Marine planktonic communities from Hawaii Ocean Times Series Station (HOT/ALOHA) Mark Anderson (University of Chicago) Ildiko Frank (UCSC) Yvonne Lipsewers (NIOZ, Netherlands) Sara Cuadros Orellana (CEBio, Brazil) Lise Øvreas (University of Bergen) Judy Wan (NASA)
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Marine planktonic communities from Hawaii Ocean Times Series Station (HOT/ALOHA )
Marine planktonic communities from Hawaii Ocean Times Series Station (HOT/ALOHA ) Mark Anderson (University of Chicago) Ildiko Frank (UCSC) Yvonne Lipsewers (NIOZ, Netherlands ) Sara Cuadros Orellana ( CEBio , Brazil) Lise Øvreas (University of Bergen) Judy Wan (NASA). - PowerPoint PPT Presentation
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Marine planktonic communities from Hawaii Ocean Times Series Station (HOT/ALOHA)
Mark Anderson (University of Chicago)Ildiko Frank (UCSC)
• Bidirectional DNA sequencing of fosmid clones (~ 10,000 sequences per depth)• ~ 64 Mbp of DNA sequence total
Sequencing methodology
Questions:
Differences in the environmental parameters microbial community composition?
Dominant populations?
Functional variations ?
Abundance profile differences?
Community similarity based on genus countCompare Genome Genome Clustering Genus, Hierarchical Clustering / PCA
10 m130 m 770 m 4,000 m
Phylogenetic DistributionCompare Genome PhyloDist Metagenomes vs Genomes Gene Count (60+)
Virus
10 m130 m 770 m 4,000 m
Phylogenetic DistributionCompare Genome PhyloDist Metagenomes vs Genomes Gene Count (60+)
Cren Eury Nano
10 m130 m 770 m 4,000 m
Cyano ProteoActino Bacteroidetes
Phylogenetic DistributionCompare Genome PhyloDist Metagenomes vs Genomes Gene Count (60+)
VerrucoPlanctomycFirmicChloroflex
Upper (10 m)Chloro Max. (130 m) Abyss (4,000 m)
Phylogenetic DistributionCompare Genome PhyloDist Radial Tree Customize (Phyla) / Bar
Gene of interestFind Genes Gene Search “rhodopsin”
Gene of interestFind Genes Gene Search “nitrogenase”
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Function ProfileFind Function COG Browser Click "Flagellum structure and biogenesis" Search All Add Selected to Function Cart Compare Genomes Function Profile View Function vs. Genomes Search Name for "type"
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Function ProfileFind Function COG COG Browser “Cell Motility” Search COG Name “Type” Select all / Add to Function Cart Compare genomes Function Profile View Functions vs. Genomes Filter “Flagellar”
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Function ProfileFind Gene Gene Search “Transposase”
Conclusion:
Differences in the environmental parameters microbial community composition? Light (rhodopsin) Nutrients (nitrogenase)
Dominant populations? Proteobacteria
Functional variations? Flagellar proteins – no pattern Transposase – abundant at depth