Current Research

We study the ecology, chemistry, and biology of microorganisms in the environment. Microbes are the engines of carbon and nutrient cycling through ecosystems. The goal of our research is to uncover the biochemical mechanisms that microbes use to drive these large-scale processes. To do this, we use a combination of biochemical analyses and sequencing technologies to identify direct, mechanistic links between the genetic architecture, community structure, and biochemical functions of microbes in complex environments. We focus on organisms in Kingdom Fungi, because they are directly responsible for moving energy and elements between the biosphere and the atmosphere, but are less well understood than plants, animals, and bacteria. Fungi also make beautiful macrostructures that have a long and interesting history in human society, and now are also aiding us in new studies of molecular-level fungal processes in the environment.

Current research includes: 1) Molecular mechanisms and biogeochemical consequences of fungal species interactions. Diversity of decomposer microorganisms often has positive or negative effects on total decay rates. These patterns can arise from synergistic and antagonistic interactions between decomposer species, yet we still do not have a mechanistic understanding of the biological processes that determine the outcome of these interactions or their influence on ecosystem-level biogeochemistry. We are identifying the molecular-level factors that regulate these processes using a combination of -omics, modeling, and community ecology approaches. 2) Secretomes of plant-fungal interactions. Mycorrhizal fungi are a ubiquitous group of fungi that associate symbiotically with live plant roots, providing nutrients and water to plants in exchange for sugar. Mycorrhizal fungi associate with over 90% of plant families, yet we still know little about the molecular basis of functional diversity among different mycorrhizal species. Our research uses new analytical chemistry techniques to quantify, visualize, and map the biochemical processes that mycorrhizal fungi use to acquire nutrients and transform the soil environment. 3) Resistance and resilience of microbial guilds and biogeochemical functions to climate change. This project aims to link ecosystem changes to the microbial communities that may drive them. At its core, the project is examining the responses of plant growth and soil biogeochemistry to rapid climate-induced changes in the Northeastern U.S. We are characterizing the microbial community drivers of these ecosystem responses through identification of total microbial community composition, active microbial communities, and genomic relationships between microbial stress tolerance and biogeochemical function.

Selected Publications

  • Saifuddin M, Segré D, Bhatnagar JM, Finzi AC (2019) Microbial carbon use efficiency predicted from genome-scale metabolic models. Nature Communications 10: 3568.
  • Averill C, Cates L, Dietze MC, Bhatnagar JM (2019) Spatial vs. temporal controls over soil fungal community similarity at continental and global scales. ISME Journal 13: 2082–2093.
  • Averill C, Dietze MC, Bhatnagar JM (2018) Continental scale nitrogen pollution has shifted forest mycorrhizal associations, driving losses of soil carbon. Global Change Biology 00: 1-10.
  • Bhatnagar JM, KG Peay, and KK Treseder. 2018. Litter chemistry influences decomposition through activity of specific microbial functional guilds. Ecological Monographs 88: 429-444.
  • Ramirez KS, CG Knight, M de Hollander, FQ Brearley, B Constantinides, A Cotton, S Creer, TW Crowther, J Davison, M Delgado-Baquerizo, E Dorrepaal, DR Elliott, G Fox, RI Griffiths, C Hale, K Hartman, A Houlden, DL Jones, EJ Krab, FT Maestre, KL McGuire, S Monteux, CH Orr, WH van der Putten, IS Roberts, DA Robinson, JD Rocca, J Rowntree, K Schlaeppi, M Shepherd, BK Singh, AL Straathof, JM Bhatnagar, C Thion, MGA van der Heijden, FT de Vries. (2017) Detecting macroecological patterns in bacterial communities across independent studies of global soils. Nature Microbiology 113: 285-293.
  • Siletti C, CA Zeiner, Bhatnagar JM (2017) Distributions of fungal melanin across species and soil. Soil Biology and Biochemistry 113: 285-293.
  • Peay KG, P Kennedy, JM Talbot (2016) Dimensions of biodiversity in the Earth mycobiome. Nature Reviews Microbiology 14: 434-447.
  • Talbot JM, F Martin, A Kohler, B Henrissat, and KG Peay (2015) Functional guild predicts the enzymatic role of fungi in litter and soil biogeochemistry. Soil Biology and Biochemistry 88: 441-456.

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