Voyage to See What's at the Bottom

by Roberto and Elio
 

Ever wonder what do the creatures living in marine sediment use as food sources? It turns out that much of the food in such sediments comes from the creatures that lived in the water column, but then died and their remains sank to the bottom. The sinking cadavers may be as big as those of whales or as small as those of bacteria. Dead algae may be as big as giant kelp or as small as members of the picoplankton. And what is the fate of the cadavers once they reach the bottom? It turns out that their DNA is a significant component of this food resource. Eleven years ago, here in STC, we had a post commenting on articles from marine scientists Dell'Anno and Danovaro and colleagues (here and here) that described the abundance and residence time of DNA in ocean se­di­ments. We were struck by the sheer magnitude of the amount of DNA estimated to be present in the top 10 cm of the world's marine sediments. About 10⁷ metric tons of extracellular DNA were estimated to be deposited on the ocean floor every year! But of course, that area is huge so it's im­portant to consider the amount of extracellular DNA (cadaver-derived) relative to that of the or­gan­isms living in the sediment. This was still very impressive, extracelular DNA was estimated to be six- to eight-fold more abundant than that from all of the live organisms in the top 10 cm of sediment.
 

A scene from the bottom of the ocean (deep benthos). Source

Fast forward to the present and consider the implications of this work for metagenomic analyses of marine sedi­ments. Such analyses would use as substrate for deep se­quencing the total sediment DNA, a minority of this being from local (benthic) residents and the majority from orga­nisms that never saw the sea bottom while they were ali­ve. Given that the papers we commented on eleven ago were published when metagenomic analyses were in their infancy, we wondered whether those results had some influence in the way marine sediment analyses (and metagenomic studies in general) are done today. So we did a quick analysis by simply glancing at subsequent papers that have cited the original paper by Dell'Anno and Danovaro. We were delighted to find out that the paper has not been forgotten, the Web of Science shows that paper has been cited 146 times. After a cursory reading of those abstracts, perhaps the most reassuring fact that stood out was that many of the metagenomic analyses used both DNA and RNA substrates for amplifications (given the short half-life of RNA, there is very little of it outside cells in contrast to DNA). That way, the genes from living cells can be distinguished from those from extra­cel­lular DNA. One particular paper published in 2015 by An­drea Torti and colleagues did a very thorough analysis of the origin and dynamics of the extra­cel­lular DNA pools in marine sediments. We found one speculation of theirs very appealing and pro­vocative, namely that "extracellular DNA may provide an integrated view of the biodiversity and ecological processes occurring on land, in marine water columns, and sediments themselves, the­re­by acting as an archive of genetic information which can be used to reconstruct past changes in source environments."  Enter a new tool  in our quest to reconstruct the past!
 

On a final note, this issue of extracellular DNA influencing metagenomic analyses is clearly not li­mited to the ocean floor. In this regard, it was nice to find among the citing articles, one published last year by Paul Carini and colleagues whose title says it all: "Relic DNA is abundant in soil and ob­scures estimates of soil microbial diversity." Bottom line (pun intended), it was a nice exercise to revisit an old post and see what influence the work of over a decade ago has had on the field. That's impact.