Unmasking Ecosystems: The Novel Role of Environmental DNA in Detecting Life Forms

Researchers from the Laboratory for the Conservation of Endangered Species (LaCONES) at the CSIR-Centre for Cellular and Molecular Biology (CCMB) in Hyderabad, have developed a new non-invasive method to assess the total biodiversity of any ecosystem by sequencing the DNA fragments found in the environmental samples such as water, soil or air . Their study, published in the journal Ecological Indicators, shows that this method can detect all kinds of organisms, including viruses, bacteria, archaea, and eukaryotes such as fungi, plants, insects, birds, fishes and other animals from just a few litres of water sample without any direct capture or counting of species.

What is environmental DNA?

Environmental DNA (eDNA) is DNA shed by all organisms into their surroundings through natural processes during their lifetime or after death . By filtering out eDNA from environmental samples, reading their sequences, and comparing them with a large database of reference sequences from all the known species, the researchers can identify the source of the eDNA and estimate the total taxonomic diversity of an ecosystem.

How does it work?

The researchers, Mr. S. Manu and Dr. G. Umapathy at CSIR-CCMB developed a lysis and PCR-free molecular approach to extract and read the genetic information encoded in eDNA. They tested their method in the highly biodiverse wetland ecosystem of Chilika Lagoon in Odisha, India’s largest brackish water lagoon, with the Chilika Development Authority’s help. By comparing over 10 billion sequences of eDNA fragments from multiple seasonal samples with a large database of reference sequences from all the known species, the researchers were able to detect organisms across the tree of life. They estimated that the total taxonomic diversity of Chilika Lagoon is about 1071 families across the tree of life, comprising approximately 799 families of eukaryotes, 230 families of bacteria, 27 families of archaea, and 13 families of DNA viruses. The researchers also found the relative abundances of families of organisms vary significantly across different locations and seasons in the ecosystem. This indicates that the method can also help monitor the changes in biodiversity across space and time.

Why is it important?

The new method is cheaper, faster, and highly scalable to large freshwater and marine ecosystems which can help in monitoring and conserving the rich biodiversity of our country. Vinay K. Nandicoori, Director of CCMB, said that the new method is moving from being a physics problem to an engineering one. LaCONES is a CSIR-Centre for Cellular and Molecular Biology (CCMB) laboratory headquartered in Hyderabad.

The current methodologies for eDNA-based bioassessment are limited to approaches where only specific species or groups of related taxa are looked for. The new method can overcome these limitations and improve detection of organisms, from microbes to mammals, even if they are low in abundance. The method can also help in identifying invasive species, endangered species, pathogens and pollutants that may affect the ecosystem health.

The method has potential applications in various fields such as ecology, conservation biology, environmental monitoring, biogeography, forensics, epidemiology and public health.

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