Contemporary environmental variation determines microbial diversity patterns in acid mine drainage

Abstract

A wide array of microorganisms survive and thrive in extreme environments. However, we know little about the patterns of, and controls over, their large-scale ecological distribution. To this end, we have applied a bar-coded 16S rRNA pyrosequencing technology to explore the phylogenetic differentiation among 59 microbial communities from physically and geochemically diverse acid mine drainage (AMD) sites across Southeast China, revealing for the first time environmental variation as the major factor explaining community differences in these harsh environments. Our data showed that overall microbial diversity estimates, including phylogenetic diversity, phylotype richness and pairwise UniFrac distance, were largely correlated with pH conditions. Furthermore, multivariate regression tree analysis also identified solution pH as a strong predictor of relative lineage abundance. Betaproteobacteria, mostly affiliated with the ‘Ferrovum' genus, were explicitly predominant in assemblages under moderate pH conditions, whereas Alphaproteobacteria, Euryarchaeota, Gammaproteobacteria and Nitrospira exhibited a strong adaptation to more acidic environments. Strikingly, such pH-dependent patterns could also be observed in a subsequent comprehensive analysis of the environmental distribution of acidophilic microorganisms based on 16S rRNA gene sequences previously retrieved from globally distributed AMD and associated environments, regardless of the long-distance isolation and the distinct substrate types. Collectively, our results suggest that microbial diversity patterns are better predicted by contemporary environmental variation rather than geographical distance in extreme AMD systems.

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage

“…Figure 1. The genera detected in AMD samples from 14 mining areas across South China (data from [24]). The font size is proportional to the average relative abundance of the specific genus in microbial communities of AMD ecosystems.…”

“…were found to be predominant at the late oxidation stage, which was usually characterized by low pH (<3.0) and a high concentration of metals [47,49,50], revealing their favorable adaptation of harsh environmental conditions and indispensability in such ecosystems Figure 1. The genera detected in AMD samples from 14 mining areas across South China (data from [24]). The font size is proportional to the average relative abundance of the specific genus in microbial communities of AMD ecosystems.…”

“…Based on high-throughput molecular approaches, much research has been conducted to investigate the microbial community variations across diverse environmental gradients, as summarized by Huang et al [5]. However, the microbes are more susceptible to environmental variations than to spatial distances, which results in an environmentally dependent distribution pattern of microbial communities [5,24,50].…”

“…In our investigation of AMD (pH < 4.0) in South China, diverse environmental factors were applied to explain the variation of microbial community assembly [24,29]. The environmental factors were clustered into three groups based on statistical correlations (Figure 3a).…”

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach

“…Indeed, environmental changes often affect taxonomic composition and abundance in microbial communities (Allison and Martiny 2008), which may have a strong effect on soil health and plant productivity (Chaparro et al 2012). Several works have been performed inspecting bacterial community variation both in cross sectional (different sites at the same time) and longitudinal studies (the same site studied over time) (Bartram et al 2014;Chen et al 2013;Costello et al 2009;Kuang et al 2012;Logares et al 2013;Pini et al 2012;Smith et al 2012).…”