For many years underwater visual surveys have been widely used to survey coral reef ecosystems across the world, and have been crucial in many coral reef monitoring programs. The drawbacks of using visual surveys are that they generally need to be conducted using SCUBA, which makes them time-consuming, logistically challenging, and potentially expensive. They are also limited to the expertise of the surveyor and open to human error. 

There is now a new method for surveying these complex ecosystems that can be used on its own as well as to compliment visual surveys. Scientists have now begun using environmental DNA (eDNA). This method analyses the DNA strands that are naturally expelled from organisms into the water column. The advantage of eDNA is that it can relatively quickly and inexpensively assess species diversity. The novel technique takes advantage of the fact that organisms constantly shed DNA into the environment, leaving behind genetic material that can be detected and analyse with molecular biology tools. Despite the increasing use of eDNA to catalog the presence of marine animals, finding a consistent correlation between the abundance of organisms and the quantity of DNA remains elusive to researchers. 

What Are The Advantages Of Using eDNA?

Tropical coral reef ecosystems, and the people who depend on them, are increasingly impacted by climate change. The scarcity of data on marine organisms, especially in contrast to terrestrial research, is primarily due to the mysterious existence of the associated fauna and reef habitat complexity. The use of eDNA has been cited as superior to other traditional biological survey methods (such as visual surveys) in terms of the amount of species observed and does so with non-invasive sampling. The use of genetic approaches in the aquatic world is at the cutting edge of high-resolution biological data processing. In order to achieve its maximum potential, marine eDNA strategies need to switch from species identification to population diversity and accessibility analysis.

The use of eDNA could allow the identification of cryptic and under-recorded animals, while visual surveys include ground-covering and comparison of the two methods. The mixture of approaches also makes it possible to associate trends of distribution of range changing tropical species with resident temperate species. The use of eDNA is a paradigm change from conventional reef survey methods to a theoretically reliable and effective surveillance method. The use of genetic approaches in the aquatic world is at the cutting edge of high-resolution biological data processing.

Metabarcoding

The method of eDNA uses ‘metabarcoding’, a technique in which all of the DNA in a water sample is analyzed in one step with DNA sequencing. Coral DNA sequences are then classified and counted to determine the abundance of various species of corals in each reef. Degraded reefs have very little coral eDNA , while reefs with more live corals have a much greater eDNA coral signature. Therefore, eDNA also allows researchers to track changes in coral reef health and the composition of the associated coral reef community. The method also allows researchers to detect rare species that could otherwise be missed by traditional visual-based survey methods. Currently, researchers are applying the use of eDNA metabarcoding monitoring to communities that are extremely difficult to visually assess, such as deep reefs that provide potential refuge from climate change for temperature-sensitive species.

The Challenges Of Using eDNA

There are also numerous concerns about the evidence arising from the use of environmental DNA. One obstacle for this sort of eDNA analysis is the continuous flow of water, which makes it impossible to know where the DNA in a given sample originally originated from. Scientists are very aware that they need a greater understanding of where the water in the samples have come from. Often, coral reefs are open, coastal areas and which are not overly affected by current. Although the impact of water flow is yet to be quantified, the consensus among researchers is that DNA degrades rapidly in marine ecosystems so the DNA within eDNA water samples have likely come from the general area. 

Another problem is that the biomass of each group of species at a site can theoretically be measured by the proportion of their eDNA contained in a water sample from that site. Yet this assumes that all these species dump their DNA at about the same time, which is not generally the case. Different species will shed mucus at different rates, certain fish poop more than others, and the abundance of reproductive material in the water will change seasonally. 

Certain species and ecosystems are ideally suited to performing population surveys using eDNA than others. The surface area of coral species, for example, is a good proxy for their individual biomass, and it is fair to conclude that all coral species are shed at comparable rates, making coral a good target for eDNA surveying. As coral is such a vital part of reef ecosystems, coral cover is an important marker of overall reef health, making it an important organism to study.

Due to rising water temperatures due to global warming, as well as direct human influences such as pollution, coral cover worldwide is increasingly degrading. Mass coral bleaching outbreaks have occurred during the past five years due to a spike in ocean temperature. According to UNESCO, by the end of this century, the coral in all 29 World Heritage sites that contain reefs could cease to exist if greenhouse gas emissions continue at their current rate. Coral reef ecosystems support more than 4,000 fish species globally and provide food, coastline protection, and incomes for millions of people worldwide. Therefore, it is vital to be able to effectively monitor and survey reef health and degradation, which eDNA analysis can make easier and more affordable to do.

Looking Ahead

The use of eDNA has been shown to be able to efficiently track coral cover and biomass by fast surveys using comparatively limited amounts of seawater. This novel and new approach could help with existing monitoring efforts, particularly where visual surveys by divers are logistically challenging. The use of eDNA promises coral reef surveys that are cheaper, faster and have the potential to capture more data and be able to be used in areas which are difficult to survey by other methods. Whilst eDNA remains in its infancy, with many questions left to answer, researchers are optimistic about the future of this method and its application to aid marine conservation. As the application of eDNA becomes more standardized and obstacles begin to be ironed out, it will be interesting to see how the use of eDNA becomes more widely used over the coming years.