Humans have always been fascinated by the extremes of our world, from the highest mountain to the deepest ocean. Today we are beginning to understand these much more clearly. The latest scientific research at the deepest part of the ocean has revealed something extraordinary - biodiversity is extensive and flourishing despite the extreme conditions.
On March 6, Cell featured one commentary and three research articles as a cover story, systematically revealing the ecological characteristics of the hadal zone at water depths exceeding 6,000 meters. These findings mark the latest results from the Mariana Trench Environment and Ecology Research (MEER) Project, a collaboration launched in 2021 by BGI Group, the Institute of Deep-sea Science and Engineering (IDSSE) of the Chinese Academy of Sciences, Shanghai Jiao Tong University, and other Chinese scientific institutions.
On March 6, 2025, Cell published a set of articles - including one commentary and three research papers - reporting the latest findings from the Mariana Trench Environment and Ecology Research (MEER) Project. This collection was featured as a cover story in the latest issue of Cell.
The MEER Project: Unveiling the Deepest Ecosystem on Ocean
Information on dives and sampling from the MEER Project and its main scientific findings.
The hadal zone, while covering just 1–2% of the ocean floor, accounts for the deepest 45% of the ocean’s vertical depth. It is a realm of extreme conditions, where immense pressure, total darkness, limited food sources, and near-freezing temperatures create an environment that commonly considered inhabitable by only a few specialized organisms.
Through in-depth discussions and collaborations, researchers from multidisciplinary fields uncovered the features and environmental adaptations of hadal microorganisms, invertebrates (amphipods), and vertebrates (fishes), and brought novel understanding of the unexpected flourishing ecosystem in the deepest ocean regions.
Researchers mapped a specialized food chain - from microbes to amphipods to fishes - and discovered unique “Convergent Adaptation” strategies shared between two representative animals and microbes. These adaptations, shaped by the extreme deep-sea environment, transcend species boundaries.
Microbes: Flourishing in the Extreme with Remarkable Adaptations
Thanks to the development of an integrated method using latest automation and sequencing technology for environmental samples, the largest and most comprehensive hadal microbial metagenome dataset to date was created.
Their findings uncovered an extraordinary diversity of hadal microorganisms, with over 7,564 newly identified species-level genomes, nearly 90% of which had never been documented in public databases.
To survive at the deepest sea levels on earth, hadal microorganisms have developed a unique set of evolutionary traits for energy intake and pressure resistance. By analyzing distinct ecological processes and microbial genomic/metabolic traits, scientists have identified two distinct adaptation strategies.
Extraordinary novelty and adaptation strategies of the Deepest Ocean microbiome revealed by the MEER dataset.
Some microorganisms have evolved streamlined genomes, highly specialized in functions that allow them to adapt to the extreme environment in deepest ocean. For example, Thermoproteota decomposes aromatic compounds - commonly existed in pollutants - as an energy source, allowing it to thrive in nutrient-limited environments. Additionally, it has developed strong antioxidant systems to withstand high pressure and low temperatures.
Others have developed versatile genomes with diverse metabolic abilities, enabling them to adapt to rapidly changing localized environments. Organisms like Chloroflexota can form biofilms, resist antibiotics, and develop flagella, giving them an advantage in the deepest marine ecosystem.
The research team also speculated the driving force behind the evolution of these microorganisms. Typically, random changes in DNA shape the evolution of most microbiomes, which in turn gradually influence ecosystems. However, in the hadal zone, these random forces had little impact. Instead, extreme conditions - such as crushing pressure and scarce food - consistently selected certain microbes. This process drove the unique microbial diversity and extraordinarily high novelty observed in the Mariana Trench samples.
Amphipods: Tiny Titans of the Deep
Beyond microorganisms, the research team made fascinating discoveries about Hirondellea gigas (H. gigas), an amphipoda species that thrives at depths of 6,800 to 11,000 meters - where pressure is equivalent to balancing an SUV on a fingertip.
Chromosome-level assembly of the amphipod Hirondellea gigas from the Mariana Trench and the genomic characters related to repetitive sequences
The research team successfully generated a chromosome level genome assembly for H. gigas, spanning a large genome size of 13.92 gigabytes (Gb). This represents the first-ever genome of the animal from the deepest ocean. Notably, more than 70% of the H. gigas genome consists of repetitive sequences, which may contribute to its ability to withstand deep-sea pressure.
Furthermore, they generated 245.97 terabytes (Tb) of whole-genome sequencing data, the largest dataset ever sequenced for a single marine species. Despite their extreme habitat, H. gigas populations showed no genetic differentiation across depths, suggesting they can migrate freely across a 4,000-meter vertical range. However, the genomes of H. gigas vary depending on their geographical location. Specifically, populations in the West Philippine Basin, located 1,500 km away, differ from those in the Mariana and Yap Trenches. This finding suggests that geographic isolation influences genetic evolution.
Additionally, researchers found that the interactions between H. gigas and its symbiotic microbes in intestine may play a vital role in helping H. gigas adapt to its extremely high-pressure and food-scarce environment.
Deep-Sea Fish: Evolutionary Marvels of the Ocean
The researchers also examined 11 species of deep-sea fish, uncovering remarkable genetic adaptations that allow them to survive in extreme depths.
Sampling information and morphological characteristics of deep-sea fish species.
Genetic analysis suggests that some deep-sea fish lineages date back to the mid- or early Cretaceous period, surviving multiple mass extinction events. Most modern deep-sea fish colonized these depths after the Cretaceous–Paleogene extinction event, which wiped out the dinosaurs.
Many deep-sea fish have lost the ability to see visible light, but some species, such as deep-sea Aulopiformes and Beryciformes, have retained vision genes that may help them detect bioluminescent signals from other deep-sea creatures. Hadal snailfish, on the other hand, have completely lost photopic vision but have enhanced low-light vision genes.
A key discovery found that many deep-sea fish species below 3,000 meters have undergone a unique genetic transformation in the rtf1 gene, which may be the key to maintaining stable gene expression under extreme pressure.
One of the most surprising findings challenges a long-standing scientific assumption about deep-sea adaptation. Previous research suggested that trimethylamine-N-oxide (TMAO), a compound that stabilizes proteins under high pressure, increases in fish as depth increases. However, this study found no significant rise in TMAO levels in fish living below 6,000 meters, prompting a reassessment of previous deep-sea research methods.
Disturbingly, the team discovered persistent organic pollutants - industrial waste compounds - in both fish and sediment samples from the Challenger Deep in the Mariana Trench and the Philippine Trench. This alarming finding underscores the far-reaching impact of human activities, even in the most remote and extreme environments on earth.
A New Era in Deep-Sea Exploration
These findings significantly advanced the world’s understanding of life in the deepest parts of the ocean, revealing unprecedented biodiversity and evolutionary adaptations in these remote ecosystems. All genomic data generated by this research, including information on deep-sea microbes, amphipods, and fish, has been made freely accessible to the global scientific community through online platforms.
"Our study not only redefines our understanding of the limits of deep-sea life but also unveils an 'extreme survival manual' written through hundreds of millions of years of evolution,” explained Dr. Xun Xu, Director of BGI-Research, the scientific research arm of BGI Group. “Deciphering these life forms is both a journey of scientific exploration and a renewed responsibility for humanity. In the future, with technological advancements and global scientific collaboration, the deep sea may reveal more secrets about the origins, adaptation, and symbiosis of life - offering critical insights for the sustainable stewardship of earth's ecosystems."
The research papers can be accessed here:
MEER: Extraordinary flourishing ecosystem in the deepest ocean
https://doi.org/10.1016/j.cell.2024.12.037
Microbial ecosystems and ecological driving forces in the deepest ocean sediments
https://doi.org/10.1016/j.cell.2024.12.036
The amphipod genome reveals population dynamics and adaptations to hadal environment
https://doi.org/10.1016/j.cell.2025.01.030
Evolution and genetic adaptation of fishes to the deep sea
https://doi.org/10.1016/j.cell.2025.01.002