Capturing the ocean's microbial diversity

Tim Williams (left) and David Wilkins in the Aurora Australis laboratory preparing to filter water samples
Tim Williams (left) and David Wilkins in the Aurora Australis laboratory preparing to filter water samples (Photo: Laura Smith, UTAS) (Photo: Laura Smith, UTAS)
Filtration apparatusA schematic showing which marine microorganisms the different filters collect. A Google Earth map showing the location of the microbial sample sites

During the Mertz Glacier voyage a team of microbiologists from the University of New South Wales collected water samples to learn more about microbes (bacteria, archaea* and viruses) and their role in Southern Ocean ecosystems.

The ocean is the largest microbial environment on Earth, yet until very recently we have lacked the technology needed to study more than a tiny fraction of its enormous diversity. Our microbiology group at the University of New South Wales is working to develop an inventory of the microbial ecosystems of the Southern Ocean, including which microorganisms are present and the metabolic and ecological processes they perform. Our study also aims to establish a baseline against which environmental changes, such as the temperature and ocean acidification effects of climate change on microbial ecosystems, can be measured. This baseline will help refine predictive models for these changes.

We collected twenty-four 400 litre seawater samples during the marine science voyage of the Aurora Australis in January and February this year. The ship made a 1500 km transect of the Southern Ocean from Tasmania to the Antarctic coast, allowing us to sample the full breadth of Southern Ocean environments, from warmer sub-tropical waters to the cooler subantarctic and frigid Antarctic zones.

Our seawater samples were collected from both the surface and the deeper layers where maximal chlorophyll concentrations exist in the water column (chlorophyll is a photosynthetic pigment present in algae and other phytoplankton). This is typically where the highest density of marine microbes is found. The seawater was pumped through a fine 20 μm mesh (1 μm = 0.001 mm) to remove non-microbial organisms, then through three consecutive filters of increasing fineness (3.0 μm, 0.8 μm, 0.1 μm) to collect the microbial component (biomass). The different filters capture microbes of different size ranges.

Back in the lab in Sydney, the microbial biomass will be removed from the filters for metagenomic, metatranscriptomic and metaproteomic analysis. Metagenomics is a recently developed technique which allows DNA from an entire microbial community to be sequenced in a single process. This gives researchers a wealth of crucial data on what kinds of microbes and genes have been selected for in that community, letting us answer questions about how the microorganisms are adapted to the environment and what ecosystem roles they play.

Metatranscriptomics and metaproteomics involve similar analyses of the total RNA and protein components of the community, respectively. While metagenomics can tell us what genes the microorganisms possess, not all genes are ‘expressed’ (transcribed into RNA, which is then translated into functional proteins) at the same levels, or at all times.

Identification of the RNA and proteins will tell us what particular genes are actually being expressed by the microbes, giving a more complete picture of community processes. Proteins, such as enzymes, will tell us what metabolic processes are occurring, such as the conversion of atmospheric gases into biomass.

This work contributes to the Australian Southern Ocean Genome-Based Microbial Observatory (ASOMO), established in 2008, which aims to understand the genomic and functional differences that occur in microbial populations. Related research was previously published in the Australian Antarctic Magazine 14: 8, 2008.

TIM WILLIAMS, DAVID WILKINS, MATTHEW DeMAERE, FEDERICO LAURO and RICK CAVICCHIOLI

University of New South Wales

* Archaea are an ancient group of microorganisms distinct from bacteria and eucarya. R. Cavicchioli. Archaea – timeline of the third domain. 2011. Nature Reviews Microbiology 9: 51-61.