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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 SKopac@wesleyan.edu April 2014. Bacteria have evolved to inhabit virtually all terrestrial habitats.

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Tough Times in Death Valley Soils: Geochemical Stressors and Diversification of the Bacillus subtilis-B. licheniformisClade

Sarah Kopac

PhD candidate

Wesleyan University

SKopac@wesleyan.edu

April 2014

bacteria have evolved to inhabit virtually all terrestrial habitats
Bacteria have evolved to inhabit virtually all terrestrial habitats

Vibrio fischeri

Deinococcusradiodurans

Bacteroidesfragilis

Wu et al. 2009

what characteristics of the environment cause bacteria to speciate
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
Ecologically distinct groups exist within species

North-facing

South-facing

Koeppel et al. 2008. PNAS 105:2504.

ecologically distinct groups exist within species1
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.

soil conductivity boron and copper levels vary over a transect
Soil conductivity, boron and copper levels vary over a transect

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4 transects x 20+ levels x 3 replicates

soil parameters
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
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
Roughly thirtyputative ecotypes have been demarcated from 588 strains

B. subtilis

subclade

B. licheniformis

subclade

growth experiments show boron tolerance is ecotype specific
Growth experiments show boron tolerance is ecotype-specific

Ecotype A

Ecotype B

Ecotype C

p=1E-6Brackets=95% CI

in summary
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
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?
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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

Shyam Desai

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