After revealing an unsuspected diversity of bacteria able to make calcium carbonate inside their own cells, scientists are now tracing the history of this ability.
A new study shows that some methane-consuming bacteria may have acquired this ability from cyanobacteria, through the horizontal transfer of a gene between very distantly related organisms.
A little over a year ago, we told you the story of these remarkable bacteria that form minerals from CO2 inside their own cells. A team from BIAM and its partners showed at the time that this ability was far more widespread than previously thought, some bacteria devote more than half their cell volume to it.
One question remained: how did such different bacteria come to acquire this remarkable ability? A new study, led by Karim Benzerara (IMPMC) together with Caroline Monteil, Dan Chevrier, and Christopher Lefèvre (BIAM), now provides a piece of the puzzle.
New bacteria join the club
This time, the researchers turned to the Methylococcaceae, a family of aerobic methanotrophic bacteria that use methane as an energy source. Two cultivable species from this family, Methylococcus geothermalis and Methylococcus mesophilus, also produce amorphous calcium carbonate inside their cells. Electron microscopy and spectroscopy confirm what these inclusions are: each cell contains at least a dozen of them, with an average diameter of about 120 nanometres.
An unexpected clue in their DNA
The researchers searched for this gene, ccyA, across 858 genomes from the order Methylococcales. It encodes a protein called calcyanin, whose function remains unknown but which serves as a marker in cyanobacteria.
« We already knew that a few Methylococcales genomes carried a gene related to ccyA, but we didn’t know whether it was truly a functional marker in these bacteria. We were able to confirm it in the strains we tested: they do make these minerals. » Karim Benzerara
The gene turned up in 39 of the 112 Methylococcaceae genomes surveyed, around 35%. Most of these genomes come from environmental metagenomes (DNA fragments collected directly from nature without isolating the corresponding organism). Five genomes came from strains that can be cultured in the lab, and of those, two, Methylococcus geothermalis and Methylococcus mesophilus, could be tested experimentally. These two confirmed that the presence of the gene does go with calcium carbonate production.
More surprising still: the calcyanin protein in Methylococcaceae closely resembles that of Microcystis, a cyanobacterial genus far away on the tree of life. This resemblance is stronger than with any other type of cyanobacteria tested, and holds for both the sequence of the protein and the predicted structure.
« Having shown that this ability was far more widespread among bacteria than we thought, we’re now trying to understand its evolutionary history. This new study shows that, in some groups, it may have passed from one bacterial lineage to another through horizontal gene transfer. » Caroline Monteil
When the methane cycle meets the carbonate cycle
This discovery links two processes that had, until now, been studied separately. The Methylococcaceae in question consume methane, and methane oxidation produces CO2 — which should, if anything, dissolve the surrounding calcium carbonate rather than cause it to precipitate. For carbonate to form regardless inside the cells, an additional mechanism, not yet identified, must be at work. Nor do the researchers yet know what proportion of the carbon from methane ends up stored this way: it would therefore be premature to see these bacteria as a new carbon sink. Their discovery does, however, reveal a previously unrecognised connection between the methane cycle and the biological formation of calcium carbonate.
A gene that may have travelled from one bacterium to another
In microorganisms, a gene can sometimes be passed directly from one organism to another with no family relationship involved. This is called horizontal transfer. The analyses suggest that an ancestor of the Methylococcaceae acquired ccyA in this way, from an ancestor of the cyanobacterium Microcystis. The gene was then passed on to different lineages, before being lost in some of them. The transfer itself was not directly observed; it is simply the scenario that most simply explains the similarities found.
X-ray cryo-tomography of Methylococcus geothermalis cells. A) X-ray absorption map: the closer to red, the higher the calcium concentration. B) Volume reconstruction of the same cells; calcium-rich granules appear in pink. Scale bar: 500 nm. © Benzerara et al., 2026.
A scientific story built step by step
BIAM’s earlier study had revealed the diversity of bacteria able to make this type of mineral, without explaining where the ability came from. This new paper shows that another family, the Methylococcaceae, does indeed carry ccyA, acquired by transfer from cyanobacteria. The precise function of the gene, the mechanisms of calcium transport, and the biological advantage of these minerals still remain to be worked out. Having measured how many bacteria are capable of making these minerals, the researchers are now starting to understand how this ability may have spread over the course of evolution.
Scientific publication
Karim Benzerara et al. Intracellular Amorphous Calcium Carbonate Biomineralization in Methanotrophic Gammaproteobacteria Was Acquired by Horizontal Gene Transfer From Cyanobacteria. Environmental Microbiology, 2026, 28:e70270. DOI: 10.1111/1462-2920.70270.
Institutions involved
Sorbonne Université, Muséum national d’Histoire naturelle et CNRS, IMPMC ; Aix-Marseille Université, CEA, CNRS, BIAM ; CNRS, Université Paris-Saclay et AgroParisTech, Laboratoire Écologie Société et Évolution ; Institut Pasteur ; ALBA Synchrotron ; Synchrotron SOLEIL.