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Published byJoseph Hubbard Modified over 9 years ago
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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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22º45’, 158º 00’ W Oct 2002 – Dec 2003 Time and location of sampling
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Vertical profiles of physico-chemical parameters at the ALOHA Station 10 70 130 200 500 770 4000
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Genome NameDepth (m)BasesGC (%)GenesEnzymesEnzymes (%)KEGG (%)COG (%)Pfam (%) 1_Upper_euphotic1074825954911252154813.7614.8045.7340.46 6_Upper_euphotic7010828386491606716049.9810.9438.2134.86 2_Base_of_chrolophyll_max1306091158537696103013.3813.7143.8037.53 3_Below_base_of_euphotic20078296145111155131411.7812.0845.4140.10 5_Below_upper_mesopelagic50087645925213784188313.6614.7549.4142.87 7_Oxygen_minimum_layer770118115974816686240714.4315.1950.4144.65 4_Deep_abyss4000110288215416740227313.5813.8550.7044.92 Metagenome Statistics Bidirectional DNA sequencing of fosmid clones (~ 10,000 sequences per depth) ~ 64 Mbp of DNA sequence total Sequencing methodology
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Questions : Differences in the environmental parameters microbial community composition? Dominant populations? Functional variations ? Abundance profile differences?
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Community similarity based on genus count Compare Genome Genome Clustering Genus, Hierarchical Clustering / PCA
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10 m 130 m 770 m 4,000 m Phylogenetic Distribution Compare Genome PhyloDist Metagenomes vs Genomes Gene Count (60+) Virus
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10 m 130 m 770 m 4,000 m Phylogenetic Distribution Compare Genome PhyloDist Metagenomes vs Genomes Gene Count (60+) Cren Eury Nano
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10 m 130 m 770 m 4,000 m CyanoProteoActinoBacteroidetes Phylogenetic Distribution Compare Genome PhyloDist Metagenomes vs Genomes Gene Count (60+) VerrucoPlanctomycFirmic Chloroflex
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Upper (10 m) Chloro Max. (130 m) Abyss (4,000 m) Phylogenetic Distribution Compare Genome PhyloDist Radial Tree Customize (Phyla) / Bar
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Gene of interest Find Genes Gene Search “rhodopsin”
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Gene of interest Find Genes Gene Search “nitrogenase” * ?
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Function Profile Find 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 Profile Find 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 Profile Find Gene Gene Search “Transposase”
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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 Abundance profile differences? Cyanobacteria
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