Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

Abstract

Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions.

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

“…The overall alpha-diversity of the microbial community was widely observed to significantly relate to the acidification process. Liu et al investigated the microbial communities in filed mine tailings at different acidification stages (pH range 2.0-7.0) and described a strong correlation between the pH and the diversity of microbes including the number of phylotypes and phylogenetic diversity (PD) [25]. This gradual decrease of microbial diversity during the acidification of mine tailings was also found in other studies of natural AMD environments [29,48,54], possibly owing to the stronger selective pressure on microorganisms.…”

“…For example, according to the result of a simulated experiment of oxidative dissolution of pyrite, the most dominant genera were Tumebacillus, Alicyclobacillus, and Ferroplasma at the early, mid, and final stage, respectively [47]. A detailed microbial community investigation in a natural AMD-generating environment indicated that the key species involved in different acidification stages varied greatly, and the relative abundances of most dominant lineages were significantly correlated with acidity [25]. In many studies, archaea (mostly Ferroplasma spp.)…”

“…In generating AMD, the dissolving of sulfide minerals by associated microbes decreases the solution pH and releases a high amount of metals. To date, several attempts have been made to investigate the microbial community dynamics related to the acidification process of the mine tailings [14,25,47]. Remarkable shifts in microbial community composition and structure have been found at different oxidation stages, most likely due to the distinct environmental gradients produced during AMD generation [48][49][50].…”

“…There is a growing interest in predicting the taxonomy and function-based microbial distribution patterns across environmental gradients [67][68][69]. Environment variations, especially the pH, should be strong predictors of the microbial diversity and the relative abundance of dominant lineages in community [24,25]. In our previous study, artificial neural networks (ANN) were applied to predict the taxonomic and functional structure of AMD ecosystems in response to environment variations [29].…”

Land-use changes influence soil bacterial communities in a meadow grassland in Northeast China

“…Conversely, DNA-characterization-based highthroughput methodologies, such as sequencing and subsequent sequence alignment, can directly detect microbial community composition and variations in species with low richness (Shi et al, 2014;Zhao et al, 2014). These methodologies have also been widely adopted to assess the genetic structure and diversity of microbial communities in various environments (Quince et al, 2009;Golebiewski et al, 2014;Liu et al, 2014;Portune et al, 2014;Ren et al, 2014;Singh et al, 2014;Thomson et al, 2015).…”