Inorganic carbon dynamics and their relation to autotrophic community regime shift over three decades in a large, alkaline river

How much of the excess CO 2 in running waters comes from in‐stream respiration of organic carbon? To answer this, we developed a 30‐yr metabolism‐carbonate system database at an hourly resolution for the Loire River, France, a large, alkaline river. We asked the following questions: what are the intra‐annual patterns of in‐stream (“internal”) CO 2 production, what processes drive these patterns, and how do these patterns depend on autotrophic community composition? We estimated internal CO 2 production as the ratio of net ecosystem production to CO 2 water‐to‐air flux (FCO 2 ). We also estimated the daily ecosystem quotient (EQ, O 2 released: dissolved inorganic carbon [DIC] consumed) and the prevalence of non‐CO 2 autotrophic DIC uptake pathways under CO 2 depletion. Median internal CO 2 production was 49% of FCO 2 in the Loire from 1990 to 2022. The river predictably shifted from a heterotrophic, CO 2 source to an autotrophic, CO 2 sink as a function of discharge, leading to four trophic‐flux (“trophlux”) states: autotrophic‐sink, autotrophic‐source, heterotrophic‐sink, and heterotrophic‐source. During autotrophic states (41% of the time), CO 2 depletion (FCO 2 ≤ 0, median pCO 2 = 135 μ atm) led to the use of and of CO 2 released by CaCO 3 precipitation as alternative DIC sources to autotrophs to support their high rates of primary production (occurring on average for 33% of the growing season). Finally, during a period of phytoplankton dominance, the median EQ was 1.3, which was reduced to 1.0 under macrophyte dominance. This work describes a dynamic coupling among autotrophic communities, calcium carbonate equilibria, and discharge‐controlled FCO 2 that together imply lower‐than‐predicted FCO 2 magnitude and greater‐than‐predicted internal CO 2 production for the Loire River.