Tips/Tricks For Maintaining Maximum Bacterial Diversity on Live Rock

[livinlifeinBKK]

Hey guys, so I'm a pretty big fan of wild (ocean) collected live rock and love the biodiversity it brings to a tank especially the bacterial biodiversity which we aren't really able to replicate artificially. However, I'm aware that due to competition among bacterial strains as well as environmental conditions in aquariums a bit of that biodiversity is lost and I was just curious if anyone had any tips or anything like that they believe helps to maintain as much of that original bacterial biodiversity as possible. I'd be really interested in hearing if anyone does.

 

[Spare time]

There really isn't a good answer to this in my opinion. The bacterial species density and ratios will fluctuate over time depending on a lot of factors. You would need to know each species, their energy sources, preferred micro-habitat, etc. Its just not practical. However, you can definitely do things to keep the water column bacterial numbers up, such as avoiding protein skimmers (or running them on a timer), not using UV, doing smaller water changes at a time, etc. The only other thing I could thing of would be to regularly dose something like AF life source (assuming the desireable bacteria are alive, able to survive storage and, then able to survive the movement to a reef aquarium habitat).

 

[HudsonReefer2.0]

I just added a # of live sand from aqua biomics lil over a month ago. They give a break down of the bacterial strains. Followed directions. So far so good. May add more in future after sending a water sample for analysis.

 

[Spare time]

I just added a # of live sand from aqua biomics lil over a month ago. They give a break down of the bacterial strains. Followed directions. So far so good. May add more in future after sending a water sample for analysis.

Wait they actually had some available? lol

 

[shakacuz]

Wait they actually had some available? lol

sign up for the stocking notifications. i recently bought their sand to help with some dino’s/cyano. with some dosing of MB7 and MB clean. it was gone almost within two weeks

aquabiomics is a good source for a wide variety of bacteria

 

[HudsonReefer2.0]

Wait they actually had some available? lol

Yeah wait list notifications

 

[Spare time]

sign up for the stocking notifications. i recently bought their sand to help with some dino’s/cyano. with some dosing of MB7 and MB clean. it was gone almost within two weeks

aquabiomics is a good source for a wide variety of bacteria

I might. It depends if I'm starting a new tank or not lol

 

[HudsonReefer2.0]

I might. It depends if I'm starting a new tank or not lol

I added to my existing. Figured why not. Lol.

 

[jabberwock]

I have been trying to achieve this with my latest build (25 gallon lagoon AIO) by starting a tank with small amounts of "live rock" from two different LFS. I believe this inherently introduces diversity because it is two separate sources. This "live rock" has been sourced from maintenance clients that have taken down tanks and has been maintained in tubs at the store. It even has some coralline algae on it. I also added some ceramic media to increase surface area. It is only about 1.5 pounds of actual rock.

I am dosing with Dr. Tim 's ammonia in order to build up some nutrients for the actual ocean live rock that I will be driving to Tampa to pick up in 9 days (20 pounds). I will go through a 90 day observation period of the ocean live rock with a single fish. All of this will occur with no sand and lights out.

So far, so good.

 

[fishface NJ]

I just added a # of live sand from aqua biomics lil over a month ago. They give a break down of the bacterial strains. Followed directions. So far so good. May add more in future after sending a water sample for analysis.

Wow $49 for a 10 oz container of water with sand. Next time I'm in Cape Coral/Sanibel FL I'll go scuba diving and bring some sand to my NJ home

 

[jabberwock]

Wow $49 for a 10 oz container of water with sand. Next time I'm in Cape Coral/Sanibel FL I'll go scuba diving and bring some sand to my NJ home

Don't post about it unless you have a collection permit...

 

[fishface NJ]

Don't post about it unless you have a collection permit...

didn't know one could not take 3 oz of sand from the beach or ocean

 

[jabberwock]

didn't know one could not take 3 oz of sand from the beach or ocean

technically that sort of thing IS regulated, so just don't admit to it on the internet.

 

[livinlifeinBKK]

Thanks for the replies guys, I know there isn't exactly a "cut and dry" answer to this question but I just wanted to hear you guys' opinions...i actually do have AF Life Source and dose it fr time to time. Of course, there's no telling how mucj of the original bacteria are still alive in there but it can't hurt

 

[Nano sapiens]

I do not know where this idea came about that reef associated bacteria/archaea can go extinct in a system via competition. You'd need something like an oxidizing agent (ex.: chlorine) in sufficient concentration or heat, or possibly cold, beyond the microorganism's tolerance to actually kill them off completely.

Bacteria, once added, are really resilient. Specific species may be outcompeted to the point that they might not show up on an rDNA test (like Aquabiomics), but they are still there and either active in limited numbers or possibly in a dormant state. If conditions change to their liking, however, they can multiply and become visible in the microbiome tests.

Adding bottled bacteria to try and achieve a diverse microbiome is an incorrect use of the product since nearly all reef associated bacteria/archaea can't even be cultured in a lab. 'Bottled bac' has it's uses for establishing the initial nitrogen cycle quickly and digesting organic matter, but this is a far cry from all the thousands of bacteria/archaea species found on a reef or in a thriving reef aquarium that are the main contributors to making the whole system work. It has also been shown that these bottled bacteria typically do not persist (beyond residual numbers) after a few weeks.

 

[ISpeakForTheSeas]

since nearly all reef associated bacteria/archaea can't even be cultured in a lab.

Not trying to be argumentative here, so I apologize if it comes across that way, as I’m just genuinely curious - I’ve seen this claim repeated a few times now on the forum here and I’m wondering why people say this, as I’ve actually been looking into a number of different marine bacterial strains, and labs do actively culture literally thousands of the common bacteria species we find in reef and reef-associated systems. Granted, the places with the largest number of strains seem to all be European and almost exclusively unavailable to the general population, and most of these strains are definitely not easy or cheap to come by regardless, but, to my knowledge, labs actually can and do culture a good, significant number of these species (I don’t know that I could say they culture or could culture most of the species at this point, as I honestly don’t know a ballpark number to work with for how many different species might exist, but I certainly wouldn’t feel confident saying that we can’t culture the vast majority of them).

Again, I’m not trying to be combative here, I’m just genuinely wondering why this belief is held and if there is a solid, logical reasoning/explanation behind it.

 

[Nano sapiens]

Not trying to be argumentative here, so I apologize if it comes across that way, as I’m just genuinely curious - I’ve seen this claim repeated a few times now on the forum here and I’m wondering why people say this, as I’ve actually been looking into a number of different marine bacterial strains, and labs do actively culture literally thousands of the common bacteria species we find in reef and reef-associated systems. Granted, the places with the largest number of strains seem to all be European and almost exclusively unavailable to the general population, and most of these strains are definitely not easy or cheap to come by regardless, but, to my knowledge, labs actually can and do culture a good, significant number of these species (I don’t know that I could say they culture or could culture most of the species at this point, as I honestly don’t know a ballpark number to work with for how many different species might exist, but I certainly wouldn’t feel confident saying that we can’t culture the vast majority of them).

Again, I’m not trying to be combative here, I’m just genuinely wondering why this belief is held and if there is a solid, logical reasoning/explanation behind it.

No worries, always good to question an unsubstantiated statement as it keeps everyone honest

I have heard Aquabiomics's founder, DR. Eli Meyer, mentioned the difficulty of culturing the vast majority of marine associated microbes in his video talks, but let's look to some scientific articles for the evidence:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815769/

'The potential for using marine microbes for biodiscovery is severely limited by the lack of laboratory cultures. It is a long‐standing observation that standard microbiological techniques only isolate a very small proportion of the wide diversity of microbes that are known in natural environments from DNA sequences. A number of explanations are reviewed. The process of establishing laboratory cultures may destroy any cell‐to‐cell communication that occurs between organisms in the natural environment and that are vital for growth. Bacteria probably grow as consortia in the sea and reliance on other bacteria for essential nutrients and substrates is not possible with standard microbiological approaches...'


More recent article show that some progress is being made:

https://www.researchgate.net/public...s_for_culturing_activedormant_marine_microbes

'Microorganisms are ubiquitous in the ocean environment and they play key roles in marine ecosystem function and service. However, many of their functions and phenotypes remain unknown because indigenous marine bacteria are mostly difficult to culture. Although many novel techniques have brought previously uncultured microbes into laboratory culture, there are still many most-wanted or key players that need to be cultured from marine environments. This review discusses possible reasons for ‘unculturable microbes’ and categorizes uncultured bacteria into three groups: dominant active bacteria, rare active bacteria, and dormant bacteria. This review also summarizes advances in cultivation techniques for culturing each group of unculturable bacteria...'


https://link.springer.com/article/10.1007/s42995-021-00093-z

'Microorganisms (both pro- and eukaryotes) occur in all marine environments with an estimated abundance of 103–1010 cells/cm3 in sediments and 104–107 cells/ml in seawater; in these habitats they play key roles in marine biogeochemical cycles (Overmann and Lepleux 2016). Surveys employing molecular marker-based high-throughput sequencing and sophisticated metagenomic approaches have revealed the vast diversity of microorganisms in marine environments and have substantially expanded the tree of life (Castelle and Banfield 2018; Hug et al. 2016; Nayfach et al. 2020). However, many of the novel lineages have no cultured representatives. In fact, most (> 99%) of the marine microorganisms have not been cultured under laboratory conditions (Hofer 2018; Jiao et al. 2020) and are seen as “microbial dark matter” (Lok 2015)...'

My impression after exploring this in a bit more depth is that 'uncultured' doesn't necessarily equate to 'not possible to culture'. From what I can see, the topic is receiving more attention and serious efforts are underway to add to the list of 'culturable marine microbes' using a variety of standard and novel culture techniques.

 

[ISpeakForTheSeas]

No worries, always good to question an unsubstantiated statement as it keeps everyone honest

I have heard Aquabiomics's founder, DR. Eli Meyer, mentioned the difficulty of culturing the vast majority of marine associated microbes in his video talks, but let's look to some scientific articles for the evidence:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815769/

'The potential for using marine microbes for biodiscovery is severely limited by the lack of laboratory cultures. It is a long‐standing observation that standard microbiological techniques only isolate a very small proportion of the wide diversity of microbes that are known in natural environments from DNA sequences. A number of explanations are reviewed. The process of establishing laboratory cultures may destroy any cell‐to‐cell communication that occurs between organisms in the natural environment and that are vital for growth. Bacteria probably grow as consortia in the sea and reliance on other bacteria for essential nutrients and substrates is not possible with standard microbiological approaches...'


More recent article show that some progress is being made:

https://www.researchgate.net/public...s_for_culturing_activedormant_marine_microbes

'Microorganisms are ubiquitous in the ocean environment and they play key roles in marine ecosystem function and service. However, many of their functions and phenotypes remain unknown because indigenous marine bacteria are mostly difficult to culture. Although many novel techniques have brought previously uncultured microbes into laboratory culture, there are still many most-wanted or key players that need to be cultured from marine environments. This review discusses possible reasons for ‘unculturable microbes’ and categorizes uncultured bacteria into three groups: dominant active bacteria, rare active bacteria, and dormant bacteria. This review also summarizes advances in cultivation techniques for culturing each group of unculturable bacteria...'


https://link.springer.com/article/10.1007/s42995-021-00093-z

'Microorganisms (both pro- and eukaryotes) occur in all marine environments with an estimated abundance of 103–1010 cells/cm3 in sediments and 104–107 cells/ml in seawater; in these habitats they play key roles in marine biogeochemical cycles (Overmann and Lepleux 2016). Surveys employing molecular marker-based high-throughput sequencing and sophisticated metagenomic approaches have revealed the vast diversity of microorganisms in marine environments and have substantially expanded the tree of life (Castelle and Banfield 2018; Hug et al. 2016; Nayfach et al. 2020). However, many of the novel lineages have no cultured representatives. In fact, most (> 99%) of the marine microorganisms have not been cultured under laboratory conditions (Hofer 2018; Jiao et al. 2020) and are seen as “microbial dark matter” (Lok 2015)...'

My impression after exploring this in a bit more depth is that 'uncultured' doesn't necessarily equate to 'not possible to culture'. From what I can see, the topic is receiving more attention and serious efforts are underway to add to the list of 'culturable marine microbes' using a variety of standard and novel culture techniques.

Thank you for your detailed response! I’m glad to see this is not an entirely baseless claim - and I appreciate the caveat/clarification you added in your last paragraph there; you’ve given me some good reading material here - particularly on those “unculturable microbes.”

 

[livinlifeinBKK]

Thank you for your detailed response! I’m glad to see this is not an entirely baseless claim - and I appreciate the caveat/clarification you added in your last paragraph there; you’ve given me some good reading material here - particularly on those “unculturable microbes.”

I actually learned about that through my studies a while back and remember being so surprised I double check with my professor to confirm if that was true or not which he confirmed (I don't recall right off what the literature was that I was reading at the time as this was a while back or I'd cite it). If I were to guess, it's the isolation of a pure culture that's the most difficult part (not just culturing in general...I'd expect most could be cultured in a mixed culture using spread plate method or similar assuming the media employed can supply needed nutrition and match salinity requirements)

 

[livinlifeinBKK]

I do not know where this idea came about that reef associated bacteria/archaea can go extinct in a system via competition. You'd need something like an oxidizing agent (ex.: chlorine) in sufficient concentration or heat, or possibly cold, beyond the microorganism's tolerance to actually kill them off completely.

Bacteria, once added, are really resilient. Specific species may be outcompeted to the point that they might not show up on an rDNA test (like Aquabiomics), but they are still there and either active in limited numbers or possibly in a dormant state. If conditions change to their liking, however, they can multiply and become visible in the microbiome tests.

Adding bottled bacteria to try and achieve a diverse microbiome is an incorrect use of the product since nearly all reef associated bacteria/archaea can't even be cultured in a lab. 'Bottled bac' has it's uses for establishing the initial nitrogen cycle quickly and digesting organic matter, but this is a far cry from all the thousands of bacteria/archaea species found on a reef or in a thriving reef aquarium that are the main contributors to making the whole system work. It has also been shown that these bottled bacteria typically do not persist (beyond residual numbers) after a few weeks.

Yeah I agree that bottled bacteria wouldn't be an effective way to achieve biodiversity...the reason i mentioned competition between bacterial species actually was something I learned from an Aquabiomics talk but you're probably right in saying that they may just not be detectable due to population size