recent article - live rock as bio filter

[msn711]

Just looking for clarification...your article seems to imply that most SW aquariums are using live rock that isn't really beneficial as a biological filter because of its lack of animal life. What, then, is serving as the biological filter in these aquariums? Many of them seem to be successful in terms of keeping their chosen species alive and healthy, so something has to be going on. And if the live rock isn't the bio filter, then why spend so much money on it? Also, doesn't the bacteria living in the surface of the rock aid in biological filtration?

[rshimek]

Hi,

The bacteria that are doing the filtration live on surfaces and I suspect most surfaces in an aquarium are covered with them. However, that really is not enough of a bacterial bed to be effective. In tanks with a sand bed, of course, the sand bed is being the filter.

As to why spend so much money for it? Well.... some of it looks pretty. :D

If the live rock has a good animal population in it pumping water through it, and some does, it may be acting as a filter.

However, the bottom line is that I don't think that the standard paradigm of a "biological" filter really is valid. I think in most cases in our systems, the algae in the tank are what is removing the nitrogenous compounds.

[pwhitby]

Ron,

I can accept your argument that diffusion through a rock is probably low and water will not really travel an appreciable distance, however, in terms of bacteria, it doesnt really have to. One of the things to consider is the formation of biofolms, and mixed layer biofilms. I think that the surface of all inert structures are coated with a two layer biofilm, the inner is comprised of anaerobes, breaking nitrates to N2 and O2 while the outer is aerobes. The aerobes protect the anaerobes and provide the nitrates. Such proximity of growth leads to a remarkably efficient system. This system is negated when we add a wet-dry type filter. In this case the anaerobes predominantly grow on the filter. Since the oxygen is extremely high at the filter they are unable to mask the anaerobes and we get a an uncoupled nitrogen cycle. The nitrates build up.

My point with this is it may not be the porosity of the rock but more the extremely large surface structure of an organically derived material. Microscopically, the surface of coral skeletons and live rock dereived from them is incredibly ridged and provides the massive surface area to permit such growth of large bacterial populations.

Just my thoughts,

Regards,

[rshimek]

Hi Paul,

I agree that might well be the place where some filtration occurs.
But, I don't think there is enough surface area there or "filtration" of the wastes produced by our systems. There is also some good evidence that the whole concept of anaerobes being the source of nitrogen reduction is incorrect, at least on real reefs; see this article, I believe, for more information: Capone, D. G. et al., 1992. Microbial nitrogen transformation in unconsolidated reef sediments, Marine Ecology Progress Series. 80:75-82; also: Stimson and Larned, 2000. Nitrogen efflux from the sediments of a subtropical bay and the potential contribution to macroalgal nutrient requirements Journal of Experimental Marine Biology and Ecology. 252:(2)159-180.

However, one of the (maybe) more minor points of the article is that there is no hard data about any of this. We can postulate all sorts of ways for filtration to occur, but until we do some collection of data we won't know about any of it.

I am convinced that the standard idea of the rock providing filtration is simply wrong, and the purpose of the article is get people thinking about it. :D

[pwhitby]

I think one of the ways to go about this would really be to estimate what the bacterial requirement would be to reduce a set concentration of ammonia to N2 and O2. Bacteria are extremely efficient, as im sure you are aware. Given biomass data we could figure the depth of bacteria required over porous surfaces.

I think at the end of the day the variables are too great to really get a good handle on this, but I do think anecdotal evidence as the wet dry filter I mention above may provide insights.

I know a number of tanks where the wet filter (usually a biowheel) once removed and allowed to be submersed experience a drop in nitrates over a relatively short period. It may be informative to creat such a set up, a clean tank with a biowheel and an ammonia source. Let it run and then immerse the wheel. Periodic sampling of the wheel matrix will indicate if nitrate decrease corresponds to increase in anaerobes.

Having established if bacteria are the players we can then move on.

Either way..........its an interesting and stimulating topic.

[Northside Reef]

LOL, sure drop a bomb like “Live rock hit or myth� then run for cover for a few days.

We see how it is.

Frank…

[pwhitby]

I actually spent a few hours yesterday looking into natural and industrial (still bacterial) rates of denitrification. For industrial processes the rates can be as high as kilograms nitrogen in the form of ammonia denitrified per meter squared of biofilm surface area. Of course these sytems are highly tuned. In natural sediments the rates are much lower but are still in the the region of mg Ammonia nitogen processed per meter squared. So........the surface area of live rock is more than adequate for denitrification. I think one of the issues I have with the article is the explanation of the requirement for "Porosity". By taking this to mean that the solutes in the water have to penetrate the rock is most probably wrong. Biofilms grow over the surface of the rock, and every other structure. They are not particularly deep, maybe a few microns in depth. Thus they are readily able to snag the ammonia and nitrites they are denitrifying. The rock is porous, and thus the surface of the rock is very pitted and broken. Thus we probably have something along the orders of 10-100 sq M of surface area in most of our tanks. This surface area is constantly bathed in water flowing in our tank.

I hope no one that reads this article pulls their live rock out. This article is not based on an understanding of microbiology. Instead it brings into play inverts as the main players in denitrification by providing water flow. The assumption that this water flow is needed at all is most probably erroneous.

Paul.

[birdman204]

I am curious as to the brand of test kits being used, or that the author would request aquarists use. I would like to help out with the study mentioned at the end of the article. I have a few tanks up and running for varying amounts of time. 1 here at work contains 100% cultured rock. Thanks
-Ryan-

[sdmike]

I've been in the aquarium hobby since the early 80s. In that time, I've seen LOTS of things come and go, but the basics still remain.

I've just started a reef and have been curious how a rock "filters" water. Seems hard to believe...

I'm not 100% convinced that LR/LS is the ONLY answer and that an additional form of filtration isn't a bad thing. We'll just have to see what biologists come up with in the next few years as we figure more and more out.

Thanks for clarifying,

M

[Dr.Salt]

I hope no one that reads this article pulls their live rock out. This article is not based on an understanding of microbiology. Instead it brings into play inverts as the main players in denitrification by providing water flow. The assumption that this water flow is needed at all is most probably erroneous.

Paul, your thoughts are accurate and appreciated.

Calcium carbonate is also the ideal chemical substrate for these bacteria.

[rshimek]

The standard explanation given throughout the reef literature is that the porosity of the rock allows for the growth of bacteria in an internal environment that is condusive for the bacterial growth. The point of the article is that the rock isn't likely porous enough for that, and that water will not move into it in any case. And as with a lot of other myths in the hobby, there are no data supporting the dogma.

The rock surface may well be acting as a base for the appropriate bacteria, however, there is no evidence or data from aquaria to support that either.

I would love to see any actual data you have that support your claims.

[dldorsey]

Dr. Shimek,

Thanks for a great article and a healthy dose of skepticism in general.

I must point out that at from a geologic perspective, which is what we're dealing with once the oragnisms become the limestone we call "live rock", porosity is indirectly related to the ability for water to flow through a rock.

For a full description you must also consider the permeability of the rock, or how well interconnected the pores of the rock are. You can have a very porous rock that is completely impermeable and would therefore not allow any "flow" what so ever.

It would be interesting if you could have a geologist analyze various live rock samples for both their porosity and permeability. I'd be interested to see results from rock of various origins and ages.

Thanks for being a scientific voice for those of us looking beyond the marketing hype.

Danny Dorsey

[BobB]

Originally posted by rshimek
Hi,

The bacteria that are doing the filtration live on surfaces...

Hi Dr. Shimek,

What a great, thought-provoking article! I'm a marine microbiologist and particularly interested in biofilms. I also have a scientific and hobbyist interest in coral reefs. In reading and thinking about liverock, it occurs to me that we need to keep a couple of points in mind. First, the use of the work 'porosity'. I think many reef aquarists envisage pores as in swiss cheese, but this may be wrong, or at least inaccurate from the point of view of bacterial cells. At 0.5-2.0 um in size, bacterial cells look at a world where porosity is more appropriately measured in micrometers, maybe even nanometers. So, a piece of calcareous liverock may be extremely porous at the micrometer scale, while being seemingly solid at the macroscale that we see. I think its entirely conceivable that most well-aged liverock, having come from old reefs, is extremely porous at the level of the bacterium.
The second point is the concept of bacteria being on the 'surface'. Again, I think we (as humans) have an ill-defined idea of what a surface is to a bacterium. The available evidence suggests that living bacteria are found in 'dense' stone several mile below the surface of Earth, as well as in halide crystals (with no macroscopically perceptible pores). Thus, I would suggest that it is entirely possible, indeed likely, that bacteria are capable of colonizing the entire liverock, from exterior surface to the inner core (multiple inches below the surface). It would be fascinating to section liverock and examine it with modern molecular tools for both the presence and the metabolic activities of potential bacterial colonizers. I wager that bacterial cells would be found far below the surface of what appears to us as solid, nonporous liverock.
This said, I bet we can all agree that macroscopic pores are also extremely necessary for the best carbon and nitrogen utilization and decomposition in liverock bacterial communities. As your article says these provide a wonderful means of circulation that aids in transport of the wastes through the liverock, as well as providing additional niches for a host of invertebrates, each (by the way) with its own thriving community of bacterial symbionts and commensals. Good quality liverock is truly alive at both macro- and microscopic levels.
Thanks once again for a stimulating article.

BobB

[rshimek]

Hi Folks,

My [thanks] to all the responders here.

The idea of the article was to challenge the dogma and that appears to have been successful.

I would love to see some of you folks that have the equipment and specialized knowhow to examine some of the questions raised here to spend a bit of your hard-to-come by spare time and get some more information about what has been hitherto treated so simplistically.

[Lazyreefer]

I disagree Dr. Ron.

With all the PHD"s and MD's on this thread perhaps you guys could cure Parkinson's disease instead.

[G-money]

Originally posted by rshimek
I would love to see some of you folks that have the equipment and specialized knowhow to examine some of the questions raised here to spend a bit of your hard-to-come by spare time and get some more information about what has been hitherto treated so simplistically.

I agree. But alas, I lack the equipment and the larger portion of the know-how. :D
I would especially like to see bacteria more incorporated into the equation. Since they are no doubt covering every square micrometer of every accessible surface of the rock, I'd go out on a limb and guess they may be more responsible for movements in and out of the rock than all other factors (biologic and other) combined.

[rshimek]

Hi Graham,

Bacteria do a lot of things, but they don't move water much, particularly in comparison to burrowing animals. Without water movement in and out of the rock, there isn't going to be much exchange with the external water.

Now, maybe they don't have to move it, if the processes are occurring on the rock surface or in biofilms. In these cases, we don't need "live" rock at all. And, of course, in many cases what we have is definedly "dead rock."

[pwhitby]

The persistance that water has to enter the rock to any significant degree is, in all likely hood, false. You have to understand bacteriology, and in particular, the incredible ability of biofilms to utilize nutrients in a water column. You ask for scientific evidence Ron.... Well I am sure you will agree that denitrification is predominantly a two part process catalyzed by bacteria. This process is utilized commercially and industrially by companies around the world to remove pollution from waste waters. That it works and is highly succesful is a fact. f you want scientific evidence that is does work I can post paper after paper. Biofilms grow on surfaces. Any surface. All they need is a solid base to grow. The surface of rock (irrespective of whether we call it live or dead) is highly pitted. This is referred to as porous. I enclose the definition of porous.
--------------------
[adj] full of pores or vessels or holes
[adj] allowing passage in and out; "our unfenced and largely unpoliced border inevitably has been very porous"
[adj] able to absorb fluids; "the partly porous walls of our digestive system"; "compacting the soil to make it less porous"
-----------------------

Since it is full of holes, both marcroscopic (those we can see) and microscopic (those we can not see) the surface structure of the rock is extremely high per unit weight. Coupled with the sand beds in our tanks, this is more than sufficient to suffice. To say that water has to be actively transported through the rock or else we don't get denitrification is incorrect. In industrial filters there are no invertebrates.

I think what it comes down is the long term use of the word porosity. We know that rock can not absorb water. It can take it into cavities, that is all. However, the two layer biofilm is probably able to satisfy the requirements of the aerobes and anaerobes.

As BOBb sums it up, porosity and diffusion mean different things at the microscopic level.

With refernce to the rates of diffusion that you quote in your article. You say that the only motive force capable of moving water is invertebrate action. What is missing from this argument is the total volume of water moving at any one time. If it is a few cubic millimeters of water diffusing then it is insufficient, however this is a totally dynamic process. The entire nutrient content of the water volume in the rock is moving. This provides a very scenario to the one you suggest. In fact it probably accounts for a greater nutrient flow than is capable by invertebrates.

Finally,
There are flaws in your proposed experiment. If you hypothesize that movement of animals through rock exchanges water, then insertion of a hypodermic needle will certainly create that movement. If the user is to avoid drawing up water from outside the rock by negative pressure then they can not draw water from the rock faster than diffusion can replace/balance the nutrients. From your figures this would be 3.6mm per hour. Thus, to take approxiamtely 5 mls to water sample would require several days of drawing a sample. Thus the data is invalid.

The only way to measure inernal Oxygen is by use of a microprobe installed in situ.

Also, depending on the tank, the invertebrate life is going to be quite diverse in each rock. If your statements are correct, then it will be impossible to interpret the data in any cogent fashion.

I am not saying this to rain on your article, however, as a person who works with bacteria daily and designs experiments that have to be extremely rigorous and reproducible, I feel that you should adress the design you propose.

I do think it would be great to look at various rocks and determine the cavitation of the structure (lets avoid porosity as a term for a while). If anyone has access to electron microscopes it would be neat to look at a number of fresh live rock specimens from various places.

Regards,
Paul.

[rshimek]

Originally posted by pwhitby

Hi,

The persistance that water has to enter the rock to any significant degree is, in all likely hood, false.

Perhaps, but there no data supporting the alternative suggestion.

Well I am sure you will agree that denitrification is predominantly a two part process catalyzed by bacteria.

While denitrification is definitely done by bacteria, it is incompletely understood and there are significant problems with the standard models cited in the so-called reef literature.

To say that water has to be actively transported through the rock or else we don't get denitrification is incorrect. In industrial filters there are no invertebrates.

The rock may or may not be porous. If it is, water is not going to be passively moved through it. So the contribution of any internal bacteria to any process in the tank water is nil. If there sufficient bacteria on the surface of the rock for denitrification, that is great! I'd love to see it. It would mean we wouldn' t need the so-called live rock at $$$ per pound and could do with any substrate in the tank.

You may well be right. I have no argument with your hypothesis. However, you don't have any data to show that occurs in an aquarium. Industrial processes, as I understand them use significant water movement over the biofilms. Given the boundary effects of rock like this I doubt there is sufficient water movement at the rock/water interface to provide the exchange necessary. I will freely admit I have no data to back this up, but I also see no data to contradict my statement. :D

... In fact it probably accounts for a greater nutrient flow than is capable by invertebrates.

I don't agree. So.. how would you show it?


There are flaws in your proposed experiment..... Thus the data is invalid.

Not invalid - but inconclusive. However, it would give some indications of water conditions within the rock. For example, if we got significant indications of sulfides, etc. I doubt anybody could get a good sample of pore water from inside the rock; I have spent a lot of time working with environmental chemists getting interstitial water from within sediments and that is hard enough. However, if we can get some data to play with. :D

The only way to measure inernal Oxygen is by use of a microprobe installed in situ.

Yep, and since you can't get one into the rock, you can't do it that way. So... try for some indirect measurements. :D

Also, depending on the tank, the invertebrate life is going to be quite diverse in each rock.

Actually, I think there won't be much invertebrate life within the rock at all. And that will be fairly conclusive.

If your statements are correct, then it will be impossible to interpret the data in any cogent fashion.

I disagree.

[SPasse]

Dr Ron,

I copied this posting from another thread; some of these points have already been discussed.

Some observations/questions:

If we consider the “ammonia cycle� subset of biological filtration, if it is not occurring in/on the live rock, where is it occurring? Perhaps this is also “urban reef legend� but I was always under the impression that nitrogen cycle bacteria require a surface to “colonize� rather that being free floating. Maybe this was more of an oxygen gradient/concentration issue that an “attachment� issue.

Even in a reef tank devoid of a “fish population� one can add a given quantity of ammonia (as ammonium chloride) has with the appropriate test kits, observe the decline (conversion/) of ammonia to nitrite to nitrate. Not that I could quantify this but this occurred in tanks with nothing but “water and fish� and perhaps a limited amount of a course gravel substrate

In my experience, it is the conversion of nitrate to nitrogen gas (at a rate that kept nitrate levels at <10ppm) that required a given ration of live rock, a DSB, or some kind of purpose built de-nitrification device, such as a “coil denitrater� In other words, a sufficiently sized “zone� with the appropriate (~1ppm) concentration of oxygen was required to “host� the bacteria responsible for converting nitrate to nitrogen gas.

If it is indeed the critters that make the “exchange� work on live rock, this would also be a positive indicator for DSBs as the relative “critter� population densities should be much higher in a sand bed that in a given “mass� of live rock. Also as a sand substrate is continually being broken up/moved around by the sand critters, the porosity/permeability would also be much higher.

In any case, good luck with your investigation.

Regards,

Scott

[pwhitby]

Ron,

let me try and address a few of your points.

denitrification is poorly understood. ?

Which aspects are poorly understood? It is pretty thoroughly researched area. A simple search on the medical databases alone yields in excess of 1,100 papers on the subject. The genetic and phenotypic basis of denitrification is thoroughly described in the literature. I agree it is not described well in the reef literature, but then why should it be. Why do you think it will be different in a reef tank as opposd to anywhere alse on the planet.

a really nice overview for readers not familiar with the process can be found here
http://www.ozestuaries.org/indicators/Def_denitrification.html


the rock may or may not be porous. If it is, water is not going to be passively moved through it. So the contribution of any internal bacteria to any process in the tank water is nil. If there sufficient bacteria on the surface of the rock for denitrification, that is great! I'd love to see it. It would mean we wouldn' t need the so-called live rock at $$$ per pound and could do with any substrate in the tank.

You may well be right. I have no argument with your hypothesis. However, you don't have any data to show that occurs in an aquarium.

Well.............Once again, why do you think this process will not be the same in an aquatic environment. The rock does not to be "live" per se. It needs to have a great surface area, or as you say, be porous. Coral rock, by its very nature, has the characteristics that makes it ideally suited for our tanks. It can come dried up or wet from the ocean, but given time will be heavily colonized by bacteria.

as for in situ measurement of oxygen, it is possible. Take a rock, drill a hole and push the probe in and seal it. Let it equillibrate and monitor the oxygen level over a few days and read the results. This would be far more precise than the method you propose. Of course it requires expensive apparatus.

Actually, I think there won't be much invertebrate life within the rock at all. And that will be fairly conclusive.

how will this be determined since A. you can not see inside a rock, and B. many inverts are microscopic.

One has to understand that baacteria perceive a very different world from us. A good understanding of bacteriology is required to thoroughly grasp the nuances of this process and aquatic microbiology.


as a scientist you know that "some data" is not good data. You say the data is not invalid but that it is inconclusive. If you make speculations on that data set and people read that they will ultimately make false assumptions. In addition, i do not understand why you would pursue generating inconclusive data.

Paul.

[TimV]

Disclaimer: I work with pwhitby, so you can take that as you may.

Ron,

I am a microbiologist. Although not an environmental microbiologist, my PhD work was at one of the top environmental microbiology departments in the country. As such, I have spent a great deal of time studying the nitrogen cycle and sitting in seminars where these processes were discussed. As such, you can choose to respect my opinion on these matters, or not.

My biggest problem with your experiment is your assumption that some data is better than no data. In many cases this is true. But bad data is not better than no data and can be detrimental. The experiment you have designed will not work.

1. As designed, this experiment would require a level of precision that can not be obtained by asking others to help. Even the rate at which the syringe is inserted and samples drawn with cause the data to be all over the map. There are just too many variables and no amount of anova or manova statistical manipulations could fix that.

2. If you want to test oxygen concentrations deep in a rock, drill a rock, place several oxygen probes and measure in situ. No other way of doing it would be valid.

3. If you really want to find out what might be occuring farther into the rock, here is a simple experimental design. Take several rocks, from the same tank. The larger the rock, the merrier. Take cores of the rock, prep for DNA and perform quantitative PCR analysis of what bacteria are there. If your nitrifiers and denitrifiers are present, that would tell you quite a bit.

I think more than anything, you too greatly discount the importance of the porosity of the rock. By porosity, I do not mean the ability of water to diffuse into the center of the rock. I mean the incredible surface area present in the rock. I would not doubt if there are many, many square kilometers of surface area. Base rock, from my experience does not have this porosity. Fiji rock left on your front porch for 6 months would probably be as good as fresh shipped Fiji given a month or so for bacterial colonization. But this likely would not apply to million-year old rock quarried from dry land.

Ron, you hold a great deal of respect and influence within this community. With that influence comes an enormous responsibility to the community. It is important that if you want to foray into a new subject, that you do so correctly. Radical speculation into an area, that for the most part is well understood, just for the sake of rocking the boat is a bit irresponsible. This is not a peer-reviewed journal; however the laymen that read this forum and the magazine will take your comments at face value. Trained scientists understand such speculation and can judge whether they feel the data supports the conclusions. We are also unlikely to act upon incomplete data or poorly obtained data. Unfortunately, others may not because they feel if a respected scientist says so, it must be true. This leads to people changing important aspects of their perfectly tuned system, just because this study says this might work better, only to find all their corals bleached and dying.

Just my educated opinion, everyone can take that as you may.

Tim

[rshimek]

Originally posted by pwhitby

Paul,

let me try and address a few of your points.

I agree it is not described well in the reef literature, but then why should it be. Why do you think it will be different in a reef tank as opposd to anywhere alse on the planet.

See the references I provided earlier. Where and how denitrification occurs on reefs and by whom is not clear.

Well.............Once again, why do you think this process will not be the same in an aquatic environment.

It might be, but many processes that occur in natural aquatic environment don't work the same in our systems. Why are you convinced they should be the same?

It can come dried up or wet from the ocean, but given time will be heavily colonized by bacteria.

I am not contesting that point at all, what I am quesitioning is the role of the bacteria in various places on the rock.

how will this be determined since A. you can not see inside a rock, and B. many inverts are microscopic.

Take a piece of the rock, fix it in a decalcifying fixative which will preserve dissolve the rock and preserve the animals. Examine the sample microscopically and enumerate them.

One has to understand that baacteria perceive a very different world from us.

So do small invertebrates... and their role in this process is critical.

as a scientist you know that "some data" is not good data

Fur shoore, but it gets you started.

Interestingly enough, I also know that it should be data "are" rather data is. The singular is datum. :D

. In addition, i do not understand why you would pursue generating inconclusive data.

I don't think the data that would be produced would be inconclusive. I think they will be indicative and from that other testable hypothesis can be generated.

What I don't understand is why you are opposed to trying to test your hypothesis/supposition/

There are precious few real data in the reef aquarium literature, generally people throw various references back and forth at one another trying to have a verbal equivalent of a ****ing match. This solves nothing. People simply holler about their assumptions. You may be right in what you say. If so, good. But show some data - from aquaria - to back it up.

[pwhitby]

Sorry, bad link,

this one should work

http://www.ozestuaries.org/indicators/Def_denitrification.html

[rshimek]

Originally posted by TimV

Hi Tim,

Disclaimer: I work with pwhitby, so you can take that as you may.

My, my... this really has got you guys going. Glad to see it. :D

The experiment you have designed will not work.

Okay. Design a better one and proceed to do the work. Just jump off the assumption bandwagon and get some real data.

Base rock, from my experience does not have this porosity. Fiji rock left on your front porch for 6 months would probably be as good as fresh shipped Fiji given a month or so for bacterial colonization. But this likely would not apply to million-year old rock quarried from dry land.

Measurements???? Data??? You are assuming again.

....changing important aspects of their perfectly tuned system, just because this study says this might work better, only to find all their corals bleached and dying.

We have no "perfectly tuned systems." we have barely passable systems. Most animals found on natural reefs do not persist in aquaria for any number of reasons, most likely due to inappropriate nutrition. If people can get solid advice about incrasing the capability of their systems to handle appropriate levels of foods, it would result in a whole lot less animal mortality. I have not advised anybody to "get rid" of their live rock. Actually, I would like them to get real LIVE rock rather than the pale substitute we know see being imported.

[pwhitby]

Ron,

My hypothesis is established. It does not need to be reproven. Multiple papers exist on denitrification in marine environs and sediments. YOU state that this may not be so. If you make a statement like that in a journal read by thousands then at least be able to prove it. Dont ask those of us that disagree with you to prove you wrong. You propose an experiment. The problems have been pointed out, redesign it so it will work. The problem here is that people read the journal and will accept it as fact. They will never come here and read this thread.

And yes I do know the difference between datum and data.

[TimV]

I just designed an experiment for you. See number 3.

Here's another as simple timecourse experiment. Small nano tanks, add radiolabeled acetate. The denitrifiers are going to assimilate the acetate as their carbon source. At various times, take out a rock, thin section it and image it by autoradiography. You could not only test whether the bacteria are present, but rates of diffusion and can sample to positively ID what bacteria are there. If you have a lab and appropriate radiation license, you could do this experiment for less than a thousand dollars. If it works, you'll have the preliminary results to support a grant looking at larger systems and rocks. Not only that, you could publish it in a respected peer-reviewed journal (JBact or JAppliedMicro would eat that up). Hell, you could compare aquacultured rock versus collected, even different sources. The point being, either of these experiments are a hell of a lot better than the bad experiment you designed (no offense intended). Your experiment is badly designed. The data will be bad. The conclusions will be bad. I'm not saying that what you want to find out is not worthy. But your results won't be inconclusive, they will be bad. It would be incredibly irresponsible to even publish them on the forum.

Unfortuately, I can't justify performing these experiments as they would be a gross mismanagement of our research funds since we study pediatric infectious diseases. But you are free to try these if you may. I'll even assist you in designing PCR primers and technical help. If you don't access to the facilities to perform these experiments, than frankly, you should leave the microbiology to the microbiologists.

Swallow your pride and admit that the experiment won't work. I've given you reasons why, if you disagree than defend your methodology. Don't just hide behind the logical fallacy that we are just speculating and need to prove our assumptions. As scientists, we need to be able to take constructive criticism of our experimental designs and modify them as such.

Tim

[Dr.Salt]

Originally posted by rshimek
While denitrification is definitely done by bacteria, it is incompletely understood and there are significant problems with the standard models cited in the so-called reef literature.
Originally posted by rshimek
See the references I provided earlier. Where and how denitrification occurs on reefs and by whom is not clear.

You are obviously not aware of these.


Atkinson, MJ. 1987. Alkaline phosphatase activity of coral reef benthos. Coral reefs. Heidelberg etc., vol. 6, no. 2, pp. 59-62.

Moriarty, DJW; Hansen, JA. 1990. Productivity and growth rates of coral reef bacteria on hard calcareous substrates and in sandy sediments in summer. AUST. J. MAR. FRESHWAT. RES., vol. 41, no. 6, pp. 785-794.

Sorokin, YuI. 1981. Periphytonic and benthic microflora on the reef: Biomass and metabolic rates. THE REEF AND MAN. PROCEEDINGS OF THE FOURTH INTERNATIONAL CORAL REEF SYMPOSIUM. VOLUME 2., 1981, pp. 443-448.

Vacelet, E; Thomassin, BA. Microbiology in coral reefs: A review. 1982. ECOLOGY OF BENTHOS IN A CORAL ENVIRONMENT, Oceanis. Serie de documents oceanographiques. Paris, pp. 85-97.

Webb, KL; DuPaul, WD; Wiebe, W; Sottile, W; Johannes. 1975. Enewetak (Eniwetok) Atoll: aspects of the nitrogen cycle on a coral reef. Limnology and Oceanography. Vol. 20, no. 2, pp. 198-210.

Webb, KL; Wiebe, WJ. 1975. Nitrification on a coral reef. Can. J. Microbiol. Vol. 21, no. 9, pp. 1427-1431

[tim1]

timV,
how would section the rock?, unless it was fixed.I would think it would crumble and be useless...just a random thought..

we will have to talk about our jobs one of these days too...
peds research..a.i dupont here...

[TimV]

Originally posted by tim1
timV,
how would section the rock?, unless it was fixed.I would think it would crumble and be useless...just a random thought..

Good point. Out of curiousity I took a piece of dry rock and cut it with a hacksaw (No diamond blade). One side did crumble a bit but it might not be as bad with a more appropriate blade. But even the ability to hack the rock in half would do the trick.

I'd love to do an artificial system using GFP-labeled Nitrosomonas and Nitrobacter species (both are available). But that would be a bit iffy. I think there is also a GFP-labeled Pseudomonas denitrificans. Probably other denitrifiers also.

we will have to talk about our jobs one of these days too...
peds research..a.i dupont here...

That would be nice. PM me sometime.

Tim

[pwhitby]

Dr Salt, Tims 1 and V...

Having reread the article the main problem, apart from the experimental design at the end... is that of diffusion of solutes through water. Ron speculates that diffusion alone is insufficient for solutes to penetrate the rock matrix and thus invertebrates are required to provide the correct blend of anaerobic environment and solute level. This is based on a misunderstanding of bacteriology and maybe a desire to implicate his specialist field of invertebrate biology in this process.


Let me cite an example, somewhat similar to the rock-denitrification issue. There is another aquatic environment we are all familiar with. Our mouths. This is an environ constantly bathed in moisture, or to be more specific saliva. I am sure that we can all agree that the mouth is a very aerobic place. The teeth can be the "live rock" in this scenario. On our teeth are bacteria. Some cause no problems what so ever and are just there because they like to hang out in our mouths. Some cause cavities. The latter are anaerobes. These guys take the sugars we eat and destroy our teeth. So....this means that the surface layer of our teeth is, in places, anaerobic and fed nutrients by diffusion. This is on the surface!!!! not deep inside the tooth but right at the surface. It is anaerobic because of biofilms. These are thin layers of densely packed bacteria. This simple example should adequately demonstrate the distance solutes (in this case sugars) need to pass from an aerobic environment to an anaerobic one. Please note, that in the majority of our mouths there are not invertebrates facilitating this process.

The point I am trying to make here is that bacteria can form an aerobic layer across an incredibly thin distance of a biofilm. As a side note, both cavity formers in our teeth and denitrifiers on rock can erode the surface they are on, thus making small pits that are probably even more anerobic.

In Rons article he states that.........
For a significant amount of gas exchange to occur there has to be continual movement of the water into and out of the rock. Given the minuscule pore sizes in these rocks, the water movement cannot be generated by water currents outside the rock. The resistance to movement of water in small tubes, such as the pores in live rock, is considerable. The only motive force sufficient to move enough water through the rock, so that it may act as an efficient denitrating site, is the force generated by the animals, mostly the worms, living in their burrows

maybe the above example demonstrates to him just how little a distance molecules need to diffuse, probably less than the thickness of one of the legs of the invertebrates he implicates.

Regards,

Paul.

[jfinch]

These biofilms are very interesting. I would assume they also exist on freshwater surfaces. Why is that rock in a freshwater tank doesn't perform denitrication? At least not to the extent that live rock does in a reef tank. I've kept african cichlid tanks with as much rockwork as any saltwater reef, but I've always had to do a water change to keep nitrates in check. Why would it work in saltwater and not fresh?

[pwhitby]

Jfinch,

Good point. I have often considered just that issue. I think it comes down to the higher stock levels we often have in freshwater tanks.

I also think that the sand plays a part in the process. I have no idea whether the roles played by rock and sand are equal on a wight-weight basis or if there is an optimal sand size or stuff like that.

Do you have more fish in your cichlid tank than a SW tank?
Are you using a filter like a biowheel type. These have been postulated to uncouple the denitrification process.

Thanks for your thoughts.

Paul

[Machiavelli]

On a slight, but still related, aside. I believe the best way to answer a question such as this and others would be to create a volunteer collaberative organization which tries to network hobbyists who are in relevant scientific fields. In this way you would be able to pool the community's scientific resources, as well as their respective access to equipment. Try and work out some funding, and you would have the beginnings of actual aquarium science. Not merely marine biology studies haphazardly applied to our home aquariums, but actual research geared towards answering and resolving questions we face--with the ultimate goal being increased survival rates for the animals we keep.

Very likely a pipe-dream, but one of my strongest wishes for this hobby is that some more hard research could be done for it.

While some here might argue that Shimek's "rocking the boat" was irresponsible, I believe it has had the fantastic consequence of drawing out other scientists. This in itself is a tiny step in the right direction.

[jfinch]

pwhitby,

Yes, my cichlid tanks have been more stocked then my reefs (perhaps overstocked with regard to biofilms?). I've always used either biowheels or a classic style wet/dry system for biological filtration in my freshwater tanks, never in my reef. The other major difference between the two type of tanks is the amount of plant uptake. I would guess that coral (rather zooxanthellae) and other alages in a reef tank are pretty efficent at ammonia/nitrate uptake. That is missing in the freshwater tanks I've kept.

Do biofilms just develop on their own or are there conditions that are more condusive to growth?

[pwhitby]

Biofilms are ubiquitous. In fact, there is a great deal of research on preventing biofilm development. Biofilms are extremely useful, as far as bacteria are concerned. Bacteria in a biofilm are very resistant to antibiotics. In some biofilms there is differentiation within the film to an almost organized situation. For example, Pseudomonas aeruginosa (a human pathogen) will develop a biofilm and the as it grows it will develop a structure similar to a seed case which will open up and spill new P. aeruginosa into the environment.

Do a Google search on biofilms if you are interested. you will find tons of information on them.

Regards,

Paul.

[jfinch]

Thanks, I'll google a bit :)

[rshimek]

Hi,

My, my, some interesting responses.

TimV. Thanks for the experimental design, but there is no way I can do that. So, unless you boys take the ball and play with it, it will remain undone.

Paul and Tim et al.,

As I see your supposition, it would be that the biofilms on the surfaces of the rock in our systems is sufficient to act as the so-called biological filter. I see no problem with that other than it lacks any quantitative data from aquaria to support it.

You have stridently made the point that the surface area on the rock provides (more than) sufficient surface are for this process. Maybe so, still no quantitative data. That would take determining a nitrogen budget for the tanks, and that hasn't been done, either.

I would be willing to concede those points, however.

The question, then is, "Why have "so-called" live rock at all? There is no demonstrated movement of water through it; so the porosity issure shouldn't have any bearing. Chunks of lava rock should do just as well. For that matter, why have rock at all. I believe Paul mentioned in an earlier post (if I may paraphrase) that the fractal surface of/within the biofilm provides more than enough surface area to perform the denitrification processes. That surface should be present upon all surfaces in the tank. The walls, bottom, etc. If there is any type of unconsolidated sediment the surface area present there should be orders of magnitude greater than is present on the rock.

So... Whether the rock is "live," "dead," or even present, shoulld be inconsequential for this "filtration."

I would venture to say that the concept of "live rock" being necessary for biofiltration is a myth and that you folks have given the reason why it is. :D

Any rock will do, or not. - any surface will do.

Of course, you do still have to provide some data. :D

[pwhitby]

Once again Ron you fail to get the point. Bacteria see a very different world to us. A glass surface is quite smooth. Coral based rock is not. The actual microscopic surface is orders of magnitude higher than the macroscopic surface. The same may well be true with sand particles derived from coralline rock (but maybe not that derived from shells or silica). The difference with the rock over the sand is that water circulates between rocks and not as readily through sand beds. 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?

What makes rock, sediments, sand etc diferent is that there exists zontaion within the very surface layers that leads to decreased oxygen levels at that point. The glass walls are constantly bathed in water and thus the oxygen potential may be too high for effective denitrification. That last point is supposition on my part. It may not be...

It amazes me that you keep asking for scientific proof yet you write a misinfomed article for the public without researching the field and with an apparent disregard for the subject matter itself.

So Ron.........
Give me the scientific proof to support your theory. Dont use my arguments and those of others. Prove us wrong.

You state that....
There is only one problem related to the use of live rock as an effective source of biological filtration. For the rock to be the site of efficient biological filtration, water has to be passed slowly and steadily through the rock. The most likely way that will happen is by the activities of the myriad of animals that live in the rock. Of course, for this to happen there must be animals living in the rock, and lots of them. Therein lies the problem with using live rock as a biological filter. Live rock comes from many sources in today's hobby, and the products that these vendors provide are by no means uniform in their capability to provide biological filtration.

You make this statement based on what assumptions?
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.

2. That only animals can move water through rock. Again, this premise relies on your assumption above.

I say that the surface area of rock, from a coral skeleton, be it so called live or dried rock added to a tank, will have more than sufficient surface area for this process. Do you dispute the fact that coral rock has an enormous microscopic surface area. The very fact that it does is why coral skeletons are use in bone reconstruction. If you disagree........PROVE IT.

You are always very quick to get others to prove their statements without doing so yourself.
As TimV states, you have influence on this forum. Your responsibility is to educate people. Not offer speculation couched as science.

Paul.

[pwhitby]

For the benefit of others,

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.

http://parasite.natur.cuni.cz/jirovec/index.php?show_big=lpm251.jpg

As you can see, the coral skeleton (dark) comprises very little of the actual body of the coral rock itself. You can clearly see the amount of surface area available for bacterial attachment. This is just a single dimension. Once you take into account the entire structure, there is enormous surface area.

Since the magnification is relatively low, it is not possible to see all the other small pores in the coral skeleton.

Just for clarification of what I mean by high microscopic surface area.

Paul.

[gregt]

Any chance you have a microscopic image of glass at roughly the same magnification? Just for side by side comparison.

[pwhitby]

At the same magnification it would look absolutely flat. Thats why we use glass slides to sit these specimens on. In the picture the coral section sits on glass.

I did try to find electron micrographs of glass and coral, but couldnt.


Paul.

[pwhitby]

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

[gregt]

Thanks! :thumbsup:

[SPasse]

Hi All,

Perhaps this would be an interesting experiment.

“Control Tank�

1 Set a “sterile� tank with synthetic saltwater.

2 Add ammonium chloride to the water to achieve a TBD concentration.

3 Introduce “pure� nitrogen cycle bacteria.

4 Plot the decay curve of ammonia, nitrite, and nitrate.

“Tank with additional semi porous media� 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 “semi porous media� 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 “permeability� issues.

Regards,

Scott

[rshimek]

Originally posted by pwhitby

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 (http://porites.geology.uiowa.edu/database/corals/glossary/comorph.gif) or here. (http://www.reef.crc.org.au/images/aboutreef/corals/coralpolyp_diagram.jpg), 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.

[pwhitby]

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.

[pwhitby]

"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.

[gregt]

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.

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.

[pwhitby]

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.

[SPasse]

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 “cycling� FO tanks with no live critters whatsoever, at least nothing that did not precipitate out of the air. The only purposely added “fuel� 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 “anoxic� environment was necessary to host the bacteria that converts nitrate to nitrogen gas.

Greg,

I think that the term “live rock� covers the entire gambit of material from that which is only colonized by bacteria up to that which hosts an entire ecosystem of “higher order� “plants� and critters. How live is you rock is perhaps the question.

Regards,

Scott

[rshimek]

Originally posted by pwhitby

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. :D

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.

[pwhitby]

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.

[rshimek]

Originally posted by pwhitby


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. :D 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.

[pwhitby]

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.

[rshimek]

Originally posted by pwhitby

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. :D

[SPC]

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

[pwhitby]

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.

[pwhitby]

Interesting point steve.

Paul.

[TimV]

Originally posted by SPC
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

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

[rshimek]

Originally posted by TimV

Hi,

Problem is that they are not going to get light inside the rock.

That's incorrect. The rock is not opaque. There is plenty of light inside the rock for them, and there is light actually to a depth of close to a meter in most coral sandy sediments. All biogenic "rock" on coral reefs is filled with algae. In fact, most of our live rock is not of coral origin at all it is algally derived. Take a good close look at the "live" rock in your systems and see how much of it is clearly of coral derivation; it ain't much.

... why then would algae be so successful?

Because there is plenty of light, and the algae extend filaments to the surface of the rock.

[gregt]

Take a good close look at the "live" rock in your systems and see how much of it is clearly of coral derivation; it ain't much.


Can you provide references to back up this statement? As I understand it, except for aquacultured rock, the vast majority of live rock is past coral collected directly from the rubble zone. That is easy to verify visual by a visit to your LFS. :confused:

[rshimek]

Originally posted by pwhitby

Paul,

it was data and datum. Not bacterias.

No, in this case it was algaes... as in: "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."

singular and plural : alga and algae. :D

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.

As long as water can cross the boundary layers in suffient amounts, I agree it could work on any rock to some extent. I don't see any quantitative information to convince that it does work in aquarium systems to a significant degree.

I think that in natural situations that if the bacteria in the rock function in this way at all, it is the bacteria in the internal cavities that provide most of the denitritfication occurring in the rock, and that those bacteria get their water from ventilation by animals.

Also that it was your intent to prove that "live rock" is devoid of animal life.

No, my intent was to find out how much of the original animal life within the rock had survived. In a natural situation there are immense numbers of animals in the rock. I was curious how many of them made it into our so-called live rock.

[rshimek]

Originally posted by gregt

Greg,

Can you provide references to back up this statement?

Check out the initial Odum and Odum 1955 paper I cited in my article, and work this way in time if you wish. Alternatively get the information from Eric B.

As I understand it, except for aquacultured rock, the vast majority of live rock is past coral collected directly from the rubble zone.

Most of the coral reef is formed by green algae which cement coral animal skeletal fragments together with their own calcareous secretions. Most of the "live" coral rock is indeed "coral" rubble, but most "coral rubble" is mixture of coral skeletal remains, coralline algae (green not red), and straight algal remains. "Pure" coral skeletal remains generally make up a very small amount and contribute a very small amount to the structure of reefs. In terms of origin and in terms of biomass and in terms of calcareous mass, a coral reef is mostly made up of algae.

[TimV]

Originally posted by rshimek
Paul,

[b]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.


First of all, as stated, the incredible surface area present within the rock makes any argument that water cannot diffuse fast enough a bit silly. It doesn't have to. The concentration gradient caused by depletion of NH4 is going to drive more into the biofilm. The nitrite produced by the Nitrosomonas species will be immediately taken up and converted to nitrate by Nitrobacter species. But here is the point: in a coupled nitrification-denitrifaction mixed biofilm, the NO3 doesn't need to diffuse either. A layer of bacteria even 100 um deep will allow for anaerobic conditions for the deepest bacteria in the matrix. This is basic oral biology (ever had a cavity?). In the lab, I've perfected methods of transformation of bacteria through induction of competence by transient anaerobiosis conditions. It is as simple as letting the bacteria settle in as little as 1 mm of culture media.

Another point is that even if these biofilms do not exist, that doesn't mean that the denitrifiers cannot work in the rock even with the low levels of diffusion you state. You neglect the fact that many of the known denitrifiers have been demonstated to be chemotactic to nitrate. They can move within the anoxic zones of the rock to get to whereever needed and can do this very rapidly. In this scenario, the nitrification and denitrification is still coupled, in the sense that the nitrate production is still occuring within the rock. Of course this is speculation, but it is supported by anecdotal evidence. I can't count the times that I or Paul have suggested to members of our club to remove their biowheels from their tanks. Every one of them have reported nitrate levels dropping to near undetectable levels shortly thereafter. I think the wheels are just so efficient in attracting the nitrifiers (but preventing the denitrifiers) that it completely uncouples the system. If invertebrates were able to assist in moving water through rock to the anoxic zones, or if algae dominated the denitrification in the tank, the biowheels would not have an effect on the system. Clearly, speculation that the nitrification and denitrification occurs in the rock (or sandbed) is well founded. The coupling of the system means that it is so efficient, that it is only limited by the rate at which it can access NH4.



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.


If all you are trying to do is prove that people don't need "live" rock, you're just trying to reinvent the wheel. A simple survey is all you would need to do to show that. I know many people that do not have a single rock from either the Pacific or Florida aquaculture farms in their system that do not have detectable nitrates in their tanks. There are probably many customers of Hirocks that can attest to their success. It may take slightly longer to develop the proper flora for nitrification/denitrification, but it will occur, likely even without intervention as these bacteria are so ubiquitous.

The only reason to buy Fiji or Marshall island rock, imo, is because you like the shapes. With as long as they sit on docks, you need to cure it for so long that it is pointless to think it will be ready much before the hawaiian base rock. Now, this next statement is completely speculative, but here is is anyway. The base rock from Florida, while coming with lots of "life", is unlikely to be as good a source of biological filtration as either wild-collected "live" rock or the hawaiian rock. I've got a few pieces that were actually dry when I obtained them. They are extremely dense (dry weight for for similar sized rocks was twice as much for the Florida rock than for wet Marshall island rock I purchased). That is de facto evidence that is is not as porous as other rock. It is fossilized and practically limestone (coming from a non-geologist, mind you, don't nitpick). Now, will that rock work. Probably. As well as Fiji or marshall? Not likely. But I highly doubt we are taxing our systems to that extent that it makes a difference.

Here's another experiment. It won't be short term, but it will won't be terribly expensive. Three small tanks with "live" Fiji, "live" Florida aquacultured, or with dead Hawaiian rock. It would preferable to use equivalent wet-weight of each in their respective tanks. Determine how long it takes for each to cycle (Add several clams or something to really get the ammonia level initially up.) Follow the time course of nitrification/denitrification. Then after an appropriate time (at least a few months after the last tank has finished cycling) start dosing exogenous ammonia. Follow nitrate levels. Ramp up ammonia additions and determine that nitrification/denitrification capacities of the system.

Statistically reliability would require at least an n of 3 for each condition, but I'd be willing to let that slide a bit for the sake of preliminary results. If someone is willing to donate 9 20 gallon tanks and the appropriate rock, I'd be willing to do it.

Thing is, the only reason why I even got involved in this discussion, is that the only thing I hate worse than having no information is having bad information. Rock works. I don't much care why but if it is that important to you, I'm willing to help. I don't mind giving my time and expertise to the community (as long as it isn't financial, my wife would kill me :) ) Just please abandon that original experiment as unworkable (and possibly irrelevant).

Hey, I do want you to succeed. I'm also a native Montanan (born and raised) and we do need to stick together.

[gregt]

Originally posted by rshimek
Greg,

Can you provide references to back up this statement?

Check out the initial Odum and Odum 1955 paper I cited in my article, and work this way in time if you wish. Alternatively get the information from Eric B.

As I understand it, except for aquacultured rock, the vast majority of live rock is past coral collected directly from the rubble zone.

Most of the coral reef is formed by green algae which cement coral animal skeletal fragments together with their own calcareous secretions. Most of the "live" coral rock is indeed "coral" rubble, but most "coral rubble" is mixture of coral skeletal remains, coralline algae (green not red), and straight algal remains. "Pure" coral skeletal remains generally make up a very small amount and contribute a very small amount to the structure of reefs. In terms of origin and in terms of biomass and in terms of calcareous mass, a coral reef is mostly made up of algae.


Thank you for responding. I understand your point.

[NicoleC]

Originally posted by TimV
Here's another experiment. It won't be short term, but it will won't be terribly expensive. Three small tanks with "live" Fiji, "live" Florida aquacultured, or with dead Hawaiian rock. It would preferable to use equivalent wet-weight of each in their respective tanks. Determine how long it takes for each to cycle (Add several clams or something to really get the ammonia level initially up.) Follow the time course of nitrification/denitrification. Then after an appropriate time (at least a few months after the last tank has finished cycling) start dosing exogenous ammonia. Follow nitrate levels. Ramp up ammonia additions and determine that nitrification/denitrification capacities of the system.


While fascinating and useful from a buyer's perspective, I don't think this experiment would be very useful in discerning the role of invertebrates in the process. There are too many variables such as the collection sites, time out of the water, etc. These might be alleviated somewhat by getting a Fiji supplier like Walt Smith to ship rock for the experiment in water and not rinsed, similar to the way Tampa Bay ships their rock.

If one wishes to just study the value of the cavitations themselves in the biological filter, wouldn't "dead" rock from all three sources be a more controlled experiment? It eliminates the concern that the supposedly live rock being used is too lifeless to perform the functions being hypothesized.

For example, if the rock with more interior cavitations is a better biological filter while dead, we can determine that the action of the invertebrates are not the sole source of benefit.

[pwhitby]

Since you still wish to argue grammar.......

You originally corrected my use of the word data. You then said I misused the word bacteria. That was my point, but like I said, lets stick with science.

I stated that surface structure and biofilms can account for the denitrification we have in our systems.

You say that without animals diffusion is not powerful enough to deal with this.

You also say that most rock is probably devoid of life. I totally agree.

So.........how do you get denitrification on all those tanks with no substrate. The rock has no animals. There is no substrate, yet we have denitrification.

You asked for the scientific proof of my statements. I gave you pictures of coral surface areas (which you still fail to acknowledge). I use a simple example to show how short a distance is required to establish anoxia. These are facts. I have shown you why I think my scenario works.

You have still to give me one piece of evidence that it does not.
I am still waiting for evidence.

At least provide the same courtesy you demand of others.

finally, as a complete aside. Other people will read this. They may not be scientists. I understand terms such as "benthic boundary layer effect " since my first degree was marine biology and biochemistry. Others may not. Please let them people know what you mean, so they can understand. Just a thought...

Paul.

[pwhitby]

Greg T and Ron.

The fact that on a reef there is a large biomass of algae has no relation to what goes on in a tank. Several times Ron has said that things on a reef and in our tanks are completely different. I agree.

I do believe that on a reef the rock is not the site of denitrification. Lets face it, the ocean is pretty huge and the life in it is miniscule when compared to our tanks. The vast amount of phytoplanktonic organisms may well just take up nitrates and grow on it as a nutrient.
Thus the requirement for denitrification may be a great deal lower than in our closed systems. Stating that on a reef the rock is full of algae has no bearing on the situation in our tanks.

Paul.

[pwhitby]

As a final point, before I turn in for the night. In your hypothesis, or supposition, animals move water through their burrows, and thus move solutes. Ok...so then what? What happens a few millimeters from the animals burrow? This is the basic fallacy of your argument. The situation there is the same at the rock surface...or water-rock boundary.

Your hypothesis is based on the single fact that solutes in water have to penetrate the rock to an appreciable depth to creat anaerobic environs. I have shown that that is not required.

Goodnight all.

Paul.

[rshimek]

Originally posted by pwhitby

Hi Paul,

You originally corrected my use of the word data. You then said I misused the word bacteria.

No, I said you misused the word algaes...

So.........how do you get denitrification on all those tanks with no substrate. The rock has no animals. There is no substrate, yet we have denitrification.

I agree with you that surface films, on substrates like glass and sand will account for denitrification. In fact, they may do most of the denitrification.

You asked for the scientific proof of my statements. I gave you pictures of coral surface areas (which you still fail to acknowledge).

The rock is not - just - coral skeleton. In fact, coral skeleton may be a small component of most reef rock; that was really my point to Greg. Yes, your pictures are pretty. But, coral skeleton is an immediate substrate and gets colonized as soon as it is exposed. First, by bacteria - and then by algae and animals. In a short time it is largely covered and along with it all the initial porosity. My recollection is that the calcareous algal depositions are a lot less porous and may simply seal the coral porosity behind them.

Look at the rock in your tank, Paul, it is probably covered with coralline algae. I would bet you would be hard pressed to find any "fresh-looking" coral skeleton. I spent a bit of gazing into my tank this afternoon and while I can see a lot of surface irregularities, they are almost on "secondary" surface such as on coralline aglae or surfaces modified by animals.

I use a simple example to show how short a distance is required to establish anoxia. These are facts. I have shown you why I think my scenario works.

I will concede your scenario works - but with the following caveats.

1) Not much, if any original coral skeleton is present and exposed. So talking about coral skeletal prosity is really a starting point, and largely irrelevent. We/you need to address porosity of the rock not the skeleton.

2) I haven't the references I need here to argue with you further. The library at Montana State is pathetic on these subjects, and the nearest library where I could do work is at the U Wash, about 750 miles away. Bottom line, it ain't gonna get done. So...

3) I could take a look at the surfaces of some of these rocks with the local SEM, it is an excellent machine. Looking for surface porosity and bacteria would be kinda fun, but... it costs about $350/hour for non-faculty users and since I am not teaching now, I fall into that category. I can't afford it.

Bottom line, I will concede that you may be right. My understanding of the initial use of porosity - in 1990 or so - when the arguement was first posed - was that the people were discussing the pores in the rock created by the burrowing organisms. Not the pores in the rock made by coral formation, and I wrote the article in that mindset.

In your hypothesis, or supposition, animals move water through their burrows, and thus move solutes. Ok...so then what? What happens a few millimeters from the animals burrow? This is the basic fallacy of your argument.

I don't see any fallacy in the argument. The water is moved by the organisms into the rock, and bacteria lining the burrows as well as the animals, remove most of the oxygen as the water passes over the animals. The burrows are longer than the animals in them and this creates quite a good low oxygen environment behind and even surrounding the animals. Thus, the linings become the site of denitrification. In essence, as I see it, "your" biofilms are not on the surface of the rock but lining the burrows in it. That pumped water continues through the rock and exits either through some other burrow or through the cracks in the rock. Paul, these burrows are tightly packed, and in small rocks almost completely fill them. That the rocks have been burrowed out is what makes reef rock light, not the coral skeleton porosity. Much of the initial coral skeleton porosity is covered, filled in, or simply obliterated by the action of the subsequent occupying organisms. Then the rock becomes so much burrowing ground for the animals. Did you read the article? I mentioned the data collected and published by Kohn and Lloyd looking at rocks, and the number of worms in them; in many cases there were several burrowing worms per square centimeter, and these were not tiny worms. I was a student in that lab when they took apart those rocks. In good, really LIVE rock, the rock is honeycombed with the burrows. There are precious few areas where the rock is more than a millimeter or two from a burrow. Additionally, in such rocks the surface of the rock doesn't have a thin boundary layer of almost stagnant water over it, the action of the animals moving in, out, and around the rock disturbs and, in fact, destroys the boundary layer.

So... this rock is not fresh coral skeleton. It is highly altered material which has been actively excavated by burrowing organisms. Frankly, I think the original coral skeletal porosity is probably irrelevent.

In any case, as I said, I am willing to concede that with our "dead" once-live rock your scenario may work and may be the major site of denitrification. Presently, although I am not convinced, I can't get either the data or the references I need to resolve this. I would like to see some indication from aquarium data that it does work, but those data will be lacking too, I guess.

I think your scenario is at least a potential reasonable explanation some of the denitrification we see in our systems, and as such I would request that you, and Tim, if he wants, write up an article for submission and potential publication in Reefkeeping. I would recuse myself from the editorial process if you like. You would be paid for the article, and you probably have spent more time arguing with me than it would take to write a decent article of about 3000 words. This would be a nice way to recover some of your losses.

[pwhitby]

Thanks for the reply Ron.


Regarding your statements above. Yes it would be great to look at some established rock and have a look at the internal surface structure. The ideal way would be Electron Microscopy. I have access to such, but as you say the cost is prohibitive. Light microscopy, or even macrophotography of cut rock may yield insight.
I also spent the last few days with my nose pressed against the glass viewing rocks. I do see a great deal of surface structure. As to how far this extends beneath the surface of the rock, I do not know, however, I will endeavour to find out.

The entire crux of both our arguments revolves around diffusion and the internal characteristics of the rock.

There must be some way we can begin to analyze this in a scientifically robust fashion.

There are other issues beyond those we both raise. For example, in the larger scheme of things, how much denitrification occurs in the sand as opposed to the rock. How much nitrogen (in whatever fashion) is removed by macroalgae as opposed to removed by denitrification. Again, these issues are not lightly tackled.

I am not sure what I could add by writing an an article. The points I would make I have tried to make above, but as we both know, we need real scientific data on which we can base our assumptions and hypothesis. In the absence of that we are left with speculation. In my personal opinion, this will not help the readers and the other members of this forum.

At the end of the day we have denitrification occurring. To break down the mechanisms of how this occurs is beyond our collective limited resources.

I propose that we (and by that all of us) put our collective heads together and try to figure out some of the fundamentals of this very important process. There are many experts on here and you are conversant with the forum infrastructure. You are an expert in your chosen field, how can we recruit other experts in the fields of hydrodynamics, geology, physics, bacteriology in a way we can openly discuss these issues. Do you think this would be a good idea?

Regards,

Paul.

[SPC]

Good morning all,

I have noticed that live rock will shed detritus, in fact, it will do this for many months without any input of nutrients or water flow in the vessel it is housed in. What animal/process is at work here?
Steve

[Machiavelli]

I propose that we (and by that all of us) put our collective heads together and try to figure out some of the fundamentals of this very important process. There are many experts on here and you are conversant with the forum infrastructure. You are an expert in your chosen field, how can we recruit other experts in the fields of hydrodynamics, geology, physics, bacteriology in a way we can openly discuss these issues. Do you think this would be a good idea?


What a fantastic idea! Why didnt I think of that? :p

[rshimek]

Originally posted by pwhitby

Hi Paul,

The entire crux of both our arguments revolves around diffusion and the internal characteristics of the rock.

Yes, I think we were talking about several different things and using the same terms in an unintentionally ambiguous manner.

I am not sure what I could add by writing an an article. The points I would make I have tried to make above

Yes, but, as you pointed out, not many folks will actually read through these threads, and fewer of them will comprehend some of the fine points. I think your discussions of biofilms, etc, might well be illuminating to general readers, and might well bring some more folks interested in this problem "out of the woodwork."

I propose that we (and by that all of us) put our collective heads together and try to figure out some of the fundamentals of this very important process. There are many experts on here and you are conversant with the forum infrastructure. You are an expert in your chosen field, how can we recruit other experts in the fields of hydrodynamics, geology, physics, bacteriology in a way we can openly discuss these issues. Do you think this would be a good idea?

I think it would be a great idea - and to fall back to my paragraph above - an article discussing the issue would be a great place to start. :D

[rshimek]

Originally posted by SPC

Hi Steve,

I have noticed that live rock will shed detritus, in fact, it will do this for many months without any input of nutrients or water flow in the vessel it is housed in. What animal/process is at work here?


It could be any number of things. The detritus is simply critter crap, more than likely. I suspect that it is formed by some suspension feeding animals; some of the worms I alluded to in the posts above or some small burrowing bivalves are probably the most likely culprits.

[G-money]

Why hasn't anyone brought up the fact that a person without a sandbed of any sort can have no detectable nitrate in a tank based solely on live rock and skimming?

I realize the sensitivity of the average aquarium test kit is far below the threshold required to allow algae growth, but still - if there wasn't anything there taking care of the nitrate, where would it go? In time, unless it was being eliminated, it would have to accumulate in algae or nitrogen-fixing bacterial biomass and you'd see it. Many folks don't.

That doesn't prove or disprove anything, but it's a pretty good "anecdote" suggesting the denitrification capability of live rock, no?

[rshimek]

Graham,

The discussion was not whether or not live rock was functional, but how it was functional and if I what percieved of as the standard explanation was a valid one.

[G-money]

Sure, but the how and whether are related.
You claim that water cannot be moved in and out of rocks without a sufficient amount of critters doing the work - assumingly less than are found on the average "poorly-shipped/maintained" rock judging from your claims. Yet many of us still find the capacity for denitrification more than sufficient. Why? Where's the need for improvement? What's broke?

It may be "shocking" to know that there are people out there with perfectly adequate denitrification using things like darkness-cured and starved live rock (resulting in LOTS of die-off before use). The critters you speak of just aren't that important for denitrification. There have to be other primary mechanisms at hand...meaning the inherent structure of the rock is of far more fundamental importance than what's on or in it. That's why us suckers buy it. :)

I'd also be interested to hear from people who have stocked their tanks with mostly man-made (aragocrete) type "live rock" and have no sandbed. Do they have denitrification issues?

[G-money]

Originally posted by G-money
...meaning the inherent structure of the rock is of far more fundamental importance than what's on or in it.

I don't mean to include bacteria in the "what's in or on it".

[Ronald]

Recall flow and pressure relationships described by Bernoulli and used by the Wright bros as well as sailers etc. Flow across the rock particularly perpendicular to the pores will result in net low pressure at the pore orifice and should result in movement of h20 throughout the rock. We are dealing with much more than diffusion here, we have flow! Check out the specifics here (http://scienceworld.wolfram.com/physics/BernoullisLaw.html) and let me know what you think.

Ron A

[Ronald]

OK guys I know I am really late to this discussion, but I do have free access to clinical CT and MRI units and could easily image a "live rock" or dead one or even a live coral in a saltwater bath. Resolution isn't that of EM, but the rock stays in tact. I could get .625mm sections at .1mm intervals and display them in 3D and as sections. i could use density threshold techniques to calculate the volume of solid rock vs air or water using standard pixel counting algorithms (or is it algorithma? :D ) and get a percentage of air vs rock (error rate likely +/-5%). Anybody interested?

Ron A

[pwhitby]

Sorry Ronald, I was out of town at a conference.

The imaging sounds like a good idea. PM me and lets talk.

Paul.

[lilko]

Hm... My, my... DSB is no longer good, live rock sucks as well... My, my... I think I will start 100% water changes every day tomorrow :) Or maybe I should change hobby all together!!!

Sorry for my BS, but I am glad to see some brains finally getting into your preachings Dr. rschimek :)

[tdwyatt]

Writing in Marine Pollution Bulletin, the editors decried the decline scientific objectivity. They wrote that, "It is both wrong and dangerous for a scientist to become personally and inflexibly 'attached' to a theory....Becoming inflexibly attached to a theory, whether or not a scientist considers it his or her own, prevents that scientist from thinking of more useful theories." (Chapman & Giddings 1997) As we continue this reexamination, readers should keep the words of Chapman and Giddings in mind. The hobby benefits most by viewing any proposed explanation for inexplicable phenomena with some skepticism. As we will show, despite the author's confidence, his hypothesis is far from proved, and his conclusions far from fact. Thanks Richard (Harker) this sums up the total experience to date.

[spamin76]

I would just like to point out that not all rock is created equal - what is sold as live rock comes from a tremendously large range from the pacific and atlantic - the age and make up of the rock could have significant differences on the rocks supposed ability to filter - ultimately I think there are far too many uncontrollable factors in this experiment to give it much validity in the final outcome - even separate pieces of rock from a small specific geographical area can have different levels of porosity and composition. Some live rock could be useful and some could not but unless you take measurements and reading on every piece of live rock in every holding tank and every aquarium currently set up there is no established control that you are getting even a minorly representative sample - not to mention the rock which is currently being acquacultured in the wild. Ultimately - this seems like a shot in the dark - live rock is not a geologically or even biologically consistent term - marshall rock is not fiji is not carribean is not tongan - and even all marshall is not necessarily alike. It just seems like the scope is too broad to determine anything all that useful from studying the rock. Just a thought though. I am not a micro-biologist - though I do know a thing or two about some aspects of geology.

I certainly understand what you mean that treatment of the rock before it reaches the tank could dramatically effect its potential as a filter.

I am just not sure how useful any eventual conclusions will be from this study even if you can likely establish that the benefits of live rock is largely overstated - I would like to say that I am partially sceptical of claims associated with live rock - so I am sympathetic - but also it makes a tank look much more fabulous - that and some of the creatures from the live rock are astoundingly resillient - I have had rock with significant die off recover tremendous amounts of bio-diversity of even some supposedly fragile sponges, worms, and tunicates over the period of several months. Amazing things have come out of my rock which were not vissibly there when I purchased it and put it in the tank. Some of the rock has been in a tank by itself for sometime so the creatures that survived the shipping process came in on the rock. On a weekly basis I look in my tank and see new things I have never seen before.
Eventually it may conceivably be possible for the live rock to regenerate a certain degree of it's natural bioload if proper conditions are provided which might render it more useful for filtration.
Again, just a thought.

[ikinne1]

You all forget about the meager simplicities!
Recall that ol' coot that instructed you in Biology 101...put aside his talks on the Krebs Cycle and Blastopheres. Remember it's all about the Reynolds Number.
Surface area is the key to reef keepers' problems. Fluidized bed filters had the RIGHT idea, but the wrong reasoning. Live rock is the way to go based on solely the magic number. With cycled live rock and a great skimmer, you are money...($$$)....to use the parlance of our times, Maude Lebowski.
Discard Dr. Skimmer's lengthy articles on salt effectiveness. I know we've better things to do. Email me directly @ ikinne1@lsu.edu for a straight-up answer (i.e. my opinion). I'm more than qualified: 135gallon x 2 : 1- SPS/LPS. 1-dedicated 135gallons to a 13-year-old hermit crab. He deserves it! PS- it isn't dedicated...he shares it with 23 other schoalling fishes.
58g nano cube. 10g nano cube.

[lavann]

hi,

i'm new to this forum(not a scientist) and the thread is quite interesting, i did a search on google and found an experiement that was done by the society of petroleum engineers, called the spontaneous water imbibition into diatomite.

here's link
http://ekofisk.stanford.edu/supria/pubsdirectory/spe46211.pdf

from what i can understand they proved that water went into the rock through capillary action, so i guess that it's possible for live rock to do the same.

i think you could replicate the experiment if you had the equipment and substitute diatomite with live rock.

[reefhippie]

I always love it when I stumble into an area that is not thoroughly researched. It leaves room for some crazy ideas! Here's one I thought I'd toss out on the table, based on some well known facts a few wild assumptions.

Everything we know about ocean life is that it's full of teamwork, living things helping other living things in the quest for survival, and a coral reef can be seen as one big living thing, or it can be seen as millions and millions of small living things, not unlike our own neighborhoods.

The "Berlin Method" suggests that live rock is necessary for the health and well being of corals in captivity, based on its ability to "filter", and we know that corals themselves can act as filters.

We know that corals need excellent water quality, low levels of ammonia, nitrites, nitrates, yada yada yada, and high levels of calcium in the wild, so they obviously need these things in our home aquariums. And if they survive only in these conditions in the wild, something is obviously contributing to the quality of the water there.

We also know that high levels of calcium is also benificial to coralline algea growth, so we can effectively say that coralline itself contains contrentated levels of calcium, which is benificial to corals, and help them grow and spread out. Light alone won't do this.

And since corals are porous, could they not be acting as some sort of a ventalation system, a passagway into the center of the rock, not unlike the branches in our lungs? We assume that the corals are "reaching out" for more light, but maybe there's more to it than that.

One interesting point that this article pointed out for me, was the use of glue to attach the coral frags to the live rock. If corals do in fact provide such a passage, an air passage, a nitrogen gas passage, a waste passage, or whatever, it would make sense that the glue would block these passagways, clogging the ventricles, so to speak. Afterall, glue is not a natural coral reef ingredient.

Thank you for the very thought provoking article.

[reefhippie]

I remember reading that it was the photosynthetic bacteria, by and large, that assisted in the nitrogen gas break-down process within the live rock. If this is true, then maybe corals exist because of those photosynthetic organisms desperately trying to survive under the shade of the coralline algae. In other words, corals are the result of photosynthetic organisms and calcium-based algae, as a way of bringing in light, and passing out nitrogen gases. Thus, corals need them, and they need the corals.

So in theory (mine anyway), the coral only knows that it needs sunlight and nutrients to survive, and so in our home aquariums, whether there is glue between itself and the live rock is unimportant because we have expensive protein skimmers and calcium reactors.

[mjbock]

I have noticed a misconception in the extreme. It would appear as though Dr. Ron proposes that organisms larger than bacteria are the only mechanism for water movement through "live rock". I content that this is likely untrue. Given that water movements inside an aquarium will set up pressure differentials within the tank and therefore on a piece of rock, these pressure differentials provide a motive force. Obviously this assumes that the pores in the live rock are at least to some degree connected. A similar motive force has been found in sediments. As water moves along sand ridges porewater has been demonstrated to migrate through the ridges (I wish I had the reference but I don't remember where I saw it). Thus water migrates through sediments in response to movement in the overlying water. As everyone is so found of pointing out, I do not have direct evidence to support this contention as it applies to live rock but it is a reasonable extrapolation.

In my view all three mechanisms for water movement: advection diffusion, pumping by organisms, and flow induced by pressure differentials are of potential importance. No Dr. Ron, the boundary layer effect is not sufficient to mean there is "no flow at the surface of the rock" think about turbulent eddies etc, as shown in any good fluid dynamic text. The no-slip condition is really only a theoretical construct that approximates observations and breaks down totally in turbulent flow. As we all know, true and complete laminar flow is a rare thing. However, I agree the flow at the boundary is not sufficient for feeding and gas exchange for macrofauna, I have spent many hours watching worms etc in feeding in flow and have published many a paper on the topic.

I must comment this argument triggers memories of the whole "bacteria rule the biochemistry of the ocean" versus bacteria are just food for everything else arguments that permeated by time in graduate school.

[jfritter]

Fascinating, although I did not see logic applied in this discussion. If there is denitrifying bacteria on the LR, then they are performing as desired. If they were not, they would not be there.. Their sufficency without the additional surface area of the LR would depend on the bioload and the substrate.