Increased rates of horizontal gene transfer in psychrophile genomes and potential links to the Phanerozoic climate record

Jeff S. Bowman, Eric Collins, Jody W. Deming

bowmanjs@ldeo.columbia.edu

• Why HGT might be elevated in psychrophile genomes • Introduce method for evaluating genomic plasticity in a

population • Application of this method, psychrophiles vs. mesophiles • Potential links between gene acquisition and the

Phanerozoic climate record

Why HGT might be elevated in cold environments

Junge et al. 2001

2

-15 °C

Wells and Deming, 2006

HGT may be elevated by phage-bacteria and bacteria-bacteria contact rates in ice environments

HGT may be elevated by phage-bacteria and bacteria-bacteria contact rates in ice environments

Infection rates and phage diversity may be higher in low temperature environments

3

Anesio and Bellas, 2011

Why HGT might be elevated in cold environments

Method for evaluating genomic plasticity in a population

Quantifying genomic plasticity

Are psychrophiles more genetically plastic than mesophiles?

Bowman et al., 2014, in prep 4

Genomic plasticity = gene loss + HGT + gene duplication

Method for evaluating genomic plasticity in a population

Maximum-likelihood tree of psychrophile and mesophile strains used in this analysis Bowman et al., 2014, in prep

5

Method for evaluating genomic plasticity in a population

Bowman et al., 2014, in prep

divG = abs(16S – CV) 16S: 16S distance CV: amino acid compositional vector distance (Qi et al., 2004) Values transformed • mean = 0 • variance = 1 • range between 0

and 1

6

Method for evaluating genomic plasticity in a population

Bowman et al., 2014, in prep

divG = abs(16S – CV) 16S: 16S distance CV: amino acid compositional vector distance (Qi et al., 2004) Values transformed • mean = 0 • variance = 1 • range between 0

and 1

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Transposase (blue)

Integrase/ Recombinase (green)

Phage specific

Chapter 5 – Horizontal gene transfer (HGT) in psychrophile genomes

Bowman et al., 2014, in prep

divG = abs(16S – CV) 16S: 16S distance CV: amino acid compositional vector distance (Qi et al., 2004) Values transformed • mean = 0 • variance = 1 • range between 0

and 1

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Octadecabacter antarcticus divG = 0.09

Octadecabacter arcticus

divG = 0.25

Results, psychrophiles vs. mesophiles

Blue = psychrophiles, Orange = mesophiles • Distribution of 16S distances nearly identical between the two groups • Distribution of compositional vectors distances, divG, and divG are all

significantly different (p = 2.49 x 10-8, 3.5 x 10-6, 0.01) by the Mann-Whitney or Students T-tests

• Preliminary (limited sample size) evidence for enhanced plasticity in psychrophile genomes

Bowman et al., 2014, in prep 9

Estimating time since acquisition for probable HGT events

During glacial maximum… • Psychrophile range is expanded • More ice environments • More temperate phage?

Veizer et al., 2003

Temperature anomalies during Phanerozoic Eon

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Estimating time since acquisition for probable HGT events

Bowman et al., 2014, in prep

Distribution of HGT event probabilities

• Identify likely HGT events by anomalous GC content

• Estimate time since acquisition with GC amelioration method (Lawrence and Ochman, 1997)

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GC

anom

aly

Psychrophiles

Mesophiles

Estimating time since acquisition for probable HGT events

= period when Earth’s temp was below the current mean

= mass extinction event

= 10 My running mean

Psychrophiles

Mesophiles

Monte-Carlo analysis for psychrophiles

562.74

-757.61

Bowman et al., 2014, in prep 12

Conclusions + acknowledgements

• Developed a new method for evaluating genomic plasticity between populations

• Preliminary evidence for higher genomic plasticity among psychrophiles compared to mesophiles

• For psychrophiles, strong correlation between time since acquisition for putative HT genes and geologic cold periods

This presentation and code for methods linked from: www.ldeo.columbia.edu/~bowmanjs