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Summer Research Project 2023
- Title: Going Underground: Unearthing the Role of Roots and Microbes in a Changing World
- Group Project Leader: Serita Frey
- Mentors: Carina Berlingeri; Nikhil Chari; Kristen DeAngelis; Serita Frey; Thomas Muratore; Benton Taylor
- Collaborators: Shersingh Joseph Tumber-Dávila
- Project Description:
Soil microorganisms play key roles in carbon (C) and nutrient cycles, as decomposers of organic matter and symbionts of plants. They drive decomposition in temperate forests as the primary producers of the extracellular enzymes that break down lignin and cellulose, two of the most abundant compounds in plant biomass. Soil microorganisms are also sensitive to environmental change, with shifts in the microbial community in response to global change drivers having significant consequences for soil C storage and feedbacks to climate through soil C loss. Roots and their mycorrhizal partners also represent an important and understudied facet of belowground ecology, and root-mycorrhizal interactions will likely be impacted by global change in ways that influence nutrient cycling process. Three sub-projects (described below) will “dig deeper” into the world beneath our feet.
Students will work with their mentor(s) early in the program to develop a research question and approach that meets their interests and skillset. Students should indicate which sub-project is of most interest (see below for descriptions). Students will meet daily to weekly with their primary mentor(s). The entire project team will meet every two weeks as a larger group to hear from collaborators and discuss progress and challenges.
Sub-project 1: Dual mycorrhizal colonization at Harvard Forest (1 student)
Mentor: Carina Berlingeri; Collaborators: Benton Taylor
Nearly 85% of plants depend on root-colonizing mycorrhizal fungi for key functions such
as nutrient and water acquisition, making mycorrhizal partnerships important drivers of global patterns of plant productivity and nutrient cycles. There are two dominant types of mycorrhizae exhibiting contrasting nutrient acquisition strategies: AM fungi show preferential foraging for phosphorus and inorganic nitrogen whereas EM fungi display preference for organic and inorganic nitrogen. Historically, plant species were thought to only associate with one type of mycorrhizal fungi, but more recent evidence shows that some plant species can associate with multiple mycorrhizal types simultaneously resulting in dual colonization. Dual colonization can be an advantageous strategy as the preferred nutrient acquisition strategies of each mycorrhizal type can complement each other and jointly alleviate N and P limitation. Despite the potential benefits to dual colonization, it is not as ubiquitous as single mycorrhizal colonization, suggesting potential costs of dual colonization such as a high requirement to support both fungal types. Deepening our understanding of the mechanisms that regulate dual mycorrhizal colonization can provide fundamental insights into the costs and benefits of plant-mycorrhizal partnerships and the global patterns of primary production that these partnerships support.
To better understand the ecological drivers of dual mycorrhizal colonization, we will be 1) assessing patterns of dual colonization along a natural gradient of mycorrhizal dominance (i.e., AM, EcM, and mixed forest stands) in adult trees, and 2) experimentally isolating the environmental regulators and plant physiological responses to dual colonization. The majority of this work will be conducted in the field, but there will be a substantial amount of microscopy work in the lab. Field work will include conducting bi-weekly plant physiological measurements using a LiCor (i.e., chlorophyll-fluorescence, heights, stomatal conductance, etc.) on planted seedlings, mature root collection, and collecting one-time environmental variables in each site (fungal diversity, spore density, soil nutrients, and light availability). Lab work will include DNA extraction, root staining, and mycorrhizal colonization using microscopy. Field measurements and lab skills will be developed during the course of the summer. The student should feel comfortable walking 3-4 miles a day, navigating a large research site, and working alone in the woods.
Sub-project 2: Root exudation in response to soil warming and nitrogen (2 students)
Mentors: Nikhil Chari, Thomas Muratore; Collaborators: Ben Taylor, Serita Frey
Rapid climate change raises questions about how plants will allocate carbon (C) under warming, and how this will influence the terrestrial C sink. Plants take up C by fixing atmospheric CO2 and allocate that C to many different pools, including pumping it into the soil as root exudates. Previous work at Harvard Forest has found that root exudation by trees decreases in response to experimental soil warming, potentially decreasing C flux belowground. Root exudation can be an effective strategy for plants to “prime” soil microbes into releasing nitrogen (N) from the soil. However, warmer soil temperatures may have a similar priming effect on soil microbes, which could explain why exudation is not as necessary (and, thus, is downregulated) in warmer soils. This summer, we want to test this hypothesis by measuring root exudation in response to interactive effects of soil warming and N addition in a long-term experiment at the Harvard Forest.
Alongside the growing appreciation of root exudates in the terrestrial C cycle is the ever-expanding world of mycorrhizal fungi — a symbiotic relationship between tree roots and soil fungi. Harvard Forest is dominated by ectomycorrhizal fungi (EMF); however, there is a small but significant contribution of arbuscular mycorrhizal fungi (AMF). EMF and AMF differ in their ability to acquire soil nutrients for their host plant, and AMF may be better suited for the global changes forecast for the New England region. Global change factors such as soil warming and N addition may create soil conditions that allow for overlap in the niches of EMF and AMF, with consequences on the terrestrial C cycle. In addition to testing to above hypothesis, we will also explore how mycorrhizal fungi mediate root exudation rates under soil warming and N addition.
For this project, two students will collaborate to measure root exudation in long-term soil warming and N addition plots. We will ask how soil warming, N, and their interaction affect root exudation rates of trees that associate with either EMF or AMF. Students can expect to spend the first few weeks of the program learning how to collect root exudates and identifying mycorrhizal root types in the field. Over the next 8 weeks, students will complete several exudate collection campaigns. Students will also analyze measured root systems for a series of root traits including length, area, and biomass, root C and N, and mycorrhizal colonization. Exudate samples will then be analyzed for both total dissolved organic carbon and specific metabolite composition.
Sub-project 3: Does niche or fitness drive soil microbial acclimation to long-term warming? Mentor: Kristen DeAngelis (1 student)
Microbes are central actors in biogeochemical cycling, and how microbes respond to climate change will affect soil health and plant nutrient availability. Over 30 years of experimental warming, soils have thermally acclimated to warming, showing an attenuated response of respiration to temperature increase. Perhaps due to the more limiting substrate availability, stable isotope probing studies have shown that microbial turnover is slower in heated soils compared to controls when assayed at similar temperatures. Additionally, soils have lost almost a third of soil carbon due to accelerated decomposition of soil organic matter. The increased microbial role in soil organic matter decomposition is evident in gene expression of microbial communities as well as in adaptation of carbohydrate degradation traits. These data point to possible explanations of fitness and niche selection as forces that are driving microbial response to long-term warming.
The goal of this study is to investigate how long-term warming has altered the growth and temperature sensitivity among soil microbial populations using the quantitative stable isotope probing (QSIP) technique. We have conducted a lab incubation experiment of soils from the Prospect Hill long-term warming experiment, where heated soils exposed to 30 years of +5?C warming and control soils were incubated at 15?C and 25?C in the lab for 7 days in the presence of 18O (heavy) or 16O (natural abundance) water. We extracted DNA from these soils at the end of the one-week incubation, separated each into 12 fractions based on density gradient ultracentrifugation, and conducted QPCR and sequencing on 9 fractions from each sample. The REU student will analyze these data to obtain turnover times for each taxon in each sample, and perform a statistical phylogenetic analysis to test whether fitness (ancestral traits) or niche (derived traits) are stronger drivers of growth rate at each temperature as well as temperature sensitivity of growth. This is a purely computational project, and the successful student will develop programming skills in R, Markdown, and Unix as well as statistical and bioinformatics skills.
General requirements for all students on the overall project: We are looking for students excited about ecosystem ecology, microbial ecology, and soils. Interest and motivation are the main requirements. Students will be expected to help one another with the different sub-projects, gaining exposure to all aspects of the overall project, thus collegiality and teamwork are also important expectations. - Readings:
Frey, S.D. 2019. Mycorrhizal fungi as mediators of soil organic matter dynamics. Annual Review of Ecology, Evolution and Systematics 50, 237–259.
Phillips, R.P., Brzostek, E., Midgley, M.G., 2013. The mycorrhizal-associated nutrient economy: a new framework for predicting carbon–nutrient couplings in temperate forests. New Phytologist 199, 41–51.
Teste, F.P., M.D. Jones, and I.A. Dickie. 2020. Dual-mycorrhizal plants: their ecology and relevance. New Phytologist. 225(5): 1835-1851. - Research Category: Soil Carbon and Nitrogen Dynamics, Physiological Ecology, Population Dynamics, and Species Interactions, Large Experiments and Permanent Plot Studies, Group Projects
