Subterranean estuaries extend inland into density-stratified coastal carbonate aquifers containing a surprising diversity of endemic animals (mostly crustaceans) within a highly oligotrophic habitat. How complex ecosystems (termed anchialine) thrive in this globally distributed, cryptic environment is poorly understood. Here, we demonstrate that a microbial loop shuttles methane and dissolved organic carbon (DOC) to higher trophic levels of the anchialine food web in the Yucatan Peninsula (Mexico). Methane and DOC production and consumption within the coastal groundwater correspond with a microbial community capable of methanotrophy, heterotrophy, and chemoautotrophy, based on characterization by 16S rRNA gene amplicon sequencing and respiratory quinone composition. Fatty acid and bulk stable carbon isotope values of cave-adapted shrimp suggest that carbon from methanotrophic bacteria comprises 21% of their diet, on average. These findings reveal a heretofore unrecognized subterranean methane sink and contribute to our understanding of the carbon cycle and ecosystem function of karst subterranean estuaries.

Karst subterranean estuaries (KSEs) extend into carbonate platforms along 12% of all coastlines. A recent study has shown that microbial methane (CH4) consumption is an important component of the carbon cycle and food web dynamics within flooded caves that permeate KSEs. In this study, we obtained high‐resolution (~2.5‐day) temporal records of dissolved methane concentrations and its stable isotopic content (δ13C) to evaluate how regional meteorology and hydrology control methane dynamics in KSEs. Our records show that less methane was present in the anoxic fresh water during the wet season (4,361 ± 89 nM) than during the dry season (5,949 ± 132 nM), suggesting that the wet season hydrologic regime enhances mixing of methane and other constituents into the underlying brackish water. The δ13C of the methane (−38.1 ± 1.7‰) in the brackish water was consistently more 13C‐enriched than fresh water methane (−65.4 ± 0.4‰), implying persistent methane oxidation in the cave. Using a hydrologically based mass balance model, we calculate that methane consumption in the KSE was 21–28 mg CH4·m−2·year−1 during the 6‐month dry period, which equates to ~1.4 t of methane consumed within the 102‐ to 138‐km2 catchment basin for the cave. Unless wet season methane consumption is much greater, the magnitude of methane oxidized within KSEs is not likely to affect the global methane budget. However, our estimates constrain the contribution of a critical resource for this widely distributed subterranean ecosystem.

Subsurface mixing of seawater and terrestrial-borne meteoric waters on carbonate landscapes creates karst subterranean estuaries, an area of the coastal aquifer with poorly understood carbon cycling, ecosystem functioning, and impact on submarine groundwater discharge. Caves in karst platforms facilitate water and material exchange between the marine and terrestrial environments, and their internal sedimentation patterns document long-term environmental change. Sediment records from a flooded coastal cave in Cozumel Island (Mexico) document decreasing terrestrial organic matter (OM) deposition within the karst subterranean estuary over the last ∼1,000 years, with older sediment likely exported out of the cave by intense storm events. While stable carbon isotopic values (δ13Corg ranging from −22.5 to −27.1‰) and C:N ratios (ranging from 9.9 to 18.9) indicate that mangrove and other terrestrial detritus surrounding an inland sinkhole are the primarily sedimentary OM supply, an upcore decrease in bulk OM and enrichment of δ13Corg values are observed. These patterns suggest that a reduction in the local mangrove habitat decreased the terrestrial particulate OM input to the cave over time. The benthic foraminiferal community in basal core sediment have higher proportions of infaunal taxa (i.e., Bolivina) and Ammonia, and assemblages shift to increased miliolids and less infaunal taxa at the core-top sediment. The combined results suggest that a decrease in terrestrial OM through time had a concomitant impact on benthic meiofaunal habitats, potentially by impacting dissolved oxygen availability at the microhabitat scale or resource partitioning by foraminifera. The evidence presented here indicates that landscape and watershed level changes can impact ecosystem functioning within adjacent subterranean estuaries.