Hans-Werner
Valuable Member
- Joined
- Aug 24, 2016
- Messages
- 1,506
- Reaction score
- 2,301
It is just my guess, what I conclude from my own observations and experiments.
Bacteria...let's really start understanding them! part one
- Thread starter flampton
- Start date
- Tagged users None
- Joined
- Sep 21, 2018
- Messages
- 6,734
- Reaction score
- 7,216
Your observations remind us that our reef systems are really pseudo-reefs, not even captive reefs. There is simply no way that we can scale down the physical forces, duplicate the physical events and certainly not reproduce the microbial flora of a reef. The best we can do is figure out what our captive creatures can tolerate and supply it.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.
- Joined
- Dec 28, 2016
- Messages
- 22,922
- Reaction score
- 22,033
I was alluding to the comments that I believe Hans Werner made - that diversity is lost in (paraphrased) a poorly functioning tank.
- Joined
- May 22, 2016
- Messages
- 6,594
- Reaction score
- 10,183
the best quality films I was able to examine were from taking a microscope slide or similar and stick it down in the sand near some nuisance growth for a few days. This one got colonized by some cyano and a pinch of everything else.
Two normal shots, two heat-fixed (on my coffee warmer) and stained with methylene blue.
The stained shots reveal two structures that didn't show in the normal version:
super tiny filaments far far thinner than cyano
and an occasional pocket of dense single-cells
SMSREEF
Valuable Member
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"
So another question, can we achieve a more diverse biome by having some of these different zones in our tank? Leaving out the parrotfish that will pulverize my coral
Plus I only have 60 gallons.For instance, the main display with rock, sand, corals, inverts with high flow.
In the sump, a refugium with macroalgae, inverts, some mud and lower flow, another section in the sump dark with minimal flow (not sure what I would put in here, maybe a bag of oysters).
In my case, I’m not thinking of diversity for diversities sake, but to create a food web of bacteria and other organisms that works together to remove waste and supply ammonia and food for the coral in the main display.
SMSREEF
Valuable Member
Very interesting!the best quality films I was able to examine were from taking a microscope slide or similar and stick it down in the sand near some nuisance growth for a few days. This one got colonized by some cyano and a pinch of everything else.
Two normal shots, two heat-fixed (on my coffee warmer) and stained with methylene blue.
The stained shots reveal two structures that didn't show in the normal version:
super tiny filaments far far thinner than cyano
and an occasional pocket of dense single-cells
I will put a few slides into different areas in my tank and see what they look like after a week or 2. My stain should be here in a week or so.
1. Sand in main display.
2. Rock lower tank
3. Rock higher tank
4. Refugium sand
5. Refugium Macroalgae
6. Dark sump with low flow
7. I also have a bucket of mud and macros I just collected from the beach so I’ll stick a slide in there too.
Hans-Werner
Valuable Member
- Joined
- Aug 24, 2016
- Messages
- 1,506
- Reaction score
- 2,301
Yes, I noticed a better "revitalization" of the tanks after adding some biopolymers which are found in or prepared from algae. I think these diverse algal biopolymers are something that contributes to the natural biodiversity in reefs. Algal biopolymers are diatom slimes, slimes and gels of macroalgae, cellulose fibers etc..
Maybe it was not the worst ideal to discard a part of the growth from algal turf scrubbers back into the aquarium after drying, as one of my books describes (I think it was "Dynamic Aquaria" by Walter H. Adey).
The growing, dying and breakdown of algae may create some extra microbial biodiversity for sure.
Bizzie
Community Member
Thanks for sharing your knowledgeWell 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
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.
- Joined
- Dec 28, 2016
- Messages
- 22,922
- Reaction score
- 22,033
I agree with this - I sent in multiple samples from various parts of my tank and got extremely different results from different areas and different methods of sampling. My guess that time of day sampled (which I didn't check) will also make a difference. I guess you could make sense out of sequential data if:Well unfortunately I'm not sure the operation is going to help you much. There can be a completely different microbiome in every nook and cranny of your tank. Basically miniature ecosystems throughout. That being said I think the info is pretty fun, and if you get joy out of it doesn't matter.
1. You have a specific place you're sampling from each time (which the kits from Aquabiomics suggests)
2. You do the sampling the same way each time
3. Every now and then you send duplicate samples as a control.
The problem even with this is - how do you pick the area to sample from - to be sure you're measuring true 'diversity'. I can tell an interesting anecdote - using the method from Aquabiomics - my tank was on the very 'low level' of diversity. When I ran my hand (to create a bit of flow) over my rock work and this a little stirring up of the water - the tank was one of the highest diversity scores recorded. I also tend to agree with you that adding 'new bacteria' is not likely to increase diversity unless only for a very short time.
EDIT: I sent multiple tests from the same tank using various methods. @AquaBiomics was nice enough to do this - without knowing the areas the samples were from. First - All of the results were accurate (i.e. controls showed no bacteria, some samples from non-reef tanks showed this) - and duplicate samples (i.e. samples that were taken at the same time and place) were nearly identical.
Last edited:
- Joined
- Dec 28, 2016
- Messages
- 22,922
- Reaction score
- 22,033
Im curious - did you see any variation etc in your diversity over time? Did you see any correlation? IMHO - I think the testing is 'interesting' - i.e. to me it is interesting to compare my tank to others - but to me its not what bacteria is 'added' to a tank (or mud or sand, etc) - its the available nutrients in the tank that will eventually decide how diverse - and which bacteria will predominate in a tank. I know this is heresy - but IMHO - the clamoring for diversity is over-rated - as compared to focusing on good maintenance routines, etc.
- Joined
- Dec 28, 2016
- Messages
- 22,922
- Reaction score
- 22,033
I probably wasn't as clear as I could have been. You are of course correct - my idea was that concept of 'strong' vs. 'weak' is in great part due to availability of nutrients - or the microenvironment - both at a 'local' and 'global' level - and those levels over time. That said, here is another example - lets say you take 2 different hypothetical strains of bacteria that use the same nutrients but the doubling time of Strain A is 5x faster than Strain B and you put them in a situation where the required nutrients were present. Very soon - there would likely only be 'strain A' in the culture - even if nutrient levels were kept constant. Additionally, bacteria, fungi, etc also compete by releasing 'toxins' - that help limit competition (I,e. various fungi releasing antibiotics) - that favor their growth over bacteria.
GlassMunky
2500 Club Member
Well I got a bunch of test results but without really anything to understand what those results mean.
mover the course of 6 months or so I never once got a reply back to any of my questions regarding results.
my he only time I ever got an email was when I left a negative review on their google business page.
even after that happened, I still didn’t get answers to any of my questions about the results.
So it’s not really a useful service
GlassMunky
2500 Club Member
But yes the graphs and stuff changed from month to month.
a couple months it said a fish pathogen showed up, then disappeared while a couple months earlier it was also absent.
I’m not sure how trustworthy the test results are to be honest.
There is another interesting facet of zonation in the reef tank I just thought of: catalase positive vs catalase-negative bacteria (if someone ever concerned over that division at all, its at least zonation set naturally)
is this angle is terribly far off flampton:
anyone knows if you gargle 3% peroxide a human mouth will froth, even after brushing, like a wild dog. we're gut-lined in catalase-positive bacteria of genus tbd, but peroxide sets them off most assured.
put in palm of hand...Ive never seen anyone's frizzle ever...there may be some depending on handlings but my hands do not froth in the palm no matter how iong 3% sits, so we have some basic catalase- positive natural zonation for human skin vs epithelial cells in the mouth
and its consistent person to person, very interesting
in reefs, so many people are dosing peroxide in various was for a decade now, patterns stand out. most lps corals will froth around the edges markedly when direct 3% accidentally hits them
but actual live rock, stewing in the same water, does not usually bubble its like adding distilled water droplets/unreactive. try some on a test section submerged just lift out and dribble on some 3% see if it bubbles.
a tuft of hair algae? hardly ever bubbles when directly treated, that's why many think the perx won't kill the tuft in the same hour treated...but in 48 hours its walloped because bubbles or not something is getting oxidized when peroxide is on it, topically at least.
even though we mix these waters strongly, zonations for catalase + v - bacteria clades still differentiate in reefing/interesting pattern imo.
is this angle is terribly far off flampton:
anyone knows if you gargle 3% peroxide a human mouth will froth, even after brushing, like a wild dog. we're gut-lined in catalase-positive bacteria of genus tbd, but peroxide sets them off most assured.
put in palm of hand...Ive never seen anyone's frizzle ever...there may be some depending on handlings but my hands do not froth in the palm no matter how iong 3% sits, so we have some basic catalase- positive natural zonation for human skin vs epithelial cells in the mouth
and its consistent person to person, very interesting
in reefs, so many people are dosing peroxide in various was for a decade now, patterns stand out. most lps corals will froth around the edges markedly when direct 3% accidentally hits them
but actual live rock, stewing in the same water, does not usually bubble its like adding distilled water droplets/unreactive. try some on a test section submerged just lift out and dribble on some 3% see if it bubbles.
a tuft of hair algae? hardly ever bubbles when directly treated, that's why many think the perx won't kill the tuft in the same hour treated...but in 48 hours its walloped because bubbles or not something is getting oxidized when peroxide is on it, topically at least.
even though we mix these waters strongly, zonations for catalase + v - bacteria clades still differentiate in reefing/interesting pattern imo.
OP
OP
flampton
Ecological Reefing
Lost track of this thread again, will be trying to get the whole series complete over holiday break.
Anyways...
I think you're misunderstanding the point of catalase. It's an enzyme that breaks down hydrogen peroxide to water and oxygen. This protects the cell(s) from the oxidizing agent. It's very important protein for most aerobes as hydrogen peroxide is produced during respiration.
Thus bubbles (oxygen) means protection of the cell(s). When we use it in our mouths we overwhelm some of the catalase positive bacteria but mainly are killing those that lack catalase (obligate anaerobes especially). Plus some of the catalase activity is from our own cells. Put a drop of peroxide on some blood and you'll see those bubbles.
Your skin has very few bacteria in comparison to the mouth and as well the H2O2 has no access to living tissue. So really shouldn't see bubbling unless there's a cut. You might get a reaction in moister areas (more bacteria) such as arm pits etc...
So not seeing bubbles is a good thing. It means it has a better chance of working on that surface.
Now I'm not a algal biologist but will suggest they do likely have catalase but it's not penetrating the cell wall very well.
- Joined
- May 22, 2016
- Messages
- 6,594
- Reaction score
- 10,183
The bubbling in response to peroxide is a confusing signal in our tanks. The bubbling is decomposition of the peroxide, by catalase Etc. Which could mean that the peroxide is being broken down without being able to damage the cells. But also there are many things that are quite sensitive to peroxide that also bubble a lot. Cyanobacteria comes to mind as the best example. My interpretation is that they possess ways to deal with peroxide and other reactive oxygen species because they are generated in small amounts by photosynthetic machinery. But the cyano probably have those enzymes precisely because they are sensitive to h202 Etc and need the protection. (So if we overwhelm it they are fatally damaged.)
That's my best attempt anyway.
That's my best attempt anyway.
OP
OP
flampton
Ecological Reefing
If you see bubbling rest assured if it's biological it is the activity of catalase you're witnessing, but I should have mentioned it's a cytoplasmic enzyme (resides inside the cell). Which means that the H2O2 has already entered the cell. Enough H2O2 will kill any cell. The sensitivity of various organisms that produce catalase to protect from hydrogen peroxide is a complicated discussion and revolves around other proteins (peroxidases), kinetics, redox states, metals etc...
Interestingly
Just found a paper suggesting Ulva rigida (macro algae) relies more on ascorbate peroxidase than catalase (4:1). This is interesting as peroxidases do not produce oxygen. So would show limited 'bubbling'. Yet this also means the algae would have limited protection from outside hydrogen peroxide as ascorbate peroxidase is found within the chloroplasts (an organelle/compartment inside the cell that is responsible for photosynthesis)
Last edited:
- Joined
- Dec 28, 2016
- Messages
- 22,922
- Reaction score
- 22,033
H2O2 will kill both catalase positive and catalase negative cells - in the concentrations used from 'a bottle'. The levels of H2O2 produced intracellularly I believe is quite a bit smaller than for example 3% H2O2. Thus - though catalase will protect against H2O2 produced by the organism itself - it will not be enough to protect against 3% H2O2. All of our cells have catalase as well. The difference between Skin and Mouth is that the skin is covered with a layer of keratin (i.e which is a relative rather than complete 'barrier'). The cells lining the mucus membranes (in the mouth) - do not have as much protection thus - a lot of the 'foaming' you're seeing is probably your own cells being damaged and exposing their catalase - rather than the 'bacteria' themselves (for example - saliva contains epithelial cells white blood cells, etc as well as bacteria). BTW - leaving H2O2 on the skin too long can be extremely damaging - and for the most part its not recommended for wound cleaning anymore. Thus to answer your question - I do not think the foaming on the skin relates to catalase positive or negative bacteria. BTW - the example you used with 'living rock' vs 'LPS' is the same scenario - the living rock doesnt bubble - because there is not a lot of cells there - LPS bubbles becasue of the catalase in its cells. But - in both cases (LR and LPS) - damage is occurring to the cells present - with or without bubbling.
hobby can't make any leaps into assumptions about what peroxide does in reefing yet, its untested. Biofilm insulations everywhere, dice roll differently. Try to imagine the level of skepticism facing peroxide use in 2011, the statement that it kills cells was causing literal reef hysteria. Lost two good id's over that row lol/hasta thereeftank and will miss ya reefcentral.
in hindsight...
peroxide dosing helps vs harms, stinging rebuke potential. its used daily
in fish disease control threads
in cyano and dino threads, Troylee has referenced it for us ten years running in a sticky. not showing harm at all.
so it burns teased out cells, on a slide, agreed and I would agree it burns a top layer/within the microcontact zone with water but one thing about a million reports on peroxide dosing into reefing has provided is a stern reminder the rules change within the box
someone does need to get us some detailed testing though on the matter, especially using today's meters for bacterial presence.
3% peroxide is so harmless these are my findings:
I cannot recall in ten thousand posts a single time an overdose of 3% killed a tank's biofilter. Not once. we got ten thousand .25 ammonia reports admitted, but doesn't everybody...
we saw corals wiped out in overdose posts. but not a need to wait 30 days to restart a totally killed system, or any days delay actually.
since ORP meters have universally reported a paradoxical drop in orp after adding into tank water vs the initially-guessed huge boost, we got another new proofing there and nowadays we even have seneye meters hooked to tanks- showing no change in ammonia processing, which matches about a million dose outcomes on file. more opposites to the rules are happening vs being in-line with the rules regarding dosing peroxide into a reef tank.
ill go on record stating peroxide doesn't do measurable harm in a reef when dosed correctly, and even when grossly overdosed the bacteria simply can't be measured as harmed
ok bring on the laser microscopy to confirm/deny Ill enjoy the updates. they need to align with a million peroxide dose search results we can all source in order to be valid findings in my opinion. Doing a big water change kills bacteria
switching out sandbeds because we move homes, or want eden flakes/valid moves. that kills bacteria
skimming kills (exports) bacteria
cleaning biomedia kills (exports permanently) bacteria
but in context, there's no consequence, the hobby wants to know the consequence zone not just a blanket eval
____________________________________________________________________
regarding peroxidase / catalase updates am reading through what you all have posted nice job. that's good biology to read up on.
in hindsight...
peroxide dosing helps vs harms, stinging rebuke potential. its used daily
in fish disease control threads
in cyano and dino threads, Troylee has referenced it for us ten years running in a sticky. not showing harm at all.
so it burns teased out cells, on a slide, agreed and I would agree it burns a top layer/within the microcontact zone with water but one thing about a million reports on peroxide dosing into reefing has provided is a stern reminder the rules change within the box
someone does need to get us some detailed testing though on the matter, especially using today's meters for bacterial presence.
3% peroxide is so harmless these are my findings:
I cannot recall in ten thousand posts a single time an overdose of 3% killed a tank's biofilter. Not once. we got ten thousand .25 ammonia reports admitted, but doesn't everybody...
we saw corals wiped out in overdose posts. but not a need to wait 30 days to restart a totally killed system, or any days delay actually.
since ORP meters have universally reported a paradoxical drop in orp after adding into tank water vs the initially-guessed huge boost, we got another new proofing there and nowadays we even have seneye meters hooked to tanks- showing no change in ammonia processing, which matches about a million dose outcomes on file. more opposites to the rules are happening vs being in-line with the rules regarding dosing peroxide into a reef tank.
ill go on record stating peroxide doesn't do measurable harm in a reef when dosed correctly, and even when grossly overdosed the bacteria simply can't be measured as harmed
ok bring on the laser microscopy to confirm/deny Ill enjoy the updates. they need to align with a million peroxide dose search results we can all source in order to be valid findings in my opinion. Doing a big water change kills bacteria
switching out sandbeds because we move homes, or want eden flakes/valid moves. that kills bacteria
skimming kills (exports) bacteria
cleaning biomedia kills (exports permanently) bacteria
but in context, there's no consequence, the hobby wants to know the consequence zone not just a blanket eval
____________________________________________________________________
regarding peroxidase / catalase updates am reading through what you all have posted nice job. that's good biology to read up on.
Last edited:
- Joined
- Dec 28, 2016
- Messages
- 22,922
- Reaction score
- 22,033
I use an oxydator - I do not use it to 'kill bacteria' or 'kill anything' - the concentration that anyone is using would seem to be far too low to 'kill anything' - unless its direct contact (i.e. sprayed directly onto algae, etc). Is there really a thinking/concept out there that aside from increasing dissolved O2 - some - that there is another benefit to H2O2? H2O2 when exposed to organics and even light - rapidly decomposes to O2 and H2O - I cannot conceive it floating around the tank - killing bacteria on rocks or anywhere else Right?
Similar threads
