IUBio

Definition of a biofilm - Again

Jan Kreft Kreft at cardiff.ac.uk
Tue Jul 27 02:44:03 EST 1999


Dear Rob and others,
true, when we get down into details, we need to be more precise with those 
distinctions I outlined. But for the moment, the developmental perspective 
you have added is more important.
If we talk about the growth of a biofilm, then it makes perfect sense to 
refer to the whole sequence of stages from the single attached cell (and 
even earlier, the not-yet-attached cell) to the ageing biofilm as a 
growing biofilm. And call a torn-off streamer a torn-off streamer rather 
than a floc, after all, this torn-off piece is clearly related to the 
structure it was torn-off from. This is even clearer with arms, as 
torn-off arms can't live on their own and will always remain torn-off arms 
while the streamers might give rise to other structures after having been 
washed into the waste carboy eventually. 
But, still, if we look at a stage in a developmental cycle as such, it is 
clearer to use a specific term, e.g. single attached cell.
To use another analogy, the development of a frog from the fertilized egg 
to the adult frog. Clearly, the fertilized egg is going to be a frog, but 
is not a frog itself (it is just that: a fertilized egg of a frog), only 
the last stage is what we call a frog. 
Thus, the developmental view doesn't invalidate "static" definitions, but 
links a set of defined static objects (snapshots as you call them) into a 
sequence in time (movie), which can represent a succession of ecosystems 
or the ontogeny of an organism. The link will be a causal one in those 
cases. 
The developmental perspective is very useful but should not be seen as an 
argument for broadening definitions in order to incorporate 
developmentally related stages. 
Best, Jan.
PS: Whatever happens to the empty lines in our mails? Where do they get 
lost? 
On 23 Jul 1999, Robert J. Palmer Jr. wrote:
> 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 
> >distinctions. 
> 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 
> for.... 
> >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"...... 
> Rob


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