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Transcript
International Census of Marine Microbes
Explore the diversity, relative abundance,
and environmental context of all
microbial life forms in the oceans
Bacteria
Archaea
Eukarya
Viruses
International - Global Coverage
Competitive Tag Sequencing - 869 samples 660 completed
~13.5 million tag sequences
Final Data set will exceed 18 million tag sequences
Microbial Population Structure of the World’s Ocean
Arctic Chukchi Beaufort
Amazon-Guianas Water
Lau Hydrothermal Vent
Anaerobic Protist Project
Amundsen Sea Antarctica
Azorean Shallow Vents
Azores Waters Project
Blanes Microbial Observatory
Baltic Sea Proper
Black Sea Redox
Census Antarctic Marine
Cariaco Basin
Caribbean Coral Bacteria
Deep Subseafloor Sediment
Coastal Microbial Mats
Coastal New England
Coral Reef Sediment
Deep Arctic Ocean
Deep Ocean Flux
Deep Sea Eukarya
Frisian Island Sylt
Guaymas Methane Seeps
Gulf of Aqaba
Global Protist Survey
Hood Canal Washington
Hawaii Ocean Time-Series
IOMM Cooperative Run
Gulf of Maine
LaCAR Cooperative Run
Lost City
Mount Hope Bay
Helgoland
New Zealand Sediment
Ocean Drilling Project
English Channel
Surreptitious Algal Bacteria
Station M Sediments
Sponges
Spatial Scaling Diversity
Humboldt Marine Ecosystem
Black Sea
Phenotypic Diversity
Named species:
Bacteria and Archaea: 9,000
Protists: 200,000
Microbial creatures of untold diversity
dominate every corner of our biosphere.
Estimates of 10 - 100 X diversity of animals.
The number of different kinds of bacteria in
the oceans could eclipse 5 to 10 million
Deep Sequencing
Total Unique V6 Tag Sequences
Total OTUs at 3% Difference
Chao1 Estimator of Richness at 3% Difference
ACE Estimator of Richness at 3% Difference
Bacteria
Archaea
30,108
18,537
5,979
1,931
36,869
37,038
2,754
2,678
Huber et al. 2007 Science
Evenness
FS312 Axial Sea Mount - Mkr 52 Difuse Flow
FS312 Axial Sea Mount - Bag City Difuse Flow
112R 550 M -25.000°E, 50.400°N
115R 4,121 M -25.000°E, 50.400°N
Acidobacteria
Soil-Kellogg-5 species
Soil-Kellogg-no plants
Marine vs. Soil
Evenness
Actinobacteria
Firmicutes
Deferrebacteres
Cyanobacteria
Chloroflexi
Bacteroidetes
Gemmatimonadetes
Lentisphaerae
Nitrospira
Planctomycetes
Proteobacteria
Verrucomicrobiae
Abundance
How many microbes can you find in a few
drops of seawater?
~ 1,000,000 Bacteria
~ 1,000,000 Archaea
~10-10,000 Protists
~10,000,000 Viruses
10,000,000,000,000,000,000,000,000,000
Microbial Cells in the Ocean
Visualization
http://vamps.mbl.edu
Detection of Anthropogenic Impacts
Human
fecal
profile
Lake Water
Bacteroidetes
Firmicutes
Combined Sewage overflow
Detection of Anthropogenic Impacts
Human
fecal
profile
1001
1101
1201
Firmicutes
1301
1401
1501
1601
1701
1801
1901
2001
Lake Water
Combined Sewage overflow
2101
Concept of the Rare Biosphere
• Low abundance taxa in rank-ordered, taxon abundance curves
• Microbial abundance curves are “long-tail distributions”
Taxon-rank distribution curve
High Abundance for microbial communities
Populations
Low Abundance
Populations
The Rare Biosphere
•
•
•
The tail is much greater than previously known
Diversity eclipses all prior estimates of
•Bacterial, Archaeal and Eukaryl diversity
Never-before-seen populations
Explaining the Rare Biosphere
• Biogeography
• Dispersal from yet to be discovered endemic
sites
Global Distribution of Abundant Tags
Explaining the Rare Biosphere
•
•
•
•
•
Biogeography
Dispersal from yet to be discovered endemic sites
Keystone species
Always rare - possibly slow growing or dormant
Persistently rare but capable of becoming
abundant
“Seed” organisms
Genomic novelty
• Analogous to heterozygosity in animals or plants
• Products of historical ecological change?
• Responders to environmental shifts
May serve as sentinel for global change
Limits to Knowledge
Operational issues for the Rare Biosphere:
•Definition of microbial diversity - key data •Start and length of the long tail
•Existence of viral, archaeal and eukaryl Rare Biosphere
•Tools necessary to define limits of the rare biosphere
•Criteria for targeting studies of rare biosphere members
Questions about the Rare Biosphere and how can we seek answers?
•Is the Rare Biosphere globally distributed?
or does the Rare biosphere reflect dispersal from endemic sites?
•Does membership in the Rare Biosphere shift across different spatial/temporal scales?
•What mechanisms determine membership in the Rare Biosphere?
•Why is there a rare biosphere?
•Do microbes in the rare biosphere compete for niche space?
•Is the rare biosphere a nearly unlimited source of genetic information that can
transfer between microbial populations?
•How important are reservoirs in protecting microbial diversity?
•Do rare organisms have a selective advantage?
•Are there specific mechanisms that allow low-abundance populations
to become dominant in response to environmental shifts?
•How does the rare biosphere shape the environment past, present and future?
•How might rare organisms impact human health and well being?
•Can the rare biosphere serve as a sentinel for global change?
•Do rare microbes play a key role in preserving biodiversity?
Acknowledgements
ICoMM Scientific Organizing
Committee:
Mitchell Sogin
Jan de Leeuw
David Patterson
Lucas Stal
Gerhard Herndl
Stefan Schouten
ICoMM Secretariat:
Linda Amaral-Zettler
ICoMM IT Specialist:
Phillip Neal
Anne Thessen
ICoMM Scientific Advisory Council:
John Baross (Chair)
Robert Andersen
Felipe Artigas
Antje Boetius
D. Chandramohan
Kazuhiro Kogure
Carlos Pedros-Alio
Francisco Rodriguez-Valera
ICoMM 454 participants:
Paula Aguiar
David Kirchman
Robert Andersen
Connie Lovejoy
Felipe Artigas
Els Maas
Stefan Bertilsson
Ana Martins
Christina Bienhold
Alison Murray
Henk Bolhuis
Jan Pawlowski
William Brazelton
Martin Polz
David Caron
Thomas Pommier
D. Chandramohan
Anton Post
Andrei Chistoserdov James Prosser
Marco Coolen
Alban Ramette
Mark Dennett
Michael Rappe
Steve D’Hondt
Anna-Louise
Slava Epstein
Reysenbach
Katrina Edwards
Gabrielle Rocap
Rima Franklin
Juliette Rooney-Varga
Eric Gaidos
James Staley
Victor Ariel Gallardo Thorsten Stoeck
Gunnar Gerdts
Shinichi Sunagawa
Jack Gilbert
Andreas Teske
Koji Hamasaki
Michael Wagner
Julie Huber
Gordon Webster
David Karl
Patricia Yager