Transcript samplings are not sufficient. There was no consensus about optimal

The goal of the International Census of Marine
Microbes (ICoMM) is to establish an international
organizational framework for exploring microbial
diversity in marine environments.
http://icomm.mbl.edu
International Census of Marine Microbes
http://icomm.mbl.edu/
PIs:
Mitchell L. Sogin
Jan W. de Leeuw
Marine Biological Laboratory (MBL)
The Royal Netherlands Institute for
Sea Research (NIOZ)
Secretariat: Linda Amaral-Zettler
Marine Biological Laboratory (MBL)
Organizing Committee:
Gerhard Herndl (NIOZ)
David J. Patterson (MBL)
Stefan Schouten (NIOZ)
Lucas Stal (NIOO)
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http://icomm.mbl.edu
International Census of Marine Microbes
To assess & explain the
diversity, distribution & abundance of
marine microbial life
The Known, the Unknown, the Unknowable
Number of microbial cells in the oceans is astronomical !!!
100,000,000,000,000,000,000,000,000,000
Microbial Cells in the Oceans
Relative abundance and productivity of Marine Life
Size
Biomass
Primary
Secondary
Production Production
___________________________________________________
Prokaryotes <3µm
82%
91%
Protists <0.3mm
18%
9%
Zooplankton < 3 cm
0.3%
93%
Swimmers <3m
0.07%
7%
Megafauna > 3m
0.01%
0.5%
____________________________________________________
Millions Tons Carbon 145,000
50,000
7,400
N.R. Pace
International Census of Marine Microbes
http://icomm.mbl.edu
Goal: To report what is Known,what is Unknown but
knowable, and what may be Unknowable about the
diversity of marine micro-organisms by the year 2010.
ICOMM is an international research coordination network.
Objective: to forge a large-scale strategic plan and to build
a cyberinfrastructure for a census of marine microbes.
ICOMM has limited resources for small pilot-scale studies.
ICOMM is not a funding source for research projects!
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Questions that Drive ICoMM:
How does diversity relate to function and ecosystem
processes?
How does the choice of gene influence diversity assessments
and inference about presence or absence of functional
groups in a complex community?
What scales of heterogeneity – spatial, temporal are most
appropriate for the census?
How can we link diversity at different scales?
What is the optimal measure of microbial diversity?
Scientific Advisory Council
(Chair) John Baross
Technology Working Group
(Chair) Rudi Amann
Informatics and Data Management Working Group
(Chair) Paddy Patterson
Benthic Systems Working Group
(Chair) Katrina Edwards
Open Ocean and Coastal Systems Working Group
(Chair) Dave Karl
After four meetings of four working groups and the SAC
What Have We Learned?
1. Information about community composition and relative numbers
of different kinds of organisms is of key importance to most
microbial oceanography investigations.
2. The metric is molecular; sequences, lipids, possibly proteins.
3. Contextual information is essential for meaningful interpretations.
4. The dynamic nature of the marine environment requires temporal
sampling and therefore greater resource demands.
5. Sampling scales range from sub-millimeter to kilometer.
6. The Census is a big job; even in its most simple form, conventional
technology will be insufficient!
Today’s typical microbial surveys (sequences from 500-1000
amplicons) capture only a fraction of the population structure.
Benthic systems working group meeting:
Southampton Oceanography Center January 14th-15th 2005
Dr. Katrina J. Edwards, (CHAIR) WHOI ([email protected])
Prof. Steven D'Hondt, GSO Univ. of Rhode Island
Prof. David Paterson, Univ St. Andrews
Prof. James Prosser, Univ Aberdeen
Prof. Andreas Teske, Univ N Carolina
Prof. Bo Barker Joergensen, MPI
Prof. Anna-Louise Reysenbach, Portland State Univ
Dr. Mitchell L. Sogin, MBL (ICoMM Organizing committee)
Prof. Paul Tyler, Univ Southampton PI of ChESS
Dr. Stefan Schouten, NIOZ (ICoMM Organizing committee)
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Eva Ramirez Llorda – Secretariat of ChESS
Technology working group meeting:
Max Planck Institute (MPI) Bremen Jan 31st - Feb 1st 2005
Rudolf Amann, (MPI), Bremen (Chair) [email protected]
Guiseppe D’Auria, (UMH), Alicante, Spain
Jan W. de Leeuw, (NIOZ)
Frank Oliver Glöckner, (MPI), Bremen
John Heidelberg, (TIGR), MD, USA
Gerhard Herndl (NIOZ)
Michael Kühl, Marine Biological Laboratory, Helsingor, Denmark
Eric Mathur, Diversa Corporation, San Diego, CA, USA
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Mitchell L. Sogin, (MBL), Woods Hole, MA, USATIFF (Uncompressed)
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Open ocean and coastal systems working group
University of Hawaii May 10th-11th 2005
David Karl (Chair) (University of Hawaii)
Peter Burkhill (Southampton Oceanography Center)
William Li (Bedford Institute of Oceanography)
Forest Rohwer (San Diego State University)
Daniel Vaulot (Roscoff)
Bess Ward (Princeton)
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Recommendations of Open Ocean and Coastal Water Group
1. Microbial population studies must be integrated with
contextual information.
2. A functional census is as important as a taxonomic census.
3. ICoMM should promote use of common protocols / techniques
that can be calibrated across different laboratories.
4. ICoMM must convince database community about importance
of contextual data.
5. Federated data bases preferred over single monster data base.
6. Predictive modeling must be developed.
7. Microbial oceanographers must cross train in microbiology,
molecular biology, biogeochemistry and bioinformatics.
Recommendations of Open Ocean and Coastal Water Group
Sampling issues
1. Scientific questions will dictate the sampling strategy
2. Sampling density will be contingent upon technology
efficiency and available resources.
3. In general, single point (as opposed to temporal) samplings
are not sufficient.
4. There was no consensus about optimal
sampling strategies
Biogeochemical provinces: a basis for examining geographic variation
Longhurst (1995) Ecological Geography of the Sea. Academic Press
The Hawaii Ocean Time-series (HOT)
• Established in
1988 as part of the
U.S. JGOFS
program
• Primary
objectives:
characterize timedependent
dynamics in
carbon, nitrogen,
and phosphorus
inventories and
fluxes.
Recommendations of Open Ocean and Coastal Water Group
Sampling issues
1. Scientific questions will dictate the sampling strategy
2. Sampling density will be contingent upon technology
efficiency and available resources.
3. In general, single point (as opposed to temporal) samplings
are not sufficient.
4. There was no consensus about optimal sampling strategies
5. Sampling strategies should include globally distributed
surveys and intensive studies of localized ecosystems.
6. Nested approach required to sample at different scales.
The census will require contributions from an
international network of microbial oceanographers.
Big questions in science demand
community-based efforts:
Examples include:
Physics: Community development of Accelerators
Astronomy: Instruments and programs from Keck to Hubble
Human Genome: Consortia of public and private laboratories
Microbial Oceanography is even more complex:
It requires massive amounts of data (genetic, physiological,
biogeochemical), major computational capabilities, extensive
modeling and BIOLOGY.
Possible technical solutions:
1.
Ether-bound membrane lipids:
the hallmark
of the
archaea
DNA sequencing:
PCR amplicons,
amlicons,
metagenomics
metagenomics
Expensive ~$1-2/read, difficult to detect minor members
2. Lipidomics
O
HO
O
Species-specific
(membrane) lipids carry biosynthetic, evolutionary,
(palaeo)-environmental and metabolic information but must be isolated
from cultures.
HO
3. DNA arrays
OH
OH
OH
OH
Only detect what is spotted
or printed on array.
Archaea
4. Proteomics
Bacteria
Eucarya
Current technology works in low diversity systems
5. Tag sequencing strategies (akin to barcode of life)
Low levels of phylogenetic information but given adequate reference
data base, has minimal computational overhead and can be very
affordable.
For a census of marine microbes, target genes must be
good evolutionary markers - i.e. adequately conserved to allow
phylogenetic inference!
Challenge of monitoring Bacterial populations
1.
2.
3.
Sequencing costs (~$1/read) constrain the size of molecular surveys.
Today’s typical microbial surveys (sequences from 500-1000
amplicons) capture only a fraction of the population structure.
Difficult to detect under-represented members of microbial communities
Communities dominated by a few abundant taxa will mask appearance of rare
community members.
Therefore surveys of a few hundred rRNA genes cannot fully describe a
microbial community.
TAG sequencing - a potential solution
1.
2.
3.
4.
Sequence short hypervariable regions in rRNAs
Identify nearest relatives in reference database of Variable region sequences
Use full length sequences from reference database match to infer taxonomy
Provides estimate of relative number of rRNAs in an environmental DNA
sample.
Conserved
Variable
TRANSAT cruise following the flow of the North Atlantic Deep Water (NADW)
Gerhard J. Herndl
Map of the TRANSAT cruise tracks. Stations occupied during TRANSAT-1 (6 Sep – 4 Oct
02) are indicated by red dots, TRANSAT-2 (9 May – 6 Jun 03) stations are in yellow.
Global Distribution of Hydrothermal Systems
Van Dover et al. 2002
Axial
Seamount
NEPTUNE