This is what I've dreamed of for so long! Testing for microbes in our tanks!

Huskymaniac

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Hi Randy,

Thanks for posting this detailed description. So many interesting things to explore here.

First I want to mention the pathogen. As you describe, there are lots of different types of P. damselae (including 2 subspecies with multiple strains), many of which are really nasty for a broad range of fish. It's so-named for its occurrence in the Damsel family, but the range is so broad I hesitate to say which aquarium fish it infects. I believe there are some fish disease experts on the forum though, maybe @Humblefish has some thoughts on this bug? It causes diseases called Photobacteriosis or pasteurellosis, which are widely described in the aquaculture literature but I can find little information on saltwater aquarium fish.

A few details I can contribute -
  • This exact same bug is found in about 1 out of 8 tanks. None of mine have it so I cannot comment on effects or lack thereof. But several others have reported no symptoms in their fish. It might be interesting to compare fish lists, especially if we can find out what it infects outside of the Damsel family.
  • At the DNA sequence level, this marker cannot distinguish between different strains, since it is a perfect match to multiple strains both the piscidida and damselae subspecies. I want to emphasize this point -- the data in hand can't distinguish between strains that are pathogenic for fish, humans, both, or neither.
  • Some researchers consider this group some of the most dangerous pathogens in global aquaculture (source), because it is globally distributed, infects a broad range of fish, and has a high mortality rate upon infection.
I didnt know which if any bacterial fish pathogens to expect in a broad survey of aquariums. So I searched for all the names I could find in the literature (over 40). This bug is the only known fish pathogen I've seen, and it shows up repeatedly but not universally (about 1 out of 8 tanks). Considering the range of possible effects I think its worth paying attention to, but I don't want to either falsely alarm or reassure anyone.

While we're on the subject of zoonoses in aquariums, I always search for Mycobacterium marinum and am happy to report I have not found it yet. I've known someone infected by M. marinum (it causes Aquarium granuloma) so while it's rare its far from unheard of.

I will say, I'm the farthest thing from a germ phobe and have accidentally gargled my share of tank water while siphoning. But after spending so much time looking at aquarium microbiomes this year I am paying special attention to keep any open cuts out of the water, at the very least...

Just looking through the message boards it seems uronema marinum is so common these days. Is it possible that what people are thinking is u. Marinum is actually p. Damselae?
 

PSXerholic

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That will be interesting! Hope you're doing well, I know my colleague who had an M. marinum infection from a cut on her hand was frustrated how long it took to heal. This bug hasnt shown up yet on the tests yet but that's consistent with the relative rarity of these infections among reef keepers. If it is there, we will find it...
Interesting!
Don't want to derail the thread, but when I was dealing with the severe TN issues in the beginning of this year, and honestly haven't paid attention to laboratory cleanliness levels while dealing with all sort of bacteria likely from the tank and corals I took apart while working with the microscope, I felt I had several subsequent body inflammations for a few months from this work on the tank!
That was no fun, at some point I thought it may be the result of the tank pathogens, and good friend and my Dentist treated me with a variety of Antibiotics such as Amoxicillin, Metrodinazole and Tetracycline which resolved after weeks of treatment all symptons I had in joints, teeth and hands! You can imagine the Restroom was my most visited location with those all after each other :cool: Might of course be coincidence, which I doubt. Lessons learned for sure!
 

AquaBiomics

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Just looking through the message boards it seems uronema marinum is so common these days. Is it possible that what people are thinking is u. Marinum is actually p. Damselae?
Thanks for bringing this up. I have been wondering the same thing, whether this known fish pathogen, present in 1 of 8 tanks, might be causing misdiagnosed diseases.

I stocked fish directly from importers and wholesalers directly into my experimental tanks without any medication or QT, and none of these tanks (12) has P. damselae. Neither do any of my home tanks. So it is far from universal in the hobby, but at 1/8 tanks its common enough I'd like to know if this is a pathogenic strain.

Would love to get the input of the resident fish disease experts on this one! What undiagnosed or misdiagnosed diseases in the hobby might be attributable to P. damselae? This may help in tracking down a sick fish to test...
 

FishDoc

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Finally someone has done it. To be able to test for microbes strains in our tanks!

This could be very helpful!

This is an exciting premise indeed. It is interesting to think that someone could now forcibly quantify the average biome arrays found in the average home aquaria and target specific proportions in certain densities and potentially create a reef vitality to target a certain tank volume and/or bioload size. Very cool!
 

Lapras

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This is pretty cool. A question, sorry if already asked:

does shipping temperature affect your analysis? like, depending on transit temp, will any of the bacteria suddenly increase/decrease significantly?
 

taricha

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Not really. They are just looking for bacterial DNA, they don't actually need live viable bacterial cells.
 

taricha

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@AquaBiomics
I wonder if this critter has shown up in people's tanks?
Dinoroseobacter shibae
Dinoroseobacter shibae DFL12T, a member of the globally important marine Roseobacter clade, comprises symbionts of cosmopolitan marine microalgae, including toxic dinoflagellates....D. shibae DFL12T is able to synthesize the vitamins B1 and B12 for which its host is auxotrophic. Two pathways for the de novo synthesis of vitamin B12 are present, one requiring oxygen and the other an oxygen-independent pathway. The de novo synthesis of vitamin B12 was confirmed to be functional, and D. shibae DFL12T was shown to provide the growth-limiting vitamins B1 and B12 to its dinoflagellate host. The Roseobacter clade has been considered to comprise obligate aerobic bacteria. However, D. shibae DFL12T is able to grow anaerobically using the alternative electron acceptors nitrate and dimethylsulfoxide
 

AquaBiomics

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This is pretty cool. A question, sorry if already asked:

does shipping temperature affect your analysis? like, depending on transit temp, will any of the bacteria suddenly increase/decrease significantly?
We "fix" (i.e., kill and preserve) the bacteria prior to shipping the sample. These fixed samples appear to be stable for days to weeks at room temperature or higher. Theyre exposed to these temps for only a day or two during shipping then stored in the freezer til analysis.
 

AquaBiomics

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@AquaBiomics
I wonder if this critter has shown up in people's tanks?
Dinoroseobacter shibae
Really interesting question, I like these because you never know, maybe I'll look in the database and find out something new!

Turns out we havent detected any member of this genus yet. There are lots of members of this genus in the DB, so if it was there we should see it. We do see lots of Rhodobacteraceae (the same family) in most tanks (one of the top 4 most abundant families), and many of these are not classified below the family level. So I can't rule out the presence of a related bug with similar functions, but can say we havent seen this one specifically yet.

I have not sampled a tank with a full blown dinoflagellate problem though...
 

Huskymaniac

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Really interesting question, I like these because you never know, maybe I'll look in the database and find out something new!

Turns out we havent detected any member of this genus yet. There are lots of members of this genus in the DB, so if it was there we should see it. We do see lots of Rhodobacteraceae (the same family) in most tanks (one of the top 4 most abundant families), and many of these are not classified below the family level. So I can't rule out the presence of a related bug with similar functions, but can say we havent seen this one specifically yet.

I have not sampled a tank with a full blown dinoflagellate problem though...

Sent you two samples. One of the tanks has a Dino problem!!!!
 

taricha

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Turns out we havent detected any member of this genus yet. There are lots of members of this genus in the DB, so if it was there we should see it. We do see lots of Rhodobacteraceae (the same family) in most tanks (one of the top 4 most abundant families)
I repeat myself, but I'm constantly re-amazed at how powerful this analysis is. Wowed that you already had eyes out (in the database) for that genus. I knew reports were showing a good amount of rhodobac. so I thought there was a chance this guy might be hiding in there.

One of the tanks has a Dino problem!!!!
look forward to it.
 

MnFish1

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Just to bump this up a bit. I have been in communication with Eli (@AquaBiomics) - sent in 8 blinded samples today - from various times - and places in my tank (and outside the tank) - will look forward - with his permission to publish the results. The problem is - I have 8 more tests I could have done:). His methods seem quite sound - and appropriate - and it will be interesting to see the answers. More to follow
 

Nano sapiens

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Just received my Aquabiome test results for a 11+ year old non-filtered (no mechanical/chemical filtration, just live rock/live sand) 12g nano. Couple of my takeaways:

  1. Diversity & balance higher than 50th percentile of tested reef tanks
  2. Balance Score (Correlation with Typical Abundance) shows similarities and differences compared to the 'typical' reef tank
  3. Huge relative abundance of Pelagibacteraceae (Gram-negative, rod-shaped, free-living Bacteria (Alphaproteobacteria), aerobic & chemoheterotrophic, previously called SAR11, thought to be the most abundant bacterial group in the ocean worldwide. Well-adapted for life in the low-nutrient waters of the open ocean. Require reduced sulfur compounds, glycine, and dissolved organic carbon for growth). Distant runner ups: Hyphomicrobiaceae (Gram-negative Bacteria (Alphaproteobacteria), mostly rod-shaped, some free-living, Mostly aerobic & chemoheterotrophic, some photoheterotrophic, Extremely diverse, widely distributed and highly abundant in marine habitats including open ocean, sediments, and algal biofilms. Degrade sulfur-containing compounds (e.g. sulfite, DMSP). Many use methylated amines (MA) as primary nitrogen source) & Rhodobacteraceae (Gram-negative Bacteria (Alphaproteobacteria), mostly rod-shaped, some free-living, Mostly aerobic & chemoheterotrophic, some photoheterotrophic, Extremely diverse, widely distributed and highly abundant in marine habitats including open ocean, sediments, and algal biofilms. Degrade sulfur-containing compounds (e.g. sulfite, DMSP). Many use methylated amines (MA) as primary nitrogen source)
  4. Typical ammonia−oxidizing microbes (with the exception of Nitrososphaeraceae (0.00026), which apparently is not typically registered in samples).
  5. Nitrite−oxidizing Nitrospiraceae lower than typical
  6. No Cyanobacteria species found
  7. No Fish pathogen species found
  8. No Coral pathogen species found
From the test reports I've seen online, there appears to be a general trend of decreasing diversity with age. This tank actually has a higher diversity (66%) compared to the 50th percentile. This is interesting and perhaps a bit surprising because the only significant additional bacteria are from occasional new specimens (~ once or twice a year, perhaps, on average) and weekly feeding of live earthworms from the compost heap. The system has never been subjected to any commercial 'fix-it' products (Vibrant, Chemi-clean, etc.) and hasn't had a melt-down (knocks on wood). Both the live rock and most of the live sand are over 20 years old (came from a previous long-lived aquarium). Since the sand bed had a very light dusting of coca-cola colored brown algae in places on the sand bed I suspected cyano, but no Cyano in the report.

Any thoughts, Eli?


Ralph.
 

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Nano sapiens

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Just received my Aquabiome test results for a 11+ year old non-filtered (no mechanical/chemical filtration, just live rock/live sand) 12g nano. Couple of my takeaways:

  1. Diversity & balance higher than 50th percentile of tested reef tanks
  2. Balance Score (Correlation with Typical Abundance) shows similarities and differences compared to the 'typical' reef tank
  3. Huge relative abundance of Pelagibacteraceae (Gram-negative, rod-shaped, free-living Bacteria (Alphaproteobacteria), aerobic & chemoheterotrophic, previously called SAR11, thought to be the most abundant bacterial group in the ocean worldwide. Well-adapted for life in the low-nutrient waters of the open ocean. Require reduced sulfur compounds, glycine, and dissolved organic carbon for growth). Distant runner ups: Hyphomicrobiaceae (Gram-negative Bacteria (Alphaproteobacteria), mostly rod-shaped, some free-living, Mostly aerobic & chemoheterotrophic, some photoheterotrophic, Extremely diverse, widely distributed and highly abundant in marine habitats including open ocean, sediments, and algal biofilms. Degrade sulfur-containing compounds (e.g. sulfite, DMSP). Many use methylated amines (MA) as primary nitrogen source) & Rhodobacteraceae (Gram-negative Bacteria (Alphaproteobacteria), mostly rod-shaped, some free-living, Mostly aerobic & chemoheterotrophic, some photoheterotrophic, Extremely diverse, widely distributed and highly abundant in marine habitats including open ocean, sediments, and algal biofilms. Degrade sulfur-containing compounds (e.g. sulfite, DMSP). Many use methylated amines (MA) as primary nitrogen source)
  4. Typical ammonia−oxidizing microbes (with the exception of Nitrososphaeraceae (0.00026), which apparently is not typically registered in samples).
  5. Nitrite−oxidizing Nitrospiraceae lower than typical
  6. No Cyanobacteria species found
  7. No Fish pathogen species found
  8. No Coral pathogen species found
From the test reports I've seen online, there appears to be a general trend of decreasing diversity with age. This tank actually has a higher diversity (66%) compared to the 50th percentile. This is interesting and perhaps a bit surprising because the only significant additional bacteria are from occasional new specimens (~ once or twice a year, perhaps, on average) and weekly feeding of live earthworms from the compost heap. The system has never been subjected to any commercial 'fix-it' products (Vibrant, Chemi-clean, etc.) and hasn't had a melt-down (knocks on wood). Both the live rock and most of the live sand are over 20 years old (came from a previous long-lived aquarium.

Editing with a cell phone...not so good.
Will respond to Eli's email later...

Ralph.
 
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MnFish1

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What was the difference between the 'swab' and the 'water'. was there any ammonia reducing bacteria in the free water? Thanks.
Just received my Aquabiome test results for a 11+ year old non-filtered (no mechanical/chemical filtration, just live rock/live sand) 12g nano. Couple of my takeaways:

  1. Diversity & balance higher than 50th percentile of tested reef tanks
  2. Balance Score (Correlation with Typical Abundance) shows similarities and differences compared to the 'typical' reef tank
  3. Huge relative abundance of Pelagibacteraceae (Gram-negative, rod-shaped, free-living Bacteria (Alphaproteobacteria), aerobic & chemoheterotrophic, previously called SAR11, thought to be the most abundant bacterial group in the ocean worldwide. Well-adapted for life in the low-nutrient waters of the open ocean. Require reduced sulfur compounds, glycine, and dissolved organic carbon for growth). Distant runner ups: Hyphomicrobiaceae (Gram-negative Bacteria (Alphaproteobacteria), mostly rod-shaped, some free-living, Mostly aerobic & chemoheterotrophic, some photoheterotrophic, Extremely diverse, widely distributed and highly abundant in marine habitats including open ocean, sediments, and algal biofilms. Degrade sulfur-containing compounds (e.g. sulfite, DMSP). Many use methylated amines (MA) as primary nitrogen source) & Rhodobacteraceae (Gram-negative Bacteria (Alphaproteobacteria), mostly rod-shaped, some free-living, Mostly aerobic & chemoheterotrophic, some photoheterotrophic, Extremely diverse, widely distributed and highly abundant in marine habitats including open ocean, sediments, and algal biofilms. Degrade sulfur-containing compounds (e.g. sulfite, DMSP). Many use methylated amines (MA) as primary nitrogen source)
  4. Typical ammonia−oxidizing microbes (with the exception of Nitrososphaeraceae (0.00026), which apparently is not typically registered in samples).
  5. Nitrite−oxidizing Nitrospiraceae lower than typical
  6. No Cyanobacteria species found
  7. No Fish pathogen species found
  8. No Coral pathogen species found
From the test reports I've seen online, there appears to be a general trend of decreasing diversity with age. This tank actually has a higher diversity (66%) compared to the 50th percentile. This is interesting and perhaps a bit surprising because the only significant additional bacteria are from occasional new specimens (~ once or twice a year, perhaps, on average) and weekly feeding of live earthworms from the compost heap. The system has never been subjected to any commercial 'fix-it' products (Vibrant, Chemi-clean, etc.) and hasn't had a melt-down (knocks on wood). Both the live rock and most of the live sand are over 20 years old (came from a previous long-lived aquarium). Since the sand bed had a very light dusting of coca-cola colored brown algae in places on the sand bed I suspected cyano, but no Cyano in the report.

Any thoughts, Eli?


Ralph.
 

Scrubber_steve

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What was the difference between the 'swab' and the 'water'. was there any ammonia reducing bacteria in the free water? Thanks.
Don't know if you've read this article?

Eli on the water test performed on a newish Battle Corals tank -
"One of the things that really stood out about your tank for me is the high levels of nutrient-processing microbes. Ammonia-oxidizing microbes made up almost 8% of your sample, which is higher than about 85% of aquariums I’ve tested, about twice as high as the average sample. Your sample also had high levels of nitrite-oxidizing bacteria (0.9%), which is among the highest of any tanks tested (higher than 96% of samples), and over 3-times higher than the average sample."
 

MnFish1

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Don't know if you've read this article?

Eli on the water test performed on a newish Battle Corals tank -
"One of the things that really stood out about your tank for me is the high levels of nutrient-processing microbes. Ammonia-oxidizing microbes made up almost 8% of your sample, which is higher than about 85% of aquariums I’ve tested, about twice as high as the average sample. Your sample also had high levels of nitrite-oxidizing bacteria (0.9%), which is among the highest of any tanks tested (higher than 96% of samples), and over 3-times higher than the average sample."
Yes - thanks - I was referring to the fact that there are 2 samples taken - one thats in the water column, the other a swab - that is not - I was curious if there was a difference between samples
 
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