[Taxacom] Three kinds of bacteria (Negibacteria the oldest)

[Kenneth Kinman]

Dear All,

       This afternoon I found a more recent (2014) paper by Cavalier-Smith online.  It seems that Chloroflexi turned out to be primitive Posibacteria, not primitive Negibacteria.  Therefore, he now accepts that the root of the universal tree life lies within Posibacteria, making it a bit older than the Negibacteria.  However, the Archaebacteria are still the youngest of the three kinds of bacteria. and being a misnomer, perhaps more researchers will begin using a qualifier such as "a.k.a. Metabacteria".


        As for the Three Domain classification, Cavalier-Smith really takes Woese to task, saying "Likewise, his fundamental misinterpretations of the tree of life and the evolutionary significance of archaebacteria that so severely misled a generation of researchers will not maintain their distorting stranglehold over phylogenetic thinking, if the rising generation of vigorous, less-prejudiced younger researchers demands proper emphasis on cell-biological, palaeontological, and 3D ultrastructural and crystallographical evidence of molecular morphology (Jékely 2006<http://cshperspectives.cshlp.org/content/6/9/a016006.full#ref-128>, 2008<http://cshperspectives.cshlp.org/content/6/9/a016006.full#ref-129>; Valas and Bourne 2009<http://cshperspectives.cshlp.org/content/6/9/a016006.full#ref-203>; Keeling 2013<http://cshperspectives.cshlp.org/content/6/9/a016006.full#ref-136>), in addition to the limited presently dominant one-dimensionality of sequences, when reconstructing the history of life."

        And he also says: "My key distinction was ignored for decades, partly because Woese’s repeated historically inaccurate, naïve tirades against morphology (Woese 1994<http://cshperspectives.cshlp.org/content/6/9/a016006.full#ref-215>) led many biochemists to ignore bacterial envelope biology. Confusions caused by such myopia are clearing."


Here are weblinks to Figure 3 and to the whole paper:


http://cshperspectives.cshlp.org/content/6/9/a016006/F3.expansion.html

http://cshperspectives.cshlp.org/content/6/9/a016006.full


________________________________
From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of Kenneth Kinman <kinman at hotmail.com>
Sent: Friday, December 15, 2017 12:49 PM
To: taxacom
Subject: Re: [Taxacom] Three kinds of bacteria (Negibacteria the oldest)

Hi Tony,

        I would assume that Cavalier-Smith argued against this splitting up of the Unibacteria (Posibacteria in Bacteria and Archaebacteria in Archaea).  But the 2015 classification is a consensus, and I can only hope future versions will not split up the Unibacteria.

        I do like the primary division of life into Superkingdoms Prokaryota and Eukaryota (sometimes referred to as Empires instead of Superkingdoms).  Superkingdoms and Empires are fine, but category Domain carries too much baggage.

        Like Ernst Mayr, I prefer Archaebacteria over Archaea, but there is nothing really archaic about it.  I guess it too late to adopted the name Metabacteria (proposed about 1990), so we're probably stuck with Archaebacteria.

                         ----------------Ken


________________________________
From: Tony Rees <tonyrees49 at gmail.com>
Sent: Friday, December 15, 2017 12:21 PM
To: Kenneth Kinman
Cc: taxacom
Subject: Re: [Taxacom] Three kinds of bacteria (Negibacteria the oldest)

Hi Ken,

In Ruggiero et al's 2015 classification of living organisms (on which T. Cavalier-Smith is an author), Archaea and Bacteria are recognised at kingdom level, with no subkingdoms defined in Archaea, and subkingdoms Negibacteria and Posibacteria recognised in Bacteria. All are in "superkingdom" Prokaryota, as opposed to Eukaryota (for the other/big stuff).

Quoted from that paper:
"We have chosen to adopt the classification in current use by the Catalogue of Life. It is derived from the TOBA [Taxonomic Outline of Bacteria and Archaea] and recognizes Bacteria and Archaea as equivalent in rank to the eukaryote kingdoms." (Elsewhere is is noted that TOBA and List of Prokaryotic Names with Standing in Nomenclature (LPSN) "treat Bacteria and Archaea as separate domains but are silent about the category of kingdom".)

That is the explanation offered, not sure if it answers your question...

Best regards - Tony

Tony Rees, New South Wales, Australia
https://about.me/TonyRees



On 16 December 2017 at 04:21, Kenneth Kinman <kinman at hotmail.com<mailto:kinman at hotmail.com>> wrote:
Dear All,
        I am puzzled why the prokaryotes are still classified as Domains Bacteria and Archaea.  The most fundamental divide should actually be between Negibacteria (which possess the outer negibacterial membrane) on the one hand, and the Posibacteria and Archaebacteria (which have lost that outer membrane).   Cavalier-Smith 1998 proposed the name Unibacteria for Posibacteria + Archaebacteria (since they have only the one membrane, not two).
      Cavalier-Smith, 2006 ("Rooting the tree of life by transition analyses") shows that Negibacteria are the oldest of the three taxa, and Archaebacteria are actually the youngest.   I am pretty sure that is why eubacterial trees are so screwed up, because using Archaebacteria as the outgroup will misroot them (Archaebacteria are actually an ingroup, not an outgroup).
      Anyway, the names Negibacteria and Posibacteria were proposed 30 years ago (Cavalier-Smith, 1987), and they are excellent names which subdivide the Eubacteria into two large and important taxa.  So why aren't they being used in databases like Catalogue of Life and NCBI's Taxonomy Browser, etc. ?  The Three Domain classification of life is outdated and should have been discarded a long time ago.
                    -----------------Ken Kinman
Cavalier-Smith, 2006:
        https://openi.nlm.nih.gov/detailedresult.php?img=PMC1586193_1745-6150-1-19-2&req=4

Evolutionary relationships among the four major kinds o | Open-i<https://openi.nlm.nih.gov/detailedresult.php?img=PMC1586193_1745-6150-1-19-2&req=4>

openi.nlm.nih.gov<http://openi.nlm.nih.gov>
Evolutionary relationships among the four major kinds of cell. The horizontal red arrow indicates the position of the universal root as inferred from the first



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