Analyzing a Bacterial Method for Dinoflagellates (and cyano?)

[CoralClasher]

I’m on day three of round three all fish look good corals are staying open this round I’ve noticed more of a fishy smell this round. I still see a few Dino but I have to hunt for them. I just used the last of the Dr. Tim’s one and only that I have. Can I use the eco-balance bacteria for the day five dose or should I get more? I have plenty of the waste away.

 

[Dan_P]

Cyano color differences can be tied to lights, but also to nutrient content of the food that drives it. In my sump, cyano is green (under whiter / yellower LED light) , and in my DT always red (bluer T5 light).

Assuming the cyanobacteria are the same species/strain, then I favor the nutrient explanation, particularly a difference in the nitrogen source. One the locations is possibly requiring higher amount of energy to extract nitrogen. Organic vs inorganic N or NO3 v NH3. Just a thought for your consideration.

 

[Cruz_Arias]

I’m on day three of round three all fish look good corals are staying open this round I’ve noticed more of a fishy smell this round. I still see a few Dino but I have to hunt for them. I just used the last of the Dr. Tim’s one and only that I have. Can I use the eco-balance bacteria for the day five dose or should I get more? I have plenty of the waste away.

I would rather continue with the One and Only, due to the bacterial density alone...

The Eco-Balance does not seem to have the same population count...

 

[CoralClasher]

Day four and this is the best bacteria bloom I’ve seen yet. Can you clarify days 4-7 skimmer to be turned on? Do I only run skimmer when I add peroxide without skimmer cup on?

 

[Cruz_Arias]

Day four and this is the best bacteria bloom I’ve seen yet. Can you clarify days 4-7 skimmer to be turned on? Do I only run skimmer when I add peroxide without skimmer cup on?

At this point I would use hydrogen peroxide into the air intake of the skimmer... and yes, with the collection cup off (this is depending of nutrient level)

 

[Pyrosteve]

Giving this a trying after a couple blackouts and H2O2. Thought I had them beat after a couple weeks but I had to do a large water change after med treatment and must have bottomed out my nutrients again. They returned with a vengeance. I started to aerate yesterday and added my first dose today. Some questions. Skimmer is off but should UV be off as well in the beginning? After what dose should I see the bloom/cloudiness? Also should lights be on, reduced or off (since most bacteria does better in the dark?)? GAC, yes or no?

 

[Idoc]

Giving this a trying after a couple blackouts and H2O2. Thought I had them beat after a couple weeks but I had to do a large water change after med treatment and must have bottomed out my nutrients again. They returned with a vengeance. I started to aerate yesterday and added my first dose today. Some questions. Skimmer is off but should UV be off as well in the beginning? After what dose should I see the bloom/cloudiness? Also should lights be on, reduced or off (since most bacteria does better in the dark?)? GAC, yes or no?

The UV is indiscriminate and would kill the good bacteria you want to bloom during the treatment.

I saw the largest bloom after the first dosing.

 

[Pyrosteve]

The UV is indiscriminate and would kill the good bacteria you want to bloom during the treatment.

I saw the largest bloom after the first dosing.

Ok. that's was I figured. No Bloom yet. What about light? Should it be kept normal, reduced, blues only or off?

 

[Idoc]

Ok. that's was I figured. No Bloom yet. What about light? Should it be kept normal, reduced, blues only or off?

I kept my lights on there normal schedule during the treatment and things worked out well. Im not sure if there would be a difference with or without lights.

 

[CoralClasher]

I just finished round three man it was a bumpy ride but well worth it!! You will get 0 readings of nutrients your corals will go into Hurricane mode don’t freak out things will be fine if you follow the directions. I removed all filters and left the lights on normal. I added phosphate round one probably didn’t need to tho.

 

[Pyrosteve]

On day 4 of treatment and I have a bloom now. Turned off the UV and everything is covered. It looks like the bacteria choked out all the dinos and any other algae so I'm optimistic. I'm a little worried that the CUC with starve tho. Nitrates are 0 so I'm hoping I don't get return visit once this is done.

Here's what I started with...

Coral frags are not happy. I've been using a turkey baster a couple times a day to keep them clear.

 

[Pyrosteve]

I noticed my sump is frothing foaming up. Is this normal?

Some of the bloom...

and where I'm at now...no sign of the dinos

 

[Idoc]

I noticed my sump is frothing foaming up. Is this normal?

Some of the bloom...

and where I'm at now...no sign of the dinos

I had that foam in the sump and overflow area of my tank. I just scooped it out after i was done with the treatment.

My nutrients were zero as well since the bacteria we are adding are described to take down those nutrients. I dosed no3/po4 immediately after the treatment so they weren't zero!

 

[CoralClasher]

I had that foam in the sump and overflow area of my tank. I just scooped it out after i was done with the treatment.

My nutrients were zero as well since the bacteria we are adding are described to take down those nutrients. I dosed no3/po4 immediately after the treatment so they weren't zero!

My phosphate came back a few days after round 2 and 3, nitrogen has not showed up yet.

 

[taricha]

Why Do Large Carbon Doses Suppress Cyano (in my system)?
A big part of this method is about using bacteria to digest the waste that fuels nuisance growth, and the other big part is about using large carbon dose to tweak bacterial behavior.
In the spirit of taking things apart, I wanted to take a closer look at the large carbon dose part, and why large doses of organic carbon suppress cyano growth in my system. It appears to disrupt cyano's ability to exploit accumulations of waste.

Usually in my tank, algae dying (from vibrant) results in debris material that supports cyano growth, but if I do a large daily carbon dose (while keeping vibrant), the cyano recedes despite the debris source still being produced.
So I turned cyano off/on/off to investigate.

(left: while dosing carbon no cyano on dying algae, middle: no carbon dosing and lots of red cyano, right: heavy carbon dosing and re-disappearance of cyano. The carbon dosing here is 2/3 of the carbon dose recommended in the method.)
Bulk water parameters were not dramatically changed. PO4 stayed around ~0.10 and NO3 tests zero...if you don't look too closely. More on that in a bit.

So why is the cyano receding?
In the sump there's an interesting stringy cyano colony that goes through color shifts when I dose large amounts of carbon. It goes from deep emerald green -> light green -> yellow, and when carbon dosing stops, it reverses.
This sort of color transition in cyano has been known for decades to be associated with N depletion.
"...the alga [cyanobacteria] lost its characteristic blue-green color and took on the light brown to golden color of a diatom. Experimentation showed that it was not the wavelength of light, but rather the depletion of nitrogen from the medium, and that alone, which was responsible for the color shift. In this and further work ..., it was determined that the color shift was due to a selective disappearance of chlorophyll and phycocyanin, thereby unmasking the carotenoids; that a yellowed culture could be made to return to green, sometimes within 24 hours, upon the addition of minute amounts of nitrogen..."
paper link
Other research in the 60 years since, has fleshed out how in nutrient deprivation, the cells become photobleached, and reduce their light-harvesting pigments while keeping more photoprotective carotenoids.

So I ran some spectrum test on samples from the cyano during increased carbon dosing, and I found the exact pigment shifts described above that are associated with N depletion.

On the left is the colony of cyano, on the right are the spectral measurements from the sample. Black is the actual measured spectra, grey dotted line is a fit made from the pigments listed in the graph header. Different colored lines represent different pigments that add up to the gray dotted line.
Top: emerald green cyano - 10/21 - note the strong phycocyanin (blue line).
Middle: light-green - 10/25 - Phycocyanin almost collapsed and Chlorophyll A is slightly reduced compared to carotenoids.
Bottom: yellow - 10/28 - total collapse of phycocyanin, and Chlorophyll A reduced compared to carotenoids which become dominant.

Additionally, the pigments not only shifted, the overall pigment density of these samples decreased during this process. Below compares absorption from light-harvesting pigments, to the scattering by the material after bleached with a couple of drops of sodium hypochlorite.

Solid lines are raw absorbance (normalized to 1) and the dotted lines represent what scattering remained when the sample was bleached.
The 10/21 - emerald green sample - blue line had over half 58% of its absorbance from actual pigments.
10/25 - light-green sample - working pigments had dropped to 40%
10/28 - yellow sample - pigment absorbance was only 13% of sample.

This indicates that by the end there was severe light-harvesting pigment loss, major photobleaching of the sample. It suggests that a lot of the sample was dead at this point (the strands detached from the pipe 4 days later) , All this data points to nutrient (Nitrogen) deprivation.

So what NO3 was actually measured?
10/8 - During heavy carbon dosing
NO3 - 0
PO4 - 0.09

10/21 - During no carbon, at height of cyano
NO3 - 0.40ppm
PO4 - 0.11

I then vacuumed and gently shook a sample out of the sand/debris
NO3 - 0.70
PO4 - 0.17

11/1 - Heavy Carbon Dosing - water
NO3 - 0.0
PO4 - 0.08

11/1- Sand/debris
NO3 - 0.0

My interpretation here is that the detectable NO3 values from the no-carbon dosing are not themselves near enough to grow happy cyano (h/t @Dan_P), but they are small indicators in the water of much larger nutrient transfers happening in the debris. That sand/debris reads higher (near double) is one indicator of that. Another is that I sucked up sand and debris, and filtered down to 150 microns leaving only dust in 200mL water. After bubbling for 2 days in the dark it produced 1.6ppm NO3. The water volume was totally arbitrary, I could have bubbled the debris dust in much smaller water volume and read much higher NO3 concentration.
The point is, it's a constant ongoing production of N from the debris, but in the presence of large carbon dose, even that source of N seems to be snuffed out by other bacterial actors before cyano can get it. Bacterial strings and films are visible in all surfaces during this carbon dosing process, and my skimmate tripled, compared to no-carbon.

Congrats to those who read this far. Hope you found something interesting.

 

[Dan_P]

Why Do Large Carbon Doses Suppress Cyano (in my system)?
A big part of this method is about using bacteria to digest the waste that fuels nuisance growth, and the other big part is about using large carbon dose to tweak bacterial behavior.
In the spirit of taking things apart, I wanted to take a closer look at the large carbon dose part, and why large doses of organic carbon suppress cyano growth in my system. It appears to disrupt cyano's ability to exploit accumulations of waste.

Usually in my tank, algae dying (from vibrant) results in debris material that supports cyano growth, but if I do a large daily carbon dose (while keeping vibrant), the cyano recedes despite the debris source still being produced.
So I turned cyano off/on/off to investigate.

(left: while dosing carbon no cyano on dying algae, middle: no carbon dosing and lots of red cyano, right: heavy carbon dosing and re-disappearance of cyano. The carbon dosing here is 2/3 of the carbon dose recommended in the method.)
Bulk water parameters were not dramatically changed. PO4 stayed around ~0.10 and NO3 tests zero...if you don't look too closely. More on that in a bit.

So why is the cyano receding?
In the sump there's an interesting stringy cyano colony that goes through color shifts when I dose large amounts of carbon. It goes from deep emerald green -> light green -> yellow, and when carbon dosing stops, it reverses.
This sort of color transition in cyano has been known for decades to be associated with N depletion.
"...the alga [cyanobacteria] lost its characteristic blue-green color and took on the light brown to golden color of a diatom. Experimentation showed that it was not the wavelength of light, but rather the depletion of nitrogen from the medium, and that alone, which was responsible for the color shift. In this and further work ..., it was determined that the color shift was due to a selective disappearance of chlorophyll and phycocyanin, thereby unmasking the carotenoids; that a yellowed culture could be made to return to green, sometimes within 24 hours, upon the addition of minute amounts of nitrogen..."
paper link
Other research in the 60 years since, has fleshed out how in nutrient deprivation, the cells become photobleached, and reduce their light-harvesting pigments while keeping more photoprotective carotenoids.

So I ran some spectrum test on samples from the cyano during increased carbon dosing, and I found the exact pigment shifts described above that are associated with N depletion.

On the left is the colony of cyano, on the right are the spectral measurements from the sample. Black is the actual measured spectra, grey dotted line is a fit made from the pigments listed in the graph header. Different colored lines represent different pigments that add up to the gray dotted line.
Top: emerald green cyano - 10/21 - note the strong phycocyanin (blue line).
Middle: light-green - 10/25 - Phycocyanin almost collapsed and Chlorophyll A is slightly reduced compared to carotenoids.
Bottom: yellow - 10/28 - total collapse of phycocyanin, and Chlorophyll A reduced compared to carotenoids which become dominant.

Additionally, the pigments not only shifted, the overall pigment density of these samples decreased during this process. Below compares absorption from light-harvesting pigments, to the scattering by the material after bleached with a couple of drops of sodium hypochlorite.

Solid lines are raw absorbance (normalized to 1) and the dotted lines represent what scattering remained when the sample was bleached.
The 10/21 - emerald green sample - blue line had over half 58% of its absorbance from actual pigments.
10/25 - light-green sample - working pigments had dropped to 40%
10/28 - yellow sample - pigment absorbance was only 13% of sample.

This indicates that by the end there was severe light-harvesting pigment loss, major photobleaching of the sample. It suggests that a lot of the sample was dead at this point (the strands detached from the pipe 4 days later) , All this data points to nutrient (Nitrogen) deprivation.

So what NO3 was actually measured?
10/8 - During heavy carbon dosing
NO3 - 0
PO4 - 0.09

10/21 - During no carbon, at height of cyano
NO3 - 0.40ppm
PO4 - 0.11

I then vacuumed and gently shook a sample out of the sand/debris
NO3 - 0.70
PO4 - 0.17

11/1 - Heavy Carbon Dosing - water
NO3 - 0.0
PO4 - 0.08

11/1- Sand/debris
NO3 - 0.0

My interpretation here is that the detectable NO3 values from the no-carbon dosing are not themselves near enough to grow happy cyano (h/t @Dan_P), but they are small indicators in the water of much larger nutrient transfers happening in the debris. That sand/debris reads higher (near double) is one indicator of that. Another is that I sucked up sand and debris, and filtered down to 150 microns leaving only dust in 200mL water. After bubbling for 2 days in the dark it produced 1.6ppm NO3. The water volume was totally arbitrary, I could have bubbled the debris dust in much smaller water volume and read much higher NO3 concentration.
The point is, it's a constant ongoing production of N from the debris, but in the presence of large carbon dose, even that source of N seems to be snuffed out by other bacterial actors before cyano can get it. Bacterial strings and films are visible in all surfaces during this carbon dosing process, and my skimmate tripled, compared to no-carbon.

Congrats to those who read this far. Hope you found something interesting.

You are so thorough! You rock! As the applause die down, Dan is heard saying “I have another research project in mind for you in 2020”.

As I follow along, I keep wondering whether the explanation for the dinoflagellate paradox “they appear at low nutrients” is wrong. Low nutrients stress every organism, even dinoflagellates and yet many aquarist claim dinoflagellates seem to appear at very low nutrients but disappear at higher nutrients. This paradox is often explained as loss of competition for nutrients but overlooks the fact that dinoflagellates are also suffering at low N and P. I hope you have on your to-do list “explain dinoflagellate paradox”. Turning dinoflagellates on-and-off would raise your status to “superhero”.

 

[taricha]

I hope you have on your to-do list “explain dinoflagellate paradox”. Turning dinoflagellates on-and-off would raise your status to “superhero”.

Currently, you're having more luck culturing dinos, so you're closer than I am to that ambitious project.
But, I'll ponder it a bit.

 

[scottrotton]

@taricha @Dan_P

I managed to come up with something that has work for me, you may be interested in as ive never seen it suggested anywhere. but here goes, this helped me battle Cyano, Dinos where all other methods failed.

1, i removed the sand bed very slowly and Chaeto (after this dinos continued to grow on rocks etc but nether the less this is what i did)
2, 3 day black out, i have a very powerful COB 70 watt 400k LED, this was turn on 24/7 idea is to give the dinos and CYano somewhere to settle that isnt in the main display, when lights are off they did indeed all move to refugium area.
3, turn lights back on, let Dinos grow, start dosing 0.1ppm phos and 3ppm daily as my levels are undetectable.
4, at this point Dinos should overrun you refugium, this is where I use a scraper to remove them and the Cyano, drain refugium chamber below the over flow baffles. Does does H2o2 1 ml per liter of estimated water. leave for 1 hour
5, drain rest of refugium then fill chamber with clean Salt water to same level as previous, do the same again.
6, if you have Cyano you should start seeing it die, sometimes water will turn pink. Drain again then fill chamber to normal level.
7, Dose beneficial bacteria to the main display whilst you do this, i used Waste away and AF Pro Bio S and Np Pro
8, Blow rocks with turker baster daily to stop organics settling, if no detritus comes off you may skip this step.
9, continue steps 4-7 until you see Dino stop

After i started doing this coraline algae exploded and covered my entire tank within 3-4 weeks, a good signal balance is back on track. No more signs of Cyano or Dinos, in both sump or Display

 

[taricha]

@scottrotton
Some comments from me:
If I read this correctly, You do a 3 day display blackout with sump/fuge light on - to concentrate dinos and cyano in the fuge.
In the fuge you kill (large dose of oxidizer possible because you've cut off return to tank) and export dino/cyano
You use a lot of blasting flow in display to help move debris to the sump.

The idea of using blackouts to move dinos out of their established comfortable niche is something we use a lot in the main dino thread. Because although they can survive on heterotrophy, they will seek out a comfortable light level.

What I find interesting is that you got big masses of dinos AND cyano in the fuge. Dino makes sense. The dino cells in the fuge were almost certainly the same cells that were in the tank. They pick up and move en mass. Cyano mats do no such thing, implying that cyano cells and filaments built new mats in the fuge in a short time. My guess is that enough debris and loose filaments/cells came over to the fuge to make establishing new big mats possible in short time.
Also interesting is the possible effect of oxidizer on the debris. I know you exported a bunch of it, but I wonder if there's a possibility peroxide changed the composition of what remained.

An interesting aside to think about.

 

[scottrotton]

@scottrotton
Some comments from me:
If I read this correctly, You do a 3 day display blackout with sump/fuge light on - to concentrate dinos and cyano in the fuge.
In the fuge you kill (large dose of oxidizer possible because you've cut off return to tank) and export dino/cyano
You use a lot of blasting flow in display to help move debris to the sump.

The idea of using blackouts to move dinos out of their established comfortable niche is something we use a lot in the main dino thread. Because although they can survive on heterotrophy, they will seek out a comfortable light level.

What I find interesting is that you got big masses of dinos AND cyano in the fuge. Dino makes sense. The dino cells in the fuge were almost certainly the same cells that were in the tank. They pick up and move en mass. Cyano mats do no such thing, implying that cyano cells and filaments built new mats in the fuge in a short time. My guess is that enough debris and loose filaments/cells came over to the fuge to make establishing new big mats possible in short time.
Also interesting is the possible effect of oxidizer on the debris. I know you exported a bunch of it, but I wonder if there's a possibility peroxide changed the composition of what remained.

An interesting aside to think about.

Pretty much spot on i forgot to add i removed as much of the cyano and dino before i did the blackout. Worth a try if someone else struggles, i would say this is 99% eliminated from my main display and minimal growth in the sump


this is what it looked like after a few days