On episode five of Bonding Over Science, host Dawn Stringer chats with Professor of Ecology and Evolutionary Biology and Earth System Science Steven Allison about how he uses Environmental Molecular Sciences Laboratory capabilities to uncover mysteries from the Earth beneath our feet. Allison explains how his research could help us understand severe events, like wildfire patterns, and how they affect soil microbiomes. Allison is researching how well microbial communities respond and rejuvenate when exposed to extreme environmental disturbances like wildfires.
Interested in learning more about this topic?
Read the web feature on wildfire research.
Dawn Stringer: Wildfires have been filling the headlines all summer, and thanks to researchers working with the Environmental Molecular Sciences Laboratory, science could be moving closer to predicting these events and learning how they’re changing the world around us.
I’m Dawn Stringer with Bonding Over Science, join me in learning more about how events like wildfires could be altering soil microbiomes.
Dawn Stringer: We all learn from a young age how to prevent wildfires from Smokey the Bear, but there’re many other environmental factors that can contribute to these events that are deeper than we can see.
Today’s guest explains how EMSL is helping researchers like him understand these factors as they change with an evolving environment.
Steven Allison: My name is Steve Allison, and I'm a professor of ecology and evolutionary biology, as well as Earth systems science at the University of California, Irvine. And my research studies the role of microbes in ecosystems and how those microbes respond to environmental changes like climate change and drought, and what the consequences of those changes would then be for our climate, our atmosphere, our soil and ecosystems.
Dawn Stringer: How did you get interested in that topic?
Steven Allison: I guess I have to go back to probably my high school days or even childhood. I was interested in ecology from a fairly young age. My parents would take us out to various places. During the summers I lived in eastern Pennsylvania and there wasn't a whole lot to do in the summers, honestly. So fortunately my parents would take us on trips, me and my sister through like the Eastern United States at first, and then we would make trips out to Yellowstone or California, the West Coast. We went to Alaska one year, so that was pretty amazing. So I was always interested in nature, you know, kind of being outdoors and seeing some of these iconic ecosystems. So then when I got to high school, I had a chance to take an AP biology class where we actually went to the Virgin Islands to study the recovery of corals and marine organisms from a hurricane that had come through a couple of years ago. So that was a really fun experience and got me interested in biology. So I went to college at Penn State and studied biology and minored in chemistry there. So I kind of started broadening out from the biology focus to include some chemical interests, which I think is showing up in my collaboration with EMSL today. After that I got into research as an undergraduate studying plant–insect interactions, and then I wanted to go bigger and study the, the role of microbes in those ecosystems.
So that was the topic of my dissertation and that ultimately opened doors because at that time we knew that microbes were important, but we didn't have the tools yet, the sequencing and omics and other advanced molecular tools that we have now. And so that was [what] I was all developing at the time. And so it's been nice over the course of my research career to be able to use those as tools and approaches to understand and probe microbiomes in a way that we could not do, say, 20 years ago.
Dawn Stringer: Can you explain, I read a little bit about your research and wildfires are included in there, what role do they play in your research, in the environment, climate change, things like that?
Steven Allison: Yeah, of course. There are a lot of impacts we expect to see from climate change. It's not just, you know, warming of average temperatures, but we expect to see changes in rainfall and snowpack, temperature extremes, wind patterns, and all that. So here in southern California, much of California or even the western United States, we're expecting a lot of these factors to develop together.
And, you know, we may have drier conditions. We may have more sources of fuel up there, invasive species, and we may have more sources of ignition for fires, you know, more interactions between people on the ground and the impacts of climate change. So that's what we're seeing here. And in addition to the drought conditions that we saw basically up until this year, we got very wet in California, conditions were dry, and we were contending with drought.
But then also the wildfire risks. So we're seeing increases in precipitation extremes, but we're also seeing increased frequencies of wildfire. And again, that's partly due to the climate conditions, but also largely due to the fact that here in Southern California, there are 20 million people living in the area and there are a lot more sources of ignition.
So basically, anywhere, anytime you have the potential for a wildfire, the conditions are really dry, humidity is low, the winds are strong, you know, there's almost always an ignition source around. So we're kind of just holding our breath, waiting to see when that's going to happen. And that's you know, that is what happens increasingly often as we see these large fires burn up right to the edge of a city, and they have impacted our research here in Irvine.
In 2007, there was a big fire and in 2020, another fire that affected our research site.
Dawn Stringer: So how important is it to study these wildfire trends and the impact it has on the Earth beneath our feet? The microbes?
Steven Allison: Wildfire has a big impact on all components of the environment. So, of course, it burns the plants that are there, what fuel the fire. But it can also affect the surface soils and even deeper into the soil, depending on how strong that fire is and how high the temperatures get. So here in California, a lot of our ecosystems are adapted to fire.
Fire is a natural part of the ecosystem, but we're seeing much more frequent fires, which is not natural, and that may have different consequences. But we are very interested in how the fires affect the microbes that live in the soil, that provide these really important services and benefits to ecosystems, including plants, people, and the other inhabitants there.
Dawn Stringer: What's the missing piece that with your research you're hoping to find between the genomic data and the microbial metabolism?
Steven Allison: Well, there are many steps between the microbes and the other living components of our environment and the climate or the benefits that we see from our natural environments. So there's beautiful landscapes that we may go hiking in or enjoy and that are storing carbon and probably helping us avoid more dangerous climate change. So yeah, we’re really interested in knowing what are all the, the links between, you know, say, an individual population of bacteria and those broader important parts of the landscape that we, that we care about.
Not that I don't care about microbes, we do care about microbes for the sake of the science and fundamental understanding. But I think if we want to connect the microbiomes that are present in our environment, with the factors that are really important to society, then we have to put this puzzle together. And so that's really what we're focusing on here, and especially how that puzzle is going to be scattered or affected by wildfire and other aspects of climate change.
So, you know, the basic principles of biology are that you start with genes, you know, our genetic material that's encoded in our DNA. And that's the case for bacteria and fungi and, you know, the microbes that live in the environment as well. So that's the blueprint for what they can do. And then the next level is to say, well, what are they actually doing at a given time?
And so for that, we can look at the expression of DNA. So we look at, you know, what genes are transcribed, what are showing up in the environment, you know, out of that blueprint, what's actually being built? And then the part that's built are the proteins and the metabolites. So the chemical compounds that are produced by microbes or, you know, our own bodies, and we can look at metabolites in the human blood.
And so the microbes don't have blood, but they do nonetheless have pathways and they make metabolites. And those are really important for how they interact with each other, how they interact with plants or plant roots and the impacts that they have on the soil and the environment. So then you [have] all these microbes, you know, trillions of microbes, you know, in a given patch of soil, for example, and they're all interacting and producing these metabolites.
And so then the next thing to do is to say, well, how does this all come together? And what does that mean for the plants in the system? What does that mean for how the soil and the plants might recover from wildfire? Is there a role in, you know, the prevalence of pathogens or the growth of the plants that we can attribute to this pathway from genes to transcription to proteins and metabolites?
So again, there's a lot of steps in that piece, which is why biology is really interesting to me. But we really need to probe each of those pieces very carefully and with the, you know, sophisticated instruments that we have at a facility like EMSL in order to really see what's going on in that puzzle.
Dawn Stringer: Which instruments at EMSL are helping you answer some of these questions?
Steven Allison: Yeah, EMSL has a really nice array of sophisticated instruments and you know, there's some that I'm not even touching because they have such a wide array of possibilities. But the kind of workhorse basic instrument that we're using is liquid chromatography mass spectrometry, so LCMS, and basically that is simpler than it sounds. You, you take a sample, so some sample that contains the microbiomes, for example, that we want to study or the plant material that we’re interested in, maybe that burned up in the fire. And you mix it with some, some liquid, some solvents, some water, and extract out those metabolites and then you can separate them out. So there's a separation phase, that's the chromatography phase.
And then there's the mass spectrometry phase which takes the separated metabolites and identifies them by using like a chemical fingerprinting approach. So that, that's one of the techniques that we're using. And it's nice because we can, you know, we can kind of just look at what's there. We don't have to necessarily know what we're looking for, and it'll give us an indicator, like a list of the metabolites that are in the, in the soil or in the plant material or in the microbes.
And then we're also using another technique to look at the quantities of these chemicals. So we kind of get a list of what's there, but if we want to know exactly how much, then we may look at this NMR technique, nuclear magnetic resonance. And that's just a way to kind of focus in on certain chemical compounds and quantify, measure how much there is in a given sample.
We're also looking at the structure of the soil. So, you know, the fire came through and we're interested in the physical structure, like what does the soil look like from a microbial perspective. So that, that requires imaging and 3D and we’re using X-ray computed tomography to do that. And that’ll give us an image of what the soil actually looks like and if it’s been affected by the wildfire.
So those are the main techniques we’re using. And then, of course, there’s a lot of analysis that has to happen after you do the measurements, and EMSL is helping us with that as well.
Dawn Stringer: When all is said and done, what’s your overall goal with understanding all of the aspects of this project?
Steven Allison: Well, my goal is that ultimately we could actually predict what will happen in an ecosystem, right. We really want to know what the future holds in terms of climate change and wildfire. You know, how bad is this going to be or are there ways or opportunities that we can make it better, ways that we can prevent the worst from happening?
So what I’d like to do is to take all the data on the genes, the blueprints that we have, and then the expression of those genes, as well as these metabolite data that we’re getting from EMSL, and then we have a mathematical model and we can take all that information. We have a team of postdoctoral scholars who are figuring out how to use that information and put it into the mathematical model, and a mathematical model can make predictions about how the microbes [are] interacting and what that means for soil carbon storage, for example, how this soil is going to continue to store carbon, which is going to help us with the climate problem.
Are they going to continue to cycle nutrients which we need for plant growth and sustaining plants that are experiencing drought or climate change? And so that’s the goal, is that we can make predictions, that we use our understanding to make predictions and know what's going to happen. And that we can do that at larger scales. So, you know, microbes are tiny and we can't see them.
They're microscopic, but they're abundant, they're really important. And we have to figure out how to take our knowledge of their genes and their physiology and their metabolism, and then use that to understand a whole ecosystem. So we can also use our mathematical models for that.
Dawn Stringer: Can you explain how you heard about EMSL?
Steven Allison: So I've known about EMSL for a while. So one of my first grants that I received as a professor was in 2010 from the Department of Energy Genomic Sciences program. When you're fortunate enough to get one of these grants, you are able to go into the program PI meeting, principal investigator meeting. And so that's an opportunity for all of the people who are funded by that program to come together, usually outside Washington, D.C., and to meet each other and talk about the challenges and opportunities of their projects.
And they also always have a session during that meeting on the capabilities of the program, and EMSL is always featured as one of those capabilities, right? Because like I said before, you have all of these instruments that can really probe the chemistry and biology and the, you know, the interactions between microbes and their environment. And so that would appear every year I would go to this meeting.
And so I knew about the programs and opportunities and instruments at EMSL, so that's where I found out about it. And it was nice that we finally had the opportunity to actually take advantage of those instruments.
Dawn Stringer: Those are all the questions I had for you today. Is there anything you'd like to talk about that we haven't touched on yet?
Steven Allison: Well, I would say just that, you know, this is a long-term experiment. And we've had our trials and tribulations with the weather and the fires and, you know, the disturbance in our research sites. So I think this project comes at a good time, though, because we were actually able to see this system go through a fire and collect samples before and after and then have the opportunity to probe those samples in such great detail with these sophisticated molecular and chemical techniques.
And so I don't know how, when we'll ever get to have that opportunity again. And it's been really nice that, you know, they happened to align. I mean, of course, we weren't happy when our field site burned down in 2020 during that fire, but we were positioned because we've been working there to take advantage of that as an opportunity for learning and new knowledge about how the system changes with fire, which again is an increasingly frequent occurrence in our system.
So I guess we're trying to make lemonade out of lemons. And it's been really nice that we have a background of collaborators and opportunities through email and through our funding agencies to keep that work going and to see how it pans out over the, over the years.
Dawn Stringer: Awesome. We're excited to see where your research goes in the future.
Steven Allison: Awesome. Yes, I am too. You never know what's going to happen.
Dawn Stringer: Thank you for listening to Bonding Over Science, I’m Dawn Stringer for the Environmental Molecular Sciences Laboratory.
We don’t have time to cover it all, so don’t forget to check out EMSL-DOT-PNNL-DOT-GOV for a full article on this topic featuring who I spoke with today. And don’t forget to follow us on all social media platforms for the latest and greatest news coming from EMSL!
Dawn Stringer: EMSL is a Department of Energy, Office of Science national user facility that accelerates scientific discovery and pioneers new capabilities to understand biological and environmental processes across temporal and spatial scales. EMSL leads the scientific community toward a predictive understanding of complex biological and environmental systems to enable sustainable solutions to the nation’s energy and environmental challenges. If you’re interested in working with EMSL, learn more at emsl.pnnl.gov, that’s E-M-S-L-DOT-P-N-N-L-DOT-G-O-V.