Multiple factors drive the abundance and diversity of the diazotrophic community in typical farmland soils of China

Singh B, Zhu YG, Hu HW, Li PP, Han YL, Han LL, Zhang QB, Wang JT, Liu SY, Wu CF, Ge AH, Zhang LM, He JZ. Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development

Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil-plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.

Soil microbial diversity and network complexity drive the ecosystem multifunctionality of temperate grasslands under changing precipitation

Soil microbiomes play a critical role in regulating ecosystem multifunctionality. However, whether and how soil protists and microbiome interactions affect ecosystem multifunctionality under climate change is unclear. Here, we transplanted 54 soil monoliths from three typical temperate grasslands (i.e., desert, typical, and meadow steppes) along a precipitation gradient in the Mongolian Plateau and examined their response to nighttime warming, decreased, and increased precipitation. Across the three steppes, nighttime warming only stimulated protistan diversity by 15.61 (absolute change, phylogenetic diversity) but had no effect on ecosystem multifunctionality. Decreased precipitation reduced bacterial (8.78) and fungal (22.28) diversity, but significantly enhanced soil microbiome network complexity by 1.40. Ecosystem multifunctionality was reduced by 0.23 under decreased precipitation, which could be largely attributed to the reduced soil moisture that negatively impacted bacterial and fungal communities. In contrast, increased precipitation had little impact on soil microbial communities. Overall, both bacterial and fungal diversity and network complexity play a fundamental role in maintaining ecosystem multifunctionality in response to drought stress. Protists alter ecosystem multifunctionality by indirectly affecting microbial network complexity. Therefore, not only microbial diversity but also their interactions (regulated by soil protists) should be considered in evaluating the responses of ecosystem multifunctionality, which has important implications for predicting changes in ecosystem functioning under future climate change scenarios.

Symbiotic diazotrophs in response to yak grazing and Tibetan sheep grazing in Qinghai-Tibetan plateau grassland soils

Grazing by local livestock is the traditional human practice in Qinghai-Tibetan Plateau grassland, and moderate intensity grazing can maintain high productivity and diversity of alpine grassland. Grazing ecosystems are often nitrogen-limited, but N2-fixing communities in response to yak grazing and Tibetan sheep grazing in Qinghai-Tibetan Plateau grassland have remained underexplored. In this study, we applied quantitative PCR quantitation and MiSeq sequencing of nifH under yak grazing and Tibetan grazing through a manipulated grazing experiment on an alpine grassland. The results showed that the grazing treatments significantly increased the soil ammonium nitrogen (AN) and total phosphorus (TP), but reduced the diazotrophs abundance. Compared with no grazing treatment, the composition of diazotrophs could be maximally maintained when the ratio of yak and Tibetan sheep were 1:2. The foraging strategies of grazing livestock reduced the legumes biomass, and thus reduced the diazotrophs abundance. Data analysis suggested that the direct key factors in regulating diazotrophs are AN and TP, and the changes of these two soil chemical properties were affected by the dung and urine of herbivore assemblages. Overall, these results indicated that the mixed grazing with a ratio of yak to Tibetan sheep as 1:2 can stabilize the soil diazotrophsic community, suggesting that MG12 are more reasonable grazing regimes in this region.

Microbiota and functional analyses of nitrogen-fixing bacteria in root-knot nematode parasitism of plants

BACKGROUND

Root-knot nematodes (RKN) are among the most important root-damaging plant-parasitic nematodes, causing severe crop losses worldwide. The plant rhizosphere and root endosphere contain rich and diverse bacterial communities. However, little is known about how RKN and root bacteria interact to impact parasitism and plant health. Determining the keystone microbial taxa and their functional contributions to plant health and RKN development is important for understanding RKN parasitism and developing efficient biological control strategies in agriculture.

RESULTS

The analyses of rhizosphere and root endosphere microbiota of plants with and without RKN showed that host species, developmental stage, ecological niche, and nematode parasitism, as well as most of their interactions, contributed significantly to variations in root-associated microbiota. Compared with healthy tomato plants at different developmental stages, significant enrichments of bacteria belonging to Rhizobiales, Betaproteobacteriales, and Rhodobacterales were observed in the endophytic microbiota of nematode-parasitized root samples. Functional pathways related to bacterial pathogenesis and biological nitrogen fixation were significantly enriched in nematode-parasitized plants. In addition, we observed significant enrichments of the nifH gene and NifH protein, the key gene/enzyme involved in biological nitrogen fixation, within nematode-parasitized roots, consistent with a potential functional contribution of nitrogen-fixing bacteria to nematode parasitism. Data from a further assay showed that soil nitrogen amendment could reduce both endophytic nitrogen-fixing bacteria and RKN prevalence and galling in tomato plants.

CONCLUSIONS

Results demonstrated that (1) community variation and assembly of root endophytic microbiota were significantly affected by RKN parasitism; (2) a taxonomic and functional association was found for endophytic nitrogen-fixing bacteria and nematode parasitism; and (3) the change of nitrogen-fixing bacterial communities through the addition of nitrogen fertilizers could affect the occurrence of RKN. Our results provide new insights into interactions among endophytic microbiota, RKN, and plants, contributing to the potential development of novel management strategies against RKN. Video Abstract.

Nodule-associated diazotrophic community succession is driven by developmental phases combined with microhabitat of Sophora davidii

Nodule-associated nitrogen-fixing microorganisms (diazotrophs) residing in legume root nodules, and they have the potential to enhance legume survival. However, the succession characteristics and mechanisms of leguminous diazotrophic communities remain largely unexplored. We performed a high-throughput nifH amplicon sequencing with samples of root nodules and soil in the three developmental phases (young nodules, active nodules and senescent nodules) of the Sophora davidii (Franch.) Skeels root nodules, aiming to investigate the dynamics of nodule-endophytic diazotrophs during three developmental phases of root nodules. The results demonstrated the presence of diverse diazotrophic bacteria and successional community shifting dominated by Mesorhizobium and Bradyrhizobium inside the nodule according to the nodule development. The relative abundance decreased for Mesorhizobium, while decreased first and then increased for Bradyrhizobium in nodule development from young to active to senescent. Additionally, strains M. amorphae BT-30 and B. diazoefficiens B-26 were isolated and selected to test the interaction between them in co-cultured conditions. Under co-culture conditions: B. diazoefficiens B-26 significantly inhibited the growth of M. amorphae BT-30. Intriguingly, growth of B. diazoefficiens B-26 was significantly promoted by co'culture with M. amorphae BT-30 and could utilize some carbon and nitrogen sources that M. amorphae BT-30 could not. Additionally, the composition of microbial community varied in root nodules, in rhizosphere and in bulk soil. Collectively, our study highlights that developmental phases of nodules and the host microhabitat were the key driving factors for the succession of nodule-associated diazotrophic community.

Semi-solid state promotes the methane production during anaerobic co-digestion of chicken manure with corn straw comparison to wet and high-solid state

Total solid content (TS) is an important factor for biogas production during anaerobic digestion. In this study, we explored the influence of different TS (5% wet, 15% semi-solid and 25% solid state) on the relative cumulative methane production (RCMP) during anaerobic co-digestion of chicken manure with corn straw. Results showed that total ammonium nitrogen and free ammonia nitrogen concentration increased with the increase of TS. Ammonium nitrogen in treatments at 15% TS was 2.25-2.76 times as high as that at 5% TS, which was below 3 times. The highest chemical oxygen demand removal and RCMP were obtained in the treatment of 15% TS with a ratio of 2:1 chicken manure: corn straw (based on TS). The RCMP in the treatments of 15% TS were 3.63-4.59 times higher than that of 5% TS based on the volume of substrates. The abundance of Caldicoprobacter improving the degradation of corn straw was significantly positively correlated with the RCMP, and the average abundance of Caldicoprobacter at 15% TS was 8.33 and 7.02 times higher than that at 5% and 25% TS, respectively. Structural equation models analysis suggested that TS significantly impacted the RCMP by indirectly impacting free ammonia nitrogen and microbial abundance. These findings indicated semi-solid state (15% TS) decreased ammonia nitrogen releasing and improved the abundance of Caldicoprobacter, and increased RCMP during anaerobic co-digestion of chicken manure with corn straw.

Land use alters diazotroph community structure by regulating bacterivores in Mollisols in Northeast China

Changes in land use can generate environmental pressures that influence soil biodiversity, and numerous studies have examined the influences of land use on the soil microbial communities. However, little is known about the effects of land use on ecological interactions of soil microbes and their predators. Diazotrophs are key soil microbes that play important functional roles in fixing atmospheric nitrogen. In this study, we investigated the co-association of diazotroph community members and patterns of diazotroph and bacterivore networks under different long-term land uses including cropland, grassland, and bare land. Diazotroph community was characterized by high-throughput sequencing. The results indicated that land use type influenced the dominant genera of diazotrophs and shaped the occurrence of specific indicator diazotroph taxa. Co-existing pattern analysis of diazotrophs and bacterivores indicated that grassland converted from cropland increased the complexity of diazotroph and bacterivore network structure. The number of nodes for diazotrophs and bacterivores was higher in grassland than in cropland and bare land. Random forest analysis revealed that six bacterivore genera Cephalobus, Protorhabditis, Acrobeloides, Mesorhabditis, Anaplectus, and Monhystera had significant effects on diazotrophs. Bacterivores were found to have predominantly negative effects in bare land. Different bacterivores had differing effects with respect to driving changes in diazotroph community structure. Structural equation model showed that land use could control diazotroph community composition by altering soil properties and regulating abundance of bacterivores. These findings accordingly enhance our current understanding of mechanisms underlying the influence of land use patterns on diazotrophs from the perspective of soil food webs.

Land use indirectly affects the cycling of multiple nutrients by altering the diazotrophic community in black soil

BACKGROUND

Diazotrophic bacteria, as one of most important group of soil microorganisms, play critical roles in multiple ecosystem functions (i.e., multifunctionality). However, little information is available about the diazotrophic community in driving soil nutrient cycling and multifunctionality at different depths with distinct vegetation in the black soil region of northeastern China. To learn the interactions among land use, cycling of multiple nutrients and the diazotrophic community, we performed this study in grassland (GL), forested land and a cropland (CL) in soils at depths of 0-15 cm and 15-35 cm.

RESULTS

The highest nifH gene abundances were found in the CL treatment, while the highest diazotrophic species richness and diversity were detected in the GL in both soil layers. The nifH gene abundance was directly/positively correlated with soil bulk density and negatively correlated with land use and soil depth. The index of multiple nutrient cycling was directly/negatively affected by soil depth and indirectly/positively affected by land use. Land use directly/negatively affected soil pH and thus indirectly affected the diazotrophic community composition and the nutrient cycling index. The diversity and community composition of the diazotrophs together accounted for 95% of the differences in the multiple nutrient cycling index.

CONCLUSION

Soil diazotrophic communities undertake important roles in maintaining nutrient cycling and soil multifunctionality at depths of 0-15 cm and 15-35 cm layers with different land uses of the black soil region of China. © 2021 Society of Chemical Industry.

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.

Meta-analysis of diazotrophic signatures across terrestrial ecosystems at the continental scale

Biological nitrogen fixation performed by diazotrophs forms a cornerstone of Earth's terrestrial ecosystem productivity. However, the composition, diversity and distribution of soil diazotrophs are poorly understood across different soil ecosystems. Furthermore, the biological potential of the key diazotroph species in relation to key environmental parameters is unknown. To address this, we used meta-analysis approach to merge together 39 independent diazotroph amplicon sequencing (nifH gene) datasets consisting of 1988 independent soil samples. We then employed multiple statistical analyses and machine-learning approaches to compare diazotroph community differences and indicator species between terrestrial ecosystems on a global scale. The distribution, composition and structure of diazotroph communities varied across seven different terrestrial ecosystems, with community composition exhibiting an especially clear effect. The Cyanobacteria were the most abundant taxa in crust ecosystems (accounting for ~45% of diazotrophs), while other terrestrial ecosystems were dominated by Proteobacteria, including Alpha-, Beta- and Gamma-Proteobacteria (accounting for ~70% of diazotrophs). Farmland ecosystems harboured the highest and crust ecosystems the lowest alpha and phylogenetic diversities. Azospirillum zeae, Skermanella aerolata and four Bradyrhizobium species were identified as key indicator species of potential diazotroph activity. Overall, diazotroph abundances and distribution were affected by multiple environmental parameters, including soil pH, nitrogen, organic carbon, C:N ratio and annual mean precipitation and temperature. Together, our findings suggest that based on the relative abundance and diversity of nifH marker gene, diazotrophs have adapted to a range of environmental niches globally.

Global diversity and distribution of mushroom-inhabiting bacteria

Mushroom-forming fungi are important sources of food and medicine in many regions of the world, and their development and health are known to depend on various microbes. Recent studies have examined the structure of mushroom-inhabiting bacterial (MIB) communities and their association with local environmental variables, but global-scale diversity and determinants of these communities remain poorly understood. Here we examined the MIB global diversity and community composition in relation to climate, soil and host factors. We found a core global mushroom microbiome, accounting for 30% of sequence reads, while comprising a few bacterial genera such as Halomonas, Serratia, Bacillus, Cutibacterium, Bradyrhizobium and Burkholderia. Our analysis further revealed an important role of host phylogeny in shaping the communities of MIB, whereas the effects of climate and soil factors remained negligible. The results suggest that the communities of MIB and free-living bacteria are structured by contrasting community assembly processes and that fungal-bacterial interactions are an important determinant of MIB community structure.

Variations of Bacterial and Diazotrophic Community Assemblies throughout the Soil Profile in Distinct Paddy Soil Types and Their Contributions to Soil Functionality

Soil microbiota plays fundamental roles in maintaining ecosystem functions and services, including biogeochemical processes and plant productivity. Despite the ubiquity of soil microorganisms from the topsoil to deeper layers, their vertical distribution and contribution to element cycling in subsoils remain poorly understood. Here, nine soil profiles (0 to 135 cm) were collected at the local scale (within 300 km) from two canonical paddy soil types (Fe-accumuli and Hapli stagnic anthrosols), representing redoximorphic and oxidative soil types, respectively. Variations with depth in edaphic characteristics and soil bacterial and diazotrophic community assemblies and their associations with element cycling were explored. The results revealed that nitrogen and iron status were the most distinguishing edaphic characteristics of the two soil types throughout the soil profile. The acidic Fe-accumuli stagnic anthrosols were characterized by lower concentrations of free iron oxides and total iron in topsoil and ammonia in deeper layers compared with the Hapli stagnic anthrosols. The bacterial and diazotrophic community assemblies were mainly shaped by soil depth, followed by soil type. Random forest analysis revealed that nitrogen and iron cycling were strongly correlated in Fe-accumuli stagnic anthrosol, whereas in Hapli soil, available sulfur was the most important variable predicting both nitrogen and iron cycling. The distinctive biogeochemical processes could be explained by the differences in enrichment of microbial taxa between the two soil types. The main discriminant clades were the iron-oxidizing denitrifier Rhodanobacter, Actinobacteria, and diazotrophic taxa (iron-reducing Geobacter, Nitrospirillum, and Burkholderia) in Fe-accumuli stagnic anthrosol and the sulfur-reducing diazotroph Desulfobacca in Hapli stagnic anthrosol. IMPORTANCE Rice paddy ecosystems support nearly half of the global population and harbor remarkably diverse microbiomes and functions in a variety of soil types. Diazotrophs provide significant bioavailable nitrogen in paddy soil, priming nitrogen transformation and other biogeochemical processes. This study provides a novel perspective on the vertical distribution of bacterial and diazotrophic communities in two hydragric anthrosols. Microbiome analysis revealed divergent biogeochemical processes in the two paddy soil types, with a dominance of nitrogen-iron cycling processes in Fe-accumuli stagnic anthrosol and sulfur-nitrogen-iron coupling in Hapli stagnic anthrosol. This study advances our understanding of the multiple significant roles played by soil microorganisms, especially diazotrophs, in biogeochemical element cycles, which have important ecological and biogeochemical ramifications.

Slope aspect determines the abundance and composition of nitrogen-cycling microbial communities in an alpine ecosystem

Slope aspect is an important topographic feature that can influence local environmental conditions. While strong effects of slope aspect on aboveground and belowground communities have been frequently elucidated, how slope aspect affects soil nitrogen (N) cycling microbes remains unclear. Here, we characterized the communities of soil N-cycling microbes on south- and north-facing slopes in an alpine ecosystem, by quantifying (qPCR) and high-throughput sequencing six genes involved in N-fixation (nifH), nitrification (archaeal and bacterial amoA) and denitrification (nirK, nirS and nosZ). We found that the abundance, diversity and community composition of major N-cycling microbes differed dramatically between the two slope aspects, and these variances could be well explained by the aspect-driven differences in environmental conditions, especially soil temperature and moisture. The response patterns of different N-cycling groups to slope aspect were much inconsistent, especially for those with similar functions (i.e. ammonia-oxidizing archaea vs. bacteria, nirK- vs. nirS-reducers), indicating strong niche differentiation between these counterparts. We also observed strong preferences and distinct co-occurrence patterns of N-cycling microbial taxa for the two slope aspects. These findings highlight the importance of slope aspect in determining the abundance, species distribution and community structure of N-cycling microbes, and consequently influencing N-cycling processes and ecosystem functioning. This article is protected by copyright. All rights reserved.

Short-Term Legacy Effects of Mercury Contamination on Plant Growth and nifH-Harboring Microbial Community in Rice Paddy Soil

Methylmercury (MeHg), which is formed in rice paddy soil, exhibits strong neurotoxicity through bioaccumulation in the food chain. A few groups of microorganisms drive both mercury methylation and nitrogen fixation in the rhizosphere. Little is known about how the shifted soil microbial community by Hg contamination affects nitrogen fixation rate and plant growth in paddy soil. Here, we examined how stimulated short-term Hg amendment affects the nitrogen fixing microbial community and influences plant-microbe interactions. Soil was treated with low (0.2 mg/kg) and high (1.1 mg/kg) concentrations of Hg for 4 weeks; then, rice (Oryza sativa) was planted and grown for 12 weeks. The nitrogen-fixation rate and rice growth were measured. The diversity and structure of the microbial community were analyzed by sequencing the nifH gene before and after rice cultivation. Hg treatments significantly decreased the nitrogen fixation rate and dry weight of the rice plants. The structure of the nifH-harboring community was remarkably changed after rice cultivation depending on Hg treatments. Iron- or sulfate-reducing bacteria, including Desulfobacca, Desulfoporosimus, and Geobacter, were observed as legacy response groups; their abundances increased in the soil after Hg treatment. The high abundance of those groups were maintained in control, but the abundance drastically decreased after rice cultivation in the soil treated with Hg, indicating that symbiotic behavior of rice plants changes according to the legacy effects on Hg contamination. These results suggested that Hg contamination can persist in soil microbial communities, affecting their nitrogen-fixation ability and symbiosis with rice plants in paddy soil.

Evolutionary origin and ecological implication of a unique nif island in free-living Bradyrhizobium lineages

The alphaproteobacterial genus Bradyrhizobium has been best known as N₂-fixing members that nodulate legumes, supported by the nif and nod gene clusters. Recent environmental surveys show that Bradyrhizobium represents one of the most abundant free-living bacterial lineages in the world's soils. However, our understanding of Bradyrhizobium comes largely from symbiotic members, biasing the current knowledge of their ecology and evolution. Here, we report the genomes of 88 Bradyrhizobium strains derived from diverse soil samples, including both nif-carrying and non-nif-carrying free-living (nod free) members. Phylogenomic analyses of these and 252 publicly available Bradyrhizobium genomes indicate that nif-carrying free-living members independently evolved from symbiotic ancestors (carrying both nif and nod) multiple times. Intriguingly, the nif phylogeny shows that the vast majority of nif-carrying free-living members comprise an independent cluster, indicating that horizontal gene transfer promotes nif expansion among the free-living Bradyrhizobium. Comparative genomics analysis identifies that the nif genes found in free-living Bradyrhizobium are located on a unique genomic island of ~50 kb equipped with genes potentially involved in coping with oxygen tension. We further analyze amplicon sequencing data to show that Bradyrhizobium members presumably carrying this nif island are widespread in a variety of environments. Given the dominance of Bradyrhizobium in world's soils, our findings have implications for global nitrogen cycles and agricultural research.

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.

Depth-dependent variability of biological nitrogen fixation and diazotrophic communities in mangrove sediments

BACKGROUND

Nitrogen-fixing prokaryotes (diazotrophs) contribute substantially to nitrogen input in mangrove sediments, and their structure and nitrogen fixation rate (NFR) are significantly controlled by environmental conditions. Despite the well-known studies on diazotrophs in surficial sediments, the diversity, structure, and ecological functions of diazotrophic communities along environmental gradients of mangrove sediment across different depths are largely unknown. Here, we investigated how biological nitrogen fixation varied with the depth of mangrove sediments from the perspectives of both NFR and diazotrophic communities.

RESULTS

Through acetylene reduction assay, nifH gene amplicon and metagenomic sequencing, we found that the NFR increased but the diversity of diazotrophic communities decreased with the depth of mangrove sediments. The structure of diazotrophic communities at different depths was largely driven by salinity and exhibited a clear divergence at the partitioning depth of 50 cm. Among diazotrophic genera correlated with NFR, Agrobacterium and Azotobacter were specifically enriched at 50-100 cm sediments, while Anaeromyxobacter, Rubrivivax, Methylocystis, Dickeya, and Methylomonas were more abundant at 0-50 cm. Consistent with the higher NFR, metagenomic analysis demonstrated the elevated abundance of nitrogen fixation genes (nifH/D/K) in deep sediments, where nitrification genes (amoA/B/C) and denitrification genes (nirK and norB) became less abundant. Three metagenome-assembled genomes (MAGs) of diazotrophs from deep mangrove sediments indicated their facultatively anaerobic and mixotrophic lifestyles as they contained genes for low-oxygen-dependent metabolism, hydrogenotrophic respiration, carbon fixation, and pyruvate fermentation.

CONCLUSIONS

This study demonstrates the depth-dependent variability of biological nitrogen fixation in terms of NFR and diazotrophic communities, which to a certain extent relieves the degree of nitrogen limitation in deep mangrove sediments. Video Abstract.

Sugar and organic acid availability modulate soil diazotroph community assembly and species co-occurrence patterns on the Tibetan Plateau

Metabolites can mediate species interactions and the assembly of microbial communities. However, how these chemicals relate to the assembly processes and co-occurrence patterns of diazotrophic assemblages in root-associated soils remains largely unknown. Here, we examined the diversity and assembly of diazotrophic communities and further deciphered their links with metabolites on Tibetan Plateau. We found that the distribution of sugars and organic acids in the root-associated soils was significantly correlated with the richness of diazotrophs. The presence of these two soil metabolites explains the variability in diazotrophic community compositions. The differential concentrations of these metabolites were significantly linked with the distinctive abundances of diazotrophic taxa in same land types dominated by different plants or dissimilar soils by same plants. The assembly of diazotrophic communities is subject to deterministic ecological processes, which are widely modulated by the variety and amount of sugars and organic acids. Organic acids, for instance, 3-(4-hydroxyphenyl)propionic acid and citric acid, were effective predictors of the characteristics of diazotrophic assemblages across desert habitats. Diazotrophic co-occurrence networks tended to be more complex and connected within different land types covered by the same plant species. The concentrations of multiple sugars and organic acids were coupled significantly with the distribution of keystone species, such as Azotobacter, Azospirillum, Bradyrhizobium, and Mesorhizobium, in the co-occurrence network. These findings provide new insights into the assembly mechanisms of root-associated diazotrophic communities across the desert ecosystems of the Tibetan Plateau.Key points• Soil metabolites were significantly linked to the diversity of diazotrophic community.• Soil metabolites determined the assembly of diazotrophic community.• Sugars and organic acids were coupled mainly with keystone species in networks.

Interactions between soil compositions and the wheat root microbiome under drought stress: From an in silico to in planta perspective

As wheat (Triticum aestivum) is an important staple food across the world, preservation of stable yields and increased productivity are major objectives in breeding programs. Drought is a global concern because its adverse impact is expected to be amplified in the future due to the current climate change. Here, we analyzed the effects of edaphic, environmental, and host factors on the wheat root microbiomes collected in soils from six regions in Belgium. Amplicon sequencing analysis of unplanted soil and wheat root endosphere samples indicated that the microbial community variations can be significantly explained by soil pH, microbial biomass, wheat genotype, and soil sodium and iron levels. Under drought stress, the biodiversity in the soil decreased significantly, but increased in the root endosphere community, where specific soil parameters seemingly determine the enrichment of bacterial groups. Indeed, we identified a cluster of drought-enriched bacteria that significantly correlated with soil compositions. Interestingly, integration of a functional analysis further revealed a strong correlation between the same cluster of bacteria and β-glucosidase and osmoprotectant proteins, two functions known to be involved in coping with drought stress. By means of this in silico analysis, we identified amplicon sequence variants (ASVs) that could potentially protect the plant from drought stress and validated them in planta. Yet, ASVs based on 16S rRNA sequencing data did not completely distinguish individual isolates because of their intrinsic short sequences. Our findings support the efforts to maintain stable crop yields under drought conditions through implementation of root microbiome analyses.

Depth-dependent influence of biochar application on the abundance and community structure of diazotrophic under sugarcane growth

Despite progress in understanding diazotrophic distribution in surface soils, few studies have investigated the distribution of diazotrophic bacteria in deeper soil layers. Here, we leveraged high-throughput sequencing (HTS) of nifH genes obtained to assess the influence of biochar amended soil (BC) and control (CK), and soil depths (0–20, 20–40 and 40–60 cm) on diazotrophic abundance and community structures, soil enzyme activities and physio-chemical properties. Multivariate ANOVA analysis revealed that soil depth had profound impact on majority of the soil parameters measured than fertilization. Although soil physio-chemical properties, enzymes activities, diazotrophic genera and enriched operational taxonomic units (OTUs) were significantly influenced across the entire soil profiles, we also observed that BC amended soil significantly increased cane stalk height and weight, nitrate (NO₃^-), ammonium (NH₄⁺), organic matter (OM), total carbon (TC) and available potassium (AK), and enhanced diazotrophic genera in soil depth 0–20 cm compared to CK treatment. Soil TC, total nitrogen (TN), OM and NH₄⁺ were the major impact factors shifting diazotrophic community structures in soil depth 0–20 cm. Overall, these results were more pronounced in 0–20 cm soil depth in BC than CK treatment.

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.

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.

The Root Microbiome of Salicornia ramosissima as a Seedbank for Plant-Growth Promoting Halotolerant Bacteria

Root−associated microbial communities play important roles in the process of adaptation of plant hosts to environment stressors, and in this perspective, the microbiome of halophytes represents a valuable model for understanding the contribution of microorganisms to plant tolerance to salt. Although considered as the most promising halophyte candidate to crop cultivation, Salicornia ramosissima is one of the least-studied species in terms of microbiome composition and the effect of sediment properties on the diversity of plant-growth promoting bacteria associated with the roots. In this work, we aimed at isolating and characterizing halotolerant bacteria associated with the rhizosphere and root tissues of S. ramosissima, envisaging their application in saline agriculture. Endophytic and rhizosphere bacteria were isolated from wild and crop cultivated plants, growing in different estuarine conditions. Isolates were identified based on 16S rRNA sequences and screened for plant-growth promotion traits. The subsets of isolates from different sampling sites were very different in terms of composition but consistent in terms of the plant-growth promoting traits represented. Bacillus was the most represented genus and expressed the wider range of extracellular enzymatic activities. Halotolerant strains of Salinicola, Pseudomonas, Oceanobacillus, Halomonas, Providencia, Bacillus, Psychrobacter and Brevibacterium also exhibited several plant-growth promotion traits (e.g., 3-indole acetic acid (IAA), 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, siderophores, phosphate solubilization). Considering the taxonomic diversity and the plant-growth promotion potential of the isolates, the collection represents a valuable resource that can be used to optimize the crop cultivation of Salicornia under different environmental conditions and for the attenuation of salt stress in non-halophytes, considering the global threat of arable soil salinization.

Genetic and Morphological Diversity of Indigenous Bradyrhizobium Nodulating Soybean in Organic and Conventional Family Farming Systems

Organic farming systems are gaining popularity as agronomically and environmentally sound soil management strategies with potential to enhance soil microbial diversity and fertility, environmental quality and sustainable crop production. This work aimed at understanding the effect of organic and conventional farming on the diversity of soybean nodulating bradyrhizobia species. Field trapping of indigenous soybean Bradyrhizobium was done by planting promiscuous soybeans varieties SB16 and SC squire as well as non-promiscuous Gazelle in three organic and three conventional farms in Tharaka-Nithi County of Kenya. After 45 days of growth, 108 nodule isolates were obtained from the soybean nodules and placed into 13 groups based on their morphological characteristics. Genetic diversity was done by polymerase chain reaction (PCR) targeting 16S rDNA gene using universal primers P5-R and P3-F and sequencing was carried out using the same primer. High morphological and genetic diversity of the nodule isolates was observed in organic farms as opposed to conventional farms. There was little or no genetic differentiation between the nodule isolates from the different farms with the highest molecular variation (91.12%) being partitioned within populations as opposed to among populations (8.88%). All the isolates were identified as bradyrhizobia with close evolutionary ties with Bradyrhizobium japonicum and Bradyrhizobium yuanminense. Organic farming systems favor the proliferation of bradyrhizobia species and therefore a suitable environmentally friendly alternative for enhancing soybean production.

Long-term chemical fertilization-driving changes in soil autotrophic microbial community depresses soil CO2 fixation in a Mollisol

Soil is the largest C pool in the terrestrial ecosystem. Numerous studies have been devoted to the decomposition of soil organic C as influenced by agricultural management. However, little is known about the effect of fertilization on the microbial CO₂ fixation potential. Here, we examined the atmospheric CO₂ fixation rates and structure of autotrophic cbbL-containing bacterial communities and accA-containing archaeal communities in response to 38 years of chemical and/or organic fertilizer application in a Mollisol. The autotrophic microbial abundance and community composition were analyzed by quantitative polymerase chain reaction and high throughput sequencing, respectively. Our results showed that chemical fertilization additions significantly decreased CO₂ fixation rates by 57%, but organic manure use resulted in no notable differences compared to no fertilizer regimes (0.38 mg CO₂ kg^-1 soil d^-1) through stable isotope methods. The declining soil pH and increasing Olsen-phosphorus in soils with chemical fertilization dramatically reduced the cbbL gene diversity and accA gene abundances and altered both the autotrophic bacterial and archaeal community compositions. The changes in CO₂-fixation rate were more greatly attributed to the shifts in autotrophic bacterial community composition than to the diversity and abundance. The C fixation potentials were positively correlated with the relative abundances of Acidiphilium and Methylibium but were negatively related to those of Azospirillum and Nitrosospira. Both composition and abundance of the autotrophic archaeal community contributed together to the CO₂ fixation activities. Our finding suggests that long-term chemical fertilization has a strong impact on the soil microbial CO₂ fixation activity and autotrophic microorganisms in upland soils and highlight the important roles of the CO₂ fixing process in soil organic carbon sequestration.

Long-term nitrogen fertilization shaped the nifH, nirK, and nosZ gene community patterns in red paddy soil in south China

To understand the diversities of diazotrophs and denitrifiers in red paddy soil under long-term fertilization conditions, nifH, nirK, and nosZ libraries were constructed by PCR-RFLP. nirK gene diversity proved to be lower than that of nosZ and nifH, and nirK and nosZ genes were more sensitive to different fertilization treatments than the nifH gene was. The 3 libraries were dominated by diverse microbes, including the Alpha, Beta, Gamma, and Delta subclasses of the Proteobacteria. Long-term addition of urea with straw mulch and azophoska increased the abundance of nonsymbiotic diazotrophs, which indicated that nonsymbiotic diazotrophs were responsible for the majority of the nitrogen-fixing ability in paddy soil. In addition, a potential link between nifH and nosZ was found due to the existence of nitrogen fixers, such as Bradyrhizobium and Ralstonia, in the nosZ library. The main chemical factors affecting the 3 genes were identified: pH was the most important factor of the nifH community; the nirK gene was more affected by pH and organic matter; available potassium and the carbon-to-nitrogen ratio significantly influenced the community structure of the nosZ gene.

Soil metabolome correlates with bacterial diversity and co-occurrence patterns in root-associated soils on the Tibetan Plateau

Metabolites in root-zone soils mediate microbe-to-microbe interactions and govern the overall microbial community. However, how chemicals relate to diversity and co-occurrence patterns of bacterial communities in root-associated soils is still poorly understood. Here, we studied the relationships of soil metabolome with bacterial community diversity and co-occurrence patterns in root-associated soils across different land types on the Tibetan Plateau. The soil metabolome mainly encompassed a range of organic acids, and sugars and sugar derivatives, which were widely negatively correlated with bacterial alpha-diversity. Compared to the investigated environmental variables, metabolites accounted more for the variations in the Shannon diversity and bacterial community compositions. Compared to sugars, organic acids accounted more for bacterial community compositions at high taxonomic ranks, while reversed at genus and species levels. The relative abundances of some bacterial genera and metabolites were closely linked to soil types and plant genotypes. The differential compounds were significantly correlated with the distinctive bacterial taxa across land types and plant genotypes. Keystone species in co-occurrence network, such as Bradyrhizobium, Bryobacter, and Microvirga were significantly correlated with sugars and organic acids. Structural equation modeling revealed that sugar metabolism can play a crucial role in altering the bacterial community diversity. This study provides new insights into the ecological mechanism that maintains bacterial community in the root-associated soils on the Tibetan Plateau.

Revealing structure and assembly for rhizophyte-endophyte diazotrophic community in mangrove ecosystem after introduced Sonneratia apetala and Laguncularia racemosa

Biological nitrogen fixation (BNF) mediated by diazotrophic communities is a major source of bioavailable nitrogen in mangrove wetlands, which plays important roles in maintaining the health and stability of mangrove ecosystems. Recent large-scale mangrove afforestation activities have drawn great attention due to introduced mangrove species and their potential impacts on bio-functionalities of local ecosystems. However, the effects of introduced mangrove species on diazotrophic communities remain unclear. Here, we analyzed rhizosphere and endosphere diazotrophic communities between native mangrove species (Avicennia marina) and introduced mangrove species (Sonneratia apetala and Laguncularia racemose) by sequencing nifH gene amplicons. Our results showed that S. apetala and L. racemose introduction significantly (P < 0.05) increased nutrition components (e.g., total carbon and total nitrogen) in rhizosphere, as well as the diazotrophs richness in rhizosphere and endosphere. The relative abundance of clusters III diazotrophs in the rhizosphere and Rhizobium in the endosphere were significantly increased with L. racemosa or S. apetala introduction. Fe and pH were the main environmental factors driving the divergence of endophyte-rhizophyte diazotrophs between native and introduced mangroves. The correlation-based network analyses indicated that the interaction among rhizophyte-endophyte diazotrophs is more harmonious in native mangrove, while there exist more competition in introduced mangroves. These findings expand our current understanding of BNF in mangrove afforestation, and providing new perspectives to sustainable management of mangrove ecosystem.