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Bacteria...let's really start understanding them! part one

https://www.triton.de/en/
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flampton

flampton

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Flampton

I hope in future works we get to see practical application of bacteria alongside their metabolic differences and classifications



That thread is very impactful to me.

It is a microcosm of today's hobby view on what cycling bacteria do, whether classic nitrifiers or heterotrophs stepping up to the plate can carry a bioload, in the end people simply want to know when they can start to reef.


False notions in what filter bacteria are doing drive sales in this hobby to the tune of hundreds of thousands of dollars spent to unstick cycles that never were stuck. bottle bac sellers tell us cycles can stall, and have a product ready to remedy.

Our hobby cannot even agree of whether nitrite testing should factor. of course everyone says it should, but they will ignore 200 nitrite positive reef starts we have on file with updates as well, rules are broken daily in reef tank cycling and we need formal works on that. We have enough data to permanently exclude nitrite measurement in reef tank cycling, but it is ignored. Offsetting stuck nitrite readings is a large driver of bottle bac sales...we collect those reaction purchase threads for pattern study as well.


It is very important to state that in understanding bacteria, we must be able to simply cycle reef tanks consistently. That is currently not the case for the hobby, nobody is in agreement on what we should measure, how long we should wait etc


there are some people in agreement: the twenty thousand or so reef tanks set up at MACNA conventions all to meet the start date, the sales date, of the convention. given the right motivation and bacterial understanding, we can either be stuck in a cycle for 80 days or we can have the reef ready by this friday, two days from now, and never fail.

I say until we can cycle reef tanks consistently in this hobby, we don't really understand the bacteria though they might classify in different ways and perform known functions when evaluated alone/not in a meshing of tank life.
I will talk more about this in the nitrogen cycling or lack thereof in the next post. Currently rewriting this post as an article. It will be much improved.

I thought of you when I was checking out the patent for Marineland Bio-Spira (Freshwater) and Instant Ocean Biospira (Saltwater). It is advertised as instant cycling and truly is the only product I would trust if forced in this direction. Why would I trust this one, well I read the science within the patent. This patent only focuses on the ammonia oxidizing bacteria in their product, haven't looked for the nitrite utilizing bacteria patent yet as it is less important.


Basically if you go down to bacterial additive test IX-
They added their bacteria and 6 ocellaris clownfish to a 10 gallon aquarium and fed twice daily. The control had the same setup but received no bacteria. The bacteria treated tanks reached 0 ammonia in 9 days, while untreated took 17 days. What is I believe more important to this test was that the mean maximum ammonia concentration in treated was 0.4 ppm while in the untreated tank it was 1.72ppm. That is a huge difference! Still toxic but obviously much less so. And that is with six clowns in a ten gallon sterilized new tank setup.
 

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Dear all

When reading this post what kind of visual aids would you think would make this article easier to understand?
I think the growth phases graph would be a good addition.

I wonder if our use of carbon has some kind of effect on quorum sensing and what effects that means for the community of microbes. I think it could inhibit diversity or at worst allow pathogens to grow unregulated (maybe part of the reason for some RTN or other issues?)

obviously this is speculation but a study on the effects of carbon would be interesting.
 

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Very interesting read but I haven't understood where you're going with this. What's your goal?

Reef tanks have an anti-scientific nature because they require an opposite approach to the conventional path that a researcher follows.

A researcher finds a niche subject and dives deep into it. On the other hand, understanding a reef tank requires connecting dots from many different areas.

I recently saw a live on youtube where someone who studies coral feeding was presenting his case on how important it is to feed the corals and I wonder how many tanks were thrown out of balance after that talk.

I have little understanding of the roles of bacteria and I do know that their balance holds one of the master keys to keep a tank stable but I don't have the faintest idea how to intervene in a positive way when there's problems.

It seems that the Anna Karenina effect is as much valid in families as it is in the biome of reef tanks: happy families are all alike, unhappy families are dysfunctional each in its own way.
 

Randy Holmes-Farley

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I think the growth phases graph would be a good addition.

I wonder if our use of carbon has some kind of effect on quorum sensing and what effects that means for the community of microbes. I think it could inhibit diversity or at worst allow pathogens to grow unregulated (maybe part of the reason for some RTN or other issues?)

obviously this is speculation but a study on the effects of carbon would be interesting.
Why presume a problem? Why not equally valid, presume organic carbon dosing makes these problems less likely?
 
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flampton

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Very interesting read but I haven't understood where you're going with this. What's your goal?

Reef tanks have an anti-scientific nature because they require an opposite approach to the conventional path that a researcher follows.

A researcher finds a niche subject and dives deep into it. On the other hand, understanding a reef tank requires connecting dots from many different areas.

I recently saw a live on youtube where someone who studies coral feeding was presenting his case on how important it is to feed the corals and I wonder how many tanks were thrown out of balance after that talk.

I have little understanding of the roles of bacteria and I do know that their balance holds one of the master keys to keep a tank stable but I don't have the faintest idea how to intervene in a positive way when there's problems.

It seems that the Anna Karenina effect is as much valid in families as it is in the biome of reef tanks: happy families are all alike, unhappy families are dysfunctional each in its own way.
I thought that was clear. I'm trying to get people to understand more about the bacteria in their reef tanks. Now what they do with that knowledge is up to them. I have my own reefing hypotheses and so that will take me in my direction, others will have their hypotheses and it can take them a completely different direction. However on these boards and the like people use language and situations without fully understanding the role of bacteria.

So to sum up will I tell you to carbon dose or feed your corals aminos or add unknown product number 8? No. However you'll now truly know how these things work at the bacterial level, well...excepting product number 8 :D . As well as what could be the downstream consequences to these additions.

Basically I want people to develop informed opinions rather than trust their gut or some other random reefer.
 
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Why presume a problem? Why not equally valid, presume organic carbon dosing makes these problems less likely?
im referring to GAC removing quorum sensing molecules reducing microbes' ability to communicate and interfering with growth cycles.
carbon dosing absolutely will increase the sheer number of microbes, or at least their metabolism, but what can we do to encourage microbial diversity is what my question is aimed at.
 

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Good info!
 

Randy Holmes-Farley

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im referring to GAC removing quorum sensing molecules reducing microbes' ability to communicate and interfering with growth cycles.
carbon dosing absolutely will increase the sheer number of microbes, or at least their metabolism, but what can we do to encourage microbial diversity is what my question is aimed at.
There is certainly no data in aquaria, but I'd be shocked if removing organic molecules multiple feet away from the bacteria interferes with quorem sensing, which is usually very short in distance effect, and the literature talks about "long distance" quorem sensing acting over 1 cm.
 

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I will talk more about this in the nitrogen cycling or lack thereof in the next post. Currently rewriting this post as an article. It will be much improved.

I thought of you when I was checking out the patent for Marineland Bio-Spira (Freshwater) and Instant Ocean Biospira (Saltwater). It is advertised as instant cycling and truly is the only product I would trust if forced in this direction. Why would I trust this one, well I read the science within the patent. This patent only focuses on the ammonia oxidizing bacteria in their product, haven't looked for the nitrite utilizing bacteria patent yet as it is less important.


Basically if you go down to bacterial additive test IX-
They added their bacteria and 6 ocellaris clownfish to a 10 gallon aquarium and fed twice daily. The control had the same setup but received no bacteria. The bacteria treated tanks reached 0 ammonia in 9 days, while untreated took 17 days. What is I believe more important to this test was that the mean maximum ammonia concentration in treated was 0.4 ppm while in the untreated tank it was 1.72ppm. That is a huge difference! Still toxic but obviously much less so. And that is with six clowns in a ten gallon sterilized new tank setup.
As the inventor and holder of those patents (and more) and author of a few associated papers (See link) - if you have questions or would like to have a discussion I'd be glad to answer questions

AEM papers

Patents
 
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flampton

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As the inventor and holder of those patents (and more) and author of a few associated papers (See link) - if you have questions or would like to have a discussion I'd be glad to answer questions

AEM papers

Patents
Just checked out your nitrite patent as well as your articles. Very nice! Thanks for linking those. As far as questions I might have a few down the line.
 

brandon429

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flampton I know the scope of your post is the review of bacterial clades and function, am only inserting these broad scope challenges because they highlight misinformation about function. and timing and consistency tank to tank

On your coming works I won’t add these in but wanted to show how the hobby needs some refereeing

Bacteria myth busting:




what If reef tank cycles do not stall?

I have about four hundred posts for proof, to me that’s a rather decent paradigm shattering for the hobby. It turns out that when we add water bacteria to water, and feed, no cycle takes longer than a cycling chart to complete even if salinity is slightly high or low, or whether ammonia was dosed high or low (no, 8 ppm doesn’t stall that’s tested as well in several threads, Dr Reef has the best one)


the notion of stalled cycles is a massive, massive, massive sales driver for the hobby. People feel a cycle is stalled due to nitrite presence or ammonia presence on a nine dollar test kit and they click buy.


when we are learning about bacteria, I’d like to reference the hundreds and hundreds of claims that cycles are stalled yet we have no trouble unstalling them with one water change.



prep for semantics debate on stalling: in a lab, on a cold slide, cells teased out may stall one another.

In a display tank with rock and sand, everyone’s starting cycle, they cannot be stalled, we show for years.

Every forum has stall posts daily, they’re all false. With a water change they can begin in most cases



clearing out filthy wastewater sure has ranging time tank to tank and tester to tester, but if you just change out the wastewater what’s left underneath is a provable functioning biofilter. Thats how we’ve been fixing the four hundred. We do not have to wait weeks and weeks for wastewater to clear to be cycled, why has nobody told us that?

ever notice how forum posters always stall, but macna instant reefs have not for two decades? Because cycles don’t stall, conventions can start sales on time. Sellers don’t stall, buyers do.

seneye nh3 meters are leading the charge against stuck cycle claims, owning one or reading posts from the owners brings insight into how cycles timeframes work and if they’re inconsistent tank to tank.

to know what cycling bacteria do, we can now get seneye readings on bacterial experiments in displays full of activated surface area.
 
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brandon429

why did you put a reef in that
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mini rants are ok if serving as October threadbump

As soon as digital nh3 testing becomes commonly available, and replaces titration guessing for test reads (which in turn allows or disallows a start date/action set for a reef tank) the field of bottle bac sales and application is going to shift dramatically

in my opinion the shift will go away from what I must buy to supplement a perceived stall or a loss or a lack of bacteria for filtration (98% of bottle bac sales) and into specific targeting bacteria for certain care regimen boosts like notable detritus breakdown or disease competition help

the way reef cycling handles itself rather consistently is going to change purchase impulses once we get readers that show us how cycles work

currently, we all debate what is .25 or .5 and hard yellow zero.

good thing for retail industry that’s still eight years out, in the mean time we’ll all continue to feel nh3 is never going to be controlled without our purchases allowing it.

seeing what nh3 does, and when it does it with or without retail help, is going to revolutionize reef cycling in 2028.


as flampton outlines what bacteria do and how they classify we can get insights into what’s going on even before the good testers are available.
 
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flampton

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So everyone as you hopefully wait patiently for my article ( I'm writing the whole thing as one instead of parts). You can get a sneak preview on my thoughts on nitrogen flux in your aquarium here. I'm having a unfortunately somewhat circular conversation but it might have some value. Sometimes it might get too technical and so don't fret as the article will simplify and go over all the popular methods of managing nitrogen in the aquarium and how it all works. Again to be clear my article will not jam a specific style down your throat.

 

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I thought that was clear. I'm trying to get people to understand more about the bacteria in their reef tanks. Now what they do with that knowledge is up to them. I have my own reefing hypotheses and so that will take me in my direction, others will have their hypotheses and it can take them a completely different direction. However on these boards and the like people use language and situations without fully understanding the role of bacteria.

So to sum up will I tell you to carbon dose or feed your corals aminos or add unknown product number 8? No. However you'll now truly know how these things work at the bacterial level, well...excepting product number 8 :D . As well as what could be the downstream consequences to these additions.

Basically I want people to develop informed opinions rather than trust their gut or some other random reefer.
I like your original post - BUT - Based on what I have learned from @AquaBiomics and some of those threads - there is no such thing as a 'correct' bacterial population in a tank. There is a fair bit of variability - depending on where and how samples were taken. In other words there are great looking tanks with bacteria xyz and terrible looking tanks with xyz. So - though it was a great review of the types of bacteria in aquaria - I was also unclear on where this was going? - and I still dont understand - after reading your last response. Unless you know what bacteria are in your tank - its impossible to know whether any product will help or hurt. There is a fair bit of information out there that adding bacteria to 'increase diversity' (as a goal) - does not help - either the bacteria that are in the tank out compete the newcomers - or the newcomers outcompete the established bacteria. From my understanding - contrary to what might be intuition - the longer a tank is running - the less diverse it can become.
 
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