Variations in deep-sea microbial composition and assembly mechanisms under different culture strategies

Deep-sea sediments harbor diverse microbial resources with immense biotechnological potential. Cultivating of these microorganisms is essential for studying their physicochemical properties, ecological functions, and resource development but remains a significant challenge. This study investigated the effects of different cultivation conditions on microbial diversity, community composition, coexistence patterns, and assembly processes from Yap Trench sediments (4,159-6,682 m depth). Results indicated that 44-55% of the microbial diversity was captured from the original sediments under high-pressure cultivation conditions, significantly higher than the 6-18% obtained under atmospheric pressure. Communities cultivated under high-pressure oligotrophic conditions closely resembled in situ microbiota, forming complex co-occurrence networks with high modularity and predominantly positive interactions, indicative of cooperative relationships enhancing community stability. However, serial subculturing and atmospheric cultivation favored pressure-tolerant groups like Proteobacteria. The deterministic processes (particularly heterogeneous selection) of community assembly were enhanced under high-pressure conditions, despite stochastic processes remaining the dominant mechanism. These findings highlight the adaptive responses of deep-sea microbial communities to extreme environmental pressures and underscore the importance of simulating high-pressure oligotrophic conditions for enriching diverse microbial groups. This study advances our understanding of deep-sea microbiology and provides a framework for exploring microbial functions and resources in extreme environments.