Exploring the abyss through recent advances in microbial profiling technologies

Abstract The deep ocean is home to a diverse array of microbial communities crucial for biogeochemical cycling and functioning of the planet. However, marine diversity remains poorly understood due to extreme environmental conditions such as high pressures, wide temperature ranges, and limited food resources. Traditional measures like taxonomic diversity are inadequate in assessing the functional roles of species within these communities. This review examines recent advancements in metagenomics, metatranscriptomics, metaproteomics, and single-cell genomics, which have transformed our ability to study deep-sea microbes. These technologies provide insights into the metabolic capabilities and ecological functions of microorganisms thriving in this challenging environment. The concept of microbial dark matter underscores the prevalence of uncultivated taxa in the deep ocean, whose ecological roles and contributions to biogeochemical processes remain largely unexplored. Integrated multi-omics approaches have begun to unravel the complexities of deep-sea microbial ecosystems, revealing a highly diverse “rare biosphere” alongside dominant populations. These findings challenge conventional views of microbial diversity and highlight the need for comprehensive strategies to characterize and understand the functional diversity of deep-sea microbial communities. This synthesis emphasizes the importance of advancing our knowledge of deep-sea microbiomes to better comprehend their contributions to global nutrient cycles and ecosystem dynamics. Continued research efforts using cutting-edge molecular techniques will be essential for unraveling the intricate relationships and adaptive strategies of these microbial communities in response to environmental pressures in the deep ocean.