|
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)
Microbial
Collections
Lead
Scientist: Russell Brainard, Emmanuel Irizarry
Soto
Target Habitats: Water, sediment
Target Organisms: Microbes
Description:
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).
 An
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:
Day-by-day
activities of the expedition.
Journals:
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:
Interviews with expedition participants, scientists,
vessel crew, educators, etc.
Features:
Highlights or special information such as interesting
discoveries, articles or related research.
|
Talk About It!
