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The Assembly of Bacterial Genomes from Soil Metagenomes
Daniel Burkhardt
Kristen DeAngelis (Faculty Sponsor)
Department of Microbiology
University of Massachusetts Amherst
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How can we use this… …to learn about this?
Actual metagenome reads (a.k.a. DNA from the soil!)
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The planet’s climate is warmingIPCC 2013 Summary for Policymakers – Figure 12.5
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Soil is a major source of carbonhttp://genomicscience.energy.gov/carboncycle/
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Microbes turn carbon into energy and CO2
Organic carbon
Microbes
Carbon dioxide
ATP
“Stuff”Respiration
Carbon dioxide
ATP
“Stuff”
Fermentation
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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
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We can test the effect of warming on soil through artificial warming experimentsFrom the Harvard Forest in Petersham, MA
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Warming elicits a tri-phasic response in soil respiration at the Harvard Forest
Mellilo, unpublished
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Change in respiration is accompanied by changes in carbon community
Warming decreases available C
Warming affects microbial abundance
DeAngelis, submitted
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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
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The Humpty-Dumpty Problem
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The binning process:
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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)
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The basis of differential coverage binning
Coverage: 2 Coverage: 5
Sample 1 Sample 2Our goal:
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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
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What does this… …have to do with this?
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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
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Thanks to…