophic Diazotrophs to N2 Fixation in a Eutrophic River: Free-Living vs. Aggregate-Associated

Recent studies have indicated that heterotrophic diazotrophs are highly diverse and fix N₂ in aquatic environments with potentially adverse conditions for diazotrophy, such as oxic and rich in total nitrogen. In this study, we compared the activity and diversity of heterotrophic diazotrophs associated with aggregates (>12 μm) to free-living cells in the eutrophic Qishon River during the winter and summer seasons. Overall, measured heterotrophic N₂ fixation rates in the Qishon River ranged between 2.6–3.5 nmol N L^–1 d^–1. Heterotrophic N₂ fixation was mainly associated with aggregates in the summer samples (74 ± 24%), whereas during the winter the bulk diazotrophic activity was mostly ascribed to the free-living fraction (90 ± 6%). In addition, immunolabeled micrographs indicated the presence of aggregate-associated heterotrophic diazotrophs in both seasons, while phototrophic diazotrophs were also captured during the winter. The richness of free-living and aggregate-associated heterotrophic diazotrophs were overall similar, yet the evenness of the later was significantly smaller, suggesting that few of the species gained advantage from particle lifestyle. The differences in the activity, micro-localization and diversity of the diazotrophic community were mostly attributed to spatiotemporal changes in the ambient C:N ratios (total organic carbon, TOC: total nitrogen) and the TOC concentrations. Taken together, our results shed new light on the contribution of heterotrophic diazotroph associated with aggregates to total heterotrophic N₂ fixation in oxic, highly eutrophic aquatic environments.

A robust approach to estimate relative phytoplankton cell abundances from metagenomes

Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.

Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef

The role of diazotrophs in coral physiology and reef biogeochemistry remains poorly understood, in part because N2 fixation rates and diazotrophic community composition have only been jointly analyzed in the tissue of one tropical coral species. We performed field-based 15N2 tracer incubations during nutrient-replete conditions to measure diazotroph-derived nitrogen (DDN) assimilation into three species of scleractinian coral (Pocillopora acuta, Goniopora columna, Platygyra sinensis). Using multi-marker metabarcoding (16S rRNA, nifH, 18S rRNA), we analyzed DNA- and RNA-based communities in coral tissue and skeleton. Despite low N2 fixation rates, DDN assimilation supplied up to 6% of the holobiont's N demand. Active coral-associated diazotrophs were chiefly Cluster I (aerobes or facultative anaerobes), suggesting that oxygen may control coral-associated diazotrophy. Highest N2 fixation rates were observed in the endolithic community (0.20 µg N cm-2 per day). While the diazotrophic community was similar between the tissue and skeleton, RNA:DNA ratios indicate potential differences in relative diazotrophic activity between these compartments. In Pocillopora, DDN was found in endolithic, host, and symbiont compartments, while diazotrophic nifH sequences were only observed in the endolithic layer, suggesting a possible DDN exchange between the endolithic community and the overlying coral tissue. Our findings demonstrate that coral-associated diazotrophy is significant, even in nutrient-rich waters, and suggest that endolithic microbes are major contributors to coral nitrogen cycling on reefs.

Diversity and abundance of diazotrophic communities of seagrass Halophila ovalis based on genomic and transcript level in Daya Bay, South China Sea

Seagrass ecosystems are among the most productive marine ecosystems, and diazotrophic communities play a crucial role in sustaining the productivity and stability of such ecosystems by introducing fixed nitrogen. However, information concerning both total and active diazotrophic groups existing in different compartments of seagrass is lacking. This study comprehensively investigated the diversity, structure, and abundance of diazotrophic communities in different parts of the seagrass Halophila ovalis at the DNA and RNA level from clone libraries and real-time quantitative PCR. Our results indicated that nearly one-third of existing nitrogen-fixing bacteria were active, and their abundance might be controlled by nitrogen to phosphorus ratio (N:P). Deltaproteobacteria and Gammaproteobacteria were dominant groups among the total and active diazotrophic communities in all samples. These two groups accounted for 82.21% and 70.96% at the DNA and RNA levels, respectively. The genus Pseudomonas and sulfate-reducing bacteria (genera: Desulfosarcina, Desulfobulbus, Desulfocapsa, and Desulfopila) constituted the significant fraction of nitrogen-fixing bacteria in the seagrass ecosystem, playing an additional role in denitrification and sulfate reduction, respectively. Moreover, the abundance of the nitrogenase gene, nifH, was highest in seawater and lowest in rhizosphere sediments from all samples. This study highlighted the role of diazotropic communities in the subtropical seagrass ecosystem.

Temperate southern Australian coastal waters are characterised by surprisingly high rates of nitrogen fixation and diversity of diazotrophs

Biological dinitrogen (N₂) fixation is one mechanism by which specific microorganisms (diazotrophs) can ameliorate nitrogen (N) limitation. Historically, rates of N₂ fixation were believed to be limited outside of the low nutrient tropical and subtropical open ocean; however, emerging evidence suggests that N₂ fixation is also a significant process within temperate coastal waters. Using a combination of amplicon sequencing, targeting the nitrogenase reductase gene (nifH), quantitative nifH PCR, and ¹⁵N₂ stable isotope tracer experiments, we investigated spatial patterns of diazotroph assemblage structure and N₂ fixation rates within the temperate coastal waters of southern Australia during Austral autumn and summer. Relative to previous studies in open ocean environments, including tropical northern Australia, and tropical and temperate estuaries, our results indicate that high rates of N₂ fixation (10-64 nmol L^-1 d^-1) can occur within the large inverse estuary Spencer Gulf, while comparatively low rates of N₂ fixation (2 nmol L^-1 d^-1) were observed in the adjacent continental shelf waters. Across the dataset, low concentrations of NO₃/NO₂ were significantly correlated with the highest N₂ fixation rates, suggesting that N₂ fixation could be an important source of new N in the region as dissolved inorganic N concentrations are typically limiting. Overall, the underlying diazotrophic community was dominated by nifH sequences from Cluster 1 unicellular cyanobacteria of the UCYN-A clade, as well as non-cyanobacterial diazotrophs related to Pseudomonas stutzeri, and Cluster 3 sulfate-reducing deltaproteobacteria. Diazotroph community composition was significantly influenced by salinity and SiO₄ concentrations, reflecting the transition from UCYN-A-dominated assemblages in the continental shelf waters, to Cluster 3-dominated assemblages in the hypersaline waters of the inverse estuary. Diverse, transitional diazotrophic communities, comprised of a mixture of UCYN-A and putative heterotrophic bacteria, were observed at the mouth and southern edge of Spencer Gulf, where the highest N₂ fixation rates were observed. In contrast to observations in other environments, no seasonal patterns in N₂ fixation rates and diazotroph community structure were apparent. Collectively, our findings are consistent with the emerging view that N₂ fixation within temperate coastal waters is a previously overlooked dynamic and potentially important component of the marine N cycle.

PPIT: an R package for inferring microbial taxonomy from nifH sequences

MOTIVATION

Linking microbial community members to their ecological functions is a central goal of environmental microbiology. When assigned taxonomy, amplicon sequences of metabolic marker genes can suggest such links, thereby offering an overview of the phylogenetic structure underpinning particular ecosystem functions. However, inferring microbial taxonomy from metabolic marker gene sequences remains a challenge, particularly for the frequently sequenced nitrogen fixation marker gene, nitrogenase reductase (nifH). Horizontal gene transfer in recent nifH evolutionary history can confound taxonomic inferences drawn from the pairwise identity methods used in existing software. Other methods for inferring taxonomy are not standardized and require manual inspection that is difficult to scale.

RESULTS

We present Phylogenetic Placement for Inferring Taxonomy (PPIT), an R package that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. After users place query sequences on a reference nifH gene tree provided by PPIT (n = 6317 full-length nifH sequences), PPIT searches the phylogenetic neighborhood of each query sequence and attempts to infer microbial taxonomy. An inference is drawn only if references in the phylogenetic neighborhood are: (1) taxonomically consistent and (2) share sufficient pairwise identity with the query, thereby avoiding erroneous inferences due to known horizontal gene transfer events. We find that PPIT returns a higher proportion of correct taxonomic inferences than BLAST-based approaches at the cost of fewer total inferences. We demonstrate PPIT on deep-sea sediment and find that Deltaproteobacteria are the most abundant potential diazotrophs. Using this dataset we show that emending PPIT inferences based on visual inspection of query sequence placement can achieve taxonomic inferences for nearly all sequences in a query set. We additionally discuss how users can apply PPIT to the analysis of other marker genes.

AVAILABILITY

PPIT is freely available to non-commercial users at https://github.com/bkapili/ppit. Installation includes a vignette that demonstrates package use and reproduces the nifH amplicon analysis discussed here. The raw nifH amplicon sequence data have been deposited in the GenBank, EMBL, and DDBJ databases under BioProject number PRJEB37167.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Barcoding a can of worms: testing cox1 performance as a DNA barcode of Nematoda

Accurate taxonomic identifications and species delimitations are a fundamental problem in biology. The complex taxonomy of Nematoda is primarily based on morphology, which is often dubious. DNA barcoding emerged as a handy tool to identify specimens and assess diversity, but its applications in Nematoda are incipient. We evaluated cytochrome c oxidase subunit I (cox1) efficiency as a DNA barcode for nematodes scrutinising 5241 sequences retrieved from BOLD and GenBank. The samples included genera with medical, agricultural, or ecological relevance: Anguillicola, Caenorhabditis, Heterodera, Meloidogyne, Onchocerca, Strongyloides, and Trichinella. We assessed cox1 performance through barcode gap and Probability of Correct Identification (PCI) analyses, and estimated species richness through Automatic Barcode Gap Discovery (ABGD). Each genus presented distinct gap ranges, mirroring the evolutionary diversity within Nematoda. Thus, to survey the diversity of the phylum, a careful definition of thresholds for lower taxonomic levels should be considered. PCIs were around 70% for both databases, highlighting operational biases and challenges in nematode taxonomy. ABGD inferred higher richness than the taxonomic labels informed by databases. The prevalence of specimen misidentifications and dubious species delimitations emphasise the value of integrative approaches to nematode taxonomy and systematics. Overall, cox1 is a relevant tool for integrative taxonomy of nematodes.

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms.

Video Abstract

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A catalog of 47 million genes was generated from 370 globally distributed metagenomes

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Meta-omics data integration disentangled the mechanisms of changes in transcript pools

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Transcript pool changes of metabolic marker genes show distinct mechanistic patterns

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Community turnover as a response to ocean warming may be strongest in polar regions

NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes

MOTIVATION

The nitrogen (N) cycle is a collection of important biogeochemical pathways in the Earth ecosystem and has gained extensive foci in ecology and environmental studies. Currently, shotgun metagenome sequencing has been widely applied to explore gene families responsible for N cycle processes. However, there are problems in applying publically available orthology databases to profile N cycle gene families in shotgun metagenomes, such as inefficient database searching, unspecific orthology groups and low coverage of N cycle genes and/or gene (sub)families.

RESULTS

To solve these issues, this study built a manually curated integrative database (NCycDB) for fast and accurate profiling of N cycle gene (sub)families from shotgun metagenome sequencing data. NCycDB contains a total of 68 gene (sub)families and covers eight N cycle processes with 84 759 and 219 146 representative sequences at 95 and 100% identity cutoffs, respectively. We also identified 1958 homologous orthology groups and included corresponding sequences in the database to avoid false positive assignments due to 'small database' issues. We applied NCycDB to characterize N cycle gene (sub)families in 52 shotgun metagenomes from the Global Ocean Sampling expedition. Further analysis showed that the structure and composition of N cycle gene families were most strongly correlated with latitude and temperature. NCycDB is expected to facilitate N cycle studies via shotgun metagenome sequencing approaches in various environments. The framework developed in this study can be served as a good reference to build similar knowledge-based functional gene databases in various processes and pathways.

AVAILABILITY AND IMPLEMENTATION

NCycDB database files are available at https://github.com/qichao1984/NCyc.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Diazotroph Diversity and Nitrogen Fixation in Summer Active Perennial Grasses in a Mediterranean Region Agricultural Soil

Summer-growing perennial grasses such as Panicum coloratum L. cv. Bambatsi (Bambatsi panic), Chloris gayana Kunth cv. Katambora (Rhodes grass) and Digitaria eriantha Steud. cv. Premier (Premier digit grass) growing in the poor fertility sandy soils in the Mediterranean regions of southern Australia and western Australia mainly depend upon soil N and biological N inputs through diazotrophic (free living or associative) N fixation. We investigated the community composition and diversity (nifH-amplicon sequencing), abundance (qPCR) and functional capacity (15N incubation assay) of the endophytic diazotrophic community in the below and above ground plant parts of field grown and unfertilized grasses. Results showed a diverse and abundant diazotrophic community inside plant both above and below-ground and there was a distinct diazotrophic assemblage in the different plant parts in all the three grasses. There was a limited difference in the diversity between leaves, stems and roots except that Panicum grass roots harbored greater species richness. Nitrogen fixation potentials ranged between 0.24 and 5.9 mg N kg-1 day-1 and N fixation capacity was found in both the above and below ground plant parts. Results confirmed previous reports of plant species-based variation and that Alpha-Proteobacteria were the dominant group of nifH-harboring taxa both in the belowground and aboveground parts of the three grass species. Results also showed a well-structured nifH-harboring community in all plant parts, an example for a functional endophytic community. Overall, the variation in the number and identity of module hubs and connectors among the different plant parts suggests that co-occurrence patterns within the nifH-harboring community specific to individual compartments and local environments of the niches within each plant part may dictate the overall composition of diazotrophs within a plant.

Analysis of nifH DNA and RNA reveals a disproportionate contribution to nitrogenase activities by rare plankton-associated diazotrophs

BACKGROUND

Holobionts comprising nitrogen-fixing diazotrophs and phytoplankton or zooplankton are ubiquitous in the pelagic sea. However, neither the community structure of plankton-associated diazotrophs (PADs) nor their nitrogenase transcriptional activity are well-understood. In this study, we used nifH gene Illumina sequencing and quantitative PCR to characterize the community composition and nifH expression profile of PADs with > 100 μm size fraction in the euphotic zone of the northern South China Sea.

RESULTS

The results of DNA- and RNA-derived nifH gene revealed a higher alpha-diversity in the active than in the total community. Moreover, the compositional resemblance among different sites was less for active than for total communities of PADs. We characterized the 20 most abundant OTUs by ranking the sum of sequence reads across 9 sampling stations for individual OTUs in both nifH DNA and RNA libraries, and then assessed their phylogenetic relatedness. Eight of the 20 abundant OTUs were phylogenetically affiliated with Trichodesmium and occurred in approximately equal proportion in both the DNA and RNA libraries. The analysis of nifH gene expression level showed uneven attribute of the abundance and nitrogenase activities by the remaining 12 OTUs. Taxa belonging to cluster III and Betaproteobacteria were present at moderate abundance but exhibited negligible nitrogenase transcription activity. Whereas, the abundances of Richelia, Deltaproteobacteria and Gammaproteobacteria were low but the contribution of these groups to nitrogenase transcription was disproportionately high.

CONCLUSIONS

The substantial variation in community structure among active dizatrophic fractions compared to the total communities suggests that the former are better indicators of biological response to environmental changes. Altogether, our study highlights the importance of rare PADs groups in nitrogen fixation in plankton holobionts, evidenced by their high level of nitrogenase transcription.

Unprecedented bacterial community richness in soybean nodules vary with cultivar and water status

BACKGROUND

Soybean (Glycine max) and other legumes are key crops grown around the world, providing protein and nutrients to a growing population, in a way that is more sustainable than most other cropping systems. Diazotrophs inhabiting root nodules provide soybean with nitrogen required for growth. Despite the knowledge of culturable Bradyrhizobium spp. and how they can differ across cultivars, less is known about the overall bacterial community (bacteriome) diversity within nodules, in situ. This variability could have large functional ramifications for the long-standing scientific dogma related to the plant-bacteriome interaction. Water availability also impacts soybean, in part, as a result of water-deficit sensitive nodule diazotrophs. There is a dearth of information on the effects of cultivar and water status on in situ rhizobia and non-rhizobia populations of nodule microbiomes. Therefore, soybean nodule microbiomes, using 16S rRNA and nifH genes, were sampled from nine cultivars treated with different field water regimes. It was hypothesized that the nodule bacteriome, composition, and function among rhizobia and non-rhizobia would differ in response to cultivar and soil water status.

RESULTS

16S rRNA and nifH showed dominance by Bradyrhizobiaceae, but a large diversity was observed across phylogenetic groups with < 1% and up to 45% relative abundance in cultivars. Other groups primarily included Pseudomonadaceae and Enterobacteriaceae. Thus, nodule bacteriomes were not only dominated by rhizobia, but also described by high variability and partly dependent on cultivar and water status. Consequently, the function of the nodule bacteriomes differed, especially due to cultivar. Amino acid profiling within nodules, for example, described functional changes due to both cultivar and water status.

CONCLUSIONS

Overall, these results reveal previously undescribed richness and functional changes in Bradyrhizobiaceae and non-rhizobia within the soybean nodule microbiome. Though the exact role of these atypical bacteria and relative variations in Bradyrhizobium spp. is not clear, there is potential for exploitation of these novel findings of microbiome diversity and function. This diversity needs consideration as part of bacterial-inclusive breeding of soybean to improve traits, such as yield and seed quality, and environmental resilience.

Temporal variability of diazotroph community composition in the upwelling region off NW Iberia

Knowledge of the ecology of N2-fixing (diazotrophic) plankton is mainly limited to oligotrophic (sub)tropical oceans. However, diazotrophs are widely distributed and active throughout the global ocean. Likewise, relatively little is known about the temporal dynamics of diazotrophs in productive areas. Between February 2014 and December 2015, we carried out 9 one-day samplings in the temperate northwestern Iberian upwelling system to investigate the temporal and vertical variability of the diazotrophic community and its relationship with hydrodynamic forcing. In downwelling conditions, characterized by deeper mixed layers and a homogeneous water column, non-cyanobacterial diazotrophs belonging mainly to nifH clusters 1G (Gammaproteobacteria) and 3 (putative anaerobes) dominated the diazotrophic community. In upwelling and relaxation conditions, affected by enhanced vertical stratification and hydrographic variability, the community was more heterogeneous vertically but less diverse, with prevalence of UCYN-A (unicellular cyanobacteria, subcluster 1B) and non-cyanobacterial diazotrophs from clusters 1G and 3. Oligotyping analysis of UCYN-A phylotype showed that UCYN-A2 sublineage was the most abundant (74%), followed by UCYN-A1 (23%) and UCYN-A4 (2%). UCYN-A1 oligotypes exhibited relatively low frequencies during the three hydrographic conditions, whereas UCYN-A2 showed higher abundances during upwelling and relaxation. Our findings show the presence of a diverse and temporally variable diazotrophic community driven by hydrodynamic forcing in an upwelling system.

Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils

With the likelihood that changes in global climate will adversely affect the soil C reservoir in the northern circumpolar permafrost zone, an understanding of the potential role of diazotrophic communities in enhancing biological N₂ fixation, which constrains both plant production and microbial decomposition in tundra soils, is important in elucidating the responses of soil microbial communities to global climate change. A recent study showed that the composition of the diazotrophic community in a tundra soil exhibited no change under a short-term (1.5-year) winter warming experiment. However, it remains crucial to examine whether the lack of diazotrophic community responses to warming is persistent over a longer time period as a possibly important mechanism in stabilizing tundra soil C. Through a detailed characterization of the effects of winter warming on diazotrophic communities, we showed that a long-term (5-year) winter warming substantially enhanced diazotrophic abundance and altered community composition, though soil depth had a stronger influence on diazotrophic community composition than warming. These changes were best explained by changes in soil moisture, soil thaw duration, and plant biomass. These results provide crucial insights into the potential factors that may impact future C and N availability in tundra regions.

Tundra ecosystems are typically carbon (C) rich but nitrogen (N) limited. Since biological N₂ fixation is the major source of biologically available N, the soil N₂-fixing (i.e., diazotrophic) community serves as an essential N supplier to the tundra ecosystem. Recent climate warming has induced deeper permafrost thaw and adversely affected C sequestration, which is modulated by N availability. Therefore, it is crucial to examine the responses of diazotrophic communities to warming across the depths of tundra soils. Herein, we carried out one of the deepest sequencing efforts of nitrogenase gene (nifH) to investigate how 5 years of experimental winter warming affects Alaskan soil diazotrophic community composition and abundance spanning both the organic and mineral layers. Although soil depth had a stronger influence on diazotrophic community composition than warming, warming significantly (P < 0.05) enhanced diazotrophic abundance by 86.3% and aboveground plant biomass by 25.2%. Diazotrophic composition in the middle and lower organic layers, detected by nifH sequencing and a microarray-based tool (GeoChip), was markedly altered, with an increase of α-diversity. Changes in diazotrophic abundance and composition significantly correlated with soil moisture, soil thaw duration, and plant biomass, as shown by structural equation modeling analyses. Therefore, more abundant diazotrophic communities induced by warming may potentially serve as an important mechanism for supplementing biologically available N in this tundra ecosystem.

UCYN-A3, a newly characterized open ocean sublineage of the symbiotic N2 -fixing cyanobacterium Candidatus Atelocyanobacterium thalassa

The symbiotic unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is one of the most abundant and widespread nitrogen (N₂ )-fixing cyanobacteria in the ocean. Although it remains uncultivated, multiple sublineages have been detected based on partial nitrogenase (nifH) gene sequences, including the four most commonly detected sublineages UCYN-A1, UCYN-A2, UCYN-A3 and UCYN-A4. However, very little is known about UCYN-A3 beyond the nifH sequences from nifH gene diversity surveys. In this study, single cell sorting, DNA sequencing, qPCR and CARD-FISH assays revealed discrepancies involving the identification of sublineages, which led to new information on the diversity of the UCYN-A symbiosis. 16S rRNA and nifH gene sequencing on single sorted cells allowed us to identify the 16S rRNA gene of the uncharacterized UCYN-A3 sublineage. We designed new CARD-FISH probes that allowed us to distinguish and observe UCYN-A2 in a coastal location (SIO Pier; San Diego) and UCYN-A3 in an open ocean location (Station ALOHA; Hawaii). Moreover, we reconstructed about 13% of the UCYN-A3 genome from Tara Oceans metagenomic data. Finally, our findings unveil the UCYN-A3 symbiosis in open ocean waters suggesting that the different UCYN-A sublineages are distributed along different size fractions of the plankton defined by the cell-size ranges of their prymnesiophyte hosts.

Phylogenetic Diversity of Nitrogenase Reductase Genes and Possible Nitrogen-Fixing Bacteria in Thermophilic Chemosynthetic Microbial Communities in Nakabusa Hot Springs

Chemosynthetic microbial communities develop and form dense cell aggregates in slightly alkaline sulfidic hot springs in the temperature range of 70–86°C at Nakabusa, Japan. Nitrogenase activity has recently been detected in the microbial communities collected. To identify possible members capable of nitrogen fixation, we examined the diversities of 16S rRNA and nitrogenase reductase (NifH) gene sequences in four types of chemosynthetic communities with visually different colors and thicknesses. The results of a 16S rRNA gene analysis indicated that all four microbial communities had similar bacterial constituents; the phylum Aquificae was the dominant member, followed in abundance by Thermodesulfobacteria, Firmicutes, and Thermotogae. Most of the NifH sequences were related to sequences reported in hydrothermal vents and terrestrial hot springs. The results of a phylogenetic analysis of NifH sequences revealed diversity in this gene among the communities collected, distributed within 7 phylogenetic groups. NifH sequences affiliated with Aquificae (Hydrogenobacter/Thermocrinis) and Firmicutes (Caldicellulosiruptor) were abundant. At least two different energy metabolic pathways appeared to be related to nitrogen fixation in the communities analyzed; aerobic sulfur/hydrogen-oxidizing bacteria in Aquificae and fermentative bacteria in Firmicutes. The metabolic characteristics of these two dominant phyla differed from those previously inferred from nitrogenase activity assays on chemosynthetic communities, which were associated with hydrogen-dependent autotrophic sulfate reduction. These assays may correspond to the observed NifH sequences that are distantly related to the known species of Thermodesulfovibrio sp. (Nitrospirae) detected in the present study. The activities of nitrogen-fixing organisms in communities may depend on redox states as well as the availability of electron donors, acceptors, and carbon sources.

A database of metazoan cytochrome c oxidase subunit I gene sequences derived from GenBank with CO-ARBitrator

The Cytochrome C Oxidase subunit I gene ("COI") is the de facto standard for animal DNA barcoding. Organism identification based on COI requires an accurate and extensive annotated database of COI sequences. Such a database can also be of value in reconstructing evolutionary history and in diversity studies. Two COI databases are currently available: BOLD and Midori. BOLD's submissions conform to stringent sequence and metadata requirements; BOLD is specific to COI but makes no attempt to be comprehensive. Midori, derived from GenBank, has more sequences but less stringent standards than BOLD, resulting in higher error rates. To address the need for a comprehensive and accurate COI database, we adapted the ARBitrator algorithm, which classifies based only on sequence properties and has successfully auto-curated bacterial genes mined from GenBank. The adapted algorithm, which we call CO-ARBitrator, built a database of over a million metazoan COI sequences. Sensitivity and specificity are significantly higher than Midori. Specificity is comparable to what BOLD achieves with data quality prerequisites. Results and software are publicly available.

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and thus microbial primary productivity. Until now, cyanobacterial populations have been viewed as the main suppliers of bioavailable nitrogen in this habitat. Although PCR amplicon surveys targeting the nitrogenase reductase gene have revealed the existence of diverse non-cyanobacterial diazotrophic populations, subsequent quantitative PCR surveys suggest that they generally occur in low abundance. Here, we use state-of-the-art metagenomic assembly and binning strategies to recover nearly one thousand non-redundant microbial population genomes from the TARA Oceans metagenomes. Among these, we provide the first genomic evidence for non-cyanobacterial diazotrophs inhabiting surface waters of the open ocean, which correspond to lineages within the Proteobacteria and, most strikingly, the Planctomycetes. Members of the latter phylum are prevalent in aquatic systems, but have never been linked to nitrogen fixation previously. Moreover, using genome-wide quantitative read recruitment, we demonstrate that the discovered diazotrophs were not only widespread but also remarkably abundant (up to 0.3% of metagenomic reads for a single population) in both the Pacific Ocean and the Atlantic Ocean northwest. Our results extend decades of PCR-based gene surveys, and substantiate the importance of heterotrophic bacteria in the fixation of nitrogen in the surface ocean.

nifPred: Proteome-Wide Identification and Categorization of Nitrogen-Fixation Proteins of Diaztrophs Based on Composition-Transition-Distribution Features Using Support Vector Machine

As inorganic nitrogen compounds are essential for basic building blocks of life (e.g., nucleotides and amino acids), the role of biological nitrogen-fixation (BNF) is indispensible. All nitrogen fixing microbes rely on the same nitrogenase enzyme for nitrogen reduction, which is in fact an enzyme complex consists of as many as 20 genes. However, the occurrence of six genes viz., nifB, nifD, nifE, nifH, nifK, and nifN has been proposed to be essential for a functional nitrogenase enzyme. Therefore, identification of these genes is important to understand the mechanism of BNF as well as to explore the possibilities for improving BNF from agricultural sustainability point of view. Further, though the computational tools are available for the annotation and phylogenetic analysis of nifH gene sequences alone, to the best of our knowledge no tool is available for the computational prediction of the above mentioned six categories of nitrogen-fixation (nif) genes or proteins. Thus, we proposed an approach, which is first of its kind for the computational identification of nif proteins encoded by the six categories of nif genes. Sequence-derived features were employed to map the input sequences into vectors of numeric observations that were subsequently fed to the support vector machine as input. Two types of classifier were constructed: (i) a binary classifier for classification of nif and non-nitrogen-fixation (non-nif) proteins, and (ii) a multi-class classifier for classification of six categories of nif proteins. Higher accuracies were observed for the combination of composition-transition-distribution (CTD) feature set and radial kernel, as compared to the other feature-kernel combinations. The overall accuracies were observed >90% in both binary and multi-class classifications. The developed approach further achieved >92% accuracy, while evaluated with blind (independent) test datasets. The developed approach also produced higher accuracy in identifying nif proteins, while evaluated using proteome-wide datasets of several species. Furthermore, we established a prediction server nifPred (http://webapp.cabgrid.res.in/nifPred) to assist the scientific community for proteome-wide identification of six categories of nif proteins. Besides, the source code of nifPred is also available at https://github.com/PrabinaMeher/nifPred. The developed web server is expected to supplement the transcriptional profiling and comparative genomics studies for the identification and functional annotation of genes related to BNF.

Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP - A Bioinformatics Pipeline for Analyzing nifH Amplicon Data

Diazotrophic microorganisms introduce biologically available nitrogen (N) to the global N cycle through the activity of the nitrogenase enzyme. The genetically conserved dinitrogenase reductase (nifH) gene is phylogenetically distributed across four clusters (I-IV) and is widely used as a marker gene for N2 fixation, permitting investigators to study the genetic diversity of diazotrophs in nature and target potential participants in N2 fixation. To date there have been limited, standardized pipelines for analyzing the nifH functional gene, which is in stark contrast to the 16S rRNA gene. Here we present a bioinformatics pipeline for processing nifH amplicon datasets - NifMAP ("NifH MiSeq Illumina Amplicon Analysis Pipeline"), which as a novel aspect uses Hidden-Markov Models to filter out homologous genes to nifH. By using this pipeline, we evaluated the broadly inclusive primer pairs (Ueda19F-R6, IGK3-DVV, and F2-R6) that target the nifH gene. To evaluate any systematic biases, the nifH gene was amplified with the aforementioned primer pairs in a diverse collection of environmental samples (soils, rhizosphere and roots samples, biological soil crusts and estuarine samples), in addition to a nifH mock community consisting of six phylogenetically diverse members. We noted that all primer pairs co-amplified nifH homologs to varying degrees; up to 90% of the amplicons were nifH homologs with IGK3-DVV in some samples (rhizosphere and roots from tall oat-grass). In regards to specificity, we observed some degree of bias across the primer pairs. For example, primer pair F2-R6 discriminated against cyanobacteria (amongst others), yet captured many sequences from subclusters IIIE and IIIL-N. These aforementioned subclusters were largely missing by the primer pair IGK3-DVV, which also tended to discriminate against Alphaproteobacteria, but amplified sequences within clusters IIIC (affiliated with Clostridia) and clusters IVB and IVC. Primer pair Ueda19F-R6 exhibited the least bias and successfully captured diazotrophs in cluster I and subclusters IIIE, IIIL, IIIM, and IIIN, but tended to discriminate against Firmicutes and subcluster IIIC. Taken together, our newly established bioinformatics pipeline, NifMAP, along with our systematic evaluations of nifH primer pairs permit more robust, high-throughput investigations of diazotrophs in diverse environments.

Sewage outburst triggers Trichodesmium bloom and enhance N2 fixation rates

The southeastern Mediterranean Sea (SEMS) is a warm and sunlit marine environment with low ambient N concentration, thus considered ideal for diazotrophy by autotrophic diazotrophs such as Trichodesmium. Despite the favorable conditions, N₂ fixation rates are often low and Trichodesmium has hardly been spotted in the SEMS. This study reports on the occurrence of a Trichodesmium bloom in the SEMS which was ascribed to T. erythraeum according to DNA fingerprinting of the nifH gene. We found that this bloom (1407 ± 983 cells L⁻¹) was triggered by an intense outburst of raw sewage that supplied high concentrations of N, P and dissolved organic carbon (DOC), which resulted in low N:P (~12:1) and exceptionally high C:P (~1340:1) ratios. We surmise that these conditions provided favorable conditions for Trichodesmium bloom to form via mixotrophic metabolism. As a result, a fourfold increase in N₂ fixation was recorded, which contributed ~70% to new primary production and spur a sharp increase in phytoplankton activity and biomass. The conclusions of this study point on a new paradigm for bloom-forming T. erythraeum which is tightly linked to anthropogenic sources and prompt microbial productivity in oligotrophic marine environments such as the SEMS.

Diversity and Activity of Diazotrophs in Great Barrier Reef Surface Waters

Discrepancies between bioavailable nitrogen (N) concentrations and phytoplankton growth rates in the oligotrophic waters of the Great Barrier Reef (GBR) suggest that undetermined N sources must play a significant role in supporting primary productivity. One such source could be biological dinitrogen (N₂) fixation through the activity of “diazotrophic” bacterioplankton. Here, we investigated N₂ fixation and diazotroph community composition over 10° S of latitude within GBR surface waters. Qualitative N₂ fixation rates were found to be variable across the GBR but were relatively high in coastal, inner and outer GBR waters, reaching 68 nmol L^-1 d^-1. Diazotroph assemblages, identified by amplicon sequencing of the nifH gene, were dominated by the cyanobacterium Trichodesmium erythraeum, γ-proteobacteria from the Gamma A clade, and δ-proteobacterial phylotypes related to sulfate-reducing genera. However, diazotroph communities exhibited significant spatial heterogeneity, correlated with shifts in dissolved inorganic nutrient concentrations. Specifically, heterotrophic diazotrophs generally increased in relative abundance with increasing concentrations of phosphate and N, while Trichodesmium was proportionally more abundant when concentrations of these nutrients were low. This study provides the first in-depth characterization of diazotroph community composition and N₂ fixation dynamics within the oligotrophic, N-limited surface waters of the GBR. Our observations highlight the need to re-evaluate N cycling dynamics within oligotrophic coral reef systems, to include diverse N₂ fixing assemblages as a potentially significant source of dissolved N within the water column.

Distinct ecological niches of marine symbiotic N2 -fixing cyanobacterium Candidatus Atelocyanobacterium thalassa sublineages

A recently described symbiosis between the metabolically streamlined nitrogen-fixing cyanobacterium UCYN-A and a single-celled eukaryote prymnesiophyte alga is widely distributed throughout tropical and subtropical marine waters, and is thought to contribute significantly to nitrogen fixation in these regions. Several UCYN-A sublineages have been defined based on UCYN-A nitrogenase (nifH) sequences. Due to the low abundances of UCYN-A in the global oceans, currently existing molecular techniques are limited for detecting and quantifying these organisms. A targeted approach is needed to adequately characterize the diversity of this important marine cyanobacterium, and to advance understanding of its ecological importance. We present findings on the distribution of UCYN-A sublineages based on high throughput sequencing of UCYN-A nifH PCR amplicons from 78 samples distributed throughout many major oceanic provinces. These UCYN-A nifH fragments were used to define oligotypes, alternative taxonomic units defined by nucleotide positions with high variability. The data set was dominated by a single oligotype associated with the UCYN-A1 sublineage, consistent with previous observations of relatively high abundances in tropical and subtropical regions. However, this analysis also revealed for the first time the widespread distribution of the UCYN-A3 sublineage in oligotrophic waters. Furthermore, distinct assemblages of UCYN-A oligotypes were found in oligotrophic and coastally influenced waters. This unique data set provides a framework for determining the environmental controls on UCYN-A distributions and the ecological importance of the different sublineages.

Unusual marine unicellular symbiosis with the nitrogen-fixing cyanobacterium UCYN-A

Nitrogen fixation - the reduction of dinitrogen (N₂) gas to biologically available nitrogen (N) - is an important source of N for terrestrial and aquatic ecosystems. In terrestrial environments, N₂-fixing symbioses involve multicellular plants, but in the marine environment these symbioses occur with unicellular planktonic algae. An unusual symbiosis between an uncultivated unicellular cyanobacterium (UCYN-A) and a haptophyte picoplankton alga was recently discovered in oligotrophic oceans. UCYN-A has a highly reduced genome, and exchanges fixed N for fixed carbon with its host. This symbiosis bears some resemblance to symbioses found in freshwater ecosystems. UCYN-A shares many core genes with the 'spheroid bodies' of Epithemia turgida and the endosymbionts of the amoeba Paulinella chromatophora. UCYN-A is widely distributed, and has diversified into a number of sublineages that could be ecotypes. Many questions remain regarding the physical and genetic mechanisms of the association, but UCYN-A is an intriguing model for contemplating the evolution of N₂-fixing organelles.

Diazotroph Diversity in the Sea Ice, Melt Ponds, and Surface Waters of the Eurasian Basin of the Central Arctic Ocean

The Eurasian basin of the Central Arctic Ocean is nitrogen limited, but little is known about the presence and role of nitrogen-fixing bacteria. Recent studies have indicated the occurrence of diazotrophs in Arctic coastal waters potentially of riverine origin. Here, we investigated the presence of diazotrophs in ice and surface waters of the Central Arctic Ocean in the summer of 2012. We identified diverse communities of putative diazotrophs through targeted analysis of the nifH gene, which encodes the iron protein of the nitrogenase enzyme. We amplified 529 nifH sequences from 26 samples of Arctic melt ponds, sea ice and surface waters. These sequences resolved into 43 clusters at 92% amino acid sequence identity, most of which were non-cyanobacterial phylotypes from sea ice and water samples. One cyanobacterial phylotype related to Nodularia sp. was retrieved from sea ice, suggesting that this important functional group is rare in the Central Arctic Ocean. The diazotrophic community in sea-ice environments appear distinct from other cold-adapted diazotrophic communities, such as those present in the coastal Canadian Arctic, the Arctic tundra and glacial Antarctic lakes. Molecular fingerprinting of nifH and the intergenic spacer region of the rRNA operon revealed differences between the communities from river-influenced Laptev Sea waters and those from ice-related environments pointing toward a marine origin for sea-ice diazotrophs. Our results provide the first record of diazotrophs in the Central Arctic and suggest that microbial nitrogen fixation may occur north of 77°N. To assess the significance of nitrogen fixation for the nitrogen budget of the Arctic Ocean and to identify the active nitrogen fixers, further biogeochemical and molecular biological studies are needed.

Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation

Chemosynthetic symbioses are partnerships between invertebrate animals and chemosynthetic bacteria. The latter are the primary producers, providing most of the organic carbon needed for the animal host's nutrition. We sequenced genomes of the chemosynthetic symbionts from the lucinid bivalve Loripes lucinalis and the stilbonematid nematode Laxus oneistus. The symbionts of both host species encoded nitrogen fixation genes. This is remarkable as no marine chemosynthetic symbiont was previously known to be capable of nitrogen fixation. We detected nitrogenase expression by the symbionts of lucinid clams at the transcriptomic and proteomic level. Mean stable nitrogen isotope values of Loripes lucinalis were within the range expected for fixed atmospheric nitrogen, further suggesting active nitrogen fixation by the symbionts. The ability to fix nitrogen may be widespread among chemosynthetic symbioses in oligotrophic habitats, where nitrogen availability often limits primary productivity.

The chemosynthetic symbionts of the bivalve Loripes lucinalis and nematode Laxus oneistus are found to encode nitrogen fixation genes, with evidence for active nitrogen fixation.

Rapid annotation of nifH gene sequences using classification and regression trees facilitates environmental functional gene analysis

The nifH gene is a widely used molecular proxy for studying nitrogen fixation. Phylogenetic classification of nifH gene sequences is an essential step in diazotroph community analysis that requires a fast automated solution due to increasing size of environmental sequence libraries and increasing yield of nifH sequences from high-throughput technologies. A novel approach to rapidly classify nifH amino acid sequences into well-defined phylogenetic clusters that provides a common platform for comparative analysis across studies is presented. Phylogenetic group membership can be accurately predicted with decision tree-type statistical models that identify and utilize signature residues in the amino acid sequences. Our classification models were trained and evaluated with a publicly available and manually curated nifH gene database containing cluster annotations. Model-independent sequence sets from diverse ecosystems were used for further assessment of the models' prediction accuracy. The utility of this novel sequence binning approach was demonstrated in a comparative study where joint treatment of diazotroph assemblages from a wide range of habitats identified habitat-specific and widely-distributed diazotrophs and revealed a marine - terrestrial distinction in community composition. Our rapid and automated phylogenetic cluster assignment circumvents extensive phylogenetic analysis of nifH sequences; hence, it saves substantial time and resources in nitrogen fixation studies.

Marine Non-Cyanobacterial Diazotrophs: Moving beyond Molecular Detection

The nitrogen input through biological N₂ fixation is essential for life in vast areas of the global ocean. The belief is that cyanobacteria are the only relevant N₂-fixing (diazotrophic) organisms. It has, however, now become evident that non-cyanobacterial diazotrophs, bacteria and archaea with ecologies fundamentally distinct from those of cyanobacteria, are widespread and occasionally fix N₂ at significant rates. The documentation of a globally relevant nitrogen input from these diazotrophs would constitute a new paradigm for research on oceanic nitrogen cycling. Here we highlight the need for combining rate measurements and molecular analyses of field samples with cultivation studies in order to clarify the ecology of non-cyanobacteria and their contribution to marine N₂ fixation on local and global scales.

Contribution of mono and polysaccharides to heterotrophic N2 fixation at the eastern Mediterranean coastline

N2 fixation should be a critical process in the nitrogen-poor surface water of the eastern Mediterranean Sea. Despite favorable conditions, diazotroph abundance and N2 fixation rates remains low for reasons yet explained. The main goal of this study was to investigate the limiting nutrients for diazotrophy in this oligotrophic environment. Hence, we conducted dedicated bottle-microcosms with eastern Mediterranean Sea water that were supplemented with mono and polysaccharides as well as inorganic nitrogen and phosphorous. Our results indicate that the diazotrophic community expressing nifH was primarily represented by heterotrophic Proteobacteria. N2 fixation and heterotrophic bacterial activity increased up-to tenfold following two days of dark incubations, once seawater was supplemented with organic carbon substrate in the form of glucose (monosaccharides) or gum-xanthan (polysaccharide surrogate). Furthermore, our results point that carbon-rich polysaccharides, such as transparent exopolymer particles, enhance heterotrophic N2 fixation, by forming microenvironments of intense metabolic activity, high carbon: nitrogen ratio, and possibly low O2 levels. The conclusions of this study indicate that diazotrophs in the eastern Mediterranean coast are primarily limited by organic carbon substrates, as possibly in many other marine regions.

Bacterial Mobilization of Nutrients From Biochar-Amended Soils

Soil amendments with biochar to improve soil fertility and increase soil carbon stocks have received some high-level attention. Physical and chemical analyses of amended soils and biochars from various feedstocks are reported, alongside some evaluations of plant growth promotion capabilities. Fewer studies investigated the soil microbiota and their potential to increase cycling and mobilization of nutrients in biochar-amended soils. This review is discussing the latest findings in the bacterial contribution to cycling and mobilizing nitrogen, phosphorus, and sulfur in biochar-amended soils and potential contributions to plant growth promotion. Depending on feedstock, pyrolysis, soil type, and plant cover, changes in the bacterial community structure were observed for a majority of the studies using amplicon sequencing or genetic fingerprinting methods. Prokaryotic nitrification largely depends on the availability of ammonium and can vary considerably under soil biochar amendment. However, denitrification to di-nitrogen and in particular, nitrous oxide reductase activity is commonly enhanced, resulting in reduced nitrous oxide emissions. Likewise, bacterial fixation of di-nitrogen appears to be regularly enhanced. A paucity of studies suggests that bacterial mobilization of phosphorus and sulfur is enhanced as well. However, most studies only tested for extracellular sulfatase and phosphatase activity. Further research is needed to reveal details of the bacterial nutrient mobilizing capabilities and this is in particular the case for the mobilization of phosphorus and sulfur.

Mesopelagic N2 Fixation Related to Organic Matter Composition in the Solomon and Bismarck Seas (Southwest Pacific)

Dinitrogen (N₂) fixation was investigated together with organic matter composition in the mesopelagic zone of the Bismarck (Transect 1) and Solomon (Transect 2) Seas (Southwest Pacific). Transparent exopolymer particles (TEP) and the presence of compounds sharing molecular formulae with saturated fatty acids and sugars, as well as dissolved organic matter (DOM) compounds containing nitrogen (N) and phosphorus (P) were higher on Transect 1 than on Transect 2, while oxygen concentrations showed an opposite pattern. N₂ fixation rates (up to ~1 nmol N L^-1 d^-1) were higher in Transect 1 than in Transect 2, and correlated positively with TEP, suggesting a dependence of diazotroph activity on organic matter. The scores of the multivariate ordination of DOM molecular formulae and their relative abundance correlated negatively with bacterial abundances and positively with N₂ fixation rates, suggesting an active bacterial exploitation of DOM and its use to sustain diazotrophic activity. Sequences of the nifH gene clustered with Alpha-, Beta-, Gamma- and Deltaproteobacteria, and included representatives from Clusters I, III and IV. A third of the clone library included sequences close to the potentially anaerobic Cluster III, suggesting that N₂ fixation was partially supported by presumably particle-attached diazotrophs. Quantitative polymerase chain reaction (qPCR) primer-probe sets were designed for three phylotypes and showed low abundances, with a phylotype within Cluster III at up to 10³nifH gene copies L^-1. These results provide new insights into the ecology of non-cyanobacterial diazotrophs and suggest that organic matter sustains their activity in the mesopelagic ocean.

High levels of heterogeneity in diazotroph diversity and activity within a putative hotspot for marine nitrogen fixation

Australia's tropical waters represent predicted 'hotspots' for nitrogen (N2) fixation based on empirical and modelled data. However, the identity, activity and ecology of diazotrophs within this region are virtually unknown. By coupling DNA and cDNA sequencing of nitrogenase genes (nifH) with size-fractionated N2 fixation rate measurements, we elucidated diazotroph dynamics across the shelf region of the Arafura and Timor Seas (ATS) and oceanic Coral Sea during Austral spring and winter. During spring, Trichodesmium dominated ATS assemblages, comprising 60% of nifH DNA sequences, while Candidatus Atelocyanobacterium thalassa (UCYN-A) comprised 42% in the Coral Sea. In contrast, during winter the relative abundance of heterotrophic unicellular diazotrophs (δ-proteobacteria and γ-24774A11) increased in both regions, concomitant with a marked decline in UCYN-A sequences, whereby this clade effectively disappeared in the Coral Sea. Conservative estimates of N2 fixation rates ranged from <1 to 91 nmol l(-1) day(-1), and size fractionation indicated that unicellular organisms dominated N2 fixation during both spring and winter, but average unicellular rates were up to 10-fold higher in winter than in spring. Relative abundances of UCYN-A1 and γ-24774A11 nifH transcripts negatively correlated to silicate and phosphate, suggesting an affinity for oligotrophy. Our results indicate that Australia's tropical waters are indeed hotspots for N2 fixation and that regional physicochemical characteristics drive differential contributions of cyanobacterial and heterotrophic phylotypes to N2 fixation.