A powerful "Borg" DNA makes methane-eating bacteria stranger than ever

Methane-eating archaebacteria have engulfed ancient life forms.
Rupendra Brahambhatt
A digital illustration of Borgs.
A digital illustration of Borgs.

Jenny Nuss/Berkeley Lab

If you think carbon dioxide is the most powerful greenhouse gas, think again. When it comes to heating the Earth, methane is 80 times more effective than CO2 and is responsible for 30% of the total global warming our planet experiences. This is why archaebacteria that consume methane and reduce their concentration in our environment are of great importance, as they help us fight climate change.

But how are these archaebacteria able to consume the suffocating methane gas? While looking for an answer to this question, in 2021, a team of researchers at the Lawrence Berkeley National Laboratory came across special DNA packets within an anaerobic methane-eating bacteria, Methanoperedens. These DNA packets were surprisingly different from the main chromosome of the bacteria, and they even had the power to boost the metabolic activity of the microorganism.

The researchers named these extrachromosomal elements (ECEs) “Borgs.” Now in a recently published study, they have shed light on the role that Borg DNA plays in methane consumption and various other ecosystem services that the microbes provide.

Borgs are metabolism boosters for the microbes

During their study, the researchers collected samples from anoxic (oxygen-deficient) soils, aquifers, and riverbeds. They were looking for the genes that allowed the methane-eating archaebacteria to survive and participate in the various natural cycles involving elements like nitrogen and carbon. The researchers identified 19 ECEs or borgs within Methanoperedens that contained genes capable of breaking down methane.

They claim that when it comes to dealing with methane, the ECEs were as powerful as the genome of the microbe. Some Borg DNA packets are so good at consuming methane that all they need is only a cell to express the genes, and they can take care of the rest of the mechanism that is required to perform the task.

While explaining the distinct nature of the ECEs, authors Jill Banfield and Marie Schoelmerich told IE, “Borg DNA is clearly distinct from the main chromosome of microorganisms for several reasons. Borg DNA does not encode ribosomal machinery (the ribosome is the protein synthesis machine of any living organism), nor full metabolic pathways, or energy-conserving systems. Yet they do encode genes that are essential for the central processes of their hosts, indicating that they can augment and expand the metabolic capabilities of them.”

Chloroplast, the special cell organelle in plants that traps sunlight and turns the same into chemical energy through photosynthesis, is believed to have formed as a result of plants engulfing ancient microbes that performed photosynthesis. Similar to this theory, the authors of the current study also assume that Borgs have also resulted from the remains of the many other microbes that were previously consumed by Methanoperedens.

This could be the reason why Borg DNA contains a variety of genes and is so different from the main chromosome of the microbe. However, during their research, the researchers also noticed that not all Methanoperedens samples contained distinct ECEs.

How could studying Borgs benefit humanity?

ECEs are basically portable DNA packets that allow the quick transfer of genes between different microbes, such as bacteria, archaea, and viruses. The current study reveals that Borg DNA elements carry signatures of recent gene transfer from their inferred Methanoperedens host. How this DNA is transferred is not known yet, but it has important implications for the interplay between the ECE and its host.

For example, the authors suggest that it creates an interdependence between the main chromosome and ECE so that the ECE can be used to evolve assimilated genes to create new versions (this could be lethal if done in the main chromosome) and copy numbers of the ECE that can be adjusted (to meet environmental conditions) independent of the main genome (Borgs can have copy numbers up to 8x of the main host chromosome).

All these aspects are believed to be important in facilitating the adaptation, evolution, and survival of these organisms (in this case, Methanoperedens). Now the question is how the knowledge of Borgs could be useful to humans.

“Our research has several important implications. Firstly, by illuminating the existence of ECEs such as Borgs, and understanding their function, we can think about ways to harness them for biotechnological and, ultimately, agricultural engineering purposes, for example. This could be pursued by amending environments such as rice paddies or cow rumen with genetically-tailored methane-consuming microorganisms,” Schoelmerich told IE.

The researchers further suggest that since Borgs harbor a myriad of novel protein machinery, they could give rise to new genome editing tools. Plus, they could also help us in studying the biology and evolution of various other complex organisms like Methanoperedens. However, a limitation of the study is that there are no existing cultures of Borgs and their hosts.

This prevents them from further studying the ECE interplay and its importance in methane oxidation in the laboratory at this point. They are currently tackling this problem and working on establishing bioreactors to cultivate Borgs and their hosts.

The study is published in the journal Nature.


Anaerobic methane oxidation exerts a key control on greenhouse gas emissions1, yet factors that modulate the activity of microorganisms performing this function remain poorly understood. Here we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins through studying groundwater, sediments and wetland soil where methane production and oxidation occur. Four curated, complete genomes are linear, up to approximately 1 Mb in length and share genome organization, including replichore structure, long inverted terminal repeats and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are highly divergent archaeal extrachromosomal elements with a distinct evolutionary origin. Gene sequence similarity, phylogeny and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as ‘Borgs’. We identified at least 19 different Borg types coexisting with Methanoperedens spp. in four distinct ecosystems. Borgs provide methane-oxidizing Methanoperedens archaea access to genes encoding proteins involved in redox reactions and energy conservation (for example, clusters of multihaem cytochromes and methyl coenzyme M reductase). These data suggest that Borgs might have previously unrecognized roles in the metabolism of this group of archaea, which are known to modulate greenhouse gas emissions, but further studies are now needed to establish their functional relevance.