Gill DNA once written off as contamination turns up chemosynthesis genes in reef-fish bacteria

The hamlet dataset was built for a different question. Sequencing whole gill tissue returns everything in it, fish and microbe alike, and the team used the fish DNA for its work on how hamlets evolved ^[3][4]. "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 of fish ecology at the University of Oldenburg ^[5]. "One day we thought, why don't we take the opposite view, look at the gill microbiome and neglect the fish DNA?" ^[6]

More than 95% of the extracted DNA came from the fish ^[7]. The microbes had less than one part in twenty of the data, drawn from hundreds of gill samples ^[8][2]. From that fraction the team reconstructed 70 bacterial genomes in 17 groups ^[9]. The paper is in PLOS Genetics, with co-authors at HIFMB in Oldenburg, the University of Hong Kong and the University of Chicago ^[1][18].

Against a seawater control, the gill community was completely different from the microbes in the surrounding water, and the authors take that to mean the microbiome is specialized for the gill and does not simply mirror the water passing over it ^[10].

The surprise came from the most widespread bacteria on the gills. They carry every gene needed for chemosynthesis, fixing carbon dioxide with energy from oxidising inorganic compounds where plants use sunlight ^[11]. "We detected the DNA of proteobacteria of the Burkholderiaceae family with chemosynthetic potential," said Sabrin Abdelghany, the lead author and a former Ph.D. student at ZMT ^[12]. "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," she said ^[13].

Abdelghany's word is "potential," because a genome lists what an organism could do. The account of the study does not report any measurement of carbon fixation on the gill, of which genes are switched on, or of anything passing from bacterium to fish ^[11][12].

Whether the fish benefits was not tested. "The gills are a major interface between the fish body and the external environment," said Martin Helmkampf, a ZMT co-author ^[15]. "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." ^[15] Puebla said: "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." ^[14] The authors conclude that the gill microbiome could play a role in fish metabolism, immunity and health ^[16].

I think the reuse matters beyond hamlets. The microbial reads came along as a side effect of sequencing fish tissue, in the portion the team had planned to discard ^[3][4]. I'd expect other host-genome datasets to repay the same second look, but the evidence so far covers one genus of reef fish in one region ^[2]. Helmkampf compared the work to "walking through a jungle for the first time, starting to describe the organisms that live there and wondering how they may interact." ^[17]