Slides for my guest lecture in a graduate seminar class.

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!