Abstract Description

Microbialites are lithifying microbial mats that form layered organo-mineral structures through biologically mediated carbon uptake and carbonate precipitation. Fossils of these formations, dating back ~3.4 billion years, represent the earliest evidence of cellular life on Earth. Modern microbialites are globally distributed, thriving in both extreme and temperate environments and have recently been shown to be amongst the most efficient biological carbon sinks on the planet. Their diversity and resilience make microbialites ideal systems for investigating how taxonomically diverse microbial communities coordinate complex metabolic networks to drive mineralization and adapt to diverse environments. The fundamental question we aimed to answer in this study was to investigate how these communities are formed, by tracking the recruitment and succession of bacterial species in nascent freshwater microbialites on the southeast coast of South Africa over 3 years. We analysed 784 metagenome-assembled (bacterial) genomes (MAGs) including 87 high-quality MAGs. Phylogenomic tools, average nucleotide identity (ANI), autoMLST, and PhyloPhlAn, were employed to resolve evolutionary relationships and lineage-specific traits, resulting in the prioritization of 55 strains for further analysis. Functional annotation via KEGG orthology identified key metabolic pathways associated with early colonizers and putative keystone taxa. Keystone taxa encoded metabolic traits central to microbialite formation, including carbon fixation and nitrogen cycling. We used stable isotope uptake studies to assess rates of carbon uptake and nitrogen assimilation, linking active metabolisms to functional potential. Our findings provide unprecedented insight into how specialized microbial communities are recruited from the environment and evolve to form mature stable communities that can persist for millions of years in a changing environment.