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

[SMSREEF]

Who here has seen bacteria they think are in a sample and are not using oil immersion?

if you're not on leica you aint seeing bacteria (in someone's home, aware labs might have other approaches though I don't know of any. it had to be oil immersion/ $1500 scope back when I was in the game at a meatpacking plant)

I haven’t. Only algae, protists and the lagers cells. Even if we have a good scope, probably the best ID we could make is Gram- or Gr+ bacteria.

Labs can use DNA testing and other testing for an ID.

 

[SMSREEF]

I have to disagree here, diversity has a clearly defined meaning.

And diversity has been strongly associated with ecosystem functions in a variety of settings, including coral reefs.

Intact, functional reefs have higher diversity in the water column bacteria than degraded reefs.

New tanks, or dry rock tanks, have far lower diversity than established or live rock tanks.

There are many questions to be asked about diversity, but its not a buzzword, its a concept that has been central to the study of Ecology for a century or more.

I agree with you about diversity being key in a reef tank. I have anecdotal evidence from my 60 cube I set up with dead rock and bagged “live” sand which is just dead with likely some bacterial spores.

I had nothing but problems at first with nuisance microbes getting out of control. I used many different bottles bacteria products and they did not help.

I credit adding real live rock with micro fauna and live sand from the Keys with increasing the diversity in the tank and allowing there to be competitors to the other microbes that were out of control.

Diversity means competition. Competition means no one thing is going to be able to overpopulate.

just look at what happens in the human gut. A person can be living with C Diff and never have a problem until they are put on an antibiotic that kills off some of the diversity in the gut. Without the competition, C Dfff numbers explode and the person gets sick.

Heck, Medicine is now using fecal transplants to cure C Diff infections to increase the “diversity” of the gut bacterial strains.

A live sand transplant or live rock transplant from a reef when a tank is having issues seems like a good idea to me.

 

[taricha]

Who here has seen bacteria they think are in a sample and are not using oil immersion?

some of the organisms present here in this sample I took of Brown Jelly I believe are bacteria. A few have a spirochete-like form. (I could be wrong and none of the ~1 micron wiggles are bacteria.) This is just 400x compound microscope + max smartphone zoom. Brown round cells are zooxanthellae (~10 microns) for scale.

 

[brandon429]

That’s neat I’d never heard of ones viewable at 400 but with all the new discoveries such as nitrification being taken on by multiple genera surely there are sizes variants tbd as well

 

[Hans-Werner]

If you take a fresh substrate sample from the tank you will hardly find bacteria with 400 x magnification. If the sample contains some organics and detritus and you forget about the sample in your backbag and you find it a few days later you will find bacteria with 400 x magnification. The rotting bacteria are bigger than the "normal" bacteria under low nutrient conditions.

 

[MnFish1]

Who here has seen bacteria they think are in a sample and are not using oil immersion?

if you're not on leica you aint seeing bacteria (in someone's home, aware labs might have other approaches though I don't know of any. it had to be oil immersion/ $1500 scope back when I was in the game at a meatpacking plant)

You do not need oil immersion to see bacteria you can see them with magnifications of 400x. More detail with 1000x. There are microscopes that do 1600 x - online (google) - for less than 200$

 

[MnFish1]

I haven’t. Only algae, protists and the lagers cells. Even if we have a good scope, probably the best ID we could make is Gram- or Gr+ bacteria.

Labs can use DNA testing and other testing for an ID.

IMO, microscopes are not used to identify bacterial strains. You can tell motile vs non-motile, You can tell cocci from rods, etc. Gram stains are used to divide bacteria into 2 broad categories - then they are further identified by various culture techniques - or more frequently now-a days - genetic analysis.

 

[MnFish1]

I agree with you about diversity being key in a reef tank. I have anecdotal evidence from my 60 cube I set up with dead rock and bagged “live” sand which is just dead with likely some bacterial spores.

I had nothing but problems at first with nuisance microbes getting out of control. I used many different bottles bacteria products and they did not help.

I credit adding real live rock with micro fauna and live sand from the Keys with increasing the diversity in the tank and allowing there to be competitors to the other microbes that were out of control.

Diversity means competition. Competition means no one thing is going to be able to overpopulate.

just look at what happens in the human gut. A person can be living with C Diff and never have a problem until they are put on an antibiotic that kills off some of the diversity in the gut. Without the competition, C Dfff numbers explode and the person gets sick.

Heck, Medicine is now using fecal transplants to cure C Diff infections to increase the “diversity” of the gut bacterial strains.

A live sand transplant or live rock transplant from a reef when a tank is having issues seems like a good idea to me.

Last things first - The goal of fecal transplants is to out-compete C. diff. As you said, C. diff is caused because a lot of 'normal flora' is wiped out by antibiotics. Thus - C. Diff overgrows. Fecal transplants are used RARELY - most of the time C.Diff is killed by antibiotics that do not kill common 'gut' bacteria. But - in an analogy to our tanks - if you did a fecal transplant in a 'normal person' - they would not have a more 'diverse' bacterial population necessarily.

From a literature standpoint - from my reading - adding bacteria to an already established tank does not necessarily result in more 'diversity' - though the population may change.

From a personal experience standpoint - My tank was set up with 'dry rock' and bacteria. within 3 months my 'dead rock' was 'live rock' from a bacterial standpoint. To me one of the debate issues mentioned here is the assumption that the more bacteria you have the better. This, I think is incorrect.

 

[MnFish1]

some of the organisms present here in this sample I took of Brown Jelly I believe are bacteria. A few have a spirochete-like form. (I could be wrong and none of the ~1 micron wiggles are bacteria.) This is just 400x compound microscope + max smartphone zoom. Brown round cells are zooxanthellae (~10 microns) for scale.

The small rapidly moving things appear to be motile bacteria (the swimming ones) - it's impossible (as you said) - to determine whether some of the other 'spots' are detritus - or non-motile bacteria - and there is no way to tell.

 

[AquaBiomics]

the one problem as I think you remember - one test from my tank showed one of the least diverse. another from mt tan was one of the most diverse... I thin different measurement parameters in the same tank can give widely divergent results

I'm not sure we ever reviewed a full key to your unknown samples - maybe I missed a post or message. I'd be curious to hear more. I seem to remember, wasnt your very diverse tank sample collected after you intentionally stirred up your tank in some way?

My tests of duplicate samples from the same tank have shown nearly identical diversity scores. Even measurements taken a month apart have typically shown very similar scores, aside from perturbations like the introduction of a diseased coral or live sand.

 

[MnFish1]

I have to disagree here, diversity has a clearly defined meaning.

And diversity has been strongly associated with ecosystem functions in a variety of settings, including coral reefs.

Intact, functional reefs have higher diversity in the water column bacteria than degraded reefs.

New tanks, or dry rock tanks, have far lower diversity than established or live rock tanks.

There are many questions to be asked about diversity, but its not a buzzword, its a concept that has been central to the study of Ecology for a century or more.

This is a good point - that said - we're not talking about broad ecological systems - like a reef or a rainforest. I'm not sure where there is evidence that suggests that merely increasing diversity will help a tank. While I can see your points of the observations about new vs live rock vs established tanks - and bacteria levels in teh water column - part of me tends to wonder about correlation and causation. I.e. is the low bacteria diversity in the water column of a 'poorly functioning tank' a result of whatever caused the poor functioning - or is it a result of the lack of diversity

 

[AquaBiomics]

Is that genus found in reef tank samples

Although there are plenty of other members of the family Thiotrichaceae, nearly all of which are classified to the genus level, I don't see any evidence of Beggiatoa in samples I've taken.

 

[brandon429]

Im still shocked to know you can see bacteria even as aggregates at 400x, any strain we'd encounter from a reef... always something new in biology that really wows me

 

[MnFish1]

I'm not sure we ever reviewed a full key to your unknown samples - maybe I missed a post or message. I'd be curious to hear more. I seem to remember, wasnt your very diverse tank sample collected after you intentionally stirred up your tank in some way?

My tests of duplicate samples from the same tank have shown nearly identical diversity scores. Even measurements taken a month apart have typically shown very similar scores, aside from perturbations like the introduction of a diseased coral or live sand.

Yes - that was the only difference - I can tell you all of them now if you like - it could be an interesting part of the discussion:
Sample ----- Description
121 - Sample of RO water - and swab RO container (just to see)
122 - Saliva and skin swab
123 - Mid day, Middle water - swab of side of tank
124 - Mid day, after creating strong flow over the live rock - and a swab of the live rock itself
125 - Duplicate of Sample 123 (a type of control)
126 - Mid Day, Sump water, and swab of side of sump
127 - Intake of skimmer and Swab of Skimmate container
128 - Fixative only (negative control)

 

[AquaBiomics]

This is a good point - that said - we're not talking about broad ecological systems - like a reef or a rainforest. I'm not sure where there is evidence that suggests that merely increasing diversity will help a tank. While I can see your points of the observations about new vs live rock vs established tanks - and bacteria levels in teh water column - part of me tends to wonder about correlation and causation. I.e. is the low bacteria diversity in the water column of a 'poorly functioning tank' a result of whatever caused the poor functioning - or is it a result of the lack of diversity

I definitely agree that correlation vs causation has not been established here.

Even if we interpret these relationships as causal - and conclude that increasing diversity has a benefit - in my view, diversity itself is probably not the real cause. Even if we were able to demonstrate that increasing diversity had a benefit, I suspect the real underlying reason would be that we had increased the levels of specific beneficial types of microbes.

Its easy to construct hypothetical examples where increasing the diversity can be detrimental (e.g. adding a bunch of novel pathogens), or where decreasing the diversity is beneficial (e.g. by introducing silver bullet drugs that selectively kill only a specific set of pathogens).

The apparent benefits of diversity, in my view, probably stem from the aggregate benefits of a large number of interacting microbes, whose many functions in the marine ecosystem we have barely scratched the surface on understanding.

Lacking that knowledge, I think increasing diversity is a reasonable strategy for trying to introduce the unknown beneficial microbes from the ocean into our tank ecosystems. (*as long as its from a source we can rationally expect to house natural marine microbial communities)

 

[MnFish1]

I definitely agree that correlation vs causation has not been established here.

Even if we interpret these relationships as causal - and conclude that increasing diversity has a benefit - in my view, diversity itself is probably not the real cause. Even if we were able to demonstrate that increasing diversity had a benefit, I suspect the real underlying reason would be that we had increased the levels of specific beneficial types of microbes.

Its easy to construct hypothetical examples where increasing the diversity can be detrimental (e.g. adding a bunch of novel pathogens), or where decreasing the diversity is beneficial (e.g. by introducing silver bullet drugs that selectively kill only a specific set of pathogens).

The apparent benefits of diversity, in my view, probably stem from the aggregate benefits of a large number of interacting microbes, whose many functions in the marine ecosystem we have barely scratched the surface on understanding.

Lacking that knowledge, I think increasing diversity is a reasonable strategy for trying to introduce the unknown beneficial microbes from the ocean into our tank ecosystems. (*as long as its from a source we can rationally expect to house natural marine microbial communities)

I see one issue with the logic - Once the diverse population is established - lets say after adding ocean water - what happens to it? the stronger species survive - and the weaker ones die off - resulting in less diversity (if any of the added bacteria survive in the first place) - so - to me this implies that to maintain 'diversity' - which we don't know is beneficial in a reef tank to begin with - we have to keep adding more and more bacteria/ocean water - and with each addition - increase the likelihood of adding 'problems'. Right?

 

[SMSREEF]

Last things first - The goal of fecal transplants is to out-compete C. diff. As you said, C. diff is caused because a lot of 'normal flora' is wiped out by antibiotics. Thus - C. Diff overgrows. Fecal transplants are used RARELY - most of the time C.Diff is killed by antibiotics that do not kill common 'gut' bacteria. But - in an analogy to our tanks - if you did a fecal transplant in a 'normal person' - they would not have a more 'diverse' bacterial population necessarily.

From a literature standpoint - from my reading - adding bacteria to an already established tank does not necessarily result in more 'diversity' - though the population may change.

From a personal experience standpoint - My tank was set up with 'dry rock' and bacteria. within 3 months my 'dead rock' was 'live rock' from a bacterial standpoint. To me one of the debate issues mentioned here is the assumption that the more bacteria you have the better. This, I think is incorrect.

I guess it’s all dependent on what you consider “live rock”. I do not consider dead rock with a film of nitrifying bacteria live rock. But I know a lot of people and businesses do. That’s kind the problem with reefing, there are no rules with this. How in the world are they selling “dry live rock”?

I think dead rock would take years to be truely be considered “live”. Even if placed in the ocean like KP or TBS do.

There is plenty of anecdotal evidence on the board of the problems people have with new tanks started with dead rock. It certainly seems a lot worse than it was when we started with live rock 20 years ago. But maybe its due to the ability to keep nutrients so low nowadays.

Back to C Diff... Fecal transplants are rarely used, but they are the most effective tool for antibiotic resistant C Diff. It saved one of my family member’s lives.

My comparison was not meant to say a bacteria transplant in an established tank would be a good thing. I do think there is evidence that a transplant in a new tank or one that has an organism that is growing out of control has benefits.

My problem was chrysophytes and the live rock and sand transplant really made a difference in my tank.

 

[MnFish1]

I guess it’s all dependent on what you consider “live rock”. I do not consider dead rock with a film of nitrifying bacteria live rock. But I know a lot of people and businesses do. That’s kind the problem with reefing, there are no rules with this. How in the world are they selling “dry live rock”?

I think dead rock would take years to be truely be considered “live”. Even if placed in the ocean like KP or TBS do.

There is plenty of anecdotal evidence on the board of the problems people have with new tanks started with dead rock. It certainly seems a lot worse than it was when we started with live rock 20 years ago. But maybe its due to the ability to keep nutrients so low nowadays.

Back to C Diff... Fecal transplants are rarely used, but they are the most effective tool for antibiotic resistant C Diff. It saved one of my family member’s lives.

My comparison was not meant to say a bacteria transplant in an established tank would be a good thing. I do think there is evidence that a transplant in a new tank or one that has an organism that is growing out of control has benefits.

My problem was chrysophytes and the live rock and sand transplant really made a difference in my tank.

Thanks - yes - I wasn't talking just about nitrifying bacteria. Every time you add a piece of coral - or a fish or a CUC or anything else - you will add other bacteria - which will populate its own 'niche'. I guess one way to see that thats true - is look at the speed that Coraline algae grows in a 'new' - dry rock tank. (And Coraline algae grows slowly as compared to bacteria) very few people 'add Coraline algae' directly - but over months - assuming conditions are correct - it spreads. Here is something I'd be interested in hearing your opinion about - Take a fish store - They set up a frag tank - with a filter, etc - My GUESS is that they do not leave it to cycle for 3-6 weeks-months as some do here (because nothing good occurs quickly in the hobby, right) - yet they can grow SPS. Most LFS I see (who have frag tanks) - do not have Dinos or brown algae covering everything. This is my anecdotal opinion - the reason for 'the uglies' with new tanks - dry rock is perhaps a diversity issue - but were this teh case - it would be rapidly solved by adding ocean water - or live sand. I think it more relates to not putting enough living stuff (Coral) and leaving large areas of bare rock - but thats my heretical opinion:)

 

[SMSREEF]

Thanks - yes - I wasn't talking just about nitrifying bacteria. Every time you add a piece of coral - or a fish or a CUC or anything else - you will add other bacteria - which will populate its own 'niche'. I guess one way to see that thats true - is look at the speed that Coraline algae grows in a 'new' - dry rock tank. (And Coraline algae grows slowly as compared to bacteria) very few people 'add Coraline algae' directly - but over months - assuming conditions are correct - it spreads. Here is something I'd be interested in hearing your opinion about - Take a fish store - They set up a frag tank - with a filter, etc - My GUESS is that they do not leave it to cycle for 3-6 weeks-months as some do here (because nothing good occurs quickly in the hobby, right) - yet they can grow SPS. Most LFS I see (who have frag tanks) - do not have Dinos or brown algae covering everything. This is my anecdotal opinion - the reason for 'the uglies' with new tanks - dry rock is perhaps a diversity issue - but were this teh case - it would be rapidly solved by adding ocean water - or live sand. I think it more relates to not putting enough living stuff (Coral) and leaving large areas of bare rock - but thats my heretical opinion:)

I see your points. I think we are kinda saying the same thing. Adding living stuff makes a more functional ecosystem in the tank. In adding the corals and life you talk about, you also add other microbes. In adding live sand and live rock you do too. I don’t know if I would put ocean water in that same category though.

About the fish store, My guess is that they would not cycle a tank for 6 months either, but would probably start with some good live rock from other tanks (at least in the sump). Also the blues would likely be turned up so high that you would never see anything brown;)

 

[flampton]

I have to disagree here, diversity has a clearly defined meaning.

And diversity has been strongly associated with ecosystem functions in a variety of settings, including coral reefs.

Intact, functional reefs have higher diversity in the water column bacteria than degraded reefs.

New tanks, or dry rock tanks, have far lower diversity than established or live rock tanks.

There are many questions to be asked about diversity, but its not a buzzword, its a concept that has been central to the study of Ecology for a century or more.

As long as you're talking about bottled products, I absolutely agree. Of course live sand, mud, and rock add a lot of new microbial diversity.

Agreed, this pattern is still holding up in the data I have in hand. (Although there are so few old tanks that the high end of the curve remains sparser than I would like)

I definitely agree that correlation vs causation has not been established here.

Even if we interpret these relationships as causal - and conclude that increasing diversity has a benefit - in my view, diversity itself is probably not the real cause. Even if we were able to demonstrate that increasing diversity had a benefit, I suspect the real underlying reason would be that we had increased the levels of specific beneficial types of microbes.

Its easy to construct hypothetical examples where increasing the diversity can be detrimental (e.g. adding a bunch of novel pathogens), or where decreasing the diversity is beneficial (e.g. by introducing silver bullet drugs that selectively kill only a specific set of pathogens).

The apparent benefits of diversity, in my view, probably stem from the aggregate benefits of a large number of interacting microbes, whose many functions in the marine ecosystem we have barely scratched the surface on understanding.

Lacking that knowledge, I think increasing diversity is a reasonable strategy for trying to introduce the unknown beneficial microbes from the ocean into our tank ecosystems. (*as long as its from a source we can rationally expect to house natural marine microbial communities)

Well that was quite a ride. Disagrees that diversity in the reef forum world has become a buzzword, and that it has a clearly defined meaning..

Then says adding bottled bacteria is probably not adding diversity. When by definition it does....

Then says well it's probably not the diversity but getting an aggregate of unknown beneficial microbes that's probably important. And that by throwing live rock and live sand in that we're attempting to introduce this consortium. That by increasing 'diversity' will hopefully get more beneficial organisms. Thus straight up repeating what I've said (see below). Yet then saying the diversity must come from marine sources. So not really looking for diversity, but specifc groups from specifc locations.

So the definition of this word diversity has taken on various meanings within your own comments. And is not the actual definition of diversity which has no positive or negative connotations. It's just a measure of the amount of different things in a fixed space. And increasing diversity is increasing the amount of new things.

https://www.merriam-webster.com/dictionary/buzzword
So tell me again how is the ill-defined and very in style reefing word 'diversity' not a buzzword???

This is what I said originally....
Diversity is a buzzword that unfortunately doesn't mean anything. What you want is to establish a ecosystem that by design (and luck) will allow the flow of nutrients added or produced in the tank to benefit the organisms of interest while limiting the pest organisms. Which means that you'll likely have to add marine sourced substrates as there is no product on the shelves that has the organisms you'll likely need to be successful, especially early on. Now this could be said you're adding diversity. I get that. But I can also go in my backyard and grab some dirt and throw that in, again diversity.