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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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slide1

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)

LiseØvreas (University of Bergen)

Judy Wan (NASA)

slide2

Time and location of sampling

22º45’, 158º 00’ W

Oct 2002 – Dec 2003

slide4

Sequencing methodology

  • BidirectionalDNA sequencing of fosmid clones (~ 10,000 sequences per depth)
  • ~ 64 Mbpof DNA sequence total

Metagenome Statistics

slide5

Questions:

Differences in the environmental parameters  microbial community composition?

Dominant populations?

Functional variations ?

Abundance profile differences?

slide6

Community similarity based on genus count

Compare Genome  Genome Clustering  Genus, Hierarchical Clustering / PCA

slide7

Phylogenetic Distribution

Compare Genome PhyloDistMetagenomesvs Genomes Gene Count (60+)

10 m

130 m

770 m

4,000 m

Virus

slide8

Phylogenetic Distribution

Compare Genome PhyloDistMetagenomesvs Genomes Gene Count (60+)

10 m

130 m

770 m

4,000 m

Cren

Nano

Eury

slide9

Phylogenetic Distribution

Compare Genome PhyloDistMetagenomesvs Genomes Gene Count (60+)

10 m

130 m

770 m

4,000 m

Actino

Bacteroidetes

Cyano

Firmic

Planctomyc

Proteo

Verruco

Chloroflex

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Phylogenetic Distribution

Compare Genome PhyloDist Radial Tree

 Customize (Phyla) / Bar

Upper (10 m)

Chloro Max. (130 m)

Abyss (4,000 m)

slide11

Gene of interest

Find Genes  Gene Search  “rhodopsin”

slide12

Gene of interest

Find Genes  Gene Search  “nitrogenase”

?

*

slide13

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"

*

slide14

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”

*

*

slide15

Function Profile

Find Gene Gene Search “Transposase”

slide16

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