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Dinos are one of those reefing topics that is intensively emotional. Many reefers decommissioned or restarted their aquarium due to dinos,  while many others claims that dino can be wiped out by simply adding product X or equipment Y. Truth is, if the aquarist takes correct actions, dino problem does not automatically means high casualties or tank reset. On the other hand,  what some aquarists' triumph against dino, may in fact be victory against a less insidious foe. Let's take a closer look at dinoflagellates to understand better what we are dealing with. 

I would like to start by discussing two myths about dinos. 


1. All dinos are the same/similar

There are about 2000 different species of dinoflagellate, almost half as much as that of corals. These different species of dino occupies different niche in the ecosystem. It's therefore unhelpful to consider all dinos the same,  especially when it comes to considering treatments for dino bloom. 

2. We can identify dino infestation just by looking at the aquarium. 

Of course,  there are certain signs which  point strongly towards dino outbreak. For example, stringly bubbly brown films hanging on the coral.  We can only have positive identification once the sample is observed under microscope. See a brown patch on the sand bed?  Is that diatom, dino, or cyano?  Identification with naked eyes is unsatisfactory.  To make matter worse, several different species of dinos may look the same to our eyes,  but require somewhat different approaches to overcome them. Therefore,  the first step of winning against dino is to know exactly which species of dino we are dealing with. If not,  any action we take is just a shot ib the dark. 


As my aquarium is in the midst of a dino outbreak,  it's a perfect opportunity for me to take a closer look at the topic of dinos.  

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Biology of Dinoflagellates

Dinoflagellates are single cell microorganisms. While often considered algae,  they are sometimes considered to be protozoa. This is unsuprising,  because dino exhibits both characteristics of algae and protozoa -They can photosynthesize, and they can move around and prey on other organisms as well. In fact,  without dinoflagellate,  we can forget about having most coral reefs. This is because the zooxanthelle,  or rather,  the Symbiodinium in the photosynthetic corals, is a group of dinoflagellate. So yay!  We need dino in our tank. 

Of course,  we only worry about  those dino which makes our aquarium ugly and kills our corals,  right?  So we shall focus on the harmful aglae (yes,  it's a scientific term). 


The Whirling Whip

Dinoflagellate is the combination of two words: dino,  which means whirling;  flagellate,  which means whip. Dinos are equipped with two whips,  which helps them to move around rather effectively. 


Take a look at this amphidinium from my aquarium. Looking at the brown cell on the right, you should be able to make out two different whips. One goes around the "beak" on the left side of the cell,  another is a longer one fixed on the right side. The whirling motion of the flagella allows the dino to move and orientate itself. 

There are many other species of dino, which will look completely different under the microscope, but they will all have the two flagella characteristic of this phylum. 


The Harmful Algae

How does some dinoflagellate harm our aquariums?  There are two main processes:

Firstly, dino compete with other aquariumn residents for nutrients. When conditions are favorable, dino reproduce rapidly. They can divide every day, and they can produce sexually as well. This rapid growth is fueled by aggressive consumption of nutrients in the aquarium, depriving other corals, and leads to their demise. 

Secondly, many dino produce toxin as a mean of defence, or as a weapon to suppress their competition. As a result, few animals are willing to graze on the dino.  On the other hand, if the dino population is wiped out through some medication, these released toxin can spell disaster for the rest of the aquarium. 

One other process, while not harming the aquarium directly,  make dino difficult to overcome. Being able to move,  dino regularly migrates, especially at night. Some species launch themselves into water column, spreading to claim new territories, while others migrate deeper into the sand bed,  hiding from potential predators. Speaking of protection, some dino are even armored with a theca


Having taken note of these processes, it's possible to fomulate strategies to manage the dino situation after the offending species is identified. 

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The dino bloom in my aquarium are largely Amphidinium sp. This genus of dino are often mis-identified as diatoms, because,  to the naked eyes,  they are almost identical. 

The macroscopic appearance of amphidinium bloom is a brown dusty appearance on the sand bed. There is very little stringy mucus.  Unlike diatoms though, amphidinium generally does not encroach onto the rock work. 


During night migration,  unlike many dinos which migrate into water column, amphidinium migrates deeper into the sandbed instead. 

Microscopically, amphidinium does not have an armored shell (theca). It can be identified by the asymmetric cleft,  which looks like a beak. 


It has two flagella (whips)  which helps it to move rather effectively in water.  It has a nucleus, and it is capable of both asexual and sexual reproduction;  can even form inactive cysts when the environment is less than ideal. 

If we consider the characteristic of amphidinium, there is no doubt that it's a resilient organism, difficult to control in an aquarium setting. Since it does not migrate into water colomn, UV is ineffective against it. Due to its fast reproductive rate, it can easily overwhlem other macro and microalgae. The only "good" thing about it is that it has very low toxicity. Therefore the clean up crews does not perish during amphidinium outbreak. 

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Treating the Amphidinium Situation  

Since amphidinium does not migrate to the water column, we can't use UV to reduce its population;  since it stays on sandbed,  and even migrate into the sand at night, hydrogen peroxide is not very effective against it. Algaecides such Dino-X may reduce, even eliminate some species of dino, but there is no guarantee, not to mention it will likely cause havoc in my already sullied ecosystem. 

Since amphidinium does not affect corals much, and are of negligible toxicity, There is a tried and tested strategy for amphidinium bloom : silicate dosing. 



No,  silicates do not kill amphidinium. We elevate the silicate level in the reef aquarium to 2ppm or higher,  so that diatoms are encouraged to grow. When diatom population rises, they start to compete with amphidinium and eventually suppress them. When diatom finally drives the amphidinium population to extremely low levels, the silicate level can be slowly brought down,  and the diatoms will decline in step with the silicate level.  As long as there are other micro-organism to occupied the newly opened niche, the amphidinium problem is resolved.  Not only that, we end up with a healthier ecosystem with robust microbe population. This will make the aquarium more resilient against future outbreaks. 

I'm 2+ weeks into this silicate dosing regime. Outwardly the sand bed looks worse. The brown patches are darker.  But microscopically, it's nothing but good news. There is finally more diatom cells compared to amphidinium cells,  and the number of amphidinium cells decreased significantly. 

The following two microscope videos for comparison:

 Nov 9th.  Note the large numbers of amphidinium cells. (400x magnification) 

 Nov 23, notice there are much less amphidinium cells,  even as the field of view is wider (200x). Also note the large number of beautiful diatoms. 


This is not a "solve the problem today" method, nor is it effective against all type of dinoflagellate. There are some pointers regarding silicate dosing,  which I will discuss in the next post. Until then,  always remember, it's essential to ID the dino before treating them. 


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Silicates for Amphidinium 

Let's address the elephant in the room: silicate?  Is this one of those evil contaminants we need to remove from the aquarium?  Isn't silicate gonna cause nuisance algae to grow in the aquarium?  Just like phosphate and nitrate? Don't we use all sorts of filters (such as ro/di) to remove every bit of silicate. 

Most of the time,  there are some truth to it. However in dealing with amphidinium, silicate is crucial because it is the fuel for diatom growth. Diatoms require silicate to build frustules, which is the beautiful glass like shell. 


Other than fueling diatoms,  silicate can also help in the growth of sponges. There are little other side effects for silicate dosing. All in all,  a very safe and effective way to overcome amphidinium. 

Chemically,  sodiun silicate is a colorless solution with very high pH.  Being a strong alkali,  it can cause skin irritation and injuries. Therefore it is important to be careful when handling the solution. 


Tips for Silicate Dosing 

There are a few quirky observations when dosing silicate. It's good to keep these in mind. 

1. Start slow,  and test the silicate level. Although silicate is not harmful in a reef tank,  there is no need to increase the concentration to extremely high levels. In the beginning, when there is little diatoms, the silicate uptake is small. There is no point in dosing a large amount everyday when starting off. Raise the silicate to 2-4ppm or so,  and keep it there. 

2. High flow. Silicate has a pH as high as kalkwasser, and is more concentrated. Therefore when adding silicate to the aquaeium, it will cause temporary cloudiness just like dosing kalkwasser or kh supplements. The cloudiness will clear away on its own,  but dosing in to high flow area is certainly recommended. 

3. KH.  Just like adding alkali such as kalkwasser,  silicate will increase the kh of an aquarium. It's essential to adjust the kh dosing,  to take into account of these additional kh added. 

4. Phosphates.  Phosphate media, Such as aluminum oxide or GFO, will remove silicate the same way they do phosphate. Keep these media offline when dosing silicate. In addition, the silicate level in the aquarium can cause false reading for some phosphate test kits. Don't be alarmed when phosphate reading is very high. 

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Turning the (Red)Tide

Dosing of silicate encouraged diatom to bloom;  and in turn, drive amphidiniun slowly out of business. 

After a month of silicate dosing,  the amount of amphidium is much less.  Even detritus sample from the sand contains much less cells than before. 


This is the image of bits of detritus.  A large number of diatom cells can be seen. Dino?  Not so much. 


A 400x image confirmed the cells are indeed diatoms. 


Macroscopically, it doesn't look much different than before. Afterall, diatoms are brown. But I'm certain the red tide has turned. Given time,  amphidinium would be completely suppressed. 

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Special Report on Dino Situation 

Well,  the situation is slowly coming under control. The sand bed still quite brown. However, microscopic investigation is very encouraging. 


As seen from the image (100x) above, the field of view is filled by diatoms. Witj only a few dino in sight. 


Multiple species of diatom. Very encouraging. 


Under 400x magnification,  even the aggregates are compose of mostly diatoms. 


Identifying the algae under microscope no only allows for a correct diagnosis, it also helps us to monitor the effectiveness of treatment. Without it, it is a lot to ask a reefer to look at visually unchanging brown sand for many months, and believe the method is working. 

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On 12/25/2021 at 2:24 PM, Andyreefer said:

The unconventional method of using diatom to suppress Dino! :yeah:


Many reefer has been doing this for a long time actually. 

The process is well documented. 

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New Year Updates

I'm near the end of the dino outbreak. The sand bed is still brown though due to diatoms.  The plan is continue to grow diatoms for another month or two,  the cutting back on silicate dosing slowly. 


FTS under daylight-ish illumination 



FTS under weak actinics + UV



Direction 2022

There are a few general direction I will pursue in 2022.

1. Coral nutrition 

2. Bio diversity 

3. Light spectrum for growth and color

I will document some of these process along the way. 

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The Non-Photosynthetics

I have been collecting some NPS corals, and tries to integrate them in to my reef scape. So far, things has been going well. In addition to seeing good polyp extension (which suggest good feeding response), I can observe encrusting (for sea fans) and new baby polyps (for sun corals).

The whole tank is broadcast fed with freeze dried plankton twice a day (before I leave for work at 6am, and in the evening at 7pm, approximately). It's also being supported by mulms produced by zeo reactor with hourly flushing.

Picture time!



Alcyonium palmatus. Chilli coral. Easy to get feeding. However it seems that it can exude enough chemicals to serverly injure the corals it touches. It does open day and night.



Rhizotrochus typus. Large solitary polyp. I do not target feed at all, instead, rely on the available planktons in the water column. As an experiment, I would like to evaluate the feasibility of having only planktonic feeding for this coral. It opens its polyp intermittently during both day and night.



Dendronepthea sp. Carnation coral. Large contrast between extended and contracted state. Opens intermittently during both day and night.



Tubastrea aurea. Orange sun coral. Mounted it inverted under a rock overhang. Exposed to very high flow, but larges under shade. Opens as the lights dim.



Tubastrea micrantha. Black sun coral. It opens as the light dims. It seems that it does not extend it's polyps when there is some level of UV spectrum. It has since budded a few baby polyps.



Acalycigorgia sp. Blueberry sea fan. This is a tiny nub I shared with another reefer. It has encrusted at the base. It opens day and night.



Alconarian sp. Fiji multi-colored seafan (not sure about the species ID). The polyps stays open most of the time. The base encrust rapidly.



Gorgonia ventalina. Purple sea fan. Polyps are out almost all the time.


Primnoa pacifica. Red tree coral. It's not in a good shape. After two month of it added into the aquarium, there is finally polyps appearing.

That's all for now.

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Dino Update

The outbreak of dino (large cell amphidinium)  has finally come under control. 

I have eased off dosing of silicate,  and diatom started to receed as well.  Samples from the aquarium shows very few dino cells. And greatly increased biodiversity. 

Opting for a non-algaecial method preserves the biodiversity, which in turn bolster the robustness of the ecosystem. Hopefully this will discourage further outbreaks. 


Hello, white sand. 

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Light and Corals

Light is a critical factor for coral health. Many corals contain zooxanthellae, which produce food through photosynthesis. Many corals produces chromaproteins and fluorescent proteins to cope with their environment. In addition, corals, even non-photosynthetic ones, relies on the light to synchronize their daily activities. 





Let's first consider what sun light really is. Without going in to much of the technicalities,  let us consider the sunlight as streams of photons. These photons travels from the sun, pass through our atmosphere, enters the water, and lands on the corals. The number of photons lands on 1 cm^2 of area in one second is called photosyntheic photon flux density (PPFD). In reefing hobby,  we call this PAR. While this is not correct, but it's kind of deeply rooted in our hobby. 

These photons however, are not all the same. Photons can carry different amount of energy. This difference in energy is inversely proportional to the wavelength of the photons. The shorter the wavelength, the more energy the photons have. We, or corals,  can't split photons. If a photon has too much or too little energy, they are not useful for the corals. 

Now if we were to consider only PAR, then we are looking at a rather incomplete picture. While we know how many photons we have, we don't know what types of photons we have. This is less of a problem in the days of T5 and metal halides. The bulbs and tubes have a known spectrum, and we need only to determine the intensity. With the advent of LEDs,  we can no longer take the spectrum for granted. The type and the number of diodes, the setting of the light profile,  these will have a big impact on coral growth and coloration. 

In the next few posts, I will try and discuss the impacts of several interesting spectrums,  and we can take a good hard look (metaphorically of course) at our lights. 

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So,  how does the light intensity affect corals. Let me outline a few important points. 

compensation point (CP): animal needs to use carbohydrate to produce energy,  and for corals and it's zooxanthelle, photosynthesis is how they (mostly)get this carbonhydrate. CP is the light level where the produced food is exactly the same as the food uses up by the organism.  If the light level is lower than the CP, corals will not have any excess nutrients to grow. 

photo-saturation (PS) : at this light level,  the zooxathelle in the coral is photosynthesizing at the fastest possible rate. At this level,  the lighting is optimal for coral growth. 

photo-inhibition (PI) : too much of good thing is not good  after all. If the amount of light exceed the PS level,  photos inhibition sets in. The photosystem in the chlorophyll become inactivated by the light,  and overall efficiency decreases. Corals will have to make changes to adapt to this level of light.  They can do so by reducing the zooxanthelle density, or by production protective pigments. 

It's important to take note, that for different corals,  or even same coral at different water conditions, the amount of light for CP,  PS, and PI can be very different. Also,  there are studies which may suggest that these factors are also spectrum depended. So all in all,  a very complicated matter. We will slowly look at different facets of this in the next few posts. 






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Have you ever wondered why one of the most popular LED light profile is called AB+?  Well I guess one of the reason is that the spectrum attempts to match the absorption peaks of chlorophyll a (Chl a) and chlorophyll b (Chl b),  both of which are found in zooxanthelle. 

Consider this adsorption spectra (source: Wikipedia


The highest absorption peaks for Chl a and Chl b ranges from 420 nm to 490 nm range. These wavelengths correspond to violet and blue light. Therefore, most of the modern reef lights produce a large amount of blue light. These caters well to the need of Chl a and b. 

On the other side of the spectrum, the 650 nm to 680 nm range correspond to amber and red spectrum. These wavelength also contribute to photosynthesis. Many reef lights provide these wavelengths through red diodes,  and to a lesser extend, white LEDs. 

It'a also worthwhile to note that the absorption is very low in the green region. On the other hand, human eyes are very sensitive to green light. Therefore some output from green diodes can make the reef aquarium looks much brighter,  while not contributing much to coral growth. 



There are a few caveats concerning the above (simplified)  information. 

1. There are more pigments in zooxanthelle than Chl a and b. There are beta-carotene, xanthophyllChl f, etc.  They do make use of other part of the spectrum. However,  Chl a and b are the dominant pigments in coral system. 

2. The absorption spectrum of Chl a and b extends well in to sub 400 nm wavelengths (UV-a),  while Chl f absorption spectrum extended into the IR region. The reason most absorption spectrum shows 400 nm -700 nm is because this is the range defined for PAR. 

3. This discussion of spectrum is with reference only to photosynthesis. This is not a discussion for coral color (yet). 


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Crazy Lights


I have finally finish my light collection for my aquarium with the latest addition of OR3 light bars. Let me share about how my light system changes into the current form as I try to adapt to the animals I keep.

I started running this 4.5x2.5x2.5 aquarium with two Wyatt lights. The 240w light, a local enterprise, gives good spread, PAR and value for money. Since my aquascape is offset to one side, my two light sets are offset from the centre as well.




It worked well, giving corals plenty of light to grow, while largely stay off the glass and minimized algae growth. There is one problem, however. Since the light shines from the top, and shaded by the top corals and rock, the amount of light reaching the front is very limited. I dislike the pale underside of colonies; nor do I want my corals to grow steeply towards the light rather than plating out. I decided to provide an angled fill light near the front edge of the aquarium. I did not opt for a light bar or a lower powerwd light. This is because I need the fill light tobe equal in quality and quantity, so that the coral can color up evenly. 3 lights now.




The addition fo the third 240w light brings a lot more color to the viewing side. But soon I encountered a new problem. As I start to introduce clams to my aquarium, it is apparent that my open sand bed 2.5' down does not have nearly enough light to support them. Solution? One more light.




Moving on, the amount of light is sufficient at all depths. The coverage is good. Time to start to look into the quality of light. I become interested in the role of UV spectrum in growth and color of corals. I have since installed customized OR3 light bar, supplying 385, 420 nm radiation to the coral. The result is very obvious so far. Finally. Today the second light bar with 365 and 740nm diodes are in. My light is set.




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The journey of Acropolis comes to an end. 

Long story short,

Tenetti tang decided to start pecking on lps suddenly.

I moved out the lps and clams, then decided to get some dwarf angels since there is only sps left.

Flame angel and multibar angel proceed to wipe out my sps collection.

The last fish purchase also brought in some parasites, many fishes died from bleeding.

Hence, a reset.

Coming soon, Acropolis 2.0

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