Spatial heterogeneity of GHG dynamics across an estuarine ecosystem

Coastal ecosystems are critical components of the global carbon cycle, exerting a disproportionate influence on the carbon budget despite their limited spatial extent. Although they have gained more attention in the past decade, detailed studies of GHG dynamics across the land-ocean continuum, including shallow-water estuaries, remain relatively scarce even though they are active sources of the three most potent greenhouse gases (GHGs): carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). Such shallow coastal ecosystems are highly heterogeneous, shaped by strong physical, biogeochemical, and biological gradients. Together with the spatial variation in coastal biodiversity, these gradients significantly influence carbon cycling at both local and global levels. However, large uncertainties persist due to limited measurements, emphasizing the need for improved constraints on GHG budgets. Surface seawater partial pressure of CO2 (pCO2), CH4, and N2O concentrations, along with seawater physical and biogeochemical properties, and air-sea gas exchange, were measured at 21 sites in southwest Finland (Baltic Sea). Sampling progressed from estuarine inner bays to the outer archipelago, covering diverse soft-sediment habitats, from sheltered to exposed areas, across a salinity gradient. Seawater pCO2 and N2O concentrations ranged from undersaturated (160 ppm and 9 nmol L−1, respectively) to supersaturated (2521 ppm and 25 nmol L−1, respectively), compared to the atmosphere, resulting in an uptake of -36 and -0.0021 mmol m−2 d−1, and a release up to 220 and 0.0383 mmol m−2 d−1, respectively. CH4 concentrations were consistently supersaturated (19 to 469 nmol L−1) compared to the atmosphere, resulting in a net source to the atmosphere from 0.014 to 1.39 mmol m−2 d−1. Freshwater input from the Karjaanjoki River and its mixing with seawater shaped the overall spatial patterns of GHGs. However, deviations from this salinity-driven control were seen in sheltered sites within the archipelago, where elevated pCO2 and CH4 concentrations likely reflected biological processes, including enhanced organic matter respiration and methanogenesis in warm, late-summer shallow waters, where limited oxidation favoured CH4 accumulation. At exposed and semi-sheltered sites, mixing processes exerted greater control, resulting in lower GHG concentrations. Our results show that both physical mixing and biological processes influence coastal GHG dynamics, with benthic ecosystems potentially playing a key but still poorly constrained role. The overall budget of air–sea GHG exchanges was dominated by CO2 fluxes, with CH4 consistently acting as a source, and N2O alternating between source and sink. High environmental variability in shallow coastal systems leads to strong fluctuations in the balance between GHG production and consumption, which needs to be considered when evaluating their role in the global carbon budget.