Coral Holibiont

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To further understand the biochemistry of the Coral Holibiont requires an understanding of physics, chemistry, micro biology.

When Felderman said that photosynthesis was the combining of the inorganic & the organic world, he got my attention.

Conclusions​

Coral reefs have been characterized as oases of biological productivity in a marine desert (Capone, 1992). The surrounding oligotrophic (= nutrient depleted) waters provide little sustenance to the reef biota. As a consequence, complex nutrient recycling webs have evolved on reefs to retain and reutilize essential elements like nitrogen and carbon. The carbon cycle on reefs is multifaceted and is beginning to be unraveled. Reliable measurements of dissolved organic carbon (DOC) levels are critical for this goal, and the introduction of the Shimadzu TOC Analyzer represents an unequivocal leap forward in research capability. On thriving reefs, most carbon input originates with atmospheric CO2, which is “fixed” via photosynthesis first into carbohydrates, and then into a multitude of other organic molecules. Much of this carbon, which is generated by the zooxanthellae in corals, is reemitted as coral mucus. This coral contribution significantly enriches the pool of DOC.
This DOC is prime food for a large variety of reef microbiota, including bacteria, both in the water column and in the corals themselves, and microplankton, etc. Finally, these microflora and microfauna serve as food for a variety of filter feeders, including, again, the corals. Thus, the interdependency of reef organisms, both large and small, is revealed as the carbon-based nutrients are recycled. The surrounding oligotrophic ocean serves as a buffer which can absorb excess nutrients that might otherwise prove harmful to reef inhabitants and modulate the levels of dissolved species by import and export, depending on relative (reef vs. open ocean) concentrations. Our captive reefs fall far short of this nutrient commerce model; we have, of course, no open ocean buffer to dilute away waste and so we rely on water changes to perform this vital function, and it remains unclear whether our aquaria contain all of the components, in appropriate proportions, of authentic reefs necessary to promote efficient nutrient recycling. Nevertheless, what we do seems to work, at least most of the time. But, what happens when things go wrong? Circumstantial evidence from Rohwer’s studies implicates DOC imbalances in coral mortality, with runaway bacterial growth as a likely mediating culprit. Can these observations inform aquarists, and is there a response that might ameliorate the problem? Certainly the first step is to establish a baseline of TOC ( DOC) levels in healthy reef aquaria under different husbandry protocols. In this article, data has been presented that accomplishes this goal, and further, validates these TOC numbers by comparison to TOC/DOC levels on healthy reefs around the world. In addition, the surprisingly minimal impact of protein skimming on TOC levels was revealed. On this point, it is apparent that if TOC levels can be monitored to assay the effects of one skimmer (the H&S A200 in this case), then they can be monitored to measure the impact of different types of skimmers operating on an experimental tank. In addition, these types of experiments also can be used to probe more directly and quantitatively the TOC removal capabilities of Granular Activated Carbon (GAC) that was hinted at in the tank #2 vs. tank #3 comparison. These types of experiments might allow, for the first time, a quantitative evaluation of skimmer and, independently, GAC performance which is divorced from the hype and misinformation that seems to surround these areas of marine aquarium maintenance/equipment. These experiments are ongoing and results will be reported in due course.

Finally, the goal of identifying approaches to halt incidents of coral mortality in reef tanks may benefit from data collection from “sick” tanks rather than the healthy aquaria examined in this study. If tanks undergoing coral crashes have an unusually high (or low) amount of TOC in the water but otherwise have acceptable water parameters, then a new and otherwise unappreciated villain will be in hand. Under these circumstances, what can the aquarist do? One experiment described by Ferrier-Pagès on Galaxea provides food for thought. Specimens of this coral were treated with the combined antibiotics penicillin, streptomycin, and amphotericin; subsequent bacterial uptake of DOC, which Rohwer identified as a mechanism for coral mortality when occurring in excess, ceased.
As I reread some of this thread, I decided to resurrect the thread and see where it goes.
Let the good times roll.
 

Beuchat

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Dear Patrick, thanks a lot for recommending my book!

Just to let you know, I’ve actually just released a new revised and expanded edition. It ended up being over 600 pages long, so it had to be split into two volumes. For now it’s only available in Spanish, but I hope to finish the translation soon.

In the photo below you can see one of my assistants posing with the new books.

About the Old Testament verses, I’d say you don’t need to take them too literally. We all know you can keep extraordinarily beautiful aquariums from a completely atheist point of view 😂
IMG_5001.jpg
 
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@Beuchat

Does the expanded addition of your book include anything about gene expression within the bacterial community of the Coral Holibiont? If it does, I will bring you to the forefront of current discussion about using sequencing dna science.
 

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Hi Patrick,

I have not included the description of that technique. I belive It is a technique with great potential to better understand the microbiome of the holobiont, scientifically very interesting but of limited practical usefulness for the average hobbyist.
 

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Hi guys, regarding the new edition of Reefkeeping Fundamentals, it has benn just released, revised and widely expanded in two books with more than 300 pages each. The ratio of legacy versus new information is about 50/50. Delta information is focused on the following topics:

- The optimal light spectrum.
- Comparation HQI, T5, LEDS
- Electrical installation
- Tank dimensions, placement, etc
- Coral Fluorescent photography
- Water recirculation
- Nitrate&Phosphate balance (a new paradigm)
- Disruptive & highly effective method to eradicate nuisance dinoflagelates outbreaks
- Water changes nutrient export simulations
- Deep dive on DSBs and carbon dosing techniques
- Deep dive on lanthanum clhoride
- Addition of amonia as N source to zooxantelae.
- Biological role of trace elements
- Deep dive on balling system and Calcium reactors
- Determination of alkalinity additives consumption rates.
-The organic method for alkalinity suplementation.
- 9 reef tank examples. From minimalist natural systems to fully automated High-Tech Reefs.

Vol 1.1. https://www.amazon.com/dp/B0GPNZYSKB

Captura de pantalla 2026-02-27 a las 8.37.31.jpg


Vol 1.2. https://www.amazon.com/dp/B0GPNM6KY8

Captura de pantalla 2026-02-27 a las 8.37.57.jpg


I hope this series of books will be usefull to the reefing comunity . Thanks for reading!
 
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Hi guys, regarding the new edition of Reefkeeping Fundamentals, it has benn just released, revised and widely expanded in two books with more than 300 pages each. The ratio of legacy versus new information is about 50/50. Delta information is focused on the following topics:

- The optimal light spectrum.
- Comparation HQI, T5, LEDS
- Electrical installation
- Tank dimensions, placement, etc
- Coral Fluorescent photography
- Water recirculation
- Nitrate&Phosphate balance (a new paradigm)
- Disruptive & highly effective method to eradicate nuisance dinoflagelates outbreaks
- Water changes nutrient export simulations
- Deep dive on DSBs and carbon dosing techniques
- Deep dive on lanthanum clhoride
- Addition of amonia as N source to zooxantelae.
- Biological role of trace elements
- Deep dive on balling system and Calcium reactors
- Determination of alkalinity additives consumption rates.
-The organic method for alkalinity suplementation.
- 9 reef tank examples. From minimalist natural systems to fully automated High-Tech Reefs.

Vol 1.1. https://www.amazon.com/dp/B0GPNZYSKB

Captura de pantalla 2026-02-27 a las 8.37.31.jpg


Vol 1.2. https://www.amazon.com/dp/B0GPNM6KY8

Captura de pantalla 2026-02-27 a las 8.37.57.jpg


I hope this series of books will be usefull to the reefing comunity . Thanks for reading!
Thank you.
IMO, too much emphasis is put on bacteria as tanks mature. In the beginning, you need and want bacteria but as tanks get more and more corals, algae, micro critters who can use and process fish waste directly for the benefit of themselves and the whole ecosystem, bacteria fall by the wayside still existing but performing a less important function. What was once a danger is now a savior (ammonia). I think that many researchers miss this. Most hobbyists do.

Regarding DOC/sugars, the best way to get them is through zoox, as explained... yet people try and cut the light quality and quantity in their tanks for a myriad of reasons. You can make corals look very good and also have them producing lots of sugars for your tank if you are good at your craft. This bunk that somehow corals do best in only blue light is a disaster over time and was based in only one small micro fact ignoring many others - akin to simple sugars are great while vigorously exercising so I am going to eat simple sugars all of the time.

For me, the largest problem with encouraging a holobiont is that people only want to focus on what they can see on test kits or get immediate results from. This leads to wanting to add waste products not knowing what they actually do - no3 and po4 are waste products. They go to chemicals that leave a void in the ecosystem chain (like @Beuchat explained) and cause long term damage - often exacerbated by bogus manufacturer claims and the blind leading the blind in online discussions.

What people need to focus on is really complex, but if you suggest a). studying real sources, learning from really good hobbyists, having patience, building for the future and learning some biology and chemistry vs b). watching a BRS video, getting a bunch of test kits and dosing XYZ because ReefBro123 online told you to do something.... most people will take B. However, I do appreciate all of the things that experienced hobbyists, researchers, etc. write since I want to be in A.
After revisiting this post it reminded me of @Randy Holmes-Farley theory on bacteria in captive reef tanks outcompeting coral for nutrients.

@Beuchat any thoughts.
 

Beuchat

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Thank you.

After revisiting this post it reminded me of @Randy Holmes-Farley theory on bacteria in captive reef tanks outcompeting coral for nutrients.

@Beuchat any thoughts.
Well, in the end all the organisms inside the aquarium compete for nutrients (if they occupy the similar trophic niche). For example, ammonia is food for zooxanthellae and for nitrifying bacteria. But at the same time, the waste products of some organisms are nutrients for others. For instance, the CO₂ released by certain heterotrophic bacteria is used by zooxanthellae and algae.

It is a recycling network of extraordinary complexity, in which each species of organism, from bacteria to phytoplankton and zooplankton, feeds and releases organic and inorganic compounds that are utilized by others. This is the food web that sustains all life in the aquarium and makes the water habitable for fish and corals
 

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