Bacterial Diversity Methods

[Agathos]

Do bacteria suffer after a long period of inbreeding as animals do?

No, they reproduce asexually creating almost identical clones of themselves.

Would the bacteria that were initially started in my tank in 1972 still be re producing?Just a theory.

If they were well adapted to your tank when they were first introduced, and the tank has not changed a lot, yes. The chances are very high that your tank now contains descendants of the bacteria that was introduced initially.

I don't know what bacteria are prevalent in reef tanks, but a fairly common marine bacteria is Vibrio natriegens. This is actually the fastest growing bacteria I am aware of. Under ideal conditions it can divide every 11 minutes! (Ideal conditions means that everything it needs for growth and division is available in excess, of course such conditions over time are only found in artificial labs environments.) If this bacterium is in your tank and has been there since the start, (this is pure guesswork from my side), and we say that it has divided every 120 minutes rather than every 11 minutes (since the conditions are far from ideal), what you have now in your tank is the 166440th generation of this organism . (Lots of generation for adaptive evolution, so the descendants could quite well be evolved to fit your tank better, let's call it Vibrio paulius. Actually, that is probably more generations than what we humans so far have been through since our species came to be).

 

[capnfritz]

My initial response would be YES - in favor of bio diversity.
But....it would still need to be nutured, and supplimented with "refreshing" doses of given cultures.

So, it seems to me that we would still want or find it desireable to do so in a more knowing manner, lest we have more problems to tend to!

Thats my point exactly.

 

[Agathos]

Off topic elaboration on bacteria and inbreeding:

Inbreeding is what happens when closely related individuals reproduce sexually, e.g. by sharing genes. Closely related individuals have a higher probablility of sharing some detrimental allele (gene copy that is usually masked by a "healthy" gene copy). Offspring of such matings could results in two copies of "sick" allele and no copies of the "healthy" allele, resulting in different problems. That's why you shouldn't have children with your siblings, or cousings, and why in most cultures this is regarded as taboo.

Bacteria do not breed at all, they reproduce through asexual division, or "cloning". So offspring will, in theory, by identical to their parent. If the parent enjoys a specific reef tank, the progeny should, too. They are all equally genetically equipped to thrive under those conditions. There is no degradation of the genetic material in the population (inbreeding does not cause "degradation of the genepool, either, just unfortunate combinations of specific alleles).

 

[Agathos]

Thats my point exactly.

I have some colleagues that work on studying bacterial populations in marine environments. I could talk to them and hear how much it would cost to add samples from reefs to their current work. Ideally we should follow the fate of one reef tank from set-up and through the years, but it could also be interesting to see the differences between a handful reef tanks with different age, to see if there's a general trend that older reefs contain less bacterial diversity.

More technically, what this study would involve is cloning of DNA from the reef tank (free DNA would be found everywhere, and can easily be amplified) and then sequence this DNA in an effort to establish what species it originates from. Such methods not only identify the bacteria present, but can also be used to quantify relative numbers of different species.

 

[mhaith]

I have some colleagues that work on studying bacterial populations in marine environments. I could talk to them and hear how much it would cost to add samples from reefs to their current work. Ideally we should follow the fate of one reef tank from set-up and through the years, but it could also be interesting to see the differences between a handful reef tanks with different age, to see if there's a general trend that older reefs contain less bacterial diversity.

More technically, what this study would involve is cloning of DNA from the reef tank (free DNA would be found everywhere, and can easily be amplified) and then sequence this DNA in an effort to establish what species it originates from. Such methods not only identify the bacteria present, but can also be used to quantify relative numbers of different species.

What would be quite interesting is to also track some of the specific traits of each tank to identify beneficial bacterial strains that can outcompete cyano or specifically consume some of the nasties in our tanks.
Just think, a bacterial dose(s) that specifically targets flatworms, ich, etc.?

(Maybe if we can identify specific commercial viability, funding will appear?)

 

[cmbspd]

While technically correct that bacteria don't reproduce sexually, bacteria actually trade quite a lot genes among clones and even "species". This happens through viral infections and also specific behaviors, called conjugation, where bacteria trade small fragments of DNA called plasmids that contain one or a few genes. This helps to explain how antibiotic resistant traits can quickly spread across a population of bacteria.

It is also a potential mechanism by which introducing a new bacterial culture could influence much of the tank community without necessarily reaching high levels. You could easily be introducing a gene for a utilizing some nutrient that the existing bacteria cannot metabolize for instance.

Bacteria also have very high mutation rates so that it doesn't take too many generations before "clones" are genetically distinguishable from their parents. And with bacteria, generation times are in tens of minutes!

Off topic elaboration on bacteria and inbreeding:

Inbreeding is what happens when closely related individuals reproduce sexually, e.g. by sharing genes. Closely related individuals have a higher probablility of sharing some detrimental allele (gene copy that is usually masked by a "healthy" gene copy). Offspring of such matings could results in two copies of "sick" allele and no copies of the "healthy" allele, resulting in different problems. That's why you shouldn't have children with your siblings, or cousings, and why in most cultures this is regarded as taboo.

Bacteria do not breed at all, they reproduce through asexual division, or "cloning". So offspring will, in theory, by identical to their parent. If the parent enjoys a specific reef tank, the progeny should, too. They are all equally genetically equipped to thrive under those conditions. There is no degradation of the genetic material in the population (inbreeding does not cause "degradation of the genepool, either, just unfortunate combinations of specific alleles).

 

[Paul B]

If this dies, for instance from some antibiotics produced by another organism added to the tank, or from some unfavourable shift in tank parameters, or something else, this could potentially have very bad consequences for the tank. I don't know how likely this is, though.

I think it is very likely in many tanks. Especially older tanks. I have personally used Chemi Clean and Red Slime remover many times over the years. Red Slime remover is basically an antibiotic that would tend to kill (or weaken) some but not all types of bacteria. Also in the beginning the tank had copper in it continousely for a couple of years. If any of you remember, before reef tanks, ich was very prevelant and we used copper extensively. I am not sure what that did to the bacterial diversity but I would imagine it could shift the numbers of dominent bacteria to a different type that was more resistant to copper or an antibiotic.
In that case, I would assume adding "wild" bacteria from the sea "may" have a positive effect.
Do any of you have a theory as to why ich does not seem to effect my tank, could bacterial additions possably have anything to do with that?

 

[ctripi]

Could any of the microbiolgists comment regarding the risk/benefits of carbon dosing ? If this is off topic please disregard.

My thoughts that this might result in a fragile situation favoring a narrow spectrum of bacterial species. This seems hazardous and potentiates those tanks for crash if husbandry is less than perfect. I mean, dosing carbon sources to help with nutrient issues already suggests less than biologically-balanced husbandry right?

Might I also risk disagreeing with Randy regarding risk of die-off. My understanding that a die-off, aside from leading to a cycling of sort, liberates endo/exotoxins that might again promote whole tank distress in various ways.

 

[Agathos]

What would be quite interesting is to also track some of the specific traits of each tank to identify beneficial bacterial strains that can outcompete cyano or specifically consume some of the nasties in our tanks.
Just think, a bacterial dose(s) that specifically targets flatworms, ich, etc.?

(Maybe if we can identify specific commercial viability, funding will appear?)

I don't know if this would be possible. Cyanobacteria are especially adapted to thrive under very specific conditions. Under these very specific conditions cyano bacteria are the bacteria that will grow and dominate. The best way to change this is to make the conditions less suitable for cyanos and more suitable for the bacteria you want. So out-competition of cyano under conditions where cyano are evolved to function optimally, I think could be hard. What we do instead is change the water chemistry (adjust concentrations of phosphates, nitrates, etc) to make the environment slightly less suitable for cyano and slightly more suitable for the beneficial bacteria, causing a shift in population sizes where the cyano population again becomes small and negligible.

When it comes to bacteria that targets other organisms, like flatworms and other parasites, the only way I can see this happen is not as a form of direct competition, but through production of chemicals that are toxic to them and only them, e.g. antibiotics. Unfortunately, most antibiotics are broad-range (and would effect other beneficiary members of our tanks) or highly selective to target other organisms that compete for the same resources, in other words other microorganisms that occupy niches overlapping with the bacteria's (parasites unfortunately do not fit this criteria).

 

[Agathos]

While technically correct that bacteria don't reproduce sexually, bacteria actually trade quite a lot genes among clones and even "species". This happens through viral infections and also specific behaviors, called conjugation, where bacteria trade small fragments of DNA called plasmids that contain one or a few genes. This helps to explain how antibiotic resistant traits can quickly spread across a population of bacteria.

Yes, and I would love to discuss this in more detail since I have been working with broad-host-range plasmids on my PhD. I actually wrote a paragraph about this in my former post but deleted it since I saw it slightly off topic .

It is also a potential mechanism by which introducing a new bacterial culture could influence much of the tank community without necessarily reaching high levels. You could easily be introducing a gene for a utilizing some nutrient that the existing bacteria cannot metabolize for instance.

Yes, this is possible, and it's an intriguing thought.

Bacteria also have very high mutation rates so that it doesn't take too many generations before "clones" are genetically distinguishable from their parents. And with bacteria, generation times are in tens of minutes!

Hence Vibrio paulius.

 

[Agathos]

I think it is very likely in many tanks. Especially older tanks. I have personally used Chemi Clean and Red Slime remover many times over the years. Red Slime remover is basically an antibiotic that would tend to kill (or weaken) some but not all types of bacteria. Also in the beginning the tank had copper in it continousely for a couple of years. If any of you remember, before reef tanks, ich was very prevelant and we used copper extensively. I am not sure what that did to the bacterial diversity but I would imagine it could shift the numbers of dominent bacteria to a different type that was more resistant to copper or an antibiotic.
In that case, I would assume adding "wild" bacteria from the sea "may" have a positive effect.

I think you are completely right. This would be analogous to taking probiotics after being treated with penicillins so as to inoculate your stomach with good bacteria again.

Do any of you have a theory as to why ich does not seem to effect my tank, could bacterial additions possably have anything to do with that?

It's hard to say. One thought is that good bacteria that normally colonizes the fish skin might be absent and this would help ich to infest the fish. If these bacteria don't really enjoy life in reef tanks, they may be lost over time, opening up for skin parasites. And a remedy could be to continuously add them to the tank. But if so, ich should be more prevalent the older the tank is, and I don't know if that is true. But it could be a similar mechanisms, so yes, it's plausible. Another explanation is also that you treat your fish very well .

 

[Agathos]

Could any of the microbiolgists comment regarding the risk/benefits of carbon dosing ? If this is off topic please disregard.

My thoughts that this might result in a fragile situation favoring a narrow spectrum of bacterial species. This seems hazardous and potentiates those tanks for crash if husbandry is less than perfect. I mean, dosing carbon sources to help with nutrient issues already suggests less than biologically-balanced husbandry right?

Again, I am just speculating. Carbon dosing, as far as I understand this practice, is to add some carbon containing molecule that work as a good carbon source for bacteria so as to stimulate a higher population of these bacteria which will again consume nitrogen and phosphate compounds from the tank which otherwise would be toxic or promote growth of less beneficial organisms?

If so, I would think that the type of carbon molecule that is dosed has big importance. Different bacteria can import and metabolize different carbon molecules at different efficiencies. So dosing carbon compound A may promote growth of one set of bacteria, while dosing carbon compound may promote growth of an entirely different set. Dosing a compound that few bacteria have evolved to be able to catabolize will only help these to grow, while dosing with e.g. glucose may promote lots of bacteria to grow. At the same time you don't want to dose with something that stimulates growth of bad guys.

So in theory I think it is possible, boosting the biological filter is a good idea and should be possible by making the good bacteria more content (either through giving them more places to live, i.e. more rocks, more water surface area, or by giving them more food in the form of carbon) so that they reach higher concentrations, but I don't think it is trivial which carbon compound is chosen, and I am afraid that the optimal compound may actually be somewhat tank specific.

 

[Paul B]

Another explanation is also that you treat your fish very well .

Well, I did stop whipping them in the 80s

 

[ctripi]

There exists antecdotal reports on RC that different carbon-sources yield differing results. I think the thread suggested straight glucose was potentially detritmental for that individuals system.

Paul......I always envisioned a Vibrio spp having a NYC accent

 

[Paul B]

Paul......I always envisioned a Vibrio spp having a NYC accent

Well my tank was originally started in NYC and the original water was collected from under the Whitestone bridge which connects the Bronx to Queens and begins the East River that passes Manhattan so, yes, maybe they do have NY accents. But you need to lean real close to the glass to hear them.

 

[ctripi]

Here is the glucose thread I mentioned = Glucose additions causes cyano & algal problems in addition to coral problems.

http://www.reefcentral.com/forums/showthread.php?t=1781320

 

[elegance coral]

When it comes to increasing microbial diversity in diversity depleted mature reef tanks, the idea is not to add foreign microflora, but to replenish with those that have already been lost.

How can we do that when we don't know what bacteria have been lost, and we would rarely know what bacteria we are adding to the system?

What I fear then will happen is not a collapse of the established ecosystem, but that the introduced species will die off rapidly. They have already died off once, during the initial competition, and they will face much harder competition now when the first survivors have colonized the tank environment fully and established themselves at optimal concentration.

I think that pretty much says it all. Why would we want to replenish bacteria that have proven their inability to survive in our system? Most of us strive to keep nutrients low. Adding microbes, knowing they will simply die and release the nutrients they contain, seems kinda counter productive to me.:hmm5:

I thought it was linked to adding specimen that is ALREADY infested, or linked to changes in tank parameters (light, temperature, water chemistry, etc) that cause outbreaks of already present pathogens.

Adding a host along with its parasite to a system that doesn't contain them would be adding to the biodiversity of the system, correct?
Maybe I should have worded my post a little better. I said these problems "can" be linked to adding biodiversity. I didn't mean to imply that these types of outbreaks are always caused by adding to the biodiversity. Most systems, probably all systems, house bad guys. As long as the system remains healthy, we may not see signs of their existence. If the health of the system plummets for some reason, we stop feeding like we should, or don't keep up with water changes, these problem microbes often show their face. This clearly isn't caused by adding to the biodiversity.

 

[elegance coral]

IMHO Biodiversity is one of those things that sounds great until you really start looking into what it will, and will not, do for a system. There are countless references in aquarium literature to how wonderful biodiversity is, and how we should all constantly strive to increase it, but I have yet to find one that holds water. Our systems create jobs that must be accomplished on a microbial level for our systems to remain healthy. We need strong, numerous, and well adapted microbes to accomplish these jobs. As our systems mature, so do these microbial populations. What benefit could possibly come from throwing new, and often unknown, microbes into such a healthy and stable system??????

 

[philbo32]

It's hard to say. One thought is that good bacteria that normally colonizes the fish skin might be absent and this would help ich to infest the fish. If these bacteria don't really enjoy life in reef tanks, they may be lost over time, opening up for skin parasites. And a remedy could be to continuously add them to the tank. But if so, ich should be more prevalent the older the tank is, and I don't know if that is true. But it could be a similar mechanisms, so yes, it's plausible. Another explanation is also that you treat your fish very well .

I agree it is difficult to form any conclusions on how bacteria on fish affect whether your fish will get whitespot as to my knowledge there has been no work in this area to identify what the individual role of the bacteria that do colonize fish.

Plus a fishes immune system has a lot to do with whether the fish will get whitespot, there is a scientific study 4 years ago which looked at a vaccine to white spot this would include injecting fish with a dead stage of Cryptocaryon irritans (http://www.sciencedirect.com/scienc...serid=10&md5=8cc5ebadf95de1a9e252e89c80f2f347) and it worked to immunize groupers. Other studies have found fish that have recovered from white spot can become immune for 6 months and can become carriers of the disease (http://www.sciencedirect.com/scienc...serid=10&md5=5447fb8fdbe4c0e5a2f51cdf76aa01d2).

Another paper of a fishes resitance to Cryptocaryon irritans after it had previously been infected = http://www.int-res.com/articles/dao/1/d001p019.pdf

 

[Paul B]

Philbo, interesting links, thanks.

As our systems mature, so do these microbial populations. What benefit could possibly come from throwing new, and often unknown, microbes into such a healthy and stable system??????

IMO, even healthy and stable systems could get a boost from an addition of new bacteria which may possably be better at converting nitrates. Many older systems especially systems with DSBs lose much of their nitrate converting means forcing people to change water to lower nitrates.
I understand that there are bacteria in every part of a tank but I don't think new bacteria would have a hard time working with or replacing bacteria already there. Our guts are loaded with bacteria and we could eat something with a disease causing bacteria that can make us very ill.
I am sure there are many bacteria in the sea that will out compete the bacteria already present in a tank. Even though the newcomer bacteria has far less numbers, it is not like in a war where the army with the superior numbers usually wins.
On the north east coastlines of the US, under every rock used to be green crabs. They were all over the place. About 40 years ago a Japanese ship was believed to import a species of Japanese shore crab in their ballast water.
Now there are no green crabs but under every rock there are dozens of Japanses shore crabs. These crabs are the same size and have the same diet as the resident green crabs yet a few of the alien crabs took over the entire ecosystem of the eastern US.
These new comer crabs are a little faster and a little hardier than the green crabs (I have kept them for years)
I understand that bacteria are not crabs but this was done one at a time.
Could this not happen with bacteria?

This is where these species come from. This is in NY harbor, (taken from my boat)