Conserved bacterial genomes from two geographically isolated peritidal stromatolite formations shed light on potential functional guilds

Abstract

Summary Stromatolites are complex microbial mats that form lithified layers. Fossilized stromatolites are the oldest evidence of cellular life on Earth, dating back over 3.4 billion years. Modern stromatolites are relatively rare but may provide clues about the function and evolution of their ancient counterparts. In this study, we focus on peritidal stromatolites occurring at Cape Recife and Schoenmakerskop on the southeastern South African coastline, the former being morphologically and structurally similar to fossilized phosphatic stromatolites formations. Using assembled shotgun metagenomic analysis, we obtained 183 genomic bins, of which the most dominant taxa were from the Cyanobacteria phylum. We identified functional gene sets in genomic bins conserved across two geographically isolated stromatolite formations, which included relatively high copy numbers of genes involved in the reduction of nitrates and phosphatic compounds. Additionally, we found little evidence of Archaeal species in these stromatolites, suggesting that they may not play an important role in peritidal stromatolite formations, as proposed for hypersaline formations.

Bacterial community structure and metabolic potential in microbialite‐forming mats from South Australian saline lakes

“…While the mat samples harboured a similar cohort of phyla, they were very heterogeneous at the lowest taxonomic level with only 4 ASVs shared among the five lake communities (Figure 3; Table S3) and were distinctly clustered according to their location (PERMANOVA; p = .0001, F = 2.0738) and/or conductivity (PERMANOVA; p = .0002, F = 2.2922) on PCoA ordination (Figure 4). These observations are largely in agreement with previous studies of microbialite‐forming mats from hypersaline Shark Bay, Western Australia (Ruvindy et al, 2016), thrombolites from hypersaline Lake Clifton, Western Australia (Warden et al, 2016), thrombolites (Mobberley et al, 2013), stromatolites from Little Darby Island, The Bahamas (Casaburi et al, 2016), microbialites and non‐ lithifying mats from freshwater habitats along the Trans‐Mexican volcanic belt (Iniesto et al, 2021) and stromatolites from the peritidal eastern coast of South Africa (exposed to both fresh and marine water) (Waterworth et al, 2021). Interestingly, sediment samples were also clustered with mat samples according to lake/conductivity.…”

Metabolomics Spatial Survey of Modern Stromatolites from South Africa and Characterization of Ibhayipeptolides

“…The Schoenmakerskop microbialite system comprises mature microbialite formations with an abundance of superficial cyanobacteria as indicated by the diverse mosaic of bacterial taxa reported previously 12,35 and detected here. We found that metabolites and microorganisms differ between core samples of microbialites submerged in the pool throughout the tidal cycle compared to surface microbialites exposed between tides.…”

“…These observations motivated us to focus our subsequent analyses on substrate core samples, particularly in light of the known capability of cyanobacteria to produce biologically active metabolites and their central role in structuring microbialite microbial consortia. 16,29,35 Sunburst plots of the CANOPUS output for substrate samples from flag sites 1 (surface) and 7 (submerged) (Fig. S13) display limited divergence of compound superclasses between sites, but revealed significant differences at the class level in metabolites present at each site.…”

“…12 These formations are now known to be ubiquitous along the coastline of southern Africa, from Brandsebaai in the west to Tofo, Mozambique in the east. 13 The Schoenmakerskop stromatolite formation is one of these sites and has been the subject of a number of studies by the hydrochemical, 34 microbial, 12,35 and associated metazoan research communities. [36][37][38][39] Given these studies, which provided evidence for the presence of new and known cyanobacterial and other taxa related to known producers of specialized metabolites with varied biological functions, we selected the Schoenmakerskop microbialite system as a study site to collect parallel samples for microbial community analysis and untargeted metabolite profiling across a gradient of salinity and nutrient input.…”

Genomic and Functional Variation of the Chlorophyll d-Producing Cyanobacterium Acaryochloris marina

“…The closest matches in the antiSMASH database of microbial secondary metabolites [ 32 ] were paenibactin and myxochelin. Homologs of these genes were detected by BLAST in an assembly of the cyanobacterium Leptolyngbya from metagenome data obtained for a South African peritidal stromatolite (NCBI BioProject PRJNA612530, assembly SM1_1_3) [ 77 ]. It is not clear whether this cluster was inherited from a common ancestor or independently acquired.…”