Soils are the invisible workhorses of forest ecosystems, housing roots that acquire water and nutrients for plants and fostering soil microbial communities that drive critical functions such as carbon storage, nutrient cycling, and greenhouse gas exchange with the atmosphere. Yet despite their fundamental importance, we understand far less about belowground responses to environmental change than we do about aboveground dynamics. As forests in New England and across the world face the many pressures of increasing climatic change, understanding how root and soil systems adapt to altered temperature, water, atmospheric chemistry, and tree community composition across different landscape contexts has become critical for predicting forest resilience and carbon cycling.
Within this project group, students will engage in complementary subprojects to investigate how changing environmental conditions shape tree roots, soil microbes, and the integral partnerships between the two. These projects will take place across a wide variety of settings at the Harvard Forest, including the Black Gum Swamp, the ForestGEO census plot, and several large-scale manipulation experiments. All of these projects share a common focus on measuring belowground traits and processes, including root biomass, root-microbial associations, water and nutrient cycling, and carbon dynamics to understand how temperate forest ecosystems cope with stress and how these responses will influence broader ecosystem processes like carbon storage and greenhouse gas emissions. Together, these complementary projects will advance our fundamental knowledge of belowground systems and our understanding of how plant-soil-microbe interactions will respond to a rapidly changing world.
Subproject 1 - Thirsty Roots in Fragmented Forests: How Water Availability Shapes Belowground Resource Strategies
Forest fragmentation doesn't just change what we see above ground, it transforms the hidden world beneath our feet. When forests are cleared, trees left standing at newly created edges face dramatically altered environments: more sunlight, warmer soils, shifting moisture patterns, and different nutrient availability. While we know trees at edges often respond by growing more leaves and branches to capture abundant light (the "walling off effect"), we understand far less about how their root systems adapt to these new conditions. Do roots proliferate into newly available space? Do they change their architecture to cope with altered water and nutrient supplies? And critically, how do increasingly common hydrological extremes, intense rainstorms alternating with prolonged droughts, affect these belowground strategies? This summer research project leverages the Climate Interactions with Forest Fragmentation (CLIFF) experiment at Harvard Forest, which uniquely combines forest structural gradients (from open clearings through edge habitats to interior forest) with experimental precipitation manipulations (simulated drought and supplemental watering), allowing us to investigate how root systems respond to the interacting effects of fragmentation and water availability, questions increasingly relevant as climate change intensifies both processes.
As a summer researcher, you'll investigate how dominant tree species adjust their fine root systems along environmental gradients created by forest fragmentation, and how these patterns shift under contrasting drought and extreme precipitation treatments. You'll begin by establishing sampling transects and installing root ingrowth cores across the CLIFF experimental plots, then spend the majority of your summer conducting hands-on laboratory analyses measuring root biomass distribution, fine root traits (specific root length, diameter, branching patterns), vertical rooting patterns, and mycorrhizal colonization—all key indicators of how trees acquire water and nutrients under different conditions. Your data will help answer critical questions: Are fragmented forests more vulnerable to drought stress? Do edge trees exhibit greater root plasticity that might buffer them against water extremes? This project offers an ideal blend of outdoor fieldwork at a world-renowned research site and detailed laboratory analysis while addressing fundamental questions about forest resilience and carbon storage in human-altered landscapes facing climate change, providing you with comprehensive training in root ecology methods, trait-based plant ecology, data analysis, and scientific communication.
Subproject 2 - Deep roots and soggy boots: tree root dynamics in saturated conditions
Wetlands are among the most important ecosystems for global carbon cycling and are the largest natural source of atmospheric CH4, a greenhouse gas roughly 27 times more potent than CO2 in terms of radiative forcing. Persistently high water tables create anoxic conditions that support methane-producing microbes, making anaerobic respiration the dominant driver of CH4 generation in these systems. Once produced, CH4 can reach the atmosphere through several pathways, including molecular diffusion through the water column, ebullition of gas bubbles, and plant mediated transport through wetland vegetation. Recent research suggests that tree stems can serve as a particularly important plant-mediated transport pathway for CH4 emissions, acting both as conduits that vent soil-derived CH4 to the atmosphere and as potential sources of CH4 produced locally within anaerobic microsites inside the wood (Barba et al., 2019; Covey & Megonigal, 2019).
At Harvard Forest’s Black Gum Swamp, preliminary data indicate strong species-specific differences in stem CH4 fluxes among black gum (Nyssa sylvatica), red maple (Acer rubrum), and eastern hemlock (Tsuga canadensis) trees (Gerwitzman et al., in prep). The goal of this project is to investigate whether belowground traits help explain these differences. We will collect peat cores around each focal species and separate intact roots to quantify root biomass, morphology, and functional traits. These measurements will allow us to test whether variation in root system structure influences plant-mediated CH4 transport from soils into tree stems, and subsequently out to the atmosphere.
As a summer researcher, your project will begin with several weeks of field sampling in the Black Gum Swamp (collecting a series of peat cores), followed by laboratory analyses of root traits and biomass throughout the summer. This work will contribute to resolving the mechanisms underlying tree-mediated wetland CH4 emissions, an important and still poorly understood component of the global CH4 cycle.
Subproject 3 - Understanding how tree-microbe partnerships impact decomposition dynamics
Temperate forests are anomalous in their high diversity of tree-microbial partnerships, particularly their relatively even distribution of trees associating with the two major groups of mycorrhizal fungi: arbuscular mycorrhizae (AM) and ectomycorrhizae (EM). These contrasting mycorrhizal partnerships influence the leaf chemistry of the host tree and the community of microbes inhabiting the soil around the tree’s roots. For example, it has been hypothesized that AM-associated trees tend to produce more easily decomposable leaves, which are quickly broken down in the soil and the mineralized nutrients from those leaves are preferentially taken up by the AM fungi themselves. In contrast, EM-associated trees produce leaves that are chemically resistant to decomposition, but the EM fungi inhabiting the soil at the base of these trees has a large suite of extracellular enzymes that can break down this recalcitrant leaf litter. While previous work has demonstrated differences in nutrient cycling in AM and EM dominated forest stands, we lack direct field evidence that leaf litter chemistry and decomposition fundamentally drive these patterns.
This project will work in a newly established leaf litter transplant experiment where the leaf litter in AM and EM dominated tree stands has been replaced with leaf litter of the opposite mycorrhizal type in an effort to identify the effects of altered leaf litter chemistry on belowground biogeochemical processes. The team will use a variety of methodological approaches to assess how these leaf litter treatments impact decomposition rates, soil pH and nutrient availability, and soil microbial communities. The results from this work will help us understand the stability of AM and EM partnerships in tree communities over long timescales and will allow us to make direct predictions of how climate change driven shifts in the tree species community will impact critical processes like decomposition and nutrient cycling.
Subproject 4 - Linking soil microbial diversity to tree community structure and function
The ability for forests to grow and capture atmospheric carbon depends on both the availability of soil nutrients and the composition of soil microbial communities. Because forests are highly heterogeneous, understanding fine-scale interactions among trees, microbes, and the physical environment is essential for predicting forest productivity and carbon cycling. Free-living soil microorganisms influence nutrient supply by either releasing nutrients through decomposition or temporarily immobilizing them. Additionally, antagonistic soil microorganisms can inhibit plant growth. Mutualistic microbial symbionts, such as ectomycorrhizal (EcM) and arbuscular mycorrhizal (AM) fungi, benefit their host plants by aiding in nutrient and water uptake, increasing stress resistance, and defending against pathogens. Despite rapidly growing interest in mycorrhizal impacts on forest productivity, we lack direct data on how soil microbes and abiotic conditions together drive spatial patterns of tree growth.
To address this gap, this project will integrate the mapped, repeatedly censused tree community of the Harvard Forest ForestGEO plot with new soil microbial metagenomic data and soil abiotic measurements collected over the summer. This project will offer an undergraduate researcher an opportunity to explore how above and belowground processes interact to influence forest growth. Specifically, we will investigate 1) the spatial coupling between aboveground tree-mycorrhizal-strategy and belowground soil microbial diversity 2) how do soil abiotic factors and nutrient availability shape the abundance of EcM and AM fungi and 3) how relative EcM and AM abundance explain variation in tree growth rates across species and soil properties. These patterns of forest growth underpin one of Earth’s largest carbon sinks, understanding its controls is essential for predicting carbon capture under global change.
General requirements for all overall project, regardless of sub-project:
1. Students can expect to spend ~50% of their time in the field. The ideal candidate has a positive attitude in group environments and is comfortable working under a range of conditions (e.g., hot and humid, cool and rainy, buggy, etc.)
2. An inquisitive nature and comfortable asking questions
3. Experience using R or the motivation to learn. This will be the primary software used for data analysis and visualization
4. Capable of walking 2+ miles (in a day) on and off trails to visit field sites
5. Capable of working in teams to help run the larger experiment, which may include time working on helping set-up/take-down parts of the experiment, or helping others with fieldwork that may not be directly related to your specific project, but related to the broader success of the overall experiment.
Reinmann AB and Hutyra LR. 2017. Edge effects enhance carbon uptake and its vulnerability to climate change in temperate broadleaf forests. Proceedings of the National Academy of Sciences 114(1): 107-112. DOI: 10.1073/pnas.1612369114
Smith et al. 2018. Piecing together the fragments: elucidating edge effects on forest carbon dynamics. Frontiers in Ecology and the Environment 16: 213-221.
Herbst, M., Roberts, J. M., Rosier, P. T. W., Taylor, M. E., & Gowing, D. J. (2007). Edge effects and forest water use: A field study in a mixed deciduous woodland. Forest Ecology and Management, 250(3), 176–186. https://doi.org/10.1016/j.foreco.2007.05.013
Barba, J., Bradford, M. A., Brewer, P. E., Bruhn, D., Covey, K., Van Haren, J., Megonigal, J. P., Mikkelsen, T. N., Pangala, S. R., Pihlatie, M., Poulter, B., Rivas?Ubach, A., Schadt, C. W., Terazawa, K., Warner, D. L., Zhang, Z., & Vargas, R. (2019). Methane emissions from tree stems: A new frontier in the global carbon cycle. New Phytologist, 222(1), 18–28. https://doi.org/10.1111/nph.15582
Covey, K. R., & Megonigal, J. P. (2019). Methane production and emissions in trees and forests. New Phytologist, 222(1), 35–51. https://doi.org/10.1111/nph.15624
Abramoff, R. Z., Warren, J. M., Harris, J., Ottinger, S., Phillips, J. R., Garvey, S. M., Winbourne, J., Smith, I., Reinmann, A., Hutyra, L., Allen, D. W., & Mayes, M. A. (2024). Shifts in belowground processes along a temperate forest edge. Landscape Ecology, 39(5), 100. https://doi.org/10.1007/s10980-024-01891-3A
Phillips, RP, E. Brzostek, and M.G. Midgley. (2013). The mycorrhizal-associated nutrient economy: a new framework for predicting carbon-nutrient couplings in temperate forests. New Phytologist. 199: 41-51.
Prescott, C.E., and S.J. Grayston. (2013). Tree species influence on microbial communities in litter and soil: current knowledge and research needs. Forest Ecology and Management. 309: 19-27.
Plant Life Belowground Blogs by Grady Welsh (Tumber-Dávila Lab Manager):
Life Lessons in Root Identification: https://plantlifebelowground.wordpress.com/2025/10/29/life-lessons-in-root-identification/
Identifying Fine Roots: https://plantlifebelowground.wordpress.com/2025/10/15/identifying-fine-roots/