Metagenomic and Metatranscriptomic Study of Microbial Metal Resistance in an Acidic Pit Lake.

Diana Ayala-Muñoz,Jennifer L Macalady,Estelle Couradeau,Carmen Falagán,Javier Sánchez-España,William D Burgos

doi:10.3390/microorganisms8091350

Diana Ayala-Muñoz, Jennifer L Macalady + Show 4 more

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https://doi.org/10.3390/microorganisms8091350

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Abstract

Cueva de la Mora (CM) is an acidic, meromictic pit lake in the Iberian Pyrite Belt characterized by extremely high metal(loid) concentrations and strong gradients in oxygen, metal, and nutrient concentrations. We hypothesized that geochemical variations with depth would result in differences in community composition and in metal resistance strategies among active microbial populations. We also hypothesized that metal resistance gene (MRG) expression would correlate with toxicity levels for dissolved metal species in the lake. Water samples were collected in the upper oxic layer, chemocline, and deep anoxic layer of the lake for shotgun metagenomic and metatranscriptomic sequencing. Metagenomic analyses revealed dramatic differences in the composition of the microbial communities with depth, consistent with changing geochemistry. Based on relative abundance of taxa identified in each metagenome, Eukaryotes (predominantly Coccomyxa) dominated the upper layer, while Archaea (predominantly Thermoplasmatales) dominated the deep layer, and a combination of Bacteria and Eukaryotes were abundant at the chemocline. We compared metal resistance across communities using a curated list of protein-coding MRGs with KEGG Orthology identifiers (KOs) and found that there were broad differences in the metal resistance strategies (e.g., intracellular metal accumulation) expressed by Eukaryotes, Bacteria, and Archaea. Although normalized abundances of MRG and MRG expression were generally higher in the deep layer, expression of metal-specific genes was not strongly related to variations in specific metal concentrations, especially for Cu and As. We also compared MRG potential and expression in metagenome assembled genomes (MAGs) from the deep layer, where metal concentrations are highest. Consistent with previous work showing differences in metal resistance mechanisms even at the strain level, MRG expression patterns varied strongly among MAG populations from the same depth. Some MAG populations expressed very few MRG known to date, suggesting that novel metal resistance strategies remain to be discovered in uncultivated acidophiles.

Highlights

Water with elevated concentrations of dissolved metals is harmful to most life forms including animals, plants, and microorganisms
We learned that single-celled eukaryotes in the genus Coccomyxa dominate the surface layer of Cueva de la Mora (CM), archaea dominate the deep layer, and a combination of bacteria and Coccomyxa are abundant at the chemocline
Several intriguing patterns emerged from our exploration of metal resistance genes and gene expression in these extreme acidophile communities

Summary

Introduction

Water with elevated concentrations of dissolved metals is harmful to most life forms including animals, plants, and microorganisms. Heavy metal cations cause toxicity by promoting oxidative stress or by binding to protein sites not made for them, causing the proteins to malfunction [1]. Antioxidants such as glutathione protect cells from reactive oxygen species (ROS) and free radicals such as superoxide radicals [1]. As(V), can disrupt the function of a variety of proteins (including those involved in ROS consumption) because of its structural similarity to phosphate [3]. Because of the pH-dependent solubility of many minerals, systems with the highest concentrations of toxic metal(loid)s are usually acidic

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