The Bacterial “Rip Clean” Method

Subsea

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I have some comments about protein skimmers skewing specific bacteria populations. First only microbes in bulk water are removed. Second, not all microbes in bulk water are attracted to foam fractionators bubbles. Ken Feldermen articles in Advanced Aquaria on carbon dosing & protein skimmers focused on this point in the conclusion section of peer reviewed research papers. I have pasted two points of interest.

Manipulating Bacterial Growth​

A “limiting nutrient” is a nutrient that has the ability, though its presence or absence, to restrict the utilization of other nutrients. Bacterial growth rates, bacterial carbon production, and bacterial growth efficiency all increase with the addition of organic carbon supplements in certain groups of marine bacteria (Carlson, 1996). The presence of a readily assimilated carbon source has been demonstrated to increase the uptake of ammonium in certain groups of marine bacteria (Goldman, 2000). The availability of a particular nutrient can not only affect a bacterial population’s growth rate, but also the metabolic functioning of the population. The availability of organic carbon has been shown to not only limit the growth rate of denitrifying bacteria, but also to limit the rate at which denitrification takes place (Brettar, 1992). Chemical entities other than organic carbon, such as inorganic phosphate, also can function as limiting nutrients (Rivkin, 1997). Indeed, given the rapid and dynamic shifts in marine bacteria metabolic behavior over time in response to changing nutrient availability, it may be inappropriate to describe marine bacteria as being limited by a single nutrient.

The frequency with which nutrient enrichments are supplemented has the potential to exert a significant effect on bacteria populations. Nutrient regimes of different periodicities have been shown to result in mixed heterotrophic bacterial communities with distinct physiological properties. It also was observed that the interplay between various bacterial strains and other participants within the microbial community may be equally as important as the selective forces of the environment in structuring microbial communities. Perhaps most interestingly, when replicate bacterial cultures were subjected to identical nutrient supplementation, the microbial community functionality was conserved despite the fact that community compositions were significantly different (Carrero-Colon, 2006). Thus, there appears to be a great deal of bacteria community plasticity in response to environmental changes, one of the hallmarks of bacteria as a successful species over evolutionary time.

The Coral Holobiont​

A coral’s holobiont is comprised of close associations between the coral animal itself, its symbiotic zooxanthellae, and a diversity of associated microbes including bacteria, archaea, algae, and fungi. These associations can take place in the coral’s immediate environment, on its surface, within its tissues, and within its skeleton (if present). This paradigm emphasizes the potential contributions of each component to the overall function and health of the coral (Rypien, 2010). The dynamic nature of these relationships can be seen in a comparison between freshly collected corals from the Red Sea region that were then placed into marine aquaria. A microbial community shift in the bacteria inhabiting the surface mucus layer was documented for collected corals when placed into the captive marine aquarium. The differences that emerged between corals from natural and captive environments suggested an adaptation of the mucus bacterial communities to the different conditions (Kooperman, 2007).

Disruptions within a coral’s holobiont have the potential to negatively impact the coral’s health. Altered bacterial community structures have been linked to both coral disease and bleaching (Kvennefors, 2010). Coral bleaching occurs if the endosymbiosis between corals and their symbiots disintegrates during stress (Ainsworth, 2008). Even so, shifts in the holobiont’s bacterial community component may not be a direct cause of coral bleaching. While bacterial communities play important roles in coral stasis and health, environmental stressors appear to be the primary triggers for coral bleaching, and bacterial involvement in patterns of bleaching appear to be the result of opportunistic colonization (Ainsworth, 2008).

PS: Second paragraph in conclusion

Aquaria subjected to active filtration via skimming present water column bacteria populations that are approximately 1/10 of those observed on natural reefs. The consequences of this disparity on the long-term health of the tank’s livestock are not known. How do reef tank organisms adapt to such a bacteria-deficient environment? Is the whole food web in an aquarium perturbed, or are there compensatory mechanisms that maintain an appropriate energy transduction through all of the trophic levels? Is “old tank syndrome” related to possible nutritional deficiencies stemming from this bacteria “gap”? Alternatively, could “old tank syndrome” be symptomatic of a gradual decrease of bacterial diversity as a consequence of selective skimmer-based removal of only bubble-susceptible bacteria? At present, it is not possible to go beyond speculation on these points – further research is needed.
 
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Subsea

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My whole point in reef husbandry is diversity. I choose to enhance microbe diversity as well as micro fauna & fana by bringing in diver collected sand & rock and nurturing them. The dual 55G tanks on this stand reflect my Laissez Faire reef husbandry.

High nutrient mixed Caribbean lagoon gardens focusing on filter feeders. Both tanks are sumpless & skimmerless and fishless. Apex predators are Sally Lightfoot Crab and six Pepoermint shrimp. While we may differ on our wording of carbon, I add carbon & elements in several forms; live phytoplankton, live mussels cracked open for consumption, frozen mysis, liquid seaweed and ammonia when needed.

Added 250ml of phyotoplankton, 5ml of liquid seaweed and 5ml of ammonia. I don’t believe in limiting nitrogen in reef tanks. I do believe in limiting phosphate as it seems to come in with the air. So to deal with phosphate I add ammonia and trace elements to encourage nutrient recycling and sequestration into desirable biomass. Thats my story and I am sticking to it.

image.jpg
 
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Subsea

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This is starting point of Dual 55G Skid tanks. Initially set up to process 200lbs of diver collected live rock & 50 lbs of live sand from Gulf Live Rock. The top 55G display is skimmerless, sumpless and fishless, with a powerful biochemical filter that uses a reverse flow thru 2” of aroggonite to perform powerful oxidation chemistry and the cryptic void in plenum is the habitat for the “sponge loop” that feeds detritus to the microbial loop and recycles POC back into the system as DIC which feeds photosynthesis that converts carbon dioxide into glucose.

In instrumentation, we call this ” a positive feedback loop”.

In Nature, we call this “Sustainable Maraculture”

PS: Top apex predators are Sally Lightfoot Crab and six Peppermint Shrimp.


Dual 55G tanks
Because this is a thread about bacteria and management of bacteria using diverse filter feeders specific enzymes, I will use liquid seaweed (inorganic carbon & little nitrogen) to favor growth for everyone and compliment that with phytoplankton as an organic carbon source.

There are no fish in this tank, I choose to favor amphipods & copepods as my gardeners, I can see them better than the bacteria. I also have much green macro algae and several red macros. Included in this tank are a variety of ornamental sponges, with my most recent joy two deep water NPS Gorgonions. The flame scallop is hiding and healthy.

I should note, that I occasional dose 5ml of ammonia when lights come on.

Note the last picture of muscle shell on sand bottom. Twenty four hours ago, I took live mussel from r
image.jpg image.jpg image.jpg image.jpg image.jpg image.jpg image.jpg image.jpg
Just added 250 ml of phyto, 5 ml of liquid seaweed, 5 ml of ammonia and two fresh live mussels cracked open.
 
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I have some comments about protein skimmers skewing specific bacteria populations. First only microbes in bulk water are removed. Second, not all microbes in bulk water are attracted to foam fractionators bubbles. Ken Feldermen articles in Advanced Aquaria on carbon dosing & protein skimmers focused on this point in the conclusion section of peer reviewed research papers. I have pasted two points of interest.

Manipulating Bacterial Growth​

A “limiting nutrient” is a nutrient that has the ability, though its presence or absence, to restrict the utilization of other nutrients. Bacterial growth rates, bacterial carbon production, and bacterial growth efficiency all increase with the addition of organic carbon supplements in certain groups of marine bacteria (Carlson, 1996). The presence of a readily assimilated carbon source has been demonstrated to increase the uptake of ammonium in certain groups of marine bacteria (Goldman, 2000). The availability of a particular nutrient can not only affect a bacterial population’s growth rate, but also the metabolic functioning of the population. The availability of organic carbon has been shown to not only limit the growth rate of denitrifying bacteria, but also to limit the rate at which denitrification takes place (Brettar, 1992). Chemical entities other than organic carbon, such as inorganic phosphate, also can function as limiting nutrients (Rivkin, 1997). Indeed, given the rapid and dynamic shifts in marine bacteria metabolic behavior over time in response to changing nutrient availability, it may be inappropriate to describe marine bacteria as being limited by a single nutrient.

The frequency with which nutrient enrichments are supplemented has the potential to exert a significant effect on bacteria populations. Nutrient regimes of different periodicities have been shown to result in mixed heterotrophic bacterial communities with distinct physiological properties. It also was observed that the interplay between various bacterial strains and other participants within the microbial community may be equally as important as the selective forces of the environment in structuring microbial communities. Perhaps most interestingly, when replicate bacterial cultures were subjected to identical nutrient supplementation, the microbial community functionality was conserved despite the fact that community compositions were significantly different (Carrero-Colon, 2006). Thus, there appears to be a great deal of bacteria community plasticity in response to environmental changes, one of the hallmarks of bacteria as a successful species over evolutionary time.

The Coral Holobiont​

A coral’s holobiont is comprised of close associations between the coral animal itself, its symbiotic zooxanthellae, and a diversity of associated microbes including bacteria, archaea, algae, and fungi. These associations can take place in the coral’s immediate environment, on its surface, within its tissues, and within its skeleton (if present). This paradigm emphasizes the potential contributions of each component to the overall function and health of the coral (Rypien, 2010). The dynamic nature of these relationships can be seen in a comparison between freshly collected corals from the Red Sea region that were then placed into marine aquaria. A microbial community shift in the bacteria inhabiting the surface mucus layer was documented for collected corals when placed into the captive marine aquarium. The differences that emerged between corals from natural and captive environments suggested an adaptation of the mucus bacterial communities to the different conditions (Kooperman, 2007).

Disruptions within a coral’s holobiont have the potential to negatively impact the coral’s health. Altered bacterial community structures have been linked to both coral disease and bleaching (Kvennefors, 2010). Coral bleaching occurs if the endosymbiosis between corals and their symbiots disintegrates during stress (Ainsworth, 2008). Even so, shifts in the holobiont’s bacterial community component may not be a direct cause of coral bleaching. While bacterial communities play important roles in coral stasis and health, environmental stressors appear to be the primary triggers for coral bleaching, and bacterial involvement in patterns of bleaching appear to be the result of opportunistic colonization (Ainsworth, 2008).

PS: Second paragraph in conclusion

Aquaria subjected to active filtration via skimming present water column bacteria populations that are approximately 1/10 of those observed on natural reefs. The consequences of this disparity on the long-term health of the tank’s livestock are not known. How do reef tank organisms adapt to such a bacteria-deficient environment? Is the whole food web in an aquarium perturbed, or are there compensatory mechanisms that maintain an appropriate energy transduction through all of the trophic levels? Is “old tank syndrome” related to possible nutritional deficiencies stemming from this bacteria “gap”? Alternatively, could “old tank syndrome” be symptomatic of a gradual decrease of bacterial diversity as a consequence of selective skimmer-based removal of only bubble-susceptible bacteria? At present, it is not possible to go beyond speculation on these points – further research is needed.
That is a great article, some of this limitation can also directly affect bacteria diversity that many aim for, introducing diversity through live rock it’s easy keeping that diversity feed and multiplying in a system may be difficult in a carbon limited system.
 

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Thanks Subsea for that read!

Last night I added my 1/4 dose after lights out. That was my 2nd dose. This time I turned off the skimmer for an hour to let the actif settle in and not get skimmed out.
This morning I peaked in the sump and noticed some cyano staring to form with the tell tale bubbles.

I think shutting off the skimmer for an hour or 2 after dose is the way to go while doing treatment just so it's not immediately skimmed out.
 

Subsea

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Please keep updating this pictures and any other observations you see whether they are positive or negative.
Lights on for 1 hour. Black patch looks more vigorous this morning.
 

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Just a thought. Assuming high nutrients isn’t an issue… wouldn’t we want to run skimmers with the drains open so we’re not removing the bacteria’s we’re trying to grow?
High nutrients in the form of phosphates and nitrates normally aren’t an issue, it’s the high organic nutrients that usually tend to be the root cause of issues that lead to a system imbalance In young systems without many competition.
Most of the bacteria removed via skimming is pelagic and a good way to remove nutrients from a system if bacteria predators aren’t in place, if the bacteria is not removed they will become available again in the water column, in a system like subsea that has many microbe predators those nutrients end up in those predators mass and not released into the water column until they are removed from the system or perish.
there is many ways in aquaria to transfer, recycle or remove nutrients and all them are fine to use imo.
 

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Just a thought. Assuming high nutrients isn’t an issue… wouldn’t we want to run skimmers with the drains open so we’re not removing the bacteria’s we’re trying to grow?
Kudos to your point. @Lasse injects skimmate into his plenum void which is being used as an anaerobic digester to reduce organics to minerals.
 

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Would you consider stop ammonia dosing for a few days?
Because you highlighted limit nitrogen, I have stopped adding ammonia or liquid seaweed in 75G twenty five year mature system, as of 1 week ago when biofloc regime was started. I am adding live phytoplankton and feeding live mussels and that is the most I will do to change my husbandry for biofloc test run.
 
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p1u5h13r4m24

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High nutrients in the form of phosphates and nitrates normally aren’t an issue, it’s the high organic nutrients that usually tend to be the root cause of issues that lead to a system imbalance In young systems without many competition.
Most of the bacteria removed via skimming is pelagic and a good way to remove nutrients from a system if bacteria predators aren’t in place, if the bacteria is not removed they will become available again in the water column, in a system like subsea that has many microbe predators those nutrients end up in those predators mass and not released into the water column until they are removed from the system or perish.
there is many ways in aquaria to transfer, recycle or remove nutrients and all them are fine to use imo.
I was suggesting in means to rebuilding the bacteria were trying to grow temporarily shutting down the skimmers. If all we were doing was just removing organics couldn’t we just use GAC?
I thought I read somewhere that skimming removed beneficial bacteria’s but I may be wrong.
 

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Once the heterotrophic bacteria population helps control the competition of ammonia to be used by nuisances (cyano, dino); what is the next step in how we can allow corals to uptake ammonia for faster growth?
Please keep in mind that corals are filter feeders. They can catch small plankton from bacterioplankton to eggs, larvae, copepods and small polychaets. If you strengthen the food web, more nutrients will be "packed" in all kinds and development stages of organisms. Additionally corals have symbiotic nitrogen fixing bacteria. In my experience it is nearly impossible to starve corals from nitrogen. What may happen is a change from deep colors to pastel colors.
 

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Because flame scallop had some black Cynobacteria on outer shell and what looked like a moving worm on inner flesh, I attempted to remove worm with suction from Turkey baster AND bivalve latched onto Turkey Baster tube, as I retreated, I pulled scallop away from his hiding place.

After I blew cyno off shell exterior, note the orange color of red macro that is dying due to cyno mat consuming red macro algae that was previously there, similar to picture #2

image.jpg image.jpg
 

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Please keep in mind that corals are filter feeders. They can catch small plankton from bacterioplankton to eggs, larvae, copepods and small polychaets. If you strengthen the food web, more nutrients will be "packed" in all kinds and development stages of organisms. Additionally corals have symbiotic nitrogen fixing bacteria. In my experience it is nearly impossible to starve corals from nitrogen. What may happen is a change from deep colors to pastel colors.
Hans,
What you discribe is the “microbial loop”, which is how I reef.
 

Subsea

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Biochemistry is quite complex. As a marine engineer whose first job was superintendent of municipal waste water treatment plant, I am all about the bugs & the “little people” in the microbial loop”. A micro biologist on nano reef called bacteria the “microbial overlords”.
When you brought up the two bacteria groups:

“The reasoning for using carbohydrates that will stimulate heterotrophic decomposers (organic matter reducing bacteria) vs etanol or acetic acid that stimulates the pelagic bacteria (No3 and po4 reducing bacteria)”

@Timfish & I see another contributor in the big picture. As you pointed out, not all carbon is the same. His point of reference comes from Dutch researches on the sponge loop“ in Caribbean reefs. To briefly summarize
(Timfish will get more detailed if you ask him.) briefly:

As primary producers, all photosynthetic organisms have exudates of DOC (dissolved organic carbon). Coral exudates are lipids & proteins while algae exudates are carbohydrates. In effect, the sugar in carbohydrates suffocate coral with algae. This happened in the Caribbean some decades ago due to a virus killing 95% of urchins on many reefs.

As a reefer for 51 years, I have collected and thrown away a garage of STUFF to run a reef tank. For the last 30 years before retiring from deep water drilling, I worked a schedule 28 days on with 28 days off as a subsea engineer. During those early years there was limited economical automation. With that focus, I found that recycling nutrients (sequestration) was the way to go. During the next 30 years I experimented with different marine ecosystems and have come to appreciate numerous inverts including flame scallops & sea apples. I attribute this to diversity of micro flora & fauna that is brought in with diver collected uncured live sand & live rock.

The three platforms of biochemistry for recycling nutrients are bacteria, algae including coral zooanthelia and “cryptic sponges”.

To complicate nutrient pathways, gas exchange is a major contributor of nutrient exchange between water and air: bringing in oxygen to complete chemistry required to grow, bringing in nitrogen gas to be converted into ammonia by “nitrogen fixation” bacteria and because Earth is a carbon based planet, carbon dioxide dissolves readily into water to form alkalinity which when combined with photosynthesis forms glucose which is carbon for the reef.

@sixty_reefer
Outstanding thread. My long post was intended to be a new thread. Not knowing your background, I assume you are a micro biologist and I desire to know WHY things happen, so I am following your thread.

@Paul B
Any thoughts on this thread?
I will repost this from early in this thread: post #88
 

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Biochemistry is quite complex. As a marine engineer whose first job was superintendent of municipal waste water treatment plant, I am all about the bugs & the “little people” in the microbial loop”. A micro biologist on nano reef called bacteria the “microbial overlords”.
When you brought up the two bacteria groups:

“The reasoning for using carbohydrates that will stimulate heterotrophic decomposers (organic matter reducing bacteria) vs etanol or acetic acid that stimulates the pelagic bacteria (No3 and po4 reducing bacteria)”

@Timfish & I see another contributor in the big picture. As you pointed out, not all carbon is the same. His point of reference comes from Dutch researches on the sponge loop“ in Caribbean reefs. To briefly summarize
(Timfish will get more detailed if you ask him.) briefly:

As primary producers, all photosynthetic organisms have exudates of DOC (dissolved organic carbon). Coral exudates are lipids & proteins while algae exudates are carbohydrates. In effect, the sugar in carbohydrates suffocate coral with algae. This happened in the Caribbean some decades ago due to a virus killing 95% of urchins on many reefs.

As a reefer for 51 years, I have collected and thrown away a garage of STUFF to run a reef tank. For the last 30 years before retiring from deep water drilling, I worked a schedule 28 days on with 28 days off as a subsea engineer. During those early years there was limited economical automation. With that focus, I found that recycling nutrients (sequestration) was the way to go. During the next 30 years I experimented with different marine ecosystems and have come to appreciate numerous inverts including flame scallops & sea apples. I attribute this to diversity of micro flora & fauna that is brought in with diver collected uncured live sand & live rock.

The three platforms of biochemistry for recycling nutrients are bacteria, algae including coral zooanthelia and “cryptic sponges”.

To complicate nutrient pathways, gas exchange is a major contributor of nutrient exchange between water and air: bringing in oxygen to complete chemistry required to grow, bringing in nitrogen gas to be converted into ammonia by “nitrogen fixation” bacteria and because Earth is a carbon based planet, carbon dioxide dissolves readily into water to form alkalinity which when combined with photosynthesis forms glucose which is carbon for the reef.

@sixty_reefer
Outstanding thread. My long post was intended to be a new thread. Not knowing your background, I assume you are a micro biologist and I desire to know WHY things happen, so I am following your thread.

@Paul B
Any thoughts on this thread?
Biochemistry is quite complex. As a marine engineer whose first job was superintendent of municipal waste water treatment plant, I am all about the bugs & the “little people” in the microbial loop”. A micro biologist on nano reef called bacteria the “microbial overlords”.
When you brought up the two bacteria groups:

“The reasoning for using carbohydrates that will stimulate heterotrophic decomposers (organic matter reducing bacteria) vs etanol or acetic acid that stimulates the pelagic bacteria (No3 and po4 reducing bacteria)”

@Timfish & I see another contributor in the big picture. As you pointed out, not all carbon is the same. His point of reference comes from Dutch researches on the sponge loop“ in Caribbean reefs. To briefly summarize
(Timfish will get more detailed if you ask him.) briefly:

As primary producers, all photosynthetic organisms have exudates of DOC (dissolved organic carbon). Coral exudates are lipids & proteins while algae exudates are carbohydrates. In effect, the sugar in carbohydrates suffocate coral with algae. This happened in the Caribbean some decades ago due to a virus killing 95% of urchins on many reefs.

As a reefer for 51 years, I have collected and thrown away a garage of STUFF to run a reef tank. For the last 30 years before retiring from deep water drilling, I worked a schedule 28 days on with 28 days off as a subsea engineer. During those early years there was limited economical automation. With that focus, I found that recycling nutrients (sequestration) was the way to go. During the next 30 years I experimented with different marine ecosystems and have come to appreciate numerous inverts including flame scallops & sea apples. I attribute this to diversity of micro flora & fauna that is brought in with diver collected uncured live sand & live rock.

The three platforms of biochemistry for recycling nutrients are bacteria, algae including coral zooanthelia and “cryptic sponges”.

To complicate nutrient pathways, gas exchange is a major contributor of nutrient exchange between water and air: bringing in oxygen to complete chemistry required to grow, bringing in nitrogen gas to be converted into ammonia by “nitrogen fixation” bacteria and because Earth is a carbon based planet, carbon dioxide dissolves readily into water to form alkalinity which when combined with photosynthesis forms glucose which is carbon for the reef.

@sixty_reefer
Outstanding thread. My long post was intended to be a new thread. Not knowing your background, I assume you are a micro biologist and I desire to know WHY things happen, so I am following your thread.

@Paul B
Any thoughts on this thread?
Pardon fat fingers and double post.
 

Subsea

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Due to ice storm, I lost power for 20 minutes and expect further disruptions. On previous homestead, I had 14K automatic propane generator with transfer switch. Here, I have battery operated air pumps that come on when electricity goes off.

image.jpg
 

Subsea

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Short power outage seemed to be ignored by reef tank inhabitants.

However, as I look closer at black mat, a detachment from sandbed is occurring.

PS: After 5 years in this tank, I have come to understand some of the feeding strategies of male green mandarin. He is very interested in looking under the mat.

The last picture shows male green mandarin in scallops depression and a part of female feeding on detritus at rock base.
image.jpg image.jpg image.jpg
 
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