Nitrogenase gene diversity and microbial community structure: a cross-system comparison

Functional responses of key marine bacteria to environmental change - toward genetic counselling for coastal waters

Coastal ecosystems deteriorate globally due to human-induced stress factors, like nutrient loading and pollution. Bacteria are critical to marine ecosystems, e.g., by regulating nutrient cycles, synthesizing vitamins, or degrading pollutants, thereby providing essential ecosystem services ultimately affecting economic activities. Yet, until now bacteria are overlooked both as mediators and indicators of ecosystem health, mainly due to methodological limitations in assessing bacterial ecosystem functions. However, these limitations are largely overcome by the advances in molecular biology and bioinformatics methods for characterizing the genetics that underlie functional traits of key bacterial populations - "key" in providing important ecosystem services, being abundant, or by possessing high metabolic rates. It is therefore timely to analyze and define the functional responses of bacteria to human-induced effects on coastal ecosystem health. We posit that categorizing the responses of key marine bacterial populations to changes in environmental conditions through modern microbial oceanography methods will allow establishing the nascent field of genetic counselling for our coastal waters. This requires systematic field studies of linkages between functional traits of key bacterial populations and their ecosystem functions in coastal seas, complemented with systematic experimental analyses of the responses to different stressors. Research and training in environmental management along with dissemination of results and dialogue with societal actors are equally important to ensure the role of bacteria is understood as fundamentally important for coastal ecosystems. Using the responses of microorganisms as a tool to develop genetic counselling for coastal ecosystems can ultimately allow for integrating bacteria as indicators of environmental change.

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

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

Micromanaging the nitrogen cycle in agroecosystems

While large inputs of synthetic nitrogen fertilizers enable our current rate of crop production and feed a growing global population, these fertilizers come at a heavy environmental cost. Driven by microbial processes, excess applied nitrogen is lost from agroecosystems as nitrate and nitrous oxide (N₂O) contaminating aquatic ecosystems and contributing to climate change. Interest in nitrogen-fixing microorganisms as an alternative to synthetic fertilizers is rapidly accelerating. Microbial inoculants offer the promise of a sustainable and affordable source of nitrogen, but the impact of inoculants on nitrogen dynamics at an ecosystem level is not fully understood. This review synthesizes recent studies on microbial inoculants as tools for nutrient management and considers the ramifications of inoculants for nitrogen transformations beyond fixation.

nifH gene expression and diversity in geothermal springs of Tengchong, China

Terrestrial hot springs have been suggested to harbor diverse diazotrophic lineages by using DNA-based nifH gene phylogenetic analysis. However, only a small amount of diazotrophs were ever confirmed to perform nitrogen fixation. In order to explore the compositions of active diazotrophic populations in hot springs, the in situ expression and diversity of nifH and 16S rRNA genes were investigated in the sediments of hot springs (pH 4.3-9.1; temperature 34-84°C) in Tengchong, China, by using high-throughput sequencing. The results showed that active diazotrophs were diverse in the studied Tengchong hot springs. The main active diazotrophs in high-temperature hot springs were affiliated with Aquificae, while those in low-temperature hot springs belonged to Cyanobacteria and Nitrospirae. Such dominance of Aquificae and Nitrospirae of diazotrophs has not been reported in other ecosystems. This suggests that hot springs may harbor unique active diazotrophs in comparison with other type of ecosystems. Furthermore, there were significant differences in the phylogenetic lineages of diazotrophs between hot springs of Tengchong and other regions, indicating that diazotrophs have geographical distribution patterns. Statistical analysis suggests that the expression and distribution of nifH gene were influenced by temperature and concentrations of ammonia and sulfur seem in Tengchong hot springs. These findings avail us to understand element cycling mediated by diazotrophs in hot spring ecosystems.

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

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

Degradation reduces the diversity of nitrogen-fixing bacteria in the alpine wetland on the Qinghai-Tibet Plateau

Biological nitrogen fixation is a key process in the nitrogen cycle and the main source of soil available nitrogen. The number and diversity of nitrogen-fixing bacteria directly reflect the efficiency of soil nitrogen fixation. The alpine wetland on the Qinghai-Tibet Plateau (QTP) is degrading increasingly, with a succession toward alpine meadows. Significant changes in soil physicochemical properties accompany this process. However, it is unclear how does the soil nitrogen-fixing bacteria change during the degradation processes, and what is the relationship between these changes and soil physicochemical properties. In this study, the nifH gene was used as a molecular marker to further investigate the diversity of nitrogen-fixing bacteria at different stages of degradation (none, light, and severe degeneration) in the alpine wetland. The results showed that wetland degradation significantly reduced the diversity, altered the community composition of nitrogen-fixing bacteria, decreased the relative abundance of Proteobacteria, and increased the relative abundance of Actinobacteria. In addition to the dominant phylum, the class, order, family, and genus of nitrogen-fixing bacteria had significant changes in relative abundance. Analysis of Mantel test showed that most soil factors (such as pH, soil water content (SWC), the organic carbon (TOC), total nitrogen (TN), and soil C:P ratio) and abundance had a significant positive correlation. TOC, TN, total phosphorus (TP), soil C:P ratio and Shannon had a significant positive correlation with each other. The RDA ranking further revealed that TOC, SWC, and TN were the main environmental factors influencing the community composition of nitrogen-fixing bacteria. It is found that the degradation of the alpine wetland inhibited the growth of nitrogen-fixing bacteria to a certain extent, leading to the decline of their nitrogen-fixing function.

Altitudinal niches of symbiotic, associative and free-living diazotrophs driven by soil moisture and temperature in the alpine meadow on the Tibetan Plateau

Legume-associated symbiotic diazotrophs contribute more to nitrogen (N) fixation than non-symbiotic diazotrophs in many terrestrial ecosystems. However, the percentage of legume biomass is low in alpine meadows on the Tibetan Plateau. Therefore, non-symbiotic diazotrophs may play important roles in N fixation in alpine meadow soils. Moreover, Tibetan alpine meadows are fragile and sensitive to global climate change, and the investigating of the key factor driving soil diazotrophic community still entails several challenges. To address these issues, we investigated diazotrophic spatial distribution and diversity along the elevational gradient between 3200 and 4200 m in the alpine meadow using amplicon sequencing of nifH gene. The result clearly showed that soil moisture and temperature were key factors driving soil diazotrophic community structures. Both altitude and soil depth significantly differentiated diazotrophic community composition. Alpha diversity indices of diazotrophic communities showed unimodal distribution along elevation gradient, strongly affected by soil moisture. Altitudinal niches were occupied by different diazotrophs. Soils at lower elevations were dominated by symbiotic diazotrophs and associative diazotrophs related to high biomass of plant hosts, while those at higher elevations were dominated by free-living psychrophiles such as Polaromonas. Furthermore, high moisture stimulated free-living anaerobes at middle elevations, such as Geobacter and Anaeromyxobacter, while suppressed legumes and symbiotic Mezorhizobium. Soil temperature not only directly affected temperature-sensitive diazotrophs, but also indirectly affected them through plants and soil properties such as pH and ammonium content. Our results suggest that climate change may strongly affect biological nitrogen fixation (BNF), and free-living diazotrophs may play important roles in BNF of alpine meadow system on the Tibetan Plateau.

Comparison of bacterial diversity, root exudates and soil enzymatic activities in the rhizosphere of AVP1-transgenic and non-transgenic wheat (Triticum aestivum L.)

AIMS

Soil microbial communities are among the most diverse communities that might be affected due to transgenic crops. Therefore, risk assessment studies on transgenes are essentially required as any adverse effects may depend not only on the specific gene and crop involved but also on soil conditions.

METHODS AND RESULTS

The present study deals with the comparison of bacterial populations, root exudates, and activities of soil enzymes in non-transgenic and AVP1-transgenic wheat rhizosphere, overexpressing vacuolar H+pyrophosphatase for salinity and drought stress tolerance. Amounts of organic acids and sugars produced as root exudates and activities of dehydrogenase, phosphatase, and protease enzymes in soil solution showed no significant differences in AVP1-transgenic and non-transgenic wheat rhizosphere, except for urease and phenol oxidase activities. The higher copy number of nifH gene showed the abundance of nitrogen-fixing bacteria in the rhizosphere of AVP1-transgenic wheat compared with non-transgenic wheat. nifH gene sequence analysis indicated the common diazotrophic genera Azospirillum, Bradyrhizobium, Rhizobium, and Pseudomonas in AVP1-transgenic and non-transgenic wheat except for Zoogloea detected only in non-transgenic wheat. Using 454-pyrosequencing of 16S rRNA gene from soil DNA, a total of 156, 282 sequences of 18 phyla were obtained, which represented bacterial (128,006), Archeal (7,928), and unclassified (21,568) sequences. Proteobacteria, Crenarchaeota, and Firmicutes were the most abundant phyla in transgenic and non-transgenic wheat rhizosphere. Further comparison of different taxonomic units at the genus level showed similar distribution in transgenic and non-transgenic wheat rhizosphere.

CONCLUSION

We conclude that AVP1 gene in transgenic wheat has no apparent adverse effects on the soil environment and different bacterial communities. However, bacterial community depends on several other factors not only genetic composition of the host plants.

SIGNIFICANCE OF THE STUDY

The present research supports introduction and cultivation of transgenic plants in agricultural systems without any adverse effects on indigenous bacterial communities and soil ecosystem.

Obtaining Osmo-resistant Mutants in Nitrogen-Fixing Bacteria Isolated from Saline Soils

Annually, about, more than 7% of the Earth's land area becomes inappropriate for agriculture subsequently of salinization and desertification. Biofertilizers based on halophilic nitrogen-fixing bacteria can restore saline soils and stimulate plant growth, having a positive effect on germination, development of stems and roots, and fruiting. The aim of this work was to obtain osmo-resistant (Osm-r) nitrogen-fixing mutants isolated from saline soils of Armenia and selection of the best ones. To achieve this goal, we have obtained a collection of Osm-r strains based on soil nitrogen-fixing bacteria without the use of genetically modified technologies, which is an innovation in sphere of soil microbiology, and, especially, in nitrogen-fixing microorganisms. These mutants were obtained on the basis of Agrobacterium sp. Y-2 and Agrobacterium sp. M-1 nitrogen-fixing strains, both spontaneously and induced. Four strains with the higher nitrogen-fixing ability, which kept their vital activity in an environment with a high concentration of salts, were selected from collection of mutants. Selected strains in the future can become the basis for creating a new, effective, environmentally friendly biofertilizer for saline soils because they are plasmidless and have the highest priority for intensive use in agriculture.

Exploring Functional Diversity and Community Structure of Diazotrophic Endophytic Bacteria Associated with Pennisetum glaucum Growing under Field in a Semi-Arid Region

Diazotrophic endophytic bacteria (DEB) are the key drivers of nitrogen fixation in rainfed soil ecosystems and, hence, can influence the growth and yield of crop plants. Therefore, the present work investigated the structure and composition of the DEB community at different growth stages of field-grown pearl millet plants, employing the cultivation-dependent method. Diazotrophy of the bacterial isolates was confirmed by acetylene reduction assay and amplification of the nifH gene. ERIC-PCR-based DNA fingerprinting, followed by 16S rRNA gene analysis of isolates recovered at different time intervals, demonstrated the highest bacterial diversity during early (up to 28 DAS (Days after sowing)) and late (63 DAS onwards) stages, as compared to the vegetative growth stage (28–56 DAS). Among all species, Pseudomonas aeruginosa was the most dominant endophyte. Assuming modulation of the immune response as one of the tactics for successful colonization of P. aeruginosa PM389, we studied the expression of the profile of defense genes of wheat, used as a host plant, in response to P. aeruginosa inoculation. Most of the pathogenesis-related PR genes were induced initially (at 6 h after infection (HAI)), followed by their downregulation at 12 HAI. The trend of bacterial colonization was quantified by qPCR of 16S rRNAs. The results obtained in the present study indicated an attenuated defense response in host plants towards endophytic bacteria, which is an important feature that helps endophytes establish themselves inside the endosphere of roots.

Nitrogen fixation by diverse diazotrophic communities can support population growth of arboreal ants

BACKGROUND

Symbiotic ant-plant associations, in which ants live on plants, feed on plant-provided food, and protect host trees against threats, are ubiquitous across the tropics, with the Azteca-Cecropia associations being amongst the most widespread interactions in the Neotropics. Upon colonization of Cecropia's hollow internodes, Azteca queens form small patches with plant parenchyma, which are then used as waste piles when the colony grows. Patches-found in many ant-plant mutualisms-are present throughout the colony life cycle and may supplement larval food. Despite their initial nitrogen (N)-poor substrate, patches in Cecropia accommodate fungi, nematodes, and bacteria. In this study, we investigated the atmospheric N2 fixation as an N source in patches of early and established ant colonies.

RESULTS

Via 15N2 tracer assays, N2 fixation was frequently detected in all investigated patch types formed by three Azteca ant species. Quantified fixation rates were similar in early and established ant colonies and higher than in various tropical habitats. Based on amplicon sequencing, the identified microbial functional guild-the diazotrophs-harboring and transcribing the dinitrogenase reductase (nifH) gene was highly diverse and heterogeneous across Azteca colonies. The community composition differed between early and established ant colonies and partly between the ant species.

CONCLUSIONS

Our data show that N2 fixation can result in reasonable amounts of N in ant colonies, which might not only enable bacterial, fungal, and nematode growth in the patch ecosystems but according to our calculations can even support the growth of ant populations. The diverse and heterogeneous diazotrophic community implies a functional redundancy, which could provide the ant-plant-patch system with a higher resilience towards changing environmental conditions. Hence, we propose that N2 fixation represents a previously unknown potential to overcome N limitations in arboreal ant colonies.

Effects of Solar Radiation on the Cyanobacteria: Diversity, Molecular Phylogeny, and Metabolic Activity

Cyanobacteria bloom is a global aquatic ecological problem that seriously threatens human health and social development. The outbreak of cyanobacteria bloom is affected by various environmental factors, among which light dose is an essential factor. In this study, the growth changes of cyanobacteria under different amounts of natural light were studied by simulating different depths of Taihu Lake, and we used 16S rRNA and non-targeted metabolomics for sequencing to reveal the effects of light on the diversity of cyanobacteria and coexisting microorganisms, and to analyze the changes of related genes, functional structures and internal metabolism involved in nitrogen cycling. The result shows that excessive and insufficient light could limit the growth, photosynthesis, and EPS secretion of cyanobacteria, resulting in an antioxidant stress response. At the same time, the amount of natural light affects the vertical distribution of cyanobacteria, and under the condition of 1/3 natural light, cyanobacteria first appeared to float. In addition, the amount of natural light affects the diversity, abundance, and metabolites of cyanobacteria and coexisting microorganisms, and the expression of nifH, nirK, and nirS, three nitrogen-fixing genes, is significantly different in different genera. This study provides valuable information on the molecular mechanism of the effects of the amount of natural light on cyanobacteria bloom.

Insight into soil nitrogen and phosphorus availability and agricultural sustainability by plant growth-promoting rhizobacteria

Nitrogen and phosphorus are critical for the vegetation ecosystem and two of the most insufficient nutrients in the soil. In agriculture practice, many chemical fertilizers are being applied to soil to improve soil nutrients and yield. This farming procedure poses considerable environmental risks which affect agricultural sustainability. As robust soil microorganisms, plant growth-promoting rhizobacteria (PGPR) have emerged as an environmentally friendly way of maintaining and improving the soil's available nitrogen and phosphorus. As a special PGPR, rhizospheric diazotrophs can fix nitrogen in the rhizosphere and promote plant growth. However, the mechanisms and influences of rhizospheric nitrogen fixation (NF) are not well researched as symbiotic NF lacks summarizing. Phosphate-solubilizing bacteria (PSB) are important members of PGPR. They can dissolve both insoluble mineral and organic phosphate in soil and enhance the phosphorus uptake of plants. The application of PSB can significantly increase plant biomass and yield. Co-inoculating PSB with other PGPR shows better performance in plant growth promotion, and the mechanisms are more complicated. Here, we provide a comprehensive review of rhizospheric NF and phosphate solubilization by PGPR. Deeper genetic insights would provide a better understanding of the NF mechanisms of PGPR, and co-inoculation with rhizospheric diazotrophs and PSB strains would be a strategy in enhancing the sustainability of soil nutrients.

Nitrogen Fixation Influenced by Phosphorus and Nitrogen Availability in the Benthic Bloom-forming Cyanobacterium Hydrocoleum sp. Identified in a Temperate Marine Lagoon

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.

Paradigms of actinorhizal symbiosis under the regime of global climatic changes: New insights and perspectives

Nitrogen occurs as inert and inaccessible dinitrogen gaseous form (N₂ ) in the atmosphere. Biological nitrogen fixation is a chief process that makes this dinitrogen (N₂ ) accessible and bioavailable in the form of ammonium (NH₄ ⁺ ) ions. The key organisms to fix nitrogen are certain prokaryotes, called diazotrophs either in the free-living form or establishing significant mutual relationships with a variety of plants. On such examples is ~95-100 MY old incomparable symbiosis between dicotyledonous trees and a unique actinobacterial diazotroph in diverse ecosystems. In this association, the root of the certain dicotyledonous tree (~25 genera and 225 species) belonging to three different taxonomic orders, Fagales, Cucurbitales, and Rosales (FaCuRo) known as actinorhizal trees can host a diazotroph, Frankia of order Frankiales. Frankia is gram-positive, branched, filamentous, sporulating, and free-living soil actinobacterium. It resides in the specialized, multilobed, and coralloid organs (lateral roots but without caps), the root nodules of actinorhizal tress. This review aims to provide systematic information on the distribution and the phylogenetic diversity of hosts from FaCuRo and their micro-endosymbionts (Frankia spp.), colonization mechanisms, and signaling pathways. We also aim to provide details on developmental and physiological imperatives for gene regulation and functional genomics of symbiosis, phenomenal restoration ecology, influences of contemporary global climatic changes, and anthropogenic impacts on plant-Frankia interactions for the functioning of ecosystems and the biosphere.

Molecular Analysis of Soil Bacterial Community Structures for Environmental Risk Assessment with Varieties of Genetically Modified Soybean and Hot Pepper

With the advance in gene technology, genetically modified (GM) crops have increased in recent years. GM crops offer us various benefits. However, there are potential risks of GM crops for the environment. In this study, the impacts of transgenic plants on soil microbial community structures were assessed. Two varieties of soybean (Glycine max L.) and hot pepper (Capsicum annuum L.), which introduced the herbicide-resistant gene, bar, were used in this study. The effects of GM crops on soil microbial community structures were investigated using a cultural method, the denaturing gradient gel electrophoresis (DGGE) procedure, and 16S rRNA gene sequencing on the Illumina platform. Additionally, the persistence of transgenes was monitored using a quantitative real-time PCR procedure. The cultural method, DGGE analysis, and the amplicon-based community profile indicated that soil microbial communities were not significantly different between GM and non-GM lines. The level of the bar gene in GM soybean plots greatly increased when the crops were actively growing, but thereafter gradually decreased to the initial level. Meanwhile, the level of the bar gene in GM hot pepper plots repeatedly increased and decreased according to the flowering stages. These results indicated that soil microbial community structures were not significantly affected.

Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems

Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N₂O), a potent greenhouse gas.

Global Grassland Diazotrophic Communities Are Structured by Combined Abiotic, Biotic, and Spatial Distance Factors but Resilient to Fertilization

Grassland ecosystems cover around 37% of the ice-free land surface on Earth and have critical socioeconomic importance globally. As in many terrestrial ecosystems, biological dinitrogen (N2) fixation represents an essential natural source of nitrogen (N). The ability to fix atmospheric N2 is limited to diazotrophs, a diverse guild of bacteria and archaea. To elucidate the abiotic (climatic, edaphic), biotic (vegetation), and spatial factors that govern diazotrophic community composition in global grassland soils, amplicon sequencing of the dinitrogenase reductase gene-nifH-was performed on samples from a replicated standardized nutrient [N, phosphorus (P)] addition experiment in 23 grassland sites spanning four continents. Sites harbored distinct and diverse diazotrophic communities, with most of reads assigned to diazotrophic taxa within the Alphaproteobacteria (e.g., Rhizobiales), Cyanobacteria (e.g., Nostocales), and Deltaproteobacteria (e.g., Desulforomonadales) groups. Likely because of the wide range of climatic and edaphic conditions and spatial distance among sampling sites, only a few of the taxa were present at all sites. The best model describing the variation among soil diazotrophic communities at the OTU level combined climate seasonality (temperature in the wettest quarter and precipitation in the warmest quarter) with edaphic (C:N ratio, soil texture) and vegetation factors (various perennial plant covers). Additionally, spatial variables (geographic distance) correlated with diazotrophic community variation, suggesting an interplay of environmental variables and spatial distance. The diazotrophic communities appeared to be resilient to elevated nutrient levels, as 2-4 years of chronic N and P additions had little effect on the community composition. However, it remains to be seen, whether changes in the community composition occur after exposure to long-term, chronic fertilization regimes.

Identification of key microorganisms in facultative stabilization ponds from dairy industries, using metagenomics

Wastewater stabilization ponds are a natural form of wastewater treatment. Their low operation and maintenance costs have made them popular, especially in developing countries. In these systems, effluents are retained for long periods of time, allowing the microbial communities present in the ponds to degrade the organic matter present, using both aerobic and anaerobic processes. Even though these systems are widespread in low income countries, there are no studies about the microorganisms present in them and how they operate. In this study, we analised the microbial communities of two serial full-scale stabilization ponds systems using whole genome shotgun sequencing. First, a taxonomic profiling of the reads was performed, to estimate the microbial diversity. Then, the reads of each system were assembled and binned, allowing the reconstruction of 110 microbial genomes. A functional analysis of the genomes allowed us to find how the main metabolic pathways are carried out, and we propose several organisms that would be key to this kind of environment, since they play an important role in these metabolic pathways. This study represents the first genome-centred approach to understand the metabolic processes in facultative ponds. A better understanding of these microbial communities and how they stabilize the effluents of dairy industries is necessary to improve them and to minimize the environmental impact of dairy industries wastewater.

Comparing the effects of algae and macrophyte residues' degradation on biological nitrogen fixation in freshwater lake sediments

The degradation and mineralization of organic residues are important factors that drive biochemical processes in lake ecosystems. However, the effect of organic matter's degradation on biological nitrogen fixation (BNF) in freshwater lake sediments remains poorly understood. This study investigated the response of sediment nitrogen fixation to the degradations of algae and macrophyte residues through continuous flow mesocosms combined with nifH sequencing analysis and isotope tracing. The results suggested that the active nitrogen fixation of sediments only occurred in the first two weeks of the rapid degradation of organic residues. Degradation of algae and macrophytes residues quickly increased the nifH abundance and the nitrogenase activity (NA) in sediments; however, the maximum NA triggered by algae's degradation (658.2 ± 16.8 ng g^-1 day^-1) was six times higher than that induced by the degradation of macrophytes residues. There was no significant difference in NA of sediments with the degradation of Potamogeton and Phragmites. Redundancy analysis (RDA) showed that the variation of diazotrophic community in sediment was significantly (p < 0.01) correlated with the concentrations of SO₄^2- and NH₄⁺ in overlying water and the Fe(II) content and Eh in sediment. Overall, the BNF of sediments can quickly respond to the degradation of organic residues, and the degradation of algae has a stronger promoting effect on the nitrogen fixation in sediments than that of macrophyte residues.

Nitrogen fixation: a poorly understood process along the freshwater-marine continuum

Although N₂ fixation is a major component of the global N cycle and has been extensively studied in open-ocean and terrestrial ecosystems, rates and ecological dynamics remain virtually unknown for the inland and coastal aquatic ecosystems (lakes, wetlands, rivers, streams, estuaries) that connect terrestrial and marine biomes. This is due to the diversity of these habitats, as well as the traditional paradigm that N₂ fixation rates were low to nonexistent, and therefore not important, in these ecosystems. We identify three major research themes to advance understanding of aquatic N₂ fixation: 1) the biological diversity of diazotrophs and variability of N₂ fixation rates, 2) the ecological stoichiometry of N₂ fixation, and 3) the upscaling of N₂ fixation rates from genes to ecosystems. Coordinating research across these areas will advance limnology and oceanography by fully integrating N₂ fixation into ecological dynamics of aquatic ecosystems from local to global scales.

Phyllosphere fungal communities of rubber trees exhibited biogeographical patterns, but not bacteria

Phyllosphere microbiomes play an essential role in maintaining host health and productivity. Still, the diversity patterns and the drivers for the phyllosphere microbial community of the tropical cash crop Rubber tree (Hevea brasiliensis) - are poorly understood. We sampled the phyllosphere of field-grown rubber trees in South China. We examined the phyllosphere bacterial and fungal composition, diversity and main drivers of these microbes using the Illumina® sequencing and assembly. Fungal communities were distinctly different in different climatic regions (i.e. Xishuangbanna and Hainan Island) and climatic factors, especially mean annual temperature, and they were the main driving factors of foliar fungal communities, indicating fungal communities showed a geographical pattern. Significant differences of phyllosphere bacterial communities were detected in different habitats (i.e. endophytic and epiphytic). Most of the differences in taxa composition came from Firmicutes spp., which have been assigned as nitrogen-fixing bacteria. Since these bacteria cannot penetrate the cuticle like fungi, the abundant epiphytic Firmicutes spp. may supplement the deficiency of nitrogen acquisition. And the main factor influencing endophytic bacteria were internal factors, such as total nitrogen, total phosphorus and water content of leaves. External factors (i.e. climate) were the main driving force for epiphytic bacteria community assembly. Our work provides empirical evidence that the assembly of phyllosphere bacterial and fungal differed, which creates a precedent for preventing and controlling rubber tree diseases and pests and rubber tree yield improvement.

Influence of environmental factors on the tropical peatlands diazotrophic communities from the Southern Brazilian Atlantic Rain Forest

The tropical peatlands of southern Brazil are essential for the maintenance of the Atlantic Rain Forest, one of the 25 hotspots of biodiversity in the world. Although diazotrophic microorganisms are essential for the maintenance of this nitrogen limited ecosystem, so far studies have focused only on microorganisms involved in the carbon cycle. In this work, peat samples were collected from three tropical peatland regions during dry and rainy seasons and their chemical and microbial characteristics were evaluated. Our results showed that the structure of the diazotrophic communities in the Brazilian tropical peatlands differs in the evaluated seasons. The abundance of the genus Bradyrhizobium showed to be affected by rainfall and peat pH. Despite the shifts of the nitrogen fixing population in the tropical peatland caused by seasonality it showed to be constantly dominated by α-Proteobacteria followed by Cyanobacteria. In addition, more than 50% of nifH gene sequences have not been classified, indicating the necessity for more studies in tropical peatland, since the reduction of N supply in the peatlands stimulates the recalcitrant organic matter decomposition performed by peatland microorganisms, influencing the C stock.

Biochar Addition Altered Bacterial Community and Improved Photosynthetic Rate of Seagrass: A Mesocosm Study of Seagrass Thalassia hemprichii

Seagrass meadows, as typical “blue carbon” ecosystems, play critical ecological roles in the marine ecosystem and decline every year. The application of biochar in soil has been proposed as a potential soil amendment to improve soil quality and mitigate global climate change. The effects of biochar on soil bacterial activities are integrally linked to the potential of biochar in achieving these benefits. However, biochar has been rarely applied in marine ecosystems. Whether the application of biochar could work on the seagrass ecosystem remained unknown. In this study, we investigated the responses of sediment and rhizosphere bacterial communities of seagrass Thalassia hemprichii to the biochar addition derived from maize at ratios of 5% by dry weight in the soil during a one-month incubation. Results indicated that the biochar addition significantly changed the sedimental environment with increasing pH, total phosphorus, and total kalium while total nitrogen decreased. Biochar addition significantly altered both the rhizosphere and sediment bacterial community compositions. The significant changes in rhizosphere bacterial community composition occurred after 30days of incubation, while the significant variations in sediment bacterial community composition distinctly delayed than in sediment occurred on the 14th day. Biochar application improved nitrification and denitrification, which may accelerate nitrogen cycling. As a stabilizer to communities, biochar addition decreased the importance of deterministic selection in sediment and changed the bacterial co-occurrence pattern. The biochar addition may promote seagrass photosynthesis and growth by altering the bacterial community compositions and improving nutrient circulation in the seagrass ecosystem, contributing to the seagrass health improvement. This study provided a theoretical basis for applying biochar to the seagrass ecosystem and shed light on the feasible application of biochar in the marine ecosystem.

Graphical Abstract

Single-cell genomics-based analysis reveals a vital ecological role of Thiocapsa sp. LSW in the meromictic Lake Shunet, Siberia

Meromictic lakes usually harbour certain prevailing anoxygenic phototrophic bacteria in their anoxic zone, such as the purple sulfur bacterium (PSB) Thiocapsa sp. LSW (hereafter LSW) in Lake Shunet, Siberia. PSBs have been suggested to play a vital role in carbon, nitrogen and sulfur cycling at the oxic-anoxic interface of stratified lakes; however, the ecological significance of PSBs in the lake remains poorly understood. In this study, we explored the potential ecological role of LSW using a deep-sequencing analysis of single-cell genomics associated with flow cytometry. An approximately 2.7 Mb draft genome was obtained based on the co-assembly of five single-cell genomes. LSW might grow photolithoautotrophically and could play putative roles not only as a carbon fixer and diazotroph, but also as a sulfate reducer/oxidizer in the lake. This study provides insights into the potential ecological role of Thiocapsa sp. in meromictic lakes.

Discovery of nondiazotrophic Trichodesmium species abundant and widespread in the open ocean

Filamentous and colony-forming cells within the cyanobacterial genus Trichodesmium might account for nearly half of nitrogen fixation in the sunlit ocean, a critical mechanism that sustains plankton's primary productivity. Trichodesmium has long been portrayed as a diazotrophic genus. By means of genome-resolved metagenomics, here we reveal that nondiazotrophic Trichodesmium species not only exist but also are abundant and widespread in the open ocean, benefiting from a previously overlooked functional lifestyle to expand the biogeography of this prominent marine genus. Near-complete environmental genomes for those closely related candidate species reproducibly shared functional features including a lack of genes related to nitrogen fixation, hydrogen recycling, and hopanoid lipid production concomitant with the enrichment of nitrogen assimilation genes. Our results elucidate fieldwork observations of Trichodesmium cells fixing carbon but not nitrogen. The Black Queen hypothesis and burden of low-oxygen concentration requirements provide a rationale to explain gene loss linked to nitrogen fixation among Trichodesmium species. Disconnecting taxonomic signal for this genus from a microbial community's ability to fix nitrogen will help refine our understanding of the marine nitrogen balance. Finally, we are reminded that established links between taxonomic lineages and functional traits do not always hold true.

Community Composition and Co-Occurrence Patterns of Diazotrophs along a Soil Profile in Paddy Fields of Three Soil Types in China

Diazotrophs play a key role in biological nitrogen (N₂) fixation. However, we know little about the distribution of the diazotrophic community along the soil profile in paddy fields. Here, we used Illumina MiSeq sequencing, targeting the nitrogenase reductase (nifH) gene, to investigate changes with depth (0-100 cm) in the diazotrophic community in paddy soils of three regions (Changshu, Hailun, and Yingtan) in China. The results indicated that most diazotrophs belonged to the phylum Proteobacteria, accounting for 78.05% of the total number of sequences. The diazotrophic diversity was generally highest in the 10-20 cm layer, and then significantly decreased with soil depth. Principal coordinate analysis and PERMANOVA indicated that the diazotrophic community structure was significantly affected by region and soil depth. There were obvious differences in the composition of the diazotrophic community between the topsoil (0-40 cm) and the subsoil (40-100 cm). Anaeromyxobacter, Sideroxydans, Methylomonas, Nostoc, Methanocella, and Methanosaeta were enriched in the topsoil, while Geobacter, Azoarcus, Bradyrhizobium, and Dechloromonas were concentrated in the subsoil. Furthermore, co-occurrence network analysis showed that the diazotrophic network in the topsoil was more complex than that in the subsoil. Distance-based redundancy analysis indicated that soil total C and N content and pH were the main factors influencing the vertical variation in the diazotrophic community. These results highlighted that depth has a great impact on the diazotrophic diversity, community composition, and co-occurrence patterns in paddy soil.

Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean

Biological nitrogen fixation contributes significantly to marine primary productivity. The current view depicts few cyanobacterial diazotrophs as the main marine nitrogen fixers. Here, we used 891 Tara Oceans metagenomes derived from surface waters of five oceans and two seas to generate a manually curated genomic database corresponding to free-living, filamentous, colony-forming, particle-attached, and symbiotic bacterial and archaeal populations. The database provides the genomic content of eight cyanobacterial diazotrophs including a newly discovered population related to known heterocystous symbionts of diatoms, as well as 40 heterotrophic bacterial diazotrophs that considerably expand the known diversity of abundant marine nitrogen fixers. These 48 populations encapsulate 92% of metagenomic signal for known nifH genes in the sunlit ocean, suggesting that the genomic characterization of the most abundant marine diazotrophs may be nearing completion. Newly identified heterotrophic bacterial diazotrophs are widespread, express their nifH genes in situ, and also occur in large planktonic size fractions where they might form aggregates that provide the low-oxygen microenvironments required for nitrogen fixation. Critically, we found heterotrophic bacterial diazotrophs to be more abundant than cyanobacterial diazotrophs in most metagenomes from the open oceans and seas, emphasizing the importance of a wide range of heterotrophic populations in the marine nitrogen balance.

Elevated pCO2 alters the interaction patterns and functional potentials of rearing seawater microbiota

Mean oceanic CO₂ values have already risen and are expected to rise further on a global scale. Elevated pCO₂ (eCO₂) changes the bacterial community in seawater. However, the ecological association of seawater microbiota and related geochemical functions are largely unknown. We provide the first evidence that eCO₂ alters the interaction patterns and functional potentials of microbiota in rearing seawater of the swimming crab, Portunus trituberculatus. Network analysis showed that eCO₂ induced a simpler and more modular bacterial network in rearing seawater, with increased negative associations and distinct keystone taxa. Using the quantitative microbial element cycling method, nitrogen (N) and phosphorus (P) cycling genes exhibited the highest increase after one week of eCO₂ stress and were significantly associated with keystone taxa. However, the functional potential of seawater bacteria was decoupled from their taxonomic composition and strongly coupled with eCO₂ levels. The changed functional potential of seawater bacteria contributed to seawater N and P chemistry, which was highlighted by markedly decreased NH₃, NH₄⁺-N, and PO₄^3--P levels and increased NO₂^--N and NO₃^--N levels. This study suggests that eCO₂ alters the interaction patterns and functional potentials of seawater microbiota, which lead to the changes of seawater chemical parameters. Our findings provide new insights into the mechanisms underlying the effects of eCO₂ on marine animals from the microbial ecological perspective.

Physiological impact of flavonoids on nodulation and ureide metabolism in legume plants

Legume plants from Fabaceae family (phylogenetic group composed by three subfamilies: Caesalpinioideae, Mimosoideae, and Papilionoideae) can fix atmospheric nitrogen (N₂) into ammonia (NH₃) by the symbiotic relationship with rhizobia bacteria. These bacteria respond chemotactically to certain compounds released by plants such as sugars, amino acids and organic acids. Root secretion of isoflavonoids acts as inducers for nod genes in rhizobia and ABC transporters and ICHG (isoflavone conjugates hydrolyzing beta-glucosidase) at apoplast are related to the exudation of genistein and daidzein in soybean roots. Biological nitrogen fixation (BNF) occurs inside the nodule by the action of nitrogenase enzyme, which fixes N₂ into NH₃, which is converted into ureides (allantoin and allantoic acid). In this review, we bring together the latest findings on flavonoids biosynthesis and ureide metabolism in several legume plant species. We emphasize how flavonoids induce nod genes in rhizobia, affecting chemotaxis, nodulation, ureide production, growth and yield of legume plants. Mainly, isoflavonoids daidzein and genistein are responsible for nod genes activation in the rhizobia bacteria. Flavonoids also play an important role during nodule organogenesis by acting as auxin transporter inhibitors in root cells, especially in indeterminate nodules. The ureides are the main N transport form in tropical legumes and they are catabolized in leaves and other sink tissues to produce amino acids and proteins needed for plant growth and yield.

UCYN-A/haptophyte symbioses dominate N2 fixation in the Southern California Current System

The availability of fixed nitrogen (N) is an important factor limiting biological productivity in the oceans. In coastal waters, high dissolved inorganic N concentrations were historically thought to inhibit dinitrogen (N2) fixation, however, recent N2 fixation measurements and the presence of the N2-fixing UCYN-A/haptophyte symbiosis in nearshore waters challenge this paradigm. We characterized the contribution of UCYN-A symbioses to nearshore N2 fixation in the Southern California Current System (SCCS) by measuring bulk community and single-cell N2 fixation rates, as well as diazotroph community composition and abundance. UCYN-A1 and UCYN-A2 symbioses dominated diazotroph communities throughout the region during upwelling and oceanic seasons. Bulk N2 fixation was detected in most surface samples, with rates up to 23.0 ± 3.8 nmol N l-1 d-1, and was often detected at the deep chlorophyll maximum in the presence of nitrate (>1 µM). UCYN-A2 symbiosis N2 fixation rates were higher (151.1 ± 112.7 fmol N cell-1 d-1) than the UCYN-A1 symbiosis (6.6 ± 8.8 fmol N cell-1 d-1). N2 fixation by the UCYN-A1 symbiosis accounted for a majority of the measured bulk rates at two offshore stations, while the UCYN-A2 symbiosis was an important contributor in three nearshore stations. This report of active UCYN-A symbioses and broad mesoscale distribution patterns establishes UCYN-A symbioses as the dominant diazotrophs in the SCCS, where heterocyst-forming and unicellular cyanobacteria are less prevalent, and provides evidence that the two dominant UCYN-A sublineages are separate ecotypes.

Diversity and Variation of Asymbiotic Nitrogen-Fixing Microorganisms in Alpine Grasslands on the Tibetan Plateau

Asymbiotic nitrogen-fixing (ANF) bacteria contribute a substantial amount of nitrogen in ecosystems, especially in those with low symbiotic nitrogen fixation (SNF) capability. Degradation of alpine grassland is widespread on the Tibetan Plateau and sown grassland has become one of the main strategies for grassland restoration. However, the diversity and community structure of ANF bacteria in different grassland types remain unknown. The aim of this study was to fill this gap. Soil samples were obtained from 39 grassland plots selected from three counties in the eastern Tibetan Plateau. The plots were classified as natural grassland (NG), sown grassland (SG), lightly degraded grassland (LDG), and severely degraded grassland (SDG). ANF microbial communities of the four grassland types were compared at the level of community and species diversity by 16S rRNA high-throughput sequencing technology. The phylum Proteobacteria accounted for &gt;72% of the ANF bacteria. The community structures of soil ANF bacteria differed significantly (p &lt; 0.01) among grassland types. We concluded that: (1) planting gramineous forage could possibly mitigate the decrease in diversity of soil ANF bacteria caused by grassland degradation; and (2) the diversity of soil ANF bacteria in alpine grassland of the Tibetan Plateau is closely related to grassland degradation and restoration.

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

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

Comparative evaluation of biochar, pelelith, and garbage enzyme on nitrogenase and nitrogen-fixing bacteria during the composting of sewage sludge

This study investigated the effects of garbage enzyme (GE), pelelith (PL), and biochar (BC) on nitrogen (N) conservation, nitrogenase (Nase) and N-fixing bacteria during the composting of sewage sludge. Results showed that the addition of GE, PL, and BC reduced NH₃ emissions by 40.9%, 29.3%, and 67.4%, and increased the NO₃-N contents of the end compost by 161.4, 88.2, and 105.8% relative to control, respectively, thus increasing the TN content. Three additives improved Nase, cellulase, and fluorescein diacetate hydrolase (FDA) activities and the abundances of nifH gene, and the largest increase was BC, followed by PL and GE. In addition, the additives also markedly influenced the succession of N-fixing bacteria, and significantly increased the abundance of Proteobacteria during the whole process. The BC and PL additions strengthened the sensitivity of N-fixing bacteria to environmental variables, and FDA, TN, moisture content, and NO₃-N significantly affected the N-fixing bacteria at genus level.

Nitrogen Fertilization and Native C4 Grass Species Alter Abundance, Activity, and Diversity of Soil Diazotrophic Communities

Native C4 grasses have become the preferred species for native perennial pastures and bioenergy production due to their high productivity under low soil nitrogen (N) status. One reason for their low N requirement is that C4 grasses may benefit from soil diazotrophs and promote biological N fixation. Our objective was to evaluate the impact of N fertilization rates (0, 67, and 202 kg N ha-1) and grass species (switchgrass [Panicum virgatum] and big bluestem [Andropogon gerardii]) on the abundance, activity, diversity, and community composition of soil diazotrophs over three agricultural seasons (grass green-up, initial harvest, and second harvest) in a field experiment in East Tennessee, United States. Nitrogen fertilization rate had a stronger influence on diazotroph population size and activity (determined by nifH gene and transcript abundances) and community composition (determined by nifH gene amplicon sequencing) than agricultural season or grass species. Excessive fertilization (202 kg N ha-1) resulted in fewer nifH transcripts compared to moderate fertilization (67 kg N ha-1) and decreased both richness and evenness of diazotrophic community, reflecting an inhibitory effect of high N application rates on soil diazotrophic community. Overall, cluster I and cluster III diazotrophs were dominant in this native C4 grass system. Diazotroph population size and activity were directly related to soil water content (SWC) based on structural equation modeling. Soil pH, SWC, and C and N availability were related to the variability of diazotrophic community composition. Our results revealed relationships between soil diazotrophic community and associated soil properties, adding to our understanding of the response of soil diazotrophs to N fertilization and grass species in native C4 grass systems.

Comparison of Diazotrophic Composition and Distribution in the South China Sea and the Western Pacific Ocean

The variation of diazotrophs has been elusive in multiple SCS and WPO regions due to insufficient data. Therefore, the dynamics of diazotrophic composition and distribution were investigated in this study, based on high-throughput sequencing and quantitative PCR of the nifH gene. We found that Proteobacteria dominated the diazotrophic community in the river-impacted SCS and cyanobacteria and Proteobacteria were more abundant in the ocean-dominated SCS and WPO. The qPCR analysis showed that cyanobacterial Trichodesmium was abundant in the Pearl River plume and in the SCS basin influenced by the Kuroshio intrusion, and it also thrived in the subequatorial region of the WPO. Unicellular cyanobacteria UCYN-A were mainly detected in the river-impacted area, UCYN-B was abundant in the WPO, UCYN-C had a relatively high abundance in the ocean-dominated area, and a preponderance of γ-Proteobacteria γ-24774A11 was observed in the ocean-dominated SCS and pelagic WPO. Diazotrophic communities had significant distance-decay relationships, reflecting clear biogeographic patterns in the study area. The variations of diazotrophic community structure were well explained by dissolved inorganic nitrogen, dissolved inorganic phosphate by an eigenvector spatial variable PCNM1. These results provide further information to help determine the ecological mechanism of elusive diazotrophic communities in different ocean ecosystems.

Habitat heterogeneity induces regional differences in sediment nitrogen fixation in eutrophic freshwater lake

Biological nitrogen fixation (BNF) in sediments is an important source of bioavailable nitrogen in aquatic systems. However, the effect of habitat change caused by eutrophication on nitrogen fixation within sediments is still unclear. In this study, nitrogen fixation rates and diazotroph diversities in sediments with heterogeneous ecological status in one eutrophic lake were investigated by using an isotope tracer method and sequencing of nitrogen-fixing (nif) genes. The results showed that both nitrogenase activity (NA) and nifH abundance in sediments of blooms area were higher than those in vegetation-dominated habitats. Correlation analysis showed that NA was correlated closely to nifH abundance, dissolved sulfide, and iron. The diazotrophic assemblage contained mainly Proteobacterial sequences belonging to Cluster I and III, and the variations of diazotrophic community could be explained by total nitrogen content, total phosphorus content, organic matters, sulfides, ammonium and iron content. Moreover, the co-occurrence network analysis showed the Alphaproteobacteria shaped the major interactions in diazotrophic community, and sediment properties had stronger effect on diazotrophic community in cyanobacteria-dominated habitat. This study revealed that habitat heterogeneity in eutrophic lakes shaped different succession of BNF in sediments and cyanobacterial blooms significantly improved the nitrogen-fixing activity in sediments, which broadened our understanding of nitrogen cycle and nutrient management in eutrophic freshwater lakes.

Enantioselective effects of cyflumetofen on microbial community and related nitrogen cycle gene function in acid-soil

Cyflumetofen (CYF) is a novel chiral acaricide widely used in commercial crops to control mites. The environmental risks exposed by CYF in the soil, especially at the enantiomer level, remain unclear. We found that the (+)-CYF enantiomer was preferentially degraded in acid-soil, resulting in (-)-CYF enrichment. 16S rRNA and qPCR analysis indicated that decreased bacterial abundance by 12.79-61.80% and 2.52-52.48% in (-)-CYF treatment and (+)-CYF treatment, respectively. Diversity was also decreased with (-)-CYF treatment. Interestingly, several beneficial bacteria, for instance, Alphaproteobacteria (class), Sphingomonadaceae (family), and Arthrobacter (specise) were more enriched following (-)-CYF. The abundance of N₂-fixing bacteria showed a sustained reduction with time, and the decrease was 3.24-72.94% with (-)-CYF and 25.37-73.11% with (+)-CYF treatment. Compared with the (+)-CYF treatment could positively promote nitrification, while the treatment (-)-CYF significantly reduced the abundance of amoA gene; namely it significantly negatively affected the nitrification in the nitrogen cycle. Through our further research, we found that Actinobacteria, Alphaproteobacteria, Lysobacter; Sphingomonas, Patescibacteria, Saccharimonadia, and Saccharimonadales showed synergistic effects with the nitrogen cycling-related genes nifH and amoA. These results contribute to a comprehensive environmental risk assessment of CYF in acid-soil at the enantiomer level.

Factoring distinct materials and nitrogen-related microbes into assessments of nitrogen pollution risks during composting

The aim of this study was to evaluate nitrogen pollution risks from distinct materials composting with the discrepancy of component, including chicken manure, municipal solid and straw waste (CM, MSW, SW). Results showed total nitrogen maximum mean concentrations were observed in CM (39.57 g/kg). Pollution risks in CM were continuous, while MSW and SW mainly concentrated during heating phases. Microbial analysis confirmed that pollution risks from ammonification and nitrification were more prevalent in CM. The risks of pollution caused by nitrate reduction accompanied N₂O were the most serious in MSW. The multifunctional nitrogen-related microbes Pseudomonas and Bacillus were affected by microenvironments and contributed to different pollution risks. Furthermore, PICRUSt analysis identified the "inferred" key genes (pmoC-amoC, nrfH, nifD etc.) related to nitrogen pollution risks. This study evaluated nitrogen pollution risks and proposed the future directions, providing theoretical basis and feasible optimization measures for the mitigation of nitrogen pollution during composting.

The Abundance of the nifH Gene Became Higher and the nifH-Containing Diazotrophic Bacterial Communities Changed During Primary Succession in the Hailuogou Glacier Chronosequence, China

Primary successional ecosystems and the related soil development are often N limited. To date, N₂-fixing communities during primary succession in alpine ecosystems have remained underexplored. In this study, we applied quantitative PCR (qPCR) quantitation and targeted amplicon sequencing of nifH in the Hailuogou Glacier foreland to investigate the succession of N₂-fixing communities in five sites along a 62-year chronosequence. The abundance of the nifH gene increased along the primary succession in the chronosequence and correlated positively with pH, acetylene reduction activity, and water, organic C, total and available N, and available P contents. The increases in alpha diversity along the chronosequence may have been partly due to less competition for resources. In contrast to the clear separation based on soil properties, the changes in the diazotrophic community composition lacked a clear trend and were associated mostly with changes in soil available K and organic C contents. The changes among differentially abundant genera were possibly due to the changes in plant coverage and species composition. The whole primary succession of the diazotrophic communities was consistent with stochastic community assembly, which is indicative of low competitive pressure.

Gamma4: a genetically versatile Gammaproteobacterial nifH phylotype that is widely distributed in the North Pacific Ocean

Despite the increasing reports of non-cyanobacterial diazotrophs (NCDs) in pelagic waters, only one NCD (GammaA) has been relatively well described, whose genome and physiology are still unclear. Here we present a comprehensive analysis of the biogeography and ecophysiology of a widely distributed NCD, Gamma4. Gamma4 was the most abundant Gammaproteobacterial NCD along transects across the subtropical North Pacific. Using quantitative PCR, Gamma4 was detectable throughout the surface waters of North Pacific (7°N-55°N, 138°E-80°W), whereas GammaA was detected at <2/3 of the stations. Gamma4 was abundant during autumn-winter and positively correlated with chlorophyll a, while GammaA thrived during spring-summer and was positively correlated with temperature. Environmental clones affiliated with Gamma4 were widely detected in pelagic waters, oxygen minimum zones and even dinoflagellate microbiomes. By analysing the metabolic potential of a genome of Gamma4 reconstructed from the Tara Oceans dataset, we suggest that Gamma4 is a versatile heterotrophic NCD equipped with multiple strategies in scavenging phosphate (and iron) and for respiratory protection of nitrogenase. The transcription of nitrogenase genes is putatively regulated by Fnr-NifL-NifA and GlnD-GlnK systems that respond to intracellular oxygen and glutamate concentration. These results provide important implications for the potential life strategies of pelagic NCDs.

Straw Mulching and Nitrogen Fertilization Affect Diazotroph Communities in Wheat Rhizosphere

Diazotrophs that carry out the biological fixation of atmospheric dinitrogen (N₂) replenish biologically available nitrogen (N) in soil and are influenced by the input of inorganic and organic substrates. To date, little is known about the effects of combined organic substrate addition and N fertilization on the diazotroph community composition and structure in purple soils. We investigated the effects of N fertilization and straw mulching on diazotroph communities by quantifying and sequencing the nifH gene in wheat rhizosphere. The abundance and richness of diazotrophs were greater the higher the fertilization level in the mulched treatments, whereas in the nonmulched treatments (NSMs), richness was lowest with the highest N fertilization level. The abundance and α-diversity of diazotrophs correlated with most of the soil properties but not with pH. At the genus level, the relative abundances of Azospirillum, Bacillus, and Geobacter were higher in the NSMs and those of Pseudacidovorax, Skermanella, Azospira, Paraburkholderia, Azotobacter, Desulfovibrio, Klebsiella, and Pelomonas in the mulched treatments. The differences in community composition between the mulched and the NSMs were associated with differences in soil temperature and soil organic carbon and available potassium contents and C:N ratio. Overall, straw mulching and N fertilization were associated with changes in diazotroph community composition and higher abundance of nifH gene in alkaline purple soils.

Agricultural practices modulate the bacterial communities, and nitrogen cycling bacterial guild in rhizosphere: field experiment with soybean

BACKGROUND

Modern agricultural management approaches are often dependent on the application of chemicals, resulting in adverse impacts on human and environmental health. Therefore, for sustainable agriculture, there is a need to implement integrated agriculture practices that can maintain natural soil microbiome and enhance crop production. Various agricultural approaches influence crop production by impacting the functional bacterial community entailed in biogeochemical cycles, for example, nitrogen (N) cycle. This study aimed to assess the rhizospheric N cycling community of soybean under three agricultural practices, namely, conservation agriculture (CA), conventional treatment (CT), and organic agriculture (OA) for two consecutive years (2017 and 2018).

RESULTS

A field experiment was designed under soybean-wheat cropping system employing CA, CT, and OA modules that included different practices of tillage, crop bedding pattern, crop residue retention, and nutrient application. Assessment of bacterial communities contributing to N transformation was performed with quantitative polymerase chain reaction (qPCR) of important markers (nifH, amoA, narG, and nirK).

CONCLUSION

Results concluded that the practice of conservation agriculture comprising of raised bed, zero tillage, crop residue retention, and application of NPK (nitrogen, phosphorus, potassium) nutrients favorably affected the plant attributes and the abundance of N cycling bacterial community over the two consecutive years. The outcome revealed the mechanistic principle behind enhanced plant growth under conservation agriculture, and opened up the possibility of regulating the N cycling bacterial community to develop sustainable and productive agro-ecosystems. © 2020 Society of Chemical Industry.

Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields

Previous studies have shown the sugarcane microbiome harbors diverse plant growth promoting microorganisms, including nitrogen-fixing bacteria (diazotrophs), which can serve as biofertilizers. The genomes of 22 diazotrophs from Colombian sugarcane fields were sequenced to investigate potential biofertilizers. A genome-enabled computational phenotyping approach was developed to prioritize sugarcane associated diazotrophs according to their potential as biofertilizers. This method selects isolates that have potential for nitrogen fixation and other plant growth promoting (PGP) phenotypes while showing low risk for virulence and antibiotic resistance. Intact nitrogenase (nif) genes and operons were found in 18 of the isolates. Isolates also encode phosphate solubilization and siderophore production operons, and other PGP genes. The majority of sugarcane isolates showed uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six strains with the highest overall genotype scores were experimentally evaluated for nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid, and indole acetic acid. Results from the biochemical assays were consistent and validated computational phenotype predictions. A genotypic and phenotypic threshold was observed that separated strains by their potential for PGP versus predicted pathogenicity. Our results indicate that computational phenotyping is a promising tool for the assessment of bacteria detected in agricultural ecosystems.

Long-term organic and inorganic fertilization alters the diazotrophic abundance, community structure, and co-occurrence patterns in a vertisol

Diazotrophs play a critical role in converting air-inactive nitrogen to bio-available nitrogen. Assessing the influences of different fertilization regimes on diazotrophs is essential for a better understanding of their maintenance of soil fertility and agricultural sustainability. In this study, we targeted the nifH gene to investigate the effects of different long-term fertilization on the diazotrophic community in a vertisol, using real-time quantitative polymerase chain reaction (PCR) and MiSeq sequencing. Five fertilization regimes were tested: no fertilizer (CK), chemical nitrogen, phosphorus, and potassium fertilizer (NPK), organic fertilizer (O), chemical NPK plus organic fertilizer with an equivalent application rate of nitrogen (NPKO), and chemical NPK plus organic fertilizer with a high application rate of nitrogen (HNPKO). Our results showed that fertilization significantly affected the diazotrophic activity, abundance and composition. NPK tended to reduce the activity, abundance, operational taxonomic units (OTU)-richness and alpha-diversity of the diazotrophs, while O had the opposite effect. The effects of inorganic and organic fertilization on the diazotrophs depended on the N application rate, showing that the diazotrophic activity, abundance, and alpha-diversity in NPKO were higher than that of HNPKO. For the diazotrophic community structure, CK, O, and NPKO were grouped and separated from NPK and HNPKO. The diazotrophic community structure strongly correlated with the soil pH, electrical conductivity (EC), total carbon content (TC), and total nitrogen content (TN), among which pH was the major factor shaping the diazotrophic community structure. Different network patterns were observed between the long-term organic and non-organic fertilizers, suggesting that the organic amendment resulted in a more complicated diazotrophic community than the non-organic amendments. Rhizobium was the most important hub connecting members in the community. These results indicated that organic amendments are beneficial to diazotrophic activity, abundance, OTU richness, alpha-diversity, and the diazotrophic communities' potential interactions, which may enhance biological nitrogen fixation in vertisols.

Impact of Intercropping on the Diazotrophic Community in the Soils of Continuous Cucumber Cropping Systems

Diazotrophs are important soil components that help replenish biologically available nitrogen (N) in the soil and contribute to minimizing the use of inorganic N fertilizers in agricultural ecosystems. However, there is little understanding of how diazotrophs respond to intercropping and soil physicochemical properties in cucumber continuous cropping systems. In this study, using the nifH gene as a marker, we have examined the impacts of seven intercropping plants on diazotrophic community diversity and composition compared to a cucumber continuous cropping system during two cropping seasons. The results showed that intercropping increased the abundance of the nifH gene, which was negatively correlated with available phosphorous in the fall. Diazotrophic diversity and richness were higher in the rape-cucumber system than in the monoculture. Multivariate regression tree analysis revealed that the diversity of the diazotrophic communties was shaped mainly by soil moisture and available phosphorous. Skermanella were the dominant genera in all of the samples, which increased significantly in the mustard-cucumber system in the fall. There was no effect of intercropping on the structure of the diazotrophic community in this case. Non-metric multidimensional scaling analysis showed that cropping season had a greater effect than intercropping on the community structure of the diazotrophs. Overall, our results suggest that intercropping altered the abundance and diversity rather than the structure of the diazotrophic community, which may potentially affect the N fixation ability of continuous cropping systems.

Seasonal and long-term effects of nutrient additions and liming on the nifH gene in cerrado soils under native vegetation

Biological nitrogen fixation (BNF) represents the main input source of N in tropical savannas. BNF could be particularly important for Brazilian savannas (known as Cerrado) that show a highly conservative N cycle. We evaluated the effects of seasonal precipitation and nutrient additions on the nifH gene abundance in soils from a long-term fertilization experiment in a Cerrado's native area. The experiment consists of five treatments: (1) control, (2) liming, (3) nitrogen (N), (4) nitrogen + phosphorus (NP), and (5) phosphorus (P) additions. The nifH gene sequence was related to Bradyrhizobium members. Seasonal effects on N-fixing potential were observed by a decrease in the nifH relative abundance from rainy to dry season in control, N, and NP treatments. A significant reduction in nifH abundance was found in the liming treatment in both seasons. The findings evidenced the multiple factors controlling the potential N-fixing by free-living diazotrophs in these nutrient-limited and seasonally dry ecosystems.

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.

Microscale heterogeneity of the soil nitrogen cycling microbial functional structure and potential metabolism

Soil aggregates, with complex spatial and nutritional heterogeneity, are clearly important for regulating microbial community ecology and biogeochemistry in soils. However, how the taxonomic composition and functional attributes of N-cycling-microbes within different soil particle-size fractions under a long-term fertilization treatment remains largely unknown. Here, we examined the composition and metabolic potential for urease activity, nitrification, N₂ O production and reduction of the microbial communities attached to different sized soil particles (2000-250, 250-53 and <53 μm) using a functional gene microarray (GeoChip) and functional assays. We found that urease activity and nitrification were higher in <53 μm fractions, whereas N₂ O production and reduction rates were greater in 2000-250 and 250-53 μm across different fertilizer regimes. The abundance of key N-cycling genes involved in anammox, ammonification, assimilatory and dissimilatory N reduction, denitrification, nitrification and N₂ -fixation detected by GeoChip increased as soil aggregate size decreased; and the particular key genes abundance (e.g., ureC, amoA, narG, nirS/K) and their corresponding activity were uncoupled. Aggregate fraction exerted significant impacts on N-cycling microbial taxonomic composition, which was significantly shaped by soil nutrition. Taken together, these findings indicate the important roles of soil aggregates in differentiating N-cycling metabolic potential and taxonomic composition, and provide empirical evidence that nitrogen metabolism potential and community are uncoupled due to aggregate heterogeneity.