Aquarium dna

[joseserrano]

Heard the owner of this company for the second time on reef bum podcast. Interesting concept, but unsure if this is really worth doing.

https://aquabiomics.com/

 

[mattyzang]

i did it on my tank, although i'm dumb and did the wrong one. i meant to do the eDNA test, but bought the microbiome one

http://www.socalireefs.com/index.php?threads/mattzangs-im-100-ext.103226/post-1091206

it's interesting for sure? i don't feel like i really have any biome issues with my tank, so i suppose it would've been more useful if i did. maybe like never ending dinos or crazy cyano. or even better some kind of pathogen killing corals or something

they're actually retesting mine with their next batch, i forget the scientific reasoning why, but they said it might increase the diversity score

my review would be: it's pretty damn expensive for what it is, but it's interesting. i feel like if you have one of those tanks that inexplicably kills stuff it'd be very interesting to see. i had some very sporadic fish deaths and wanted to make sure i didn't have something in there doing it, so now i can feel better that fish just randomly die lol

oh and it takes forever to get results. i think i initially sent mine in early august, and i guess they're super slammed with tests, so it is what it is, but i didn't get results until early September, so it's not like an ICP test

 

[mattyzang]

the Dr. Eli dude sent me a follow-up which apparently he does for every test, so that's cool

Hi Matt,



I'm writing to follow up personally on this automated email and share my perspective on your report.



First I need to point out that while reviewing your report I noticed the filter sample didnt produce as many sequences as we would like (the swab sample from the biofilm worked normally and produced plenty of data). This can reduce the sensitivity of the test and leads to underestimates of diversity. So we will re-run the filter sample in the upcoming run and update the report when the new data are available. I want to be clear that I don't expect much if anything to change - we are re-running it only because we have a strict rule that all samples have to pass our QC thresholds. The report actually looks fine and is a useful first look at your tank's microbial community, especially the biofilm including the nitrifying community.



The report shows a community with lower than usual diversity. This score is certainly underestimated because of the low coverage in the filter sample, since that's where most of the diversity comes from. So I expect it to increase in the updated report, likely into the normal range.



Your sample received a high balance score, indicating a community similar to that of the typical healthy, mature reef tank. This score is not affected much by coverage, so its already a reasonably good estimate of your community. The composition of this community looks great at a family level. The only unusually abundant group - Pelagibacteraceae - is actually a positive sign. This group is the most abundant on natural reefs and in many reef tanks, where it serves as a useful indicator of community maturity since it takes a long time to reach high levels in the community. But in many tanks this group is artificially removed by UV sterilizers. Since our database includes many of these tanks, the "typical" levels are actually an underestimate. For tanks without UV, the levels seen in your sample are common. This looks like an appropriate community composition at this level.



The nitrifying community showed mixed results. We found ammonia oxidizers at typical levels but no sign of any nitrite oxidizers. Its possible we'll pick something up on re-sequencing of the filter sample, but these are actually more abundant in the biofilm sample thats already well represented in your data. So this looks like a real result. This group is surely present somewhere in an established tank, but this result indicates they are present at low levels at most in your biofilm community.



I would only interpret this as a problem if the tank is having issues with nutrient control or nuisance algae. Some tanks manage nutrients thorugh other processes that effectively outcompete nitrifiers for nutrients, resulting in low nitrifying communities without any problem. I see that you use ethanol for carbon dosing, so perhaps this accounts for the low nitrifying community. Its actually pretty common and again I would not consider it a problem on its own.



We found no evidence of any pathogens in the system. This is good, and probably an accurate description of the system. But the main reason I want to re-run the sample is so we can have more confidence in this negative result. With low coverage we can miss pathogens present at very low levels in the sample; higher coverage increases the sensitivity for detecting them. It looks like you don't have any reason to expect pathogens in your tank, based on sample registration. So far we have found none, and overall a healthy and typical microbial community.



I'll email again when the updated results are ready. I hope this is useful.



Thanks,



-Eli

so it's interesting that i apparently lack decent nitrifiers as i do struggle to keep po4/no3 low. granted, muh fish load, but due to high nutrients i now carbon dose off and on as it seems more efficient than water changes to lower nitrates. po4 doesn't seem to get lower no matter what, so now i have a gfo reactor

maybe my carbon dosing caused the lack of nitrifiers? maybe i added too many fish too fast? not really sure

i've also done reef flux multiple times, so maybe that played a role in screwing with something

 

[joseserrano]

The thing that keeps me from doing it is he said, the abundance has to be pretty high in your water column for it to be found. So aefw, coral disease,… have to be pretty present for it to be found in a semi random x ml of your water sample.

 

[mattyzang]

The thing that keeps me from doing it is he said, the abundance has to be pretty high in your water column for it to be found. So aefw, coral disease,… have to be pretty present for it to be found in a semi random x ml of your water sample.

yeah idk how accurate it really is. you swirl a cotton swab in your main drain and the other one i think you swabbed inside the return jet. i definitely thought, well it would seem weird to get dna of aefw or something here, but i also have zero clue how dna would be found. maybe it's just everywhere in the tank?