The ‘omics of Organic Matter – Using Molecular Tools to Decipher SOC Persistence in a Changing World

A. PEYTON SMITH Assistant Professor of Soil Carbon Dynamics, Department of Soil and Crop Sciences, College of Agriculture and Life Sciences, Texas A&M University Author

06/07/2023 Added

14 Plays

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Uncertainties in predicting the soil’s response to global change arise from the often complex and dynamic interactions between biological, geochemical and physical processes occurring below ground. This talk will explore how microbial and molecular tools can reveal fundamental mechanisms that regulate the persistence of organic matter in soils.

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[00:00:00.780]The following presentation
[00:00:02.250]is part of the Agronomy and Horticulture Seminar Series
[00:00:05.850]at the University of Nebraska Lincoln.
[00:00:08.130]Welcome everyone
[00:00:09.570]to another week of the seminar series.
[00:00:12.180]This week it's a pleasure to introduce Dr. Peyton Smith
[00:00:16.890]from Texas A&M University, one of our visiting speakers,
[00:00:20.490]which we're always very excited about.
[00:00:22.980]You've met with faculty, graduate students.
[00:00:25.742]It's maybe more faculty,
[00:00:27.510]and so it's been a great quick trip to Lincoln,
[00:00:33.330]and we're glad to have you here.
[00:00:34.980]Dr. Smith, you have a bachelor's
[00:00:38.640]from University of Washington,
[00:00:41.190]a master's from Yale, and a PhD from Wisconsin, Madison.
[00:00:46.740]She's also spent time at the Pacific Northwest National Lab
[00:00:50.670]in Eastern Washington near-
[00:00:53.429]Tri-Cities. Tri, okay.
[00:00:54.943]All right, so lots of experience
[00:00:58.231]in the area of soil carbon dynamics
[00:01:03.510]with a focus on small scale processes,
[00:01:07.260]chemical, physical, biological,
[00:01:10.590]and how those things affect carbon nutrient movements
[00:01:14.490]at larger landscape scale.
[00:01:16.470]So of course, very applicable, important,
[00:01:19.410]and increasingly discussed area today.
[00:01:23.460]So we're glad to hear you tell us more
[00:01:26.190]about the omics of soil organic carbon today.
[00:01:31.260]I will note for those of you in the room,
[00:01:34.860]we'll pass the microphone around to you individually
[00:01:38.340]per usual to pose your questions
[00:01:39.990]so the online group can hear.
[00:01:42.510]Those of you online,
[00:01:43.350]please feel free to enter your questions into the Q and A.
[00:01:48.090]It's a Q and A, not the chat, right?
[00:01:49.830]Yes. Q and A,
[00:01:51.000]but we'll find them either way.
[00:01:52.170]And I'll pose those to Peyton at the end.
[00:01:55.650]So with that, I'll give the microphone figuratively to you.
[00:02:00.371]All right. (host chuckles)
[00:02:01.440]Peyton, thanks. Thank you.
[00:02:02.670]And thank you so much for coming and for inviting me.
[00:02:05.550]This is my first time hanging out in Lincoln, Nebraska,
[00:02:09.270]and it was a short time,
[00:02:10.620]but I look forward to hopefully one day coming back
[00:02:13.110]and meeting more.
[00:02:14.520]So today I'm gonna talk about my research.
[00:02:18.961]But first, a little bit of who I am.
[00:02:21.780]Maybe you haven't heard of me.
[00:02:23.550]I am coming from Texas A&M University.
[00:02:26.100]I have now been there for almost five years.
[00:02:28.980]And so, but I am not a Texan.
[00:02:31.740]I'm actually born and raised in Wisconsin.
[00:02:33.720]So I've got our lovely state soil here,
[00:02:35.307]the antigo silt loam.
[00:02:36.990]Beautiful alpha soil, rich in carbon.
[00:02:41.040]And from Wisconsin, actually, how many people here
[00:02:43.710]even in high school was like, "I'm gonna be in soils or ag"?
[00:02:47.550]Raise your hand.
[00:02:49.920]So there's a few chosen ones who knew right off the bat.
[00:02:53.160]I had no idea.
[00:02:54.330]I didn't even know soils was a field whatsoever.
[00:02:57.120]I didn't really think about it.
[00:02:58.770]You know, I just walked on it all day
[00:03:00.120]and didn't even respect it.
[00:03:01.470]So it really wasn't until much later on in my career
[00:03:06.120]that I heard about soil.
[00:03:07.230]So I ended up doing my undergraduate degree in Washington.
[00:03:11.283]I was really attracted by the large old growth forest,
[00:03:14.610]the big trees there.
[00:03:15.720]So I went to the College of Forest Resources,
[00:03:17.966]which is no more.
[00:03:18.930]I think it's the School of the Environment right now.
[00:03:21.570]And from there, I really heard the word microalgae,
[00:03:24.930]and my whole world kind of blew open
[00:03:27.330]and I just wanted to study the soil,
[00:03:29.280]I wanted to study the organisms within the soil,
[00:03:31.740]and really understand those reactions
[00:03:33.333]and how all of these amazing giant trees were able to thrive
[00:03:38.070]in this environment.
[00:03:39.570]So most of my work right now
[00:03:41.550]is kind of a mix between biogeochemistry
[00:03:43.740]and microbial ecology, but my position,
[00:03:47.580]I was hired as a soil carbon dynamics,
[00:03:49.590]professor of soil carbon dynamics,
[00:03:51.240]which was very fitting
[00:03:53.130]because even if I say I'm a biogeochemist,
[00:03:55.110]I really just care about carbon right now.
[00:03:58.590]So it was a really fitting position to apply for.
[00:04:03.120]But before I got there,
[00:04:03.953]I also spent some time working in India
[00:04:07.710]and Costa Rica as well.
[00:04:09.480]And so I was able to see soils from really around the world.
[00:04:14.430]And then I did my master's in Connecticut.
[00:04:18.450]So I really like to switch coasts here too
[00:04:20.940]and continents.
[00:04:22.950]And from there, I really then got the urge
[00:04:26.250]to study soil.
[00:04:29.220]And I went to a forestry school for my master's too
[00:04:31.860]and I thought all these forest, these tree people,
[00:04:34.470]they keep making me wanna study the above ground,
[00:04:36.559]but the below ground is where it's all happening.
[00:04:39.540]And so I was like,
[00:04:40.627]"I'm gonna go back home to my beautiful state of Wisconsin
[00:04:44.755]and do my PhD in a department that's purely soils."
[00:04:49.890]There's no agronomy or crops involved, no offense to those,
[00:04:53.280]to study it.
[00:04:55.110]But I was like, "I just want to be in soil."
[00:04:57.240]So I was able to come back to Wisconsin
[00:05:00.790]and do my PhD there.
[00:05:02.850]I did more work in Kenya and Puerto Rico as well,
[00:05:06.676]which then led me to the national lab,
[00:05:10.290]and then now at Texas.
[00:05:11.430]And so you can slightly see
[00:05:13.560]it's kind of a bad resolution here,
[00:05:15.600]but this is what I'm working with here in Texas.
[00:05:18.270]And you might see that dark color and think,
[00:05:19.897]"Ah, look at all of that organic matter."
[00:05:21.729]No.
[00:05:22.950]No, that is like 1% organic matter and that's a vertisol.
[00:05:27.510]So we've got quite different properties
[00:05:29.580]than the beautiful Midwestern soils that myself grew up with
[00:05:33.390]and that you all get to work with.
[00:05:35.074]So it's been quite an adventure,
[00:05:38.370]and I'm very happy to be here today
[00:05:39.870]to talk about the work that I've been doing
[00:05:42.000]across all these different countries and institutions,
[00:05:46.440]which has to do with carbon.
[00:05:48.660]So I don't probably have to spend a lot of time justifying
[00:05:51.060]why it's important.
[00:05:51.900]Carbon has become a national interest.
[00:05:55.658]I feel like soil carbon,
[00:05:57.120]I was reading a yogurt container
[00:05:58.590]that talked about increasing soil carbon, and I thought,
[00:06:01.777]"I never would've thought 15 years ago,
[00:06:04.410]like my breakfast would be telling me about soil carbon."
[00:06:07.229]So it's really become a household name.
[00:06:09.210]We've really realized how important that the soil is
[00:06:11.850]in terms of keeping that carbon in there.
[00:06:15.150]So we know that soils act as both the sink of carbon,
[00:06:18.840]the largest terrestrial sink.
[00:06:20.520]We like to say in all of our proposals,
[00:06:22.890]but it's also a really significant biological source.
[00:06:25.290]It's one of our largest biological contributors
[00:06:28.200]to greenhouse gases as well.
[00:06:30.990]And one thing that we're noticing is in this changing world,
[00:06:34.140]whether it's land use change, climate change,
[00:06:36.420]extreme weather patterns,
[00:06:38.370]we're really unsure about the capability of soils
[00:06:40.530]to continue holding that mass reservoir.
[00:06:44.910]And if you're wondering how our ability to predict
[00:06:49.050]the capability of soils to hold onto carbon,
[00:06:53.100]this is a paper that's a decade old,
[00:06:55.994]but I could probably use these models right now.
[00:06:58.890]These are a series of different earth system models,
[00:07:01.380]and all of them are predicting
[00:07:03.008]what the change is going to be in the next coming years.
[00:07:08.280]And you can see that it's not just magnitude
[00:07:11.670]that changes with these models,
[00:07:13.320]it's the direction of change.
[00:07:15.120]So we have some models predicting
[00:07:16.560]that soils are gonna actually hold more carbon
[00:07:18.997]than they're doing now, and then we have some that are like,
[00:07:20.887]"No, they're gonna start to lose it."
[00:07:23.670]And so what I'm really interested in
[00:07:25.110]is like why do we see such variation
[00:07:28.560]and how are we able to use the knowledge that we have
[00:07:32.250]about the biology, the chemistry, the mineralogy,
[00:07:35.340]the physics to better improve these models
[00:07:38.640]so we can really start understanding
[00:07:41.970]how much our soils are gonna be helping us
[00:07:44.520]with storing all this carbon in the future?
[00:07:46.860]So I think one of the reasons why these models
[00:07:50.310]are not performing as well,
[00:07:52.350]let's see if I can get this going,
[00:07:53.970]is because soils are such a heterogeneous mixture
[00:07:57.780]of different aggregate sizes.
[00:07:59.730]These aggregates are clumped together,
[00:08:01.860]forming different cores of different sizes.
[00:08:04.260]These cores are connected or not connected
[00:08:06.990]by varying pore channels, varying sites.
[00:08:10.560]It's connectivities, it's a very complex network.
[00:08:13.227]And so you can imagine with this diversity,
[00:08:15.600]we have such a diversity of the organisms there,
[00:08:19.440]but also the type of carbon that's there.
[00:08:23.910]And so a lot of my work is trying to understand
[00:08:27.750]all of these interactions
[00:08:29.040]and how they occur in this physical space.
[00:08:31.680]So this is just a scanning, or this is an x-ray tomography,
[00:08:35.340]and this is actually not even very high resolution.
[00:08:38.310]It's just eight millimeters by eight millimeters,
[00:08:40.650]and you can still see how heterogeneous
[00:08:44.160]just a tiny eight millimeters of soil can be.
[00:08:47.880]And really, I didn't necessarily want to study micros.
[00:08:52.500]But unfortunately, they're the agents of change
[00:08:54.600]when it comes to any sort of biogeochemical reactions
[00:08:58.574]that's driving these ecosystem processes.
[00:09:01.590]And so they're central when it comes to nutrient cycling,
[00:09:06.544]disease transmission bioremediation,
[00:09:09.840]but more specifically, I'm really interested in their role
[00:09:13.560]in decomposition activities
[00:09:15.630]and how they cycle organic matter.
[00:09:20.220]One thing that we're noticing about a lot of organic matter
[00:09:22.650]that's hanging out in soils
[00:09:24.210]is it has been through the microbial machinery
[00:09:26.820]or biomass at some point.
[00:09:28.740]So it's somehow been utilized or turned over,
[00:09:31.770]or perhaps even a byproduct of decomposition,
[00:09:35.863]a microbial exudate.
[00:09:38.313]And so I was stuck studying them.
[00:09:40.440]And so if you think about this simple model
[00:09:42.840]that we have of just carbon going in, carbon coming out,
[00:09:47.730]well, we know that there's a lot more that goes on.
[00:09:51.060]And so if we're trying to even get it a little further,
[00:09:54.510]a lot of our models are like,
[00:09:55.770]whoa, we're gonna have carbon as two pools.
[00:09:57.990]We're gonna have a slow pool, we're gonna have a fast pool,
[00:10:00.720]then we, sometimes there's a passive pool.
[00:10:02.628]There's so many different types of models out there.
[00:10:05.970]But if you are a microorganism
[00:10:08.280]and you're living in a pore channel,
[00:10:10.320]it's not like you see a piece of carbon,
[00:10:11.327]you're like, "Ah, this is the slow pool carbon.
[00:10:14.280]I think I'll wait 'til I get one of those active pieces."
[00:10:17.160]And so really trying to bring along
[00:10:19.470]that ecological significance into our models,
[00:10:22.170]I think will improve.
[00:10:24.810]But if it was that easy to do, we'd probably be doing it.
[00:10:28.050]And so you can see that we can add a lot more arrows,
[00:10:30.990]a lot more pools.
[00:10:32.700]And I even have a paper that I love where we say,
[00:10:36.067]"Get rid of pools."
[00:10:37.500]There's no such thing as a pool.
[00:10:39.000]Let's talk about probabilities.
[00:10:42.360]But for simplicity, we're gonna go with the pool.
[00:10:45.060]And today I just want to bring up
[00:10:47.970]things like low molecular weight carbon
[00:10:50.130]and high molecular weight carbon
[00:10:51.990]because carbon is not all the same.
[00:10:54.960]Once it gets into the soil, where it's coming from,
[00:10:57.690]what it's chemical structure is like
[00:11:01.410]can really vary for how well it's likely
[00:11:04.380]to absorb to a mineral,
[00:11:06.750]how likely it's going to be consumed,
[00:11:08.880]or how likely it's going to be transported away with water.
[00:11:14.062]But there's many different types of ways
[00:11:17.430]you can characterize carbon.
[00:11:18.750]I'm just gonna be talking about
[00:11:19.890]low and high molecular weight in this talk.
[00:11:23.910]But so really, you've got that carbon
[00:11:26.040]going through the microbial biomass, some of it.
[00:11:28.500]You've got it breaking down
[00:11:29.990]into some of these lower molecular weight,
[00:11:32.160]you have some of this higher molecular weight,
[00:11:34.170]but what we've noticed is that
[00:11:35.670]when it comes to that stable pool,
[00:11:38.550]it doesn't have to be a high molecular weight
[00:11:41.250]or it doesn't have to be something that's really complex
[00:11:45.180]lignin-like in order to stick around.
[00:11:47.850]That oftentimes, we have very simple sugars
[00:11:51.180]that can persist in the soil for decades.
[00:11:55.200]And so some of these low molecular weight things
[00:11:56.745]we can think of like aminos, some saccharides.
[00:12:01.110]High molecular weight, you can think of more of those waxes,
[00:12:03.956]lignins, and some of our more complex proteins as well.
[00:12:08.580]And really what we're interested in, right?
[00:12:10.170]Is getting those, getting that carbon into a pool,
[00:12:14.670]into something that's gonna be there
[00:12:16.534]for a lot longer than even just five or 10 years.
[00:12:21.360]So to kind of get us started of all these different things
[00:12:25.140]that I've brought up is I can pretty much think about
[00:12:28.158]ways carbon stays in soils
[00:12:30.600]in kind of thinking about the biological,
[00:12:32.700]the chemical, the neurological, and the physical.
[00:12:35.430]So when it comes to the biological or the microbiome,
[00:12:40.440]a lot of times we're thinking about,
[00:12:41.273]all right, so what is that functional potential
[00:12:43.560]of the microorganism?
[00:12:45.120]So does it have the gene
[00:12:48.450]to produce the enzyme to catalyze the reaction,
[00:12:51.420]to break down something like the lignin?
[00:12:53.490]If it does break, lignin will be used up.
[00:12:55.950]If it doesn't, it won't.
[00:12:57.840]So depending on who's there in the community,
[00:13:00.240]you've got a lot of fungi,
[00:13:04.357]especially some of these more polypores
[00:13:06.150]that easily have peroxidase enzymes to break it down.
[00:13:09.300]You're not gonna see lignin persist,
[00:13:11.280]but that may not be something that you're gonna see
[00:13:13.697]in more of a grassland environment.
[00:13:16.980]And so the microbiome,
[00:13:18.270]we know that that functional potential is gonna matter.
[00:13:20.695]So not just can they do it,
[00:13:22.860]but also how much of them are there?
[00:13:25.770]Historically, we spent a lot of time
[00:13:29.400]thinking about the molecular composition, right?
[00:13:31.830]So has everyone heard of like humic and folic acids?
[00:13:35.628]You know, so one being something that is less complex,
[00:13:39.480]easy to degrade?
[00:13:40.740]Well, we used to think
[00:13:42.540]that if you had a lot of aromatic rings,
[00:13:44.430]you were gonna stick around for a lot longer.
[00:13:47.280]But what we're realizing
[00:13:48.726]is sometimes it's not that chemical makeup,
[00:13:52.380]it's not how aromatic, how complex it can be.
[00:13:55.110]It actually depends
[00:13:57.060]on whether or not it sorbs to a colloidal surface.
[00:14:01.020]And you can have low molecular weight
[00:14:04.080]or some of that easier labial carbon
[00:14:06.540]easily sorbed onto a surface and rendered unavailable
[00:14:09.330]for microbial turnover and decomposition.
[00:14:12.660]And so now we've realized that really,
[00:14:14.700]this mineral interactions,
[00:14:16.200]these mineral organic associations
[00:14:18.690]are really important in keeping that carbon in soils.
[00:14:23.850]But more importantly, in my opinion,
[00:14:27.960]it's not just whether it's sorbed,
[00:14:29.157]but where is it located in that physical matrix?
[00:14:32.370]Because maybe you have a functional microbiome.
[00:14:35.040]It can degrade the type of carbon that you have there.
[00:14:38.580]And that carbon is freely available, it's not sorbed,
[00:14:41.940]but maybe it's in a pore space
[00:14:44.280]where it's so small and it's isolated
[00:14:46.980]that almost all of the oxygen is no longer there
[00:14:49.219]and oxygen takes such a long time
[00:14:51.150]to diffuse through any water-filled force base.
[00:14:53.940]So in that situation,
[00:14:55.917]you switch it to a different metabolism even.
[00:14:59.550]And maybe that carbon will not be decomposed.
[00:15:02.460]So for me, to try to understand how carbon stays in soils,
[00:15:07.680]I try to take a very holistic approach
[00:15:11.280]and really try to attack
[00:15:13.873]some of these questions with looking at both the biology,
[00:15:18.180]the neurology, and the chemistry
[00:15:20.910]in thinking about where that location is in the soil.
[00:15:25.380]And I generally do this in the context of global change.
[00:15:29.130]So a lot of the questions we ask in my lab are like,
[00:15:31.950]what are those dominant mechanisms?
[00:15:33.630]Do we have more of a biological control
[00:15:37.326]or like the microbiome that's driving
[00:15:39.570]what carbon gets turned over?
[00:15:41.340]Or are we having more of a chemical?
[00:15:43.500]Like is it because this organic matter
[00:15:46.700]is not available?
[00:15:50.520]But then also thinking about the interactions
[00:15:53.010]between the biological, the chemical, these physical,
[00:15:56.160]and how these interactions can really drive
[00:15:59.370]not just the stabilization, so how much carbon stays there,
[00:16:02.760]but what gets blown off usually as a greenhouse gas?
[00:16:07.770]And really, in the context of global change.
[00:16:10.193]And for that, I mean land use change or climate change.
[00:16:14.460]And especially right now,
[00:16:16.261]a lot of my work focus is on drought,
[00:16:18.433]which is something that we experience in Texas every year.
[00:16:23.640]So it's a wonderful place to live
[00:16:25.320]if you'd like to study drought.
[00:16:28.110]You know, so how does it also influence these things?
[00:16:31.650]So my talk is about the omics
[00:16:33.510]and I would love to talk to you about all of the omics,
[00:16:35.970]but I cannot today.
[00:16:38.400]So, but just to kind of go over
[00:16:40.380]what some of these omics are,
[00:16:41.939]we've got metagenomics, metatranscriptomics,
[00:16:45.060]metaproteomics, metabolomics.
[00:16:46.710]I'm somehow on a timer.
[00:16:50.430]So metagenomics is like, "Who's there?"
[00:16:54.540]Metatranscriptomics is kind of like,
[00:16:55.927]"Ah, but what are they doing?"
[00:16:57.870]So what are those genes that are more active there?
[00:17:01.170]So for proteomics, you're looking at proteins.
[00:17:04.054]Oftentimes these are kind of more of these
[00:17:06.060]high molecular weight.
[00:17:08.460]And a lot of folks in proteomics
[00:17:10.890]think that this is a better indicator
[00:17:12.880]of what functional activities are more persistent
[00:17:16.909]compared to the transcriptomics.
[00:17:19.260]And today I'm gonna talk a little bit more about
[00:17:21.600]metabolomics.
[00:17:23.021]And so these can be more low molecular weight substrates.
[00:17:27.000]And usually these byproducts of reactions
[00:17:31.350]in the soil.
[00:17:32.183]So today I'm gonna give you some examples of metabolites,
[00:17:36.013]but I'm also gonna talk about
[00:17:38.400]kind of this other tool that I use,
[00:17:40.530]which is a high resolution mass spectrometry
[00:17:43.860]where I can get the molecular formula
[00:17:48.360]of thousands of organic matter compounds
[00:17:51.810]in one environmental sample.
[00:17:54.180]Okay, again, sorry, this was on a
[00:17:57.450]auto advance or something.
[00:17:58.964]So for this in particular,
[00:18:03.339]we don't have the omic name for it, but for me I'm like,
[00:18:06.810]it's kind of the omics of soil organic matter.
[00:18:09.510]And the one thing that I think is really powerful
[00:18:11.400]about using this tool
[00:18:13.140]is once I understand the molecular formula
[00:18:15.840]and a little bit about what that carbon looks like,
[00:18:18.630]we can actually map it to different metabolic pathways
[00:18:22.140]and start to infer some of the microbial metabolic functions
[00:18:26.970]occurring in the soil.
[00:18:29.100]And using some of this information too,
[00:18:32.040]we can kind of get at some of both the abiotic
[00:18:34.617]and the biotic transformations
[00:18:36.810]occurring with the organic matter.
[00:18:38.180]I'll talk to you a little about this.
[00:18:40.170]So this is one of the machines I work with.
[00:18:43.650]This is FTICR,
[00:18:45.720]which is fourier-transform ion cyclotron resonance.
[00:18:50.130]In particular, this is a 21 Tesla magnet.
[00:18:52.950]So there's a lot of power there.
[00:18:55.830]Basically, spinning your electrons,
[00:18:58.284]extremely high resolution.
[00:19:01.440]The one thing about it,
[00:19:02.340]so I don't know if you've seen normal spectra,
[00:19:04.320]but I mean this one, it's so high resolution
[00:19:07.170]that it's just all faded together,
[00:19:09.630]but you can really start to see
[00:19:11.430]and point out individual compounds with carbon,
[00:19:16.110]hydrogen, oxygen, nitrogen, sulfur,
[00:19:19.500]and phosphorus.
[00:19:21.150]So those are the main elements that you can get.
[00:19:24.930]So and unfortunately,
[00:19:26.769]we can't also get the calcium
[00:19:28.965]or all of these or some of these other,
[00:19:31.470]but you can get a pretty good profile
[00:19:34.603]of the type of organic matter compounds in the soil.
[00:19:37.914]So with this, you can do several things.
[00:19:40.770]You can use this kind of van Krevelen diagram
[00:19:43.680]where you're looking at different elemental ratios.
[00:19:46.980]And from it, you can infer
[00:19:48.450]different types of compound classes.
[00:19:50.790]So you can look at something
[00:19:52.500]that would be like a lipid-like compound,
[00:19:54.390]a protein-like compound, tannin-like,
[00:19:56.850]something that would be more aromatic.
[00:19:58.740]So your condensed hydrocarbons.
[00:20:01.530]So, and in addition, so you can look at
[00:20:04.470]what type of compounds just have
[00:20:06.903]carbon, hydrogen, and oxygen.
[00:20:08.970]All right, what are ones that have a nitrogen?
[00:20:11.280]What about nitrogen and sulfur?
[00:20:12.900]So there's several different ways
[00:20:13.980]that you can use this information
[00:20:16.260]and classify it to get a better idea
[00:20:18.030]of what your organic matter looks like.
[00:20:21.390]But it's also a metabolomic tool as well.
[00:20:24.690]And so we've also used it to identify metabolites.
[00:20:28.590]And one of the other powers about it
[00:20:30.240]being so high resolution
[00:20:32.880]is you can actually look at two peaks
[00:20:36.210]and look at the molecular mass changes in those
[00:20:39.540]and realize which elements were possibly lost or gained
[00:20:43.470]within a reaction.
[00:20:45.090]So something as simple as this compound experienced
[00:20:48.600]protonation or deprotonation.
[00:20:51.450]So again, it can be biotic or abiotic.
[00:20:55.740]So I'm not gonna go through all of the details of it,
[00:21:00.330]but with that it means that I can start taking
[00:21:04.080]some of those signatures,
[00:21:05.430]and then also looking at these different keg pathways,
[00:21:08.478]these metabolic pathways, and start identifying
[00:21:13.680]where I've seen those transformations in the pathway,
[00:21:17.910]and then in my sample whether I've seen evidence
[00:21:20.400]of the reaction for products.
[00:21:22.470]And so in some of our work, we've been able to narrow down
[00:21:25.380]some of the carbon cycling to decreases
[00:21:29.280]in the lysine pathways
[00:21:31.740]that really had to do with osmolytes
[00:21:33.690]and the fact that one of our sites was experiencing
[00:21:36.706]a lot less moisture.
[00:21:39.900]And so I really enjoy this tool
[00:21:41.910]because I feel like I can get a lot of information
[00:21:45.360]for just one sample.
[00:21:48.600]So I'm gonna present two examples of this today for you.
[00:21:53.460]The first one is gonna be more of the using it
[00:21:56.400]as metabolomic approach.
[00:21:58.110]And for this, we're gonna be looking at the metabolomic
[00:22:01.110]of root exudates.
[00:22:02.160]We're gonna be doing this in response to drought.
[00:22:05.460]And so this one is focusing more
[00:22:07.080]on plant-soil-microbe interactions.
[00:22:09.510]And then the second one,
[00:22:11.730]I'm actually gonna bring you to a tropical forest,
[00:22:13.855]get you out of the Nebraska cropping systems a bit,
[00:22:17.610]and we're gonna start looking at land use change
[00:22:20.820]and how that influences the molecular composition of carbon
[00:22:24.210]and how that may be related to how much CO2
[00:22:26.887]is being released
[00:22:29.798]in payment for ecosystem service plantations.
[00:22:33.960]So those are the two examples.
[00:22:36.240]I also have like 90 other slides at the end,
[00:22:39.120]so if you have anything else you wanna know, just ask me.
[00:22:43.470]Okay, so root exudates.
[00:22:46.980]So root exudates are a really important source
[00:22:49.680]of carbon in the soils as well.
[00:22:51.060]I think a lot of the times we think of these
[00:22:54.396]especially in forestry as the litter
[00:22:56.400]falling to the forest floor and being decomposed,
[00:22:59.550]but plants actually contribute
[00:23:01.491]a significant portion of their photosynthesis into the soil,
[00:23:06.687]and these can sometimes even be up to 40%,
[00:23:10.770]which is quite a bit.
[00:23:13.650]And that is not for all plants
[00:23:16.740]because we've seen some that are quite lower than that.
[00:23:19.890]But so not only are they putting that carbon into the soil,
[00:23:24.210]but once it gets in there,
[00:23:25.852]there's a variety of different pathways that it can go.
[00:23:30.240]And so thinking about these,
[00:23:31.740]usually what they are are these secondary metabolites.
[00:23:36.067]Either primary or secondary.
[00:23:38.190]We say they're plant-derived, but to be honest,
[00:23:42.090]we don't know.
[00:23:43.530]Because we have endophytes that live in roots.
[00:23:45.960]You cannot separate what they have produced from the roots.
[00:23:50.951]I mean, we've even tried using different isotopes
[00:23:53.670]to try to tease out,
[00:23:56.070]but it's not a very clear picture.
[00:24:00.330]So again, we've got
[00:24:01.260]more of these low molecular weight compounds,
[00:24:02.968]acids, organic acids, phenolic, et cetera.
[00:24:07.050]But what we've noticed is that also,
[00:24:09.480]there are these high molecular weight compounds.
[00:24:11.610]I think when most people think about these exudates,
[00:24:13.890]they're thinking about these more easy to decompose things.
[00:24:17.700]But really, they're also producing
[00:24:19.860]a lot of mucilage and proteins.
[00:24:22.139]So these root exudates are super important
[00:24:25.080]for a variety of different functions in the soil.
[00:24:27.515]So one, for me, they're really great
[00:24:31.320]for aggregation, roots,
[00:24:33.060]mycorrhizal hyphae produce these as well.
[00:24:36.858]They're really great for enmeshing soil particles together.
[00:24:42.180]But a lot is what we're knowing
[00:24:44.190]about what the signaling it's doing for microorganisms.
[00:24:46.980]So some of our theories now
[00:24:49.050]are that we've got signaling compounds
[00:24:51.870]that are recruiting beneficial microorganisms
[00:24:54.660]that in turn help the plant
[00:24:56.400]withstand some sort of abiotic or biotic stress.
[00:25:00.480]So they're also a delicious food for microorganisms.
[00:25:05.700]If you look in the soil,
[00:25:06.750]most of the microorganisms are gonna be congregated
[00:25:09.060]around those root tips
[00:25:11.220]or anywhere where that root is exuding
[00:25:13.329]this delicious carbon,
[00:25:15.485]which means that you're gonna see a lot of respiration
[00:25:19.800]or CO2 release around those areas from the microorganisms
[00:25:24.930]in addition to the roots.
[00:25:27.570]So we were really interested
[00:25:29.910]in looking at these root exudates
[00:25:33.630]and trying to profile all of these metabolites
[00:25:36.270]and maybe see if we can start to identify
[00:25:38.190]some of these signaling metabolites,
[00:25:41.040]and then also look at the microbial community,
[00:25:44.040]subject our plants to different drought stresses,
[00:25:47.910]and see kind of when do we start seeing
[00:25:49.561]a change in the microbiome, when do we start seeing changes
[00:25:52.350]in the root exudation profiles,
[00:25:54.810]and then can we use these root exudates as substrates
[00:25:59.431]or can we create inoculants
[00:26:01.440]out of changes in that microbiome
[00:26:03.270]that may stimulate root exudation?
[00:26:08.820]So that's what the whole project is about,
[00:26:11.610]really under this overarching hypothesis
[00:26:13.740]that these exudates
[00:26:16.710]also are important for signaling to these microbiome.
[00:26:20.880]So this is the work of Harrison and Heng-An.
[00:26:23.760]Harrison is a master's student who is transforming
[00:26:27.090]or turning into a PhD student this summer.
[00:26:29.460]He just got a NASA fellowship for it.
[00:26:31.170]And Heng-An is a postdoc on this project.
[00:26:33.060]This is funded by the Ag Microbiome Program in NIFA.
[00:26:37.650]And so our first objective
[00:26:39.120]was really just to start to profile these metabolomes,
[00:26:43.170]and then root exudates, and then really starts to connect it
[00:26:47.610]to changes in the microbiome.
[00:26:50.730]And then, looking at kind of whether or not,
[00:26:57.145]if we can use these substrates to initiate changes
[00:27:00.360]or use the microbiome to initiate changes
[00:27:02.190]in root exudation.
[00:27:03.150]I'm just gonna present the first objective
[00:27:04.680]because we've just got data from this this week
[00:27:09.210]that I threw into this presentation
[00:27:11.188]'cause it's always fun to get new data.
[00:27:14.640]So the stuff I'm gonna present today
[00:27:16.083]is gonna be just on the root exudates
[00:27:19.590]and a lot of the ones through what we've done,
[00:27:21.443]both the metagenome, metatranscriptome, and the metabolome,
[00:27:25.540]those are all at sequencing labs right now
[00:27:28.920]and we might see the data in the next year
[00:27:32.370]whenever they get to it.
[00:27:33.600]So we chose to do this in cotton.
[00:27:36.150]And if you're wondering why that cotton flower is pink,
[00:27:38.670]that's actually just from the growth chamber lights.
[00:27:41.550]So that really is a beautiful white flower.
[00:27:46.050]But so we pretty, we used an aeroponic system
[00:27:49.650]because even though you got rid of that soil,
[00:27:54.360]and for me as a soil scientist to start doing experiments
[00:27:57.630]without soil was really hard because I was like, why?
[00:28:01.920]Why would you do that to the core plant?
[00:28:04.017]But for the first part, we really wanted to get a good idea
[00:28:07.410]of what do these root exudates look like?
[00:28:09.870]We haven't even explored what the metabolome looks like
[00:28:13.590]and how that changes as the plant grows.
[00:28:16.740]And so with the aeroponic system,
[00:28:18.060]we were able to do it non-destructively
[00:28:20.100]and we were able to do it continuously.
[00:28:22.350]And so we grew plants in a growth chamber
[00:28:24.930]and we were also able
[00:28:27.570]to then change the fertigation that we were giving them.
[00:28:32.250]But you can imagine that the same setup you can use
[00:28:35.070]to either change the nutrient status
[00:28:37.725]to see how that changes.
[00:28:39.105]So it's a really great system for trying to manipulate
[00:28:43.349]what you're giving the plant.
[00:28:46.230]And so we collected the root exudates,
[00:28:49.710]did some extractions,
[00:28:50.760]and sent them in to get the metabolome.
[00:28:54.780]So for this particular,
[00:28:56.310]I wanted to talk about some of the treatments that we did.
[00:28:58.710]And truthfully, we didn't start them off
[00:29:02.040]aeroponically, right?
[00:29:03.180]So we wanted to germinate them on paper,
[00:29:05.760]throw them in hydroponics
[00:29:06.840]so we didn't dry them out completely,
[00:29:08.880]and really once they entered that first square stage
[00:29:12.570]is when we shifted them over to
[00:29:14.730]kind of the aeroponic system,
[00:29:16.500]which generally was between days 20 and days 30
[00:29:19.830]at the time.
[00:29:22.140]And so we use several different cotton varieties.
[00:29:24.990]I think I'm just gonna present maybe one today,
[00:29:28.521]but we use both drought susceptible varieties
[00:29:31.770]and also a variety that had been bred for drought tolerance
[00:29:37.087]that surprisingly did worse under drought.
[00:29:41.430]And we gave it two phases.
[00:29:43.110]So we did a water deficit phase,
[00:29:44.910]and we pretty much did it until the plants looked like
[00:29:47.820]they were going to completely die,
[00:29:50.490]which for us was that day left
[00:29:53.340]in which we thought we might lose
[00:29:54.870]a lot of our experimental replications.
[00:29:56.760]And then we decided to say,
[00:29:58.230]well, what happens when they recover?
[00:30:00.630]'Cause something that we experience a lot
[00:30:02.760]is drought, and then a giant downpour.
[00:30:06.450]And so we will often flip flop in Texas
[00:30:10.080]for what we're dealing with.
[00:30:11.340]And so we kind of wanted to replicate and just see,
[00:30:13.650]well what happens then
[00:30:14.940]when you add water back into the system at full rate?
[00:30:19.025]Okay, so this next slide
[00:30:20.880]is a video that Harrison put together and it's so fast,
[00:30:24.900]and I am too old to understand how to slow it down.
[00:30:27.930]I tried.
[00:30:28.950]But I'm gonna talk through a little bit.
[00:30:31.230]So we've got the control plants on this side
[00:30:33.810]and the drought ones on this side.
[00:30:35.820]And so it kind of starts out with like the baseline.
[00:30:38.130]We haven't done any drought, there's recovery.
[00:30:41.490]So you can see they look,
[00:30:43.320]they're growing bigger on both sides.
[00:30:45.750]And then we started initiating drought.
[00:30:47.640]It takes a couple days,
[00:30:49.320]and you can really start to see the plants start to wilt,
[00:30:52.282]and then recovery, and they flush back up.
[00:30:56.820]So let's start looking at what happens to the metabolome.
[00:31:01.110]All right, so for these graphs,
[00:31:02.542]what we're looking at are both unique and shared
[00:31:06.750]metabolites.
[00:31:07.583]So the darker color here, this is your drought,
[00:31:10.950]the wider is the control, and then shared.
[00:31:14.100]So at the beginning,
[00:31:16.230]these weren't statistically different or anything,
[00:31:18.960]but as that drought goes on, what we noticed,
[00:31:22.140]well, one, the total number of metabolites increases,
[00:31:25.500]that's the plant grows, right?
[00:31:26.670]So now you're looking at an increasing diversity
[00:31:30.180]of compounds that are being released.
[00:31:32.190]But we noticed that we saw
[00:31:34.440]relatively more unique compounds
[00:31:36.540]in those drought-induced plants than we did.
[00:31:40.950]And then when we got back to recovery,
[00:31:43.410]we noticed that it took a little bit of time,
[00:31:45.510]but then they went back to having a very similar metabolome
[00:31:49.320]in terms of the number of unique compounds.
[00:31:53.430]Okay, so the other thing that we looked at,
[00:31:56.970]this is an UpSet plot and it's really small.
[00:31:59.760]So I'm gonna talk you through it a little bit.
[00:32:03.060]What this is is it kind of goes over
[00:32:05.400]all of these unique metabolites.
[00:32:08.430]So these are just counts of unique metabolites.
[00:32:10.530]And then these are the dates.
[00:32:11.760]Day 2, 4, 7, 9 11.
[00:32:14.970]And if the bars connect, it means you saw those metabolites,
[00:32:19.500]they were shared across all.
[00:32:21.540]So we had several metabolites that were shared
[00:32:23.880]across all of the days of drought.
[00:32:26.250]So those, we think, all right,
[00:32:29.367]either there's something,
[00:32:30.750]even though they were unique to the drought treatment,
[00:32:33.107]this is something that you see a change
[00:32:36.330]as soon as some of the water deficit begins.
[00:32:39.480]But what we noticed is it really happened
[00:32:41.550]towards the end of that drought.
[00:32:42.960]So when we were looking at nine days,
[00:32:45.115]is when we had like 481
[00:32:49.230]unique metabolites.
[00:32:52.140]Shared between day nine and day 10 or 11,
[00:32:55.680]we had 576.
[00:32:57.873]So quite a difference.
[00:33:00.030]And then you'll notice at that day 11,
[00:33:04.560]when those plants were very wilted
[00:33:07.410]and were looking like they were going to die,
[00:33:10.320]they dropped back down again.
[00:33:12.690]So thinking about that data,
[00:33:15.570]and then mapping it to those keg databases,
[00:33:18.960]what we noticed was that
[00:33:21.392]I will show you is that here's a whole list.
[00:33:25.560]And that's the thing is you kind of get a list
[00:33:27.300]of like the different processes
[00:33:29.340]is that the majority of ones we were seeing
[00:33:31.740]were at the end like day nine and 11.
[00:33:34.027]A lot of these had to do with phenylpropanoids,
[00:33:37.020]flavonoids.
[00:33:39.510]And for that, if you're looking at some of those,
[00:33:42.420]here's your flavonoids, phenylalanines, et cetera,
[00:33:46.920]this is something that we have started to see
[00:33:48.750]in the literature.
[00:33:49.680]And not just in row crops or anything.
[00:33:53.040]We've actually started to see it in trees as well.
[00:33:56.220]And so we also started seeing
[00:33:58.008]some of these secondary metabolite biosynthesis
[00:34:01.455]and started kind of focusing in
[00:34:03.522]on what those metabolites could be.
[00:34:06.630]So daidzein,
[00:34:08.436]this is something that we've seen in the literature
[00:34:10.890]as being important for soybean root exudates,
[00:34:14.700]and they're thinking that this is really involved
[00:34:16.380]in getting some nitrogen fixation synthesis going.
[00:34:20.940]I mean, what is it called?
[00:34:24.210]Bio symbiosis.
[00:34:27.266]So we're starting to see some interesting profiles.
[00:34:30.630]And this I also just want you
[00:34:32.340]to kind of just take an overall look at this network.
[00:34:35.880]So this right here has to do with those transformations.
[00:34:39.330]It's a network analysis
[00:34:40.920]and you usually look at it as how connected it can be.
[00:34:43.170]You look at things like edges and nodes.
[00:34:46.110]But I just want you to kind of like step back
[00:34:48.360]and look at the full pictures
[00:34:49.620]and see how across the days that network analysis looks.
[00:34:54.060]So this is kind of how all of these compounds
[00:34:57.553]are connected to these transformations.
[00:35:00.630]So we start at two, day four,
[00:35:02.760]we start to see a lot more complexity in that metabolome,
[00:35:07.050]skipping some days and boom, this is the day nine.
[00:35:09.990]So you can see that the networks
[00:35:12.030]have really increased in complexity and connectivity.
[00:35:16.740]And then once those plants are very wilted,
[00:35:19.110]you can see that complexity even start to disperse as well.
[00:35:24.736]So we, we're really excited to kind of see this,
[00:35:28.440]to really look at it.
[00:35:29.460]Another thing that we noticed is that
[00:35:33.240]most of the nitrogen compounds
[00:35:35.310]were the ones that were increasing the drought.
[00:35:37.470]And so this is where
[00:35:38.970]we just looked at the end of the treatment.
[00:35:41.820]Well this is our,
[00:35:44.970]oh that says carbon, but it's actually nitrogen.
[00:35:47.040]Sorry about that.
[00:35:49.080]No, that is, oh wait, sorry.
[00:35:51.240]This is what happened when you throw your student slide in.
[00:35:53.264]So this first one is just that concentration
[00:35:57.084]and it is nitrogen,
[00:35:58.528]but this is when we normalize it by the root biomass.
[00:36:03.210]So we had some plants that we deconstructed
[00:36:05.400]at the end of the treatment.
[00:36:07.680]And so for both of those,
[00:36:08.760]no matter whether it was how much nitrogen that was overall
[00:36:11.730]exuded that concentration or whether it was normalized
[00:36:13.830]by how much of that root, biomass was there,
[00:36:16.590]there was a significant increase in the amount of nitrogen
[00:36:19.930]that was released after that deficit,
[00:36:23.670]but also even after recovery.
[00:36:25.920]And that's not something we noticed
[00:36:27.450]with the carbon compounds surprisingly.
[00:36:31.860]When we started to look at those nitrogen compounds,
[00:36:34.650]we actually see that it's mostly focused
[00:36:38.490]with metabolites that include both nitrogen and phosphorus
[00:36:43.950]or nitrogen, phosphorus, and sulfur.
[00:36:47.580]But it wasn't with the ones that we saw
[00:36:50.340]with just organic matter with nitrogen
[00:36:53.190]or metabolites with nitrogen
[00:36:54.810]or in the absence of sulfur or phosphorus.
[00:36:59.040]And then when it was the recovery,
[00:37:00.300]it was pretty much that increase
[00:37:01.770]was just driven by metabolites that had sulfur as well.
[00:37:07.776]This is just a response ratio
[00:37:11.310]of the drought to the control for how much nitrogen
[00:37:15.630]was present in those metabolites.
[00:37:17.400]And what I love is it really follows
[00:37:19.050]kind of what we saw with that.
[00:37:22.050]You know, the rest of our metabolome profile
[00:37:24.360]is that once those plants wilted,
[00:37:27.120]it really did shut down some of those processes.
[00:37:29.340]But really kind of at the height of drought,
[00:37:31.710]these plants are really leaking quite a bit of nitrogen.
[00:37:37.200]There's lots of summaries for this,
[00:37:39.960]but I've already gone over lots of time.
[00:37:42.910]But one thing I wanted to say
[00:37:46.290]is like this is kind of our first step
[00:37:48.330]and we don't have a lot of full metabolomes
[00:37:51.270]of root exudates overall,
[00:37:52.560]especially once they go with plant growth.
[00:37:55.650]And so we've brought it into the soil,
[00:37:58.230]so we're starting to look at that microbiome as well.
[00:38:01.717]But if you're wondering what this has to do
[00:38:03.690]with soil carbon,
[00:38:06.660]so one thing about root exudates is that
[00:38:09.810]some of the recent literature is showing
[00:38:11.790]that they do have quite an affinity to soil minerals.
[00:38:16.380]And a lot of the community right now is very concerned
[00:38:19.560]that these root exudates are replacing previously protected
[00:38:23.956]or mineral stable carbon.
[00:38:28.110]And so what we're doing with these root exudates,
[00:38:30.060]we've collected quite a bit,
[00:38:31.517]we are now using them as substrates
[00:38:34.260]in soils of different mineralogy
[00:38:35.970]and different surface areas,
[00:38:38.370]and even using secretion measures to look at where,
[00:38:43.110]which mineralogy may sorb these root exudates more.
[00:38:46.590]And while some may think that we are replacing old carbon,
[00:38:51.570]there's part of me that thinks, well, we may be replacing it
[00:38:55.140]with something that's low molecular weight,
[00:38:56.820]something that maybe is easier or more available
[00:39:00.570]for microorganism to decompose.
[00:39:02.640]And so if we're seeing kind of more easily degradable carbon
[00:39:05.910]getting stable on colloids, to me that seems like a win.
[00:39:11.490]And so that, so stay tuned.
[00:39:15.570]And if you're going to AGU this year,
[00:39:17.303]we put enough proposal to have an entire session
[00:39:19.800]on root exudation,
[00:39:21.390]whether it's looking at carbon sequestration
[00:39:24.690]and root exudation or whether it's looking at omics
[00:39:27.510]or even just looking at it in terms of nutrient mining.
[00:39:32.490]Okay.
[00:39:33.450]So here's the awesome team that's a part of this project.
[00:39:38.373]Malak Tfaily at University of Arizona
[00:39:40.530]is our FTICR genius,
[00:39:44.340]and I've been working with her for about 10 years now.
[00:39:46.980]Okay.
[00:39:48.390]So I don't have a whole lot of time
[00:39:50.670]to talk to you about tropical forests and the molecular,
[00:39:56.040]but this is Kathy Quinonez's work, she's my PhD student.
[00:40:00.240]We go down to Costa Rica every year.
[00:40:02.460]This is a project also
[00:40:03.510]with a lot of different collaborators.
[00:40:06.630]And both here and in Costa Rica.
[00:40:10.740]And in addition, I run an RU program.
[00:40:14.640]And so we spend a month in Costa Rica every summer.
[00:40:17.400]And a lot of the work that you're gonna see
[00:40:19.260]was helped because these RU students
[00:40:22.470]have contributed to running them
[00:40:24.600]and they all get to be co-authors
[00:40:26.010]and they've all presented at AGU.
[00:40:28.410]And so I don't wanna present this work without highlighting
[00:40:31.650]the hard work that these undergrads do.
[00:40:34.326]In this particular project, it's in Costa Rica,
[00:40:37.080]there's lots of different forests.
[00:40:40.080]Similar to most countries from the tropics,
[00:40:42.786]deforestation was very common about a hundred years ago.
[00:40:46.200]We've started to see a lot more afforestation activities
[00:40:49.500]occurring.
[00:40:51.720]But what's really nice is that even though
[00:40:55.860]it's lost a lot of its natural forest land,
[00:40:58.320]some of these programs like payment for ecosystem services
[00:41:02.610]has convinced land owners
[00:41:04.590]to protect the existing forest that they have
[00:41:07.260]or convert the pastures that used to be forest
[00:41:10.500]into plantations.
[00:41:12.930]So this is a soil map by the way of Costa Rica.
[00:41:17.130]So if you are someone who just thought oxisols
[00:41:19.800]were in the tropics, I'm telling you right now,
[00:41:22.530]it's very diverse.
[00:41:24.960]and most of these soils have andic properties.
[00:41:27.630]So I'm gonna go through this fast.
[00:41:31.650]So we try to study,
[00:41:33.930]we used a space for time approach
[00:41:35.520]to really look at some of these plantations
[00:41:37.980]to say we know they're storing above ground carbon,
[00:41:41.130]but what's happening below ground?
[00:41:43.200]And so we pretty much used adjacent native forests,
[00:41:48.966]active pastures,
[00:41:50.520]and then also plantations that were grown
[00:41:52.410]from those pastures.
[00:41:54.540]So it did, in terms of our study site,
[00:41:57.570]it took quite a lot of time to try to find pastures
[00:42:01.110]that all had very, like the same grasses
[00:42:04.717]because that's gonna change some of the carbon dynamics
[00:42:08.130]to find native forest ecosystems
[00:42:10.410]that were also very similar,
[00:42:12.120]that had similar species dominance.
[00:42:15.360]And even though we sampled like 10 different sites,
[00:42:19.200]we were only able to like really get three main sites
[00:42:23.340]that had kind of all three land uses,
[00:42:26.880]and then at least two different plantation species.
[00:42:31.380]And so whenever you're working with this natural system,
[00:42:35.480]it's really hard.
[00:42:37.470]We found five sites, and then we went back a second year,
[00:42:40.920]and two of them had already logged,
[00:42:43.350]and so we couldn't continue to track the carbon there,
[00:42:47.130]but we could say what happens with land use change
[00:42:49.573]in real time.
[00:42:51.690]Okay, so speeding through, we've got several different sites
[00:42:55.380]across where we've tried to
[00:42:57.222]kind of keep some of these parameters constant
[00:43:01.680]in terms of mean annual temperature,
[00:43:03.270]mean annual precipitation, species composition.
[00:43:06.750]Our plantation species were monocultures
[00:43:10.020]and they were actually native forests,
[00:43:11.970]which is very unique to this area.
[00:43:14.220]So we did several things where we looked at carbon,
[00:43:18.960]we looked at permanganate oxidizable carbon,
[00:43:21.330]which some people use as kind of an active carbon pool.
[00:43:24.660]We did cumulative respiration,
[00:43:26.850]we did it both in incubation form, we also did it in situ,
[00:43:29.985]measuring it from the soil itself.
[00:43:32.220]And then we used that fourier-transform
[00:43:33.780]ion cyclotron resonance
[00:43:35.070]to also look at the molecular composition
[00:43:37.290]of the organic matter.
[00:43:38.430]So we're not just looking at metabolites now.
[00:43:40.800]We're looking at the whole thing.
[00:43:44.040]So let's see here.
[00:43:47.070]420.
[00:43:47.960]So I really should stop in like five minutes.
[00:43:50.610]So I'm gonna tell you a little bit about this.
[00:43:54.300]We're gonna go too fast.
[00:43:57.930]Alright, we saw land use effect, right?
[00:44:00.270]And it wasn't that surprising.
[00:44:02.040]So basically, native forests
[00:44:03.600]had a higher concentration of carbon
[00:44:06.000]compared to the pastures,
[00:44:09.720]and we'll just focus on kind of the organic carbon.
[00:44:13.890]But when we started to look at kind of that nested
[00:44:17.487]different species, we noticed that that land use effect
[00:44:20.477]was actually not just plantations.
[00:44:24.570]That each plantation,
[00:44:25.500]depending on the different species that was planted there
[00:44:28.130]really ended up mattering, which is not surprising as well.
[00:44:33.330]So this is more, we'll just do this.
[00:44:37.890]When we look at the respiration, we actually,
[00:44:40.560]despite the fact that you kind of see a decrease
[00:44:43.470]in those bars up there, it's not significant at all.
[00:44:46.710]Of course, when we normalize it to carb,
[00:44:48.480]how much carbon was actually in the soil,
[00:44:50.910]we're going to see a lot more of the carbon
[00:44:53.640]that was in the soil being respired in those pastures
[00:44:56.040]compared to the native forest.
[00:44:58.680]Usually, the PES plantation species were often in between.
[00:45:02.580]We normalize this
[00:45:04.230]based on how much total carbon was in the soil.
[00:45:07.290]And we also thought if permanganate oxidizable carbon
[00:45:10.440]is really an active pool,
[00:45:12.570]then it should be correlated with how much is blown off.
[00:45:15.990]And we normalized it by that as well.
[00:45:18.742]We didn't actually see a species effect.
[00:45:21.720]So when it came to respiration, it was more of a land use.
[00:45:26.100]Let's just get to the fun molecular stuff.
[00:45:28.350]Okay, so we did see
[00:45:31.260]changes in the molecular composition
[00:45:33.570]and they were mostly associated with the native forest.
[00:45:36.356]So we saw differences in things like lipids and lignin
[00:45:42.240]and in organic matter compounds that had nitrogens
[00:45:45.570]and sulfurs.
[00:45:47.520]But what I really wanna talk about are aromatics.
[00:45:51.090]So we can also look at
[00:45:53.100]how complex these structures are
[00:45:56.640]for the specific compounds.
[00:46:00.360]And what we saw, we did see a species effect,
[00:46:03.510]but the native forest,
[00:46:05.040]especially compared to those pastures,
[00:46:08.040]had a lot more aromatics.
[00:46:12.600]So one of the things that I really like to look at,
[00:46:16.740]so this is called the nominal oxidation state of carbon.
[00:46:20.610]And so for this you can think about,
[00:46:23.880]and oftentimes you're thinking about Gibbs free energy,
[00:46:26.520]nominal oxidation states,
[00:46:27.960]and more like anaerobic environments.
[00:46:29.730]But in soils we have so many agnatic microcytes
[00:46:32.520]that we're really discovering that a lot of them
[00:46:34.200]are actually driving some of these respiration
[00:46:37.573]patterns that we see overall.
[00:46:40.530]And so you can think about if you see an increase
[00:46:43.860]in that nominal oxidation state,
[00:46:46.680]it's kind of like it's more thermodynamically available
[00:46:49.260]for a microbe to break that down.
[00:46:50.910]So think increase,
[00:46:52.500]more likely that that's gonna be turned over to CO2.
[00:46:56.550]And what we noticed,
[00:46:57.660]and this is the distribution of all the different compounds
[00:47:00.780]of organic matter in the soils,
[00:47:02.730]is that when it came to the native forest,
[00:47:05.370]we actually had kind of these two peaks.
[00:47:08.341]You know, especially relative to these pastures.
[00:47:11.670]And you can see by the tree species it really differed.
[00:47:14.850]So we almost see one emerge with our terminalia species,
[00:47:19.350]but so what this is kind of indicating
[00:47:21.120]is that we actually have kind of two main cools of carbon
[00:47:25.440]that's associated with these native forests.
[00:47:27.540]And one of them is most likely
[00:47:30.180]more thermodynamically favorable
[00:47:32.070]compared to the other one.
[00:47:33.270]And so we're really starting to think that,
[00:47:35.010]well, we see more aromatics there,
[00:47:36.840]we've almost have two pools.
[00:47:38.790]And so that may be the reason why
[00:47:41.310]we're seeing a lot more carbon accumulating
[00:47:43.710]in these native forests compared to the pastures.
[00:47:47.040]And the thing about these plantations
[00:47:49.830]is they're only 15 years since they've been grown.
[00:47:53.700]And so some of them,
[00:47:54.540]they often have these intermediate values between pastures.
[00:47:57.960]And so it's one of these things where maybe with time,
[00:48:01.320]they could start developing a profile
[00:48:02.850]that looks more like a native forest.
[00:48:05.730]But really, if you were a landowner,
[00:48:08.400]you are not keeping your plantation for a hundred years.
[00:48:12.030]You should be logging it and making that incentive,
[00:48:15.661]for those trees as well.
[00:48:18.690]And so really,
[00:48:20.190]when it comes to kind of the ones that we studied,
[00:48:22.200]and we've gone back and done this
[00:48:23.280]in several other areas too.
[00:48:25.260]What we're really noticing is that a lot of that carbon
[00:48:29.670]that was lost with deforestation
[00:48:31.650]is not being recovered in a 15-year time period.
[00:48:35.460]Which is not all that surprising
[00:48:37.080]as pathogenesis takes a long time.
[00:48:41.280]But the one thing about this, and I'll end here,
[00:48:44.340]is in the beginning I mentioned,
[00:48:47.130]oh, we spent all this time back in the day
[00:48:49.980]thinking about the molecular or the recalcitrant
[00:48:52.620]of the organic matter as driving that carbon stabilization.
[00:48:56.970]And really it's the microbes and the spatial location.
[00:49:01.020]And yet a lot of the studies that I've done is showing
[00:49:05.280]that the molecular composition indeed does matter.
[00:49:09.090]And what I can really relate it to
[00:49:11.070]is kind of how it's usually this nos value,
[00:49:14.880]this thermodynamic favorability.
[00:49:18.418]It often correlates with respiration
[00:49:21.140]in a variety of systems.
[00:49:22.560]I've done incubations where I've done it
[00:49:24.870]in completely anaerobic systems, in mixed systems,
[00:49:27.750]and very oxic systems.
[00:49:29.610]And this seems to be something
[00:49:31.710]that's constantly correlating
[00:49:34.890]with how much CO2 is being blown off.
[00:49:38.760]So really if you're thinking about
[00:49:41.760]some of these tools overall,
[00:49:43.800]I've just given you kind of one example
[00:49:45.313]of one that I've been able to use
[00:49:47.100]to really kind of get into that molecular profile
[00:49:50.760]of organic matter,
[00:49:51.900]but then also looking at metabolites of root exudates
[00:49:54.852]to really start to explore some of these
[00:49:57.117]biochemical interactions occurring in soils.
[00:50:01.860]And if you're interested in doing something like this,
[00:50:06.600]this capability is available to all of you.
[00:50:09.480]So the Environmental Molecular Sciences laboratory
[00:50:13.920]is a user facility that DOE runs.
[00:50:16.860]Every year they have two proposal calls.
[00:50:19.260]You don't even have to be a PI.
[00:50:21.000]You can be a graduate student,
[00:50:22.740]and you can submit a user proposal.
[00:50:25.170]They can be sometimes competitive
[00:50:26.640]depending on how many people submit them.
[00:50:29.010]But if you want this technology
[00:50:32.340]and your proposal gets selected, they will run this.
[00:50:35.820]And also, talk you through some of the data analysis
[00:50:39.450]'cause there is a bit of coding involved with some of this.
[00:50:42.360]But it's a really wonderful resource.
[00:50:45.660]Or if you wanna do some of the other cool toys
[00:50:47.430]that they have like nanos and (indistinct).
[00:50:50.067]And so, yeah.
[00:50:52.950]And with that, I'll take questions.
[00:50:55.230]Thank you.
[00:50:56.063]That clocks fast.
[00:50:56.896]We do have time for questions.
[00:50:59.418]But yeah, any here in the room or online?
[00:51:04.920]That was an excellent presentation.
[00:51:07.560]I have an offbeat type question.
[00:51:10.530]Farmers in the Midwest who grow corn-
[00:51:12.780]Yeah. are inundated
[00:51:14.580]by all these biologicals
[00:51:18.300]that they can apply to their corn
[00:51:20.520]and maybe get better yields.
[00:51:23.430]So what are the chances,
[00:51:25.410]you talked a lot about carbons and exudates
[00:51:27.629]and this sort of thing.
[00:51:30.870]These biological products, they,
[00:51:32.760]some people get good results,
[00:51:34.230]some don't get so good results.
[00:51:37.680]What you've talked about here
[00:51:39.540]would seem to have a bearing on the results.
[00:51:43.140]Is that feasible?
[00:51:44.787]I think they do have a bearing on the results,
[00:51:47.460]especially when it comes to some of our more exudate work.
[00:51:51.210]And I might get myself in trouble here
[00:51:53.453]because you're gonna hear an opinion.
[00:51:56.400]If you really gonna wanna manage for microbes,
[00:51:58.943]you are gonna wanna manage your carbon in essence.
[00:52:03.900]I think, and even though we are trying to
[00:52:06.570]develop certain inoculants for certain situations,
[00:52:10.710]I really feel like a lot of those are snake oil.
[00:52:17.407]I'm getting myself in trouble here,
[00:52:18.870]but it's because if you are trying to apply some,
[00:52:22.890]and rarely do I see them working ubiquitously
[00:52:26.220]across all systems and environments.
[00:52:28.500]I think that you can, actually, you can.
[00:52:30.990]You can create cultures or stimulants
[00:52:34.064]for specific systems, for specific environments,
[00:52:37.740]specific crops.
[00:52:39.780]But I think when you try to market something
[00:52:42.360]for all of these,
[00:52:43.800]what's gonna work for a cotton growing in a vertisol
[00:52:46.620]in Texas is not gonna work for corn in Nebraska most likely.
[00:52:51.496]So I don't know if that helps, but I think that,
[00:52:57.060]like for example,
[00:52:59.100]Harrison is really interested in trying to use,
[00:53:03.300]kind of collect these exudates
[00:53:04.920]and he's been putting it in like fake martian regolith,
[00:53:08.743]and then using that regolith that has had root exudates
[00:53:13.980]grow wheat in.
[00:53:17.619]And I think that there's use
[00:53:19.980]for things like that when he's trying to say like,
[00:53:21.720]okay, so how can we start cultivating crops on Mars
[00:53:25.440]using what we have?
[00:53:28.140]And so, but overall, like part of me,
[00:53:32.010]I'm like if you're gonna wanna manage for microbes,
[00:53:33.990]manage for carbon in my head, but I am very carbon bias.
[00:53:41.580]Other questions in the room or online maybe?
[00:53:47.340]Yeah, Bruce.
[00:53:51.330]In your first study there with the cotton-
[00:53:53.580]Yeah. with your misting
[00:53:55.260]and everything going through drought and in recovery,
[00:53:59.550]is there an impact on the air composition
[00:54:04.800]within those chambers?
[00:54:06.030]You know, is there oxygenation differences
[00:54:09.240]in terms of what you have in those chambers
[00:54:11.970]or would that change results?
[00:54:13.701]Oh, it would absolutely change results.
[00:54:16.710]And so one thing
[00:54:19.800]that I like about it better
[00:54:21.810]if you're going to try to collect root exudates
[00:54:25.530]is if a lot of times people collect them hydroponically,
[00:54:29.920]but then you're kind of losing all of those root exudates
[00:54:32.413]and in this case,
[00:54:34.346]they're kind of always staying in that system.
[00:54:36.630]And then so when you do kind of your flushes,
[00:54:39.510]you're able to get them all
[00:54:41.010]and not worry that you've lost any.
[00:54:45.660]But I think, I don't, I mean it's not just the air pressure,
[00:54:49.020]but almost everything I think with those aeroponics
[00:54:52.680]can change it.
[00:54:53.550]And we have replicated it in the greenhouse three times
[00:54:58.073]using the same varieties.
[00:55:00.216]And each time, a new thing will come up
[00:55:03.720]and it's usually happens to do with,
[00:55:06.660]well, usually it has to do
[00:55:08.100]with more of like changes in temperature
[00:55:11.028]because our growth chambers die
[00:55:14.910]mid-experiment one time and we had to redo that.
[00:55:17.171]But no, I think a lot of those change,
[00:55:20.190]I wouldn't worry so much about,
[00:55:26.910]yeah, I hadn't thought about the air pressure per se
[00:55:30.660]and everything's pretty, like the humidity was the same
[00:55:33.660]in each of those kind of buckets.
[00:55:35.010]We did monitor that, but that's a good question.
[00:55:38.790]I think, so for me,
[00:55:41.940]I think it's great for collecting these exudates,
[00:55:43.980]but I actually, I think that what we see
[00:55:46.680]when we grow things aeroponically
[00:55:48.540]is gonna be completely different than what is gonna happen
[00:55:51.829]when that plant is in the soil
[00:55:53.970]because I do think that it's a conversation.
[00:55:56.370]And so I'm really in-
[00:55:57.270]Particularly when you get a 12-inch rain
[00:55:58.800]and that's gonna change the-
[00:56:00.270]Yes. air composition
[00:56:02.010]very much in those soils. Absolutely.
[00:56:04.530]And so that is even why like collecting root exudates
[00:56:07.380]and there's tons of papers on all the different methods
[00:56:09.480]is there's no good method.
[00:56:13.320]And especially when you're doing things out in the field,
[00:56:15.462]I mean people have even put like little caps
[00:56:17.760]on certain roots as well.
[00:56:19.940]But again, it's like once you get it
[00:56:22.290]in the absence of its real environment,
[00:56:24.000]and I do think that there is an interaction
[00:56:25.830]that happens with the rhizobiome and the root exudates,
[00:56:30.000]but it's like, it's not only that,
[00:56:31.770]but it's like what that microbiome is doing.
[00:56:33.390]You're also, that's changing the amount of hydrogen,
[00:56:36.150]you're changing the pH,
[00:56:38.070]which absolutely is gonna change everything.
[00:56:42.877]So I can't wait to try to see what this looks like in soil.
[00:56:46.003]I can tell you my data is gonna have very high aero bars.
[00:56:53.970]Any more questions?
[00:56:58.200]I have one.
[00:56:59.033]You talked about the complexity of understanding
[00:57:02.370]the fate of the pools.
[00:57:06.210]Is that, given the,
[00:57:09.750]you mentioned the variability and conditions,
[00:57:12.284]more extremes, is that getting more complex
[00:57:16.410]or more, I guess more for us to influence
[00:57:18.183]what degree of influence might we have over that fate
[00:57:22.860]and what does it look like moving forward?
[00:57:28.290]You mean are you talking about with extreme,
[00:57:30.090]like extreme weather? Yeah, right.
[00:57:31.860]Like what projecting this into.
[00:57:34.356]Well, I think what's really difficult right now
[00:57:37.110]is even the studies that we're doing right now in the field,
[00:57:40.530]like and we've been doing stuff,
[00:57:42.540]we've been tracking carbon for five years.
[00:57:46.470]Since I moved to Texas, we have actually not had one.
[00:57:50.370]There's been no typical year.
[00:57:52.837]And everyone's just like, "This isn't typical."
[00:57:55.590]And every year, I've been there, I'm like,
[00:57:56.433]"I don't know what y'all think typical is,"
[00:57:58.961]because it's been crazy
[00:58:02.523]because we are experiencing extreme weather right now.
[00:58:06.030]And so I think it's really hard because my,
[00:58:09.630]especially with my students,
[00:58:10.740]it's like as they've been collecting this data
[00:58:12.360]and seeing these trends, part of me is like your baseline,
[00:58:16.590]your baseline is already been influenced.
[00:58:21.210]And so for me, that's why,
[00:58:25.080]I love about land grant institutions
[00:58:26.965]in experimental stations is we, hopefully,
[00:58:30.660]hopefully you guys even have archived soils.
[00:58:32.580]So we can even measure some of these things on stores,
[00:58:36.570]soils that have been stored for 50 or 100 years.
[00:58:39.360]So we can actually say like,
[00:58:40.747]"Okay, well what did it look like?"
[00:58:43.230]And then of course to use our wonderful modelers.
[00:58:46.170]We can hopefully use the little information we have
[00:58:48.540]to really give us a fuller picture.
[00:58:52.050]But I don't know because I think that
[00:58:55.740]it's really hard to,
[00:58:57.420]cause I don't know what the baseline is.
[00:58:58.590]Hmm. I feel like
[00:58:59.670]it's constantly shifting and it has been in my entire time.
[00:59:08.310]Great presentation, Peyton.
[00:59:11.330]In the beginning, you discussed and also argue about,
[00:59:14.970]like studying soil organic carboning models
[00:59:18.750]and pools and fluxes.
[00:59:21.090]And I wanna know like what are your thoughts
[00:59:23.610]on the microbial efficiency and the MENDs model
[00:59:28.740]that is looking into
[00:59:31.980]the studying stable carbon
[00:59:35.190]that mainly is driven by the microbial use efficiency
[00:59:38.070]of what is there in the soil.
[00:59:40.800]So would you mind to share- Yes.
[00:59:42.330]with us your thoughts? I actually would.
[00:59:44.010]So there are a plethora
[00:59:46.170]of really innovative models coming out
[00:59:49.140]where they're trying to incorporate microbial
[00:59:51.390]and MEND is one of them.
[00:59:54.510]So the one thing about,
[00:59:57.210]so carbon use efficiency or microbial carbon use efficiency
[01:00:00.916]really differs depending on how you measure it.
[01:00:03.360]And so I think what's difficult
[01:00:05.760]is we haven't like standardized any of those procedures
[01:00:08.880]and all of the conditions that we use to measure it
[01:00:11.430]are also, it's like I have folks
[01:00:14.640]who measure it using carbonity.
[01:00:16.420]We've got folks who just use it looking at biomass
[01:00:19.920]and respiration and normalizing that.
[01:00:22.350]But not everyone's using the same moisture content,
[01:00:26.970]the same temperature.
[01:00:28.842]So that's the thing is like microbial use efficiency.
[01:00:31.890]I wish it was so much better to measure.
[01:00:35.220]So, but I think, but I really like that one.
[01:00:38.070]I think the other thing that's coming out of that group,
[01:00:40.140]like Francesca Cotrupo's group is,
[01:00:43.590]which I didn't bring up today.
[01:00:44.730]I actually have several slides on it after this,
[01:00:47.473]is dividing it into like particulate organic matter,
[01:00:51.750]looking at light fractions, looking at heavy palm,
[01:00:55.710]looking at mineral associated organic matter.
[01:00:57.630]So fractioning the organic matter
[01:00:59.760]into kind of your POM or your MAM.
[01:01:01.380]MAM is that mineral associated.
[01:01:04.560]And we've even done this within aggregate sizes.
[01:01:07.290]So within macro aggregates, we've looked at
[01:01:08.970]how much of it is mineral associated,
[01:01:10.530]how much of it is particulate, micro aggregate,
[01:01:12.780]silk and clay fractions.
[01:01:15.882]Those pools
[01:01:17.640]seem to work much better as well.
[01:01:22.020]And I think because they have
[01:01:23.670]more of an ecological relevance
[01:01:27.210]to what is occurring in the soil environment as it is.
[01:01:31.025]And I think those are also,
[01:01:34.200]they kind of, again,
[01:01:35.400]they kind of like have an indirect microbial component
[01:01:39.720]just based on like the lability
[01:01:42.720]and things that are usually mineral associated
[01:01:44.970]have usually been stuck to minerals
[01:01:46.620]via like microbe exudates or things like that.
[01:01:51.930]But no, I really,
[01:01:53.310]it's really nice to see some of these microbial models
[01:01:56.370]come out.
[01:02:02.310]Thank you.
[01:02:03.143]Well, join me in thanking Dr. Smith one more time.
[01:02:07.590]Okay.
[01:02:08.423]Yeah, if anyone online, last chance to pose a question.
[01:02:12.150]If not, I'll say in the meantime,
[01:02:15.720]two more weeks left in the seminar series.
[01:02:17.970]Next week, please come back and join us for robotic tools
[01:02:22.380]and climate smart ag.
[01:02:25.800]Anything?
[01:02:27.960]All right. Well, thank you.
[01:02:29.228]Thank so much. Thank you.
[01:02:30.281]I appreciate it.
[01:02:31.681](crowd applauding)

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The ‘omics of Organic Matter – Using Molecular Tools to Decipher SOC Persistence in a Changing World

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