# nitrogen cycle water quality



## rsskylight04 (Nov 9, 2013)

Who knows about the bacteria that cycle ammonia and nitrates in aquarium water. How can I encourage the best possible environment for good bacteria growth. Any info is well appreciated


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## Romad (Jun 28, 2009)

Have you read these sticky threads on the nitrogen cycle and bacteria in the freshwater tank? This will be a good start.

http://www.tropicalfishkeeping.com/...nners-guide-freshwater-aquarium-cycle-213418/

http://www.tropicalfishkeeping.com/freshwater-general-articles/bacteria-freshwater-aquarium-185721/


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## beaslbob (Oct 17, 2012)

rsskylight04 said:


> Who knows about the bacteria that cycle ammonia and nitrates in aquarium water. How can I encourage the best possible environment for good bacteria growth. Any info is well appreciated


 
You add fast growing live plants.

my .02


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## Flear (Oct 5, 2012)

ammonia is produced by a ton of different methods of non-photosynthetic oxigen rich environment
how ammonia is produced isn't a concern, we know it's going to be produced in massive enough quantities we are very thankful for other bacterial processes that break it down.

it's not simple, 

once ammonia is produced, it depends on your ph what happens first
if the ph is low, then you get ammonium, (under 6.5 is almost all ammonium)
ammonium is safe, very safe
above 6.5 you start having small amounts of ammonia (this is the toxic one)
at about 9.5 it's about 50/50

i don't know squat about ammonium being converted
i know plants can use ammonium directly, ... plants are good

i don't know the names of the types of bacteria either, only the processes involved in the nitrogen cycle, the simplified nitrogen cycle

the first one converts ammonia to nitrites, ... i've as toxic as ammonia, i've also heard more toxic, ... i dono
next, ... roll the dice, we hope the next one will convert to nitrates
a bad roll could convert to ammonia again, ... is this likely no, but lets follow the simple cycle and leave it at that

nitrates are still toxic, but safer than what the tank has gone through
plants can use nitrates easily.

i have heard (and forgotten about light levels that help or limit one of these bacteria (converting to nitritres or nitrates), i think it needs dark, ... so pick an opaque substrate (an idea i had for a time was sand blasting glass beads, perfectly round for sensitive skins of some fish), but if it inhibits or limits the nitrogen cycle into nitrates, it's not worth it in my mind.

if you've got sufficient plants then you don't have to do water changes due to nitrates (possibly for other reasons, but not for nitrates)

if you don't have plants, you have 2 choices
change water, or ...
pick live rock (give it time to culture) and another bacteria steps into the picture

converts nitrates into harmless nitrogen gas, ... this is only done in anoxic environments (if i have the right word), ... without oxigen environments, ... deep inside the live rock, osmosis will bring in nitrates, and move out nitrogen gas.

could also bring about the same process with a deep sand bed (5" or more of substrate)
don't listen to the fears about the Deep sand bed if you have plants, don't clean a deep sand bed
don't disturb your DSB, just leave it alone, ... it will accumulate a ton of nutrients till you are wondering (after a few years) why you have mud in the bottom of the tank
oh ya, and if you have plants the roots will bring oxigen into the substrate, and defeat the process of converting nitrates into nitrogen gas.

but if you have plants the plants will reduce the nitrates and once more things are healthy

for marine tanks, coral rock is what's used, ... just left alone it cultures and all is good
for freshwater if you want your PH low, don't use this as the calcium will bring your PH to 8 or more
porous lava rock is a good alternative

regardless of the live rock options, i am sure the measures are the same, X pounds of life rock per gallon of water, i don't remember, have a look in marine/coral sections to find out

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long story short, don't care about any of the above, so long as your ammonia and nitrites are near zero it's good, for new tanks this is expected to take 4-6 weeks.
if you have plants you can have nitrates up to 40

if you have live rock & plants, you might have nitrogen deficiencies in your plants
if you have a DSB and plants, your plants are going to be undoing the anoxic layer and no denitrification is going to be happening

once things are reduced to nitrates, pick one means of handling it, and/or you can combine with water changes

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a more complicated nitrogen cycle
add ammonium into the mix
and there are bacteria that can convert various nitrogen molecules into all kinds of other different nitrogen molecules, ... some of these are toxic to have in tanks, some go against the nitrogen cycle. ... the simplified nitrogen cycle wins out as nitrogen compounds that are produced in abundance will also promote bacteria that process the compounds into the regular simplified nitrogen cycle till things balance out in a stable cycle

cyano bacteria can also play a part in the nitrogen cycle
from what i've seen of cyano it's limited/controlled with oxigenated water flow, ... still water down at the substrate can be a bad breeding ground for cyano, once started it's much harder to remove then never having it to begin with, ... so far cyanobacteria is the only source i've heard of that we have commonly available to our aquariums that can directly make use of dissolved N2 gas in the water, i don't remember where it converts it to on the nitrogen cycle of our aquariums., ... overall not a good thing to have in our tanks though, ... there are cyano strains that are safe, but others are toxic and nothing will eat it.


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## rsskylight04 (Nov 9, 2013)

*thank*

Thanks for your very detailed answer. Do you know, where is the main population of good bacteria? Is it the filter... or the substrate... or the water itself? Also is it ok to move substrate from my established tank to a new tank? Will it help cycle the tank or is it just a waste of my valuable bacteria? Does it help to move slimy rocks frommy old tank to the new one? Thanks for the knowledge, you guys are great!


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## Flear (Oct 5, 2012)

rsskylight04 said:


> Who knows about the bacteria that cycle ammonia and nitrates in aquarium water. How can I encourage the best possible environment for good bacteria growth. Any info is well appreciated


"best", ... sorry about this, ... i will never think of someone who wants "best" as a person who knows anything about what they're asking

there is no such thing as "best"
best for what ?
best for plants
best for completing the nitrogen cycle
best for what ?

as for best for the nitrogen cycle itself, ... i've never looked into that
what kind of substrate, particle size, light, temperature, PH, oxigen, ... and other.

if you're only worried about the nitrogen cycle, don't
think about what you want to get out of it, think about what you want in the tank that you are concerned about the nitrogen cycle for, but just the nitrogen cycle, ... like worrying about if your tires are 30psi or 40 psi when your already late for an interview

what do you have in your tank ?
do you have plants ?
do you have other critters ?
water changes ?
light ?
PH ?
nutrients ?
new or established tank ?

even then all these questions boil down to:
new or established tank ?
plants or not ?

and notice none of these questions are about feeding (overfeeding can increase ammonia, then through bacterial conversions result in nitrates) unless it's extreme

from personal experience:
do you have snails ?
if your fish are small enough (or your snails large enough) they will eat dead fish and you will never experience an ammonia spike, ... larger fish not so much (unless your snail population is beyond extreme)

do you have any creatures that deal with dead/dying things in the tank (most people don't)

do you need to worry about the nitrogen cycle ?
no

unless your building a tank your throwing dead things into
on the net somewhere (another forum) a lady has a tank with a DSB, she describes going as far as burying the dead fish and critters to provide nutrients under the substrate for plants, ... never an ammonia spike, ... so there's a lot of leniency in things, a lot of room to not care till you get so far into extreme, and even then, there's ways to handle it.


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## Flear (Oct 5, 2012)

where the majority of the bacteria is ?
wherever the majority of the surface area is

if you've got gravel & a bunch of sponges in your filter, then your filter has the majority of the bacteria
if you've got sand then regardless of the filter, that's the majority of your bacteria
if you've got a bare bottom tank (actually a serious way some set there tanks up who have coral) then the surfaces inside the tank (including everything else in the tank)

if that's your question "where is the bacteria"
just look for a substrate with lots of surface area, use sand instead of gravel
personally i'd stick with 2" or less if you don't have plants and don't clean your substrate on a regular basis.

if you have plants, as deep a substrate as you want
if you have coral, might be better without a substrate at all, go bare bottom
it's more important to know what is in your tank instead, then worry about the substrate later, or where your bacteria is going to culture that keeps the nitrogen cycle healthy
if your replacing your filters on a regular basis, then don't count it


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## rsskylight04 (Nov 9, 2013)

*thanks#2*

I have a very well established 75 gall with 1 jack dempsey and 2 pictus cats. My reason for asking is that this tank has been up and running for 6 years with never a problem. I want to really understand what is going so good in there so that I might reproduce the resultts in other tanks... instead of crossing my fingers and hoping for the best. Sounds like plants are very good for the water, but I can't have any... the dempsey shreds them just for fun! Based on your posts and the excellent reference materials written by byron, I guess the deep gravel bed that I have in my tank has helped to keep it so stable. Water is crystal clear and fish are very healthy. Flear is right that there is no one best way to maintain a tank, my focus is on optimal waterquality fot my fish. Thanks for the intelligence!


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## Flear (Oct 5, 2012)

java fern & anubias are very resistant plants, ... just look for plants safe for a goldfish tank


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## Hallyx (Jun 11, 2011)

Flear takes the nitrogen cycle too casually for my taste. A strong cycle keeps nitrous toxins at 0.0ppm, done right. An unstable cycle can crash creating dangerous ammonia spikes. A large or rapidly-increased bioload can be easily overload too small a bacteria colony, leading to ammonia spikes.

I started my research into the nitrogen cycle here: Aquarium Nitrogen Cycle | Cycling Methods | Ammonia & Nitrates


Strohmeyer is an old-school professional aquarist. While there may be a few ways to promote a cycle, his are good fundamentals. This article will specify which bacteria do which job in what order. 

Research and experiment have shown me that lots of O2 and a temperature around 84* F encourage the cycle, along with hard water and high pH, and darkness. I suppose you already know that soft water and low pH (below 6.5) will discourage the cycle.

Heavy planting removes ammonia before the bacteria can get to it. So a planted tank has a smaller bacteria colony; but, then, a larger one is not necessary. Some people call this a "silent cycle." I find the term inaccurate and misleading.


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## rsskylight04 (Nov 9, 2013)

*just what I was looking for!*

Thank you hallyx for the excellent post and informative link. I am a perfectionist when it comes to my fishtanks. I don't just want to know what to do, I want to know why I'm doing it and exactly what is happening to make it work. Ive often wondered if plants in the tank take nutrients from bacteria-your information confirms that this is true. Also, info on temp and hardness/ph is very useful to me. Your wisdom is very well appreciated.


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## Hallyx (Jun 11, 2011)

rsskylight04 said:


> I don't just want to know what to do, I want to know why I'm doing it and exactly what is happening to make it work.


Exactly so. I couldn't agree with you more.


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## Flear (Oct 5, 2012)

Hallyx, 

yup, i found the PH problem first hand, that was devastating  i lost half my fish when the PH shifted from below 6.5 to above.

prior to that my aim was to have PH 7.0-7.5 (concerned about snails)
i was familiar with ammonium, but wasn't aware i was dealing with any
at the time i had just removed 2 shopping bags worth of plants i had let get beyond overgrown when i trimmed everything down

i had heard that darkness helps the cycle, but had forgotten what part of the nitrogen cycle it's key too, ... and a refresher is good. prior to that i was thinking of sand-blasting glass beads, only to realize later (after farther reading) it will inhibit the nitrogen cycle due to being transparent (would look neat though 

i am on the fence about plants and ammonia, in the hobby i have seen a lack of recognition about ammonium, which has left me in doubt when people say plants absorb ammonia

i had not thought about the bacteria colony vs. how heavy the tank is planted, ... good to keep that in mind.
i had no knowledge of what optimum parameters was for developing the bacteria colony, thank you so much 

i dono about all nitrous toxins at 0, nitrates i have only heard they are good for plants and up to 40ppm is optimal.


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## Hallyx (Jun 11, 2011)

Ammonia (NH3) converts to ammonium (NH4) by grabbing a hydrogen ion (H+) from the water at lower pH. It loses that ion at higher pH becoming toxic free ammonia, as you found out, Flear. 

Here's a chart which shows the percentage of ammonium versus free ammonia relative to pH and temperature, which is also a factor..
CNYKOI - Ammonia calculator


Plants absorb ammonia in preference to other nitrogen compounds and convert it to ammonium to provide energy to break the C from the CO2 to build plant mass, releasing O2 which your nitrifying bacteria need. How it does this in conjunction with photosynthesis is something I'm not quite clear on. Rickey knows this stuff really well.

You lost lot of ammonia/ammonium processing capacity from your system when you (over)-trimmed your plants. When your pH went up, ammonium reverted to free ammonia and decimated your fish.

It's not that the bacteria need darkness so much as they need less UV radiation. Darkness seems to help the cycle a little. Not as much as O2 and warmth (~84*)

Sand-blasting glass beads seems to me to be an interesting choice as substrate. Is that what you mean? Being on the bottom, it wouldn't matter regarding darkness. They're out of the way, as it were.

In a plantless tank, all the ammonia is oxidized by the nitrifying bacteria. In a NPT all the ammonia is consumed by the plants. Anywhere along that spectrum, the dominant factor gets dibs, the leftovers go the other.

I'm under the impression that nitrate is converted to ammonia before it's used. I'm having a hard time getting accurate confirmation of this. But, if your plants are absorbing all the ammonia, you won't see nitrate at all. Nitrate is an end product of the nitrogen cycle.

Nitrate may be good for plants, but no amount of nitrate is optimal for livestock.


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## rsskylight04 (Nov 9, 2013)

Hallyx, the link you provided in previous post is exceptional, I'm going to have to re read a few times... long time scince I took any chemistry. Great stuff! I think every aquarist should read that. Again, thanks for the help.


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## Flear (Oct 5, 2012)

sandblasting glass beads are an over-kill for substrate use.

they're round for delicate fish
they're fine (like play-sand)
make compacting impossible due to their shape
lots of pore-space for water to keep O2 levels high inside the substrate

the company that manufactures them also produces a ceramic bead for foundry casting, ... but i don't know where they sell it to, ... that i think is white, but opaque, solving translucency issues (if any)

the issues with the glass beads would be translucency, allowing light to pass through, sure glass inhibits UV to a degree, but it doesn't block it, if that's an important factor, an opaque substrate becomes of higher value.

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as for ammonia/ammonium & nitrates

bits i've come across don't talk about ammonia, makes me a little confused

they talk about nitrates & ammonium
plants prefer ammonium, failing that their next choice is nitrates that they convert to ammonium

i wish i could find information on ammonia vs ammonium for plant uptake

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when it comes to nitrates, the option is to follow what reef tanks are doing with live rock
dead coral rock is great as it allows the bacteria to live safely in O2 deprived water deeper inside the live rock there it can process nitrates into N2, completing the nitrogen cycle, for freshwater if your PH is high (for a chichlid tank sure) can go the same route, ... if your PH is lower then lava-rock would do the job i think (that info is really hard to find


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## rsskylight04 (Nov 9, 2013)

*question*

I have very hard water, does that keep ph low? Is it good for bacteria?


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## Hallyx (Jun 11, 2011)

Flear said:


> the issues with the glass beads would be translucency, allowing light to pass through, ... an opaque substrate becomes of higher value.


The transparency of the substrate doesn't matter. It's down-sun of the system. I run bare-bottom tanks. I just mentioned darkness as a minor cycling aid.



Flear said:


> ... failing that their next choice is nitrates that they convert to ammonium
> 
> i wish i could find information on ammonia vs ammonium for plant uptake


I bet the members over at the "_Advanced Planted Tank_" section of this forum could answer that question.

Not many freshwater keepers use live rock. Strohnmeyer discuses how to complete the cycle through to N2 outgassing in his article I referred to. For Betta, it's just easier to do water changes. Lava rock is sometimes used to raise KH (hardness) causing a rise in pH.

Hard water (high GH and/or KH) keeps pH high and stable, hard to manipulate up or down. Hard water is good for the growth of nitrifying bacteria.


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## rickey (Jul 7, 2013)

Flear said:


> as for ammonia/ammonium & nitrates
> 
> bits i've come across don't talk about ammonia, makes me a little confused
> 
> ...


I can pull some articles relating to the chemistry if want them, I'll pull them at work so we don't have to buy for them, but I can quarentee a headache before you get it all figured out.
R


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## Forestfish (Nov 17, 2013)

Wow, this is an amazing post !


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