Intracellular amorphous calcium carbonate biomineralization in methanotrophic gammaproteobacteria was acquired by horizontal gene transfer from cyanobacteria

Benzerara, K.; Millet, M. L.; Skouri-Panet, F.; Gaschignard, G.; Mehta, N.; Bezard, M.; Caumes, G.; Chevrier, D.; Dezi, M.; Duverger, A.; Guigner, J.-M.; Gutierrez-Preciado, A.; Lefevre, C. T.; Lopez-Garcia, P.; Menguy, N.; Monteil, C. L.; Pehau-Arnaudet, G.; Penard, E.; Pereiro, E.; Scandola, C.; Travert, C.; Vantelon, D.; Duprat, E.; Callebaut, I.; Moreira, D.

doi:10.64898/2025.12.07.689555

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bioRxiv · 10.64898/2025.12.07.689555

Intracellular amorphous calcium carbonate biomineralization in methanotrophic gammaproteobacteria was acquired by horizontal gene transfer from cyanobacteria

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Abstract

Some bacteria genetically control the biomineralization of intracellular amorphous calcium carbonates (iACC) with potential implications for microbial physiology, evolution, bioremediation and biogeochemical cycling. Until now, this capacity has been documented in Cyanobacteria, the giant gammaproteobacterium Achromatium and a few magnetotactic Pseudomonadota and Nitrospirota. Here, we report the discovery of iACC biomineralization in members of the Methylococcaceae, a family of aerobic methanotrophic Gammaproteobacteria. A homolog of the ccyA gene, previously considered a diagnostic marker for iACC formation in Cyanobacteria, was identified in several Methylococcaceae genomes, based on a search of the conserved C-terminal (GlyZip)3 domain of the encoded calcyanin protein, with a sequence coverage higher than 60% and an E-value lower than 1e-20. Moreover, two cultivated strains, Methylococcus geothermalis and Methylococcus mesophilus, whose genomes contained the ccyA gene, were consistently shown to form iACC granules. The ccyA genes of Methylococcaceae and Microcystis share higher sequence similarity (47%) than with other Cyanobacteria (around 30%) within their common (GlyZip)3 domain, suggesting horizontal gene transfer (HGT) from an ancestral Microcystis-like cyanobacterium to Methylococcaceae. This finding extends the known taxonomic distribution of ccyA and suggests that the capability to biomineralize iACC was acquired by HGT, possibly in environments such as those close to the oxyclines of lakes, where Cyanobacteria and Methylococcaceae commonly co-exist. The discovery of iACC in methane-oxidizing Methylococcaceae highlights a previously unrecognized coupling between calcium carbonate biomineralization and methane cycling in aquatic environments, suggesting that iACC formation may play an overlooked role in microbial carbon storage and local geochemical regulation.

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Benzerara, K., Millet, M. L., Skouri-Panet, F., Gaschignard, G., Mehta, N., Bezard, M., Caumes, G., Chevrier, D., Dezi, M., Duverger, A., Guigner, J.-M., Gutierrez-Preciado, A., Lefevre, C. T., Lopez-Garcia, P., Menguy, N., Monteil, C. L., Pehau-Arnaudet, G., Penard, E., Pereiro, E., Scandola, C., Travert, C., Vantelon, D., Duprat, E., Callebaut, I., Moreira, D.. 2025-12-07. Intracellular amorphous calcium carbonate biomineralization in methanotrophic gammaproteobacteria was acquired by horizontal gene transfer from cyanobacteria. https://doi.org/10.64898/2025.12.07.689555

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