Hypothesis

Beneficial coral-associated bacteria that metabolize dimethylsulfoniopropionate (DMSP) produce sulfide (H2S) as a byproduct, which directly stimulates the host carbonic anhydrase (CA) enzyme activity in the calcifying epithelium. Elevated CA activity increases the conversion of bicarbonate to CO2, facilitating proton export and thereby raising the pH of the calcifying fluid (pH_cf) under ocean acidification (OA). This microbially mediated boost in pH_cf supplies the necessary energetic advantage for sustained aragonite precipitation, linking bacterial DMSP turnover to coral calcification resilience.

Mechanistic Basis

Recent work shows that Endozoicomonas marisrubri and Mameliella alba enhance Symbiodiniaceae growth via DMSP metabolism and vitamin biosynthesis [https://academic.oup.com/femsre/article/47/2/fuad005/7071893]. DMSP cleavage by bacterial DMSP lyases yields dimethyl sulfide (DMS) and, alternatively, sulfide through dissimilatory pathways. Sulfide is known to act as a signaling molecule that can upregulate CA expression in various marine invertebrates. In corals, CA is a key enzyme that supplies CO2 for calcification while removing protons, thus elevating pH_cf [https://pmc.ncbi.nlm.nih.gov/articles/PMC5740286/]. We propose that bacterial-derived sulfide acts as a transcriptional co‑activator for host CA genes, increasing Vmax of the enzyme and allowing the coral to maintain pH_cf at 1.6–2.2× seawater DIC levels even when external pH drops.

Predictions and Experimental Design

1. Metabolite Measurement – Corals inoculated with DMSP‑metabolizing bacteria will show elevated seawater sulfide concentrations relative to aposymbiotic or bacteria‑free controls under OA conditions.
2. CA Activity – Host CA activity (measured via esterase assay) will be significantly higher in sulfide‑exposed corals, correlating with sulfide concentration.
3. pH_cf and Calcification – Using pH-sensitive microelectrodes or fluorescent dyes, pH_cf will be higher and calcification rates (buoyant weight or alkalinity anomaly) will be maintained in sulfide‑treated corals compared with controls under identical low pH.
4. Genetic Response – Quantitative PCR will reveal upregulation of host CA transcripts (e.g., CA4, CA9) only when both bacteria and DMSP are present.

Experiment: Fragment Orbicella faveolata nubbins, assign to four treatments (i) ambient pH + native microbiome, (ii) low pH (pH 7.6) + native microbiome, (iii) low pH + antibiotics to reduce bacterial load, (iv) low pH + antibiotics + addition of a cultured DMSP‑degrading Endozoicomonas strain. Maintain for 6 weeks, monitor sulfide, CA activity, pH_cf, calcification, and Symbiodiniaceae photosynthetic efficiency.

Potential Outcomes and Falsifiability

• Support: A significant increase in sulfide, CA activity, pH_cf, and calcification in treatment (iv) relative to (iii) would confirm the proposed microbial‑driven mechanism.
• Refutation: If sulfide addition does not elevate CA activity or pH_cf, or if calcification remains low despite high sulfide, the hypothesis is falsified, indicating that bacterial DMSP metabolism does not directly fuel host calcification under OA.
• Alternative: Should CA activity rise without changes in sulfide, other bacterial metabolites (e.g., vitamins, nitrogen compounds) may be responsible, prompting refinement of the mechanistic link.

This hypothesis is directly testable, integrates microbiology, biogeochemistry, and cellular physiology, and addresses the critical knowledge gap of how microbiome‑derived metabolites energetically support the pH_cf upregulation essential for coral calcification under acidification stress [https://www.whoi.edu/press-room/news-release/scientists-identify-how-ocean-acidification-weakens-coral-skeletons/] [https://news-oceanacidification-icc.org/2026/03/02/persistence-of-coral-reef-structures-into-the-twenty-first-century/].