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We're going away for Christmas and the Mrs asked me I was going to take a book with me to read. Me thinks I'll be content sat around the pool reading all these fantastic papers that you've posted Darrel. 👍
 
Hi all,
Me thinks I'll be content sat around the pool reading all these fantastic papers
I've got another one for you, <"Sustained nitrogen loss in a symbiotic association of Comammox Nitrospira and Anammox bacteria">. This one would describe a system analogous to the <"denitrifying media"> and <"Biocenosis" buckets"> discussed in other <"UKAPS threads">.
  • Comammox successfully encapsulated and demonstrates nitrification activity in hydrogel beads.
  • Comammox-Anammox co-culture shows signs of cooperation in near complete removal of ammonia-N.
  • Comammox occupies aerobic outer zone while Anammox inhabits underneath oxygen-depleted layer.
  • Comammox confirmed as major nitrifier and successfully suppressed canonical NOBs and hence nitrate accumulation.
Separation_Anammox_Comammox.jpg

....... Following initial bead fabrication, cells were dispersed in the polymer matrix while they mainly appeared on the peripheral layer of the beads after 86 days of incubation (Fig. 3). While the Comammox organisms N. inopinata (green) was randomly distributed just after immobilization, it formed a thin layer at or near the hydrogel surface following the incubation period. In particular, Comammox cells resided in between the oxygenated edge of the hydrogel beads and the Anammox cells (red), which were situated in a deeper (presumably anoxic) layer. .......
* Ekaterina Y. Gottshall, Sam J. Bryson, Kathryn I. Cogert, Matthieu Landreau, Christopher J. Sedlacek, David A. Stahl, Holger Daims, Mari Winkler, (2021) "Sustained nitrogen loss in a symbiotic association of Comammox Nitrospira and Anammox bacteria", Water Research, 202,

cheers Darrel
 
Hi @dw1305 & Everyone,

I have extracted the following from the Planet Catfish reference:

"For whatever reason some aquarists are resistant to the idea that plants can be an important component of biological filtration, but it is the honest truth".

I have demonstrated to my own satisfaction that plants alone are able to purify the aquarium water to such an extent that no additional filtration is necessary. I'll try to locate my thread here on UKAPS where I gave details of my setup.

JPC
 
Hi Folks,

Here it (hopefully) is:


JPC
 
Hi Folks,

Obviously, as a hobbyist, I am unable to investigate the presence of AOB or AOA in my tank. But, I guess I could possibly eliminate any stray microbes by passing the tank water through a UV-C sterilizer. Just a thought.

JPC
 
Hi all,
Obviously, as a hobbyist, I am unable to investigate the presence of AOB or AOA in my tank. But, I guess I could possibly eliminate any stray microbes by passing the tank water through a UV-C sterilizer. Just a thought.
I'm not sure it will make any difference to the microbial community. Even though you say you that you just have plants, you really have plant / microbe biofiltration, even if you only have floating plants and don' t have a filter or any substrate.

Cheers Darrel
 
Hi all,

I've added it onto an existing PlanetCatfish thread <"Using deep gravel and bacteria to control nitrogen - Page 6">. I'd say the reception has been both mixed and underwhelming.

cheers Darrel
Hahaha.

I recognise one or two of the usernames in those threads from past debates about plant/biofiltration on other aquatic forums, not really surpising to see that certain individuals still don't like to accept new data that is super-relavent to their hobby, even nearly 10 years on😅.

Crazy to me that some can have such a dogmatic attitude to microbiology...but I guess many "fishkeepers" aren't neccesarily interested in science (which is absolutely fine too, just wish they wouldent pretend to understand the literature they reference lol).

UKAPS is full of amazing threads like this that not only allow readers to apply cutting-edge science to improve plant/fish health, but also help foster a greater interest in understanding the complex biochemical reactions going on all around us everyday.

Thanks so much for all the content you share Darrel! 😊
 
Hi all,
but I guess many "fishkeepers" aren't necessarily interested in science
I think generally everyone wants to see posts of fantastic aquariums with healthy plants and fish, if you like aquarium eye-candy to scroll through, but I think there is a <"more serious discussion"> to be had as well.

I understand it is a bit of a niche interest, and also that we all have <"faith positions"> and tend to look for <"confirmation bias">.

Really I'm interested in the <"coffee, not the froth">, but it isn't always easy to <"work out which is which">, and that is where some science comes in handy.

cheers Darrel
 
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I'm not sure it will make any difference to the microbial community. Even though you say you that you just have plants, you really have plant / microbe biofiltration, even if you only have floating plants and don' t have a filter or any substrate.
Hi @dw1305

Point taken. To be honest, no sooner had I submitted my post when I realized that there would be microbes on the various surfaces.

JPC
 
I'd guess we are nowhere near the end of it yet.
Myself, I've read a bunch of nitrification related papers a while ago. I gave up trying to remember all those taxa involved in nitrification preferring various conditions regarding ammonia concentration, carbon availability, oxygen concentration, mass flow, temperature, light, organic carbon concentration, heterotrophic microbes competition etc. etc. I always use the simplest term nitrifying microbes (as opposed to nitrifying bacteria) and that's that. We don't possess means to determine.
Just three points of practical relevance:
1. I've made quite a many experiments relating to cycling new tanks. I've never detected comammox processes. Nitrite spike was always present. That does not imply necessarily that comammox microbes are not present in our tanks, yet it suggests that it takes quite a while before they develop.
2. I've detected that full nitrification is delayed in the presence of heterotrophic bacteria. The fastest way to establish nitrification is without any organic stuff, only mineral salts (including ammonium, naturally). No fish food!
3. There are many nitrifying microbes, each of them enjoying competitive advantage within very specific conditions. I guess that different nitrifying communities develop within filters and within tank substrate.
 
Hi all,
I've never detected comammox processes. Nitrite spike was always present. That does not imply necessarily that comammox microbes are not present in our tanks, yet it suggests that it takes quite a while before they develop.
That was partially <"why I asked"> the Dr Newton the "time" and "inoculum" questions. "Time" is the question <"I'd really like the answer to">, but I still think "plants in active growth" and six weeks "growing in" circumvent it (as an issue in nitrification) by doing <"the heavy lifting">, even if the microbial flora isn't fully developed.

Just to show how fast things are moving at the sharp end of microbial research, COMAMMOX Nitrospira, <"Long-term microbial community structures and dynamics in a commercial RAS during seven production batches of Atlantic salmon fry (Salmo salar)">4 which we didn't know existed ten tears ago, are now looking to be more important than either AOA or AOB in low ammonia situations (like our filters etc). <"https://journals.asm.org/doi/full/10.1128/AEM.01390-18">1
I've detected that full nitrification is delayed in the presence of heterotrophic bacteria. The fastest way to establish nitrification is without any organic stuff, only mineral salts (including ammonium, naturally). No fish food!
Same for me, I like to keep all the <"organic matter out of the filter">. This is largely because <"I don't want organic matter to compromise dissolved oxygen levels">, either by <"physical clogging"> or by stimulating <"heterotrophic microbial decomposition">.
There are many nitrifying microbes, each of them enjoying competitive advantage within very specific conditions. I guess that different nitrifying communities develop within filters and within tank substrate.
Again I'm sure you are right, that is very much what the follow-up paper paper says, as well as the conclusion from <"Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira">3 etc.
1. Xia, F., Wang, J.G., Zhu, T., Zou, B., Rhee, S.K. and Quan, Z.X., (2018). "Ubiquity and diversity of complete ammonia oxidizers (comammox)". Applied and environmental microbiology, 84(24),
2. Zala Schmautz, Jean-Claude Walser, Carlos A. Espinal, Florentina Gartmann, Ben Scott, Joël F. Pothier, Emmanuel Frossard, Ranka Junge, Theo H.M. Smits, (2022) "Microbial diversity across compartments in an aquaponic system and its connection to the nitrogen cycle", Science of The Total Environment, 852,
3. Bartelme, R.P., McLellan, S.L. and Newton, R.J., (2017). Freshwater recirculating aquaculture system operations drive biofilter bacterial community shifts around a stable nitrifying consortium of ammonia-oxidizing archaea and comammox Nitrospira. Frontiers in microbiology, 8, p.101.
4. Stine Wiborg Dahle, Sunniva Ingebrigtsen Gaarden, Julia Fossberg Buhaug, Roman Netzer, Kari J.K. Attramadal, Tobias Busche, Marianne Aas, Deni Ribicic, Ingrid Bakke, (2023)
"Long-term microbial community structures and dynamics in a commercial RAS during seven production batches of Atlantic salmon fry (Salmo salar)",Aquaculture, 565


cheers Darrel
 
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Hi all,
I would be interested to know if it would be possible to cycle a tank in a sub 5 PH (say 4 - 4.5) environment?
I'm going to guess it will still occur, but at a slower rate, and possibly it will take longer to establish. It is back to the relative proportion of <"sat waiting" or "found it">. I'll keep looking and see if I can find anything specific.

I'm going to guess that in the longer term (again I've no idea of the time scale) that "found it" will occur and an appropriate assemblage (for: low pH, low ammonia loading and high dissolved oxygen level) of nitrifying microbes will always develop <"https://pubs.acs.org/doi/abs/10.1021/acs.est.2c03299">***.
....... Integrated 16S rRNA gene amplicon sequencing, fluorescence in situ hybridization (FISH), and metagenomic sequencing methods demonstrated the selective enrichment of comammox bacteria when the MBBR was operated at a dissolved oxygen (DO) concentration above 6 mg O2/L. The dominance of comammox Nitrospira over canonical ammonia oxidizers (i.e., Nitrosomonas) was attributed to the low residual ammonium concentration (0.02–0.52 mg N/L) formed in the high-DO MBBR...........Moreover, the ammonia-oxidizing activity of comammox Nitrospira-dominated biofilms was susceptible to the oxygen supply, which dropped by half with the DO concentration decrease from 6 to 2 mg O2/L. These features collectively suggest a low apparent oxygen affinity for the comammox Nitrospira-dominated biofilms in the high-DO nitrifying MBBR.
This paper found lower levels of nitrification at lower pH, <"https://pubs.acs.org/doi/10.1021/acs.est.8b04177">*, but that the presence of plants ameliorated this.
......Here, we employed quantitative polymerase chain reactions and next-generation sequencing to evaluate the bacterial communities and their links to nitrogen transformations for improving NUE (Nitrogen Use Efficiency ) s in four bench-scale plant-based floating-raft aquaponics (pak choi, lettuce, chive, and tomato) and three pH levels (7.0, 6.0, and 5.2). Low relative abundance of nitrifiers in plant roots and biofilters suggested nitrogen loss, which decreased NUE in aquaponics. Low pH level was a major factor that shifted the microbial communities and reduced the relative abundance of nitrifiers in aquaponic systems, leading to total ammonia nitrogen accumulation in recirculating water. In plant roots, the abundance of nitrite-oxidizing bacteria (e.g., Nitrospira spp.) did not decrease at low pH levels, suggesting the benefit of growing plants in aquaponics for efficient nitrification and improving NUE......
There are quite a few for Rice growing, I'll need to go through them when I have time, but this (Oil-palm based) one looks quite useful <"https://journals.asm.org/doi/full/10.1128/mSystems.00309-20">**
.......... Ammonia oxidizer activity decreased following acidification of the forest soils but increased after liming of the oil palm soils, leading to a trend of a reversed net nitrification rate after pH modification. AOA and AOB nitrification activity was dependent on pH, but AOB were more sensitive to pH modification than AOA, which demonstrates a greater stability of AOA than AOB under conditions of short-term perturbation. In addition, these results predict AOB to be a good bioindicator of nitrification response following pH perturbation during land-use conversion. AOB and/or comammox species were active in all soils along the land-use gradient, even, unexpectedly, under acidic conditions, suggesting their adaptation to native acidic or acidified soils.........
* Sumeth Wongkiew, Mee-Rye Park, Kartik Chandran, and Samir Kumar Khanal (2018) "Aquaponic Systems for Sustainable Resource Recovery: Linking Nitrogen Transformations to Microbial Communities" Environmental Science & Technology 52:21, pp12728-12739
**Zhao, J., Meng, Y., Drewer, J., Skiba, U.M., Prosser, J.I. and Gubry-Rangin, C., (2020). "Differential ecosystem function stability of ammonia-oxidizing archaea and bacteria following short-term environmental perturbation". Msystems, 5(3),
*** Jing Zhao, Min Zheng, Zicheng Su, Tao Liu, Jie Li, Jianhua Guo, Zhiguo Yuan, and Shihu Hu (2022) "Selective Enrichment of Comammox Nitrospira in a Moving Bed Biofilm Reactor with Sufficient Oxygen Supply" Environmental Science & Technology 56:18, pp. 13338-13346


cheers Darrel
 
Hi all,
There are many nitrifying microbes, each of them enjoying competitive advantage within very specific conditions. I guess that different nitrifying communities develop within filters and within tank substrate.
I've just been re-reading this thread from 2012 <"Alfagrog for reducing Nitrates?">. It had some input from (former) member @Greg's Pea, who had worked as an <"industrial microbiologist"> and is generally quite an interesting thread.
Anaerobic digestion has always intrigued me but large scale installations just aren't done in this country. The dutch on the other hand love AD and i'd be very interested to see its application to the hobby more.
One thing that has changed is that large scale Anaerobic Digestion plants are <"now really popular">, partially because they produce methane (CH4) that you can <"convert to electric and sell to the grid">, although the financial advantages of this <"have been curtailed by the UK Government">.

I'm still not sure they have any application to aquariums, but you could potentially make use of the <"anaerobic ANAMMOX"> process, if you had a <"spatial or temporal separation"> between the aerobic and anaerobic phases.

cheers Darrel
 
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Hi all,
As the science of the aquarium’s microbiom is so complex, what is currently “best practice” for cycling an aquarium?
Personally I always advice <"plant and wait">. It just works.

If you have a look at <"Correspondence with Dr Ryan Newton - School of Freshwater Sciences, University of Wisconsin—Milwaukee"> it describes where the science is at the moment.

Dr Newton says:
...... Nitrifiers are present in many environments because they can live with comparably low external nutrients (carbon particularly). There are a couple of good possibilities, 1) the water - most municipal water systems contain some number of nitrifiers, which then come out of your residence tap; 2) the plants - nitrifiers are also commonly associated with plants. Or, it could be they drift in from the air - seems less likely, but it is not impossible.

If you do need to add nitrifiers the best source is from an aquaponics or aquaculture system that is already running and removing ammonia. Some water or sediment/soil or part of the biobilter (if there is one) is an excellent starter. Without this source as an inoculum then you could add some roots from plants from any other tank that is running - these are likely to have nitrifiers associated with them. A small clipping put into the tank would be enough.

In some lab tests we found that adding previous material from a running biofilter could reduce ammonia oxidation start-up time from 2-3 weeks to 2-3 days. We also tested a commercial product of nitrifiers & it did decrease the time to ammonia oxidation start-up. It was slower than our biofilter material transfer, but much quicker than doing nothing.........

cheers Darrel
 
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