Summary Microeukaryotes play key ecological roles in the microbial web of aquatic ecosystems. However, large knowledge gaps urgently need to be filled regarding the biogeography with associated shaping mechanisms and co‐occurrence patterns of microeukaryotes under freshwater‐saltwater gradients, especially true in tropical regions. Here, we investigated microeukaryotes of six mixed freshwater‐saltwater regions in the Pearl River Estuary and surrounding coasts in southern China, with salinity ranging 0.1–32.0% and distances spanned up to 500 km, using molecular ecological methods. Results indicate that the biogeography of abundant and rare microeukaryotic communities was similar, both their co‐occurrence patterns and biogeographical patterns were driven by deterministic and stochastic processes. The environmental factors with higher selective pressure than dispersal limitation meant that the role of deterministic process in structuring communities was more significant than that of stochastic process, and salinity played important role in structuring both microeukaryotic communities and networks. The abundant communities had stronger influence on entire microeukaryotic communities and seemed to be more sensitive to environmental changes than their rare counterparts, while rare ones had stronger interspecific relationships. Finally, the geographic scale and environmental gradients of study regions should firstly be clarified in future research on the ecological processes of microeukaryotes before conclusions are drawn.

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Blue holes are unique geomorphological features with steep biogeochemical gradients and distinctive microbial communities. Carbon cycling in blue holes, however, remains poorly understood. Here we describe potential mechanisms of dissolved carbon cycling in the world's deepest blue hole, the Yongle Blue Hole (YBH), which was recently discovered in the South China Sea. In the YBH, we found some of the lowest concentrations (e.g., 22 μM) and oldest ages (e.g., 6,810 years before present) of dissolved organic carbon, as well as the highest concentrations (e.g., 3,090 μM) and the oldest ages (e.g., 8,270 years before present) of dissolved inorganic carbon observed in oceanic waters. Sharp gradients of dissolved oxygen, H2S, and CH4 and changes in bacterially mediated sulfur cycling with depth indicated that sulfur‐ and/or methane‐based metabolisms are closely linked to carbon cycling in the YBH. Our results showed that the YBH is a unique and easily accessible natural laboratory for examining carbon cycling in anoxic systems, which has potential for understanding carbon dynamics in both paleo and modern oceans—particularly in the context of global change.