Genomic convergence and geographical divergence: multi-scale salinity adaptation mechanisms of microbiomes in shale gas flowback and produced water.

Authors

Xinjie Shi, Siyu Duan, Yulian Zhang, Bowen Hou, Lilan Zhang

Published in

Water research. Volume 309. Issue Pt B. Pages 127270. Nov 03, 2026. Epub Nov 03, 2026.

Abstract

Shale gas flowback and produced water (FPW) represents a spatially heterogeneous artificial hypersaline ecosystem, in which the salt‑tolerance‑related genetic repertoire of indigenous microorganisms and the mechanisms shaping in‑situ community salinity adaptation patterns remain poorly clarified. Here, we collected metagenomic data from major shale gas-producing regions worldwide, encompassing 68 FPW samples from five basins: the Sichuan Basin, Anadarko Basin, Denver-Julesburg Basin, Western Canadian Sedimentary Basin, and Permian Basin. Based on these data, we constructed a genomic dataset comprising 699 high-quality MAGs to unravel the multi-scale salt adaptation mechanisms of the FPW microbiomes. Genomic results revealed that over 80% of FPW microbes encoded salt-in and salt-out pathways, demonstrating widespread genetic functional redundancy across geographically isolated basins. Despite convergent genomic potential, FPW microbiomes exhibited basin-specific adaptive differentiation, with Sichuan and Permian Basins favoring the salt‑in pattern and Anadarko Basin favoring the salt‑out pattern. Given the high conservation of gene repertoires and the physicochemical differences across basins, such salinity adaptation patterns decoupling between genomic repertoire and community adaptation may be driven primarily by environmental filtering. Machine learning identified trehalose metabolism genes (e.g., K00697, K17311 and K17313) and K⁺ uptake genes (e.g., K03498) as the biomarkers governing salt‑out and salt‑in pattern biases, respectively. Metabolic cross-feeding mediated by trehalose public metabolites, supported by keystone taxa of Thermotogota and Bacillota, potentially further enhanced community-level salt tolerance via interspecific metabolic synergy. This study elucidates the hierarchical adaptation mechanism coupling intrinsic genomic potential and local environmental filtering, providing novel ecological insights into microbial salinity adaptation and theoretical support for hypersaline wastewater biological treatment.

PMID:
42998561
Bibliographic data and abstract were imported from PubMed on 08 Nov 2026.

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