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The goal of the International Census of Marine Microbes (ICoMM) is to establish an international organizational framework for exploring microbial diversity.

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Presentation on theme: "The goal of the International Census of Marine Microbes (ICoMM) is to establish an international organizational framework for exploring microbial diversity."— Presentation transcript:

1 The goal of the International Census of Marine Microbes (ICoMM) is to establish an international organizational framework for exploring microbial diversity in marine environments. The goal of the International Census of Marine Microbes (ICoMM) is to establish an international organizational framework for exploring microbial diversity in marine environments.

2 PIs: Mitchell L. Sogin Marine Biological Laboratory (MBL) Jan W. de Leeuw 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) International Census of Marine Microbes

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4 International Census of Marine Microbes To assess & explain the diversity, distribution & abundance of marine microbial life To assess & explain the diversity, distribution & abundance of marine microbial life The Known, the Unknown, the Unknowable

5 Number of microbial cells in the oceans is astronomical !!! 100,000,000,000,000,000,000,000,000,000 Microbial Cells in the Oceans

6 SizeBiomassPrimary SecondaryProduction ___________________________________________________ Prokaryotes <3µm82%91% Protists <0.3mm18% 9% Zooplankton < 3 cm 0.3% 93% Swimmers <3m 0.07% 7% Megafauna > 3m 0.01% 0.5% ____________________________________________________ Millions Tons Carbon 145,00050,000 7,400 Relative abundance and productivity of Marine Life

7 N.R. Pace

8 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 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! International Census of Marine Microbes

9 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?

10 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

11 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 amplicons) capture only a fraction of the population structure.

12 Dr. Katrina J. Edwards, (CHAIR) WHOI 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) Eva Ramirez Llorda – Secretariat of ChESS Benthic systems working group meeting: Southampton Oceanography Center January 14 th -15 th 2005

13 Technology working group meeting: Max Planck Institute (MPI) Bremen Jan 31 st - Feb 1 st 2005 Rudolf Amann, (MPI), Bremen (Chair) 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 Mitchell L. Sogin, (MBL), Woods Hole, MA, USA

14 Open ocean and coastal systems working group University of Hawaii May 10 th -11 th 2005 David KarlDavid Karl (Chair) (University of Hawaii) PeterPeter Burkhill (Southampton Oceanography Center) William Li (Bedford Institute of Oceanography) Forest RohwerForest Rohwer (San Diego State University) Daniel VaulotDaniel Vaulot (Roscoff) Bess Ward Bess Ward (Princeton)

15 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

16 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 Recommendations of Open Ocean and Coastal Water Group Sampling issues

17 Biogeochemical provinces: a basis for examining geographic variation Longhurst (1995) Ecological Geography of the Sea. Academic Press

18 The Hawaii Ocean Time-series (HOT) Established in 1988 as part of the U.S. JGOFS program Primary objectives: characterize time- dependent dynamics in carbon, nitrogen, and phosphorus inventories and fluxes.

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20 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. Recommendations of Open Ocean and Coastal Water Group Sampling issues

21 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. The census will require contributions from an international network of microbial oceanographers. Big questions in science demand community-based efforts:

22 Possible technical solutions: 1.DNA sequencing: PCR amlicons, metagenomics Expensive ~$1-2/read, difficult to detect minor members Possible technical solutions: 1.DNA sequencing: PCR amlicons, metagenomics Expensive ~$1-2/read, difficult to detect minor members 2.Lipidomics Species-specific (membrane) lipids carry biosynthetic, evolutionary, (palaeo)-environmental and metabolic information but must be isolated from cultures. Bacteria Archaea Eucarya Ether-bound membrane lipids: the hallmark of the archaea Possible technical solutions: 1.DNA sequencing: PCR amlicons, metagenomics Expensive ~$1-2/read, difficult to detect minor members 2.Lipidomics Species-specific (membrane) lipids carry biosynthetic, evolutionary, (palaeo)-environmental and metabolic information but must be isolated from cultures. 3.DNA arrays Only detect what is spotted or printed on array. Possible technical solutions: 1.DNA sequencing: PCR amlicons, metagenomics Expensive ~$1-2/read, difficult to detect minor members 2.Lipidomics Species-specific (membrane) lipids carry biosynthetic, evolutionary, (palaeo)-environmental and metabolic information but must be isolated from cultures. 3.DNA arrays Only detect what is spotted or printed on array. 4.Proteomics Current technology works in low diversity systems Possible technical solutions: 1.DNA sequencing: PCR amplicons, metagenomics Expensive ~$1-2/read, difficult to detect minor members 2.Lipidomics Species-specific (membrane) lipids carry biosynthetic, evolutionary, (palaeo)-environmental and metabolic information but must be isolated from cultures. 3.DNA arrays Only detect what is spotted or printed on array. 4.Proteomics 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!

23 Challenge of monitoring Bacterial populations 1.Sequencing costs (~$1/read) constrain the size of molecular surveys. Today’s typical microbial surveys (sequences from amplicons) capture only a fraction of the population structure. Difficult to detect under-represented members of microbial communities 2.Communities dominated by a few abundant taxa will mask appearance of rare community members. 3.Therefore surveys of a few hundred rRNA genes cannot fully describe a microbial community. 1.Sequence short hypervariable regions in rRNAs 2.Identify nearest relatives in reference database of Variable region sequences 3.Use full length sequences from reference database match to infer taxonomy 4.Provides estimate of relative number of rRNAs in an environmental DNA sample. TAG sequencing - a potential solution

24 Conserved Variable

25 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. TRANSAT cruise following the flow of the North Atlantic Deep Water (NADW) Gerhard J. Herndl

26 Van Dover et al Global Distribution of Hydrothermal Systems

27 NEPTUNE Axial Seamount


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