SUMMARY
Stromatolites are complex microbial mats that form lithified layers and ancient forms are the oldest evidence of 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. Using assembled shotgun metagenomic data we obtained 183 genomic bins, of which the most dominant taxa were from the Cyanobacteriia class (Cyanobacteria phylum), with lower but notable abundances of bacteria classified as Alphaproteobacteria, Gammaproteobacteria and Bacteroidia. We identified functional gene sets in bacterial species conserved across two geographically distinct stromatolite formations, which may promote carbonate precipitation through the reduction of nitrogenous compounds and possible production of calcium ions. We propose that an abundance of extracellular alkaline phosphatases may lead to the formation of phosphatic deposits within these stromatolites. We conclude that the cumulative effect of several conserved bacterial species drives accretion in these two stromatolite formations.
ORIGINALITY-SIGNIFICANCE Peritidal stromatolites are unique among stromatolite formations as they grow at the dynamic interface of calcium carbonate-rich groundwater and coastal marine waters. The peritidal space forms a relatively unstable environment and the factors that influence the growth of these peritidal structures is not well understood. To our knowledge, this is the first comparative study that assesses species conservation within the microbial communities of two geographically distinct peritidal stromatolite formations. We assessed the potential functional roles of these communities using genomic bins clustered from metagenomic sequencing data. We identified several conserved bacterial species across the two sites and hypothesize that their genetic functional potential may be important in the formation of pertidal stromatolites. We contrasted these findings against a well-studied site in Shark Bay, Australia and show that, unlike these hypersaline formations, archaea do not play a major role in peritidal stromatolite formation. Furthermore, bacterial nitrogen and phosphate metabolisms of conserved species may be driving factors behind lithification in peritidal stromatolites.
Footnotes
* The title of the manuscript has changed. * The format has been altered for submission to a different journal * Background information regarding sample site geochemistry was updated and expanded upon. * Investigation into potential endolithic activity was deemed weak and has been removed from the previous version. * Discussion of loss of phoR in phosphate transport and implication for role in phosphatic structure development was deemed weak and has been removed. * Methods for functional gene abundance was changed substantially. All raw data and scripts utilized to curate data are also now available in a GitHub repo. * Description of sampling sites during collection includes several more key details. * Analysis of Archaeal bins has been included in this version for comparison to archaeal communities identified in hypersaline stromatolites. * Re-analysis of Shark Bay metagenomic data for comparative purposes has been removed from this version. * Nearly all figures from the previous were discarded and replaced with different figures. Only Figure 2 remains the same. * Substantial reduction in number of supplementary figures as a result of summarizing data/results.
https://github.com/samche42/Conserved_Stromatolite_bacteria_manuscript.git
