Biomineralization in the Toadfish microbiome

Calcium carbonate production in the ocean is dominated by planktonic microeukaryotes such as coccolithophores and foraminifera (Feely et al 2004. Science 305: 362–66). However, an alternative and remarkable carbon sink in the ocean has been greatly overlooked, that is piscine carbonate. Marine teleost fish precipitate CaCO3 in their intestines as part of their osmoregulatory strategy. Based on the estimate that marine fish biomass is around 800-2,000 million tons, this carbonate precipitation by fish can represent up to 15% of the total calcium carbonate deposition in the ocean (Wilson et al 2009. Science 323: 359–62). More recent ocean fish biomass estimates are 10 times higher (Irigoien et al. 2014. Nat Com 5: 3271), so this percentage could be even higher. Oceanic acidification due to elevated atmospheric CO2 is predicted to have major impacts on calcifying organisms, decreasing the CaCO3 production rates in calcifying marine plankton and corals as ambient CO2 increases (Orr et al 2005. Nature 437: 681–86). On the other hand, the production of carbonate precipitates by fish will accelerate as a result of both increasing seawater temperatures and CO2 concentrations. Biomineralization mechanisms in plankton and corals depend on the seawater concentrations of CO2 or HCO3 which change with pH as CO2 concentration increases (Wilson et al 2009). Fish, in contrast, use endogenous CO2 to produce HCO3 ions that rise to very high concentrations within the gut lumen. Thus, the contribution of fish to marine carbonate production will putatively increase in the future and become an even more important component of the inorganic carbon cycle (Heuer et al 2016. Sci Rep 6: 1–8). Despite carbonate precipitation being critical for fish rehydration and survival and having captured the attention of fish biologists for decades, the molecular mechanisms that regulate this reaction are still unknown. Strikingly, no candidate genes putatively involved in this process have been identified so far when analyzing the genome and the transcriptome of the Gulf Toadfish, the model organisms used to study this process. The impossibility to identify these genetic mechanisms within the fish genome lead us to consider the hypothesis that it is gut microbiota responsible for the carbonate precipitation. The involvement of bacteria in calcium carbonate deposition in marine environments is a well-known phenomenon that has been linked to photosynthesis, sulfate reduction, the nitrogen cycle, and saltern environments (Hammes et al 2002. Rev Env Sci Bio 1: 3–7). So, the carbon precipitate capabilities of bacteria are proven in the free-living environment. As well, bacteria have been linked in mammals to the development of kidney stones (Schwaderer et al 2017. Ann Trans Med 5: 3–8). There are different types of kidney stones, being the most common ones composed of calcium oxalate crystals (CaC2O4). It has been observed that bacteria are capable of producing calcium coated shells or calcium derived metabolic byproducts that would act as crystallization centers for the formation of renal calculi (Kose et al 2018. Sci Rep 8: 1–13). The lack of genomic clues in the fish genome and the proven capability of bacteria to precipitate carbonates outside and inside animal hosts makes a compelling case to test the hypothesis that members of the fish microbiome are responsible for piscine carbonate deposition. Considering the significant contribution of piscine carbonates to the global ocean carbon budget, it is of paramount importance to determine the genomic mechanisms involved in this process. A full understanding of the microbial role on piscine carbonate deposition will help to improve carbon dynamics modeling and to design alternative carbon sequestration and ocean acidification mitigation strategies.