16S rRNA gene amplicon sequence analysis of water, microbial mat, and microbialite samples from Laguna Pozo Bravo.

The prokaryotic composition of water, soft microbial mat and microbialite samples from Laguna Pozo Bravo (ENA accession number: ERP120954) was determined with the MGnify metagenomic analysis pipeline v.5.0 (MGnify accession number: MGYS00005312) through the taxonomic assignment of the 16S rRNA gene amplicon sequences (SILVA release 132). Alpha diversity metrics (Shannon index) were calculated using the R package phyloseq. The phyloseq package was also employed to perform a principal coordinate analysis (PCoA) based on Bray-Curtis dissimilarity. The core input to phyloseq was a combination of the following components, which can be assembled into a single phyloseq object: (1) OTU/ASV abundance table (otu_table) – matrix of counts (rows or columns = taxa, the other = samples). (2) Sample metadata (sample_data) – a data.frame with sample-wise covariates; row names must match sample IDs in the abundance table. (3) Taxonomic classification (tax_table) – matrix of taxonomic ranks for each OTU/ASV; row names must match the taxa names in the abundance table.