Jessica Moore: Root-microbe-ecologist Interactions

Jessica Moore’s research “Plant roots stimulate the decomposition of complex, but not simple, soil carbon” is shortlisted for the 2020 Haldane Prize prize for early career researchers. Here, she talks about her inspiration for the project as well as her experience as a first-generation college student and the importance of a support network.

Jessica Moore is a microbial and ecosystem ecologist currently working in the Biosciences Division at Oak Ridge National Laboratory.
Jessica Moore is a microbial and ecosystem ecologist currently working in the Biosciences Division at Oak Ridge National Laboratory.

Recently, there has been a lot of discussion around how roots and microbes interact within the soil matrix due to the importance of their interactions in ecosystem processes and calls for improving predictions of ecosystem responses to global changes. A general question in plant ecology is: to what extent do roots stimulate microbial decomposition of organic matter? There is mixed evidence for facilitation, where it is thought that roots exude simple carbon compounds that alleviate microbial energy limitation. We posit that the evidence is mixed because the effects are often measured in bulk soil. In our paper, we used a rhizosphere model and conducted a field study using stable isotopes to track C decomposition, and we show that roots stimulated microbial decomposition of complex soil carbon but not simple soil carbon.

Schematic of hypothesized interactions between roots, mycorrhizal fungi, and soil decomposer microbes. We hypothesized that roots and mycorrhizal fungi would stimulate microbial decomposition of organic matter. In the left panel, roots and mycorrhizal fungi have access to soil and enzymatic activity and CO2 flux (blue arrow) is moderately higher than the middle panel where only mycorrhizal fungi are present, and much higher than the right panel where roots and mycorrhizal fungi are excluded. Schematic was originally published by Moore et al. in Journal of Ecology (DOI 10.1111/1365-2745.12484).
Schematic of hypothesized interactions between roots, mycorrhizal fungi, and soil decomposer microbes. We hypothesized that roots and mycorrhizal fungi would stimulate microbial decomposition of organic matter. In the left panel, roots and mycorrhizal fungi have access to soil and enzymatic activity and CO2 flux (blue arrow) is moderately higher than the middle panel where only mycorrhizal fungi are present, and much higher than the right panel where roots and mycorrhizal fungi are excluded. Schematic was originally published by Moore et al. in Journal of Ecology (DOI 10.1111/1365-2745.12484).

We hypothesized that root-microbe interactions affect pools of soil carbon differently because decomposition of complex soil carbon demands more microbial energy than decomposition of simple carbon substrates. Clearly plants influence soil microbial activity, but theoretical development of plant-microbe-soil dynamics has not kept pace with empirical research. Here, we directly validated rhizosphere theory by manipulating root access to soil in a forest and measuring soil carbon responses. Using stable isotopes, we showed roots differently affect soil carbon pools. While microbial processes are at the forefront of carbon cycle theory, roots are not explicitly represented in most soil carbon models. We compared modelled hypotheses with explicit root-microbe interactions and varying degrees of microbe-C substrate affinity to the trends observed in our forested field site. This is the first step toward representing roots in carbon cycle models.

Gas and soil samples were collected from PVC mesocosms inserted into soil. Photo taken at Marcell Experimental Forest, MN.
Gas and soil samples were collected from PVC mesocosms inserted into soil. Photo taken at Marcell Experimental Forest, MN.

Significance of the Experiment

Our paper highlighted the critical importance of soil microbes in ecosystem processes for me. The different mesh sizes we used in our root and fungal hyphal exclusion cores likely limited bacteriovore grazers, altered abundance of microbes that can produce antibiotics during interference competition, and modified the playing field for resource competition and facilitation. Although we did not characterize the microbial community in this study, I think that would be an interesting area to explore in a future study. Since this work was completed, I have worked in new experiments and investigated the soil microbiome in more depth. I am especially curious about how the microbiome responds to environmental perturbations. How do soil microbial communities vary in composition and function under global change pressures, and how does that affect ecosystem processes they play a role in? My PhD work was in ecosystem ecology and today I focus on these key ecosystem players – microbes – investigating macro-scale questions by manipulating and measuring at the micro-scale.

Carbon dioxide fluxes in the PVC mesocosms were measured using an infrared gas analyzer (LiCor 6400).
Carbon dioxide fluxes in the PVC mesocosms were measured using an infrared gas analyzer (LiCor 6400).

I enjoy combining empirical field research with ecosystem models to reveal processes that neither approach could reveal on its own. The model used ground-truthed data about site characteristics such as temperature and precipitation. Then, we developed different versions of the model that represented different hypothetical scenarios. It’s the most detailed and concrete way to formulate a scientific hypothesis, in my experience. Finally, we collected data from the field experiment to compare with what the model projected in each hypothetical scenario. Combining the model with experimental data made it possible to study in situ root-microbe interactions that influence carbon cycling.

What Motivated Me to Pursue Ecology

Jessica Moore uses a hammer corer to excavate soils. PVC mesocosms were filled with the soil and placed into the same hole the soil was collected from. A mesocosm laying on the ground here shows the windows lined with stainless steel mesh, which was large enough to allow roots, fungi, and most soil fauna to enter.
Jessica Moore uses a hammer corer to excavate soils. PVC mesocosms were filled with the soil and placed into the same hole the soil was collected from. A mesocosm laying on the ground here shows the windows lined with stainless steel mesh, which was large enough to allow roots, fungi, and most soil fauna to enter.

I didn’t know about ecology when I began college. Like many who declare Biology as a major, I was on track to pursue a Medical degree. One day in my introductory biology class, I struggled to understand alternation of generations in mosses and asked the professor after class for clarification. She did something pivotal for me: she took me outside. On hands and knees in the lawn outside the lecture hall, she fingered through the grasses to find a moss sporophyte. “Aha! This is the reproductive organ for the moss!”, she excitedly told me. This real-world view was much easier to comprehend than the textbook diagram. Up until that point I did not know that one could conduct science outdoors in such a non-sterile and uncontrolled environment. Isn’t science done in a lab? In petri dishes and flasks by someone wearing nitrile gloves and a lab coat? Realizing the dirty work of ecology thrilled me and I signed up for every field-based class the following semester. I took field botany, field mycology, field ecology, and a summer course called “The Battle Between Lava and Life” which combined geology and biology on a two-week field trip across the Pacific Northwest US. These courses got me thinking about how the natural world works and how interconnected all the processes were. At the end of my biology series the professor challenged us to think of one question for the final exam that would tie together all that we had learned over the year. The question I thought of was: “Describe the pathway and all the factors that affect how a carbon atom flows through an ecosystem starting in the atmosphere, through photosynthesis, through the consumer food web, into the detrital food web, and through cellular respiration back to the atmosphere.” My question was returned to me with a note at the top of the page: Come see me after class. Every undergrad’s dreaded request from a professor. I stepped into her office and she said, “Have you considered graduate school? I know an ecosystem ecologist and I think you’ll be very interested in her work”. My career path was forever changed.

Although I desired a career in ecology research, I had no idea where to start. I am a first-generation college student — the first in my family to pursue a PhD and the first generation to move so far from home for my career. It was imperative that I found advisors and a support group of other first-generation students who were also pursuing graduate school. I was the only ecologist in the bunch, but the field of study wasn’t the thing that brought us together. We shared the burdens of figuring out how to finance this major life change, how to tell our families we’d be moving away, and how to get reconnected into a support system in a new place. We could not ask our parents for help because this path was unfamiliar territory for them, too. An added challenge was that I had already started a family and needed to figure out how to manage raising a child and doing science so far away from grandparents who could babysit. All of these challenges I met with perseverance because ecology isn’t just a job for me; it’s my passion and part of who I am.

Passionate about Ecology

An ecologist on vacation. Jessica Moore enjoys exploring the outdoors in her work and in her free time. Photo taken at Cumberland Island National Seashore, GA.
An ecologist on vacation. Jessica Moore enjoys exploring the outdoors in her work and in her free time. Photo taken at Cumberland Island National Seashore, GA.

In my spare time, I thoroughly love spending time outdoors. I enjoy taking my two children on backpacking adventures through Appalachia where we hike, rock climb, and bird watch. When I’m unplugged from technology in the wilderness, I remember why ecology is my passion. I see the trees in the forest and think about the fungi they’re interacting with in the soil. I see the birds and wonder where they migrated from, what they’re eating in this neck of the woods, and whether global changes have pressured phenological shifts in their diet. I share my passion for nature and synthesizing observations with K-12 students. I enjoy volunteering to teach hands-on ecosystem science lessons for students in primary and intermediate schools and I have taught a summer field course on mycology for primary school students. When I return to my lab after a weekend outdoors or time spent inspiring youth, I am refreshed and energized to continue working on the research questions I am innately passionate about.

Just as ecological systems are densely interconnected networks with many players interacting with one another and the environment, so too are ecologists. One piece of advice that was influential for me that I pass along to others is to continuously build your network and engage with the broader scientific community. A single scientist on their own will have a limited skill set and perspective, while a team of scientists will be better equipped with diverse perspectives to holistically address perplexing natural phenomena. We cannot do our work in isolation. We will learn more working among diverse colleagues. Try sharing your research ideas with groups of people who do not study exactly what you study because they will invariably have a perspective different than yours and see your research from a new angle. When attending professional conferences, ask the presenters questions about their work. Attend poster sessions where the dialogue is more informal and there are more opportunities for scientific discussion. Chat with junior scientists as well as senior scientists, those in your field and those tangential to your field. I once attended an American Geophysical Union conference talk on Mars geochemistry; the person sitting next to me asked “What planet do you study?”. “Earth” was my response and we both laughed. You never know what future research collaborations, employment opportunities, or fresh ideas you may gain from expanding your professional network.

Read the article in full here.

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