Eva Dale  0:00  
From the heart of the Ohio State University on the Oval, this is Voices of Excellence from the College of Arts and Sciences, with your host, David Staley. Voices focuses on the innovative work being done by faculty and staff in the College of Arts and Sciences at The Ohio State University. From departments as wide ranging as art, astronomy, chemistry and biochemistry, physics, emergent materials, mathematics and languages among many others, the college always has something great happening. Join us to find out what's new now.

David Staley  0:32  
My guest today over Zoom is Virginia Rich, Associate Professor and a Director of the EMERGE Biology Integration Institute in the Department of Microbiology at The Ohio State University, College of the Arts and Sciences. Her areas of expertise include global change microbiology, microbial meta omics and genes to ecosystems inquiry, each of which we're going to be learning about today. Dr. Rich, welcome to Voices.

Virginia Rich  1:01  
Thank you so much for the opportunity to be here. I'm really excited, but I apologize that I'm coming down with a cold and so my voice is scratchy, but I'll do my best.

David Staley  1:10  
That's all we ask, thank you. Well, I'm very interested to learn about these areas of research as you engage in, so I'd like you to first tell us about what global change microbiology is.

Virginia Rich  1:21  
Yeah, thank you. This is an incredibly important and growing field. There was a seminal paper a few years ago called "Scientists Warning to Humanity: Global Change Microbiology", and it was part of the scientists warning to humanity series that groups of experts have been putting out over the last decade or so about key areas of climate change science that need to be addressed and that need to be elevated in the way we're considering them. So, global change microbiology is one of these, because as my friend, the biogeochemist Scott Saleska, who's a professor at University of Arizona, as he says, there's a what's called a big biology problem in climate science, which is that even if we knew how all the humans will respond - how much fossil fuel use they will consume, what kind of diet, whether vegetarian or not, they will pursue, what their home water usage will be, all of those things - even if we can predict humans, ecological and climate change footprint, what that would be in the coming decades, it's much harder to pin down how the biosphere as a whole will respond, and that's because responses are emergent. They're not additive, and what I mean by that is that if you think about a classroom of kids, for example, I have school aged children, and so when we think about the dynamics in a classroom, if you are having a one on one interaction with each different student in that classroom, you might have a very different outcome than when you get all of the students together and try to have the same conversation, and that's a very simple example of what emergent behavior can look like the same thing happens in ecosystems where the way one organism, like a tree or a deer or a microbe responds to one piece of climate change like warming might be very different from how another organism responds and how the two of them respond when undergoing that experience together might be quite different, again, in a non additive way. And I mentioned one piece of climate change and heating there, because, of course, each organism is also responding to the other parts of climate change, which is the changing amount of precipitation, both the amount overall in different parts on the planet, and the tempo of that precipitation, different nutrient deposition in different parts of the planet, etc. And so, when we think about organismal responses to each of those things separately, even one individual organism will respond in an emergent, rather than additive, way to the whole suite of climate change experiences that they're having.

David Staley  4:28  
Well, and I want to be clear about this - you mentioned this article, "Scientists Warning to Humanity Microorganisms and Climate Change" - you were, in fact, one of the authors on that paper. 

Virginia Rich  4:36  
Yes, I did have that privilege. Yeah, I just played a small role.

David Staley  4:40  
As you described it, though you were making it sound as if you weren't involved in it, and I wanted our listeners to understand that you were indeed one of the authors of this very important paper. So, you describe the complexities involved here in trying to understand climate change, even if we could understand the full effect of humans on the climate, it would be really difficult to determine how the biosphere would respond. So, how do we do it? How does a microbiologist then try to understand that? What methods do you employ to try to figure out this really complex problem?

Virginia Rich  5:16  
That's a great question, and I'd like to, if I may, I would like to back up for a second just clarify two things. One, there is no ambiguity that climate change is happening and that it is human caused, and two, there is no disagreement about the fundamental premise that there's a lot of problems coming our way because of climate change. Where the uncertainty is, where this big biology problem that my friend Scott frames this as, where that comes into play is our projections for the rate of climate change, sort of feedbacks overall as we go into the next century, and also the hot spots where things are really going to be problematic for us, and so that's the essential piece for not only focusing our research dollars for solving ongoing questions, but also focusing our policy dollars on where we should try to mitigate and build resilience into our systems. So, a perfect example is, you know, the public already has a sense that sea level rise is happening, and so we are focusing policy resources in low lying coastal communities, okay, and people are getting an increasing sense that fire severity is increasing and fire frequency is increasing, and so our dry land management strategies are changing. And so, there's already happening a very vital focusing of our efforts in specific places to try to build the most resilient human wild interface we can this century, and so this big biology problem is central to that piece, right? It's to knowing how fast things are going to go to heck and where we can target our resources to minimize that. So I just wanted to make that point before we moved on. 

David Staley  7:19  
Thank you.

Virginia Rich  7:19  
 Yeah, thanks. So then your question was, so how are we doing this? And I would back up a second say I actually moved here from an environmental science department, and while my PhD training is in microbial ecology, my undergraduate training was actually in integrative biology. And so, although the current academic hat I wear in my department is as a microbiologist, I'm fundamentally an environmental scientist, and so I am part of the subset of microbiologists that are passionately driven by understanding how microorganisms contribute to ecosystems, and specifically how they contribute, in key ways, to ecosystem outputs. And by system outputs, what we mean are things like in a wastewater treatment plant a system output would be how well you remove emerging contaminants, or it might be how well you remove antibiotics, or it might be how well you immobilize some of the pulse of nutrients that come in in a wastewater treatment plant. It could be, you know, your system might be here in Columbus, we think a lot about brewing, right? And there's a lot of breweries that go on. And so your system output, in that case, might be the flavor, the alcohol content of the brew that you're creating. So we can define system output based on the system that we're looking at. And these are all ecosystems. A wastewater treatment plant is an ecosystem. A brewing - that is an ecosystem. Okay? So with that definition of the system output is something we're defining based on the thing we care about for that ecosystem, then we can look at the ecosystem as a whole and see how it's giving rise to that system output. And the microorganisms in pretty much every ecosystem we look at the microorganisms are really central to that. So microorganisms are the drivers of planetary biogeochemistry. Many of the biogeochemical cycles that we know about are dominated by microorganisms. They do a lot of transformations that humans cannot do. And if all multicellular life on the planet ended tomorrow, a lot of the biogeochemical cycles on the planet would kind of keep chugging along not that different. Okay, so when we're thinking about system outputs, it's really important that we consider the microorganisms, and that's true not only in the ecosystem scale, or thinking about brewing or wastewater treatment, but certainly about crops and agriculture, that's another thing that's really important here in Ohio, that's part of our legacy and one of the key things Ohio is known for, agriculture. And there's an increasing recognition, although this has been around for a long time, that what's happening below ground with the microorganisms in the soil environment, which is sort of code for all the chemistry and microbiology that's happening there, that that really is predictive of things like crop yields as well as things like crop resilience to drought. So there's a particular subset of global change microbiology that's focusing a lot on, you know, crop resilience to climate change and how we can partner successfully with the microorganisms to help support our agricultural systems. So you've heard me talk about how microorganisms are central to system outputs, and how the interactions among them and the feedbacks to them are really complex, fascinating and consequential to how we manage our industrial, municipal and planetary ecosystems. It's one of the reasons why here in OSU, I'm so excited and appreciative that the new center of microbiome science has been launched because that brings together people who think about microbiomes from all over campus, from the School of Environment and Natural Resources to the geology folks to medicine. It brings all of us together, so we can share our best practices in how to glue all of these different layers of information together, because it's not straightforward. What's more, the center of microbiome science provides a bunch of training in things like informatics tools that is essential for processing this complex meta omics data. And any given lab, you know, I run a pretty small lab. We've got maybe five to seven people at any one time, but in any given lab, there's not critical mass of expertise to cover all of the different tools that my people need to know. And so by having this centralized training structure, I can send my people there and say, go take this class. Go interact with these people. They even have, like, working group office hours, and it is phenomenal. And so, I would just like to put in an appreciative plug for that organization, because it's really transforming how my lab is able to function so - but none of those were answering your question, I'm sorry, David.

David Staley  12:45  
And maybe we've already moved into this area, but I'd like to know more about what microbial metaomics is.

Virginia Rich  12:51  
Yes, yes, you were asking me about methods, and I got excited, still talking about the why of all of this, but now let's talk about the how. So how do we look at these systems, and how do we look at these microorganisms? Well, in the systems that I'm involved in, interdisciplinarity is absolutely essential, because no one lab can be measuring all of the things if we're thinking about a system output being, for example, the emissions of a greenhouse gas. That's one of the main things we're focused on. At my side, in Arctic Sweden, we think about how thawing permafrost gives rise to methane emissions, which can then accelerate climate change. So if we're interested in measuring that, like I'm mostly a microbiologist, I don't measure landscape scale methane emissions. So it's really vital that I partner with biogeochemists who can use things like chamber measurements, automated chamber closures and measurements, to look at emissions people who work at Eddy flux towers, which are these cool towers that sit above the landscape and sip the air and then measure the gasses that are in the air that have been blown past that tower. It's important that I partner with plant biologists who can really understand how the plants are taking up the CO two in our systems, and also modelers, because at the end of all of this, all of this like looking at all of the angels dancing and all the heads of the pins at the end of this, we really want to be able to distill what we've learned into better predictions. And the way you do that is by partnering with very clever modelers who are willing to talk to like the microbiologists who are down in the weeds. And we get together and we say, okay, you use these parameters in your models, but now my measurements tell me that that parameter is changing in a way that your model doesn't account for. So how can we build in a realistic improvement in parameters to get a more accurate projection of where this system is going, or to go back to our earlier examples, where we should target our. Sources. So the way we do this is by interdisciplinarity within microbiology, the kinds of tools we use are, for example, that word, that mouthful word that you used a minute ago, microbial meta omics. So people will have heard probably of the term genomics, and that's because for several decades now, the human genome has been sequenced in various states of completeness, and there's been a lot of media coverage about the human genome. And so this word genomics has been sort of bandied around publicly. What it means is looking at the information encoded in the genome, which is the DNA for a given organism. When we talk about meta genomics, which is a particular subset of meta omics, generally meta genomics, the meta refers to the community level. Okay, so with, like, Facebook's rebranding as meta, people might have this in their mind, anyway, that this prefix meta, or this term meta, is like, oh, yeah, this is the community okay. So think about, think about using that same prefix. Now for genomics, it's like, the community level genomics. So what we go out into is we extract the DNA from a system, and we sequence it. And so just the same way that two decades ago, pioneers in the field of genomics established a good foundational blueprint for the human genome, we've been trying to go through as microbial scientists, and I would say biologists more broadly, and categorize the genomes that are present in our different focal organisms and ecosystems. So people have been looking at the genomes of Drosophila, the fruit fly, or C elegans, the nematode, or, you know, your favorite crop species, as well as, of course, lots of pathogens. So people have seen this in the news a lot as we think about the genomes of different covid variants and understanding how those are changing over time. So what we do is we go out and we do this for an entire soil system. Now it's not quite the full ecosystem, because I'm not going out and I'm not also sequencing the genomes of every single plant in our system. But what we do is we take soil cores, we take those back to the lab, we mix them with chemicals that allow the DNA to be released from all the cells, and then we prepare that DNA for sequencing and sequence it. And that gives us we do it's called short read sequencing. So we sequence little pieces of it, and that gives us genetic information as Ts, Cs and Gs, from a myriad of organisms in that environment. How many of those organisms we capture depends on how much sequencing we do. At the end of it, what we're left with, what the sequencing center sends back to us is a lot like 2000 different puzzles all mixed together in a big bag. Oh, dear, all the pieces of those puzzles mixed together. They're not complete puzzles. And what's more, you might have 200 boxes of one puzzle and one box of another puzzle, and they're all mixed together. So now what you can do is a couple of different things. You can say, hey, what puzzles were there in the first place? Can I just figure out how many puzzles there were? Is it 2000 Is it 3000 then you might say, I want to know about puzzles with bridges. How many of these puzzles have bridges? How many puzzles have flowers? Then you might want to get really clever and say, Can I start putting these puzzles together, like, can I reconstruct each individual puzzle separately, even if I can't do that for all of the puzzles, if I can do it for some of the puzzles, that starts to let me see much more clearly the landscape of puzzles that I started with, if you will. So going back now to our genomes, the conceptual analogs to what I was describing are that you get back all of your DNA sequences you would like to know what organisms are there. That's not a difficult problem, and you don't need metagenomics to do that. You can do that with just a single gene, marker gene, we call it the fingerprint gene, 16 SRNA. So you can do that in a simpler way. But what metagenomics allows you to do is also look for all the puzzles that contain bridges, so all of the organisms that have the potential to process and break down an antibiotic, or all the organisms that have the potential to make some greenhouse gas that you're worried about them producing or reciprocally consuming that greenhouse gas. By putting some subset of the puzzles back together again, which computational tools are letting us do in more and more sophisticated ways, then you can start to say, Okay, now. I have a whole section of this organism's genome that I have pieced together from all of these little puzzle pieces with some high degree of confidence saying this, you know, 70% complete puzzle, or 90% complete puzzle comes from the same species of microbe, then you can start saying, okay, for that individual microbe. I know who it is, like what lineage it is on the tree of life. I know that it contains a bridge. I also know that it contains flowers. So like I know that it can produce greenhouse gasses, I know that it can also interact in a syntrophic partnership with some other organisms in my site. And what's more, I can tell from its genome that it has the potential to interact with plants at my site in some important way, for example. So that's the kind of information you can start to get from meta genomes. Kind of those three different key pieces. So with that foundation in place of what metagenomics gets you, how is that different from this strange term you mentioned meta omics? Well, meta omics includes metatranscriptomics, metaproteomics and meta metabolomics as well. Again, lots of big mouthful words, but the point is that those look at other pieces of the ecosystem, other molecules within the ecosystem. So the metagenomics looked at DNA. Let's just think about metatranscriptomics Briefly. Metatranscriptomics looks at the RNA and specifically, as much as possible, the messenger RNA. So if audience members stretch their minds back to like the high school biology class that they took about messenger RNA and how genes are expressed, DNA is transcribed into messenger RNA, and then it is translated into protein. So and this is important and cool, if we think about all those different puzzle pieces in the environment, those are maps of the potential of all of these different organisms to do their ecosystem function, whatever, whatever the things are that they're doing, which is basically just survive and procreate from their perspective, but just the same way that every single cell in our bodies, with a few exceptions, has the same DNA. And yet our toe is quite different from our kidney. Cell is quite different from our nose a given organism in the environment that has the same DNA can manifest in that ecosystem in very different ways, just like our kidney versus our toe versus our nose. Okay, so understanding what genes they're expressing is really key to understanding how they're actually active in that environment, and that's actually what differentiates our toe from our nose from our kidney cell, is what genes are being expressed. So that's why we use this broad phrase meta omics when we're trying to think about methods to characterize what organisms are there, what they have the potential to do, and then what they are actually doing. And so it's really key to have kind of all of those pieces together as much as possible. Of course, the farther you get down in that, the more it costs and the more complex the data management. But that's the overall idea.

Janet Box-Steffensmeier  23:16  
Did you know that 23 programs in the Ohio State University, College of Arts and Sciences are nationally ranked as top 25 programs, with more than 10 of them in the top 10. That's why we say the College of Arts and Sciences is the intellectual and academic core of the Ohio State University. Learn more about the college@artsandsciences.osu.edu

David Staley  23:42  
Well, I'm just amazed at not just the interdisciplinarity, but the scope, I guess, of this work. And I'm interested in how, well how one organizes this and I assume that this is what the eMERGE biology integration Institute does. Maybe tell us a little more about this institute, and especially how sort of knowledge is organized by this institute.

Virginia Rich  24:05  
So the National Science Foundation in 2019 announced a new program, a new funding program, called the biology integration institutes and our team had been working together for about a decade in characterizing a specific ecosystem where permafrost is thawing rapidly due to climate change, and the greenhouse gas emissions from this site are rapidly changing in a way that will accelerate climate change. We call it a positive feedback, but it's not a good thing. So we try to avoid the word positive when we're talking more broadly, because it's an accelerant, is what it is. Because methane packs a wallop as a greenhouse gas. It's about 30 times more potent than CO two than carbon dioxide, and so thinking about the changing methane emissions for. Systems like this is really important. So we've been working together for about a decade to understand this system. And just like model organisms, things like fruit flies and nematodes have been so important to advancing biology in the last 70 to 100 years, our group and a number of other groups now see model ecosystems, although you won't see this term used very much, but fundamentally, this is what we're talking about. We're talking about model ecosystems, just like people have looked at model organisms, model ecosystems for understanding how ecosystems respond in these holistic and emergent ways. To really figure that out, you have to get heaps of data over multiple years, and that is a hard thing to do. We've been really fortunate in being able to obtain funding, over the years from the Department of Energy, for the first decade, to really characterize and try to understand using those microbial meta omics methods and in partnerships with biogeochemists to look at greenhouse gas emissions, plant people modelers from some of the national labs to really characterize this one site. When National Science Foundation released their biology integration Institute funding opportunity, our team was like, Oh, this is the thing we've been waiting for, because it was about, let's see, four times the size of the previous funding calls. So the funding cap for this program was 12 and a half million dollars over five years, and we knew that having generated data and made a lot of important discoveries, including an entirely new methanogenic order of organisms that we were poised to really take this next step and look at this emergence phenomenon. And so the EMERGE acronym is not a proper acronym, but it stands for emergent ecosystem response to change, and we're doing that through a paired research and training framework, and we brought on a bunch of new team members to complement and expand our existing expertise. And so we're probably double or triple in size from what we were before. And now we have five years starting in 2020 of stable funding, so a difficult part of all this was what we launched right as the pandemic was getting going, so we launched in September of 2020. In spite of that, we've been able to bring together more than 90 scientists, over more than 15 organizations, including universities and national lab facilities, primarily here in the United States, but also including colleagues in Australia and in Sweden itself, of course, to establish a new level of integrated tools and concepts for trying to plug together the different pieces of how an ecosystem works and how it responds to change over time. And that part is an important piece that we haven't had a chance to talk about yet, but is really at the heart of EMERGE. It's not just about how the bags of genes in these ecosystems give rise through a lot of complex interactions and differing gene expression give rise to system outputs. That's the first part of it. That's what we call the genes to ecosystems part. Okay, so how do you scale from bags of genes and lists of genes to actual system outputs? Genes to ecosystems? But it's also, and this is one of the novel things about our institute, it's also about the flip side of that- how the ecosystem is feeding back year over year to the genes. What we mean by this is that ecosystems are not static, and so understanding how the system is responding to climate change drivers right now, how it's responding to temperature, how it's responding to changing precipitation, fires, whatever it is right now, is not necessarily going to be how that system is responding in five years, because biology changes the way that it has been framed by two of our team members, Scott Saleska, whom you heard me mentioned before, and Regis Ferriere, both at The University of Arizona, is as the three A's. So assembly, acclimation and adaptation. So assembly, in this context, means how communities are changing. As conditions change, not all the same organisms can survive anymore, and different organisms will come in and take over just the same way that, like cockroaches and rats and pigeons live in cities, as an environment changes, the organisms that are present change. Okay, so that's the assembly piece. Acclimation, in the context of the framework that we're looking at, refers to changing gene expression. So just the same way that your listeners, when they go on vacation somewhere warm, will find that after a week or so, they're not bothered by the heat as much anymore, because they've acclimated, so too can organisms acclimate by, for example, changing their gene expression. Adaptation is the final piece, which is changing the actual gene content in organisms, and this comes back to Darwinian selection. So if you have different mutants present in the environment, some of those can survive better. And so even for the same lineages that stay present through this time, their actual genetic repertoire may shift over time. So it's those three A's, assembly, acclimation and adaptation, that capture at least a chunk of how an ecosystem can change over time in response to climate change. And so if you want to understand how system outputs are going to look in 10 years, in 20 years, in 50 years, you can't just think about how the current system is responding. You have to learn the rules for how the system is changing in response to that changing environment.

David Staley  31:18  
Why are you a microbiologist, as opposed to, I don't know, an historian or a poet, how did you end up as a microbiologist?

Virginia Rich  31:26  
So funny question, I used to want to be a poet, and then I realized I was really bad at it.

David Staley  31:30  
 Oh, okay.

Virginia Rich  31:32  
I got some good feedback in high school that, like, it really wasn't my forte, and I really liked biology, and there is this glorious poetry to the biological world.

David Staley  31:43  
What do you mean by that?

Virginia Rich  31:44  
You know, next time your listeners go outside, and you know, I'm gonna wax solely poetic right now, but you know you go outside and you look at how sort of the individual phonemes of your ecosystem are interacting to create this absolutely beautiful poems and prose everywhere you look, it's just stunning, and it's complex, and it's clever, and it's cool. So to me, I go outside and I look around just my neighborhood here, here in Columbus, Ohio, I live in the city, and it's the trees and the flowers, especially this time of year. Oh, my goodness. I think all of us see that kind of poetry around us. So I got really interested in the kinds of interactions, and organisms, and beauty of the biological world. And over time, you know, I got a degree in Molecular and Cellular Biology with an emphasis in genetics. I got a degree in Integrative Biology, so a double degree as an undergraduate, and then I took a little time off because I was like, Okay, this is cool, but I don't know where I'm going next. And for younger listeners, I want to trumpet the benefits of taking time off after college. It can be tempting to go straight on to graduate school if you think you maybe want to do science long term, but you don't have to. You can take a break and be a lab technician, you know, do something else for a while. I TAed, I was a lab technician for like, two, two and a half years, and then I realized that, like, if I was gonna do this, I probably needed to go back to graduate school, and I probably needed to not wait any longer, because when you've been out of school for a little while, you're like, Oh, why would I go back to school? So you got to kind of move on with things after a little bit. But I'm a big fan of taking that time off, because it lets you figure out where your niche could be if you're not already clear, which I was not. So I knew I really liked molecules and genes, and I knew I really liked ecosystems. I had a good girlfriend of mine, and she studied forests, and I went and visited her down in Puerto Rico, where she was working in the forest down there and doing ecological research, and that was so cool, but forests were overwhelming. There's so much like it's patchiness and habitat differences across the forest that seemed just really complicated to me and hard, and so I naively at that time, was like, oh, microbial ecology that will somehow be more attractable because it is small. It turns out that all of that patchiness and complexity in forests is amplified like 100 fold at the microscopic scale, but I didn't know that at that point. I didn't really fully fathom that, which seems, you know, again, it was naive, but it's like, oh, they'll be tractable, and I can look at, you know, the genes from them more easily. And so I started into a PhD in microbial ecology, and was really hooked because of what I continue to learn about the importance of these organisms in understanding ecosystem function. So then I kept continuing on this path, and I did a postdoc with a biogeochemist because I knew that that piece of it was critical too. So, I'm not really a microbiologist I'm still more of like an environmental scientist, but microbes are such an important entry point and sort of foundation for how ecosystems work, and a great tool. For us to develop new methods, conceptual methods and actual like laboratory methods, for understanding how systems respond, and also they're a great intervention point. Right? As we move increasingly into the era of climate change mitigation and management, we need to have tools at our disposal, and microbes are something we can work with quickly in the lab to understand those possible levers, if you will.

David Staley  35:30  
Virginia Rich, thank you.

Virginia Rich  35:33  
David Staley, thank you.

Eva Dale  35:35  
Voices from the Arts and Sciences is produced and recorded at The Ohio State University, College of Arts and Sciences Technology Services Studio. Sound engineering by Paul Kotheimer. Produced by Doug Dangler. I'm Eva Dale.

Transcribed by https://otter.ai