Bottled Bacteria, AquaBiomics. Just what's in your bottles

[BeanAnimal]

The primary point of this thread is learning what is in the bottles. But, if you just try a bit harder you can make this an ammonia prediction and tank cycling thread. I have faith in you.

 

[BeanAnimal]

This hypothesis is reasonable, but the bacteria identified as S. marcescens is ~44% of the bottle's bacterial contents.

Still possibly infected culture, unintended but untested due to poor QC or methodology?

 

[Garf]

what that thread did for reefing:

see pages 5-6 onward, actual Dr. Tim speaking. how often do we see that here, q and a from him.


we can see basic utility from common bottle bac strains.


**if you read the details of that experiment you see a unique thing/action that no other testers for bottle bac have done: the 100% water change trick. I'll let readers discern why that was done. has to do with implantation rates per maker, a big deal for reefers who value surface area.

Considering my earlier comments on the "Three body problem" I'm thinking about the possibility that these bacterias are releasing exudates or taking surface that prevent natural saltwater reef bacterias taking hold, hence the horrendous wait period for seeming "stability" in dry rock start ups. Sure, they cycle in a couple or 3 weeks, but longer term? Cycling is the easiest bit, in my book.

 

[A_Blind_Reefer]

Considering my earlier comments on the "Three body problem" I'm thinking about the possibility that these bacterias are releasing exudates or taking surface that prevent natural saltwater reef bacterias taking hold, hence the horrendous wait period for seeming "stability" in dry rock start ups. Sure, they cycle in a couple or 3 weeks, but longer term? Cycling is the easiest bit, in my book.

This is why I’m hanging out quietly at the back of the room. I’ve been in the hobby for many years (which doesn’t mean anything other than I could have been doing it wrong all along) and never had issues like I did with my current setup. A bare bottom, dry rock, bacteria in a bottle start….. yes I’m an idiot and fell into the hype of this is how things are nowadays. No hitchhikers, ultra low nutrient, ultra low maintenance…. It will even do your laundry, clean the house and cook dinner. Total nightmare, never again. Three years to get to what I would call stable and another two or three fighting semi-frequent rtn/stn. To the point that I ran a full course of cipro. I know, it was a last resort effort. I also let it ride in the tank after treatment in hopes that the one or two percent per day auto water change after, diluted the meds to the point of being safe-ish. Trying not to jinx myself but I haven’t had a necrosis event in well over a year. I started dosing ammonium about eight months ago or so and that appears to be of benefit (I can’t tell anything with my vision but non-reefers that visit comment on its progress). I also just recently started vinegar as well. Fingers crossed that I’m feeding the good over the bad but who knows….

 

[Solo McReefer]

There is money for researching things for the sake of knowledge and implications outside of money making goals. For example, conservation is one that isn't directly about money.

 

[Solo McReefer]

One problem would be that the results would no doubt get back to the vendors. If two products appear identical, or one doesn't have good results, you'll see a LOT of activity where the companies will try to protect their brands. I ran into this twice - when I ran some sea salt testing, and then with my carbon / HLLE research - in both cases I was approached by manufacturers in a very aggressive way.

I also wonder if these products are all just bacteria cultures? Fritzyme's name implies that it has some enzymes in it.

I also think you'll find that some of these products are identical. I was told by a friend who was visiting one of these companies in Texas, that their back lot was littered with empty carboys from another bacteria supplier just down the road from them.

Tim Hovenac invented a line of these products, and given the original research he has published on this topic, he really knows his stuff. Most of the other companies don't have actual R&D departments.

KZ Fillings Extraction Team

 

[.AcroKiller.]

This is why I’m hanging out quietly at the back of the room. I’ve been in the hobby for many years (which doesn’t mean anything other than I could have been doing it wrong all along) and never had issues like I did with my current setup. A bare bottom, dry rock, bacteria in a bottle start….. yes I’m an idiot and fell into the hype of this is how things are nowadays. No hitchhikers, ultra low nutrient, ultra low maintenance…. It will even do your laundry, clean the house and cook dinner. Total nightmare, never again. Three years to get to what I would call stable and another two or three fighting semi-frequent rtn/stn. To the point that I ran a full course of cipro. I know, it was a last resort effort. I also let it ride in the tank after treatment in hopes that the one or two percent per day auto water change after, diluted the meds to the point of being safe-ish. Trying not to jinx myself but I haven’t had a necrosis event in well over a year. I started dosing ammonium about eight months ago or so and that appears to be of benefit (I can’t tell anything with my vision but non-reefers that visit comment on its progress). I also just recently started vinegar as well. Fingers crossed that I’m feeding the good over the bad but who knows….

Pm sent about ammonia dosing with carbon dosing.

 

[A_Blind_Reefer]

Pm sent about ammonia dosing with carbon dosing.

Ah, thanks for letting me know here as I can’t tell when I get messages here

 

[telegraham]

Still possibly infected culture, unintended but untested due to poor QC or methodology?

I tested two bottles that were purchased several years apart. One bottle lived in my garage for a couple years, and that was the first bottle I tested. Because I thought I had contaminated the first bottle, I purchased the second bottle and tested. Very similar contents with a bug identified as S. marcescens being the primary bacteria.

Maybe:
The original source provided by Tim was contaminated with S. marcescens (or something that's identified as S. marcescens), Tim didn't know, and the juice has been made that way all along.
The E-B manufacturer is working with source that became contaminated over time.
The E-B manufacturer isn't performing their work as aseptically as they should, they aren't using sterile disposables, and their gear is funky.
AquaBiomics is misidentifying S. marcescens.

I'm sure there are other possibilities. It's been three months. No word from Tim. I know one other curious mind has tested E-B, and they are seeing what I'm seeing.

 

[Spare time]

Or is it?

It depends. I write grants so yes some are about solving questions rather than something purely about money.

 

[BeanAnimal]

I tested two bottles that were purchased several years apart. One bottle lived in my garage for a couple years, and that was the first bottle I tested. Because I thought I had contaminated the first bottle, I purchased the second bottle and tested. Very similar contents with a bug identified as S. marcescens being the primary bacteria.

Maybe:
The original source provided by Tim was contaminated with S. marcescens (or something that's identified as S. marcescens), Tim didn't know, and the juice has been made that way all along.
The E-B manufacturer is working with source that became contaminated over time.
The E-B manufacturer isn't performing their work as aseptically as they should, they aren't using sterile disposables, and their gear is funky.
AquaBiomics is misidentifying S. marcescens.

I'm sure there are other possibilities. It's been three months. No word from Tim. I know one other curious mind has tested E-B, and they are seeing what I'm seeing.

I think that leaves with far more questions than it answers.

 

[AquaBiomics]

I tested two bottles that were purchased several years apart. One bottle lived in my garage for a couple years, and that was the first bottle I tested. Because I thought I had contaminated the first bottle, I purchased the second bottle and tested. Very similar contents with a bug identified as S. marcescens being the primary bacteria.

Maybe:
The original source provided by Tim was contaminated with S. marcescens (or something that's identified as S. marcescens), Tim didn't know, and the juice has been made that way all along.
The E-B manufacturer is working with source that became contaminated over time.
The E-B manufacturer isn't performing their work as aseptically as they should, they aren't using sterile disposables, and their gear is funky.
AquaBiomics is misidentifying S. marcescens.

I'm sure there are other possibilities. It's been three months. No word from Tim. I know one other curious mind has tested E-B, and they are seeing what I'm seeing.

I want to comment on the possibility of misidentifying S. marcescens from these data. (I know you and I have discussed this but not sure if its been brought up in the thread)

The sequence is a perfect (100%, 253 of 253 base pairs) match for S. marcescens. There are hundreds of isolates for this species in the database, all labeled with this species name, and all are identical for this marker. The list of perfect matches also includes some un-named isolates that are only annotated to the genus level (always Serratia).

There are two other possible species matches - S. nematodiphila and S. fluorescens. These are the only two species in the database that it could be confused with.

So overall: its definitely Serratia, definitely not any of the other genera in the database. It could be any one of the many different strains of S. marcescens, or it could be one of these two species (S. nematodiphila and S. fluorescens.)

S. marcescens is a widely reported contaminant in lab cultures, and survives in a pretty wide range of conditions. So thats what I think we're looking at. But I've tried to state the real range of uncertainty above, so readers can draw their own conclusions.

 

[Solo McReefer]

I think that leaves with far more questions than it answers.

The answer, seems to me, is not to use the product until the questions are answered

By the other questions

One of which, what other bottles have it as well

Anyway, I have no doubt that every corporation who makes Bug Juice right now has sequenced every other bottle of bug juice on the market.

It's not like "they" don't already know what's in their competitors bottles

The people who don't know, are reefers. And there are a lot of reefers who actively don't want to know, "No, don't tell me what's in the blue bottle. I don't want to know"

Another question would be, is it really S marcescens. It could be a related strain

 

[Scott Campbell]

I have not, but I think it is an excellent tool to answer specific, focussed questions.

Testing of bacterial additives for composition, and what effects that has on the bacteria in a tank over time seems well suited for it.

Let me give another example that is both directly tied to the exact topic of this thread, and helps clarify my comments relating to folks potentially having different opinions on which bacteria are desirable vs undesirable.

Some readers here are aware of my hypothesis that the vilification of ammonia has lead to products that may actually do more harm than good, and are doing a disservice to the hobby. The constant drumbeat that nitrifiers are desirable and should be frequently added directly or promoted by adding media to house them may be hurting reef tanks. The hypothesis is that these actions cause ammonia to be converted to nitrate faster than it otherwise would, causing corals to have to use more energy to process nitrate than their preferred N source of ammonia.

Using these bacteria tools to determine which additives contain nitrifiers, and help some reefers possibly avoid them could be very useful . It could also help reefers understand what effects these additives and media additions or removal can have on the amount of nitrifying bacteria in their aquaria..

Thus, I am not at all against using the tool to answer specific questions. If folks have reasons to be concerned about problematic levels of pathogens, that too could be useful.

I’m much less convinced about other issues such as relating to biodiversity.

Randy

I found this article provides compelling evidence that bacterial diversity is indeed important in our aquariums and that monitoring the bacterial make-up of our tank (via tests by Aquabiomics) could be extremely helpful. It also supports my long-standing belief that sponges are a critically important component of a reef aquarium. I have no confidence bottled bacteria will be helpful in any way. But I do believe regularly adding live sand (from Tampa Bay Saltwater or Aquabiomics) provides an enormous benefit to the tank.

DOC is The Most Important Parameter For A Healthy Reef Tank: Here’s a New Method to Manage It | Reef Builders | The Reef and Saltwater Aquarium Blog

In this article, I will provide an overview of my take on the current zeitgeist of reefing and explain why the entire industry is ignoring a critical aspect of coral care. I will explain what issues…

reefbuilders.com

 

[Randy Holmes-Farley]

Randy

I found this article provides compelling evidence that bacterial diversity is indeed important in our aquariums and that monitoring the bacterial make-up of our tank (via tests by Aquabiomics) could be extremely helpful. It also supports my long-standing belief that sponges are a critically important component of a reef aquarium. I have no confidence bottled bacteria will be helpful in any way. But I do believe regularly adding live sand (from Tampa Bay Saltwater or Aquabiomics) provides an enormous benefit to the tank.

DOC is The Most Important Parameter For A Healthy Reef Tank: Here’s a New Method to Manage It | Reef Builders | The Reef and Saltwater Aquarium Blog

In this article, I will provide an overview of my take on the current zeitgeist of reefing and explain why the entire industry is ignoring a critical aspect of coral care. I will explain what issues…

reefbuilders.com

Thank you very much. I appreciate getting to read it.

I'll make a few comments on it since I strongly agree with some of it, and do not agree with some other aspects.

1. I agree that the effects of organics has always been a huge missing link in our understanding of reef aquaria. Some of these effects are mediated through (or caused by) microorganisms and others are not. Bacterial effects are likely an important aspect of the effects we see, but they should not be viewed as the only ones. Most of the organisms in our tanks can take up and use certain organics directly, and many are subject to toxic or inhibitory effects of other organics.

2. I think that for the reasons outlined in 1, studying the relationship between organics and bacterial populations and potential coral diseases is a great thing to study.

3. The discussion of sources and sinks of organic carbon in the article certainly seems reasonable.

4. I am much less convinced that DOC as a broad brush measure is the best way to get such info, but perhaps it is the only accessible one at the moment. As an analogy, if one wanted to get a correlation between heavy metals (which is a single standard test for pharmaceuticals, for example) and coral health, it would be hugely difficult to get a good understanding of the complexities since some are toxic, some are needed elements, and some are both depending on concentration. Why would we assume organics are not equally or more complicated (since there are far, far more different organics in a reef tank than there are different metals).

5. I'm a little concerned about the referenced literature studies of things like glucose showing changes in bacterial populations due to the extremely high levels tested to show an effect. It's like dosing an animal the human equivalent of 1,000 splenda packets a day and seeing an effect, so then reporting that splenda causes X. In one of the studies mentioned in the article, the amount of different sugars tested was 500 uM. In a second one is was 25 ppm glucose.

"Each treatment was amended with 500 μM of the corresponding sugars. The concentration was chosen to elicit rapid microbial responses"

Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton - The ISME Journal

Coastal pollution and algal cover are increasing on many coral reefs, resulting in higher dissolved organic carbon (DOC) concentrations. High DOC concentrations strongly affect microbial activity in reef waters and select for copiotrophic, often potentially virulent microbial populations. High...

www.nature.com

For glucose, 500 uM means 90 mg/L. That's 90 ppm of glucose. Ken Feldman, a reefer and scientist referred to in the article has shown total organic carbon levels of every organic added together is only on the order of 1-2 ppm. To add far more than that level of a single species seems like a great exaggeration of how much the natural DOC in a reef aquarium will drive particular species.

6. Again, while I'm not discounting the idea that reef tanks might be much better off at low average DOC, and I recommend doing so for many reasons, the simple idea of high total DOC from organic carbon dosing as a significant cause of coral disease seems to not correlate well with the large number of folks who do dose organic carbon and only rarely get a coral disease problem. It is certainly a real effect that some do, and has been a concern since the first days of organic carbon dosing, but it's importance might be somewhat downplayed by the fact that most people dosing large amounts of, say, acetic acid, do not detect coral problems. They may get bacterial shifts for sure. But in the absence of seeing a problem, then the issue becomes one of risk vs gain. FWIW, a moderate dose of 50 mL of vinegar a day into a 100 gallon tank is adding 7 ppm of acetic acid (2.6 ppm organic carbon). That exceeds Ken's values for the total of all DOC in a typical reef aquarium (1-2 ppm), and yet is only rarely associated with actually seen coral diseases. Thus, it seems reasonable to me that if DOC causes coral diseases, it is not all DOC, but some subset of DOC.

 

[Scott Campbell]

Thank you very much. I appreciate getting to read it.

I'll make a few comments on it since I strongly agree with some of it, and do not agree with some other aspects.

1. I agree that the effects of organics has always been a huge missing link in our understanding of reef aquaria. Some of these effects are mediated through (or caused by) microorganisms and others are not. Bacterial effects are likely an important aspect of the effects we see, but they should not be viewed as the only ones. Most of the organisms in our tanks can take up and use certain organics directly, and many are subject to toxic or inhibitory effects of other organics.

2. I think that for the reasons outlined in 1, studying the relationship between organics and bacterial populations and potential coral diseases is a great thing to study.

3. The discussion of sources and sinks of organic carbon in the article certainly seems reasonable.

4. I am much less convinced that DOC as a broad brush measure is the best way to get such info, but perhaps it is the only accessible one at the moment. As an analogy, if one wanted to get a correlation between heavy metals (which is a single standard test for pharmaceuticals, for example) and coral health, it would be hugely difficult to get a good understanding of the complexities since some are toxic, some are needed elements, and some are both depending on concentration. Why would we assume organics are not equally or more complicated (since there are far, far more different organics in a reef tank than there are different metals).

5. I'm a little concerned about the referenced literature studies of things like glucose showing changes in bacterial populations due to the extremely high levels tested to show an effect. It's like dosing an animal the human equivalent of 1,000 splenda packets a day and seeing an effect, so then reporting that splenda causes X. In one of the studies mentioned in the article, the amount of different sugars tested was 500 uM. In a second one is was 25 ppm glucose.

"Each treatment was amended with 500 μM of the corresponding sugars. The concentration was chosen to elicit rapid microbial responses"

Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton - The ISME Journal

Coastal pollution and algal cover are increasing on many coral reefs, resulting in higher dissolved organic carbon (DOC) concentrations. High DOC concentrations strongly affect microbial activity in reef waters and select for copiotrophic, often potentially virulent microbial populations. High...

www.nature.com

For glucose, 500 uM means 90 mg/L. That's 90 ppm of glucose. Ken Feldman, a reefer and scientist referred to in the article has shown total organic carbon levels of every organic added together is only on the order of 1-2 ppm. To add far more than that level of a single species seems like a great exaggeration of how much the natural DOC in a reef aquarium will drive particular species.

6. Again, while I'm not discounting the idea that reef tanks might be much better off at low average DOC, and I recommend doing so for many reasons, the simple idea of high total DOC from organic carbon dosing as a significant cause of coral disease seems to not correlate well with the large number of folks who do dose organic carbon and only rarely get a coral disease problem. It is certainly a real effect that some do, and has been a concern since the first days of organic carbon dosing, but it's importance might be somewhat downplayed by the fact that most people dosing large amounts of, say, acetic acid, do not detect coral problems. They may get bacterial shifts for sure. But in the absence of seeing a problem, then the issue becomes one of risk vs gain. FWIW, a moderate dose of 50 mL of vinegar a day into a 100 gallon tank is adding 7 ppm of acetic acid (2.6 ppm organic carbon). That exceeds Ken's values for the total of all DOC in a typical reef aquarium (1-2 ppm), and yet is only rarely associated with actually seen coral diseases. Thus, it seems reasonable to me that if DOC causes coral diseases, it is not all DOC, but some subset of DOC.

I am also not concerned about the effects of carbon dosing or additional algae growth in a refugium. Which the author states as possible issues. But my tank is filled with masses of sponges. So in addition to encouraging bacterial growth to lower nitrates, carbon dosing just feeds the sponges in my tank. But without sponges, too much carbon dosing may be adding to DOC levels which may encourage bacterial growth that is not beneficial to the corals. I suspect every tank has a different capacity to pull DOC out of the water column. Regarding algae - the author already admits you need a lot of herbivores. So algae is going to grow regardless. Additional algae growth in a refugium that also protects microfauna populations seems like a trivial worry.

I did find it interesting that corals need access to a varied selection of bacterial types to create the optimum holobiont. And that DOC can encourage bacterial growth that is at odds with the bacteria the corals prefer.

 

[Dan_P]

Thank you very much. I appreciate getting to read it.

I'll make a few comments on it since I strongly agree with some of it, and do not agree with some other aspects.

1. I agree that the effects of organics has always been a huge missing link in our understanding of reef aquaria. Some of these effects are mediated through (or caused by) microorganisms and others are not. Bacterial effects are likely an important aspect of the effects we see, but they should not be viewed as the only ones. Most of the organisms in our tanks can take up and use certain organics directly, and many are subject to toxic or inhibitory effects of other organics.

2. I think that for the reasons outlined in 1, studying the relationship between organics and bacterial populations and potential coral diseases is a great thing to study.

3. The discussion of sources and sinks of organic carbon in the article certainly seems reasonable.

4. I am much less convinced that DOC as a broad brush measure is the best way to get such info, but perhaps it is the only accessible one at the moment. As an analogy, if one wanted to get a correlation between heavy metals (which is a single standard test for pharmaceuticals, for example) and coral health, it would be hugely difficult to get a good understanding of the complexities since some are toxic, some are needed elements, and some are both depending on concentration. Why would we assume organics are not equally or more complicated (since there are far, far more different organics in a reef tank than there are different metals).

5. I'm a little concerned about the referenced literature studies of things like glucose showing changes in bacterial populations due to the extremely high levels tested to show an effect. It's like dosing an animal the human equivalent of 1,000 splenda packets a day and seeing an effect, so then reporting that splenda causes X. In one of the studies mentioned in the article, the amount of different sugars tested was 500 uM. In a second one is was 25 ppm glucose.

"Each treatment was amended with 500 μM of the corresponding sugars. The concentration was chosen to elicit rapid microbial responses"

Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton - The ISME Journal

Coastal pollution and algal cover are increasing on many coral reefs, resulting in higher dissolved organic carbon (DOC) concentrations. High DOC concentrations strongly affect microbial activity in reef waters and select for copiotrophic, often potentially virulent microbial populations. High...

www.nature.com

For glucose, 500 uM means 90 mg/L. That's 90 ppm of glucose. Ken Feldman, a reefer and scientist referred to in the article has shown total organic carbon levels of every organic added together is only on the order of 1-2 ppm. To add far more than that level of a single species seems like a great exaggeration of how much the natural DOC in a reef aquarium will drive particular species.

6. Again, while I'm not discounting the idea that reef tanks might be much better off at low average DOC, and I recommend doing so for many reasons, the simple idea of high total DOC from organic carbon dosing as a significant cause of coral disease seems to not correlate well with the large number of folks who do dose organic carbon and only rarely get a coral disease problem. It is certainly a real effect that some do, and has been a concern since the first days of organic carbon dosing, but it's importance might be somewhat downplayed by the fact that most people dosing large amounts of, say, acetic acid, do not detect coral problems. They may get bacterial shifts for sure. But in the absence of seeing a problem, then the issue becomes one of risk vs gain. FWIW, a moderate dose of 50 mL of vinegar a day into a 100 gallon tank is adding 7 ppm of acetic acid (2.6 ppm organic carbon). That exceeds Ken's values for the total of all DOC in a typical reef aquarium (1-2 ppm), and yet is only rarely associated with actually seen coral diseases. Thus, it seems reasonable to me that if DOC causes coral diseases, it is not all DOC, but some subset of DOC.

The author might not have understood the DDAM model and is possibly exaggerating the risk of DOC. The model is that as algae growth increases, it is their exudates that is feeding the bacteria and shifting the bacteria metabolism to the abundant carbohydrate. The DDAM authors aren’t talking about any ol’ DOC. And besides vinegar dosing and the popularity of using macro algae to manage nitrate levels seems to even go against the idea of there being consequences of elevated DOC from algae in the reef aquarium. As time allows, I will dig deeper into the references.

 

[Solo McReefer]

What does DDAM mean?

 

[SDchris]

What does DDAM mean?

DOC, Disease, Algae, Microbes
It describes a model in natural environments that shifts from a reduction in top predators (like sharks) to increased benthic algae and it's relationship to disease, algae and microbes.

 

[Dan_P]

What does DDAM mean?

Dissolved organic carbon (DOC), Disease, Algae, Microorganism. The model predicts that when the percent area coverage of macro algae on a reef increases, the amount of DOC decreases and there is an increase in bacteria biomass. The bacteria biomass increase also involves a shift to heavier populations of bacteria species that have the potential to cause disease.