From owner-biofilms@net.bio.net Thu Jul 01 12:57:00 1999 Path: biosci!biosci!not-for-mail From: Bob McLean Newsgroups: bionet.microbiology.biofilms Subject: Re: Biofilm Treatment with Polymers Date: 1 Jul 1999 06:57:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 85 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <3.0.6.32.19990701075209.007afd80@leela.swt.edu> NNTP-Posting-Host: net.bio.net Hi Mary, First let me welcome you to the biofilm field. Although activity on this discussion group is low right now, the field as a whole is really progressing well. I am a little unclear about your definition of polymers. Do you refer to plastics, polypeptides, polysaccharides? In any case, there are a number of antifouling agents on the market right now. Often they are marketed under the generic names as biocide, slimicide, etc. You might try searching for medical references using medline (http://igm-01.nlm.nih.gov/index.html). As well I would recommend using other indexing services such as chemical abstracts, biological abstracts, etc. Try keywords such as biofilm, control, antifouling, as well as specific names of the chemicals that you are interested in. In response to your question about measuring biofilms, chemical and spectrophotometric analyses are certainly easy. In my experience, they are about an order of magnitude less sensitive than conventional sonication (with a bath sonicator) and dilution plating. Other approaches include growing biofilms with radiolabelled bacteria and enumerating with a scintillation counter, doing acridine orange direct counts. There is a new volume of Methods in Enzymology (vol 310, edited by Ron Doyle) devoted entirely to biofilms, which is due to be published in the next few months. This volume will have a pretty comprehensive and up to date list of techniques for biofilm work. Best wishes and good luck, Bob McLean At 11:04 PM 6/29/99 -0400, you wrote: >I am researching topics for my graduate project and my advisor would >like to do some work with biofilms. >My current work involves the use of polymers as drug treatments and we >are just getting into the anti-infective field. It would be nice if I >could mesh the two together (or so I thought). >When I did a literature search nothing comes up with polymers and >biofilms. However through web surfing I have found a number of >commercial companies out there that manufacture polymers and use them >for treatment of industrial waste water, paper mills, cooling towers >etc. An example of this is Buckman Laboratories, who market a >polyionene compound for biofilm eradication. Have any of these >companies published their data? Maybe I am searching in the wrong >place, is PubMed an unreasonable place to look for this information? My >thought had been to look at commercially available polymers of differing >molecular weight and different charge densities and see what effect they >would have on established biofilms. There is no sense in my reinventing >the wheel if the information is out there. Can any of you out there >offer some helpful suggestions? Just to clarify, I am not talking about >the polymers as surface components but as soluble antimicrobials. >Another question (if I may take up some more of your time) was about >quantifying biofilms after treatment. I had come across a method that >uses crystal violet to stain the biofilm, extracting it with DMSO, and >measuring the absorbance in a spec. It appealed to me because of its >simplicity and ease of use. Any objections or cautions about this >approach? >Thank you in advance for your replies. >Mary Pitruzzello >pitruzzello@mediaone.net > > > >------------------------------------------------------------------- >To reply to the group as well as to the originator, make sure that >the address biofilms@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. > > > ___________________________________________________________________________ R.J.C. (Bob) McLean, Ph.D. Dept. Biology Southwest Texas State University 601 University Drive San Marcos, Tx 78666 USA (512)245-3365 phone (512)245-8713 FAX Email: RM12@swt.edu http://www.bio.swt.edu/biofac/mclean/mclean.html ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Thu Jul 01 12:57:00 1999 Path: biosci!biosci!not-for-mail From: P.Stoodley@exeter.ac.uk (paul stoodley) Newsgroups: bionet.microbiology.biofilms Subject: Re: Biofilm Treatment with Polymers Date: 1 Jul 1999 06:57:02 -0700 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 109 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: References: <37798945.8D5DB9F2@mediaone.net> NNTP-Posting-Host: net.bio.net Carl, I have recently conducted some work on the rheological properties of in situ biofilms which behaved like viscoelastic polymer gels: STRUCTURAL DEFORMATION OF BACTERIAL BIOFILMS CAUSED BY SHORT TERM FLUCTUATIONS IN FLUID SHEAR: AN IN-SITU INVESTIGATION OF BIOFILM RHEOLOGY. Paul Stoodley, Zbigniew Lewandowski, John D. Boyle, and Hilary M. Lappin-Scot which is currently in press for Biotechnoogy and Bioengineering. Ian Sutherland has characterized a number of extracted and purified biofilm polymers: Sutherland, I.W. 1994. Structure-function relationships in microbial exopolysaccharides. Biotech. Adv. 12: 393-447. Sutherland, I.W. 1996. A natural terrestrial biofilm. J. Ind. Microbiol. 17: 281-283. and a good review can be found by D.G. Allison - Biofilm, Volume 3, Paper 2 (BF98002) 1998 Online Journals - URL:http://www.bdt.org.br/bioline/bf Exopolysaccharide production in bacterial biofilms. other refs that may be of interest - Performance evaluation of disinfectant formulations using poloxamer-hydrogel biofilm-constructs AU: Wirtanen_G, Salo_S, Allison_DG, MattilaSandholm_T, Gilbert_P JN: JOURNAL OF APPLIED MICROBIOLOGY, 1998, Vol.85, No.6, pp.965-971 The use of poloxamer hydrogels for the assessment of biofilm susceptibility towards biocide treatments AU: Gilbert_P, Jones_MV, Allison_DG, Heys_S, Maira_T, Wood_P JN: JOURNAL OF APPLIED MICROBIOLOGY, 1998, Vol.85, No.6, pp.985-990 As far as the crystal violet method goes - I have used it to stain biofilm on glass surfaces and it stuck to just about everything - I assume it also stained the conditioning film so I would be a bit worried about overestimating biomass. Although it might be useful as a crude comparative measure. Other methods are to scrape it off dry it and weigh it but this may not be technically possible for your apparatus and you have the problem of dealing with very small quantities and making sure that it is all scraped off. You could possibly "digest" the biofilm and report the COD. I use a microscopic method in which I look at surface area covered and average thickness. The problem with this method is taking enough measurements to be representative and making the assumption that the biofilm in the viewing area is the same as in the places where it is difficult to observe - i.e. corners. probably the most common method is to "scrape and plate" and give values of CFU/unit area. Good luck, Paul. On 30 Jun 1999 17:09:59 -0700 "Carl J. Pitruzzello" wrote: > I am researching topics for my graduate project and my advisor would > like to do some work with biofilms. > My current work involves the use of polymers as drug treatments and we > are just getting into the anti-infective field. It would be nice if I > could mesh the two together (or so I thought). > When I did a literature search nothing comes up with polymers and > biofilms. However through web surfing I have found a number of > commercial companies out there that manufacture polymers and use them > for treatment of industrial waste water, paper mills, cooling towers > etc. An example of this is Buckman Laboratories, who market a > polyionene compound for biofilm eradication. Have any of these > companies published their data? Maybe I am searching in the wrong > place, is PubMed an unreasonable place to look for this information? My > thought had been to look at commercially available polymers of differing > molecular weight and different charge densities and see what effect they > would have on established biofilms. There is no sense in my reinventing > the wheel if the information is out there. Can any of you out there > offer some helpful suggestions? Just to clarify, I am not talking about > the polymers as surface components but as soluble antimicrobials. > Another question (if I may take up some more of your time) was about > quantifying biofilms after treatment. I had come across a method that > uses crystal violet to stain the biofilm, extracting it with DMSO, and > measuring the absorbance in a spec. It appealed to me because of its > simplicity and ease of use. Any objections or cautions about this > approach? > Thank you in advance for your replies. > Mary Pitruzzello > pitruzzello@mediaone.net > > > > ------------------------------------------------------------------- > To reply to the group as well as to the originator, make sure that > the address biofilms@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. > ---------------------- Paul Stoodley Environmental Tel: 01392 264348 Microbiology Fax: 01392 263700 Research email: p.stoodley@exeter.ac.uk Group Exeter University Biological Sciences Hatherly Laboratories Prince of Wales Road Exeter EX4 4PS. UK. --- ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Thu Jul 01 12:57:00 1999 Path: biosci!biosci!not-for-mail From: "David B. Hedrick" Newsgroups: bionet.microbiology.biofilms Subject: Re: Biofilm Treatment with Polymers Date: 1 Jul 1999 06:57:30 -0700 Organization: Hedrick Services Lines: 126 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <377B3A58.617B@icx.net> References: <37798945.8D5DB9F2@mediaone.net> Reply-To: davidbhedrick@icx.net NNTP-Posting-Host: net.bio.net Hello Mary: I hope I can help. > I am researching topics for my graduate project and my advisor would > like to do some work with biofilms. > My current work involves the use of polymers as drug treatments and we > are just getting into the anti-infective field. It would be nice if I > could mesh the two together (or so I thought). > When I did a literature search nothing comes up with polymers and > biofilms. However through web surfing I have found a number of > commercial companies out there that manufacture polymers and use them > for treatment of industrial waste water, paper mills, cooling towers > etc. I would expect the polymers used for drug treatment to be very different from those used to treat industrial biofilms. I expect drug-treatment polymers either deliver active ingredients dissolved in the polymer or have an effect on tissues by the nature of the polymer. Polymers used industrially against biofilms are largely competing for good bacterial attachment sites on surfaces. Industrial biocides are ususally small soluble molecules. Rarely does industry want to make the biofilm more healthy. > An example of this is Buckman Laboratories, who market a > polyionene compound for biofilm eradication. Have any of these > companies published their data? Companies don't publish data on their products because the ingredients are often so simple that customers are tempted to make their own product. Also liability exposure. What's in Coke? What's in ice cream? What's in shampoo? Coke is carbonated prune juice. You wouldn't want to eat store ice cream if you knew it's composition (polysorbate 60, anyone? sodium alginate?). Shampoo is so easy and cheap to make, they have to put smells and colors and sparkles and lots of commercials in it so you perceive a difference. > Maybe I am searching in the wrong > place, is PubMed an unreasonable place to look for this information? Yes. Sounds like a medical database to me. Try Agricola (Latin for farmer) at . Before a high-tech product is sold, the research behind it is often in the scientific literature. Finding the original research from the company site is like finding your girlfriends bra-strap by her mother's instructions. A company site is rarely scientific literature. Remember, PR = BS. OK. You have to look for the original government funded research that this company's product is based upon. Sigh. Go through the entire company site, follow every link, look at everything. Write down every person's name that appears anywhere. If someone made an important discovery that made money, they might still be in the company. If you have access to corporate information, get the names of the largest stock-holders. Now search the scientific literature for those names. Go back and look for names of specific chemical compounds or processes. Search the literature for those. You now have a large list of names and a large list of chemicals/processes, which in your literature search (I like Agricola, Chem Abstracts is comprehensive and sadistic, Biological Abstracts is big and obscure, there are others) give you huge numbers of matches. Most of those you eliminate by scanning the title. Read some of those abstracts, and of those, some of those articles. By this time, what you are searching for has changed because you have learned a lot. Remember to check in the government documents and patent records. Remember to be nice to the librarians. 30 seconds of being polite to a librarian could save you days. > My > thought had been to look at commercially available polymers of differing > molecular weight and different charge densities and see what effect they > would have on established biofilms. The trick in industrial settings (and anyone feel free to correct me, I'm extrapolating) is to kill the biofilm with a soluble biocide, then protect the clean surfaces with a polymer that competes with the bacteria. Attached bacteria are notoriously difficult to remove or kill. Much easier to prevent attachment. > There is no sense in my reinventing > the wheel if the information is out there. Can any of you out there > offer some helpful suggestions? Just to clarify, I am not talking about > the polymers as surface components but as soluble antimicrobials. Why use a polymer as an antimicrobial when sodium hypochlorite (bleach) works so well? As a drug, bleach has it's limitations. 8^) But in industrial water treatment, it's pretty good. > Another question (if I may take up some more of your time) was about > quantifying biofilms after treatment. I had come across a method that > uses crystal violet to stain the biofilm, extracting it with DMSO, and > measuring the absorbance in a spec. It appealed to me because of its > simplicity and ease of use. Any objections or cautions about this > approach? Cool, if it works on your system. I hadn't heard of that method. I usually look for biofilm biomass in systems like soils and bioreactors. Don't think it would work on those. You started your post with your graduate advisor suggesting you look at biofilms. Your medical background blinds you to the biofilms around you. Take a glass from your cupboard, fill it with water from your tap, and set it on a shelf. There were some bacteria on the inside surface of your glass, but they are out-numbered by the bacteria that came with your tapwater. Don't worry. The tapwater bacteria are selected by their ability to survive hypochlorite, not their infectivity in humans. A week later, there is a barely visible scum on the water surface and a definite slimeyness on the inside of the glass. Soil is a large biofilm thinly spread across the fractal surfaces of clay, silt, and sand particles. Plant leaves have a biofilm called the phyllosphere. Plant roots, the rhizosphere (or rhizoplane, I can never remember). Your skin, as well as every body orifice, has it's own microbial community. So does every other animal. And plant. Biofilms can increase or decrease the corrosion of metals. There are lots of biofilms out there, and we don't have any idea most of what's going on. I hope I was of some help. > Thank you in advance for your replies. > Mary Pitruzzello > pitruzzello@mediaone.net -- Or, you could hire me. ~DBH Technical writing, literature search, and data analysis at the interface of chemistry and biology. davidbhedrick@icx.net David B. Hedrick P.O. Box 16082 Knoxville, TN 37996 ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Fri Jul 02 06:51:00 1999 Path: biosci!biosci!not-for-mail From: a.hunt@lancaster.ac.uk (Amelia Hunt) Newsgroups: bionet.microbiology.biofilms Subject: Re:Biofilm Treatment with Polymers Date: 2 Jul 1999 00:51:09 -0700 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 47 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <199907011937.UAA04335@unixb.lancs.ac.uk> NNTP-Posting-Host: net.bio.net Hello Mary, With regards biofilm quantification. If it is purely a bacterial biofilm that you are looking at, then I would recommend removing the biofilm by a combination of scraping and sonicating (find the best combination for your own work) and then use 4',6 diamidino 2 phenylindole (DAPI) at a final concentration of 0.1µg/ml or greater to stain cells. Then enumerate using epifluorescence microscopy. There are lots of papers that describe this method e.g. Porter, K.G. & Feig, Y.S. 1980. Limnol. Oceanogr. 25(5) 943-948 (seminal paper) and Zweifel & Hagstrom. 1995. Appl. Environ. Microbiol. 61(6) 2180 - 2185 gives details of methods to exclude non-nucleoid containing bacteria - should you be concerned... For planktonic studies DAPI and, with reservations, acridine orange (AO) provide the best methods to estimate bacterial numbers. Bacteria visualised by these methods can also be used to estimate biovolume and from this, biomass. Here at Lancaster, we also use direct counts by these methods rather than plate counts which have been proven to be an underestimate of actual bacterial numbers. With regards using polymers as biocides (of which I know absolutely nothing about) - maybe an examination of some ecology papers examining the ability of recalcitrant organic carbon molecules to inhibit microbial metabolism could prove interesting with respect to the ability of these to move into biofilms.e.g., Freeman C & Lock, MA. 1992. Appl. Environ. Microbiol. 58 2030 - 2033. Hope this is of some help Love Amelia Dr Amelia P. Hunt Biological Sciences I.E.N.S. Lancaster University Lancaster LA1 4YQ --- ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Wed Jul 07 09:38:00 1999 Path: biosci!biosci!not-for-mail From: Araya Ruben Alonso Newsgroups: bionet.microbiology.biofilms Subject: biofilm diversity Date: 7 Jul 1999 03:38:40 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <3.0.6.32.19990707192450.0079b7d0@em.phs.osaka-u.ac.jp> NNTP-Posting-Host: net.bio.net hello For to study the microbial diversity of lotic bacterial associated to biofilms by DGGE analysis. How I can to know if the DNA fragment size obtained (for universal primer), is representative to the microbial diversity?. Someone can suggest me something?. thanks in advance for any help Ruben Araya araya@phs.osaka-u.ac.jp ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Wed Jul 07 17:38:00 1999 Path: biosci!biosci!not-for-mail From: Cindy MORRIS Newsgroups: bionet.microbiology.biofilms Subject: Re: Biofilm Treatment with Polymers Date: 7 Jul 1999 11:38:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 73 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <1.5.4.32.19990707153813.0068f800@avi-maur.avignon.inra.fr> NNTP-Posting-Host: net.bio.net Dear Biofilm group: Concerning the message from Mary Pitruzzello and the discussion that followed, I have 2 comments. The first concerns the use of crystal violet to quantify biofilms. The second remark concerns my rebuttal of the definition of some terms proposed by David B. Hedrick (a technical writer). *** *** Concerning use of crystal violet to quantify biofilms: For the past year my lab has been trying to adapt a crystal violet-based staining method to the quantification of bacteria adhering to a surface. This method is based on the technique described by Sonak, S. and Bohsle, N. (1995. "A simple method to assess bacterial attachment to surfaces". Biofouling 9:31-38). After multiple trials, we have abandoned this technique because it is i) almost impossible to calibrate and ii) seems to have a very high threashold of sensitivity (ie you need about 10E5 to 10E6 bacteria per ml to detect CV that is not due to background residual) and iii) CV never stops diffusing out of the cells; the more you rinse, the more you remove; it is difficult to decide when to stop. For more details, you can discuss with my student, Tristan Boureau (boureau@avignon.inra.fr) who will be at the indicated address until mid Sept. What are the alternatives?; well, it depends on how you want to go about it. If you can do direct measures by coupling viability stains to confocal microscopy, that would probably give interesting results. Also, check out one of my recent articles (Morris C.E., Monier J.M., Jacques M.A. 1998. A technique to quantify the population size and composition of the biofilm component in communities of bacteria in the phyllosphere. Applied and Environmental Microbiology 64:4789-4795.) Even if you don't use the technique we propose, you might find the introduction and discussion useful: we present many of the different approaches for quantification of biofilm populations that have been used so far in the literature. *** *** In his response to Mary's question, DB Hendrick states that: >"Plant leaves have a biofilm called the phyllosphere. Plant roots, the >rhizosphere (or rhizoplane, I can never remember). >Your skin, as well as every body orifice, has it's own microbial >community. " 'Phyllosphere', 'phylloplane', 'rhizosphere', 'rhizoplane', ARE NOT biofilms. "Phyllo" is the Greek combining form for leaf, "rhizo" for root, and the more familiar words "plane" for surface and "sphere" for (you guessed it!!) sphere. Hence, rhizoplane is the root surface. The rest of them you can figure out for yourselves. To more correctly state his proposition, DB Hendrick could have said that the phylloplane of numerous plants harbor large populations of micro-organisms (up to ca. 10E8 per leaf), of which some may be aggregated into biofilms. But, the vast majority of the phylloplane (about 90-98%) is virgin territory. The presence of biofilms in the rhizosphere is less well known, but the rhizosphere harbors a rich microbial population. Furthermore, DB Hendrick also insinuates that microbial community = biofilm. Perhaps it is very likely that the organisms assembled in a biofilm function as a community; but just because that organisms function as a community does not imply that they are biofilms!! Sorry to be so severe, but I think that a professional technical writer should be a bit more careful in use of terminology. Sincerely Cindy E. Morris INRA - Station de Pathologie Vegetale B.P. 94 84143 Montfavet, France tel : (33) 490-31-63-84 fax : (33) 490-31-63-35 e-mail : morris@avignon.inra.fr ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Thu Jul 08 12:37:00 1999 Path: biosci!biosci!not-for-mail From: "8"@rindow.sjc.u-tokai.ac.jp Newsgroups: bionet.microbiology.biofilms Subject: Help find incubator waterbath and media porer striliser Date: 8 Jul 1999 06:37:35 -0700 Organization: Customer of Planet Online Lines: 15 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <7m1i9m$eah$1@news8.svr.pol.co.uk> NNTP-Posting-Host: net.bio.net hi there Can some one help me find old incubator, waterbath and media porer in south of england area. some mlso in nhs trust might have this. thanks reply appriciated on jblab@technologist.com ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@net.bio.net is included in the "To:" field. See the BIOFILMS homepage at http://www.im.dtu.dk/biofilms for info on how to (un)subscribe and post to the Biofilms newsgroup. 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See the BIOFILMS homepage at http://www.im.dtu.dk/biofilms for info on how to (un)subscribe and post to the Biofilms newsgroup. From owner-biofilms@net.bio.net Sun Jul 11 08:16:00 1999 Path: biosci!biosci!not-for-mail From: gerne@my-deja.com Newsgroups: bionet.microbiology.biofilms Subject: Re: Biofilm Treatment with Polymers Date: 11 Jul 1999 02:16:12 -0700 Organization: Deja.com - Share what you know. Learn what you don't. Lines: 137 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <7m8oo7$hc7$1@nnrp1.deja.com> References: <3.0.6.32.19990701075209.007afd80@leela.swt.edu> NNTP-Posting-Host: net.bio.net If you consider destruction of the biofilm as a possible route you might also want to consider cytometric assessment methods. I worked on dental biofilms and there scraping and sonication worked well on 24 hour plaque(see http://www.cyto.purdue.edu/flowcyt/research/micrflow/gerhard/gerhard.htm ) but with older plaque the dextran matrix did not shift any more. Plating does not work to obtain absolute counts as you can not identify the guys that grow on your aerobe and your anaerobe plates and the ones that grow on both, let alone thet a lot of those guys only grow when next to their best friend. If you want to quantify the biomass of a biofilm any bulk measurement will fail as it can not cope with the heterogeneity of the cells. However you could consider measuring total DNA by fluorimetry and postulating an average DNA content. Good luck Gerhard In article <3.0.6.32.19990701075209.007afd80@leela.swt.edu>, Bob McLean wrote: > Hi Mary, > First let me welcome you to the biofilm field. Although activity on this > discussion group is low right now, the field as a whole is really > progressing well. > I am a little unclear about your definition of polymers. Do you refer to > plastics, polypeptides, polysaccharides? In any case, there are a number > of antifouling agents on the market right now. Often they are marketed > under the generic names as biocide, slimicide, etc. You might try > searching for medical references using medline > (http://igm-01.nlm.nih.gov/index.html). As well I would recommend using > other indexing services such as chemical abstracts, biological abstracts, > etc. Try keywords such as biofilm, control, antifouling, as well as > specific names of the chemicals that you are interested in. > In response to your question about measuring biofilms, chemical and > spectrophotometric analyses are certainly easy. In my experience, they are > about an order of magnitude less sensitive than conventional sonication > (with a bath sonicator) and dilution plating. Other approaches include > growing biofilms with radiolabelled bacteria and enumerating with a > scintillation counter, doing acridine orange direct counts. There is a new > volume of Methods in Enzymology (vol 310, edited by Ron Doyle) devoted > entirely to biofilms, which is due to be published in the next few months. > This volume will have a pretty comprehensive and up to date list of > techniques for biofilm work. > Best wishes and good luck, > Bob McLean > At 11:04 PM 6/29/99 -0400, you wrote: > >I am researching topics for my graduate project and my advisor would > >like to do some work with biofilms. > >My current work involves the use of polymers as drug treatments and we > >are just getting into the anti-infective field. It would be nice if I > >could mesh the two together (or so I thought). > >When I did a literature search nothing comes up with polymers and > >biofilms. However through web surfing I have found a number of > >commercial companies out there that manufacture polymers and use them > >for treatment of industrial waste water, paper mills, cooling towers > >etc. An example of this is Buckman Laboratories, who market a > >polyionene compound for biofilm eradication. Have any of these > >companies published their data? Maybe I am searching in the wrong > >place, is PubMed an unreasonable place to look for this information? My > >thought had been to look at commercially available polymers of differing > >molecular weight and different charge densities and see what effect they > >would have on established biofilms. There is no sense in my reinventing > >the wheel if the information is out there. Can any of you out there > >offer some helpful suggestions? Just to clarify, I am not talking about > >the polymers as surface components but as soluble antimicrobials. > >Another question (if I may take up some more of your time) was about > >quantifying biofilms after treatment. I had come across a method that > >uses crystal violet to stain the biofilm, extracting it with DMSO, and > >measuring the absorbance in a spec. It appealed to me because of its > >simplicity and ease of use. Any objections or cautions about this > >approach? > >Thank you in advance for your replies. > >Mary Pitruzzello > >pitruzzello@mediaone.net > > > > > > > >------------------------------------------------------------------- > >To reply to the group as well as to the originator, make sure that > >the address biofilms@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. > > > > > > > ________________________________________________________________________ ___ > R.J.C. (Bob) McLean, Ph.D. > Dept. Biology > Southwest Texas State University > 601 University Drive > San Marcos, Tx 78666 > USA > (512)245-3365 phone > (512)245-8713 FAX > Email: RM12@swt.edu > http://www.bio.swt.edu/biofac/mclean/mclean.html > > ------------------------------------------------------------------- > To reply to the group as well as to the originator, make sure that > the address biofilms@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. > > Sent via Deja.com http://www.deja.com/ Share what you know. Learn what you don't. ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Sun Jul 11 11:07:00 1999 Path: biosci!biosci!not-for-mail From: Claus Sternberg Newsgroups: bionet.microbiology.biofilms Subject: Summer vacation Date: 11 Jul 1999 05:07:40 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <4.1.19990711135516.00aaa280@pop.dtu.dk> NNTP-Posting-Host: net.bio.net To: Biofilms newsgroup. Dear All, This is just a small notice to inform you that I will be away for the next week or so. This means that messages sent to the Biofilms newsgroup will not be forwarded to the list until I get back. With the low traffic this should not be a big problem, but I you posted something and wonder why it doesn't appear on the newsgroup - you now know why! I will deal with the incoming messages as soon as I am back. Best regards, and a nice summer to you all! Claus Sternberg July 11 1999 Biofilms newsgroup moderator ------------------------------------------------------------------- * Claus Sternberg, PhD * * Department of Microbiology Technical University of Denmark * * Building 301 DK 2800 Lyngby Denmark * * Phone: (+45) 45 25 25 15 FAX: (+45) 45 93 28 09 * * E-mail: cs@im.dtu.dk * * URL: * * PGP Public Key available on request * ------------------------------------------------------------------- ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Mon Jul 12 06:58:00 1999 Path: biosci!biosci!not-for-mail From: Jean Barbeau Newsgroups: bionet.microbiology.biofilms Subject: Denture biofilms Date: 12 Jul 1999 00:57:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hella, Working on denture biofilms, we want to study the physico-chemical conditions that prevail within these biofilms. We sample intact denture plaque by using cryosectioning embedding medium after freezing the denture. By this way, we can obtain sections for microscopic observations. Are there some probes or techniques that can be used to determine the aerobic or anaerobic as well as pH status of fresh biofilms? Thanks Jean Barbeau adjoint aux vices-doyens et responsable des études supérieures Faculté de médecine dentaire Université de Montréal Montréal, Québec CP 6128, Succursale Centre-Ville H3C 3J7 ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Mon Jul 19 15:11:00 1999 Path: biosci!biosci!not-for-mail From: Bob McLean Newsgroups: bionet.microbiology.biofilms Subject: Re: Denture biofilms Date: 19 Jul 1999 09:11:15 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 62 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <3.0.6.32.19990714111236.007a8250@leela.swt.edu> NNTP-Posting-Host: net.bio.net Jean, There are a number of fluorescent probes which will measure redox potential, pH, Ca levels, viability, gram reaction, gene expression etc. Molecular Probes (a major manufacturer of such products - web site http://www.probes.com ) will give you technical data showing fluorescence correlation with e.g. pH or Ca levels. Even with this information, it is best if you perform correlation studies under your experimental conditions. Several people have published some very nice work in this area. Among others, I would look for papers by Zbignew Lewandowski and Gil Geesey (Montana State), Rob Palmer (University of Tennessee, Knoxville), Darren Korber and John Lawrence (Saskatoon, Saskatchewan, Canada), and the biofilm group in Lyunby Denmark (Claus Sternberg, Soren Molin, et al). I hope this information is helpful. Bob McLean At 02:04 PM 7/11/99 -0500, you wrote: >Hella, >Working on denture biofilms, we want to study the physico-chemical >conditions that prevail within these biofilms. We sample intact denture >plaque by using cryosectioning embedding medium after freezing the denture. >By this way, we can obtain sections for microscopic observations. >Are there some probes or techniques that can be used to determine the >aerobic or anaerobic as well as pH status of fresh biofilms? >Thanks >Jean Barbeau >adjoint aux vices-doyens et responsable des études supérieures >Faculté de médecine dentaire >Université de Montréal >Montréal, Québec >CP 6128, Succursale Centre-Ville >H3C 3J7 > > > >------------------------------------------------------------------- >To reply to the group as well as to the originator, make sure that >the address biofilms@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. > > > ___________________________________________________________________________ R.J.C. (Bob) McLean, Ph.D. Dept. Biology Southwest Texas State University 601 University Drive San Marcos, Tx 78666 USA (512)245-3365 phone (512)245-8713 FAX Email: RM12@swt.edu http://www.bio.swt.edu/micro/mclean/mclean.html ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Mon Jul 19 15:11:00 1999 Path: biosci!biosci!not-for-mail From: Kurt De Meyer Newsgroups: bionet.microbiology.biofilms Subject: VITEK (BioMérieux) Date: 19 Jul 1999 09:11:15 -0700 Organization: EUnet Belgium, Leuven, Belgium Lines: 18 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <378CD44E.2DA2156D@ping.be> NNTP-Posting-Host: net.bio.net Hello, I'm a graduate student bio-engineer and doing my probationary period at a medical laboratory. There i'm working with the Vitek (BioMérieux). If anyone has information about the biochemical tests that occur in the system and the advantages and disadvantages of the Vitek, or know articles about the Vitek, could you please be so kind to let me know. Many thanks in advance. Kurt De Meyer. ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Mon Jul 19 15:11:00 1999 Path: biosci!biosci!not-for-mail From: "David B. Hedrick" Newsgroups: bionet.microbiology.biofilms Subject: Re: Biofilm Treatment with Polymers Date: 19 Jul 1999 09:11:16 -0700 Organization: Hedrick Services Lines: 70 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <378BC742.6926@icx.net> References: <1.5.4.32.19990707153813.0068f800@avi-maur.avignon.inra.fr> Reply-To: davidbhedrick@icx.net NNTP-Posting-Host: net.bio.net X-Complaints-To: abuse@icx.net NNTP-Posting-Date: 13 Jul 1999 23:12:46 GMT X-Mailer: Mozilla 3.01C-KIT (Win95; U) My goodness, Cindy. We have a large number of bacteria, and other organisms, attached to a surface. What else is required for it to be considered a biofilm? I think your response was rather arch and superior. I hope you had fun, "correcting" my "proposition", and acusing me of "insinuating". If you're going to be caustic, at least spell my name correctly. I was speaking informally, encouraging her to investigate other types of biofilms, or whatever you want to call microorganisms attached to surfaces. It wasn't for publication and I don't think I deserved your nastyness. > In his response to Mary's question, DB Hendrick states that: > >"Plant leaves have a biofilm called the phyllosphere. Plant roots, the > >rhizosphere (or rhizoplane, I can never remember). > >Your skin, as well as every body orifice, has it's own microbial > >community. " > 'Phyllosphere', 'phylloplane', 'rhizosphere', 'rhizoplane', ARE NOT > biofilms. "Phyllo" is the Greek combining form for leaf, "rhizo" for root, > and the more familiar words "plane" for surface and "sphere" for (you > guessed it!!) sphere. Hence, rhizoplane is the root surface. The rest of > them you can figure out for yourselves. > To more correctly state his proposition, DB Hendrick could have said that > the phylloplane of numerous plants harbor large populations of > micro-organisms (up to ca. 10E8 per leaf), of which some may be aggregated > into biofilms. But, the vast majority of the phylloplane (about 90-98%) is > virgin territory. The presence of biofilms in the rhizosphere is less well > known, but the rhizosphere harbors a rich microbial population. > Furthermore, DB Hendrick also insinuates that microbial community = biofilm. > Perhaps it is very likely that the organisms assembled in a biofilm function > as a community; but just because that organisms function as a community > does not imply that they are biofilms!! > Sorry to be so severe, but I think that a professional technical writer > should be a bit more careful in use of terminology. > > Sincerely > Cindy E. Morris > INRA - Station de Pathologie Vegetale > B.P. 94 > 84143 Montfavet, France > tel : (33) 490-31-63-84 > fax : (33) 490-31-63-35 > e-mail : morris@avignon.inra.fr > > ------------------------------------------------------------------- > To reply to the group as well as to the originator, make sure that > the address biofilms@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. -- ~DBH Technical writing, literature search, and data analysis at the interface of chemistry and biology. davidbhedrick@icx.net David B. Hedrick P.O. Box 16082 Knoxville, TN 37996 ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Tue Jul 20 06:35:00 1999 Path: biosci!biosci!not-for-mail From: Bob McLean Newsgroups: bionet.microbiology.biofilms Subject: need for definitions Date: 20 Jul 1999 00:35:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 42 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <3.0.5.32.19990719133028.007aa7e0@leela.swt.edu> NNTP-Posting-Host: net.bio.net Hi everyone, Last summer at ISME8 (8th International Symposium on Microbial Ecology) a question was raised as to a true "definition" of a biofilm. While I am sure that we can all agree that dental plaque and the slime-coated rocks in rivers are two examples of biofilms, we need to reach some sort of consensus on this definition. I pose the following questions for discussion: 1) Does one adherent microorganism constitute a biofilm? 2) If not, then how many do we need to start referring to an adherent population as a biofilm? 3) At what point would the term "microcolony" apply? 4) Do biofilms require metabolically active organisms? 5) If metabolism is required, then what type of metabolism should be essential (proton motive force, respiration, biosynthesis, etc)? 6) On the lighter side, has anyone given their lab a good nickname? (My lab at Southwest Texas State University has adopted the name "Slime Gang") It is sometimes tempting to get confrontational during some of these discussions. I have a lot of respect for the participants in this discussion group, both on a personal and a professional level. I would encourage people to enjoy the science (including my first five comments) and when possible have fun (my comment 6). Sincerely, Bob McLean ___________________________________________________________________________ R.J.C. (Bob) McLean, Ph.D. Dept. Biology Southwest Texas State University 601 University Drive San Marcos, Tx 78666 USA (512)245-3365 phone (512)245-8713 FAX Email: RM12@swt.edu http://www.bio.swt.edu/micro/mclean/mclean.html ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Tue Jul 20 07:53:00 1999 Path: biosci!biosci!not-for-mail From: sparge@globalnet.co.uk (Andy Spragg) Newsgroups: bionet.microbiology.biofilms Subject: Re: Biofilm Treatment with Polymers Date: 20 Jul 1999 01:53:08 -0700 Organization: GXSN Lines: 52 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <3793b1fd.173593037@news.globalnet.co.uk> References: <1.5.4.32.19990707153813.0068f800@avi-maur.avignon.inra.fr> NNTP-Posting-Host: net.bio.net On 19 Jul 1999 09:11:16 -0700, "David B. Hedrick" wrote: >My goodness, Cindy. >We have a large number of bacteria, and other organisms, attached to a >surface. What else is required for it to be considered a biofilm? I >think your response was rather arch and superior. Hear hear! I think YOUR original response was first-class. If it lacked anything, IMHO, it lacked only inasmuch as it sketched the definitional boundary of a biofilm _insufficiently_ broadly. Cindy had written (in part): >> Furthermore, DB Hendrick also insinuates that microbial community = biofilm. >> Perhaps it is very likely that the organisms assembled in a biofilm function >> as a community; but just because that organisms function as a community >> does not imply that they are biofilms!! >> Sorry to be so severe, but I think that a professional technical writer >> should be a bit more careful in use of terminology. As a professional mathematical modeller, I have a passing interest in biofilms in the very broadest sense of the word (I personally have no qualms about thinking about e.g. life on the surface of a planet, as a biofilm). This interest has been catalysed by a friend and ex-colleague of mine, who has been working in the area for several years since obtaining his PhD in the subject. I rate his intellectual capability for deep and questioning thought very highly, and when he tells me that he has one biofilm-related question which to date no-one who purports to be expert in the field has been able to answer to his satisfaction, I rate that as a fairly telling observation. The question is this: "How is membership of a biofilm defined?" It seems to me that the answer to this question is intimately related to the answer to the question: "How is a biofilm defined?" and it in turn seems to me that the dogmatic Cindy ought to be admirably placed to answer both these questions satisfactorily. If she cannot, then I venture that she should think a little more carefully before admonishing others for insufficient terminological caution. Andy Spragg Speculate to accumulate; catabolize to anabolize; reculer pour mieux sauter. ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Tue Jul 20 09:26:00 1999 Path: biosci!biosci!not-for-mail From: P.Stoodley@exeter.ac.uk (paul stoodley) Newsgroups: bionet.microbiology.biofilms Subject: Re: need for definitions Date: 20 Jul 1999 03:25:53 -0700 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 113 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: References: <3.0.5.32.19990719133028.007aa7e0@leela.swt.edu> NNTP-Posting-Host: net.bio.net Bob, this is a good point and I would even add a few more definitions that may need to be made - even for the more obviously recognized biofilms. Many biofilms are heterogeneous consisting of groups of cells, which are referred to by a number of different terms (microcolonies, cell clusters, stacks, fronds, streamers, corn cobs, mounds etc.). Some of these are descriptive and are used to try to give some idea of morphology or shape of the structure. I like the term "micro-colonies" because it conveys the idea of a grouping of cells at a specific location on a surface, however, in a mixed species biofilms it may be misleading to some because it implies that each microcolony is a mono-culture of clones. Another consideration are the spaces between the cell clusters (sometimes called voids or channels). Are these an integral part of the biofilm? For example, when we talk about the thickness of a biofilm attached to a solid surface do we refer to the distance from the surface of a hypothetical plane which lays across the peaks of a biofilm or an average thickness which takes into account the spaces between the microcolonies and will be somewhat less than the maximum thickness. The same goes for cell density. Is it more useful to talk about the density of cells in the biomass portion of the biofilm or the density of cells in the biomass + spaces portions of the biofilm? It may be useful to start thinking about biofilms in terms of primary, secondary and tertiary structures. For example the primary structure could be cells, EPS, and in some cases an inorganic component (sediments, scale corrosion products etc.) For now I will concentrate on cells and EPS as primary structures. These can then be arranged in many different ways, possibly depending on the environmental conditions in which a particular biofilm is accumulating. Some secondary structures may be "cell clusters, mounds, streamers, ripples, microcolonies, stacks, fronds etc. AS WELL as the spaces between them (voids and channels). Finally, the secondary structures may be combined to give an overall tertiary biofilm structure. So we might have a base film + streamers, or micro-colonies + streamers + ripples etc. etc. It might be an interesting exercise to invite the group to post all of the different types of biofilms that they observe and see if they can be classified into groups so that when someone talks of an "A -type or fluffy" biofilm it is understood what is meant. I imagine that this sort of thing has been done already for larger ecosystems such as forests or grasslands. Defining things is a balancing act between the usefulness of being able to convey generalisations rapidly and the risk of limiting our scope of thinking by excluding certain areas because of rigid definitions. A couple question that have come up at the last two Biofilm Club meetings at Gregynog UK are "is there a universal biofilm definition" and "would such a definition be useful". I am not sure if the answers were Yes or No! It will be interesting to see if the group thinks that this topic is worthy of debate. Paul Stoodley Exeter University Center for Biofilm Engineering On 20 Jul 1999 00:35:12 -0700 Bob McLean wrote: > Hi everyone, > Last summer at ISME8 (8th International Symposium on Microbial Ecology) a > question was raised as to a true "definition" of a biofilm. While I am > sure that we can all agree that dental plaque and the slime-coated rocks in > rivers are two examples of biofilms, we need to reach some sort of > consensus on this definition. I pose the following questions for discussion: > 1) Does one adherent microorganism constitute a biofilm? > 2) If not, then how many do we need to start referring to an adherent > population as a biofilm? > 3) At what point would the term "microcolony" apply? > 4) Do biofilms require metabolically active organisms? > 5) If metabolism is required, then what type of metabolism should be > essential (proton motive force, respiration, biosynthesis, etc)? > 6) On the lighter side, has anyone given their lab a good nickname? (My > lab at Southwest Texas State University has adopted the name "Slime Gang") > It is sometimes tempting to get confrontational during some of these > discussions. I have a lot of respect for the participants in this > discussion group, both on a personal and a professional level. I would > encourage people to enjoy the science (including my first five comments) > and when possible have fun (my comment 6). > Sincerely, > Bob McLean > ___________________________________________________________________________ > R.J.C. (Bob) McLean, Ph.D. > Dept. Biology > Southwest Texas State University > 601 University Drive > San Marcos, Tx 78666 > USA > (512)245-3365 phone > (512)245-8713 FAX > Email: RM12@swt.edu > http://www.bio.swt.edu/micro/mclean/mclean.html > ---------------------- paul stoodley University of Exeter --- ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Tue Jul 20 14:06:00 1999 Path: biosci!biosci!not-for-mail From: Keith.Rose@bristol.ac.uk (Keith Rose) Newsgroups: bionet.microbiology.biofilms Subject: Re: need for definitions Date: 20 Jul 1999 08:06:22 -0700 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 33 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: References: <3.0.5.32.19990719133028.007aa7e0@leela.swt.edu> NNTP-Posting-Host: net.bio.net Hi all, I've been mulling over this question about "what is a biofilm" ever since the memorable debate during the Biofilms symposium at the Sheffield BDSR a few years ago. There really is a place for the type of definition that Paul mentioned, to make it immediately obvious what "type" of biofilm one is talking about, but this wouldn't really make it clear what is and what isn't a biofilm. For my part, I suggested that a convenient definition would be any system in which the contents of the extracellular fluid are significantly different from the fluid at the biofilm surface (Rose and Turner, BBA 1379, 185-190). This could also go some way to defining the boundaries of the biofilm. Cheers, Keith ---------------------- Dr R.K. Rose Restorative Dentistry Bristol Dental Hospital Lower Maudlin Street Bristol BS1 2LY UK +117 9284334 (fax +117 9284778) --- ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Tue Jul 20 14:06:00 1999 Path: biosci!biosci!not-for-mail From: "Jaime Finguerut" Newsgroups: bionet.microbiology.biofilms Subject: Hiding the attachment region of bacteria Date: 20 Jul 1999 08:06:22 -0700 Organization: Centro de Tecnologia Copersucar Lines: 34 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <1901A865D3@azul.ctc.com.br> NNTP-Posting-Host: net.bio.net Dear Friends: I was reading the messages of the denture biofilms and I decided to ask you a, perhaps, too generic question. I would like to know if there is a way to prevent the formation of biofilms (specially in the bucal cavity) hiding or saturating the attachment area of the bacteria. I read some messages about the use of polymeric material as coatings but my question would be also related to substances that mimic the way the bacteria use to attach (pili, lectins, adhesins, etc) that we can use, before the bacteria began making the biofilm. In a certain way antibodies do this job, but they are produced by the human host and not added. Do you know any references about this kind of strategy ? Is it feasible, I mean looking for a similar way the bacteria attach and using it to prevent the attachment? I thank you in advance for your kind help. Best Regards ------------------------------------ Jaime Finguerut (Mr., chem.eng.) Copersucar Cx.Postal 162 Piracicaba Sao Paulo BRAZIL 13400-970 fax +55 19 429 8109 jaime@azul.ctc.com.br ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Tue Jul 20 14:06:00 1999 Path: biosci!biosci!not-for-mail From: Tim Charlton Newsgroups: bionet.microbiology.biofilms Subject: Biofilms definition? Date: 20 Jul 1999 08:06:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 56 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <3794660C.B09FB9A@unsw.edu.au> NNTP-Posting-Host: net.bio.net Dear All, As a first pass at Bob MacLean's challenge for a definition of a biofilm.... "Biofilm" is useful as a general descriptive term because it covers a range of conditions. I think that it would be a red herring to try and give "biofilm" a definition that is narrow, being restricted to just one or a limited number of states. I therefore like a definition such as " organisms which occupy the interface between two phases e.g. liquid-solid, liquid-gas or solid-gas". References to biofilms often describe organisms fixed at the interface encased in an exopolyer matrix. Nivens DE et al [J of Ind Micro. 15, 263-276] cites Characklis and Marshall (eds.) i.e. cells immobilised at a substratum and frequently embedded in an organic polymer matrix of microbial origin..... which is not necessarily uniform in time or space [Characklis and Marshall (eds.) Biofilms ; a basis for an interdisciplinary approach, 1990]. I think that this is one reasonable definition. I wouldn't get too hung up about where the interfacial regions begin or end but simply to describe dynamic processes between the substratum and the bulk pahse such as detachment/attachment and concentration gradients. The interfacial region will also be dynamic being defined by the living surface which may have solid and liquid properties such as a hydrated polymer gel. Scale is an issue in defining the interfacial region and in this light I like Andy Spragg's view from space which sees the thin veneer of green and blue on the surface of the earth as a biofilmm. It is also useful to go down from the microbial scale (microns) to the molecular scale (nano-attometres) because chemical interactions must also influence microbial behaviour. (As an aside I am interested in bringing a bit more aquatic chemistry into the study of microbial biofilms.) The job is then becomes to use more descriptive terms to define the way the organisms behave within this interfacial region. Andy Spragg's original question of how is membership of a biofilm defined is interesting. For example research by Paul March and Helen Dalton at UNSW shows a members of a bacterium (SW8) that detaches from one colony and moves to another. Even though the individual that are on the move are not attached it is probably useful to consider them still part of the biofilm and the detachment/reattachment behaviour as a biofilm process. In summary then I would like to see an emphasis upon relationships, dynamic processes and scale. Perhaps the emphasis should be on authors to apply a set of descriptive terms in their introduction to define the boundaries of their "biofilm worlds". Regards Tim Charlton ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Tue Jul 20 14:06:00 1999 Path: biosci!biosci!not-for-mail From: paul stoodley Newsgroups: bionet.microbiology.biofilms Subject: Re: need for definitions Date: 20 Jul 1999 08:06:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 136 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I am not sure if this meassge already went out to the group since I did not put "biofilms@net.bio.net" in the address. Sorry for those who have already seen it but I have added a ps to the end. Paul Stoodley. Bob, This is a good point and I would even add a few more definitions that may need to be made - even for the more obviously recognized biofilms. Many biofilms are heterogeneous consisting of groups of cells, which are referred to by a number of different terms (microcolonies, cell clusters, stacks, fronds, streamers, corn cobs, mounds etc.). Some of these are descriptive and are used to try to give some idea of morphology or shape of the structure. I like the term "micro-colonies" because it conveys the idea of a grouping of cells at a specific location on a surface, however, in a mixed species biofilms it may be misleading to some because it implies that each microcolony is a mono-culture of clones. Another consideration are the spaces between the cell clusters (sometimes called voids or channels). Are these an integral part of the biofilm? For example, when we talk about the thickness of a biofilm attached to a solid surface do we refer to the distance from the surface of a hypothetical plane which lays across the peaks of a biofilm or an average thickness which takes into account the spaces between the microcolonies and will be somewhat less than the maximum thickness. The same goes for cell density. Is it more useful to talk about the density of cells in the biomass portion of the biofilm or the density of cells in the biomass + spaces portions of the biofilm? It may be useful to start thinking about biofilms in terms of primary, secondary and tertiary structures. For example the primary structure could be cells, EPS, and in some cases an inorganic component (sediments, scale corrosion products etc.) For now I will concentrate on cells and EPS as primary structures. These can then be arranged in many different ways, possibly depending on the environmental conditions in which a particular biofilm is accumulating. Some secondary structures may be "cell clusters, mounds, streamers, ripples, microcolonies, stacks, fronds etc. AS WELL as the spaces between them (voids and channels). Finally, the secondary structures may be combined to give an overall tertiary biofilm structure. So we might have a base film + streamers, or micro-colonies + streamers + ripples etc. etc. It might be an interesting exercise to invite the group to post all of the different types of biofilms that they observe and see if they can be classified into groups so that when someone talks of an A -type or fluffy or whatever, biofilm it is readily understood what is meant. I imagine that this sort of thing has been done already for larger ecosystems such as forests or grasslands. For definitions to be useful they should be able to convey ideas and generalisations rapidly and yet not be so rigid that they limit our scope of thinking. A couple question that have come up at the last two Biofilm Club meetings at Gregynog UK are "is there a universal biofilm definition" and "would such a definition be useful". I am not sure if the answers were Yes or No! It will be interesting to see if the group thinks that this topic is worthy of debate. PS. I am also interested to hear what the group thinks about "EPS" vs "slime"? I believe that the term "slime" was first used in a biofilm context to descripe the slippery material that coated wetted surfaces. This was then changed to EPS (extracellular polymeric sugars or extracellular polysaccharides) to give a more specific technical description of the composition of the slime i.e. sugars. Costerton also used the term "glycocaylix" but this is associated with the "slime" around individual cells not the material that makes up the matrix of the biofilm. (Is EPS a mixture of individual glycocalicies?). However, now it is shown that the EPS can contain protiens and nucleic acids so the term EPS has been subtly changed by some to mean Extracellular Polymeric Substances. It seems that we have now gone full circle. We have a term "EPS" which sounds more technical than slime but in fact does not give any more specificity. Why not go back to bacterial "slime" again until we can define EPS a little better? Or if we like the acronym EPS why not extracellular polymeric slime? I have just done some work on P. aeruginosa and mixed culture biofilms which showed that these biofilms did rather behave like slug slime! Paul Stoodley Exeter University Center for Biofilm Engineering On 20 Jul 1999 00:35:12 -0700 Bob McLean wrote: > Hi everyone, > Last summer at ISME8 (8th International Symposium on Microbial Ecology) a > question was raised as to a true "definition" of a biofilm. While I am > sure that we can all agree that dental plaque and the slime-coated rocks in > rivers are two examples of biofilms, we need to reach some sort of > consensus on this definition. I pose the following questions for discussion: > 1) Does one adherent microorganism constitute a biofilm? > 2) If not, then how many do we need to start referring to an adherent > population as a biofilm? > 3) At what point would the term "microcolony" apply? > 4) Do biofilms require metabolically active organisms? > 5) If metabolism is required, then what type of metabolism should be > essential (proton motive force, respiration, biosynthesis, etc)? > 6) On the lighter side, has anyone given their lab a good nickname? (My > lab at Southwest Texas State University has adopted the name "Slime Gang") > It is sometimes tempting to get confrontational during some of these > discussions. I have a lot of respect for the participants in this > discussion group, both on a personal and a professional level. I would > encourage people to enjoy the science (including my first five comments) > and when possible have fun (my comment 6). > Sincerely, > Bob McLean > ___________________________________________________________________________ > R.J.C. (Bob) McLean, Ph.D. > Dept. Biology > Southwest Texas State University > 601 University Drive > San Marcos, Tx 78666 > USA > (512)245-3365 phone > (512)245-8713 FAX > Email: RM12@swt.edu > http://www.bio.swt.edu/micro/mclean/mclean.html > ---------------------- paul stoodley University of Exeter ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Tue Jul 20 14:06:00 1999 Path: biosci!biosci!not-for-mail From: "Robert J. Palmer Jr." Newsgroups: bionet.microbiology.biofilms Subject: Re: need for definitions Date: 20 Jul 1999 08:06:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 65 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi Bob, Good points, especially for those just getting into the field and for proposal/paper reviewers on the fringes of the field. My 2 cents worth: >1) Does one adherent microorganism constitute a biofilm? Absolutely, especially if you are working with pure cultures. Many of us believe the suite of physiological changes that constitute "the biofilm phenotype" begins at attachment. What happens later in time and space depends on what other organisms (those of the same phenotype or of different phenotpyes) enter the equation. Also, as I stated in the Biofilms Workshop at ASM last May, we need to start thinking about interfaces rather than adherence to substrata - any interface that will allow aggregation and (most importantly) activity of biomass. The community that develops there, whether of a single phenotype or of multiple phenotypes, constitutes a "biofilm". It would be interesting to compare the sorts of physiological changes that take place through simple aggregation (clumps of bacteria that are not really adherent to a substratum) with those that occur through aggregation at an interface or through true adherence to a substratum. >2) If not, then how many do we need to start referring to an adherent >population as a biofilm? Question of scale, observers's perspective and all that. If you are examining an event at the community level, then there had better be a community present. I have made my case for single-cell studies above. >3) At what point would the term "microcolony" apply? Colony implies discrete units. Microcolony implies small discrete units. Discrete units implies some sort of discretion. Psuedomonads in flowing in vitro systems form tiny clumps of cell before these clumps coalesce into a carpet of cells. Here the definition might best be approached by a spatial equation: growth (or accumulation, in the case of motile cells) in Z must be greater than growth in XY. Only a time-resolved approach can yield reliable data here. >4) Do biofilms require metabolically active organisms? What's your definition of "metabolically active"? >5) If metabolism is required, then what type of metabolism should be >essential (proton motive force, respiration, biosynthesis, etc)? I'd vote for minimal metabolism (repair). Now we are delving into the definition of alive vs dead. Start thinking about spores and desiccated cells. Cases exists where cyanobacterial cells from botanical specimens (dried sheets, like pressed flowers) have been recultured after nearly a century.... As you can tell, I'm an extremist. If you are concerned about the impact of biofilms in real-world processes such as corrosion, infection, etc., then perhaps the metabolic bar ought to be raised a bit. >6) On the lighter side, has anyone given their lab a good nickname? (My >lab at Southwest Texas State University has adopted the name "Slime Gang") >It is sometimes tempting to get confrontational during some of these >discussions. I have a lot of respect for the participants in this >discussion group, both on a personal and a professional level. I would >encourage people to enjoy the science (including my first five comments) >and when possible have fun (my comment 6). I prefer stodgy names like "Biofilm Imaging Facility" that can be converted to lighter-sounding acronyms (BIF). Rob Palmer CEB/UT ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Tue Jul 20 18:33:00 1999 Path: biosci!biosci!not-for-mail From: Cindy MORRIS Newsgroups: bionet.microbiology.biofilms Subject: Re: need for definitions Date: 20 Jul 1999 12:33:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 77 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <1.5.4.32.19990720170720.006b0008@avi-maur.avignon.inra.fr> NNTP-Posting-Host: net.bio.net The debate about the definition of the term "biofilm" is timely. Some of the existing definitions have implications that make it difficult to know when it is appropriate to use this term. When my research group observed that matrix-enclosed microbial aggregates were ubiquitous on leaf surfaces, we hesitated quite some time before deciding to call them "biofilms" in our publications. I have a very pragmatic opinion about the definition of the term "biofilm "resulting from my lab's debate about whether or not we could accurately use this term and my belief that definitions should help us communicate clearly and avoid confusion. 1) The definition of biofilm should account for phenomena not already described by other terms. Two competitor terms are "attached / adhering" cells and "colonies / microcolonies". "Attached cells" could adequately describe single cells adhering to a surface. Hence, I think that it is confusing to use "biofilm" to describe the attachment of single cells. "Colony" generally evokes an aggregated clonal population; matrices and attachment are not essential. 2) The definition of biofilm (or any other term for that matter) should not lead to confusion between the myriad properties that this phenomenon might or might not have and the basic essential characteristics. The point of some of the early definitions of biofilms, such as that of Characklis and Marshall (1990): "A biofilm consists of cells immobilized at a substratum and frequently embedded in an organic polymer matrix of microbial origin." was probably to distinguish planktonic, solitary cells from sessile, aggregated cells enrobed in a matrix. Many of the potential consequences for the ecology of the microorganisms harbored in biofilms are obvious from this definition. Hence, this definition gives a good starting point for investigations into all of the other properties that biofilms might have. If on top of a basic definition we add properties that perhaps cannot be generalized (type of metabolism; the size of channel space for example), we risk to foster schisms in biofilm research. For example, I have heard about debate concerning the fact that biofilms in unsaturated environments are not true biofilms. Biofilms were first observed in aquatic (or fluid-containing) environments and there seems to be a need for fluid implicit in some definitions of biofilms. Bacteria are essentially sessile for most of the time that they are on leaf surfaces (except for the ephemeral periods of free moisture on the leaf). For leaf surfaces the term "planktonic" doesn't have any sense. Hence, it can be argued that what we call biofilms in the phyllosphere might not be true biofilms. But, the aggregation of cells of divers microbial species, combined to the production of an exopolymeric matrix has the potential for a profound impact on the ecology epiphytic bacteria. The properties of biofilms in water-saturated and unsaturated environments might not all be the same, but should we create definitions that lead to incompatibilities between them? I vote for a definition that includes 1) contact with a surface, 2) presence of an exopolymeric matrix, 3) the presence of more that one cell. This definition then can give way to what distinguishes the behavior of biofilms: the potential for cell-to-cell communication and metabolic exchange, AND protection from divers stresses and the creation of chemical gradients due to the presence of the matrix, AND contact-induced phenotypes. ********** On the lighter side: we don't have a nickname for my lab, but we did have lots of laughs trying to come up with the appropriate term to describe "planktonic" bacteria on leaf surfaces. As I suggested above, "planktonic" is inappropriate for bacteria on leaf surfaces. Among the losing terms to replace planktonic were "asocial" and "lonely". I think that with all of the communication going on inside of biofilms, "lonely" may someday find its place in our writing to describe the organisms that are excluded. Cindy E. Morris INRA - Station de Pathologie Vegetale B.P. 94 84143 Montfavet, France tel : (33) 490-31-63-84 fax : (33) 490-31-63-35 e-mail : morris@avignon.inra.fr ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Tue Jul 20 18:33:00 1999 Path: biosci!biosci!not-for-mail From: "K.E.Cooksey" Newsgroups: bionet.microbiology.biofilms Subject: Definition of a biofilm Date: 20 Jul 1999 12:33:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <3.0.6.32.19990720113809.007abbb0@gemini.oscs.montana.edu> NNTP-Posting-Host: net.bio.net I don't want to sound as though I am older than I am, but why do we need another definition of a biofilm? Perhaps the first review of biofilm engineering and biology was published 16 years ago by the late Bill Characklis and I. In it we defined a biofilm in the following way : ....immobilized cells grow, reproduce, and produce extracellular polmer substances that frequently extend from the cell, forming a tangled mass of fibers lending structure to the entire assemblage which shall be termed a biofilm. The term biofilm does not necessarily imply a surface accumulation that is uniform in time and/or space. We dveloped this into a shorter version that defines a biofilm as "the accumulation of microbial cells , their products and inorganic particles at a wetted surface ".[ to take into the account that natural biofilms accumulate lots of silt]. Let's not re-invent the wheel! Keith Cooksey, Research Professor As part of the final part of the review we mentioned 13 areas that we felt were in need of further work. It is interesting to see how many of these STILL need further work! The reference is Adv in Appl. Microbiol. 29 93-137 [1983] ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Tue Jul 20 21:59:00 1999 Path: biosci!biosci!not-for-mail From: sparge@globalnet.co.uk (Andy Spragg) Newsgroups: bionet.microbiology.biofilms Subject: Re: Definition of a biofilm Date: 20 Jul 1999 15:59:39 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 39 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <3794ea09.253488617@smtpmail.globalnet.co.uk> References: <3.0.6.32.19990720113809.007abbb0@gemini.oscs.montana.edu> NNTP-Posting-Host: net.bio.net On 20 Jul 1999 12:33:16 -0700, "K.E.Cooksey" wrote: >I don't want to sound as though I am older than I am, but why do we need >another definition of a biofilm? Let's not re-invent the wheel! >We developed ... a shorter version that defines a biofilm as "the >accumulation of microbial cells , their products and inorganic particles at >a wetted surface ".[ to take into the account that natural biofilms >accumulate lots of silt]. I'm mainly interested (see the "Biofilm treatment with polymers" thread) in the definition of a biofilm as a means to an end, namely the definition of _membership_ of a biofilm. Does your definition help with this one? Don't think so: - Are grazing protozoa members of a biofilm? Not by your definition - but a case could be made. - What about Tim Charlton's example of a motile bacterium which can move from one colony to another? Does it belong? Do any other microorganisms which are "facultative planktonic", to coin a phrase? Not by your definition (at least, not as far as I can see) - but membership seems very plausible in this case. - What about adventitious microbes? Your definition would say yes - but it seems a bit unjust to exclude the ones that got there my design, and include the ones that got there by accident. It's a nice concise definition and it probably captures most of what most people understand by the term biofilm, but it seems to me that the last word has certainly not been said thereby. What do others think? Andy Spragg Speculate to accumulate; catabolize to anabolize; reculer pour mieux sauter. ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Tue Jul 20 22:01:00 1999 Path: biosci!biosci!not-for-mail From: "Jaime Finguerut" Newsgroups: bionet.microbiology.biofilms Subject: Rapid ID kits for LAB Date: 20 Jul 1999 16:01:52 -0700 Organization: Centro de Tecnologia Copersucar Lines: 33 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <21E50738619@azul.ctc.com.br> NNTP-Posting-Host: net.bio.net Dear Friends of Lactacid: We are needing some advice finding a laboratory or a firm that would like to develop a simple, rapid and cheap test kit to detect the presence of a certain lactic acid bacteria (Lactobacillus fermentum strains) that are able to induce flocculation in our industrial alcoholic fermentation process. This test kit must (perhaps) be developed not for the bacteria itself but for detecting the protein (s?) responsible for the co-flocculation phenomena. We have considerable evidence that most of the flocculation problems we have are directly related to Lacobacillus infection and it is certainly mediated by lectins, that attach to the mannose moiety of the cell wall of the bacteria. We can send a lyophil of a typical strain that is able to co-flocculate with our yeast. If possible reply directly to me (jaime@azul.ctc.com.br) I thank you in advance for your kind help. ------------------------------------ Jaime Finguerut (Mr., chem.eng.) Copersucar Cx.Postal 162 Piracicaba Sao Paulo BRAZIL 13400-970 fax +55 19 429 8109 jaime@azul.ctc.com.br ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Tue Jul 20 22:01:00 1999 Path: biosci!biosci!not-for-mail From: jeffrey.nickerson@ummed.edu Newsgroups: bionet.microbiology.biofilms Subject: Postdoctoral Position Available Date: 20 Jul 1999 16:01:52 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <01JDSHFZ2RMQ8WW18Y@wccf.mit.edu> NNTP-Posting-Host: net.bio.net Postdoctoral Position(s) Available Candidates should have a strong background in cell biology, biochemistry, or molecular biology. We are studying structural proteins of the nucleus that have a role in RNA processing. One of these proteins is concentrated in the interchromatin granule clusters (splicing speckles) of the nucleus but a sub-population is highly enriched in long nuclear tracks. These tracks often originate at splicing speckles and terminate near the nuclear periphery- suggesting that they may be involved in the transport of RNA, protein, or complexes within the nucleus and toward the cytoplasm. The postdoctoral associate would determine the role that this nuclear protein may play in transport, in the spatial organization of RNA splicing, and in the structure of nuclear tracks. The experimental approach will integrate molecular and microscopy techniques. The University of Massachusetts Medical School is a growing institution located within the greater Boston area. The Department of Cell Biology has especially strong research programs in nuclear and chromatin structure, cytoskeletal function, and mitotic architecture. Good core facilities for microscopy and molecular biology are available within the department. Interested candidates should contact: Jeffrey A. Nickerson, Ph.D. (Jeffrey.Nickerson@ummed.edu) Department of Cell Biology and Cancer Center University of Massachusetts Medical School 55 Lake Avenue North Worcester, MA 01655 (508) 856-2312 (508) 856-5612 FAX { GOTOBUTTON BM_1_ Jeffrey.Nickerson@ummed.edu} ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Wed Jul 21 08:33:00 1999 Path: biosci!biosci!not-for-mail From: "Paul S" Newsgroups: bionet.microbiology.biofilms Subject: PDI "discovery series" scanner and SUN computer.....HELP Date: 21 Jul 1999 02:33:40 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <7n32ug$57$1@autumn.news.rcn.net> NNTP-Posting-Host: net.bio.net The computer reports a bad IDPROM when booted, and now the "Discovery Series" software used to run the scanner no longer works. It reports that the current user is not authorized to use the software. OS is Open Windows (ver 4.??) I think. Equipment is about 9 years old. The PDI name and equipment has been bought by BioRad, and they have adopted it for Mac and PC, no longer SUN. They do not provide any support for the older SUN system. Are the two problems related? If so, is there a fix or workaround? ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Wed Jul 21 14:29:00 1999 Path: biosci!biosci!not-for-mail From: "Robert J. Palmer Jr." Newsgroups: bionet.microbiology.biofilms Subject: Re: Definition of a biofilm Date: 21 Jul 1999 08:29:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 59 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I don't think anyone is reinventing the wheel here. Bob brought up some points that are frequently raised WITHIN the biofilm community, and as such are even more pertinent to those entering a burgeoning field. For example, does a single cell qualify as a biofilm by your definition? I would suggest not, but only by virtue of the wording that requires "accumulation". However a single cell can be immobilized and can produce extracellular material. Let's say it divides. Do those two cells now constitute a biofilm as an "accumulation"? They certainly fit all the other requirements of either of your definitions. The Characklis-edited magnum opus (to which many individuals made very important contributions) is still the Bible of biofilm research despite its heavy emphasis on engineering aspects and desptite our recognition that biofilms are NOT black boxes whose physical (and physiological) characteristertics can be modeled like a bomb blast. I too am a bit bothered by all this worry about what constitutes a biofilm - it has been and always will be an operating definition subject to interpretation and "waffle". Discussion certainly does a minimal amount of damage, and open discussion in this (and other) forums helps clarify to which camps we all belong. Rob Palmer CEB/UT >I don't want to sound as though I am older than I am, but why do we need >another definition of a biofilm? Perhaps the first review of biofilm >engineering and biology was published 16 years ago by the late Bill >Characklis and I. In it we defined a biofilm in the following way : >....immobilized cells grow, reproduce, and produce extracellular polmer >substances that frequently extend from the cell, forming a tangled mass of >fibers lending structure to the entire assemblage which shall be termed a >biofilm. The term biofilm does not necessarily imply a surface accumulation >that is uniform in time and/or space. >We dveloped this into a shorter version that defines a biofilm as "the >accumulation of microbial cells , their products and inorganic particles at >a wetted surface ".[ to take into the account that natural biofilms >accumulate lots of silt]. >Let's not re-invent the wheel! >Keith Cooksey, Research Professor >As part of the final part of the review we mentioned 13 areas that we felt >were in need of further work. It is interesting to see how many of these >STILL need further work! >The reference is Adv in Appl. Microbiol. 29 93-137 [1983] > >------------------------------------------------------------------- >To reply to the group as well as to the originator, make sure that >the address biofilms@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. ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Thu Jul 22 07:42:00 1999 Path: biosci!biosci!not-for-mail From: "David B. Hedrick" Newsgroups: bionet.microbiology.biofilms Subject: Re: Definition of a biofilm - Again Date: 22 Jul 1999 01:42:33 -0700 Organization: Hedrick Services Lines: 82 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <379678F2.7B12@icx.net> References: Reply-To: davidbhedrick@icx.net NNTP-Posting-Host: net.bio.net Dear Robert and all: I'd like to suggest that the term "biofilm" be used to distinguish attached microbes from free-living or planktonic organisms. A single bacterium (AKA "lonely") still derives benefits from attachment - often higher carbon availability, not being swept away, etc. How many "lonely" bacteria are there in a square centimeter? Isn't it just a matter of degree, and a subjective opinion at that, whether 2 bacteria are close enough together to qualify as a biofilm? People like Robert with his lovely laser confocal microscope can routinely measure the distance between organisms. But those of us using chemical or molecular techniques have no way of determining whether the organisms are disperse or clustered on the surface. Short of hiring Rob, that is. The purpose of a semantic discussion should be to obtain the simplest usable definition, so that we can go on to use it. Problems in definition I've run into are with things that look like biofilms but are free-floating in water. Methanosarcina grow in clumps under most cultural conditions, and are more resistant to toxins (oxygen in this case) when clumped. Many aqueous systems have solid particles such as silt and clay which are often colonized. Do the bacteria colonizing a clay particle many times their size act like planktonic or biofilm organisms? Then what about the flocs that the bioreactor people are always complaining about? > > I don't think anyone is reinventing the wheel here. Bob brought up some > points that are frequently raised WITHIN the biofilm community, and as such > are even more pertinent to those entering a burgeoning field. > For example, does a single cell qualify as a biofilm by your definition? > I would suggest not, but only by virtue of the wording that requires > "accumulation". However a single cell can be immobilized and can produce > extracellular material. Let's say it divides. Do those two cells now > constitute a biofilm as an "accumulation"? They certainly fit all the > other requirements of either of your definitions. The Characklis-edited > magnum opus (to which many individuals made very important contributions) > is still the Bible of biofilm research despite its heavy emphasis on > engineering aspects and desptite our recognition that biofilms are NOT > black boxes whose physical (and physiological) characteristertics can be > modeled like a bomb blast. > I too am a bit bothered by all this worry about what constitutes a biofilm > - it has been and always will be an operating definition subject to > interpretation and "waffle". Discussion certainly does a minimal amount of > damage, and open discussion in this (and other) forums helps clarify to > which camps we all belong. > Rob Palmer > CEB/UT > >I don't want to sound as though I am older than I am, but why do we need > >another definition of a biofilm? Perhaps the first review of biofilm > >engineering and biology was published 16 years ago by the late Bill > >Characklis and I. In it we defined a biofilm in the following way : > >....immobilized cells grow, reproduce, and produce extracellular polmer > >substances that frequently extend from the cell, forming a tangled mass of > >fibers lending structure to the entire assemblage which shall be termed a > >biofilm. The term biofilm does not necessarily imply a surface accumulation > >that is uniform in time and/or space. > >We dveloped this into a shorter version that defines a biofilm as "the > >accumulation of microbial cells , their products and inorganic particles at > >a wetted surface ".[ to take into the account that natural biofilms > >accumulate lots of silt]. > >Let's not re-invent the wheel! > >Keith Cooksey, Research Professor > >As part of the final part of the review we mentioned 13 areas that we felt > >were in need of further work. It is interesting to see how many of these > >STILL need further work! > >The reference is Adv in Appl. Microbiol. 29 93-137 [1983] > > -- ~DBH Technical writing, literature search, and data analysis at the interface of chemistry and biology. davidbhedrick@icx.net David B. Hedrick P.O. Box 16082 Knoxville, TN 37996 ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Thu Jul 22 09:51:00 1999 Path: biosci!biosci!not-for-mail From: Cindy MORRIS Newsgroups: bionet.microbiology.biofilms Subject: Re: Definition of a biofilm - Again Date: 22 Jul 1999 03:51:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 42 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <1.5.4.32.19990722094533.00692b7c@avi-maur.avignon.inra.fr> NNTP-Posting-Host: net.bio.net Dear All: here are some additional arguements for the debate relative to the most recent message of DB Hedrick: > A single >bacterium (AKA "lonely") still derives benefits from attachment - often >higher carbon availability, not being swept away, etc. ** So, in the case of attachement of a single cell, why is the description "attached cell" not sufficient?? If we call it a biofilm, this implies that there are other properties that a single attached cell might not have. Would we need to say "a single-celled non-matrix-enclosed biofilm"? >How many >"lonely" bacteria are there in a square centimeter? Isn't it just a >matter of degree, and a subjective opinion at that, whether 2 bacteria >are close enough together to qualify as a biofilm? *** I would argue that in many cases it is NOT a subjective opinion. The significance of a biofilm being more that one cell is that there is a potential for "communication" (genetic or chemical exchange) between the cells; that the cells function as a tissue and have behaviors that the single cell cannot have. This communication cannot take place if the bacteria are not sufficiently close and if there is not a vehicle (matrix, pili, etc) for transporting the message . Hence, I would argue that single, attached cells that do not have the potential for communication are "single attached cells". Cindy E. Morris INRA - Station de Pathologie Vegetale B.P. 94 84143 Montfavet, France tel : (33) 490-31-63-84 fax : (33) 490-31-63-35 e-mail : morris@avignon.inra.fr ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Thu Jul 22 20:34:00 1999 Path: biosci!biosci!not-for-mail From: Jan Kreft Newsgroups: bionet.microbiology.biofilms Subject: Re: Definition of a biofilm - Again Date: 22 Jul 1999 14:34:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 119 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: Reply-To: Jan Kreft NNTP-Posting-Host: net.bio.net 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. 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"). 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.). 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. Jan. Jan Kreft Phone +44 (0)1222 875278 Cardiff School of Biosciences Fax +44 (0)1222 874305 Cardiff University E-mail Kreft@cardiff.ac.uk PO Box 915, Cardiff CF10 3TL, UK On 22 Jul 1999, David B. Hedrick wrote: > Dear Robert and all: > I'd like to suggest that the term "biofilm" be used to distinguish > attached microbes from free-living or planktonic organisms. A single > bacterium (AKA "lonely") still derives benefits from attachment - often > higher carbon availability, not being swept away, etc. How many > "lonely" bacteria are there in a square centimeter? Isn't it just a > matter of degree, and a subjective opinion at that, whether 2 bacteria > are close enough together to qualify as a biofilm? People like Robert > with his lovely laser confocal microscope can routinely measure the > distance between organisms. But those of us using chemical or molecular > techniques have no way of determining whether the organisms are disperse > or clustered on the surface. Short of hiring Rob, that is. > The purpose of a semantic discussion should be to obtain the simplest > usable definition, so that we can go on to use it. > Problems in definition I've run into are with things that look like > biofilms but are free-floating in water. Methanosarcina grow in clumps > under most cultural conditions, and are more resistant to toxins (oxygen > in this case) when clumped. Many aqueous systems have solid particles > such as silt and clay which are often colonized. Do the bacteria > colonizing a clay particle many times their size act like planktonic or > biofilm organisms? Then what about the flocs that the bioreactor people > are always complaining about? > > > > I don't think anyone is reinventing the wheel here. Bob brought up some > > points that are frequently raised WITHIN the biofilm community, and as such > > are even more pertinent to those entering a burgeoning field. > > For example, does a single cell qualify as a biofilm by your definition? > > I would suggest not, but only by virtue of the wording that requires > > "accumulation". However a single cell can be immobilized and can produce > > extracellular material. Let's say it divides. Do those two cells now > > constitute a biofilm as an "accumulation"? They certainly fit all the > > other requirements of either of your definitions. The Characklis-edited > > magnum opus (to which many individuals made very important contributions) > > is still the Bible of biofilm research despite its heavy emphasis on > > engineering aspects and desptite our recognition that biofilms are NOT > > black boxes whose physical (and physiological) characteristertics can be > > modeled like a bomb blast. > > I too am a bit bothered by all this worry about what constitutes a biofilm > > - it has been and always will be an operating definition subject to > > interpretation and "waffle". Discussion certainly does a minimal amount of > > damage, and open discussion in this (and other) forums helps clarify to > > which camps we all belong. > > Rob Palmer > > CEB/UT > > >I don't want to sound as though I am older than I am, but why do we need > > >another definition of a biofilm? Perhaps the first review of biofilm > > >engineering and biology was published 16 years ago by the late Bill > > >Characklis and I. In it we defined a biofilm in the following way : > > >....immobilized cells grow, reproduce, and produce extracellular polmer > > >substances that frequently extend from the cell, forming a tangled mass of > > >fibers lending structure to the entire assemblage which shall be termed a > > >biofilm. The term biofilm does not necessarily imply a surface accumulation > > >that is uniform in time and/or space. > > >We dveloped this into a shorter version that defines a biofilm as "the > > >accumulation of microbial cells , their products and inorganic particles at > > >a wetted surface ".[ to take into the account that natural biofilms > > >accumulate lots of silt]. > > >Let's not re-invent the wheel! > > >Keith Cooksey, Research Professor > > >As part of the final part of the review we mentioned 13 areas that we felt > > >were in need of further work. It is interesting to see how many of these > > >STILL need further work! > > >The reference is Adv in Appl. Microbiol. 29 93-137 [1983] ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Fri Jul 23 07:32:00 1999 Path: biosci!biosci!not-for-mail From: "K.E.Cooksey" Newsgroups: bionet.microbiology.biofilms Subject: Re: Definition of a biofilm/SHOULD HAVE GONE TO ALL SUBSCRIBERS Date: 23 Jul 1999 01:32:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 78 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: <3.0.6.32.19990722162155.007b3820@gemini.oscs.montana.edu> NNTP-Posting-Host: net.bio.net >Date: Wed, 21 Jul 1999 09:29:45 -0600 >To: "Robert J. Palmer Jr." >From: "K.E.Cooksey" >Subject: Re: Definition of a biofilm >In-Reply-To: >References: <3.0.6.32.19990720113809.007abbb0@gemini.oscs.montana.edu> > >Rob ; I see your point. One organism is not a biofilm[ look up the meaning of film!], two are a film, albeit a small one , but I think we are entering the " angels on a pin" realm here. I agree that biofilms are not black boxes that can be modeleled easily. I fought contantly with Bill Characklis at coffee many mornings about such. Other examples of academic arguements might include what are the diffrences between biochemistry, biological chemistry and molecular biology? Debates have raged there too. It's all a matter of perspective. I also remember working in Berkeley with Roger Stanier : He believed that there were about 5 Pseudomonads sp.- now because of 16S technology we have dozens. It all depends whether one is a lumper or a splitter. The same can be said of the biofilm debate. > >Keith > > > >At 08:15 AM 7/21/1999 -0400, you wrote: >>I don't think anyone is reinventing the wheel here. Bob brought up some >>points that are frequently raised WITHIN the biofilm community, and as such >>are even more pertinent to those entering a burgeoning field. >> >>For example, does a single cell qualify as a biofilm by your definition? >>I would suggest not, but only by virtue of the wording that requires >>"accumulation". However a single cell can be immobilized and can produce >>extracellular material. Let's say it divides. Do those two cells now >>constitute a biofilm as an "accumulation"? They certainly fit all the >>other requirements of either of your definitions. The Characklis-edited >>magnum opus (to which many individuals made very important contributions) >>is still the Bible of biofilm research despite its heavy emphasis on >>engineering aspects and desptite our recognition that biofilms are NOT >>black boxes whose physical (and physiological) characteristertics can be >>modeled like a bomb blast. >> >>I too am a bit bothered by all this worry about what constitutes a biofilm >>- it has been and always will be an operating definition subject to >>interpretation and "waffle". Discussion certainly does a minimal amount of >>damage, and open discussion in this (and other) forums helps clarify to >>which camps we all belong. >> >>Rob Palmer >>CEB/UT >> >>>I don't want to sound as though I am older than I am, but why do we need >>>another definition of a biofilm? Perhaps the first review of biofilm >>>engineering and biology was published 16 years ago by the late Bill >>>Characklis and I. In it we defined a biofilm in the following way : >>>....immobilized cells grow, reproduce, and produce extracellular polmer >>>substances that frequently extend from the cell, forming a tangled mass of >>>fibers lending structure to the entire assemblage which shall be termed a >>>biofilm. The term biofilm does not necessarily imply a surface accumulation >>>that is uniform in time and/or space. >>>We dveloped this into a shorter version that defines a biofilm as "the >>>accumulation of microbial cells , their products and inorganic particles at >>>a wetted surface ".[ to take into the account that natural biofilms >>>accumulate lots of silt]. >>>Let's not re-invent the wheel! >>>Keith Cooksey, Research Professor >>>As part of the final part of the review we mentioned 13 areas that we felt >>>were in need of further work. It is interesting to see how many of these >>>STILL need further work! >>>The reference is Adv in Appl. Microbiol. 29 93-137 [1983] >>> ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Fri Jul 23 13:19:00 1999 Path: biosci!biosci!not-for-mail From: "Robert J. Palmer Jr." Newsgroups: bionet.microbiology.biofilms Subject: Re: Definition of a biofilm - Again Date: 23 Jul 1999 07:19:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net and still more.. >>How many >>"lonely" bacteria are there in a square centimeter? Isn't it just a >>matter of degree, and a subjective opinion at that, whether 2 bacteria >>are close enough together to qualify as a biofilm? >*** I would argue that in many cases it is NOT a subjective opinion. The >significance of a biofilm being more that one cell is that there is a >potential for "communication" (genetic or chemical exchange) between the >cells; that the cells function as a tissue and have behaviors that the >single cell cannot have. This communication cannot take place if the >bacteria are not sufficiently close and if there is not a vehicle (matrix, >pili, etc) for transporting the message . Hence, I would argue that single, >attached cells that do not have the potential for communication are "single >attached cells". Your point about communication is clearly important. Biofilms offer the advantage of CLOSE communication. However, all the types of communication you mentioned are known to occur in planktonic cells (and, we would postulate, single attached cells), so perhaps these factors are not operable in defining a biofilm - they are operable as advantages of the biofilm habitat, such as access to nutrients unvailable (or sparsely available) in the bulk liquid. Rob Palmer ------------------------------------------------------------------- To reply to the group as well as to the originator, make sure that the address biofilms@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. From owner-biofilms@net.bio.net Fri Jul 23 13:19:00 1999 Path: biosci!biosci!not-for-mail From: "Robert J. Palmer Jr." Newsgroups: bionet.microbiology.biofilms Subject: Re: Definition of a biofilm - Again Date: 23 Jul 1999 07:19:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 89 Sender: daemon@net.bio.net Approved: biofmod@im.dtu.dk Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net 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" structu