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Here, we combined hydrogeochemical profiling, 16S rRNA gene amplicon sequencing, indicator species analysis, null-model inference, and predictive functional profiling to characterize community composition, assembly processes, and functional potential across 88 samples at South Sumujaran Lake, Badain Jaran Desert, China. The samples spanned fresh groundwater in two transects, brackish-to-saline groundwater in the transition zone, and hypersaline lake water along a hydrologically connected continuum, covering a more than 300-fold range in salinity. Despite hydrological connectivity, lake water communities were almost completely distinct from those in the two groundwater transects and the transition zone. The transition zone also supported a distinct set of indicator taxa, suggesting that its community composition was not explained by mixing alone. Assembly processes shifted along the continuum: dispersal limitation was the most prevalent process system-wide and occurred within the two low-salinity groundwater transects but not in the transition zone or hypersaline lake, whereas homogeneous selection increasingly structured communities toward these higher-salinity zones. Predicted functional profiles differed little between the two groundwater transects but markedly between groundwater and lake water. This zone-specific pattern helps explain how steep solute gradients structure microbial communities along hydrologically connected flow paths in groundwater-fed terminal lakes of arid regions.<\/jats:p>","DOI":"10.1093\/femsec\/fiag113","type":"journal-article","created":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T11:37:30Z","timestamp":1791027450000},"source":"Crossref","is-referenced-by-count":0,"title":["Microbial community assembly along a groundwater\u2013hypersaline lake continuum in the Badain Jaran Desert"],"prefix":"10.1093","volume":"102","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9165-9828","authenticated-orcid":false,"given":"Meiqing","family":"Lu","sequence":"first","affiliation":[{"name":"The University of Hong Kong CUG-HKU Joint Centre for Coastal Groundwater and Ecosystem Studies, Department of Earth and Planetary Sciences, , Hong Kong SAR ,","place":["China"]},{"name":"Archaeal Biology Centre, Synthetic Biology Research Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Key Laboratory of Marine Microbiome Engineering of Guangdong Higher Education Institutes, Institute for Advanced Study, Shenzhen University , Shenzhen 518060 ,","place":["China"]},{"name":"Shenzhen Institute of Research and Innovation, The University of Hong Kong , Shenzhen 518057 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaolang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Florida Atlantic University Department of Geosciences, , Boca Raton, FL 33431 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiu Jimmy","family":"Jiao","sequence":"additional","affiliation":[{"name":"The University of Hong Kong CUG-HKU Joint Centre for Coastal Groundwater and Ecosystem Studies, Department of Earth and Planetary Sciences, , Hong Kong SAR ,","place":["China"]},{"name":"Shenzhen Institute of Research and Innovation, The University of Hong Kong , Shenzhen 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