Great Crested Newt eDNA Analysis: What are the benefits of GCN eDNA within ecology?

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GCN eDNA

Great Crested Newt eDNA has been probably the best revolution within environmental science this decade.

Despite this, we still keep getting asked, what is it? How does it work? And How is GCN eDNA allowing us to be at the forefront of ecology?

With the rapid development of technology and industry, as well as increasing human activity in nature, lots of pollution and contaminated particles are entering the ecosystem on a daily basis. Many populations of organisms are exposed to substances that disrupt their normal growth and development and disrupt their genetic structure and variability in the long run. Environmental pollution is a growing problem and requires the development of sensitive methods to investigate the effect of pollution at different levels for all organisms.

Many research methods have been developed in the last decade that focuses on extracting the DNA from the environment without disrupting the normal daily life of wildlife species. One of the most recognised methods is environmental DNA or eDNA.

When the entire ecosystems are studied, one of the main problems that arise is how to accurately isolate all possible organisms that are found in an environment. This is especially problematic for many bacteria and microscopic organisms as usually their survival conditions are related to coexistence with other organisms within the same environment.

For example, if ecologists try to grow bacteria in a petri dish that is in a soil or water sample, they will generally grow only about 5 percent of the total diversity of species that are actually in that sample in such laboratory conditions. If they then sequence the genes of those 5 percent, they will not receive a clear representation of what exists in that environment.

Therefore, the scientists simply bypassed the need to separate and breed all possible species in the sample and simply isolated all the DNA that a sample contained, regardless of which species it belonged to, and then analysed such data with a computer and associated it with each individual species. This way, instead of 5 percent of the gene content, they could see up to 100 percent of all the genes that an environment contains.

The same method was used in September 2019 when geneticist Neil Gemmell and his team sampled the eDNA from Loch Ness in Scotland in search of the existence of the legendary lake monster Nessie.

Prof. Gemmell’s team sadly didn’t find Nessie, but his important research allowed the science, which is now behind great crested newt eDNA to continue developing.

What is Great Crested Newt eDNA?

Great Crested Newt eDNA is DNA extracted from the habitats where we assume these organisms live. Sources of environmental or eDNA can be found in faeces, shed skin, carcasses, damaged tissues, and other metabolic waste, and is detected by sampling the outdoor environment like water or soil.

The most common definition of GCN or great crested newt eDNA emphasises that the biological source of eDNA does not need to be presented during the DNA extraction. This is where the beauty of eDNA method truly lies – we are provided with tons of information without harming the species in their habitat.

Great crested newts (Triturus cristatus) are protected in the UK under the Wildlife and Countryside Act (1981) and the Conservation of Habitats and Species Regulations (2010). Due to this fact, ecologists and scientists are urging developers and others involved in the land-use change to use non-invasive surveys as much and often as possible to preserve the endangered and protected species like great crested newts.

Pressures and threats for the newt’s habitat arise due to the disappearance of small standing ponds and ponds that this species needs to breed. Throughout karst landscapes, such as limestone, dolomite, and gypsum, this species is endangered by the abandonment of ponds that are no longer used for human activity (livestock, irrigation). It is also endangered by construction, various land reclamation projects, concreting, neglecting, or draining ponds and watering places, all of which lead to the disappearance of habitats and populations of the great crested newts.

Pesticides are considered one of the biggest threats to the development of eggs and larvae because they can cause deformities. Moreover, introduced fish species such as gambusia have also been registered as threats to eggs and larvae. These fish feed on eggs and compete with larvae for food.

Using the great crested newt eDNA, ecologists can successfully determine the presence of the great crested newt and initiate activities that will lead to their protection. Furthermore, by not causing any harm, this method has been approved by Natural England, and unlike other methods, provides cheaper, faster, and much more reliable results.

great crested newt edna

What is DNA and How Great Crested Newt eDNA is extracted from water samples?

DNA is a genetic, hereditary material presented in the cells of organisms of all living things, from the simplest to the most complex.

It consists of two polynucleotide chains linked by hydrogen bonds. Each chain consists of a large number of interconnected nucleotides, and each nucleotide consists of sugars deoxyribose, phosphate, and a nitrogen base. Each sugar is bound to one of the four nitrogenous bases: adenine (A), thymine (T), cytosine (C), guanine (G). The variability of the base order and the large length of the DNA molecule ensures the storage of a large amount of information in the DNA.

DNA extraction is the process of purifying DNA from a sample by a combination of physical and chemical methods. The methods used to isolate DNA depend on the sample size. Despite the various methods, there are some similarities between them. In general, their goal is to separate the DNA found in the cell nucleus from other cellular components. DNA isolation is required for genetic analysis, which is used for scientific, medical, or other purposes.

The most common way of great crested newt eDNA analysis involves taking a sampling of a small volume of water that is sent to the laboratory for further extraction. The concentration of newts’ DNA is relatively high between April and June as this is their breeding season. If you suspect their presence, you should try to do the sampling as early as possible. Kit for sample collection has to include ethanol preservative and dedicated equipment to ensure the DNA will not experience degradation over time. Once the tubes with samples arrive in the laboratory, the DNA is extracted and isolated to be tested for the quantitative polymerase chain reaction inhibition.

During this analysis, the great crested newt eDNA is separated from the DNA of other living organisms, like water organisms, bacteria, or viruses. This way, the pure GCN eDNA can be amplified and analysed using fluorescent imaging.

Thanks to the high sensitivity of the methodology, the results can indicate either the presence or absence of the great crested newts.

In short, great crested newt eDNA is a safer, faster, and more cost-efficient solution than traditional methods.

Benefits of GCN eDNA over traditional methods

Traditional survey methods include visual searches, egg searching, torching, netting, and bottle trapping. Methods require many people to be involved which is not always effective and can include higher labour costs. That’s just to find out whether great crested newts even live within a water source.

Moreover, some can result in more harm for the newts like their suffocation within the nets or bottles. But the bottom line is that the subject of research has to be presented in the environment during the surveys – something that great crested newt eDNA methods bypass and have minimum effect on the natural habitat. Biggs et al. (2014) estimate that this method has more than 99% detection efficiency while others have less than 80% – bottle trapping along with torching being the highest one with 76%.

Although if great crested newt eDNA return a positive result for their presence, these methods may be required for mitigation purposes, GCN eDNA cuts valuable time and money from the very start. If great crested newt eDNA analysis returns a negative result that the costs saved are significant, as the use of traditional methods is null.

But, what are the traditional methods used during newt surveys?

Egg searching

This method includes visual searching for the newts’ eggs during their breeding season. Although it sounds relatively easy, this method depends on the presence of the eggs, and once detected, they are in danger to be seen by predators. When surveyors unfold the leaves during the search, the eggs are left exposed which means this method comes with greater risk for their ultimate protection.

Torching

Night torching is a less invasive method as it does not include their capturing for observation. However, the surveyors have to use recommended candlepower in order to distinguish between different newt species. Also, depending on the used torches, the results can vary and can result in poor work. Moreover, torching results in the pond being disturbed physically for an extended period.

Netting

This method can be useful for observation and relocation of great crested newts in their natural habitat. However, surveyors have to be careful as newts can easily be caught between the frame and the net. This method is not as effective as other methods and can be harmful to the creatures. Finally, during the relocation other species can be caught in the net, and transferred to the habitat they usually do not occupy, disturbing the current life in the pond.

Bottle trapping

Bottle trapping is as effective as eDNA but comes with a high price: newts are trapped inside the bottle for examination, and if the process is not set up the right way, it can result in their drowning. Even the most experienced surveyors are reluctant to use this method due to the high mortality rate. This method is used alongside torching or when is not possible to do visual surveys due to the heavily vegetated areas.

The results can also be inconclusive as empty bottles do not necessarily mean there are no newts in the pond.

To conclude, great crested newt eDNA is much more sensitive as a method than other standard techniques. It can detect newts at relatively low densities, more quickly and without disturbing the species in their environment.

Therefore, it is considered to be a non-invasive method and one that puts animals’ rights before the scientific results.

How Great Crested Newt eDNA is helping ecologists to save protected species?

By being able to detect newts’ presence in the environment thus providing a way of their monitoring, conservation, and protection. Great crested newt eDNA is helping us as ecologists to save the endangered species from extinction due to the extensive human activity within their natural habitat, in a fast, safe and cost-effective way.

The greatest result of this method manifests in the ability to gain a better insight into the prevalence and threats of this species. Some of the measures for their protection can be encouraging the local community to maintain ponds, wetlands, and lakes where great crested newts exist. This can be achieved by removing waste, and excessively overgrown plants.

Particular attention should be paid to the prevention of the spread of invasive fish species into water habitats (gambusia, catfish, etc.). Pesticide use should be reduced and environmental solutions promoted.

Informing the public about the importance of smaller ponds and enabling active participation in the maintenance of these habitats. Popularising the construction of smaller ponds on private land where there are populations of large great crested newts can also be beneficial.

However, we feel that further research is needed as well as the establishment of long-term monitoring programs at various locations to ensure long term success. The future of newt preservation might lay in the cheap and rapid analysis that great crested newt eDNA provides to researchers, ecologists, and surveyors all around the world.

In the UK, where great crested newts are a protected species, their number is rapidly declining, and one reason can be that people are not aware of their presence in the construction sites. Other methods can be effective but require extensive knowledge, previous training, obtaining licences, and can result in the significant disturbance of their natural habitat. Furthermore, some of the methods carry a potentially mortal danger to the species.

Great crested newt eDNA is a simple method of finding the newt’s DNA in their natural habitat, without the need for their physical presence, and using those results to educate, preserve and protect the species. The specter of great crested newt eDNA benefits is wide, from just getting the confirmation of their existence to the general protection of the endangered species in the UK.

Helping species to recover often depends on acquiring valuable information about the population and the threats they encounter during the breeding. Getting meaningful information can help ecologists to undertake specific measures in order to prevent large-scale consequences.

Using GCN eDNA as a method, we can get beneficial and useful results in an inexpensive and effective way that might save this incredible amphibian species from extinction.

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