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  #51  
Old 07/22/2007, 06:57 AM
pjf pjf is offline
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Proprietary Bacterial Filtration

I’ve created a table summarizing the proprietary bacterial filtration methods that you have graciously supplied references for.




















































Bacterial Filtration
Proprietary System Bacteria Bacteria Type Primary Nutrients Export Method References
Polyp Lab Custom bacterial strains Aerobic, biofilm forming Organic carbon, amino acids Skimming dead biofilms www.polyplab.com/reefresh.html
Prodibio Nitrosomonas europea Aerobic, chemolithoautotrophic ammonia-oxidizing Trace elements, phospholipids, amino acids, marine type fatty acids, vitamins, carotenoids N2 gas http://www.robsreef.com/Merchant2/me...t_Code=pbkreef http://www.robsreef.com/Merchant2/me..._Code=pbdigest
http://genome.jgi-psf.org/draft_micr...arde.home.html
http://aem.asm.org/cgi/reprint/62/8/2888.pdf
Nitrobacter winogradskyi Aerobic, chemolithoautotrophic nitrite-oxidizing
Paracoccus denitrificansHeterotrophic, denitrifying in anaerobic conditions
Pseudomonas stutzeriiHeterotrophic, denitrifying in anaerobic conditions
Zeolite Nitrosomonas europea Aerobic, chemolithoautotrophic ammonia-oxidizing Glucose, amino acids Skimming heterotrophic bacteria, filter changes http://www.reefcentral.com/forums/sh...hreadid=905996 http://aem.asm.org/cgi/reprint/62/8/2888.pdf
Nitrobacter winogradskyi Aerobic, chemolithoautotrophic nitrite-oxidizing


My first impressions are:


  • Both the Polyp Lab and the Zeolite methods appear to be proprietary variants of carbon dosing where nitrifying bacteria are used to oxidize ammonia and nitrites to nitrates and heterotrophic bacteria are used to consume nitrates for skimmer export.

  • Probidio appears to “push the envelope” by supplying denitrifying bacteria (Bio-Digest) that convert ammonia, nitrites and nitrates to gaseous nitrogen. Do you have any information that shows how to culture and sustain Paracoccus denitrificans and Pseudomonas stutzerii in a marine aquarium?

  #52  
Old 07/23/2007, 03:07 PM
mesocosm mesocosm is offline
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Greetings All !

Quote:
Originally posted by pjf
... Do you have any information that shows how to culture and sustain Paracoccus denitrificans and Pseudomonas stutzerii in a marine aquarium?
In a marine aquarium? We need to be careful with what we make of the research literature here ... many marine bacteria have proven to be surprisingly difficult to culture. In terms of culturing, the media formulae presented in the "Materials and Methods" section of the research literature is probably the best place to look for specific culturing techniques. Even so, there is some interesting stuff out there ...

For a good sampling on the type of stuff available for Paracoccus denitrificans, check out this stuff ...

Google Search Results
http://www.google.com/search?as_q=&h...s=&safe=images


For a good sampling on the type of stuff available for Pseudomonas stutzerii, check out this stuff ...

Google Search Results
http://www.google.com/search?num=50&...2+&btnG=Search






Google is okay for this type of stuff, but better is ...Scirus.

Scirus
Advanced Search Interface
http://www.scirus.com/srsapp/advanced/index.jsp?q1=


Scirus results for Paracoccus denitrificans:
http://www.scirus.com/srsapp/search?...&ds=web&sa=all

Scirus results for Pseudomonas stutzerii + "denitrification" ...
http://www.scirus.com/srsapp/search?...n%22&t=all&g=r

See the difference? ...




Having ranted all that, I would add that "getting bacteria to grow" isn't the thing that I'm interested in ... I'm interested in getting them to metabolize stuff. For that, we're going to need to add things beyond the C:N:P relationship. For example ...

Quote:
As part of an effort to identify other genes involved in the regulation of denitrification, mutants with pleiotropic defects in the ability to utilize N-oxyanions and N-oxides as electron acceptors for anaerobic growth were sought. One such mutant, whose anaerobic growth is severely impaired when nitrate, nitrite, or N2O is used as an electron acceptor, was unexpectedly discovered to have a mutation in a cobalamin (vitamin B12) biosynthesis gene. Analysis of this mutant provided evidence that P. denitrificans expresses a cobalamin-dependent ribonucleotide reductase, which is required for growth only under anaerobic conditions.

From:

Anaerobic Growth of Paracoccus denitrificans Requires Cobalamin: Characterization of cobK and cobJ Genes
Neil Shearer, Andrew P. Hinsley, Rob J. M. Van Spanning, and Stephen Spiro
J Bacteriol. 1999 November; 181(22): 6907–6913.
http://www.pubmedcentral.nih.gov/art...gi?artid=94164
Please don't get lost in the techno-babble, folks ... all it's saying is that in order for Paracoccus denitrificans to do denitrification (under the experimental conditions), the genes to produce the enzymes to do the actual metabolization have to be within the genetic code of the strain (which is not always the case), and that another chemical (in this case vitamin B12) has to be present to facilitate the denitrifying reaction.

And some folks say that vitamins are useless in marine aquaria ...


It should also be pointed out that the rates and products of metabolism can vary widely between strains. For example ...
Quote:
A comparison was made of denitrification by Pseudomonas stutzeri, Pseudomonas aeruginosa, and Paracoccus denitrificans. Although all three organisms reduced nitrate to dinitrogen gas, they did so at different rates and accumulated different kinds and amounts of intermediates. Their rates of anaerobic growth on nitrate varied about 1.5-fold; concomitant gas production varied more than 8-fold. Cell yields from nitrate varied threefold. Rates of gas production by resting cells incubated with nitrate, nitrite, or nitrous oxide varied 2-, 6-, and 15-fold, respectively, among the three species. The composition of the gas produced also varied markedly. ...

From:

Comparison of denitrification by Pseudomonas stutzeri, Pseudomonas aeruginosa, and Paracoccus denitrificans.
C A Carlson and J L Ingraham
Appl Environ Microbiol. 1983 April; 45(4): 1247–1253.
http://www.pubmedcentral.nih.gov/art...i?artid=242446
Again ... please don't be put off by the techno-babble, folks. All it's saying is that different strains do different things, under different conditions. Hardly surprising.



JMO ... FWIW, maybe nothing.
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  #53  
Old 07/23/2007, 03:14 PM
mesocosm mesocosm is offline
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Greetings All !


Quote:
Originally posted by pjf
... Both the Polyp Lab and the Zeolite methods appear to be proprietary variants of carbon dosing where nitrifying bacteria are used to oxidize ammonia and nitrites to nitrates and heterotrophic bacteria are used to consume nitrates for skimmer export. ...
I don't think the differences are that straightforward ... JMO.


Quote:
Originally posted by pjf
... Probidio appears to “push the envelope” by supplying denitrifying bacteria (Bio-Digest) that convert ammonia, nitrites and nitrates to gaseous nitrogen. ...
Again, I don't think the differences are that straightforward ... JMO ...




In terms of the "variable sets", I would suggest these:

(1) The inclusion of some form of culture vessel (aka "reactor");
(2) The specific strains of the bacterial inoculant;
(3) The specific formulation of carbon source(s) and metabolic "participants"(*);
(4) The type of media for the culture vessel (if applicable);
(5) The "dosing schedule";
(6) User experience(s).

(*) ... includes weak acids, weak bases, vitamins, amino acids, minerals, and ionic compounds.


I hasten to add ... there's a "broader context" of variables including circulation within the ecosystem (mass transfer), filtration configuration (primarily the protein skimmer selection), the lighting configuration, and ... "husbandry".

While I like your chart immensely (nicely done!), I feel the need to point something out ... I've danced the Bacterioplankton Boogaloo Shing-a-ling way too long to put all that much faith in what the manufacturers of these systems have to say about their products. Their product descriptions are remarkably ... uninformative.

Using what are essentially profit-oriented promotional materials as definitive descriptions strikes me as more than casually risky. Even so, it's not like I think they're lying (.... I don't believe they are. They've just choosen to not tell us all that much...), and it seems to me that they have presented enough of the basics to be useful for a limited, critical examination of what their products actually do.



JMO ... your mileage will vary.
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  #54  
Old 07/23/2007, 04:19 PM
onetrickpony onetrickpony is offline
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I am really enjoying this thread

So far it has ranged from
Nitrogen-limitation
Glutamate or glutamine
Vitamins, B-12
Trace metals, enzymes
Italians wild & crazy reef keepers- hormones

“Our captive marine ecosystems are much more analogous to a laboratory culture vessel than they are to full-blown, natural marine ecosystems�

If are reef aquariums are culture vessels, is there a recipe( lots of $$$$ being spent on someone’s secrete recipe) that one could use to feed our tanks to get the benefits we are all looking for , other than just throwing in a good multivitamin & glutamate along with good reef keeping practices –Light, water, Flow

Mesocosm do you dose in your reef setup

Thanks
Ken
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  #55  
Old 07/24/2007, 08:45 PM
pjf pjf is offline
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Question Cracks in Holy Grail?

The "Holy Grail" of natural nitrate reduction (NNR) has been the cultivation of anoxic denitrifying bacteria in live rock and in deep sand beds. Yet, there is very little information available to the average aquarist about obtaining and sustaining denitrifying bacteria. One is left to believe that denitrifying bacteria are autotrophic, ubiquitous in marine aquaria, and need no special provisions other than porous rock, fine aragonite sand, and nitrogenous wastes. However, these assumptions are being challenged.

• Except for Probidio, I have yet to found readily available sources for denitrifying bacteria, such as Pseudomonas stutzeri and Paracoccus denitrificans. The sources for these bacteria tend to be university laboratories. Has anyone independently verified that these bacteria exist in the Probidio BIO-DIGEST product?

• Both Pseudomonas stutzeri and Paracoccus denitrificans were isolated from soil samples and they can be cultured in Luria-Bertani broth (10 grams tryptone, 5 grams of yeast extract, 10 grams of NaCl, 1 liter water). Is there any evidence that they reduce nitrogenous wastes to N2 gas in natural marine reefs?

• Both Pseudomonas stutzeri and Paracoccus denitrificans are heterotrophic. What nutrients will they need beyond what is normally available (nitrogenous wastes, phosphates) in a marine aquarium?
  #56  
Old 07/26/2007, 07:46 PM
mesocosm mesocosm is offline
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Greetings All !


Quote:
Originally posted by pjf
... Yet, there is very little information available to the average aquarist about obtaining and sustaining denitrifying bacteria. ...
Here's a good, general, non-techno-babble article about denitrification ...

What is: Denitrification?
Dr. Timothy Hovanec
http://www.marineland.com/science/reports/report1.asp

From the article ...
Quote:
Another problem is to provide a constant source of the organic carbon required by the bacteria. This means mixing it up and delivering it at the correct infusion rate which will change over time. There is not enough naturally occurring organic material in an aquarium to keep the process going. Exactly how do this for an aquarium is not well documented.
Sound familiar? ...

BTW ... Hovanec does pretty good work. You can find some of it here:
http://www.marineland.com/science/dr...ms_reports.asp




Quote:
Originally posted by pjf
... I have yet to found readily available sources for denitrifying bacteria ... The sources for these bacteria tend to be university laboratories.
Sources for heterotrophic bacteria literally abound because of their tolerance for commercial processing, distribution, and storage ... denitrifying bacteria do not present the same set of tolerance(s). Happily, there is an excellent, relatively economical source of denitrifiers for our systems ... live rock. Unfortunately, I've never found any clinical identification of the strains involved, which makes the targeting of specific nutrients problematic.




Quote:
Originally posted by pjf
... Has anyone independently verified that these bacteria exist in the Probidio BIO-DIGEST product?
You'd have to ask the Prodibio folks. I've never used their products, nor have I seen any independent verification of their products' contents (... call me a fool, but I tend to accept their general descriptions).




Quote:
Originally posted by pjf
... What nutrients will they need beyond what is normally available (nitrogenous wastes, phosphates) in a marine aquarium?
Remembering that this opinion is just that (deserving of all of the skepticism and critical examination you care to muster) ... (1) a small diversity of short-chain, organic carbon compounds ... (2) some form of acetate ... (3) small concentrations of amino acids ... (4) small concentrations of vitamins.

Which amino acids? Hehe ... let the user decide.

Which vitamins? Remembering that this is just opinion ...
B1 (Thiamine. Weak S source);
B2 (Riboflavin. Multiple metabolic pathway involvement, and is a cofactor of FAD);
B3 (Niacin. Energy metabolism pathways, and NAD & NADH derivatives);
B5 (Pantothenic acid. Multiple anabolic & catabolic pathways);
B7 (Biotin. Catalysis of fatty acids, and gluconeogenesis);
B9 (Folic acid. Involved in production & maintenance of new cells);
B12 (Cobalamin, aka Cyanocobalamin. Previously cited).

JMO ...

I would remind everyone that this listing of vitamins is largely speculative on my part. While there is documentation for the potential metabolic roles I suggest, almost none of the documentation is specific to denitrifiers. Indeed, as you sift through the literature, you're going to discover that the role of specific vitamins vs. marine bacteria is largely ill-defined. This is why I presented links to the various media earlier ... so far it's the best "linkage source" I've found. Looking forward to seeing other folks' sources.

And I hasten to add ... it's not as simple as just dumping some of these compounds into the mix and automatically getting enriched bacterial metabolic behavior. There are inhibition pathways in play as well.




Quote:
Originally posted by pjf
... Is there any evidence that they reduce nitrogenous wastes to N2 gas in natural marine reefs?
The majority of research literature that I've found on the reduction of NO3 to N2 has to do with marine sediments (not typically associated with reefs, with the sediments in reef lagoons being the exception). Even so, here's one for you ...

Quote:
In fact, our nitrification rates would be underestimates since losses by denitrification were not included; available evidence (Wiebe 1985) suggests that denitrification occurs widely in the reef environment, with quantitatively important rates. This situation is in sharp contrast to that in oceanic waters, where bacterial nitrification is negligible compared to consumption by phytoplankton (Hattori et al. 1980) and the capacity for NH4 oxidation is two orders of magnitude lower than for NH4 uptake by phytoplankton (Wada and Hattori 1971).

Nitrification in reef corals
Limnol. Oceonogr., 35(3), 1990, 725-730
http://www.aslo.org/lo/toc/vol_35/issue_3/0725.pdf




JMO ... FWIW
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  #57  
Old 07/26/2007, 07:51 PM
mesocosm mesocosm is offline
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Greetings All !


Veering a little off topic ...


Nitrification in reef corals
Limnol. Oceonogr., 35(3), 1990, 725-730
http://www.aslo.org/lo/toc/vol_35/issue_3/0725.pdf


Some extracts ...

Quote:
... equivalent to 17% of the NH4 consumption and 21% of the uptake by zooxanthellae showing an effective competition for NH4 by nitrifiers. NH4 utilization rates were equal to inorganic N production rates, and NO3 production rates were equal to NO3 uptake rates by zooxanthellae, suggesting close coupling between these processes.
Quote:
Density of nitrifying bacteria associated with living corals may vary from 4 to 260 x 10^3 cells ... [4,000 to 260,000 nitrifying bacteria cells per mg coral tissue].
Quote:
Coral reefs present a contrast, with apparently low levels of ambient inorganic N but high primary productivities, implying that in the absence of any significant input of nutrients from external sources recycling processes must operate efficiently. The various processes known to be responsible for recycling N in the marine environment are N fixation, ammonification, nitrification, uptake and assimilatory reduction, denitrification, and dissimilatory N03- reduction.
Quote:
In symbiotic associations, particularly in corals where the density of zooxanthellae is of the order of [1,000,000] cells cm^2 (Drew 1972), it is reasonable to expect that nitrification will have to compete with assimilatory removal of NH4.





What's the point? Look back at the second quote. They've documented from 4,000 to 260,000 nitrifying bacteria cells per mg of coral tissue. If you think that "dosing stuff" is just manipulating the micro-beasties doing nitrification & denitrification ...

... you may do well to think again.





JMO ... Your mileage will vary.
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  #58  
Old 07/29/2007, 02:03 PM
pjf pjf is offline
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Lightbulb Aerobic DSBs and Sugar Dosing

Here are 4 hypotheses that should be evaluated in the light of our discussion regarding carbon dosing of heterotrophic denitrifying bacteria:

• Denitrifying bacteria in deep sand beds and live rock are heterotrophic and must be dosed with organic carbon, amino acids and vitamins for sustenance.


The efficacy of deep sand beds (DSB) is loudly debated in many forums. Both pristine aquariums and tank crashes have been attributed to deep sand beds. Denitrifying bacteria in the DSB are often assumed to require little effort to obtain and even less effort to upkeep. Perhaps nitrate export requires a more certain acquisition and a more measured sustenance of denitrifying bacteria.

“Analysis of the bacteria found on live rock and in live sand needs to be done with reef aquariums in which live rock and live sand provide the bulk of biological filtration.” - Delbeek & Sprung, The Reef Aquarium, Volume 3, page 258.

“Various strains of heterotrophic bacteria are known to function as denitrifiers under certain conditions. Spotte (1992) lists the following genera: Alcaligenes (=Achromobacter), Azospirillum, Bacillus, Chromobacterium, Corneobacterium, Flavobacterium, Halobacterium, Kingella, Neissera, Paracoccus, Propionibacterium, Pseudomonas, Spirillum, Thiobacillus, Vibrio and Xanthomonas.” - Delbeek & Sprung, ibid, page 261.

I believe the Spotte (1992) reference cited by Delbeek & Sprung is his 1992 book, Captive Seawater Fishes: Science and Technology (ISBN-13: 978-0471545545).

• Anaerobic denitrification occurs in aerobic bacterial substrates.


If true, this may obviate the need for deep sand beds and massive pieces of live rock that lack porosity. The following is from Delbeek & Sprung (ibid, p. 260):

“It has been shown that nitrification and denitrification occur in aerobic layers, where they are termed coupled since the processes occur simultaneously, mediated by bacteria in close proximity. Here anoxic microsites provide a habitat for anaerobic bacteria, while being surrounded by aerobic pore waters (Jenkins and Kemp, 1984).”

I believe that the reference to Jenkins and Kemp (1984) is this one:

The Coupling of Nitrification and Denitrification in Two Estuarine Sediments
Mark C. Jenkins, W. Michael Kemp
Limnology and Oceanography, Vol. 29, No. 3 (May, 1984), pp. 609-619.

I have not been able to acquire the complete Jenkins and Kemp article but the first page states that nitrification and denitrification occurs simultaneously within fecal pellets and within plant detrital particles. This suggests that bacterial substrates need not be very deep to create the anoxic “microsites” for denitrification.

• Aim for an aerobic DSB, not an anaerobic DSB.


Under low oxygen conditions, some bacteria can use sulfate (SO4) to metabolize organic material, producing hydrogen sulfide (H2S) as a byproduct. Randy Holmes-Farley found no sulfide odors or black metal sulfide deposits in the core samples of his 1”-2” oolitic sand bed and of his 6” DSB which he believes is kept well oxygenated (http://reefkeeping.com/issues/2005-12/rhf/index.php).

• Sugar dosing is not “green.”


If we provide our macroalgae refugia with light, fish poop, and maybe iron, we expect to reap more macroalgae to export plus higher water quality. In contrast, the idea of dosing organic chemicals to heterotrophic bacteria in the aquarium itself runs counter to our agrarian and husbandry instincts.

While we do dose molasses to accelerate our sewage treatment processes, it is done “in vitro” away from our homes. The sewage treatment plant is our “refugium.” In contrast, the sugar dosing of aquariums is done “in situ.” We would object to molasses usage if it was dosed into our drinking water. I wonder if the fish and the corals would object to sugar dosing if we could only hear them.
  #59  
Old 07/31/2007, 05:34 AM
MCsaxmaster MCsaxmaster is offline
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Ok, admittedly, I've only skimmed this thread for lack of time to do much else

Let me just hit on a few things though.

Quote:
Bertoni's doubt is correct. Unless something is seriously out of wack ... as in Tank-O-Death out of wack ... marine aquaria are simply not CO2 limited (... or inorganic carbon limited, for that matter).
Yes, mostly...kinda sorta....ok, here's what I mean. It has generally been thought that marine organisms able to utilize HCO3- as a source of carbon (which most autotrophs can) were not C-limited in NSW because there is relatively so darn much of it. Let me just note that organisms that can use bicarbonate (as well as CO2) are still using CO2 as the substrate for rubisco, but they may start by taking bicarbonate from the sea water and converting it to CO2 with carbonic anhydrase, for instance. What folks are learning (of interest because atmospheric CO2 is shooting ever higher) is that carbon fixation for a lot of marine critters is NOT necessarily saturated at current levels. Now, increased concentration of inorganic carbon (as CO2 or HCO3-) may or may not actually increase the growth rates of a lot of marine organisms, even if they do fix it faster when it is more available. They may simply make more carbohydrates which they already have a sufficient supply of for their growth needs. While there are exceptions, generally marine producers DO NOT respond substantially to increased inorganic C above today's levels in terms of their net growth. So, a calcium reactor probably isn't going to benefit the diatoms in your tank that much

Quote:
Organic carbon limitation is an entirely different issue, but at this point we're no longer talking about autotrophic marine bacteria ... we're now talking about heterotrophic marine bacteria (in all their various forms).
Absolutely!!! The heterotrophic bacteria in the ocean or a river or your aquarium couldn't care less how much inorganic carbon there is, at least in terms of getting and food or energy from it. CO2 is as useless to a heterotrophic microbe as it is to us. They respire it from burning organic material--it is a waste product to them, just as it is to us.

I think the question really relates to what is limiting the uptake of inorganic N and P in our aquariums. In other words, why don't all the producers in the tank just suck all of them up until they both are at undetectable concentrations.

The answer, I think, is that often, we really don't know what exactly is limiting the growth of all the various primary producers in our tanks. Iron limitation could be a factor in a lot of tanks. Grazing (benthic algae) and supsension feeding (planktonic producers) could be a major issue, and most likely IS a major issue in structuring algal/microbial communities and helping determine rates of nutrient uptake. Competition between coralline algae and turf and macroalgae is probably significant. Competition between corals and algae is probably significant.

The question, I think, is how is that we can have a tank in captivity with elevated nitrate and phosphate where those levels remain elevated for a long time and we don't see ridiculous algal blooms. In nature when nutrients become elevated, primary producers bloom, suck up the nutrients, and eventually get grazed down. That happens every spring in temperate seas and every upwelling in places that get upwellings (including coral reefs). Unless the nutrient input is significant and sustained, however, the concentration drops back down after all the producers suck it up, unless they are limited by some other factor (e.g., iron limitation in southern ocean, light limitation in polar regions in the winter). Something or some things in certain aquaria limit the production of primary producers when nutrients are elevated yet the tank is not completely overgrown with algae. The same happens in nature though, which is worth considering. Most reef algae in nature are NOT nutrient limited even at the very low nutrient concentrations found in reef water. They've adapted to this condition over evolutionary time and don't need high concentrations to get sufficient nutrients. They are still limited in nature though, and hence they don't take over the reef (unless something gets monkied up). The same can and does happen in every aquarium that is not overgrown with algae.

So, how do we increase primary production to lower dissolved nutrients? Well, dosing sugar and vodka and whatnot seems to work, although it's probably the most dangerous and potentially disasterous method I can think of off hand (besides raising the aquarium to a pH of 12 to precipitate phosphate, or something else that would kill every last darn thing). Providing more space and refuge from grazing could help (refuge from grazing, refugium...huh, huh, wink, wink). Dosing iron might help in some situations. Dosing other minor nutrients might help to, though that is largely unexplored. I'm sure there are many other things that could be done too that we just don't have a good appreciation of yet.

Anyway, that's my piece. Hopefully it was at least partially sensical as I've not had that much sleep

Oh, and Starbuck's is raising their prices, so that $3.95 won't work so well anymore. Buggers.....

Chris
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  #60  
Old 07/31/2007, 05:37 AM
MCsaxmaster MCsaxmaster is offline
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And one last thing to add, corals are HUGE sources of DOC on reefs and the production of zooxanthellae (half of which is lost daily as mucus and DOC) is really one of the major sources of primary production on the reef. Instead of dosing sugar/vodka/vinegar/fruit loops (I'm sure somebody has tried it) just growing more corals and algae in the tank would provide more DOC which could enhance microbial production and denitrification in what is arguably a very safe way. It's hard (but probably not impossible) to 'overdose' coral mucus.

Food for thought (pun intended),

Chris
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  #61  
Old 07/31/2007, 07:19 AM
mesocosm mesocosm is offline
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Greetings All !


Quote:
Originally posted by MCsaxmaster
Ok, admittedly, I've only skimmed this thread for lack of time to do much else ...
Many thanks for taking the time ! ... I know you've got lots going on. When I sent the PM asking you to take a quick scan of this one to check for any serious blunders on my part, I figured it would be awhile as the life of a research slave ... errrr .... grad student ... doesn't abound with lots of free time. The quick response is much appreciated.

For those who aren't familiar with Chris' work here on RC, you may wish to take a few moments and check these out ...

The Nutrient Dynamics of Coral Reefs:
Part I, Biogeochemical Cycles

Chris Jury
Reefkeeping Magazine - August, 2006
http://reefkeeping.com/issues/2006-08/cj/index.php


The Nutrient Dynamics of Coral Reefs:
Part II, The Oceanic System

Chris Jury
Reefkeeping Magazine - October, 2006
http://reefkeeping.com/issues/2006-10/cj/index.php


The Nutrient Dynamics of Coral Reefs:
Part III, Land and Sea

Chris Jury
Reefkeeping Magazine - November, 2006


The Nutrient Dynamics of Coral Reefs:
Part IV, The Sky Above

Chris Jury
Reefkeeping Magazine - December, 2006
http://reefkeeping.com/issues/2006-12/cj/index.php


Chris ... again ... Many Thanks!


Quote:
Originally posted by pjf
Here are 4 hypotheses that should be evaluated in the light of our discussion regarding carbon dosing ...
I wish ... really wish ... that I was ready to talk 'hypotheses' about this whole carbon dosing thing. At this point, I'm really only prepared to discuss the general underlying principles and mechanisms. The chemolithotrophs that we're talking about come in a variety of strains which do different things, to different substrates, under different conditions ... and we're not at all certain about the combination of strains that are 'in play' in our systems.

Until the equivalent of a Salifert test kit for bacterial strains in marine aquaria becomes available to hobbyists (something that is generally reliable, inexpensive, and easy to use), the issue of which micro-beasties are actually present & doing what they do ... is going to remain problematic.

Even so, it seems to me that if we're clear and methodical, we might very well come up with a set of basic principles which are of use to reefkeepers, and independent of any particular product line or brand.

JMO ...


BTW, here's another one that touches on several of the issues involved in this thread ...

what do anaerobic bacteria eat ?
(RC, Snarkeys, 10.22.06)
http://archive.reefcentral.com/forum...hreadid=955973


JMO ... your mileage will vary.
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  #62  
Old 07/31/2007, 07:21 AM
mesocosm mesocosm is offline
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Greetings All !


Quote:
Originally posted by MCsaxmaster
... I think the question really relates to what is limiting the uptake of inorganic N and P in our aquariums. In other words, why don't all the producers in the tank just suck all of them up until they both are at undetectable concentrations. ... we really don't know what exactly is limiting the growth of all the various primary producers in our tanks. ... Something or some things in certain aquaria limit the production of primary producers when nutrients are elevated yet the tank is not completely overgrown with algae. ... So, how do we increase primary production to lower dissolved nutrients? ...
Indeed ... This is fundamental stuff.


JMO
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  #63  
Old 07/31/2007, 07:52 AM
MCsaxmaster MCsaxmaster is offline
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Quote:
Many thanks for taking the time ! ... I know you've got lots going on. When I sent the PM asking you to take a quick scan of this one to check for any serious blunders on my part, I figured it would be awhile as the life of a research slave ... errrr .... grad student ... doesn't abound with lots of free time. The quick response is much appreciated.
No worries. I thought I'd get here early this morning so I could leave by 8 or 9. The darn indoor air has sufficient CO2 that it has sufficiently dropped the pH in some sea water I'm using so that I've had to spend and extra 2 hrs aerating the darn stuff with CO2-free air to bring the pH up to friggin normal, so I had some down time while that's been happening.

Quote:
For those who aren't familiar with Chris' work here on RC, you may wish to take a few moments and check these out ...
Thanks for the plug. If I can get a bit of time to do some typing I plan to pick that back up, because it's far from 'completed'....

Oh, and just a refinement of something I said. We'd like to be able to generally increase primary production in tanks so as to suck up dissolved nutrients, but only to the extent that we don't cause other problems (e.g., algae taking over a tank, zooxanthellae growing out of control, dinoflagellate blooms, etc.).

cj
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  #64  
Old 07/31/2007, 09:10 AM
Flint&Eric Flint&Eric is offline
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i too have only skimmed over this here at work, but it has been by far one of the best threads on here in a very long time. it's great to see such bright minds debating and conversing with tact...a rare thing these days

ok carry on....
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  #65  
Old 08/01/2007, 09:52 AM
mesocosm mesocosm is offline
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Quote:
Originally posted by Flint&Eric
... debating and conversing with tact ... a rare thing these days

ok carry on....
Shouldn't be too surprising ... good stuff is often the result of moving away from personality and/or product driven opinion, while simultaneously grounding the discussion in objective research literature.

Those who've been watching this topic evolve during the past few years may appreciate a more subtle, entertaining dynamic: A junior moderator of an obscure, irrelevant forum in ZeoVille has called in someone with some serious academic & analytic game who holds the perspective that, "dosing sugar and vodka and whatnot seems to work, although it's probably the most dangerous and potentially disasterous method I can think of off hand" ... to scour his opinions and reasoning regarding bacterioplankton & carbon-dosing strategies for technical blunders and logic-flaws ...

... in a ReefCentral forum.


Quote:
We have crossed some strange boundary, and the world has taken a turn to the surreal.

Captain Miller
Saving Private Ryan
...


FWIW, it turns out that there's a group of folks who, recognizing its importance, have coined a phrase for the sort of thing that's going on here ... critical inquiry.



JMO



BTW, any product smack that includes a reference to "fruit loops" ... well ... you've simply got to love it.
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Last edited by mesocosm; 08/01/2007 at 10:02 AM.
  #66  
Old 08/01/2007, 09:54 AM
mesocosm mesocosm is offline
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Greetings All !



Quote:
Originally posted by onetrickpony
... If are reef aquariums are culture vessels, is there a recipe (lots of $$$$ being spent on someone's secrete recipe) that one could use to feed our tanks to get the benefits we are all looking for, other than just throwing in a good multivitamin & glutamate along with good reef keeping practices ...
You might be interested in this one ...

Growth of marine bacteria in batch and continuous culture under carbon and
nitrogen limitation

Joel C. Goldman & Mark R. Dennett
Limnol. Oceanogr., 45(4), 2000, 789–800

Full Article (pdf)
http://www.aslo.org/lo/toc/vol_45/issue_4/0789.pdf


Folks who are interested in what a "baseline" formula might look like really ought to consider taking a look at Table 1 within the article. Various combinatins of glutamate, glucose, ammonium, amino acids, citrate, and acetate were examined in terms of GEE (gross growth efficiency), specific growth rates (u), C:N ratios, and N recovery. I would suggest that folks also take a few moments to distinguish between the numbers that were generated with mid vs. end exponential growth phase.

JMO ...



Quote:
Originally posted by onetrickpony
... Mesocosm do you dose in your reef setup
I don't have any personal reef systems operating at the moment. I'm currently working with transshipment receiving & holding systems (six stand alone systems ranging from 600G to 2500G), and anemone & commensal shrimp propagation systems.

"Dosing" is definitely a part of their future ...



JMO ... HTH
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  #67  
Old 08/01/2007, 01:54 PM
Flint&Eric Flint&Eric is offline
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i must keep this short, as i am at work ( shhh dont tell )
the dosing of the bac strains for these systems seems to be based on the "life cycle" of the bacteria...or so i have read, with the additional supplements being added daily/weekly/ etc. to keep levels to par.

what would be the effect to keep a drip via peri pump of the carbon, nitrogen, and vitamins? why cant we dose aa's and vitamins with our top off? would there be much benefit without the regular addition of bacs, or lead to nutrient problems?

i'd assume this would keep biomass and overall params more stable, what about then the effect of nutrient surges (pappone, comes to mind)?


i apologize about the vagueness of these questions, but i'm curious to hear your ideas regarding them... please take them which ever route your mind fancies.


eric
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  #68  
Old 08/01/2007, 08:18 PM
mesocosm mesocosm is offline
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Quote:
Originally posted by Flint&Eric
... the dosing of the bac strains for these systems seems to be based on the "life cycle" of the bacteria ...
If by "life cycle" you mean the exponential growth phase ... okay. I think of it more in terms of (A) increase in biomass, (B) sequestration of specific compounds/elements dependent upon siderophores, (C) export via skimming, and (D) recycling through "feeding".

JMO ...



Quote:
Originally posted by Flint&Eric
... or so i have read ...
Any links to product line explanations other than the materials presented by Korallen-Zucht ?



Quote:
Originally posted by Flint&Eric
... with the additional supplements being added daily/weekly/ etc. to keep levels to par. ...
It's always seemed to me that the "sweet spots" for dosing schedules are dynamic, hence the need for regular, consistent interpretation ... and adjustment ... by the hobbyist.

JMO ...



Quote:
Originally posted by Flint&Eric
... what would be the effect to keep a drip via peri pump of the carbon, nitrogen, and vitamins? ...
A continuous drip strikes me as a "schedule" which might produce some very nasty outcomes, in very short order ... although dilution might be a way around this issue. Even so, a "pulsed" pattern of nutrient additions ... at relatively low concentrations, with at least 48 hours in between pulses ... has always struck as a better strategy than either continuous, or large infrequent dosing patterns. JMO.



Quote:
Originally posted by Flint&Eric
... why cant we dose aa's and vitamins with our top off? ...
We can do anything we want, can't we? ...

Hehe ... even so, I would be concerned about negative synergy between what's being mixed together in the top off. It's not like amino acids and vitamins can be randomly mixed together without any concern for how they're interacting with one another ... to say nothing of what might be present in the "top off" (unless we're talking about distilled water). For example, there was a recent thread in this forum which talked about precipitation issues when adding an amino acid to RODI water (I've lost track of the link ... sorry).



Quote:
Originally posted by Flint&Eric
... would there be much benefit without the regular addition of bacs, or lead to nutrient problems? ...
This is an opinion-realm in which I'm doing some serious re-assessment ... I'll post more when I have something meaningful to say.



Quote:
Originally posted by Flint&Eric
... i'd assume this would keep biomass and overall params more stable ...
In terms of critical inquiry, I think making assumptions about what's going on with the free-living, and biofilm bacterial populations in our systems (whether they're targeted by carbon & nutrient dosing, or not) introduces what is potentially a huge error.



Quote:
Originally posted by Flint&Eric
... what about then the effect of nutrient surges (pappone, comes to mind)? ...
What about it? ...

Are you certain "nutrient surges" is what's going on? ...

Hehe ... seriously ... I don't view the "Pappone Method" as a bacterioplankton strategy. I'd have to see a lot more details about it before I would describe it as anything more than an interesting food recipe.





JMO ... HTH
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  #69  
Old 08/01/2007, 08:26 PM
MCsaxmaster MCsaxmaster is offline
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Gary,

A question: why would infrequent larger additions of...well, whatever, seem preferable? From my armchair position over here (ewww, it's comfy ) it would seem to me that the smallest, most frequent additions feasible of whatever we're adding would generally be the way to go. Curious on your thoughts...

cj
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  #70  
Old 08/01/2007, 10:07 PM
mesocosm mesocosm is offline
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Quote:
Originally posted by MCsaxmaster
A question: why would infrequent larger additions of...well, whatever, seem preferable? ...
I don't believe that larger, infrequent supplementation is the optimal route. Quite the contrary, "... a "pulsed" pattern of nutrient additions ... at relatively low concentrations, with at least 48 hours in between pulses ... has always struck as a better strategy than either continuous, or large infrequent dosing patterns."



Quote:
Originally posted by MCsaxmaster
... it would seem to me that the smallest, most frequent additions feasible of whatever we're adding would generally be the way to go. ...
Indeed ...

The reasoning behind my preference for a 48 hour "gap" between nutrient additions is to allow the bacterial guild to more fully metabolize pre-existing (not dosed) nutrients from the water column ... as opposed to just consuming whatever is being supplemented.

The last thing I would want is an explosive exponential growth phase, accompanied by a potentially problematic dissolved oxygen shift.



At this point, my twisted little mind wanders off onto a couple of different tangents ...

(1) This is an argument that a minimum of N-compounds should be dosed. After all, I'm trying to get the bacterial guild to consume N-compounds already extant within the water column. This would seem to argue for a formula composed primarily of a (carbon source) + (a coreactant, like a vitamin ... or small set of coreactants, like a vitamin & an electron donor) + (a substrate, like Fe or S ... maybe);

(2) The "correct" dosing interval is, I must admit, puzzling to me ... and I don't claim to have a particularly good rationale for choosing 48 hours (think "arbituary"). If the replication interval is 3 hours (3 hours for 1 bacterial cell to become 2 bacterial cells), then I'm talking about something on the order of 16 "generations" between nutrient dosing. I readily concede that this interval may not be optimal.

(3) "Bacterial growth by feeding on nutrient supplements" isn't the only thing going on ... bacterial death, bacterial competitive interactions, predation by bacteriovorous micro-beasties (like ciliates), efficiency of utilization differences between free-living vs. biofilm communities, and shifts in attachment/detachment dynamics are also going on. This is what I mean about not making assumptions regarding the actual behavior dynamics of the free-living and biofilm populations in our systems. What we're talking about are non-linear sets of events.

(4) Amino acids in 'food for bacteria' formulae may be nothing more than just a convenient, economical weak nitrogen source ... and that bacteria may not be the principal consumers of this weak nitrogen source. After all, don't the chemolithotrophs we're probably talking about really want ammonium as their primary N source?



On another sub-tangent ... one I may regret posting ... I'm becoming increasingly of the opinion that amino acids aren't particularly good "raw materials" for the processes which produce chromatophores within corals. Maybe a good "energy" source, but I don't believe that the ...

[amino acids supplementation] ---> [directly enriched coral coloration]

... model represents what is actually going on with amino acid dosing, despite the credible, legitimate observations & correlations of many experienced reefkeepers. I have the distinct sense that something else is going on (... how's that for 'critical inquiry' ?!!). I want to say that the enriched coloration is a secondary consequence of what amino acids are doing to a coral's associated microbiota ... both outside, and within, the coral tissue.



JMO ... Let the Beating Begin.
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  #71  
Old 08/02/2007, 02:44 AM
MCsaxmaster MCsaxmaster is offline
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  #72  
Old 08/02/2007, 02:45 AM
MCsaxmaster MCsaxmaster is offline
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Gary, forgive me, but I'm not following why dosing on a 48 hr schedule (pulsing) would seem preferable? Why would a 48 hr pulsed schedule of dosing whatever be preferred to, for instance, constant dosing?

cj

p.s. The fruit loop dosing experiment is a failure for me so far, though this tends to only occur once daily, in the mornings
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  #73  
Old 08/02/2007, 06:58 AM
mesocosm mesocosm is offline
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Greetings All !


For some reason I have this strange visual of sitting next to a reef aquarium, constantly spooning fruit loops into the tank ...



Consider what's happening with a continuous drip: constant presentation of an additional (relative to what was already present) bacterial food source into the water column, resulting in a constantly increasing bacterial biomass that takes a while to catch up to the nutrient content (both dosed & extant) of the water column ... with an associated continual increase in dissolved O2 consumption.

At some point a classic predator vs. prey dynamic is reached. The population graph would look like the simultaneous graphs of owls vs. field mice in a riparian habitat ... steep-sloped growth rates, followed by rapid population crashes, followed by steep-sloped growth rates, followed by rapid population crashes ... et cetera. This is not the type of "stability" I'm looking for, if for no other reason than that the graphs of the nutrient concentration(s) in the water column are oscillating around the maxima. This is to say nothing of all the fun and games issues of rapid O2 depletion also lurking near the maxima of the graph.

(Note: Not that there aren't ways to deal with this by periodically removing significant portions of the bacterial biomass before it's population crash. For example, LdrHawke experimented with growing the bacterial biomass on floss which was removed/replaced at regular intervals ... along with periodic air bubble pulses throughout the system. See the 'DSB Heresy' thread in the Advanced Forum.)

I'm suggesting a preference for a "time lag" between nutrient pulses so that I get the same kind of graph ... but one that oscillates around the minima (in terms of the nutrient concentration of the water column). In other words, I only want a relatively brief exponential growth phase so that I still get nutrients stripped out of the water column, without assuming the risks associated with the O2 depletion and crash of a larger bacterial biomass.

As I posted earlier ... my selection of 48 hours is arbituary. I'm completely open to the suggestion that a 3 hour dosing interval (for example) ... using a very dilute nutrient formula ... might be more optimal. But at some point there's the issue of husbandry "convenience".


For some reason I have this strange visual of sitting next to a reef aquarium, constantly spooning fruit loops into the tank ...





JMO ... Looking forward to reading the perspective of others.
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  #74  
Old 08/02/2007, 09:02 AM
Flint&Eric Flint&Eric is offline
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Quote:
If by "life cycle" you mean the exponential growth phase ... okay. I think of it more in terms of (A) increase in biomass, (B) sequestration of specific compounds/elements dependent upon siderophores, (C) export via skimming, and (D) recycling through "feeding".
actually yes!

Quote:
Any links to product line explanations other than the materials presented by Korallen-Zucht ?
i honestly dont read their direct "literature" very much, i'm sure you understand why...but i've heard it thrown out on the board a few times.

Quote:
At some point a classic predator vs. prey dynamic is reached. The population graph would look like the simultaneous graphs of owls vs. field mice in a riparian habitat ... steep-sloped growth rates, followed by rapid population crashes, followed by steep-sloped growth rates, followed by rapid population crashes ... et cetera. This is not the type of "stability" I'm looking for, if for no other reason than that the graphs of the nutrient concentration(s) in the water column are oscillating around the maxima. This is to say nothing of all the fun and games issues of rapid O2 depletion also lurking near the maxima of the graph.
makes sense. the reason i primarily is/was interested in a constant drip is it would allow a system such as zeo or ultra to be doable. i am out of town too often to keep up with dosing. i'd be interested to see the results of trying a constant drip... i'll let hugo go first...


Quote:
Hehe ... even so, I would be concerned about negative synergy between what's being mixed together in the top off. It's not like amino acids and vitamins can be randomly mixed together without any concern for how they're interacting with one another ... to say nothing of what might be present in the "top off" (unless we're talking about distilled water). For example, there was a recent thread in this forum which talked about precipitation issues when adding an amino acid to RODI water (I've lost track of the link ... sorry).
oh trust me i know i've found a small mix of aminos that can be mixed...lots of frustrating and interesting trial and error has taken place to find that out. i was dripping a small amount in with top off to keep increased PE 24/7. now with heavier stocking levels, the tank get's aa's once a week...any more and algae pops up.

eric
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  #75  
Old 08/02/2007, 11:20 AM
MiddletonMark MiddletonMark is offline
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Quote:
Originally posted by mesocosm
Hehe ... seriously ... I don't view the "Pappone Method" as a bacterioplankton strategy. I'd have to see a lot more details about it before I would describe it as anything more than an interesting food recipe.
Careful what can of worms you open

I tried to bring up this thought on some of the Pappone threads, and had a large # of folks state that Pappone must have a carbon source/sugar, and that said carbon source is a vital and distinguishing part that makes it completely different from any sugar/carbon-lacking food.

To me, the distinguishing character of Pappone is the varied and nutritious seafood mix [vs. LFS food/bottled suppliments/etc] ... vs. the minor carbon source, but apparently we're wrong

Anyway, back to reading/lurking mode.
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