Environmental DNA reveals secret reef inhabitants

A global sampling of seawater is used by an international research team to determine which tropical reef fish are found where. They used the residual DNA from the animals in the seawater to identify species and families. However, not all fish can be traced this way.

The coral reefs of tropical corals are beautiful, colorful, and rich in species. Coral reefs are home for as many as 8,000 species, according to researchers.

Global warming and human activities are making coral reefs disappear at an alarming pace. It is not yet known how many species of reef fish are there and where they are distributed.

Many fish species are secretive and live in close quarters. For the most part, biodiversity research has relied on visual observations of divers (or catching fish) to determine the presence and extent of fish in an area.

A new approach to ecology is now available: environmental DNA (eDNA). This new approach allows organisms to leave their genetic material, or parts thereof, in the environment.

Researchers can use this approach to collect water samples from one place, extract the DNA (fragments), and sequence them. The order of DNA building block components can be determined. They can then compare the sequences with reference sequences that are derived from reliable specimens. This will allow them to determine if the species is found at the location.

This is the method that an international team of researchers led by researchers at the University of Montpellier and ETH Zurich used to study the occurrence of fish reefs.

The researchers collected 226 water samples from 26 locations in 5 tropical marine areas between 2017 and 2019. They isolated the DNA and analyzed it, which they then assigned the species or families.

One-sixth more diversity detected

The researchers discovered a 16% higher diversity of reef fishes by using eDNA rather than traditional survey methods such as visual observation during dives. Loc Pellissier is Professor of Ecosystems and Landscape Evolution at ETH Zurich. “We can detect many fish species and their families much faster with the eDNA method than we can with observations alone,” he says. He is one the two leading authors of a study published in the scientific journal. Proceedings of the Royal Society B – Biological Sciences. Although the DNA analysis was completed in two years, the visual observations that supported the study were made by countless observers over 13 years.

Researchers discovered more species living in open water (pelagic), in reef-bound species (cryptobenthic), and in caves and crevices of reefs (cryptobenthic). These fish are less frequently seen or identified by divers.

Many of the pelagic species are more comfortable in open water or at greater depths. Some species belong to families that do not tolerate coral reefs or avoid divers, such as tuna and mackerel in the family Scombridae, as well as sharks in the Carcharhinidae family (requiemsharks, e.g. The blacktip reef shark

These species are important because they actively participate in coral reef function through their pelagic larval stage or their nocturnal migrations. This is why it is often overlooked the importance of these fishes in the ecosystem.

Visual observations are (still!) necessary

However, not all species can easily be recorded using eDNA. Pellissier states that these species-rich families are only partially covered by reference databases. A significant amount of the eDNA present in water samples has not been assigned due to these gaps.

Researchers are busy sequencing DNA of additional fish species to further improve the approach. However, divers will still be required to record some species not easily detected by eDNA. They also need to collect additional information such as fish sizes and biomass which cannot yet be recovered from the eDNA.

Extraordinary diversity in Coral Triangle

Researchers also confirmed earlier findings that species compositions vary widely between marine bioregions. The “Coral Triangle” of Borneo and Papua New Guinea is home to a high level of fish diversity. It is five times more than in the Caribbean. There are many herbivores, including coral-eating species.

Pellissier explains that this is due to the fact the Coral Triangle was (and continues to be) extremely tectonically dynamic, resulting in a wide range habitats. This marine area’s surface temperature was also more stable during the Ice Ages, which was why it was able to support a high degree of diversity.

The Caribbean, however, was more affected by the ice ages and its coral reefs, fish stocks, and other natural phenomena, shrank during cold periods. Additionally, the Isthmus of Panama formed over 2.7 million years ago. This, among other things changed the Caribbean’s ocean currents. Both events led to higher levels of extinctions.