Taxonomical and functional microbial community selection in soybean rhizosphere

Abstract

This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors.

Microbial Assembly in Agroecosystems — From the Small Arise the Big

“…In this study [4], they showed that there was a selection process at both taxonomic and functional levels operating in the assembly of the rhizospheric community, with different community structure compared to the bulk soil community. The phyla Actinobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, Chlamydiae, Tenericutes, Deferribacteres, Chlorobi, Verrucomicrobia and Aquificae were selected in the rhizosphere.…”

“…The model undergoing this approach is based on zero-sum dynamics of a metacommunity. Indices deriving from this view are being also used for local communities [32], with recent applications in studies related to the patterns of microbial assembly in agroecosystems and rhizosphere [4,21] A more comprehensive picture of the application of these paradigms in microbial ecology studies can be reached by both theoretical (e.g. Classic Metapopulation -neutral) and numerical (e.g.…”

“…In an experimental research, [4] studied the process of microbial selection in the rhizosphere from bulk soil reservoir under agricultural management of soybean in Amazon forest soils. They used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities and to test the validity of neutral and niche theories to explain the community assembly in the rhizosphere.…”

“…Zero-Sum Model -neutral, Broken-Stick Model -niche-based) models. The models describe the organization of microorganisms into communities, at the local level [4], and along metacommunities, at the regional level [21] (e.g. Rates of dispersal and immigration coefficient).…”

“…Recently, metagenomic libraries from soil microbial DNA are being used as template [3], in order to evaluate the effects of the conversion of forest into agriculture [4]. The dimension 2 has been assessed by biochemical assays of production/consumption of microbial-mediated greenhouse gases and microbial enzyme activities in soil [5][6][7][8].…”