# Dummy Question #002: Bacteria turning waste into Ammonium?



## niko (Jan 28, 2004)

If you care to have some kind of order in the information you get from this discussion please read Dummy Question #001:
http://www.aquaticplantcentral.com/...67-dummy-question-001-fish-waste-ammonia.html

So:

*How do we care for the bacteria that turns the fish waste into Ammonium?*

I personally make sure they floss and brush their teeth before going to bed: 









What do you do so they stay healthy?

--Nikolay


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## prBrianpr (Nov 18, 2007)

I dont think that we need to care them. With fish pooping all the day the bacteria have plenty of food. i also think that some of it also live inside the fish.


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## niko (Jan 28, 2004)

PrBrianPr,

You answered exactly the way I was hoping someone will.

*US planted tank folk as a whole do not pay attention to the full range if biofiltration.*

Here's a ridiculous situation:

1. Look at the sections of the APC forum:
http://www.aquaticplantcentral.com/forumapc

We see:
--> No section called "Filtration"
--> Nice and active section "Algae"
--> Nice and active section "Fertilizing"
--> PPS and EI are stickies.

Japanese and German know-how don't matter. The Japanese know only how to make cool tanks and market them smart. Germans only know how to make overrated Eheim filters and ugly looking tanks.

You know how I fix all mechanical problems with my car? I take it to the car wash. No need to check the engine. (Maybe an occasioinal glance to make sure it's still there allright.)









And when planted tanks give me problems I play with fertilizers, water changes, and light. No need to check the filter. (Maybe an occasonal rinse to make me feel good allright.)









Let's see how many more bored souls will click on Dummy Question #002 before I ask Dummy Quesion #003.

--Nikolay


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## Dryn (Sep 6, 2007)

Ambushed!!! Duck and Cover... Return Fire!!! NOOO... they got prBrianpr. He was so young too.


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## Dryn (Sep 6, 2007)

Seriously, this is definately a topic that isn't considered very often. The understanding of soil and water bacteria in terrestrial plants is becoming more an more detail in recent years. This may be a source of information for our hobby. I've read some of the book though. It is very, very complicated and detailed.


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## houseofcards (Feb 16, 2005)

So it sounds like you are poking fun at the instructions that come with most canister filters most notably the Eheims that give very long durations between cleaning.


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## Natalia (Sep 15, 2008)

Bacteria that convert fish/plant waist or sludge into ammonia/ ammonium are the heterotrophic bacteria, mainly from genus Bacillus and Pseudomonas. They are fast-growing and pretty resistant to different conditions, can live in almost any PH, fresh or salt water, with or without oxygen. In this sense, you do not need to create anything special to maintain their population. 

The two problems with those bacteria is 1) that they can compete for the food source with nitrifying bacteria, thus reducung the efficiency of nitrification and 2) in low oxygen conditions (at night for instance) they can convert nitrate back into ammonia. 

Therefore one may want to keep their population in check by removing the excess of sludge from the substrate/ filter.


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## niko (Jan 28, 2004)

Oh this is starting to get interesting! Maybe. Let's see how long I can keep the attention using my convoluted jokes.

*Dryn*,

I do shoot in all directions. Meaning exactly where the planted tank hobby is in the US - all over the place. At least I use a laughing gas pistol. The corny kind of laughing gas.

Yes, pretty lame. But somewhat better than not sharing what I know.

*Dryn* (hm... name sounds familiar...),

The topic of how waste actually turns into Ammonium is pretty lame. Some interesting information concerning aquariums and "waste -->NH4" popped up in 1966. Yes, 43 years ago! Of course that we are not going to consider information that is almost 50 years old. We're modern folk with rimless tanks and we stress on Aquascaping!

And fighting algae with modern approaches.

*HouseOfCards*,

I could say I wonder why Eheim suggests not to clean their filters too often. But I won't. I'm sure they either know something special or they are just plain stupid.

Hard to say. But what we know is that we have wonderful space-age ways of running planted tanks clean as a whistle from Day 1. Every time:

Look here:
http://www.aquaticplantcentral.com/forumapc/fertilizing

And here:
http://www.aquaticplantcentral.com/forumapc/algae

What kind of a person would argue that that's not a wealth of information right at your fingertips?

*Natalia*,

"Heterotrophic" is the word! But I'm not sure it will catch on. It doesn't suggest anything cool. I'll call them 'Uncool" for now.

From what I understand the Uncool bacteria are indeed very hardy. So hardy that you can buy them in a bottle:









You can't buy the bacteria that we all have in our canister filters bottled like that. They throw tantrums and just die.

The Uncool bacteria could act idiotic too - they can actually make NH4! Oxygen drops and here they go providing a free buffet for all the algae passing by.

Say, Natalia, do you speak any foreign languages? Be careful what you say - your answer can open an entire new world for you. Maybe that's what knowledge is supposed to do. From what I see you have gone to many places but not visited this particular new world yet.

Google translantion works ok but after reading the results from that undoubtedly amazing software miracle I feel like hammers have been pounding my head for a century. And I start to speak funny too. Meaning - nothing unusual for me actually. Anyway;

We have arrived to a good enough answer to the original question ("How do we care for the bacteria that turns the fish waste into Ammonium?"):

*1. The bacteria that turns waste into NH4 must never be starved for Oxygen.*
*2. The bacteria that turns waste into NH4 must never be allowed to turn NO3 back to NH4.*

But that does not necessarily mean we need to make sure our canister filter is nice and clean. Because... maybe, (and only maybe) they don't live there.

Are they in the substrate? I personally really hope they are in my tank's substrate. I guess they are because if they were not there then I'd probably have 3 year old mountain of fish poop that is growing every day.

So now I hope you understand - The Uncool heterotrophic bacteria that turns fish waste into NH4 is an elusive creature. We don't even have a good notion where it is. Much less how to take care of it.

Maybe like the Cool bacteria doing NH4-->NO2-->NO3 as we speak the Uncools are all over - in/on the substrate, on the plants, on the glass, on the decorations, in the canister filter.

This writing is getting too long for the average planted tank reader. Why should we really care about some obscure bacteria?

Because it's a huge part of the answer "Why do I have algae?".

Here, instead of giving away what others know better than me (an I just recently learned) I'll distract you with Dummy Question #003:
*"What is COD and why should we care about it?"*
http://www.aquaticplantcentral.com/...dummy-question-003-what-s-cod.html#post513582

--Nikolay


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## Shad0w (Nov 13, 2006)

what will happen to the "cool bacteria" when there is no/limited NH4 available? Do they die? or Hibernate (not what do you call it)?


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## niko (Jan 28, 2004)

Shadow,

Here in our highly scientific discussion we joyfully invented two new names:

1. "Cool" 
The bacteria that turns NH4 into NO3.
We all know about them, care about them, like them. They are the popular kids. 

2. "Uncool"
The bacteria that turns waste into NH4.
They do crazy important work. Without them the Cool bacteria will have a hard time looking pretty.

I have the feeling that you may have meant "Uncool" when you said "Cool".

But I maybe wrong for once in my life. 

In any case - it is damn hard to remove all the NH4 from a tank. so the bacteria will always find something to eat.

"High-bear-Nate"... (I think that's how it's spelled but I maybe wrong):
The bacteria also likes to form "spores" - meaning that when something is not to their liking they pull out cute little sleeping bags and zip up in them. Honestly I don't know if our own Cool pet bacteria actually can form spores. But they will stay in your tank through rain and cold. You can kill them using chemicals (or just plain tap water) but they will never die because your lush plants ate all the NH4 before the bacteria woke up.

--Nikolay


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## Shad0w (Nov 13, 2006)

I actually mean the bacteria that convert NH4 into NO3.

I'm asking because if the tank full of healthy growing plants and plants take all the NH4 and NO3. We dose NO3 so I assume NH4 from fish is not enough. In this scenario would the bacteria die from starvation?


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## Philosophos (Mar 1, 2009)

Ammonification is a matter of oxidization. Whether it's heat, bacteria or fungi, something has to do it. In the case of our tanks, some of these bacteria are the same that cause infections in stressed fish. Familiar names like pseudomonas, streptomycis and bacillus are included in this very large group of bacteria.

Fish expel some NH4 flat out. The odd fish produces urea, but in our tanks that just converts directly to NH4 as a necessity of basic chemistry, not microbiology.

Whether the ammonia or ammonium is a matter of ionization, and exists as one or the other depending on pH and temperature.

All of these colonies are something I leave to my aerobic substrate and the wonder of soil sediment. I like my mechanical filtration to remove waste, not back-leech it into the column. As such, I clean my filters every 2-4 weeks on any high maintenance tank.


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## niko (Jan 28, 2004)

See!

We are back to square 1 - discussing the Cool bacteria (NH4-->NO3).

I'm trying to talk about a novel idea that is nothing new really, but we have forgotten it very, very well. So far I've started 3 threads and the discussion is barely moving. 

Let me tell you something simple. It's about advertisement. Marketing if you wish:

PPS and EI are the two dominant methods of running a planted tank. Both of them are here today because of a lot of talk, arguments, discussion, and efforts. I personally laugh at both of them. But my point is - it took a lot to establish them as pillars of the planted tank society. 

Here I'm talking about things that we must know. Things that have been known for a long time but most of us haven't even heard of. Enough car washing, let's look at the engine to find answers to many problems.

Maybe one day in the future certain aquarium site will actually have a section called "Filtration". And a few others.


Shadow,

The bacteria that convert NH4 to NO3 (and I call "Cool") will die from starvation only if they really don't have anything to eat for a very long time. Maybe they turn into dormant spores maybe they die. Here's how I know they are very hardy:

Unplug your canister filter. Disconnect the hoses. Leave the water inside. 

Start a new tank a month later, even 2 months, even 3 months later. You will see that the tank cycles very quickly - 3-4 days at most. That's because the bacteria in the filter did not die. They had nothing to eat, maybe each other allright. But as long as the biomedia didn't dry you will have a miraculously fast cycling. 

Philosophos,

I see you are placing your bet on the Cool bacteria that turns NH4 into NO3. Most of us to the same.

You are also removing waste through your mechanical filtration. I have tried that too completely convinced that I can filter the hell out of the aquarium water and make it so clean that I can't see it. I even designed my own diatom filter that could run 24/7. What an monumentally idiotic idea!

I didn't see you say anything about the Uncool bacteria turning waste into NH4.

Most of us are missing many basic things about running an aquarium. Not only planted. That's why I have started this series of threads.

--Nikolay


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## Natalia (Sep 15, 2008)

Niko,
I think you are wrong about the nitrifying bacteria. They are strictly aerobic and will die without an adequate oxygen supply. They do not form spores. In you filter that has been left for 1-2-3 month these bacteria are dead. But you have a lot of heterotrophic bacteria which can feed on ammonia among other things. Although these bacteria are not the most efficient nitrifiers, they can cycle your tank when present in huge numbers. This is how the commercial products like Cycle, etc. work I think.


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## niko (Jan 28, 2004)

Natalia,

If you read carefully you will see that I make fun of our collective ignorance. My own ignorance first!

My conclusions are often based on personal observations. As wrong as they can be.

I'm glad you are throwing light on what could be happening in an old disconnected canister filter. 

You mentioned that heterotrophic bacteria could actually take care of the cycling in a new tank. But from what I have read recently I understand that there are quite a few conditions which have to be right for the Uncool heterotrophic bacteria to actually work.

So we are starting to see that things about filtration are quite complicated. We could loose interest right here. Stick to our old easy ways. 

Good thing I have a vast storage of somewhat funny tricks to keep the pursuit of knowledge going. 

Personally I'll now try to find out the following:
1. How fast Uncool heterotrophic bacteria can eat NH4 and make NO3.
2. Optimal conditions for Uncool bacteria to convert NH4 to NO3 (something that normally the Cool bacteria does.)

--Nikolay


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## prBrianpr (Nov 18, 2007)

Nitrifing bacteria not make sporeS? so the companies are lieing??? I read the Bacteria products and says that contain nitrifing Bacteria not heterotrophic. I always use a lot of plants and bacteria products in new setups, this not prevent spikes in amonia but this method is very usefull. The spikes not always appear, only in few setups and down the spikes to almost safe levels, I also use a percent of water from a cycled tank so I make a tank in one day with fish and nothing bad happend.


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## niko (Jan 28, 2004)

After the last post we could start discussing 3 things:

1. The biology of Nitrifying bacteria (the ones that convert NH4 to NO3).
2. How realistic are aquarium company's claims for this or that.
3. How to cycle a new tank.

All 3 will take the attention away from the topic of heterotrophic bacteria - the bacteria that converts waste to NH4.

The same bacteria that we as a whole apparently have no clue about. All we can say is "Uhm, yeah.. they exists... somewhere."

Honestly, at this point all I want is for everybody that cares to read this thread to remember that *heterotrophic bacteria break down organics and produce NH4. That NH4 is then converted by other bacteria to NO3.*

And next time someone asks "Why do I have algae?" please ask them about the organics in their tank. Don't limit yourself to the lights, fertilization and the other lame sad violin melodies.

--Nikolay


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## Shad0w (Nov 13, 2006)

prBrianpr said:


> Nitrifing bacteria not make sporeS? so the companies are lieing??? I read the Bacteria products and says that contain nitrifing Bacteria not heterotrophic. I always use a lot of plants and bacteria products in new setups, this not prevent spikes in amonia but this method is very usefull. The spikes not always appear, only in few setups and down the spikes to almost safe levels, I also use a percent of water from a cycled tank so I make a tank in one day with fish and nothing bad happend.


My though also.

Many company selling bacteria in the bottle, does it really work? What kind of bacteria inside?

How about PSB (Photosynthetic bacteria) product? It contains Polyclonal euryhalious and eurythermic photosynthetic bacteria.


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## Philosophos (Mar 1, 2009)

niko said:


> Philosophos,
> 
> I see you are placing your bet on the Cool bacteria that turns NH4 into NO3. Most of us to the same.
> 
> You are also removing waste through your mechanical filtration. I have tried that too completely convinced that I can filter the hell out of the aquarium water and make it so clean that I can't see it. I even designed my own diatom filter that could run 24/7. What an monumentally idiotic idea!


I do it because not cleaning your filter will reduce flow rate and wear on the filter harder. It's also easier to just remove the waste than to deal with waiting for every feeding to break down, along side the rest of the organics left over from the process. Skipping out on the filtration is a wonderful idea until you go and try to spawn any fish in the hobby that requires clean water. Watch what happens to your hatch rates for that matter.

At this point you've pretty much sat around calling everyones ideas idiotic (including some of the biggest contributors in the hobby), but haven't offered any sources to support your assertions. It might be an idea to present a bit more of a formal case if you're going to fling epithets all over the place at the same time.


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## mudboots (Jun 24, 2009)

I wish someone using zero filtration would chime in to offer how it's working, good, bad or indifferent. 

I have zero filtration, though some water movement, but 2 stupid moments (trying to battle pea soup with oops-i-dental h2o2 overdoses) left so much plant debris (nearly every single leaf in the tank) that it took a long time for it all to decompose, and now I am kind of waiting out some mild green water that spiked while I was on vacation (no water movement at the time, no inputs of nutrients to the fish or otherwise, but CO2 production from the substrate...). Since restoring the unfiltered water movement I have noticed a decline in the diatom sludge and visible organics, but still have quite a bit of GSA and staghorn here and there.


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## Diana K (Dec 20, 2007)

For more info about nitrifying bacteria (NH3/NH4 ---> NO3) and the research that has gone into identifying these species, have a look here.

http://www.drtimsaquatics.com/Library_Presentations/SciencePapers/SciencePapers.html

Basically:
Most 'bacteria in a bottle' products do not have the correct species of nitrifying bacteria. They may have heterotrophic bacteria, and other sorts, but the bacteria that do most of the work in an aquarium of turning ammonia or ammonium into nitrate does not enter a spore stage where they can be reliably bottled and sold at room temperature. These species are harder to culture and ID in the lab. Hetertrophic bacteria are present, and were identified many years ago, and can be bottled, and this is what is usually in the bottles of 'cycle boosting' stuff. Not useless bacteria, just not the bacteria that end up doing most of the ammonia to nitrate processing in a mature tank.


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## niko (Jan 28, 2004)

*Philosophos*,

Go back up this thread and read my posts. Carefully this time.

Today you ask me to give links, to "present a formal case", to serve it all on a silver tray.
Yesterday I explained why I will not:
http://www.aquaticplantcentral.com/...dummy-question-003-what-s-cod.html#post513649

Read my posts carefully. Is all of this worth following or not? Main thing - the reading should bring some kind of fun. It's our hobby not a sumo performance:









Here's one (of many) annoying ideas:
If I have to clean my filter because it gets plugged up then my filtration setup is not good. Or at least it's obsolete.

If you feel like it - Google away to find out why. Try youtube. Try googling in other languages too. I'm not joking.

As far as the "biggest contributors in the hobby" are concerned - I could say that there is T. Amano and at maybe one or two more persons. I don't think their names are known well. I exclude DianaK because I know nothing about The-El-Das Natural. Also to me people like TexGal are huge contributors to the hobby because they keep it light and fun.

*Mudboots*,

Zero filtration, only water movement - I've done it! Once:

Strong light. CO2. Very light fish load. Light feeding every 2-3 days.Medium planting.

Chinese canister filter broke. Left the tank with just a powerhead for 3-4 weeks. No algae issues. No other isssues. Plants actually started to grow a little faster starting Day 2 without a canister.

Possible explanation:
1. NH3/NH4 that was consumed by the bacteria in the canister was now available to the plants.
2. Light fish load did not produce too much organics. So there was not much to turn into NH4.

Conclusions (pathetic, from only 1 tank, but when noone is looking I try to secretly think):
An established tank is a very stable system.
A filter (canister or not) is just an insurance in case there is a considerable disbalance.

*DianaK*,

Most of us assume we know a lot of the basics of running an aquarium (planted or not). But we don't. I hope that the close-to-home example of commercially sold bacteria will motivate at least some people to try to find out more info on things we all think we know.

--Nikolay


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## houseofcards (Feb 16, 2005)

"Organics apparently are in the very beginning of what causes problems in our tanks. It's wise to get to know them as good as possible."

--Nikolay

This for me is the key. It leads to all problems. The filter could be an enemy just as easy as it could be a friend.


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## prBrianpr (Nov 18, 2007)

well, I use bacteria in products and works for me. Can reduce but not prevent spikes, be carefully with the addition of fish the first 2 weeks.


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## Philosophos (Mar 1, 2009)

niko said:


> *Philosophos*,
> 
> Go back up this thread and read my posts. Carefully this time.


I didn't read that thread a first time; just this one.



niko said:


> Today you ask me to give links, to "present a formal case", to serve it all on a silver tray.
> Yesterday I explained why I will not:
> http://www.aquaticplantcentral.com/...dummy-question-003-what-s-cod.html#post513649
> 
> Read my posts carefully. Is all of this worth following or not? Main thing - the reading should bring some kind of fun. It's our hobby not a sumo performance


And your reason is sort of poorly thought out given that you're content to tell people that their ideas are outright wrong, but without any real detail as to why.

I appreciate information given directly to me; you haven't bothered to show that people sometimes appreciate having information given to them freely. When a good link to a journal gets posted, I read it because it has been given freely. It is something I'm not going to pay $25 for or dance around with the author while they give me their conclusions but not their method.



niko said:


> Here's one (of many) annoying ideas:
> If I have to clean my filter because it gets plugged up then my filtration setup is not good. Or at least it's obsolete.
> 
> If you feel like it - Google away to find out why. Try youtube. Try googling in other languages too. I'm not joking.


And here's a prime example of what you're doing. You aren't telling me why it's not good filtration, you're not backing up you're facts, you're just making a broad statement then telling me to google it without narrowing down who's theory you're going with. You haven't even bothered to ask me more details about my opinion to see my point of view before judging it.

I'm going to respectfully withdraw from this thread; I have better things to do with my time than having my ideas insulted without giving me anything to think about. Or perhaps I should say, "everything you are going to say on this thread is wrong, just google it."


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## niko (Jan 28, 2004)

The spirit of argument is horrible isn't it?

Now that the sporadic opposition is lost we are on to bigger and better things. Maybe. It depends on our open minds.

Hopefully the 3 threads hinting about some "secret" knowledge have done their job - at least some people are now aware that:

*1. There are 2 groups of bacteria that take care of the dirt in our tanks.*
*2. It's a good idea to pay attention to any information about biofiltration that we come across.*

Dummy Question #4 will touch on "someting completely different" - substrate.

--Nikolay


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## mudboots (Jun 24, 2009)

This is some good "un-discussion", and I hope Dan isn't really offended to the point that he's bowing out for good. 

On one hand I see the frustration, on the other, I happen to be one of those folks who can actually learn this way, seeing the ideas of differing points of view typed out vaguely, leaving lots of room for "hmmmmm, I wonder...", so I can absorb it and research, rather "google" it, at my leisure. So for several knowledgable people to go back and forth helps the folks like me who really didn't know what they were getting into in the first place.

Regarding filtration, I have always thought of it as the enemy of low maintenence (obviously realizing that some may see it as the shining key to their respective systems). If I need filtration it's because there's something in the water I don't want, so if the filter breaks down I'm in trouble. If I can figure out what's in there that I don't like (excess "stuff"), where it's coming from (fish, feeding, et cetera), how to utilize it instead of remove it (bacteria, plants...), how much, and on and on, then I'll have the perfect tank (for me, and me only since we all have very different ideas and goals). Of course at the moment I still have mildly green water with a healthy stand of various algaes, so obviously I've got something wrong. So many things to try to balance...and I will admit as well that I am one of those who was not aware of what types of bacteria I had, only that there were bacteria in there, hopefully happy, and hopefully doing their jobs.

Note - also on filtration, something I am trying on a 10 gallon (only 5 gallons of water though) newt-arium, because I have a small in-the-tank filter for the "water fall" effect, is using the small, black, large-pored insert that usually comes with these filters without any carbon packs (the white inserts). I'm wondering if this will lead to a bacterial colony in the matrix of the larger mesh to polish the water without ever clogging. So far so good, but this has only been a couple months, and it's not really comparable to true aquarium conditions because the water also beats against rock and has lots of air exposure.


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## Diana K (Dec 20, 2007)

"I exclude DianaK because I know nothing about The-El-Das Natural."

Very small note.. I sounds like you are confusing me with Diana Walstad. Probably not, but it just sounds a bit like it.

We are separate people. She might be on the list of people who have influenced this hobby. (She sure is on MY list!) 
I certainly would not be on anyone's list of 'influencing the aquarium hobby'


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## Andy Ritter (Nov 26, 2008)

niko said:


> Japanese and German know-how don't matter. The Japanese know only how to make cool tanks and market them smart. *Germans only know how to make overrated Eheim filters and ugly looking tanks*.


Whoa, Nikolay, what's up with that comment? I realize that everyone is entitled to their own opinions, but there really isn't any need for cheap shots. I personally love the way the German tanks look. One of my first planted tank books was The Optimum Aquarium, and I think that there are lots of examples of beautiful aquariums in it. As far as opinions go, I personally don't care for the way Iwagumi styled tanks look (not to mention that I would bet that if you could ask the fish what they thought, that they would prefer to have some hiding places so they would feel more comfortable). However, I don't care what type of planted tank makes anyone else happy. The only one that I'm concerned about is in my den, and the only person that has to like it is me (well, my wife has some say so as well). The main difference is that I'm not going to publicly criticize an entire way of setting up an aquarium.

Andy


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## niko (Jan 28, 2004)

Andy,

Throughout all these Dummy writings I use double talk. That is typing one thing, meaning another. Serving everything on a plate, clear and easy to digest does no good to anyone.

In the quote that you pointed out I make fun of extreme opinions. I exagerate the notion that all Japanese tanks/equipment are nice and all German tanks/equipment are obsolete looking and ugly. 

Here's a valuable information that could be a starting point for someone's fruitful journey: Everything that I hint about in the 10 Dummy Questions is information taken from Japanese and German sites. It's information as valuable as it can be. As proven as it can be. And it's out there for anyone to find and read. Exactly what we need to know if we could get rid of extreme opinons and open our minds about this hobby.

So I hope now you see understand more why I find it amusing to make fun of extreme opinions. Just trying to force people to read my posts more carefully and hopefully make them have their own opinion.

--Nikolay


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## goldier (Feb 13, 2010)

I’m quite amused at reading these threads. Ah, the frustration through the great effort to achieve the perfection may have led some people to abandon all unnecessarily (and costly) strapping of accessories, and to return to the nature of a pond in the woods. When my water at home is in trouble, I’d go ask the pond fairy – she has never disappointed me


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## Reginald2 (Feb 8, 2009)

I enjoyed the dummy series, even if they were a little bloviated . Interesting and fun, what more do you want for nothing?


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