Using deep gravel and bacteria to control nitrogen

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Re: Using deep gravel and bacteria to control nitrogen

Post by MarcW »

Thanks for your input Darrel.

As someone that routinely kills java fern, it'd be great if you could let me know a few plants which could survive with low light and not planted in the substrate?

Anubias do OK, but don't really seem to grow in my tanks, java fern is OK in some tanks but dies in others, maybe that's to do with temperature rather than lighting, it does OK in my lower tanks but not at the top of the rack where the water is 2-4c higher.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
MarcW wrote: 05 Sep 2019, 15:02 .......As someone that routinely kills java fern, it'd be great if you could let me know a few plants which could survive with low light and not planted in the substrate?

Anubias do OK, but don't really seem to grow in my tanks, java fern is OK in some tanks but dies in others........
Have you still got the moss that came with the Asellus etc.? That should grow OK low light.

The best low light plant for me is Bolbitis heudelotii, it does much better in low nutrients and soft water than Java Fern (Microsorum pteropus).

I've also found that some of the selected cultivars of Java Fern (like "Needle Leaf" and "Trident") aren't anything like as good growers low tech as the ordinary variety.

Bolbitis isn't a quick grower, but it is a bit like Anubias, you don't really notice it growing but eventually it forms a reasonable clump (below).

Image

It isn't cheap to buy, and even more expensive as a "mother plant", (presumably because it isn't a quick grower even emersed), but your more than welcome to some of mine.

cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by MarcW »

Hi Darrel, yes I still have the moss it's in a tank with the Asellus, hopefully that'll grow to a decent sized clump.

Your comments about the java fern variants match with my experience, now I've thought about it, the narrow leaved version has all died, the few I have remaining are all the normal type and growing OK.

I've ordered some Bolbitis heudelotii to try out thanks for the tip.
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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin »

Here is what Tropica says about the heudelotti:
Bolbitis comes from West Africa, a fern with very beautiful transparent green leaves, 15-40 cm tall and wide. When planting do not cover the rhizome because it will rot, and it is best to plant Bolbitis heudelotii on a root or stone. Keep the plant in position with fishing line until it has gained a hold. Easy to propagate by splitting the horizontal rhizome. Growth can be increased considerably by supplying CO2, and is only optimal in soft, slightly acidic water.
from https://tropica.com/en/plants/plantdeta ... WS%29/4407

I seem to recall I tried to plant it where there was decent flow/circulation. I am not sure if that was an urban aquarium myth or good advice.

As for the AOA and AOB. I am not ready to accept the conclusions of Sauder. L. whose name appears on all of the studies I have read so far which conclude AOA are the dominant ammonia oxidizers in aquariums. Science has no idea how much ammonia a single cell of either organism is able to oxidize. The current science usually counts the number of of archaeal and bacterial amoA genes to determine numbers. I believe some AOB have more than one amoA gene. Further, the most recent research appears to indicate that there is an amoA gene in Nitrospira and this organism can oxidize ammonia to nitrate directly.
Although, AOA were numerically dominant over AOB, a presumed third ammonia-oxidizer was also present in the biofilter sand matrix. Identification of Nitrospira-like amoA (Figure 7B) in the biofilter and the strong correlation between the abundance of the Nitrospira nxrB uwm-2 gene and this Nitrospira amoA, suggests a complete ammonia-oxidizing Nitrospira spp. resides in the UWM biofilter. In fact, we found that the comammox amoA was the most abundant ammonia-oxidizing gene in the biofilter (on average 1.9X that of AOA amoA).
(Sorry I am not great at proper crediting, but the complete paper can be read here https://www.frontiersin.org/articles/10 ... 00101/full )

Original Research ARTICLE
Front. Microbiol., 30 January 2017 | https://doi.org/10.3389/fmicb.2017.00101

Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira

Ryan P. Bartelme, Sandra L. McLellan and Ryan J. Newton*
School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
TwoTankAmin wrote: 06 Sep 2019, 19:14I seem to recall I tried to plant it where there was decent flow/circulation. I am not sure if that was an urban aquarium myth or good advice.
I'm not sure. None of my plants are fixed to anything, so they tend to end up out of the direct flow from the filter.

The photo above is in my kitchen tank, rain-water and low nutrients and that plant grew from a single rhizome with three or four leaves in ~five or six years.
TwoTankAmin wrote: 06 Sep 2019, 19:14As for the AOA and AOB. I am not ready to accept the conclusions of Sauder. L. whose name appears on all of the studies I have read so far which conclude AOA are the dominant ammonia oxidizers in aquariums. Science has no idea how much ammonia a single cell of either organism is able to oxidize. The current science usually counts the number of of archaeal and bacterial amoA genes to determine numbers. I believe some AOB have more than one amoA gene.
There is a fair bit of research from waste water treatment. "Unraveling the active microbial populations involved in nitrogen utilization in a vertical subsurface flow constructed wetland treating urban wastewater" (https://www.sciencedirect.com/science/a ... 9717301006). This is "The more important role of archaea than bacteria in nitrification of wastewater treatment plants in cold season despite their numerical relationships" (https://www.sciencedirect.com/science/a ... 5418306961)
TwoTankAmin wrote: 06 Sep 2019, 19:14......Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable The more important role of archaea than bacteria in nitrification of wastewater treatment plants in cold season despite their numerical relationships Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira

Ryan P. Bartelme, Sandra L. McLellan and Ryan J. Newton*
I'm pretty sure that people will carry on finding the complete nitrifier "COMAMMOX Nitrospira" wherever they look. My guess is also that people will keep on finding novel nitrifying micro-organisms, whether they are bacteria or archaea.

cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin »

I have one problem generalizing from waste water studies which find Nitrobacter is the dominant nitrite oxidizer. The one thing I think has been established beyond any doubt is that Nitrobacter is not found in any meaningful level, if found at all, in aquariums. It is suited to oxidizing higher levels of nitrite than is found in tanks. Nitrospira is what is regularly detected.

Combine this with the discovery of Nitrospira capable comammox and there is a whole host of microorganisms that are likely at work dealing with ammonia in our tanks. I have come to believe there is probably no single dominant bacteria or archaea across the universe of tanks. Rather each tank will have its own particular balance. I am also pretty sure the exact complement of nitrifying organisms in a tank can change over time as the ammonia loading and other parameters change.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
TwoTankAmin wrote: 07 Sep 2019, 19:34 ......I have come to believe there is probably no single dominant bacteria or archaea across the universe of tanks. Rather each tank will have its own particular balance. I am also pretty sure the exact complement of nitrifying organisms in a tank can change over time as the ammonia loading and other parameters change......
I think that is where we are now.

I'll attempt to keep up with the scientific literature, but I probably won't have a proper trawl through it again before Christmas.

cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
dw1305 wrote: 07 Sep 2019, 20:19 ..........I'll attempt to keep up with the scientific literature, but I probably won't have a proper trawl through it again before Christmas........
Another paper has come my way:

Zhao et al. (2015) "Microbial community and removal of nitrogen via the addition of a carrier in a pilot-scale duckweed-based wastewater treatment system" (https://www.sciencedirect.com/science/a ... 241401774X).

It is a plant/microbe bio-filtration paper, and it quantifies the net contributions, to nitrogen removal, of a floating plant (Duckweed - Lemna japonica) and microbial biofilm in a Duckweed based waste water treatment. It also investigates why the nitrogen balance might be slightly different when you use Water Hycanth (Eichornia crassipes) as a floating plant.

They attribute these differences in nitrification to the much larger root area of Eichornia, when compared to Lemna, with this expanded rhizosphere supporting a much larger volume of microbial biofilm.

What is really interesting is that when they added a plastic carrier to the effluent flow (to act as a surrogate "root surface" in the Lemna treatment), to give a comparable area for microbial biofilm adhesion.

They found that the addition of a carrier improves nitrogen (N) removal in a duckweed system and that abundant N-removal microbes on the carrier biofilm contribute to improved N removal.

cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
TwoTankAmin wrote: 06 Sep 2019, 19:14.....As for the AOA and AOB. I am not ready to accept the conclusions of Sauder. L. whose name appears on all of the studies I have read so far which conclude AOA are the dominant ammonia oxidizers in aquariums.........
This is a paper where they didn't find any AOA, but they found a range of novel AOB.

Hüpeden, J. et al (2020) "Taxonomic and functional profiling of nitrifying biofilms in freshwater, brackish and marine RAS biofilters" Aquacultural Engineering 90.
In the freshwater biofilters >99 % of the total AOB reads were assigned to uncultured ammonia oxidizing bacteria with Nitrosomonas communis Nm2 as the closest relative (96 % sequence similarity to the 16S rRNA gene). .....................

In the freshwater biofilters >99 % of the total NOB reads were classified to the genus Nitrospira, which had Ns. defluvii as closest known relative (99 % similarity to the 16S rRNA gene)........

At each RAS, a site-specific nitrifying community was identified. The majority of reads was affiliated with unknown members of Nitrosomonas and Nitrospira, representing several potentially novel species within these genera, which were currently not possible to culture by traditional techniques. The comprehensive phylogenetic analysis to determine the closest taxonomically described species revealed a co-existence of different, Nitrosomonas-like AOB and Nitrospira-like NOB in all biofilters with one representative being the predominant ammonia or nitrite oxidizer at each RAS, respectively.......

The presence and in some cases dominance of AOA over AOB in aquaria and RAS biofilters was reported previously (Bartelme et al., 2017; Brown et al., 2013; Sakami et al., 2012; Sauder et al., 2011) and growth of AOA at low ammonia concentrations has been demonstrated for enriched and isolated representatives (Nicol et al., 2011; Sauder et al., 2012). In other studies, the quantity of AOA in RAS was reported negligible or zero (Foesel et al., 2008; Keuter et al., 2017). The load of ammonia was discussed as important factor for the coexistence of AOA and AOB in RAS, since AOA have a higher affinity towards ammonia than AOB and could be outcompeting AOB at lower concentrations (Brown et al., 2013; Martens-Habbena et al., 2009; Roalkvam et al., 2020). Mostly, AOA dominate in niches characterized by low nutrients, low pH and low DO (Erguder et al., 2009) as well as elevated temperature (Taylor et al., 2017). These parameters are not valid here and in our study, archaeal reads were not present in the 16S rRNA amplicon sequencing data set. In addition, no archaeal amoA sequences were found by specific PCR and no typical cells of AOA were detected via electron microscopic investigation of the biofilms
cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

Thanks Darrel, for keeping this up to date. I'm learning a lot.

Cheers, Eric
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
Last one for a bit.

This paper looks at the interaction between dissolved organic carbon (DOC), nitrification and the microbial assemblage. The paper is open source, and should be available to every-one:

Navada, S., Knutsen, M.F., Bakke, I. et al. (2020) Sci Rep 10.
Nitrifying biofilms deprived of organic carbon show higher functional resilience to increases in carbon supply
........ the organic carbon to ammonia nitrogen (C/N) supply ratio can influence resource competition between heterotrophic and nitrifying bacteria for oxygen and space. We investigated the impact of acute and chronic changes in carbon supply on inter-guild competition in two moving bed biofilm reactors (MBBR), operated with (R1) and without (R0) external organic carbon supply. The microbial and nitrifying community composition of the reactors differed significantly. Interestingly, acute increases in the dissolved organic carbon inhibited nitrification in R1 ten times more than in R0.

A sustained increase in the carbon supply decreased nitrification efficiency and increased denitrification activity to a greater extent in R1, and also increased the proportion of potential denitrifiers in both bioreactors...... Specifically, efficient removal of organic matter before the nitrification unit can improve the robustness of the bioreactor to varying influent quality.

Thus, maintaining a low C/N ratio is important in nitrifying biofilters when acute carbon stress is expected or when anoxic activity (e.g. denitrification or H2S production) is undesirable, such as in recirculating aquaculture systems (RAS).
Which I think can be digested as:

"a lot of of organic matter in your filter reduces nitrification, but increases denitrification".

Which partially explains why not using your filter as a syphon, not letting the filter media get too gungy and having a pre-filter, helps with nitrification.

I'm a "nitrate factory" fan, nitrate (NO3-) can always be mopped up by plants and water changes.

cheers Darrel
Last edited by dw1305 on 09 Sep 2020, 16:42, edited 4 times in total.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
bekateen wrote: 09 Sep 2020, 15:16Thanks Darrel, for keeping this up to date. I'm learning a lot.
Cheers, Eric
I am as well, but it's back to the old problem, trying to line up all the moving bits and then work out what they actually mean in practice.

I was thinking about this in terms of marine aquarists using Vodka, or similar, as a carbon source. I assume they do it (and it works by this mechanism) to increase denitrification in the deep sand bed.

Is it still in vogue? I assume some-one will know

cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

Here's a new video about the fish store in San Francisco where the owner uses the deep gravel and never does water changes. We've discussed earlier in this thread why that is not so simple, but it's still a cool pet store. Enjoy:

https://youtu.be/watch?v=rg1u-XVMU3Q
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
Three years on I'm going to resurrect this old thread, because it contains bits that are relevant. I've recently had some correspondence with Dr Newton at the University of Wisconsin (his is the lab. referenced by @TwoTankAmin earlier in the thread).

I contacted him after reading: Bartelme RP, Smith MC, Sepulveda-Villet OJ, Newton RJ. (2019). "Component microenvironments and system biogeography structure microorganism distributions in recirculating aquaculture and aquaponic systems". mSphere 4:e00143-19.
It is well worth a read and he very kindly both replied to my email and answered the questions I asked, which were:
1. If we planted an aquarium and waited for the plants to "grow in" over ~6 weeks, where does the initial inoculum of AOA and comammox Nitrospira come from? and

2. If we did need to add them? What would be the best source of initial inoculum?
and his reply was
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.

2. 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. However, the microbes present in the system from the commercial product disappeared over a few weeks and were replaced by those more common to our system. So, it seems some products could help “jump-start” the process, but it will be a lot less predictable and ultimately may not determine what microbe succeed in the long run.
cheers Darrel
Last edited by dw1305 on 24 Jul 2023, 18:12, edited 1 time in total.
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Re: Using deep gravel and bacteria to control nitrogen

Post by TwoTankAmin »

@dw1305
TY for posting this Darrel.

Years ago I used to read the bacteria came into tanks from the air. I did not accept this as the normal route. I worked in Saudi Arabia int the late 1970s. I was there when it was 130F in the shade and you could not see your sweat because it evaporated as fast as you made it. There is no way floating bacteria were surviving in that dry air. We had a Brit who built a sw water tank and stocked it with fish and water from the Arabian Gulf. His tank had to cycle from the water not the air.

Here is a better explanation:

Bradley, Tyler C., Charles N. Haas, and Christopher M. Sales. 2020. "Nitrification in Premise Plumbing: A Review" Water 12, no. 3: 830. https://doi.org/10.3390/w12030830
Abstract
Nitrification is a major issue that utilities must address if they utilize chloramines as a secondary disinfectant. Nitrification is the oxidation of free ammonia to nitrite which is then further oxidized to nitrate. Free ammonia is found in drinking water systems as a result of overfeeding at the water treatment plant (WTP) or as a result of the decomposition of monochloramine. Premise plumbing systems (i.e., the plumbing systems within buildings and homes) are characterized by irregular usage patterns, high water age, high temperature, and high surface-to-volume ratios. These characteristics create ideal conditions for increased chloramine decay, bacterial growth, and nitrification. This review discusses factors within premise plumbing that are likely to influence nitrification, and vice versa. Factors influencing, or influenced by, nitrification include the rate at which chloramine residual decays, microbial regrowth, corrosion of pipe materials, and water conservation practices. From a regulatory standpoint, the greatest impact of nitrification within premise plumbing is likely to be a result of increased lead levels during Lead and Copper Rule (LCR) sampling. Other drinking water regulations related to nitrifying parameters are monitored in a manner to reduce premise plumbing impacts. One way to potentially control nitrification in premise plumbing systems is through the development of building management plans
full paper here https://www.mdpi.com/2073-4441/12/3/830

The part about which starter bacteria has been put forward by Dr. Hovanec for years. In one of his patent applications and I think also in one of his papers they did a test with a bacterial starter and they found that bacteria was gone once the tank was cycled.
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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

Thanks Darrel and TTA. All good info. From Darrel's post, this affirms my experience that a "good squeeze" from a dirty sponge filter into a new clean tank with a new sponge filter can cycle the tank in days. For the most part, that's all I do now.

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Re: Using deep gravel and bacteria to control nitrogen

Post by cwindram »

I plan to try a deep substrate as an experiment in a tank that I'll be setting up soon. I'd seen that video by Aquarium Coop on Ocean Aquarium in San Francisco, and found it fascinating. Maybe a bit off-topic, but I have always used plants to control nitrogen... all of my tanks have live plants, and there is never any measurable nitrate in them, in fact I sometimes add a general fertilizer to help grow the plants. I've got a recent setup (50 gals) going that's almost exclusively emergent plants, and this leaves lots of swimming space in the tank. No cats are visible in the photo, but this tank has Platydoras, Mochokiella, Microglanis, Tatia, and a fish that is probably
a Pseudopimelodus.
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Re: Using deep gravel and bacteria to control nitrogen

Post by bekateen »

cwindram wrote: 07 Dec 2022, 22:18I'd seen that video by Aquarium Coop on Ocean Aquarium in San Francisco, and found it fascinating.
Hi cwindram,

This thread was started after I visited Ocean Aquarium (a couple of years before the Aquarium Coop video) and I talked to the owner about his tanks. He was encouraging me to give it a try. I think he has a really unique system, and it definitely works well for him, but I think there are a few aspects which are difficult to recreate in many home tanks.
1) Most of his tanks are packed with plants, esp. java moss and other floating stem plants, to the point that it's often difficult to see what's in the tank. That's fine if that's the effect you want, but if you want a tank with open area or water current, that becomes less practical.
2) While he doesn't do outright water changes, he does do a lot of water replacement. First, his tanks are mostly uncovered, so he's often topping the tanks with clean water to compensate for evaporative water loss. Second, he does sell fish, and when he does, he removes water for bagging and has to replace it.

Obviously, none of these steps amount to the water changes we do in most home tanks, but my experience (and if you read this whole thread, you learned this) is that I'm a relatively bad plant keeper because my tanks mostly have high current and low low light. So for me, the model doesn't work as well.

I love your emergent plants in your tank. How are you supporting them in the tank? I presume there are poles (it looks like bamboo) holding the baskets in place, but am I seeing that right?

Thanks,
Eric
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Re: Using deep gravel and bacteria to control nitrogen

Post by aquaholic »

I have not read through all the posted pages on this topic but my city council water often has high levels of ammonia, partly because of chloramine dose fluctuations and partly because of cleaning activities. There is no prior warning, no indication how long this lasts and with several fish rooms, having to delay a scheduled water change day creates problems.

I solved this issue very easily with a slow constant drip (automatic) water change that displaces old water out. No timers, valves, mechanical devices. There are multiple other benefits to constant drip but this solved the poor water quality issue instantly and removes nitrate build up issue at the same time.

I run a few hundred tanks on central filtration systems, all bare bottom but do keep several 55 gallon drums full of gravel to keep biofilm - aquatic stability. They have not been disturbed for almost 15 years.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
bekateen wrote: 07 Dec 2022, 21:21 .........From Darrel's post, this affirms my experience that a "good squeeze" from a dirty sponge filter into a new clean tank with a new sponge filter can cycle the tank in days. For the most part, that's all I do now......
I think you are right Eric, I'm guessing that nearly all people use the "good squeeze" method if they can.

We've also had some correspondence with Dr Tim Hovanec (on UKAPS) fairly recently, which again may be of interest to some members.

cheers Darrel
Last edited by dw1305 on 31 Jan 2023, 15:28, edited 1 time in total.
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Re: Using deep gravel and bacteria to control nitrogen

Post by cwindram »

[quote]...my experience (and if you read this whole thread, you learned this) is that I'm a relatively bad plant keeper because my tanks mostly have high current and low low light. So for me, the model doesn't work as well.

I love your emergent plants in your tank. How are you supporting them in the tank? I presume there are poles (it looks like bamboo) holding the baskets in place, but am I seeing that right?

Thanks,
Eric[/quote]

Yes, Eric, there are bamboo crossbars, with plastic plant pots zip tied to them. I've tried various methods of supporting the plants, this seems to the best system I've come up with here yet. Most of the pots don't have any substrate, just a bare root plant, and the roots tend to grow through the drainage holes in the pots over time. A few of the plants have a bit of gravel or "fuller's earth" in the pot...which is like a clay gravel which provides some minerals to the plant. And some of the plants are grown in a "breeder box" which hangs over the side, which has circulation driven by an airline. Anyway, you can have plenty of water movement inside the tank with this method, and it doesn't disturb the plants. And because the plants are at the top of the tank, light levels can be kept low in the tank itself. (Couldn't figure out how to use the quote function correctly - maybe somebody could educate me on this).
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
cwindram wrote: 07 Dec 2022, 22:18 ....... Maybe a bit off-topic, but I have always used plants to control nitrogen... all of my tanks have live plants, and there is never any measurable nitrate in them, in fact I sometimes add a general fertilizer to help grow the plants. I've got a recent setup (50 gals) going that's almost exclusively emergent plants, and this leaves lots of swimming space in the tank. ........
Not off topic for me. I tell people that planted systems (with "plant / microbe" biofiltration, there is no "plant only" biofiltration), particularly like yours where plants have access to atmospheric CO2 and oxygen, are an order of magnitude more effective than "microbe only" systems, but they don't all believe me.

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.
bekateen wrote: 08 Dec 2022, 04:07...... my experience (and if you read this whole thread, you learned this) is that I'm a relatively bad plant keeper because my tanks mostly have high current and low low light. So for me, the model doesn't work as well.
@beekateen I understand that, and high current does, to some degree, mitigate against low dissolved oxygen levels. High levels of dissolved oxygen are the key metric, it doesn't really matter how you get there, I just like a system without (m)any "single points of failure" in the way that @aquaholic outlines for their drip system.
aquaholic wrote: 08 Dec 2022, 05:58..... but my city council water often has high levels of ammonia, partly because of chloramine dose fluctuations and partly because of cleaning activities. There is no prior warning, no indication how long this lasts and with several fish rooms, having to delay a scheduled water change day creates problems.

I solved this issue very easily with a slow constant drip (automatic) water change that displaces old water out. No timers, valves, mechanical devices. There are multiple other benefits to constant drip but this solved the poor water quality issue instantly and removes nitrate build up issue at the same time.

I run a few hundred tanks on central filtration systems, all bare bottom but do keep several 55 gallon drums full of gravel to keep biofilm - aquatic stability. They have not been disturbed for almost 15 years.
Could you add a floating plant to the drums? I know you are limited with what you can grow in Australia. I think that, dependent on which state you live in, that Nile Cabbage / Water Lettuce (Pistia stratiotes) might be an option?

cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by aquaholic »

I deliberately keep light levels low in my fish rooms to reduce tank maintenance however to provide the vivid pop of intense natural colours that all wild caught fish have, I culture 3 x 2000L tubs of green water algae on a weekly rotation which is flood fed (opening a valve) through my tanks - adult brood stock and growout stages all benefit. Additionally I have a 6m long bed of scoria containing edible pandan plants. The water table level rises and falls within the scoria via a siphon (no moving parts) so essentially a wet - dry filter. Plants get fed to the fish. I'm constantly asked for submersed pandan for peoples ponds so some gets sold when I need to remove excess.

I also have anoxic baskets on one system and anoxic like baskets with plants on another. Both seem to work but it's very hard to beat automatic (constant drip) water changes as essentially there is nothing to do. Very small drainage hoses can be used to remove slow drips to waste for anyone wondering how to provide drains.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
aquaholic wrote: 08 Dec 2022, 14:12 ...... I culture 3 x 2000L tubs of green water algae on a weekly rotation which is flood fed (opening a valve) through my tanks - adult brood stock and growout stages all benefit. Additionally I have a 6m long bed of scoria containing edible pandan plants. The water table level rises and falls within the scoria via a siphon (no moving parts) so essentially a wet - dry filter. Plants get fed to the fish. I'm constantly asked for submersed pandan for peoples ponds so some gets sold when I need to remove excess.........
Perfect system.

You might be interested in: Bartelme RP, Oyserman BO, Blom JE, Sepulveda-Villet OJ, Newton RJ. (2018) "Stripping Away the Soil: Plant Growth Promoting Microbiology Opportunities in Aquaponics." Front Microbiol. 22;9:8.

cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by aquaholic »

Hello Darrel,
Thank you for the article suggestion. Interesting but inconclusive reading creating unsatisfactory learnings.

I think we already know the importance of microbial activities especially in plant root zones. Similar to moving bed bio reactors - biofilm filters (bacterial colony diversification) providing superior biological filtration over traditional nitrification bacteria there is so much we don't know or understand yet we don't need to fully understand to obtain benefits. I changed from wet - dry filtration to MBBR after running both side by side in comparison tests for several years. The wet - dry filters were adequate but MBBR were better (for me) as multiple filtration passes are provided per single water pass. Despite me trawling through many scientific articles on biofilm research for many years, it was enough to simply acknowledge we can still benefit without knowing exactly how or why.

The struggle over fish - plants - soil outlined was easy for me. I prioritise fish over plants so all the plants are expendable and plant density - diseases are never an issue. Plants provide spawning material, refuge, fish and human food, as well as improved water quality. While I'm sure fractional improvements are possible, expanding an imperfect system is practical and easy way to boost performance.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
aquaholic wrote: 11 Dec 2022, 05:48Thank you for the article suggestion. Interesting but inconclusive reading creating unsatisfactory learnings.
I think you are right, we are still very much in a "shades of grey" world. Personally I think we are at the beginning of the discovery of novel ammonia oxidising microbes (AOM), and that the next ten years will be as least as revelatory as the last ten.
aquaholic wrote: 11 Dec 2022, 05:48I think we already know the importance of microbial activities especially in plant root zones.
I wish, I do, but I think that generally aquarists are still a long way behind where the science is. Personally I'm very sceptical, a bit of a luddite, a great believer in KISS & "if it ain't broke don't fix it" solutions, but I think you have to embrace solid science. I'm old enough to remember when yellow tinted, aged water was regarded as an elixir of life, rather than an inevitably toxic brew, and plants as purely decorations* and irrelevant to biological filtration. Judging from a lot of more email correspondence we still have a remarkably large number of people who haven't fully bought in to the importance of plants*, the rhizosphere, AOA, COMAMMOX Nitrospira etc.
aquaholic wrote: 11 Dec 2022, 05:48Similar to moving bed bio reactors - biofilm filters (bacterial colony diversification) providing superior biological filtration over traditional nitrification bacteria there is so much we don't know or understand yet we don't need to fully understand to obtain benefits. I changed from wet - dry filtration to MBBR after running both side by side in comparison tests for several years. The wet - dry filters were adequate but MBBR were better (for me) as multiple filtration passes are provided per single water pass. Despite me trawling through many scientific articles on biofilm research for many years, it was enough to simply acknowledge we can still benefit without knowing exactly how or why.
Moving Bed Bioreactors (MMBR) definitely give you most bang for your buck. This is from "Elliott, O., et al. (2017) "Design and Manufacturing of High Surface Area 3D‐Printed Media for Moving Bed Bioreactors for Wastewater Treatment." Journal of Contemporary Water Research & Education 160 pp. 144-156."
........ The specific surface area and topology of a biofilter media carrier is one of the most important parameters that determines the performance and efficiency of the system. In this work, mathematical models and 3D printing technologies were used to design and fabricate complex media designs that provide high specific surface area and refugia to protect biofilm from premature sloughing. Several gyroid based designs were proposed with specific surface area well beyond 2300 m2/m3. However, wall thicknesses and pore sizes that are prone to clogging determined a design that yields 1168 m2/m3 (133% larger than the baseline commercial K1 Kaldnes). Several moving bed bioreactors were constructed for laboratory testing with inoculation provided by wastewater from a fisheries operation. Preliminary results indicate that the 3D printed media can withstand the prevalent conditions in moving bed bioreactors, and that the NH3 removal rate of gyroid media is comparable to that of K1 Kaldnes........
aquaholic wrote: 11 Dec 2022, 05:48The struggle over fish - plants - soil outlined was easy for me. I prioritise fish over plants so all the plants are expendable and plant density - diseases are never an issue. Plants provide spawning material, refuge, fish and human food, as well as improved water quality. While I'm sure fractional improvements are possible, expanding an imperfect system is practical and easy way to boost performance.
I was originally interested in plants purely as aids to water quality, but I now realise that I had severely underestimated the synergistic effect in plant /microbe biological filtration.

cheers Darrel
Last edited by dw1305 on 12 Dec 2022, 10:54, edited 8 times in total.
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Re: Using deep gravel and bacteria to control nitrogen

Post by dw1305 »

Hi all,
TwoTankAmin wrote: 07 Dec 2022, 17:56TY for posting this Darrel.

Years ago I used to read the bacteria came into tanks from the air. I did not accept this as the normal route. I worked in Saudi Arabia int the late 1970s. I was there when it was 130F in the shade and you could not see your sweat because it evaporated as fast as you made it. There is no way floating bacteria were surviving in that dry air.
I'll guess that atmospheric transfer isn't that important, but I can also see that it will happen in most circumstances, purely because the fauna and flora of ephemeral water bodies is incredibly proficient at finding new "puddles".

Because of that I'm also going to guess that organisms (like AOA, AOB, Nitrospira etc), which are orders of magnitude smaller and more numerous, are always going to find your tank sooner or later.

I can see why my tanks might be slightly different to the norm, and why that might mean they get an appropriate starting inoculum of microbes and become "cycled" without any direct intervention* on my part.

*I use rainwater, I always have running tanks and from these I transfer plants, substrate, filter mulm, and these are all going to be inoculum sources, supplying an appropriate oligotrophic assemblage of archaea and bacteria .

cheers Darrel
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Re: Using deep gravel and bacteria to control nitrogen

Post by Procrypsis »

+2 on the RO system.
I run mine and capture the "waste water" to flush toilets, laundry, etc. Nothing goes to waste.
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