Habitat heterogeneity drives microbial community assembly and functional specialization in extremely arid ecosystems

ABSTRACT Extreme arid ecosystems present significant environmental challenges, yet the mechanisms by which habitat heterogeneity (e.g., salinity gradients, soil–sediment contrasts) shapes microbial community assembly and functional specialization remain poorly understood. This study integrated culture-dependent and culture-independent approaches to investigate microbial diversity, assembly processes, and metabolic potential across wasteland soils, desert soils, and saline lake sediments in the Turpan–Hami Basin. High-throughput sequencing revealed habitat-specific patterns, with lake sediments exhibiting significantly greater OTU richness and Shannon diversity than wasteland and desert soils ( P < 0.05). These shifts were driven by salinity-dependent taxonomic succession, notably the dominance of Gammaproteobacteria , Halobacteria, and Desulfobacteria in hypersaline lakes. Ecological assembly processes diverged across habitats, with deterministic processes (heterogeneous/homogeneous selection) dominated in deserts and moderate saline lakes, whereas stochastic processes (dispersal limitation, drift) prevailed in wastelands and hypersaline systems. Metabolic profiling highlighted habitat-specific functional specialization: terrestrial systems were characterized by nitrogen-cycling, while saline lakes displayed partitioned sulfur metabolism (e.g., sulfate respiration in high-salinity sediments). Co-occurrence network analyses revealed greater topological complexity in freshwater lakes than in extreme environments, reflecting contrasting resilience strategies. Cultivation strategies informed by sequencing results recovered 4.02% to 21.76% of the sequence-detected genera, significantly improving access to the uncultured majority. These findings demonstrate that habitat heterogeneity drives microbial community assembly and functional evolution in extremely arid ecosystems, underscoring the value of integrating omics with cultivation to uncover microbial dark matter. IMPORTANCE Understanding microbial adaptation in hyperarid environments is crucial for predicting ecosystem responses to extreme stressors. This study provides an integrative framework linking environmental heterogeneity to microbial community assembly and metabolic specialization across diverse habitats in one of Earth’s driest basins. Our findings demonstrate that deterministic environmental filtering dominates community assembly in deserts and moderately saline lakes, whereas stochastic processes prevail in wastelands and hypersaline systems. Habitat‑specific metabolic specialization is evident, with nitrogen cycling being key in terrestrial soils and sulfur metabolism central to saline lakes. By significantly improving the recovery of uncultured diversity through targeted strategies, this study bridges a major gap between molecular surveys and cultivable microorganisms. These findings advance ecological theory on community assembly and offer a model for studying microbial resilience and functional evolution under extreme aridity.

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