Photosynthesis and respiration cause distinct chemical microenvironments within cyanobacterial aggregates. Here, we used microsensors and a diffusion–reaction model to characterize gradients in carbonate chemistry and investigate how these are affected by ocean acidification in Baltic vs. Pacific aggregates (Nodularia and Dolichospermum vs. Trichodesmium). Microsensor measurements of O2 and pH were performed under in situ and expected future pCO2 levels on Nodularia and Dolichospermum aggregates collected in the Baltic Sea. Under in situ conditions, O2 and pH levels within the aggregates covered ranges of 80–175% air saturation and 7.7–9.4 in dark and light, respectively. Carbon uptake in the light was predicted to reduce HCO3− by 100–150 μmol/L and CO2 by 3–6 μmol/L in the aggregate center compared to outside, inducing strong CO2 depletion (down to 0.5 μmol/L CO2 remaining in the center) even when assuming that HCO3− covered 80–90% of carbon uptake. Under ocean acidification conditions, enhanced CO2 availability allowed for significantly lower activity of carbon concentrating mechanisms, including a reduction of the contribution of HCO3− to carbon uptake by up to a factor of 10. The magnification of proton gradients under elevated pCO2 that was predicted based on a lower buffer capacity was observed in measurements despite a concurrent decrease in photosynthetic activity. In summary, we provide a quantitative image of the inorganic carbon environment in cyanobacterial aggregates under present-day and expected future conditions, considering both the individual and combined effects of the chemical and biological processes that shape these environments.

In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2022-04-28.