Sequencing secrets of whole microbial communities
For the first time whole microbial communities and their functions, in Antarctica and the Southern Ocean, are being examined using DNA sequencing technology.
Dr Rick Cavicchioli and his colleagues from the University of New South Wales, and collaborators at the J. Craig Venter Institute and the US Department of Energy Joint Genome Institute, are using 'metagenomics' to sequence the DNA in entire environmental samples, rather than the traditional method of sequencing the genomes of single, cultured species. This approach will not only provide the scientists with a more rapid and expanded view of microbial diversity and function in the southern polar region, but will set a precedent for the capacity to use the technique on Antarctic and Southern Ocean samples.
'The southern polar region plays a critical role in maintaining microbial processes that are essential for the health of the world's ecosystems, yet we know very little about them,' Dr Cavicchioli says.
'Metagenomics offers an unprecedented means to reveal the secrets of Antarctic and Southern Ocean microorganisms and to learn about the unique, cold-adapted processes that they perform and their ability to adapt to global warming.'
About 75% of the earth's biosphere is cold and 'psychrophiles' (cold-loving organisms) can be found in permanently, seasonally and artificially (such as refrigerated) cold environments. However, the functional role of psychrophilic microbes in cold environments – such as the processing or organic and inorganic carbon and nitrogen compounds – has only recently been appreciated.
Photo: Jeff Hoffman
'Over the next five years the ASOMO program plans to compare whole water samples of archaea and bacteria collected in the same locations in different seasons, to understand the genomic and functional differences that occur in the populations,' Dr Cavicchioli says.
'This will provide information on the diversity, energy generating processes and adaptive capabilities of the microbes, and enable predictions to be made about the impact of continued global warming.'
Metagenomics will also be used to examine the potential effects of increases in oceanic carbon dioxide (ocean acidification) on microbial communities.
The findings will contribute to a database of information collected for the Census of Antarctic Marine Life – a major Australian-led project of the International Polar Year – of which CEAMARC is a part.
Photo: Jeff Hoffman
If the metagenomics approach proves successful, Dr Cavicchioli says it will open up opportunities for a range of other investigations including:
• comparing microbial communities in geographically isolated regions of Antarctica, to understand the degree of diversity within similar but separate areas;
• studying microbes that cannot be cultured in the laboratory; and
• studying microbial communities that contribute to the successful cleanup of contaminated sites.
This article is based on a paper by Dr Cavicchioli that appeared in Microbiology Australia, September 2007, pp 98-103.
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