ISU ENVSCI690 Graduate Seminar Slides
1 like493 views
The document summarizes a presentation about environmental science research in the Germs Lab. The lab uses genomics and other innovative methods to understand microbial communities and their role in the environment. Key projects examine how land use impacts soil health and microbial diversity across different states. Advanced sequencing technologies have enabled large datasets to be generated at low cost, helping researchers better understand microbial functions in ecosystems.
ISU ENVSCI690 Graduate Seminar Slides
- 1. Adina Howe Agricultural and Biosystems Engineering (slides available from ww.germslab.org) ENVIRONMENTAL SCIENCE RESEARCH IN THE GERMS LAB Genomics and Environmental Research in Microbial Systems
- 2. Who am I? • Mechanical Engineer • Environmental Engineer • Microbiologist • Bioinformatician • Big data-‐er • Teacher • Mentor • Trainer
- 3. What is my research mission? We are changing the environment that we live in. To preserve environmental integrity, we must understand and manage the impacts of global change. Scientific research (and data) must inform our decisions and policy. GERMS uses innovative scientific methods to evaluate and understand our complex and changing world.
- 4. How will GERMS do this? Put simply, our vision is to… Monitor, evaluate, and manage our microbial communities and their services in the environment.
- 5. A DEFINING-‐THE-‐ RELATIONSHIP TALK WITH OUR MICROBIAL NEIGHBORS
- 6. Can we live without them? • Assigned reading (Gilbert and Neufeld, 2014): (many questions on why this was assigned) • Why was this published? • Is it useful? • What are the impacts/consequences of research? • Boundary conditions • What are three biggest challenges to our society, for the world, for our future, for the state of Iowa? • What can understanding microbiology / microbial ecology / environmental do to help? ???
- 7. Super challenges of our shared future
- 8. The role of our microbial partners? neighbors? MICROBES IN ECOSYSTEMS NATURE AIR WATER SOIL MICROBIOMES HUMANS/ANIMAL ENGINEERED BIOREACTORS WASTEWATER
- 9. Understanding community dynamics in the environment • Who is there? • What are they doing? • How are they doing it? Kim Lewis, 2010
- 10. Sequencing the code of life http://www.iflscience.com/chemistry/do-‐try-‐home Who? What? How? Why? (Experimental Design)
- 11. Transforming technology? Stein, Genome Biology, 2010 E. Coli genome 4,500,000 bp ($4.5M, 1992) 1990 1992 1994 1996 1998 2000 2003 2004 2006 2008 2010 2012 Year 0.1 1 10 100 1,000 10,000 100,000 1,000,000 DNA Sequencing, Mbp per $ 10,000,000 100,000,000
- 12. Rapidly decreasing costs with today’s sequencing technologies Stein, Genome Biology, 2010 Next Generation Sequencing 4,500,000 bp (E. Coli, $200, presently) 1990 1992 1994 1996 1998 2000 2003 2004 2006 2008 2010 2012 Year 0.1 1 10 100 1,000 10,000 100,000 1,000,000 DNA Sequencing, Mbp per $ 10,000,000 100,000,000
- 13. Effects of low cost sequencing… First free-‐living bacterium sequenced for billions of dollars and years of analysis Personal genome can be mapped in a few days and hundreds to few thousand dollars
- 14. Postdoc experience with data 2003-‐2008 Cumulative sequencing in PhD = 2000 bp 2008-‐2009 Postdoc Year 1 = 50 Gbp 2009-‐2010 Postdoc Year 2 = 450 Gbp
- 15. Computational reconstruction of genes. Titus Brown
- 16. IN THE NEWS: 80% of Americans polled support WARNING: This product contains deoxyribonucleic acid (DNA). The Surgeon General has determined that DNA is linked to a variety of diseases in both animals and humans. In some configurations, it is a risk factor for cancer and heart disease. Pregnant women are at very high risk of passing on DNA to their children. Washington Post, Jan, 2015
- 17. Super challenges of our shared future
- 18. BACK ON TRACK…
- 19. The shifting experimental continuum Single Isolate Pure Culture Enrichment Mixed Cultures Natural systems
- 20. Something old, something new, something borrowed, something blue SOME GERMS RESEARCH PROJECTS
- 21. SOILS (SOMETHING OLD): HOW DOES LAND USE CHANGE SOIL ECOSYSTEM HEALTH?
- 22. Great Prairie (where is this?)
- 23. Paired Treatments in 3 States
- 24. Diverse genes present in soil affecting health, nutrient availability, and C/N/P cycling 0 100 200 300 400 aminoacidmetabolism carbohydratemetabolism membranetransport signaltransduction translation folding,sortinganddegradation metabolismofcofactorsandvitamins energymetabolism transportandcatabolism lipidmetabolism transcription cellgrowthanddeath replicationandrepair xenobioticsbiodegradationandmetabolism nucleotidemetabolism glycanbiosynthesisandmetabolism metabolismofterpenoidsandpolyketides cellmotility TotalCount KO corn and prairie corn only prairie only Howe et. al, PNAS, 2014 • Incredible soil biodiversity (only able to sample 10% with our significant efforts – largest published) • Many functions shared between corn and prairie (red) • Prairie soils have many more unique functions à How important are these unique functions? à Does biodiversity provide stability? à Can we recover these functions after land conversion?
- 25. GUTS (SOMETHING NEW): HOW DO MICROBES IN OUR BODIES AFFECT OUR HEALTH?
- 26. We are supraorganisms 26
- 27. Gut microbiota interacts with genetics and environment to influence our health 27 Source: Zhao, 2013 Obesity Intestinal inflammation IBD diseases Diet has a greater potential to shape the structure and function of gut than host genetics. Direct influence on health state
- 28. Two baseline diets (with a perturbation) Low-‐fat (LF) baseline diet Milk-‐fat (MF) baseline diet Age (wk) 4 5 6 7 8 9 10 11 12 13 14 Diet Switch Washout (Return to Baseline) Baseline 28 LF / 10% Fat / Complex Carbs MF / 37% Fat / Simple Sugars MF LF MF LF
- 29. Two baseline diets (with a perturbation) Low-‐fat (LF) baseline diet Milk-‐fat (MF) baseline diet Age (wk) 4 5 6 7 8 9 10 11 12 13 14 Diet Switch Washout (Return to Baseline) Baseline 29 LF / 10% Fat / Complex Carbs MF / 37% Fat / Simple Sugars MF LF MF LF Viruses can: • Wipe out specific populations of bacteria • Transfer genes (functions) to bacteria • Expand or destroy “niches” of bacteria
- 30. How do bacteria and viruses respond to diet changes? • Bacteria • Broadly, bacteria will return to baseline conditions even when on an alternate diet (within 24 hours). • Observed under both diets • Viruses • When grown on low fat diet, response was similar to bacteria, return to baseline communities. • Response was diet-‐specific: milk fat diet mice viruses became different and did not have any trends towards return to original (in this experiment)
- 31. WATER (SOMETHING BLUE): CAN WE PROVIDE BETTER TOOLS TO MONITOR WATER QUALITY?
- 32. How do we monitor water quality now?
- 33. How do we monitor water quality now? Data Type Example Cost per sample / Frequency of sampling Precision / Water quality information Challenges Water properties chemical analysis of water quality narrow range of information about services in ecosystem Traditional integrity indicators presence of coliform bacteria detection methods lack specificitity and are often imprecise Phytoplankton community characterization cyanotoxin detection through fractionation of ammonia detection of toxicity may not reveal source Microbial community characterization (16S rRNA) abundance of genes present and assoiated with all cyanobacteria characterization of microbial community structure may not reveal gene function; data volume large for public understanding Proposed MAVeRiC genes (DNA) abundance of genes present associated with specific source of pollution identifying relevant genes of interest to water quality; DNA reveals genes present but not necessarily actively expressed Proposed MAVeRiC genes (RNA) abundance of genes expressed and present associated with specific source pollution identifying relevant genes of interest to water quality
- 34. Scalable, quantitative tools to monitor microbial responses in complex environments Estimating risks from pathogens Biotic integrity of a healthy water system Sources of non point pollution Role of waters in stabilizing climate change Microbial genetic biomarkers can capture…
- 35. !! ! B D 24 Samples (216 targets per sample) Nutrients Toxicity Diversity (Broad and specific) !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! CA Lake%1 Lake%2% … Lake%132 Total%Biodiversity%Indexes % Bacteria(+(Archaeea 10 8 … 2 Bacteria1specific 2 0 10 Archaea1specific Fungal1specific Specific%Biodiversity%Indexes Cyanobacteria1specific 2 8 … 9 Mycrocystis(sp.1specific 8 2 … 9 Cylindrospermopsis(sp.1specific 4 2 … 0 Nutrient%Indexes % Nitrogen(fixation(index 2 4 … 7 Denitrification(index 3 3 … 5 Phosphorus(cycling(index 10 10 … 5 Carbon(cycling(index 5 7 … 4 Cyanobacteria(nitrogen(fixation 4 6 … 8 Phosphate1solubilizing(rhizobacteria 4 2 … 0 Toxicity%Indexes % Microcystis(gene(presence 8 9 … 4 Microcystis(gene(activity 7 9 … 5 B I O D I V E R S I T Y F U N C T I O N Project with John Downing, Chris Filstrup, and Fan Yang
- 36. Color test for Ebola virus à color test for environmental contaminants? http://www.kurzweilai.net/synthetic-‐biology-‐ on-‐ordinary-‐paper-‐a-‐new-‐operating-‐system
- 37. Color test for environmental contaminants? http://www.kurzweilai.net/synthetic-‐biology-‐ on-‐ordinary-‐paper-‐a-‐new-‐operating-‐system
- 38. Three things to take home: 1. Microbes are not simple, and today’s emerging (emerged?) technology is allowing to access their complexity. 2. There is incredible microbial diversity (millions) – and these are systems/resources that we need to monitor, understand, and manage. 3. Environmental science is an inter-‐disciplinary science, microbial data (but not alone) is a huge opportunity to address our questions.
- 39. Thank you! QUESTIONS? • Collaborators: • Kirsten Hofmockel& Fan Yang (ISU, EEOB) • John Downing & Chris Filstrup (ISU, EEOB) • Daina Ringus & Gene Chang (University of Chicago) • Folker Meyer & Sarah Owens (Argonne National Laboratory) • GERMS Lab Jin Choi Ryan Williams Recruiting NOW!