The Bacterial “Rip Clean” Method

beesnreefs

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Thanks @Subsea

From what I've read it's not the ammonia form of nitrogen that's the issue it nitrates. Shantz and Burkpile have looked at nitrogen (one paper reviewed the data from 44 different published studies) and it was nitrates that caused the most issues wiht corals, not ammonia. A quote from one of their papers I think points out the complexity we are dealing with:

"the response of corals to increasing nutrient availability was context dependent, varying with coral taxa and morphology, enrichment source, and nutrient identity"



Adding labile DOC, aka carbon dosing, does promote heterotrophic bacterial growth. There's lots of research demonstrating that. Unfortunately, ta major difference between coral DOC and algal DOC is coral DOC is largely refractory and promotes autotrophic microbial processes (read oxygen conserving) while algal DOC is largely labile and promotes heterotrophic microbial processes (read oxygen consuming. Adding labile DOC to promote heterotrophic microbial prcesses can have an immidiate or acute effect on corals. It can promote heterotrophic microbial growth in corals microbiomes and can literally suffocate corals as heterotrophic bacteria suck up oxygen using labile DOC to consume the refractory DOC available. Excess labile DOC can also have chronic effects on corals taking years to have obvious negative effects on corals (Old Tank Syndrome)

As Subsea pointed out, sponges are a variable. A huge variable as it turns out depending on how a species feeds. Some feed exclusively off DOC and remove it 1000X faster than the bacterioplankton in a system. While they may mitigate the negative effects on labile DOC in a system they do process DOC differentially depending on it's source. DOC from corals results in different compounds than DOC from algae. We don't know yet how artificial sources of labile DOC effect microbial prcesses but considering the mountain of peer reviewed research showing labile DOC causes coral death I'd wouldn't use it.


Here's a data bomb

Nitrogen stuff

Nitrogen cycling in hte coral holobiont


Ammonium Uptake by Symbiotic and Aposymbiotic Reef Corals

Amino acids a source of nitrogen for corals

Urea a source of nitrogen for corals

Diazotrpophs a source of nitrogen for corals

Ammonia uptake by Anemones

Elevated ammonium delays the impairment of the coral-diniflagellate symbiosis during labile carbon pollution

DOC Stuff

"Coral Reefs in the Microbial Seas" This video compliments Rohwer's book of the same title (Paper back is ~$20, Kindle is ~$10), both deal with the conflicting roles of the different types of DOC in reef ecosystems. While there is overlap bewteen his book and the video both have information not covered by the other and together give a broader view of the complex relationships found in reef ecosystems


Maintenance of Coral Reef Health (refferences at the end)


Global microbialization of coral reefs (Increased microbial loads negatively impact coral reefs)

Indirect effects of algae on coral: algae‐mediated, microbe‐induced coral mortality

Influence of coral and algal exudates on microbially mediated reef metabolism.
Coral DOC improves oxygen (autotrophy), algae DOC reduces oxygen (heterotrophy).

Role of elevated organic carbon levels and microbial activity in coral mortality

Effects of Coral Reef Benthic Primary Producers on Dissolved Organic Carbon and Microbial Activity
Algae releases significantly more DOC into the water than coral.

Pathologies and mortality rates caused by organic carbon and nutrient stressors in three Caribbean coral species.
DOC caused coral death but not high nitrates, phosphates or ammonium.

Visualization of oxygen distribution patterns caused by coral and algae

Biological oxygen demand optode analysis of coral reef-associated microbial communities exposed to algal exudates
Exposure to exudates derived from turf algae stimulated higher oxygen drawdown by the coral-associated bacteria.

Microbial ecology: Algae feed a shift on coral reefs

Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages.

Sugar enrichment provides evidence for a role of nitrogen fixation in coral bleaching

Elevated ammonium delays the impairment of the coral-dinoflagellate symbiosis during labile carbon pollution
(here's an argument for maintaining heavy fish loads if you're carbon dosing)

Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton

Unseen players shape benthic competition on coral reefs.

Allelochemicals (DOC) Produced by Brown Macroalgae of the Lobophora Genus Are Active against Coral Larvae and Associated Bacteria, Supporting Pathogenic Shifts to Vibrio Dominance.

Macroalgae decrease growth and alter microbial community structure of the reef-building coral, Porites astreoides.

Macroalgal extracts induce bacterial assemblage shifts and sublethal tissue stress in Caribbean corals.

Biophysical and physiological processes causing oxygen loss from coral reefs.



Sponge Stuff

BActeria and Sponges


Element cycling on tropical coral reefs.
This is Jasper de Geoij's ground breaking research on reef sponge finding some species process labile DOC 1000X faster than bacterioplankton. (The introduction is in Dutch but the content is in English.)

Sponge symbionts and the marine P cycle

Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges

Differential recycling of coral and algal dissolved organic matter via the sponge loop.
Sponges treat DOC from algae differently than DOC from corals

A Vicious Circle? Altered Carbon and Nutrient Cycling May Explain the Low Resilience of Caribbean Coral Reefs

Surviving in a Marine Desert The Sponge Loop Retains Resources Within Coral Reefs
Dissolved organic carbon and nitrogen are quickly processed by sponges and released back into the reef food web in hours as carbon and nitrogen rich detritus.

Natural Diet of Coral-Excavating Sponges Consists Mainly of Dissolved Organic Carbon (DOC)

The Role of Marine Sponges in Carbon and Nitrogen Cycles of COral Reefs and Nearshore Environments.

And since we're discussing favorable and not so favorable bacteria here's a paper looking at how different corals and polyps are influencing the bacteria in the water column.
Aura-biomes are present in the water layer above coral reef benthic macro-organisms

Thanks for the data bomb @Timfish! I’ll do my best to read through everything you’ve shared

If you had to summarize your takeaway from all the data, what would it be? What action steps would you recommend to a typical Reefer?
 
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sixty_reefer

sixty_reefer

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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’m am sorry to disappoint you, I’m no micro biologist, just another aquarists like many on here, I just took an interest for nutrients as I find the subject fascinating.
this is just a result of many years reading papers and discussing the subject with fellow aquarists, and personal experimentation to find answers. I still have much to learn.
 

Subsea

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Here is what @Paul B says about detritus & MULM



  • paul b
    Oracle Reefer
  • WAMAS Speaker
  • Gender:Male
  • Location:Long Island NY
  • #1
June 10, 2016
I think one of the most important, and least understood or mentioned things in a reef tank is "mulm". That stuff that grows in the dark portions of a tank if it is set up long enough. "Mulm" is a combination of algae, sponges, bacteria, pods, worms, detritus, poop and any thing else that can be propagated or grown in the dark. I realize most people would immediately get out the sponge, razor blade or grenade to remove it but there is a word I like to use to describe those people. That word is "wrong". Mulm is a natural product that you will find in the sea all over the world. Our tanks run on bacteria, algae and a food chain. Bacteria and a food chain are dependent on having a place to reproduce. Mulm is the perfect place. Rocks and glass are flat surfaces that are only two dimensional. Mulm makes these places three dimensional allowing much more space for bacteria and microscopic organisms to grow and do the macarana. (Then love to dance) Pods, which are needed for any small fish also need to eat and their numbers are directly related to how much food they can get their hands on (or whatever pods use to eat with) The more food, the more pods, the more pods, the easier to keep smaller fish. Larger fish such as copperbands and angels also eat pods.
Many people try to keep fish such as pipefish, mandarins or other dragonettes in a sterile tank and while feeding them a couple of times a day with tiger pods or some other expensive food. Those types of fish will not live for long in such a tank and they certainly won't spawn which I consider the "only" criteria to determine the state of health for any paired fish.
Mulm (after a while, maybe a few years) should grow on the back and sides of glass as well as under rocks.
Here in this picture of my clingfish, the mulm appears green. It is really brownish and that fish is on the side of my tank. I brightened up the picture and turned it sideways because it was in the dark and the fish was hard to see.
There is a thick layer of it on the back of my tank where my mandarins and pipefish like to hunt. My long spined urchin also grazes there most of the time as there is not much algae in my tank for him to eat. He is many years old as are the mandarins and pipefish and they are dependent on this food source.
A sterile tank IMO is the biggest problem we have keeping certain fish healthy.
Sterile is good in an operating room but very bad in a tank.

2015-08-162005.50.07_zpsb11pthli.jpg

I recently took this off Kauai Hawaii. The rocks are covered in Mulm. You can see a spotted moray eel in the center.

2013-10-19094135_zps8e697d16.jpg

This was in the Caribbean. The mulm provides food for those fry.
Fry_zps89b3dc30.jpg

This is off a mangrove Island in Key Largo Florida. Notice the growth on the roots.

Fish%20in%20Mangrove_zpsd99p2bgw.png

I know many people will disagree with me. That is fine. But everything I propose I post pictures to back up my theories. None of my ideas come from re-hashed, inside the box rumors.

 

Timfish

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I forgot a link


Thanks for the data bomb @Timfish! I’ll do my best to read through everything you’ve shared

If you had to summarize your takeaway from all the data, what would it be? What action steps would you recommend to a typical Reefer?


Feed your fish. Do your water changes it's the only way to reduce all the DOC and all the microbial stuff and lets corals promote what's beneficial for them (I like weekly ~5%). Keep PO4 between .03 mg/l and .5 mg/l. Corals don't need nitrate so keep it low.
 
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sixty_reefer

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What do you mean when you say use a source of Doc for cleaning for yellow water and film algae on glass?

Does that mean carbon dosing with something like tropic marin other line of carbon dosing such as NP Bacto Balance, Elimi-NP, etc?
The organic carbon won’t remove the yellow tint from the water it will prevent that from happening by reducing organics that if stay too long in the water column will cause the water going yellow.
 

reefluvrr

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The organic carbon won’t remove the yellow tint from the water it will prevent that from happening by reducing organics that if stay too long in the water column will cause the water going yellow.
I am sorry, I am trying to understand what this means. I feel like a kid again trying to grasp physics concepts again.:)

Organic carbon dosing grows what type of bacteria that reduces organics. Also can you help explain what are these types of organics? Are the organics the cause for the water to go yellow in your sentence?
 

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I’m am sorry to disappoint you, I’m no micro biologist, just another aquarists like many on here, I just took an interest for nutrients as I find the subject fascinating.
this is just a result of many years reading papers and discussing the subject with fellow aquarists, and personal experimentation to find answers. I still have much to learn.
Not disappointed. I seek to know more about what I love and have evolved to nutrient recycling with nutrient export to be fragging and selling coral. I do very limited water change and only when gravel vac for 11 months. On month 12, I do two 100% water changes to get system back to normal reef parameters. Because I don’t do high alkalinity demanding SPS, I rely on alkalinity and trace mineral management thru passive dissolving of aragonite in sandbed.
 
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brandon429

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if you guys drive this thread to page eight and there's no new jobs clearly being started, that's a functional crime of science



and of potential-> to get change in the hobby, by doing live time jobs. never ever think that someone's take on reefing is 1/10th as important as their ability to do outbound jobs to satisfactory completion when everyone is watching.

don't give weight or credence to anything that is a typed set of paragraphs and not pictures of a live time job, started recently on this path, soon to be tracked out three months by a willing and engaged tank owner.
 

Subsea

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if you guys drive this thread to page eight and there's no new jobs clearly being started, that's a functional crime of science



and of potential-> to get change in the hobby, by doing live time jobs. never ever think that someone's take on reefing is 1/10th as important as their ability to do outbound jobs to satisfactory completion when everyone is watching.

don't give weight or credence to anything that is a typed set of paragraphs and not pictures of a live time job, started recently on this path, soon to be tracked out three months by a willing and engaged tank owner.
Brandon,
To compare or equate the average reef hobbiest work thread with peer reviewed scientific articles is a “crime against science”
 

brandon429

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in the very least, writers should be scanning pages to see if a new page is about to load without a new work job started

then they'd withhold until they secured a job at least for that page before it loads a new reading page

minimum one tank job per page among any amount of discourse is an acceptable rate in my opinion

but not ever three straight pages without a job, that's a crime. I predict ten straight pages are coming/hoping to head that off
 

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Can’t see this product mention algae, just long chain polymers but I remember some other carbon dosing product that claims to be algae derived. Agar is algae derived. Just a thought. Not really related but the wife bought reef enhance and live rock enhance, looks all the world like bakers yeast, lol.
I really hope that tropic marine hasn’t discontinued this product.
does it turn jelly like?
 

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@sixty_reefer

I can’t find it now, about a month ago on this website on experiment forum, carbon dosing in addittion to Guillard f/2 fertilizer was used for enhanced phytoplankton production. In that experiment, I think by Peace River, the carbon source was critical. Seems like some overlapping science.
 

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if you guys drive this thread to page eight and there's no new jobs clearly being started, that's a functional crime of science



and of potential-> to get change in the hobby, by doing live time jobs. never ever think that someone's take on reefing is 1/10th as important as their ability to do outbound jobs to satisfactory completion when everyone is watching.

don't give weight or credence to anything that is a typed set of paragraphs and not pictures of a live time job, started recently on this path, soon to be tracked out three months by a willing and engaged tank owner.
For clarification are you looking for people fixing other people's tank similar to what you do? Or are you looking for hobbiest to start using the product (if we can even get it any longer) and documenting the process with images etc?
 
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sixty_reefer

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I am sorry, I am trying to understand what this means. I feel like a kid again trying to grasp physics concepts again.:)

Organic carbon dosing grows what type of bacteria that reduces organics. Also can you help explain what are these types of organics? Are the organics the cause for the water to go yellow in your sentence?

Yellow water comes from the decay and decomposition of organic matter (fish food, uneaten food etc) dissolving into the water for a period of time, by reducing that time with encouraging more bacteria to consume those nutrients the formation of yellow water is drastically reduced.

on here I’m proposing to use biofloc technology that uses carbohydrates to stimulate the growth of heterotrophic bacteria
( Pseudoalteromonadaceae, Bacillaceae amongst others) responsible for reducing organic matter in aquaria, this are the common sources of inorganic nitrogen (ammonia) that can cause many nuisances

 

Dburr1014

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if you guys drive this thread to page eight and there's no new jobs clearly being started, that's a functional crime of science



and of potential-> to get change in the hobby, by doing live time jobs. never ever think that someone's take on reefing is 1/10th as important as their ability to do outbound jobs to satisfactory completion when everyone is watching.

don't give weight or credence to anything that is a typed set of paragraphs and not pictures of a live time job, started recently on this path, soon to be tracked out three months by a willing and engaged tank owner.
My actif is coming in February 1st or 2nd.
I'm going to start right away.
I also just bought this so I'm going to start dosing this daily until I get it. I don't think it would hurt any.

16743282562384420414753800566567.jpg
 
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sixty_reefer

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Can’t see this product mention algae, just long chain polymers but I remember some other carbon dosing product that claims to be algae derived. Agar is algae derived. Just a thought. Not really related but the wife bought reef enhance and live rock enhance, looks all the world like bakers yeast, lol.

does it turn jelly like?

we do many things in our reefs that aren’t designed to control algae, the product isn’t claiming to do it though. But it claims to be “nutrition for bacteria” and it claims that “accelerates the break dow of excessive nutrients and contaminants by converting them into increased available nutrition for filter feeders” that won’t kill algae on its own just reduce the source of energy and increase food for trophic levels

wend mixed with tank water becomes cloudy not noticed the jelly in the container is just in powder form.
 

Garf

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carbon dosing in addittion to Guillard f/2 fertilizer
From memory, phyto (or some types anyway) can grow in low light using organics, but only 60% of the normal growth rate. Add light and it may make sense that growth is increased. A bit like photosynthesis using both red and deep red spectrums is greater than using either red or deep red then adding them together.
 

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