Dr. Kevin Novak Anoxic Filtration System.

[flampton]

And that's just it. The belief that a facultative anaerobe will always prefer oxygen is exactly entry level. Emphasis on entry level. I suppose when one first starts out one will learn this definition even now, though I really wish this is changed.

We have realized that 'facultative anaerobe' is a poor descriptor that should not be reserved for 'organisms that prefer oxygen by can respire anaerobically', and had to be redefined to match with newer understandings of microbial physiology.

The electron transport chain is not always as straightforward as is often taught in entry level biology. Not all of the 'archetypal' protein complexes are always present, and you also have other membrane-bound proteins (or protein complexes) that can utilize a range of electron donors and acceptors beyond what you learn early on.

A common case is the lack of the archetypal complex III, which is the cytochrome c reductase complex that transfers electrons from an electron-transfer quinol to a c-type cytochrome. This is what is necessary in the conventional model to allow electrons donated from NADH at the very start of the electron transport chain to be transferred to oxygen as the terminal electron acceptor. In the absence of this complex or another protein/protein complex capable of the same function, something else needs to be responsible for reducing c-type cytochromes. Certain D-lactate dehydrogenases come to mind here.

However, this is relatively inefficient, as well, you actually need D-lactate then for there to be aerobic respiration. Like, a lot of it for effective aerobic respiration. At the same time, the organism may be able to utilize electrons from NADH, which is a lot more of a 'common' energy source than D-lactate, for anaerobic respiration - often with fumarate as the terminal electron acceptor, but not always. So, you can have an organism that cannot efficiently generate energy aerobically, but a lot more so anaerobically.

As more and more microbial species are characterized, more is known about the diversity of energy production and it became really important to define their respiratory capacities better. There are also microorganisms that can thrive in both high and low oxygen levels, or those that can respire (effectively) in all oxic conditions. It's not just about what electron acceptors are utilized, but also about the type and diversity of electron donors too.

Hope that helps clear this all up for you.

Lol, take the L. I want the definition changed. Yeah buddy.

Just an FYI the majority of bacteria I work with lack complex III. You know what they all create more energy with? Oxygen. This is because they can produce more ATP/e-. There is no possibly way for an alternative electron acceptor to produce more ATP/e- because physics. Doesnt matter what limitations are found in the system.

Now if a facultative anaerobes cannot access enough oxygen it may resort to alternative electron acceptors which by definition must produce less energy. Inefficiencies in the system do not alter this fact. Or if they lack the ability they must utilize fermentation, which is extremely inefficient, e.g. the facultative anaerobe Saccharomyces cerevisiae.

Now you keep saying preferred, so I'm guessing you'll try to hunt down a weirdo organism that will be reported to 'prefer' an alternative to oxygen. However preferred is ill defined. If the organism utilizes an alternative electron acceptor when it has a choice, it will not change the fact that it can produce more ATP/e- with oxygen. And thus why would it choose the poor source?Usually because It's found in a extreme niche. And anyways when we find organisms that make these strange choices we never redefine the majority, but would create another definition for this grouping. In this instance we would add a modifier e.g. nitrate-preferring facultative anaerobe.

However as this is just a reefing forum, I promise everyone reading you don't need to ever consider this information. It's truly pointless in the discussion of this filter.

 

[Azedenkae]

Alright, let me address this one at a time.

Lol, take the L. I want the definition changed. Yeah buddy.

The term 'facultative aerobe' has been used for a very, very, very long time. I am surprised you don't think facultative aerobes really a thing. So no, I am not going to 'take the L' just because you, ironically calling me out on wanting to change a definition, yourself decided that something that has been long used is not really a thing.

Just an FYI the majority of bacteria I work with lack complex III. You know what they all create more energy with? Oxygen. This is because they can produce more ATP/e-. There is no possibly way for an alternative electron acceptor to produce more ATP/e- because physics. Doesnt matter what limitations are found in the system.

Now if a facultative anaerobes cannot access enough oxygen it may resort to alternative electron acceptors which by definition must produce less energy. Inefficiencies in the system do not alter this fact. Or if they lack the ability they must utilize fermentation, which is extremely inefficient, e.g. the facultative anaerobe Saccharomyces cerevisiae.

Okay, so let me explain this in more detail.

Without complex III, but presuming you have another protein/protein complex that can utilize something other than electron-transfer quinol as the electron donor, you have electrons transferred from the electron donor to a c-type cytochrome, then to oxygen. With that, the cytochrome c oxidase is able to translocate (conventionally) protons across the cell membrane, and the gradient drives the ATPase to generate ATP. Cool. Yes, indeed oxygen as the terminal electron acceptor is the best option when it comes to electron acceptors.

But you are looking at this in a vacuum.

When you have ATP production anaerobically for the same organism, they have the advantage that NADH can arise from so many different metabolic processes. Let's go with two that you should know and is common, glycolysis and the TCA cycle. From glucose, an organism can synthesize quite a lot of NADH, and so yeah while the electron transfer from NADH to fumarate does not generate as much energy per one molecule of NADH, the advantage is it gets to happen a lot more than transfer of electrons from D-lactate to oxygen. And this, is where such an organism does better anaerobically than aerobically. Thus, facultative anaerobe.

If you do so much work with microorganisms lacking complex III, you should really know this.

Now you keep saying preferred, so I'm guessing you'll try to hunt down a weirdo organism that will be reported to 'prefer' an alternative to oxygen. However preferred is ill defined. If the organism utilizes an alternative electron acceptor when it has a choice, it will not change the fact that it can produce more ATP/e- with oxygen. And thus why would it choose the poor source?Usually because It's found in a extreme niche. And anyways when we find organisms that make these strange choices we never redefine the majority, but would create another definition for this grouping. In this instance we would add a modifier e.g. nitrate-preferring facultative anaerobe.

I guess this is more subjective, because it is a matter of point of view as to whether we should or should not redefine the majority. I am a proponent of 'for' (clearly), because no matter how small or big a discovery is, if it changes the way we need to think about our research then it should redefine what we know/use/do.

Though that is kind of moot in this case, because again, the term 'facultative aerobe' has been used for a long time, and guess what, yes they use it to refer to organisms that prefer aerobic respiration rather than anaerobic respiration (although they are capable of both), as opposed to 'facultative anaerobes' which is the opposite.

You may argue against it, opting to never use the term 'facultative aerobe' or opt to believe it is not really a thing, but that is on you for deciding to do so. But unfortunately for you, the term 'facultative aerobe' is a thing and is used. I mean Google Scholar is a thing if you want to try to search for 'facultative aerobe' there and see how it is being used.

 

[flampton]

Alright, let me address this one at a time.

The term 'facultative aerobe' has been used for a very, very, very long time. I am surprised you don't think facultative aerobes really a thing. So no, I am not going to 'take the L' just because you, ironically calling me out on wanting to change a definition, yourself decided that something that has been long used is not really a thing.

Okay, so let me explain this in more detail.

Without complex III, but presuming you have another protein/protein complex that can utilize something other than electron-transfer quinol as the electron donor, you have electrons transferred from the electron donor to a c-type cytochrome, then to oxygen. With that, the cytochrome c oxidase is able to translocate (conventionally) protons across the cell membrane, and the gradient drives the ATPase to generate ATP. Cool. Yes, indeed oxygen as the terminal electron acceptor is the best option when it comes to electron acceptors.

But you are looking at this in a vacuum.

When you have ATP production anaerobically for the same organism, they have the advantage that NADH can arise from so many different metabolic processes. Let's go with two that you should know and is common, glycolysis and the TCA cycle. From glucose, an organism can synthesize quite a lot of NADH, and so yeah while the electron transfer from NADH to fumarate does not generate as much energy per one molecule of NADH, the advantage is it gets to happen a lot more than transfer of electrons from D-lactate to oxygen. And this, is where such an organism does better anaerobically than aerobically. Thus, facultative anaerobe.

If you do so much work with microorganisms lacking complex III, you should really know this.

I guess this is more subjective, because it is a matter of point of view as to whether we should or should not redefine the majority. I am a proponent of 'for' (clearly), because no matter how small or big a discovery is, if it changes the way we need to think about our research then it should redefine what we know/use/do.

Though that is kind of moot in this case, because again, the term 'facultative aerobe' has been used for a long time, and guess what, yes they use it to refer to organisms that prefer aerobic respiration rather than anaerobic respiration (although they are capable of both), as opposed to 'facultative anaerobes' which is the opposite.

You may argue against it, opting to never use the term 'facultative aerobe' or opt to believe it is not really a thing, but that is on you for deciding to do so. But unfortunately for you, the term 'facultative aerobe' is a thing and is used. I mean Google Scholar is a thing if you want to try to search for 'facultative aerobe' there and see how it is being used.

Facultative aerobe is a term used by scientists who don't understand the nomenclature. Non-microbiologists or foreign groups who receive poor translations.

You seem to be arguing about metabolic flexibility.

To end this I want to you to name one organism that reproduces faster utilizing one of the these alternate electron acceptors if it has a choice? Preferably one that would exist in a freshwater or saltwater aquarium.

I'll wait...

 

[Azedenkae]

Facultative aerobe is a term used by scientists who don't understand the nomenclature. Non-microbiologists or foreign groups who receive poor translations.

You seem to be arguing about metabolic flexibility.

To end this I want to you to name one organism that reproduces faster utilizing one of the these alternate electron acceptors if it has a choice? Preferably one that would exist in a freshwater or saltwater aquarium.

I'll wait...

Here we go: https://www.sciencedirect.com/science/article/abs/pii/037810979090043P

Desulfovibrio desulfiricans CSN

I had to choose an article describing a microorganism that 1) can both utilize oxygen and other electron acceptors for respiration as opposed to just clearing oxygen through other means, but 2) nonetheless grew slower or had no growth under oxic conditions. In fact, this strain prefers oxygen as the electron acceptor: https://academic.oup.com/femsec/article-pdf/17/4/271/18088826/17-4-271.pdf, as we have been discussing, but yeah, quoting the article, 'poor or no growth was obtained in aerated shaken cultures'. I mean I guess the article also says 'microaerophilic growth was observed in stabilized oxygen gradients' so there is that. But well, there we go. A microorganism that grows more poorly in oxic than anoxic conditions, even though it can generate ATP with oxygen. Facultative anaerobe!

Though I suppose you will probably find some excuse to dismiss the articles, like 'oh they are too old' or something.

By the way, Nature, Nature Microbiology, and ISME all have articles referring to facultative aerobes. Or describing something as facultatively aerobic, if you want to be specific. Those are top tier journals that publish a lot of work in biology, and microbiology in particular (Nature Microbiology and ISME more so). I would say it is pretty freaking valid to consider facultative aerobe as 'really a thing' given that.

But hey, maybe that's just me. In my field we do generally value publications in those journals highly. You can opt for otherwise I suppose. Your choice.

 

[KrisReef]

Neat discussion.
Can anyone tell me how a bacteria decides which metabolic route to take? Do they read the literature and then make a decision based upon information from a pH meter or do they have an upstream O2 sensor that informs them of the best path based upon what is coming next? They do have an awesome living setup for such simple creatures.

 

[Azedenkae]

Neat discussion.
Can anyone tell me how a bacteria decides which metabolic route to take? Do they read the literature and then make a decision based upon information from a pH meter or do they have an upstream O2 sensor that informs them of the best path based upon what is coming next? They do have an awesome living setup for such simple creatures.

Now I am just imagining bacteria just like shopping in a bacterio-depot for various proteins and stuff.

But yeah, they do have some really cool setup, yeah. There are some pretty nifty functions that some microbes have, such as the capacity to generate sodium instead of proton motive force to drive ATP synthesis, many of which not surpringly are found in marine environments. Then there are those that can invade eukaryotic cells and live within the cells themselves. Oh and let's not forget the chemolithoheterotrophs and chemoorganoautotroph, which are kinda weird, but cool. The former is kind of weird, relying on inorganic compounds as the energy source, but organic compounds as the carbon source.

 

[KrisReef]

I was actually thinking about the bacteria family, with like the last 36 generations gathering together at the Thanksgiving table, and after the blessing is said Grandpa turns and says to Grandma; "Please pass me the protons."

There was another thread on here recently asking people what they liked most about their tanks and a few people gave the microbes proper credit.

 

[Azedenkae]

I was actually thinking about the bacteria family, with like the last 36 generations gathering together at the Thanksgiving table, and after the blessing is said Grandpa turns and says to Grandma; "Please pass me the protons."

There was another thread on here recently asking people what they liked most about their tanks and a few people gave the microbes proper credit.

Lol.

And yeah. Microbes are awesome. That's why I decided to study them instead of well, anything else. XD I think I might be going crazy and turning into one of those 'I CAN SOLVE EVERYTHING WITH WHAT I SPECIALIZE IN!' scientists. Hope not. But I do think microbes can solve a lot of problems.

 

[Hot2na]

Novak is a Pimp..He copied the Jaubert style plenum and put it in a freshwater tank...Pioneer ? Hardly....

 

[flampton]

Here we go: https://www.sciencedirect.com/science/article/abs/pii/037810979090043P

Desulfovibrio desulfiricans CSN

I had to choose an article describing a microorganism that 1) can both utilize oxygen and other electron acceptors for respiration as opposed to just clearing oxygen through other means, but 2) nonetheless grew slower or had no growth under oxic conditions. In fact, this strain prefers oxygen as the electron acceptor: https://academic.oup.com/femsec/article-pdf/17/4/271/18088826/17-4-271.pdf, as we have been discussing, but yeah, quoting the article, 'poor or no growth was obtained in aerated shaken cultures'. I mean I guess the article also says 'microaerophilic growth was observed in stabilized oxygen gradients' so there is that. But well, there we go. A microorganism that grows more poorly in oxic than anoxic conditions, even though it can generate ATP with oxygen. Facultative anaerobe!

Though I suppose you will probably find some excuse to dismiss the articles, like 'oh they are too old' or something.

By the way, Nature, Nature Microbiology, and ISME all have articles referring to facultative aerobes. Or describing something as facultatively aerobic, if you want to be specific. Those are top tier journals that publish a lot of work in biology, and microbiology in particular (Nature Microbiology and ISME more so). I would say it is pretty freaking valid to consider facultative aerobe as 'really a thing' given that.

But hey, maybe that's just me. In my field we do generally value publications in those journals highly. You can opt for otherwise I suppose. Your choice.

We would never refer to Desulfovibrio as a facultative anaerobe because it is NOT one. As they're unable to maintain life with oxygen as the terminal electron acceptor they would be classified as an obligate anaerobe (for some species/strains) and aerotolerant anaerobe (for others).

I know you keep referring to your field. However since you couldn't immediately come up with anything relevant (let alone a model organism) means your likely a senior undergrad or first year grad student (maybe an overzealous tech?). Best advice I can give you is to learn to accept when you're wrong. You'll get no where in any scientific field with this attitude. And frankly if you're at a decent school your advisors will absolutely destroy you until you figure this out.

 

[Azedenkae]

We would never refer to Desulfovibrio as a facultative anaerobe because it is NOT one. As they're unable to maintain life with oxygen as the terminal electron acceptor they would be classified as an obligate anaerobe (for some species/strains) and aerotolerant anaerobe (for others).

To end this I want to you to name one organism that reproduces faster utilizing one of the these alternate electron acceptors if it has a choice?

You only asked for an organism that reproduces faster with an alternate electron acceptor while still having ozygen as a possible, I gave you one. Yes it took me some time, but I gave you what you asked.

Plus, if you read into the papers you'd see it respires with oxygen but can't grow very well in oxic conditions such as in a "aerated shaken cultures".

they're unable to maintain life with oxygen as the terminal electron acceptor they would be classified as an obligate anaerobe (for some species/strains) and aerotolerant anaerobe (for others). Buuut I guess being wrong can only apply to me? I mean you can't be wrong, can't you? It has to be someone else. Okay cool.

 

[flampton]

Neat discussion.
Can anyone tell me how a bacteria decides which metabolic route to take? Do they read the literature and then make a decision based upon information from a pH meter or do they have an upstream O2 sensor that informs them of the best path based upon what is coming next? They do have an awesome living setup for such simple creatures.

This is actually very close to the truth. Their genetic material encode for the various sensing mechanisms (can be pH, O2, light, etc) AND the decisions in response to what those sensors are saying. So basically the manual has already been memorized.

 

[flampton]

You only asked for an organism that reproduces faster with an alternate electron acceptor while still having ozygen as a possible, I gave you one. Yes it took me some time, but I gave you what you asked.

Plus, if you read into the papers you'd see it respires with oxygen but can't grow very well in oxic conditions such as in a "aerated shaken cultures".

they're unable to maintain life with oxygen as the terminal electron acceptor they would be classified as an obligate anaerobe (for some species/strains) and aerotolerant anaerobe (for others). Buuut I guess being wrong can only apply to me? I mean you can't be wrong, can't you? It has to be someone else. Okay cool.

No, I'm wrong constantly.

If you can't stand being wrong how will you ever reject a hypothesis?

Face it you came on here and thought you'd put me in my place and since you're limited in info you spouted garbled scientific examples with 'big' words about a new paradigm in 'your' field that requires a major restructuring of 'your' field's definitions....to someone who's an actual doctor in 'your' field.

 

[Azedenkae]

No, I'm wrong constantly.

If you can't stand being wrong how will you ever reject a hypothesis?

Face it you came on here and thought you'd put me in my place and since you're limited in info you spouted garbled scientific examples with 'big' words about a new paradigm in 'your' field that requires a major restructuring of 'your' field's definitions....to someone who's an actual doctor in 'your' field.

I realize you are a PhD in the same field as I am, but I don't think that it negates everything I presented, niche or otherwise. It ie still good to really listen to others and well, see what they have to say and if it makes sense. Sometimes, it can drastically alter your deeply ingrained viewpoints. I mean not always, you can consider the situation and make a decision either way as you think makes sense. I have learnt so much from my fellow reefers and had significant changes of views, even recently.

In this case though.

You said facultative aerobes are not really a thing, well there are publications in top tier journals referring to them.

You said there is no way anaerobic growth could be better than aerobic growth if both options are available, I gave one explanation as to why that could be possible.

You asked for an example of such a microorganism that can utilize oxygen and other compounds as electron acceptors, yet grow better in anoxic than oxic conditions. I gave you an example.

But none of that is good enough for you. None of it. So I am done. Have a good day sir or madam.

 

[revhtree]

Please keep the posts from getting personal. Be kind and friendly and or please just ignore one another. Thanks.

 

[Azedenkae]

Please keep the posts from getting personal. Be kind and friendly and or please just ignore one another. Thanks.

Thanks for the reminder. Will do.

 

[Crashjack]

Please keep the posts from getting personal. Be kind and friendly and or please just ignore one another. Thanks.

... not only that, you are going to to be responsible for making my head explode.

 

[Hermie]

Basically Dr Novak focuses on maximizing denitrification processes in freshwater systems. Do the applications work in saltwater?

Plenums + biocenosis baskets

 

[Hermie]

Well Dr. Novak also has a ton of credentials and he says it works in saltwater so I'll at least give a listen to the guy who's trying to be helpful instead of the guy being an egotistical jerk. Who cares what your signature says doesn't make you the authority on everything especially when you won't even explain why you think what you do.

There's a simple way to settle all this,

tests + experiments

 

[Hermie]

It wont, it's a type of zeolite. Same stuff that the zeovit system uses.

baked clay is not zeolite, zeolite is a specific type of rock mainly made of aluminum