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Tough Times in Death Valley Soils: Geochemical Stressors and Diversification of the Bacillus subtilis -B. licheniformis Clade. Sarah Kopac PhD candidate Wesleyan University [email protected] April 2014. Bacteria have evolved to inhabit virtually all terrestrial habitats. - PowerPoint PPT Presentation
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Tough Times in Death Valley Soils: Geochemical Stressors and Diversification of the Bacillus
subtilis-B. licheniformis Clade
Sarah KopacPhD candidate
Wesleyan [email protected]
April 2014
Bacteria have evolved to inhabit virtually all terrestrial
habitats
Wu et al. 2009
Deinococcus radiodurans
Vibrio fischeri
Bacteroides fragilis
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
South-facing
North-facing
Koeppel et al. 2008. PNAS 105:2504.
Ecologically distinct groups exist within species
South-facing
North-facing
Koeppel et al. 2008. PNAS 105:2504.
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.
Death Valley National Park
Soil conductivity, boron and copper levels vary over a
transect
123456789
1011121314151617181920
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. subtilissubclade
B. licheniformissubclade
Ecotypes differ in their associations with iron
1
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
1
11
1
1
1
1
1
1
111
1
1
1
1
…as well as four additional soil dimensions
1
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
1
11
1
1
1
1
1
1
111
1
1
1
1
ParameterP
value
Iron 0.002
Phosphorus 0.0083
NO3-N 0.016
Soil pH 0.032
% clay 0.0897
Copper tolerance also differs across strains
Growth experiments show boron tolerance is ecotype-specific
p=1E-6 Brackets=95% CIEcotype 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 committeeFrederick CohanAnnie BurkeDanny KrizancMichael Singer
Undergraduates (Krizanc)Diego CalderonCarlos FransiscoLing KeAaron PlaveWei Wang
Undergraduates (Cohan)
Alexa BoselSophie BreitbartJon ChabonClaire ConwayShyam DesaiWesley HoMelanie KorenMfundi MakamaJanine PetitoJess SherryNoor TellBrianne WeimannGreg Wong
MA/BAs and PhDs
Stephanie AracenaRob ClarkClaire FournierMenherit GoodwynMichelle TiptonJane Weidenbeck
CollaboratersAlex RooneyHeather KlineJohannes Sikorski
p=0.761171
Ecotypes have similar growth at 0mM boron