Home Cellular science Methane-Eating “Borgs” Assimilated Earth Microbes

Methane-Eating “Borgs” Assimilated Earth Microbes

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A digital illustration inspired by the methane-eating Archaea and the Borg who assimilate them. Credit: Jenny Nuss/Berkeley Lab

A newly discovered type of transfer DNA structure with a sci-fi name appears to play a role in balancing atmospheric methane.

In star trek, the Borg are a ruthless, hive-mind collective that assimilates other beings in an effort to take over the galaxy. Here on the non-fictional planet Earth, the Borg are bundles of DNA that could help humans fight climate change.

Last year, a team of scientists discovered DNA structures in a methane-consuming microbe called Methanoperedens which seem to supercharge the body’s metabolic rate. They named the genetic elements “Borgs” because the DNA they contain contains assimilated genes from many organisms. In a study published October 19 in the journal Nature, the researchers, led by Jill Banfield, describe the curious collection of genes within Borgs. They are also beginning to study the role these DNA bundles play in environmental processes, such as the carbon cycle.

“Imagine a single cell capable of consuming methane. Now you add genetic elements in this cell that can consume methane in parallel and also add genetic elements that give the cell greater capacity. It basically creates a condition for consuming methane on steroids, if you will. — Kenneth Williams

First contact

Methanoperedens are a type of archaea (single-celled organisms that look like bacteria but represent a separate branch of life) that break down methane (CH4) in soils, groundwater and the atmosphere to support cellular metabolism. Although Methanoperedens and other methane-consuming microbes live in various ecosystems around the world, they are thought to be less common than microbes that use photosynthesis, oxygen or fermentation for energy. However, they play an outsized 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 around 30% of human-caused global warming. The gas is emitted naturally by geological processes and by methane-generating archaea; however, industrial processes are releasing stored methane into the atmosphere in worrying quantities.

Banfield is a researcher at the faculty Lawrence Berkeley National Laboratory (Berkeley Lab) and Professor of Earth and Planetary Sciences and Environmental Science, Policy and Management at University of California, Berkeley (UC Berkeley). She studies how microbial activities shape large-scale environmental processes and how, in turn, environmental fluctuations alter the planet’s microbiomes. As part of this work, she and her colleagues routinely sample microbes in different habitats to see which genes of interest the microbes use for survival, and how those genes might affect global cycles of key elements, such as carbon, l nitrogen and sulfur. The team is looking at genomes in cells as well as the portable bundles of DNA known as extra-chromosomal elements (ECEs) that transfer genes between bacteria, archaea and viruses. These elements allow microbes to quickly obtain beneficial genes from their neighbors, including those that are only distantly related.

Jill Banfield and Kenneth Williams

Jill Banfield and Kenneth Williams take a water sample from the East River in Colorado to study the microbial life in the ecosystem. Credit: Roy Kaltschmidt/Berkeley Lab

Scientists have discovered evidence for a whole new type of ECE by studying Methanoperedens sampled from the soil of a seasonal pond in California. Unlike the circular strands of DNA that make up most plasmids, the best-known type of extra-chromosomal element, the new ECEs are linear and very long – up to a third of the length of the whole Methanoperedens genome. After analyzing additional samples of subterranean soils, aquifers and riverbeds in California and Colorado containing methane-consuming archaea, the researchers discovered a total of 19 distinct ECEs which they dubbed Borg. Using advanced genome analysis tools, the team determined that many sequences within the Borg are similar to methane-metabolizing genes within the current Methanoperedens genome. Some of the Borg even encode all of the cellular machinery needed to eat methane on their own, as long as they’re inside a cell that can express the genes.

“Imagine a single cell capable of consuming methane. Now you add genetic elements in this cell that can consume methane in parallel and also add genetic elements that give the cell greater capacity. It basically creates a condition for consuming methane on steroids, if you will,” explained co-author Kenneth Williams, Banfield’s senior scientist and colleague in Earth and Environmental Sciences at the Berkeley Lab. . Williams conducted research at the site in Rifle, Colorado, where the best-characterized Borg was recovered, and is also chief field scientist of a research site on the East River near Crested Butte, in Colorado, where some of Banfield’s current sampling takes place.

The East River site is part of the Ministry of Energy Watershed Function Scientific Interest Area, a multidisciplinary research project led by Berkeley Lab that aims to link microbiology and biochemistry with hydrology and climate science. “Our expertise brings together what are often thought of and treated as completely disparate fields of investigation – the big science that connects everything from genes to watersheds and atmospheric processes.”

The resistance is futile a disadvantage

Banfield and fellow researchers at UC Berkeley’s Institute for Innovative Genomics, including co-author and longtime collaborator Jennifer Doudna, speculate that the Borg may be residual fragments of whole microbes that have been gobbled up. by Methanoperedens to aid metabolism, the same way plant cells exploited once free photosynthetic microbes to obtain what we now call chloroplasts, and how an ancient eukaryotic cell consumed the ancestors of today’s mitochondria. Based on the similarities in the sequences, the engulfed cell could have been a relative of Methanoperedensbut the overall diversity of genes found in the Borg indicates that these DNA packages were assimilated from a wide range of organisms.

Regardless of origin, it’s clear that the Borg have existed alongside these archaea, shuttling between genes, for a very long time.

In particular, some Methanoperedens were found without Borg. And, in addition to recognizable genes, Borg also contain unique genes coding for other metabolic proteins, membrane proteins, and extracellular proteins almost certainly involved in the electronic conduction necessary for energy generation, as well as others. proteins that have unknown effects on their hosts. Until scientists can cultivate Methanoperedens in a lab environment, they won’t know for sure what abilities different Borg grant, why certain microbes use them, and why others don’t.

A likely explanation is that the Borg act as a storage locker for metabolic genes that are only needed at certain times. In progress methane monitoring research showed that methane concentrations can vary widely throughout the year, typically peaking in the fall and dropping to lowest levels in early spring. The Borg therefore offer a competitive advantage to methane-eating microbes like Methanoperedens during times of plenty when there is more methane than their native cellular machinery can break down.

Plasmids are known to serve a similar purpose, rapidly spreading genes for resistance to toxic molecules (like heavy metals and antibiotics) when the toxins are present in high enough concentrations to exert evolutionary pressure.

“There is evidence that different types of Borg sometimes coexist in the same host Methanopreredenes cell. This opens up the possibility that the Borg can spread genes across bloodlines,” Banfield said.

Bold exploration of the universe (microbial)

Since publishing their preprint article last year, the team began follow-up work to better understand how the Borg can affect biological and geological processes. Some researchers comb through datasets of genetic material from other microorganisms, looking for evidence that the Borg exist in association with other species.

While her colleagues use methods in the lab, co-author Susan Mullen, a graduate student in Banfield’s lab, will get her feet wet with some very scenic fieldwork. She recently started a project to sample microbes in the East River floodplains throughout the year to assess how seasonal changes in the abundance of Borg and other microbes known to be involved in the methane cycle are correlated with seasonal fluxes of methane.

According to the authors, years later, carefully cultivated microbes filled with Borg could be used to reduce methane and curb global warming. All of this benefits the collective – life on Earth.

Reference: “The Borg are giant genetic elements with the potential to expand metabolic capacity” by Basem Al-Shayeb, Marie C. Schoelmerich, Jacob West-Roberts, Luis E. Valentin-Alvarado, Rohan Sachdeva, Susan Mullen, Alexander Crits-Christoph, Michael J. Wilkins, Kenneth H. Williams, Jennifer A. Doudna and Jillian F. Banfield, October 19, 2022, Nature.
DOI: 10.1038/s41586-022-05256-1