Autotrophic and symbiotic diazotrophs dominate nitrogen-fixing communities in Tibetan grassland soils

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome

BACKGROUND

Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome.

RESULTS

After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments).

CONCLUSION

Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.

Impacts of Managed Vegetation Restoration on Arbuscular Mycorrhizal Fungi and Diazotrophs in Karst Ecosystems

The crucial functional arbuscular mycorrhizal fungi (AMF) and diazotrophs play pivotal roles in nutrient cycling during vegetation restoration. However, the impact of managed vegetation restoration strategies on AMF and diazotroph communities remains unclear. In this study, we investigated the community structure and diversity of AMF and diazotrophs in a karst region undergoing managed vegetation restoration from cropland. Soil samples were collected from soils under three vegetation restoration strategies, plantation forest (PF), forage grass (FG), and a mixture of plantation forest and forage grass (FF), along with a control for cropland rotation (CR). The diversity of both AMF and diazotrophs was impacted by managed vegetation restoration. Specifically, the AMF Shannon index was higher in CR and PF compared to FF. Conversely, diazotroph richness was lower in CR, PF, and FG than in FF. Furthermore, both AMF and diazotroph community compositions differed between CR and FF. The relative abundance of AMF taxa, such as Glomus, was lower in FF compared to the other three land-use types, while Racocetra showed the opposite trend. Among diazotroph taxa, the relative abundance of Anabaena, Nostoc, and Rhizobium was higher in FF than in CR. Soil properties such as total potassium, available potassium, pH, and total nitrogen were identified as the main factors influencing AMF and diazotroph diversity. These findings suggest that AMF and diazotroph communities were more sensitive to FF rather than PF and FG after managed vegetation restoration from cropland, despite similar levels of soil nutrients among PF, FG, and FF. Consequently, the integration of diverse economic tree species and forage grasses in mixed plantations notably altered the diversity and species composition of AMF and diazotrophs, primarily through the promotion of biocrust formation and root establishment.

Precipitation affects soil nitrogen fixation by regulating active diazotrophs and nitrate nitrogen in an alpine grassland of Qinghai-Tibetan Plateau

Soil asymbiotic nitrogen (N) fixation provides a critical N source to support plant growth in alpine grasslands, and precipitation change is expected to lead to shifts in soil asymbiotic N fixation. However, large gaps remain in understanding the response of soil asymbiotic N fixation to precipitation gradients. Here we simulated five precipitation gradients (10 % (0.1P), 50 % (0.5P), 70 % (0.7P), 100 % (1.0P) and 150 % (1.5P) of the natural precipitation) in an alpine grassland of Qinghai-Tibetan Plateau and examined the soil nitrogenase activity and N fixation rate for each gradient. Quantitative PCR and high-throughput sequencing were used to measure the abundance and community composition of the soil nifH DNA (total diazotrophs) and nifH RNA reverse transcription (active diazotrophs) gene. Our results showed that the soil diazotrophic abundance, diversity and nifH gene expression rate peaked under the 0.5P. Soil nitrogenase activity and N fixation rate varied in the range 0.032-0.073 nmol·C2H4·g-1·h-1 and 0.008-0.022 nmol·N2·g-1·h-1 respectively, being highest under the 0.5P. The 50 % precipitation reduction enhanced the gene expression rates of Azospirillum and Halorhodospira which were likely responsible for the high N fixation potential. The 0.5P treatment also possessed a larger and more complex active diazotrophic network than the other treatments, which facilitated the resistance of diazotrophic community to environmental stress and thus maintained a high N fixation potential. The active diazotrophic abundance had the largest positive effect on soil N fixation, while nitrate nitrogen had the largest negative effect. Together, our study suggested that appropriate precipitation reduction can enhance soil N fixation through promoting the abundance of the soil active diazotrophs and decreasing soil nitrate nitrogen, and soil active diazotrophs and nitrate nitrogen should be considered in predicting soil N inputs in the alpine grassland of Qinghai-Tibetan Plateau under precipitation change.

Soil microbial subcommunity assembly mechanisms are highly variable and intimately linked to their ecological and functional traits

Revealing the mechanisms underlying soil microbial community assembly is a fundamental objective in molecular ecology. However, despite increasing body of research on overall microbial community assembly mechanisms, our understanding of subcommunity assembly mechanisms for different prokaryotic and fungal taxa remains limited. Here, soils were collected from more than 100 sites across southwestern China. Based on amplicon high-throughput sequencing and iCAMP analysis, we determined the subcommunity assembly mechanisms for various microbial taxa. The results showed that dispersal limitation and homogenous selection were the primary drivers of soil microbial community assembly in this region. However, the subcommunity assembly mechanisms of different soil microbial taxa were highly variable. For instance, the contribution of homogenous selection to Crenarchaeota subcommunity assembly was 70%, but it was only around 10% for the subcommunity assembly of Actinomycetes, Gemmatimonadetes and Planctomycetes. The assembly of subcommunities including microbial taxa with higher occurrence frequencies, average relative abundance and network degrees, as well as wider niches tended to be more influenced by homogenizing dispersal and drift, but less affected by heterogeneous selection and dispersal limitation. The subcommunity assembly mechanisms also varied substantially among different functional guilds. Notably, the subcommunity assembly of diazotrophs, nitrifiers, saprotrophs and some pathogens were predominantly controlled by homogenous selection, while that of denitrifiers and fungal pathogens were mainly affected by stochastic processes such as drift. These findings provide novel insights into understanding soil microbial diversity maintenance mechanisms, and the analysis pipeline holds significant value for future research.

Microbiome resistance mediates stimulation of reduced graphene oxide to simultaneous abatement of 2,2',4,4',5-pentabromodiphenyl ether and 3,4-dichloroaniline in paddy soils

Paddy soils near electrical and electronic waste recycling sites generally suffer from co-pollution of polybrominated diphenyl ethers and 3,4-dichloroaniline (3,4-DCA). This study tested the feasibility of reduced graphene oxide (rGO) to stimulate the simultaneous abatement of 2,2',4,4',5-pentabromodiphenyl ether (BDE99) and 3,4-DCA in percogenic paddy soil (PPS) and hydromorphic paddy soil (HPS). rGO improved the debromination extent of BDE99 and the transformation rate of 3,4-DCA in PPS, but did not affect their abatement in HPS. The inhibition of specific fermenters, acetogens, and methanogens after rGO addition contributed to BDE99 debromination by obligate organohalide-respiring bacteria (OHRB) in PPS, but relevant soil microbiomes (e.g., fermenters, acetogens, methanogens, and obligate OHRB) responded little to rGO in HPS. For 3,4-DCA, the enhanced activities of nitrogen-metabolic chloroaniline degraders by rGO increased its transformation rate in PPS, but was compensated by the decreased biotransformation from 3,4-DCA to 3,4-dichloroacetanilide after the addition of rGO to HPS. The discrepant stimulation of rGO between PPS and HPS was mediated by soil microbiome resistance. rGO has the application potential to stimulate the simultaneous abatement of polybrominated diphenyl ethers and chloroanilines in paddy soils with relatively low microbiome resistance.

Diazotrophic abundance and community structure associated with three meadow plants on the Qinghai-Tibet Plateau

Symbiotic diazotrophs form associations with legumes and substantially fix nitrogen into soils. However, grasslands on the Qinghai-Tibet Plateau are dominated by non-legume plants, such as Kobresia tibetica. Herein, we investigated the diazotrophic abundance, composition, and community structure in the soils and roots of three plants, non-legume K. tibetica and Kobresia humilis and the legume Oxytropis ochrocephala, using molecular methods targeting nifH gene. Diazotrophs were abundantly observed in both bulk and rhizosphere soils, as well as in roots of all three plants, but their abundance varied with plant type and soil. In both bulk and rhizosphere soils, K. tibetica showed the highest diazotroph abundance, whereas K. humilis had the lowest. In roots, O. ochrocephala and K. humilis showed the highest and the lowest diazotroph abundance, respectively. The bulk and rhizosphere soils exhibited similar diazotrophic community structure in both O. ochrocephala and K. tibetica, but were substantially distinct from the roots in both plants. Interestingly, the root diazotrophic community structures in legume O. ochrocephala and non-legume K. tibetica were similar. Diazotrophs in bulk and rhizosphere soils were more diverse than those in the roots of three plants. Rhizosphere soils of K. humilis were dominated by Actinobacteria, while rhizosphere soils and roots of K. tibetica were dominated by Verrumicrobia and Proteobacteria. The O. ochrocephala root diazotrophs were dominated by Alphaproteobacteria. These findings indicate that free-living diazotrophs abundantly and diversely occur in grassland soils dominated by non-legume plants, suggesting that these diazotrophs may play important roles in fixing nitrogen into soils on the plateau.

The effectiveness of sewage sludge biochar amendment with Boehmeria nivea L. in improving physicochemical properties and rehabilitating microbial communities in mine tailings

Biochar amendment can be adopted to improve soil substrate, in turn facilitated phytoremediation. However, improvements to the properties of tailings following different feedstocks of biochar amendment in phytoremediation, particularly the impacts on nitrogen cycle and the related nitrogen-fixing microorganisms remain unclear. In this study, a 100-day pot experiment was designed to determine the co-effects of different combinations of woody and non-woody biochar, namely hibiscus cannabinus core biochar (HB), sewage sludge biochar (SB), chicken manure biochar (MB) and two crops (Cassia alata L., Boehmeria nivea L.). It was found that, on the one hand, biochar amendment directly immobilized heavy metal (loid) contamination in the tailings; on the other hand, biochar amendment, particularly non-woody SB, improved soil properties (i.e., the combination of SB with crops increased the total nitrogen content by 4.7-7.5 times). This indirectly improved phytostabilization (i.e., SB increased crop height 1.5-1.8 fold, root length 3.3-3.7 fold, decreased NH4NO3-extractable Pb, Cu, Cd and also increased the relative abundance of nitrogen-fixing bacteria such as Mesorhizobium, Bradyrhizobium, and Rhizobium). Besides this, redundant analysis shown that the carbon, nitrogen sources, and pH provided by the biochar were identified as the key factors associated with the nitrogen-fixing bacteria. Through the comprehensive evaluation of different biochar amendment in phytoremediation, it was found that the non-woody SB got higher comprehensive score (3.1-3.6) in biochar amendment in phytoremediation, especially in Boehmeria nivea L. Thus, the combination of non-woody SB and Boehmeria nivea L. improved microbial function, while the microorganisms in turn promoted crop growth. Our results revealed the prospect of using non-woody SB assisted Boehmeria nivea L. for phytoremediation in multi-metal mine tailings.

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.

Effect of endophytic diazotroph Enterobacter roggenkampii ED5 on nitrogen-metabolism-related microecology in the sugarcane rhizosphere at different nitrogen levels

Sugarcane is an important sugar and energy crop worldwide, requiring a large amount of nitrogen (N). However, excessive application of synthetic N fertilizer causes environmental pollution in farmland. Endophytic nitrogen-fixing bacteria (ENFB) provide N nutrition for plants through biological N fixation, thus reducing the need for chemical fertilizers. The present study investigated the effect of the N-fixing endophytic strain Enterobacter roggenkampii ED5 on phytohormone indole-3-acetic acid (IAA), N-metabolism enzyme activities, microbial community compositions, and N cycle genes in sugarcane rhizosphere soil at different N levels. Three levels of 15N-urea, such as low N (0 kg/ha), medium N (150 kg/ha), and high N (300 kg/ha), were applied. The results showed that, after inoculating strain ED5, the IAA content in sugarcane leaves was significantly increased by 68.82% under low N condition at the seedling stage (60 days). The nitrate reductase (NR) activity showed a downward trend. However, the glutamine synthase (GS) and NADH-glutamate dehydrogenase (NADH-GDH) activities were significantly enhanced compared to the control under the high N condition, and the GS and NR genes had the highest expression at 180 and 120 days, respectively, at the low N level. The total N content in the roots, stems, and leaves of sugarcane was higher than the control. The 15N atom % excess of sugarcane decreased significantly under medium N condition, indicating that the medium N level was conducive to N fixation in strain ED5. Metagenome analysis of sugarcane rhizosphere soil exhibited that the abundance of N-metabolizing microbial richness was increased under low and high N conditions after inoculation of strain ED5 at the genus level, while it was increased at the phylum level only under the low N condition. The LefSe (LDA > 2, p < 0.05) found that the N-metabolism-related differential microorganisms under the high N condition were higher than those under medium and low N conditions. It was also shown that the abundance of nifDHK genes was significantly increased after inoculation of ED5 at the medium N level, and other N cycle genes had high abundance at the high N level after inoculation of strain ED5. The results of this study provided a scientific reference for N fertilization in actual sugarcane production.

Green waste and sewage sludge feeding ratio alters co-composting performance: Emphasis on the role of bacterial community during humification

Composting with five levels of green waste and sewage sludge was compared to examine how feeding ratios affected composting performance with special focus on humification, and the underlying mechanisms. The results showed that the raw material ratio persistently affected compost nutrients and stability. Humification and mineralization were promoted by higher proportion of sewage sludge. Bacterial community composition and within-community relationships were also significantly affected by the raw material feeding ratio. Network analysis indicated that clusters 1 and 4 which dominated by Bacteroidetes, Proteobacteria, and Acidobacteria shown significantly positive correlation with humic acid concentration. Notably, the structural equational model and variance partitioning analysis demonstrated that bacterial community structure (explained 47.82% of the variation) mediated the effect of raw material feeding ratio on humification, and exceeded the effect of environmental factors (explained 19.30% of the variation) on humic acid formation. Accordingly, optimizing the composting raw material improves the composting performance.

The relationships between heavy metals and bacterial communities in a coal gangue site

Coal is the main source of energy for China's economic development, but coal gangue dumps are a major source of heavy metal pollution. Bacterial communities have a major effect on the bioremediation of heavy metals in coal gangue dumps. The effects of different concentrations of heavy metals on the composition of bacterial communities in coal gangue sites remain unclear. Soil bacterial communities from four gangue sites that vary in natural heavy metal concentrations were investigated using high-throughput sequencing in this study. Correlations among bacterial communities, heavy metal concentrations, physicochemical properties of the soil, and the composition of dissolved organic matter of soil in coal gangue dumps were also analyzed. Our results indicated that Actinobacteriota, Proteobacteria, Chloroflexi, Acidobacteriota, and Gemmatimonadota were the bacterial taxa most resistant to heavy metal stress at gangue sites. Heavy metal contamination may be the main cause of changes in bacterial communities. Heavy metal pollution can foster mutually beneficial symbioses between microbial species. Microbial-derived organic matter was the main source of soil organic matter in unvegetated mining areas, and this could affect the toxicity and transport of heavy metals in soil. Polar functional groups such as hydroxyl and ester groups (A_226-400) play an important role in the reaction of cadmium (Cd) and lead (Pb), and organic matter with low molecular weight (S_R) tends to bind more to mercury (Hg). In addition to heavy metals, the content of nitrogen (N), phosphorus (P), and total organic carbon (TOC) also affected the composition of the bacterial communities; TOC had the strongest effect, followed by N, SOM, and P. Our findings have implications for the microbial remediation of heavy metal-contaminated soils in coal gangue sites and sustainable development.

Assessing the Effect of Slope Position on the Community Assemblage of Soil Diazotrophs and Root Arbuscular Mycorrhizal Fungi

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

Biogeographic Pattern and Network of Rhizosphere Fungal and Bacterial Communities in Panicum miliaceum Fields: Roles of Abundant and Rare Taxa

Unraveling how microbial interactions and assembly process regulate the rhizosphere abundant and rare taxa is crucial for determining how species diversity affects rhizosphere microbiological functions. We assessed the rare and abundant taxa of rhizosphere fungal and bacterial communities in proso millet agroecosystems to explore their biogeographic patterns and co-occurrence patterns based on a regional scale. The taxonomic composition was significantly distinct between the fungal and bacterial abundant and rare taxa. Additionally, the rare taxa of bacteria and fungi exhibited higher diversity and stronger phylogenetic clustering than those of the abundant ones. The phylogenetic turnover rate of abundant taxa of bacteria was smaller than that of rare ones, whereas that of fungi had the opposite trend. Environmental variables, particularly mean annual temperature (MAT) and soil pH, were the crucial factors of community structure in the rare and abundant taxa. Furthermore, a deterministic process was relatively more important in governing the assembly of abundant and rare taxa. Our network analysis suggested that rare taxa of fungi and bacteria were located at the core of maintaining ecosystem functions. Interestingly, MAT and pH were also the important drivers controlling the main modules of abundant and rare taxa. Altogether, these observations revealed that rare and abundant taxa of fungal and bacterial communities showed obvious differences in biogeographic distribution, which were based on the dynamic interactions between assembly processes and co-occurrence networks.

Soil diazotrophic abundance, diversity, and community assembly mechanisms significantly differ between glacier riparian wetlands and their adjacent alpine meadows

Global warming can trigger dramatic glacier area shrinkage and change the flux of glacial runoff, leading to the expansion and subsequent retreat of riparian wetlands. This elicits the interconversion of riparian wetlands and their adjacent ecosystems (e.g., alpine meadows), probably significantly impacting ecosystem nitrogen input by changing soil diazotrophic communities. However, the soil diazotrophic community differences between glacial riparian wetlands and their adjacent ecosystems remain largely unexplored. Here, soils were collected from riparian wetlands and their adjacent alpine meadows at six locations from glacier foreland to lake mouth along a typical Tibetan glacial river in the Namtso watershed. The abundance and diversity of soil diazotrophs were determined by real-time PCR and amplicon sequencing based on nifH gene. The soil diazotrophic community assembly mechanisms were analyzed via iCAMP, a recently developed null model-based method. The results showed that compared with the riparian wetlands, the abundance and diversity of the diazotrophs in the alpine meadow soils significantly decreased. The soil diazotrophic community profiles also significantly differed between the riparian wetlands and alpine meadows. For example, compared with the alpine meadows, the relative abundance of chemoheterotrophic and sulfate-respiration diazotrophs was significantly higher in the riparian wetland soils. In contrast, the diazotrophs related to ureolysis, photoautotrophy, and denitrification were significantly enriched in the alpine meadow soils. The iCAMP analysis showed that the assembly of soil diazotrophic community was mainly controlled by drift and dispersal limitation. Compared with the riparian wetlands, the assembly of the alpine meadow soil diazotrophic community was more affected by dispersal limitation and homogeneous selection. These findings suggest that the conversion of riparian wetlands and alpine meadows can significantly alter soil diazotrophic community and probably the ecosystem nitrogen input mechanisms, highlighting the enormous effects of climate change on alpine ecosystems.

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.

Compositional and Metabolic Responses of Autotrophic Microbial Community to Salinity in Lacustrine Environments

The compositional and physiological responses of autotrophic microbiotas to salinity in lakes remain unclear. In this study, the community composition and carbon fixation pathways of autotrophic microorganisms in lacustrine sediments with a salinity gradient (82.6 g/L to 0.54 g/L) were investigated by using metagenomic analysis. A total of 117 metagenome-assembled genomes (MAGs) with carbon fixation potentially belonging to 20 phyla were obtained. The abundance of these potential autotrophs increased significantly with decreasing salinity, and the variation of sediment autotrophic microbial communities was mainly affected by salinity, pH, and total organic carbon. Notably, along the decreasing salinity gradient, the dominant lineage shifted from Desulfobacterota to Proteobacteria. Meanwhile, the dominant carbon fixation pathway shifted from the Wood-Lungdahl pathway to the less-energy-efficient Calvin-Benson-Bassham cycle, with glycolysis shifting from the Embden-Meyerhof-Parnas pathway to the less-exergonic Entner-Doudoroff pathway. These results suggest that the physiological efficiency of autotrophic microorganisms decreased when the environmental salinity became lower. Metabolic inference of these MAGs revealed that carbon fixation may be coupled to the oxidation of reduced sulfur compounds and ferrous iron, dissimilatory nitrate reduction at low salinity, and dissimilatory sulfate reduction in hypersaline sediments. These results extend our understanding of metabolic versatility and niche diversity of autotrophic microorganisms in saline environments and shed light on the response of autotrophic microbiomes to salinity. These findings are of great significance for understanding the impact of desalination caused by climate warming on the carbon cycle of saline lake ecosystems.

IMPORTANCE The Qinghai-Tibetan lakes are experiencing water increase and salinity decrease due to climate warming. However, little is known about how the salinity decrease will affect the composition of autotrophic microbial populations and their carbon fixation pathways. In this study, we used genome-resolved metagenomics to interpret the dynamic changes in the autotrophic microbial community and metabolic pathways along a salinity gradient. The results showed that desalination drove the shift of the dominant microbial lineage from Desulfobacterota to Proteobacteria, enriched autotrophs with lower physiological efficiency pathways, and enhanced coupling between the carbon cycle and other element cycles. These results can predict the future response of microbial communities to lake desalination and improve our understanding of the effect of climate warming on the carbon cycle in saline aquatic ecosystems.

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.

Soil Microbial Community Varied with Vegetation Types on a Small Regional Scale of the Qilian Mountains

Clarifying the response of soil microbial communities to the change of different vegetation types on a small regional scale is of great significance for understanding the sustainability of grassland development. However, the distribution patterns and driving factors of the microbial community are not well understood in the Qilian Mountains. Therefore, we characterized and compared the soil microbial communities underlying the four vegetation types in a national natural reserve (reseeded grassland, swamp meadow, steppe meadow, and cultivated grassland) using high-throughput sequencing of the 16S rRNA and ITS. Meanwhile, the plant community and soil physicochemical characteristics were also determined. The results showed that bacterial and fungal communities in all vegetation types had the same dominant species, but the relative abundance differed substantially, which caused significant spatial heterogeneities on the small regional scale. Specifically, bacteria showed higher variability among different vegetation types than fungi, among which the bacterial and fungal communities were more sensitive to the changes in soil than to plant characteristics. Furthermore, soil organic carbon affected the widest portion of the microbial community, nitrate-nitrogen was the main factor affecting bacteria, and aboveground plant biomass was the main factor affecting fungi. Collectively, these results demonstrate the value of considering multiple small regional spatial scales when studying the relationship between the soil microbial community and environmental characteristics. Our study may have important implications for grassland management following natural disturbances or human alterations.

Effects of Underground Coal Mining on Soil Spatial Water Content Distribution and Plant Growth Type in Northwest China

The impact of coal mining subsidence on surface ecology involves the influence of several ecological elements such as water, soil, and vegetation, which is systematic and complex. Given the unclear understanding of the synergistic change patterns of the water-soil-vegetation ecological elements in the influence of coal mining in the west, this paper investigates the impact of coal mining on the surface ecology, especially the distribution of soil water content (SWC). In 2020, this study collected 3000 soil samples from 60 sampling points (at depth of 0-10 m) and tested the SWC. All samples come from three different temporal and spatial areas of coal mining subsidence in the desert mining area of Northwest China where soil types are mainly aridisols. At the same time, the interactions among deep SWC and surface soil physical and chemical properties, surface SWC and soil fertility, and pH were analyzed. The spatial variability of soil moisture is reflected by kriging interpolation, and SWC values at different depths are predicted as a basis for monitoring the environmental impact of different coal mining subsidence years. The research has shown that the ground subsidence leads to a decrease in SWC value and changes in surface soil pH, physical and chemical properties, and covering vegetation, which have occurred from the beginning of coal mining. The impact of coal mining on the SWC of the unsaturated zone is mainly at the depth of 0-6 m, where SWC is not directly related to the nutrient content of the surface soil. The overall settlement of the ground will stir up simultaneous decline in the quality of deep SWC and topsoil. The findings of this investigation suggest that changes in the soil structure caused by coal mining subsidence are the key factor in SWC loss. Timely monitoring and repairing 0-6 m ground fissures, as well as selecting shrubs on the surface is the best choice for the restoration of the ecological environment and prevention of soil erosion in this area.

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.

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.

Mobilization of soil phosphate after 8 years of warming is linked to plant phosphorus-acquisition strategies in an alpine meadow on the Qinghai-Tibetan Plateau

Phosphorus (P) is essential for productivity of alpine grassland ecosystems, which are sensitive to global warming. We tested the hypotheses that (1) mobilized 'calcium-bound inorganic P' (Ca-P_i ) is a major source of plant-available P in alpine meadows with alkaline soils after long-term warming, (2) mobilization of Ca-P_i is linked to effective plant carboxylate-releasing P-acquisition strategies under warming, and (3) the mobilization is also related to plant nitrogen (N)-acquisition. We conducted an 8-year warming experiment in an alpine meadow (4635 m above sea level) on the Qinghai-Tibetan Plateau. A significant increase in P concentration in both aboveground and belowground biomass indicates an increased mobilization and assimilation of P by plants under warming. We observed a significant decrease in Ca-P_i , no change in moderately-labile organic P, and an increase in highly resistant organic P after warming. There was no increase in phosphatase activities. Our results indicate that Ca-P_i , rather than organic P was the major source of plant-available P for alpine meadows under warming. Higher leaf manganese concentrations of sedges and forbs after warming indicate that carboxylates released by these plants are a key mechanism of Ca-P_i mobilization. The insignificant increase in Rhizobiales after warming and the very small cover of legumes show a minor role of N-acquisition strategies in solubilizing phosphate. The insignificant change in relative abundance of mycorrhizal fungi and bacteria related to P cycling after warming shows a small contribution of microorganisms to Ca-P_i mobilization. The significant increase in leaf N and P concentrations and N:P ratio of grasses and no change in sedge leaf N:P ratio reflect distinct responses of plant nutrient status to warming due to differences in P-acquisition strategies. We highlight the important effects of belowground P-acquisition strategies, especially plant carboxylate-releasing P-acquisition strategies on responses of plants to global changes in alpine meadows.

Using molecular detection for the diversity and occurrence of cyanobacteria and 2-methylisoborneol-producing cyanobacteria in an eutrophicated reservoir in northern China

Aquatic ecosystems and drinking water supply systems worldwide are increasingly affected by taste and odor episodes. In this study, molecular approaches including next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) were used to study the diversity and dynamics of cyanobacteria and 2-methylisoborneol (2-MIB)-producing cyanobacteria in Yuqiao Reservoir, a eutrophicated drinking water reservoir in Tianjin city, northern China. NGS revealed that the entire cyanobacterial community consisted of 16 genera, with Planktothrix (28.8%), Pseudanabaena (18.4%), Cylindrospermosis (7.8%), and Microcystis (7.6%) being the dominant genera, while microscopic examination identified only eight cyanobacterial genera. NGS of the 2-MIB synthesis gene revealed that Pseudanabaena and Planktothricoides were the main 2-MIB producers, with Pseudanabaena being dominant. This finding demonstrated that NGS can identify 2-MIB producers quickly and accurately and it can thus play an important role in the practical monitoring of aquatic ecology. The qPCR test showed 2-MIB synthesis gene with 4.27 × 10⁶ copies/L to 2.24 × 10⁹copies/L occurring at the three sampling sites. The mic gene copy number increased before the 2-MIB concentration increased, indicating that forecasting role in dealing with the 2-MIB concentration by gene copy number. Predicting 2-MIB by qPCR in the field must be verified with additional studies. The combination of NGS and qPCR can be an even more comprehensive method to provide early warning information to managers of reservoirs and water utilities facing taste and odor incidents. This is the first amplicon NGS dataset based on 2-MIB gene to study the diversity and dynamics of 2-MIB-producing cyanobacteria.

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.

Nutrients available in the soil regulate the changes of soil microbial community alongside degradation of alpine meadows in the northeast of the Qinghai-Tibet Plateau

The alpine meadow in the Qinghai-Tibet Plateau has been seriously degraded due to human activities and climate change in recent decades. Understanding the changes of the soil microbial community in response to the degradation process helps reveal the mechanism underlying the degradation process of alpine meadows. We surveyed and analyzed changes of the vegetation, soil physicochemical properties, and soil microbial community in three degradation levels, namely, non-degradation (ND), moderate degradation (MD), and severe degradation (SD), of the alpine meadows in the northeastern Qinghai-Tibet Plateau. We found that as the level of degradation increased, plant cover, plant density (PD), above-ground biomass (AGB), plant Shannon-Wiener index (PS), soil water content (SWC), soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), total potassium (TK), available nitrogen (AN), available phosphorus (AP), and available potassium (AK) decreased significantly, while the soil pH increased from 7.20 to 8.57. Alpine meadow degradation significantly changed the composition of soil bacterial and fungal communities but had no significant impact on the diversity of the microbial communities. Functional predictions indicated that meadow degradation increased the relative abundances of aerobic_chemoheterotrophy, undefined_saprotroph, and plant_pathogen, likely increasing the risk of plant diseases. Redundancy analysis revealed that in ND, the soil microbial community was mainly regulated by PS, PH, PD, SWC, and soil pH. In MD, the soil microbial community was regulated by the soil's available nutrients and SOC. In SD, the soil microbial community was not only regulated by the soil's available nutrients but also influenced by plant characteristics. These results indicate that during alpine meadow degradation, while the changes in the plants and soil environmental factors both affect the composition of the soil microbial community, the influence of soil factors is greater. The soil's available nutrients are the main driving factors regulating the change in the soil microbial community's composition alongside degradation levels.

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.

Succession of diazotroph community and functional gene response to inoculating swine manure compost with a lignocellulose-degrading consortium

Diazotroph community contributes to the nitrogen mass and improves the agronomic quality of composting product, but their responses to microbial inoculation during composting are unclear. In this study, the lignocellulose-degrading consortium was inoculated at different levels (0%: CK (control) and 10%: T) to investigate their effects on the variations in the diazotroph community and functional gene during composting. In the later composting phase, the nifH gene copy number was 17.50-25.28% higher in T than CK. The nitrogenase abundance in CK and T were 0.042% and 0.046% in composting product, respectively. Network analysis indicated that inoculation affected the co-occurrence patterns of the diazotroph community and changed the keystone species composition. Partial least-squares path modeling showed that available carbon sources and the succession of the diazotroph community mainly determined the increased abundance of nifH gene. Microbial inoculation stimulated the diazotrophs activities, and was conducive to the nitrogen production in composting product.

Variation, distribution, and diversity of canonical ammonia-oxidizing microorganisms and complete-nitrifying bacteria in highly contaminated ecological restoration regions in the Siding mine area

Canonical ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete-nitrifying bacteria (comammox) exist in a variety of ecosystems. However, little is known about AOA, AOB and comammox or their contributions to nitrification in the soils of heavily degraded and acidic mine regions. In the present study, the activity, richness, diversity and distribution patterns of AOA, AOB and comammox in the Siding mine area were investigated. Nemerow's multifactor pollution index (P_N) values indicated that the soil in all three areas in the Siding mine area was highly contaminated by Cd, Pb, Zn, Mn and Cu. The AOA, AOB and comammox amoA gene copy numbers exhibited significant positive correlations with Pb and Zn levels and P_N values, which indicated that the populations of AOA, AOB and comammox underwent adaptation and reproduction in response to pollution from multiple metals in the Siding mine area. Among them, the abundance of AOA was the highest, and AOA may survive better than AOB and comammox under such severely pollution-stressed and ammonia-limited conditions. The phyla Thaumarchaeota and Crenarchaeota may play vital roles in the soil ammonia oxidation process. Unlike AOA, AOB may use soil available phosphorus to help them compete for NH₃ and other limiting nutrients with AOA and heterotrophs. Moreover, soil organic matter was the main factor influencing the species diversity of AOB, the β-diversity of AOB and comammox, and the community composition of AOA, AOB and comammox. Our research will help to explain the role and importance of AOA, AOB and comammox in the different ecological restoration regions in the Siding mine area.

Different tillage practices change assembly, composition, and co-occurrence patterns of wheat rhizosphere diazotrophs

Tillage has a considerable effect on the soil ecosystem and its services, including microbial communities. Harnessing beneficial microbes is a sustainable way to optimizing crop management and agricultural production. Although diazotrophs play a major role in global biological nitrogen fixation, the effects of tillage on diazotrophic communities in the rhizosphere are not fully understood. In the present study, we investigated the diazotrophic community in wheat rhizosphere soil under different tillage treatments in a long-term experiment, i.e., plow tillage (considered as conventional tillage), chisel plow tillage (considered as conservation tillage), and zero tillage (considered as conservation tillage). Tillage led to a divergent distribution in the rhizosphere diazotrophic community and significant changes in community structure. Tillage caused specific responses from members/modules of the rhizosphere diazotrophic community co-occurrence network, and the relative abundance of keystone taxa was higher under conservation tillage than under conventional tillage. The increased abundance of tillage-sensitive modules under conservation tillage had a broad and significant positive correlation with rhizosphere nutrient availability, whereas the opposite was true for conventional tillage. Differences in nutrients under different tillage practices may lead to different assembly processes of diazotrophs. Overall, our findings indicate that tillage significantly affects the assembly and composition of the rhizosphere diazotrophic community, emphasizing the importance of improved substrate availability for rhizosphere diazotrophic modules under conservation tillage. This knowledge could deepen our understanding of the rhizosphere functional microbial community (e.g., biological nitrogen fixation).

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.

The composition of antibiotic resistance genes is not affected by grazing but is determined by microorganisms in grassland soils

Grazing is expected to exert a substantial influence on antibiotic resistance genes (ARGs) in grassland ecosystems. However, the precise effects of grazing on the composition of ARGs in grassland soils remain unclear. This is especially the case for grassland soils subject to long-term grazing. Here, we investigated ARGs and bacterial community composition in soils subject to long-term historic grazing (13-39 years) and corresponding ungrazed samples. Using a combination of shotgun metagenomics, amplicon analyses and associated soil physicochemical data, we provide novel insights regarding the structure of ARGs in grassland soils. Interestingly, our analysis revealed that long-term historic grazing had no impacts on the composition of ARGs in grassland soils. An average of 378 ARGs, conferring resistance to 14 major categories of antibiotics (80%), were identified in both grazing and ungrazed sites. Actinobacteria, Proteobacteria and Acidobacteria were the most prevalent predicted hosts in these soils and were also shown to harbour genetic capacity for multiple-resistant ARGs. Our results suggested that positive effects of bacterial community composition on ARGs could potentially be controlled by affecting MGEs. Soil properties had direct effects on the composition of ARGs through affecting the frequency of horizontal gene transfer among bacteria. Twelve novel ARGs were found in S. grandis steppe grasslands, indicating that different vegetation types might induce shifts in soil ARGs. Collectively, these findings suggest that soil properties, plants and microorganisms play critical roles in shaping ARG patterns in grasslands. Together, these data establish a solid baseline for understanding environmental antibiotic resistance in grasslands.

Depression of soil nitrogen fixation by drying soil in a degraded alpine peatland

Soil biological nitrogen fixation (BNF) represents a major pathway through which nitrogen enters pristine peatlands. Many peatlands have been undergoing human-induced changes in environmental factors, while environmental changes dramatically affect the community composition and activity of nitrogen-fixing prokaryotes (i.e., diazotrophs). However, the impact of peatland degradation on soil BNF remains unclear. By carrying out a field campaign, we examined how soil BNF varies along a natural gradient from pristine marshes to moderately-degraded meadows and sandy meadows on the Zoige Plateau. Plant and topsoil samples from four pristine marshes, three moderately-degraded meadows, and three sandy meadows were collected to determine the potential rate of nitrogen fixation (R_Nfix), abundance of the nifH gene, diazotrophic community composition, and soil and plant characteristics. Our results showed that topsoil R_Nfix varied in the range 0.018-3.00 μmol N g d.w.^-1 day^-1 (i.e. 21.74-1632.37 mg N m^-2 day^-1) across the ten sites, being lowest in sandy meadows and highest in pristine marshes. Topsoil R_Nfix and diazotrophic abundance were positively correlated with soil water content, sedge cover, plant biomass, soil organic carbon content, and total nitrogen and phosphorus contents. Soil water content, which affected most plant and soil characteristics, had dominant influences on the abundance and community structure of diazotrophs. The R_Nfix was closely correlated with the abundance of dominant diazotroph groups. The community composition of diazotrophs differed markedly among sites of different degradation levels. Proteobacteria was the most abundant diazotrophic phylum across the ten sites. Heterotrophic diazotrophs acted as the major contributor to BNF, especially in pristine marshes and moderately-degraded meadows. We conclude that soil water content was the main factor driving the depressed soil BNF during peatland degradation in Zoige, due to soil water effects on plant cover and biomass, soil organic carbon and total phosphorus, and the abundance and community structure of diazotrophs.

Ridge Tillage Improves Soil Properties, Sustains Diazotrophic Communities, and Enhances Extensively Cooperative Interactions Among Diazotrophs in a Clay Loam Soil

Reduced tillage practices [such as ridge tillage (RT)] have been potential solutions to the weed pressures of long-term no tillage (NT) and the soil-intensive disturbances caused by conventional tillage [such as moldboard plow (MP) tillage]. Although soil diazotrophs are significantly important in global nitrogen (N) cycling and contribute to the pool of plant-available N in agroecosystems, little is currently known about the responses of diazotrophic communities to different long-term tillage practices. In the current study, we investigated the differences among the effects of NT, RT, and MP on soil properties, diazotrophic communities, and co-occurrence network patterns in bulk and rhizosphere soils under soybean grown in clay loam soil of Northeast China. The results showed that RT and MP led to higher contents of total C, N, and available K compared to NT in both bulk and rhizosphere soils, and RT resulted in higher soybean yield than NT and MP. Compared to NT and RT, MP decreased the relative abundances of free-living diazotrophs, while it promoted the growth of copiotrophic diazotrophs. Little differences of diazotrophic community diversity, composition, and community structure were detected between RT and NT, but MP obviously decreased diazotrophic diversity and changed the diazotrophic communities in contrast to NT and RT in bulk soils. Soil nitrogenous nutrients had negative correlations with diazotrophic diversity and significantly influenced the diazotrophic community structure. Across all diazotrophs' networks, the major diazotrophic interactions transformed into a cooperatively dominated network under RT, with more intense and efficient interactions among species than NT and MP. Overall, our study suggested that RT, with minor soil disturbances, could stabilize diazotrophic diversity and communities as NT and possessed highly positive interactions among diazotrophic species relative to NT and MP.

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

Biological nitrogen fixation plays an important role in nitrogen cycling by transferring atmospheric N2 to plant-available N in the soil. However, the diazotrophic activity and distribution in different types of soils remain to be further explored. In this study, 152 upland soils were sampled to examine the diazotrophic abundance, nitrogenase activity, diversity and community composition by quantitative polymerase chain reaction, acetylene reduction assay and the MiSeq sequencing of nifH genes, respectively. The results showed that diazotrophic abundance and nitrogenase activity varied among the three soil types. The diazotrophic community was mainly dominated by Bradyrhizobium, Azospirillum, Myxobacter, Desulfovibrio and Methylobacterium. The symbiotic diazotroph Bradyrhizobium was widely distributed among soils, while the distribution of free-living diazotrophs showed large variation and was greatly affected by multiple factors. Crop type and soil properties directly affected the diazotrophic ɑ-diversity, while soil properties, climatic factors and spatial distance together influenced the diazotrophic community. Network structures were completely different among all three types of soils, with most complex interactions observed in the Red soil. These findings suggest that diazotrophs have various activities and distributions in the three soil types, which played different roles in nitrogen input in agricultural soil in China, being driven by multiple environmental factors.

Nitrogen fertilizer and Amorpha fruticosa leguminous shrub diversely affect the diazotroph communities in an artificial forage grassland

Soil diazotrophs have been known to be essential in biological nitrogen (N) fixation, which contributes to the sustainability of agricultural ecosystems. However, there remains an inadequacy of research on the effects of different N inputs from N fertilization and from symbiotic N fixation associated with legumes on the diazotroph communities in agricultural ecosystems. Hence, we investigated the variations in diazotroph abundance and community composition as well as the soil properties with different N inputs in the Guimu-1 hybrid elephant grass cultivation on karst soils in China. We conducted six different N treatments: control, Amorpha fruticosa planting at a spacing of 1.5 × 2 m (AFD1), A. fruticosa planting at a spacing of 1 × 2 m (AFD2), N fertilization (N), A. fruticosa planting at a spacing of 1.5 × 2 m with N fertilization (AFD1N), and A. fruticosa planting at a spacing of 1 × 2 m with N fertilization (AFD2N). Our results showed that the interaction between sampling time and N fertilization significantly affected the diazotroph abundance. In July, the diazotroph abundance significantly decreased in the N fertilization treatments: N, AFD1N, and AFD2N, compared to that in the control. The richness and Chao1 estimator of diazotrophs significantly increased in AFD2N and AFD1 correspondingly in December and July, relative to those in the control. Co-occurrence networks showed species-species interactions with high negative correlations that occurred more in the control than in the N input plots. The N input from N fertilization and legume planting directly increased the ammonium N and nitrate N and consequently affected the dissolved organic N and pH of the soil, thereby altering the diazotroph abundance and richness. Our findings demonstrated that both N fertilization and legumes could reduce the interspecific competition among diazotroph species by providing greater N availability in the forage grass.

Insight to key diazotrophic community during composting of dairy manure with biochar and its role in nitrogen transformation

Analyzing diazotrophic community may help to understand nitrogen transformation in composting and improves the final compost quality. In this study, diazotrophic community dynamics were investigated in terms of nifH gene during dairy manure and corn straw composting with biochar addition using high-throughput sequencing. Biochar decreased the diversity of diazotrophic community and altered diazotroph community structure during composting. At phylum level, Proteobacteria, Actinobacteria and Firmicutes were dominant diazotrophic communities throughout composting process. Biochar addition registered higher correlation coefficient (R) between physicochemical factors (temperature, ammonium (NH₄⁺-N) and nitrate (NO₃^--N)) and diazotroph community composition. Rhodopseudomonas and Pseudoxanthomonas was the key diazotrophic communities influencing NH₄⁺-N transformation in control (CK) and biochar compost (BC), respectively, while for NO₃^--N transformation Clostridium and Bradyrhizobium in CK, Azospira and Methylocystis in BC served as predominant factors. These results indicated that addition of biochar altered the key diazotroph communities influencing nitrogen transformation. Furthermore, some diazotrophs (e.g. Rhodopseudomonas, Bradyrhizobium and Azospira) affecting NH₄⁺-N and NO₃^--N transformation were also observed to be mediating total nitrogen (TN). Interestingly, interactions between diazotrophic communities were observed and these interactions could also influence nitrogen transformation.

Effects of different legume species and densities on arbuscular mycorrhizal fungal communities in a karst grassland ecosystem

Legumes can increase nitrogen (N) input to soil via N₂ fixation, and arbuscular mycorrhizal fungi (AMF) can colonize legumes, which further promotes the acquisition of nutrients such as phosphorus (P). Nevertheless, little is known about how different legume species or planting densities affect soil AMF communities. We measured soil AMF abundance, diversity, and community composition in two legume species that had been planted at two densities in a karst grassland. Five treatments were used: control (CK), Amorpha fruticosa at 1.5 × 2 m density (AFD1), A. fruticosa at 1 × 1 m density (AFD2), Indigofera atropurpurea at 1.5 × 2 m density (IAD1), and I. atropurpurea at 1 × 1 m density (IAD2). The results showed that A. fruticosa plots were significantly richer in Redeckera spp., while I. atropurpurea plots were richer in Septoglomus. AMF abundance in AFD1, AFD2, and IAD1 was significantly higher than in CK, but AMF abundance in IAD2 was significantly lower than that in the other treatments. AMF richness and Chao1 estimator in AFD1 were significantly higher than in CK. Funneliformis, Septoglomus, and Acaulospora were significantly more abundant in IAD2 than in the other treatments. The interaction between legume species and density had a significant effect on AMF abundance and community composition. AMF abundance and diversity were significantly negatively and positively correlated with available P and microbial biomass N, respectively. These results suggest that different species and densities of legumes may increase available N, which could improve AMF abundance and alleviate soil P deficiencies. Planting A. fruticosa or I. atropurpurea at a low density may be an effective method to increase AMF colonization of roots, and thus, nutrient transport in karst grasslands.

Dairy soil bacterial responses to nitrogen application in simulated Italian ryegrass and white clover pasture

Through clearing and use of fertilizer and legumes, areas of southwestern Australia's unique coastal sand plains can support relatively low-cost dairies. However, the ancient, highly weathered nature of the soils in this region makes the dairies susceptible to a range of threats, including nutrient leaching and erosion. Despite this, Western Australian dairy cows typically produce up to 5,500 L of milk per head annually supported by inorganic nitrogen (N) fertilizer (commonly 50:50 urea and ammonium sulfate) at rates up to <320 kg of N/ha per year. Where hotspots exist (up to 2,000 kg of N/ha per year), total N exceeds pasture requirements. We investigated plant and soil bacteria responses to N fertilizer rates consistent with Australian legislated production practices on dairy farms for pure and mixed swards of white clover (Trifolium repens) and Italian ryegrass (Lolium multiflorum) in a long-term pasture experiment in controlled glasshouse conditions. Although the soil bacterial community structure at phylum level was similar for white clover and Italian ryegrass, relative abundances of specific subgroups of bacteria differed among plant species according to the N fertilizer regimen. Marked increases in relative abundance of some bacterial phyla and subphyla indicated potential inhibition of N cycling, especially for N hotspots in soil. Ammonium concentration in soil was less correlated with dominance of some N-cycling bacterial phyla than was nitrate concentration. Changes in bacterial community structure related to altered nutrient cycling highlight the potential for considering this area of research in policy assessment frameworks related to nutrient loads in dairy soils, especially for N.

Upland Soil Cluster Gamma dominates methanotrophic communities in upland grassland soils

Aerobic methanotrophs in upland soils consume atmospheric methane, serving as a critical counterbalance to global warming; however, the biogeographic distribution patterns of their abundance and community composition are poorly understood, especial at a large scale. In this study, soils were sampled from 30 grasslands across >2000 km on the Qinghai-Tibetan Plateau to determine the distribution patterns of methanotrophs and their driving factors at a regional scale. Methanotroph abundance and community composition were analyzed using quantitative PCR and Illumina Miseq sequencing of pmoA genes, respectively. The pmoA gene copies ranged from 8.2 × 10⁵ to 1.1 × 10⁸ per gram dry soil. Among the 30 grassland soil samples, Upland Soil Cluster Gamma (USCγ) dominated the methanotroph communities in 26 samples. Jasper Ridge Cluster (JR3) was the most dominant methanotrophic cluster in two samples; while Methylocystis, cluster FWs, and Methylobacter were abundant in other two wet soil samples. Interestingly, reanalyzing the pmoA genes sequencing data from existing publications suggested that USCγ was also the main methanotrophic cluster in grassland soils in other regions, especially when their mean annual precipitation was <500 mm. Canonical Analysis of Principal Coordinates including all soil samples indicated that the methanotrophic community composition was significantly correlated with local environmental factors, among which mean annual precipitation and pH showed the strongest correlations. Variance partitioning analysis showed that environmental factors and spatial distance were significant factors affecting the community structure of methanotrophs, and environmental properties were more important factors. Collectively, these findings indicate that atmospheric methane may be mainly oxidized by USCγ in upland soils. They also highlight the key role of water availability and pH in determining the abundance and community profiles of grassland soil methanotrophs.