recent article - live rock as bio filter
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Although a bad pic, this is a cross section of a piece of glass. It is actually medieval glass that showed signs of stress cracking with age.
It is approximately the same magnification. The surface edge is at the top of the picture. As you can see. it is quite smooth and not pitted....even though it is really old.
I am sure Dr. Ron is not proposing that the glass walls are the main sites of denitrification. I showed the pics to show others that there is most likely more than enough surface area within the outer edges of coral rock to suffice as a base for baceterial growth.
Hopefully these pics will demonstrate that.
Paul
It is approximately the same magnification. The surface edge is at the top of the picture. As you can see. it is quite smooth and not pitted....even though it is really old.
I am sure Dr. Ron is not proposing that the glass walls are the main sites of denitrification. I showed the pics to show others that there is most likely more than enough surface area within the outer edges of coral rock to suffice as a base for baceterial growth.
Hopefully these pics will demonstrate that.
Paul
Hi All,
Perhaps this would be an interesting experiment.
ââ"šÂ¬Ã…"œControl Tankââ"šÂ¬Ã‚Â
1 Set a ââ"šÂ¬Ã…"œsterileââ"šÂ¬Ã‚ tank with synthetic saltwater.
2 Add ammonium chloride to the water to achieve a TBD concentration.
3 Introduce ââ"šÂ¬Ã…"œpureââ"šÂ¬Ã‚ nitrogen cycle bacteria.
4 Plot the decay curve of ammonia, nitrite, and nitrate.
ââ"šÂ¬Ã…"œTank with additional semi porous mediaââ"šÂ¬Ã‚ possible candidates would include:
http://www.drsfostersmith.com/product/prod_display.cfm?pcatid=3609&Ne=40000&R=7854&N=2004+113066
Or perhaps some scraped & baked branching tonga LR.
Hypothesis:
Ammonia, Nitrite, decay would be accelerated in the ââ"šÂ¬Ã…"œsemi porous mediaââ"šÂ¬Ã‚ media tank, but nitrate decay would occur at a much higher rate in the semi porous media tank.
Perhaps a third tank would contain only additional smooth surface media to try to differentiate between the ââ"šÂ¬Ã…"œpermeabilityââ"šÂ¬Ã‚ issues.
Regards,
Scott
Perhaps this would be an interesting experiment.
ââ"šÂ¬Ã…"œControl Tankââ"šÂ¬Ã‚Â
1 Set a ââ"šÂ¬Ã…"œsterileââ"šÂ¬Ã‚ tank with synthetic saltwater.
2 Add ammonium chloride to the water to achieve a TBD concentration.
3 Introduce ââ"šÂ¬Ã…"œpureââ"šÂ¬Ã‚ nitrogen cycle bacteria.
4 Plot the decay curve of ammonia, nitrite, and nitrate.
ââ"šÂ¬Ã…"œTank with additional semi porous mediaââ"šÂ¬Ã‚ possible candidates would include:
http://www.drsfostersmith.com/product/prod_display.cfm?pcatid=3609&Ne=40000&R=7854&N=2004+113066
Or perhaps some scraped & baked branching tonga LR.
Hypothesis:
Ammonia, Nitrite, decay would be accelerated in the ââ"šÂ¬Ã…"œsemi porous mediaââ"šÂ¬Ã‚ media tank, but nitrate decay would occur at a much higher rate in the semi porous media tank.
Perhaps a third tank would contain only additional smooth surface media to try to differentiate between the ââ"šÂ¬Ã…"œpermeabilityââ"šÂ¬Ã‚ issues.
Regards,
Scott
Paul,
On the contrary, Paul, it is you who are missing the point.
The same may well be true with sand particles derived from coralline rock (but maybe not that derived from shells or silica).
It is not.
The difference with the rock over the sand is that water circulates between rocks and not as readily through sand beds.
Water flows between rocks that are separated by given distances. It will not flow through rock groups that are closer than those distances. Those distances are determined by the bulk flow of the water above the rock and the surface heterogeneity of the rock. The benthic boundary layer effect will prevent water from appreciably moving close to rocks with much surface heterogeneity. This is why organisms embedded or living in or on those surfaces extend filtration devices or gills above the surfaces. Water will not appreciably circulate in those benthic boundary layer regions unless something in those regions moves it.
Water moves quite readily though sediments, but it has to be moved through them in the same manner it has to be moved through rocks.
Your statement also makes it seem that you believe that the glass walls have the same surface properties as coral based rock. Do you actually believe that?
Of course not, but it was your statement that water has to enter the rocks that indicates that the surface heterogeneity was largely unimportant.
The glass walls are constantly bathed in water and thus the oxygen potential may be too high for effective denitrification.
Hmmm... I thought the rock in the aquarium was also contantly bathed in water...
1. That denitrification occurs deep inside a rock. Thus you discount that this process may occur within a short distance inside rock. PROVE IT TO ME. Show me the science behind your assumption.
This was a restatement of the common phrase that the porosity of the rock lead to denitrification inside the rock. I don't believe that denitrification occurs within the rock we have as I don't believe there is sufficient water change.
I did discount that sufficient denitrification might occur on the rock surface. I don't accept that that hypothesis has been shown to function in aquaria, but I will accept that it may be possible. If so, however, so-called live rock is unnecessary for it, any rock should work fine, particularly any rock of biogenic origin, including limestone.
2. That only animals can move water through rock. Again, this premise relies on your assumption above.
Name another motive force.
Do you dispute the fact that coral rock has an enormous microscopic surface area.
Of course not. But water isn't moving thorugh it.
The very fact that it does is why coral skeletons are use in bone reconstruction.
Which is not relevent to this discussion at all.
And then there is your attempt to mislead....
"Here is a picture of a cross section of a dead coral. It is a light micrograph. The coral is sat on a glass slide."
No, Paul, this is an image of a section of limestone.
As you can see, the coral skeleton (dark) comprises very little of the actual body of the coral rock itself.
Actually both the light and the dark regions are likely parts of the coral skeleton, but it is difficult for a novice to interpret this image. You should have pointed out that the light areas are simply less dense regions of rock and are not "open" spaces. Not all skeletal materials deposited by corals are of equal density and this is a good example of that.
You might check out
this diagram or here. , for how to try to interpret the image.
You can clearly see the amount of surface area available for bacterial attachment.
Actually, you can see no surface area at all. It is the interior of a limestone rock.
However, even if coral is highly porous, and you really out to check out some of the autoradiographs of coral skeletons to verify your supposition that it is, water still has to be pumped though it. It will not - and cannot flow passively through these materials.
Try this self-experiment. Take a piece of capillary tubing. Fill it with colored water. Put it in your aquarium. How long will it be before that colored water flows out of the tubing? Seconds... Hours.... Days....
For cavities as small as this, or smaller, in the inside or even on the surface of the corals water flow is nil. Without the water flow, there won't be any biological filtration as there will be no exchange of any materials.
Scott,
Interesting experiment, and not too far from several we have talked about, however, life is never so simple. The problem comes down to what else do these bacteria need to eat. You see they may need all manner of different types of food stuffs, such as dissolved orgnic carbon sources, amino acids and stuff.
One way round this would be to filter sterilize some old tank water, with known nitrates and all the other dissolved organic compounds. Then use this in ther experiment you describe.
We would need several tanks for each condition to allow statistics.
There are other problems, but Its a good idea.
AT the end of the day, without high end equipment we just can prove these things. We can only go by inference and current knowledge.
I guess if we want to expand on your experiment....how many people currently run a tank with no live rock, and have no nitrates.
Nice idea, and a good starting point Scott.
Paul.
Interesting experiment, and not too far from several we have talked about, however, life is never so simple. The problem comes down to what else do these bacteria need to eat. You see they may need all manner of different types of food stuffs, such as dissolved orgnic carbon sources, amino acids and stuff.
One way round this would be to filter sterilize some old tank water, with known nitrates and all the other dissolved organic compounds. Then use this in ther experiment you describe.
We would need several tanks for each condition to allow statistics.
There are other problems, but Its a good idea.
AT the end of the day, without high end equipment we just can prove these things. We can only go by inference and current knowledge.
I guess if we want to expand on your experiment....how many people currently run a tank with no live rock, and have no nitrates.
Nice idea, and a good starting point Scott.
Paul.
"Here is a picture of a cross section of a dead coral. It is a light micrograph. The coral is sat on a glass slide."
No, Paul, this is an image of a section of limestone..
Actually it is a section of fossilized coral. You are correct, it is probably fossilized within limestone, but that section is still a coral skeleton. As you point out a little later....Actually both the light and the dark regions are likely parts of the coral skeleton, but it is difficult for a novice to interpret this image.
so you do acknowledge that it is a coral skeleton.
In honesty, I wasnt posting this for you Ron. It was to show people the open structure throughout an entire coral skeleton.
In fossilized rock I think that crystalline deposits may close some of those pores, thats why limestone and fossilized coral is so dense. A dried piece of fiji rock is very light. ergo...its pretty full of air.
This site is beyond reproach. I think it shows the exact thing I am talking about. Please take a moment to look at it, then feel free to dispute the large surface area of the coral skeleton.
http://www.advancedaquarist.com/issues/july2002/feature.htm
Ron, I will try one more time. The distances I am talking about are mere milimeters into a coral based rock. I agree it doesnt have to be live rock. I have said that many times. Thats why i prefer to be a little more specific when I say coral-based rock. Your entire argument dismisses biofilms. Yes I know biofilms are a relatively newly described phenomenon, but they do exist.
Paul.
No, Paul, this is an image of a section of limestone..
Actually it is a section of fossilized coral. You are correct, it is probably fossilized within limestone, but that section is still a coral skeleton. As you point out a little later....Actually both the light and the dark regions are likely parts of the coral skeleton, but it is difficult for a novice to interpret this image.
so you do acknowledge that it is a coral skeleton.
In honesty, I wasnt posting this for you Ron. It was to show people the open structure throughout an entire coral skeleton.
In fossilized rock I think that crystalline deposits may close some of those pores, thats why limestone and fossilized coral is so dense. A dried piece of fiji rock is very light. ergo...its pretty full of air.
This site is beyond reproach. I think it shows the exact thing I am talking about. Please take a moment to look at it, then feel free to dispute the large surface area of the coral skeleton.
http://www.advancedaquarist.com/issues/july2002/feature.htm
Ron, I will try one more time. The distances I am talking about are mere milimeters into a coral based rock. I agree it doesnt have to be live rock. I have said that many times. Thats why i prefer to be a little more specific when I say coral-based rock. Your entire argument dismisses biofilms. Yes I know biofilms are a relatively newly described phenomenon, but they do exist.
Paul.
gregt
Premium Member
How do you define "live rock" in context with your article (and this conversation)?
I've always thought the common definition of "live rock" to be any rock that contains a full compliment of denitrifying bacteria. I always thought that most aquarists agreed that "live" had nothing to do with "visible" life on the rock. Perhaps I am in the minority in assuming this definition, but a clarification in definitions would be helpful at any rate.
I would define ...
live rock as the stuff we buy, wet from the ocean. it may or may not have algaes and/or other life on it
Dead rock as the stuff we get dried, but originally from the ocean.
Both, in my opinion will work equally well in denitrification so long as they are coral based rock and a bacterial population has had time to colonize it.
Paul.
live rock as the stuff we buy, wet from the ocean. it may or may not have algaes and/or other life on it
Dead rock as the stuff we get dried, but originally from the ocean.
Both, in my opinion will work equally well in denitrification so long as they are coral based rock and a bacterial population has had time to colonize it.
Paul.
Paul,
problem comes down to what else do these bacteria need to eat.
Does nitrogen cycle bacteria need anything else to eat?
I am dating myself here, but I remember ââ"šÂ¬Ã…"œcyclingââ"šÂ¬Ã‚ FO tanks with no live critters whatsoever, at least nothing that did not precipitate out of the air. The only purposely added ââ"šÂ¬Ã…"œfuelââ"šÂ¬Ã‚ was the ammonium chloride. Where were the DOCs etc. coming from?
I am also thinking about those coil denitrators. They had, lots of surface area and (in theory) got the oxygen content down to around 1ppm. Urban legend? was that this ââ"šÂ¬Ã…"œanoxicââ"šÂ¬Ã‚ environment was necessary to host the bacteria that converts nitrate to nitrogen gas.
Greg,
I think that the term ââ"šÂ¬Ã…"œlive rockââ"šÂ¬Ã‚ covers the entire gambit of material from that which is only colonized by bacteria up to that which hosts an entire ecosystem of ââ"šÂ¬Ã…"œhigher orderââ"šÂ¬Ã‚ Ã¢â"šÂ¬Ã…"œplantsââ"šÂ¬Ã‚ and critters. How live is you rock is perhaps the question.
Regards,
Scott
problem comes down to what else do these bacteria need to eat.
Does nitrogen cycle bacteria need anything else to eat?
I am dating myself here, but I remember ââ"šÂ¬Ã…"œcyclingââ"šÂ¬Ã‚ FO tanks with no live critters whatsoever, at least nothing that did not precipitate out of the air. The only purposely added ââ"šÂ¬Ã…"œfuelââ"šÂ¬Ã‚ was the ammonium chloride. Where were the DOCs etc. coming from?
I am also thinking about those coil denitrators. They had, lots of surface area and (in theory) got the oxygen content down to around 1ppm. Urban legend? was that this ââ"šÂ¬Ã…"œanoxicââ"šÂ¬Ã‚ environment was necessary to host the bacteria that converts nitrate to nitrogen gas.
Greg,
I think that the term ââ"šÂ¬Ã…"œlive rockââ"šÂ¬Ã‚ covers the entire gambit of material from that which is only colonized by bacteria up to that which hosts an entire ecosystem of ââ"šÂ¬Ã…"œhigher orderââ"šÂ¬Ã‚ Ã¢â"šÂ¬Ã…"œplantsââ"šÂ¬Ã‚ and critters. How live is you rock is perhaps the question.
Regards,
Scott
Paul,
so you do acknowledge that it is a coral skeleton.
It it is the altered remains of what once was a coral skeleton. Now it's a rock.
In honesty, I wasnt posting this for you Ron. It was to show people the open structure throughout an entire coral skeleton.
Then you should have posted an image of one.
In fossilized rock I think that crystalline deposits may close some of those pores, thats why limestone and fossilized coral is so dense. A dried piece of fiji rock is very light. ergo...its pretty full of air.
Which is misleading. In the water on the reef it is largely filled with algae (many of which are cyanobacteria; but also with green algae). In fact, if it is "live" while it is porous, most of those pores are filled with algal material.
Ron, I will try one more time. The distances I am talking about are mere milimeters into a coral based rock.
Paul, I will try one more time. That distance is just too far for water to move under most conditions in marine environments. See Steve Vogel's book on "Life in Moving Fluids." The problem of water flow over such small distances is not inconsequential. You are found of saying that I don't know much about bacterial interactions, but you ought to check out the properties of water flow in small constricted spaces. You seem to think it is both rapidly moving and easily moved, and it is neither.
Your entire argument dismisses biofilms.
Of course it doesn't. My argument assumes that biofilms are everywhere and that the bacteria in them do their biofilmy things with dispatch.
The whole argument devolves to water movement and how it occurs and is generated. It isn't a passive process.
The very surface heterogeneity that gives these rocks their habitat for biofilms prevents much water flow through them. This is why the water has to be moved by a propulsive force generated near to the biofilm within the boundary layer. Even the outer layers of the rocks, will have very slow exchange rates with the overlying water.
It simply boils down to the fact that expensive "live" rock is immaterial if the surface of any rough rock will do. In that case, the use of so-called live rock as "a biological filter" is a myth.
Scott,
Its probable that the life on the rocks provided enough stuff for the denitrifying bacteria to grow. Yes they really do need much more than nitrate. If they dont have carbon and other element sources they can not grow new cell walls, proteins etc.
The original idea of coil denitrators was as you stated. I played with them in my youth. They worked really well with a very slight sugar solution (like 10 gm sugar per liter water...then added a few mls per day) added to them. The problem was tuning them. Once they became too anoxic they could produce Hydrogen sulfide....and that stuff stinks, as im sure you know. Its also toxic.
HTH.
P.
Its probable that the life on the rocks provided enough stuff for the denitrifying bacteria to grow. Yes they really do need much more than nitrate. If they dont have carbon and other element sources they can not grow new cell walls, proteins etc.
The original idea of coil denitrators was as you stated. I played with them in my youth. They worked really well with a very slight sugar solution (like 10 gm sugar per liter water...then added a few mls per day) added to them. The problem was tuning them. Once they became too anoxic they could produce Hydrogen sulfide....and that stuff stinks, as im sure you know. Its also toxic.
HTH.
P.
I would define ...
live rock as the stuff we buy, wet from the ocean. it may or may not have algaes and/or other life on it
I don't think there is a definition of this stuff, really. Paul's definition above may work for a microbiologist, I suppose. It doesn't do it for me.
I prefer visible things on it.Dead rock as the stuff we get dried, but originally from the ocean.
I would consider most of the stuff shipped from the various collectors at the present time as "dead" rock. Most of the microscopic and macroscopic life on it, with the exception of the bacteria has been killed.
I think the most effective "biological filter" will be found in a rock with significant animal life present in it. In effect, this life would maximize water flow over and through the surfaces and interstices that the bacteria live on. Without such animal life, the bare surface of the rock will/may act as a biological filter but the amount that it will do so is open to conjecture.
Ron,
Is your argument, in a nutshell...that passive diffusion of solutes in a static water column inside a rock structure is insufficient to bathe the biofilm. ??
yes or no.
Because... so far I have shown the incredible surface area open to biofilms. These great surfaces are available with milimeters of the external water (stuff in the tank which will be flowing) and even closer to water filled regions of the rock (stuff semi-encapsulated by the rock matrix and essentially not moving). You personally state that solutes in water difuse at 0.0001M per second, or, 0.1mm per second, so in ten seconds we have diffused 1 mm into a rock. Wait a minute and we have solutes diffused 6mm. Thus, diffusion in my model can account for the process.
The above is based on fact.
I still would like to see any facts you have quoted.
As for the initial picture I showed not being a coral skeleton but limestone, thats semantics. The essential structure is the same, which was the point, but then i proved that again. I noticed you didnt question surface area on the advanced aquarist study. Nice pictures arent they.
Paul.
Is your argument, in a nutshell...that passive diffusion of solutes in a static water column inside a rock structure is insufficient to bathe the biofilm. ??
yes or no.
Because... so far I have shown the incredible surface area open to biofilms. These great surfaces are available with milimeters of the external water (stuff in the tank which will be flowing) and even closer to water filled regions of the rock (stuff semi-encapsulated by the rock matrix and essentially not moving). You personally state that solutes in water difuse at 0.0001M per second, or, 0.1mm per second, so in ten seconds we have diffused 1 mm into a rock. Wait a minute and we have solutes diffused 6mm. Thus, diffusion in my model can account for the process.
The above is based on fact.
I still would like to see any facts you have quoted.
As for the initial picture I showed not being a coral skeleton but limestone, thats semantics. The essential structure is the same, which was the point, but then i proved that again. I noticed you didnt question surface area on the advanced aquarist study. Nice pictures arent they.
Paul.
Paul,
Is your argument, in a nutshell...that passive diffusion of solutes in a static water column inside a rock structure is insufficient to bathe the biofilm. ??
No. My argument is that that passive of solutes in a static water colum inside a coral rock is insufficient to have any appreciable exchange with the water surrounding the rock structure.
Because... so far I have shown the incredible surface area open to biofilms.
You have indicated that there is porosity of the rock. If the rock is truly alive on the reef, the interior is filled with algae, and if it is dead in a tank, it may or may not have much of anything in it.
Thus, diffusion in my model can account for the process.
Yes, it can; provided the diffusion occurs over the benthic boundary layer. And if it does, then we don't need any "live" rock. My initial argument was that live rock needed water pumped through it to function as a filter. I expected to show from subsequent examinations of the rock that it had no effective pumping animal life in it; which would have been supported by any chemical data I could obtain from inside the rock. And it follows from that , that having "live" rock is immaterial, and any reasonable substrate should do, which was going to be the point of any subsequent discussion on the subject.
As for the initial picture I showed not being a coral skeleton but limestone, thats semantics. The essential structure is the same.
No, it is not a priori the same; for any fossil it has to be shown to be similar. See the term "diagenesis."
Oh, and by the way, from an earlier post, macroalgaes sounds a lot like bacterias... the singular is alga, and the plural, algae.
Hi Ron,
I'm a bit confused on this point:
In fact, if it is "live" while it is porous, most of those pores are filled with algal material.
The whole argument devolves to water movement and how it occurs and is generated. It isn't a passive process.
If the water movement within the rock is insufficient to support bacterial processes, how do the alage survive within this same environment?
Steve
I'm a bit confused on this point:
In fact, if it is "live" while it is porous, most of those pores are filled with algal material.
The whole argument devolves to water movement and how it occurs and is generated. It isn't a passive process.
If the water movement within the rock is insufficient to support bacterial processes, how do the alage survive within this same environment?
Steve
Ron,
it was data and datum. Not bacterias. Interestingly data is commonly used in both singular and plural, but this is a debate on our science, not our grammar....anyway back to the science...
I said...Thus, diffusion in my model can account for the process.
you replied........Yes, it can; provided the diffusion occurs over the benthic boundary layer. And if it does, then we don't need any "live" rock. My initial argument was that live rock needed water pumped through it to function as a filter. I expected to show from subsequent examinations of the rock that it had no effective pumping animal life in it; which would have been supported by any chemical data I could obtain from inside the rock. And it follows from that , that having "live" rock is immaterial, and any reasonable substrate should do, which was going to be the point of any subsequent discussion on the subject.
This seems a very different opinion from your article which states that....
Rock without animals in it will not be effective at being a filtration medium as there is no way for the interior porosity and presumptive bacterial beds to be functional without a way of moving water through the rock, and the only way that movement may be accomplished is by animal action.
so now I am confused.
Your reply to me in the above post would seem to indicate you have taken my stance that animals are not needed and that coral based rock, be it originally live or dried, can and does act as a site of denitrification. Also that it was your intent to prove that "live rock" is devoid of animal life.
Can you clarify that for me. Is your meaning "any other porous substrate that satisfies the requirements of nutrient flow and appropriate anaerobiosis"
Thanks,
Paul.
it was data and datum. Not bacterias. Interestingly data is commonly used in both singular and plural, but this is a debate on our science, not our grammar....anyway back to the science...
I said...Thus, diffusion in my model can account for the process.
you replied........Yes, it can; provided the diffusion occurs over the benthic boundary layer. And if it does, then we don't need any "live" rock. My initial argument was that live rock needed water pumped through it to function as a filter. I expected to show from subsequent examinations of the rock that it had no effective pumping animal life in it; which would have been supported by any chemical data I could obtain from inside the rock. And it follows from that , that having "live" rock is immaterial, and any reasonable substrate should do, which was going to be the point of any subsequent discussion on the subject.
This seems a very different opinion from your article which states that....
Rock without animals in it will not be effective at being a filtration medium as there is no way for the interior porosity and presumptive bacterial beds to be functional without a way of moving water through the rock, and the only way that movement may be accomplished is by animal action.
so now I am confused.
Your reply to me in the above post would seem to indicate you have taken my stance that animals are not needed and that coral based rock, be it originally live or dried, can and does act as a site of denitrification. Also that it was your intent to prove that "live rock" is devoid of animal life.
Can you clarify that for me. Is your meaning "any other porous substrate that satisfies the requirements of nutrient flow and appropriate anaerobiosis"
Thanks,
Paul.
Last edited:
TimV
New member
SPC said:
First a few crude definitions:
Photoautotroph - uses light as energy and able to fix carbon from CO2.
Chemiautotroph - uses inorganic sources for energy (for example NH4, NO3- or NO2- in this situation) and able to fix its own carbon from CO2
Algae can be strictly photoautotrophic. Problem is that they are not going to get light inside the rock. So any algae living in there would, imo, have to be surviving as a chemoautotroph. Therein lies the issue with Ron's argument. If some of the most efficient, and evolved, chemoautotrophs are unable to get adequate nutrition to flourish within the rock, why then would algae be so successful? I could buy the argument that algae prodominates within live coral (explanations as simple as microbial antagonism and antibacterial substances produced by the corals themselves) but not on rock.
TimV
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