Microbial Metabolome of an Arid Ecosystem


The purpose of this team is to create a VIP on the Microbial Metabolome of an Arid Ecosystem. Resource availability has the potential to impact soil ecosystem functioning, regulate microbial life, drive microbe-microbe interactions, and control biogeochemical cycling. This effect is extremely evident in arid soil ecosystems, where essential resources, such as water and carbon, are already limited. As climate change progresses, deeper droughts and rewetting will further alter, and possibly transform, these ecosystems with a direct impact on community composition, function and stability. The subject of how below-ground microbial communities acclimate and adapt to rapid environmental change, especially in arid ecosystems, is not well explored. Furthermore, the relative roles of microbial functional diversity in driving the ecological and evolutionary responses of terrestrial ecosystems to current and future environmental change is understudied. It is therefore vital to incorporate knowledge of the microbial “unseen majority” if we were to understand how humans and other life forms on Earth can withstand predicted climate change. Fortunately, the field of metabolomics is ready to radically reform our understanding of how changes in resource availability could influence microbiome functioning but is, arguably, one of the greatest challenges yet in modern discovery. This is because diversity of the soil metabolites (of plant and microbial origin) far exceeds any other complexity on earth. In fact, less than 2 % of spectra in an untargeted metabolomics experiment can be annotated. This means that the vast majority of information collected by metabolomics is “dark matter,” chemical signatures that remain uncharacterized. Thus to assess microbiome responses to changes in resource availability, the unmet need is to also develop and apply new computational solutions for better metabolite annotation and characterization.

The team will work on identifying novel biomarkers (metabolites) related to drought under natural conditions and in response to changing water conditions pre-, during and post- monsoon season across five years. Samples will be collected from Saguaro National Park before, during and after the monsoon season. The data generated under this project will not only help build or improve predictive models of organismal responses to environmental changes but also inform solutions to critical societal challenges, including natural resource management and resilience to environmental change, and will enable future mitigation plans that increase carbon sequestration and decrease the positive atmospheric feedbacks that would accelerate climate change.

Issues Involved or Addressed

  • Team-based research program that bridges the gap between metabolomics and environmental ecosystem processes.
  • Improve predictive models of organismal responses to environmental changes in an arid ecosystem.
  • Learning metabolomics pipelines that are applicable to diverse disciplines (environment, clinical studies, pure cultures).
  • Access to the state-of-the-art tools that will help with career goals.
  • Professional development training to help in the workforce.

Methods and Tech

  • Metabolite extraction.
  • Metabolite clean-up.
  • Metabolite data collection using mass spectrometry.
  • Metabolite data annotation using Python through MetaboDirect and MetaboTandem python pipelines.
  • Data interpretation in the context of metabolism and ecology.

Academic Majors of Interest

  • Environmental Science
  • Ecology & Evolutionary Biology
  • Plant Sciences
  • Natural Resources and the Environment
  • Geosciences

Preferred Interests and Preparation


  • Interest in molecular understanding of ecological processes
  • familiarity with chemistry and biology terms


  • Teamwork skills
  • Attention to detail
  • Enthusiasm and personal drive
  • Initiative
  • Willingness to learn

Team Advisor