Article haven

[blueheaven]

As the school holidays are here, I am contributing my free time to write articles to help beginners understand better of the different aspects of reefkeeping.

This is an article that I have written some time ago. Hope it helps.

Here's my article on Sandbeds

Many people have conflicting ideas on setting up a refugium, especially one with a sandbed. I have seen set ups with a DSB (Deep Sand Bed) of about 4" to 6" thick. And sadly, a lot of people think that just by putting in some sand and macroalgae, they have a working refugium. I firmly say NO.

In my opinion, its important to know and understand the thing you are doing before doing it. Although sandbed dynamics are still being researched, I will provide the current information available.

Bacteria and zones

The main purpose of adding a sandbed is to allow bacteria to colonise on its surface. Many people think of diseases when the word "bacteria" is mentioned. The bacteria we are talking about here are those that convert certain compounds to another form.

There are mainly 2 groups of bacteria, namely the aerobic and anaerobic. Aerobic refers to the presence of air and anaerobic refers to the absence of air.

And the confusion comes as each group will split into 2 groups. The 2 groups are the autotrophs and heterotrophs. Autotroph meaning the organism is able to synthesize its own food from inorganic substances and heterotroph meaning

an organism that cannot synthesize its own food and dependent on organic substances.

Basically, there are 3 groups of bacteria we are interested in. The aerobic autotrophs, aerobic heterotrophs and anaerobic heterotrophs. The aerobic heterotrophs will break down organic substances into inorganic compounds (eg. ammonia). These inorganic compounds are then taken up by aerobic autotrophs which will perform nitrification. The anaerobic heterotrophs will perform denitrification.

The aerobic autotrophs are usually found on the suface layer of sand since they need oxygen and light to synthesize food. The other area around the top 1/3 of the sandbed will be colonised by aerobic heterotrophs. And as oxygen levels decrease down the sandbed, anaerobic heterotrophs will colonize there.

An important point to note is that anaerobic zone actually consisted of 2 different zones. The zone that has oxygen concentrations of 0.5-2 ppm (test conducted by Sam Gamble) is named as the "anoxic" by Bob Goemans. This zone will contain facultative (bacteria that live with or without oxygen) bacteria that fully oxidize nitrate back to nitrogen gas.

The other zone that has no oxygen at all will consist of anaerobic heterotrophs with only convert nitrate into ammonium which is a better fertilizer than nitrates for algae.

This explains why I think that really deep sandbeds are not good as your ultimate goal is to achieve an anoxic zone. The recommended sandbed depth should be 3"-3.5"

Grain size and size of refugium

Normally, people try to use the smallest grain size for their sandbed. This differs between systems and I shall explain.

It is good to have small grain size as it increases the surface area for bacteria to colonise. But this only applies to systems which have the skimmer output there or any other source of oxygenated water. If the area is in lowly oxygenated water, the oxygen diffusion will be limited to the upper layers.

For those people who have lowly oxygenated water in their sandbeds, it is advised to use bigger grain sizes and a bigger sandbed. This will allow oxygen to diffuse deeper faster.

Infauna and their importance

The word "infauna" is new to many people. It actually means the fauna (animals) IN the sandbed. So why do these animals make such an importance in sandbeds? The infauna consist of mini-stars, micro-stars, worms, flatworms and a myraid of other small animals. These infauna will constantly shift the sand and their action will prevent the sandbed from reaching a completely anaerobic zone. This action also ensures that the sand does not clump together as a result of precipitation and bacterial actions.

I really hope that LFS will start to bring in recharge kits consisting of these infauna that reefers can add to their sandbed. If not, these animals will come as hitchhikers on live rock.

Quorum Gene Sensing

This is a relatively new concept to sandbed dynamics and it involves bacteria. Quorum sensing is actually a way bacteria produce this gene that senses the population of the bacteria. The researched bacteria is the Vibiro spp. and it is found that the bacteria will produce toxins that kill human cells in high populations.

It will be interesting to do research on the nitrifying bacteria and see whether they will be detrimental in high population sizes. And we could see whether we can stop the production of the Quorum gene .

This comes to the end of my article and I hope readers will find this useful and I will type another article on different types of sumps next.

The top information on different types of bacteria and zones are from Sand Mail, FAMA Aug 2004 by Bob Goemans

[damien]

Good effort! Keep it up!

[Lin]

hey, itz intersting and i m sure i noe alittle more~ theres still alot more to learn..CHEERS

[blueheaven]

If you want to do a follow-up on my article, you are invited to do so.

And others who wish to contribute their articles can post them here

[blueheaven]

I'm currently working on my article on NSW and synthetic salt

In the meantime, here's another article from me

Coral Colouration

Usually, people buy corals that look exotic and contain intense colours only to find out that that precious specimen has eventually turned into a dirty brown tan. Most of these people either sell away these specimens or even throw them away. Then, they visit the LFS again and purchase another specimen. Such actions are very damaging to reefs and inhumane.

Some may ask, why does "expert" reefers here are able to have such colourful specimens in their tanks? And usually this aquarist eventually backs out from this hobby as he cannot get the satisfaction he wants.

Basically, there are 4 main components that contribute to nice colours in corals. These are water quality, lighting, nutrition and genetics.

Water Quality

Water quality is top priority in aspect to colouration. After proper cycling of the tank, ammonia and nitrites are of little concern. The main concern here is nitrates. Although nitrates are very much least toxic than the former two chemicals but it is a good fuel for algae. So what has coral colouration got to do with nitrates?

Majority of corals contain zooxathellae, one celled algae, in their tissues. These special symbiotic algae are the ones that are responsible for coral colouration. These algae are golden brown in colour and corals have a special enzyme that forces the algae to secrete sugars they produce from photosynthesis. So how does these brown algae produce bright colours?

Going into deeper biology, we know that fluorescent proteins are synthesized when the promoter is stimulated or activated. The stimulus we are interested in is UV exposure. Zooxathellae produce coloured pigments that act as photoprotection from harmful ultraviolet rays. Ultraviolet rays also stimulate the fluorescent proteins and make them glow.

Getting back to nitrates, high nitrate concentration will cause a massive algal bloom within the coral. Although zooxathellae produce colours, the high density of these symbiotic algae actually masked the colours produced. This results in the browning of certain corals. So the first step to ultimate coral colouration is to achieve an undetectable nitrate level.

Lighting

We all know that everything we see around us are actually reflections of light into our eyes. Even if you have the most powerful lighting system, your corals may seem bland as the amount of colour that is reflected into your eyes are low. People using 6500k bulbs generally see corals as yellowish with reds more prominent. This is due to the spectrum of the bulb that leans towards the red region of the 7 colours of white light. 10000k bulbs generally give a more uniformed colouration as it is considered a full spectrum bulb. 14000k to 20000k bulbs bring out the blues and purples better.

Therefore, using a powerful and strong light does not necessary mean that corals will show their nice colours. In fact, using too powerful lights will cause an increase in photsynthesis of zooxathellae so much so that the coral itself suffers as well.

Nutrition

A few years back, people think that providing strong lighting for corals and the byproducts of photosynthesis is enough for the coral to survive. Recently, there has been an emphasis on feeding corals to provide more nutrition. Basically, increased feeding and external nutrition for corals have positive results from more intense colouration to faster growth.

With special regards to SPS, it has also been speculated that addition of halogens also results in the coral becoming a solid colouration but long term usage has not been recorded.

For corals with a visible "mouth", it is recommended that the aquarist feed them small shrimps or scallops and for smaller polyped specimens, it is recommended that specialised food such as Golden Pearls be fed.

Genetics

Lastly, the type of colours you want from a coral depends on its genes. If a coral has genes that makes it naturally brown, there is no use trying to colour it up. That's why you see people collecting specimens from all over the world to add special strains of corals. Coral farmers are also looking into reproducing the special strains for distribution. Therefore, do not blame anyone when your yuma or stylo does not turn out as nice as other reefer's.

This marks the end of my second article and I hope that other reefers will share their articles here. Do look out for other articles I will be writing in th future.

[giantbicycle]

Wow!!got it,....well done bro..

Opps, Pm me if u are done considering me in the.****..

[jOsHiE]

regarding your article of size of sand for the refugium.... u said "It is good to have small grain size as it increases the surface area for bacteria to colonise. But this only applies to systems which have the skimmer output there or any other source of oxygenated water. If the area is in lowly oxygenated water, the oxygen diffusion will be limited to the upper layers."

wat do u mean that the skimmer out put there... so if i were to do a dsb in my second compartment of my sump and my skimmer in my third compartment... means i should use #grade 1 sand instead???

[blueheaven]

Basically what i am saying here is that if the water entering your DSB is lowly oxygenated, you are better off with grade #1 sand

A guage of whether is oxygenated or not is whether there is any compartment where the water is splashing, or if you are using a powerful skimmer that aerates your water vigorously.

But in any case, try not to exceed 5" in depth so as not to create a totally anaerobic region

[shoelevy]

hm...can i ask u sth?

i quote "The anaerobic heterotrophs will perform denitrification."

denitrification is a process where no3 is converted to n2 gas rite?

so no3 is food for the heterotrophs ya?

according to "Autotroph meaning the organism is able to synthesize its own food from inorganic substances and heterotroph meaning

an organism that cannot synthesize its own food and dependent on organic substances."

since no3 is not an organic compound since it contains no C atoms...so the anaerobic bact doesn't feed on organic comp so according to yr definition, shouldn't the anaerobic bacts be called autotrophs instead of heterotrophs?

jus sth that puzzled me...no offense to shoot u blueheaven

[blueheaven]

Ok I'll see to the issue later cause I need to go out now

[blueheaven]

hm...can i ask u sth?

i quote "The anaerobic heterotrophs will perform denitrification."

denitrification is a process where no3 is converted to n2 gas rite?

so no3 is food for the heterotrophs ya?

according to "Autotroph meaning the organism is able to synthesize its own food from inorganic substances and heterotroph meaning

an organism that cannot synthesize its own food and dependent on organic substances."

since no3 is not an organic compound since it contains no C atoms...so the anaerobic bact doesn't feed on organic comp so according to yr definition, shouldn't the anaerobic bacts be called autotrophs instead of heterotrophs?

jus sth that puzzled me...no offense to shoot u blueheaven

Ok, somehow I had reviewed this thread and I will explain it to you

An organism being an autotroph is able to synthesize foos for itself in the prescence of light, somewhat like photosynthesis.

Since the bacteria is unable to use light to make its own food, it cannot be classified as an autotroph

[blueheaven]

Read a similar article today from FAMA

The writer pointed out quorum sensing too in his article. Seems like this field is kind of exciting to explore. (BTW the part on quorum sensing came solely from me and I had not noticed that the foreigners also thought of the same thing)

Would propose a research project on quorum sensing with regards to reef systems

[blueheaven]

I had just reviewed this thread and I had prepared a follow up on the sandbed article.

From Ammonium to Nitrogen

As previously stated, in a zone which is totally anaerobic, ammonium will be produced rather than nitrogen gas. This can be a problem as ammonium is a very good fertiliser for nuisance algae.

But recent research conducted in the Black Sea found that bacterium from the order Planctomycetales is able to convert ammonium to nitrogen gas together with nitrite.

This process termed Anammox stands for anaerobic ammonium oxidation. Nutrient profiles, fluorescent RNA probes, 15N tracer experiments and the distribution of specific "ladderane" membrane lipids show that the ammonium that is diffusing upwards is consumed by anammox bacteria just below the aerobic zone.

This shows that anammox actually plays a part in the Nitrogen Cycle in the sea and occurances in captive systems is a new field that is worth researching. By showing how deeper sandbeds can actually be a zone for the colonisation of anammox bacteria might just unlock a new methodology for sandbed keeping and who knows what benefits it can hold?

Next up will be a follow up on the black substance usually found in sandbeds so stay tuned!!

The above information about anammox bacteria are from nature publishing group, www.nature.com

[qazwer]

wow bro blueheaven,

I'm sure to learn more here ...

for you!!!

Qazwer

[blueheaven]

bro..that isnt true

autotrophs are organisms capable of synthesizing its own organic substances from inorganic compounds.

organisms which synthesis organic compunds in the presence of light via photosynthesis like plants are called photoautotrophs and they are a kind of autotroph...not all autotroph requires light

just my 2 cents

Yeah I was about to correct that statement but I need more info

Thanks a lot decentkid

[blueheaven]

Also take note that the aerobic autotrophs will synthesize food from light and that's why they are found in the surface zone.

[jem]

two thumbs up for you bro!..Blueheaven -> next anthony calfo?...

[blueheaven]

Nah, I cannot compare to Anthony

He is my Master

[blueheaven]

Follow up on black sunstance in sandbeds will be posted on Saturday

Stay tuned

[blueheaven]

Black substance in sandbeds

I am definately sure that any aquarists who have kept sandbeds before would have come across the statement that a black layer would be formed. Some say this is hydrogen sulphide, some say this is cyanobacteria. Actually, this black stuff is none other than FeS or Iron sulphide.

Iron sulphide itself is a brown precipitate and due to the intense colour, we often perceive it as black. All sulphides are toxic to organisms and thus, this chemical is not good for reefs.

This compound is formed by sulphate reducers which being anaerobic bacteria, usually thrive under mats of the cyanobacterium Lyngbya sp. or in any anaerobic region. Thus, in anaerobic regions of sandbeds, a "black" layer of FeS is formed.

FeS can be oxidised in the sediment by MnO2 or maganese oxide into FeOOH, S, Mn and H2O. It can also be oxidised into sulphuric acid by autotrophic or mixotrophic bacteria and will be neutralised by calcium carbonate into calcium sulphate.

All in all, the black substance is not much of a worry BUT it indicates that the sandbed has a totally anaerobic zone and this should be the main worry of aquarists

[blueheaven]

And if anyone are writing articles on any aspect of reefkeeping, pls feel free to post it here

[klim]

Black substance in sandbeds

I am definately sure that any aquarists who have kept sandbeds before would have come across the statement that a black layer would be formed. Some say this is hydrogen sulphide, some say this is cyanobacteria. Actually, this black stuff is none other than FeS or Iron sulphide.

Iron sulphide itself is a brown precipitate and due to the intense colour, we often perceive it as black. All sulphides are toxic to organisms and thus, this chemical is not good for reefs.

This compound is formed by sulphate reducers which being anaerobic bacteria, usually thrive under mats of the cyanobacterium Lyngbya sp. or in any anaerobic region. Thus, in anaerobic regions of sandbeds, a "black" layer of FeS is formed.

FeS can be oxidised in the sediment by MnO2 or maganese oxide into FeOOH, S, Mn and H2O. It can also be oxidised into sulphuric acid by autotrophic or mixotrophic bacteria and will be neutralised by calcium carbonate into calcium sulphate.

All in all, the black substance is not much of a worry BUT it indicates that the sandbed has a totally anaerobic zone and this should be the main worry of aquarists

Hi Blueheaven,

How long will this "Black" Substance developed? In that case, if we turn the sand often , will this substance develpe?

I have a lots of snail, big and small, also starfishes, will this help to prevent it from happening?

Appreciate your advice.

[blueheaven]

Hi bro, the rate of production of this ppt will be limited by the amount of anaerobic bacteria you have. Usually this develops about 3-4 months of having a sandbed but technically, this process will occur as long as you have a very deep sandbed.

It is not advisable to have too many organisms to disturb the sandbed as you disrupt the oxygen diffusion rate for any specific area and ultimately disrupt the different zones. Remember, the bacteria we are talking about here is facultative

[Kelmen]

Black substance in sandbeds

...

All in all, the black substance is not much of a worry BUT it indicates that the sandbed has a totally anaerobic zone and this should be the main worry of aquarists

I'm confusing here. So, should we worry about it or not?

And shall we leave it alone, or work on something to remove\reduce it?

[blueheaven]

You should not worry about the black stuff but more on how to achieve the anoxic zone in your sandbed. The black stuff are just "indicators" to tell you that the sandbed has a totally anaerobic zone