Analyzing a Bacterial Method for Dinoflagellates (and cyano?)

neilp2006

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Random?
If bacteria and waste water treatment is a key component in your day to day career, wouldn't it be prudent to know all aspects of what processes every component does? I would tend to think so.

If you're disagreeing with me based on a personal opinion or personal feeling towards me, great. Please identify your distaste of me; not the science behind the regimen.
I said random because that’s what i would be doing. Random pubmed searches for a bacterium based on the terms ‘bacteria’ ‘consume’ ‘Dinoflagellates’ ‘waste water’

You see how that can be construed as ‘random’, right?

Since YOU have inside knowledge regarding YOUR experience in waste water treatment, and YOU KNOW the strain you are referring to- no, I don’t think that the info you are providing is random. But without the strain name, I can’t find any eveidence that what you are saying has any basis in scientific fact, because I can’t read the papers.

I have no issue with you. I don’t even know you. I was simply asking for references to the ‘fact’ of a ‘bacterial strain that aggressively eats dinoflagellates’. As a 24 year medical microbiologist, I’ve yet to encounter a bacterial strain that directly consumes protists.

I’m willing and ready to learn, but without a starting point, I can’t do the research.

Also- you have this incredibly apropos information that would greatly benefit everyone reading the thread, yet seem unwilling to share it. I can’t parse that.

And frankly- I’ve yet to a see any science behind the regimen, since there are no scientific articles detailing research done that follows core scientific principles.

Here, in this forum, let’s not pretend we are doing science. If we want to do that, then let’s treat it like science. Let’s identify the most qualified people based on their scientific training, do controlled experiments, publish and debate it. Have discourse.

Not get super defensive and think someone has a beef with you two posts into a series of questions regarding the validity of a statement that was made.

I mean you no disrespect, I seriously don’t. But these threads have a tendency to drive their own baseless narrative that can cause damage. There are several key posts above detailing why this protocol may be a bas idea, and people are still just throwing bacteria and vodka into their tanks without really understanding the biology of it. I think it is a responsibility of people with specific knowledge that They share that knowledge to the group and help everyone benefit. That’s includes calling out statements tjat they feel are inaccurate or wrong, or don’t pertain to our closed environments.

Best regards
 
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Cruz_Arias

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Ahh... I figured it was a bit of miscommunication.

I'll see if I'd be able to publically post the specialized bacterial strain. Dr. Tim H. should have the strain name if he discovered his strain suggested in the regimen.

It does act similarly to the proprietary waste water aerobic thermophilic bacterial strains which react very very similarly to correct volume carbon dosing and additional efficient oxygenation to the digestive systems.

I appreciate your curiosity and feedback, Neil... it's always a pleasure to exchange ideas with another educated.
 

neilp2006

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Ahh... I figured it was a bit of miscommunication.

I'll see if I'd be able to publically post the specialized bacterial strain. Dr. Tim H. should have the strain name if he discovered his strain suggested in the regimen.

It does act similarly to the proprietary waste water aerobic thermophilic bacterial strains which react very very similarly to correct volume carbon dosing and additional efficient oxygenation to the digestive systems.

I appreciate your curiosity and feedback, Neil... it's always a pleasure to exchange ideas with another educated.
Glad we could get it sorted. That’s an incredibly interesting biology to me- I’ve never heard of it in the medical field or in other fields. Must admit- I havent studied environmental works all that much.

Don’t worry about the strain name. No need to get into the hassle of trying to share potential trade secrets. The fact you are willing to share it demonstrates a lot. I didn’t totally follow that you knew Dr Tim has cultivated such a strain- I figured you were extrapolating from your waste water work and made an assumption. For that, I apologize. If Dr Tim has cultivated such a strain and is including it in the waste away product, then I don’t doubt that it may be directly acting upon the protists as hypothesized.

I’m really hoping that this approach reaches a maturity level where it can be trusted to work as long as people follow the protocol. There are many biological relationships underlying how our tanks perform and work (or not!) that we simply don’t appreciate, and it’s slways more complicated than a ‘n’ bullet point protocol. But with proper guidance and a scientific based approach, and clear rationale for doing things, I don’t doubt a valid biological based protocol can be found that lets us achieve control over these issues.

Best regards
 
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Cruz_Arias

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If Tim Havonec is in R2R, I think he would be an authority to speak about his product?

Just a thought, Neil. Perhaps a moderator would be able to invite him to this discussion?
 
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Cruz_Arias

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The engulfing bacteria are non-discriminatory in what organics they consume, Neil. If dying or weak dinoflagellates are small enough to be "surrounded" and consumed, that bacteria would not care. (I don't think they have feelings LOL)

They are a digestive type of bacteria (Waste Away) that, when exposed to oxygen and a carbon source (vodka), increase their metabolism to consume sludge organics. The nitrifying bacterial strain (One and Only) also responds favorably to an increased carbon source and oxygen.

In regards to efficient oxygenation (as indicated with the bubbling method) the smaller and finer the bubbles, the more surface area per mL the fresh air (low co2) has to impact the water... with the osmotic pressures (partial pressures) of the o2 (higher concentration) is imposing on the water, it tends to force out the CO2 out of solution.

Hence the need for more efficient and directed aeration (not vigorous and uncontrolled bubbling)

Rippling and disturbing the surface of the water in an area of high CO2 concentration dissolves the gas at the surface of the water... if it's high in CO2, guess what's being dissolved at the point of surface agitation?

CO2 has a higher affinity to dissolve in water than O2. That has been proven in many scientific studies. (I take no credit for their work, but use the studies as a point of reference)

As the bacteria (bacterial population increases) the O2 consumption goes up, the CO2 production also goes up... the only way to remove the CO2 is not by photosynthesis, but rather by infusion of O2 back into the water.

Water is like a sponge. It can only hold so much gas and solute until it's full. If you want to remove one, you can force it out (in the case of CO2) with another soluble gas (oxygen) via osmosis and increased gas/liquid surface area interface.






Glad we could get it sorted. That’s an incredibly interesting biology to me- I’ve never heard of it in the medical field or in other fields. Must admit- I havent studied environmental works all that much.

Don’t worry about the strain name. No need to get into the hassle of trying to share potential trade secrets. The fact you are willing to share it demonstrates a lot. I didn’t totally follow that you knew Dr Tim has cultivated such a strain- I figured you were extrapolating from your waste water work and made an assumption. For that, I apologize. If Dr Tim has cultivated such a strain and is including it in the waste away product, then I don’t doubt that it may be directly acting upon the protists as hypothesized.

I’m really hoping that this approach reaches a maturity level where it can be trusted to work as long as people follow the protocol. There are many biological relationships underlying how our tanks perform and work (or not!) that we simply don’t appreciate, and it’s slways more complicated than a ‘n’ bummer piint protocol. But with proper guidance and a scientific based approach, and clear rationale for doing things, I don’t doubt a valid biological based protocol can be found that lets us achieve control over these issues.

Best regards
 
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Cruz_Arias

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In regards to pH to Alkalinity, I would like to borrow from Randy.

In normalized systems, the meq/L of Alkalinity is around 2.4 to 3.4 which translates to approximately 7.0 dKH to 8.4 dKH.
The linearization in the article states that in higher concentrations of CO2, the pH of the water shifts.

Most systems (lately) are at an elevated dKH (8.4 to 9.6) and are barely maintaining a pH of 8.0

So the Day 0 of pre-aeration with fresh, low CO2 air, is vital to bring up the available D.O. as well as the ensuing days of bubbling 24/7 to mechanically force out the CO2 being produced by the increased bacterial loads.

The assumption that most tanks are 90 to 95% D.O. saturated is erroneous. Based on the aforementioned facts.


Alk to pH.png
dKHchart_zps4e61b88d.jpg
 
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neilp2006

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The macrophage bacteria are non-discriminatory in what organics they consume, Neil. If dying or weak dinoflagellates are small enough to be "swallowed" and consumed, that bacteria would not care. (I don't think they have feelings LOL)

They are a digestive type of bacteria (Waste Away) that, when exposed to oxygen and a carbon source (vodka), increase their metabolism to consume sludge organics. The nitrifying bacterial strain (One and Only) also responds favorably to an increased carbon source and oxygen.

In regards to efficient oxygenation (as indicated with the bubbling method) the smaller and finer the bubbles, the more surface area per mL the fresh air (low co2) has to impact the water... with the osmotic pressures (partial pressures) of the o2 (higher concentration) is imposing on the water, it tends to force out the CO2 out of solution.

Hence the need for more efficient and directed aeration (not vigorous and uncontrolled bubbling)

Rippling and disturbing the surface of the water in an area of high CO2 concentration dissolves the gas at the surface of the water... if it's high in CO2, guess what's being dissolved at the point of surface agitation?

CO2 has a higher affinity to dissolve in water than O2. That has been proven in many scientific studies. (I take no credit for their work, but use the studies as a point of reference)

As the bacteria (bacterial population increases) the O2 consumption goes up, the CO2 production also goes up... the only way to remove the CO2 is not by photosynthesis, but rather by infusion of O2 back into the water.

Water is like a sponge. It can only hold so much gas and solute until it's full. If you want to remove one, you can force it out (in the case of CO2) with another soluble gas (oxygen) via osmosis and increased gas/liquid surface area interface.
A macrophage is a specialized type of mammalian cell that forms part of the immune system.its name literally means ‘big eater’ because it eats cells and components from lysis that are smaller than it. There are no ‘macrophage bacteria’. I think this is where our small issue is coming from, an incorrect use of the nomenclature.

Even sludge digesting bacteria don’t literally ingest the sludge to break it down. They secrete degradative enzymes that further break down the sludge, then import ions and macromolecules through specific transporters. Bacteria have too rigid an outer membrane to engulf and swallow ‘prey’ so they rely on extracellular degradation and importation of breakdown products.
 

Cruz_Arias

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You might be right, Neil...

Maybe the terminology is not consistent. What I'm talking about is the predatory type of bacteria that aggressively attacks sludge and consumes particulates by means of phagocytosis.

In the waste water world we call those guys, "macrophage bacteria". How would you like for me to refer to them as? Predatory bacteria, phagocytic bacteria?

They can consume particulates (not just secreting enzymes) that can be many times it's own size, and when exposed to normalized levels of oxygen (300 to 400ppm) increases it's voracity in bacterial film (and other organic film) digestion.
 

neilp2006

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You might be right, Neil...

Maybe the terminology is not consistent. What I'm talking about is the predatory type of bacteria that aggressively attacks sludge and consumes particulates by means of phagocytosis.

In the waste water world we call those guys, "macrophage bacteria". How would you like for me to refer to them as? Predatory bacteria, phagocytic bacteria?

They can consume particulates (not just secreting enzymes) that can be many times it's own size, and when exposed to normalized levels of oxygen (300 to 400ppm) increases it's voracity in bacterial film (and other organic film) digestion.
Ok, sure.

We can agree to call it something else, but all I’m saying is that a bacterial cell literally, physically cannot change its membrane conformation in order to engulf a particulate of any size. It’s just not physically possible. They lack at least 2 layers of physical components required to do it.

Unicellular organisms that phagocytose particles are very common- but none of them are bacteria.

Whatever this process is- it’s not phagocytosis. You and your colleagues may be calling them ‘phagocytosis bacteria’ But that is not a classification that actually exists. You guys know what that name represents- other people don’t.

The last part offers a clue though. Under high O2, these organisms exhibit an increase in their ‘appetite’ for bacterial biofilms. That right there indicates they aren’t bacteria. My hunch is that you are talking about some sort of ameboid organism, but not a bacterium
 
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Cruz_Arias

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Ok, sure.

We can agree to call it something else, but all I’m saying is that a bacterial cell literally, physically cannot change its membrane conformation in order to engulf a particulate of any size. It’s just not physically possible. They lack at least 2 layers of physical components required to do it.

Unicellular organisms that phagocytose particles are very common- but none of them are bacteria.

Whatever this process is- it’s not phagocytosis. You and your colleagues may be calling them ‘phagocytosis bacteria’ But that is not a classification that actually exists. You guys know what that name represents- other people don’t.

The last part offers a clue though. Under high O2, these organisms exhibit an increase in their ‘appetite’ for bacterial biofilms. That right there indicates they aren’t bacteria. My hunch is that you are talking about some sort of ameboid organism, but not a bacterium
They are bacteria, Neil. Not making this stuff up. :) There is no equity in stating a fantasy.
 

neilp2006

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Ok, now, I’m not discounting the existence of predatory bacteria, and I’m well versed in the existence of Bdellovibrio like organisms. I was involved in reasesrch in the early 2000’s looking at ways to engineer bdellovibrio for use against antibiotic resistant staphylococcus .

It literally says in that paper “ predate..,by secretion of lytic enzymes...cytoplasmic invasion... or epibiosis”

This discussion is whether or not Waste Away contains a bacterial strain that performs phagocytosis in order to ‘eat’ dinoflagellates.

Nowhere in that paper is phagocytosis mentioned, largely because phagocytosis doesn’t occur in bacteria and mentioning it in this paper would have been an immediate ‘fail’ that stopped publication. Bacteria physically can not perform phagocytosis

I’m sure they are bacteria. I mean, you’ve told me they are, so why doubt it. I’m also 100% sure that they aren’t performing phagocytosis .


I think I’m going to bow out. This discussion isn’t useful for the thread And we seem to be disagreeing over a naming issue.

Regards
 

Cruz_Arias

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So now, we'll call it bacterial "surrounding" of the dinoflagellates. If that's more acceptable, @neilp2006

I'll take your lead in your field of expertise, you're probably more experienced at this level of taxonomy and interactions.

It was explained to me by a micro-biologist in the field that the "bugs consumed other bugs and digested them"

If I am incorrect, I stand corrected.

Regards,
 
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Victoria M

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Thank you for sharing that paper. @Cruz_Arias . It was an interesting read. I am not familiar with those types of bacteria and I find it very interesting. I am more familiar with human illness causing bacteria.
I think Neil that the article was congruent with what you said. it clearly used terms such as lysis, attachment, ect. and it did use the term wolf pack to describe a predatory tactic of bacteria. multiple cells ganging upon prey cell, or cells. A single cell did not engulf another cell. It does not use the terms macrophage or phagocytosis which are very specific biological terms, with very specific meaning, as you already stated.
it is a matter of nomenclature. an unintentional misuse of a term by someone along the way.
I read a very interesting statement by Dr. Tim regarding his avoidance of these types of threads. His reasons for avoiding them were very solid and hilarious. If I can find it will send it to you. to sum it up. He earned his doctorate with his study of bacteria, and he is not going to argue with every ones google doctorate. He said it much nicer though.
I get into this very situation with patients. The doctor lays out a medical plan of care, shares tests results, ect asks if anyone has any questions, they say "no" then he leaves. They usually ask me what that all meant. LOL. Then later I get to hear the family and patient telling other family members what the doctor said. Then I get to explain again what everything means. finding ways to explain medical talk in ways that non medical folks understand is my specialty. lol. that is just a joke folks.
 

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Then I get to explain again what everything means. finding ways to explain medical talk in ways that non medical folks understand is my specialty. lol. that is just a joke folks.
Victoria. - this is where I make my money too but in software technology between the technologists and the sales people. My interaction would be more nurse to patient and sometimes doctor to nurse. I am not good enough to go doctor to patient. Too much of a tech to layman, but it’s something I am working of. Explaining technology to my 86 year old father. My mother gets enough.
 
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taricha

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@Cruz_Arias thanks so much for hopping in the thread.
Just to be clear, I wouldn't be dissecting nor inviting others to pick apart the details here if there weren't clearly great potential and a lot of success in this kind of approach.
The assumption that most tanks are 90 to 95% D.O. saturated is erroneous. Based on the aforementioned facts.
Yeah the way I said that was not true, and overstated. (but O2 and CO2 don't push each other out in general.)
I'd rephrase to most systems that are reef lit and skimmed reach 90 to 95% of max dissolved oxygen at some point during a daily 24 hour cycle. They also drop to 70% or less during each cycle.
Eric Borneman - Need To Breathe part 3 (see figures2,4,5,6,7,8,9.) Also my lit and skimmed tank showed similar profile.
Tanks that are either not reef lit or skimmed, could be way below those values.
So if I'm already touching 90%+ in each daily cycle, 24 hours of pre-aeration is not going to move the needle much on the O2. But hours of outside air (if it was indoors before) will definitely drop the CO2 tank levels, and raise the pH - which is still worth doing.

I also said earlier that bacteria consuming the ethanol floods the system with CO2, and that may be true, but I need to re-measure more carefully before I can trust my measurement that it was the vodka and not the high ambient indoor CO2 that I was measuring increase the tank CO2.


Even sludge digesting bacteria don’t literally ingest the sludge to break it down. They secrete degradative enzymes that further break down the sludge
we'll call it bacterial "surrounding" of the dinoflagellates.
In this hobby lots of things are described as "eating" other things that really they can't ingest in a literal vertebrate sense. I just always charitably assume "eating" is a shorthand for some process of an organism establishing proximity to another, causing its downfall through some chemical or biological action, and benefitting from the nutrients liberated from the organism's death.
 
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taricha

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Let's shift gears a bit... good Qs here I'd been meaning to post about anyway.
With regard to stepwise waste reduction, are we guessing at how much waste we need to clear when we choose Waste Away?

And with regard to carbon dosing, is the thinking that ethanol will help heterotrophic bacteria consume organic matter that it would not ordinarily consume in the absence of a simple carbon source?
If you had a lot of grunge and did a Waste-Away pre-step, you wouldn't really have to do much guessing. You can measure if it's enough or too much with your built in optical turbidity sensors. [a.k.a. you can see if the tank is cloudy with your eyes :) ]. The Dr Tim's Recipe says turn off skimmer,UV, ozone, but if cloudy water is detected turn them back on immediately.
When the waste-away step doesn't generate cloudy water, then that tells you that you don't have a ton of easily digestible grunge anymore, and the bloom that you'll create in the steps of the method ought to proceed predictably and within manageable ranges.

The ethanol effect I've been thinking about a bit. When I started, I got cloudy water, then I let it fade to barely cloudy. I was able to re-start the cloudiness by addition of a little more waste-away and another dose of vodka. Since the water was already slightly cloudy there was plenty of bacteria, it's not that more bacteria re-invigorated. It must be the ethanol that re-intensified the bloom.
Is every addition of a large amount of ethanol helping the bacteria digest more grunge? Or toward the end does more and more ethanol mostly grow more and more bacteria. I lean toward the latter explanation that after a certain point, the additional ethanol makes more bacteria (but I'm running a side experiment on debris digestion to check this point.) I think the large amount of ethanol is responsible for very cloudy water and considerable mass of bacteria on surfaces as I posted pics of earlier.

Which brings me to this thought. Another mechanism by which this method would help against cyano is actually quite simple. You are to siphon visible clumps and mats out daily. And growing large bacterial populations in thriving thick mats means they are seeking out particulate goodies and entwining and incorporating all those particulates into the mat structure, allowing you to more efficiently remove them by siphoning. So I'm not sure if the ethanol allows more grunge to be digested, but it definitely does allow more grunge to be grabbed by bacteria, and therefore removed from the system.
 

Dan_P

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Let's shift gears a bit... good Qs here I'd been meaning to post about anyway.

If you had a lot of grunge and did a Waste-Away pre-step, you wouldn't really have to do much guessing. You can measure if it's enough or too much with your built in optical turbidity sensors. [a.k.a. you can see if the tank is cloudy with your eyes :) ]. The Dr Tim's Recipe says turn off skimmer,UV, ozone, but if cloudy water is detected turn them back on immediately.
When the waste-away step doesn't generate cloudy water, then that tells you that you don't have a ton of easily digestible grunge anymore, and the bloom that you'll create in the steps of the method ought to proceed predictably and within manageable ranges.

The ethanol effect I've been thinking about a bit. When I started, I got cloudy water, then I let it fade to barely cloudy. I was able to re-start the cloudiness by addition of a little more waste-away and another dose of vodka. Since the water was already slightly cloudy there was plenty of bacteria, it's not that more bacteria re-invigorated. It must be the ethanol that re-intensified the bloom.
Is every addition of a large amount of ethanol helping the bacteria digest more grunge? Or toward the end does more and more ethanol mostly grow more and more bacteria. I lean toward the latter explanation that after a certain point, the additional ethanol makes more bacteria (but I'm running a side experiment on debris digestion to check this point.) I think the large amount of ethanol is responsible for very cloudy water and considerable mass of bacteria on surfaces as I posted pics of earlier.

Which brings me to this thought. Another mechanism by which this method would help against cyano is actually quite simple. You are to siphon visible clumps and mats out daily. And growing large bacterial populations in thriving thick mats means they are seeking out particulate goodies and entwining and incorporating all those particulates into the mat structure, allowing you to more efficiently remove them by siphoning. So I'm not sure if the ethanol allows more grunge to be digested, but it definitely does allow more grunge to be grabbed by bacteria, and therefore removed from the system.

Hey, have you looked at WasteAway in a test tube in any manner, say, turbidly vs mg of organic material? Turbidity vs type of organic matter? Have you looked at the longevity of the bacteria? Do they peter out?
 
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taricha

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Hey, have you looked at WasteAway in a test tube in any manner, say, turbidly vs mg of organic material? Turbidity vs type of organic matter? Have you looked at the longevity of the bacteria? Do they peter out?
On your last question they do fade away - run out of easy meals I suspect. Dr Tim makes a gel that slow releases waste-away over month for that reason (bacteria don't stay in system indefinitely).
Test tubes? Once unsuccessfully. Giving it another shot.
IMG_20190910_165801.jpg

(grunge that had built up in a neglected algae tank over months, tested vs 3 different "grunge eating" bacterial blends with and without ethanol.)
So right now my observations are based on my aquarium.
 
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