Louca lab, UO

About

People

Research

Publications

Software

Data

Blog

Join

Internal

Microbiology of Big and Little Soda Lake, Nevada

This page provides supplemental data to the following article:
Habibi-Soufi, H., Tran, D., Louca, S. (2024). Microbiology of Big Soda Lake, a multi-extreme meromictic volcanic crater lake in the Nevada desert. Environmental Microbiology 26:e16578

Article abstract
Big Soda Lake, Nevada, is a multi-extreme meromictic lake, whose hypersaline hyperalkaline bottom waters feature permanent anoxia and high concentrations of arsenic, sulphide and ammonia. These properties make Big Soda Lake—and the adjacent Little Soda Lake—a fascinating system for exploring life's boundaries, discovering novel microbial taxa and identifying biotechnologically useful strains. To date, the taxonomic diversity and metabolic capabilities of microorganisms in this system remain largely unknown. Here, we fill this gap using microbiome surveys across the Big and Little Soda Lake water columns, including 16S rRNA sequencing, fungal ITS2 sequencing and gene- and genome-resolved metagenomics. We accompany these surveys with measurements of salinity, pH, temperature, oxygen, ammonium and ammonia concentrations. Our analyses reveal rich bacterial communities, taxonomically and functionally differentiated along Big Soda Lake's oxycline and, to lesser extent, between lakes. Fungal communities were dominated by a small number of families, while nearly no archaea were detected. Pathways related to perchlorate reduction, anoxygenic phototrophy, fermentation, dissimilatory metabolism of arsenite/arsenate, sulphur compounds, nitrogen compounds and hydrogen, were particularly prevalent. A total of 129 high-quality bacterial and archaeal metagenome-assembled genomes (completeness ≥ 80%, contamination ≤ 5%) were recovered, yielding insight into the taxonomic distribution of microbial metabolic pathways.

Data overview
The data provided below for download include standard downstream products derived from the 16S rRNA amplicon sequences and shotgun metagenomic sequences, such as OTU-per-sample tables and gene-per-sample tables.

The raw sequence data are available on the NCBI SRA under BioProject accession PRJNA993288. In particular, raw 16S rRNA amplicon sequences are available under run accessions SRR25252478-SRR25252483, raw ITS2 amplicon sequences are available under run accessions SRR25252615-SRR25252620, and raw metagenomic sequences are available under run accessions SRR25242035-SRR25242040.

Downloads

	Phylogenetic tree of prokaryotic ASVs.
	Phylogenetic tree of prokaryotic OTUs (99% identity).
	Table listing prokaryotic ASV read counts per sample.
	Taxonomic classifications for prokaryotic ASVs.
	Table listing OTU read counts per sample.
	Representative sequences of prokaryotic 16S rRNA ASVs.
	Phylogenetic tree of fungal ASVs.
	Phylogenetic tree of fungal OTUs (99% identity).
	Table listing fungal ASV read counts per sample.
	Table listing fungal OTU read counts per sample.
	Taxonomic classifications for fungal ASVs.
	Representative sequences of fungal ITS2 ASVs.
	Table listing relative abundances of genes in each sample.
	Table listing genes found in each MAG.
	Table listing metabolic functions found in each sample, based on gene-centric metagenomics.
	Phylogenetic tree of high-quality bacterial MAGs.
	Fasta files of all high-quality MAGs.
	Overview of all MAGs, including qualities, taxonomic identities and genome summary stats.