Genome-resolved metagenomics reveals seasonally defined life strategies in hypersaline sediments

Abstract

Abstract Background. Hypersaline sediments are long-standing models for microbial adaptation and are increasingly regarded as reservoirs of novel biosynthetic potential, including surface-active compounds. Inferences about biosurfactant production in such communities have rested largely on taxonomic affiliation, targeted single-gene surveys or metabolite detection, rather than on genome-resolved evidence that the pathways are encoded. The seasonal restructuring of these communities has also rarely been resolved at genome level. Results. We sequenced summer and winter sediments from the hyperarid Qaidam Basin on the northern Tibetan Plateau, recovering 44 metagenome-assembled genomes and 1,468 biosynthetic gene clusters from 2.98 Gbp of assembly. Evaporative and cryoconcentration processes raised winter porewater chloride by two to three orders of magnitude relative to summer. The community switched between osmoadaptation strategies. Summer sediments were dominated by salt-in haloarchaea with acidic proteomes and rhodopsin phototrophy, whereas winter sediments were dominated by salt-out bacteria with near-neutral proteomes and winter-enriched compatible-solute biosynthesis. The salt-in bacterium Salinibacter occupied the expected intermediate position, providing an internal control. The winter surface-active response was envelope-associated rather than secreted, comprising phospholipase-derived lysophospholipids, desaturase-mediated membrane remodelling, substitution of phospholipids by phosphorus-free ornithine and sulfoquinovosyl lipids, and capsular exopolysaccharide export. Dedicated secreted biosurfactant pathways were not detected. Of 69 NRPS clusters, only one carried the starter condensation domain diagnostic of lipopeptide assembly, and it matched no characterised reference. Profile-based, read-level and orthology-based searches independently recovered no complete lipopeptide, rhamnolipid or trehalolipid pathway. Apparent biosurfactant genes in 40 of 44 genomes resolved to housekeeping homologues upon domain verification, and an independent catalogue of 1,773 regional genomes reproduced the same absence. Conclusions. Surface activity in this hypersaline community is retained at the cell envelope rather than secreted, and dedicated biosurfactant biosynthesis is not a community-level trait. Because both taxonomic affiliation and gene-name annotation overestimate this capacity, genome-resolved verification is required before biosynthetic potential inferred from extreme environments is treated as real.