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Chemical gradients between fresh, brackish and saline waters shape biogeochemical reactions and organic matter transformation within subterranean estuaries. In the Yucatan Peninsula’s karst subterranean estuary (KSE), methane and dissolved organic matter generated during the anaerobic decomposition of tropical forest vegetation are transported into flooded cave networks where microbial consumption greatly reduces their concentrations in the groundwater. To test the hypothesis that chemoclines associated with salinity gradients of the KSE are sites of methane oxidation, we obtained methane concentration and δ13C profiles of unprecedented vertical resolution from within a fully-submerged cave system located 6.6 km inland from the coastline using the ‘OctoPiPi’ (OPP) water sampler. Along a 12–24 cm thick low-salinity-halocline at ∼4.5 m water depth, salinity increased from fresh to brackish (0.2–1.8 psu), methane concentrations decreased, and δ13C values increased, as expected for microbial methane oxidation. The underlying brackish water had elevated oxygen concentrations compared to the always anoxic freshwater, suggesting that aerobic methane oxidation is the dominant process facilitating methane consumption. By contrast, as salinity increased from 1.8 to 36 psu through a 24–36 cm thick high-salinity-halocline between the meteoric lens and the saline groundwater at ∼20 m water depth, methane concentrations and δ13C values were constant. Conservative mixing and kinetic isotope models incorporating the methane data confirm a hotspot for microbial methane oxidation at the low-salinity-halocline. At least 98% of methane originating in the anoxic freshwaters was removed before its transport via channelized flow towards the coastline. These findings provide novel insight into the spatial constraints of methane dynamics within a karst subterranean estuary.

Seasonal precipitation affects methane accumulation and turnover in tropical karst subterranean estuaries, the region of the coastal aquifer where hydrological and biogeochemical processes regulate material exchange between the terrestrial and marine environments. However, the impact of extreme weather events (e.g., tropical storms and hurricanes) on subsurface carbon cycling linked to coastal karst landscapes is unknown. In this study, we present a 5-month long hydrologic and chemical record from inland and coastal portions of the extensive Ox Bel Ha cave system in the northeastern Yucatan Peninsula. The record encompasses wet and dry seasons and includes effects from Tropical Storm Hanna during October 2014. Intense rainfall coincides with an episodic increase in water level and sudden shifts in salinity, indicating a spatially widespread hydrologic response. The most profound effect of the storm was a vanishing pulse of dissolved oxygen to ~0.7 mg l-1 that declined to zero along with the disappearance of methane that had built up during the wet season. A positive shift in methane’s stable carbon isotope content from −62.6 ± 0.6‰ before the storm to −44.0 ± 2.4‰ after the storm indicates microbial methane oxidation was the primary mechanism for the loss of methane from the groundwater. Post-storm methane concentrations, which never reached pre-storm levels, suggest the tropical storm had long-lasting (months) effects on carbon cycling. These findings demonstrate that mixing and oxygen delivered during storm-induced hydrologic forcing has an outsized biogeochemical effect within typically stratified karst subterranean estuaries.

The Yucatán Peninsula, Mexico is a carbonate platform well-known for extensive karst networks of densely stratified aquifer ecosystems. This aquifer supports diverse anchialine fauna, including species of the globally distributed atyid shrimp genus Typhlatya. Four species (T. campecheae, T. pearsei, T. dzilamensis and T. mitchelli) are endemic to the Peninsula, of which three are federally listed in Mexico. This first integrative evaluation [i.e., molecular (public and newly generated), morphological, broad geographic and type locality sampling, and environmental data] of Yucatán Typhlatya reveals considerable species identity conflict in prior phylogenetic assessments, broad species ranges and sympatry within cave systems, five genetic lineages (three known and two new to science) with the endangered T. campecheae herein classified as junior synonym of the vulnerable T. pearsei. Ancestral/divergence reconstructions support convergent evolution of a low-salinity/stenohaline ancestor of a post-Paleogene arc Yucatán+Cuba Typhlatya clade within a euryhaline/anchialine-adapted atyid clade, and secondary adaptation of the coastal-restricted euryhaline [2-37 psu] T. dzilamensis (unknown conservation status), of which the remaining four species lineages are low-salinity/stenohaline adapted found in both inland and coastal regions. This study demonstrates the need for integrative/interdisciplinary approaches when conducting biodiversity assessments in complex and poorly studied aquifers.

Biogeochemical processing of dissolved organic matter, including methane, along sharp salinity gradients in subterranean estuaries greatly alters the composition of submarine groundwater discharge into the marine environment. Along the margins of coastal carbonate (karst) platforms, which account for ~25% of all coastlines, subterranean estuaries extend kilometers inland within porous bedrock, flooding extensive cave networks. This environment harbors a poorly understood, but globally dispersed, anchialine fauna (invertebrates with subterranean adaptations) and characteristic microbial communities. In Mexico’s Yucatan Peninsula, microbial processing of methane and dissolved organic carbon (DOC), originating from overlying tropical soils, is the critical link for shuttling organic matter to higher trophic levels of the food web within the coastal aquifer. To better understand carbon turnover during organic matter transformations in this habitat, we collected samples for stable and radiocarbon analyses targeting the biotic and abiotic components of the carbon cycle. In the freshwater, radiocarbon signatures of terrestrially originated DOC (pMC = 105.1; [DOC] = 517 µM; δ13C = ˗27.8 ‰) and methane (pMC = 101.6; [CH4] = 6460 nM; δ13C = ˗71.5 ‰) correspond with modern 14C ages, suggesting these sources of energy within the habitat are comprised of modern carbon fixed recently by photosynthesizing primary producers at the land surface. By contrast, DOC in the deeper saline groundwater is significantly lower in concentration (21 µM), and substantially older (pMC = 47.3, equates to 6010 ± 95 14C yrs). Similarly, dissolved inorganic carbon (DIC) in the freshwater is significantly younger (pMC = 86.5, equates to 1170 ± 15 14C yrs) than in the deeper saline water (pMC = 58.4, equates to 4320 ± 25 14C yrs). These findings demonstrate that important sources of nutrition for the food web are intimately linked to the overlying subaerial habitat, which suggests these ecosystems are highly vulnerable to nearby land use alterations. Furthermore, this study provides new insights into carbon turnover during the process of methane production/consumption, carbon exchange, and organic matter transformation before the emission of the dissolved constituents into coastal oceans from karst subterranean estuaries. Radiocarbon and stable isotopic analyses of the resident fauna will allow us to evaluate the ecological effects of the rapid top-down transfer mechanism for methane and DOC. Beyond better understanding the sources and fate of these carbon sources, our findings have the potential to support management and conservation efforts aimed at coastal groundwater ecosystems.

The potential of subterranean environments as models to address major evolutionary and ecological questions has been highlighted in the literature. They represent partially isolated, discrete units offering several replicates of the same evolutionary processes. Species occurrence data of these environments is abundant, although sparse in the literature or gathered in databases established according to regional, taxonomical, or ecological criteria. We here present a newly assembled dataset consisting of records of aquatic animals in all types of caves or wells from all over the world. Literature sources were gathered from Google Scholar by independently searching for each metazoan phylum/arthropod order, as well as the key words “cave”, “groundwater”, “well”, or “stygobite”, in English, Galician, Spanish, Portuguese, Catalonian, French, Italian, Hungarian, Greek, German, Polish, Russian, and Serbo-Croatian. The relevance of each source was confirmed after checking the title and the abstract. For each selected source, we examined its reference list in order to identify studies that were not published in journals indexed in the databases we searched. From the 6852 selected references, we manually extracted all records that concerned either occurrence of a species in a given geographical area or occurrence of any taxon in a particular cave or well. occurrence of a species in a given geographical area or occurrence of any taxon in a particular cave or well. Records were classified as primary or secondary, depending on whether they provided new information or referred to already publish records, allowing us to identify redundant information in posterior analyses. Information for each access point was organized in as a gazetteer, including synonym names, geographical, ecological, and geological information. Following this strategy, we have obtained 48,800 records (32,769, primary) from 1957 references checked so far. Most records are amongst fish and crustaceans. In contrast, few data exist for other groups that are comparatively diverse outside caves, such as Nematoda. Relevant information will be included in World Register of Marine Cave Species (Fig. 1).

New records for 17 species of crustaceans from anchialine systems in the Yucatan Peninsula, Mexico, are presented. The records come from explorations in Dzilam de Bravo, Yucatan, and from Puerto Aventuras and the Nohoch Nah Chich and Ox Bel Ha cave systems near Tulum in Quintana Roo, Mexico. For five of the 17 species dealt with here, the records presented constitute the second time those species are reported after their original descriptions. For the alpheid shrimp Yagerocaris cozumel, we present the first record of the species for continental Yucatan and for the atyid shrimp Jonga serrei, the second record from Mexico. Depth data are provided for all species.