An ITiMS Podcast
The University of Michigan's Integrated Training in Microbial Systems (ITiMS) program supports University of Michigan doctoral students exploring the burgeoning field of microbiome studies. In this podcast, ITiMS students explore microbial topics through games and conversation around research, government, and business roles.
Episode 2
In this episode, ecology PhD student Nicholas walks us through different topics about what life is like among microbes in the soil environment. We touch on soil decomposition and nutrient cycles, plant disease, biofilms, and patterns of biodiversity.
Producer: Nicholas Medina
Co-hosts: Freida Blostein and Emily Crossette
Guest: Jo Handelsman, Keith Heidecorn
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Transcript
0:00 HEIDECORN: I think people kind of, for most things don’t think about soil as something that--as a solution--but all these crops, everything, originates from the soil--healthy soils are, key.
[music]
0:24 MEDINA: Hey listeners! Welcome to the second episode of our podcast mini-series about the crisis, science, and solutions for soils. If you missed our first episode about the global crisis, you can find the link in the description. This episode will highlight some ideas about how microbes work in soils, with clips from interviews with Professor Jo Handelsman, director for the Wisconsin Institute for Discovery at the University of Wisconsin-Madison--and Keith Heidecorn, VP of Business Development and Emerging Technologies at Locus Fermentation Solutions, and VP of Sustainability at Locus Agricultural Solutions. We’re your hosts—Freida Blostein and Emily Crossette. I’m Nicholas Medina. All of us are PhD students studying microbes in various ways as part of the Integrated Training in Microbial Systems, or ITiMS program at the University of Michigan. My projects study how soil microbes are organized into different communities depending on the physical structure of soil and the foraging activity of invertebrates in agricultural lands.
BLOSTEIN: And I’m an epidemiologist studying how the oral microbes that live in our mouths can contribute to ongoing chronic health problems, like dental decay and periodontitis.
CROSSETTE: And I’m an environmental engineer, so I study the microbial ecology in engineered water and wastewater treatment process, and currently I’m studying how storage impacts the manure microbiomes that are applied to land.
2:04 MEDINA:So again, in this episode, we’ll touch on what microbes do for soil: taking on topics of decomposition, plant disease, metabolism, soil aggregation, biofilms, and some interesting questions for future research.
2:24 BLOSTEIN:We’ll start with the reality that soil is a major reservoir of nutrients for land plants, and we can thank soil microbes for recycling all of those nutrients for us. Professor Handelsman talked to us about the key functions of soil microbes for society.
2:39 HANDELSMAN: They decompose plants and animals that have died in the soil, and that’s a way of bringing the nutrients that are released from those carcasses, so to speak, into the rest of the biological system and recycle the nutrients in them. Every nutrient in soil—nitrogen, phosphorus, sulfur, and certainly carbon—is processed by microbes. That’s essentially the difference between soil and rock, is that we have a very active microbial community that is metabolically quite robust and is having an effect on the nutrients.
3:20 CROSSETTE: So, it sounds like most of the nutrients from rocks are released for plant growth by microbes. This means that plants without microbes would not get the nutrients they need to live.
MEDINA:And when we talked to Keith it also seems like some microbes wouldn’t be able to live without their plants.
3:40 HEIDECORN: We’ve seen, through all our treatments, no matter what, we increase that root mass, and root masses are an important indication of how much carbon could potentially be in the soil, because roots exude about 20 to 30% of their sugars through the roots of the plants. So, the more roots you have, the bigger the roots, that means that more sugars are feeding the microbial populations in there, and those microbial populations are in turn putting more carbon in the soil.
4:10 MEDINA:So to follow up here, plant roots have a strong effect on the soil right around them. And this is called the rhizosphere. And the effect is that the plants give away carbon in the form of sugars to nearby microbes who give the plant other nutrients in return from the soil. It’s a strong partnership that plants and soil microbes have, especially because almost half of the sugar that plants make from photosynthesis goes into the soil.
BLOSTEIN:Wow, who would have known that plants were so generous?
CROSSETTE: Yeah, or that microbes follow the Golden Rule philosophy: they treat others just like others treat them.
4:55 MEDINA:So, this connection between soil microbes and plant roots, essentially all happening in the brown part of nature, begs the question: Does what happens below ground affect other parts of the plant above ground, in the green part of nature?
CROSSETTE: I’m sure Keith’s answer would be yes. Changing the soil microbes can actually prevent the wilting of plants. This is important for warmer regions of the United States growing citrus plants, where there is a non-soil bacteria that’s causing what’s called Citrus Greening Disease.
MEDINA:From some research, this bacteria is spread by insects and infects the above-ground part of the plant.
5:40 HEIDECORN: It doesn’t actually kill the tree, it just reduces its ability to grow efficient oranges and citrus, and so they drop earlier, they’re not getting the numbers they’re getting.
5:55 BLOSTEIN:So this bacterial group, now called Liberibacter, includes strands from the United States, Asia, South America, and Africa. Is there more we should know about how the bacteria causes disease?
MEDINA:Well, it seems like it lives in the sap of the plant so it could be eating sugar in there, or maybe its proteins on the cell just look so foreign that the plant’s immune system reacts to its presence. I imagine it can just get so complicated.
BLOSTEIN:Probably just as complicated as human disease.
CROSSETTE: Okay, let’s run with this hypothesis that bacteria are stealing the plants’ sugars. Could it be eating other molecules, too?
BLOSTEIN:Well, sugar is usually the easiest and most rewarding.
CROSSETTE: Well, I know that from experience.
BLOSTEIN: Right. So, similar to microbes in soil like fungi, mini bacteria breathe kind of like human cells do, so, they get energy and they produce carbon dioxide.
CROSSETTE: It’s a good thing they don’t have teeth.
MEDINA: I don’t get it.
CROSSETTE: You don’t get it? We’re talking about - Frida studies periodontal diseases and they eat only sugar!
BLOSTEIN: Yeah, right, if bacteria had teeth there would be a lot of bacterial cavities, I guess?
CROSSETTE: Sorry, I just had to throw that in there.
7:19 MEDINA: No, that’s good. And so bacteria can eat lots of other things, too, which is why they’re so involved in cycling key nutrients in soil. In general, microbial metabolism can be broken down into where cells get their energy and matter. Cells that get their energy and matter from carbon-carbon bonds are called chemoheterotrophs: “chemo” meaning chemical energy and “hetero” meaning organic matter. On the other hand, plants are photoautotrophs: “photo” meaning light energy and “auto” meaning inorganic matter.
CROSSETTE: So there are definitely other types of microbes in soil who can get their energy from non-carbon elements, like sulfur, iron, and nitrogen, but those microbes are idiots because sugar is definitely the best.
[music]
8:20 MEDINA:So just like last episode, we also have a microbe trivia game throughout this one. We’ll give you three clues, and you should have a guess as to the name of the microbe by the end of the episode. Here’s the first clue: This microbe is a molding fungus that produces a chemical that prevents cell wall synthesis in bacteria, so it’s a common antibiotic that has helped save lives since 1928. This fungus’s antibiotic is often used to treat bacterial infections, like pneumonia, strep throat, meningitis, syphilis, and gonorrhea according to the National Library of Medicine.
9:11 BLOSTEIN: Yeah, why can microbes have so many different diets and how can they eat all of these things at the same time in soil? From a soil ecology perspective, it turns out that some of this can be explained by the actual structure of the soil environment.
9:28 HANDELSMAN: Probably one of the most interesting aspects of soil microbiology to me is the fact that soil microbes produce these long sticky polysaccharides which act as the glue that binds soil particles together. If you imagine the difference between a rich healthy garden soil where you have clumps and clods that are stuck together and are quite large compared with, for example, beach sand, where there’s much less aggregation and the individual grains are all separate, that’s generated by the microbes of the soil who produce these polysaccharides that stick the particles together.
10:13 MEDINA: So this probably explains why Professor Handelman’s favorite soil is the beloved Mollisol of the midwestern United States, a system that has been created and nourished by Native American fire management and is the basis of the U.S. agricultural economy.
CROSSETTE: One really quick question – Do you also have a favorite soil?
10:37 HANDELSMAN: Well, it’s interesting. It depends on the level at which you ask or answer that question. So, there are 12 broad soil groups in soil classification. And the best one in my opinion is the Mollisol, which is the most agriculturally productive soil in the world. It’s vied for and loved by anyone who has it and it’s wanted by all the countries and regions that don’t have it. It’s typical of the U.S. Midwest. It’s I think the greatest gift that this country has in terms of natural resources. So Mollisols are pretty important and they’re also pretty rare so they’re probably my favorite, but of course, I have a general commitment just because it’s the Wisconsin state soil to a particular Mollisol called the Antigo Silt Loam which is the Wisconsin state soil.
11:40 CROSSETTE: Soil structure and specifically these clumps, or aggregates, are really important for mediating microbial activity in soil, and it seems like microbes themselves are actually making these sticky sugar glues that hold the soil particles together. So they must benefit from these structures, right?
BLOSTEIN: Well, what’s known for sure is that less decomposition happens inside of aggregates because there’s less oxygen inside of them, which many microbes need - especially fungi - to respire, just like us.
MEDINA: Outside of soil aggregates there are larger spaces between aggregates filled with air and water which are called macropores. Water and air flows quickly through these macropores and brings along fresh carbon and nutrients for microbes to use that are living on the surfaces of those soil aggregates. Inside the soil aggregates, there are still pores, but they’re way smaller, called micropores. These are less than 30 micrometers wide, and are better at restricting carbon and nutrient flow and trapping dead plant matter that would otherwise be eaten by other microbes. So soil aggregates in general tend to be a reservoir of soil nutrients because there’s less microbial activity.
CROSSETTE: Oh, so this is why healthy microbe soil interactions prevent the runoff from nutrients! They’re essentially creating this glue that traps nutrients that could otherwise, you know, infiltrate into water that’s run off or seep into groundwater, and keeping those within the rhizosphere.
MEDINA: Exactly - the more aggregation a soil has, the better it can hold onto water and nutrients and the less erosion you have, thanks to soil microbes.
13:44 BLOSTEIN: Okay, but I have a question about all of this: These soil pores are super small. How do you soil scientists even know that all of this is going on inside of clumps of dirt?
MEDINA: Well, it turns out that you can take a “cat” scan - CT scan - of soil, just like medical professionals do for humans, but just at a really small scale. This is called a micro-CT scanner. It can let you see pores inside of aggregates, including trapped organic matter.
BLOSTEIN: That’s pretty cool. Like you can literally see into soils just the way that we can see into human brains or something when we give people CAT scans.
MEDINA: Yeah, though it is expensive to use - even for researchers.
14:37 CROSSETTE: Well, for the small price of a couple of cans of cat food a day you can get your do-it-yourself at-home CAT-scanner!
MEDINA: Listeners, Emily has two pet cats.
BLOSTEIN: Yeah, but I feel like that would not be as effective. I think we should just plan the experiment the right way. I’ll go find some protocols and dog-ear the pages.
MEDINA: And Frieda has a pet dog.
[music]
13:07 MEDINA: Here’s our second clue for our microbe trivia: This fungus includes species that are key to giving blue cheeses their color and funky taste. Also, you might find some of this microbe growing at home on any old oranges or bread.
15:30 MEDINA: Actually, speaking of dogs and microbes, did you know that dog owners have more diverse microbiomes than people without dogs?
CROSSETTE: I really hope it’s the same for cats, too. I wonder what about the dogs… Do you think it has anything to do with them licking their skin or their fur?
15:46 BLOSTEIN: Yeah, I mean saliva definitely has bacteria in it. That’s what I spend a lot of my time studying. Saliva is like constantly washing over our tongues and our gums and our teeth which are all coated in these coalitions of bacteria that we call biofilms. And if you ever like run your tongue over your teeth and they feel slimy, that’s what you’re feeling. Biofilms form when bacterial communities attach to surfaces and form what’s called an extracellular polymeric substance. And that’s what that sticky goo is, and it helps the bacteria stick together. Biofilms like that are super cool because, kind of like soil aggregates, they can allow bacteria to thrive in different ways or be more fit than any single bacteria would be alone. Biofilms are everywhere, and I imagine they’re probably in soil, too, right?
MEDINA: Yeah, biofilms are common on soil aggregate surfaces, and they help increase the species diversity of those microbial communities. They help microbes and cells survive together better by holding more water and nutrients. And again, this makes soil aggregates reservoirs of biodiversity.
BLOSTEIN: Maybe just like our pets’ saliva is doing for our skin microbiomes!
MEDINA: Probably, yes.
CROSSETTE: Yeah, I bet there’s also a ton of fur microbiomes, too.
BLOSTEIN: Yeah, like sloths have whole communities of algae and these eukaryotic organisms that live in their fur. I don’t even want to think about it though. My dog is so disgusting. I love her, but she’s very gross.
CROSSETTE: Well back to soil. So, overall, aggregation in microbial polysaccharide production seems like an important part of microbiology in general. In soil, they can affect its structure to slow down erosion by water and wind, which is affecting our Great Plains soils of the U.S. Midwest.
BLOSTEIN: For more information on erosion and the soil crisis, check back into Episode 1. Again, the link is in the description.
CROSSETTE: Okay, so to get back to soil, we’ve learned that aggregation and these microbial products like sugars and sticky goo seem to be a really important part of microbiology in general. Specifically in soil, they can affect its structure to slow down erosion by water and wind, and this is really critical for maintaining the soils of the Great Plains of the United States.
MEDINA: So all of this microbial, gluey substances - could they be what save us from the soil crisis?
CROSSETTE: Sadly, it’s more complicated than that. For a follow-up to this, you’ll have to check out our next episode, Episode 3.
[music]
18:52 MEDINA: Here’s our third and final clue to help you guess our mystery microbe: This fungus has recently had a plush doll made after it that kind of looks like a tree or an octopus, and in this form it probably functions to provide tactile emotional support to humans.
19:16 MEDINA:Finally, listeners, we’ve come to our last topic of the episode, which is about future directions for research in soil microbiology. So, a simple way of framing most related ideas here are with asking the question of “Why are there so many species of microbes in soil?”
19:37 HANDELSMAN: So, I think there’s a long way to go in understanding particularly soil communities. Soil is probably the most biologically complex environment on earth and has the highest density of species of any ecosystem we know of, and so a really important part of soil ecology is the production of these glues that bacteria produce, and that’s something that my lab is very interested in is how do bacteria take the nutrients fed to them by the roots of plants and turn them into these polysaccharides that have such a dramatic effect on soil structure.
20:21 CROSSETTE: So one reason could be the formation of soil structure itself. Soil has millions of aggregates, and each one of those can have its own slightly different combination of microbial cells.
MEDINA:Yeah, and this is similar to a fundamental idea in ecology, which is that having separate populations of even just one or two species can change the outcomes of competition between them. Separating populations into different habitats can reduce competition between some species, and therefore help them survive, and even coexist, with different species that they otherwise wouldn’t live with.
BLOSTEIN: Okay, that’s interesting – so, does it matter how many total species are interacting?
MEDINA:In ecology, total species is shown to vary by habitat size. So originally, this data comes from islands in the Caribbean, where larger islands, like Cuba, have more species of larger organisms, or macrobes, than smaller ones, like Puerto Rico, and that’s because larger islands also have more individuals of each species which lowers the chance that population will go extinct.
BLOSTEIN: And the same theory could apply to the soil microbial diversity then, if we kind of think of each soil aggregate being its own separate, little island.
MEDINA: Yeah. There are also other explanations for soil biodiversity, like dormancy and the transfer of useful genes that give bacteria new functions, but we’ll save those for another time.
CROSSETTE: So, Dr. Handelsman and her colleagues, much like geniuses in a superhero movie, work together to build a synthetic microbial community with organisms originating from soil. This synthetic community they appropriately named THOR, which stands for “The Hitchhikers of the Rhizosphere.” Let’s hear how THOR will help us better understand microbial interactions.
22:39 HANDELSMAN: Where we’re hoping to take this model system, which is made of three very typical soil organisms representing the three major phyla in soil, is to understand their interactions with each other and, just, I mean you’d think that three organisms would be rather simple and we have all the tools that you might want to study them: We have full genome sequence, we can do genetics, we have metabolomic data, and, in spite of all of what we have and there being only three organisms, we find the interactions so complex. And just as one small example - one of the organisms among THOR produces an antibiotic, but it only produces it in the presence of the organism that it actually kills with the antibiotic. So, the inducer of antibiotic production is actually the victim, as well. And then in the same system, the third member of THOR protects the victim from death by the antibiotic.
BLOSTEIN: So to recall, out of those three bacteria, the first one can kill other cells by making an antibiotic.
CROSSETTE: Yes. That’s Pseudomonas, and it’s a pretty common genus actually.
MEDINA: And then, there’s another victim that dies from the antibiotic?
BLOSTEIN: Yeah, that’s Flavobacterium.
CROSSETTE: And then there’s a savior of that lethal interaction who stops the production of the antibiotic.
MEDINA: I’m following.
24:07 HANDELSMAN: And that’s just one molecule, and all the different directional interactions that we know of - and there are probably others - just with one molecule and three members of the community. And so, when you then multiply that complexity by, you know, another factor of 100 in terms of the size and composition of the real community in the soil, you begin to realize just how hard this problem is. So, what we’re trying to do is develop models with THOR, with just three members, that we can then test and see if they validity at a total community, the natural community level, and if those models can predict behavior of the natural community. So that remains to be done, but that’s the kind of work that I think is really going to break open our understanding of the soil and root microbiome because we have to simplify the problem. We’ve got to reduce the degrees of complexity and the complexity of the community itself.
25:21 MEDINA:So, I imagine this is happening among a lot more species. Even if we were to just focus on a single clump of soil, right?
BLOSTEIN: And this really shows how useful soil can be in so many different ways, and soil microbes, too. It’s amazing that we can exploit some of these bacteria to make biocide compounds for us, right, because that can help us in medicine. And it’s not even just bacteria - fungi make antibiotics, too. Did you know that there are fungi that we use to make antibiotics? One of my favorite funguses is responsible for an antibiotic that has saved so many lives…
MEDINA: Wait, wait wait - that’s for our listeners! To guess at the end of the episode.
BLOSTEIN: Oh, sorry, I just got really excited about fungi. They’re so much fun, you guys!
CROSSETTE: So to move on, all of these potentially biocidal interactions are good for biodiversity?
MEDINA: Well, I mean, food webs in general, going back to ecology, are apparently filled with indirect interactions like these. In one study, ecologists use models to show that indirect interactions of two species with a third or fourth species can increase the average length of food chains. So, in theory, indirect interactions like these could support higher diversity in soils. Especially if you include all the predatory bugs, and viruses, and bacteriophages that eat the bacteria and fungi.
CROSSETTE: There is so much to explore about microbial diversity, and how studying and understanding microbes can help us save soils.
In our next episode, we will talk about the benefits we get from soil microbes, and how we might be able to help microbes help us save the soils.
[music]
27:34 MEDINA: It’s time to reveal our mystery microbe of this episode’s microbe trivia, so gather your thoughts, phone a friend, and guess: What is this microbe?
[music]
The answer is…penicillium! Aptly named after the antibiotic treatment we know as “penicillin,” the penicillium fungus can defend against bacteria by blocking bacterial cell wall synthesis.
If you guessed it, or didn’t, the prize is - new knowledge! So, be sure to spread it to your friends and family!
That’s all for this episode, folks. We hope you learned a lot about what microbes do in soil. We sure did while researching for this project. We’d like to thank our guests again, Professor Jo Handelsman and Keith Heidecorn, along with the ITiMS Community, for helping give this podcast life. We also thank the Burroughs Wellcome Fund for supporting the ITiMS Program as a whole. Until next time!
References:
Bairey, E., Kelsic, E. & Kishony, R. High-order species interactions shape ecosystem diversity. Nat Commun7, 12285 (2016). https://doi.org/10.1038/ncomms12285.
Gabriel L. Lozano, Juan I. Bravo, Manuel F. Garavito Diago, Hyun Bong Park, Amanda Hurley, S. BrookPeterson, Eric V. Stabb, Jason M. Crawford, Nichole A. Broderick, Jo Handelsman. mBio Mar 2019, 10 (2) e02846-18; DOI: 10.1128/mBio.02846-18.
Kravchenko, A.N., Guber, A.K., Razavi, B.S. et al. Microbial spatial footprint as a driver of soil carbon stabilization. Nat Commun10, 3121 (2019). https://doi.org/10.1038/s41467-019-11057-4.
MacArthur RH, Wilson EO (1967). The theory of island biogeography. Princeton, N.J: Princeton University Press. ISBN978-0-691-08836-5.
Rillig, M., Muller, L. & Lehmann, A. Soil aggregates as massively concurrent evolutionary incubators. ISME J11, 1943–1948 (2017). https://doi.org/10.1038/ismej.2017.56.
Music: (YouTube Audio Library)
“Earth Bound” by Slynk
“Lobo Loco” by Bazar
“Mid-Air Machine” by Four Corners
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