EMeyer

No, I'm familiar with this work including in corals but don't do this for a few reasons. Since there arent primers that universally amplify all viruses, it would be more expensive. And since we know even less about marine viruses than marine bacteria, I think it would be hard to develop a market for it. I still struggle to convince hobbyists that bacteria matter, despite the amount of money people spend pouring bottles of ""live bacteria"" into their tanks

The only sample I'm finding from you is in august 2019, does that sound about right? If so, based on my records, it looks like your tank had a very low balance score similar to what John's later developed. Both of your tanks had very low levels of Pelagibacteraceae, but each of your tanks included different atypical families in its place. Both tanks also had elevated levels of Vibrionaceae. Keep in mind Pelagibacteraceae is the most abundant group in the ocean (a top contender for the most abundant organisms on the planet), and Vibrionaceae includes quite a few known pathogens. So I think its plausible these specific deviations from the typical pattern are functionally important.

I looked into your parasite test results (18s rDNA) from the Aug 2020 sample, I don't recall if we discussed those before? None of the usual suspects for fish or coral parasites (including AEFW) are present in that sample, but I do see a candidate that may be worth following up on. The sample had Brooklynella sinensis at high levels (>300 identical DNA sequences from this species). This isnt Brooklynella hostilis (the cause of the fish disease), but a close relative. I can't find any useful info on this parasite so far. Since my 18S database isnt as well developed as my 16s (microbiome) db, I can't immediately do a full search, but I can say that none of the other samples run in that batch showed any evidence of Brooklynella sinensis. So this gives you some sense of how rarely it shows up in samples, which is why it caught my eye on manual review of the output. Hope some of this was helpful!

I'll add that I looked into your Vibrio in more detail. The Vibrionaceae in your sample consist of several types not classified beyond the family level, a few Vibrio sp. (i.e. classified to the genus level), and Vibrio fortis. This composition hasnt changed over the time we've sampled your tank; these types have always been there. They've just increased in abundance. So I see no evidence any new, problematic Vibrio were introduced.

Looking back into your microbiome results, you'll recall we didnt find any smoking gun pathogens in your sample from Aug 2020. I do notice that your microbial community, while remaining diverse, has become very atypical over time. In May 2019 it was nearly a model for a typical community, with a high balance score (0.7). All of the top 5 most abundant families in the typical microbiome were present at similar levels in your tank at that time. By Nov 2019 that had changed - your balance score had fallen to 0.3. Since that time, it's continued to fall, from 0.19 in Jan 2020 to 0.1 in Aug 2020. Several of the major families that are typically abundant have become very rare in your tank (Pelagibacteraceae and Flavobacteriaceae). Vibrionaceae have increased substantially over this time. I always say, an atypical community (low balance score) should not on its own be interpreted as necessarily evidence of a problem. But in your case, if we're asking about possible reasons for the issues youre having with corals, we can say for sure that the microbial community has gone from very typical to very atypical over the past year or so. I see some parallels between your sample and the sample I took from my Euphyllia tank while it was suffering from BJD. I'm not suggesting the same pathogen is involved, just that both are show some of the same disruptions. The most effective ways I've found to rapidly improve my aquarium's microbiome are live sand/mud, and more recently, in-tank treatments with low doses of antibiotics. I don't think we're at an antibiotic stage with your tank yet, but have you tried any additions of live sand or mud? Also, considering the pretty dramatic change in your tank's microbiome over the past year, can you think of any changes you've made that may explain it? Id be especially interested to hear about any sterilizing effects e.g. UV or ozone, since those seem to be associated with reductions in Pelagibacteraceae.

I finally got around to writing this up on Reef2Reef. https://www.reef2reef.com/threads/experimenting-with-in-tank-antibiotic-treatments-for-brown-jelly-disease.782438 A quick summary: So, anybody got brown jelly in your tanks?

snail eggs.

advice for new reefers? go ahead and get the live rock now instead of trying for 2-3 years to get a sterile box of rocks and glass to turn into an ecosystem. more beneficial than any silly expensive piece of equipment you'll be sold, and speeds up your tanks development better than anything else.

I have an interesting finding from my most recent round of sequencing that I thought I'd share. In this unreplicated case study, I found that an in-tank antibiotic treatment appears to have cleared up an outbreak of brown jelly disease (BJD), without causing any problems for the rest of the microbiome or any detectable problems for livestock. If anyone is having BJD issues, and would like to try this treatment, I'd love to sample your tank before and after the treatment to replicate this finding. I'm busy with Turkey today, so it'll be a few days before I can post the data here. This post is just a teaser. Here is what I've found A specific Bacterium (an undescribed species in the genus Acrobacter) is associated with BJD that sporadically shows up in newly imported Euphyllia The BJD can be transmitted by placing an affected coral in an otherwise healthy tank, resulting in disease and stress in several Euphyllia species An in-tank treatment with a specific low dose of a commonly used aquarium antibiotic appears to have arrested this problem and allowed the affected corals to recover samples of the aquarium microbiome before and after the treatment show that The abundance of the suspected pathogen (Arcobacter sp.) is greatly reduced by the treatment The diversity and balance of the aquarium microbiome were not damaged by the treatment; in fact, both scores increased following the antibiotic treatment, along with the relative abundance of nitrifying microbes. So, anybody got BJD? Message me if so... I'll update with data when I can...

Dremels are my go to tool for coral fragging. I like the diamond blade - its a wheel, I think its sold for cutting tile. Maybe $20-30 at Home Depot. I'm jealous of the specialized band saws. Someday!

cuttlefish eggs! Good luck, those are awesome.

Bumping this as a reminder and for a few additions to the list. I am also looking for common aquarium pests and *known* varieties of nuisance algae. (e.g. Bryopsis) Rather than come up with a long comprehensive list, if its something that you want to keep out of your tank, and you have a specimen of it, I want to sequence its DNA. (I already have plenty of specimens of vermetid snails and bristleworms. Funny enough I have no aiptasia currently, but I can probably get some locally). Brown jelly disease.... this is still high on my list. I've got a bunch of samples from one tank but would love to get samples from a different tank. Coral parasites of any kind... Acro eating flatworms, Euphyllia eating flatworms, red bugs, black bugs... (RTN/STN are not on my list, since these appear to be bacterial and we already have a great database for that) Thanks!

I'll be curious to hear how this goes. I tried this with some orange and purple capricornis a while back. They wouldnt fuse for me, and the purple took over (I ended up with 6 mini colonies of purple cap instead of 6 grafted frags) It probably depends a lot on which varieties you start with, what colors are these? (unsure because of the blue) I still think the grafted varieties in the hobby are products of somatic mutation rather than true grafting but I keep trying!

Glad I'm not the only one. If my corals crashed as often as my chaeto does, I think I'd have left the hobby long ago. It goes through boom/bust cycles in most of my tanks, and I cant figure it out. I've tried dosing iron etc, nothing helps. I always just grab some from one of my other tanks and transfer it over to restart the chaeto. So far this has worked but if all my chaeto ever crashes at once I'm gonna be screwwwed.

I should clarify that the study I cited was from a lagoon at Heron Island on the GBR, where there is limited exchange with the open ocean during part of the day. So these effects are probably different here than in the open ocean. Still, its a typical coral habitat so I figured it was a relevant number to add to the discussion. I'm often struck by the fact that on real reefs, most of the parameters we try to keep stable in our aquariums, are not stable at all. Temperature, light, pO2, pCO2, pH, alkalinity. The only cycle we ever try to mimic is light. The others, we (the reefkeeping community) try to maintain at stable levels, in some cases levels that aren't near the average. But I hadnt really dug into the alkalinity part until your post, I'm still doing manual dKH titrations so I don't see these patterns

So cool. This is incredible that the hobby is getting to the point we can detect and think about adjusting these daily fluctuations in alkalinity. Since pH isnt stable on natural reefs, I was motivated to look at the research literature to ask, how does your variation in alkalinity compare to natural coral reefs? This study (reference here) also found alkalinity dropped during the daytime by about 7%. (Its shown as "TA", for total alkalinity) I guess the daytime drop in alkalinity is driven by photosynthesis? Interesting that this pattern is opposite the variation in corals' demand for alkalinity. I suspect the increased demand after lights out has to do with the falling pH, which will convert carbonate into bicarbonate. Corals take up bicarbonate, so it would make sense that uptake would increase at night when the pH falls and the bicarbonate rises. I think thats how it works, anyway!

Just dropping in to say F bristleworms. I feel more compassion towards yellowjackets.

Still looking for 40 breeder (at least 1, maybe 2) 4'x2' shallow frag tank Not desperate but would also buy 29 gallon 55 gallon

Gambling on aquarium equipment, how can I resist? 5 + my freebie: 3 on the nero 3 on the mp40

I agree. I've been able to accomplish what I wanted to with the Apex, but man, it'd sure be easier if they just included some of the basic elements present in every other language I've used. Cmon, Neptune, just give me some kind of loop!

The new coral shed is close to finished... so now I need tanks to fill it! Still looking for frag tanks and 40b.

Ha, I hadnt thought about that. Sure, I can keep any information about what parasites a person may have in their tank confidential. My purposes don't require even knowing where the parasite came from, just what it is. To be clear, the goal here isnt building a database of what's in various peoples tanks (like with the microbiome). The goal is more specific identification. Currently, when I analyze an eDNA sample from an aquarium, I can tell it has corals, fish, snails, shrimp, etc. because I find their DNA in the water. I also find parasite DNA in the water. For stuff like Cryptocaryon (already in the database) I can get a clear identification. For other parasites (e.g. montipora eating nudibranch), if I detected their DNA it would show up as a close match to some kind of Mollusk because that exact species is not in the database. By getting known parasite sequences in the database, I'll be able to identify these things when they show up in water samples. So everyone can feel free to send me parasites and say you got them from Petco or something

I'm focusing on parasites for this test -- the algae test would be good to ID Dinos but I'm keeping that on the back burner for now. I can run the algae test on your recent sample and see what shows up..

Thats great to hear, I'd love to take some off your hands! If we can get one in a tube, I'm confident we can get a sequence from it for comparison with environmental DNA from tanks including yours.

Hi all, I'm working on expanding my database for my eDNA test, which I'm currently using to detect common fish parasites like Cryptocaryon or Uronema in water samples. I'd like to expand to include common coral parasites. If you encounter any of the following parasites, and are able to collect a sample, could you please send them to me? Acropora-eating flatworms Montipora-eating nudibranchs Red bugs Euphyllia-eating flatworms Anything else I'm forgetting? I'm also interested in expanding my database on bacteria associated with Brown Jelly Disease, so if you encounter any BJD, I would love a sample of that too! All samples can be preserved using the strongest proof alcohol you have on hand (151 proof is ideal but really, even standard vodka or whiskey will do). Pickle the parasite in a small amount of booze, store it in the freezer, and send me a message -- I will send you a prepaid shipping envelope (and if you are interested, a free microbiome sampling kit to analyze your tank)