Core Microbiota in Agricultural Soils and Their Potential Associations with Nutrient Cycling

Abstract

Revealing the ecological roles of the core microbiota in community maintaining and soil nutrient cycling is crucial for understanding ecosystem function, yet there is a dearth of continental-scale studies on this fundamental topic in microbial ecology. Here, we collected 251 soil samples from adjacent pairs of maize and rice fields at a continental scale in eastern China. We revealed the major ecological roles of the core microbiota in maintaining complex connections between bacterial taxa and their associations with belowground multinutrient cycling. By identifying the habitat preferences of the core microbiota, we built a continental atlas for mapping the spatial distributions of bacteria in agro-soils, which helps forecast the responses of agricultural ecosystems to anthropogenic disturbance. The multinutrient cycling index for maize and rice soils was related to bacterial α-diversity and β-diversity, respectively. Rice soils exhibited higher bacterial diversity and closer bacterial cooccurrence relationships than maize soils. In contrast to the macro- or microecological latitudinal richness patterns in natural terrestrial ecosystems, the bacteria in maize soils showed higher richness at high latitudes; however, this trend was not observed in rice soils. This study provides a new perspective on the distinct bacterial biogeographic patterns to predict the ecological roles of the core microbiota in agro-soils and thus helps manage soil bacterial communities for better provisioning of key ecosystem services. IMPORTANCE Disentangling the roles of the core microbiota in community maintaining and soil nutrient cycling is an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the spatial atlas and ecological roles of the core microbiota. A systematic, continental-scale survey was conducted using agro-soils in adjacent pairs of maize (dryland) and rice (wetland) fields across eastern China. The results indicate that the core microbiota play major ecological roles in maintaining complex connections between bacterial taxa and are associated with belowground multinutrient cycling. A continental atlas was built for mapping the bacterial spatial distributions in agro-soils through identifying their habitat preferences. This study represents a significant advance in forecasting the responses of agricultural ecosystems to anthropogenic disturbance and thus helps manage soil bacterial communities for better provisioning of key ecosystem services—the ultimate goal of microbial ecology.

Soil pH and temperature regulate assembly processes of abundant and rare bacterial communities in agricultural ecosystems

“…Here, we showed that soil pH and MAT mediated the balance between stochastic and deterministic assembly for abundant and rare sub‐communities, respectively, in agro‐ecosystems. It is not surprising that soil pH influences the assembly of abundant sub‐communities because pH is known to affect bacterial community composition and diversity at multiple scales (Fierer and Jackson, ; Rousk et al ., ; Jiao et al ., ). In the present study, the increased role of stochasticity in acidic environments may mean that adapted lineages of abundant taxa accumulate in acidic soils.…”

“…This implies that rare species might not be waiting for favourable conditions based on the homogenized habitats in maize or rice fields. Rice soils possessed more rare taxa than maize soils, which could be due to the presence of both aerobic and anaerobic taxa due to saturation-unsaturation cycles in rice fields (Jiao et al, 2019). Rare taxa, which are more abundant in rice fields, can increase functional redundancy and resiliency to environmental disturbances (Yachi and Loreau, 1999;Pedrós-Alió, 2012;Lynch and Neufeld, 2015).…”

“…We used high-throughput sequencing data from studies of soil bacterial diversity in fields cultivated with maize and rice (Jiao et al, 2019). The sampling sites extend from 18.30 N to 48.35 N and 87.61 E to 99.91 E across eastern China.…”

“…Microbial diversity was analysed using high-throughput sequencing of the V4-V5 regions of the 16S rRNA gene on a HiSeq2500 platform (Illumina Inc., San Diego, CA). Sequences were filtered for quality control, split into OTUs using a 97% similarity cut-off and assigned to taxonomic groups (Jiao et al, 2019).…”

“…In the present study, we aim to (i) explore the biogeographic patterns of abundant and rare bacterial taxa in agro‐ecosystems and (ii) uncover the underlying environmental factors regulating assembly processes of abundant and rare bacterial taxa. These questions could be well addressed based on the existing high‐throughput sequencing data sets obtained from adjacent pairs of maize (water unsaturated) and rice (water saturated) cultivated fields across eastern China (Jiao et al ., ). Our results highlight the importance of considering the different linkages between environmental conditions and ecological processes in governing the assembly of abundant and rare taxa in agro‐ecosystems.…”