Why are all systems running out of bacteria?

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gbroadbridge

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Truly honest question, supposing that we are not adding bleach to our systems. What’s happening to the bacteria this days? Is it dying and if it’s dying how can we introduce new bacteria, if we can’t even sustain the ones we were supposed to have, it seems to be the new trend, add as many as you can. Is microbe diversity really achieved this way?
I always had in mind that diversity was achieved with a stable system and if it’s stable are we really loosing out on something?
What makes you think we're running out of bacteria. They're everywhere.

Some tanks can develop a lack of biodiversity when one bacterial strain is outcompeted by another, but that's nothing new. They'll come back when needed.

New tanks, starting with sterile materials (bereft of useful bacteria for a marine ecosystem), need bacteria introduced either from some media from an existing tank (preferred) or from a bottle (which will not contain a complete useful biome). Adding animals and coral over time will increase diversity.

I believe bottled products are useless once a tank is up, running and stable - say after a couple of years.
 

damsels are not mean

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I am no microbiologist but I would think adding a single coral frag would bring in more diversity than all the bottled products combined. If you want that biodiversity get some live rock. Even the stuff rotting in buckets at your LFS is good for seeding whatever diversity we are after. Ideally some rock from a trusted friend's old tank.
 
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Why are all systems running out of bacteria?​


Due to the large number of mostly beginner questions asking if their systems need additional bottled bacteria on a regular basis, I can see why you may think this is a real thing.

The problem is not that bacteria are being lost from a properly set up system (only the unwise introduction of chemicals hostile to microbial life and catastrophic events can cause this), it's that a system is often not being set up properly in the first place. Dry rock and dry sand by themselves certainly do not make for a diverse and populous community of microorganisms!

Way back in the early days of reef keeping here in the US we followed one rule and that was either use all live rock (preferred) or if not available/too expensive at least a mix of ~50/50 base rock and quality live rock for the top. Base rock was usually from a reef's 'rubble zone' that got tossed around by wave action so much that not much grew on it (or could have been from an aquarist's sump) and the live rock was the premium rock from calmer reef areas that had lots of coralline, macro algae, sponges, etc. Bacteria was never an issue for a properly operating system and no one ever 'ran out of it' ;)

Case in point: My 14 year old reef has higher biodiversity than the average 5 year old system (Aquabiomics test) and most of the live rock (Indo-pacific) and sand is 25 year old. This doesn't speak to loss any possible loss of bacteria, but it's well known that a diverse community of microorganisms will populate every available niche (substrates and free living).
We’ll said, that’s a great approach to reef keeping
 
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I am no microbiologist but I would think adding a single coral frag would bring in more diversity than all the bottled products combined. If you want that biodiversity get some live rock. Even the stuff rotting in buckets at your LFS is good for seeding whatever diversity we are after. Ideally some rock from a trusted friend's old tank.
That’s always been my thoughts too
 
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sixty_reefer

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I think that bacteria get skimmed out over time or filtered out depending on what type of mechanical filtration is used.

I know Dr. Tim makes good products. The results can actually be measured. You can easily measure your nutrient levels and then dose Waste Away or Eco-balance in a dirty tank. Wait 24-48 hrs and measure again. Both are concentrated products. The first time I used Waste Away I heard a strange gurgling noise coming from my tank early that morning. When I went to investigate the pipes were making a funny noise which wasn’t the case before I dosed. The pipes became much cleaner allowing better water flow. At that point I realized how effective specific bacteria like (Waste Away) or [Heterotrophic bacteria] could be. Only 1/2 half dose was very effective. I typically don’t even do that much anymore. I just do 1/4 dose currently and it’s been effective at fighting Dino’s (helps outcompete them), but also doesn’t drop my nutrient levels too aggressively.

The question is how much do we need in the system and how to measure when their gone? I don’t really want to pay for an Aquabiomics test every 2 months so I try to watch the algae growth and look at nutrient numbers as a few ways to blindly measure the amount of bacteria in the system. Probably not the best indicators, but pay $100 for a test is too much for me.

Like mentioned above…when I dose Ecobalance or Waste Away it’s consuming nutrients, but there is a decline as time passes. Are they being skimmed out this fast? Should the skimmer be off for a few hours daily and if so can this be measured looking at nutrient levels (specifically phosphate) to understand how well this works and how long it should be off. We know Heterotrophic bacteria can divide in 20 minutes so this will work for them, but what about Nitrifiers? Will they be able to compete for surface area as we know they do not multiply nearly as fast or will they get outcompeted? Should we put competitors in the system that can grow much faster and steal all the available micronutrients that our Nitrifiers need? However, they must still be in the system since we know these bacteria are Ammonia and Nitrite Oxidizer’s. I guess the question I have is how to properly balance them both. A lot of other questions in my mind also.

Also, how big of a role do trace elements play with the bacterial diversity or population? I suspect it’s important as I’ve noticed a much healthier tank keeping the Trace’s in range as opposed to them being depleted or low. Could be coincidence though.? The water is more clear, algae doesn’t seem to be as aggressive, nutrients are much easier to manage, corals are happier with better polyp extension. Maybe this is due to traces alone and not so much the bacteria, but I do feel that the microbiology as a whole need phosphate and a lot of different trace elements to not only grow, but to thrive and populate in the tank.

@Dr Tim’s Aquatics?
I have no doubt in the quality of the products we are being offered, I’m more in the thought why do a stable mature system needs the addition of so much diversity, where did things go wrong, all the bacteria that comes in the bottle was supposed to already be in the system. What happened to the bacteria that was in the tank for the need to add more
 

Dan_P

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Exactly. It’s so silly to me how people are trying to collect bacteria like it’s Pokémon cards.

As far as I’m concerned, I believe “not enough bacteria” is just a catch all to explain why corals are dying. But logically, it doesn’t make sense to me. Corals share symbiosis with zooxanthellae. As long as the parameters are in proper range, there’s some organic matter to feed the corals, light, and flow: I fail to see how not having enough bacteria could cause an issue.

Unless your corals are starving to death so you feed bacteria.

Here’s a thought provoking question: ever seen those reef shows where they quickly set up exhibit tanks and fully stock it with corals? Do you think those people needed to worry about EDNA sequencing and collecting mud from places? Probably not. It’s bogus IMO.

I stopped worrying about bacteria. With dry rocks, they often leach nutrients and there’s a lot of competition for open territory. If algae grows and smothers corals, that’s not good.
Coral do have and need bacteria to live, but there is no connection between coral health and bottled bacteria. I am not certain whether anyone has demonstrated a link between coral health and the presence of live rock from the ocean ( a potential source of bacteria).

Bottled bacteria were initially sold as miracle cures for the waste disposal process in the aquarium. Unproven claims like grunge and detritus reduction cover these product bottles. Then the vendors and aquarists upped the claims to include using these products for the elimination of nuisance algae. All we have is anecdotal data which puts all the claims of benefits of bottled bacteria (not cycling bacteria) in with claims of seeing Big Foot.
 

Reefahholic

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I have no doubt in the quality of the products we are being offered, I’m more in the thought why do a stable mature system needs the addition of so much diversity, where did things go wrong, all the bacteria that comes in the bottle was supposed to already be in the system. What happened to the bacteria that was in the tank for the need to add more
I believe It gets skimmed and filtered out over time. Maybe not depleted, but I think the population may become lower and need to be supplemented.
 
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I believe It gets skimmed and filtered out over time. Maybe not depleted, but I think the population may become lower and need to be supplemented.

Think about it this way. If you were to somehow manage to remove 1/2 of the total number of bacteria from a typical reef aquarium what would the remaining bacteria do? They'd immediately get busy and start reproducing to fill the void! On one end, some of our bacteria can replicate within the hour and some might take a few days, but within a relatively short period of time bacterial numbers would be back to whatever the system's microorganism physical holding capacity is (determined by how much space, both substrate and free living volume, is available in the system).
 

Nano sapiens

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Where is the bacteria found? On the corals themselves?

Microorganisms (such as bacteria, archaea, fungii, etc.) are found just about everywhere in nature so for reef aquariums that includes anything (substrates like sand, rock, plastic piping, glass, the fish, etc. and also the water column). So yes, corals have their own species specific set of microbial communities living in and on them, which is typically called the 'Microbiome' (or sometimes 'Holobiont').
 
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JCM

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Why are all systems running out of bacteria?​


Due to the large number of mostly beginner questions asking if their systems need additional bottled bacteria on a regular basis, I can see why you may think this is a real thing.

The problem is not that bacteria are being lost from a properly set up system (only the unwise introduction of chemicals hostile to microbial life and catastrophic events can cause this), it's that a system is often not being set up properly in the first place. Dry rock and dry sand by themselves certainly do not make for a diverse and populous community of microorganisms!

Way back in the early days of reef keeping here in the US we followed one rule and that was either use all live rock (preferred) or if not available/too expensive at least a mix of ~50/50 base rock and quality live rock for the top. Base rock was usually from a reef's 'rubble zone' that got tossed around by wave action so much that not much grew on it (or could have been from an aquarist's sump) and the live rock was the premium rock from calmer reef areas that had lots of coralline, macro algae, sponges, etc. Bacteria was never an issue for a properly operating system and no one ever 'ran out of it' ;)

Case in point: My 14 year old reef has higher biodiversity than the average 5 year old system (Aquabiomics test) and most of the live rock (Indo-pacific) and sand is 25 year old. This doesn't speak to loss any possible loss of bacteria, but it's well known that a diverse community of microorganisms will populate every available niche (substrates and free living).

Yes all of this. We all used to start with real live rock and bottled bacteria would've been laughed at. I dont believe it's a coincidence that we see so many problems these days while most people are using dry rock and sand to start tanks.

I started my new tank last year with real rock pulled straight from the ocean. It looked and behaved "mature" from the start and I've never had any of the problems I see posted here so frequently. Sure I have some patches of algae that grow, but so does every natural reef out there. Bacterial diversity has never been a concern.
 

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Truly honest question, supposing that we are not adding bleach to our systems. What’s happening to the bacteria this days? Is it dying and if it’s dying how can we introduce new bacteria, if we can’t even sustain the ones we were supposed to have, it seems to be the new trend, add as many as you can. Is microbe diversity really achieved this way?
I always had in mind that diversity was achieved with a stable system and if it’s stable are we really loosing out on something?
I have not heard of this as being a problem before except when maybe when there have been crashes or possibly when meds have been used on fish that might also affect the bacterial balance. Was there a study done on this? I would like to read the sources you got this info from. It's entirely possible that in our closed systems the bacteria eventually gets stripped out and needs to be replenished so I would like to read more about this.
 
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Think about it this way. If you were to somehow manage to remove 1/2 of the total number of bacteria from a typical reef aquarium what would the remaining bacteria do? They'd immediately get busy and start reproducing to fill the void! On one end, some of our bacteria can replicate within the hour and some might take a few days, but within a relatively short period of time bacterial numbers would be back to whatever the system's microorganism physical holding capacity is (determined by how much space, both substrate and free living volume, is available in the system).
I’ve noticed something odd when skimming. I’ve never liked cleaning the cup but thought aeration was of utmost importance, so I’ve had one on for ages. Four or 5 weeks ago I removed the skimmer and just ran the needle wheel pump in the sump (never tried that before). For the first few weeks I got a foam head on the sump surface, as you would expect. Then the foam head disappeared. This can only be due to bacteria consuming it surely. Makes me think that folks are not allowing the bacteria to develope in the foam when skimming and it ends up as a self fulfilling prophecy.
 

Dan_P

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Where is the bacteria found? On the corals themselves?
Yes, but it seems they come equipped with them. I don’t recall anyone claiming you have to adjust their biome to keep them healthy in a new aquarium, though it is just a matter of time before somebody starts selling a coral biome elixir.
 

Forty-Two

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Where is the bacteria found? On the corals themselves?
They indeed do. I read a couple of articles about it but I don’t have them handy at the moment (and too tired to find them). There was also a study done on dying Florida corals.

During the study it came to light that corals
have their own micro biome which is critical to their survival. This has fed a few theories that we may be better off stocking a new tank heavily with corals to propagate bacteria as healthy bacteria counts and types are essential to a healthy reef. Sorry for the digress there - anyhoo turns out what was happening in Florida was that septic tanks were leaking into the ocean and that ‘bad bacteria’ was settling on the corals and disrupting the micro biome of the corals and this causing them to die.

Back to the original topic - the issue today - the reason the Op sees so many posts about this topic is because of two reasons in my opinion:

1) there are some large vendors out there that have convinced folks that starting a tank with dry rock is a normal and viable way to start a reef tank - without mentioning that rock from the Ocean has had thousands of years to collect the necessary life forms on it conducive to life - and yes - you could buy dry rock and eventually get there but chances are it’s going to be much more expensive and many more interventions will be needed to achieve that - but hey - it lines their pocketses right?
2) There is a legit shortage of live rock these days, and a shortage of dry rock from the Ocean(ie: Tonga/Indonesian etc). I suspect that if demand were higher there would be a method to supply it - but see point #1. The Ocean has a lot of rock in it - and I’m not sure that rock from a reef is necessary - somewhat porous rubble from the Ocean is still likely better that Marco rock or “Real reef rock”. Regardless bio-diversity is a major problem these days as a result.
 

Nano sapiens

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It's entirely possible that in our closed systems the bacteria eventually gets stripped out and needs to be replenished so I would like to read more about this.

As mentioned earlier, the typical reef aquarium microbiome will be at a certain system specific maximum density for the given substrates, water volume and nutrients provided. If any bacteria are removed (water changes, gravel vacuuming, etc.), the remaining bacteria will repopulate in a relatively short period of time. So any stripping is only temporary and replenishment is a given in a properly functioning aquatic system.

Now over time, the composition of the microbiome (microorganism community) can change due to a variety of factors. And at this point all we can say is that if the reef aquarium is functioning properly (animals are healthy, algae is controlled), then the microbiome (whatever microorganism community it happens to be made up out of) are in a proper state of dynamic equilibrium ('a state of balance between continuing processes').
 
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monicalooze

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Bacteria can be a funny thing. There are so many stains that compete for similar resources. One thought I have on this is the use of “man made live rock”. Everyone has shifted to dry rock or cultured rock. I think that has a serious effect on bacteria balance. Not saying it’s not good to be sustainable but real live rock carries a lot of micro fauna that can be very benificial.
Started a tank approximately 3.5 mos ago with live rock from KP aquatics. I will literally never do it with dry rock again. I'm feeding enough zooplankton and phytoplankton to create an algae forest the size of the Amazon, and there is literally no algae. The water is absolutely crystal clear. I've found some icky pests, like a leopard polyclad flatworm that ate three of my snails, a mithrax crab that ate a bunch of macros and a photosynthetic sponge, and there's a couple crabs I'm still working on catching, but overall it's a lot more fun and the tank is far more stable than my 2.5 year old tank, which is still struggling - you can tell something is out of whack, but it's none of the normal parameters or anything one can test for. My relationship with the new tank hasn't been "abusive" (heh.) and I have all sorts of cool tunicates, brittlestars, a pistol shrimp, fan-worms, sponges, and other things I haven't yet identified.

I got into the hobby because I love the ocean, and it's much more fun (for me) to create a natural ecosystem using natural filtration methods than have a perfectly neon, sterile, SPS tank. To each their own. Neither one is better or worse, but I do think beginners would be more likely to stick with the hobby if they traded dry rock for live. The struggle is real otherwise.
 
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