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Mysterious strands of DNA that apparently assimilate the genes of many different organisms in their environment have been discovered in a California backyard.
Scientists have named these elements “Borgs”, and their discovery could help us understand not only the evolution of microorganisms, but also their interactions within their ecosystems and their role in the wider environment.
According to geomicrobiologist Jill Banfield of the University of California at Berkeley, Borgs could make an extremely important discovery.
“I have not been so excited about a discovery since CRISPR”, she said on twitter. “We found something enigmatic that, like CRISPR, is associated with microbial genomes.”
An article describing the structures has been uploaded to the bioRxiv preprint server and is currently awaiting peer review.
The first of the Borgs was discovered in mud mined from Banfield’s backyard. She was working with geneticist Basem Al-Shayeb of UC Berkeley to identify viruses that infect anoxic microbes called archaea that live in wetlands, Scientific journal reports.
Environmental DNA is a great way to identify the range of organisms that inhabit an ecosystem. But in their mud ball, Banfield and Al-Shayeb found something funny: a DNA structure made up of nearly a million base pairs. It’s enormous.
A closer examination of the sequence revealed even more peculiarities: more than half of the genes were new; it had mirrored sequences at the end of each strand; and it showed structures compatible with the ability to self-replicate.
Intrigued, the researchers turned to DNA databases to see if they could find anything else that resembled their discovery. They identified 19 sequences that appeared to match the profile.
It is not clear what these DNA structures are, but they are certainly fascinating. They belong to a class of structures called extrachromosomal elements, or ECEs, which can be found outside of chromosomes that contain most of an organism’s genetic material.
ECEs are huge and self-replicating, and they can be found inside or outside cell nuclei; examples include plasmids and viral DNA.
“We can neither prove that they are Archean viruses or plasmids or mini-chromosomes, nor prove that they are not,” the researchers write in their article.
Borgs are much bigger than other ECEs, however, according to Banfield: one-third the size of their host microbes.
Sequencing revealed that the Borgs they found have some characteristics in common with a genus of archaea called Methanoperedens which oxidize methane, suggesting that the structures may be associated with these particular microbes. In fact, the Borg could be critically involved in this process.
This is of interest to scientists like Banfield, because the process reduces the amount of methane in the atmosphere. Since methane is a potent greenhouse gas, learning how microbes drive it could have implications for climate science.
however, Methanoperedens can’t be grown in the lab – not yet, anyway. One problem with environmental DNA is that it can be contaminated with other genetic material in the same environment.
Indeed, Borgs seem to share many gene sequences from other elements and microbes; researchers interpret this to mean that ECEs have absorbed and assimilated these genes and elements – hence the name, after the alien race of the hive spirit of Star Trek.
It is possible, however, that these shared genes are evidence of environmental contamination. Until Methanoperedens can be cultured in the laboratory, isolated from these contaminating influences, it may not be possible to definitively declare that these genetic structures are a new discovery.
Nonetheless, the discovery is intriguing. If the Borg are real, they could increase the ability to Methanopederens‘ability to oxidize methane. This suggests that unknown processes may be at play and that these ECEs play a previously unknown role in regulating the atmosphere.
“The Borgs carry numerous metabolic genes, some of which produce variants of the Methanoperedens proteins that may have distinct biophysical and biochemical properties,” the researchers write in their paper.
“Assuming these genes expand and increase Methanoperedens energy metabolism, Borgs can have far-reaching biogeochemical consequences, including reduced methane fluxes, with significant and unforeseen climatic implications. “
The results are available on the bioRxiv preprint site.
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