Sarah Kopac
PhD candidate
Wesleyan University
SKopac@wesleyan.edu
April 2014
Bacteria have evolved to inhabit
virtually all terrestrial habitats
Vibrio fischeri
Deinococcus radiodurans
Bacteroides fragilis
Wu et al. 2009
What characteristics of the environment
cause bacteria to speciate?
• What environmental factors cause speciation?
• Are some environmental dimensions more difficult to adapt
to than others?
• Can we predict which parts
of the environment are
evolutionarily relevant
to bacteria that colonize
Spacecraft and/or
extra-terrestrial bodies?
Ecologically distinct groups exist within
species
North-facing
South-facing
Koeppel et al. 2008. PNAS 105:2504.
Ecologically distinct groups exist within
species
Ecotype Simulation analysis of three
protein-coding genes in Bacillus simplex.
Note: All strains are identical for 16S
rRNA!
= one recognized species
Ecotype Simulation:
Rejects a priori criteria.
Identifies species clusters based on
analysis of population dynamics.
North-facing
South-facing
Koeppel et al. 2008. PNAS 105:2504.
Death Valley National Park
Soil conductivity, boron and copper
levels vary over a transect
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4 transects x 20+ levels x 3 replicates
Soil parameters
• pH
•
• Electrical conductivity •
(salinity)
•
• Lime estimate
•
• % organic matter
•
• Nitrate:N
•
• Phosphorus
• Potassium
Zinc
Iron
Manganese
Copper
Boron
Texture
(sand/clay/silt)
588 strains were isolated from the soil
• Screened for Bacillus subtilis-licheniformis
• gyrA gene sequenced from each
Roughly thirty putative ecotypes have
been demarcated from 588 strains
B. subtilis
subclade
B. licheniformis
subclade
Ecotypes differ in their associations with iron
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0%
20%
40%
60%
80%
100%
…as well as four additional soil dimensions
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Parameter
P value
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Iron
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0.002
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Phosphorus
0.0083
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NO3-N
0.016
Soil pH
0.032
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% clay
0.0897
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0%
20%
40%
60%
80%
100%
Copper tolerance also differs across
strains
Growth experiments show boron
tolerance is ecotype-specific
Ecotype A
Ecotype B
Ecotype C
In summary…
• Closely related ecotypes differ in their ecologies
– Associations with iron, phosphorous, NO3-N, pH, %
clay
• Strains and/or ecotypes differ in their tolerance
for boron and copper
• Adaptations to other parameters (salinity, lime,
organic matter, potassium, zinc, manganese)
might be more ancient, and therefore more
difficult
Further questions
• Is there a genetic basis to differences in
growth tolerance?
• Which combinations of environmental
dimensions are most commonly associated
with speciation?
• Are resource-based pressures also influencing
speciation in this system?
Thesis committee
Frederick Cohan
Annie Burke
Danny Krizanc
Michael Singer
Undergraduates (Krizanc)
Diego Calderon
Carlos Fransisco
Ling Ke
Aaron Plave
Wei Wang
Undergraduates (Cohan)
Alexa Bosel
Sophie Breitbart
Jon Chabon
Claire Conway
ShyamDesai
Wesley Ho
Melanie Koren
MfundiMakama
Janine Petito
Jess Sherry
Noor Tell
Brianne Weimann
Greg Wong
MA/BAs and PhDs
Stephanie Aracena
Rob Clark
Claire Fournier
MenheritGoodwyn
Michelle Tipton
Jane Weidenbeck
Collaboraters
Alex Rooney
Heather Kline
Johannes Sikorski
Ecotypes have similar growth at
0mM boron