Podcast: Here's some dirt, part 1

Soil is so much more than the word dirt may imply, as I learned speaking with soil and ecosystems researchers at the NIOO, the Netherlands Institute of Ecology
Podcast: Here's some dirt, part 1

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This podcast episode digs into dirt or, rather, as it is scientifically called, soil.

A while ago I wrote about soil research for Nature Methods. The story is called Soil researchers dig deeper into dirt.  Here, I am sharing more of what I heard in reporting that piece. 

Traditionally, soil science is mostly physics and chemistry and not about the critters in the soil. Soil ecologists take a more holistic view as you will hear in this podcast. 

It's with Dr. Ciska Veen,  soil and ecosystems researcher at the Netherlands Institute of Ecology (NIOO-KNAW) and Dr. Wim van der Putten, who heads terrestrial ecology at NIOO-KNAW. 

You will hear about their work and that of their colleagues in greenhouses and in the field. Also hear about their Soil-tron, which is a way to do experiments in the field with soil with intact layers and that is extracted in columns. It's a way to do field experiments in a more controlled way so one can make measurements and time series. 

A drone shot of the Soil-tron at The Netherlands Institute of Ecology

(The Netherlands Institute of Ecology

A photo of the Soil-tron at the Netherlands Institute of Ecology

(The Netherlands Institute of Ecology) 

Two researchers at work at the Soil-tron

(The Netherlands Institute of Ecology

A researcher working at the Soil-tron

(The Netherlands Institute of Ecology

You can listen to the podcast right here or find this podcast on streaming services such as Apple podcasts,  Google podcastsSpotify,  Amazon Music, Gaana and wherever else you find your podcasts. 

Note: These podcasts are produced to be heard. If you can, please tune in. Transcripts are generated using speech recognition software and there’s a human editor. But a transcript may contain errors. Please check the corresponding audio before quoting.

Transcript: Here’s some dirt

Ciska Veen 
We work on soil biodiversity and functioning so that means like we look at who is in the soil and what are they doing. 

That’s Dr. Ciska Veen  soil and ecosystems researcher at the NIOO, the Netherlands Institute of Ecology (NIOO-KNAW). 

Wim van der Putten
For the quality of our life it's is really important that we just look at soil from a holistic perspective, because this is giving soil species take less management, they give more functions and return and more services. So actually, we're just fools if we don't use the soils in the proper way.

And that’s soil and ecosystems researcher Dr. Wim van der Putten, who heads terrestrial ecology at the Netherlands Institute of Ecology. 

Hi and welcome to Conversations with scientists. I’m Vivien Marx. Today’s episode digs into dirt or rather as it is scientifically called soil. Traditionally as Wim van der Putten has mentioned to me, soil science is mostly physics and chemistry and not about the critters in the soil, like invertebrates or microbes. Soil ecologists on the other hand, which Dr. Van der Putten and Dr. Veen are, is all about soil and its organisms, including microbes, and there are around 5,000 organisms of in a teaspoon of soil. There have been some separations between soil scientists and soil ecologists but in many cases soil studies involve physics and chemistry and ecology and biology. 

I asked both of scientists a number of things. Such as how to measure if soil is healthy and how might soils store more CO2. There is a balance to strike to make soil sustainable and for the long-term able to produce the food we need. And since in many areas of the world, soil is damaged, they talked about one can restore it. And yes, I did also talk about gardening tips. 

I wrote a story for Nature Methods about soil and I wanted to share more of what I had heard,  so this is how this podcast came to be.

I always like asking people about their name, also so I can maybe, sort of pronounce it, kind of right. So Dr Veen explains her name, since I wondered about the two initials GF in her scientific publications. 

Ciska  Veen [2:05]
So my name is Ciska, Ciska Veen. And the letters are actually not in the middle of the name. But my second name is actually Francisca. GF is are my only initials, but everybody calls me Cisca, Ppeople know me by Cisca, that's fine. And I use like my initials for publications. But yeah, nobody knows me by those really.

Wim van der Putten [2:25]
So it’s Wim van der Putten. If if you put in in the American way, it’s Wim van der Putten. Van der in Dutch is like if you would say 'of the'. Put is a source or a well. So it’s of the sources. 

Wim van der Putten and a number of soil scientists and soil ecologists published a perspective in Science a while ago a piece called 'Soil biodiversity needs policy without borders'. It’s about the way soil is connected globally and how important soil biodiversity is. A link to this perspective is in the show notes. https://www.science.org/doi/abs/10.1126/science.abn7248 . I found that concept of global connection a bit puzzling, how might soil be globally connected. It’s because producing food drags nutrients around the world.

Wim van der Putten [3:15]
We wanted to reach a broader audience, and then see how they could be made aware of the importance of soil for everything that is happening in life. So for the way how we can adapt to climate change. And what we are doing actually for producing food, in terms of dragging around nutrients across the world, carbon, and just making a huge footprint. But also by reducing the nutrients in one continent, for example, in South America, to overload the nutrient condition in another part of the world and in northwest Europe. So in the EU, for a long time, they didn't have this whole policy, because they said, Well, what does the soil in Spain have to do with the soil in the Netherlands?

Spain and The Netherlands are not, geographically speaking, neighbors but there is a soil connection between them, which wasn’t clear to policy makers. 

Wim van der Putten [4:10]
And this is the politicians, especially in the national politicians. And what we have learned in ecology is that ecosystems can be connected. For example, there's a famous example of swans going from geese going from the Midwestern United States to the Canadian coastal region. So because they are not being controlled in the winter, when they feed in the Midwest, there's too many of these species going to the Arctic, and they're they overgraze the wetlands in  north eastern Canada. So this type of examples is quite prominent in ecology, where you see that disconnected locations can be connected through these types of processes, like transport, or movement or so.

When we talked I mentioned the fires in Canada, which showed the Eastern seaboard of the US,  how connected that area to an area that seems far away. The forest fires in Canada,  led to this orange fog that smelled like burnt wood and made your throat scratchy and your eyes water. 

Wim van der Putten [5:20]
I saw the orange, the pictures. This is an interesting type of feedback that I'm interested in also, because these feedbacks, are much more real that we than we realize. You would assume that climate change is influenced, for example, more in regions like where New York where many people living and   using a lot of energy, then it changes the climate. And, as a consequence, more northern territories become more prone to fire because of drought, and then the fire gives smoke and that smoke goes back to the East Coast of the United States. Then it's sort of a boomerang effect. You throw out the boomerang and you get it back. It's hitting you.

Global connections in soil science can boomerang in interesting ways, wow. Soil science, as I learned reporting this story is not, classically, about biology or ecology. 

Wim van der Putten [6:15]
So soil science, classically is the ones who look at the physics and chemistry. So let's say how the house is constructed. And so the ecologist will look at the inhabitants of the house. So what are the microbes, the nematodes, the earthworms doing and actually there is a direct connection between physics chemistry and soil ecology. So ecology is actually the relationship between living organisms and their abiotic environment, the physical environment, but also to their biological environment. So, we look specifically at the organisms in soil, as a physicist and chemist chemists look at the dead components is soil, but that comprise of soil so which is like the walls and the roof of your house. They influence who can live there. But who will live there influences how these how the House is looking like. So actually, there should be constant interaction between physics, chemistry and biology. But these are sort of living apart together.

Living apart together. It sounds like there should be interactions between physics, chemistry and biology but those do not always happen. Besides bringing disciplines together to get a better picture of what is happening in soil, scientists need to decide on scale. 

Researchers might look at soil in a pot of soil or on a much later scale like a field or in a controlled environment called an ecotron. The idea is to try and draw conclusions about what is happening in the scale you are studying and to try to extrapolate from that. The different scales take different levels of effort and time and money.  At the Netherlands Institute of Ecology, the team does experiments at all the scales. Here’s Ciska Veen: 

Ciska Veen [8:15]
We do all of it. We do experiments all the way up from like, really small scale stuff in a lab where we have things in vials up to micro and mesocosms.  So those are sort of soils in small to big pots basically, up to the field. 
We work on soil biodiversity and functioning so that means like we look at who is in the soil and what are they doing in terms of nutrient cycling carbon storage, cycling water, greenhouse gas emissions, like all those kinds of things. And we measure these across all these type of experiments, basically.

In soil research you can go small, go big and work in something called ecotrons which are larger, controlled environments  and we’ll talk about those in this episode, too. Different scales get you different types of experiments and insights from those experiments.  

Ciska Veen [9:10]
There's a few nice things about going small scale and a few nice things about going big scale. So small scale means that you have a lot of control. So you can manipulate specific factors very precisely. And that can be very nice if you want to untangle what the impact of certain factor is. The disadvantage is that you're at some point, not working in a real soil or real ecosystem anymore, because you basically, there's two things for soil specifically. 
One is, you are sort of destroying the structure of the soil. So a real soil is layered. And if you take it to like your small tube, you lose that basically. And all the connections with other species are gone right? On the big scale. So that's why we also do a lot of measurements in the field. Because there you can measure in the real system with all this variation, all these interactions, and this layering of the soil, which is actually really important for a lot of processes, like the transport of water, for example, it's just determined by physics of the soil. 
But then you don't have so much control anymore, because there's a lot of variation and you miss out on like untangling very specific factors. Sometimes we of course, do manipulative experiments in the field, but it just becomes harder. 
But then you don't have so much control anymore, because there's a lot of variation and you miss out on like untangling very specific factors. Sometimes we of course, do manipulative experiments in the field, but it just becomes harder. So ecotrons are a bit of the maybe link between these very controlled experiments and fields, because they actually, yeah, they can have real soils, they can have multiple species interacting, you can manipulate stuff, because usually they're built in a controlled environment, or the backyard of an institute, something like that. 
Yeah, they're still not the real world. But they're already quite close to it  with while having some advantages that small scale experiments have. But because of that, let's say the scale of the Ecotrons and the possibility that you can still manipulate and measure things really well means that they are usually very expensive. Also, that are very big, so that you can only have, and that's a large disadvantage of ecotrons, that you can only have a few. Which means that you do not have a lot of power to manipulate either a lot of factors or do a lot of replicates. So you basically repeat your setup a few times, let's say that's what we used to do small scale experiments or field.

Ecotrons are larger and more expensive to maintain and use, there aren’t many of them. I spoke to a few scientists about their ecotrons and will come back to them in this episode and others. When researchers are working on soil, they have decisions to make about which approach to use. Here’s Ciska Veen. 

Ciska Veen [11:40]
So every approach has its advantages and disadvantages. That's why we also use all of them. We have what we call a soil-tron, which is sort of an ecotron , where we actually collected intact soil cores of one meter diameter. So they're really big mesocosms, basically, with intact soil layering. We brought them all here from the Netherlands. So we have 60 from the most abundant soil types, and now we do all kinds of manipulations and measurements on them. So there are 60.

16 or 60?  

Ciska Veen 
Six, zero, yeah. 


Ciska Veen
Yeah. So it's quite, that's quite impressive. So we had like, Wim has, so when you talk to him, you can ask for that we have this like little films or, and photos of like, it's a super big soil drill with a crane that like takes it up.

Whoa, what you're saying, take it intact, in other words, so you have those layers.

Ciska Veen 
But that like the effort, because if you want to do that, for it's one square meter, if you want to drill that into the soil, you cannot do that by hand. And you need a big truck to transport that soil. So yeah. So that's one of the things we have, which is sort of our ecocon, but we call it the soiltron.

We’ll get back to the soiltron in a moment, I just want to add Wim van der Putten in here who talks about the cycling between scales. 

Wim van der Putten
We soil ecologists, we make observations in the field. And then we try to explain those, but you can't just explain them from the field only because the field is too complex. So that's why we try to get things out of the field, by soil samples, for example, that we bring them to the to the lab, examined them, then we test certain detailed treatment effects, for example of nitrogen, or temperature or a drought in a greenhouse, or in something which is semi controlled, like an outdoor experiment, then we make conclusions about that, then we try to put that together. So we go to the field again, see if it works. If it doesn't work completely, then we just go back to the greenhouse and to the lab. So we try to go through this circle, from field to lab, greenhouse, and then back to the field. And, and by that it's sort of like an action process, we try to improve our understanding. And every time we develop new ideas, we test those ideas. And that's how we bring about process progress in this in this field.

Not all soil ecologists work this way. 

Wim van der Putten
There are people who only focus on the lab, there are people who only focus on the field. In the field, what you can do is you can find correlations, you can see patterns. In the lab, you can test these patterns. But what usually is done in the lab is that things are made so unnatural that you don't understand how the real world works. For example, if you have, if you test how a plant is affected, or one microbe that you have cultured on petri dishes, and then you put that microbe in the soil, other otherwise sterile conditions, then you can test how that microbe is interacting with the plant. But if you take a teaspoon of soil, there are 5000 species of these microbes in it, and even 10 billion individuals, so as many as people on Earth, but what we ultimately want to know is how this one microbe is affecting plants in this consortium of these 4,999 others. And that is what you cannot do in the lab. Because it takes too much time. So you can just touch on my coat and to the treat and for you will not have enough in one life just to test all these possible combinations.

In some experiments one might inoculate a soil sample and see what happens. Researchers might add one factor, one variable and then assess the difference it makes. There is fascinating interaction between plants and fungi in their roots, Toby Kiers works on this and I did a story about some of her work and this subject more generally, the link is in the show notes. I just mention her because Wim van der Putten mentions her. 

Wim van der Putten
Yes, a common thing there is that you add something. So that's to innoculate. So what people do if so they can add one microbe, for example, a lot of work on mycorrhizal fungi, which are fungi that act in symbiosis with plants. In that work, a lot of experiments have been done with one plant, one mycorrhizal fungus a nd they see how that works. And you had an interesting piece about Toby Kiers her work, and he looks at how different sort of mycorrhizal fungi trading off with plants. And then the plant is sort of trying to go for the best offer, that already is just looking at how different microbes perform or behave in relation to this amount planted video, we just take it one step or a major step further, we take this whole handful of soils, whether all the 1000s of species of microbes, and then we add that to plants, and then see how those microbes are influencing the performance of plants. And preferably, if you put the plants in a plant community, and then you are quite far towards the field situation. And by doing that, we have shown that for example, we can enhance the rate of naure restoration by just bringing in the whole soil community, the whole community of bacteria and fungi and everything which is in the soil from a site that has been restored already. And if you bring that into a sort of virgin soil or heavily disturbed soil, you can see that you not only can speed up the process of natural restoration, but you can also drive it into a certain direction.

Iteration is key also to assess what might be happening. It might seem that something  can work well in the field but you have to test that. 

Wim van der Putten
Exactly, yes. And the proof isn't eating the pudding. So ultimately, you have to try out as realistic conditions as possible. And then see if your ideas are still correct.

Back to the soiltron that they have set up. It sounds like it might be a resources others might want to try out. For now the Soiltron is for their scientists only but collaborators will eventually be able to come, visit and work there. Here’s Ciska Veen and Wim van der Putten

Ciska Veen 
I think we're always open to this. We just started it so at the moment it's affiliated to to project so at the moment, we have our own people working on it. But yeah, I think this is a better science, like if someone knocks on our door, we're always open to to listen and talk and collaborate. 

Wim van der Putten
We want to have it fully established. And then of course, we can say, well, people are invited to come over and do some work, especially if they have a specialism, which we don't have.

One study I had come across was one by Yanjie Liu and team from the Northeast Institute of Geography and Agroecology of the Chinese Academy of Sciences in Changchun, China. Ciska Veen had handled that paper, which was published in the journal Functional Ecology. The scientists did experiments in greenhouse pots and in field tests. It focused on drought but also on rewetting, which often follows natural drought. The rain does come…eventually. The scientists looked at invasive species and drought. So it turns out Yanjie Liu and team found, that invasive species are hit harder by drought. But invasive species recover faster than native plants when the rain comes after the drought. I found that surprising but I guess it goes to show you have to look at an ecosystem for a longer time, otherwise you might draw wrong conclusions. 

Ciska Veen 
Yeah, that makes a lot of sense. And that's not, even this is one example. But that's for a lot of things. And of course, this is challenging, because, let's say, in The Netherlands, for example, we also have huge issues with nutrient deposition. Let's say you would only look at drought, but don't include the extra nutrients. You might also draw wrong conclusions on what's going to happen in the future.

Nutrient deposition is not fertilizer, yes, or no?

Ciska Veen 
Yeah, it's coming from fertilizers and from industry and cars. And there's lots of reasons and I don't know if you've heard about it, but it's like a huge crisis that we're going through at the moment. Also, Belgium is in it, we have a lot of super intensive agriculture, we're both very small countries. Nature is really suffering. I mean, like really suffering. So let's say in the system's

Meaning suffering? you know, so the soils are depleted, but also that farmers are? 

Ciska Veen 
And  then forests are dying because of that. Yeah, like there's all kinds of examples. So maybe it's too much oriented, but like, for example, no birds or eggs, they don't have enough calcium anymore. So the eggs in the bones of birds, they get very fragile, so they can just break basically, like those kinds of things. So yeah, so that's a huge from the European, European Union, there's a huge sort of task put on us to reduce that. 
But of course, it affects ecosystems. So if you want to understand how global change is impacting on ecosystem, you actually also have to look at that factor. There's multiple other factors like warming, extra CO2. Yeah. 
And I think just realizing that all these factors are influencing the impact of the other factors. That's indeed what you basically got from this paper, that's really important. But it also is good to realize that you cannot usually study all of it at the same time. So we realize that we actually cannot draw maybe all the conclusions all the time. And we also realize that we need to study more of these multi-f actors together. But that's also really challenging, because you can understand like, if you add one factor, it doubles your setup, basically, but yet, add another one. And you also want to look at all the crosses, it's sort of an exponential curve, right? It's not just only doubling all the time it like, yeah, exponentially increases the number of samples that you have to take. So this is a challenge for the field.

In an experiment scientists need numbers and also controls. Let’s say they are looking at one or several factors, they need to do this multiple times and have something to compare it to, to benchmark it to.  

Ciska Veen 
And yeah, so this is a challenge. And we all know that and that's also why experiments in a way are powerful because you manipulating one factor at a time. But sometimes you know that a factor is dependent on the other one. And this is what yeah, basically what you also got from that paper, right? So if you only look at drought, but don't look at what happens as a rewetting, you don't really know the full story. 
There's also a  time issue to that. It also depends on if you're interested in what happens right after drought. Yeah, measuring immediately is fine. But if you're interested in long term effects, you might need to look at rewetting. 

To look at long-term effects of drought one would need to consider what happens when the rain does eventually come and that means the experiment runs longer and will cost more. 
I wondered what types of interactions she and her colleagues had with policymakers, there must be pressure on them to establish what is happening to the soil and people must be asking: what can we do? To fix this?  Like now. 

Ciska Veen [23:00]
Yeah, this is a very good question. It's also a bit different and depends on your depending on your own personality, I think as a scientist, so scientists are always a bit careful. Sometimes maybe too careful, because we know everything's context-  dependent. And so we want to do more research and more context. And yet at the same time, indeed, people need to fix problems now. How do I phrase this. 
Yeah, so I think there's a few things that I would like to say about this. One is we actually don't know everything, for sure. But we do have a lot of knowledge already. So one is we try to communicate that knowledge. But it's, of course, partly not up to us, we can communicate what we need to do, but then doing it is something different, right. And that involves a lot of more sort of social sciences, I think. So we are communicating what we know. And we hope that that helps to make some to solve some problems now. So that's one thing we already know a lot. 
I think the second thing is that. Yeah, we already know a lot. But of course, we don't know everything. So in the meantime, while communicating what we know, we go on with his experiments. And there's always something more to do. But that doesn't mean that we cannot communicate what we already know. So I think that should go hand in hand all the time. And even I think there's never an end to, let's say science, because every time we find out something, we also find more questions or unknowns, right? 
So I think this all this process always has to go hand in hand, we should always communicate what we know. We should also always continue finding out more, I think what we do see in our research is that we're shifting a little bit to focus on. So already my lifetime, as a scientist, I see that, that when I started, we were more focused on understanding what was happening. And now we're also more focused on steering our systems and understanding how we should do that. And that's, of course,   of much more immediate relevance to, let's say, policymakers or end users of knowledge. 

Before delving more into policy, let’s go back to the Soiltron for a moment.  Back to the Soil Ecotron at The Netherlands Istitute of Ecology. This way of doing experiments lets scientists  study soil and more factors that influence soil. Here’s Wim van der Putten. 

Wim van der Putten  [25:30]
What we soil ecologists are being accused of by soil physicists and chemists is that we take so we just mix it and then we put all kinds of things in. So and they are right, because soil has different layers, and has gradients. And so so what we did in this soil ecotron we just made steel cylinders. And we sort of drill the cylinders or we just, we have turned them into the soil with a hydraulic crane. And so we just, we just had the soil and meadow And then we just put in the silence, and then we just dug a trench next to the cylinders, we pulled them on a steel plate. And that's how we dragged them out and brought them to the to the institute here.
it's like bringing an ice core to your research station. And so we have all the structures, all the layers, the stratification, everything is intact. And then we brought them to the institute, or we could have examined them in the field as well. There's two problems there so one is that in the field, these cores can leak. So everything can can escape in every direction. And the other thing is that some of these fields are really remote. So if you want to do regular gas production measurements, like CO2 coming out of the soil, and we had to go to these fields  every week, and now we can use ever high tech equipment to measure all these different fluxes and flows. And we just have the main bond experiments and that makes it easier

The Soil Ecotron has been up and running for a few years.  It’s a way to model the different soils and to see how certain types of soil damage and depletion might be addressed. 

Wim van der Putten [27:30]
We know from other ecotron types of experiments, so outdoor experiments or field experiments, that to set up these treatments can take five year, easily. This is what we don't know. Why does it take so much time before we get this more diverse soil community established. Is it that some of these species are there they have to be woken up? Or do they have to come in higher numbers? And that does take time. So this is what we don't know. This is what we can investigate. 

The ecotron mirrors the soil types in the Netherlands and their damage. 

Wim van der Putten  [28:10]
So we have the three main types of soil in the Netherlands which is clay, sand and peat. And of each main soil type we have 20. So, we always want to have five replicates, so that we can have four treatments. And four treatments sure you can have to have two of one and two of the other treatment. And for example, we took these soil cores, soil columns from fields that were heavily managed grasslands. And we know that with these heavily managed grasslands that you get less soil biodiversity than if you go to a semi natural grassland. 

They are heavily manured. And often also they are just plowed down and resown with grasses and maybe also being sprayed with herbicides. These treatments have a negative effect on soil biodiversity. So what you then see is that you're losing out the bigger guys in the soil, and you're also losing out the fungi in the soil. So what we did with these columns, with these ecotrons, we just have we have added or inoculated live soil from more natural grasslands, to bring in, to restore the natural soil bio diversity of these systems. And then as another treatment, we have sown a more diverse mixture of plants of grass species. So we created actually very high intensive cores, we created the most extreme soil course with more diverse soil community and more plant community. And then also we have the two combinations. So we have the combination intensive grassland and with more biodiversity, and we have intensive grassland with more plant species. 
So we set up these experiments. And then when time is ripe, we  have students starting to work on them. Or, what we also do is use gradients in the field. So fields that have been restored 1,2,3,4,5 years, but also 10 years, 20 years. And then we can sample such a gradient, which is what we call a chrono sequence, so a time series. And then we have these gradients and we can sample them in one day. And it is like if you're going through time, so through 30 years time in one day.

Because soil changes over time due to many factors one needs that view of change over time. Here Wim van der Putten talks about a collaborative mesocosm experiment—a medium sized ecotron—set up in 2012 and that has been running since then. 

Wim van der Putten [30:40]  
So we have established that experiment in 2012. And that has been running for a number of years. And for example, there has been a Chinese guest researcher doing work on it. And two weeks, three weeks ago, we had a PhD thesis defense of a Chinese PhD student. She got here with a Chinese scholarship. And then we said, Okay, we have this experiment. And let's do your work in this experiment. And then she collected data. So now we have this experiment where  just different people have been doing a PhD or their guest research period. And then every time we get new results that we can put together in the end, but also these people can just do their work in a running experiment, which has quite the history. 

Soil changes, also due to our not so great influences on soil. Ecology as a science changes due to the changes in soil and more generally it changes due to many other factors. The field of ecology changes as the approaches to study ecology change. It used to be, for instance, about assessing which species are in a given environment. But soil has complexities, there are chemical and physical characteristics and there are organisms to track, many insects and microbes living in soil So there are techniques that help researchers understand who’s there and which organisms are using which resources in the soil. And As Ciska Veen explains, there are techniques she wishes were no longer ones she and other researchers can only dream about. 

Ciska Veen [32:10]
If we look at like ecology in general in the past what we've done, let's talk about plant communities. For example, we've like met the species that were there, how abundant were then all these things, but you can see them easily right. But that's like decades ago, we've moved on from there to understand, like, what drives the species? How are these communities assembled? Who's interacting with whom? What are the mechanisms underlying all of these assemblies of communities and all of the composition of communities and what they do? That's sort of easy, because you can see those community. It has been usually complex, but it's relatively easy, I think in soil were like 50 to 100 years behind, because now those metagenomic techniques were only basically mapping species, we're still at the stage of like, who's there. 
So I think, for me, what I'm increasingly interested in, but I'm not a methodsy person. So that's actually interesting in like, I'm not like the one that's inventing cool new methods in the lab. But what we're increasingly using, but it's super exciting, I think, is tracing elements in the soil, so that we can actually see who is doing what. So we're like, yeah, following this movement in ecology, basically. 
So not only seeing who's there, but what are they actually doing, because for me, that in the end is the most interesting part. And then we need the sort of more high tech methods for where we can actually trace interactions between species where we can trace elements in the soil, let's say carbon, for example, if we want to understand what carbon from above ground is actually going to the soil and staying there, we might need to trace it because we can Yeah, we cannot see otherwise where it's coming from. 
So there are for example, stable isotopes that we can use for that. And then in combination with his meta genomics techniques-- who's there techniques, let's say, then you get really cool information on like, who's actually using some of the resources you're giving? And what are you doing with it? And what is the loss as a gas, and what is staying in the soil? Was it us as a greenhouse gas, or what is staying in the soil as organic matter and is stored for longer time? What is staying in the soil as a nutrient for plants, what is lost as an N2O gas like nitrous oxides, which is a very potent greenhouse gas. 
So those kinds of questions, I think, like the tracing of these elements is really interesting also, for fundamental understanding of these systems. So that's one thing I think the other thing, what we're increasingly thinking about, and and we don't really well, there's two things that we're increasingly thinking, but we don't have the techniques yet. But that would be great tools to have a sort of in situ, continuous measurements of important processes, or soil biodiversity or whatever. 
Yeah, let's say one thing that we can measure very easily now. And as we do, for example, above ground is like air temperature. And it helps us you know, to predict the weather to predict all kinds of things. In the soil, we can also measure temperature, but there's all kinds of other things that we cannot measure easily, that would  be super nice to have to sort of continuous measurements so that we are in line with, like, weather forecasts can try to understand and forecast what's happening in the soil in real time. Yeah, in a real time, way, in a real context, way. And that's, that's not there yet. But that's something we're dreaming about a lot.

This dream of assessing soil changes in real time, right as they are happening, seems practical and important. It might involve temperature changes and many other aspects. I asked Ciska Veen more about this. 

Ciska Veen [36:00]
It’s going beyond temperature, basically. But we would like to measure things like carbon flows or like, yeah, they also refer to it sometimes lab on a chip, or you in the field take like, it's a bit of a different scale, but you take like a sample, put it on a chip, and then you see like, who's there, for example, so to not have to do all this meta genomics, like those kinds of tools or like have continuous measurements in the sun. Yeah, I know, carbon fluxes or whatever. It doesn't be all super cool. We can do a little bit of it. But it's all super specific and really expensive and it does like one measurement at a time but like having something that in situ measures yeah like sensors basically that's what we're looking for a lot.  It's very labor intensive to do all these measurements on soils, and you always have to take them out of their context into a lab. And that's not always the same. 

One issue I wondered about, also considering how labor-intensive studying soil is, is data-sharing. I come across data-sharing issues a lot in my reporting. And the practices differ widely between fields. 

Ciska Veen [37:00]
At the moment, I think this is all really under development. And we're all aware that we need to be much more open with open science is not, we're not there yet, for sure. So there's indeed like, now, if you publish a paper, you usually publish the data with it. So all these repositories that have links to papers, those data you can find there. But the sort of reality still is that if you're doing a meta analysis, or you want to fill your model, you have to actually contact a lot of authors to get the data. So that's what we're doing a lot. 

All too many papers have a note that says: data available upon request. Sometimes, maybe quite often in some fields, the data are not readily available upon request. For soil, there are a lot of resources where researchers can find data. Links to the ones that Ciska Veen mentions are in the transcript. 

Ciska Veen [37:55]
 And they also get into more or less detail depending on what you need it for. Yeah. There's a few initiatives that create like this, let's say data layers for like GIS-type of analysis, does global maps and more and more data go into that? So so there's someone Tom Granther, or I don't know if you know him, he's leading a lot of those initiatives. There's a group in Belgium, Jonas Lembrecht.  
There’s also at Wageningen University  if I look out the window, I see it. We're on the same campus. But they have like something that's called ISRIC  which is the International Center for soil something's, yeah, look it up soils. And they also have databases, for example, on major, like pH, organic matter, some of those sort of major themes that everybody always measures. 

So there's some initiatives where they tried to put this together, we at the NIOO are building something that's not yet available, but that's going to be available soon. But something that's called a Reference Center for Soils, https://www.isric.org/where we also are basically collecting all kinds of soil biodiversity measurements on as many sources as we can get our hands on. So we have a big project ourselves, or we measure already 1000 soils, but we hope to, at the end, fill that reference center with more soil so that we can sort of benchmark also like what is a good soil but all those data that are in such a place at some point should be open.

There’s a lot of those initiatives, this is only a handful. But I mean, there's more people that do this. And yeah, this will all be open at some point. There's also the initiatives, like GBiF I don't know if you know that. It's like the biodiversity database.  https://www.gbif.org/ Then the FAO has like a NETSOB. https://www.fao.org/global-soil-partnership/netsob/fr/

They're all yet startups, let's say. So none of them has a lot of data on soils in it at the moment. But everybody agrees that we should do this. And, yeah, in a few years, it will be there. Still have to contact everybody for everything.   

As is true in many areas of research, policymaking shapes the science. For soil there was something called the Soil Directive. And it leads to a need to have comparable measurements and discussion about soil health. Soil can be healthy and yet environmentally be problematic.  And I apologize here for some reason we had some disturbance in the audio all of a sudden

Wim van der Putten [40:30]
So the Soil Directive has been established in 2016. Before that time in 2006, they try to establish a Soil Directive  already. So a directive is not a law, but it's sort of an intention. And in, in the earlier version, there were five countries which were against. Unfortunately, it was also the Netherlands, but also Germany, France, the UK, which was still part of the EU then, and Austria, against. And you wonder why, because the Netherlands is just a front runner in soil research. But that's where the politics comes in. People are afraid that if so, the, the story was that we have our soil legislation is so well organized, that people if we don't want to go back to the ones who have least organized in Europe, but actually, the key problem was that this was directive, which show that in the Netherlands, things are also not so good as we claim that it is. So but that's, that's gone. So now we have a Soil Directive. And now this this summer, the EU law on soil health is being presented in the EU parliament. Now that it will be sent out for consultation to the member states, there will be a lot of discussion about it. And then in in some time, and it might take a couple of years, then this law should be approved or should be voted for. And then we have the EU Soil Law. And when we have that, then the member states have to fulfill or they have to maintain the law as well. So the question is, how to do that, and what is soil health and how to measure that. So in soil, we have two types of concepts on the soil quality. So quality is usually used to express the capacity of a soil to produce yield of crops. But actually, you can have a soil of a high quality, which is just leaking greenhouse gases to the atmosphere leaking nitrate to the groundwater, which gets clobbered if you have a rainfall of which needs to get bought, or if it's a drought period. So those soils, which have a high quality for producing yield, have a low health, because they don't produce many other ecosystem services. And so this new soil is looking at soils in a much more holistic way. So not only for producing yield, but also for controlling climate, for controlling the quality of of our surface water of the ground water buffering capacity, and so on and so on.

Having a Soil Law could be useful in some ways but it brings up other issues quickly namely a need to be able to measure soil health, if the directive is approved. Beyond laws and rules of various kinds, the EU sets up different ways of assessing soil. One project involves something called Lighthouse Farms and then there are Living Labs.Wim van der Putten explains. 

Wim van der Putten [43:35]
The European Commission has a number of missions. So we have the mission, Soil Health and Food. And that mission is responsible for the soil knowledge in the EU. And they propose to set up 100 Lighthouse Farms and  Living Labs across Europe. So what's a lighthouse farm? A lighthouse farm is something which is a farm with the use of all kinds of novel methodologies to produce crops in a more sustainable way. That way you can learn. 
A Living Lab is much bigger, it's, for example, an area of 50 by 50 kilometers, where not only farmers are there, but also the people. So in villages, or cities, but also the people who sell something farmers or who buy products from farmers. And so this whole community is influenced by the, by the health of soils. But also it's influencing the health of soils by all kinds of social interactions, economy, legal procedures, social aspects, whatever. So in a Living Lab, The EU wants to find out what not only what are the best technical solutions, but also what are the best technical and socially acceptable solutions. And that's the interesting thing of the living labs approach of the EU. And so this is also what we're trying to roll out internationally. So we had meetings of EU with Canada, and EU with the United States. And, for example, the Canadians say, Oh, we like this different approach. And likewise from approach or maybe we could also develop them in Canada. And actually, this is something that the Food and Agriculture Organization, FAO,in Rome is doing. So the United Nations has given them a task to improve the health of soils worldwide. So they also think about, can we set up these, these Living Labs or Lighthouse farms across the world, where we are constantly going to monitor  effects of what we do on soil biodiversity and the ecosystem services that it provides. And therefore get a more consistent and direct type of monitoring of the environment.

These are large-scale soil-focused programs that pull in all sorts of other aspects economic and social ones to gauge soil health and sustainability. This topic brought use back to the Science paper he and colleagues authored. Which is about calling for a global approach to soil health. 

Wim van der Putten [46:25]
The point that we made in our Science perspective, is that the EU can take care of the health of its own soils, but it should also take care of the health of the soils elsewhere. So we have a footprint. And so if we just take care of the health of soils in Europe, but then we export the need to produce a lot of food and feed to other countries, then we still have a negative footprint on soils in other regions in the world. And this is what should also be prevented by good and solid EU policy.

Since we were talking about soil and food production I thought I might ask him for soil expertise related to gardening. Do you rake the leaves away from your garden patch. Well, Wim van der Putten has some comments on that. 

Wim van der Putten [47:25]
Yeah, so it's important to take care for the organic matter in soil. So what many people do is they remove the leaves, even bring them away. And then they buy fertilizer to fertilize the soil. So the best is to go for a system as circular as possible. So rule one is keep so so manage your soil organic matter, properly, put on organic matter, the whatever the compost, prepare your own compost and put it on your land. 

Another aspect to think about is about how microbes and fungi play crucial roles in soil health. Fungi have, let’s say, interesting appetites that matter a lot in soil health. 

Wim van der Putten  [48:00]
Yeah, this is interesting. Usually the bacteria are more or less at the same level. And the fungi can go up or down. So if you look at the fungal to bacterial ratios, usually  the fungi vary. So and it's important to have enough fungi. And in order to get enough fungi, it's important not to till your soil too much. So that's why no till is better than to till. So don't just disturb the soil too much. There is a bit of a trade off, because most food crops are originating from wild plants that like to do to grow in disturbed soil. So you have to disturb the soil to some extent, but try to do it as minimal as possible. And then put organic matterl, which is preferred by fungi because they like the slow foods more than the fast. So put put slow foods for the soil organisms on your soil. And you will get more fungi. Also in combination with not just tilling the soil too much, that's basically it.

Interest in the role of microbes in soil research and thinking politically about soil have changed a lot over the course of his career. Wim van der Putten says. Although there is name calling. In Dutch some people who are too holistic about soil are called ‘wooly socks’ people.

Wim van der Putten [49:30]
It's interesting to see, soil has become really hot over the past decades. When I started out, I showed that in nature, soil pathogens influence the changes in plant community composition. In the beginning, people said, we don't believe this. We don't buy this. Now this is common good for many plant ecologists. Over time, which is more towards the whole soil. The risk is a little bit that people consider people who think from a holistic perspective as they'd like what we say --wool and socks people, so people with alternative ideas and so but actually actually, for the quality of our life it's is really important that we just look at soil from a holistic perspective, because this is giving soil species take less management, they give more functions and return and more services. So actually, we're just fools if we don't use the soils in the proper way. And the trick will be to make people aware of that just looking at soil from this all inclusive perspective is cool rather than something else.  

That was Conversations with scientists. Today’s episode was with Dr. Ciska Veen soil and ecosystems researcher at NIOO, the Netherlands Institute of Ecology (NIOO-KNAW). And Dr Wim van der Putten, who heads terrestrial ecology at the Netherlands Institute of Ecology.

The music used in the podcast is Jungle Jam by Evert Z and licensed from Artlist.io.

And I just wanted to say because there’s confusion about these things sometimes. The scientists in this podcast or the Netherlands Institute of Ecology didn’t pay to be in this podcast or pay for this podcast. This is independent journalism that I produce in my living-room. I’m Vivien Marx, thanks for listening.

Seedlings in soil and some rays of sunshine

(sarayut/Getty Images/iStockphoto)

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