20 Questions for Gurol Suel: biofilm electrical communication

January 29th, 2018 by Amy Proal

Gürol Süel is a Professor of Molecular Biology and the Associate Director of the San Diego Center for Systems Biology. His research team integrates quantitative biology approaches with mathematical modeling to identify principles of bacterial organization and coordination. Most recently, the team discovered a new form of bacterial communication that arises in biofilms: Ion channel mediated electrical signaling. For more context on this discovery, please read this article in The Atlantic Magazine.

Amy: Thanks so much for speaking with me. Your last few papers on electrical communication in bacterial biofilms blew me away. I think many other people feel similarly! How did you get interested in the topic? 

Gurol: We were very interested in trying to understand higher-order organization and behavior in bacterial communities. That’s because even though bacteria are unicellular organisms they’re not solitary. They actually live in dense communities (biofilms) that have certain features: for example they’re very resilient to stress and antibiotics.

We became interested in biofilm electrical signaling partially because we saw that in biofilms there was some kind of long-range metabolic coordination. We were having a hard time understanding how the bacterial cells could communicate so effectively over such long distances. It seemed that a simple diffusion-based mechanism (like quorum sensing) might not be sufficient to support this communication. My Ph.D. is in molecular biophysics. I also have a background in electrophysiology. For example, I used to do electrophysiology in fruit flies with photoreceptors. So drawing from that experience, I started wondering if there could be a different type of signaling process involved.

We started looking at amino acids critical for slow-range biofilm communication. The most important amino acid appears to be glutamate. Glutamate is very interesting because it’s also an excitatory amino acid in the human brain. In fact, about half of all brain activity is regulated by glutamate. Glutamate is also one of few amino acids that’s charged. So it can’t just get in and out of cells on its own because that’s energetically unfavorable. So you’ve got to have some kind of a proton motor force to actually take up the charged amino acids. And if you’re dealing with a proton motor force then the cell membrane potential is important.

Little by little we pursued this line of thought and realized that we were looking at some kind of ion channel purpose or function in this signaling process. And when you think about ion channels and membrane potentials you think about sodium and potassium – those are the most commonly utilized ions in biological systems. So we looked at both and saw that sodium wasn’t really doing anything. That wasn’t surprising because Bacillus subtilis, the microorganism that we work with, is not known to have any identified sodium channels.

Bacteria form communities called biofilms (Image: The Laboratory of Gurol Suel)

But we saw a lot of beautiful signaling and dynamics going on when we looked at potassium. Then, we took the suggested potassium ion channel and started making mutants. One thing led to another and we realized that these bacteria were communicating using potassium ion channels, in a way reminiscent of what neurons do in the brain with action potentials. Once we uncovered that, we realized that if you have these long-range electrochemical waves propagating through the biofilm, then the waves wouldn’t just stop at the edge but might propagate a distance.

That led us to the Cell paper where we said: What if there’s some kind of motile cells nearby? Would they be sensing or responding? Would they be affected by these types of signals being emitted by the biofilm? Pursuing those questions turned into a fun and intriguing study. Then we said OK – if that’s possible, what if there’s another biofilm further away: could the two biofilms sense each other and interact? That led us to the Science paper about time-sharing of limited nutrients.

Amy: Right. I enjoyed reading those papers because your experiments are so well organized. I’m interested in the redundancy between the way neurons signal and the way you found that bacteria in these biofilms are signaling. Do you think it’s possible that there are any interactions between human nerve signaling and these microbes? That they could tap into each other’s signaling?

Gurol: I mean, we don’t know. That’s the short answer. Because no one’s ever looked at that. Would it be possible? I guess it would be possible. I do know that extracellular potassium signals (the potassium ion channel mediated signals) are not specific to just neurons. We showed it now even in bacteria. But it’s also very important in plants. It’s very important in all kinds of other living organisms – because these ions are very generic, meaning they can affect extracellular charge in any membrane.

So it’s not inconceivable to think that if a bacteria releases some charged particles and there happens to be an excitable cell nearby – maybe a mammalian cell – that the mammalian cell might actually respond to that. I don’t think that’s super crazy. Right now it’s unproven but it’s something we think about.

Amy: Very interesting. What about external electromagnetic fields – do you think that our human electronic devices or any radio frequency networks we’ve set up as humans could be impacting biofilm communities?

Gurol: That’s a very good question. Again I don’t know for sure. But it’s well known that lots of organisms have electro-reception, meaning they can follow electromagnetic fields on our planet. Animals with electro-reception range from whales to birds. So if organisms can sense these fields, what you’re suggesting is probably not super crazy.

There are actually bacteria known to have small particles inside that are sensitive to magnetic fields. We also know there are documented cells that will respond to an electrical field, including bacterial cells. There’s also good work out there clearly showing that just like temperature, pressure and so forth, biological systems are sensitive to magnetic forces and electrical forces. That’s more or less well-established. What we don’t know is whether or not your cell phone is going to have anything to do with your gut microbiome or things like that. Those are the things that, to my knowledge, have not been clearly studied.

Amy: Not really. But interesting future research?

Gurol: Yeah. And as I said, there’s enough strong evidence out there showing that living organisms are sensitive to these physical external properties: pressure, temperature, pH, electrical fields, magnetic fields. That’s not a new concept. So we’ll just have to see. And I don’t know, do birds sit on electric wires because it tingles? Or is it just a good sitting place?

Amy: Haha. There was a study which showed that Interference from human electronics and AM radio signals disrupted bird migration…

Gurol: Yes I wouldn’t be surprised. I think there is enough information out there to at least create a good incentive to look at the topic in greater depth.

Amy: Yes. So I research the human microbiome. If someone asked you to describe the human microbiome knowing what you do now, how would you explain it?

Gurol: Maybe I would say that the human body is an ecological network. We’re existing together with our environment, and our environment is not just about whether it’s cold or rainy outside. Within our bodies we have countless organisms (not countless but lots of organisms) and bacteria are just one of them, in fact we probably have even more viruses than bacteria – nobody’s been able to track down everything. So we harbor a lot of organisms, especially in our gut. And I think it’s a complex interaction that we don’t fully understand. There’s always, of course, a little bit of hype – when we discover something new everyone gets excited, maybe even a little over-excited. But even if 10% of all the stuff out there on the microbiome turns out to be relevant that’s already a lot.

So I would say the microbiome is a little universe of an ecological network within our body. There’s things going on between all the bacteria. But then there’s also things going on between the bacteria and our cells, the human cells. And we have yet to fully appreciate how many and which parts of these processes are super-critical and which are processes that are interesting but maybe not as critical.

The human microbiome is an ecological network

For example, there’s always interesting studies about species composition of the microbiome – studies stating that composition is critical to this process or that process. But we have to remind ourselves that the composition of the microbiome is not a static thing. When I wake up and go to bed my microbiome is probably totally different depending on where I went to dinner and other variables.

So to some degree we can’t be super sensitive to species-specific microbiome changes, because then we would have traumatic, physiological problems throughout the day. That model just wouldn’t work. We also know that the microbiome can recover: you can take antibiotics and really flush out a lot of stuff but then you can very quickly recover your microbiome. So it’s going to be important to discern which processes have an effect but are not supercritical and which processes are actually very important. That’s the kind of stuff that makes it interesting for the future – to see where it leads us.

Amy: Many people research microbes in isolation and outside their natural environment. I know great insight can be gained from that work. But do you think there needs to be a larger push to research how microbes really act in vivo (in their natural environment)?

Gurol: Yeah. So “in vivo” is an interesting term. It’s very important when you’re dealing with something like the study of cell lines in the laboratory. Problems have appeared when people have studied these cell lines and then tried to claim things about cancer: because the cell line was taken out of its natural context. But when you’re dealing with bacteria to say “what is in vivo?” is not even very clear to me. Take the organism we work with – Bacillus subtilis. You have it right now on your eyebrows and on your skin. It’s also in your gut. It’s in the soil. It’s on your tablecloths. If you have fruits and vegetables in your fridge it’s in there. So which of those locations is “in vivo”…right? They are all very different conditions, but are all places where bacteria naturally occur.

So the question of “in vivo” is a blurred, fuzzy, and potentially misleading question: in the sense that we don’t actually know what to call “in vivo.” If you isolate bacteria in the lab it’s more clear what you’re doing. But to say “this is the proper in vivo context” – I’m putting out a little word of caution: these bacteria are capable of surviving under so many different conditions that we have to be careful.

But overall any good scientist would know that if you’re studying a cell you have to understand the context of the cell, meaning the environment of the cell. And if the environment of the cell includes other cells, and those may be the same species, or different species, then obviously that is something that needs to be taken into consideration. But one can still execute very important studies without being shackled to this vague notion of “what is in vivo?”

It’s especially important to remind people of this now, because as a scientific community are very concerned in trying to make sure that our data is reproducible, and that we have reliable results: that if I do an experiment somebody else can reproduce it. But the moment we get into these types of in vivo conditions the problem is very poorly defined. Even the eyebrow skin environment differs between two people based on fat content, pH and other variables. So we’re dealing with a lot of unknowns, and although we can pat ourselves on the back and say “hey we’re studying something in a more natural context,” we have to realize that it comes at a cost – the cost of having less defined conditions and a lack of understanding of certain things. So it’s a balance – there’s no right or wrong – but we have to understand the pros and cons of each of these approaches very carefully.

Amy: OK I see. Still, in any environment, the microbiome community should focus on studying microbe activity in addition to just species, right?

Gurol: Sure. Sure.

Amy: Ok, what about other microbes like viruses, phages, fungi. Do you think that they’re involved in this electrical of signaling as well?

Gurol: We already showed in at least one paper that two very evolutionary distant species of bacteria can communicate electrically – Pseudomonas and Bacillus. One’s gram positive and one’s gram negative, so they’re very different types of bacteria. That is an indication that this signaling is not just limited to a single species of bacteria. Although that would have been a great result too. Because then you would have to ask “how can it be that only one species evolved this thing!?” That would be kind of  interesting on it’s own also. But maybe not surprisingly that does not appear to be the case.

Bacteria use action potentials to generate electrical signals

So we are still at the ground level if you will. These discoveries are still quite recent in terms of scientific years – they’re the opposite of dog years that go extra slow. So time will tell how many other species signal electrically – which ones do, which ones don’t and what that all means. But again it goes back to the earlier question that you asked: how widespread could this be? It has something to do with the fact that the membrane potential is a very fundamental property of any cell. Any living organism that’s a cell has a potential across its membrane. It’s a very ancient set of physiological processes, so it wouldn’t be shocking in hindsight if we found that different species, and even organisms across many different kingdoms, can engage in some form of this communication.

Amy: Agreed. Can you tell me a little more about how you integrate mathematical models along with the study of actual biofilms to get your results?

Gurol: Sure, the mathematical models are quite important. We use them for two main purposes. One is to come up with very specific hypotheses. The nice thing about mathematical modeling is that you can make predictions that are hypothesis driven…more than hypothesis driven: that are mathematically supported. That is very important because not only does it mean that you can define the question you’re asking really well, but once you have experimental results you can also interpret them using the framework of a mathematical model in a way that is much more powerful.

The other reason we’re doing it is that mathematical models allow us to identify concepts, and concepts are very important because a lot of people are interested in “what is this gene?, or “what is this protein?” Those are tangible objects, and so people really like working on those things. Concepts are by definition intellectual things. That means they are not tangible, in the sense that you can’t touch it, you can’t say “here’s the protein.” But concepts are very important because they allow us to bridge across very different types of systems. So if we can use the same mathematical description to describe processes happening in very different organisms that is meaningful. You can say, “There seems to be something that is shared between two systems, and then you can say “Are they trying to solve a similar problem?” Maybe there’s some kind of evolutionary information there.

Hodgkin and Huxley

So identifying concepts is very relevant in finding connections between things that appear on the surface to be different. Like bacteria and neurons: if I you told ten years ago that they might have similarities, then people would chase you out of the room and say you’re crazy. But now we can use the mathematical formulas that were originally developed in the 1950s by the brilliant Hodgkin-Huxley team. They got a Nobel Prize for the work. They identified a mathematical framework and figured out that basic action potentials in neurons are driven by potassium and sodium flux across the membrane. We showed that you can use that same mathematical framework to explain and make predictions regarding electrical signaling in bacterial communities.

Amy: Yes absolutely. How have your results been received? It seems like pretty enthusiastically, but have you had trouble communicating this to people who have only studied microbes in isolation?

Gurol: No, I mean communicating work is a very important part of being a scientist, because knowledge not shared is like knowledge that almost doesn’t exist. If only one person knows about it, that doesn’t help anybody. So communication is critical. And when you’re communicating you cannot blame the audience for not getting something – you have to figure out how to communicate your results so that anybody can appreciate them. So we take great pride in trying to write papers that are accessible, even though obviously we have to deal with the fact that we’re communicating technical scientific work. I think this pays off in that if you’re able to explain WHY something is important, people can make their own judgement on whether it’s critical or not. The dangerous thing is if people don’t understand it and they’re just confused. Confusion leads to frustration. At that point it’s very difficult to decide if something is noteworthy or not.

Amy: I think you did a great job with communication. I like how you put the more complex math towards the back of the paper.

Gurol: We try to make sure that you can read the paper, and then if you are interested there’s more meat you can sink your teeth into. I’m sure there’s still much room for improvement but we try.

Amy: No, you did a really good job. Can you tell me little more about ion potentials and about how biofilms are able to coordinate behavior to time-share nutrients?

Gurol: Sure. So you mentioned our three latest papers that you liked. The first paper describes how potassium ion channels are utilized by bacteria in biofilm communities to send long-range electrical signals. These signals allow them to coordinate their metabolism. That was an exciting finding that set many other things into motion. In the next paper we described how these electrical signals could extend beyond a single biofilm community. If there’s planktonic motile cells swimming around (because biofilms exist in aqueous environments) it’s not crazy to think that they could be recruited into the biofilm community (even different species). We knew that bacterial motility is driven by proton motor force – the cells utilize an electrochemical gradient across the membrane to generate the energy required to churn flagella: swirly appendages that allow bacteria to swim. We said, “Well if you have electrical signals maybe they would have an effect on this process of motility.” And indeed, we found that that electrical signals can direct and attract motile cells from a distance to the community. That’s interesting because now you can see how electrical signaling can turn a single species community into one that recruits other species too.

We followed that finding up by saying, “OK so if there’s two biofilm communities – two physically separated communities at some distance – not super far away but, with respect to the size of a bacteria some significant distance – what would happen?”

We saw that if these communities share the same environment they become coupled – they can sense each other so to speak. This happens in two main ways. One is this electrical signaling which syncs communities under metabolic stress. But there’s also competition between two communities, where resources are limited and there’s only enough to sustain one community. We found that under such conditions, communities started modulating the coupling between them and transitioned to different types of dynamics: they began time-sharing the limited resources. Time-sharing is a well-known concept. Take vacation homes or cloud computing (where it’s called resource sharing). Another example would be if you have one toy and two kids that want to play with it. You have the kids take turns playing with the toy. It turns out this same strategy is being employed by these bacteria. It’s an exciting discovery because time-sharing is a very dynamic process. With vacation homes or cloud computing time-sharing is not trivial – somebody has to set up a calendar saying, “You take August I’ll take June.” So it requires some kind of higher organization or somebody who coordinates things.

Bacteria use flagella to “swim”

But we found that bacteria naturally time-share through their dynamic system behavior. They can actually transition from being in phase where they’re competing a lot (and that’s OK if there’s enough nutrients) to then switching to time-sharing behavior when nutrients are low. In that case, there’s nobody from the outside telling which colony to do what. The process naturally emerges through the interaction between the communities. It’s very interesting then that bacteria are capable of executing what appear to be nontrivial strategies for coping with limited resources.

Amy: It’s extremely interesting. Do you think we’ve underestimated bacteria? With each new study it seems that bacteria are able to do much more than we previously believed.

Gurol: I’m always amazed by any living organism. If you realize how long these guys have been around (especially bacteria) they’ve survived mass extinction, one after the other. Not just the extinction that killed dinosaurs, but also the earlier extinction where even more species disappeared.

So they’re extremely resilient. They’ve been able to colonize from the Arctic to the depths of the ocean. It’s fascinating. You know, sometimes I go to the east coast and I have trouble adjusting to the new environment! So I’m impressed by these bacterias capabilities. Also, I’m sure there’s still a lot we don’t know. It’ll be a fun future to figure out what else they can do.

Amy: I agree. I know this is jumping ahead but do you see any possible therapeutic interventions based on these findings? Maybe you could interrupt an electrical signal in a biofilm-driven illness?

Gurol: Sure. We really like doing basic research and then letting the findings lead us in those directions. But we are certainly not blind to the possibility that our discoveries may also have biomedical implications. We’re trying to be careful – we don’t want to put blinders on and just focus on one thing. But we do obviously realize that biofilms are a major public health threat. Biofilms are responsible for the majority of infections in clinics. There are people dying and billions of dollars at stake. So yes. We’re aware of these problems and are slowly trying to explore those avenues as well.

Amy: What are you going to study next?

Gurol: We’re still trying to understand some of the basics. We’re still very intrigued by this new form of communication between bacteria – what else can it do? At the other side, at the smaller scale, we’re also trying to understand if in addition to ion channels, there are other genes and proteins playing regulatory roles. So we’re diving both in the direction of more detailed depth and more rigorous research. But also going in the other direction to see “How widespread is this and what other interesting behaviors can come out of this?” I suspect this research will lead to more unexpected findings.

Amy: Is there a growing community of researchers who are getting interested in this? Or are you guys working mostly alone?

Gurol: No, there’s a growing community. In fact we’re going to have a first session on biofilm electrophysiology at the upcoming American Biophysical Society Meeting this February. There will be speakers from all kinds of different institutions and from around the world. So there’s definitely a community that’s building and I think this field has a lot of potential. It’s obviously a very small field only in its infancy, but we’re trying to draw in more people and create a connected community.

Amy: Yes. Some of papers you cite are from the 1970s. How did that earlier research play into your findings?

Gurol: As they say, we’re standing on the shoulders of giants. Smart people existed before we came along. There’s been beautiful studies done – going all the way back to Hodgkin and Huxley. In fact, I would go back as far as Luigi Galvani in the 18th century who did this beautiful experiment where he cut a frog in half and used electrodes to make the legs twitch. It really freaked people out and led to books like Frankenstein where the monster is brought to life with electrical currents. So this field goes back hundreds of years. Obviously a lot more people work on electrophysiology in the human brain because that’s an important organ and it’s easy to see the relevance. But people have looked from plants to fungi to bacteria because the ability of cells to use electrochemical potential across the membrane is so ancient.

Amy: Yes. So let’s say you were talking to a student who wanted to study biofilms or microbiology. What kind of skillset would you recommend this student get to best succeed in the field? 

Computers play a central role in the study of microbes

Gurol: First you have to learn how to think like a scientist, because once you understand how that process works you can work on anything. In terms of a more concrete skillset, the more diverse the better. If you have a unique background and have done things that others have not done then, in the future, maybe you can see things from a different perspective. You might discover something new. I’m sure my background in electrophysiology allowed me to think about biofilm signaling a little bit differently.

I’ll also say this, the future is as clear: we’re heading in a direction where being able to communicate in terms of a mathematical language is key. Also understanding large data sets and analysis – that’s not going away. So having no fear of computers and software and mathematics and physics: that will be important, because again these boundaries are blurring. I think being interdisciplinary is very important.

Amy. Yes. I wish I had a physics background. I’m jealous. Before we go would you like to leave people with any other message?

Gurol: We covered a lot of stuff. Hopefully we’ll have more stuff to talk about in the future. But I’m happy that people like you and others are taking note and finding our work interesting. In this day and age it’s very important for people in science and people in science communication to make work accessible and reach out to the public. Because the more we educate the general public and try to help them understand what science is and how it works, the better it is for our society.

Amy: I do. Thank you again for this fascinating conversation.

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