Scientists have discovered DNA sequences in wetland soil that are unlike anything ever found and which could have “important and unanticipated climate implications,” according to a new preprint study co-authored by a Nobel Prize Laureate, among other genomics researchers.
The authors of the new paper, which has not yet been peer-reviewed, named these genetic elements “Borgs” after the recurring villains in Star Trek, because they assimilate genes from other organisms.
Borgs are extrachromosomal elements, meaning that these DNA sequences are found outside the chromosomes that lie within the nucleus of most cells and that contain the majority of an organism’s genetic material. Examples of extrachromosomal elements include plasmids, which can replicate outside of a host’s chromosomes, and some viruses.
Exactly what Borgs are remains a mystery at this point, but it is clear that they share genes and proteins with organisms that oxidize methane, called methanotrophs, that belong to the genus Methanoperedens, suggesting that they acquired these elements through past gene transfers. Methanotrophs are of immense interest to climate change researchers because they reduce atmospheric emissions of methane, a potent greenhouse gas that contributes to rising global temperatures.
“Speaking for myself, I was really very excited, especially once it became clear that they carry genes directly involved in methane oxidation,” said senior author Jillian Banfield, a biogeochemist and geomicrobiologist at the University of California, Berkeley, in an email.
Banfield and her colleagues realized they were dealing with something special after sequencing DNA found in the wetlands of Lake County, California. Her team includes several researchers from the Innovative Genomics Institute (IGI), a partnership between UC Berkeley and the University of California, San Francisco that was founded by Jennifer Doudna, who received the 2020 Nobel Prize for Chemistry and is a co-author of the new study.
The researchers have studied a huge variety of microbial entities—bacteria, archaea, eukaryotes, viruses, phages, and plasmids, for instance—that inhabit watery habitats such as groundwater aquifers, soils, and vernal pools. The Borgs were clearly different from anything they had seen before, hinting at a distinct evolutionary origin.
“In studying one wetland soil (vernal pool) we identified fragments of enigmatic genomes that were clearly archaeal but could not be classified easily as any type of known genetic element,” said Banfield, who leads the Microbial Initiative at the IGI.
“We then sought them in other datasets we have generated,” she continued. Using this approach, the researchers were able to collect at least 19 examples of Borgs, and sequence four complete genomes, thereby establishing “the existence of a substantial lineage of related entities with clearly shared (and somewhat unusual) features” making them “novel extrachromosomal elements.”
The team color-coded the 19 groups—there are Orange, Lilac, and Rose Borgs, for example—and described some of their perplexing properties, including their exceptionally enormous size. The DNA sequences were most abundant in deep anaerobic (oxygen-poor) soil and sometimes exceeded actual Methanoperedens populations in these locations by eight times. Indeed, there was no consistent relationship in the abundances observed between the Borgs and the methanotrophs they interact with, adding another layer of mystery to their origins and behavior.
That said, the Borgs do clearly contain metabolic genes, which might be able to boost the energy metabolisms of Methanoperedens that host them. If so, these unique genetic elements could provide new insights into reducing methane emissions, which is a major aim for climate change mitigation plans.
“We expect that Borgs increase the overall amount of methane that a Methanoperedens can oxidize, in part by making them more able to adapt to changing conditions,” Banfield said. “Thus, one short term strategy is to figure out how to foster Methanoperedens in agricultural soils (which are already manipulated) that are more robust due to the Borgs than those without.”
The team is also interested in resolving a more basic question: what even are these Borgs? They could be “giant linear viruses,” or “plasmids unlike anything previously reported,” or perhaps “a sibling Methanoperedens lineage that underwent gene loss and established a symbiotic association within Methnoperedens,” according to the study.
To get a better handle on the countless riddles posed by these weird DNA sequences, the researchers hope to find more Borgs in other datasets. Banfield said that this research could lead to the discovery of “new mechanisms for processes that as yet, we don’t even know exist.”
“Thus, the analogy may be made to CRISPR—a system with only partially predicted function related to microbial defense against viruses, but ultimately a fantastic new toolset,” she concluded.