Sequencing secrets of whole microbial communities

Filters used to separate phytoplankton, zooplankton, microbes and viruses from Southern Ocean water samples.
Filters used to separate phytoplankton, zooplankton, microbes and viruses from Southern Ocean water samples. Filtrate containing bacteria and archaea will be sequenced. (Photo: Jeff Hoffman)
Rick Cavicchioli (left) and Torsten Thomas, from the UNSW, process microbial samples collected at Ace Lake.

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.

To help address this knowledge gap Dr Cavicchioli and his team collected 25 surface and deep-water samples (from 1.5 – 3693 m) from the Southern Ocean during the Collaborative East Antarctic Marine Census (CEAMARC) earlier this year. These, and other samples collected over the next five years, will provide a basis for examining the genomic composition of bacteria and archaea (an ancient group of microbes). The team will also use 'metatranscriptomics' and 'metaproteomics' to study the RNA and protein composition, respectively, of whole samples. (DNA codes for RNA, which provides the template for proteins, which contribute to the functional capacity of an organism, such as the ability to convert atmospheric carbon into particulate matter). The work forms part of a newly proposed Australian Southern Ocean Genome-Based Microbial Observatory (ASOMO).

'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.

The work also complements the team's research in the lakes of Antarctica's Vestfold Hills, near Davis. These saline lakes were isolated from the ocean about 5000 years ago, providing scientists with an opportunity to define the biological properties required for survival at the extreme limits of life. In 2006, the research team took samples from Ace, Deep and Organic lakes. Metagenomic analysis is expected to provide an understanding of the ecology, adaptive biology and the undiscovered properties of psychrophilic microbes in the lakes.

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.