On the trail of secret reef dwellers

Researchers demonstrate the potential of so-called environmental DNA metabarcoding for studying biodiversity in tropical reefs. © Mihtiander/iStock

Biodiversity research with “forensic” methods: A study shows which fish are found in tropical reefs is reflected in their genetic traces in the water. The process of so-called metabarcoding of environmental DNA can also be used to identify species that divers cannot see. However, visual observations remain important because the genetic reference databases do not yet cover the great diversity of fish species, the researchers say.

They populate the fascinating underwater gardens of the earth: thousands of species of fish live in the coral reefs of the various tropical sea regions. However, it is still unclear how many species there are and where exactly they occur. In addition, against the background of sad trends, better insights into biodiversity appear important: In the course of global warming and other man-made threats, ecological reef habitats are disappearing at an alarming rate. In order to accurately record this development, information about original species compositions in the various tropical reefs of the world is important. For a long time, the insights were based only on visual observations by divers or on catches. But now a new method is finding its way into biodiversity research: the detection of species through environmental DNA.

Telltale traces of genetic material

The method is based on the fact that living beings leave traces of genetic material in their habitat through excretions or particles such as skin flakes. Thanks to the ever finer detection methods of modern genetics, they can be detected in samples. If there is genetic reference data, the determined sequence sections can then be assigned to known species. In some cases this is used to identify a specific species in a habitat. In order to examine biodiversity, on the other hand, the international research team has now used the method of environmental DNA metabarcoding, in which many species in a habitat can be recorded at the same time. The scientists collected water samples from 26 locations in five tropical marine regions around the world and analyzed the DNA isolated from them. They then compared the results with reference reef fish genetic data to identify species and families.

As the team reports, the potential of the method for studying biodiversity in the tropical reefs was confirmed: The researchers found a 16 percent higher diversity of fish on average than by conventional survey methods such as visual observations during dives. “Thanks to the environmental DNA method, we can identify many fish species and families much more quickly than with observations,” emphasizes co-author Loïc Pellissier from ETH Zurich. Because the DNA analyzes were completed after only two years – the visual observations that served for comparison, however, come from 13 years of stocktaking with high personnel costs.

In detail, it was shown that fish are often among the hidden species that typically reside in the numerous caves and crevices of the underwater landscape. As a result, divers see them less often – and some of these species are very similar in appearance. In addition, many fish swimming in open water apparently escape the view, the study shows. As the scientists explain, many of these so-called pelargic species avoid humans or do not live permanently in coral reefs, such as some representatives of mackerel and tuna and special shark species. However, the detection of these fish is also very important because they can play a major role in the complex interrelationships in reef ecosystems, the researchers emphasize.

Greatest biodiversity in the Coral Triangle

In their current study, they also confirmed that species compositions differ significantly between the different tropical reef regions of the world. The fish diversity is particularly high in the so-called coral triangle between Borneo, Papua New Guinea and the Philippines. Up to five times more fish species and families live here than in the Caribbean. As the researchers explain, this has to do with the fact that the habitats in this area are very diverse. In addition, the climate in geological history was very stable there compared to other regions, which allowed a particularly high level of diversity to develop and establish itself.

The researchers conclude that environmental DNA metabarcoding can greatly enrich biodiversity research in reefs. However, they emphasize that they cannot yet completely replace visual observations. Because the reference databases only cover some fish families very incompletely. Therefore, a significant part of the environmental DNA found in the water samples could not be assigned so far. The team is therefore working on sequencing the DNA of other fish species and feeding the data into the reference databases. Diving for research will probably always remain important for other reasons. According to the researchers, this is the only way to record biometric information such as the sizes of fish and their frequency in the world’s underwater gardens.

Source: Swiss Federal Institute of Technology in Zurich, specialist article: Proceedings of the Royal Society B: Biological Sciences, doi: 10.1098/rspb.2022.0162

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