Vertical and Spatial Distribution of Microbial Sources in Mangrove Wetland Groundwater–Sediment Systems: Implications for Coastal Aquifer Dynamics

Mangrove wetlands are critical ecotones between terrestrial and marine environments, yet the spatial distribution and environmental origins of microbial communities in their groundwater–sediment systems remain poorly characterized. Microbial source tracking using the SourceTracker2 Bayesian algorithm was applied to 22 samples collected along a single mangrove wetland transect on Qi’ao Island, Pearl River estuary, China—comprising a freshwater well, supratidal and transition zones, seaward mangrove wetland piezometers, and two 60-cm sediment cores from a mangrove-vegetated and an adjacent unvegetated site. Shannon diversity of source profiles was narrowly constrained across the whole gradient (3.15 ± 0.26; coefficient of variation 8.4%) and did not differ significantly among sample groups (Kruskal–Wallis H = 7.38, p = 0.194), indicating strong diversity buffering. In contrast, source composition was strongly structured (PERMANOVA pseudo-F = 4.14, R2 = 0.56, p = 0.0001). Mangrove core sediments were dominated by sediment-associated (9.98%), rhizosphere (8.58%) and soil (6.69%) sources, whereas the adjacent non-mangrove core was dominated by freshwater sediment (17.52%) and marine sediment (9.29%) sources. Aggregating the 104 reference sources into eight ecological categories showed that vegetation- and soil-derived sources accounted for 29.5% of the mangrove core but only 20.1% of the non-mangrove core (p = 0.035), while freshwater sources showed the opposite pattern (15.3% versus 32.2%, p = 0.002). Wastewater- and host-associated sources together contributed 39.3% in mangrove wetland piezometers, identifying a pronounced anthropogenic imprint. Depth profiling revealed systematic vertical structuring in the mangrove core only, with marine and undifferentiated sediment sources decreasing with depth (β = −0.377 and −0.115% cm−1; R2 = 0.71 and 0.76; p = 0.034 and 0.025) and vegetation- and soil-derived sources increasing with depth (β = +0.375% cm−1, R2 = 0.75, p = 0.026); the non-mangrove core was vertically homogeneous. These results quantify the interplay of terrestrial, marine and anthropogenic microbial inputs in mangrove groundwater systems and provide a baseline for monitoring contaminant transport and ecosystem integrity in coastal aquifers. Because the design comprises a single transect sampled on one wet-season occasion with pseudo-replicated depth intervals, the findings should be treated as a spatially explicit baseline rather than a generalizable description of mangrove microbiomes.