News Release

Surprising discovery from first large-scale analysis of biodiversity and biogeography of viruses

Modern microbialites may be endemic remnants of ancient ecosystems

Peer-Reviewed Publication

Agency for Science, Technology and Research (A*STAR), Singapore

Viruses and bacterial viruses (known as phages) are among the most abundant life forms on the planet. Two papers published recently in Nature, March 2 and 12, 2008, analyse the geographical distribution of viral communities in modern organosedimentary structures (sedimentary features, built by the interaction of organisms and their environment) known as microbialites, the living analogues of the oldest fossils on Earth, and come up with some surprising nuggets of information.

Microbialites first appeared in the geological record, 3.5 billion years ago, and for more than 2 billion years they are the main evidence of life on Earth. A team of scientists from US and Singapore used a comparative metagenomics approach to show that phages associated with such structures are very different not only from each other but also from those found in any other ecosystem so far. The team’s findings indicate that modern microbialites are endemic remnants of ancient ecosystems.

Dr Ruan Yijun, Senior Group Leader at the Genome Institute of Singapore (GIS), said, “Using DNA sequencing technology, we were able to identify unknown viruses in various environments relevant to human health. This collaboration is the first ever large-scale effort to analyse biodiversity and biogeography of viruses in the environments around humans.”

“We have been interested in this kind of analysis since the SARS (severe acute respiratory syndrome) outbreak in 2002,” added Dr Ruan. “In pursuit of this interest, we established a virus discovery programme at GIS, resulting in the discovery of abundant viruses in the human gut (PLoS Biology, 2006) and different variants of dengue viruses. Now, with more viral metagenomic data accumulated, we are able to summarise the biodiversity and biogeography on a global scale.”

Microbialites are organosedimentary structures accreted by sediment trapping, binding and in situ precipitation due to the growth and metabolic activities of microorganisms.

Stromatolites and thrombolites are morphological types of microbialites classified by their internal mesostructure: layered and clotted, respectively.


Notes to the Editor:

Research publication:

The research findings described in the press release can be found in the March 2, 2008 issue of Nature under the title “Biodiversity and biogeography of phages in modern stromatolites and thrombolites”; and the March 12, 2008 issue of Nature under the title “Functional metagenomic profiling of nine biomes”.

Authors for March 2 paper:

Christelle Desnues1, Beltran Rodriguez-Brito1,2, Steve Rayhawk1,2, Scott Kelley1,3, Tuong Tran1, Matthew Haynes1, Hong Liu1, Mike Furlan1, Linda Wegley1, Betty Chau1, Yijun Ruan4, Dana Hall1, Florent E. Angly1, Robert A. Edwards1,2,3,5, Linlin Li1, Rebecca Vega Thurber1, R. Pamela Reid6, Janet Siefert7, Valeria Souza8, David L. Valentine9, Brandon K. Swan9, Mya Breitbart10 & Forest Rohwer1,3

1. Department of Biology,
2. Computational Sciences Research Center,
3. Center for Microbial Sciences, San Diego State University, San Diego, California 92182, USA.
4. Genome Institute of Singapore, Singapore 138672, Singapore.
5. Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.
6. Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida 33149, USA.
7. Department of Statistics, Rice University, Houston, Texas 77251, USA.
8. Departamento de Ecologı´a Evolutiva, Instituto de Ecologı´a, Universidad Nacional Auto´noma de Me´xico AP 70-275 Coyoaca´n, 04510 Mexico D.F., Mexico.
9. Department of Earth Science, University of California Santa Barbara, Santa Barbara, California 93106, USA.
10. College of Marine Science, University of South Florida, St Petersburg, Florida 33701, USA.

Authors for March 12 paper:

Elizabeth A. Dinsdale1,5*, Robert A. Edwards1,2,3,6*, Dana Hall1, Florent Angly1,4, Mya Breitbart7, Jennifer M. Brulc8, Mike Furlan1, Christelle Desnues1{, Matthew Haynes1, Linlin Li1, Lauren McDaniel7, Mary Ann Moran10, Karen E. Nelson11, Christina Nilsson12, Robert Olson6, John Paul7, Beltran Rodriguez Brito1,4, Yijun Ruan12, Brandon K. Swan13, Rick Stevens6, David L. Valentine13, Rebecca Vega Thurber1, Linda Wegley1, Bryan A. White8,9 & Forest Rohwer1,2

1 Department of Biology,
2 Center for Microbial Sciences,
3 Department of Computer Sciences, and
4 Computational Science Research Centre, San Diego State University, San Diego, California 92182, USA.
5 School of Biological Sciences, Flinders University, Adelaide, South Australia 5042, Australia.
6 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.
7 University of South Florida, College of Marine Science, 140 7th Avenue South, St Petersburg, Florida 33701, USA.
8 Department of Animal Sciences, and
9 The Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA.
10 Department of Marine Sciences, University of Georgia, Athens, 30602 Georgia, USA.
11 The J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
12 Genome Institute of Singapore, 60 Biopolis Street, 02-01, Genome, Singapore 138672, Singapore.
13 Department of Earth Science, University of California Santa Barbara, Santa Barbara, California 93106, USA.
{ Present address: Unite des Rickettsies, CNRS-UMR 6020, Faculte de medecine, 13385 Marseille, France.

About the Genome Institute of Singapore

The Genome Institute of Singapore (GIS) is a member of the Agency for Science, Technology and Research (A*STAR). It is a national initiative with a global vision that seeks to use genomic sciences to improve public health and public prosperity. Established in 2001 as a centre for genomic discovery, the GIS will pursue the integration of technology, genetics and biology towards the goal of individualized medicine. The key research areas at the GIS include Systems Biology, Stem Cell & Developmental Biology, Cancer Biology & Pharmacology, Human Genetics, Infectious Diseases, Genomic Technologies, and Computational & Mathematical Biology. The genomics infrastructure at the GIS is utilized to train new scientific talent, to function as a bridge for academic and industrial research, and to explore scientific questions of high impact.

About the Agency for Science, Technology and Research

The Agency for Science, Technology and Research, or A*STAR, is Singapore's lead agency for fostering world-class scientific research and talent for a vibrant knowledge-based Singapore. A*STAR actively nurtures public sector research and development in Biomedical Sciences, Physical Sciences and Engineering, with a particular focus on fields essential to Singapore's manufacturing industry and new growth industries. It oversees 14 research institutes and supports extramural research with the universities, hospital research centres and other local and international partners. At the heart of this knowledge intensive work is human capital. Top local and international scientific talent drive knowledge creation at A*STAR research institutes. The Agency also sends scholars for undergraduate, graduate and post-doctoral training in the best universities, a reflection of the high priority A*STAR places on nurturing the next generation of scientific talent.

For enquiries, please contact the following:

Genome Institute of Singapore
Winnie Serah Lim
Asst Manager, Corporate Communications
Tel: (65) 6478 8013
(65) 9730 7884

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