Microbial ocean Microbial ocean metagenomics metagenomics ::the central dogma meets systems ecology.the central dogma meets systems ecology.

Ed Ed DeLong DeLong - October 4, 2006 - San Diego- October 4, 2006 - San Diego

CULTIVATIONCULTIVATIONINDEPENDENT INDEPENDENT SURVEYSSURVEYS

A la Pace et al., 1986A la Pace et al., 1986

Stahl et al.ASM news

1986 ISME-4 in LjubljanaPerspectives in Microbial Ecology

(Stahl, Olsen, Lane, et al.)

GENOMIC ANALYSESUNCHARACTERIZEDNATIVE TAXA

Microbial Community Genomics & EcologyMicrobial Community Genomics & Ecology

•• Archaeal metagenomics Archaeal metagenomics

•• Comparative community genomics Comparative community genomics

•• Proteorhodopsin Proteorhodopsin ecologyecology

•• Philosophical underpinnings Philosophical underpinnings

XX

X

X

X

X

X (oxygen min)

X

X

Oceanic BAC libraries

X

X

X

X

X (oxygen min)

MB BAC libraries

1

SAR86 130 kbp BAC

1

Fast photcycle kinetics

Expression of proteorhodopsin in E. coli

ON

OFF

5 min

OFF

ON

Retinal Proteorhodopsin

+-+

+

-+ -

-

pH 0.02

LIGHT-DRIVEN PROTON PUMPING IN E. COLI(via “ SAR86” PROTEORHODOPSIN)

Oded Beja

Béjà et al. Science 289: 1902-1906 (2000)

Depth-specific differences in proteorhodopsin variants

Béjà et al. Nature 411:786-789 (2001)

Venter et al., Environmental Genome ShotgunSequencing of the Sargasso Sea,

Science 394:66-74 (2004)

PLANKTONIC ARCHAEA

Number genome fragments with target gene(s) (per 332 Mbp screened)

500

10

70

130

200

0 10 20 30 40

2824

1620

3824

312

170

Euryarchaeal 16S rRNAEuryarchaeal-type PRLinked Euryarchaeal 16S & PR

Archaeal PR gene distributions track the light gradient

NUF Frigaard

Microbial Community Genomics & EcologyMicrobial Community Genomics & Ecology

•• Comparative community genomics Comparative community genomics

•• Proteorhodopsin Proteorhodopsin ecologyecology

•• Background/Philosophical underpinnings Background/Philosophical underpinnings

•• Crenarchaeal metagenomicsCrenarchaeal metagenomics

PLANKTONIC MARINE ARCHAEAPLANKTONIC MARINE ARCHAEA

Crenarchaea Crenarchaea fix COfix CO22 - what is the - what is the reductant reductant ??

Venter et al, Science 304: 66 (2004)Venter et al, Science 304: 66 (2004)SchleperSchleper, Nat Rev Micro 3: 479 (2005), Nat Rev Micro 3: 479 (2005)Konneke Konneke et al., Nature 437: 543 (2005)et al., Nature 437: 543 (2005)TrueschTruesch, , Schleper Schleper et al., EM 7:1985 (2005)et al., EM 7:1985 (2005)Francis et al., PNAS 102:14683Francis et al., PNAS 102:14683 ( (2005)2005)Hallam Hallam et al.,et al., PLoS PLoS 4: e95 (2006)4: e95 (2006)Wuchter Wuchter et al., PNAS 103:12317 (2006)et al., PNAS 103:12317 (2006)LeiningerLeininger,, Schleper Schleper,et al. Nature 442: 806 (2006),et al. Nature 442: 806 (2006)

Reports of Reports of crenarchaealcrenarchaeal-associated -associated amoAamoA-like gene fragments-like gene fragments

ARCHAEAL NITRIFICATION ????ARCHAEAL NITRIFICATION ????

Cenarchaeum symbiosum

TCA

Hydroxypropionate cycle components in C. symbiosumHallam et al., PLoS Biol. 4: e95. 2006

Marine archaeal autotrophy

Gene name Locus cenFOS

urea transporter dur3 +

urease

α ureC +

β ureB +

γ ureA +

E ureE +

F ureF +

G ureG +

H ureH +

ammonia monooxygenase

A amoA +

B amoB +

C amoC +

hydroxylamine oxidoreductase hao -

nitrate reductase nar -

nitrite reductase nirK +

ferredoxin-nitrite reductase nirA +

Hallam et al., PLoS Biol. 4: e95. 2006

amo

hao

nir

nor

Marine archaeal NH4 oxidation

Microbial Community Genomics & EcologyMicrobial Community Genomics & Ecology

•• Comparative community genomics Comparative community genomics

•• Proteorhodopsin Proteorhodopsin ecology/physiologyecology/physiology

•• Background/Philosophical underpinnings Background/Philosophical underpinnings

•• Crenarchaeal metagenomicsCrenarchaeal metagenomics

GENOMIC PROFILES IN THE PACIFIC OCEAN NSF Press Release 06-016

Sequencing Our Seas

http://www.nsf.gov/news/news_summ.jsp?cntn_id=105769

GenomeLibraries

10 m

70 m

200 m

130 m

500 m

770 m

4000 m

PHOTIC ZONE UNIQUE SEQUENCES

DEEP WATER UNIQUE SEQUENCES

PZ

DW

Variation in COG category representation vs. depth

1) Prochlorococcus phylotypes evident2) Viral recovery maxima - 70 m3) Viral recovery decrease below PZ

THE FUTURE ???

• Explore• Experiment• Educate

Director David Karl, University of Hawaii Manoa

http://cmore.soest.hawaii.edu

C-MORE Int. HQ – Univ. Hawaii

Honolulu, Hawaii, USA

Director David Karl, University of Hawaii Manoa

C-MORE GOALS:TO UNDERSTAND

• Mechanisms that drive and sustain diversity &function in oceanic microbes (systems biology)

• Mechanisms that link organisms together inrobust networks (ecosystems biology)

THE GRAND CHALLENGE

• Establish the “parts list” or blueprint: genomicsand phylogenetic, isolate diversity

• Decode the assembly manual: gene regulation,physiology and metabolism

• Integrate across disciplines: ecogenomics,ecophysiology and systems ecology

C-MORE RESEARCH

GenomeLibraries

C-MORE CONNECTIVITYUniversity of Hawaii = Lead Institution

MBARI • WHOI • OSU • UCSC • MIT

FORMAL EDUCATION & TRAINING

curriculum, teacher training, mentoring, outreach

If interested,join us next summer

for our annualAgouron Institute-sponsored summer

training course

C-MORE“Summer at Sea”

DeLong LabDeLong Lab•• Jen Jen BraffBraff•• Kostas Konstantinidis Kostas Konstantinidis•• Jay Jay McCarrenMcCarren•• Chon MartinezChon Martinez•• Tracy Tracy MincerMincer•• Tsultrim Palden Tsultrim Palden•• Vihn Vihn PhamPham•• Virginia Rich Virginia Rich•• Dennis Ryan Dennis Ryan•• Yanmei Yanmei ShiShi•• Xin Xin He (He (uropurop))

PAST LAB MEMBERSPAST LAB MEMBERS• Oded Beja• Niels-Ulrik Frigaard• Steve Hallam• Ramon Massana• Alison Murray• Vicki Orphan• Christina Preston• Christa Schleper• Grieg Steward• Marcelino Suzuki• Jose de la Torre

CollaboratorsCollaboratorsMIT - Penny Chisholm, M. Sullivan, M. Coleman, J. MIT - Penny Chisholm, M. Sullivan, M. Coleman, J. FriasFriasU. Hawaii - Dave Karl, Matt ChurchU. Hawaii - Dave Karl, Matt ChurchPenn State, Stephan SchusterPenn State, Stephan SchusterThe C-MORE TeamThe C-MORE Team