Evolutionary histories of microbial calcification-associated genes across the tree of life

Biocalcification, a widespread process by which animals and algae form hard tissues and cellular structures, has played a major role in the global carbon cycle over the past 541 Ma. Extracellular or intracellular carbonates are formed by diverse bacteria, yet the genetic basis and evolutionary history of this process remain poorly resolved. Here, we present a large-scale survey of an intracellular calcification marker (calcyanin) and two calcification-associated genes with potential mineralization-promoting roles (carbonic anhydrase [CA] and urease) across the Bacteria and Archaea domains. High-sequence-coverage homologs of calcyanin are restricted to oxygenic cyanobacteria and consistent with vertical inheritance within seven families, suggesting a possible origin in a common ancestor of the Cyanobacteriia class, although some cases likely reflect horizontal gene transfer (HGT). In contrast, CA genes are widespread across all domains of life, with phylogenetic and structural analyses supporting independent origins of the α-, β-, and γ-classes, followed by extensive inter-phylum and possible inter-domain HGT events. Urease genes are distributed broadly and most likely originated in Pseudomonadota or Cyanobacteriota , and their phylogenetic placement is consistent with extensive bacterial and archaeal diversification and a possible bacterial contribution to plant and fungal ureases. Together, these findings not only reveal distinct evolutionary trajectories of microbial calcification-associated genes but also provide a genomic framework for generating hypotheses that microbial calcification may have interacted with ocean chemistry and the global carbon cycle since the Archaean.

IMPORTANCE

Microbes help regulate the global carbon cycle partly by influencing when and where carbonate minerals form on Earth's surface. However, the genes connected to microbial calcification have not been evaluated broadly across the bacterial and archaeal tree of life or in relation to early Earth history. Here, we analyze a previously experimentally validated intracellular calcification marker and two widespread enzymes that can influence carbonate chemistry under suitable conditions. Our results show that these gene systems have distinct and complex evolutionary histories, including inheritance within lineages, gene loss, duplication, transfer between distantly related microbes, and possible transfers between bacteria and eukaryotes. Compared with previous taxon- or gene-specific studies, this work provides a broader evolutionary view of how mineralization-promoting functions emerged, diversified, and spread across microbial lineages. It provides a genomic framework for studying how microbial physiology may have interacted with ocean chemistry and carbon cycling through Earth history.