Cruise News

By David Pearce

The microbial community is primarily responsible for recycling the nutrients which reach the sea floor. For this reason, a group of three scientists from the British Antarctic Survey (BAS) are investigating the biodiversity and community structure of microorganisms within the sediment and comparing the nutrient rich (M5) and nutrient poor (M6) sites around the Crozet Islands. This work will involve microscopy during the cruise itself, with stains that selectively mark key groups of bacteria and this will be complimented with a range of DNA based molecular techniques back in the laboratories at BAS.

Robin and Rachel demonstrate the delicate art of slicing mud! Click on the pictures for a larger version

Bacteria are very small (< 100th of a millimetre in length) and so it is often impossible to describe their taxonomy using morphological (or cell shape) characteristics alone. For this reason, we can design specific chemicals (oligonucleotide probes) which bind to particular DNA sequences which only occur in selected groups of bacteria. If these chemicals are synthesised to include a dye which fluoresces (glows) under ultra-violet light, then only those cells which contain a specific DNA sequence are stained by that chemical. These can then be detected using a special type of microscope with appropriate filters. We will also be using two further fluorescent stains: DAPI to stain all DNA in the sample, and hence estimate the total population density, and CTC which will fluoresce only in living cells, to estimate how many cells have survived the ascent to the surface. In this way we can start to build up a picture of the community structure whilst still at sea.

On return to the laboratories in Cambridge, we will extract the total community DNA from the sediment. This will be used to identify the dominant groups of bacteria present within the sample (using denaturing gradient gel electrophoresis – a technique which requires about 5000 cells per ml before identification can take place) and to construct clone libraries, which, with the assistance of a little statistics, can be used to estimate the total microbial biodiversity across each site.