Scientists Find Bacteria That Make Food From Chemicals Living in Coral Reef Fish Gills
Researchers who once threw out microbial DNA as contamination went back to it and rebuilt 70 bacterial genomes from Caribbean hamlet fish, most of them new to science. The most common ones carry every gene needed for chemosynthesis, which had never been documented in a fish.
The gills of Caribbean reef fish are home to bacteria that appear able to make their own food from chemicals rather than sunlight, a lifestyle usually associated with deep-sea hydrothermal vents, according to a study published in PLOS Genetics.
The discovery came from data scientists had long treated as garbage. Researchers at the Leibniz Centre for Tropical Marine Research in Bremen, known as ZMT, had sequenced all the DNA in hundreds of gill samples from hamlets, small colorful reef fish in the genus Hypoplectrus, from across the Greater Caribbean to study how the fish evolved. That process, called metagenome sequencing, captures the fish's own DNA along with the DNA of everything living on it.
"In the past, we focused solely on fish DNA for our work and considered microbial DNA a contaminant," said Oscar Puebla, a fish ecologist at ZMT and professor at the University of Oldenburg. "One day we thought, why don't we take the opposite view, look at the gill microbiome and neglect the fish DNA?" The team, which included researchers from the Helmholtz Institute for Functional Marine Biodiversity in Oldenburg, the University of Hong Kong and the University of Chicago, went back through the data.
More than 95% of the DNA came from the fish, leaving less than 5% from microbes. That was still enough to reconstruct 70 bacterial genomes from 17 bacterial groups, and most of them were new to science. The gill community was completely different from the microbes in the surrounding seawater, which suggests these bacteria are specialists adapted to living on gills rather than hitchhikers from the water. "The genes in these new bacterial genomes indicate that the microorganisms found in the gills can carry out a wide variety of metabolic functions, including many potential metabolic interactions both among different bacteria and between bacteria and the fish," Puebla said.
The biggest surprise was that the most widespread bacteria in the gills have all the genes needed for chemosynthesis, the ability to fix carbon dioxide using energy from breaking down inorganic compounds instead of sunlight, the way plants do. "We detected the DNA of proteobacteria of the Burkholderiaceae family with chemosynthetic potential," said Sabrin Abdelghany, a former Ph.D. student at ZMT and the study's lead author. Such bacteria have been found at deep-sea vents and living with invertebrates such as worms and mollusks, she said, "but to the best of our knowledge they have not been documented in fish."
Gills are one of the busiest surfaces on a fish's body. Besides breathing, they handle immune defense, waste removal and the balance of salt and acidity in the body, noted co-author Martin Helmkampf. The authors say the specialized microbiome they found could play a role in fish metabolism, immunity and health, though what these bacteria actually do for their hosts is still unknown. Helmkampf compared the work to "walking through a jungle for the first time." Puebla said the findings could matter both for wild fish populations and for aquaculture, where gill health is a constant concern.
