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Summer Research Project 2021

  • Title: Going Underground Sub-project 2: Microbial controls on root exudate carbon pathways in soil
  • Group Project Leader: Serita Frey
  • Mentors: Nikhil Chari; Mallory Choudoir; Kristen DeAngelis; Serita Frey; Adriana Romero-Olivares
  • Collaborators: Melissa Knorr; Relena Ribbons
  • Project Description:

    This is part of the group project, ‘Going Underground: Unearthing the Role of the Soil Microbiome in a Warmer, Fertilized World,’ which has the following overarching theme:

    Rising temperatures and atmospheric nitrogen deposition pose a threat to the health of forests in the Northeastern US where Harvard Forest is located. Mean annual temperature in the region has increased 1.5 °F since 1970. Although rates of atmospheric nitrogen deposition in the region have declined in recent years, decades-long deposition at rates of 4 to >8 kg N ha-1 yr-1 has resulted in a legacy of nitrogen-enriched soils. Previous research at Harvard Forest has documented that chronic soil warming and increased nitrogen loads alter soil microbial communities and the biogeochemical processes they mediate. We are particularly interested in microbial controls on soil organic matter (SOM) dynamics. SOM is the primary source of plant-available nutrients in terrestrial ecosystems; thus, the maintenance of SOM levels is critical for forest sustainability. Soils also represent the largest repository of carbon (C) in the biosphere and are an important source of carbon dioxide (CO2) to the atmosphere via microbial decomposition of organic materials. The overarching goal of this project is to examine microbial responses to soil warming and simulated nitrogen deposition and to understand how soil microbes influence SOM formation and stabilization.

    Since this summer program will be virtual, students on this project will utilize existing datasets to ask questions related to the overarching theme. 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: (Sub-project 1) Fungal responses to soil warming and nitrogen fertilization; (Sub-project 2) Microbial controls on root exudate C pathways in soil; or (Sub-project 3) Bacterial genomic signatures of warming-accelerated soil C loss (see full descriptions below). 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 2: Microbial controls on root exudate carbon pathways in soil (1 student; Mentors: Nikhil Chari, Ben Taylor)

    Rising atmospheric CO2 levels are projected to change the amount and composition of plant root exudates (Phillips et al. 2011), potentially shifting the nature of soil C inputs. Root exudates and other plant inputs are either microbially respired or incorporated into SOM as particulate organic matter (POM) or mineral associated organic matter (MAOM) (Lavallee et al. 2019). Whether bioenergetically favorable root exudate inputs are respired or form MAOM may depend on rates of microbial respiration versus assimilation, and the difference between these pathways may have dramatic consequences for soil C residence times.

    In this sub-project, the student will analyze data from an artificial root exudate experiment examining the effects of different artificial root exudate inputs (a simple sugar, amino acid, and organic acid) on MAOM and POM soil fractions in Harvard Forest soil (collected near one of the soil warming experiments). The student will aim to determine whether various inputs a) concentrate in the MAOM fraction, b) are largely respired, or c) are incorporated into microbial biomass. Additionally, the student will perform a literature review on the impacts of input chemistry on SOM formation pathways. Questions of note for this review are: how does litter chemistry affect the likelihood of microbial assimilation/respiration? What is the mechanistic process from microbial assimilation to SOM/MAOM formation? How are non-bioenergetically favorable inputs likely to be incorporated in the soil matrix? The data analysis and literature review will occupy the student’s time for roughly the first half of the program.

    In the second half of the program, the student will use the findings from their data analysis and literature review to develop an artificial root exudate experiment using our multi-feed syringe pump system. The student will be encouraged to develop an experiment that will specifically look at microbial controls on root exudate dynamics, including by assaying microbial biomass carbon and/or nitrogen. For example, one possible experiment would be to examine how sugar inputs along a gradient of complexity/quality are respired or concentrate in MAOM/POM/microbial fractions. However, the student is encouraged to come up with their own specific questions and comparisons. Given the virtual nature of this summer’s program, we will work with the student to develop a full research proposal and implement the experiment on our pump system under their virtual guidance, with the goal of supplementing the student’s experimental experience with experience honing critical writing skills.

    We are looking for students excited about microbiome science, ecosystem ecology, and soils. Interest and motivation are the main requirements. Experience, aptitude, or at least strong interest in data analysis and bioinformatics is desirable. 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:

    Abs, Elsa,, Scott R. Saleska, Regis Ferriere. Microbial evolution reshapes soil carbon feedbacks to climate change. bioRxiv 641399; doi:

    Anthony, M., K. Stinson, J. Moore, and S.D. Frey. 2020. Fungal responses to plant invasion are greater under soil warming than simulated nitrogen deposition. Oecologia (in press).

    Keiluweit, M., J.J. Bougoure, P.S. Nico, J. Pett-Ridge, P.K. Weber, and M. Kleber. 2015. Mineral protection of soil carbon counteracted by root exudates. Nature Climate Change 5: 588-595.

    Lavallee, J.M., J.L. Soong, M.F. Cotrufo. 2020. Conceptualizing soil organic matter into particulate and mineral-associated forms to address global change in the 21st century. Global Change Biology. 26(1): 261-273.

    Melillo, J.M., S.D. Frey, K.M. DeAngelis, W. Werner, M. Bernard, F.P. Bowles, G. Pold, M.A. Knorr, and A.S. Grandy. 2017. Long-term pattern and magnitude of soil carbon feedback to the climate system in a warming world. Science 358, 101-105.

    Morrison, E.W., A. Pringle, L.T.A. van Diepen, and S.D. Frey. 2018. Simulated nitrogen deposition favors stress-tolerant fungi with low potential for decomposition. Soil Biology & Biochemistry 125: 75-85.

    Phillips, R.P., Finzi, A.F., and Bernhardt, E.S. 2011. Enhanced root exudation induces microbial feedbacks to N cycling in a pine forest under long-term CO2 fumigation. Ecology Letters 14(2):187-194.

    Pold, G., Billings, A.F., Blanchard, J.L., Burkhardt, D.B., Frey, S.D., Melillo, J.M., Schnabel, J., van Diepen, L.T. and DeAngelis, K.M., 2016. Long-term warming alters carbohydrate degradation potential in temperate forest soils. Appl. Environ. Microbiol., 82(22), pp.6518-6530.

  • Research Category: Soil Carbon and Nitrogen Dynamics, Physiological Ecology, Population Dynamics, and Species Interactions, Large Experiments and Permanent Plot Studies, Group Projects