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You are here: /main/research expeditions/CReefs 2006/Collection/Microbes

Census of Marine Life, Census of Coral Reefs Expedition to French Frigate Shoals (October 2006)

Ship Logs

Microbial Collections

Lead Scientist: Russell Brainard, Emmanuel Irizarry Soto
Target Habitats: Water, sediment
Target Organisms: Microbes

Water and sediment samples will be taken for RNA/DNA work by means of extremely non-invasive procedures, following the CoML International Census of Marine Microbes (ICoMM) protocols.

Sampling waters for lipid analyses of water
For lipid analysis 20-100 liters of water, depending on cell densities, needs to be filtered over pre-combusted (400°C, overnight) 0.7 µm glass fiber filters (GFF). The filters are then packed in aluminum foil (the use of soft plastic should be minimized) and kept frozen in the dark. Before analysis the filters are freeze-dried.

Lipid analyses of sediment
Sediment samples can be taken by a variety of techniques including box coring and piston coring. Samples can be taken from the core by metal sampling devices (e.g. spatulas) and should be 1-10 gram in size depending on organic matter contents (e.g. for 1% OC, 100 mg of sample may already be enough). The samples can be stored frozen or freeze-dried and subsequently stored frozen in the dark, preferably in hard plastic bottles or special geochemical bags.

Sampling water for DNA/RNA extraction using a Sterivex filter
Sterivex filters are 0.22 micron capsules (Millipore) that are routinely use by ICoMM scientists concentrating water samples for further DNA or RNA sample extraction. The traditional application involves filtering a recorded volume of water through the filter using a sterile syringe (140 or 60 cc). The sterivex is then either kept frozen until further processing or else a room temperature stable buffer (such as the Puregene Lysis Buffer (Gentra Systems) or RNAlater (Ambion) is added to fill the sterivex chamber (~2 ml) and the unit is then refrigerated, frozen or shipped to its final destination. While the buffers added to the chamber are stable at room temperature and will prevent DNA/RNA degradation for limited periods of time, samples are optimally kept as cold as possible (if available, dry LN as provided in a dry shipper is ideal).

Sterivex filter assemblyAn automated filtration method can be used with the sterivex filters (shown at left), though for this project samples may be processed manually.

This allows the filtration of water from several one liter bottles at a time (using a vacuum pump) onto several sterivex filters. The sterivex filters can be used to filter up to 3L for very oligotrophic water.

Back to collection methods

Additional resources

Ship Logs

Ship Logs:
Day-by-day activities of the expedition.

Daily or semi-daily personal journal entries by the particpants in the expedition. These journals do not necessarily reflect the positions of any of the agencies connected with this project.

Interviews with expedition participants, scientists, vessel crew, educators, etc.

Highlights or special information such as interesting discoveries, articles or related research.

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