TerraGenome Roundtable ISME-13

TerraGenome Roundable – International Consortium on Soil Metagenomics

Proposer(s): Janet Jansson (LBNL), James Tiedje (MSU), Mark Bailey (Oxford, UK), Pascal Simonet (ec-Lyon), George Kowalchuk (NIOO), Dave Myrold (Oregon State Univ.), Jizhong Zhou (Oklahoma State. Univ.)

Description: Soil microbial communities are known to be drivers of major geochemical cycles, to support healthy plant growth, and to degrade organic matter and pollutants. However, little is known about the vulnerability of their key functions and how they respond to (and buffer) human-induced environmental perturbations, such as climate change and land use. The genetic resources in only a single gram of soil are huge with 1,000 times more sequences than in the human genome. However, only a fraction (less than 1%) of the microbiota extant in soil has yet been cultivated using any of an array of techniques. In addition, few environmentally isolated bacteria have been completely sequenced since most sequencing has targeted microorganisms from other ecosystems, such as extreme environments or human pathogens. Fortunately, recent advances in 2nd generation sequencing approaches have now made sequencing of the soil metagenome a real possiblity. Information gleaned from soil metagenomics holds great promise to increase our understanding of gene diversity and function in the soil environment and has potential to provide a greater understanding of soil microbial processes. This proposed roundtable will therefore bring together scientists interested in the use of metagenomics to explore the composition and function of soil ecosystems. This initiative will build upon the recently launched TerraGenome consortium (www.terragenome.org), an international consortium of scientists interested in exploring opportunities for soil metagenomics and establishing standards and protocols for metagenomic sequencing. This will be a subject discussion centered around the following 5 short 10 minute talks, leaving most room for discussion:

1. Introduction to TerraGenome & Metadata standards (James Tiedje)
2. The TerraGenome Pilot initiative: Rothamsted soil metagenomics update (Tim Vogel)
3. Short update on other soil metagenomic sequencing projects (Janet Jansson)
4. The next stage for TerraGenome (Dave Myrold)

Structured discussion led by George Kowalchuk, James Tiedje and David Myrold (Possibilities & Pitfalls). For example: (1) experiences with different sequencing platforms, (2) bioinformatics challenges, (3) trade-offs between sequencing depth and spatial/temporal variation, (4) progress in integrating with transcriptome and proteome studies. We will also aim to generate a list of current projects with some brief description of location, soil type, management, etc.

Timing:
Monday evening 17:30-19:30

TerraGenome workshop

June 2009 TerraGenome workshop

In conjunction with BAGECO-10 meeting in Uppsala, Sweden (June 15-19, 2009)
TerraGenome Workshop Date: June 14-15, 2009.

Agenda June 14, 2009:
8:00 Welcome (Pascal Simonet)
8:30 – 10:00
Short overviews (15 min. + 5 min. discussion) of on-going soil metagenomics projects (accomplishments, goals and challenges)
• Soil metagenomics – Rothamsted, UK (Penny Hirsch)
• Metasoil update (Tim Vogel)
• Grand challenges –US perspective (James Tiedje)
• Soil metagenomics – Puerto Rico (Terry Hazen)
10:00-10:30 (coffee)
10:30-11.30 (10 min. contributed presentations and 5 min. discussions)
• Soil metagenomics – Australia (Pauline Mele)
• Soil metagenomics – Japan (Yusuke Unno)
• Soil metagenomics – Argentina (Luis Wall)
• Soil metagenomics and scale (George Kowalchuk)
11.30-12.00 General discussion and summary (Mark Bailey and Janet Jansson)
12:00-13:00 (lunch)
13:00 – 13.30
Legal aspects (Tom Dedeurwaerdere)
13.30-14.00
Metadata needs & update (James Tiedje)
14.00-15.00
Metagenomic sequencing and bioinformatics update (15 min. each) Chris Detter, Patrick Chain, Jeroen Raes, Folker Meyer
15:00-15.30 (coffee)
15.30-16.30
Committee reports (25 min. + 5 min. discussion)
• Research committee report (Eric Triplett)
• Communications committee report (Tim Vogel)
16.30-17.30
Small group discussions: From Rothamsted onwards
• Utilization of the Rothamsted data for other sites and other Rothamsted soil experiments
• Grand Challenges and how to meet them
17.30-18:30
Large group summary and discussion
(Discussion leaders: Mark Bailey and Janet Jansson)

Agenda June 15, 2009:
8:30-10:00
Key issues for soil metagenomics (20 min. each + 10 min. discussion) Joe Zhou, Vigdis Torsvik, Christoph Tebbe,
• Gradients (pH, nutrients, etc.)
• Scale (time and space)
• Change and impacts (climate, anthropogenic, etc.)
• Biogeography (national and global) – comparison to Global Ocean Survey
• Bioexploration
10:00-10:30 (Coffee)
10:30-11:30
Key issues continued (20 min. each + 10 min. discussion) Laurent Phillipot, Konny Smalla, contributed)
11:30-12:00 Group discussion: Collaboration potential
o Bioinformatics
o Data storage
o Data sharing
o Shared samples
12.30 -13.30 (Lunch)
13.30-15.00 Free discussion period

Logisitcs:
The workshop will be held in Room L (Sal L in Swedish) in the “Undervisningshuset” on the Ultuna Campus of the Swedish University of Agricultural Sciences (SLU). Please see the attached map of the campus that shows the location of the Undervisningshuset.

Travel information from the airport (Arlanda International Airport) can be found on the BAGECO-10 website: http://www-conference.slu.se/bageco/ Additional general information is also on the BAGECO-10 website.

Note that the train from the airport stops in Central Uppsala. It is necessary to take a bus from the train station to the campus where the meeting is located. (see bus information detailed below). Alternatively you can take a taxi directly from your hotel or from the airport to the meeting site.

Registration (including a payment of 600 Swedish crowns (SEK) to pay for the conference room and lunch costs) and hotel booking should also be done through the BAGECO-10 website (see above).

NOTE: The registration deadline is June 6, 2009.

   

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