Influenza virus, TEM (colorized). C. Goldsmith, CDC, Wikimedia Commons
(Click on this link to listen to an audio version of this blog ….Virosphere part 2
I think that we have all become more than a little bit obsessed with viruses. I would have expected my biology friends to sit around Zooming over a coffee or a beer, talking endlessly about viral detection, mitigation, reproduction or evolution. I never would have thought, though, that my “normal” friends would be doing exactly the same thing!
We are all feeling penned in and attacked by SARS-CoV2 and all of its rapidly mutating strains. SARS-CoV2 has made this all very personal! So many things that we loved to do and so many more things that we hoped to do are now so fraught with risk that the anxiety/pleasure trade-off just doesn’t seem worth it! I can’t even stand to see a stranger’s uncovered mouth anymore (not that that was ever a high point of my day, of course)!
We talked about the virosphere before (Signs of Summer 5, July 2, 2020) and also about SARS-CoV2 (“Things to Know About Covid-19”), Mach 14, 2020). Remember the key points about a virus: it is very, very small (one hundred million or maybe even a billion times smaller than one of your own body cells)! They are very simple in structure (a short strand of DNA or RNA wrapped in protein). They are incredibly numerous (there are ten million times more viruses on Earth than there are stars in the whole Universe! Or, closer to home, there are ten thousand viral particles in every cubic millimeter of every breath you take!).
Most viruses don’t do anything to humans or most other organisms either. Many very specific features of a virus and a potential host cell have to match up before a virus has any chance of entering or influencing a cell! A few viruses, though, can get into a cell and de-rail its metabolism and possibly cause disease, and there are other viruses that can actually stick their genetic information right into a host cell’s DNA! In humans, 8% of the 3 billion base pairs in our genome are from viruses. That means that there are 240 million viral nucleotide sequences in the average human genome! Some of these viral sequences do nothing, but others do some very important things and may have been vital in our evolution as a species!
Ebola virus (colorizes SEM). U.S.Agency for International Development. Wikimedia Commons
If you consider all of the genetic information in the living systems on Earth, there is probably more information contained in the summed set of all the short, nucleic acid strands housed inside of viruses than in all of the information encoded in the long strands of DNA and RNA contained within every cellular, living organism (every plant, animal, protist, fungus and bacterium). Viruses represent, then, not only a vast reservoir of genetic information and potential, but, as I just said, they are able to transfer at least parts of this information between all types and all manners of cells. This “horizontal” transfer of genetic information between often totally unrelated species violates so many classical principles of biology that it throws the ideas of species and species boundaries and speciation itself into a chaotic jumble! It may also be a key factor in generating the unique genetic combinations that then makes evolution on Earth possible!
So where did viruses come from? Were they the earliest life forms on Earth, or did they arise from the shed nucleic acids from the earliest cellular life forms? Here are some recent papers that may help us better understand what viruses really are.
In the first decade of the 21st Century it was recognized that the DNA shed (via cells, feces, etc.) by organisms living in aquatic environments could be isolated and amplified to the point where those DNA-shedding organisms could actually be identified and even counted. Water samples from streams and lakes could be analyzed for their environmental DNA (eDNA) content to determine the composition of their biotic communities.
Simple diagram of a virus. Figure by domdomegg, Wikimedia Commons
There is a rich literature on aquatic eDNA sampling, but an excellent summary of the methods is included in a 2015 U.S. Geological Survey and Washington State University publication entitled Environmental DNA Sampling Protocol—Filtering Water to Capture DNA from Aquatic Organisms.
More recently, it has been determined that identifiable and quantifiable DNA from plants, fungi and animals (including, potentially, humans) can be obtained from the surrounding air!
Two papers on air-sampling of eDNA were published in the January 6, 2022 issue of Current Biology (Paper #1, Paper #2). Interestingly, although the two research groups worked independently of each other, both selected similar sites (zoos!) to carry out their atmospheric eDNA sampling. Their reasoning for these sampling locations (a zoo in the U.K. and a zoo in Denmark) was the exotic animal eDNA they would be looking for would not be present outside of precisely located zoo enclosures, so endemic contamination would not be a confounding factor and precise distances from the eDNA sources could be calculated.
Using vacuum systems to pass environmental air through filters, both teams were able to collect air-bourn eDNA from not only the zoo animals but also from their food hundreds of meters away from their sources! The eDNA from dozens of animals were detected and identified in each study.
In another study (conducted at my undergraduate alma mater, Texas Tech, and published in the journal BMC Ecology and Evolution (December 6, 2021)) a doctoral candidate and his advisor collected plant and fungal eDNA from previously established, passive dust and pollen collectors set out in the agricultural fields around the university. eDNA from grasses, invasive plants (including Ailanthus (:tree of heaven”)) and fungi was detected and identified. This study is quite remarkable in that that collection systems were stationary and no additional methods were used to concentrate the presumably dilute eDNA in the air. As one of the researchers put it, “Airborne eDNA continues to surprise us with how much material is in the environment!”
SARS-CoV2. Figure by Scientific Animations, Wikimedia Commons
Another aspect of environmental nucleic acids is the observation that some plants release micro RNA’s (miRNA’s) from their roots! In a paper published October 14, 2021 in the journal Nature Plants, a research group from the University of California-Riverside determined that the plant Arabidopsis thaliana (the “thale cress,” an annual plant from Eurasia and Africa that is very commonly used in molecular research) not only releases miRNA’s from its roots into its hydroponic growth medium, but that adjacent plants near the secreting individuals pick up these miRNA’s through their roots with consequential impacts on their own gene expressions (the miRNA’s interfere with mRNA activity during the translation phase of protein synthesis).
The researchers speculated that these miRNA’s may function as communication molecules alerting adjacent plants of the secreting plant’s level of stress, or these miRNA’s may be chemical instruments of competition. Plants absorbing the miRNA’s may have some critical metabolic pathway interfered with or shut down thus giving the secreting plant a competitive advantage.
miRNA’s are quite delicate molecules and its plant to plant transfer has only been observed in plants growing in liquid growth media. Future experiments are planned to see if these miRNA’s can survive and be transferred in soil.
So, we have nucleic acids floating around in surface water systems, flying around in the air and , possibly, soaking about in soil or ground (or drinking) water. Add all of these to the incredible number of viruses that are flying and floating about, and it is easy to say without exaggeration that we are constantly being plastered with nucleic acids of al kinds. It may be unlikely that an individual nucleic acid molecule could get into a host cell and cause changes, but it seems absolutely inevitable that at least one or two of all of these billions and trillions of nucleic acids hitting each and every one of us could (and would) accomplish some sort of “message” delivery!