Soil Microbial Community Function Research Articles

Soil microbial community structure and functionality changes in response to long‐term metal and radionuclide pollution

SummaryMicrobial communities are essential for a healthy soil ecosystem. Metals and radionuclides can exert a persistent pressure on the soil microbial community. However, little is known on the effect of long‐term co‐contamination of metals and radionuclides on the microbial community structure and functionality. We investigated the impact of historical discharges of the phosphate and nuclear industry on the microbial community in the Grote Nete river basin in Belgium. Eight locations were sampled along a transect to the river edge and one location further in the field. Chemical analysis demonstrated a metal and radionuclide contamination gradient and revealed a distinct clustering of the locations based on all metadata. Moreover, a relation between the chemical parameters and the bacterial community structure was demonstrated. Although no difference in biomass was observed between locations, cultivation‐dependent experiments showed that communities from contaminated locations survived better on singular metals than communities from control locations. Furthermore, nitrification, a key soil ecosystem process seemed affected in contaminated locations when combining metadata with microbial profiling. These results indicate that long‐term metal and radionuclide pollution impacts the microbial community structure and functionality and provides important fundamental insights into microbial community dynamics in co‐metal‐radionuclide contaminated sites.

Rhizosphere response to predicted vegetation shifts in boreal forest floors

The boreal forest is the single largest terrestrial store of carbon on Earth, and approximately 25% of these carbon stocks are in the forest floor. Climate change is expected to alter boreal vegetation, and aspen-dominated stands will replace conifers in Western Canada. We investigated how these vegetation shifts could affect the composition and function of soil microbial communities, using forest floor samples from the Ecosystem Management Emulating Natural Disturbance (EMEND) project in northwestern Alberta, Canada. Soil microbial communities were surveyed in rhizosphere and bulk forest floor of 17-year-old spruce clear-cuts where aspen was naturally regenerating, mature stands of aspen and spruce, and 17-year-old clear-cuts of aspen. Phospholipid fatty acid (PLFA) analysis was used to characterize microbial community composition and multiple substrate induced respiration (MSIR) to quantify microbial community functional capacity. Carbon source utilization by microorganisms was investigated through natural abundance isotope analysis of individual PLFAs. Rhizosphere samples had a significantly higher proportion of fungi and a higher gram-negative to gram-positive bacteria ratio compared to bulk soil. Fungi and gram-negative bacteria biomarkers in the rhizosphere showed 13C depletion compared to bulk forest floor, indicating that they had assimilated more newly-photosynthesized carbon than bulk forest floor microbes. Aspen trees exerted a greater influence over their rhizospheres than spruce trees in terms of microbial community composition and functional capacity, and aspen rhizospheres showed the highest basal respiration. In less than two decades, aspen regeneration in former spruce stands shifted the composition of microbial communities towards that of native aspen stands, with the rhizosphere microbiome responding more quickly than bulk forest floor. This study suggests that predicted vegetation shifts in the boreal have the potential to cause more immediate and profound changes in the rhizosphere, and emphasizes the need to include the rhizosphere in future studies.

Arbuscular Mycorrhiza and Sustainable Agriculture

Arbuscular mycorrhizal fungi (AMF) provide benefits to most crop species via enhanced nutrient uptake, increased drought and abiotic stress resistance, and reduced effects of pathogens and pests. Much remains unclear regarding the specific mechanisms influencing these processes, and the critical roles of AMF are often overlooked in planning agroecological systems. There is growing consensus, however, around the important roles AMF play in improving plant resilience and crop yield while also enhancing the functioning of soil microbial communities. Heterogeneous practices across all scales complicate the successful integration of AMF in agroecological systems. AMF symbioses with crops are passive, or stimulated by incorporation of crop wastes in soil, soil inoculation with AMF spores, or the planting inoculated of seeds. Here we suggest that AMF can have highest beneficial impacts in areas with low levels of agrochemical inputs. We argue that areas with intensive agrochemical inputs can also be made more sustainable with AMF enhancements.

Insights into the Spatiotemporal Differences of Tailings Seepage Pollution by Assessing the Diversity and Metabolic Functions of Soil Microbial Community

Insights into the Spatiotemporal Differences of Tailings Seepage Pollution by Assessing the Diversity and Metabolic Functions of Soil Microbial Community

Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates.

Sequencing PCR‐amplified gene fragments from metagenomic DNA is a widely applied method for studying the diversity and dynamics of soil microbial communities. Typically, DNA is extracted from 0.25 to 1 g of soil. These amounts, however, neglect the heterogeneity of soil present at the scale of soil aggregates and thus ignore a crucial scale for understanding the structure and functionality of soil microbial communities. Here, we show with a nitrogen‐depleted agricultural soil the impact of reducing the amount of soil used for DNA extraction from 250 mg to approx. 1 mg to access spatial information on the prokaryotic community structure, as indicated by 16S rRNA gene amplicon analyses. Furthermore, we demonstrate that individual aggregates from the same soil differ in their prokaryotic community compositions. The analysis of 16S rRNA gene amplicon sequences from individual soil aggregates allowed us, in contrast to 250 mg soil samples, to construct a co‐occurrence network that provides insight into the structure of microbial associations in the studied soil. Two dense clusters were apparent in the network, one dominated by Thaumarchaeota, known to be capable of ammonium oxidation at low N concentrations, and the other by Acidobacteria subgroup 6, representing an oligotrophic lifestyle to obtain energy from SOC. Overall this study demonstrates that DNA obtained from individual soil aggregates provides new insights into how microbial communities are assembled.

Changes in soil microbial community structure and function following degradation in a temperate grassland

Abstract Aims Grassland degradation represents a major challenge in the maintenance of grassland productivity. This process has dramatic impacts on energy flows and soil nutrient dynamics, thus directly or indirectly influencing soil microbes. Here, we aim to (i) examine changes in soil microbial composition, diversity and functionality in response to different levels of grassland degradation (i.e. non-degraded, moderately and severely degraded) in a temperate grassland in Inner Mongolia, and (ii) elucidate biotic and abiotic factors that are responsible for these changes. Methods The composition structure of soil microbial community was determined by high-throughput sequencing. The functionality of bacterial communities was examined using the tool of FAPROTAX, and functional guilds of fungal communities were quantified using the FUNGuild pipeline. Important Findings Grassland degradation significantly decreased soil bacterial diversity but it did not affect fungal diversity. Belowground biomass, soil organic carbon and total nitrogen were positively related to changes in diversity of bacterial community. Grassland degradation significantly increased the relative abundance of Chloroflexi (from 2.48% to 8.40%) and decreased Firmicutes (from 3.62% to 1.08%) of bacterial community. Degradation also significantly increased the relative abundance of Glomeromycota (from 0.17% to 1.53%) and decreased Basidiomycota (from 19.30% to 4.83%) of fungal community. The relative abundance of pathogenic fungi (Didymella and Fusarium) was decreased significantly by degradation. In addition, degradation had a significant impact on putative functionality of soil bacteria related to soil carbon and nitrogen cycling. Our results suggest that soil bacterial community is more sensitive than fungal community in response to degradation in the temperate grassland.

Vegetation richness, species identity and soil nutrients drive the shifts in soil bacterial communities during restoration process.

Soil bacteria play an essential role in functioning of ecosystems and maintaining of biogeochemical cycles. However, little is known about changes in the compositions and functional groups of soil bacterial communities during different restoration stages. The influences of aboveground vegetation and belowground soil properties on soil bacterial communities were also unclear during this process. Here we sequenced the soil bacterial communities in different stages of sand fixation. Sand fixation increased the diversity of the bacterial communities, among which the populations of Actinobacteria, Acidobacteria and Gemmatimonadetes changed significantly. The function prediction showed sand fixation increased Gram-positive and aerobic bacteria. Bacterial structure is significantly correlated with plant richness, coverage and biomass. In particular, we found species identity was an important determinant in structuring bacterial composition. Soil properties were all significantly correlated with soil bacterial community richness and diversity. Fusobacteria was strongly positively correlated with sand, Chloroflexi with total N and Gemmatimonadetes with SOM and total C. It suggested that soil nutrients (TC, TN and SOM) have large consequences for soil bacterial community dissimilarities. These results indicated that vegetation richness, especially species identity, together with improvement in soil nutrients, play key roles in driving the shifts in soil microbial community structure and function during restoration process.

The use of Biolog Eco microplates to compare the effects of sulfuric and nitric acid rain on the metabolic functions of soil microbial communities in a subtropical plantation within the Yangtze River Delta region

China has recently undergone rapid economic development. However, it is the third-largest acid rain region in the world after Europe and North America, and the acid rain problem in the Yangtze River Delta region is particularly serious. Over recent years, the type of acid rain in the Yangtze River Delta region has changed from sulfuric acid rain (SAR) into nitric acid rain (NAR) because of SO2 and NOX emission controls. This has made ecosystems more complicated. In this study, we used Biolog Eco microplates to investigate the impact of simulated SAR and NAR on soil microbial community function over a year, beginning in March 2015. The results showed that the long-term simulated acid rain treatments reduced the average well color development (AWCD) of the carbon sources in soil microbial communities. Secondly, the effects of acid type on the utilization of polymers and amino acids increased in the later stages of the simulated acid rain treatments. Furthermore, the differences in the utilization of carbon sources caused by the simulated acid rain treatments were mainly due to soil microorganism utilization of L-serine, Tween40, D-mannitol, and N-acetyl-D-glucosamine. Finally, the physical and chemical properties of the soil were not significantly correlated with the utilization of the six C groups. Our results suggested that the two types of acid rain had different effects on soil microbial community function. When the type of acid rain changed, the stability of the ecosystem was challenged and the risk of ecosystem disruption greatly increased.

Effects of Elevated CO2 on Tomato (Lycopersicon esculentum Mill.) Growth and Rhizosphere Soil Microbial Community Structure and Functionality

Although elevated CO2 (eCO2) in the atmosphere is one of the main factors influencing climate and ecosystem stability, less research on eCO2 in greenhouse soil systems has been conducted, despite their prevalence. In this article, phospholipid fatty acid (PLFA) profiling, 16S rRNA and Internally Transcribed Spacer (ITS) gene sequencing and high-throughput quantity polymerase chain reactions (HT-qPCRs) for 72 biogeochemical cycling-related genes were used to reveal the comprehensive responses of microbes to 23 days eCO2 fumigation in the soil of a tomato greenhouse. Our results indicated that eCO2 significantly increased microbial biomass (p < 0.05). The fungal community was more susceptible to eCO2 than the bacterial community; the fungal alpha diversity indices decreased significantly under eCO2 (p < 0.05) and the abundance of Ascomycota and its lower level taxa also increased significantly (p < 0.01). The absolute abundance of numerous C, N, P, S and methane cycling related genes increased significantly (p < 0.05) under eCO2. Furthermore, the microbial community structure and function were correlated with certain measured plant characteristics. Hence, the microbial ecosystem of the tomato greenhouse soil system was stimulated under eCO2. These results contribute to a greater understanding of how eCO2 in the atmosphere affects terrestrial ecosystem stability.

Development of microwave-assisted extraction and dispersive liquid–liquid microextraction followed by gas chromatography–mass spectrometry for the determination of organic additives in biodegradable mulch films

Organic additives are extensively used as ingredients in biodegradable mulch films. They are swiftly released into the environment, which may have an ecotoxicological impact on plant growth and development, as well as on soil microbial community abundance and function. Herein, a method based on the application of microwave-assisted extraction (MAE) and dispersive liquid–liquid microextraction (DLLME) was developed to analyze eighty organic additives by gas chromatography-mass spectrometry in poly(butylene adipate terephthalate) (PBAT) biodegradable mulch films. This was a comprehensive study, including the identification of organic additives, optimization of MAE and DLLME methods, analysis of isocyanate conversion, and evaluation of the matrix effect (ME). Under the optimized experimental conditions, this method exhibited excellent detection capabilities for organic additives, except for 5 kinds of isocyanates and their reaction products, with coefficients of determination R2 > 0.999 and lack of fit P > 0.05 in linear regression parameters. A negligible ME was observed. The relative recoveries were 93.0–109.8%, and the repeatability and reproducibility varied within the ranges of 2.06–8.76% and 2.38–10.23%, respectively. The limits of detection and limits of quantitation were 0.0008–0.0586 μg g−1 and 0.003–0.195 μg g−1, respectively. The developed method was further successfully applied to the analysis of organic additives in PBAT biodegradable mulch films from four different manufacturers. Interestingly, the Venn diagram and principal component analysis showed that different manufacturing origins display obvious characteristic differences in the organic additive types and concentrations.

Testosterone amendment alters metabolite profiles of the soil microbial community.

Steroid hormones are prevalent in the environment and have become emerging pollutants, but little is known about their effects on soil microbial community composition and function. In the present study, three representative soils in China were amended with environmentally relevant concentrations of testosterone and responses of soil bacterial community composition and soil function were assessed using high-throughput sequencing and nontargeted metabolomics. Our results showed that testosterone exposure significantly shifted bacterial community structure and metabolic profiles in soils at Ningbo (NB) and Kunming (KM), which may reflect high bioavailability of the hormone. Abundances of several bacterial taxa associated with nutrient cycling were reduced by testosterone and metabolites related to amino acid metabolism were downregulated. A close connection between bacterial taxa and specific metabolites was observed and confirmed by Procrustes tests and a co-occurrence network. These results provide an insight into the effects of steroid hormones on soil microbial community and highlight that nontargeted metabolomics is an effective tool for investigating the impacts of pollutants.

Salinity controls soil microbial community structure and function in coastal estuarine wetlands.

Soil salinity acts as a critical environmental filter on microbial communities, but the consequences for microbial diversity and biogeochemical processes are poorly understood. Here, we characterized soil bacterial communities and microbial functional genes in a coastal estuarine wetland ecosystem across a gradient (~5 km) ranging from oligohaline to hypersaline habitats by applying the PCR-amplified 16S rRNA (rRNA) genes sequencing and microarray-based GeoChip 5.0 respectively. Results showed that saline soils in marine intertidal and supratidal zone exhibited higher bacterial richness and Faith's phylogenetic diversity than that in the freshwater-affected habitats. The relative abundance of taxa assigned to Gammaproteobacteria, Bacteroidetes and Firmicutes was higher with increasing salinity, while those affiliated with Acidobacteria, Chloroflexi and Cyanobacteria were more prevalent in wetland soils with low salinity. The phylogenetic inferences demonstrated the deterministic role of salinity filtering on the bacterial community assembly processes. The abundance of most functional genes involved in carbon degradation and nitrogen cycling correlated negatively with salinity, except for the hzo gene, suggesting a critical role of the anammox process in tidal affected zones. Overall, the salinity filtering effect shapes the soil bacterial community composition, and soil salinity act as a critical inhibitor in the soil biogeochemical processes in estuary ecosystems.

Fungal Community, Not Substrate Quality, Drives Soil Microbial Function in Northeastern U.S. Temperate Forests

Mycorrhizal fungi can affect soil organic matter cycling through several mechanisms including priming, nutrient competition, and direct enzyme production. Differences in nutrient foraging strategies between ectomycorrhizal (EcM) and arbuscular mycorrhizal (AM) fungi produce divergent belowground dynamics: where EcM can take up organic nitrogen and directly break down soil organic matter (SOM) by producing enzymes, AM fungi are limited to scavenging mineral N. EcM-associated tree species also have leaf litter with relatively higher ratios of carbon to nitrogen (C:N), and belowground saprotrophic communities more dominated by fungi. Consequently, free-living microbes in EcM-dominated soils should experience nitrogen limitation, with subsequent increases in enzyme production and decreased carbon use efficiency (CUE). However, the relative importance of the effects of substrate quality and fungal community composition on enzyme production and CUE are unclear. To assess this distinction, we sampled the organic horizon and 10 cm of the mineral horizon in northern temperate forest soils along a gradient of EcM dominance. We characterized fungal community composition by measuring EcM relative abundances from extracted fungal DNA and the fungal to bacterial (F:B) ratios from phospholipid fatty acid (PLFA) analysis. We assessed soil substrate quality as the soil C:N ratio. Soil microbial functions were measured as potential activities of five hydrolytic and two oxidative enzymes, and microbial CUE. We found that the fungal community, represented by either the F:B ratio, EcM relative abundance, or both, affected CUE and six measured enzyme activities, while the C:N ratio affected only oxidative and chitin-targeting extracellular enzyme activities. Our results highlight the use of EcM relative dominance as a predictor of soil microbial community composition and function independent of substrate quality.

Functional and taxonomic diversity of grasshoppers differentially shape above‐ and below‐ground communities and their function

Abstract Herbivores are important drivers in both above‐ and below‐ground ecosystems. Despite their importance, studies of herbivores often focus on the effects of individual species, potentially missing the effects of herbivore diversity. Here we examine how orthopteran herbivore species and functional (i.e. diet) diversity interact with nutrient availability to shape above‐ and below‐ground ecosystems. We stocked six species of grasshoppers (Orthoptera) with two different feeding modes (i.e. grass‐only or grass‐ and forb‐feeders) at varying taxonomic compositions (0, 1 or 6 species) in field enclosures and measured their effects on above‐ground plant biomass, chemistry and richness, as well as below‐ground microbial community composition and function. We treated half the cages with nitrogen fertilizer to examine how herbivore effects may be mitigated by soil nutrient availability. Above‐ground, we predicted that grasshoppers would decrease plant biomass and richness, and increase the %N of the plant community. We also predicted that high diversity cages would have the largest decreases in plant biomass and richness, but these effects would be offset by fertilizer additions. Below‐ground, we predicted that herbivore taxonomic composition and diet would differentially shift soil microbial community composition and function. We also predicted that fertilization would decrease the soil pH and increase nutrient availability creating an interaction with herbivores that leads to shifts below‐ground community composition. We found that grasshoppers decreased plant biomass and richness, and this effect was not dependent on nutrient additions. Contrary to our predictions, we did not see the largest above‐ground changes in high diversity cages. Below‐ground, herbivore diet and fertilization, but not their interaction, shifted bacterial communities. Grasshopper taxonomic composition did not influence bacterial communities. Grasshopper taxonomic composition and diet interacted with fertilizer to increase below‐ground levels of bioavailable C and microbial biomass. Fungal communities did not respond to any treatments. The differing effects of herbivore diet versus taxonomic composition highlight the need for studies that examine multiple diversity metrics when exploring herbivore‐meditated effects on above‐ and below‐ground ecosystems. Combined, our results suggest that bottom‐up and top‐down controls are important factors to consider when studying the composition and function of grassland ecosystems. A free Plain Language Summary can be found within the Supporting Information of this article.

Excessive nitrogen addition accelerates N assimilation and P utilization by enhancing organic carbon decomposition in a Tibetan alpine steppe

High amounts of deposited nitrogen (N) dramatically influence the stability and functions of alpine ecosystems by changing soil microbial community functions, but the mechanism is still unclear. To investigate the impacts of increased N deposition on microbial community functions, a 2-year multilevel N addition (0, 10, 20, 40, 80 and 160 kg N ha−1 year−1) field experiment was set up in an alpine steppe on the Tibetan Plateau. Soil microbial functional genes (GeoChip 4.6), together with soil enzyme activity, soil organic compounds and environmental variables, were used to explore the response of microbial community functions to N additions. The results showed that the N addition rate of 40 kg N ha−1 year−1 was the critical value for soil microbial functional genes in this alpine steppe. A small amount of added N (≤40 kg N ha−1 year−1) had no significant effects on the abundance of microbial functional genes, while high amounts of added N (>40 kg N ha−1 year−1) significantly increased the abundance of soil organic carbon degradation genes. Additionally, the abundance of microbial functional genes associated with NH4+, including ammonification, N fixation and assimilatory nitrate reduction pathways, was significantly increased under high N additions. Further, high N additions also increased soil organic phosphorus utilization, which was indicated by the increase in the abundance of phytase genes and alkaline phosphatase activity. Plant richness, soil NO2−/NH4+ and WSOC/WSON were significantly correlated with the abundance of microbial functional genes, which drove the changes in microbial community functions under N additions. These findings help us to predict that increased N deposition in the future may alter soil microbial functional structure, which will lead to changes in microbially-mediated biogeochemical dynamics in alpine steppes on the Tibetan Plateau and will have extraordinary impacts on microbial C, N and P cycles.

Soil microbial community composition and function are closely associated with soil organic matter chemistry along a latitudinal gradient

Despite the important roles of microorganisms in soil organic matter (SOM) decomposition and nutrient cycling, how their biomass, community composition and function are driven by a joint effect of edaphic and environmental factors at a large spatial scale remains unclear. Moreover, a mechanistic understanding of the associations among microbial communities and SOM chemistry as a key indicator of substrate availability over large spatial scales has been lacking until now. To fill this knowledge gap, we examined how soil microbial community abundance and composition (via phospholipid fatty acid (PLFA) analysis) and function (via enzyme activities and net N mineralization) were associated with the edaphic and environmental factors from six oriental oak (Quercus variabilis) forest sites arranged across a 11° latitudinal gradient in East China. We found strong relationships between SOM chemistry as indicated by 13C nuclear magnetic resonance (NMR) spectroscopy and microbial community composition and function along this gradient. For example, the ratio of fungi to bacteria (F/B) decreased with increasing carboxyl C percentage; the lower abundance of arbuscular mycorrhizal fungi (AMF) and decreased invertase activity in the southern sites were possibly related to higher ratio of alkyl to O alkyl (A/O); urease activity increased with carboxyl C percentage. Microbial biomass (total PLFAs) had positive relationships with urease activity, net N mineralization rate, and soil pH. Mean annual precipitation (MAP) and pH were important for overall microbial community composition. Overall, our results indicate that SOM chemistry is closely related to microbial community composition and function along the latitudinal gradient and should be considered in future studies. Our study contributes to a better prediction of microbial responses to possible substrate changes brought by future environmental changes, which is urgently needed under the context of accelerating global change.

Effects of Soil Microbes on Forest Recovery to Climax Community through the Regulation of Nitrogen Cycling

Microbes, as important regulators of ecosystem processes, play essential roles in ecosystem recovery after disturbances. However, it is not clear how soil microbial communities and functions change and affect forest recovery after clear-cutting. Here, we used metagenome sequencing to systematically analyse the differences in soil microbial community composition, functions, and nitrogen (N) cycling pathways between primary Korean pine forests (PF) and secondary broad-leaved forests (SF) formed after clear-cutting. Our results showed that the dominant phyla of the two forest types were consistent, but the relative abundance of some phyla was significantly different. Meanwhile, at the genus level, the fold-changes of rare genera were larger than the dominant and common genera. The genes related to microbial core metabolic functions, virulence factors, stress response, and defence were significantly enriched in SF. Additionally, based on the relative abundance of functional genes, a schema was proposed to analyse the differences in the whole N cycling processes between the two forest types. In PF, the stronger ammoniation and dissimilatory nitrate reduction (DNRA) and the weaker nitrification provided a genetic explanation for PF dominated by ammonium (NH4+) rather than nitrate (NO3−). In SF, the weaker DNRA, the stronger nitrification and denitrification, the higher soil available phosphorus (AP), and the lower nitrogen to phosphorus ratio (N/P) comprehensively suggested that SF was faced with a greater degree of N limitation. These results offer insights into the potential relationship between soil microbes and forest recovery, and aid in implementing proper forestry management.

Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields

BackgroundPanax notoginseng is a highly valuable medicinal plant. Reduced P. notoginseng yield is a common and serious problem that arises in a continuous cropping system. Variation in the composition and function of soil microbial community is considered the primary cause of yield reduction.MethodsThis study used shotgun metagenomic sequencing approaches to describe the taxonomic and functional features of P. notoginseng rhizosphere microbiome and screen microbial taxa and functional traits related to yields.ResultsAt the family and genus level, a total of 43 families and 45 genera (relative abundance > 0.1%) were obtained, and the correlation with the yield of P. notoginseng was further analyzed. Nitrosomonadaceae, Xanthomonadaceae, Mycobacterium and Arthrobacter that were enriched in soils with higher yields were positively correlated with P. notoginseng yields, thereby suggesting that they might increase yields. Negative correlation coefficients indicated that Xanthobacteraceae, Caulobacteraceae, Oxalobacteraceae, Chitinophagaceae, Sphingomonas, Hyphomicrobium, Variovorax and Phenylobacterium might be detrimental to P. notoginseng growth. A total of 85 functional traits were significantly (P < 0.05) correlated with P. notoginseng yields. Functional traits, likely steroid biosynthesis and MAPK signaling pathway were positively correlated with P. notoginseng yields. In contrast, functional traits, such as bacterial secretion system, ABC transporters, metabolism of xenobiotics by cytochrome P450 and drug metabolism–cytochrome P450, were negatively associated with yields.ConclusionsThis study describes an overview of the rhizosphere microbiome of P. notoginseng with discrepant yields and identifies the taxa and functional traits related to yields. Our results provide valuable information to guide the isolation and culture of potentially beneficial microorganisms and to utilize the power of the microbiome to increase plant yields in a continuous cropping system.

Vertical distributions of soil microbial biomass carbon: a global dataset.

Soil microbial biomass carbon (SMBC) is important in regulating soil organic carbon (SOC) dynamics along soil profiles by mediating the decomposition and formation of SOC. The dataset (VDMBC) is about the vertical distributions of SOC, SMBC, and soil microbial quotient (SMQ = SMBC/SOC) and their relations to environmental factors across five continents. Data were collected from literature, with a total of 289 soil profiles and 1040 observations in different soil layers compiled. The associated environment data collectd include climate, ecosystem types, and edaphic factors. We developed this dataset by searching the Web of Sciene and the China National Knowledge Infrastructure from the year of 1970 to 2019. All the data in this dataset met two creteria: 1) there were at least three mineral soil layers along a soil profile, and 2) SMBC was measured using the fumigation extraction method. The data in tables and texts were obtained from literature directly, and the data in figures were extracted by using the GetData Graph digitizer software version 2.25. When climate and soil properties were not available from publications, we obtainted the data from the World Weather Information Service (https://worldweather.wmo.int/en/home.html) and SoilGrids at a spatial resolution of 250 meters (version 0.5.3, https://soilgrids.org).The units of all the variables were converted to the standard international units or commonly used ones and the values were transformed correspondingly. For example, the value of soil organic matter (SOM) was converted to SOC by using the equation (SOC = SOM × 0.58).This dataset can be used in predicting global SOC changes along soil profiles by using the multi-layer soil carbon models. It can also be used to analyse how soil microbial biomass changes with plant roots as well as the composition, structure, and functions of soil microbial communities along soil profiles at large spatial scales. This dataset offers opportunities to improve our prediction of SOC dynamics under global changes and to advance our understanding of the environmental controls.

Composition and diversity of soil microbial communities in the alpine wetland and alpine forest ecosystems on the Tibetan Plateau

While the composition and diversity of soil microbial communities play a central and essential role in biogeochemical cycling of nutrients, they are known to be shaped by the physical and chemical properties of soils and various environmental factors. This study investigated the composition and diversity of microbial communities in 48 samples of seasonally frozen soils collected from 16 sites in an alpine wetland region (Lhasa River basin) and an alpine forest region (Nyang River basin) on the Tibetan Plateau using high-throughput sequencing that targeted the V3-V4 region of 16S rRNA gene. The dominant soil microbial phyla included Proteobacteria, Acidobacteria, and Actinobacteria in the alpine wetland and alpine forest ecosystems, and no significant difference was observed for their microbial composition. Linear discriminant analysis Effect Size (LEfSe) analysis showed that significant enrichment of Hymenobacteraceae and Cytophagales (belonging to Bacteroidetes) existed in the alpine wetland soils, while the alpine forest soils were enriched with Alphaproteobacteria (belonging to Proteobacteria), suggesting that these species could be potential biomarkers for alpine wetland and alpine forest ecosystems. Results of redundancy analysis (RDA) suggest that the microbial community diversity and abundance in the seasonally frozen soils on the Tibetan Plateau were mainly related to the total potassium in the alpine wetland ecosystem, and available potassium and soil moisture in the alpine forest ecosystem, respectively. In addition, function prediction analysis by Tax4Fun revealed the existence of potential functional pathways involved in human diseases in all soil samples. These results provide insights on the structure and function of soil microbial communities in the alpine wetland and alpine forest ecosystems on the Tibetan Plateau, while the potential risk to human health from the pathogenic microbes in the seasonally frozen soils deserves attention.