Reef Chemistry Thought Experiment #1: Bacteria

[Randy Holmes-Farley Verified Community Expert]

I'm starting an occasional series of threads on thought experiments.

Things for which there's no known correct answer since they have not, and often cannot, be tested. Just fodder for in depth discussion of various topics.

We will start with a very complicated thought question.

Todays question:

What would happen in a normal, healthy, cycled reef aquarium if one added an antibiotic that killed all bacteria in the aquarium, and had no other direct effects on any other organism.

What would happen that an observer looking at the tank, and taking measurements of normal reef parameters, observe immediately and as time went by?


Let's have some intellectual fun with this!

 

[KrisReef]

Clearly the “cycled” tank is going to become an uncycled tank as the bacteria that were present to process nitrogen wastes all died with the antibiotic treatment. The rock and sand are functionally dry rock, although we don’t know if they have coralline or macro algae or corals growing on them, nor do we know what fishes or other organisms are present in the “normally” functioning reef.

For the typical reef aquarium we have at least a few species of fish and various invertebrates present that are interacting with the nitrogen cycle end products, or just fish releasing ammonia.

The ammonia level should begin to rise and be measurable on our testing.

Yet, A tank with corals and clams only may not show any immediate signs of ammonia since they take up ammonia from the water for energy and nutrients.

A shark tank may show ammonia but the presence of ammonia is not as significant for these fishes since they have urea in their blood.

Still, for the typical reef the fish present are going to show signs of ammonia poisoning and may be surface breathing and showing general signs of distress but if the antibiotics are still effective there will be no bacterial bloom and cloudy water that we usually see when excess ammonia is present in an aquarium.

I don’t know if gut bacteria were eradicated from the treatment? If they were I would expect the fish would start showing symptoms including lack of appetite and diarrhea as well.

Uptake of alkalinity may slowdown or speed up depending on what the inverts are doing with the excess dead bacteria in the water?

 

[brandon429]

my prediction:

assuming no bacteria are found on internal surfaces, they're still in the internal surfaces + waste outputs from all creatures in the tank that are heterotrophic feeders/all fish, inverts, arthropods etc

there is no setting in which animals can exist in a medicated reef wiped of it's bacteria and not have any inside them as symbionts / pathogens/ associates, so new seeding by creatures within is guaranteed

bacterial regrowth immediately starts when the course of the additive/efficacy completes

water is what's required for new bacteria growth initially, a catch point for bac that are inherently traveling around everyone's home and daily habits

the home the tank is located in will quickly seed in new bac via contamination pathways, all forms of tank maintenance involving water addition/topoff/new change water will feed in new mixed bacterial species and since the waste compounds have been building up from the animals inside + dying rotting carcasses if the waste levels got high enough, clouding of the water will occur since surfaces are no longer sufficient (vital surface area) for the degree of the new bac bloom. this will create oxygen competition and further any death cycles

a complete die off will occur based on too many variables to track unless ammonia controlling bacteria are added back quick enough to outpace bioload waste inputs and circulation/oxygen/co2 expel constants are in range to support the delicate life. after the antibiotic effectiveness clears, the tank will recycle itself/ have ammonia-controlling bacteria back on all surfaces in a week or two BUT the wastewater will be so far advanced of what it can carry it could be weeks/months before the system clears up. it will be littered with eutrophic waste and compounds and detritus all about and begin to select for plants vs hermatypic corals once the biosystem restarts, unless someone rip cleans it

after two weeks post antibacterial effectiveness date, all surfaces will be self cycled and ready to perform due to the copious input of new bacteria plus their inherent feeding in the eutrophic system, one big water change would remove all that wastewater (leaving all vital surfaces adhered in functional bacteria in slicks) and a new reef would function just like anyone's dry rock start setup that carries fish just the same

I do not predict that inherently low pH from a crashing system/dieoff/waste acid generation + rotting gas compounds will protect the system from ammonia cascading. it'll work hand in hand with oxygen stripping to kill off most or all remaining life depending on circulation rates, dilution, temp and bioload counts in my opinion. whatever the pH of the system is, enough ammonia will build to kill it if dilution and loading permits and the feeding bac bloom even if they're not nitrifiers will strip the system of oxygen at the start of the rebuilding phase

 

[KrisReef]

my prediction:

assuming no bacteria are found on internal surfaces, they're still in the internal surfaces + waste outputs from all creatures in the tank that are heterotrophic feeders/all fish, inverts, arthropods etc

there is no setting in which animals can exist in a medicated reef wiped of it's bacteria and not have any inside them as symbionts / pathogens/ associates, so new seeding by creatures within is guaranteed

bacterial regrowth immediately starts when the course of the additive/efficacy completes

water is what's required for new bacteria growth initially, a catch point for bac that are inherently traveling around everyone's home and daily habits

the home the tank is located in will quickly seed in new bac via contamination pathways, all forms of tank maintenance involving water addition/topoff/new change water will feed in new mixed bacterial species and since the waste compounds have been building up from the animals inside + dying rotting carcasses if the waste levels got high enough, clouding of the water will occur since surfaces are no longer sufficient (vital surface area) for the degree of the new bac bloom. this will create oxygen competition and further any death cycles

a complete die off will occur based on too many variables to track unless ammonia controlling bacteria are added back quick enough to outpace bioload waste inputs and circulation/oxygen/co2 expel constants are in range to support the delicate life. after the antibiotic effectiveness clears, the tank will recycle itself/ have ammonia-controlling bacteria back on all surfaces in a week or two BUT the wastewater will be so far advanced of what it can carry it could be weeks/months before the system clears up. it will be littered with eutrophic waste and compounds and detritus all about and begin to select for plants vs hermatypic corals once the biosystem restarts, unless someone rip cleans it

after two weeks post antibacterial effectiveness date, all surfaces will be self cycled and ready to perform due to the copious input of new bacteria plus their inherent feeding in the eutrophic system, one big water change would remove all that wastewater and a new reef would function just like anyone's dry rock start setup that carries fish just the same

I do not predict that inherently low pH from a crashing system/dieoff/waste acid generation + rotting gas compounds will protect the system from ammonia cascading. it'll work hand in hand with oxygen stripping to kill off most or all remaining life depending on circulation rates, dilution, temp and bioload counts in my opinion.

Great parameter model and I forgot about Dissolved Oxygen, probably moving towards zero in your scenario.0

 

[Dan_P]

I'm starting an occasional series of threads on thought experiments.

Things for which there's no known correct answer since they have not, and often cannot, be tested. Just fodder for in depth discussion of various topics.

We will start with a very complicated thought question.

Todays question:

What would happen in a normal, healthy, cycled reef aquarium if one added an antibiotic that killed all bacteria in the aquarium, and had no other direct effects on any other organism.

What would happen that an observer looking at the tank, and taking measurements of normal reef parameters, observe immediately and as time went by?


Let's have some intellectual fun with this!

Very crafty of you!

Anything depending on living bacteria, for examples predators and symbiotic organisms, sicken and could die adding to the amount of biomass of dead bacteria.This includes some algae that depend on bacteria for vitamins. All bacterial processing of organic matter and waste stops. Fungus might carry some of the digestion duty. Ammonia generated by higher organisms accumulates. DOC increases.

Photosynthetic organisms take over ammonia consumption. Organisms that consume organic matter increase in number without bacteria competition. Greening of the aquarium takes place. DOC continues to increase but as the antibiotic level declines, bacteria begin to return. Bacteria inside fish and coral might be another source of bacteria. Nuisance organism populations increase and colonize the bacteria free surfaces.

In 1-2 months the aquarium looks like a mess.

 

[brandon429]

nice catch on required metabolic nutrient limitation that's a sick catch

 

[HomebroodExotics]

I believe you would have dinos or some other sort of organism take over very quickly.

 

[Randy Holmes-Farley Verified Community Expert]

A number of folks mentioned the nitrogen cycle, but in an established reef tank with plenty of photosynthetic organisms that are happy to take up ammonia, do we know that bacteria are important at all with respect to ammonia?

 

[Dan_P]

A number of folks mentioned the nitrogen cycle, but in an established reef tank with plenty of photosynthetic organisms that are happy to take up ammonia, do we know that bacteria are important at all with respect to ammonia?

I feel the answer depends on scale. At the aquarium scale, I give a provisional “no” answer. At the biofilm scale, my answer is a solid “yes”.

Algae will consume ammonia in the water and our ammonia test result would let us sleep at night. At the biofilm level, ammonia would probably accumulate because heterotrophic bacteria growth is generally carbon limited, and this could affect which organisms are thriving on the surface. A locally high concentration of ammonia could favor a different collection of organisms than a surface depleted of ammonia by oxidation to nitrate. I would guess the depleted nitrogen condition would be esthetically pleasing to the hobby.

 

[brandon429]

really great call on photosynthetic command

-they are only working half the day, nitrifiers are round the clock

we should kill off cycling bac on test surfaces that doesn't have any extra complement of plants on it other than the microscopic inclusions all live rocks have, and test that theory, it's sound for sure

*when we do large skip cycle setups, dry starts on bottle bac, what's in the bottles added aren't plants they're monerans but that doesn't mean they remain the permanent residents doing the ammonia control

someone do a test to see if bacteria matter over time: live rock won't work as the test substrate in my opinion bc it's too porous to let antibiotics get into all crevices, some bac will survive

someone take test tiles and pack them in the display, not the sump, of a running reef 5 months, let them become live

then deactivate the bac with whatever antibiotics are indicated for the strains aquabiomics has been showing were related to ammonia control in reef tanks, then test those tiles for ammonia command in a separate test setup

 

[bushdoc]

I am assuming that ALL bacteria would cease to exist in this experiment, including those in Fish and invertebrates gut.After all Marine Fish drink sea water and would be exposed to antibiotics.
Sterilizing gut of fish would inevitably cause some diseases, gut bacteria provide some vitamins, aid immunological function and aid digestion of nutrients.
In humans altering bacterial flora leads frequently to fungal infections, in fish it might lead to parasites taking over. Killing most of bacteria would also lead to appearing of antibiotic resistent strains, which are frequently more virulent. Humans with sterilized gut ( due to prolonged course of antibiotics to fight some infection) often develop debilitating diarrhea ( Clostridium difficile), which have to be treated with even more antibiotics and frequently followed by fecal transplant ( introduction of fecal bacteria from healthy donor).
I would say that Reef Tank deprived of all bacteria would cease to exist as a reef tank and fish, corals and other invertebrates would suffer high morbidity and mortality.

 

[LadAShark]

Another thing is that corals also symbiose with various bacteria, and also consume various other bacteria.

Various sponges also rely on bacteria the same.

Another thing is that depending on how the hypothetical is approached, if it's some magical antibiotic that only kills all the bacteria, or if it's enough antibiotics to kill all bacteria have very different results. Some, if not many antibiotics are not entirely bacteria specific

Anyway, another thing not mentioned is that the amount of detritus and organic material in the reef would shoot out the roof. As far as I recall the uptake and breakdown of ATP into phosphate is also done by bacteria, and many organisms' cells do not uptake ATP, so that would be an interesting phenomenon, with phosphate not necessarily following the rise in ammonia (which, I am not sure if algae can uptake atp to keep up with).

 

[LadAShark]

I am assuming that ALL bacteria would cease to exist in this experiment, including those in Fish and invertebrates gut.After all Marine Fish drink sea water and would be exposed to antibiotics.
Sterilizing gut of fish would inevitably cause some diseases, gut bacteria provide some vitamins, aid immunological function and aid digestion of nutrients.
In humans altering bacterial flora leads frequently to fungal infections, in fish it might lead to parasites taking over. Killing most of bacteria would also lead to appearing of antibiotic resistent strains, which are frequently more virulent. Humans with sterilized gut ( due to prolonged course of antibiotics to fight some infection) often develop debilitating diarrhea ( Clostridium difficile), which have to be treated with even more antibiotics and frequently followed by fecal transplant ( introduction of fecal bacteria from healthy donor).
I would say that Reef Tank deprived of all bacteria would cease to exist as a reef tank and fish, corals and other invertebrates would suffer high morbidity and mortality.

Assuming that no bacteria ever can come to exist in the system, the truth is fungi also exist aquatically. Unforeseeable fungal infections may also be an issue in the reef as well.

 

[LadAShark]

I am assuming that ALL bacteria would cease to exist in this experiment, including those in Fish and invertebrates gut.After all Marine Fish drink sea water and would be exposed to antibiotics.
Sterilizing gut of fish would inevitably cause some diseases, gut bacteria provide some vitamins, aid immunological function and aid digestion of nutrients.
In humans altering bacterial flora leads frequently to fungal infections, in fish it might lead to parasites taking over. Killing most of bacteria would also lead to appearing of antibiotic resistent strains, which are frequently more virulent. Humans with sterilized gut ( due to prolonged course of antibiotics to fight some infection) often develop debilitating diarrhea ( Clostridium difficile), which have to be treated with even more antibiotics and frequently followed by fecal transplant ( introduction of fecal bacteria from healthy donor).
I would say that Reef Tank deprived of all bacteria would cease to exist as a reef tank and fish, corals and other invertebrates would suffer high morbidity and mortality.

Assuming that no bacteria ever can come to exist in the system, the truth is fungi also exist aquatically. Unforseeable fungal infections may also be an issue in the reef as well. Piggybacking off my previous comment, various fungi can uptake ATP, so with the presence of ATP and ammonia, we may actually end up selecting for fungal growth.

 

[KrisReef]

Assuming that no bacteria ever can come to exist in the system, the truth is fungi also exist aquatically. Unforseeable fungal infections may also be an issue in the reef as well. Piggybacking off my previous comment, various fungi can uptake ATP, so with the presence of ATP and ammonia, we may actually end up selecting for fungal growth.

How many other reefers out their get into this hobby because they were inspired by a growth in their gym socks?

 

[LadAShark]

How many other reefers out their get into this hobby because they were inspired by a growth in their gym socks?

Why else would we have sock filters?

 

[Azedenkae]

What would happen in a normal, healthy, cycled reef aquarium if one added an antibiotic that killed all bacteria in the aquarium, and had no other direct effects on any other organism.

Does this include bacteria inside other organisms? I.e. in the guts of fish, etc.

Also, I assume you would also include all archaea? Or are we really talking bacteria specifically and not all prokaryotes?

 

[Randy Holmes-Farley Verified Community Expert]

Lots of great discussion folks!

Of course, no one knows exactly what will happen, but here are some ideas of what I think might happen.

1. I think in the first few minutes, nothing visible happens.

2. Over a period of hours, what happens may depend strongly on whether there are many bacteria harboring toxins (such as cyanobacteria). Lots of dead bacteria beginning to fall apart and releasing toxins might be a severe problem for fish and some other organisms.

3. In the same time frame, the water will yellow as organics are released from dead bacteria. Interestingly, though, the lack of bacteria may slow the lowering of O2 and save the fish from an otherwise low O2 or increased hydrogen sulfide situation. Some larger organisms may thrive on the increased organics.

4. In the first hours, I doubt algae changes much. Bacteria, even if dead, are still protecting surfaces from algae attachment for a while. That will decline as they break down and fall apart, but that might take days before sufficiently bare surfaces get exposed.

5. Other organisms that consume organics will rapidly expand in numbers. Marine fungi are poorly understood, but some of these may find a new niche, maybe even covering old bacteria-covered surfaces. Other microorganisms go wild, at least compared to their normal populations. . Viruses that invade bacterial are not having a good time, but they can hang out waiting for hosts.

6. Now the reinvasion starts. The antibiotics are likely themselves broken down (by oxidation, UV, skimmed out, bound to GAC, etc.) or just precipitated into organic matter/detritus, and the concentrations drop low enough for bacteria to repopulate from the air, foods added, etc.

7. The first bacteria back are colonizing a brave new world, and some of them grow like crazy until something limits them (probably trace elements). Fish and other organisms that were Ok for a little while without bacteria may not be when they get new bacterial species on and in them. Some bacteria will be benign, or beneficial, while others will be pathogens. What these bacteria do will depend entirely on which ones get into the system first, and how fast each strain can reproduce.

8. My guess is that at least some organisms will succumb to bacterial infections, but I have no idea which ones. Others will weather the changes, and may do fine. If larger dead organisms are not removed (say, a fish), that will accelerate the problems for many other organisms

9. Eventually (months, probably, maybe a year), a new balance is attained. I expect the tank will look like crap, with lots of green algae all around, but who knows.

As to chemical parameters, here are some thoughts:

1. In the first few minutes, no big change.
2. Over hours, organics are rising, as may certain trace elements that the dead bacteria release, but not nitrate and phosphate. Alk and calcium are basically unchanged for a few hours.
3. The consumption of alk and calcium may slow as abiotic calcification is inhibited by organics. Is coral and coralline algae calcification slowed? Probably.
4 Fish and other large organisms (crabs, shrimp, etc.) will continue to pump out ammonia and phosphate for photosynthetic organisms, so as long as they are still alive, photosynthetic organisms will be getting nutrition.
5. I do not know what chemicals are released from microorganisms other than bacteria as they expand in numbers, but toxins might begin to be a problem.
6. Long term, alk and calcium demand may depend solely on which organisms survive the bacteria reinvasion.

 

[Edgecrusher28]

Lots of great discussion folks!

Of course, no one knows exactly what will happen, but here are some ideas of what I think might happen.

1. I think in the first few minutes, nothing visible happens.

2. Over a period of hours, what happens may depend strongly on whether there are many bacteria harboring toxins (such as cyanobacteria). Lots of dead bacteria beginning to fall apart and releasing toxins might be a severe problem for fish and some other organisms.

3. In the same time frame, the water will yellow as organics are released from dead bacteria. Interestingly, though, the lack of bacteria may slow the lowering of O2 and save the fish from an otherwise low O2 or increased hydrogen sulfide situation. Some larger organisms may thrive on the increased organics.

Just finished a 5 day in-tank treatment with Amoxicillin and Cephalexin and within a day or so the water had the most insane yellow tint I have ever seen (carbon reactor was not in use), ORP fell immediately from 320 to 140 and PH also dropped from 8.2 to 7.7. These numbers did not seem to fluctuate after additional doses however.

4. In the first hours, I doubt algae changes much. Bacteria, even if dead, are still protecting surfaces from algae attachment for a while. That will decline as they break down and fall apart, but that might take days before sufficiently bare surfaces get exposed.

5. Other organisms that consume organics will rapidly expand in numbers. Marine fungi are poorly understood, but some of these may find a new niche, maybe even covering old bacteria-covered surfaces. Other microorganisms go wild, at least compared to their normal populations. . Viruses that invade bacterial are not having a good time, but they can hang out waiting for hosts.

6. Now the reinvasion starts. The antibiotics are likely themselves broken down (by oxidation, UV, skimmed out, bound to GAC, etc.) or just precipitated into organic matter/detritus, and the concentrations drop low enough for bacteria to repopulate from the air, foods added, etc.

7. The first bacteria back are colonizing a brave new world, and some of them grow like crazy until something limits them (probably trace elements). Fish and other organisms that were Ok for a little while without bacteria may not be when they get new bacterial species on and in them. Some bacteria will be benign, or beneficial, while others will be pathogens. What these bacteria do will depend entirely on which ones get into the system first, and how fast each strain can reproduce.

8. My guess is that at least some organisms will succumb to bacterial infections, but I have no idea which ones. Others will weather the changes, and may do fine. If larger dead organisms are not removed (say, a fish), that will accelerate the problems for many other organisms

9. Eventually (months, probably, maybe a year), a new balance is attained. I expect the tank will look like crap, with lots of green algae all around, but who knows.

As to chemical parameters, here are some thoughts:

1. In the first few minutes, no big change.
2. Over hours, organics are rising, as may certain trace elements that the dead bacteria release, but not nitrate and phosphate. Alk and calcium are basically unchanged for a few hours.
3. The consumption of alk and calcium may slow as abiotic calcification is inhibited by organics. Is coral and coralline algae calcification slowed? Probably.
4 Fish and other large organisms (crabs, shrimp, etc.) will continue to pump out ammonia and phosphate for photosynthetic organisms, so as long as they are still alive, photosynthetic organisms will be getting nutrition.
5. I do not know what chemicals are released from microorganisms other than bacteria as they expand in numbers, but toxins might begin to be a problem.
6. Long term, alk and calcium demand may depend solely on which organisms survive the bacteria reinvasion.

 

[KrisReef]

Just finished a 5 day in-tank treatment with Amoxicillin and Cephalexin and within a day or so the water had the most insane yellow tint I have ever seen (carbon reactor was not in use), ORP fell immediately from 320 to 140 and PH also dropped from 8.2 to 7.7. These numbers did not seem to fluctuate after additional doses however.

The thought experiment perhaps was possible to make in the real world? It would be helpful to know what bacteria are alive in this tank as certainly not all were killed by the application of the two antibiotics, or were they?
Interesting that the yellow cascade of organic material is observed, and not just a thought apparently.
I’ve got more thinking to do to understand this question, a lot more than I “thought.”