Bacterial community structure of contrasting soils underlying Bornean rain forests: Inferences from microarray and next-generation sequencing methods

Soil microbial diversity is vast, and we lack even basic understanding of how this diversity is distributed ecologically. Using pyrosequencing and microarray methods, we quantified the structure of bacterial communities in two contrasting soils underlying Bornean rain forest (clay and sandy loam) that differ markedly in soil properties, aboveground tree flora, and leaf litter decomposition rates. We found significant soil-related taxonomic and phylogenetic differences between communities that, due to their proximity, are independent of climate. Bacterial communities showed distinct compositional and taxon-abundance distributions that were significantly correlated with the structure of the overlying tree community. Richness of bacteria was greater in the more resource-rich clay soil. Phylogenetic community analyses suggested that environmental filtering may be an important mechanism of community assembly in clay, compared to niche-competition in sandy loam. The Acidobacteria were the most abundant group in clay, but the Proteobacteria dominated in sandy loam. Of the ten most abundant classes, the Actinobacteria, Betaproteobacteria, Clostridia, Bacilli, and Gammaproteobacteria were more abundant in sandy loam than clay. Our study, which is the first to quantify edaphic variation in bacterial communities using high-throughput methods in soils underlying one of the most tree species rich forests on Earth, indicates an important role of plant-soil feedbacks linking the community structure of the trees and the underlying soil microbiome. We suggest the biochemical composition of carbon and nutrient resources in plant litter and soil pH and oxygen availability as important determinants of the distribution of bacterial diversity