A genome catalogue of mercury-methylating bacteria and archaea from sediments of a boreal river facing human disturbances
Data files
Feb 06, 2024 version files 1.42 GB
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README.md
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StMaurice_MAGs_aa.tar.gz
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StMaurice_MAGs_contigs.tar.gz
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StMaurice_MAGs-gff.tar.gz
Abstract
Methyl mercury is a toxic compound produced by anaerobic microbes that biomagnifies in aquatic food webs, impacting animal and human health. Genome-based explorations of Hg methylators remain limited, particularly in the context of river ecosystems. To fill this knowledge gap, we created a genome catalogue of putative Hg-methylating microorganisms (based on the presence of hgcAB) from the sediments of a river impacted by two run-of-river hydroelectric dams, logging, and a wildfire. By using genome-resolved metagenomics, we uncovered a unique and diverse assemblage of Hg methylators dominated by members of the metabolically versatile Bacteroidota and particularly enriched in butyrate fermentative microbes. By comparing diversity and abundance of Hg methylators between sites that were subjected to different disturbances, we found that ongoing disturbances, such as input of organic matter related to logging activities, were particularly favorable to the establishment of a Hg-methylating niche. Lastly, for a deeper understanding of the environmental factors shaping Hg methylator diversity, we juxtaposed the Hg-methylating genome catalogue with the wider microbial community. The results suggest that Hg methylators respond to environmental conditions similarly to overall microbial community, and therefore it is crucial to interpret the diversity and abundance of Hg methylators within their specific ecological context.
README: Metagenome-assembled genomes catalogue from sediments of a boreal river facing human disturbances
https://doi.org/10.5061/dryad.9zw3r22mz
The metagenome-assembled genomes (MAGs) included in this catalogue were generated from six combined assembly corresponding to the six sampling sites from which sediment cores were collected along the St. Maurice River. This repository contains contigs, amino acid sequences and genome features of the 850 MAGs that comprise this catalogue.
Contact information
Address correspondence to David A. Walsh, david.walsh@concordia.ca.
Description of the data and file structure
The MAGs in this catalogue underwent quality filtering based on contamination and completeness, and only high and medium-quality MAGs were retained (< 10% contamination and > 50% completeness). They were then dereplicated at ≥95% average nucleotide identity (ANI), after which only the best species representative were kept.
Each compressed folder represent different information included in this catalogue, and contain one file per MAG :
- StMaurice_MAGs_contigs.tar.gz: compressed folder containing nucleotide sequence of contigs in each MAG in FASTA format (.fa file extension);
- StMaurice_MAGs_aa.tar.gz: compressed folder containing the annotated amino acid sequence of each MAG in FASTA format (.faa file extension);
- StMaurice_MAGs_gff.tar.gz: compressed folder containing annotated genome features in General Feature format (.gff file extension).
File naming system
Files were named after each MAG, which were prefixed with the sampling site they were generated from. Please refer to the published manuscript for the exact locations of the sampling sites.
WEM-4: constructed channels
REF-2 : reference site
CA-10 : site flooded by run-of-river dam and close to area affected by wildfire
CA-6: site flooded by run-of-river dam and close to area affected by wildfire
RDC-10 : site flooded by run-of-river dam and close to logging activities
RDC-14: site flooded by run-of-river dam and close to logging activities
Sharing/Access information
Links to other publicly accessible locations of the data:
- Raw metagenomic reads are available at the European Nucleotide Archive under study accession PRJEB67532>
- Combined assemblies were deposited and annotated at the Joint Genome Institute (JGI) Genomes OnLine Database (GOLD) under study accession [Gs0164199]
Methods
Detailed methods are described in associated publication.