Expressions of Intent for IPY 2007-2008 Activities

Expression of Interest Details

PROPOSAL INFORMATION

CANADA #223: Microbial Indicators of Polar Environmental Change  (Microbial Indicators or MIPEC)

Outline
mponent of living biomass, and act as the catalysts that drive biogeochemical cycles. In fact, in their roles as major producers and consumers of green-house gases, microbial communities are significant players in regulating the ecosphere. In addition, they can be important sentinels of environmental change, as alterations in the structure and biomass of microbial communities can herald changes not only in pathways of nutrient and energy transfer in foodwebs, but also in biogeochemical cycles. Despite their abundance and likely importance in polar ecosystems, very little is known about the composition of polar microbial communities, their interactions and geochemical roles, or their response to environmental changes. The proposed research takes advantage of the high-throughput tools of molecular biology to collect high-resolution spatial data across terrestrial, freshwater and marine arctic ecosystems for the specific purpose of identifying the numerically dominant groups of viruses, bacteria and protists in each of these environments. The proposed research compliments the work proposed by Vincent et al (The Canadian Arctic Genome Project) in that we will examine a relatively large number of samples representing a variety of environments for the specific purpose of examining the numerically dominant taxa, whereas, Vincent et al. will adopt a metagenomics approach to examine a fewer number of samples, but in much more “depth” than possible using our approach. In contrast, we will target a relatively small number of taxonomically significant genes for viruses, bacteria and protists. We propose to use Serial Analysis of Ribosomal Sequence Tags (SARST), a high throughput method (http://www.microbiology.ubc.ca/Mohn/SARST.htm; Neufeld et al. 2004; Kysela et al. 2005) to sequence short regions of rDNA that are of phylogenetic significance. SARST uses a series of enzymatic reactions to link short 16S ribosomal DNA sequences (17-55 bp ribosomal sequence tags; RSTs) into concatemers (10 to 20 RSTs) that can be cloned and sequenced. This allows the taxonomic diversity of samples to be described with much less sequencing effort. In a similar way, the composition of viral communities can be inferred from sequence analysis of specific virus-associated genes. This sequence information can be translated into arrays that can be used to document temporal and spatial changes in microbial composition that result from environmental change. Ultimately, our goal is to develop a baseline understanding of the composition of microbial communities. This will not only provide the needed information to help us understand if they are changing, but will document the microbial richness of polar communities. This work will expand greatly the efforts we have begun as part of the Canadian Arctic Shelf Exchange Study References: Kysela, DT, C Palacios, ML Sogin. 2005. Serial analysis of V6 ribosomal sequence tags (SARST-V6): a method for efficient, high-throughput analysis of microbial community composition. Environ Microbiol 7: 356-64 Neufeld, JD, Z Yu, W Lam, WW Mohn. 2004. Serial analysis of ribosomal sequence tags (SARST): a high-throughput method for profiling complex microbial communities. Environ. Microbiol. 6:131-144

What significant advance(s) in relation to the IPY themes and targets can be anticipated from this project?
The project directly addresses the themes as follows: Theme 1 by documenting the composition as well as the temporal and spatial variability of Arctic microbial communities. Theme 2 by allowing temporal comparisons of communities on short and long-term time scales. Theme 3 through comparisons with datasets from the Antarctic and other regions of the globe. Theme 4 by documenting the microbial composition of terrestrial, freshwater and marine viral, bacterial and protist communities. Theme 5 by studying the occurrence of life in extreme environments. Theme 6 by documenting the influence of human societies on microbial communities and the consequent occurrence of human pathogens circulating in microbial communities.

What international collaboration is involved in this project?
We are very interested in partnering with the international community in order to access and share samples from a wide range of Arctic environments.

FIELD ACTIVITY DETAILS

Geographical location(s) for the proposed field activities:
Our goal is to obtain samples from a wide range of pristine and human affected effected environments. Ideally we would partner with other missions as each sample will only take approximate take a day to collect and process in the field. Most of the analysis needs to be done in a well equipped nucleic-acid processing facility.

Approximate timeframe(s) for proposed field activities:
Arctic: Flexible            
Antarctic: Flexible            

Significant facilities will be required for this project:
It is anticipated that logistical support will be required to collect samples from the Canadian Arctic. It is hoped this can be doe in conjunction with other programs.

Will the project leave a legacy of infrastructure?
We would provide a library of microbial DNA from a wide range of Canadian Arctic environments that would be available for analysis and bioprospecting for many years.

How is it envisaged that the required logistic support will be secured?
Consortium
Own national polar operator
Another national polar operator

Has the project been "endorsed" at a national or international level?
No. The project was discussed with the Canadian IPY Secretariat, and submission encouraged.

PROJECT MANAGEMENT AND STRUCTURE

Is the project a short-term expansion (over the IPY 2007-2008 timeframe) of an existing plan, programme or initiative or is it a new autonomous proposal?
New
It is anticipated that the samples will be collected as ancillary components to other expeditions

How will the project be organised and managed?
Overall coordination of the project will be overseen by Suttle. Financial management will be carried out by Amy Chan, a research scientist in the Suttle group. The Suttle group will be responsible for the processing and the analysis of the virus data. The Mohn group will process and analyse the rDNA data. Sequencing will be done through the NAPS sequencing facility at UBC, and the SARST data analysed using SARST related software that has been developed by the UBC Bioinformatics Centre (UBiC).

What are the initial plans of the project for addressing the education, outreach and communication issues outlined in the Framework document?
There will be undergraduate, graduate and post-doctoral training as part of the project. We will endeavour to involve the local communities with the selection of sites for sampling and communicate our findings through the links established by Arctic Net in Canada.

What are the initial plans of the project to address data management issues (as outlined in the Framework document)?
SARST data will be archived in the GEO database at the National Center for Biotechnology Information (NCBI), and the viral data will be deposited in GenBank

How is it proposed to fund the project?
Funding has not been identified for the project. The majority of costs will be for sequencing and data analysis. It will require a Canadian funding agency to commit resources for sequencing projects that have an environmental mandate. The overall cost will depend on the number of environments sampled. A reasonable first step would be 10 samples at approximately $500,000.

Is there additional information you wish to provide?
This project will provide continuity with previous projects involved with global change in the Canadian Arctic including CASES, ArcticNet and NRiSCC.

PROPOSER DETAILS

Professor Chris Suttle
University of British Columbia Department of Earth and Ocean Sciences
6270 University Blvd
Vancouver
V6T 1Z4
Canada

Tel: (604) 822-8610
Mobile:
Fax: (604) 822-6091
Email:

Other project members and their affiliation

Other Information