[Taxacom] Three Domains (was: Diversity of bacteria)

Dr.B.J.Tindall bti at dsmz.de
Thu Feb 9 08:35:24 CST 2012


Ken,
See my comments:

Quoting Kenneth Kinman <kennethkinman at webtv.net>:

> Hi Brian,
>       It is widely accepted that the original eukaryote was
> probably a chimaera formed from a fusion of an archaebacterium and a
> eubacterium, although I believe it is still controversial whether the
> archaebacterial element was the host cell or the nucleus. The close
> relationship of eukaryotes and archaebacteria was initially discovered
> through molecular sequences of the ribosomal machinery from the
> archaebacterial component.

It is widely accepted that there is a mixture of genes in the various  
groups, with eukaryotes containing genes from both members of the  
Bacteria and Archaea, Bacteria containing genes from members of the  
Archaea etc. While there would appear to be good support for the  
endosymbiont hypothesis with regards mitochondria and plastids the  
fusion of Bacteria and Archaea to give eukaryotes seems to be based on  
senarios that started their life as hypotheses where there are a  
number of potential contradictions. While there is evidence in the  
eukaryotes that parts of genomes of the contributing organisms have  
been intergrated to give chimeric genomes, such effects can also arise  
as a result of the uptake of genomic material alone.

>
>        However, many authors have strongly criticized
> Woese and his 3 domains for ignoring the overwhelming similarities
> between eubacteria and archaebacteria.  Ernst Mayr's 1998 paper "Two
> Empires or Three?" is excellent (Proc. Natl. Acad. Sci., 95:9720-9723).
> In the same journal is a paper by Margulis, Dolan and Guerrero, 2000
> ("The chimaeric eukaryote"; Proc. Natl. Acad. Sci., 97:6954-6959), in
> which the first section is entitled "Two Domains, not Three", and they
> give more data on the similarities between eubacteria and
> archaebacteria.

Margulis's work centres on the fusion of a spirochete (Bacteria) with  
a member of the Thermoplasma line of descent (Archaea), explicitly  
indicating in their diagrams that the eukaryote chimera has protein  
and lipids from the Thermoplasma ancestor. Others choose different  
starting organisms. These theories does not take into account that the  
very characteristic membrane lipids found in members of the Archaea  
would have had to have "evaporated" in the eukaryote to explain the  
current situation. There are a couple of hypotheses the suggest that  
the characteristic lipids from the archaeal partner just "evaporated".  
However, as long as a membrane remains intact in such symbioses (as in  
the case of mitochondria and plastids) the membranes retain their  
source organism characteristics. If a member of the Archaea engulfed a  
member of the Bacteria then the cytoplasmic membrane of the chimera  
should have all the hallmarks of the engulfing organism, which is not  
the case ("evaporating" the membrane gives you a dead chimera). The  
other way around there should be a inner membrane (some suggest the  
nuclear membrane) with these properties, which is also not the case.  
If you do lipid extractions of plants or animals one also sees the  
hallmarks of the plastid and mitochondrial membranes.


>
>       Then there are the many papers by R.S. Gupta which are
>
> likewise highly critical of the Three Domain classification, and he
> provides additional data which supports Thomas Cavalier-Smith's
> hypothesis that archaebacteria evolved from a subclade of the
> gram-positive bacteria (although Gupta refers to them as "Monoderms"
> rather than Unibacteria; both terms refer to the fact that they have
> only a single cell membrane, rather than two cell membranes in the
> gram-negative bacteria, which Cavalier-Smith calls Negibacteria and
> Gupta calls "Diderms").

Yes and in the middle of Gupta's "monoderm tree" is a "diderm" which  
most folks have never noticed.......

Cavalier-Smith (categorically) places a fairly late date on the  
evolution of the Archaea, which is much later than the first eukaryote  
multicellular fossils, making it rather tricky for the chimera model  
to work.....

Recent work on a number of mycolic acid containing Gram-positive  
(monoderm) taxa clearly indicate that the mycolic acids are arranged  
in an outer membrane, ie would by structural considerations would also  
be diderms.

Lake has also suggested that double membrane Bacteria arose as a  
fusion of two different Bacteria, implying that the diderm theory  
could also be questioned. Closer reading indicates one or two problems.

>
>       Anyway, these authors and many others may disagree on
> the details (Cavalier-Smith thinks Negibacteria came first and the
> Unibacteria arose by loss of the outer membrane, while Gupta thinks it
> happened the other way around), but they are all strongly critical of
> Woese's "Three Domains" for ignoring all the very fundamental
> similarities between eubacteria and archaebacteria, as well as the
> eubacterial component of the chimaeric eukaryotic cell. Woese should be
> credited for discovering that archaebacteria are a very distinct group
> of prokaryotes, but he went way overboard in elevating them to a
> separate Domain.  This is even more irritating when you consider that
> Hori and Osawa (1982), published their paper almost 30 years ago,
> presenting molecular evidence that there was nothing particularly
> "archaic" about Archaebacteria, and proposed that they be called
> Metabacteria.  That proposal made perfect sense and yet they were
> ignored.  Much of the confusion and the whole Three Domain mess could
> have been avoided if their proposal had been followed.

A key issue in the evolution of cellular systems if the origin of a  
cell membrane. While structurally conserved (in essence a hydrophilic  
- hydrophobic - hydrophilic "sandwich" in which physical limits are  
placed on the thickness of these layers) there are two very basic  
models, one based on the fatty acid model and the other the isoprenoid  
model. If you read recent papers on lipidomics you will see that a  
number of authors are picking up on these two funadamentally different  
pathways. The issue with fatty acids vs isoprenoids linked to glycerol  
is that members of two very different enzymes that carry out the  
linkage of the fatty acids vs that of the isoprenoids. Stereochemistry  
of the glycerol also comes into play which is also relevant at the  
level of the physical packing of lipid layers, which don't like  
racemic mixtures - in fact all biological systems don't like  
uncontrolled stereochemistry. The physical nature of the isoprenoid  
side chains also means that the mechanisms of controlling membrane  
intergrity at the lipid level are different in members of the Archaea  
and Bacteria/Eukarya. Stereochemical considerations also seem to put  
constraints on lipid diversity in members of the Archaea that members  
of the Bacteria do not have. Physics is the final element that tells  
you whether things work when you try to bolt them together.

Lipids can spontaneously organise - try vigorously shaking one  
teaspoon of olive oil in half a litre (one pint) of water and see how  
long the lipid droplets remain in suspension (micelles of varying size  
between that of bacterial and yeast cells form a slightly turbid  
dispension that will last for hours). Do the same thing with a fully  
apolar compound like hexadecane and you won't get a stable dispersion.

If one looks at possible early stages of evolution I would think that  
getting one membrane would be the first step and then adding a second  
a second step. One can, of course loose things by secondary loss.

All changing the name Metabacteria does is to change a name, based on  
the Metabacteria website the author would not support the origin of  
members of the Archaea within the Gram-positives and also clearly  
states that the ancestors of the eukaryotes are the Archaea.

>
>         There is actually no good evidence that I have
> ever seen presented that the so-called archaebacteria are as old as
> (much less older than) the eubacteria, and plenty of evidence to the
> contrary.   Thus Mayr's criticism of Woese for replacing Archaebacteria
> with Archaea (dropping the accurate last part of the name, -bacteria,
> and retaining the inaccurate part, archae-). This has just perpetuated
> the notion that life originated in boiling hot springs or deep-sea
> hydrothermal vents. Many chemists would tell you that this is highly
> unlikely and that life may have actually arisen at the opposite extreme
> (in water near the freezing point). I still prefer something more
> moderate (even the "warm little pond", which I believe originated with
> Darwin).

To a large degree the only way of determining the age of the early  
organisms is by the traces they left behind or by extrapolating  
backwards from known data since the early singled celled forms have  
long since disappeared. As Russel Doolittle's group showed a factor of  
2 in the "estimations" can make a big difference 2 billions years and  
4 billions years (or adding the error in the other direction of 8  
billion years).

Most of the extrapolation about conditions on Earth and the  
requirements placed on the early life forms comes from geological and  
early climate studies/extrapolation.

The interesting thing about hydrothermal vents is the sharp  
temperature gradient that may prevail. The internal water temperature  
may be 250-350°C, but within a few meters the water temperature is  
significantly lower, if this wasn't the case then all those Riftia,  
mussels, crabs and shrimps you see in the documentaries would cook  
within minutes.

>
>        In any case, I would recommend reading the papers
> in Proc. Acad. Nat. Sci. by Mayr and by Margulis, Dolan, and Guerrero.
> These are freely available at the PNAS website (pnas.org). Also R.S.
> Gupta, 1998 ("Life's third domain (Archaea): an established fact or an
> endangererd paradigm"; Theor. Popul.Biol., 54:91-204). Here is a weblink
>
> to the pubmed citation of the Mayr paper (and it has a link to the paper
>
> where it says "Free PMC Article"):
>
> http://www.ncbi.nlm.nih.gov/pubmed/9707542

If the Archaea evolved from within the Gram-positive Bacteria there  
are a number of things to be taken into consideration:
1) the fact that the genomes of members of the Archaea don't seem to  
be exculsively Gram-positive, in most cases we see the genome of  
modern day organisms reflecting the extrapolated ancestors, especially  
at the level of core genomes.
2) the sequence diversity of genes such as the 16S rRNA gene in  
members of the Archaea and Bacteria is almost equally diverse. If the  
Archaea arose in the middle of Gram-positive then the mutation rates  
in members of the Archaea would have to have increased significantly  
to become that diverse in a shorter period of time. If that is the  
case then one would not be able to do "sequence based phylogenetic  
reconstructions" without first knowing the mutation rates and one  
would also have to fix a reliable point in geological time when the  
various lines of descent arose. While there is evidence that a number  
of obligate intracellular organisms have increased mutation rates this  
is due to their life style.

I could point you to geochemical data in support of an ancient origin  
of members of the Archaea, but then I also know that this data may be  
flawed because of secondary growth of these organisms in the deposits  
studied.

I have seen alternative theories that put one half of the Archaea  
"closer to the Bacteria", the other half "closer to the Eukaryotes"
http://www.pnas.org/content/105/51/20356.full.pdf
http://rstb.royalsocietypublishing.org/content/364/1527/2197.full.pdf+html

In one takes the chimera hypothesis to it's extreme eukaryotes are  
essentially fusion products of several lines of prokaryote, meaning  
that the division prokaryote - eukaryote is largely gradistic.

It is always useful to be aware of different hypotheses and to know  
that various proponents prefer their own view point, arguing against  
the other viewpoint. Reading Mayr's paper I came across:
"The question then is does a two-domain or three-domain arrangement of  
the living world agree better with the principle of balance? So far, I  
believe only about 175 different archaebacterial groups have been  
described. It is quite likely that further research will find  
thousands, but hardly more than that. Approximately 10,000 eubacteria  
have been named. The number of species of eukaryotes probably exceeds  
30 million; in other words, it is greater by several orders of  
magnitude. The number of species of birds alone is ≈10,000, and  
there are many millions of species of insects."

Surely, as Paddy Paterson indicated in the links he sent to the  
original thread I think we know that there is a huge diversity of  
prokaryotes to be documented (both Bacteria and Archaea), which is an  
important task in hand.

Brian

>
>                       ------Ken
> Kinman
> P.S.  I didn't realize that Thomas Cavalier-Smith's kingdom (regnum)
> level names were rejected by that committee in 2008.  I realize that the
>
> Bacteriological Code doesn't deal with taxa at such high ranks, but
> neither do the Zoological or Botanical Codes.  Not sure why they felt
> the need to formlly reject the names, since there are no reasons given.
> Perhaps the paraphyly of some of the taxa was an issue with some
> members.  The notion that paraphyletic taxa are "unnatural" is certainly
>
> widespread these days, but I frankly can't see how prokaryotes in
> particular can be classified naturally without some paraphyletic taxa.
> Empire (Superkingdom) Prokaryota is certainly paraphyletic with respect
> to Empire (Superkingdom), so maybe that is why so many still gravitate
> toward Three Domains (although the latter seems to simply ignore the
> paraphyly that is obviously there beneath the window-dressing).
>
> ---------------------------------------------------------
> Brian Patrick wrote:
> Hi Ken et al.,
> Okay, so Ken stated that the 3 domain system should be abandoned because
>
> there seems to be more evidence that archaebacteria are indeed
> monophyletic with eubacteria?  Thus, we should stay at the older
> superkingdom system of Prokarya and Eukarya?
> I am definitely NOT an expert on bacteria, so I am genuinely asking
> whether this is a viable line of reasoning?  I thought that the evidence
>
> for archaebacteria being more closely related to eukaryotes was pretty
> strong (ribosomes of archaebacteria are more similar to eukaryotes and
> other evidence that is not coming to mind at this moment).
> What evidence exists for each side of this, i.e., for unifying all
> prokaryotes into a single kingdom vs. the 3 domain system wherein the 2
> superkingdom system creates paraphyly?
> This is fascinating!  The paradigm shift to 3 domains was interesting,
> but if there is now evidence to throw that into doubt for a return to
> the previous paradigm...
> Thanks again for your time!
> Best regards, Brian
> ------------------------------------------------------------
> L. Brian Patrick, Ph.D.
> Assistant Professor of Biology and Chair
> Department of Biological Sciences
> Dakota Wesleyan University
> 1200 W. University Ave.
> Mitchell, SD  57301
>
>
>
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Dr.B.J.Tindall
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