How deep-sea microbes build food in the dark using unexpected fuel
Genetic evidence from the deep Pacific Ocean shows that many microbes carry genes to make food from inorganic carbon using carbon monoxide and sulfur, rather than relying mainly on ammonia.
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Sunless energy
Miles beneath the ocean waves, sunlight never arrives. Yet life still flourishes in the pitch black. Microbes drive this world through deep sea chemoautotrophy, making their own food from dissolved inorganic carbon using chemical energy instead of sunlight.
For years, marine scientists assumed deep-sea carbon fixation depended mainly on nitrifiers. These are specialised microbes that harvest energy by oxidising ammonia. But new genetic clues suggest other chemical engines might run the abyss.
Rebuilding deep genomes
Researchers analysed 28 water samples gathered between 150 and 4,000 metres down in the Northeast Pacific Ocean. They pieced together scattered environmental DNA into 128 metagenome-assembled genomes across 13 microbial phyla.
The team screened these genomes for marker genes tied to carbon fixation and energy-releasing catabolism. Chemoautotrophs made up 11% to 26% of the sampled communities. Curiously, genes for the Calvin cycle and 3-hydroxypropionate bi-cycles outnumbered the pathways typical of nitrifiers.
Instead of ammonia, these organisms appear primed to burn different fuels. Around 77.3% of the reconstructed chemoautotrophic genomes carried genes to oxidise carbon monoxide, and 69.5% carried genes for sulfur. Only 5.5% encoded machinery to oxidise ammonia, and 3.1% had genes for methane.
Flexible survivors
Think of these microbes as hybrid off-roaders with multi-fuel tanks. They can tap carbon monoxide, sulfur, or imported organic matter when one fuel runs dry. Half encoded multiple energy-yielding pathways, and 99% carried genes to take up external organic matter. However, finding an engine under the bonnet does not guarantee the engine is running.
What we still don't know
The main caveat is that this study only measured genetic potential from reconstructed DNA. It did not directly measure active carbon fixation rates in the ocean. The samples also came from just one Pacific region. We do not yet know the real-time rates of carbon fixation driven by these pathways, or how much carbon monoxide oxidation truly contributes to global ocean carbon budgets.
Science words
- chemoautotrophy
- The process where organisms produce food from inorganic carbon using chemical energy instead of sunlight.
- dissolved inorganic carbon
- Mineral forms of carbon in water, including dissolved carbon dioxide and bicarbonate.
- nitrifiers
- Microbes that extract energy by breaking down ammonia or nitrite compounds.
- metagenome-assembled genomes
- Individual microbial genomes reconstructed by stitching together DNA fragments directly from an environmental sample.
- catabolism
- Metabolic reactions that break chemical compounds down to release energy.
Check it yourself
This story is based on a real research paper in mSystems by Salcedo, Jaffe, Dekas. We write with AI help and check it against the paper, but the original is the final word.