If you dig out a handful of soil, or a whole bucket full, what do you see? Really, not that much? Well, yes, that’s one reason the study of soil is such a challenge. It’s a lot of stuff mushed together, crumbs, roots, dead stuff, critters. Soil is a very complex, intensely 3D-structured environment. How do you map that landscape? In order to look at the fine structures of a root, scientists have to painstakingly lay them bare. If they want to catch a critter, they have to lure it into a trap. And with very tiny organisms, it’s sometimes just impossible to get that sample. In this episode, scientists share their challenges and methods, and dream of new technology to improve our understanding of soil in major ways – if it just existed! This episode features Asmeret Asefaw Berhe, Kate Scow, Maddy Thakur, Marcel van der Heijden, and podcast producers Matthias Rillig and Anja Krieger.

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TRANSCRIPT

Sound – Piha in Amazonian Forest (Brazil) by Felix Blume on Freesound, CC-0

Anja Krieger
Just imagine being in a tropical rainforest. You are in this amazingly diverse and colorful world of plants and animals. But what do you do as a soil ecologist? You kneel down, your eyes on the brown ground, taking sample by sample, which all look the same.

Sound – Soil Brush by NeoSpica on Freesound, CC-0

You can see the amazing diversity of the life you’re studying. To reveal this, you need to take your samples to the laboratory.

Theme by Sunfish Moon Light

Katie Field
I think the most difficult aspect of studying soil or soil processes is that you can’t see what’s going on. Because things are hidden, things are invisible.

Bala Chaudhary
It’s really hard (laughs), it’s really hard! And it takes a long time.

Anja
Welcome to Life in the Soil, a podcast by the plant, fungal and soil ecology lab at the Freie Universität in Berlin, Germany.

Matthias Rillig
One of the points maybe that people don’t really appreciate is how difficult it is to really gain access to some of the parameters or some of the variables to measure.

Bala Chaudhary
Anytime you take a soil sample or a core, you inherently change it.

Yong-Guan Zhu
There are so many different organisms there. We only recognize very few of them!

Toby Kiers
If I were to say the things that are difficult about studying these symbiotic fungi, I almost would keep you here all day. These guys are really difficult to bring into the lab. And the main reason why they’re difficult is that they’re symbiotic!

Asmeret Asefaw Berhe
Like every kind of scientific field, you have to keep learning. You have to keep learning and you have to keep coming up with new approaches that help us expand the knowledge base.

Vocoder sings “Life in the Soil, Life in the Soil”

Yong-Guan Zhu
We need to get a better understanding of the complexity and get to know who are there, and what they are doing, and why they are doing that.

Theme music fades.

Anja
Hello again, soil-mates, this is Anja Krieger, your host! In the first three episodes of this series on soil ecology, we introduced you to the habitat and the vast diversity of life in the soil, like fungi, nematodes, springtails and bacteria. But how do soil scientists actually study these incredibly small organisms and their tiny, tiny world? What methods and tools do they need, and what are their challenges and dreams? This is what we’re going to take a closer look at in this episode.

Music – Bundt by Blue Dot Sessions

Anja
Soil is a super exciting but also super complex world to study. I had never really thought how hard it could be before I met Matthias Rillig, my podcast co-producer. He’s the ecologist who runs the soil laboratory at Freie Universität here in Berlin.
Matthias, if you’re a soil biologist interested in the biota – how do…how do you get the creatures out? They’re very tiny.

Matthias
Yeah, so for many of them, you don’t need to get them out, all you need to get out is the DNA. So you go in the lab and extract the DNA and then you use a suitable primer pair, basically, to amplify, which means capture the group of organisms of interest, for example, fungi or bacteria, or cercozoa within the protists. But for many organisms, primers are not very well defined yet. I’m sure this will change in the future, but then you got to extract them. Also, if you want to look at them, you need to extract them. So you…there’s different methods of extraction, for example, for microarthropods, you put the moist soil in a little funnel, and you have a little vial underneath it. And then on top, you switch on a light. And so this means that the top of this funnel starts drying out very slowly and gets warmer. And so the animals don’t like that. So they will migrate down in that funnel, in the end, they will, you know, basically just fall out of that funnel into a little vial where you can collect them. And then you can, you know, you can look at them, you can identify them to species if you can. Or you can do analysis on them, you know, stable isotope contents or something or nutrient contents. And you can do further studies on them. You can also capture them live and basically use them in experiments. For fungi, you can also extract them, of course, you can plate soil dilutions out on a petri dish on agar. And then you can look at the colonies that come out, you can single out the colonies with a toothpick and then let the fungi grow individually. And then you have isolates of certain fungi. You can do the same with bacteria. But there’s estimates that like a tiny percentage, like a percent, or a 10th of a percent of bacteria are culturable. We do not know what the percentage of fungi is. Yeah, and so there’s real limitations to these culture-based methods, in terms of community analysis. And for bacteria and fungi, they’re no longer accepted, I mean, this stopped a long time ago, because they’re completely unrepresentative of what’s really there – for that you need the DNA-based methods.­­­­

Anja
What is the hardest thing for you in studying soils?

Matthias
There’s many things to say here. One of the points maybe that people don’t really appreciate is how difficult it is to really gain access to some of the parameters or some of the variables to measure…say, for example, you want to measure­­­ roots. This is pretty basic, right? I mean, the above-ground people, when they want to measure plant biomass, they just take a pair of scissors and clip it off and put it in a bag and you’re done. But when you work with roots, you know, you have to take out that entire soil. Then we have a little root-washing table where you spread that soil out, very gently spray the soil off of the roots. And then it takes many hours to get these roots out of soil and then you put it in a bag and­ then you can wait and do more measurements on it. So, very many times just obtaining your sample is very, very difficult and very time consuming. But if you want to do anything more complicated – for example, just imagine you want to measure anything over time. There is almost nothing you can measure right in place. Let’s say you want to do a seasonal cycle. So you take samples throughout the year, maybe like twice a month, take these samples back to the lab – what do you think your field site will look like? Well, it looks like Swiss cheese. Right? I mean, afterwards, that thing is just only holes, because every time you took a sample, you left a hole. And so one of the biggest problems is that almost all measurements that you can do are destructive. So that sample that you did your measurement on is gone afterwards. And that is just a huge problem, when you do any time courses, they’re just very, very difficult to do. Because that gets confounded with another factor that’s difficult about soil, is its enormous variability. So if you take your sample here, or like just a couple hand widths over there, you’ll get different values, because soil is just incredibly, it’s just heterogeneous.

Anja
So these soil maps that exist of different kinds of soils and I guess they’re also very different kinds of communities living in there, but that’s not everything, right? So that’s just like the broad types of soil, but then within those types of soils, there’s like all this variation, like even in the smallest space.

Matthias
That’s right, I mean, there’s variability at just… every scale, you know, there’s variability at the global scale, you have different soil orders, you know, there’s a taxonomy of soils just like of plants. So you have different soils in different climate regions of the Earth. And then you go to regions, you have different soils depending on the topography and the parent material, you know, what rock it is, is it in a mountain, is it next to a river? And then when you go even further down to like the scale of like, say, like the size of an office room, then, you know, you have different plants that give rise to different soils, different local disturbances and local differences and properties. And then if you zoom even further in to the scale, where that’s actually the scale relevant to the microbes, because they are small, and so to them, tiny little landscapes, if you will, they matter, then you have this crazy heterogeneity at even like the scale of a few hundred micrometers. So at every level, you have this immense heterogeneity in all kinds of parameters you care to imagine. And so yeah, that’s definitely a challenge.

Music – Heliotrope by Blue Dot Sessions

Anja
But let me tell you, soil scientists are in it for the challenge. And many of them develop some pretty cool ideas to find out more about soils. Marcel van der Heijden is one of these creative minds. He works at Agroscope, the Swiss centre of excellence for agricultural research, and at the university of Zurich. He’s the speaker of the BiodivERsA project that funds our podcast.

Marcel van der Heijden
So I think for many people, soil is dark, it’s muddy, it’s dirty, and people have not a strong connection with soil, they don’t realise how important soil is for our life, for food production.

Anja
Marcel runs the Unterhosen project. Unterhose is German and translates to “underpants”.

Marcel van der Heijden
Yes, this is a very funny project. So we start a large citizen science project. So that means we want to involve many farmers and many citizens to bury underwear in the soil as a way to assess soil quality. So the whole project is aimed to enhance the awareness of soil biodiversity and soil quality. So that’s important for agriculture, that it’s important for humans.

Anja
To bring home this message, the scientists send the participants a piece of underwear, which they can bury for two months in their soil or garden. After that, the citizen scientists send the soil sample with the underwear back to the lab, and Marcel and his team analyse it. Since only Swiss citizens can participate at the moment, I asked Marcel if I could bury my own underwear in the soil, here in Germany, to try it out.

Marcel
You, of course, can take your own underwear. But it’s, of course very important to take cotton underwear because if you get take synthetic underwear, it will not degrade.

Anja
Right, I wouldn’t want to add synthetic microfibres to my garden. The whole idea of this citizen science project is to see how fast cotton is degrading – and that tells you about the productivity of the organisms that live in your soil.

Marcel
So we look at the soil quality, we look at soil life. And then we try with these 1000 different sites, we try to see if the underwear breakdown is linked to soil quality and soil biodiversity. So its an idea is to find a proxy to test how good the soil quality is. And of course, it’s funny – everyone has something to do with underwear.

Anja
With the Underwear project, Marcel and his team try to get citizens involved in soil science – in a playful way. But they also collect real data.

Marcel
So we will get a lot of information for many different pieces of lands. The people have to give some information about land use. And then we can link the breakdown of the piece of underwear with land use, with soil quality, with soil biodiversity. So I think that’s very interesting. So it is science, sciencewise, it’s very interesting. But also there’s the social component, of course to teach about the importance of soil and to teach also about soil biodiversity and soil life. How fascinating it is.

Music – Lost Shoe by Blue Dot Sessions

Kate Scow
Primarily most bacteria exist as little rods or little cocci, little spheres.

Anja
That’s microbial ecologist Kate Scow. You might remember her from episode 3, where she told us all about some of the tiniest inhabitants of soil, the bacteria.

Kate Scow
Well, you know, the old way of seeing under a microscope for bacteria was pretty disappointing. So you go in and look at them, and you can stain them and they just like, Oh, you know, it’s like, okay, it’s boring. If you get to see an actinomycete, which is a particular kind of bacterium that has filaments, and has conidia, which are a kind of spore, there’s more to look at, they’re prettier, but a lot of bacteria just really boring.

Anja
Kate says her work is less about seeing, and more about finding out what bacteria actually do. So rather than looking through a microscope, she tests how the bacteria deal with different conditions. For her, that’s like doing an interview.

Kate Scow
So I might say, do you need oxygen? So I’ll put some of that in, and they’ll say, yeah, that helped. Then I say, do you need more, do you need maybe some nitrogen? And then, they’ll say, yeah! And the way that they’re answering me is how rapidly they break down the particular pollutant.

Anja
When Kate interviews or tests her bacteria this way, she only indirectly sees them. She gets an answer in the form of a curve showing the breakdown of a pollutant. Or she sees that the overall mass of bacteria is growing. This tells her what the organisms might be capable of. Then, she follows the classic question of a crime story: Who did it? And that’s where she needs more sophisticated technology.

Kate Scow
So I may see, like, wow, this organism really broke down this…ehm, this soil broke down these, these compounds, I wonder who did it? Or I wonder what group of organisms did it. And then I might go in and use different tools like looking at the DNA to try to do a correlation between who showed up in the DNA as maybe dominant members and the process and the ability, say, to eat the pollutant.

Anja
That way Kate can identify the bacteria that might be responsible for what just happened.

Kate Scow
It’s, it’s like indicators of them, right? I’m not seeing them as a whole body. I’m seeing them by essentially extracting their guts. (Laughs) And looking at their, you know, their constituents to give me information about who they are.

Anja
However, one question remains open after the genetic analysis. Are they dead or are they alive?

Kate Scow
It’s hard to know, like with some of the techniques we have, who’s actually living and actively engaged versus who’s dormant – like, they’re still alive, technically. But they’re really shut down, because the conditions aren’t great for them. So they’re kind of waiting it out – versus who’s, like dead. Methodologically, it can be really complex, like, if you extract DNA from soil and use that as your indicator of the organisms – you might be extracting a lot of DNA that’s of dead organisms, it’s just still hanging around, that DNA. So it might not represent who’s living, who’s actually doing the work in the soil.

Anja
The boundary between life and death is really hard to draw in soil, Kate says. But whether dead or alive, bacteria play crucial roles for the ecosystem.

Kate Scow
Sometimes they’re agents, you know, sometimes they’re actually carrying things out and you’re interested in them being alive, right? But sometimes they’re like, pools or reservoirs, you know, of nutrients. So it doesn’t really matter, like, if they’re actually alive or not. What matters is that that all this nitrogen and phosphorus and other elements like exist in them, and they will turn over.

Music – Tidal Foam by Blue Dot Sessions

Asmeret Asefaw Berhe
I joke sometimes that I don’t study living things in soil, per se. Even though I study processes those living things mediate.

Anja
Asmeret Asefaw Berhe is a professor of soil biogeochemistry at the University of California in Merced.

Asmeret Asefaw Berhe
I joke sometimes with my friends who study microbial ecology, that living things start becoming interesting to me when they die and when their organic matter enters into soil. Right, from a scientific perspective, right, that’s what I study, is what happens to their remains.

Anja
She uses sophisticated tools to examine the chemical composition of soil. That way she can study how soil interacts with the big cycles that are important for life on Earth, like the carbon and the nitrogen cycle.

Asmeret Asefaw Berhe
You know, one of my favorite methods to use in soil science is spectroscopy, which is basically this approach that uses interaction of light with matter to tell us about the properties of the matter that we’re studying, in this case soil. So we can use this tool called spectroscopy, to understand about the mineral composition of soil, the organic matter composition of soil and even how the minerals and the organic compounds are interacting in soil.

Anja
But soil is one of the most complex biomaterials we know of, and that’s a challenge. It contains materials from different rocks, from different locations, weathered at different times – and the organic matter in soil can come in a huge variety of states, and some of it can be 1000s of years old.

Asmeret Asefaw Berhe
So whenever you’re trying to use tools like spectroscopy to understand soil, then you undoubtedly have to deal with that complexity. And so these methods that are pretty straightforward to use if you are using them, you know, in typical organic chemistry lab, for example, when you come and try to apply them in a soil biogeochemistry lab, you have to spend a lot of time trying to extract information out of this diverse signature of the soil that you’re looking at. So that’s probably one of the hardest things. But at the same time, once you succeed in getting, you know, the tools to tell you the story of soil, it also tells, you know, fascinating complex stories and history of soil.

Music – Building the Sledge by Blue Dot Sessions

Anja
How can scientists tease out these stories of soil? Biologists who study bigger animals and their habitat can often directly observe them with their own eyes. So, just think of someone studying dolphins or seals in the ocean. In contrast, soil scientists are trying to peek into a miniature world.

So just like some of us wear glasses to be able to focus, soil scientists need special tools, methods, filters and lenses. Luckily, major advancements have been made in science and they have enabled some exciting discoveries over the past few decades. Soil scientists now have a whole toolbox of methods at their disposal. They can use lenses, filters, microscopes, add fluorescing colors, analyse isotopes in lipids and proteins, and sequence DNA in soil. There’s a lot of options. But for each organism or process they want to study, they need to choose a different approach. All of that makes soil an incredibly challenging, but also exciting field of research. And it’s one with many hopes and dreams, I found.

I asked soil ecologist Madhav Thakur what would he do with a lot of money.

Music –­­­­ Aourourou by Blue Dot Sessions

Maddy Thakur
So if you give me an imaginary budget, which is immense, I would like to develop some techniques of artificial intelligence, which can really monitor soil, and create immense amount of data to help us understand how the crazy complexity in the soil works. So imagine all those robotic cameras in the soil moving, capturing soil animals in the action, how they are feeding, how they’re moving. And if we can build some kind of, you know, machinery like this, it’s not only for the science, it will also capture the imagination of a lot of general public. Because people get excited when they see things they have never seen before. So if you have a picture of a black hole, everybody was like, Wow, look at that black hole!­­­­­ If you have a picture of how a soil animal in nature is feeding on another animal, that will also wow a lot of people.

Music fades out

Anja
Maddy is not the only one who dreams of this.

Matthias. Let’s say money is not a limitation. And you could invent this futuristic method or machine to help you understand soil better. Is there something that you would really love to have?

Matthias
Yeah, if I could dream something up, that doesn’t exist yet, I think it would be a device that allows me to monitor real time dynamics, biological real time dynamics in a certain volume of soil, that’s not too tiny, but you know, doesn’t need to be huge. But it could be like a couple of centimeters cubed, and just see what goes on in there, really, in real time, and how these organisms, for example, make an aggregate or how they attack a piece of soil organic matter, and actually make it stable, so that it’s stored in the soil. And how all these interactions really play out. We cannot ever see, we only get ever snapshots, we get like, you know, extractions of DNA from 250 milligrams of soil, this is our information. But this is just who’s there not really who is active. And also, definitely not who interacted with whom, because we’re actually extracting, you know, maybe like the equivalent of the country of Germany, and inferring from that, who went out to dinner with whom! (Laughs) I mean, it’s basically…that scale is very, very coarse when you think about it. And it would be really nice to have a machine that allows me to go into that pore space, and allows me to watch this in real time. I mean, what aboveground ecologists basically can do, they can also sit there and observe interactions in real time. That would be my machine, no idea how to get there. But you know, if you want to have a dream, that would be one.

Anja
So to all the millionaires and billionaires listening now to this podcast (Matthias laughs) – if you think this is exciting, and, you know, this could be an alternative to sending a car to Mars, then you know who to get in touch with!

Matthias
Mars is also cool, just for the record! (both laugh)

Theme music – by Sunfish Moon Light

Anja
And thanks to all the non-millionaires listening out there as well! This was episode 4 of Life in the Soil with Kate Scow, Marcel van der Heijden, Asmeret Asefaw Berhe, Maddy Thakur, Matthias Rillig, and me, Anja Krieger. Our story consultants were Tessa Camenzind, Milos Bielcik, Moisés Sosa Hernández and Stefanie Maaß.

If you liked our show, share it with your friends, and leave us a review on iTunes. You can get in touch with Matthias via the lab website, rilliglab.org. Cover art is by Maren von Stockhausen, music by Blue Dot Sessions and theme by Sunfish Moon Light.

Next on Life in the Soil, we’ll explore the humans impacts and global change in the Anthropocene. How do we protect and restore the precious ecosystems in the soil? So stay tuned, and join us next time!

Vocoder sings “The Life in the Soil”­­­, end of audio.

FULL CREDITS

Produced by: Anja Krieger and the Rillig Lab
Funded by: Digging Deeper / BiodivERsA
Guest experts in this episode: Asmeret Asefaw Berhe, Kate Scow, Maddy Thakur, Marcel van der Heijden
Additional Voices in intro: Yong-Guan Zhu, Bala Chaudhary, Katie Field, Toby Kiers
Story consultants: Tessa Camenzind, Milos Bielcik, Moisés Sosa Hernández, Stefanie Maaß.
Thanks for feedback: Madara Pētersone

Cover art: Maren von Stockhausen
Music: Sunfish Moon Light / Future Ecologies, Blue Dot Sessions
Sounds: Freesound.org CC-0

Listeners in Switzerland can join the citizen science project by registering before April 15, 2021: https://www.beweisstueck-unterhose.ch/

The Digging Deeper project was funded through the 2015-2016 BiodivERsA COFUND call for research proposals, with the national funders Swiss National Science Foundation, Deutsche Forschungsgemeinschaft, Swedish Research Council Formas, Ministerio de Economía y Competitividad and Agence Nationale de la Recherche.