Marine Microbial Ecology

How are field samples collected?

Ship based sampling

Samples are collected either using instruments deployed over the side of the ship or by collecting from a seawater supply line with an intake at 7 m depth in the ship's hull.

Samples for depth profiles are obtained using a Rosette sampler. The rosette has 24 x ten litre Niskin bottles that can be closed at required depths by electronic signal from the ship. The attached CTD (Conductivity, Temperature, and Depth) system sends continuous data profiling the water column's temperature, salinity and density. Water masses, oceanographic features and currents are identified from these data.

CTD sampling rosette being launched from the side of the RV Aurora Australis
Image: Fiona Scott

CTD sampling rosette being returned into the CTD bay on the side of the RV Aurora Australis at night
Image: Simon Wright

Collecting water samples from the Niskin bottles on the rosette sampler
Image: Simon Wright

Samples for phytoplankton pigment analysis (0.5 - 2 L) are filtered onto glass fibre filters and stored in liquid nitrogen (-196°C) for analysis on return to Australia.

The 12-bottle phytoplankton filtration rack used on board the RV Aurora Australis
Image: Fiona Scott

Duplicate samples are preserved for cell identification by light microscopy or electron microscopy, and cell counting by a process of sedimentation and inverted microscopy. Living cells are also examined and counted whilst on board the ship with microscopes shock-mounted to avoid vibrations from the ship's engines.

Bacteria and viruses are filtered onto black polycarbonate membrane filters, stained with dyes that bind to their DNA and RNA, and counted by fluorescence microscopy.

Large phytoplankton are collected using 20 micrometer mesh plankton nets. This method of sampling is selective but it allows comparisons of current phytoplankton communities with historic samples.

Sea ice sampling

It is difficult to sample the microbial community living within sea-ice. The protists live in brine channels that are formed between relatively fresh water ice crystals. To protect the delicate organisms, sampling and laboratory techniques must avoid large changes in salinity that occur during melting.

Ice communities are sampled using a SIPRE ice corer or Jiffy drill. The SIPRE corer provides a cylindrical section of the sea-ice from which samples are cut, melted in filtered seawater and examined for microbes.

Alternatively, a partial core hole is drilled and the microbe-containing brine is allowed to drain into it.

A Sipre-corer and part of the resultant sea-ice core
Image: Fiona Scott

Scientist operating an ice-drill
Image: Fiona Scott

Land-based (Continental station) sampling

Over-snow vehicles or small boats are used to get to collecting sites from our Antarctic stations. Sea-ice and water samples are brought back to the laboratory where there are low-temperature incubation tanks, culturing facilities and analytical equipment.

Back | Next