FW Nitrification discovery--Archaea, not Bacteria - Tropical Fish Keeping - Aquarium fish care and resources
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post #1 of 4 Old 12-15-2012, 05:41 PM Thread Starter
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FW Nitrification discovery--Archaea, not Bacteria

I have referenced this in a couple of threads, but given the immense significance I think it deserves its own thread.

Nitrification is the oxidation of ammonia into nitrite and then the oxidation of nitrite into nitrate. For decades, aquarists have assumed that nitrification was carried out by bacteria, usually deemed to be Nitrosomonas (ammonia to nitrite) and Nitrobacter (nitrite to nitrate). Dr. Tim Hovanec (1996) led a team of scientists that determined the second stage was actually carried out by Nitrospira in aquatic (as opposed to soil) environments. Nitrosomonas was confirmed to be present in marine environments but could not be detected in freshwater; subsequent research (2001) confirmed that Nitrosomonas bacteria could be enriched from freshwater, so it was assumed to be the bacteria strain responsible for FW nitrification.

[Edit: Just occurred to me to mention here that prior to Dr. Hovanec's work, or perhaps a bit earlier, most had assumed aquatic nitrification followed soil nitrification, hence the "assumed" bacteria. Dr. H proved that absolutely incorrect, and several subsequent studies by other scientists have not proven him wrong but confirmed his findings.]

Since the discovery of ammonia-oxidizing archaea (AOA) in 2008, scientists have been studying anew the nitrification process in marine and freshwater habitats. Earlier this year (2012), a team of biologists at the University of Waterloo (Waterloo, Ontario) published the results of their study which revealed that, based on amoA gene abundances, AOA were the dominant putative ammonia oxidizers in the majority of freshwater and saltwater aquaria. These results provide first evidence for the important role of AOA in freshwater aquarium filtration and suggest possible niche adaptation of AOA to conditions associated with freshwater aquarium biofilters [cited from the Introduction to the scientific paper].

For those interested, here is the complete study; the Introduction and Results sections are easier to follow and contain some very useful information.
PLOS ONE: Aquarium Nitrification Revisited: Thaumarchaeota Are the Dominant Ammonia Oxidizers in Freshwater Aquarium Biofilters

Archaea used to be classed with bacteria in the prokaryote group of organisms, but they now constitute a distinct domain of single-celled organisms.

What this means in terms of many of the oft-repeated assumptions on nitrification and bacteria I don't know, but we should be prepared for some significant re-thinking in this area.


Byron Hosking, BMus, MA
Vancouver, BC, Canada

The aquarist is one who must learn the ways of the biologist, the chemist, and the veterinarian. [unknown source]

Something we all need to remember: The fish you've acquired was quite happy not being owned by you, minding its own business. If you’re going to take it under your wing then you’re responsible for it. Every aspect of its life is under your control, from water quality and temperature to swimming space. [Nathan Hill in PFK]

Last edited by Byron; 12-15-2012 at 06:51 PM.
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post #2 of 4 Old 12-15-2012, 06:42 PM
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Vigdis Torsvik, a scientist I have long admired (in my line of work) is at the forefront of research regarding the aquatic and soil dwelling archaea nitrifyers (& mineralizers)
Centre for Geobiology :: UiB
Ammonia-loving Archaea Win Landslide Majority

Planet's Nitrogen Cycle Overturned By 'Tiny Ammonia Eater Of The Seas'

Sure makes us realize we don't have even one tenth of the facts.
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post #3 of 4 Old 12-15-2012, 07:50 PM
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"Bacterial amoA genes were abundant in both supplements, but thaumarchaeal amoA and 16S rRNA genes could not be detected." [bacterial supplements for aquariums]
"and in 12 of these biofilters AOA contributed all detectable amoA genes."
Hmm, maybe that explains why those bacterial supplements for instant cycle do not always work..
Just read the abstract so far, will print it and read it all later.

taking a break from fish-keeping.
3 lovely male betta still keep me company.
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post #4 of 4 Old 12-15-2012, 08:10 PM
"A rose by any other name"?
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