The microbiology of reef tank cycling.

Discussion in 'New to Saltwater & Reef Aquariums? Post Here' started by brandon429, Sep 20, 2015.

  1. john.m.cole3

    john.m.cole3 cyclOps R2R Supporter R2R Excellence Award Reef Squad Build Thread Contributor Hub City Reef Club

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    Fun new project for those considering doing a mix of live and dry rock. I sold off everything in my 72 DT and bought a 135 tall. I also scored some 5 year old pukani and tonga branch that has been in an individuals tank exclusively. There's about 100 pounds of rock total that has been cooking since new years. It's got some nice corraline and yellow sponges on it. My plan is to use only the prime cuts and mix in some dry Marco and Billy Hay rock.

    Do you all think I can skip cycle a 135 with 50 pounds live and 50 pounds dead rock??? I also have my marinepure brick that is 13 months old/wet.
     

  2. brandon429

    brandon429 Well-Known Member R2R Supporter R2R Excellence Award

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    yes. I believe the bioload you w start with can be handled by the living portion, the dry portion is just playing catchup. that marine pure is mighty powerful, mighty powerful stuff. Id watch out for any dried on jerky organics from the dry rock...sometimes those have to pre cure or be outer layer stripped with vinegar to liberate the protein stores that when rehydrated can contribute quite well to total ammonia loading. if those rocks are not bringing in dried beef jerky organics on the rock, formerly live benthic animals, then it just sits there neutral like when I blast my whole sandbed with tap water and peroxide.

    I like knowing what those upper trend abilities for ppm digested in 24 hours are as well from that type of work.

    ive always been curious just how much could be processed in 24 hours. not ever owning a saltwater ammonia test kit has left me guessing, but going off other posts ive seen 6 ppm digested in 24 hrs just the same.
     
    Last edited: Mar 30, 2017
  3. BoomCorals

    BoomCorals www.boomcorals.com R2R Supporter Gold Sponsor

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    In previous tanks where I did skip cycle method, I would dose ammonia to 2.0ppm to test. It was often gone in 10 hours.
     
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  4. john.m.cole3

    john.m.cole3 cyclOps R2R Supporter R2R Excellence Award Reef Squad Build Thread Contributor Hub City Reef Club

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    Got live rock? 20170330_194513.jpg
     
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  5. brandon429

    brandon429 Well-Known Member R2R Supporter R2R Excellence Award

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    I can already see coralline
     
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  6. john.m.cole3

    john.m.cole3 cyclOps R2R Supporter R2R Excellence Award Reef Squad Build Thread Contributor Hub City Reef Club

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    Hey brother, I mkay need a hand lifting this beast on the stand when it's all ready. I'd love for you to see the biological diversity on this rock I aquired. I would guess close to the quality tampa bay has to offer, but not quite that level
     
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  7. brandon429

    brandon429 Well-Known Member R2R Supporter R2R Excellence Award

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    Done Sir! I can be coaxed from the recesses of lake alan henry anytime holla

    Someone took good care of that rock no bad algae, i pinch zoomed in on the pic
     
  8. roansdad

    roansdad Active Member

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    When all is said and done and our tank is deemed "cycled" how big of a water change do you suggest befor adding any livestock? Also do I feed ammonia up until the day befor I add fish? Or when do I stop that?
     
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  9. brandon429

    brandon429 Well-Known Member R2R Supporter R2R Excellence Award

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    Thank you for posting!

    In nanos we can easily change out all the water because we took long enough in cycling so the bacteria became adhered to the surface, the water change didn't remove them it only removed the nitrate which is algae food. Do as big of a water change you can do at the end of your submersion period and when the tank passes it's last digestion test for ammonia. Over the whole course of cycling adding ammonia only once will work, and that's added early on we show so there's no need to keep adding it towards the end. We added ammonia a total of just two times in post #6 over a span of one month

    There's no set rule for number of times ammonia is dosed...once is enough, twice is nice, and any more than that means there will be lots of nitrate at the end for us to export and some true nitrite readings might be in the tank due to sheer backup, just to account for the nitrite posts that are out there before the cycling completion date elapsed. I choose adding it twice, once at the start of the submersion period and once halfway through, perfect bac feed and not too much nitrate, no nitrite will be of concern at this dosing amnt.

    For huge tanks where large water change isnt possible, they can use polyfilters designed to lock up nitrate. or bum someones marinepure block for use then giveback. heck we could easily mail around wet marinepure blocks just fine wrapped in wet newspaper they'll repopulate just fine given a shot of vodka in someone's newly cycled 200 gallon setup for example then mail the block back to whichever online friend helped out.

    The reason for nitrate consideration after cycling completes (putting emphasis on not having to test for nitrate before a cycle completes, only ammonia and submersion time matters) is so that when we begin running lights and adding animals we don't want the excess nitrate in the system as algae challenge feed. Though we weren't testing for nitrate during the cycle it's ok to test after so we know the nitrate is low to zero for the start of stocking.



    ****somebody needs to make a side business selling aged marinepure blocks and a little dosage sheet for amount of vodka to place in a new tank trying to strip nitrogen and trying to inoculate the system with hopefully nitrate-digesting bacteria. yep, we need a skip cycle marine pure block sales approach from someone with enough buckets and blocks :) to begin!
     
    Last edited: Apr 28, 2017
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  10. brandon429

    brandon429 Well-Known Member R2R Supporter R2R Excellence Award

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    Google scholar links portion of our thread. feel free to use scholar links to prove or disprove claims here so we can modify the thread into the simplest truth about cycling possible:

    http://www.nature.com/nrmicro/journal/v14/n9/full/nrmicro.2016.94.html
    marine biofilms provide resource capture (nutrients) and they insulate from effects of antimicrobial substances and actions we take in cleaning our tanks.

    ******MARINE BIOFILMS****
    post more research from this angle, please~ everything we rely on in this thread is due to marine biofilms, and surface area vastly outpacing our needs. We are not dealing with singular, unattached nitrifying bacteria in marine filtration systems...we're dealing with housed/insulated/full communities that gain benefit from existing that way (they gain feed, insulation from temp/drying/chem shocks etc)
    https://link.springer.com/article/10.1007/s00254-004-1044-x
    Our list of three things that can kill your bacteria, would be a list of twenty or better were it not for the natural ways these bacteria present in our aquaria--> housed alongside nonfiltration types in a mass with varying density depending on conditions
    http://www.aimspress.com/fileOther/PDF/microbiology/microbiol-02-00304.pdf


    *the order of deposition for new substrates is also covered in this text above, its my favorite reference so far. The way nitrifiers exist in nature is what allows them to ride over on group B rock setups just fine, and lose no net bacterial benefit. The order that they deposit after we insert a new substrate into the water means that when coralline shows up, it means nitrifiers have been there a long time provided no medication has been dosed. That's means live rock you see with real coralline is full of bacteria

    The protections afforded to nitrifiers by communal scum layer living allows us to dose strong peroxide to the system to attack a target like invasive dinos, and still not have measurable effects on nitrification under any practical dose of peroxide from any peroxide thread. We hope to build repeatable care actions from tenets of microbiology in this thread...nitrifiers are the last thing you need to consider when taking almost any action you'll take in reefing.

    Nitrifiers are not found solitary in nature:
    https://core.ac.uk/download/pdf/19096878.pdf



    Upper ammonia limits for nitrifiers
    http://www.sciencedirect.com/science/article/pii/S0304389407010928
    if my ammonia accidentally gets to 5+ ppm, will my cycle stall? No
    http://onlinelibrary.wiley.com/doi/10.1016/j.femsec.2005.05.001/full

    But it says that on the fishless cycling website so how can you say that? You are going to argue with the top microbiologist in reefing?


    Why are there so many searchable cycling threads well above 5 ppm who still oxidize ammonia at day 40? I see twenty 8 ppm tanks on the first key word search.
    Context matters, lots of people went above five. Some went to ten. All cycled by day 40 using any form of boost via ammonia and/or bottled bac.

    Nitrifiers that have been isolated in culture, away from their natural inclusions in a real reef tank, may show suppression at 5 ppm sustained ammonia. We don't encounter them in a tank setting like that... so that's why so many posts exist online where people posted 8 ppm ammonia cycling that still completed. 5 ppm ammonia, 7 ppm ammonia, isn't considered the threshold for a medication event or we'd be seeing true stalled cycles from verified ammonia readings. we do not see that after 40 days no matter how you slice it

    unless someone is doing a curing process where massive organic reserves were left on old live rock to rehydrate and rot, most cycles will complete by day 40 and only what ammonia does at that time matters.

    context of the measure matters hugely in microbiology, 5 ppm was lethal in limited settings.

    How high ppm ammonia does that state nitrifiers in sludge w tolerate? 350 ppm? how scary does 6 ppm for a few days at most sound in hindsight?

    Drying and desiccation resistance:

    https://academic.oup.com/femsle/article/79/1/65/551993/Survival-of-ammonia-oxidising-bacteria-in-air

    bacteria that enter our tank have the ability to generate protection layers to cover periods of emersion far worse than an aquarist will require for a tank move or a water change or cleaning.
     
    Last edited: Jun 21, 2017
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  11. john.m.cole3

    john.m.cole3 cyclOps R2R Supporter R2R Excellence Award Reef Squad Build Thread Contributor Hub City Reef Club

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    Cycling with dry rock and no sand using ammonium chloride 20170604_184650.jpg
     
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  12. brandon429

    brandon429 Well-Known Member R2R Supporter R2R Excellence Award

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    Last edited: Sep 7, 2017
  13. john.m.cole3

    john.m.cole3 cyclOps R2R Supporter R2R Excellence Award Reef Squad Build Thread Contributor Hub City Reef Club

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    No, I'm keeping the marinepure brick and spheres in the frag tank. Inn starting off fresh with 3 of the brightwell bricks this time.
     
  14. brandon429

    brandon429 Well-Known Member R2R Supporter R2R Excellence Award

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    nano reef aquarist working with ammonia, verifying time frames in a test tank:

    https://www.nano-reef.com/forums/to...ing-rate-of-established-tank/#comment-5529122

    what our friend Dandelion from nr.com is doing is verifying what bacteria require, and don't require from us, to do their measurable job. he has removed critical surface area in the test tank, and still able to pass the digestion test in 24 hours from a really small pico reef. imagine if this was a large tank/more surface area...


    *look at this page on marine nitrifying bacteria! it has some of the best scholar articles on common issues ive seen. its taking me hours just to peruse the first few.

    http://www.fishforums.net/threads/the-science-of-bottled-bacteria-for-cycling-aquaria.414863/
     
    Last edited: Sep 6, 2017
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  15. brandon429

    brandon429 Well-Known Member R2R Supporter R2R Excellence Award

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    https://www.nano-reef.com/forums/topic/384273-boris-12g-first-salt/

    look at Boris' quality of live rock in this nano, a prime example of uncured rock but this is very topshelf and likely to preserve most of whats brought in, this is a bunch of calcifying organisms and low plant loading, good stuff.

    we change water nicely in this system, cpr in/out regular like clockwork

    feed well, input then water change and farm whats on the rock

    see how the live rock is really dense and not tracking porous to the point it looks pumice-like? less crevices to retain huge worms misplaced for an aquarium (this is rather uncured, but, very keepable animals and plants)

    its not likely to leak ammonia with any decent transfer, and if it does the typical cpr remedy will stop it before too long.

    funny enough as we mentioned on initial pages the smell test of the container these rocks come from will indicate very accurately how well they've shipped. this group of rock if kept wet should distribute their hitchhikers well into a tank, seeding it with endless animals to observe. I would take some of this and put it in my old pico reef right now, its top shelf lr.

    he is working to guide out ammonia in trace amounts, to keep the multi varied benthic creatures that make all the color and texture.
     
    Last edited: Jul 29, 2017
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  16. brandon429

    brandon429 Well-Known Member R2R Supporter R2R Excellence Award

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    John friend check it@!
    https://www.reef2reef.com/threads/ammonia-alert-badge-and-cycle-time.318075/#post-3932278

    30 days emersed out of water on a shelf

    rock passes a verified digestion test, those bioslicks from post #130 seem to be holding up :) this is a neat thread above. might be my fav bac thread so far.

    these confirmation tests are going to be a joy


    recap for page 7

    Do bacteria seem tough or weak given our collections so far

    theres death, taxes, and bac that will continue on no matter what we withhold and that includes water for quite a long time apparently. Desiccation is still an antibacterial mode, but who are we to posit desiccation limits without some darn nice testing.
     
    Last edited: Aug 2, 2017
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  17. john.m.cole3

    john.m.cole3 cyclOps R2R Supporter R2R Excellence Award Reef Squad Build Thread Contributor Hub City Reef Club

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    I think we should start pushing the limits with testing and observation. Use X form of biomedia which is a more measuravle substance than live rock, and see how little media it takes to digest 2 ppm ammonia in 24 hours. I bet it is a lot less than the average reefer thinks. Measure time, water volume, approximate surface area of biomedia (measure in grtams maybe?). With enough testing and varying the numbers on those 3 variables would end result produce a statement like, " You need blank amount of media per water volume to process this amount of ammonia in this amount of time.
     
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  18. brandon429

    brandon429 Well-Known Member R2R Supporter R2R Excellence Award

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    Rare bump, see what's out there. If people have noticed lately in the general forum, there have been a few posts about live rock surviving quite some time out of water

    There’s been continual and constant api problems across all web forums since last update if that helps/surprises
     
    Last edited: Oct 11, 2017
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  19. john.m.cole3

    john.m.cole3 cyclOps R2R Supporter R2R Excellence Award Reef Squad Build Thread Contributor Hub City Reef Club

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    I've set up about 6 tanks since this last update. I just donate a ceramic sphere made by marinepure, make sure they have good flow, and make em wait 30 days before they add fish. Not sure if we can persuade Mother Nature to take a different course.
     
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  20. brandon429

    brandon429 Well-Known Member R2R Supporter R2R Excellence Award

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    Six man, equals dedication excellent
     
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