Bacterial Diversity Methods

[mhaith]

Assuming Bacterial Diversity in our tanks is a good thing............

and assuming a variety of bacterial strains not only consume a variety of organics but the animals in our tanks have evolved to consume/coexist with certain strains of bacteria.

Over a period of time, as with any ecosystem, certain bacterial strains dominate. With the recent focus on carbon dosing to increase the size of bacterial populations, the selective process would be accelerated, resulting in higher populatioins yet fewer strains of bacteria.

I can't help but believe we are accelerating mono-cultures within our tanks..especially mature tanks where we don't have the space or inclination to add new items with their bacterial hitchhikers into our tanks.

What are the best methods of inoculating new bacterial strains into our systems?

I guess "˜factory grown' bacterial strains provided by Zeo, Prodibio, MB7 might be a solution but I doubt it will provide the diversity sand, live rock or even a new organism will provide.

I have considered "˜trading' pieces of live rock on a regular to place in my sump for a period of time to inoculate the tank with new bacterial strains. Assuming the bacteria will migrate off the rock and into the system, what would be the preferred amount of time and method to insure proper inoculation?

Any other ideas of maintaining biodiversity or am I overreacting?

 

[philbo32]

IMO your overreacting. If you used live rock in your system then the right bacteria will be there. Plus any bacteria required by the organisms in your tank will already be with or on your organisms unless you breed them and keep the eggs/offspring in a sterile environment (which a reef tank is not a sterile environment). The term monoculture in the case of bacteria in any environment is rare if not impossible unless using laboratory techniques and specialised equipment. Bacteria are extremely resistant and will adjust to changing conditions especially given there short life cycle. Adding 'foreign' bacteria won't harm your tank but might not do anything in the long run and probably less likely to adjust and survive compared to the original bacteria in your system.

Why are you questioning the quality of the bacteria in your system? Have you had any problems with water quality? I have dosed grown bacteria in fermenters which have originated from my own tank to boost bacteria numbers. This was done whilst starting carbon dosing and to help get rid of cyano which compete for the same carbon source.

 

[mhaith]

Perhaps mono-culture was a misnomer. Is there a dispute that biodiversity decreases within a closed system?

The topic is not so much quantity of bacteria as much as diversity. I am operating under the assumption that a variety of strains is preferable in a healthy ecosystem. Do you disagree?

 

[elegance coral]

I am operating under the assumption that a variety of strains is preferable in a healthy ecosystem. Do you disagree?

I'm not philbo32, who I agree with by the way, but I would like to take a stab at your question.

We all have a variety of microbes in our systems. As the tank matures, some microbes will flourish and others will lose the battle for dominance and die off, or simply eek out an existence. It's through this battle for dominance that we acquire bacteria populations that are well suited to the conditions of our system. This is what makes for a stable environment. Adding microbes, simply for the sake of biodiversity, disrupts this stability. We see this in environments all over the world, where non-native species are introduced into a stable environment. We want stable systems, with microbial populations that have reached a balance with the system. Adding foreign microbes simply causes the microbial populations to fluctuate. Biodiversity sounds great, but it's not always a good thing. Most of us run mixed reefs to some extent. Within the first year or so, we typically add organisms from many different types of environments and from many different locations around the world. This is the time when our systems are typically unstable. We add a vast amount of biodiversity during this time simply by stocking our tanks. At some point, new additions typically decrease, and biodiversity among microbes decreases. Many people view this as a bad thing. IMHO, it is a good thing. This is the point where the strong survive and the weak don't. I'd rather have fewer species of strong, well adapted, microbes, than many different species all competing for resources causing the populations to fluctuate, and instability within the system.

 

[BadSquishy]

I'm relatively new to the forum and to the hobby for that matter, so my opinion is just that, I don't claim any great experience or depth of direct knowledge.

First, I don't believe it is practically possible to control enough of the inputs to achieve balance and stability in any but the very simplest closed systems, much less an isolated, but not closed system such as a reef tank. There too few metrics by which we can assess the "state" of the system. Sure we can measure some very basic parameters and we can exercise some gross control but nothing close to ensuring bacterial stability.

Population growth is typically non-linear and with even a few contributing terms, chaotic. Boom, bust, random pulse profiles are common. The size the system, affects the period of fluctuation and contributes to cycle extinction. "Successful" organisms are in no way excused from participation in these cycles and often show the highest fluctuations.

Cut off the deep water flows, bringing both food and bacterial diversity, to a coral reef - and the resulting stripping outflows, and the ecosystem would change dramatically from the natural open reef. Stripping is every bit as important as input. Close off a section of reef, feed and measure water parameters as we do and I suspect it would be very different, less diverse and healthy, in a very short time.

So I tend to agree with mhaith, "that biodiversity decreases within a closed system" and further that frequest stripping and replenishment of bacterial diversity tends to increase overall stability in small isolated systems.

So ultimately his/her question as to what is the best way to inoculate our systems with diverse strains (and I might add, cull established strains) of bacteria is really an excellent question. At my very shallow level of experience, I have learned the importance of frequent water changes (stripping) and to use my nose as a limited but useful tool for detecting some bacterial imbalances.

 

[Agathos]

If the assumption that microbial diversity is gradually lost as the tank matures, I believe it becomes increasingly difficult to increase diversity through adding complex cultures to the tank at later stages. This is because the mature tank contains large populations of microorganisms that have already proven themselves in competition with many others when the tank was started and diversity flourished. These are the organisms that thrive under the specific conditions given by the tank environment. Adding some new live rocks with microbial diversity will not change this, the new microorganisms will have much harder competition now facing the established large "monocultures".

 

[orthokardia]

Is anyone aware of lab quality studies that have followed bacterial ratios over time in home sized reefs? BTW-Great thread.

-bart

 

[capnfritz]

Exellent thread. For years it's been my opinion that once the chemistry is consistent, bacteria are the driving force in aquaria. I have tried various methods to validate, but unfortunately no concrete results so far. Hopefully this thread will stay up for a while and some biologists will join in.
i'm running a DT and a "control" tank with what I hope is a mixed bacterial population and results have been encouraging, sofar.

 

[mhaith]

I'm not philbo32, who I agree with by the way, but I would like to take a stab at your question.

We all have a variety of microbes in our systems. As the tank matures, some microbes will flourish and others will lose the battle for dominance and die off, or simply eek out an existence. It's through this battle for dominance that we acquire bacteria populations that are well suited to the conditions of our system. This is what makes for a stable environment. Adding microbes, simply for the sake of biodiversity, disrupts this stability. We see this in environments all over the world, where non-native species are introduced into a stable environment. We want stable systems, with microbial populations that have reached a balance with the system. Adding foreign microbes simply causes the microbial populations to fluctuate. Biodiversity sounds great, but it's not always a good thing. Most of us run mixed reefs to some extent. Within the first year or so, we typically add organisms from many different types of environments and from many different locations around the world. This is the time when our systems are typically unstable. We add a vast amount of biodiversity during this time simply by stocking our tanks. At some point, new additions typically decrease, and biodiversity among microbes decreases. Many people view this as a bad thing. IMHO, it is a good thing. This is the point where the strong survive and the weak don't. I'd rather have fewer species of strong, well adapted, microbes, than many different species all competing for resources causing the populations to fluctuate, and instability within the system.

That's a very interesting answer and not one that I expected. If I am understanding you correctly, you are saying that the microbes that should be present and survive will remain strongly seated absent of any events which might kill off, through 'unnatural inputs' such as anti-bacterials like cyano-killers, (which might just be the worst thing one could add to their system and an entirely different thread), creating stability? Stability is a great goal in the short term but.....

Your position does make sense towards stability during a certain stage of a system's lifecycle. However I am of the current opinion that as the lifecycle of a closed system matures, it will result in eventually a crash or at least a 'crisis' of the dominant species that will threaten the entire system or at least result, as resources are in more demand, a total dominance by fewer and fewer species as they crowd out the weaker species.

Wouldn't continued diversity aid in the constant evolution and health of an ecosystem despite the struggles and fluctuations that come with it?

 

[Randy Holmes-Farley]

Assuming Bacterial Diversity in our tanks is a good thing............

Personally, I've not heard a convincing rational for thinking that more diverse bacteria is clearly better.

I don't see massive bacterial die off as a substantial concern. If it happens, and I do not know if it ever has happened in any reef tank, anywhere, new ones will rapidly grow back. I expect there will be lots of natural evolution of species and populations whether we want it to happen or not, based on the changes in the system we cause by adding bacteria with foods, organsims, water, etc, and by changing tank conditions in lots of ways.

This sounds to me like a solution looking for a problem that may or may not really exist.

 

[Agathos]

Hopefully this thread will stay up for a while and some biologists will join in.

I'm a bacterial geneticist with extensive experience in microbiology.

 

[mhaith]

I'm a bacterial geneticist with extensive experience in microbiology.

In an above post you state it 'very difficult' to challenge the 'mono-cultures' which makes total sense and makes the solution to a lack of biodiversity a challenge.

However, that being said, per Randy's comment, is a lack of biodiversity a problem even needing a solution?

Isn't 'mono-cultures' one on of the primary theories of 'Old Tank Syndrome?

 

[Agathos]

In an above post you state it 'very difficult' to challenge the 'mono-cultures' which makes total sense and makes the solution to a lack of biodiversity a challenge.

However, that being said, per Randy's comment, is a lack of biodiversity a problem even needing a solution?

I really don't know. The reason one ends up with less diversity is that the bacteria and other microorganisms less adapted to the tank environment will be out-competed by the ones that are able to thrive under the specific conditions that our highly artificial reef tanks offer. In other words, we are left with those that are really good at making use of the nutrients at offer in the tanks, grow and multiply, while not being killed off by others. One would think that this is good for the tank, after all one wants a healthy population of microorganisms to serve as our biological filter, and to act as food for other lifeforms.

One problem I can think of -- but I don't know how relevant it is -- is that if the bacterial flora of the tank is dominated by a very few species, rather than many different species, the tank would be more at risk if something happened to this specific species' population. In other words, if your biological filter relies on one or a few species' population, sudden mass death of these species could have detrimental effects on the water quality of the tank, and hence other lifeforms. One might also envisage a situation where one species makes up the majority of bacteria in the tank. 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 do believe that diversity is lost, from probably a few hundred different bacterial species to perhaps half of that or less, as tanks mature. The biggest change, I would think, would be that a few species start to dominate, while the other species are kept in smaller populations. So it's more of a shift in population sizes, than out-right decimation of species. At least, that's what I would believe.

Investigating this could be done in different ways, from the rather inaccurate method of plating out bacteria on non-selective plates and counting the diversity to accurate methods of DNA sequencing metagenomic material from the tank. It would cost, though.

My prior point is that IF the case is that diversity is lost, I don't think it would be easy to stop this process. Our tanks offer a very specific chemical environment which will select for specific species. The chemical environment in nature is much more diverse, and will support much more microbial diversity. One can always try to seed mature tanks with diverse microbial cultures, but unless one add a substantial amount of new "diversified" bacteria, the newcomers will rapidly loose the fight for nutritions with the old-timers who have established themselves in the tank. And if one decides to add a large amount of new bacteria to increase the diversity for a long period, this would only lead to microbial die-off experienced in cycling of new tanks. And this is not something that most people want.

 

[capnfritz]

Just IMO, I would think it's better to drive your system with as much diversity as you can.
Particularly bacteriologicaly. My guess is "old tank syndrome" is when this basic foundation is out of equilibrium. Further, many crashes, blooms and so on. Could it be ( for instance) that the weakening of the fishes immune system and the appearance of ick, could be traced back to an abnormal bacteriological basis?
A better understanding of these basic things, would boost our sucess in our hobby.

 

[BadSquishy]

Yep, given another perspective and doing a bit more reading, I once again have to abandon preconceived notions and admit I've adopted an attractive but probably wrong position. Oh well so what elese is new.

"Personally, I've not heard a convincing rational for thinking that more diverse bacteria is clearly better."

Your right, this was an assumption made without foundation or supporting evidence, and a less rather than more diverse bacterial population is reported in healthy coral environments. Diseased environments generally show greater diversity in bacterial strains but it is unclear if this is causal, symptomatic or perhaps a little of both.

"I don't see massive bacterial die off as a substantial concern. If it happens, and I do not know if it ever has happened in any reef tank, anywhere, new ones will rapidly grow back."

Absent some significant external event, (chemical poisoning, ph flux, radical temperature swing, antbiotic etc.) aerobic autotrophs populations would appear to remain relatively stable provided a controlled nutrient source and environment...agreed.

As far as heterotrophic bacteria populations go I still see potential for blooms causing significant problems.

 

[elegance coral]

That's a very interesting answer and not one that I expected. If I am understanding you correctly, you are saying that the microbes that should be present and survive will remain strongly seated absent of any events which might kill off, through 'unnatural inputs' such as anti-bacterials like cyano-killers, (which might just be the worst thing one could add to their system and an entirely different thread), creating stability? Stability is a great goal in the short term but.....

Your position does make sense towards stability during a certain stage of a system's lifecycle. However I am of the current opinion that as the lifecycle of a closed system matures, it will result in eventually a crash or at least a 'crisis' of the dominant species that will threaten the entire system or at least result, as resources are in more demand, a total dominance by fewer and fewer species as they crowd out the weaker species.

Wouldn't continued diversity aid in the constant evolution and health of an ecosystem despite the struggles and fluctuations that come with it?

We can look at other closed, or semi-closed, systems around the world, like caves and islands, to show what happens when we add "biodiversity" to small stable systems. Look at Easter Island. It was once a lush forest with many different species of palm trees and an unknown number of animal species. Two new species were introduced. Humans and rats. The humans cut down the trees, and the rats ate the seeds of the trees. Today the forest and the animals it once supported are extinct. Caves can be very isolated environments with few species, but they are very stable. Some species living and evolving within the cave for hundreds of thousands of years, if not millions. Scientists that study these caves and the organisms that live there, go to great lengths to keep from adding "biodiversity" to the system. If mother nature calls upon a scientist while they are in such a cave, they don't leave their waste behind. They bag it up and take it with them when they leave. This isn't a pleasant task, but they understand the devastation that adding biodiversity to such a system can cause. Scientists studying the moons of Jupiter with a space probe, came to a dilemma at the end of the mission. They could crash the probe into one of the moons and hopefully learn something about it in the process, or crash it into the atmosphere of Jupiter causing the craft to burn up. The decision was made to crash the craft into Jupiter, because of the remote possibility of microbial life on the craft effecting microbes that may live on the moon. In other words, they didn't want to add to the "biodiversity" of the moon if there was any there.

In our systems, problems like Ick, internal parasites, RTN, STN, brown jelly, red bugs, flat worms, and many other problems, can all be linked to adding more biodiversity. These are extreme situations, but just examples of why "biodiversity" isn't something wonderful that we should all strive for. Our systems are like small islands, where the organisms, especially microbes, adapt to the environmental conditions, and the ecosystem becomes very stable. Each new addition of biodiversity creates fluctuations in microbial populations. These fluctuations may be small and insignificant in most cases, but I see no benefit of intentionally adding to the biodiversity of a healthy, well established system. Just MHO.

 

[Agathos]

We can look at other closed, or semi-closed, systems around the world, like caves and islands, to show what happens when we add "biodiversity" to small stable systems. Look at Easter Island. It was once a lush forest with many different species of palm trees and an unknown number of animal species. Two new species were introduced. Humans and rats.

What you are referring to here is the addition of foreign species to established ecosystems. This might cause devastating effects when this introduced species and the local species have not co-evolved to coexist in the same ecosystem, like your examples show.

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. 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.

If we are to add foreign bacteria to a reef tank, e.g. from our local oceans, one might experience that the newcomers are better at surviving and reproducing in the reef tank, and then we would see a tumultuous shift in population sizes where the old ones will diminish while the newcomers take over. This could absolutely be bad for the tank. BUT I find it highly unlikely that foreign, local bacteria would thrive more than bacteria that entered the tank at start-up and that originated from natural reefs (came as highthikers on LS).

In our systems, problems like Ick, internal parasites, RTN, STN, brown jelly, red bugs, flat worms, and many other problems, can all be linked to adding more biodiversity.

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.

 

[teesquare]

THIS is a great thread folks!
And while there may not be any clear cut answers for or against - I think the discussion is certainly healthy.
I have always wondered about the domination of specific strains of bacteria, which initially signal "tank stability" -potentially causing a long slow decline.
In the "dark ages" of this hobby, all that mattered was conversion of ammonia to nitrate. Clearly - we did not understand enough about de-nitrification, and so on.
So - why not look further into the advantages for greater bacterial diversity? With the presumption -of course - that there are known strains of bacteria that need to be avaoided? ( Disease causing ones, and others)

T

 

[capnfritz]

Saltwater covers 80% of the earths surface, so having a better understanding of bacteriological interactions would seem a win win scenario. Although coral reefs are only a small area of the oceans, I think that a comparison with a cave is unrealistic. IMO the controlling factor for reefs is location, temp. and not bac. isolation.

 

[teesquare]

Interesting capnfritz-

How then do we explain the diversity of higher life - if we cannot accept that there is at least as much bio-diversity at the single cell level? Does location, and temperature encompass the total requirement for a given set of bacteria to become dominant? It seems that nature uses a "distillation" method - often called survival of the fittest.....
Thus - would there not be MANY niches occupied by multitudes of bacteria at the little known end of the aquatic envirement? It is easier for us to make assumptions based on observation (as to the overall health and success of a tank) but - here we are talking about micro-observation. I have not seen any evidence - other than each of our anecdotal visual observation.......
Anyone aware of any long term studies that would be relevant?
T