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Molecular Biology of Biogeochemistry Scoping Workshop

On This Page

  • Overview
  • Agenda
  • Participant List
  • Related Resources
  • Workshop Report

Overview

November 8-10, 2010

The Molecular Biology of Biogeochemistry:  Using molecular methods to link ocean chemistry with biological activity.

A Scoping Workshop supported by the Ocean Carbon and Biogeochemistry (OCB) Program

Conveners:  Jim Moffett and Eric Webb
University of Southern California

Planning Committee: Bob Anderson (Columbia), Ginger Armbrust (UW), Kevin Arrigo (Stanford), Bess Ward (Princeton), Keith Moore (UCI), Ben van Mooy (WHOI)

_____________________

Application of molecular biology to biogeochemistry is based on a central premise: Organisms respond to changes in their chemical and physical environment in highly specific ways based on their individual genomes.  This response can be assessed by examining the genomes of natural assemblages of microbes, and the response itself can be examined by looking at the transcriptome (reflecting up-regulation of key genes) particularly of the several hundred marine microbes for which we now have complete gene sequences.  Ultimately transcription leads to the synthesis of proteins that, among other things, enables organisms to adapt to changing conditions or to optimize their physiology and catalyze key processes in all biogeochemical cycles.  These specific proteins can also now be studied in natural samples in the rapidly expanding field of proteomics.  Integration of these techniques with detailed biogeochemical sampling can lead to resolution of longstanding questions as well as defining new principles for ocean biogeochemistry.

This workshop will convene molecular biologists and biogeochemists to determine what genomic and proteomic tools can be applied to important problems in the carbon, nitrogen and phosphorus cycles of the ocean through an understanding of how microbes and primary producers interact with their physical and chemical environment.  The workshop is timely because of the current emphasis on large-scale observational programs such as CLIVAR and GEOTRACES as well as observatory programs using moorings and new technologies like gliders.  These programs address important problems in biogeochemistry, but many, particularly the global ones, rely primarily on chemical measurements.  With a few notable exceptions (like the Video Plankton Recorder, VPR), biological measurements are difficult to integrate into the rigorous intensive sampling demands of large sectional surveys. Molecular biological information combined with core parameters measured on GEOTRACES sections would significantly enhance the value of the entire database to OCB objectives.

Meeting Objectives  

To develop recommendations for specific molecular biological measurements carried out within large-scale global surveys that address the OCB themes of  (1) Feedbacks and climate sensitivities of biogeochemical cycles; and (2) interactions with ecosystem structure, ocean carbon production, uptake, and storage.

Key Questions

  1. What are the key parameters we would like to measure, particularly on large sectional survey cruises?
  2. How many of these parameters can we characterize in a robust, quantifiable, way, now, or in the near future?  What is reasonable based on cost?
  3. Many of these data are operationally defined.  What does that mean for these tools, and how much “operational definition” is acceptable?
  4. Given the finite number of organisms with complete genomes, how useful is the concept of autoecology (as with Prochlorococcus) for answering important questions in biogeochemistry?
  5. Is proteomics on mixed assemblages of natural organisms likely to be tractable in the foreseeable future?
  6. From the answers to the previous questions, can we develop a prioritization for what should be measured within the framework of large global surveys?
  7. How important are large, dedicated cruises, perhaps incorporating process studies, to validating molecular tools?   What are some examples?

The highest priority of the workshop is to identify tools  - genomic, transcriptomic or proteomic – that are immediately available for cruise implementation, but also those that might be available in the very near (< 5y) future. The workshop will begin with several keynote speakers covering state of the art molecular approaches and will discuss questions 1 and 2 in plenary. Next, the main group will break into working teams to continue questions 1 and 2 organized by biogeochemical focus (e.g., primary production, oxygen minimum zone, N2 fixation). Groups will reconvene in plenary to report their findings. Breakout groups will be organized at that point in terms of methodology and approach (e.g., a “Proteomics” breakout group & an “Autoecology” breakout group). We will reconvene in plenary to discuss findings, as they relate questions 6 and 7. A synthesis of the workshop presentations and discussion will be prepared by the organizers, submitted as a workshop report, which will form the basis for future field and research programs supported under the auspices of OCB.

Registration is now closed.

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Agenda

Agenda
Molecular Biology of Biogeochemistry Workshop
Wilshire Grand Hotel, Los Angeles, CA
November 8-10, 2010

Monday, November 8
730
Breakfast
845 Introduction - Jim Moffett
915 Mak Saito - CoFeMug an integrated Biogeochemical Section
945 Bob Morris  - CoFEMug proteomics
1015 Break
1030 Adam Martiny - Relating genotypic diversity to specific chemical and physical parameters
1100 Eric Webb - Functional genomics:  Controls on Trichodesmium N fixation
1130 Jed Fuhrman - Whole microbial community structure, from viruses to protists, and their interactions
1200 Lunch
1300 Ginger Armbrust - Functional Genomics II Probing controls on C fixation by eukaryotes
1330 Bethany Jenkins - Eukaryotes and Fe
1400 Karla Heidelberg -  Eukaryote genomics and metagenomics
1430 Bess Ward - Molecular and geochemical tools combined to study the N cycle in OMZs
1500 Break
1545 Steve Giovanonni – Sar11 genomics and proteomics  - focus on the processes and genes
1615 Dave Hutchins - Role of molecular biology in assessing the effects of climate change on marine ecosystems
1645 Plenary Discussion Breakout Section for Tues AM. Discussion Leader: Jim Moffett
Breakout Theme I: Identifying and prioritizing what properties of microbial assemblages we need to characterize to compliment chemical measurements within the framework of a sectional survey program.   

  1. Nutrient/micronutrient limitation of large phytoplankton that are important in C export (Arrigo, Armbrust)
  2. Physical and chemical controls on the N cycle, including chemoautotrophy (Ward, Ingalls)
  3. Evolution of functional groups across physical and chemical gradients (Martiny, Webb)
  4. Physical and chemical determinants of overall change in microbial community structure (Fuhrman, Giovanonni).
1800 Meeting Adjourns
Tuesday, November 9
0730 Breakfast
0830 Breakout Groups Meet
1000 Break
1030 Plenary session Reports from Prioritization of Parameters Groups
1100 Plenary Discussion  Assembling an array of parameters to measure on a section  Discussion Leader:  Bob Anderson
1200 Lunch
1300 Plenary Session Organize Breakout Groups
Discussion Leader: Eric Webb
Theme II  Critical Evaluation of Tools

  1. Metagenomics (Heidelberg)
  2. Gene expression (Webb, Allen)
  3. Proteomics (Saito, Morris)
  4. Phylogenetics (Fuhrman)
1330 Breakout Groups Meet
1500 Break
1530 Breakout Groups Report
1600 Plenary Discussion (continued) Assembling an array of specific tools to measure on a section
Discussion Leader: Bess Ward
1730 Organize Wed AM Breakout Groups Planning and Logistics of a Field Campaign
Theme III  Implementation of a field program
Integration with GEOTRACES and other programs (Priorities)  (Anderson, Van Mooy)
Integration with GEOTRACES and other programs (Logistics)  (Moffett, Morris)
Data Synthesis and Interpretation (Martiny, Pearson)
Validation of molecular tools – Priorities and Timeline (Fuhrman, Ward)
1800 Meeting Adjourns
1900 Group Dinner
Wednesday, November 10
0730 Breakfast
0830 Breakout Groups Meet
1015 Break
1045 Plenary Group Reports  and draft sampling plan for an actual section
Discussion Leader:  Jim Moffett
1215 Lunch
1300 Plenary Discussion  What major science issues need to be addressed to fund a stand-alone program?  Trophic issues?  Genomic data for more prevailing species?
Discussion Leader: Kevin Arrigo
1500 Workshop Ends
1530 Steering Committee Meets

Related Files

  • Agenda

Participant List

  • Participant List

Related Resources

Microbiological Targets for Ocean Observing Laboratories (MicroTOOLs) (https://sites.google.com/site/microtoolsii/)

Workshops were held to discuss the development of in situ and high throughput molecular (DNA, RNA, protein) approaches for studying the biogeochemical activities of open ocean microbes.

There are two reports from this workshop that detail discussions at the workshops, and the progress to make the first community-available microbial oligonucleotide arrays based on genes from key marine microbes and genes that encode biogeochemically important processes.

It is hoped that momentum will continue to grow, including wider participation of the marine microbial community in developing and applying this resource.

Please contact Irina Ilikchyan (iirina@ucsc.edu), Julie Robidart (jrobidart@ucsc.edu) or Jon Zehr (zehrj@ucsc.edu) for further information.

Related Files

  • MicroTOOLs Workshop I Report
  • MicroTOOLs Workshop II Report
  • Appendices

Workshop Report

Click here for a PDF file of the workshop report.

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Funding for the Ocean Carbon & Biogeochemistry Project Office is provided by the National Science Foundation (NSF) and the National Aeronautics and Space Administration (NASA). The OCB Project Office is housed at the Woods Hole Oceanographic Institution.