Stream metabolism sources a large fraction of carbon dioxide to the atmosphere in two hydrologically contrasting headwater streams

Headwater streams are control points for carbon dioxide (CO$_{2}$) emissions to the atmosphere, with relative contributions to CO$_{2}$ emission fluxes from lateral groundwater inputs widely assumed to overwhelm those from in-stream metabolic processes. We analyzed continuous measurements of stream dissolved CO$_{2}$ and oxygen (CO$_{2}$) concentrations during spring and early summer in two Mediterranean headwater streams from which we evaluated the contribution of in-stream net ecosystem production (NEP) to CO$_{2}$ emission. The two streams exhibited contrasting hydrological regimes: one was non-perennial with relatively small groundwater inflows, while the other was perennial and received significant lateral groundwater inputs. The non-perennial stream exhibited strong inverse coupling between instantaneous and daily CO$_{2}$ and CO$_{2}$ concentrations, and a strong correlation between aerobic ecosystem respiration (ER) and gross primary production (GPP) despite persistent negative NEP. At the perennial stream, the CO$_{2}$–O$_{2}$ relationship varied largely over time, ER and GPP were uncorrelated, and NEP, which was consistently negative, increased with increasing temperature. ... mehrMean NEP contribution to CO$_{2}$ emission was 51% and 57% at the non-perennial and perennial stream, respectively. Although these proportions varied with assumptions about metabolic stoichiometry and groundwater CO$_{2}$ concentration, in-stream CO$_{2}$ production consistently and substantially contributed to total atmospheric CO$_{2}$ flux in both streams. We conclude that in-stream metabolism can be more important for driving C cycling in some headwater streams than previously assumed.