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

[flampton]

So this thread got away from me for a bit...

So first off if you want to know if you can see bacteria with various magnifications. Yes depends on the species. From 0x-1000x.

So if you wondered what a bacterial type might look like under the scope, then look up its size and shape. A cocci(spherical) bacteria that is 5um will appear to be 0.5mm in diameter at 100x, 2mm at 400x and will be 5mm at 1000x.

Microscopes can be used in a scheme to help with identification. Not really needed though, just nice to have a visual sometimes.

Also 1000x is the highest allowable magnification by light microscopy, even though unscrupulous cheap suppliers might advertise higher mags.

 

[LRT]

I love this thread

 

[Hans-Werner]

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?

That is a fundamental misconception of the cause or lack of biodiversity. Biodiversity has nothing to do with strong of weak. In the case of bacteria it is all about substrates and nutrients. A very small bacterium that grows slowly and with little nutrients on a substrate, that is hard to degrade, is it strong or weak? Strong or weak doesn't matter, it may be the only bacterium that can live under these conditions and so it is without competitors on this substrate.

So microbial diversity (bacteria, fungi and some protists) is not defined by the additions of species or strains but by the diversity of "difficult" substrates and limited nutrients. On one single such "difficult" substrate a whole bunch of specialized bacteria may establish and live because the complete degradation to CO2 may be a multi-step process. A biopolymer like cellulose or lignin may be degraded to oligomers and monomers. The oligomers and monomers may be fermentet to organic acids and the organic acids finally may be respired to CO2. The polymer may be a heteropolymer degraded to a set of different oligomers and monomers nourishing a diverse set of bacteria. This is what causes biodiversity.

If you throw in substrates that each and every bacterium that comes along can respire like glucose, acetate or ethanol you will not support biodiversity. More likely oppurtunistic bacteria that show rapid growth will overgrow everything else, finally "overgrowing" and killing corals and fish. This will not be the case in a tank with a high bacterial biodiversity because both conditions mutually exclude each other. In a tank showing a high biodiversity no single substrate and no single bacterial strain will dominate. Biodiversity is an indicator, an indicator of certain conditions.

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.

If a few species overgrow everything else this is not biodiversity. If you add a diversity of species and only a few overgrow everything else this shows that the conditions were not right to maintain biodiversity. That is the real problem. Adding diversity does not help if the diversity is not sustained.

Are conditions sustaining a high biodiversity automatically good? Not necessarily for all, most likely not for opportunistic pathogens that show rapid growth with a plenty of available nutrients. This may be the cause why bacterial biodiversity is indicating "good" conditions.

I think many pathogens are introduced with their host or with one host anyway, especially in the case of fish.

 

[brandon429]

Observing bacteria under the light microscope | Microbehunter Microscopy

It is possible to use non-toxic stains (such as ink for fountain pens) to stain yogurt bacteria in-vivo. | Microbehunter Microscopy

www.microbehunter.com

I thought Oliver’s responses here read as solid material, guy seems sharp. I got to wondering if 400x opens the bac world to us, it doesn’t. But we can see many strains apparently and Id have guessed zero. Microscopy has improved since 1998 ch3ck.

 

[taricha]

This thread's generated some high quality info the last couple of pages. Great read, thanks everyone.

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

I was going to respond to this, but Hans-Werner made my argument better than I could have, and with much better specifics to illustrate.

In a tank showing a high biodiversity no single substrate and no single bacterial strain will dominate. Biodiversity is an indicator, an indicator of certain conditions.

This is a good way to think of it, IMO. Diversity of species tells us about diversity of foods/niches etc present.

I can grow way more pods and more kinds by dosing phyto than by pouring in bags of pods.

This is my anecdotal opinion - the reason for 'the uglies' with new tanks - dry rock is perhaps a diversity issue - but were this the 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

Not heretical. It's rarely noticed but invariably true that the majority of posts in dino threads are from tanks with vast deserts of rock and sand. competition matters. Large mass of Coral exerts a force over the microbiome.
Also because tanks that are thick with gorgeous corals just frankly don't care about a little patch of red/brown cyano/dinos as much as people with nearly empty tanks do.

 

[SMSREEF]

I thought Oliver’s responses here read as solid material, guy seems sharp. I got to wondering if 400x opens the bac world to us, it doesn’t. But we can see many strains apparently and Id have guessed zero. Microscopy has improved since 1998 ch3ck.

Thanks for this. It’s been a long time since I was in my micro class. I’ve been looking under the scope and never see bacteria. But I forgot we need to stain to see them.

I may order some stain and try to look at samples under the scope.

I am loving this thread and learning a lot along the way. Thanks to all who are sharing your experiences and knowledge.

 

[brandon429]

Agreed fully. This total / 8 page discussion is happening solely here and on no other boards (rc knows about Aqua’s measurements I’m talking Randy level microbiology discuss n learn with dual/duel practitioner inputs). Nice new material for reading im in a rabbit hole such that might have to call in late 30 mins

 

[MnFish1]

That is a fundamental misconception of the cause or lack of biodiversity. Biodiversity has nothing to do with strong of weak. In the case of bacteria it is all about substrates and nutrients. A very small bacterium that grows slowly and with little nutrients on a substrate, that is hard to degrade, is it strong or weak? Strong or weak doesn't matter, it may be the only bacterium that can live under these conditions and so it is without competitors on this substrate.

So microbial diversity (bacteria, fungi and some protists) is not defined by the additions of species or strains but by the diversity of "difficult" substrates and limited nutrients. On one single such "difficult" substrate a whole bunch of specialized bacteria may establish and live because the complete degradation to CO2 may be a multi-step process. A biopolymer like cellulose or lignin may be degraded to oligomers and monomers. The oligomers and monomers may be fermentet to organic acids and the organic acids finally may be respired to CO2. The polymer may be a heteropolymer degraded to a set of different oligomers and monomers nourishing a diverse set of bacteria. This is what causes biodiversity.

If you throw in substrates that each and every bacterium that comes along can respire like glucose, acetate or ethanol you will not support biodiversity. More likely oppurtunistic bacteria that show rapid growth will overgrow everything else, finally "overgrowing" and killing corals and fish. This will not be the case in a tank with a high bacterial biodiversity because both conditions mutually exclude each other. In a tank showing a high biodiversity no single substrate and no single bacterial strain will dominate. Biodiversity is an indicator, an indicator of certain conditions.


If a few species overgrow everything else this is not biodiversity. If you add a diversity of species and only a few overgrow everything else this shows that the conditions were not right to maintain biodiversity. That is the real problem. Adding diversity does not help if the diversity is not sustained.

Are conditions sustaining a high biodiversity automatically good? Not necessarily for all, most likely not for opportunistic pathogens that show rapid growth with a plenty of available nutrients. This may be the cause why bacterial biodiversity is indicating "good" conditions.

I think many pathogens are introduced with their host or with one host anyway, especially in the case of fish.

So we agree on 90 percent of what I said. Merely adding sand etc does not likely improve whatever condition that caused the lack of diversity in the first place Which is likely why @AquaBiomics has seen that older tanks lose rather than gain diversity over time. I would also suggest that in the ocean or reef where there are relatively stable conditions and relativwly stable nutrient levels your statements are 100% true. In a tank I’m not as sure

 

[flampton]

Thanks for this. It’s been a long time since I was in my micro class. I’ve been looking under the scope and never see bacteria. But I forgot we need to stain to see them.

I may order some stain and try to look at samples under the scope.

I am loving this thread and learning a lot along the way. Thanks to all who are sharing your experiences and knowledge.

Start with crystal violet. Decent general purpose stain that should get into most bacteria and eukaryotes.

And you'll need to fix the sample. Normally done with heat. I've not personally fixed a salt water specimen though and am a little concerned with crystal formation. I'll have to look into this....

 

[MnFish1]

Start with crystal violet. Decent general purpose stain that should get into most bacteria and eukaryotes.

And you'll need to fix the sample. Normally done with heat. I've not personally fixed a salt water specimen though and am a little concerned with crystal formation. I'll have to look into this....

The other issue is concentration unless your looking at an active tissue infection there will likely not be

 

[MnFish1]

The other issue is concentration unless your looking at an active tissue infection there will likely not be

Sorry my phone cut off - unless you are looking at an active infection - there will not likely be enough bacteria in just a 'water sample' unless you concentrate it somehow.

To heat fix the slide - let it air dry -then 2-3 passes (the bottom of the slide) - on a Bunsen burner. My guess is that when you stain it (where you use a fair bit if liquid - the salt crystals will go away.

 

[MnFish1]

If you want to stain your slides I would use this kit rather than crystal violet - which will show shapes - but nothing else. Additionally depending on what you're trying to fine - I would first do a 'wet mount' - (i.e. just a look of a drop of whatever - under a microscope slide) - and then do a gram stain (matching the shapes you saw under the wet mount. That in combination (looking for motility) - and the gram stain will give you a much better indication as to what you are looking at (i.e. vibrio vs something else) - but will also not be entirely 'diagnostic'

 

[SMSREEF]

Start with crystal violet. Decent general purpose stain that should get into most bacteria and eukaryotes.

And you'll need to fix the sample. Normally done with heat.

Thank you! I just ordered a small bottle on Amazon.

there will not likely be enough bacteria in just a 'water sample' unless you concentrate it somehow.

To heat fix the slide - let it air dry -then 2-3 passes (the bottom of the slide) - on a Bunsen burner.

I plan on looking at detritus and other places that may have a bacterial film, not just the water column.

I don’t have a Bunsen burner but I can use a Bic lighter right?

 

[SMSREEF]

If you want to stain your slides I would use this kit rather than crystal violet - which will show shapes - but nothing else. Additionally depending on what you're trying to fine - I would first do a 'wet mount' - (i.e. just a look of a drop of whatever - under a microscope slide) - and then do a gram stain (matching the shapes you saw under the wet mount. That in combination (looking for motility) - and the gram stain will give you a much better indication as to what you are looking at (i.e. vibrio vs something else) - but will also not be entirely 'diagnostic'

I’ll check that one out too. Thanks @MnFish1

 

[HaveFishWillTravel]

Well I’ve been on here for a month or two and I've found a really heavy misunderstanding of bacteria in the aquarium and what they're actually useful for. This is NOT another cycling thread! None of this is opinion unless I say IMO.

First before I begin I'll introduce myself. I have loved aquariums for a long time and my first tank was a 55g saltwater with a undergravel filter and dead coral skeletons. Haha that dates me a little bit. After growing up a bit more I received my masters and PhD in microbiology. My focus has been in the genetics and physiology of Gram-negative human pathogens. My focus has always been in this area because that's where the real edgey science is done. And in case you wondering its not because I think other microbiological fields can't do the top of the line science it is just that they don't have the money that we do.

Again back on topic. I'm going to break this down beginner style.

Okay first I need to introduce what bacteria are and eventually get to why certain bacterial 'types' are the most important in your aquarium. Second I need to introduce the most important concept upfront and that is if someone refers to bacteria you need to know what they're talking about. Why? Well just referring to something as a bacteria is unfortunately meaningless. That's like a doctor treating a human with malaria and then later telling her significant other that she was trying to kill one eukaryote to save the other eukaryote. Technically true but doesn't actually say much...

So for this first topic I'm only going to talk about how bacteria in our aquariums utilize their environment to make energy and acquire carbon.

Let us start with the easiest to understand. That is the
1. Chemoorganoheterotroph -these derive energy from breaking down various organic carbons and they acquire their carbon from these sources as well (they need to eat things). This population is dependent on you feeding the aquarium organic carbon, i.e. food)

2. Chemoautotrophs- these derive energy from the oxidation of electron donors in their environment and acquire carbon through fixing CO2. (Fixing CO2 is when an organism can take CO2 and make sugars from it)

3. Photoautotrophs- these derive energy from light and acquire carbon through fixation.

4. Photoheterotrophs- these derive energy from light and acquire carbon from organic sources.

And if this wasn't confusing enough these categories are not always fixed, as some organisms may switch categories under different environmental conditions.

Phew....Now let us start placing the various bacteria mentioned on the forums into categories.

Chemoorganoheterotrophs- The bacteria that utilize this methodology are the MOST abundant organisms in your aquarium. They're everywhere, on your rocks, in your rocks, in your water column, on your animals, in your animals. Everywhere! Now are they good, bad, indifferent for your aquarium? Well depends, haha! As this category is so diverse in this article I'll just break it down to the two main players we are interested in...

Bacterial pathogens- these feed on an animal you care about. In anthropomorphic terms these are bad guys. They hopefully will be in low abundance in the aquarium.

Bacterial pathogens part two- these feed on an organism you don't like...

'decaying' bacteria- these are the guys who break large 'dead' organics down to small organics. Basically they are by far the number one clean up crew in your tank. Any organic carbon that's not utilized by another animal in your tank these bacteria will eventually digest. I know you think you feed well but some way or another these bacteria will get a major piece of that pie. These are great until you have too many. These types of bacteria are sold in stores.

Okay now chemoautotrophs- This is the most well known on this board because this is were the so called cycling bacteria reside. The two basic types are the nitrifiers. They're found on the surfaces of the aquarium that have access to O2. When I discuss nitrogen in the next article I'll discuss how they fit into the dynamics of a cycling and a well established aquarium. These are also sold in stores.

Photoautotrophs- these are your favorite because this is where we find the cyanobacteria. These guys play an important role in your tanks food chain but access to high nutrients and low predators will cause blooms as you all are aware. They bring more carbon into your aquarium through fixation of CO2. They also produce oxygen by removing hydrogen from water molecules. Don't know anyone who sells cyanobacteria.

Photoheterotrophs-. These guys aren't talked about much. They're in your tank though and they play less of a role in the aquarium. They'll help with decay of organics as well. I know of at least one product that has a strain. Not an advertisement but as far as I am aware only one product, PNS probio, contains a photoheterotrophic strain.

Okay phew... Please let me know if the above helps you My next article will talk about carbon, nitrogen and phosphate flux in the aquarium in relation to the bacteria in your tank. If you have questions let me know below. If you see a mistake let me know as well.

Thanks for reading this far!
Eric

Edit:: haha I forgot to mention what bacteria are. They're single celled organisms that lack a nucleus of the domain bacteria. They can also be referred to as prokaryotes. We are eukaryotes- we have a nucleus. Sorry about that.

Excellent! Thank you. Looking forward to the next in your series.

 

[Hans-Werner]

So we agree on 90 percent of what I said. Merely adding sand etc does not likely improve whatever condition that caused the lack of diversity in the first place Which is likely why @AquaBiomics has seen that older tanks lose rather than gain diversity over time.

Yes. In my opinion the loss of diversity with time is rather caused by stability in some way. In my experience, introducing new live rock or live sand is not able to bring back the growth and diversity of the initial conditions. Besides a possible lack of some trace elements I think it is the "establishment" impeding new growth and diversity. Established and highly organized biofilms are able to break down and mineralize the organic materials, that regularily are added to the tank, in a short time. High nutrient (mainly N and P) loads even speed up this mineralization process, speeding up the nutrient increase and so on, a feedback loop. So there is no way to bring back the old diversity that evolved after the tank started.

That throws up the question whether coral reefs are really that stable? Besides minor disturbances like parrotfish and other organisms eroding and throwing around corals and creating fresh surfaces it was found that in heavily destroyed reefs, i. e. by a typhoon or a tsunami, after some time, biodiversity is highest, reaching a peak and decreasing with time.

 

[Dan_P]

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

What is a ”poorly functioning tank”?

 

[Dan_P]

Yes. In my opinion the loss of diversity with time is rather caused by stability in some way. In my experience, introducing new live rock or live sand is not able to bring back the growth and diversity of the initial conditions. Besides a possible lack of some trace elements I think it is the "establishment" impeding new growth and diversity. Established and highly organized biofilms are able to break down and mineralize the organic materials, that regularily are added to the tank, in a short time. High nutrient (mainly N and P) loads even speed up this mineralization process, speeding up the nutrient increase and so on, a feedback loop. So there is no way to bring back the old diversity that evolved after the tank started.

That throws up the question whether coral reefs are really that stable? Besides minor disturbances like parrotfish and other organisms eroding and throwing around corals and creating fresh surfaces it was found that in heavily destroyed reefs, i. e. by a typhoon or a tsunami, after some time, biodiversity is highest, reaching a peak and decreasing with time.

Would you unpack what you mean “caused by stability”? What “thing” is stable?

 

[Hans-Werner]

Little disturbances of biofilms, little chemical variation in supply of organic substances. Like the comparison with coral reef shows: there is disturbance, instability and variation, creating a spatial and temporal mosaic of zones. This is widely lacking in a tank.

 

[Dan_P]

Little disturbances of biofilms, little chemical variation in supply of organic substances. Like the comparison with coral reef shows: there is disturbance, instability and variation, creating a spatial and temporal mosaic of zones. This is widely lacking in a tank.

OK, got it.

i guess this stability “issue” says something about the adaptability of the creatures we keep in our aquariums.