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Summer Research Project 2021

  • Title: Going Underground Sub-project 3: Bacterial genomic signatures of warming-accelerated soil carbon loss
  • 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 3: Bacterial genomic signatures of warming-accelerated soil carbon loss (1 student; Mentor: Kristen DeAngelis)

    In a long-term field experiment at Harvard Forest, soil warming has resulted in a large loss of soil C (Melillo et al., 2017). The loss is mostly due to microbes, with periods of SOM decay punctuated by changes in microbial community structure and function (Pold et al., 2015). SOM quality has been degraded (Pold et al., 2016), and a study of hundreds of isolates showed that the bacteria from chronically heated soils have an increased ability to degrade complex SOM (Pold et al., 2017). Despite the evidence for evolutionary adaptation, the genetic nature of this increased bacterial capacity to degrade complex organic compounds has not been found.

    Genes, genomic markers and phylogenetics are currently used as proxies for microbial functions and feedbacks in ecosystem models. But ecosystem models span decades to a century, which is certainly enough time for molecular evolution of microbes to contribute to community acclimation to stress. Microbial adaptation to climate stress is a source of soil self-reinforcing feedbacks to the climate system that can either be stabilizing (negative) or destabilizing (positive). Evolutionary adaptation of soil microbes is suggested as mechanism of changing microbial feedbacks to the climate system over time. The student working on this project will measure changes in microbial traits due to long-term warming, and consider how measured traits could fit into evolutionary trait adaptation into microbial parameters of climate models.

    This research will examine genomes of bacterial isolates and associated data (metagenomes, metatranscriptomes) from the long-term warming experiment, in an effort to understand the nature of how bacterial organic matter degradation is altered with long-term warming. Specifically, the student will work with bacterial genomes in a comparative analysis to look for evidence of nucleotide polymorphisms, gene duplication, virally-transmitted horizontal gene transfer, or altered gene regulation that would explain observed increases in SOM degradation.

    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