isu envsci690 graduate seminar slides
TRANSCRIPT
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
Who am I?
• Mechanical Engineer • Environmental Engineer • Microbiologist • Bioinformatician
• Big data-‐er • Teacher • Mentor • Trainer
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.
How will GERMS do this?
Put simply, our vision is to…
Monitor, evaluate, and manage our microbial communities and their services in the environment.
A DEFINING-‐THE-‐ RELATIONSHIP TALK WITH OUR MICROBIAL NEIGHBORS
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?
???
Super challenges of our shared future
The role of our microbial partners? neighbors?
MICROBES IN
ECOSYSTEMS
NATURE AIR
WATER SOIL
MICROBIOMES HUMANS/ANIMAL
ENGINEERED BIOREACTORS WASTEWATER
Understanding community dynamics in the environment
• Who is there? • What are they doing? • How are they doing it?
Kim Lewis, 2010
Sequencing the code of life
http://www.iflscience.com/chemistry/do-‐try-‐home
Who? What? How? Why? (Experimental Design)
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
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10
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1,000
10,000
100,000
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DNA Sequencing, M
bp per $
10,000,000
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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, M
bp per $
10,000,000
100,000,000
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
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
Computational reconstruction of genes.
Titus Brown
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
Super challenges of our shared future
BACK ON TRACK…
The shifting experimental continuum
Single Isolate Pure Culture
Enrichment Mixed Cultures
Natural systems
Something old, something new, something borrowed, something blue
SOME GERMS RESEARCH PROJECTS
SOILS (SOMETHING OLD): HOW DOES LAND USE CHANGE SOIL ECOSYSTEM HEALTH?
Great Prairie (where is this?)
Paired Treatments in 3 States
Diverse genes present in soil affecting health, nutrient availability, and C/N/P cycling
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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?
GUTS (SOMETHING NEW): HOW DO MICROBES IN OUR BODIES AFFECT OUR HEALTH?
We are supraorganisms
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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
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
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LF / 10% Fat / Complex Carbs
MF / 37% Fat / Simple Sugars
MF
LF MF
LF
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
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)
WATER (SOMETHING BLUE): CAN WE PROVIDE BETTER TOOLS TO MONITOR WATER QUALITY?
How do we monitor water quality now?
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
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…
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24 Samples (216 targets per sample)
Nutrients ToxicityDiversity (Broad and specific)
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CA
Lake%1 Lake%2% … Lake%132Total%Biodiversity%Indexes %Bacteria(+(Archaeea 10 8 … 2Bacteria1specific 2 0 10Archaea1specificFungal1specificSpecific%Biodiversity%IndexesCyanobacteria1specific 2 8 … 9Mycrocystis(sp.1specific 8 2 … 9Cylindrospermopsis(sp.1specific 4 2 … 0Nutrient%Indexes %Nitrogen(fixation(index 2 4 … 7Denitrification(index 3 3 … 5Phosphorus(cycling(index 10 10 … 5Carbon(cycling(index 5 7 … 4Cyanobacteria(nitrogen(fixation 4 6 … 8Phosphate1solubilizing(rhizobacteria 4 2 … 0Toxicity%Indexes %Microcystis(gene(presence 8 9 … 4Microcystis(gene(activity 7 9 … 5
BIODIVERSITY
FUNCTION
Project with John Downing, Chris Filstrup, and Fan Yang
Color test for Ebola virus à color test for environmental contaminants?
http://www.kurzweilai.net/synthetic-‐biology-‐on-‐ordinary-‐paper-‐a-‐new-‐operating-‐system
Color test for environmental contaminants?
http://www.kurzweilai.net/synthetic-‐biology-‐on-‐ordinary-‐paper-‐a-‐new-‐operating-‐system
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.
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!