Bonding Over Science Episode 8—TerraForms: Synthetic Habitats for Soil Ecology

 

The Environmental Molecular Sciences Laboratory (EMSL) developed a group of platforms called TerraForms to help researchers to investigate hydrobiogeochemical processes. The platforms include custom-designed synthetic environments, microfluidics technologies, and in-house instrumentation, which simulate soil properties and visualize soil microbial and plant community dynamics.  Listen to EMSL Earth Scientist Arunima Bhattacharjee on episode 8 of the Bonding Over Science podcast as she explains TerraForms' capabilities.  

Transcript: 

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Dawn Stringer: TerraForms. It’s a process developed by EMSL Earth Scientist Arunima Bhattacharjee and Biologist Jayde Aufrecht to create a synthetic plant habitat to reproduce minerology on a small chip you can hold in the palm of your hand. 

It’s something almost out of a movie, and today, Bhattacharjee tells us how using TerraForms can help us learn more about various climate and environmental issues. 

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Dawn Stringer: So first, I just want to say thank you for joining me and being on EMSL’s podcast. 

Arunima Bhattacharjee: Yeah, it's a pleasure. I'm super excited. Always happy to share more information about TerraForms. 

Dawn Stringer: Start off by just introducing yourself and telling me a little bit about your research and the path to your research. 

Arunima Bhattacharjee: So I'm an Earth scientist and I've been at EMSL now for five years. A little over five years. And so I was hired on the soils SFA [science focus area] as a postdoc, and I started working with soil, specifically with soil microbes to see how in different moisture conditions microbes grow in soil and degrade carbon and specifically to use imaging, mass spectrometry. 

So looking at like different types of chemical, using different types of chemical imaging to understand the metabolite distribution as these microbes grow around these carbon substrates. Just wanted to make it clear that before I started my postdoc here, I was working on like all medically relevant bacteria. So coming in here, it was [a] very different experience because I was working with like one or two different microbes, which are very model microbes, I would say. 

And then as I started working on soil, it is super complex and that's the reason why I wanted to like develop these different platforms where we can specifically do like chemical imaging on them. And yeah, it was very hard to visualize soil because it's so opaque and heterogeneous. So we wanted to develop something where we retained a heterogeneity because the heterogeneity is super important. It is why we have these huge biodiversity of microbes and which we love to study and so how can we retain this biodiversity and still be able to, you know, visualize them, visualize them not only through optical imaging, just looking at them, growing, using a microscope, but also to get some chemical information spatially. What kind of metabolites they're making as they're growing around inside of like soil, like pores, while they're interacting with each other, and while they're degrading minerals or degrading different carbon sources. 

So all this information is important because once we understand them, we can build better systems for different agricultural practices. And so that's basically my research. 

Dawn Stringer: You mentioned mass spectrometry. What are some other ways that you take a look at these metabolites? 

Arunima Bhattacharjee: So definitely mass spectrometry based techniques are primarily used. And within that we use MALDI [Matrix-Assisted Laser Desorption/Ionization], we use nanoDESI [Nanospray Desorption Electrospray Ionization Mass Spectrometer], we use SIMS, NanoSIMS [Nanoscale Secondary Ion Mass Spectrometry], and all of these, so what I have realized is not one technique can be used to decipher the whole process of, you know, nutrients cycling, for example, how what kind of metabolites they're making, what metabolites, accumulate certain inorganic nutrients uptake them inside of their like inside the hyphae in case of fungus or bacteria inside of the bacteria cell. 

So we need a combination of several different techniques, which led us to make these TerraForm platforms compatible for a wide range of analysis techniques. So just to give a summary [of] mass spectrometry, which includes all the techniques that I talked about, MALDI, NanoDESI, SIMS, NanoSIMS, we can do SEM [scanning electron microscopy] on them to visualize what kind of changes are happening on the, on the surface of the minerals, how the fungal hyphae is growing within the soil force. 

We have not done transmission electron microscopy on them because you need a very tuned substrate. We have collaboration with SSRL [Stanford Synchrotron Radiation Lightsource] where we use different synchrotron-based techniques like XANES [X-ray absorption near-edge structure] and X-ray fluorescence to understand the chemical changes occurring within these minerals, the chemistry of different inorganic nutrients being taken by these microorganisms. 

Dawn Stringer: Very cool. I want to hone in a little bit on the TerraForms. It sounds really cool and I know that that's kind of a rebrand for these micro models. Can you explain to someone who doesn't know what are TerraForms? 

Arunima Bhattacharjee: Well, just as a very basic view, if you think about it, it's like these are very reduced complexity platforms. The reason for TerraForms is, soil is super complex. If you have done studies in soil, you always end up with like certain conclusions, which is not very satisfactory. You can always say this thing influences this, or a group of microbes did something, but what is that? 

We don't completely understand the mechanisms. So once you have a hypothesis, while studying soil and you want to study that hypothesis further, you go into these reduced complexity platforms. The reason I say reduced complexity is because you can start building certain elements of soil into these platforms. You can mimic the soil porosity, you can mimic certain types of aggregate size distributions. 

You can mimic mineralogy. You don't even have to mimic everything. You can mimic only one or two of these components. And then incubate microorganisms, incubate plants, by which I mean, you can grow plants. You can grow microbes. You can see how they interact within these platforms and test specific hypotheses with certain soil elements. That's basically what TerraForms are. 

And we have different platforms for users who are interested in studying plants, who are interested in studying only microbes, maybe plant microbes. Or they want high throughput, we have platforms for that as well. 

Dawn Stringer: What kind of hypotheses are being tested through these complex TerraForms? 

Arunima Bhattacharjee: Different users come in with different types of hypotheses. We have one user who's looking, at suppose there are different freeze-thaw cycles in case of like permafrost soils. You have these freeze-thaw events and so what happens when you have like freeze-thaw cycles going on and then how those certain inorganic nutrients attach to certain porosities or certain aggregates or certain minerals. 

So looking at like how mineralogy affects plant and microbe growth, what kind of metabolite distribution occurs when you have certain types of minerals present? And what happens when you have certain microbes growing inside of these platforms and interacting with these with plant roots. So, yeah, it's a wide range of hypotheses. 

Dawn Stringer: And with that said, what kind of issues are we trying to solve in this research? 

Arunima Bhattacharjee: 

Well, we typically accept user proposals that align with the EMSL mission. This particular capability fits within the Rhizosphere [Function] IRP [Integrated Research Platform] very well and also to a certain extent the biogeochemical transformation. When we talk about a lot of soil minerals, the issues that we are trying to solve is like suppose you have very nutrient impoverished soils. 

So phosphorus is a very limiting nutrient right now. And so a lot of user proposals that we get look at how can we increase the availability of phosphorus for plant growth? That’s one thing. Potassium is a macronutrient also, which is very limiting in certain soils. So how can we improve crop productivity? I guess that’s one big issue. The other issue that we look at using these TerraForms platforms are carbon sequestration on minerals, for example. 

How can we increase that? So because there’s like so much climate change happening right now, there is a big driver to sequester the carbon from the environment. And so understanding these mechanisms of like how carbon is retained on mineral surfaces, I think is really important. So I think these are some very hot topics that users come to research through user proposals and to access this capability. 

Dawn Stringer: Now in some of my research, I understand there’s a bit of a demand for these types of capabilities right now. Can you explain why? 

Arunima Bhattacharjee: I think it’s because of the reduced complexity of these platforms. So just to make it clear, this is not like the first time that anybody has done work on inside of like these tiny platforms. Well, it starts with microfluidics and microfluidics is like not very new. It’s been around for decades in biomedical engineering. And in the case of soil ecology, however, it has become more and more something that users want and people are using. 

So when I was like starting my work as a postdoc, I looked into this and I think the first ever instance of micro model use or something like going back to like 2014, 2015, something like that. The papers had started appearing there. There are researchers in Europe who use these kind of micro models. There is our collaborator at University of Connecticut who has done a lot of research on micro models growing in platforms which has these soil aggregate structures and things like that. 

So EcoFABs [fabricated ecosystems], for example, from Berkeley Lab is one example where they have done so much trials, including labs and also asking labs to use these platforms. And if you kind of look back on these, a lot of these platforms are only compatible with optical microscopy. They can extract the bulk biomass and do some omics. 

But our advantage is that all of our platforms are compatible with imaging mass spectrometry, so we can take a chemical image on these after the incubations are done. Most of these techniques are destructive. We are trying to figure out how we can in the future do nondestructive chemical imaging on these. We are not there yet, but the reason why there is a huge user demand is I think it’s because we can get chemical maps and that chemical information and metabolomic information is extremely valuable for understanding mechanisms and interaction pathways between plant, microbe, or microbe-microbe interaction apart from just getting [an] optical image. 

Dawn Stringer: Right. And I'm curious if it's easier to create this synthetic version of these habitats as opposed to doing just straight field work. 

Arunima Bhattacharjee: I don't know about that. I'm not a very field work person. I have worked with soil in the past, but someone else obtained the soil for me. It is certainly easier to incubate inside of these devices. You're able to do some very basic research. You can really look at mechanisms, but I don't think that these devices should be just used by themselves. 

I think these should be used concurrently with the existing techniques to study soil. Only then we can get a full picture. By themselves, I don't think, I mean they give you a lot of information, but it's not the full picture. 

Dawn Stringer: Which is very similar to a lot of research through EMSL. And for those who haven't visited, we have a really impressive plant lab and I've seen those rhizochips with the roots growing through them. How do you start the process of growing these TerraForms? 

Arunima Bhattacharjee: First, there is the process of fabrication itself, which we do in the EMSL clean room. And the first thing is to fabricate these devices. It is a process called photolithography through which we create these chips and we use different materials. We can use PDMS [polydimethylsiloxane], [and] cover these with membranes which are compatible with mass spectrometry. We also use different types of epoxies which are compatible with mass spectrometry, and it depends on what the user wants or what the project requires. 

If we want to embed minerals, then we typically use other different types of polymers to create that to, I guess, simulate the mineralogy that is required for certain projects. All of these devices are then mass spec compatible at the end and then a seedling is grown from a seed. It is germinated on agar plates. 

And once it is big enough to be transferred, it is transferred into the chip directly where it continues growing. The chip itself is filled with media and is maintained in a hydrated condition so that the seedling can keep growing. And so certain projects require addition of microbes. So that is done later on. We have different ports created inside of the device so that we can add microbes if required. 

One of the projects that was coming in, I guess, I'm not sure if it is funded yet, but that requested this particular platform was to look at plant bacteria and fungi interaction and how minerals are uptaken by fungi or bacteria, and transferred to the plant for example. So yeah, that's the whole process. And once the incubation is done, the chip is lyophilized and prepped for mass spec. 

But while the growth is occurring, it can be imaged by microscopy to track growth. 

Dawn Stringer: Before we wrap up, can you explain why this research is important to helping solve various environmental issues? 

Arunima Bhattacharjee: Well, primarily, again, going back to the idea of reduced complexity of these platforms is why we are able to understand mechanisms of nutrient uptake. If you have a super complex environment such as soil, then there are too many variables and you cannot really understand which variable influences how. And so I guess like this is the biggest advantage where we can have only the influence of certain variables and understand specific mechanisms which help us understand the process at a broader level. I think that's why. 

Dawn Stringer: I also want to give you the opportunity to add anything else that you think we should know. 

Arunima Bhattacharjee: I know this is a super interesting and exciting capability and there is a lot of demand. Fabricating these devices is still something that we still do it in-house. That's something we are not training users, but we would like to train users how to prep their own samples so that we can ship these chips through their respective labs. 

They can do their own incubation and growth and then prep samples and send it back to us for mass spec. And if they want to know this, I encourage people to register for the user meeting and come for these workshops where you can teach them. 

Dawn Stringer: Now can you tell us where we can learn more about you and your research? 

Arunima Bhattacharjee: It's in the EMSL website. I do have papers published, a lot of these micro model papers are coming out right now. 

Dawn Stringer: Well, thank you so much for joining me today on Bonding Over Science. 

Arunima Bhattacharjee: Yeah, it's so great cause I'm super excited as well. And, you know, this capability is something that there has been great user demand. And I'm very happy because this is something that came out from my own research. And it's really great to see people using it. 

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Dawn Stringer: This episode was recorded prior to the EMSL User Meeting workshop. If you’re interested in listening to the EMSL User Meeting recordings, you can find them on the EMSL website under EMSL-DOT-PNNL-DOT-GOV-SLASH-LEARN-SLASH-USER-DASH-MEETING and learn more about research developed at EMSL that’s benefiting users around the world. 

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Dawn Stringer: Thank you for listening to Bonding Over Science, I’m Dawn Stringer for the Environmental Molecular Sciences Laboratory.  

We don’t have time to cover it all, so don’t forget to check out EMSL-DOT-PNNL-DOT-GOV for a full article on this topic featuring who I spoke with today. And don’t forget to follow us on all social media platforms for the latest and greatest news coming from EMSL! 

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Dawn Stringer: EMSL is a Department of Energy, Office of Science national user facility that accelerates scientific discovery and pioneers new capabilities to understand biological and environmental processes across temporal and spatial scales. EMSL leads the scientific community toward a predictive understanding of complex biological and environmental systems to enable sustainable solutions to the nation’s energy and environmental challenges. If you’re interested in working with EMSL, learn more at emsl.pnnl.gov, that’s E-M-S-L-DOT-P-N-N-L-DOT-G-O-V. 

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