> Do you have a reference for the "several proteins shy of its modern
> composition" statement?

An in press paper by De Las Rivas et al. (Trends in Plant Science, Jan 2004)
highlights a few examples of this (specifically the cyanobacterial and
chloroplast/plastid oxygen evolving complex proteins).  Also any of several
great papers by William Martin (google: Bill Martin chloroplast) on
inferring the protein content of the cyanobacterial/chloroplast ancestor,
and other evolutionary themes in general.

> I was aware of the atmospheric O2 difference, thats what I was fishing
for.
> But I have not read anything on the subject for a quarter century, but the
> cyanobacteria did not live in the atmosphere, AFAIK. Chloroplasts live
> inside cells, so they have their distinct niche, obviously. I studied
> mycorhizal/plant root bacteria briefly, but not the genetics.

Definitely cyanobacteria did not live in the atmosphere, sensu stricto, but
they did have to live in the photic zone, within the reach of sunlight.  So
this implies perhaps some shallow water habitat that was in equilibrium with
the atmosphere and so probably had plenty of oxygen around.  There are some
nice current ideas in geology about a Precambrian (well, neoproterozoic)
ocean that was probably something like the modern Black Sea -- oxygenated
within the upper layer/photic zone but still highly sulfidic (anoxic and
reduced) below this level.  Cyanobacteria and early algae would have
occupied the surface layers and more primitive, obligately anaerobic
bacteria would have been dominant further down in the depths.

> I'm speaking of the niche of the "Archean cyanobacteria".  Is there a
living
> cyanobacterium that lives in the same niche?  What about the thermos??  Is
> there any habitat (or microhabitat) that exists on earth today that is
> indistinguishable, qualitatively, from that of 2 billion YA?  that is,
with
> the same temp, light, chemicals, anaerobic, etc. If so, then why would
those
> successful organisms change?  The only answer I can think of is mutation
> drift.

These are all good questions, and certainly microbiologists have spent
countless hours looking for such living fossils.  So there are modern
cyanobacteria that can live anaerobically, shutting off oxygenic
photosynthesis and oxidizing hydrogen sulfide (instead of water).  These
have even been compared to what an early Earth cyano would have been like
(e.g. by Schopf in several of his books, though his evidence for early
Archean cyanobacteria is much more controverted now than it was just a few
years ago).  But the main problem is, all known cyanobacteria have exquisite
and very complex systems for dealing with molecular oxygen at the levels
produced within the cell (ground zero of O2 production, right?).  These
adaptations would not have been required until after the development of
oxygenic photosynthesis, and so even if Schopf is right and his microfossils
are cyanos that simply haven't learned to oxidize water yet, they are going
to be completely different beasts than what we see today.

There are also thermophilic cyanobacteria (IIRC, 72 deg. C is the max known
temperature for photosynthesis) e.g. the emerald green color in many of the
hot springs of Yellowstone, but these look more or less just like any other
modern cyano that have figured out how to function at high temperatures.

> Finally, if you are a geneticist, which species living today is "least
> different" genetically from the presumed 2 billion year old version?

Another good question.  Among cyanos, members of the genus Gloeobacter
exhibit many "primitive" characteristics and are almost invariably early
branchers on phylogenetic trees, and so this was once argued to be the
"oldest living cyano".  But based on a recently completed genome,
these guys
are really not much different (based on protein content and ultrastructure)
from other cyanobacteria, and so we're still left hunting for a more
primitive organism that, as you are absolutely correct in suggesting, may be
hiding out in one of these niches.

An interesting aside, there has been several recent attempts to date the
appearance of modern groups of bacteria based on genetic analyses (and using
geological calibration points).  Though there are a lot of arguments why
these molecular clock techniques will fail when extrapolating so far back in
the Earth's history, its worth mentioning that most of these have the modern
groups of cyanobacteria appearing only around 1.5 billion years ago.

Assuming that date is correct, either our sampling sucks so far, or none of
the earliest cyanos have survived to modern times.
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