[Coral-List] Coral absorbance factor

Jeremy J. Sofonia jeremy at sofonia.com
Thu Dec 11 10:53:29 EST 2008

Dear Steve -

I would strongly recommend  a look at Beer et al. (1998):

Beer S., M. IIan, A. Eshel, A. Weil, and I. Brickner.  1998.  Use of  
pulse amplitude modulated (PAM) fluorometry for in situ measurements  
of photosynthesis in two Red Sea faviid corals.  Marine Biology  

Interestingly, you'll notice that they calculate the absorbance  
factor (FA) by accounting for the reflectance of the coral skeleton  
(Rs), subtracting this from that measured from the live coral (Rc),  
and then dividing by the reflectance of the incident light by a  
mirror (Rt).

AF = (Rs - Rc) / Rt

This is quite clever, and depending on the objective of the study  
could result in providing some very interesting results, particularly  
if one is looking at the effect of skeletal reflectance - and the  
possible variations therein ( e.g. could lead to questions into  
inter- and intra-specific differences in morphology etc).

On the other hand, utilising the water pick to remove the tissue is  
obviously a destructive technique which prohibits repeated measure on  
the same colony over time.  It also may be logistically restrictive  
if you are trying to assess corals in situ.

Besides, most corals (at least those that I've worked with)  don't  
seem to live very well without their skeletons.  By subtracting this,  
are we really understanding the natural process? If not, it may be  
important retain this information in the FA and to consider  
absorption in living corals as a 'gross' rather than 'net' function  
of the coral components.

Perhaps just:

AF = Rc - Rt

One other thing to consider:  There is variation in the strength of  
the ambient light pluse derived from the DivingPAM.  Although slight,  
it may change with factors such as ambient temperature and battery  
charge.  From some basic trials of my own, I observed this to have a  
greater effect when running the 'rapid light curves' than when  
employing a single saturation pulse.  I would recommend you also run  
a preliminary trial using the mirror to try and assess (and account  
for) how your specific machine performs.

All in all a very interesting - and I think important - part of coral  
fluorometry which has a great deal of room for further investigation  
and refinement.  I'm certainly no expert, and would be quite happy to  
hear your thoughts, and from other on the list.

Springerlink offers the .PDF of Beer et al (1998) using the following  
path:  http://www.springerlink.com/content/gyp1gpb955tde85h/

If the link doesn't work for some reason, try a Google Scholar search  
- it should get you there.

All the best,


On 10/12/2008, at 7:49 PM, Steve Dalton wrote:

> Merry Christmas to all.  I am looking at photoacclimation in two coral
> species using the PAM and want to determine sub-saturation  
> irradiance (Ek)
> of replicate fragments exposed to different light and temperatures  
> regimes.
> But, I am unable to accurately determine Ek for each treatment  
> without an
> accurate determination of absorbance factor (AF) for hard corals.   
> If anyone
> has been able to determine the mean AF for hard corals or know of any
> publications that indicate the absorbance factor for the PSII for  
> symbiont
> algae a reply would be great.  I am hoping that monitoring stressed  
> coral
> through time using Ek and ETRmax as an indication of short term
> photoacclimation.
> Cheers
> _______________________________________________
> Coral-List mailing list
> Coral-List at coral.aoml.noaa.gov
> http://coral.aoml.noaa.gov/mailman/listinfo/coral-list

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