Invisible Microbial "Oases" in the Deepest Ocean: MEER Phase II Results Published in Cell Host & Microbe

 

Recently, the Phase II findings of the Mariana Trench Environment and Ecology Research (MEER) project, jointly initiated by Shanghai Jiao Tong University, the Institute of Deep-sea Science and Engineering of the Chinese Academy of Sciences, BGI Group, and other institutions, with Professor Xiang Xiao of Shanghai Jiao Tong University serving as the convening scientist, were published as a collection in the internationally renowned journal Cell Host & Microbe. The collection comprises one Forum article and three research articles.

The publication follows the Phase I findings of the MEER project, which appeared as a cover collection in Cell in 2025, marking another major advance by the project within just one year. The new collection was also highlighted by the journal’s editors for revealing previously underappreciated genetic diversity and microbial processes in the deepest ocean.

For the first time, the research team systematically reveals the invisible microbial “oases” hidden in the hadal zone from multiple perspectives, including the hadal high-pressure activation hypothesis, proteome-level active microbial networks, global deep-sea genetic resources and protein structures, and topographic controls on hadal carbon cycling. Together, these findings advance hadal research from “depicting ecological patterns” toward a new stage of understanding underlying mechanisms and mining biological resources, underscoring China’s continuing international leadership in hadal life science.

The hadal zone, extending below 6,000 meters, represents the deepest and one of the most extreme environments on Earth and was once regarded as a “forbidden zone for life.” With the support of the full-ocean-depth human-occupied vehicle Fendouzhe, Phase I of the MEER project elucidated life-adaptation strategies and species composition in hadal ecosystems and provided the first systematic ecological portrait of the deepest marine ecosystem.

Building on this foundation, Phase II has moved further forward. Through the team’s independently developed DNA-protein co-extraction and co-analysis methodology, the researchers overcame major challenges associated with low biomass, low extraction efficiency, and the difficulty of identifying microbial activity in extreme environments. Combined with large-scale integration of global datasets, in situ high-volume filtration of hadal seawater, high-resolution mapping of hadal topography, and integrated geochemical-microbial modeling, the project has established a complete research chain spanning theoretical innovation, technological innovation, scientific discovery, and resource mining.

 

01 A New Perspective: Invisible Microbial Oases in Extreme Environments

From Hadal High-Pressure Activation to Convergent Adaptation

The Forum article systematically proposes the “hadal high-pressure activation” hypothesis and the concept of “convergent adaptation,” providing a new theoretical framework for explaining the unexpectedly high microbial biomass, diversity, and metabolic activity found in the hadal zone. The authors propose that ultra-high pressures above 60 MPa do not simply inhibit life. Instead, they may trigger the generation of reactive oxygen species (ROS), which can promote the oxidative breakdown of otherwise refractory organic compounds while accelerating microbial adaptive evolution, thereby helping to create invisible microbial “oases” at depths approaching 11,000 meters. The article further suggests that ROS-centered antioxidant strategies represent a convergent adaptation mechanism shared across diverse extreme environments and life forms, including hadal microorganisms, Mount Everest microbiomes, radiation-resistant microorganisms, and drought-tolerant plants. This perspective moves beyond the conventional paradigm of environmental inhibition versus survival resistance by proposing that extreme environmental stressors may also act as biological activators. It offers a new conceptual framework for rethinking the distribution of extreme life on Earth and for exploring the possibility of extraterrestrial life.

 

02 The Hadal Zone Is Far from Silent

Metaproteomics Decodes Active Life Networks in the Deepest Ocean

The first research article reports the first systematic metaproteomic characterization of microorganisms and viruses in hadal seawater, revealing active life networks in the deepest seawater. Using the team’s DNA-protein co-extraction and co-analysis approach, the researchers constructed the Active Protein Dataset of the Mariana Trench Environment and Ecology Research Project (MEER-APD), containing 135,073 non-redundant active proteins, more than 95% of which are hadal-specific. The study shows that, under hadal high-pressure conditions, microorganisms actively exploit refractory organic matter and expand their use of carbon and energy sources through processes including thiosulfate oxidation and heavy-metal-associated metabolism, thereby sustaining highly active metabolic networks. Temperate and virulent viruses, meanwhile, employ distinct yet complementary ecological strategies to regulate microbial communities, contributing to elemental-cycling patterns markedly different from those of the upper ocean. By moving hadal microbiology from functional prediction to comprehensive in situ validation of microbial activity, the study fundamentally challenges the traditional view of the hadal zone as a biologically “silent” environment.

 

03 Hidden Microbial Hotspots at Nearly 11,000 Meters

Topography Reshapes Microbial Ecosystems in the Deepest Ocean

The second research article further reveals that active hadal ecosystems are strongly shaped by seafloor topography, giving rise to previously overlooked microbial hotspots. Through fine-scale topographic and sediment analyses in the Challenger Deep of the Mariana Trench, the researchers found that the topographic position index (TPI) explained more local geochemical variation than water depth and emerged as an important determinant of microbial community structure and activity. Concave topographic features create previously unrecognized hidden microbial hotspots in the hadal zone, sustaining high microbial biomass, diversity, and metabolic activity. These locations may also function as interchange hubs, facilitating microbial exchange between hadal and shallower ocean regions. The findings challenge the conventional view of hadal trenches as one-way depositional sinks in which materials and microorganisms simply accumulate at depth. The population-dispersal tracking approach developed by the team has also been made openly available, providing a new tool for deep-sea carbon-budget assessment and large-scale ecological prediction.

 

04 The World’s Largest Deep-Sea Gene Resource Atlas

Unlocking the Deep Sea as an “Evolutionary Engine”

The third research article extends the work from fundamental scientific discovery to biological resource mining and potential applications. By integrating 2,138 deep-sea metagenomic samples from around the world, including hadal environments, the team constructed a deep-sea gene catalog (DSGC) containing 502 million non-redundant genes, and predicted more than 2.4 million representative protein structures, establishing the largest deep-sea gene resource atlas and protein-structure resource to date. The study identifies the deep sea as a distinctive “evolutionary engine,” characterized by stronger signals of rapid evolution. It also uncovered 392 protein domains with no detectable structural match, pointing to a substantial reservoir of previously unexplored molecular architectures.Through structure-guided screening and experimental validation, the researchers identified a divergent helicase with potential biotechnological applications that approximately doubled nanopore DNA sequencing speed relative to standard enzymes. The study provides a reusable methodological framework for exploring the genetic “dark matter” of the deep sea and translating previously inaccessible biological diversity into new opportunities for biotechnology innovation.

Taken together, the four studies form an integrated body of work spanning high-pressure activation, activity validation, global significance, and resource mining. They provide a comprehensive picture of microbial activity mechanisms and biological resource potential in the deepest parts of the ocean, while revealing the potential role of unexpectedly thriving hadal ecosystems as important hubs in global biogeochemical cycling.

Beginning with scientific exploration enabled by the full-ocean-depth human-occupied vehicle "Fendouzhe", the MEER project has gradually developed into a large interdisciplinary, cross-sector, and cross-institutional research platform that combines investigator-driven exploration with organized scientific research. Following the milestone breakthroughs of Phase I, the team did not stop at a one-time discovery. Supported by a sustainable organizational model and a dynamic research talent pipeline, it produced another series of original findings within just one year. These achievements demonstrate the sustained innovative capacity generated by organized research driven by breakthroughs in fundamental science, while also showing how deep-sea genetic resources can contribute to the development of new quality productive forces and open new possibilities for biotechnology, medicine, healthcare, and other industries. The hadal active protein dataset, the deep-sea gene and protein structure atlases, and other resources generated by this research have all been incorporated into the world's largest hadal biological database, which the MEER project continues to build. These resources are shared openly with the international scientific community through major international science programmes including the UN Ocean Decade and the UN Science Decade, contributing Chinese expertise to humanity's efforts to understand the deepest ocean and to develop deep-sea biological resources.

Links to the papers:

1. Seeking the invisible microbial oases in extreme environments (Forum)

https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(26)00306-9

2. Unveiling active microbial processes in Earth’s deepest seawater

https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(26)00282-9

3. Hadal topography incubates hidden microbial hotspots in the deepest ocean

https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(26)00275-1

4. The genetic repertoire of the deep-sea microbiome: from sequence to structure and function

https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(26)00202-7