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  1. Psinet

    Psinet Member

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    I decided I would start a topic on archaea, as noone seems to know anything about them and they are DEFINITELY affecting our aquaponics system. There is no dispute about this and I am rather bemused to find the "gurus" have never mentioned them - considering the dogma floating around regarding Nitrosomonas sp etc.

    Paraphrased between wikipedia and me:

    Archaea (/ɑrˈkiːə/ ar-KEE-ə) are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon (sometimes spelled "archeon"). They have no cell nucleus nor any other membrane-bound organelles within their cells. In the past they were viewed as an unusual group of bacteria and named archaebacteria, but the Archaea have an independent evolutionary history and show many differences in their biochemistry from other forms of life and so they are now classified as a separate domain in the three-domain system. In this system the phylogenetically distinct branches of evolutionary descent are the Archaea, Bacteria and Eukaryota (ie everything else - you and me included).

    Archaea use a much greater variety of sources of energy than eukaryotes (funghi etc): ranging from familiar organic compounds such as sugars, to ammonia, metal ions or even hydrogen gas. Archaea reproduce asexually and divide by binary fission, fragmentation, or budding; unlike bacteria and eukaryotes, no known species form spores.

    Initially, archaea were seen as extremophiles that lived in harsh environments, such as hot springs and salt lakes, but they have since been found in a broad range of habitats, including soils, oceans, and marshlands. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are now recognized as a major part of Earth's life and may play roles in both the carbon cycle and the nitrogen cycle.

    One example is the methanogens that inhabit the gut of humans and ruminants, where their vast numbers aid digestion. Methanogens are used in biogas production and sewage treatment, and enzymes from extremophile archaea that can endure high temperatures and organic solvents are exploited in biotechnology. By the end of the 20th century, microbiologists realized that archaea is a large and diverse group of organisms that are widely distributed in nature and are common in much less extreme habitats, such as soils and oceans.

    Archaea exist in a broad range of habitats, and as a major part of global ecosystems, may contribute up to 20% of earth's biomass (!!!!!!!!!!!!!!!!!!!!!!!!!!!). The first-discovered archaeans were extremophiles. Indeed, some archaea survive high temperatures, often above 100 °C, as found in geysers, black smokers and oil wells. Other common habitats include very cold habitats and highly saline, acidic, or alkaline water. However, archaea include mesophiles that grow in mild conditions, in marshland, sewage, the oceans and soils.

    Figured I would just point out that these organisms are also powering our systems. They are everywhere, and are doing an appreciable % of the earths chemical processes - possibly the MOST of any organism, including the "magical" nitrosomonas and nitrobacter.

    https://uwspace.uwaterloo.ca/bitstream/handle/10012/8239/Szabolcs_Natasha.pdf?sequence=1

    Edit: grammar/spelling/added research link
     
    Last edited: Nov 28, 2014
  2. Psinet

    Psinet Member

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    So in other words - our AP systems are overflowing with mesophile archaea which are helping power the "nitrogen cycle" amongst a host of other processes.
     
  3. Wendy in BC

    Wendy in BC New Member

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    Psinet,

    I don't have the time to google at the moment but wondered if these are a branch of prokaryotes or have they renamed prokaryotic organisms .... i'm a bit surprised that I haven't heard the term archaea?
     
  4. Psinet

    Psinet Member

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    No Wendy, they are not prokaryotes (that is - in the sense that we understand them), and that is what makes them so interesting.

    I too am suprised no APers have heard of them.
     
    Last edited: Mar 27, 2011
  5. Wendy in BC

    Wendy in BC New Member

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    Thank you, tormorrow I'll have to spend some time googling
     
  6. Psinet

    Psinet Member

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    Wiki:
    Classification is still difficult, because the vast majority have never been studied in the laboratory and have only been detected by analysis of their nucleic acids in samples from the environment. Although archaea have, in the past, been classed with bacteria as prokaryotes (or Kingdom Monera), this classification is regarded by some as outdated.[1]

    ^This is pretty much widely accepted now. But then some still argue for a flat earth.
     
  7. trout

    trout New Member

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    Hi Psinet

    I get the general impression that archaea is a very important microorganism to you.
    I am however not certain of its importance or relevance to aquaponics.
    At the end of the day we need to turn our ammonia to nitrate and that is all.

    What I suspect is far more important is how can we increase the efficency of the
    process and for that, knowing the name of the microorganism is irrelevant.

    Now I went out last night and only basically crawled out of bed now.
    Was I shocked to see that World War Three had started and nobody told me!!!!!!!!

    So let us look back over a bit of time.

    Can I draw your attention to this thread and post #33


    http://www.aquaponics.net.au/forum/showthread.php?p=23613&highlight=bacteria#post23613

    interesting who the poster is.


    At the end of my Uni course my lecturer told us to that we should understand that

    The more you know the more you realise you know nothing.

    with this in mind can I suggest you have a look at this thread.

    http://www.nature.com/ngeo/journal/v2/n9/full/ngeo613.html


    I am certain that archaea plays a role, what that role is, still needs studing

    Maybe in 20 years time we may find a totally different organism responsible.

    cheers Lou
     
  8. trout

    trout New Member

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    OK what is wrong with this forum?

    my quotes or links are not working?
     
  9. Gratilla

    Gratilla Member

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    See this:

    http://www.aquaponics.net.au/forum/showthread.php?t=2275
     
  10. Psinet

    Psinet Member

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    Archaea are important to the planet, hence me and aquaponics. And you.

    Understanding a system is the ONLY way to make it more efficient or have any desired control.

    They are definitely in our systems, and definitely have an effect. Knowing the name of the organism is obviously the first step towards improving the conditions for it.

    And that is what I am pointing out - science is not just A key to aquaponics...it is THE key.

    There is no mention of archaea on this forum, and it is very possible they play a greater role in the chemical cycle than the oft reffered candidates.
     
  11. trout

    trout New Member

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    Hi Psinet

    Due to the inability of this forum to link or highlight quotes it makes posting somewhat difficult, hence I am afraid this post will be somewhat verbose.

    I agree that Archaea are important as is everything on earth to maintain the fine equilibrium.
    [It could be argued that humans are not necessay {global warming} but lets no go there]

    you stated knowing the name is the first step, I would have thought knowing its actions
    was the first, then its structure the second again name is irrelevant.

    You stated [,There is no mention of archaea on this forum] that is true but a post of 8th February 2011 suggests something along those lines

    I have copied it below:

    Kewl... good to see another reference to the role of Nitrospira as the nitrifying bacteria responsible in the nitrogen cycle...

    I wrote this up in the BYAP mag some time ago.... but nobody seemed to pick it up...

    Basically, recent research suggests that the commonly held view of the nitrogen cycle... is wrong... or at least partially wrong...

    quote ends.

    This was post #33 on Wendys thread of filtration and was submitted by RupertofOz
    So although the name Archaea wasnt mentioned its actions were.

    Having a science background I always like to see proper studies done and not if possible rely on Wiki.
    [ please note I do like Wiki]

    The most recent journal paper that I could find was printed on 30 August 2009

    I have copied it below:

    Nature Geoscience 2, 621 - 624 (2009)
    Published online: 30 August 2009 | doi:10.1038/ngeo613

    Subject Category: Biogeochemistry

    *
    Search Pubmed for
    o H. J. Di
    o K. C. Cameron
    o J. P. Shen
    o C. S. Winefield
    o M. O’Callaghan
    o S. Bowatte
    o more authors of this article

    Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils

    H. J. Di1, K. C. Cameron1, J. P. Shen2, C. S. Winefield3, M. O’Callaghan4, S. Bowatte5 & J. Z. He2

    Abstract

    The oxidation of ammonia to nitrate, nitrification, is a key process in the nitrogen cycle. Ammonia-oxidizing archaea are present in large numbers in the ocean1, 2, 3 and soils4, 5, 6, suggesting a potential role for archaea, in addition to bacteria, in the global nitrogen cycle7, 8. However, the importance of archaea to nitrification in agricultural soils is not well understood4. Here, we examine the contribution of ammonia-oxidizing archaea and bacteria to nitrification in six grassland soils in New Zealand using a quantitative polymerase chain reaction. We show that although ammonia-oxidizing archaea are present in large numbers in these soils, neither their abundance nor their activity increased with the application of an ammonia substrate, suggesting that their abundance was not related to the rate of nitrification. In contrast, the number of ammonia-oxidizing bacteria increased 3.2–10.4-fold and their activity increased 177-fold, in response to ammonia additions. Indeed, we find a significant relationship between the abundance of ammonia-oxidizing bacteria and the rate of nitrification. We suggest that nitrification is driven by bacteria rather than archaea in these nitrogen-rich grassland soils.

    end of article.


    So, this article shows scientists that disprove the link between nitrification and archaea.

    Is this the end of the story, I hope not, But I for one will wait until all the studies are in.

    cheers Lou

    PS: I apologise for the verbosity.
     
  12. Psinet

    Psinet Member

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    No apology for verbosity needed - I have no problems with long posts.

    This is an interesting article and I also discovered it recently.

    Science and research are the key to understanding, I am sure you agree.

    Here is an abstract from another study showing why the study you referenced may have came to the conclusion they did:

    Archaea are able to perform different reductive pathways of the N-cycle, including both assimilatory processes, such as nitrate assimilation and N2 fixation, and dissimilatory reactions, such as nitrate respiration and denitrification. However, nitrogen metabolism is much less known in archaea than in bacteria. The availability of the complete genome sequences of several members of the eury- and crenarchaeota has enabled new approaches to the understanding of archaeal physiology and biochemistry, including metabolic reactions involving nitrogen compounds. Comparative studies reveal that significant differences exist in the structure and regulation of some enzymes involved in nitrogen metabolism in archaea, giving rise to important conclusions and new perspectives regarding the evolution, function and physiological relevance of the different N-cycle processes.

    So, as I would have suspected, they are not just competing with bacteria - they are co-existing with them and performing different functions, but still within the C and N-cycle process.
     
    Last edited: Oct 31, 2015
  13. trout

    trout New Member

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    Hi Psinet

    The article you quote only says they are different to bacteria and that nitrogen metabolism is much less known in archaea than in bacteria. So any importance to the nitrification ability of archaea is pure speculation.

    I fail to see the point you are trying to make.

    archaea is relatively new and we know very little about it.
    Is it important it might be
    Is it useless, it might be.

    We need more studies.

    cheers Lou
     
  14. Psinet

    Psinet Member

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    .......

    Archaea are able to perform different reductive pathways of the N-cycle.

    Comparative studies reveal that significant differences exist in the structure and regulation of some enzymes involved in nitrogen metabolism in archaea, giving rise to important conclusions and new perspectives regarding the evolution, function and physiological relevance of the different N-cycle processes.

    The point is science.

    Should I just find my own little hole in a thread and hide there with my experimentation since it is apparent it isn't very interesting or relevant to you?

    Edited: Grammar
     
    Last edited: Oct 31, 2015
  15. RupertofOZ

    RupertofOZ New Member

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    You can find the article I wrote concerning "nitrospira" in BYAP Magazine Issue 5 - May 2009... Titled "Is the accepted view of Nitrification a Myth"... page 18....

    The article is complete with cited references.... and other research has since been posted that confirms the role of "nitrospira" in conversion of nitrites to nitrates... rather than the long held view that nitrobacter are the principle nitrifying bacteria...
     
  16. Wendy in BC

    Wendy in BC New Member

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    Yes John, I remember that the microbes traditionally thougt to be involved in nitrification are infact not and remain anonymous
     
  17. trout

    trout New Member

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    Hi Psinet

    All you have done is copy and paste the last two lines of the article.

    There is no proof that archaea contribute a major part of the nitrification process in
    aquaponics.

    The article that I posted proves that side by side bacteria do a much better job.
    This was a scientific test.

    maybe if bacteria is not present archaea will step up and take over but so far
    all the proof that I have seen suggests that archaea are NOT that important in
    aquaponics.

    cheers Lou
     
  18. Psinet

    Psinet Member

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    I am not trying to prove archaea are better or worse than bacteria.

    I am making no points regarding them at all, besides.....

    ....noone has ever mentioned them, and they play a role in chemical processes in our AP systems.

    I reposted the article points because I thought they were self explanatory. They play a DIFFERENT role in the N cycle. As it states.
     
  19. RupertofOZ

    RupertofOZ New Member

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    The reference quoted by Psinet comes from a 2004 paper by Cabello, Roldan & Moreno-Vivian... (full paper cited below)...

    It begins by reaffirming the basis of the nitrogen cycle... which includes both nitrification and denitrification as parts of the complete cycle...

    And while most discussion here and on other forums focuses on the nitrification aspects of the nitrogen cycle.. as it applies to aquaponics....

    There has also been considerable discussion in past years with regard to "denitrification"... particularly during the early years of the BYAP forum...

    And the respective roles of aerobic, heterotrophic, anaerobic and even anammoxic processes... and distinctions between aquaponics and wastewater treatments where the latter two processes have much greater relevance...

    While the paper notes that Archaea may have both an assimilatory pathway, like N2 fixation and nitrate assimilation.. (such as occurs in legume nitrogen fixation)... and dissimilatory reactions, such as nitrate respiration and denitrification... essentially the anaerobic reduction of nitrates to nitrogen (N2) or nitrous oxide (NO2)....

    They begin their introduction with the caveat that little is known of such mechanisms by Archaea.... and that they primarily occur in extreme conditions...

    Psinet is correct that such "reductive" processes are an essential part of both the "nitrogen" and "carbon" cycles... essentially breaking down, putrifying, rotting and recycling those elements back into nature....

    Archaea may well serve a part in such functions, as do various other bacteria, and most certainly most fungii...

    But essentially, there is little to suggest that under normal aerobic circumstances that exist and encouraged in a balanced aquaponics system... any great degree of anaerobic denitrifrication processes occur.... they may well in some small degree...

    But I would suggest that any such occurances beyond some small degree... are not to be recommended, or encouraged... and generally represent a system that is (within an aquaponics context)... out of balance..

    And that point has been made frequently on various forums...

    Past discussions on BYAP regarding denitrification were raised by Janet Peltier, and similarly recently here by Wendy... with regard to high nitrate levels.... not a normal situation in most aquaponic systems... and a situation that has never been referenced in literature as having any adverse effects on fish health beyond levels of 450ppm+....

    Interestingly the paper cited below.. refers to the reductive processes of denitrification requiring Iron, Sulpher and Carbon... and a complete thread, while not actually naming Arcaea as such... was dedicated to incorporating a "filter" into an aquaponics system as a means of denitrification... by addition of those very elements... to lower nitrate levels...

    (Search the BYAP forum for "RSG Filter"...)

    Similarly, and I have previously posted in this regard also... admittedly without knowledge or reference to Archaea as the mechanism.... discussion has occurred on many of the koi keeping forums with regard to the use of "Bakki Showers"... not only for oxygenation, filtration, and cooling... but for supposed benefits of denitrification.... the breakdown of nitrate levels...

    Indeed I incorporated a crude implementation of a "Bakki Shower" into my trout system... for all of the reasons above....

    To conclude....

    Arcaea may well be present to some degree in aquaponics systems.. perhaps even in a "balanced" system....

    But with even the esteemed microbiologists suggesting that little is known of the processess involved...

    What practical purpose could be served by trying to encourage anaerboic or ananomoxic conditions in an aquaponics system... merely to invoke denitrification.... to breakdown nitrates...

    Why would we not instead just encourage aerobic nitrification.. to produce nitrates.... and grow more plants....


    Reference : http://mic.sgmjournals.org/cgi/reprint/150/11/3527.pdf


    .
     
    Last edited: Mar 28, 2011
  20. Psinet

    Psinet Member

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    But....the archaea proposed are aerobic.....

    In regards to any more questions regarding this topic, I would like to introduce you to some recent and directly relevant research.

    https://uwspace.uwaterloo.ca/bitstream/handle/10012/8239/Szabolcs_Natasha.pdf?sequence=1

    "In one filter, AOA were the only ammonia-oxidizers detected in the biofilm during aquarium development, suggesting that AOA were the sole contributors to nitrification in this aquarium. "

    "In start-up aquaria, early ammonia concentrations increased with fish biomass, and AOB amoA genes were strongly detected over AOA marker genes in all filters without initial AOA inoculation. Inoculation of AOA-dominated supplements into newly established biofilters improved early ammonia oxidation rates in comparison to filters supplemented with AOB or those lacking supplements."

    ...and much, much more.

    I think this paper should at least end debate on the matter and allow us to move forward.

    Furthermore, I feel that it validates my initial claims - many times over.

    I can not begin to number the times that I was lectured on 'AOB's' and nitrification whenever I proposed this over the past few years.

    The reality is, archaea are not just potentially ammonia-oxidizers - they are a given in any balanced aquaponics system and are quite likely to be THE dominating contributor to the nitrification process.

    All credit to Natasha Alexandria Szabolcs
     
    Last edited: Oct 27, 2015

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