Bacterial Analysis.

[ShaunW]

Here is where we lay out the designs. I would like to post this up so that all involved can provide any imput they may have and for full disclosure.

Christine, I've been thinking! :banghead:

So I think that we need to have a better experimental design from the beginning. I know what I would like to find out by our tests, they include:

1. Does the bacterioplankton of a reef tank compare to the natural environment?
2. How does husbandry affect this bacterial population?
3. Does bacterioplankton get affected by the very equipment that we put on reef tanks for nutrient depletion, i.e. skimmers, pumps, etc.
4. Finally, I want to put to rest the debate regarding protein skimmers removing bacteria in that I would like to know if they do or don't effectively remove bacteria, and if this is a good thing?
5. As an aside I would like to know if zeovit tanks have different bacterial populations and amounts.

Now as for our collaboration, I would like to know up front, what do you hope to determine (I told you my experimental plans above)?

I would like to have the scientific boundaries set beforehand since every scientific collaboration that I have had determines these issues in advance before a single experiment was performed. I'm sure the same is true in your job, .

Please let me know your thoughts.
Shaun.

 

[ShaunW]

So I think that we need to have a better experimental design from the beginning.

Agreed.

1. Does the bacterioplankton of a reef tank compare to the natural environment?

I like this question. Aside from quantity are you looking for some id? This is where it will get tricky/expensive--I have two ID systems here, but since most of these bacteria have not been identified and named they won't be in my databases. I can give a bit of a profile to distinguish one species from another, but for real ID we need to go to 16S ribosomal analysis.

2. How does husbandry affect this bacterial population?

yes, this is a bit of what I was getting at with water changes. do people who do huge frequent water changes decrease their available plankton? How about DSB/BB? This one will end up being very anecdotal though without setting up controlled tanks.

3. Does bacterioplankton get affected by the very equipment that we put on reef tanks for nutrient depletion.

Yes.

4. Finally, I want to put to rest the debate regarding protein skimmers removing bacteria in that I would like to know if they do or don't effectively remove bacteria, and if this is a good thing

This one will be a popular result IF we do it right--controls etc and not releasing data before it has been worked through. We can do this one once we get the other ones underway, as I think again we need controlled tanks, perhaps different skimmers etc.

5. As an aside I would like to know if zeovit tanks have different bacterial populations and amounts..

You know you're looking for trouble, right? What the hell, I could use a little excitement. If we do this one lets do more than just Zeovit--get a few different tank additives and compare. It will be more interesting, looking at several bottled additives, and will make it look less like we're out to mess with Zeovit.

My interests are somewhat evolving the more I read. In addition to how husbandry affects bacteria (which I think will be interesting to hobbyists) I am particulary interested in coral surface flora, how they vary from coral to coral within the same tank, and why/how that population difference is maintained. We know from literature that the types of bacteria found at the surface of the coral will be different from planktonic species because the available nutrients are much higher on an animal (mucus is a great food source). This may lead to some interesting things regarding sand beds (not only sand beds for denitrification, but as haven for bacteria), "sand stirring", old live rock versus newly imported, etc. Lots of interesting things there.

This ties in a bit to the projects I have proposed for my "real job", which will be to determine if corals/sponges/algae produce antimicrobial substances either exuded in the mucus or as surface-bound compounds to maintain their particular flora. Then, can I extract these compounds and use them? Right now when people do marine bioprospecting they harvest tons of organisms for analysis and then production--I am only going to look at things I can sustainably aquaculture on land, so that if I find a useful compound (for anything really--I'm going to collaborate here with a big lab in Germany that can do huge screens for all sorts of bioactivity) I can produce it with zero environmental impact.


Yes, let's set this all out well, so that we aren't redoing experiments later. Determine what resources we each have that can be useful, and plan out the sequence of things. Also, that way we can ask for the right type of samples from aquarists (and divers too) the first time...

thanks,
Christine

 

[masterswimmer]

Uuuhhhh, sounds good to me

Looking forward to reading the English version.

swimmer

 

[kimoyo]

Shaun/Christine,

Goodluck with this, looks like a very nice experiment.

 

[sihaya]

Well, this does look like a fun project. What are you guys going to do with the information you gather?

I recently proposed a hypothetical protein skimmer study design to Dr. Toonen and he was actually nice enough to write back with his input. Of course, it's not a study I could do myself. But if anyone is up for a project, I think you'd only need 6-9 tanks and they wouldn't even have to be completely identical.

 

[sihaya]

One thing... I haven't read this entire thread. But if someone hasn't already said it, I'd be careful not to confuse what the skimmer pulls out with what might be growing IN the body, cup, etc. of the skimmer itself. Bacteria grow really fast. So I'm sure there are plenty naturally growing in our skimmer cups that weren't necessarily pulled out by the skimmer itself.

 

[ShaunW]

One thing... I haven't read this entire thread. But if someone hasn't already said it, I'd be careful not to confuse what the skimmer pulls out with what might be growing IN the body, cup, etc. of the skimmer itself. Bacteria grow really fast. So I'm sure there are plenty naturally growing in our skimmer cups that weren't necessarily pulled out by the skimmer itself.

Christine and myself have discussed this at length. We have been trying to design an autoclavable skimmer cup. But it is more difficult than you think. However, sterile cups could also be used for collection, i.e. modify a 1L flask to fit on a skimmer.

 

[ShaunW]

Well, this does look like a fun project. What are you guys going to do with the information you gather?

We haven't decided but MR gets first DIBS, since both Christine and myself a loyal to this site.

I recently proposed a hypothetical protein skimmer study design to Dr. Toonen and he was actually nice enough to write back with his input. Of course, it's not a study I could do myself. But if anyone is up for a project, I think you'd only need 6-9 tanks and they wouldn't even have to be completely identical.

Could you provide more info, I would love to hear about the experimental design!

 

[sihaya]

Ok, I just read this post and eeeek! The first step in designing any study/trial/experiment is figuring out exactly what question you want to ask and if it can be answered and how. This is not as easy as it sounds. I'm telling you all right now, if you don't get the question right, you won't get the study right. This is part of my criticism of the Borneman-Lowe salt study (but that's in another thread).

So, now, let's look at these questions...

1. Does the bacterioplankton of a reef tank compare to the natural environment?

HUGELY complex question... what tank and what natural environment? when and where in said natural environment?

IMHO, this is just too big a question to start with... we need smaller steps.

2. How does husbandry affect this bacterial population?

Eek... an even bigger question!! Which bacterial, when? where? what kind of husbandry?

3. Does bacterioplankton get affected by the very equipment that we put on reef tanks for nutrient depletion, i.e. skimmers, pumps, etc.

This is a little better... still way too huge, but possibly managable if cut down. Maybe someone could start by look at one kind of bacterioplankton and one piece of equipment.

4. Finally, I want to put to rest the debate regarding protein skimmers removing bacteria in that I would like to know if they do or don't effectively remove bacteria, and if this is a good thing?

This might be a decent question, but it's going to be very tricky. As Christine and solbby are already trying to do, you'd have to find some way to distinguish bacteria growing in the skimmer from bacteria taken out by the skimmer. Then there's all the usual questions... what kinds of bacteria? which skimmers? etc...

I highly doubt this question will ever be "put to rest," but you could possible take one a look a the question with a clever study (the design of which is escaping me right now, but I suspect it's possible).

5. As an aside I would like to know if zeovit tanks have different bacterial populations and amounts.

I don't think this question will ever get answered (assuming it even could be). For one thing, we don't even know exactly what kinds zeolithe rocks zeovit is selling, if they're consistent or anything about them. But please, don't get me started on zeovit. I can just feel my blood pressure rising already.


But, like I said, I'm no expert. But I do have experience in scientific research (medical research), I've written a grant proposal, published a research paper, etc. So I do know the basics. And for what it's worth, I think you guys should take this great info you're collecting and use it to come up with one or a few good questions that you can try to answer (or find some way to narrow your huge questions down).

 

[sihaya]

But it is more difficult than you think. However, sterile cups could also be used for collection

Oh I never thought it would be easy at all!! lol But I think it's really cool that you guys are experimenting with this! :cheers:

 

[sihaya]

Btw, even though I'm in Cleveland, I'm so glad I found you all. I had no idea there were so many geeky, smart and ambitious reefers in any one spot. You even have a scientific papers sticky! Seriosuly you guys, I have an urge to move to NY now (not that I haven't had that urge many times before though...).

Sorry for not being able to spend more time on this thread right now. I'm in the middle of exams and my head is spinning. I mean, seriously, can y'all believe the EPA took 54 PAGES to define "sold waste" ?!?!

 

[Harif87]

Hey Solby, when you get your results be sure to explain in layman's terms aslo, im no bio expert (not yet anyway) but i would like to fully understand your conclusion. Also i think it would be great if, once you decide on a final procedure, post it in a single post with the steps you took. I find this thread to be all over the place, but thats just me

 

[ShaunW]

FANTASTIC! So happy you can join us! Maybe we can fly you in for one of our fragswaps! So to address your excellent points, I would like to explain myself better, since we have the same philosophy regarding experimental design, i.e. one question, limit the variables, QC, reproducible results, provide positive and negative controls:

Ok, I just read this post and eeeek! The first step in designing any study/trial/experiment is figuring out exactly what question you want to ask and if it can be answered and how. This is not as easy as it sounds. I'm telling you all right now, if you don't get the question right, you won't get the study right. This is part of my criticism of the Borneman-Lowe salt study (but that's in another thread).

So, now, let's look at these questions...

1. Does the bacterioplankton of a reef tank compare to the natural environment?

HUGELY complex question... what tank and what natural environment? when and where in said natural environment?

IMHO, this is just too big a question to start with... we need smaller steps.

So the first question is strickly in terms of bacterial counts. Is the number of bacteria the same in reef tanks verse the standard planktonic 1x106 bacteria/mL population commonly found in natural reefs (please understand that this number changes from reef to reef and from day to night, but in general the planktonic bacterial populations in the wild (bacterioplankton) are relatively well know and studied. Plenty of literature to fall back on for support.).

2. How does husbandry affect this bacterial population?

Eek... an even bigger question!! Which bacterial, when? where? what kind of husbandry?

Does feeding increase the population like the wild. Does having a skimmer verse not having one change the population. Do pumps and filter socks change the population. Does the population change from nocturnal to day? (these are many additional questions but can be easily address on one tank).

3. Does bacterioplankton get affected by the very equipment that we put on reef tanks for nutrient depletion, i.e. skimmers, pumps, etc.

This is a little better... still way too huge, but possibly managable if cut down. Maybe someone could start by look at one kind of bacterioplankton and one piece of equipment.

4. Finally, I want to put to rest the debate regarding protein skimmers removing bacteria in that I would like to know if they do or don't effectively remove bacteria, and if this is a good thing?

This might be a decent question, but it's going to be very tricky. As Christine and solbby are already trying to do, you'd have to find some way to distinguish bacteria growing in the skimmer from bacteria taken out by the skimmer. Then there's all the usual questions... what kinds of bacteria? which skimmers? etc...

I highly doubt this question will ever be "put to rest," but you could possible take one a look a the question with a clever study (the design of which is escaping me right now, but I suspect it's possible).

5. As an aside I would like to know if zeovit tanks have different bacterial populations and amounts.

I don't think this question will ever get answered (assuming it even could be). For one thing, we don't even know exactly what kinds zeolithe rocks zeovit is selling, if they're consistent or anything about them. But please, don't get me started on zeovit. I can just feel my blood pressure rising already.


But, like I said, I'm no expert. But I do have experience in scientific research (medical research), I've written a grant proposal, published a research paper, etc. So I do know the basics. And for what it's worth, I think you guys should take this great info you're collecting and use it to come up with one or a few good questions that you can try to answer (or find some way to narrow your huge questions down).

As for the others, so many reefers automatically assume that a skimmer will affect the planktonic bacterial population. It is dogma, however, NOBODY has ever proved it, nor have they ever show ANY information about it! So why is it DOGMA (I hate dogmatic ideas :tongue1: ). Take the whole concept of zeovit for example, it depends on this dogma being true.

As for actual bacterial culturing and IDing of various strains/populations, well this would be the hardest thing to do, and realistically I don't think I want to address it. Marine microbiology has many hurdles, jumping them would be hard. However, Christine is going to culture bacteria from corals. Maybe she can comment further.

 

[ShaunW]

Hey Solby, when you get your results be sure to explain in layman's terms aslo, im no bio expert (not yet anyway) but i would like to fully understand your conclusion. Also i think it would be great if, once you decide on a final procedure, post it in a single post with the steps you took. I find this thread to be all over the place, but thats just me

No problem. Right now we are still in the experimental design stage. However the pilot has begun in that the tubes for sample collection have been sent.

Christine and myself haven't fully figured out how we will present the results but most likely it will be in the form of a article. So I will put it all in layman's terms when the time comes.

 

[jackson6745]

One thing... I haven't read this entire thread. But if someone hasn't already said it, I'd be careful not to confuse what the skimmer pulls out with what might be growing IN the body, cup, etc. of the skimmer itself. Bacteria grow really fast. So I'm sure there are plenty naturally growing in our skimmer cups that weren't necessarily pulled out by the skimmer itself.

Um, would the purpose of this proposed study try to discredit the function of a skimmer?

 

[prattreef]

Nice to see this moving forward. When were the tubes sent, so I can keep an eye out for them? Randy

 

[prattreef]

I don't think so Rich. Just the claim that it is primarily bacteria that skimmers are removing and as an extension the claims of some reef products that such bacterial action is the main mechanism by which these products work. RD

 

[ShaunW]

Um, would the purpose of this proposed study try to discredit the function of a skimmer?

Not at all Rich! It is impossible to discredit a skimmer since its importance for a reef tank is FACT and UNQUESTIONABLE!

But we could possible say which skimmers are better than others with a quantitative measurement, instead of the arbitrary bubble size and statements such as "my corals look better". Also if bacterial removal happens.

 

[Harif87]

Um, would the purpose of this proposed study try to discredit the function of a skimmer?

(never mind lol), but personally i think that the idea of the must have skimmer needs to be put under the microscope. Not to discredit it, but to fully understand what and how much of it does the skimmer pull out.

 

[ShaunW]

Nice to see this moving forward. When were the tubes sent, so I can keep an eye out for them? Randy

Not 100% sure but Tuesday possibly was the day. Christine sent them out (I hope). Otherwise they will go out ASAP. We just had to "iron out" the instructions.