A digital illustration inspired by methane-eating archaea and the Borgs that assimilate them. Credit: Jenny Nuss/Berkeley Lab
Borgs may be the antagonists in Star Trek’s fictional universe, but here on Earth, these DNA structures help fight climate change.
In a study published in Nature, California researchers describe their 2021 discovery and exploration of DNA structures within a methane-consuming microbe called Methanoperedens. They named the genetic elements “Borgs” because the DNA within them contains genes assimilated from many organisms.
As part of an ongoing research project to study how environmental fluctuations alter the planet’s microbiomes, scientists with Lawrence Berkeley National Laboratory and UC Berkeley regularly sample microbes in different habitats. The team looks at the genomes within cells as well as the portable packets of DNA known as extra-chromosomal elements (ECEs) that transfer genes between bacteria, archaea and viruses.
Last year, samples of Methanoperedens—unicellular organisms that break down methane (CH4) in soils, groundwater and the atmosphere—taken from seasonal wetland pool soil showed evidence of an entirely new type of ECE. Unlike the circular strands of DNA, the new ECEs are linear and long—up to one-third the length of the entire Methanoperedens genome.
After analyzing additional samples from underground soil, aquifers and riverbeds in California and Colorado that contain methane-consuming archaea, the researchers uncovered a total of 19 distinct ECEs, which they named “Borgs.” Using advanced genome analysis tools, the scientists determined that many of the sequences within the Borgs are similar to the methane-metabolizing genes within the actual Methanoperedens genome. Some of the Borgs even encode all the necessary cellular machinery to eat methane on their own, so long as they are inside a cell that can express the genes.
“Imagine a single cell that has the ability to consume methane. Now you add genetic elements within that cell that can consume methane in parallel and also add genetic elements that give the cell higher capacity. It basically creates a condition for methane consumption on steroids,” said co-author Kenneth Williams, a senior scientist in Berkeley Lab’s Earth and Environmental Sciences Area.
Williams and his colleagues hypothesize that Borgs could be residual fragments of entire microbes that were engulfed by Methanoperedens to aid metabolism. And while the similarities in genetic sequences support that theory, the overall diversity of genes found in the Borgs supports the theory that the DNA packages were assimilated from a wide range of organisms.
Notably, the Borgs also contain unique genes encoding other metabolic proteins, membrane proteins, extracellular proteins and other proteins that have unknown effects on their hosts.
The researchers say one likely explanation is that Borgs act as a storage locker for metabolic genes that are only needed at certain times. For example, research has shown that methane concentrations vary significantly throughout the year, peaking in the fall and dropping in early spring. The Borgs, therefore, provide a competitive advantage to methane-eating microbes like Methanoperedens during periods of abundance when there is more methane than their native cellular machinery can break down.
Since discovering the genetic elements last year, the team has begun follow-up work to better understand how Borgs may affect biological and geological processes. Some researchers analyzing datasets of genetic material from other microorganisms, looking for evidence that Borgs exist in other species as well. Other researchers are sampling microbes from the floodplains of the East River throughout the year to assess how seasonal changes in Borg abundance and other microbes known to be involved in methane cycling correlate to seasonal fluxes of methane.
Ideally, the researchers say, in the future, carefully cultured microbes full of Borgs could be used to reduce methane and curb global warming.