The deep sea as the largest and maybe most hostile environment on Earth is still underexplored especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea genetic dataset comprising of 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures, revealing unprecedented microbial genetic diversity. Global sequence analysis combined with biophysical and biochemical measurements allowed us to link specific protein structures with genetic variants required for life in the deep sea and to advance biotechnology. Furthermore, estimating the rate of substitutions revealed that genes involved in replication, recombination and repair appear to be critical for microbial life in the deep sea. Among them was a structurally unique helicase which enabled ultra-rapid nanopore sequencing (390±11 bp/s). Thus, our work not only deciphers ecological drivers and evolutionary forces underpinning the deep-sea genetic diversity, but it also bridges genetic knowledge with biotechnology.

This Perspective introduces the “Mariana Trench Environment and Ecology Research (MEER)”, the first systematic study of hadal ecosystems (>6,000m) in the Mariana Trench. Using China’s “Fendouzhe” submersible (2021), 33 dives collected 227 sediment cores, seawater, and macrofauna (amphipods, snailfish). Key findings: (1) Microbial diversity—extreme novelty and adaptation to ultrahigh pressure, revealed by 92 Tb metagenomic data; (2) Macrofauna evolution—horizontal gene flow in amphipods and vertebrate colonization by snailfish; (3) Ecosystem connectivity—trenches link surface oceans and Earth’s interior, hosting microbial hotspots driving biogeochemical cycles. MEER’s open-access databases and methodologies redefine the hadal zone as a dynamic, biodiverse frontier critical to Earth’s processes.

Systematic exploration of the hadal zone, Earth’s deepest oceanic realm, has historically faced technical limitations. Here, we collected 1,648 sediment samples at 6-11 km in the Mariana Trench, Yap Trench, and Philippine Basin for the Mariana Trench Environment and Ecology Research (MEER) project. Metagenomic and 16S rRNA gene amplicon sequencing generated the 92-Tbp MEER dataset, comprising 7,564 species (89.4% unreported), indicating high taxonomic novelty. Unlike in reported environments, neutral drift played a minimal role, while homogeneous selection (HoS, 50.5%) and dispersal limitation (DL, 43.8%) emerged as dominant ecological drivers. HoS favored streamlined genomes with key functions for hadal adaptation, e.g., aromatic compound utilization (oligotrophic adaptation) and antioxidation (high-pressure adaptation). Conversely, DL promoted versatile metabolism with larger genomes. These findings indicated that environmental factors drive the high taxonomic novelty in the hadal zone, advancing our understanding of the ecological mechanisms governing microbial ecosystem in such an extreme oceanic environment.

The amphipod Hirondellea gigas is a dominant species inhabiting the deepest part of the ocean (~6,800-11000 m), but little is known about its genetic adaptation and population dynamics. Here, we present a chromosome-level genome of H. gigas, characterized by a large genome size of 13.92 Gb. Whole-genome sequencing of 510 individuals from the Mariana Trench indicates no population differentiation across depths, suggesting its capacity to tolerate hydrostatic pressure across wide ranges. H. gigas in the West Philippine Basin is genetically divergent from the Mariana and Yap Trenches, suggesting genetic isolation attributed to the geographic separation of hadal features. A drastic reduction in effective population size potentially reflects glacial-interglacial changes. By integrating multi-omics analysis, we propose host-symbiotic microbial interactions may be crucial in the adaptation of H. gigas to the extremely high-pressure and food-limited environment. Our findings provide clues for adaptation to the hadal zone and population genetics.

The deep sea, especially hadal zones, characterized by high-hydrostatic pressure, low temperatures, and near-total darkness, present some of the most challenging environments for life on Earth. However, teleost fish have successfully colonized these extreme habitats through complex adaptations. We generated genome assemblies of 12 species, including 11 deep-sea fishes. Our findings reconstructed the teleost deep-sea colonization history and revealed the overall impact of the deep-sea environment on fishes. Interestingly, our results question the previously assumed linear correlation between trimethvlamine oxide (TMAO) content and depth. By contrast, we observed a convergent AA replacement in the rtf1 gene inmost deep-sea fishes under 3,000 m, and in vitro experiments suggest that this mutation can influence transcriptional efficiency, which is likely to be advantageous in the deep-sea environment. Moreover, our study underlines the pervasive impact of human activities, as we detected the presence of persistent organic pollutants in species from the Mariana Trench.