DNA reveals chemosynthesis genes in bacteria living on coral reef fish gills
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Chemosynthetic bacteria have been documented in various marine environments and in association with invertebrate hosts such as annelid worms and mollusks, but their presence in fish appears to be a new discovery. The findings show that fish gills host a complex and specialized microbiome that is not yet well understood but could play an important role in fish metabolism, immunity and health.
Scientists from ZMT and ICBM took a closer look at the microorganisms living in the gills of coral reef fish. They used data from previous genomic studies of tropical reef fish called hamlets (Hypoplectrus spp.) across the Greater Caribbean, for which they had examined hundreds of gill samples. The findings are published in the journal PLOS Genetics.
As part of that work, the team sequenced all the DNA in the tissue samples, known as the metagenome. The result was a large trove of data that included fish DNA and DNA from microorganisms living in the gills.
The researchers initially planned to discard the microbial DNA and use the sequenced fish DNA to study the evolution of the hamlets, which they did. But then they decided to revisit the data from a different perspective.
“In the past, we focused solely on fish DNA for our work and considered microbial DNA a contaminant,” recalls Oscar Puebla, a fish ecologist at ZMT and professor of fish ecology 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 new direction led to different research questions for the team, which also included colleagues from the Helmholtz Institute for Functional Marine Biodiversity (HIFMB) in Oldenburg, the University of Hong Kong and the University of Chicago.
“Our new plan was to identify which microorganisms live in the gills of the hamlets and thus shed light on the gill microbiome, which scientists do not yet know much about,” says Sabrin Abdelghany, a former Ph.D. student at ZMT and lead author of the study.
Her co-author Martin Helmkampf from ZMT adds, “The gills are a major interface between the fish body and the external environment. They are not only important for gas exchange during breathing but also for fish immunity, excretion of waste and metabolic products, as well as body pH and salinity regulation.”
Further insights into the gill microbiome
The scientists found that more than 95% of the DNA extracted from the gills came from the hamlet hosts, with microbial DNA accounting for less than 5% of the data. Yet this small fraction was enough for the researchers to discover something new about the fish gill microbiome.
The researchers reconstructed 70 bacterial genomes from 17 bacterial groups and found that the vast majority are new to science.
They also showed that the gill microbiome was completely different from the community of microorganisms in the surrounding seawater. This suggests that the gill microbiome is specialized to live on the gills rather than merely reflecting the seawater microbiome with which the gills interact.
Puebla says, “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.”
To their surprise, Puebla’s team also observed that the most widespread bacteria in the gills have all the genes required for chemosynthesis—the ability to fix carbon dioxide using energy derived from the oxidation of inorganic compounds rather than from sunlight, as plants do.
“We detected the DNA of proteobacteria of the Burkholderiaceae family with chemosynthetic potential,” says Abdelghany. “Bacteria with such chemosynthetic abilities have been found in a variety of marine environments such as deep-sea vents or in association with invertebrates like annelid worms and mollusks, but to the best of our knowledge they have not been documented in fish.”
The gills host a complex and specialized microbiome that is still poorly understood but could play a role in fish metabolism, immunity and health, the authors conclude. Their findings raise further questions and open challenging new lines of research for the team.
Helmkampf likens the experience to “walking through a jungle for the first time, starting to describe the organisms that live there and wondering how they may interact.”
Puebla concludes: “We are clearly still at an exploration and discovery stage, and know almost nothing about the gill microbiome’s importance for fish physiology and health. This is relevant in both aquaculture environments and natural populations that are facing rapid environmental change.”
Publication details
Sabrin Abdelghany et al, Proteobacteria with chemosynthetic potential are highly prevalent in the gills of Hypoplectrus reef fishes, PLOS Genetics (2026). DOI: 10.1371/journal.pgen.1012266
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Leibniz Centre for Tropical Marine Research
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DNA reveals chemosynthesis genes in bacteria living on coral reef fish gills (2026, September 27)
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