Help with interpretation and next steps: AquaBiomics Microbiome Report

[thebookshark]

Hey folks, need some help with my Microbiome report. I have been experiencing some RTN & STN in this tank; first losses about 2 months ago and were two smooth-skinned deepwater acros. I managed to save a 3rd acro by fragging and re-gluing it and it has been doing well since. No issues for the last 2 months and then last week 2 more acros lost. No issues with any other coral species and everything in the tank is growing and doing well. Hence why I ordered the AB Microbiome test (sample that was tested for this report was collected about 5 weeks ago).

I will say that my RFAs have started to go downhill in the last month; they’ll pop up and move randomly with no changes to lighting or flow and then they can’t get re-settled and sort of wither and die. I’ve lost 2 and have another 4 currently struggling. Wondering if it could be due to the listed pathogens in the report?

I am an experienced hobbyist (20 years) and I have learned in that time to be very cautious with extreme interventions. For this reason, I am extremely reticent to nuke the tank with antibiotics. I tend to go straight to peer-reviewed research for answers and from this I’ve decided to use probiotics as my first approach to treatment of the pathogens and to get my microbiome diversity up. I have the Nyos Biotic supplement coming tomorrow. Please provide any additional recommendations you may have, particularly interested in your take, @Randy Holmes-Farley !

 

[Randy Holmes-Farley Verified Community Expert]

I think it is often hard to know whether something in such a report warrants action, and if so, what actions are most useful.

Report aside, one can add bacteria. It may or may not help.

Best, IMO, is some real ocean sand (or rock). Second is sand or rock from a good reef tank. Bottled bacteria might be useful, but may not add natural reef species.

 

[thebookshark]

I think it is often hard to know whether something in such a report warrants action, and if so, what actions are most useful.

Report aside, one can add bacteria. It may or may not help.

Best, IMO, is some real ocean sand (or rock). Second is sand or rock from a good reef tank. Bottled bacteria might be useful, but may not add natural reef species.

I do have a lot of rock in this system given its size (21G AIO). This tank is an upgrade from my 10G nano and it was transferred in January with the rock that had been in that tank for a year. I added another 17lbs of very cured LR from my LFS so it has 27 lbs of cured rock plus about 20 lbs of sand. I have very efficient nutrient export with nitrates reading at 0.38 on a Hanna ULR checker and phosphates at 0.10, also on a Hanna checker.

 

[Dan_P]

Hey folks, need some help with my Microbiome report. I have been experiencing some RTN & STN in this tank; first losses about 2 months ago and were two smooth-skinned deepwater acros. I managed to save a 3rd acro by fragging and re-gluing it and it has been doing well since. No issues for the last 2 months and then last week 2 more acros lost. No issues with any other coral species and everything in the tank is growing and doing well. Hence why I ordered the AB Microbiome test (sample that was tested for this report was collected about 5 weeks ago).

I will say that my RFAs have started to go downhill in the last month; they’ll pop up and move randomly with no changes to lighting or flow and then they can’t get re-settled and sort of wither and die. I’ve lost 2 and have another 4 currently struggling. Wondering if it could be due to the listed pathogens in the report?

I am an experienced hobbyist (20 years) and I have learned in that time to be very cautious with extreme interventions. For this reason, I am extremely reticent to nuke the tank with antibiotics. I tend to go straight to peer-reviewed research for answers and from this I’ve decided to use probiotics as my first approach to treatment of the pathogens and to get my microbiome diversity up. I have the Nyos Biotic supplement coming tomorrow. Please provide any additional recommendations you may have, particularly interested in your take, @Randy Holmes-Farley !

It will be interesting to see the Aquabiomics report after adding all the bacteria products.

 

[thebookshark]

It will be interesting to see the Aquabiomics report after adding all the bacteria products.

I ordered 20lbs of Florida harvested live sand today from LiveRockNReef. I plan to slowly siphon out my existing sand and replace it with an equal volume of the wild sand over the course of 1-2 weeks while keeping a close eye on nutrient levels. I spoke with Bill there for a while about my shipping options and explained my issues and concerns; he was very helpful. Ultimately I opted for 2-day shipping as the temperature here in Atlanta has dropped quite a bit. After it arrives I will transfer the sand to a bucket, add some freshly mixed saltwater, a heater, and a powerhead to keep it live over the course of the addition period. Between this and the probiotics I’m hoping to see significant improvements in the microbiotic diversity in a month or two. This seems the best approach over nuking the tank with antibiotics or chemicals.

 

[Dan_P]

I ordered 20lbs of Florida harvested live sand today from LiveRockNReef. I plan to slowly siphon out my existing sand and replace it with an equal volume of the wild sand over the course of 1-2 weeks while keeping a close eye on nutrient levels. I spoke with Bill there for a while about my shipping options and explained my issues and concerns; he was very helpful. Ultimately I opted for 2-day shipping as the temperature here in Atlanta has dropped quite a bit. After it arrives I will transfer the sand to a bucket, add some freshly mixed saltwater, a heater, and a powerhead to keep it live over the course of the addition period. Between this and the probiotics I’m hoping to see significant improvements in the microbiotic diversity in a month or two. This seems the best approach over nuking the tank with antibiotics or chemicals.

You are taking the additive approach rather than fixing by subtraction.

Have you considered that the coral issue is not a microbiome problem? I can’t offer an alternative, just playing devil’s advocate,

 

[thebookshark]

You are taking the additive approach rather than fixing by subtraction.

Have you considered that the coral issue is not a microbiome problem? I can’t offer an alternative, just playing devil’s advocate,

I have; however, I carefully monitor my alkalinity, salinity, and temperature and they are stable. I keep detailed records and test often. My temperature is 79-80 depending on the lights (cooler at night), I have a gravity-fed ATO with RODI and it took a bit of fandangling but I finally got it sorted and my SG stays steady at 1.025. Alkalinity has always run on the low end in this tank but is steady between 7.8-8.1 with no swings. I dose AFR for alk and elements. Calcium is steady at 380-400 and Mag at 1350-1370.

Since swings in these parameters are the other oft-cited cause of tissue necrosis and I’ve controlled for these, pathogens seem the only alternative. I don’t have flatworms, bugs, or other coral pests. If I’ve missed another possible cause please let me know.

 

[Dan_P]

I have; however, I carefully monitor my alkalinity, salinity, and temperature and they are stable. I keep detailed records and test often. My temperature is 79-80 depending on the lights (cooler at night), I have a gravity-fed ATO with RODI and it took a bit of fandangling but I finally got it sorted and my SG stays steady at 1.025. Alkalinity has always run on the low end in this tank but is steady between 7.8-8.1 with no swings. I dose AFR for alk and elements. Calcium is steady at 380-400 and Mag at 1350-1370.

Since swings in these parameters are the other oft-cited cause of tissue necrosis and I’ve controlled for these, pathogens seem the only alternative. I don’t have flatworms, bugs, or other coral pests. If I’ve missed another possible cause please let me know.

You seem to have whittled down the number of possibilities. Are you planning on another Aquabiomics test?

 

[slingfox]

I am doubtful this is a microbiome issue since many SPS keepers keep tanks and have never run an Aquabiomics. You would likely be better served running an ICP-MS test and posting the results along with a fully description of your system with photos and perhaps that will help yield more actionable feedback.

Also, how do you know you don’t have coral? What is your coral QT and dipping protocol?

The fact that you have an SPS colony which recovered and did fine after getting fragged suggests you may have a flow or lighting issue.

 

[thebookshark]

I am doubtful this is a microbiome issue since many SPS keepers keep tanks and have never run an Aquabiomics. You would likely be better served running an ICP-MS test and posting the results along with a fully description of your system with photos and perhaps that will help yield more actionable feedback.

Also, how do you know you don’t have coral? What is your coral QT and dipping protocol?

The fact that you have an SPS colony which recovered and did fine after getting fragged suggests you may have a flow or lighting issue.

Here are the results from my last ICP analysis.

I dip all frags in a Bayer Advanced solution of 2c tank water and 20 ml of Bayer for 15 minutes and soak/rinse twice in clean tank water before adding.

I have a Nero 3 on random flow all day plus my return pump at full blast. Light is an AP9X on a modified Worldwide Corals schedule. A few recent tank shots included and the lighting schedule.

 

[Justfebreezeit]

a single nero will have a hard time getting flow to the end of a 3ft tank. I know I sound like a broken record. Last time promise!

 

[thebookshark]

a single nero will have a hard time getting flow to the end of a 3ft tank. I know I sound like a broken record. Last time promise!

Haha it’s not quite 3 feet!

 

[slingfox]

Here are the results from my last ICP analysis.

I dip all frags in a Bayer Advanced solution of 2c tank water and 20 ml of Bayer for 15 minutes and soak/rinse twice in clean tank water before adding.

I have a Nero 3 on random flow all day plus my return pump at full blast. Light is an AP9X on a modified Worldwide Corals schedule. A few recent tank shots included and the lighting schedule.

The setup sounds like too little flow and too little light to support larger SPS colonies. The setup likely works fine for a mixed reef and when the SPS are small. I assume flow is the bigger issue. A common issues as SPS colonies get large is there is not enough flow at the center of the colony which causes the coral to go downhill.

The ICP also has a lot of potential areas for improvement including too low salinity and too low nitrates. Then the question is do you want o try to address the various deficiencies in trace elements onto.

Also, you cannot rule out pests with your dipping routine. One dip might kill most pests but it does nothing for the eggs. To lower pest risk further you need to dip multiple times (eg, once a week for 4-6 weeks).

 

[thebookshark]

The setup sounds like too little flow and too little light to support larger SPS colonies. The setup likely works fine for a mixed reef and when the SPS are small. I assume flow is the bigger issue. A common issues as SPS colonies get large is there is not enough flow at the center of the colony which causes the coral to go downhill.

The ICP also has a lot of potential areas for improvement including too low salinity and too low nitrates. Then the question is do you want o try to address the various deficiencies in trace elements onto.

Also, you cannot rule out pests with your dipping routine. One dip might kill most pests but it does nothing for the eggs. To lower pest risk further you need to dip multiple times (eg, once a week for 4-6 weeks).

Flow issues are definitely something I’ve considered. I do make sure my acros are high on the rock and attached in areas of strong, direct current.

I balk at the assertion there’s insufficient lighting though. This is an extremely powerful light mounted just 9” above the surface over a small tank. Most of my SPS and all of my acros are 3-5” below the surface. Last time I rented a PAR meter I was getting 400-450 in that range. I also have a small crocea clam that was just 1.25” when I bought it and it has grown to 2” in just a few months- it’s attached itself where I originally placed it, high on the rockwork about 3” directly under the light. Given its growth and small size, I really disagree that my lighting is lacking.

I have checked the affected and unaffected frags repeatedly for pests, both during the initial dip and after adding them. Further, I have a possum wrasse and peppermint shrimp that eat coral pests (I know this because some monti-eating nudis made it in, likely eggs, early on in this tank and I have been fighting them ever since- see my recent post about the methods that worked for me and newly developed coral immunity). So I really don’t think it is a pest or parasite.

I’m interested to hear everyone’s thoughts on how to determine if flow is adequate. I know dissolved O2 tests are considered pretty unreliable. I’ve also noticed that many SPS-dominant tanks have flow levels that (to me) seem to rival a hurricane compared to my experiences snorkeling in wild reefs. In Hawaii, there were definitely some strong tidal currents in the shallow reef channels but they typically flow in one direction save for turbulence from waves breaking etc. Compare this to the absolute cyclonic vortex of many reef tanks and it does make me wonder if we aren’t using extreme water turnover/high O2 to offset some other deficiency in the system- my first thought would be higher water temps that often accompany the crazy-intense lighting rigs of large SPS tanks.