Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage

Abstract

The microbial communities in acid mine drainage have been extensively studied to reveal their roles in acid generation and adaption to this environment. Lacking, however, are integrated community- and organism-wide comparative gene transcriptional analyses that could reveal the response and adaptation mechanisms of these extraordinary microorganisms to different environmental conditions. In this study, comparative metagenomics and metatranscriptomics were performed on microbial assemblages collected from four geochemically distinct acid mine drainage (AMD) sites. Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities. Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions. Organism-wide comparative analyses of the active taxa revealed environment-dependent gene transcriptional profiles, especially the distinct strategies used by Acidithiobacillus ferrivorans and Leptospirillum ferrodiazotrophum in nutrients assimilation and energy generation for survival under different conditions. Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.

Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil

“…While metagenomics, metatranscriptomics, and functional arrays are good approaches for functional analysis [18, 19], these methods are constrained by cost and difficulty [20, 21]. Recently, Langille et al [22] developed the software Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), which analyzes microbial function by combining phylogenetic analyses and genome database data to predict functional profiles.…”

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

“…In summary, microbial-mediated AMD generation results in a low alpha-diversity of microbial community at the late stage. [27,52,53]. For example, previous metagenomics study of tailings acidification showed that the sulfur oxidation was mainly performed by Thiobacillus at the early stage and by Acidithiobacillus at the late stage [50].…”

“…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 [51]. Metagenomic as well as transcriptomic analyses deciphered significant variations in microbial community function [27,52,53].…”

Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss

“…Similar to various acidophiles, Sulfobacillus spp. might generate a reversed membrane potential via the Kdp-type potassium transport system (Table S4), thereby partially deflecting the inward flow of protons (9,65,66). Additionally, genes encoding the Kef-type potassium efflux system and voltage-gated potassium channel proteins were identified in Sulfobacillus genomes.…”