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of Marine Life, Census of Coral Reefs Expedition to
French Frigate Shoals (October 2006)
Scientist: Russell Brainard, Emmanuel Irizarry
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)
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
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.
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.
should be 1-10 gram in size depending on organic matter
contents (e.g. for 1% OC, 100 mg of sample may already
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.
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
through the filter using a sterile syringe (140 or 60
cc). The sterivex is then either kept frozen until further
or else a room temperature stable buffer (such as the
Puregene Lysis Buffer (Gentra Systems) or RNAlater (Ambion)
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
temperature and will prevent DNA/RNA degradation for
limited periods of time, samples are optimally kept as
possible (if available, dry LN as provided in a dry shipper
automated filtration method can be used with the sterivex
filters (shown at left), though for this project samples
may be processed manually.
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
activities of the expedition.
or semi-daily personal journal entries by
in the expedition. These journals do not necessarily reflect
the positions of any of the agencies connected with this
Interviews with expedition participants, scientists,
vessel crew, educators, etc.
Highlights or special information such as interesting
discoveries, articles or related research.