Re: Bacteria on the SEM?!

[Ben Waggoner <bmw@xxxxxxxxxxxxxxxxxxxx>]

On Thu, 4 Apr 1996, Jim Buckman wrote:

> Does anyone have any information on identifying bacteria on the SEM by
> morphological criteria? - good papers, personal experience, etc - with
> particular reference to bacteria within shelly phosphatic material with a
> high organic content (brachiopods, or similar). I am interested in both
> modern and fossil examples, and would be pleased to hear from all
> interested parties on this subject.

My experience has been with bacteria in amber, but I also have a bit of 
experience in clinical bacteriology. Basically, identifying most bacteria 
by purely morphological criteria is well-nigh impossible -- the Gram
stain is really the bare minimum to make an ID, and you've almost got to 
have growth information (i.e. does it hemolyze on sheep's-blood agar, can 
it grow in oxygen, does it secrete catalase, etc. etc.) as well. (You 
might be able to tell Gram-positive from Gram-negative bacteria by cell 
wall structure if you can crank the magnification high enough; I've never 
tried this.)

If you can't get that information, you can sometimes make up for it: if you
know the sample's environment well, or if you can get information on
analogous environments, you may be able to find out what's likely to be 
in your sample. For instance, if you isolated and ID'd bacteria from an 
extant brachiopod shell, you might find that only a few species of, say, 
rod-shaped bacteria colonize phosphate shells (out of the kazillion or so 
rod-shaped species out there). If you know that the microenvironment in 
brachiopod shells is, say, anaerobic, you can rule out all obligate 
aerobes, and presumably all freshwater and terrestrial bacteria as well.

There are exceptions to the above, in which the bacteria do have enough
complex morphology to be identifiable fairly accurately using light or
electron microscopy. Cyanobacteria are perhaps the best examples of
bacteria that can be ID'd from morphology. Many actinomycetes are also
complex enough to ID, and sheathed bacteria (e.g. Leptothrix, which forms
a thick gelatinous sheath that contains Fe and Mn) and some other
filamentous types might be identifiable as well. Myxobacterial sporangia
can also be ID'd with light or electron microscopy -- but you're not
likely to find myxobacteria in a brachiopod shell; they tend to prefer
more luxurious habitats, like dung. Note that bacteriologists today
routinely use sequencing and tree-building to ID bacteria, and many of the
old morphological groupings don't correspond to clades (or accepted 
phenetic groupings).

I hope this helps. Good luck -- I'll be interested to see what comes out 
of this. Have you seen the papers on Cambrian phosphatic brachiopod 
structure by Galina Ushatinskaya at the Paleo Institute in Moscow? She's 
worked on bacterial diagenesis of phosphatic shells. I can send copies of 
some of her reprints (in Russian) if you're interested.

Ben Waggoner
Department of Integrative Biology
University of California
Berkeley, CA 94720 USA
bmw@uclink2.berkeley.edu

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