Scientists at the University of California, Berkeley, have discovered the unusual DNA structures within Methanoperedens — a group of archaea that break down methane in soils, groundwater, and the atmosphere — that appear to supercharge the organism’s metabolic rate. They’ve named the genetic elements ‘Borgs’ because the DNA within them contains genes assimilated from many organisms.
A digital illustration inspired by methane-eating archaea and the Borgs that assimilate them. Image credit: Jenny Nuss / Berkeley Lab.
University of California, Berkeley’s Professor Jill Banfield and colleagues study how microbial activities shape large-scale environmental processes and how, in turn, environmental fluctuations alter the Earth’s microbiomes.
As part of their work, they regularly sample microbes in different habitats to see what interesting genes microbes are using for survival, and how these genes might affect global cycles of key elements, such as carbon, nitrogen, and sulfur.
They look 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.
These elements allow microbes to quickly gain beneficial genes from their neighbors, including those that are only distantly related.
While studying Methanoperedens sampled from seasonal wetland pool soil in California, the researchers found evidence of an entirely new type of ECE.
Unlike the circular strands of DNA that make up most plasmids, the most well-known type of extra-chromosomal element, the new ECEs are linear and very 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, they uncovered a total of 19 distinct ECEs they dubbed Borgs.
Using advanced genome analysis tools, the team 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,” said Dr. Kenneth Williams, a researcher at the University of California, Berkeley.
“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, if you will.”
The authors hypothesize that the Borgs could be residual fragments of entire microbes that were engulfed by Methanoperedens to aid metabolism.
Based on the similarities in sequences, the engulfed cell could have been a relative of Methanoperedens, but the overall diversity of genes found in the Borgs indicates that these DNA packages were assimilated from a wide range of organisms.
“There is evidence that different types of Borgs sometimes coexist in the same host Methanopreredens cell,” Professor Banfield said.
“This opens the possibility that Borgs could be spreading genes across lineages.”
The findings were published in the journal Nature.
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B. Al-Shayeb et al. Borgs are giant genetic elements with potential to expand metabolic capacity. Nature, published online October 19, 2022; doi: 10.1038/s41586-022-05256-1
