Isolation of bacterial genomes from soil metagenomes
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Presentation at the 20th Annual Massachusetts State-wide Undergraduate Research Conference on April 26th, 2014.
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Isolation of bacterial genomes from soil metagenomes
- 1. The Assembly of Bacterial Genomes from Soil Metagenomes Daniel Burkhardt Kristen DeAngelis (Faculty Sponsor) Department of Microbiology University of Massachusetts Amherst
- 2. How can we use this… …to learn about this? Actual metagenome reads (a.k.a. DNA from the soil!)
- 3. The planet’s climate is warming IPCC 2013 Summary for Policymakers – Figure 12.5
- 4. Soil is a major source of carbon http://genomicscience.energy.gov/carboncycle/
- 5. Microbes turn carbon into energy and CO2 Organic carbon Microbes Carbon dioxide ATP “Stuff”Respiration Carbon dioxide ATP “Stuff” Fermentation
- 6. 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
- 7. We can test the effect of warming on soil through artificial warming experiments From the Harvard Forest in Petersham, MA
- 8. Warming elicits a tri-phasic response in soil respiration at the Harvard Forest Mellilo, unpublished
- 9. Change in respiration is accompanied by changes in carbon community Warming decreases available C Warming affects microbial abundance DeAngelis, submitted
- 10. 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
- 13. Sequence dependent strategies One 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)
- 14. The basis of differential coverage binning Coverage: 2 Coverage: 5 Sample 1 Sample 2Our goal:
- 15. 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
- 16. What does this… …have to do with this?
- 17. 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
- 18. Thanks to…
Editor's Notes
- Often think about carbonin the context of light bulbs, cars, but overlook what’s going on underneath our feet