The Assembly of Bacterial Genomes from Soil Metagenomes

Daniel Burkhardt

Kristen DeAngelis (Faculty Sponsor)

Department of Microbiology

University of Massachusetts Amherst

How can we use this… …to learn about this?

Actual metagenome reads (a.k.a. DNA from the soil!)

The planet’s climate is warmingIPCC 2013 Summary for Policymakers – Figure 12.5

Soil is a major source of carbonhttp://genomicscience.energy.gov/carboncycle/

Microbes turn carbon into energy and CO2

Organic carbon

Microbes

Carbon dioxide

ATP

“Stuff”Respiration

Carbon dioxide

ATP

“Stuff”

Fermentation

Slight increases in temperature can have drastic effects on enzyme activity

Optimum temperature

Rate of reaction in enzyme catalyzed system

Potential positive feedback loop to warming

We can test the effect of warming on soil through artificial warming experimentsFrom the Harvard Forest in Petersham, MA

Warming elicits a tri-phasic response in soil respiration at the Harvard Forest

Mellilo, unpublished

Change in respiration is accompanied by changes in carbon community

Warming decreases available C

Warming affects microbial abundance

DeAngelis, submitted

Shotgun sequencing

Original genome

Sequence fragments

Scaffolding

http://scienceblogs.com/evolgen/2007/02/07/shotgun-sequencing-a-eukaryoti/

ATCG

ATCG

TAATCG

ATCGTA

Now multiply this by 100,000

The Humpty-Dumpty Problem

The binning process:

Sequence dependent strategiesOne solution:

Try to use species specific sequence biases

G+C % Synonymous codon

choice Amino acid usage Oligonucleotide

frequency (2-8 nt sequences)

Composition dependent methods because they rely on properties of the sequences

Genomic Signature: Characterization and Classification of Species Assessed by Chaos Game Representation of Sequences Patrick J. Deschavanne,* Alain Giron,† Joseph Vilain,† Guillaume Fagot,† and Bernard Fertil†

Heat map of 7 nt-long sequence (e.g. CTAGGCT)

The basis of differential coverage binning

Coverage: 2 Coverage: 5

Sample 1 Sample 2Our goal:

Differential coverage binning

Variation in abundance…

…leads to variation in coverage

Albertsen, M. et al. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotechnol. 31, 533–538

Reassemble from these reads only

What does this… …have to do with this?

So what can we learn from these genomes?

Tie functionality to taxonomy and climate change Better interpret changes in

community Influence climate models

Discover new bacteria! Discover pathways in

bacteria without culturing them first

Understand members of the community which are affected by warming Hypothetical bacterial genome

Thanks to…