The Tfaily lab uses innovative and state-of-the-art techniques to map organic matter, scaling genes to ecosystems, in order to better predict ecosystem functions and climate impact implications. Our research spans a variety of ecosystems, including peatlands, rainforests, and watersheds.  

Focuses include: 

  • Biotic and abiotic influences on organic matter transformations and multiomics integration
    • Organic matter composition characterization
    • Microbial respiration and greenhouse gas emission 
    • Metabolite assmebly
    • Metabolomics and Multiomics integration
    • Ecosystem focuses – peatlands, rainforests, Sonoran Desert, watersheds
  • Plant-microbe-soil and Rhizosphere interactions (biogeochemical and microbial)
  • Stable Isotope Probing Metabolomics (SIP Metabolomics) 
    • Tracking plant and microbe metabolite fate using labeled isotope analytical techniques


EMERGE-BII – The National Science Foundation-funded EMergent Ecosystem Responses to ChanGE (EMERGE) Biology Integration Institute aims to develop such a framework by integrating research, training, and high-resolution field and laboratory measurements across 15 scientific subdisciplines–including ecology, physiology, genetics, biogeochemistry, remote sensing, and modeling–across 14 institutions, in order to understand ecosystem-climate feedbacks in Stordalen Mire, a thawing permafrost peatland in arctic Sweden. Rapid warming in the Arctic is driving permafrost thaw, and new availability of formerly-frozen soil carbon for cycling and release to the atmosphere, representing a potentially large but poorly constrained accelerant of climate change. EMERGE examines biological interactions and their responses to change by employing a ‘genes-to-ecosystems-to-genes’ (G2E2G) approach.

SPRUCE – the primary component of the Terrestrial Ecosystem Science Scientific Focus Area of Oakridge National Laboratory’s Climate Change Program. This study aims to assess the response of northern peatland ecosystems in Minnesota to increase in temperature and exposures to elevated atmospheric CO2 concentrations.  

B2 WALD – a stable isotope labeling experiment located in the Biosphere 2 Tropical Rainforest. This is an ecosystem-wide controlled temperature perturbation experiment coupled with isotope labeling in order to understand the implications of carbon cycling with respect to a changing climate.  

ViroSoil – This project is funded by the Department of Energy in collaboration with The Ohio State University for establishing ecological paradigms for how viruses alter soil microbiomes and nutrient cycles by developing foundational (eco)systems biology approaches.Within this overall project,we established bacterial virus (phage)-host model systems to investigate metabolic reprogramming in virus-infected cells (a.k.a. virocells). Such work is critical for establishing baseline approaches for understanding microcells across ecosystems, including soils, and to translate these findings into biogeochemical data needed to develop predictive computational models of soil microbial functioning and impacts.

Metabolomics software development: This project is Funder the Department of Energy for overcoming systems biology bottlenecks: a pipeline for metabolome data processing analyses and multi-omics integration. The overarching objective of this proposal is to optimize the analysis of complex and heterogeneous biological and environmental datasets by developing a user-friendly, open-source metabolomics data analysis pipeline that is integrable with other multi-omics data sets. Our large-scale multi-omics data integration approach is highly relevant to the DOE System Biology Knowledgebase (KBase) mission of achieving a predictive understanding of the role of compounds in diverse biological and environmental systems, and will allow us to improve biological and metabolic genome-based predictive models by integrating “true” metabolic evidence.

BRIDGES-BRIDGES is an NSF-funded interdisciplinary graduate training program in ecosystem genomics that trains diverse students to communicate (1) across the entire “genes-to-ecosystems” scale, and (2) among the different cultures of science and the people that practice science, to solve real world problems that matter.

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