Microbial ocean metagenomics : the central dogma meets...
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Transcript of Microbial ocean metagenomics : the central dogma meets...
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