DNA analysis has uncovered the presence of chemosynthetic bacteria in the gills of coral reef fish, offering new perspectives on fish metabolism, immunity, and health. Scientists from the Leibniz Centre for Tropical Marine Research (ZMT) and the Institute for Coastal Marine Biology (ICBM) studied the gill microbiomes of a group of tropical reef fish called hamlets (Hypoplectrus spp.) in the Greater Caribbean. Their findings, published in the journal PLOS Genetics, involved sequencing the metagenome of gill tissue samples, which included both the fish's DNA and that of microorganisms living in the gills. At first, the researchers focused on the fish DNA to understand the evolution of hamlets. However, they later examined the microbial DNA, which had previously been seen as contamination. This shift in approach revealed a complex and specialized gill microbiome. Though less than 5% of the DNA extracted came from microorganisms, the researchers were able to reconstruct 70 bacterial genomes from 17 distinct bacterial groups, many of which were previously unknown to science. The study found that the gill microbiome differs from the surrounding seawater microbiome, suggesting that the microorganisms are adapted to live specifically in the gills. Among the bacteria identified were members of the Burkholderiaceae family, which possess the genetic ability to perform chemosynthesis—a process in which organisms use chemical energy from inorganic compounds to fix carbon dioxide, instead of relying on sunlight. This process is commonly found in deep-sea hydrothermal vents and in certain invertebrates, but had not been previously observed in fish. The discovery suggests these bacteria might contribute to various metabolic processes in the gills, including interactions between different bacteria and between bacteria and the fish itself. This raises new questions about the role of the gill microbiome in fish physiology and health, with potential implications for aquaculture and the survival of natural fish populations in changing environments. The research team notes that they are only beginning to explore the complexity of the gill microbiome and more studies are needed to fully understand its significance.