Editor’s note: As we expand outward from Earth to other worlds we are almost certainly going to encounter things we did not expect to find – things that are unlikely or impossible on Earth. Life on other worlds may arise from a totally different set of chemical pathways than was the case on Earth. Or it may follow a very similar path. Or both. How do we estimate what could exist such that we are better prepared to search for the unexpected? Using systems such these researchers have done to identify the plethora of compounds that are possible and functional in Earth life is one way to start to figure that out.
The deep sea is a unique ‘evolutionary engine’ with one of the richest and most unexplored sources of genetic diversity on Earth, according to a major new study that has assessed its potential to transform biotechnology and DNA sequencing technologies.
Despite covering more than half of the Earth’s surface, this environment is still one of the least understood when it comes to the genes of the organisms that live there, generating and hosting vast genetic diversity that remains largely untapped.
Now in one of the most comprehensive studies of its kind, a team of almost 60 researchers from the UK and China analysed more than 2100 samples spanning global deep-sea environments to build a genetic dataset containing more than 500 million unique genes and 2.4 million predicted protein structures.
By linking genetic variation to protein structure and function, the research bridges a critical gap between basic science and real-world applications, and highlights the immense potential of deep-sea biodiversity for developing new technologies in fields ranging from biotechnology to medicine.
The findings, published today in the journal Cell Host & Microbe, reveal a remarkable paradox: while the genetic ‘blueprints’ of deep-sea life vary enormously, the essential shapes of the proteins they produce often remain strikingly similar.
This suggest that while life in the deep sea – particularly the regions at depths exceeding 1000 metres – is constantly evolving at the genetic level, it still relies on some stable, core designs to survive extreme conditions.
Co-lead author Prof Thomas Mock, from the University of East Anglia’s (UEA) School of Environmental Sciences, said: “Our findings show how we can address some of today’s biggest scientific and technological challenges by making use of microbes from the deep sea, and that these environments, with their physical isolation and extreme conditions, serve as hotspots for evolution.
“This work reframes the deep sea not merely as a reservoir of biodiversity, but as a unique evolutionary engine that actively shapes, diversifies, and hosts a range of functionally distinctive genetic traits.
“Nature has already solved many of the problems we face in technology – we just need to find and understand those solutions.”
Integrated Deep-Sea microbial Gene Catalog (DSGC)
(A) Geographic distribution of the 2,138 deep-sea samples in the DSGC.
(B) Depth breakdown of samples used in this study.
(C) Total gene count and breakdown of gene number by habitat in DSGC. The shadowed zone in the hadal ecosystem indicates the unigenes contributed by the MEER project. HVs, hydrothermal vents; MSs, methane seeps; HEs, hadal ecosystems; and OEs, other deep-sea ecosystems.
(D) Functional and taxonomic annotation of DSGC.
(E) Ternary plot showing the proportional relations of the number of effective sequences (Nf) for each Pfam family (dots). Blue dots indicate families where the DSGC’s Nf is the highest among the three catalogs.
(F) Venn diagram of unique and shared gene clusters (in millions) among DSGC, OM-RGC, and TSGC.
(G) Unique and shared gene clusters between DSGC and the Global Ocean Gene Catalog (GOGC), and the number of unigenes in exclusively DSGC gene clusters. M, millions.
Extreme environment
The deep sea is one of the most challenging environments on the planet – characterised by crushing pressure, temperatures ranging from near-freezing (< 4°C) to above 100°C at hydrothermal vents, limited oxygen and permanent darkness.
Yet it is precisely these harsh conditions that appear to drive innovation at the molecular level.
The study used sample data from habitats including hadal trenches, such as the Mariana Trench in the Pacific Ocean, hydrothermal vents and methane seeps, all home to diverse life forms.
The researchers identified key groups of proteins involved in DNA replication, recombination and repair as evolving particularly quickly. These proteins have developed specialised features that help organisms survive and function under extreme conditions like high pressure and low temperatures.
Breakthrough for DNA sequencing
Among the most promising discoveries is a unique variant of a helicase – a protein that unwinds DNA. This deep-sea version shows unusual structural features that could improve nanopore DNA sequencing – a cutting-edge technology used in research, medicine and environmental monitoring – by giving better control over how fast DNA is read.
“This is a clear example of how studying life in extreme environments can directly lead to new tools and innovations,” said first author Dr Yang Guo, of the Institute of Oceanology, Chinese Academy of Sciences, in China.
“Our work lowers the barrier to marine microbial bioprospecting, offering a practical and scalable solution for investigating deep-sea ‘genomic dark matter’.”
Dr Yuliang Dong, from BGI Research, Shenzhen, in China, added: “We expect this will not only accelerate biotechnological innovation but also incentivise broader research into extreme oceanic environments.”
Expanding understanding
The research draws on recent advancements in deep-sea sampling and AI-based protein structure prediction tools, integrating global deep-sea genetic data with advanced computational and experimental techniques, creating one of the largest resources of its kind for exploring marine life at the molecular level.
Harnessing the oceans as a biotechnological resource is an established concept that has already yielded significant bioactive discoveries advancing medicine and industry.
However, the authors say their study takes this further, expanding known marine gene diversity by more than 50 per cent and substantially broadening our understanding of the ecological and evolutionary drivers of deep sea genetic diversity, as well as providing a framework for harnessing this largely untapped biological resource.
This research was supported by the National Key Research and Development Program of China, and the ‘Pioneer’ and ‘Leading Goose’ R&D Program of Zhejiang Province.
The genetic repertoire of deep-sea microbiome: from sequence to structure and function, Cell Host and Biome
Astrobiology,
