by Mechas
I have recently come across several articles that mention work with environmental DNA, abbreviated with the catchy term eDNA. As a microbiologist, I am familiar with the term metagenomic DNA, which refers to the genetic material from a mixed community, and therefore wondered, are these terms equivalent?
Fig. 1. Citations retrieved from PubMed using the terms "environmental DNA" or "metagenomic DNA" (numbers on the left) and "metagenome" (numbers on the right). Source Mechas Zambrano
To begin with, a quick search in PubMed shows that "environmental DNA" has been around for longer and is more widely used than "metagenomic DNA" (Fig. 1). My failure to appreciate the relevance of eDNA in biological surveys probably reflects the fact that it is commonly used by scientists who work with organisms other than microbes, such as fish and amphibians. Metagenomics therefore refers to the approach used to study the metagenome, or the collection of genetic material or genomes, most of which are microbial, in a sample. The allure of eDNA lies in its potential as an accessible and efficient means for assessing biodiversity. And with this I mean the capacity to monitor and map both microbial and non-microbial species over time and across geographies.
Organisms in any environment leave traces of their DNA as the result of processes such as shedding of skin, coughing, or depositing fecal material. These fragments of genetic material become part of the eDNA in a given location and can be used for identification of these organisms. Perhaps the most common strategy for species identification involves comparison of short, standardized sequences of DNA in a method known as DNA barcoding (Fig. 2). Microbiologists usually do taxonomic profiling of bacteria and fungi by first PCR-amplifying and then sequencing conserved 16S rRNA genes or ITS (internal transcribed spacer) regions. When multiple taxa or groups of organisms are identified, the methodology is called "metabarcoding," which sounds exotic but simply means that several groups of organisms are analyzed, let's say insects or protists, in addition to bacteria or fungi. Eukaryotes are usually identified by targeting conserved mitochondrial cytochrome c oxidase I (COI) gene regions or 18S rRNA ribosomal sequences. An alternative approach to metabarcoding involves sequencing the metagenome via shotgun sequencing, a strategy that may miss less abundant organisms but offers a glimpse into the functional potential of these metagenomes.
Fig. 2. DNA barcoding scheme. Source
As with many DNA-based approaches, there are limitations to the use of eDNA. Rare species could be missed, especially in very species-diverse samples like soils. Differences in methodologies, ranging from sample collection to data processing, bias results and comparisons. We also know very little about the stability of DNA in the environment or its capacity to accurately represents the breadth of biological diversity in an ecosystem. Not surprisingly, humans also interact with their environments, leaving behind traces of their DNA that can inadvertently reveal information regarding a particular population or community. Although human DNA is usually removed from datasets to avoid ethical issues, concerns remain regarding future implementation of this technology to obtain personal information without authorization.
So why is eDNA interesting? It offers an opportunity to examine biodiversity with minimal intervention of ecosystems or the need to directly collect biological specimens. A recent study even managed to identify local biodiversity using eDNA captured during routine ambient air-quality monitoring. eDNA also delivers data on various taxonomic groups, from invisible single-celled microbes to multicellular eukaryotes. By doing so, it opens the possibility of examining the distribution of species and, perhaps more ambitiously, understanding the complex web of organisms that make up an ecosystem. Tied to technological innovations in molecular methods for DNA extraction, long-read sequencing, and bioinformatic tools, eDNA promises to enrich our understanding of species distribution and their changes over time. And, as recently shown, to inform us about ancient, million-year-old ecosystems, as well as genomes and functions from paleolithic times.
eDNA represents an exciting opportunity to explore species and biodiversity across kingdoms and to monitor changes within ecosystems and over time. How timely to embrace such a simple yet powerful strategy.
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