recent article - live rock as bio filter

[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.

. 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.

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]

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.

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]

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.

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

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

 

[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.