Daniel Petras
University of California-Riverside, CA·Microbiology & Immunology
Microbes constantly transform chemicals in their surroundings, from organic matter in seawater to drugs and pollutants in the human gut. These chemical exchanges help decide how much oxygen an ocean holds and whether gut bacteria can fend off infections.
- Fields
Microbiology & Immunology
Earth & Environmental Science
Chemistry
- Topics
metabolomics
mass spectrometry
machine learning
- Grants
- 2 known grants, through Jun 2030
What they work on
- Identify hypoxia-sensitive microorganisms and oxygenase-dependent metabolic pathways by exposing marine microbial cultures to controlled oxygen levels and measuring gene transcription.
- Identify microbial adaptations that compensate for oxygenase inhibition by low oxygen, such as up-regulation or switching to alternative pathways, extrapolated across marine and non-marine genomes.
- Detect a proposed new class of oxygenase-dependent dissolved organic matter by applying machine learning to LC-MS/MS data, validated with the KEGG pathway database and mapped across environmental datasets.
- Test how oxygen dependence of microbial oxygen use varies with productivity and respiration history, using phytoplankton-bloom mesocosms and field samples from Oregon coastal waters.
- Determine how non-antibiotic xenobiotics and their biotransformation products affect commensal gut bacteria, pathogens and specialized metabolites, using a synthetic microbiome model and functional metabolomics.
- Evolve commensal gut bacteria under xenobiotic stress to test for cross-resistance to antibiotics and changes in resilience against Salmonella enterica and Vibrio cholerae colonization.
More about the research
Both projects share an approach: mass spectrometry-based metabolomics, the large-scale measurement of small molecules, used to link microbial chemistry to how microbial communities behave.
Why it matters
Better rules linking oxygen to organic matter breakdown could improve predictions of ocean deoxygenation, which harms fisheries. They could also improve control of low-oxygen processes such as wastewater treatment and predictions of how drugs and pollutants persist. On the health side, understanding how everyday chemicals weaken the gut microbiome's defenses against Salmonella and cholera could inform future microbiome-based therapies.
Known grants
From NIH and NSF research grants. Labs often have other funding we can't see.
Closest labs
Erin McParland
Oregon State University, OR·Earth & Environmental Science
Quantify about 150 small polar extracellular metabolites in seawater across four regimes that differ in biological productivity and oxygen, using new metabolomics methods.
Winifred Johnson
University of North Carolina Wilmington, NC·Earth & Environmental Science
Identify which marine microbial groups produce which osmolytes under nitrogen stress by pairing osmolyte measurements with transcriptomics in laboratory cultures.
William Harcombe
University of Minnesota, MN·Ecology & Evolution
Test whether mutualism changes the combined effect of antibiotic pairs by running over 3,900 growth experiments comparing Escherichia coli and Salmonella enterica in monoculture versus obligate cross-feeding co-culture.
The school
University of California-Riverside: 21 labs on PI Pages, $232M a year on research, 328 research doctorates a year.
Reach out
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