Abstract
Small coastal rivers form compressed river–estuary–offshore continua that regulate biogeochemical cycling yet remain underexplored. Here we show that gradient compression is a pivotal control on sediment microbial community turnover. Using full-length 16S and ITS sequencing, we found that bacterial assembly is predominantly deterministic (> 50%), whereas fungal assembly is largely stochastic (> 66%). This divergence yields contrasting spatial outcomes: estuaries emerge as bacterial network hotspots but fungal dilution zones, while offshore selective pressure promotes functional specialisation and reduced predicted redundancy. Together, these patterns suggest ecosystems that are structurally complex yet potentially functionally vulnerable. By integrating community structure, assembly processes, and functional profiles with environmental gradients, our study proposes a mechanism by which steep gradients can erode functional redundancy and, potentially, resilience. We further show that such small-scale systems—ubiquitous worldwide—may be especially sensitive to perturbations, underscoring the need for early-warning indicators within watershed risk management.
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Data availability
All data supporting the findings of this study are openly available on Figshare (https://doi.org/10.6084/m9.figshare.30235306). Sequencing data and associated metadata are publicly available via NCBI SRA under BioProject PRJNA1280671, including BioSamples SAMN49528295–SAMN49528311 and SRA accessions SRR34096328–SRR34096344 (16S) and SRR34096417–SRR34096433 (ITS).
Code availability
All code used to generate the results and figures reported in this study is openly available on Figshare (https://doi.org/10.6084/m9.figshare.30235306).
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Acknowledgements
This work was supported by the National Key Research and Development Program of China (Grant no. 2022YFC3203603) and the Special Fund for Natural Resources Development of Jiangsu Province (Marine Science and Technology Innovation) under the project “Research on the Evaluation and Prevention Technology System of Coastal Erosion Geological Hazards in Jiangsu Province” (Grant no. JSZRHYKJ202104). We thank Shanghai Jianhai Environmental Monitoring Technology Co., Ltd. for technical and logistical support during estuarine field sampling. The authors sincerely thank the editor team and anonymous reviewers for their constructive comments and insightful suggestions, which greatly improved the quality of this manuscript.
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W.W. and Q.F. conceptualised and designed the study. J.X. conducted field sampling, laboratory experiments, statistical analyses, data visualisation, and prepared and revised the manuscript. K.W., Y.F., D.Z., and W.W. contributed to field sampling. K.W. provided expertise on the marine context, while K.Z. contributed expertise on the riverine context. Funding was secured by W.W. and K.W. W.W. supervised, reviewed, and validated the manuscript.
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Xu, J., Wan, K., Zhang, D. et al. Gradient compression drives divergent sediment bacterial and fungal assembly from river to sea.
Commun Earth Environ (2026). https://doi.org/10.1038/s43247-026-03504-0
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DOI: https://doi.org/10.1038/s43247-026-03504-0
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