[Coral-List] using F.I.S.H. on Acropora samples

Megan Huggett huggett at hawaii.edu
Thu Apr 19 18:22:59 EDT 2007

I am a regular user of FISH and the main problem with coral samples is
background autofluorescence. I would recommend trying CARD-FISH on your
samples if possible, as the amplified signal helps to overcome some of the

My work has been with algal samples rather than corals, but CARD-FISH helped
hugely with seeing cells against a highly fluorescent background.

A similar problem occurs with sponges, and I believe the authors of: Webster
et al 2001 "Phylogenetic diversity of bacteria associated with the marine
sponge Rhopaloedes odorabile" AEM 67(1) 434-444 describe photobleaching
under fluorescent lights to overcome background also.


Dr Megan Huggett
Postdoctorate Fellow
University of Hawaii
Kewalo Marine Laboratory
41 Ahui St, Honolulu, 96813, HI
Ph: (808) 539 7317
Fax: (808) 599 4817
Email: huggett at hawaii.edu

-----Original Message-----
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Subject: Coral-List Digest, Vol 46, Issue 18

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Today's Topics:

   1. [Fwd: Re:  Heat; light, food, and bleaching, continued]
      (Esther Peters)
   2. Re: Range of reef fishes? (Lad Akins)
   3. using F.I.S.H. on Acropora samples (buiscuil)
   4. tropical sponges (roberta lasagna)
   5. Temminck Fellowship at National Museum of Natural	History
      Leiden (Hoeksema, B.W.)


Message: 1
Date: Tue, 17 Apr 2007 08:49:37 -0400
From: Esther Peters <esther.peters at verizon.net>
Subject: [Coral-List] [Fwd: Re:  Heat; light, food, and bleaching,
To: Coral-List <coral-list at coral.aoml.noaa.gov>
Message-ID: <4624C261.7090106 at verizon.net>
Content-Type: text/plain; charset=us-ascii; format=flowed

Dear Tom, Pedro, Charles, Andrea, Shashank, and All,

Tom, I'm glad you wrote in at this time, because it reminded me I had
wanted to provide a few comments earlier but could not get to answering
the e-mails then!

Yes, more research is needed on carbon and energy metabolism, but I hope
we can also use the tools from histology in addition to physiology,
biochemistry, microbiology, ecology, and systematics.  As many of you
know, my interest is in understanding the structure of the coral's cells
and tissues in relation to its function (histology), or as Tom noted in
an earlier e-mail about the Goreau, Goreau, and Yonge paper, functional
anatomy.  Visual images with light and electron microscopy of what is
happening to tissue structure help us understand grossly visible
reactions (e.g., bleaching) and aid in interpretation of quantifiable
measurements of molecules (e.g., respiration, carbon).

Experimental and field observations on the histology/histopathology of
scleractinia since about 1900 have confirmed the importance of mucus
production by these organisms, the variable nature and biochemistry of
mucus production by different species, and the changes that occur in
mucus production when the coral is exposed to levels of sedimentation
and turbidity above those to which it was adapted (or other stressors).
These changes include biochemical composition, initial increases in
mucus production, and loss of mucocytes with continued stress.  This
loss is also probably related to changes in nutrient intake, not only
carbon contributed from the zooxanthellae (which might be shaded under
these conditions and not producing as much for the coral host) but also
interference with obtaining zooplankton or bacterial carbon sources.
The result is tissue atrophy and can lead to death of the polyps.  The
significance of vibrios that kill zooxanthellae and other changes that
occur in the microbial community on the mucus layer of corals is just
now being realized, which are also closely associated with mucus
changes, in more than one way.  (And then there are those coccidia I
found that are somehow associated with bleaching, but everyone seems to
forget about them!)

    But I digress...the niche partitioning based on surface-to-volume
ratios of polyps brought to light another aspect of ecological
limitations which has directed small polyp vs. large polyp studies and
what we suspected that they could eat or how well they could get rid of
sediment, but more information is necessary.  In Andrea's study of
Montipora capitata, a small-polyped coral that can obtain all its energy
requirements from zooplankton when bleached, the free edges of the
polyp's mesenteries possess a cnidoglandular band (part of the
mesenterial filament) that in some areas contains numerous large
cnidocytes producing the stinging cells known as nematocysts.  These
nematocysts are at least 80 micrometers long with extensively coiled and
spiny tubules, indicating they can aid in the capture of zooplankton.
The mesenterial filaments are convoluted and can be extruded through the
mouth to capture zooplankton.  The cnidoglandular bands also have
numerous granular gland cells, which contain acidophilic granules,
likely zymogens, digestive enzyme precursors.  The epidermal cells also
may not produce much mucus (this species is susceptible to sedimentation
in Kanahoe Bay, I understand).  So this species is indeed capable of

Conversely, the genus Porites has only small (maybe 10-20 micron)
nematocysts in its tentacles and mesenterial filaments.  It has larger
nematocysts in its gastrodermis, but they don't appear to be used in
food gathering (although more observations are needed on this!).  And
the fascinating chromophore cells of this genus are probably related to
its "more" autotrophic mode.  In addition, Porites epithelia are loaded
with mucocytes and they produce copious amounts of mucus, even when not
under sediment stress!  Perhaps they rely more on particulates and
bacteria growing on their mucus for carbon?

Yes, much more is to be learned about the Scleractinia, and histology
should be included in more studies to help interpret the functional results.

Esther Peters

Thomas Goreau wrote:

 > Estimado Pedro,
 > Thanks for your comments and reinvigorating this discussion, I'm just
 > back from coral reef restoration projects in Micronesia and Polynesia
 > and I had not seen many of the comments below. You are absolutely
 > right that little is known and much more needs to be done on both
 > carbon and energy metabolism in both bleached and normal corals, but
 > this has never been a fad issue with funding agencies.
 > My parent's first work on the fate of C-14 incorporated by
 > zooxanthella photosynthesis in the early 1950s showed that the coral
 > retained very little of the released carbon, almost all went into
 > mucus release. Later biochemical work (Trench and Muscatine, Cooksey
 > & Cooksey, Battey & Patton, etc.) confirmed that almost all
 > zooxanthellae release to the host were precursor biochemicals used in
 > mucus synthesis. The loss of these precursors causes a much greater
 > energy drain on bleached corals that must release mucus to deal with
 > sedimentation and other stresses, and almost certainly changes the
 > amount and chemical composition of mucus and the cost to the coral of
 > producing it.
 > Since corals are specialized for different types of zooplankton prey
 > (something we have long known, but which you won't find in the "peer"
 > "reviewed" literature), their ability to make up loss of this will
 > depend on their nutrition from predation. The heavy loss of mucus in
 > bleaching must impose severe limitations on coral and their nutrition
 > and environment must affect their ability to replace this. There is
 > very little good work on this, but Andrea Grottoli and colleague's
 > work is an important start.  A recent paper in Nature on the
 > biochemical utilization of mucus release of corals by Wild et al. was
 > done on corals that were releasing exceptional levels of mucus
 > because they were in the first stages of severe bleaching, but this
 > abnormal condition was not noticed by the authors, the reviewers, or
 > the editors, who refused to publish our comment pointing this out!
 > In the late 1980s Ray Hayes and I took samples of coral mucus from
 > bleached and unbleached portions of corals in Jamaica and Cayman,
 > which were analyzed for the microbial community by Kim Ritchie and
 > Garriet Smith. We found large amounts of a previously unknown Vibrio
 > species on the mucus of bleached Montastrea annularis and Porites or
 > Acropora (as I remember, I don't have it here) that did not occur on
 > mucus of the unbleached portions of the same colonies. In 1991 we
 > found large amounts of the same Vibrio found in the Caribbean on the
 > mucus of bleached Acropora, Porites, and Montastrea in the South
 > Pacific that again did not occur on the mucus from unbleached potions
 > of the same colony. We published a couple of papers on this in the
 > microbiological literature about 15 years ago. We assumed the Vibrio
 > was an opportunist specializing on the mucus of changed composition,
 > but were not able to follow through with biochemical measurements.
 > Several types of Vibrio has been known to be abundant on coral mucus
 > since the pioneering work of Hugh Ducklow and Ralph Mitchell in the
 > early 1970s.
 > Later Rosenberg, Loya, Ben Haim, Kushmaro and colleagues found Vibrio
 > associated with bleached corals and claimed it to be the cause of
 > bleaching. We suspected (incorrectly) at the time it was probably the
 > likely opportunist we had found rather than the cause of bleaching.
 > Later work with James Cervino, Ray Hayes, Garriet Smith, Shawn and
 > Sara Poulson, Rob Martinez, Fabiano Thompson, and myself have found
 > another set of Vibrios closely related to the pathogenic shellfish
 > poisoning Vibrios which cause Yellow Band Disease in Caribbean
 > Monstastreas and in several other Pacific genera, and we have shown
 > that this is not bleaching at all in that there is no expulsion of
 > the algae. Instead the bacteria attack the zooxanthellae in situ and
 > cause programmed cell death (apoptosis). Ben Haim and Rosenberg have
 > since confirmed that the same takes place with their different Vibrio
 > strains. So those Vibrios are a zooxanthella (not coral) disease, not
 > bleaching, and quite separate from the opportunistic Vibrios on the
 > mucus.
 > Furthermore the ways in which carbon and energy are partitioned will
 > differ between corals with different trophic pathways (an issue non
 > long known to coral researchers but essentially absent from the
 > published literature except for a paper by Jim Porter on niche
 > partitioning by surface to volume ratios of polyps in the early 1970s
 > and Grottoli et al's more recent work). Zac Forsman just showed me
 > his experiments in Honolulu two days ago with the same species
 > (Porites compressa and Montipora capitata)  that Andrea Grottoli
 > worked on, and he has found (working I think with Cindy Hunter and
 > Bob Richmond) that they also respond very differently to light stress
 > and the speed of water circulation. Clearly there is much more to be
 > learned!
 > Saludos,
 > Tom


Message: 2
Date: Tue, 17 Apr 2007 09:29:34 -0400
From: "Lad Akins" <Lad at reef.org>
Subject: Re: [Coral-List] Range of reef fishes?
To: "Lorenzo Alvarez Filip" <lorenzoalvarezf at yahoo.com>,
	<coral-list at coral.aoml.noaa.gov>
Content-Type: text/plain;	charset="us-ascii"

Hi Lorenzo and listers,

Sorry for the delay in this response.

Regarding your posting looking for the ranges of tropical reef fish, you may
also want to check out the Reef Environmental Education Foundation's
(REEF's) on-line database at http://www.reef.org/data/database.htm

REEF's fish survey project was developed as a volunteer survey program
patterned after the successful birding programs of Audubon, Cornell, etc.
Surveys of fish (and inverts on the US west coast) are conducted by
volunteer divers and snorkelers during regular recreational dives and
entered submitted via computer scannable form or entered on-line at
http://www.reef.org/dataentry/login.php   Data are QA/QC at REEF HQ before
passing into the publicly accessible database which now contains more than
100,000 individual surveys.  Data are currently being collected from
throughout the Tropical Western Atlantic, coastal North America, the
Tropical Eastern Pacific and Hawaii.  Data are separated by experience level
of observer and a number of standard reports, including distribution
reports, (e.g.. from TWA region at
http://www.reef.org/data/twa/species.shtml) are available free of charge on
the website.  In addition, the entire dataset or portions thereof may be
requested free of charge by researchers in need of more specific

Numerous peer reviewed publications and researchers have and are using this
information, summaries or .pdfs of which can be downloaded from the
scientific papers section of the REEF site at

The REEF Fish Survey Project was initiated to answer just the kind of
question you are asking.

I hope this info helps.  Please feel free to e-mail with any data requests
or specific questions to either Christy Semmens, REEF Director of Science -
Christy at reef.org,  or Joseph Cavanaugh, REEF Director of Field Operations -
Joe at reef.org.  For general information on the REEF organization or programs
contact Leda Cunningham, REEF's Executive Director - Leda at reef.org

Much thanks for the opportunity to provide the info!


Lad Akins
Special Projects
98300 Overseas Hwy
Key Largo  FL  33037
(305) 852-0030
(305) 942-7333 cell

-----Original Message-----
From: coral-list-bounces at coral.aoml.noaa.gov
[mailto:coral-list-bounces at coral.aoml.noaa.gov]On Behalf Of Lorenzo
Alvarez Filip
Sent: Thursday, April 12, 2007 10:02 AM
To: coral-list at coral.aoml.noaa.gov
Subject: [Coral-List] Range of reef fishes?

Dear listers,

I am looking for sources that includes information about the geographic
range of tropical reef fishes, I know the splendid work of Ross Robertson
and Gerald Allen for the tropical eastern pacific, but I don't know if
similar resources are available for other regions (e.g. Caribbean,

I'll appreciate any information that you can give to me.

Many thanks, Lorenzo

Lorenzo Alvarez-Filip
School of Environmental Sciences
University of East Anglia
Email: l.alvarez at uea.ac.uk
       lorenzoalvarezf at yahoo.com

Coral-List mailing list
Coral-List at coral.aoml.noaa.gov


Message: 3
Date: Tue, 17 Apr 2007 15:59:22 -0400
From: buiscuil <pascal.mege at gmail.com>
Subject: [Coral-List] using F.I.S.H. on Acropora samples
To: coral-list at coral.aoml.noaa.gov
	<6390f5290704171259y6311ab32i30270471b6f3fae0 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hello subscribers,
Being novice in this technique, I wonder if anyone has used fluroescence in
situ hybridization (FISH) on bacterial populations associated with coral,
especially of the genus Acropora. Well, in fact, I know some did (!) but it
is good to hear more from others, especially since I do not dispose of
everything that was described.
Using specific probes, my aim is to compare proportions of bacteria using
FISH on the one hand and using 16SrDNA sequencing on the other... The
lattest I cope with but can I use my already extracted DNA (used for the 16S
sequencing) as a substrate for the hybridization and how? My fear (well, one
of them) is to have unspecific hybridization occuring since my extracted DNA
include the whole coral sample (tissue, zoox, algae, bacteria etc). What
would you advise? Thank you for useful and guiding answers!

Pascal M?ge
PHD student - university of Puerto Rico -Rio Piedras-


Message: 4
Date: Tue, 17 Apr 2007 15:29:57 +0200 (CEST)
From: roberta lasagna <robertalasagna at yahoo.it>
Subject: [Coral-List] tropical sponges
To: coral-list at coral.aoml.noaa.gov
Message-ID: <456957.18672.qm at web27803.mail.ukl.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1

Dear listers,
  I'm trying to find informations on tropical sponges, especially with
regard to the maldivian zone.
  In particular I would like to find paper or information on
presence/absence of photosynthetic symbionts, in maldivian sponges.
  Thank you in advance.
  Kind regards.
  Roberta Lasagna
PhD student
University of Genoa (Italy)


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Message: 5
Date: Wed, 18 Apr 2007 12:08:03 +0200
From: "Hoeksema, B.W." <Hoeksema at naturalis.nl>
Subject: [Coral-List] Temminck Fellowship at National Museum of
	Natural	History Leiden
To: <coral-list at coral.aoml.noaa.gov>
	<104E1BC78864DE46B2BF048E06162FEC018232C7 at nnms26.nnm.local>
Content-Type: text/plain;	charset="iso-8859-1"

Please forward this message to possible candidates

The Temminck-Fellowship programme for visiting senior researchers at the
National Museum of Natural History 'Naturalis', Leiden, the Netherlands

Funds are available for one or more Temminck-fellows in
2007. Temminck-fellowships are intended for established, senior
researchers from other countries, preferably from outside the European
Union, in any of the fields that form the highlights of the Naturalis
research programme (see http://www.naturalis.nl). Fellowships are
available for periods of a minimum of three months to a maximum
of twelve months, and the available budget is sufficient to cover
travel and lodging for the recipient. Research costs cannot be
covered. Temminck-fellows are expected to collaborate intensively with
one or more Naturalis-researchers, and work on, e.g., scientific papers,
books, and grant proposals, all with Naturalis as their (secondary)
affiliation. Applications should be directed to paauw at naturalis.nl,
accompanied by a proposed budget, a c.v., and a detailed list of
activities to be carried out during the fellowship period.


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