eDNA

eDNA -Environmental monitoring technique

DNA is the genetic material of living organisms that contain characteristics related information of the specific organism. In modern laboratory diagnostics, DNA analysis is a very useful and sensitive tool. 

For the Diagnosis of target  DNA, there is an essential DNA sequence required for the laboratory work. This can be achieved by nucleic acid hybridization, DNA probes, and DNA chips microarray of gene probes all of these tools are essential for DNA diagnosis purposes.

DNA analysis for environmental monitoring 

Today, environmental pollution is a major problem that we face. Pollutants that cause environmental pollution degrade the purity of our environment. Some several pathogenic microorganisms and viruses may cause environmental pollution, particularly water pollution. 

DNA analysis can also be employed for the specific detection of indicator bacteria such as Escherichia coli to check the quality of potable water. By using DNA probes we can detect the specific gene of Escherichia coli that is present in the sample. The DNA analysis technique is very sensitive and is capable of identifying a single Escherichia coli cell in 100 ml of water.

It also helps to detect pathogenic organisms such as Salmonella, Vibrio, and Shigella.

eDNA -DNA analysis for environmental monitoring

The eDNA is known as Environmental DNA. eDNA is a genetic material that is obtained directly from environmental samples like soil, water, etc rather than any signs of the biological source material.

 This is a new and modern technique for monitoring the environment. This technique is fast, easy, and more accurate as compared to traditional monitoring techniques. We can detect and monitor both the aquatic and terrestrial environments. 

eDNA analysis based on molecular approach for species identification. This technique gives shows detailed results and knowledge on a different scale. This technique is also applicable to detect species occurrence and abundance.

How does eDNA technology work?

Step -1 Collection of sample for the analysis.

Selection of site from where you want to analyze with the help of eDNA. The sample is collected in a sterilized container. 

During sample collection measures the water standard properties and other registered environment parameters that influence the amount of eDNA that is present in the water. Then samples are then transported to the laboratory for analysis.

Step -2 Extraction of eDNA

The eDNA is extracted from the collected sample by using the same basic principle used in the forensic laboratory for the extraction of DNA. During experimental work in the laboratory risk of contamination should be avoided. After the extraction of DNA from the sample then DNA is saved for future analysis.

Step -3(a )Analysis of single species by extracted eDNA

Single species analysis is done by Barcoding. Barcode is a small part of DNA that is the primer copies. In a test tube mix primer, a drop of DNA, enzymes, and salts, and then placed this test tube in the PCR machine for amplification.

When the PCR machine runs then a colored curve is obtained on the computer screen that indicates the presence of species in the collected sample, if no colored curve formed it indicates that no specific species is present in the sample.

Step -3 (b)Analysis of multiple species 

Metabarcoding is used for the analysis of multiple species. DNA, primers, salts, and enzyme all are mixed in a test tube and placed in a PCR machine. To analysis the results the sample is run through NGS i.e. Next Generation Sequencing analysis.

When the analysis is done the result contains millions of different types of DNA in the form of data. To sort out the specific species from this data programming method is used that helps to separate the different DNA codes from each other. The overall process is known as bioinformatics.

Final results that we get in the form of an Excel file that helps to identify the specific species, and also helps to identify how many copies of DNA present. For each species.

Advance approaches of eDNA technique 

1. The eDNA technique is a very accurate and cost-effective technique for the detection of species in environmental samples.
2. It has the ability to monitor the salmonid aquaculture producers in the industry.
3. This technique is useful to detect the abundance of pathogens and other biological threats in the surrounding environment.
4. The monitoring of eukaryotic micro and microbial communities and populations can be detected by the eDNA technique.
5. This technique helps to detect the pathogen in freshwater aquaculture.
6. The eDNA technique is a sensitive and time-saving technique.
7. This technology has recent advances in ecotoxicology studies.
8. The eDNA technology has a wide range of applications in biological, geological, and environmental sciences.
9. This methodology is useful and important for the detection of rare and cryptic species.
10. Helps to early detection of invasive species.
11. The eDNA technique is very powerful for monitoring Biodiversity.
12. This technique is very useful to verify the environmental changes over time.
13. Species disappearing due to different actions done by human beings like factory construction and dam construction near water habitat.
14. eDNA technology helps wildlife researchers in snowy areas to analyze the presence of elusive and rare species like lynx, arctic fox, polar bears, etc on the glaciers.

The eDNA technique plays a very important role in the monitoring environment. It is a fast, cost-effective, and time-saving, technique.

Reference 

• Bohmann, K., A., Gillbert, M.T., Carvalho, G. R., Creer, S., Knapp M., et al. (2014), “Environmental DNA for wildlife biology and biodiversity monitoring”.Trends Ecol.Evol.29,358–367. doi:10.1016/j.tree.2014.04.003
• eDNA -The new environmental monitoring technique on www.dce.au.dk
• Ficetola, G.F., Miaud, C., Pompanon, F., and Taberlet, P. (2008), “Species detection using environmental DNA from water samples” .Biol. Lett.4:423.doi 10.1098/rsbl.2008.0118
• Gomes, G.B., Hutson, K.s., Domingos, J.A., Chung, C., Hayward, S., Miller, T.L., et al. (2017), “ Use of environmental DNA (eDNA) and water quality data to predict protozoan parasites outbreaks in fish farms.Aquaculture 479,467–473.doi:10.1016/j.aquaculture .2017.06.021
• https://www.ncbi.nlm.nih.gov
• Lucy peters ., et al. (2018), “Environmental DNA: ANew Low-Cost Monitoring Tool For Pathogens in salmonid Aquaculture.”Front Microbiol. https://doi.org/10.3389/fmicb.2018.03009
• Pengyuan Wang et al. (2019), “ Environmental DNA: An Emerging Tool In Ecological Assessment”.Bull Environ Contam Toxicol, 103 (5):651–656. doi: 10.1007/s00128–019–02720-z
• Philip Francis Thomsen et al. ( 2015), “ Environmental DNA — An emerging tool in the conversation for monitoring past and present biodiversity.”Biological Conservation Volume 183, Pg-4–18. https://doi.org/10.1016/j,biocon.2014.11.019 
• Thomsen, P.F., Kielgast, J., Iversen, L.L., Wiuf, C., Rasmussen, M., Gilbert, M.T., et al. (2012), “Monitoring endangered freshwater biodiversity using environmental DNA”. Mol Ecol.21,2565–2573. doi:10.1111/j.1365–294X.2011.05418.x
• Zamor, R. M., Glenn, K.L., and Hambright, K.D. (2012), “ Incorporating molecular tools into routine HAB monitoring programs: Using qPCR to track invasive Prymnesium Harmful Algae 15,1–7.doi:10.1016/j.hal.2011.10.028
• www.aquabiota.se

Image Reference :

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