IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

Definition of a biofilm - Again

Robert J. Palmer Jr. rjpalmer at utkux.utcc.utk.edu
Fri Jul 23 09:19:24 EST 1999

Now we're getting somewhere...
>Hi all, 
>I would rather prefer Keith Rose's suggestion that in order to qualify as 
>a biofilm, the structure must have a micro-environment that is different 
>from the bulk phase. Let's take trees and forests as an analogous example. 
>Now, we all have a pretty good idea of what a forest is and wouldn't call 
>a single tree a forest. We would call a tree a tree. A forest is an 
>assembly of trees that creates a habitat that differs from the habitat 
>that a single tree can create. Of course, the difference is gradual, but 
>nevertheless, we can have no doubt that there is a qualitative difference 
>between a tree and a forest, however fuzzy the borderline might be. 
>I would like to suggest that we have to make several independent 
But there are no unattached trees :) :)
>1. Single organisms versus aggregates. Biofilms would be a special case of 
>microbial aggregates, namely those that arise from attachment of cells to 
>a surface. Other special cases would be colonies on agar plates, lake 
>snow, sludge flocs, digester granules, and consortia in the original sense 
>of the term (referring to well-organized symbiotic aggregates of different 
>species, e. g. "Chlorochromatium aggregatum").
But where is the distinction? Chlorochromatium is clear (I think..., and 
may be the extreme example of a microcolonial biofilm), but digester 
granules and sludge flocs frequently have a substratum, however small, 
associated with them, much as rain drops have solid nucleation particles. 
Also, don't these flocs, consortia, and aggregates fulfill all the other 
definitions we've heard so far (communication, contact, matrix, etc)?
>2. Attached to a surface versus planctonic. Biofilms would be attached to 
>a surface, but some of the other abovementioned aggregates wouldn't be 
>(flocs etc.).
The surface is in the middle of the floc. Tthe digestor is the solar system 
and the flocs are planets and the bug (biofilms) are Earth's biosphere 
(pardon the overly simplistic analogy). Does the substratum have to be big 
and hard? Skin is not hard (usually); leaf surfaces are not hard (although 
they certainly are from the bacterium's standpoint). So, are clay 
particles (or aggregations of clay particles) or colloids within a 
bioreactor that support the aggregation (colonization?) of cells substrata? 
Just being the Devil's advocate here - that's what discussion groups are 
>3. Coming back to Paul Stoodley's primary versus higher order structure 
>distinction, I think that micro-colonies or cell-clusters are a more basic 
>structural unit than biofilms and flocs etc. as these are clearly 
>structures at a higher hierarchal level. So we have cells at the lowest 
>level of structural organization (maybe call it primary structure?), then 
>micro-colonies/cell-clusters as well as consortia at the next level 
>(secondary structure), and sludge flocs and biofilms etc. one level higher 
>(tertiary structure). And maybe stromatolites comprising several layers of 
>biofilm, dead and alive, as quaternary structures. 
>I guess the point I'm trying to make is that if we adopt a definition of 
>biofilms that includes everything under the sun, it will loose its 
>meaning. We need clearly defined terms, based on qualitative distinctions. 
>That's my two cents.
That was several dollars (pounds, guilders) worth! Here's another point to 
consider. Many here are making a case for narrowing the definition based 
on attachment to a substratum or these putative "higher order" structures. 
However, the biofilm is a temporal phenomenon. Even biochemistry is to 
some extent temporal (whaen is quaternary structure achieved, when is the 
protein folded?). I don't like the discrete-step approach. I prefer the 
developmental approach. To make another simplistic analogy, an arm is an 
arm regardless of whether it is attached to a four-year-old child or to a 
seventy-year-old woman. We all have no problems accepting the definition 
of an arm, and I would venture to say we have several definitions that are 
spatiotemporally intertwined: where the arm starts in time (limb 
formation) or space (it is the armpit from the external perspective, but 
the shoulder joint from a skeletal perspective). All this means that 
"biofilm" will continue to be an operating definition and that the 
"distinct" higher-order structures exist primarily as an artifact of our 
"snapshot" approach to examining biofilms. This is not to say that a 
morphometric approach yields no information: the stromatolite analogy being 
the most extreme arguement. However, stromatolites develop only under a 
very unique set of circumstances. Other assemblages e.g., 
Farbstreifensandwatt (there's a mouthfull!) is less ordered but still 
clearly recognizable as structures. Pure-culture P.a. biofilms also have 
structures initially (microclonies or whatever you'd care to call tham) 
that then coalesce and loose their definition to a large extent (at least 
morphologically, but how about physiologically!?).
Maybe the next Biofilms Bible will be a multivolume work with an entire 
volume dedicated to different perspectives on "what is a biofilm"......

To reply to the group as well as to the originator, make sure that
the address biofilms at net.bio.net is included in the "To:" field.

See the BIOFILMS homepage at http://www.im.dtu.dk/biofilms for info
on how to (un)subscribe and post to the Biofilms newsgroup.

More information about the Biofilms mailing list

Send comments to us at archive@iubioarchive.bio.net