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EMeyer

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EMeyer last won the day on September 5

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About EMeyer

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    Evil Damsel

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    Monroe, OR

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  1. Black box LEDs, 8 hour photoperiod. I'll grab a PAR measurement soon. But based on the dimmer switches they are all set at equal intensity, and to the eye they are equally bright. I'll also add that I use long LEDs so that each tank shares a light with its neighbor... so these effects cannot be driven by light source differences, because each "clean" tank shares a light with a "dirty" tank. (randomized block design)
  2. A diversity score of 0.48 means 48% of reef tanks in the DB had lower diversity than this sample (i.e., total number of unique bacterial types in the sample) A balance score of 0.36 describes the relationship between the levels of each microbial family in this sample, compared with the average levels across reef tanks in the DB. A score of 1 means it perfectly matches the average levels, a score of 0 means its very different. Tanks started with dry rock, in my experiments - whether bacteria in a bottle were added or not - ended up with low diversity and low balance. Only "good" live rock produced reasonable diversity and balance. While these effects were consistent in my experiment, your results may vary No, to be clear, I have not developed (and am not currently working on) a bacteria in a bottle product. (I am working on a bacterial nutrient solution but still very R&D) The different microbiomes in this case came from different sources of live rock, a bottle, or none (controls, with just dry rock). I describe the experiment in some detail here
  3. Sorry I missed this. Group 4 was a batch of live rock I got from a wholesaler. I am not aware of any retailers that carry it but the wholesaler lists it as Tonga nano branch rock. They described to me that it comes from a mariculture facility in Tonga, and is shipped to them with corals. It is real coral rubble, with some coralline algae, but no impressive surface growth (sponges, corals, tunicates, etc). Just coral rubble and bacteria and a little coralline. In contrast, the dry rock I used was dry, sterile, Pukani. This is also real coral rubble. So both the dry rock and the bacteria in a bottle tanks have this. The live rock in group 1 looked AMAZING on the surface and garbage underneath. It was that terrible purple-dyed concrete stuff, I heard someone call it "Walt Smith". On the surface it was the best live rock I've ever seen, hands down. Inside it is garbage. Literally purple concrete mixed with shells and rubble. I predict that a standard building brick would have as much internal surface area as this stuff. If I'd been buying it for a display tank I'd have had an unpleasant dispute with the vendor. For experiments, there is value in testing a wide range of options so I wasnt too upset.
  4. I encourage BRS and others to run any number of tests like that, analyzing their tanks before and after using my service Group 1 = bad live rock that looked really good Group 2 = dry rock with bacteria in a bottle Group 3 = dry rock (control) Group 4 = good live rock that didnt look too impressive at first In terms of developing microbial communities capable of processing ammonia and nitrite, I didnt see any convincing differences between the live rock sources, and the bacteria in a bottle worked great (the second dose did, anyway). Its very interesting to find that in terms of the succession of algal strains colonizing the tanks, (the uglies), there is a big difference... and ONLY the good live rock (the stuff that provided a microbiome similar to mature reef tanks) avoided the uglies. What does it take to establish a microbiome similar to a mature reef tank? My tests show that a) good live rock can do it b) not all live rock is created equal c) some bacteria in a bottle products are not effective for this goal What excites me about these findings is they provide the most convincing evidence I've seen that the benefits of a healthy aquarium microbiome extend beyond the ability to process ammonia and nitrite... These findings suggest a scoop of sand or a small piece of live rock rubble from Suncrestreef's tank would work wonders for starting a new tank...
  5. Sorry about that. I think its fixed now. There are at least 3 ways to include images and all 3 worked for my account / browser but not others! Fingers crossed
  6. The good news is, you've already got some... thats the branch rock. Turns out within a couple days of adding it to the tank, the microbiome of those tanks was already reasonably similar to established reef tanks (balance scores 0.25 - 0.4)
  7. Hi everyone, I've had a pattern developing in the lab for a while and its ready to show you. We've all started a few tanks and seen our share of the uglies. Its seen so commonly some declare it inevitable. Here are the experimental tanks I set up this spring for the cycling experiment. After concluding that experiment, I turned on the lights, and stocked each tank with a small cleanup crew and a single fish. I've been feeding daily and maintaining top off water but doing no other maintenance. Remember, this is an experiment, not a display tank Check this out. The only difference between these tanks: they started with different microbiomes. Groups 1-3 had low diversity and balance (averages: 0.1, 0.04). Group 4 had high diversity and balance (0.48 and 0.36). This is what these differences do to a tank, in visual form. The photo doesnt do it justice... and I forgot to photograph one tank completely because I got distracted taking pictures of the fish. I'm gonna work with my sister in law who is a pro photographer to capture this better. If anyone is curious enough wants to see in person, get in touch and drop by the lab! Here are close ups of the substrate in a few tanks. Which one would you want in your living room? I will update this post soon with better pics and an analysis of the microbiome in these tanks. But it was too striking a pattern not to share...
  8. Thanks everyone! I'll ship out kits early this week. All the additional spots are filled, thanks for the quick responses.
  9. Hi everyone, In our first round I was really happy with almost every aspect of how the analysis behaved. My only concern is the low sensitivity for detection of biofilm bacteria that play important roles in nutrient processing. Nitrite oxidixing bacteria (NOB) showed up in the water samples, but at low levels... in some tanks they were not detectable (i.e., fewer than 1 in 10,000 cells came from these important families), despite known activity. Fortunately, samples from my experimental tanks confirmed that tanks with nitrite oxidizing activity can have undetectable NOB in the water but nice high abundance in the biofilm (sand, in this case). So its clear we can sample and detect them. The only challenge is how to sample the biofilm in a standardized way across different aquariums. See, I like water samples because every tank has water. Some tanks don't have sand. Or sumps. Or skimmers. etc. So we can't design anything aruond sampling those parts. But they all have a few things in common. And one of these is pipes. Everyone has pipes of some kind. We may have to get creative with little AIO nano systems, but the ones I've seen have something analogous to pipes. The literature shows NOB are well established in water pipe biofilms. So although I'm hesitant to modify things, it is too early in the development to dig my heels in. The evidence is clear that we need to include a biofilm sample for improved sensitivity. So I did a lot of thinking and reading and I will have new sampling kits ready to ship out this week. The new kit includes one additional step - swabbing a submerged, interior surface of one of your pipes with a sterile swab to sample the biofilm. ----- TLDR 1. If you participated in the first round of microbiome analysis, I would like to re-sample your tanks and this time include biofilm samples. This means @badxgillen , @Tampicocoralfarms , @Lexinverts , @youcallmenny , @SuncrestReef , @Knuckledragger , @SunCrestReef , @Tandor69 , @householdofpayne , @NateDawg , @daveo ... If you are interested, please message me for the new coupon code and you can place another free order on the website. (this ensure I can track the shipment and the sample) 2. If someone else is reading this, and wants to sample your tank, please message me. I've got room for samples from another 3 people in addition to the list above. So the first 3 who want in, send me a message. [No idea why that tagging thing doesnt seem to work!]
  10. Thanks David, this makes sense. I've added that to my code, future updates will include a report date and previous versions will get pushed into an "archive" folder on the reports page. Not the lowest! I'm finishing up a writeup on the major families found in these data. This is almost ready. The short answer is - bacterial communities in the ocean are mostly determined by dissolved nutrients. Not just NO3 etc, but complex and largely unmeasured things like the specific types of DOC... I (and I believe We) dont know the specific answer with regards to aquaria. This is the subject for my next experiment beginning soon - how does the type and amount of DOC (as used in carbon dosing) affect the microbiome? Yeah, this was interesting. Part of my goal here is to establish a baseline. I expected there to be some low level of background pathogens in our tanks. Overall we only found a couple of pathogens, at very very low levels, in a few tanks. The first thing I want to emphasize is that a few subspecies in this group are pathogens, but not all. Still, this bug is clearly a member of the species, which includes some of the most important in marine aquaculture. But it could be a less pathogenic variety. I can dig deeper on this and get back to you. It may be that 16S sequence data (what we used) cannot distinguish these subspecies; that happens sometimes. I have not previously investigated this specific pathogen yet but I will be, since it is one of the few that showed up at all. My initial survey shows this pathogen causes Pasteurellosis, or Photobacteriosis. Symptoms include loss of appetite, reduced activity, lesions and hemorrhages around eyes or mouth, lesions and tubercles on internal organs, eventually leading to death. Sounds fun. The diseases caused by bacteria in this species are considered some of the most dangerous among established and emerging diseases in fish aquaculture. The literature says they are ubiquitous throughout the aquaculture industry. It can infect a broad range of fish species, although older fish become tolerant due to maturation of their immune systems. Interestingly there is good evidence that infection requires iron, and this can be deleted in marine aquariums. Antibiotics and other chemotherapies have been used in fish aquaculture to control this disease, although antibiotic resistance has developed in some strains. I base this on a brief reading of the following two free references on this subject that are available for anyone who is curious to learn more http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.731.3326&rep=rep1&type=pdf https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058529/ Whatever the case, its clear that your tank was an outlier in having such a high frequency of this bug (which ranged from absent to 10x lower than yours in most samples). The observation of such high levels without visible symptoms is an important observation to remember if we see P. damselae in other tanks. I will also be curious to compare your specific sequence data with other members of the group that show up in tanks WITH disease symptoms. I will be curious to hear if it shows up again in retesting (see upcoming post, I'll be inviting re-sampling of the same tanks with my updated sampling kit) Another great point. I've added "How long has your tank been up and running?" to the sample registration form. Thanks for the feedback, all...
  11. This is a question I wondered about too. I only have a single comparison, because I screwed up one of my sand samples. But based on this single comparison, it appears you are correct and sampling affects the NOB metric. I see ~50-fold lower AOB+AOA in the water column than in the sand. The sand had detectable NOB while the water did not. Even in the sand, NOB is ~60 times less abundant than AOB+AOA. So it makes sense that if all the sand microbes are reduced by ~50 fold in the water column then the less abundant NOB would become undetectable. Things to think about. Its easy to change the sampling protocol. Its just important that we have something everyone can do consistently. Sampling sand isnt possible for people with bare bottoms. I fail to imagine any way of sampling live rock associated microbes consistently. Water that flows constantly through a biofilm-covered aquarium seems to be the one thing all reefers have available to sample in an easy manner... and for about half of the tanks sampled it showed both AOB and NOB... I do think the variation we see here is real, but its variation in amounts rather than presence/absence. Still pondering this one. Any feedback welcome!
  12. Hi everyone, I've been working for a couple days on an update and am excited to share the results. I hope this new analysis shows the potential for this kind of data to shed light on specific groups of bacteria that aquarists are interested in. These are new dimensions to think about.... previously we've focused on overall patterns; now we'll look at specific groups of microbes aquarists care about (whether they realize it or not) I'm uploading these now.... within a few minutes, you can check out your updated reports to see new info about specific groups of interest in your samples: Nitrifying bacteria Cyanobacteria Pathogens https://aquabiomics.com/view-reports/ This is just the beginning of exploring the functional meaning of these microbiomes. A few highlights: Your tanks' microbiomes are almost completely free of known pathogens Most samples lacked any evidence of known coral or fish pathogens. A few samples showed a low level of fish pathogens. But some of them do have relatively high levels of cyanobacteria A few samples showed unusually high cyanobacterial levels compared to the rest. I see that some of these were noted as having cyanobacteria when you registered your samples. I'll be curious to hear if the cyano scores you received match with your impressions of your tank at the time or after sampling. As someone who has battled cyano in one of my tanks for almost 2 years, I am also intrigued by the thought of comparing notes on the type of cyanobacteria we're dealing with (I've broken it down by family here). Perhaps this will lead to clarity on how to win the battle (in my case, nitrate dosing made a huge difference, but that was trial and error) Your tanks vary widely in levels of nitrifying bacteria Finally, I was surprised to see this much variation in nitrifying bacteria. Since I bet some of you will be surprised too, I thought this was worth discussing. Nitrifying groups include ammonia oxidizing bacteria and archaea (AOB & AOA), and nitrite oxidizing bacteria (NOB). Almost all tanks showed comparably high levels of AOB & AOA. But there was substantial variation in NOB. Many samples showed clear evidence for one or more types of NOB, but almost as many showed no evidence of NOB at all. To be clear, I searched extensively for nitrite oxidizing bacteria. I even looked for the fifth clade that has only recently been discovered (Nitrotoga). I tried! And will keep exploring to see if there is something I have missed. But I suspect the key to understanding this variation may lie in considering that DNA sequencing measures the composition of the community, and there is a finite limit to detection of rare types. If one type "blooms" to a high abundance, the probably that rare types will not be detected increases (assuming the number of DNA sequences per sample remains constant). Like any measurement, there is a limit of detection for this analysis. In this case, its approximately 1 DNA sequence per 10,000 (i.e. 0.1 ppt or 100 ppm). Bottom line - if your sample shows up as having no NOB, I do not interpret that as absence of NOB. I interpret it as meaning that NOB are present at very low levels in your tank relative to other kinds of microbes in your tank. This variation is surprising to me. When we encounter surprising patterns there can be a tendency to assume they result from errors. And I am still digging to see if there is some way my code is missing something. But I will raise two points that I believe support this observation: Most of the known NOB were found in some tanks. So their absences from other tanks is not a systematic error in the method (e.g. gaps in the database or uneven DNA extraction efficiencies). This is a genuine difference among tanks; I just don't believe its presence vs absence. I think its quantitative. Occasionally I have put a bunch of fish in a tank that previously had a low bioload. I've seen very minor ammonia spikes from this, but much larger nitrite spikes. This would be consistent with a lower population of NOB than AOB. Anyway, as always, I will be curious to hear what you think!
  13. I've occasionally added local natural seawater to my tanks on the theory that diversity is good, and because for a while I raised cuttlefish that liked to eat a variety of local inverts (amphipods and other crustaceans). But I never observed any effects good or bad. Direct comparisons between microbiomes of natural seawater and aquariums are not common in the literature, but I expect they are very different. I'm curious now about the question "would anything from local seawater survive in our tropical aquaria?" I bet yes, but a small subset. Itd be a fun experiment though. I'll include a local sample for fun in my next batch of microbiome analysis. I have replicate aquariums set up that I could use for this; spike some with local seawater and don't spike others, then compare changes in the microbiome among tanks.
  14. I can relate to this dilemma! Two female mandarins do not like sharing space. Such pretty little fish, so peaceful normally, and all of sudden mine started attacking each other. They arent easy to catch, either.
  15. it was a pleasant surprise that there is a core microbiome shared among different tanks. I can talk more about this in a future thread; it requires data. But its not just "every tank is a unique snowflake". There is a strong pattern. Your tank is a good example. And some tanks that participants logged as having problems were also major outliers with low scores, which is cool... I will be following up with them. Also, these score show interesting patterns in experimental tanks... very low scores in brand new tanks, and big differences between dry rock, live rock, and bacteria in a bottle.... I would file all of that under "promising and hoped for" the most head scratching part is the small number of tanks with very different microbiomes but no reports of problems. Its a complex enough question I cant trust my gut to figure it out, I will have to do some stats. and its likely more samples are needed. This is my initial impression.
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