eDNA every­where for (al­most) every­thing

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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