The rhizosphere harbors complex microbial communities, whose dynamic associations are considered critical for plant growth and health but remain poorly understood. We constructed co-occurrence ...networks for archaeal, bacterial and fungal communities associated with the rhizosphere and bulk soil of wheat fields on the North China Plain. Rhizosphere co-occurrence networks had fewer nodes, edges, modules and lower density, but maintained more robust structure compared with bulk soil, suggesting that a less complex topology and more stable co-occurrence pattern is a feature for wheat rhizosphere. Bacterial and fungal communities followed a power-law distribution, while the archaeal community did not. Soil pH and microbial diversity were significantly correlated with network size and connectivity in both rhizosphere and bulk soils. Keystone species that played essential roles in network structure were predicted to maintain a flexible generalist metabolism, and had fewer significant correlations with environmental variables, especially in the rhizosphere. These results indicate that distinct microbial co-occurrence patterns exist in wheat rhizosphere, which could be associated with variable agricultural ecosystem properties.
•Rhizosphere co-association networks had low complexity and greater stability.•Microbial diversity was positively correlated with network size and connectivity.•Keystone species were predicted to maintain a flexible generalist metabolism.•Keystone species in the rhizosphere correlated less with environmental variables.
•Livestock manure had stronger impact on N-cycling gene abundances than wheat straw.•AmoA genes were more sensitive to fertilization than other N-cycling genes.•Available P was the most important ...factor affecting the abundance of N-cycling communities.
Long-term agricultural fertilization significantly affects nitrogen cycling in soils. However, there is little information about the response of different functional genes involved in the nitrogen cycle to chemical and organic fertilization, and the key factor influencing the community abundance. We investigated the influence of long-term application of chemical fertilizer (NPK) and combined with wheat straw or livestock manures on the abundance of six nitrogen cycle genes (nifH, archaeal and bacterial amoA, nirS, nirK and nosZ) by quantitative PCR. Compared with non-fertilization treatment, long-term application of NPK fertilizers significantly increased the abundance of nirK, nosZ and bacterial amoA genes but decreased archaeal amoA gene abundance, with no significant effect on the abundance of nifH and nirS genes. Compared with NPK treatment, the application of NPK+organic manure increased the abundance of all the nitrogen-cycling genes while the application of NPK+wheat straw had little effect. The abundance of amoA genes contributed the most to the variations in the abundance of the nitrogen cycling community between different fertilization strategies. Soil available P and total N were the most important factors influencing the abundance of microbial communities involved in the nitrogen cycle. These results indicated that, under the application of chemical fertilizers, the addition of livestock manures had much stronger effects on the abundance of nitrogen cycle genes than the addition of wheat straw, and bacterial and archaeal amoA genes were more sensitive to fertilization than other functional genes.
Nitrogen (N) deposition influences both above- and below-ground communities and influences ecosystem functioning. However it is not clear about direct or indirect interactions among plants, soils and ...microbes in response to nitrogen deposition. In this study, the responses of soil bacterial diversity to N enrichment were investigated at surface (0–10 cm) and sub-surface (10–20 cm) soils in a temperate steppe ecosystem. N addition (>120 kg N ha−1 yr−1) resulted in a significant shift in bacterial community composition and a decrease in bacterial OTU richness in surface soil, but the effect on the sub-surface layer was far less pronounced, even at the highest addition rate (240 kg N ha−1 yr−1). Bacterial OTU richness was significantly correlated with soil and plant characteristics. Hierarchical structural equation modeling showed that soil ammonium availability was responsible for the shift in bacterial richness, whereas the change in bacterial community composition was due to alterations in soil pH and plant composition. These results indicated that N fertilization directly affected soil bacterial richness but indirectly affected bacterial communities through soil acidification and plant community change, indicating distinct controls on soil bacterial diversity and community composition. Our results also suggest that N availability could be a good predictor for the loss of soil bacterial diversity under atmospheric nitrogen deposition.
•N deposition impacts soil bacterial community in grassland.•Different controls on soil bacterial diversity and community composition.•An integrated mechanism of plant–soil–microbe interactions.
Cropping systems have fertilized soils for decades with undetermined consequences for the productivity and functioning of terrestrial ecosystems. One of the critical unknowns is the role of soil ...biodiversity in controlling crop production after decades of fertilization. This knowledge gap limits our capacity to assess how changes in soil biodiversity could alter crop production and soil health in changing environments. Here, we used multitrophic ecological networks to investigate the importance of soil biodiversity, in particular, the biodiversity of key-stone taxa in controlling soil functioning and wheat production in a 35-year field fertilization experiment. We found strong and positive associations between soil functional genes, crop production and the biodiversity of key-stone phylotypes; soils supporting a larger number of key-stone nematode, bacteria and fungi phylotypes yielded the highest wheat production. These key-stone phylotypes were also positively associated with plant growth (phototrophic bacteria, nitrogen fixers) and multiple functional genes related to nutrient cycling. The retrieved information on the genomes clustered with key-stone bacterial phylotypes indicated that the key-stone taxa had higher gene copies of oxidoreductases (participating most biogeochemical cycles of ecosystems and linking to microbial energetics) and 71 essential functional genes associated with carbon, nitrogen, phosphorus, and sulfur cycling. Altogether, our work highlights the fundamental role of the biodiversity of key-stone phylotypes in maintaining soil functioning and crop production after several decades of fertilization, and provides a list of key-stone phylotypes linking to crop production and soil nutrient cycling, which could give science-based guidance for sustainable food production.
Arctic plant communities vary greatly over short distances due to heterogeneities in topography and hydrological conditions across the landscape. Recent evidence suggests substantial changes in ...vegetation including increasing shrub cover and density in the Arctic over the past three decades that may be in response to climate change. We investigated soil microbial biomass, nutrient availability, nitrogen (N) mineralization potential and nitrification potential in four of the principal vegetation-types across the low Arctic: dry heath, birch hummock, tall birch and wet sedge. Soil total carbon (C) and N contents, microbial biomass C, dissolved organic C (DOC) and N (DON), mineral N, and N mineralization potential differed considerably among vegetation-types. Tall birch and wet sedge soils had significantly higher DON, mineral N, and N mineralization potential than birch hummock or dry heath soils. Soil N mineralization potential across all soils was positively correlated with soil available C and N, and negatively correlated with soil total C:N ratios. Nitrification potential was negligible in all soils. These results demonstrate close relationships between soil biogeochemical properties, mineral N supply rates, and vegetation-types across an arctic landscape. Our soil N mineralization data suggest that climate warming may enhance N availability in tall birch soils more than in birch hummock soils, and therefore that increases in shrub densities across the landscape are most likely within and directly around current tall shrub patches.
•We built a correlation network using fungal and bacterial taxa.•Kinless hubs were highly positively correlated with the abundance of functional genes.•SEM results highlighted the positive effect of ...kinless hubs on the functional genes.
Microbial taxa within complex ecological networks can be classified by their universal roles based on their level of connectivity with other taxa. Highly connected taxa within an ecological network (kinless hubs) are theoretically expected to support higher levels of ecosystem functions than less connected taxa (peripherals). Empirical evidence of the role of kinless hubs in regulating the functional potential of soil microbial communities, however, is largely unexplored and poorly understood in agricultural ecosystems. Here, we built a correlation network of fungal and bacterial taxa using a large-scale survey consisting of 243 soil samples across functionally and economically important agricultural ecosystems (wheat and maize); and found that the relative abundance of taxa classified as kinless hubs within the ecological network are positively and significantly correlated with the abundance of functional genes including genes for C fixation, C degradation, C methanol, N cycling, P cycling and S cycling. Structural equation modeling of multiple soil properties further indicated that kinless hubs, but not provincial, connector or peripheral taxa, had direct significant and positive relationships with the abundance of multiple functional genes. Our findings provide novel evidence that the relative abundance of soil taxa classified as kinless hubs within microbial networks are associated with high functional potential, with implications for understanding and managing (through manipulating microbial key species) agricultural ecosystems at a large spatial scale.
The elevational patterns of diversity for plants and animals have been well established over the past century. However, it is unclear whether there is a general elevational distribution pattern for ...microbes. Changbai Mountain is one of few well conserved natural ecosystems, where the vertical distribution of vegetation is known to mirror the vegetation horizontal zonation from temperate to frigid zones on the Eurasian continent. Here, we present a comprehensive analysis of soil bacterial community composition and diversity along six elevations representing six typical vegetation types from forest to alpine tundra using a bar-coded pyrosequencing technique. The bacterial communities differed dramatically along elevations (vegetation types), and the community composition was significantly correlated with soil pH, carbon/nitrogen ratio (C/N), moisture or total organic carbon (TOC), respectively. Phylogenetic diversity was positively correlated with soil pH (P = 0.024), while phylotype richness was positively correlated with soil pH (P = 0.004), total nitrogen (TN) (P = 0.030), and negatively correlated with C/N ratio (P = 0.021). Our results emphasize that pH is a better predictor of soil bacterial elevational distribution and also suggest that vegetation types may indirectly affect soil bacterial elevational distribution through altering soil C and N status.
► We examine soil bacterial distribution along elevation. ► Bacterial communities differed dramatically along elevation. ► Bacterial diversity and community composition were correlated with soil pH. ► Soil pH is a better predictor of bacterial elevational distribution.
Black soils (Mollisols) are one of the most important soil resources for maintaining food security of China and are mainly distributed in northeast China. To understand which environmental factors ...influence the microbial communities and how the communities are distributed in the black soils, we collected 26 soil samples with different soil carbon contents across the black soil zone in northeast China, and the soil bacterial community compositions were estimated using high resolution bar-coded pyrosequencing. A total of 355,813 bacterial 16S rDNA sequences were obtained, which were classified into at least 35 bacterial groups. The dominant groups across all samples (>5% of all sequences) were Acidobacteria, Actinobacteria, Proteobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes and Planctomycetes. The composition and diversity of the soil bacterial community were dominantly affected by both soil pH and soil total carbon content, and the effect of soil pH was stronger than that of soil carbon content. Variance partitioning analysis showed that geographic distance contributed 14.75% of the bacterial community variation, and soil environmental factors explained approximately 37.52% of the variation. Pairwise analysis showed that a relatively higher diversity of the bacterial community was observed at lower latitudes, suggesting that a latitudinal diversity gradient of the bacterial community might be present in the black soil zone. In general, our results indicated that contemporary factors, such as soil pH and soil carbon content, were more important than the historical factor of geographic distance in shaping the bacterial community in the black soil zone in northeast China.
Variation partition analysis of the effects of geographic distance and soil variables on the phylogenetic structure of bacterial communities in the black soils of northeast China. Display omitted
•Bacterial communities in Mollisols were both affected by soil pH and soil C content.•The effect of soil pH on bacterial communities was stronger than soil C content.•Geographic distance was another important factor in shaping communities.•A latitudinal diversity gradient of the community was observed in the Mollisols.•Soil bacterial communities were spatially distributed in the black soil zone.
Plant biodiversity is often correlated with ecosystem functioning in terrestrial ecosystems. However, we know little about the relative and combined effects of above- and belowground biodiversity on ...multiple ecosystem functions (for example, ecosystem multifunctionality, EMF) or how climate might mediate those relationships. Here we tease apart the effects of biotic and abiotic factors, both above- and belowground, on EMF on the Tibetan Plateau, China. We found that a suite of biotic and abiotic variables account for up to 86% of the variation in EMF, with the combined effects of above- and belowground biodiversity accounting for 45% of the variation in EMF. Our results have two important implications: first, including belowground biodiversity in models can improve the ability to explain and predict EMF. Second, regional-scale variation in climate, and perhaps climate change, can determine, or at least modify, the effects of biodiversity on EMF in natural ecosystems.
Summary
Continent‐scale biogeography has been extensively studied in soils and marine systems, but little is known about biogeographical patterns in non‐marine sediments. We used barcode ...pyrosequencing to quantify the effects of local geochemical properties and geographic distance for bacterial community structure and membership, using sediment samples from 15 lakes on the Tibetan Plateau (4–1670 km apart). Bacterial communities were surprisingly diverse, and distinct from soil communities. Four of 26 phyla detected were dominant: Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria, albeit 20.2% of sequences were unclassified at the phylum level. As previously observed in acidic soil, pH was the dominant factor influencing alkaline sediment community structure, phylotype richness and phylogenetic diversity. In contrast, archaeal communities were less affected by pH. More geographically distant sites had more dissimilar communities (r = 0.443, P = 0.030). Variance partitioning analysis showed that geographic distance (historical contingencies) contributed more to bacterial community variation (12.2%) than any other factor, although the environmental factors explained more variance when combined (28.9%). Together, our results show that pH is the best predictor of bacterial community structure in alkaline sediments, and confirm that both geographic distance and chemical factors govern bacterial biogeography in lake sediments.
PDF
