Evaluation of Paleotemperature Proxy Using Coral Genome Biology

Coral skeletons are robust tools for examining past environments. However, biogenic effects during skeletal formation cause uncertainties in paleoclimate reconstructions. Thus establishing a method to separate biogenic from abiogenic effects during skeletal formation is required. We utilized an open access and searchable gene database for the staghorn coral Acropora digitifera and examined the number of genes related to the elements in seawater to assess the origin of uncertainties in geochemical proxies. We found that A. digitifera has genes that can process at least 15 chemical elements as individual substances (Ca, Na, Zn, K, C, N, Cl, S, Fe, Mg, Mn, Cu, H, Mo, and Te) and transporters for seven of these elements (Ca, Na, Zn, K, Cl, Cu, and H). The number of Ca-related genes was the highest (at least 428 genes, including 53 transporters), whereas Sr, one of the most widely used geochemical proxies, was not found in the gene database.

Moreover, we conducted RNA-seq using two A. digitifera samples that showed four fold differences in growth rates. We investigated genomes that are possibly related to metabolizing skeletal elements (Sr, Mg and Ca). Intriguingly, we did not find Sr related genes, but we identified a Mg transporter (aug_v2a.04878) that showed higher gene expressions in the fast growth sample. Therefore this gene could cause growth rate difference and might explain large individual variations reported in skeletal Mg/Ca ratios, which is problematic as a reliable water temperature proxy.

One of the most important topics in biomineralization research is whether chemical elements in marine calcifiers are controlled biogenically or abiogenically when they are transported from seawater into the skeleton. To resolve this issue, we propose that a bioinformatics approach using genome information would be an effective method. We suggest that elements without relevant coral genes make good candidates for reliable proxies. Genomic information can help us find new geochemical proxies with the fewest vital effects and also explain the robustness of geochemical proxies that are already known to be effective in reconstructing past ocean environments. We suggest that considering elements without relevant coral genes could provide effective criteria for reliable proxies (e.g. Sr/Ca, Li/Ca and U/Ca).