Ammonia to N2 gas?

[ReeferAl]

Randy,
In another forum this statement was made:

Denitrification requires full nitrification as its predecessor, as only nitrate can be converted to N2 gas. Ammonia and nitrite can't be directly converted to N2.

Is this true? It seems like I have seen that process delinealted somewhere, NH3 to N2. It's been a long time since my undergrad chemistry (it was actually my major long ago) and I don't know if the statement is factual or BS. Can you clear this up?
Thanks.
Allen

[Boomer]

That is incorrect, as the bacteria A. faecalis, for example, can convert ammonia into N2 gas through heterotrophic nitrification.

[ReeferAl]

Thanks. That's what I thought.
Allen

[Randy Holmes-Farley]

I do not know what actually happens in typical reef aquaria with respect to such details of the nitrogen cycle, and I expect that such details are not generally established. What could happen and what does actually happen are not necessarily the same.

I'm not even sure that the question is clear. If a single bacteria took up ammonia, and after several biochemical steps involving internal nitrite and nitrate, released N2, would that qualify as a yes, or is the statement intended to have ammonia be converted into N2 in a single biochemical event?

That said, it is certainly true that many organisms can take up ammonia and use it as a nitrogen source. Macroalgae, for example, can do that.

Thanks, Boomer. :)

[Mr_Quality]

Hi Randy, Boomer,

It was me who made that wild assertion. LOL. :lol:

Randy,
You are absolutely on the right track. My point was that nitrate production needs to precede conversion to N2 . A. faecalis can take ammonia all the way through to N2, but it does so stepwise, with the last step being reduction of nitrate to N2 via the enzyme, nitrate reductase.

ReeferAl,
FYI, I'm not exactly a novice in this discipline. I am a biochemist working for Becton Dickinson, a market leader in microbiological products.

[Randy Holmes-Farley]

Here's an interesting reference, followed by some of the most recent ones that I can find on the subject:


Interactions of manganese with the nitrogen cycle: alternative pathways to dinitrogen. Luther, George W., III; Sundby, Bjorn; Lewis, Brent L.; Brendel, Paul J.; Silverberg, Norman. College Marine Studies, University Delaware, Lewes, DE, USA. Geochimica et Cosmochimica Acta (1997), 61(19), 4043-4052.

Abstract

The conversion of combined nitrogen (ammonia, nitrate, org. nitrogen) to dinitrogen (N2) in marine sediments, an important link in the global nitrogen cycle, is traditionally assumed to take place only via the coupled bacterial nitrification-denitrification process. We provide field and lab. evidence that N2 can also be produced by the oxidn. of NH3 and org.-N with MnO2 in air. The reduced manganese formed in this reaction readily reacts with O2, generating reactive Mn(III, IV) species to continue the oxidn. of NH3 and org.-N to N2. Free energy calcns. indicate that these two reactions are more favorable as a couple than the oxidn. of org. matter by O2 alone. We also provide field evidence consistent with the redn. of NO3- to N2 by dissolved Mn2+. These two reactions involving nitrogen and manganese species can take place in the presence and absence of O2, resp. Our field evidence suggests that the oxidn. of NH3 and org.-N to N2 by MnO2 in the presence of O2 can outcompete the oxidn. of NH3 to NO3- in Mn-rich continental margin sediments and thereby short-circuit the nitrification/denitrification process. The MnO2 catalyzed reaction may account for up to 90% of the N2 formation in continental margin sediments, the most important N2 producing environments in the marine N cycle. The oxidn. of NH3 and org.-N by MnO2 in the presence of O2 can explain why N2 can form in oxic sediments; it can also explain why denitrification rates measured by acetylene inhibition and labeled tracers can give lower ests. than direct measurements of N2 prodn.


Anoxic nitrification in marine sediments. Mortimer, Robert J. G.; Harris, Sansha J.; Krom, Michael D.; Freitag, Thomas E.; Prosser, James I.; Barnes, Jonathan; Anschutz, Pierre; Hayes, Peter J.; Davies, Ian M. Earth and Biosphere Institute, School of Earth Sciences, University of Leeds, Leeds, UK. Marine Ecology: Progress Series (2004), 276 37-51.
Abstract

Nitrate peaks are found in pore-water profiles in marine sediments at depths considerably below the conventional zone of oxic nitrification. These have been interpreted to represent non-steady-state effects produced by the activity of nitrifying bacteria, and suggest that nitrification occurs throughout the anoxic sediment region. In this study, SNO3 peaks and mol. anal. of DNA and RNA extd. from anoxic sediments of Loch Duich, an org.-rich marine fjord, are consistent with nitrification occurring in the anoxic zone. Anal. of ammonia oxidiser 16S rRNA gene fragments amplified from sediment DNA indicated the abundance of autotrophic ammonia-oxidising bacteria throughout the sediment depth sampled (40 cm), while RT-PCR anal. indicated their potential activity throughout this region. A large non-steady-state pore-water SNO3 peak at .apprx.21 cm correlated with discontinuities in this ammonia-oxidiser community. In addn., a subsurface nitrate peak at .apprx.8 cm below the oxygen penetration depth, correlated with the depth of a peak in nitrification rate, assessed by transformation of 15N-labeled ammonia. The source of the oxidant required to support nitrification within the anoxic region is uncertain. It is suggested that rapid recycling of N is occurring, based on a coupled reaction involving Mn oxides (or possibly highly labile Fe oxides) buried during small-scale slumping events. However, to fully investigate this coupling, advances in the capability of high-resoln. pore-water techniques are required.

[Randy Holmes-Farley]

This reference typifies the kind of studies that indicate that a whole lot more may be going on than the simple process that are usually discussed in aquarium books:

Community structure of ammonia-oxidizing bacteria within anoxic marine sediments. Freitag, Thomas E.; Prosser, James I. Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK. Applied and Environmental Microbiology (2003), 69(3), 1359-1371.

Abstract

The potential for oxidn. of ammonia in anoxic marine sediments exists through anaerobic oxidn. by Nitrosomonas-like organisms, utilizing nitrogen dioxide, coupling of nitrification, managanese redn., and anaerobic oxidn. of ammonium by planctomycetes (the Anammox process). Here we describe the presence of microbial communities with the potential to carry out these processes in a natural marine sediment system (Loch Duich, Scotland). Natural microbial communities of Planctomycetales-Verrucomicrobia and b- and g-proteobacterial ammonia-oxidizing bacteria were characterized by anal. of 16S rRNA genes amplified using group-specific primers by PCR- and reverse transcription-PCR amplification of 16S rDNA and RNA, resp. Amplification products were analyzed by sequencing of clones and by denaturant gradient gel electrophoresis (DGGE). Amplification of primers specific for Planctomycetales-Verrucomicrobia and b-proteobacterial ammonia-oxidizing bacteria generated products at all sampling sites and depths, but no product was generated using primers specific for g-proteobacterial ammonia-oxidizing bacteria. 16S rDNA DGGE banding patterns indicated complex communities of b-proteobacterial ammonia-oxidizing bacteria in anoxic marine sediments. Phylogenetic anal. of sequences from clones and those excised from DGGE gels suggests dominance of Nitrosospira cluster 1-like organisms and of strains belonging to a novel cluster represented in dominant bands in 16S rRNA DGGE banding patterns. Their presence indicates a group of organisms closely related to recognized b-proteobacterial ammonia-oxidizing bacteria that may be selected in anoxic environments and may be capable of anoxic ammonia oxidn. Sequence anal. of planctomycete clone libraries and sequences excised from DGGE gels also demonstrated a diverse microbial community and suggested the presence of new subdivisions, but no sequence related to recognized Anammox organisms was detected.

[Boomer]

Thanks Randy for the follow up. I was in Minneapolis for New Years and didn't have access to my two new books that sell it out like your abstracts;

Bacterial Biogeochemistry & Microbial Ecology of the Oceans

[a4]

What about the anaomox cycle that is the conversion of ammonium to N2 in a low oxygen environment.

Anammox_biochemistry



"Based on 15N experiments, we have postulated the following mechanism for anaerobic ammonium oxidation: the anammox bacteria reduce nitrite (NO2-) to hydroxylamine (NH2OH). Next, hydroxylamine and ammonium (NH4+) are condensed to hydrazine (N2H4) and water. Finally, hydrazine is oxidized to dinitrogen gas (N2) and the electrons are used to reduce the next molecule of nitrite. Jos Schalk has purified a 183 kD enzyme with 24 haem-c cofactors. This enzyme is able to oxidise both hydroxylamine and hydrazine and is obviously an important player in anammox biochemistry, for it constitutes more than 10% (w/w) of the total cell protein. Currently, we are purifying a nitrite reducing enzyme and a hydrazine producing enzyme."

[Boomer]

Mike

I didn't know how to really reply to that post, ie. Direct from NH3 --> N2 or did he mean a single bacteria could do it. I assumed a single bacteria but yes it is still a stepped process as you said. I liked Randy's remark;

ammonia be converted into N2 in a single biochemical event?



NO

A4

What about the anaomox cycle that is the conversion of ammonium to N2 in a low oxygen environment

That still is not a single event, you are still going through conversion ;) And there is no NO3- in that process also.

the anammox bacteria reduce nitrite (NO2-) to hydroxylamine (NH2OH). Next, hydroxylamine and ammonium (NH4+) are condensed to hydrazine (N2H4) and water. Finally, hydrazine is oxidized to dinitrogen gas (N2)

[a4]

Boomer, I understand that nitrate is not used. The process shows that nitrite is used up in the process and the hydride ions come from the hydrazine.
Those hydride ions are used to reduce another nitrite to hydoxylamine. Then ammonia attacks the hyroxylamine and forms hydrazine ( the protonated hydroxyl group on the hydroxylamine looks like a good leaving group. So water leaves and hydrazine is formed.

[Mr_Quality]

The point I was making in the thread that ReeferAl referenced was that N2 production required nitrate as its substrate. In the classical nitrification-denitrification pathway, that remains true.

Based on the abstracts above though, it appears that there are alternative pathways under study, that do not involve nitrate as a precursor. And that conversion to nitrate can occur in hypoxic environments and that conversion to N2 can occur in O2 rich environments. Those are new learnings for me.

Thanks!
:idea: :idea: :idea: