Subterranean estuaries (STEs) are important coastal biogeochemical reactors facilitating unique niches for microbial communities. A common approach in determining STE greenhouse gas and nutrient fluxes is to use terrestrial endmembers, not accounting for microbially mediated transformations throughout the STE. As such, the microbial ecology and spatial distribution of specialists that cycle compounds in STEs remain largely underexplored. In this study, we applied 16S rRNA amplicon sequencing with paired biogeochemical characterisations to spatially evaluate microbial communities transforming greenhouse gases and nutrients in an STE. We show that methanogens are most prevalent at the terrestrial end (up to 2.81% relative abundance) concomitant to the highest porewater methane, carbon dioxide and dissolved organic carbon concentrations (0.41 ± 0.02 μM, 273.31 ± 6.05 μM and 0.51 ± 0.02 mM, respectively). Lower ammonium concentrations corresponded with abundant nitrifying and ammonia-oxidising prokaryotes in the mixing zone (up to 11.65% relative abundance). Methane, ammonium and dissolved organic carbon concentrations all decreased by >50% from the terrestrial to the oceanic end of the 15 m transect. This study highlights the STE's hidden microbiome zonation, as well as the importance of accounting for microbial transformations mitigating nutrient and greenhouse gas fluxes to the coastal ecosystems.

中文翻译：

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微生物组介导地下河口甲烷和氮的转化

地下河口（STE）是重要的沿海生物地球化学反应器，为微生物群落提供独特的生态位。确定 STE 温室气体和养分通量的常用方法是使用陆地端元，而不考虑整个 STE 中微生物介导的转化。因此，微生物生态学和在 STE 中循环化合物的专家的空间分布在很大程度上仍未得到充分探索。在这项研究中，我们应用 16S rRNA 扩增子测序和配对生物地球化学表征来空间评估 STE 中转化温室气体和营养物质的微生物群落。我们发现，产甲烷菌在陆地端最为普遍（相对丰度高达 2.81%），同时孔隙水甲烷、二氧化碳和溶解有机碳浓度最高（分别为 0.41 ± 0.02 μM、273.31 ± 6.05 μM 和 0.51 ± 0.02 mM） ）。较低的铵浓度对应于混合区丰富的硝化和氨氧化原核生物（相对丰度高达 11.65%）。从 15 m 横断面的陆地端到海洋端，甲烷、铵和溶解的有机碳浓度均下降了 > 50%。这项研究强调了 STE 隐藏的微生物区带，以及考虑微生物转化以减轻沿海生态系统的营养物和温室气体通量的重要性。