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Microbiological Response to Environmental Changes OMIC sensors of ecological stress

Microbiological Response to Environmental Changes OMIC sensors of ecological stress. Diverse group of microbial ecologists, molecular biologists, biogeochemists , chemists, toxicologists, system biologists, geneticists. OMICS.

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Microbiological Response to Environmental Changes OMIC sensors of ecological stress

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  1. Microbiological Response to Environmental Changes OMIC sensors of ecological stress Diverse group of microbial ecologists, molecular biologists, biogeochemists, chemists, toxicologists, system biologists, geneticists

  2. OMICS • Technologies that look simultaneously at a diverse group of molecules involved in microbial response to the environment • DNA • mRNA, sRNA • Proteins • Metabolites • Primary • Secondary

  3. Can OMIC methods detect ecological stress? • Review OMIC technologies • GENomics • TRANSCRIPTomics • PROTEOmics • METABOLomics • Explore application of OMICS in detection of ecological stress • Strengths and weaknesses • Goals to advance OMIC-based approach to sensing • Discuss relevance of OMICS-based sensing in our own research

  4. A set of basic research strategies that together offer potential for future characterization and bioremediation • Not a monitoring strategy • Lack of mechanistic understanding of normal, “baseline” microbial community state • Expensive • Labor intensive • Quality control • HUGE Data management

  5. Potential applications • Method will generate a large volume of data useful in discovery of: • Global microbial environmental response • Mechanistic biochemical pathways • Baseline physiological characterization • Community composition and dynamics • Microbial ecology Also useful in framing more focused experiments

  6. Path Forward • Establish baseline OMICS parameters for different organisms, different environments • Focus on key metabolic pathways • Improve our basic understanding of the bacterial metabolism (enzyme, pathways, metabolites) • Identify indicator organisms, parameters for environmental stress • Identify actionable stress levels

  7. Path forward • Develop, maintain standard methods to yield reproducible, consistent results • Improve sequencing methods (faster, cheaper, portable) • Develop database, establish important biomarkers for target environmental conditions • Develop data management and analysis tools

  8. Aspects of participant research that could benefit from an OMICS approach • In situ selenate source control in mine waste • Algal bloom monitoring and control • Salmonella-host bacteria interactions • Bioremediation • Biofuel enzyme discovery • See paragraphs and references from each participant in summary document

  9. SO WHAT?? • Example in wastewater treatment - Microbial communities are used in wastewater treatment - Occasionally the system crashes; wastewater treatment fails - Monitoring the health and function of microbial community using OMICS methods may be able to detect and/or prevent a system crash

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