IUBio

PCR in biofilms

Nikolai Bugaenko bugar at post.krascience.rssi.ru
Mon Jan 27 21:01:07 EST 1997


Hi,

Could somebody tell in what way are the going to derive some knowledge
obtained from PCR (see below) techniques to the physiological
peculiarities of the rather specialized (I mean, adaptated) cells in a
biofilm. Probably, one can meet a biofilm where the organisms of various
species grow, but my experience is concern with purely bacterial
(single-species) biofilms, where bacterial cells are genetically the
same, inside the film, or outside of it.

Regards, Michael G.Sadovsky
Institute of Biophysics of SD of RAS;
660036 Russia, Siberia, Krasnoyarsk
tel. +7-(3912)-494101; fax: +7-(3912)-433400;
e-mail: bugar at post.krascience.rssi.ru


b-rittmann at NWU.EDU wrote:
> 
> Indeed, the use of ribosomally targetted oligonucleotide probes overcomes
> much of the problem with culturing bias.  Of course, probing is still a new
> technology, and many aspects of it remain in the experimental, or testing,
> phase.  For example, when combined with PCR, probing should be able to
> detect cell types never before cultured.  Otherwise, we are limited to
> probing for cultured species for which we have the rRNA sequence.
> 
> Bruce Rittmann
> Northwestern University
> 
> In article <33E9D23A.5612 at sask.usask.ca>, Subramaniank at SASK.USASK.CA
> (Karthikeyan Subramanian) wrote:
> > How can we discuss the structure or biological diversity of a biofilm
> > community, when we can culture only a small percentage of the organisms
> > present, and the normal plating procedures can exclude those members....
> > which may be crucial to the biofilm function, yet present only on those
> > plates which are TNTC.
> 
> Doesn't PCR-based DNA sequencing, using "universal" ribosomal DNA primers
> and
> related methods, provide a solution to that problem?  Or am I out of touch
> with
> practical limitations to that approach.  Granted, an rDNA sequence alone
> isn't
> perfect for doing systematics and is useless for physiology, but it would
> seem
> to be useful (in theory) for quantitating populations.  Are there no tricks
> for teasing out relatively rare sequences?
> 
> R.A.Preston
> rapr at med.pitt.edu
> 
> Bruce E. Rittmann
> John Evans Professor of Environmental Engineering
> Northwestern University
> 2145 Sheridan Road
> Evanston, IL 60208-3109
> b-rittmann at nwu.edu
> 847-491-8790 (ph); 847-491-4011 (fax)



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