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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.
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#52
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Greetings All !
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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:
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:
JMO ... FWIW, maybe nothing.
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Mesocosm |
#53
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Greetings All !
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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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Mesocosm |
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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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For it was not into my ear you whispered, but into my heart. It was not my lips you kissed, but my soul.-Judy Garland |
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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
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Greetings All !
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What is: Denitrification? Dr. Timothy Hovanec http://www.marineland.com/science/reports/report1.asp From the article ... Quote:
BTW ... Hovanec does pretty good work. You can find some of it here: http://www.marineland.com/science/dr...ms_reports.asp Quote:
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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:
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JMO ... FWIW
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Mesocosm |
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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:
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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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Mesocosm |
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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. |
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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:
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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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FSM ~ Touched by His noodly appendage ~ |
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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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FSM ~ Touched by His noodly appendage ~ |
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Greetings All !
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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:
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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Mesocosm |
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Greetings All !
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JMO
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Mesocosm |
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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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FSM ~ Touched by His noodly appendage ~ |
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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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red|house|blog "i like bubbly, and i love animals - so it works out well" "there are a lot of people out there who think they have a modern house simply because they have alot of steel in it" |
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Greetings All !
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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:
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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Mesocosm Last edited by mesocosm; 08/01/2007 at 10:02 AM. |
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Greetings All !
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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:
"Dosing" is definitely a part of their future ... JMO ... HTH
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Mesocosm |
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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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red|house|blog "i like bubbly, and i love animals - so it works out well" "there are a lot of people out there who think they have a modern house simply because they have alot of steel in it" |
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Greetings All !
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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:
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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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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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FSM ~ Touched by His noodly appendage ~ |
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Greetings All !
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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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Mesocosm |
#71
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double
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FSM ~ Touched by His noodly appendage ~ |
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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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FSM ~ Touched by His noodly appendage ~ |
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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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Mesocosm |
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eric
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red|house|blog "i like bubbly, and i love animals - so it works out well" "there are a lot of people out there who think they have a modern house simply because they have alot of steel in it" |
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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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read a lot, think for yourself |
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