Last year, a team of scientists discovered DNA structures in a methane-consuming microbe called Methanoperedens that appear to increase the organism’s metabolic rate. They named these genetic elements “Borgs” because the DNA in them contains genes that have been taken up from many organisms. In a study published Oct. 19 in Nature, researchers led by Jill Banfield describe a strange collection of genes within the Borgs. They are also beginning to study the role these DNA packages play in environmental processes such as the carbon cycle.
Methanoperedens are archaea (single-celled organisms similar to bacteria, but representing a distinct branch of life) that break down methane (CH4) in soil, groundwater and the atmosphere to support cellular metabolism. Although Methanoperedens and other methane-consuming microbes live in diverse ecosystems around the world, they are thought to be less common than microbes that use photosynthesis, oxygen or fermentation for energy. Yet they play a huge role in Earth system processes by removing methane – the most potent greenhouse gas – from the atmosphere. Methane traps 30 times more heat than carbon dioxide and is estimated to be responsible for about 30 percent of human-caused global warming. The gas is naturally emitted through geological processes and methane-producing archaea; however, industrial processes are releasing stored methane back into the atmosphere in worrying amounts.
Banfield is a scientist at Lawrence Berkeley National Laboratory and a professor of Earth and Planetary Sciences and Environmental Science, Policy and Management at UC Berkeley. She studies how microbial activity shapes large-scale environmental processes and, in turn, how environmental fluctuations alter the Earth’s microbiome. As part of this work, she and her colleagues routinely sample microbes in different habitats to understand which interesting genes microbes are using to survive and how these genes may affect the global cycle of key elements such as carbon, nitrogen and sulfur. . The team studied the genome inside cells and portable DNA packages called extrachromosomal elements (ECEs), which pass genes between bacteria, archaea and viruses. These elements allow microbes to rapidly acquire beneficial genes from their neighbors, including those only distantly related.
Scientists discovered evidence of an entirely new type of ECE while studying Methanoperedens sampled from seasonal wetland pond soil in California. Unlike the circular DNA strands that make up most plasmids, the new ECEs are linear and very long—about one-third the length of the entire Methanoperedens genome. After analyzing other samples of subsurface soils, aquifers and riverbeds in California and Colorado that contained methane-consuming archaea, the researchers found a total of 19 different ECEs, which they dubbed Borgs. Using advanced genome analysis tools, the team determined that many of the sequences in the Borgs were similar to methane metabolism genes in the actual Methanoperedens genome. Some Borgs even encode all the necessary cellular machinery to eat methane on their own, as long as they’re inside a cell that expresses the gene.
“Imagine a single cell that is capable of consuming methane. Now you add genetic elements within that cell that are capable of consuming methane in parallel, and you also add genetic elements that give the cell a higher capacity. If you will, it’s basically creates a condition for methane-consuming steroids,” explains co-author Kenneth Williams. He is a senior scientist in Earth and Environmental Sciences at Berkeley Lab and a colleague of Banfield. Williams led the study at the Revel site in Colorado, where the most well-characterized Borg was found, and was also the lead field scientist at the East River research site near Christ Butte, Colorado, where some of Banfield’s current sampling efforts are located. conduct there.
The East River site is part of the Department of Energy’s Watershed Functional Sciences focus area, a multidisciplinary Berkeley Lab-led research program that links microbiology and biochemistry with hydrology and climate science. “Our expertise is in bringing together fields of investigation that are often considered and seen as completely unrelated — big science that connects everything from genetics all the way down to watersheds and atmospheric processes.”
Resistance is a disadvantage of futility
Banfield and her researchers at UC Berkeley’s Institute for Innovative Genomics — including co-author and longtime collaborator Jennifer Doudna — have hypothesized that Borgs may be remnants of whole microbes that are engulfed by Methanoperedens to aid metabolism, similar to plants How cells used formerly free-living photosynthetic microbes to obtain what we now call chloroplasts and how an ancient eukaryotic cell consumed the ancestors of today’s mitochondria. Based on sequence similarity, the phagocytosed cell may be a relative of Methanoperedens, but the overall diversity of genes found in Borgs suggests that these DNA packages were taken up from a wide range of organisms.
Regardless of origin, it’s clear that Borgs have been with these archaea for a long time and shuttle genes back and forth.
Notably, some Methanoperedens were found without Borgs. And in addition to identifiable genes, Borgs contain unique genes encoding other metabolic proteins, membrane proteins, and extracellular proteins that are almost certainly involved in electron conduction required for energy generation, and others with unknown effects on their hosts. Until scientists can grow Methanoperedens in a laboratory setting, they won’t be sure what abilities the different Borgs confer, and why some microbes use them and others don’t.
And one possible explanation is that Borgs act as storage cabinets for metabolic genes and are only needed at certain times. Ongoing methane monitoring studies have shown that methane concentrations can vary widely throughout the year, typically peaking in the fall and dropping to their lowest levels in early spring. Thus, during periods of methane abundance, when there is more methane than their native cellular machinery can break down, Borgs provide a competitive advantage to methanotrophs like Methanoperedens.
Plasmids are known to play a similar role, rapidly spreading resistance genes to toxic molecules such as heavy metals and antibiotics when concentrations of toxins are high enough to exert evolutionary pressure.
“There is evidence that different types of Borgs sometimes coexist in the same host Methanopreredens cells. This opens up the possibility that Borgs may be spreading genes across lineages,” Banfield said.
Boldly explore the (microbial) universe
Since publishing the related article as a preprint last year, the research team has begun follow-up work to better understand how Borgs might affect biological and geological processes. Some researchers are combing through datasets of genetic material from other microbes and looking for evidence that Borgs coexist with other species.
Years later, carefully cultivated Borg-laden microbes could be used to reduce methane and curb global warming, according to the researchers. It’s all for the benefit of the collective — life on Earth.