Environmental DNA and the confusion of the tree of life

Often we tend to think that natural evolution does not allow us to keep the “memory” of past species. That is, when extinctions of entire groups, and not of individual species, occur, both due to rare catastrophic events and, much more frequently, due to the gradual replacement of the old groups with new ones better adapted to an environment in perennial transformation, it means that the genetic information of ancient organisms has been lost forever, so even if the ancient traits of those organisms were to become useful again, recovering them in living organisms requires their independent re-evolution, or the evolution of functionally equivalent traits. The “genetic inventions” developed during the Darwinian evolution process, that is, are in the historical vision of evolutionism linked to their carriers: once those organisms and their genomes disappear by any accident, they are lost, unless the casual convergence on the same traits from part of other groups of living organisms.

This vision has been overcome in the last ten years, due to the emergence of a new research sector facilitated by technological development: the study of the so-called environmental DNA. In short, thanks to new and more sophisticated technologies for the collection of environmental samples, sequencing and bioinformatic reconstruction, we have realized that we live literally immersed in a “cloud” of DNA, coming from the death of the most disparate organisms and corresponding to the more diverse variety of genetic information. Moreover, this genetic information is not particularly labile: we have already seen on these pages how distinguishable fragments of the genome of ancient living beings belonging to each kingdom can persist for several million years in the environment, allowing to obtain information on entire ecosystems and moreover, from certain environments, such as sediments under the seabed, it has been possible to recover living bacteria, i.e. cells with completely intact and functioning genomic DNA, after more than 100 million years.

Now it is natural to wonder whether this environmental DNA, so ubiquitous and under certain conditions so persistent, can recover its functions by naturally transforming living organisms. If this were the case, in fact, this implies the possibility that traits that have long since disappeared, due to the extinction of their carriers, can be recovered by organisms much later than those, and not related to them; that is, characteristics that appeared somewhere in the tree of life could, if the hypothesis is true, literally “jump” from one branch to another and from one era to another, so that evolutionary bricolage could recover traits with value adaptive even long after their carriers have disappeared.

Things, at least for i bacteriathey are exactly like this: many studies have shown the possibility of these organisms to recover and reuse the environmental DNA, up to the most recent data showing that this may be one of the main mechanisms through which traits such as antibiotic resistance are propagated. Just to mention the most recent of the studies, for now published in the form of a preprint, a research group has even precisely defined the environmental conditions and the types of substrate most suitable for this exchange of DNA between different bacteria through the environment, examining their consequences in terms of evolution and co-optation of adaptive traits. These are common conditions and are those in which, moreover, the long conservation of fragments of more or less ancient DNA is also favoured; it follows that the question we asked ourselves earlier, at least in bacteria, has an affirmative answer, and in fact the reabsorption of mammoth DNA from 43,000-year-old bones has also been demonstrated in bacteria.

Now, you have to consider how well it is known from bacteria DNA can make its way into many different organisms. For plants, where the phenomenon is very frequent, it is now established that the transfer of DNA from the microbiome has guided the evolution of terrestrial forms. Furthermore, in many invertebrates, transfer of DNA from bacteria is still observed today, with various adaptive meanings; finally, even between plants and animals and in general between all types of organism the phenomenon of the transfer of DNA fragments, with an adaptive value, is by now well documented.

For these reasons, it should by now be clear to the reader that the tree of life, drawn for the first time by Darwin in his notebook, is much more tangled and confused than commonly thought from this great flow of DNA, taken from a sea of ​​genetic information in which we are constantly immersed. At times, adaptive information of very remote living beings is written in this DNA which can still be useful in modern organisms not at all related to those that evolved this information; but in any case, whether modern or very ancient, the genetic information dispersed in the environmental DNA is a reservoir of variability from which living organisms continually drawGMO by nature.