A team of researchers in the States have discovered a group of deeply unusual DNA strands in an unassuming wetland pool.
We spoke to Jill Banfield, professor of microbial metagenomics based at the University of California, Berkeley, to find out more.
You’ve discovered something you’ve called ‘Borgs’. What exactly are they?
All organisms have a genome. In fact, things that we don’t necessarily think of as living organisms have genomes too. People will be familiar with viruses, for example, or maybe plasmids. These rely on other organisms to replicate, to make copies of themselves to survive and propagate.
The Borgs are a kind of DNA-based entity – we can’t call them an organism – that lives with and depends on a kind of organism called an ‘archaean’. To put that in context, all life on Earth classifies into one of three major groups: bacteria, like E. coli, for example; eukaryotes – you and plants and fungi are all eukaryotes; then the third group are archaea.
They’re much less studied, but really interesting. They were originally thought to be extremophiles, meaning they live in extreme environments. But now we know that they’re kind of everywhere. Most recently, it’s become clear that these archaea were probably the ancestors of eukaryotes. We all go back to archaea at some point in our history.
Why did you name them after the Borg from Star Trek?
There are two ways that evolution happens. One is from parent to child, and child to their child, that’s called vertical descent. So you inherit your genome from your ancestors. And then there’s another way that organisms can innovate and change and get new capacities, and that’s called lateral gene transfer. It’s a really important second way of evolution.
It means genes can actually move around independent of organisms. Things like viruses are actually kind of important in that process. It’s not unusual to have that process happening, but the Borgs seem to be particularly involved in acquiring genes from organisms and inserting them into their own genomes [a bit like how the Borg in Star Trek assimilate different species, cultures and technology]. So that’s why we call them Borgs.
And they were found in the soil in your backyard?
I have a pretty big backyard. I’m living at the moment in the country and we have what’s called a vernal pool. It’s a pool that fills with water in the springtime and then dries out over the course of the year.
We were studying in a nearby area, and we thought, “Oh, why don’t we just take some samples from this vernal pool soil and just see if they’re interesting.” We work in lots of different environment types, studying life’s diversity and other things. It made sense to take some samples in a place that’s rarely sampled.
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How many different types of Borg have you found?
We have 19 pretty well described Borgs and four others that we are pretty sure about. I feel fairly confident that there are a lot of others out in the world that just haven’t been identified to date. The 19 different species of Borg all have somewhat different capacities, but they share common features.
One of the Borgs you’ve studied could be used to ‘eat’ methane in soil to help fight climate change. Tell us more.
First of all, let’s talk about where methane comes from. Essentially, all methane is coming from archaea called methanogens, which just means organisms that make methane. They live in places where there’s no oxygen.
They live in the subsurface where it’s dark and moist, and they’re very common in wetlands. They’re also common in places like rice paddies. Archaea that make methane exist under the ground, the methane is a gas and it can rise through the soil and enter into the atmosphere. As a greenhouse gas, it causes warming.
But there are also organisms for which methane is actually pretty good food, they eat the methane. So it’s a balance between the organisms that make methane and the organisms that eat it. A lot of different kinds of organisms can eat methane.
But a very special kind can also live without oxygen. And they live in the deep subsurface as well. They haven’t been known for all that long, but they’re really, really, really important. These organisms are the kinds of organisms that are the hosts for the Borgs. And as soon as the methane gets generated, they can eat it.
And that prevents its release to the atmosphere. Some of these methane-eating organisms do not have Borgs, but the ones that do appear to have a sort of turbocharged metabolism due to the presence of the Borg. They therefore have extra capacity to consume the methane and generate energy from it. That’s why they’re important.
Are there different useful functions that the different Borgs can perform?
The ones we know now do seem to be involved with adding to the metabolism of their hosts. So, there are two ways of looking at that question. The first is: do completely different organisms have Borgs that do different things altogether? And the answer is, we don’t know but it’s quite possible, we just need to look for them.
We haven’t found any yet. But I mean, it would be strange if this is a phenomenon of biology that only occurs in one tiny group. The second question you might be asking is: do the Borgs have other capacities that aren’t to do with methane that might be useful? And the answer is absolutely yes, because the most striking feature of these Borgs is that they have on the order of a million genes.
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We can only predict functions for a small subset of those – most of the genes are completely novel. And so there’s a lot of questions you can ask about what they might be doing with those genes, and probably it’s got something to do with their existence in a cell within a host.
Having lots of novel genes is not in itself that unusual because most viruses and bacteria, for example, are packed with genes of unknown function. But it does represent a huge potential for discovery of all sorts of interesting capabilities.
One thing I think that makes people comprehend the potential significance a little better is to point out that the CRISPR system, which is now renowned for its capacity to edit genomes, came from microbes. It was a bunch of genes of unknown function. And actually, interestingly, it’s a system of unknown function that became apparent because of its repeats; the CRISPR system has got sequence repeats in it.
That’s what was really the flag that said there’s something interesting here (read more about CRISPR on p52). And the Borg genomes are full of interesting and enigmatic repeats. I would say there are some good reasons to be looking at these genomes for new biotechnologically relevant tools.
What are the next steps?
Well, we plan to do a lot of different things, the first part of this is to answer some pretty fundamental questions. If you’ve seen any of the Twitter chats, there’s been a huge debate about whether these are, in fact, viruses.
Some people say they’re viruses and other people say they’re plasmids. And other people say we can’t really classify them as either, they are something new. I don’t know if that’s all that important because in some ways it’s a matter of nomenclature.
But underneath all that is the fundamental question of, do they exist in the cell continuously like a plasmid would? So basically exist alongside a living cell and just be part of the whole cell’s set of capacities, or are they more like a virus that comes and infects and kills the cell and then goes away? They are very different patterns. And I think understanding that is a key in understanding what these are and where to turn next to study them.
The second question is related to the tools that might arise. Are there other systems we can discover? We are going to be looking into that. I’m hoping to be able to work with collaborators at UC Berkeley to identify systems, genes and proteins that we think we can predict a function for and see if we can figure out how they’re working.
The third thing is to do with the climate. The institute that I’m associated with, the Innovative Genomics Institute at UC Berkeley, has recently launched an initiative on climate and the topic is closely linked to greenhouse gas emissions.
And one of the things we are interested in is whether or not we can learn enough about places where greenhouse gases are being formed, such as rice fields, to devise strategies to enhance the growth of organisms that will eat the methane in the soil before it goes into the atmosphere.
About our expert, Prof Jill Banfield
Jill is a professor of microbial metagenomics based at the University of California, Berkeley. Her primary research interests are in studying how microorganisms shape, and are shaped by, their natural environments