Genome-resolved metagenomics and evolutionary analysis reveal conserved metabolic adaptations in extremophile communities from a copper mining tailing
Year: 2025
Type: article
Abstract: BACKGROUND: Microbial communities in mining environments exhibit unique metabolic adaptations to extreme conditions, such as high metal concentrations and low pH. Their relatively low species complexity makes them an attractive model for fine-scale evolutionary analysis; nonetheless, genome-resolved metagenomic data from these environments are still scarce. Here, we employed genome-resolved metagenomics to analyze a high-quality Illumina-sequenced sample from the Cauquenes copper tailing in central Chile, one of the world's largest and oldest copper waste deposits. We aimed to uncover the taxonomic composition, metabolic potential, and evolutionary pressures shaping this extremophile community. RESULTS: We reconstructed 44 medium- and high-quality metagenome-assembled genomes (MAGs), predominantly from the phyla Actinomycetota, Pseudomonadota, and Acidobacteriota. Taxonomic analysis revealed limited species-level classification, with only five MAGs assigned to known species, highlighting the challenges of characterizing extreme environments. Functional profiling identified enhanced metabolic capabilities in sulfur and copper pathways, critical for survival in mining ecosystems. Using evolutionary analysis on mining MAGs using dN/dS ratios, we uncoverd strong negative selection on genes involved in sulfur, copper, and iron metabolism, indicative of a conservative evolutionary state. In contrast, genes under positive selection were linked to motility, biofilm formation, and stress resistance, suggesting adaptive mechanisms for resource acquisition and survival. CONCLUSIONS: Our study provides a metagenome-wide evolutionary analysis of mining MAGs, demonstrating that microbial communities in copper tailings are highly specialized, with conserved metabolic pathways under strong purifying selection. At the same time, the recovery of previously unclassified species of extremophiles expands the known biodiversity of mining ecosystems. These findings emphasise the challenges of leveraging these communities for biotechnological applications, such as biomining, due to their evolutionary constraints.
Source: Environmental Microbiome
Authors: Moises A. Rojas, Gladis Serrano, Jorge Torres, Jaime Ortega, Gabriel Gálvez, Emilio Vilches, Valentina Parra, Angélica Reyes-Jara, Vinicius Maracaja-Coutinho, Lorena Pizarro, Mauricio Latorre, Alex Di Genova
Language: English
Subfield: Biomedical Engineering
Field: Engineering
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $2,590
Awards: LABORATORIO NACIONAL PARA HPC, EPITRANSCRIPTOMIC REGULATION OF COMPETING ENDOGENOUS RNA NETWORKS IN CARDIAC FIBROBLASTS ASSOCIATED WITH HEART FAILURE WITH PRESERVED EJECTION FRACTION, SYSTEMS BIOLOGY CENTER FOR THE STUDY OF EXTREMOPHILE COMMUNITIES FROM MINING TAILINGS., NEW COMPUTATIONAL ALGORITHMS TO ELUCIDATE THE GENETIC ARCHITECTURE AND FUNCTIONAL IMPACT OF LARGE-SCALE REARRANGEMENT IN PREVALENT CHILEAN CANCERS, G5186520474, BCL6 A NEW TRANSCRIPTION FACTOR REGULATING CARDIOMYOCYTE HYPERTROPHY IN RAT AND HUMAN MODELS, NON-CODING RNA GLOBAL TRANSCRIPTIONAL REGULATORY NETWORK ACTIVATED BY METALS IN ENTEROCOCCUS FAECALIS., CENTER FOR MATHEMATICAL MODELING (CMM), G8263889507, METILOMA DE RESPUESTA A HIERRO EN ENTEROCOCCUS FAECALIS, CENTRO DE MODELAMIENTO MATEMATICO, THE METHYLOME TRANSCRIPTIONAL REGULATORY NETWORK ACTIVATED BY COPPER IN ENTEROCOCCUS FAECALIS.
OpenAlex ID: W4417501085