View source for Biofilm

{{Short description|Film of microorganisms on a surface}}
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{{For|biographic motion picture|Biographical film}}
{{Use dmy dates|date=April 2022}}
{{Primary sources|date=April 2021}}

[[File:Staphylococcus aureus biofilm 01.jpg|thumb|right|300px|''[[Staphylococcus aureus]]'' biofilm on an indwelling [[catheter]]]]

[[File:Algae in silicified sediment with evaporite crystals. Urgonian carbonate platform of Provence. 1.jpg|thumb|right|300px|Probable [[cyanobacteria]] in the vertical section of a silicified biofilm from the Lower Cretaceous.
Very shallow hypersaline environment of the [[Urgonian]] [[carbonate platform]] of Provence, south eastern France.]]

{{Quote box
 |width = 296px
 |title = [[IUPAC]] definition
 |quote = ''Aggregate'' of microorganisms in which cells that are frequently embedded within a self-produced matrix of extracellular polymeric substances (EPSs) adhere to each other and/or to a surface.
* A biofilm is a system that can be adapted internally to environmental conditions by its inhabitants.
* The self-produced matrix of [[extracellular polymeric substance]]s, which is also referred to as slime, is a polymeric conglomeration generally composed of extracellular ''biopolymers'' in various structural forms.<ref>{{cite journal|title= Terminology for biorelated polymers and applications (IUPAC Recommendations 2012) |journal= [[Pure and Applied Chemistry]] |year= 2012 |volume= 84 |issue= 2 |pages= 377–410 |doi= 10.1351/PAC-REC-10-12-04|doi-access = free | vauthors = Vert M, Doi Y, Hellwich KH, Hess M, Hodge P, Kubisa P, Rinaudo M, Schué F }}</ref>
}}

A '''biofilm''' is a [[Syntrophy|syntrophic]] [[Microbial consortium|community of microorganisms]] in which [[cell adhesion|cells stick to each other]] and often also to a surface.<ref name="CSH">{{cite journal | vauthors = López D, Vlamakis H, Kolter R | title = Biofilms | journal = Cold Spring Harbor Perspectives in Biology | volume = 2 | issue = 7 | article-number = a000398 | date = July 2010 | pmid = 20519345 | pmc = 2890205 | doi = 10.1101/cshperspect.a000398 }}</ref><ref name="Hall-Stoodley" /><ref name="MicrobioJ">{{cite journal | vauthors = Bamford, Natalie C, MacPhee, Cait E, Stanley-Wall, Nicola R | title = Microbial Primer: An introduction to biofilms – what they are, why they form and their impact on built and natural environments | journal = Microbiology  | volume = 169 | issue = 8 | page = 001338 | date = August 2023  | pmid = 37526065 | pmc = 7615007 | doi = 10.1099/mic.0.001338 | doi-access = free }}</ref>  These adherent cells become embedded within a slimy [[extracellular matrix]] that is composed of [[extracellular polymeric substance]]s (EPSs).<ref name="CSH"/><ref name="Hall-Stoodley" /> The cells within the biofilm produce the EPS components, which are typically a [[polymer]]ic combination of extracellular [[polysaccharide]]s, [[protein]]s, [[lipid]]s and [[DNA]].<ref name="CSH"/><ref name=Hall-Stoodley /><ref name="Aggarwal">{{cite journal | vauthors = Aggarwal S, Stewart PS, Hozalski RM | title = Biofilm Cohesive Strength as a Basis for Biofilm Recalcitrance: Are Bacterial Biofilms Overdesigned? | journal = Microbiology Insights | volume = 8 | issue = Suppl 2 | pages = 29–32 | date = January 2016 | article-number = MBI.S31444 | pmid = 26819559 | pmc = 4718087 | doi = 10.4137/MBI.S31444 }}</ref> Because they have a three-dimensional structure and represent a community lifestyle for microorganisms, they have been metaphorically described as "cities for microbes".<ref name="Watnick_2000">{{cite journal | vauthors = Watnick P, Kolter R | title = Biofilm, city of microbes | journal = Journal of Bacteriology | volume = 182 | issue = 10 | pages = 2675–9 | date = May 2000 | pmid = 10781532 | pmc = 101960 | doi = 10.1128/jb.182.10.2675-2679.2000 }}</ref><ref>{{cite news|url= https://www.quantamagazine.org/building-codes-for-bacterial-cities-20170725/|title= Building Codes for Bacterial Cities {{!}} Quanta Magazine|work= Quanta Magazine|access-date= 25 July 2017|archive-date= 26 July 2017|archive-url= https://web.archive.org/web/20170726013257/https://www.quantamagazine.org/building-codes-for-bacterial-cities-20170725/|url-status= live}}</ref>

Biofilms may form on living (biotic) or non-living (abiotic) surfaces and can be common in natural, industrial, and hospital settings.<ref name="Hall-Stoodley">{{cite journal | vauthors = Hall-Stoodley L, Costerton JW, Stoodley P | title = Bacterial biofilms: from the natural environment to infectious diseases | journal = Nature Reviews. Microbiology | volume = 2 | issue = 2 | pages = 95–108 | date = February 2004 | pmid = 15040259 | doi = 10.1038/nrmicro821 | s2cid = 9107205 }}</ref><ref name="LearGLewisGD">{{cite book | veditors = Lear G, Lewis GD | year= 2012 | title= Microbial Biofilms: Current Research and Applications | publisher= [[Caister Academic Press]] | isbn = 978-1-904455-96-7}}</ref> They may constitute a [[microbiome]] or be a portion of it. The microbial cells growing in a biofilm are [[physiology|physiologically]] distinct from [[plankton]]ic cells of the same organism, which, by contrast, are single cells that may float or swim in a liquid medium.<ref name="O'Toole_1998">{{cite journal | vauthors = O'Toole GA, Kolter R | title = Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signalling pathways: a genetic analysis | journal = Molecular Microbiology | volume = 28 | issue = 3 | pages = 449–61 | date = May 1998 | pmid = 9632250 | doi = 10.1046/j.1365-2958.1998.00797.x | s2cid = 43897816 | doi-access = free }}</ref> Biofilms can form on the [[teeth]] of most animals as [[dental plaque]], where they may cause [[tooth decay]] and [[gum disease]].

[[Microorganism|Microbes]] form a biofilm in response to a number of different factors,<ref>{{cite journal | vauthors = O'Toole GA, Kolter R | title = Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development | journal = Molecular Microbiology | volume = 30 | issue = 2 | pages = 295–304 | date = October 1998 | pmid = 9791175 | doi = 10.1046/j.1365-2958.1998.01062.x | s2cid = 25140899 | doi-access = free }}</ref> which may include cellular recognition of specific or non-specific attachment sites on a surface, nutritional cues, lack of light<ref>{{Cite journal |last=Upmanyu |first=Kirti |last2=Haq |first2=Qazi Mohd. Rizwanul |last3=Singh |first3=Ruchi |date=2022-01-01 |title=Factors mediating Acinetobacter baumannii biofilm formation: Opportunities for developing therapeutics |url=https://www.sciencedirect.com/science/article/pii/S2666517422000281 |journal=Current Research in Microbial Sciences |volume=3 |article-number=100131 |doi=10.1016/j.crmicr.2022.100131 |issn=2666-5174|pmc=9325880 }}</ref> or in some cases, by exposure of planktonic cells to sub-inhibitory concentrations of [[antibiotic]]s.<ref>{{cite journal | vauthors = Karatan E, Watnick P | title = Signals, regulatory networks, and materials that build and break bacterial biofilms | journal = Microbiology and Molecular Biology Reviews | volume = 73 | issue = 2 | pages = 310–47 | date = June 2009 | pmid = 19487730 | pmc = 2698413 | doi = 10.1128/MMBR.00041-08 }}</ref><ref>{{cite journal | vauthors = Hoffman LR, D'Argenio DA, MacCoss MJ, Zhang Z, Jones RA, Miller SI | title = Aminoglycoside antibiotics induce bacterial biofilm formation | journal = Nature | volume = 436 | issue = 7054 | pages = 1171–5 | date = August 2005 | pmid = 16121184 | doi = 10.1038/nature03912 | s2cid = 4404961 | bibcode = 2005Natur.436.1171H }} (primary source)</ref> A cell that switches to the biofilm mode of growth undergoes a [[phenotypic shift]] in behavior in which large suites of genes are differentially [[gene regulation|regulated]].<ref>{{cite journal | vauthors = An D, Parsek MR | title = The promise and peril of transcriptional profiling in biofilm communities | journal = Current Opinion in Microbiology | volume = 10 | issue = 3 | pages = 292–6 | date = June 2007 | pmid = 17573234 | doi = 10.1016/j.mib.2007.05.011 }}</ref>

A biofilm may also be considered a [[hydrogel]], which is a complex polymer that contains many times its dry weight in water. Biofilms are not just bacterial slime layers but biological systems; the bacteria organize themselves into a coordinated functional community. Biofilms can attach to a surface such as a tooth or rock, and may include a single species or a diverse group of microorganisms. Subpopulations of cells within the biofilm differentiate to perform various activities for motility, matrix production, and sporulation, supporting the overall success of the biofilm.<ref name="Labor">{{cite journal | vauthors = Momeni B | title = Division of Labor: How Microbes Split Their Responsibility | journal = Current Biology | volume = 28 | issue = 12 | pages = R697–R699 | date = June 2018 | pmid = 29920261 | doi = 10.1016/j.cub.2018.05.024 | s2cid = 49315067 | doi-access = free | bibcode = 2018CBio...28.R697M }}</ref> The biofilm bacteria can share nutrients and are sheltered from harmful factors in the environment, such as desiccation, antibiotics, and a host body's immune system. A biofilm usually begins to form when a free-swimming, planktonic bacterium attaches to a surface.<ref name="O'Toole_1998" /><ref name="Watnick_2000" />

== Origin and formation ==
=== Origin of biofilms ===
Biofilms are thought to have arisen during primitive Earth as a defense mechanism for prokaryotes, as the conditions at that time were too harsh for their survival. They can be found very early in Earth's fossil records (about 3.25&nbsp;billion years ago) as both Archaea and Bacteria, and commonly protect prokaryotic cells by providing them with homeostasis, encouraging the development of complex interactions between the cells in the biofilm.<ref name="Hall-Stoodley"/>

=== Formation of biofilms ===

The formation of a biofilm begins with the attachment of free-floating microorganisms to a surface.<ref name="O'Toole_1998" /><ref name="Watnick_2000" /> The first colonist bacteria of a biofilm may adhere to the surface initially by the weak [[van der Waals force]]s and hydrophobic effects.<ref name="pmid11397632">{{cite journal | vauthors=Briandet R, Herry J, Bellon-Fontaine M | title=Determination of the van der Waals, electron donor and electron acceptor surface tension components of static Gram-positive microbial biofilms | journal=Colloids Surf B | volume=21 | issue=4 | pages=299–310 | date=August 2001 | pmid=11397632 | doi=10.1016/S0927-7765(00)00213-7 }}</ref><ref name="pmid20438621">{{cite journal | vauthors=Takahashi H, Suda T, Tanaka Y, Kimura B | title=Cellular hydrophobicity of Listeria monocytogenes involves initial attachment and biofilm formation on the surface of polyvinyl chloride | journal=Lett. Appl. Microbiol. | volume=50 | issue=6 | pages=618–25 | date=June 2010 | pmid=20438621 | doi=10.1111/j.1472-765X.2010.02842.x | s2cid=24880220 | doi-access=free }}</ref> If the colonists are not immediately separated from the surface, they can anchor themselves more permanently using [[cell adhesion]] structures such as [[pilus|pili]]. A unique group of Archaea that inhabit [[anoxic waters|anoxic groundwater]] have similar structures called [[Hamus (archaea)|hami]]. Each hamus is a long tube with three hook attachments that are used to attach to each other or to a surface, enabling a community to develop.<ref name="archaea">{{cite web |title=7: Archaea |url=https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_(Bruslind)/07%3A_Archaea |website=Biology LibreTexts |language=en |date=6 February 2018 |access-date=10 August 2020 |archive-date=23 September 2020 |archive-url=https://web.archive.org/web/20200923100806/https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_(Bruslind)/07%3A_Archaea |url-status=live }}</ref><ref name="Brock">{{cite book | vauthors=Madigan M |title=Brock biology of microorganisms |date=2019 |publisher=Pearson |isbn=978-1-292-23510-3 |page=86 |edition=Fifteenth, Global}}</ref> Hyperthermophilic archaeon ''[[Pyrobaculum]] calidifontis'' produce bundling pili which are homologous to the bacterial TasA filaments, a major component of the extracellular matrix in bacterial biofilms, which contribute to biofilm stability.<ref name=Wang2022PNAS>{{cite journal | vauthors=Wang F, Cvirkaite-Krupovic V, Krupovic M, Egelman EH | title=Archaeal bundling pili of ''Pyrobaculum calidifontis'' reveal similarities between archaeal and bacterial biofilms | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=119 | issue=26 | article-number=e2207037119 | date=June 2022 | pmid=35727984 | pmc=9245690 | doi=10.1073/pnas.2207037119 | doi-access=free | bibcode=2022PNAS..11907037W }}</ref> TasA homologs are encoded by many other archaea, suggesting mechanistic similarities and evolutionary connection between bacterial and archaeal biofilms.<ref name=Wang2022PNAS />

[[File:A114, Lava Beds National Monument, California, USA, Golden Dome Lava Tube Cave, 2004.jpg|thumb|Biofilm of golden [[hydrophobic]] [[bacteria]]; ceiling of Golden Dome Cave, a [[lava tube]] in [[Lava Beds National Monument]]<ref>[https://www.nps.gov/places/golden-dome-cave.htm "Golden Dome Cave"] {{Webarchive|url=https://web.archive.org/web/20221213013714/https://www.nps.gov/places/golden-dome-cave.htm |date=13 December 2022 }}. National Park Service. November 6, 2021. Retrieved February 11, 2024.</ref>]]

[[Hydrophobicity]] can also affect the ability of bacteria to form biofilms. Bacteria with increased hydrophobicity have reduced repulsion between the substratum and the bacterium.<ref name="Donlan2002">{{cite journal | vauthors=Donlan RM | year=2002 | title=Biofilms: Microbial Life on Surfaces | journal=Emerging Infectious Diseases | volume=8 | issue=9| pages=881–890 | doi=10.3201/eid0809.020063 | pmid=12194761 | pmc=2732559}}</ref> Some bacteria species are not able to attach to a surface on their own successfully due to their limited motility but are instead able to anchor themselves to the matrix or directly to other, earlier bacteria colonists. [[Non-motile bacteria]] cannot recognize surfaces or aggregate together as easily as motile bacteria.<ref name="Donlan2002" />

During surface colonization bacteria cells are able to communicate using [[quorum sensing]] (QS) products such as [[N-acyl homoserine lactone]] (AHL). Once colonization has begun, the biofilm grows by a combination of cell division and recruitment. [[Polysaccharide]] matrices typically enclose bacterial biofilms. The matrix exopolysaccharides can trap QS autoinducers within the biofilm to prevent predator detection and ensure bacterial survival.<ref>{{cite journal | vauthors=Li S, Liu SY, Chan SY, Chua SL | title=Biofilm matrix cloaks bacterial quorum sensing chemoattractants from predator detection | journal=The ISME Journal | pages=1388–1396 | date=January 2022 | volume=16 | issue=5 | pmid=35034106 | doi=10.1038/s41396-022-01190-2 | pmc=9038794 | bibcode=2022ISMEJ..16.1388L }}</ref> In addition to the polysaccharides, these matrices may also contain material from the surrounding environment, including but not limited to minerals, soil particles, and blood components, such as erythrocytes and fibrin.<ref name="Donlan2002" /> 

The development of a biofilm may allow for an aggregate cell colony to be increasingly tolerant<ref>{{cite journal | vauthors=Ciofu O, Tolker-Nielsen T | title=Tolerance and Resistance of ''Pseudomonas aeruginosa'' Biofilms to Antimicrobial Agents-How ''P. aeruginosa'' Can Escape Antibiotics | journal=Frontiers in Microbiology | volume=10 | article-number=913 | date=2019 | pmid=31130925 | pmc=6509751 | doi=10.3389/fmicb.2019.00913 | doi-access=free }}</ref> or [[antibiotic resistance|resistant to antibiotics]]. Cell-cell communication or [[quorum sensing]] has is involved in the formation of biofilm in several bacterial species.<ref name="Sakuragi">{{cite journal | vauthors=Sakuragi Y, Kolter R | title=Quorum-sensing regulation of the biofilm matrix genes (pel) of Pseudomonas aeruginosa | journal=Journal of Bacteriology | volume=189 | issue=14 | pages=5383–6 | date=July 2007 | pmid=17496081 | pmc=1951888 | doi=10.1128/JB.00137-07 | doi-access=free }}</ref>

== Development ==
[[File:Mature biofilm structure.png|thumb|upright=1.8|right| {{center|'''Mature biofilm structure'''{{hsp}}<ref name="Rapacka-Zdonczyk2021">{{cite journal | vauthors = Rapacka-Zdonczyk A, Wozniak A, Nakonieczna J, Grinholc M | title = Development of Antimicrobial Phototreatment Tolerance: Why the Methodology Matters | journal = International Journal of Molecular Sciences | volume = 22 | issue = 4 | page = 2224 | date = February 2021 | pmid = 33672375 | pmc = 7926562 | doi = 10.3390/ijms22042224 | publisher = MDPI AG | doi-access = free }} [[File:CC-BY icon.svg|50px]] Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License] {{Webarchive|url=https://web.archive.org/web/20171016050101/https://creativecommons.org/licenses/by/4.0/ |date=16 October 2017 }}.</ref>}} Biofilm is characterised by heterogenous environment and the presence of a variety of subpopulations. A biofilm structure is composed of metabolically active (both resistant and tolerant) and non-active cells (viable but not culturable cells and persisters) as well as polymer matrix consisting of polysaccharide, extracellular DNA and proteins. Biofilm growth is associated with an escalated level of mutations and [[horizontal gene transfer]] which is promoted in due to the packed and dense structure. Bacteria in biofilms communicate by [[quorum sensing]], which activates genes participating in virulence factors production.<ref name="Rapacka-Zdonczyk2021" /><ref>{{cite journal | vauthors = Hall CW, Mah TF | title = Molecular mechanisms of biofilm-based antibiotic resistance and tolerance in pathogenic bacteria | journal = FEMS Microbiology Reviews | volume = 41 | issue = 3 | pages = 276–301 | date = May 2017 | pmid = 28369412 | doi = 10.1093/femsre/fux010 | publisher = Oxford University Press (OUP) | doi-access = free }}</ref>]]

Biofilms are the product of a microbial [[Developmental biology|developmental]] process.<ref>{{cite journal | vauthors = O'Toole G, Kaplan HB, Kolter R | title = Biofilm formation as microbial development | journal = Annual Review of Microbiology | volume = 54 | pages = 49–79 | date = 2000 | pmid = 11018124 | doi = 10.1146/annurev.micro.54.1.49 | doi-access = free }}</ref> The process is summarized by five major stages of biofilm development, as shown in the diagram below:<ref name="Monroe2007">{{cite journal | vauthors = Monroe D | title = Looking for chinks in the armor of bacterial biofilms | journal = PLOS Biology | volume = 5 | issue = 11 | article-number = e307 | date = November 2007 | pmid = 18001153 | pmc = 2071939 | doi = 10.1371/journal.pbio.0050307 | doi-access = free }}</ref>

[[File:biofilm.jpg|thumb|upright=1.8|left| {{center|'''Five stages of biofilm development'''{{hsp}}<ref name="Monroe2007" />}} (1) Initial attachment, (2) Irreversible attachment, (3) Maturation I, (4) Maturation II, and (5) Dispersion. Each stage of development in the diagram is paired with a [[photomicrograph]] of a developing ''P. aeruginosa'' biofilm. All photomicrographs are shown to the same scale.]]

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== Dispersal ==
Dispersal of cells from the biofilm colony is an essential stage of the biofilm life cycle. Dispersal enables biofilms to spread and colonize new surfaces. Enzymes that degrade the [[#Extracellular matrix|biofilm extracellular matrix]], such as [[dispersin B]] and [[deoxyribonuclease]], may contribute to biofilm dispersal.<ref>{{cite journal|vauthors=Kaplan JB, Ragunath C, Ramasubbu N, Fine DH |title=Detachment of Actinobacillus actinomycetemcomitans biofilm cells by an endogenous beta-hexosaminidase activity |journal=Journal of Bacteriology |volume=185 |issue=16 |pages=4693–8 |date=August 2003 |pmid=12896987 |pmc=166467 |doi=10.1128/JB.185.16.4693-4698.2003}}</ref><ref>{{cite journal|vauthors=Izano EA, Amarante MA, Kher WB, Kaplan JB |title=Differential roles of poly-N-acetylglucosamine surface polysaccharide and extracellular DNA in Staphylococcus aureus and Staphylococcus epidermidis biofilms |journal=Applied and Environmental Microbiology |volume=74 |issue=2 |pages=470–6 |date=January 2008 |pmid=18039822 |pmc=2223269 |doi=10.1128/AEM.02073-07|bibcode=2008ApEnM..74..470I }}</ref> Enzymes that degrade the biofilm matrix may be useful as anti-biofilm agents.<ref>{{cite journal |vauthors=Kaplan JB, Ragunath C, Velliyagounder K, Fine DH, Ramasubbu N |title=Enzymatic detachment of Staphylococcus epidermidis biofilms |journal=Antimicrobial Agents and Chemotherapy |volume=48 |issue=7 |pages=2633–6 |date=July 2004 |pmid=15215120 |pmc=434209 |doi=10.1128/AAC.48.7.2633-2636.2004}}</ref><ref>{{cite journal |vauthors=Xavier JB, Picioreanu C, Rani SA, van Loosdrecht MC, Stewart PS |title=Biofilm-control strategies based on enzymic disruption of the extracellular polymeric substance matrix--a modelling study |journal=Microbiology |volume=151 |issue=Pt 12 |pages=3817–32 |date=December 2005 |pmid=16339929 |doi=10.1099/mic.0.28165-0|doi-access=free }}</ref> Evidence has shown that a fatty acid messenger, [[Cis-2-Decenoic acid|''cis''-2-decenoic acid]], is capable of inducing dispersion and inhibiting growth of biofilm colonies. Secreted by ''[[Pseudomonas aeruginosa]]'', this compound induces cyclo heteromorphic cells in several species of bacteria and the yeast ''[[Candida albicans]]''.<ref>{{cite journal|vauthors=Davies DG, Marques CN |title=A fatty acid messenger is responsible for inducing dispersion in microbial biofilms |journal=Journal of Bacteriology |volume=191 |issue=5 |pages=1393–403 |date=March 2009 |pmid=19074399 |pmc=2648214 |doi=10.1128/JB.01214-08}}</ref>
Nitric oxide has also been shown to trigger the dispersal of biofilms of several bacteria species<ref>{{cite journal|vauthors=Barraud N, Hassett DJ, Hwang SH, Rice SA, Kjelleberg S, Webb JS |title=Involvement of nitric oxide in biofilm dispersal of Pseudomonas aeruginosa |journal=Journal of Bacteriology |volume=188 |issue=21 |pages=7344–7353 |year=2006 |doi=10.1128/jb.00779-06|pmid=17050922 |pmc=1636254 }}</ref><ref>{{cite journal|vauthors=Barraud N, Storey MV, Moore ZP, Webb JS, Rice SA, Kjelleberg S |title=Nitric oxide-mediated dispersal in single- and multi-species biofilms of clinically and industrially relevant microorganisms |journal=Microbial Biotechnology |volume=2 |issue=3 |pages=370–378 |year=2009 |doi=10.1111/j.1751-7915.2009.00098.x|pmid=21261931 |pmc=3815757 }}</ref> at sub-toxic concentrations. [[Nitric oxide]] has potential as a treatment for patients that have chronic infections caused by biofilms.<ref>{{cite web |url=http://www.southampton.ac.uk/biosci/research/projects/dispersal_of_biofilms_in_cystic_fibrosis.page |title=Dispersal of Biofilm in Cystic Fibrosis using Low Dose Nitric Oxide |publisher=University of Southampton |access-date=20 January 2012 |archive-date=8 December 2013 |archive-url=https://web.archive.org/web/20131208120601/http://www.southampton.ac.uk/biosci/research/projects/dispersal_of_biofilms_in_cystic_fibrosis.page |url-status=live }}</ref>

It was generally assumed that cells dispersed from biofilms immediately go into the planktonic growth phase. However, studies have shown that the physiology of dispersed cells from ''Pseudomonas aeruginosa'' biofilms is highly different from that of planktonic and biofilm cells.<ref name="auto">{{cite journal|vauthors=Chua SL, Liu Y, Yam JK, Tolker-Nielsen T, Kjelleberg S, Givskov M, Yang L |title=Dispersed cells represent a distinct stage in the transition from bacterial biofilm to planktonic lifestyles |journal=Nature Communications |volume=5 |year=2014 |doi=10.1038/ncomms5462 |pmid=25042103 |article-number=4462|bibcode=2014NatCo...5.4462C |doi-access=free }}</ref><ref name="pmid26158442">{{cite journal | vauthors = Chua SL, Hultqvist LD, Yuan M, Rybtke M, Nielsen TE, Givskov M, Tolker-Nielsen T, Yang L | title = In vitro and in vivo generation and characterization of Pseudomonas aeruginosa biofilm-dispersed cells via c-di-GMP manipulation | journal = Nat Protoc | volume = 10 | issue = 8 | pages = 1165–80 | date = August 2015 | pmid = 26158442 | doi = 10.1038/nprot.2015.067 | hdl = 10356/84100 | s2cid = 20235088 | hdl-access = free }}</ref> Hence, the dispersal process is a unique stage during the transition from biofilm to planktonic lifestyle in bacteria. Dispersed cells are found to be highly virulent against macrophages and ''Caenorhabditis elegans'', but highly sensitive towards iron stress, as compared with planktonic cells.<ref name="auto" />

Furthermore, ''Pseudomonas aeruginosa'' biofilms undergo distinct spatiotemporal dynamics during biofilm dispersal or disassembly, with contrasting consequences in recolonization and disease dissemination.<ref name="Ma 1–13">{{cite journal | vauthors = Ma Y, Deng Y, Hua H, Khoo BL, Chua SL | title = Distinct bacterial population dynamics and disease dissemination after biofilm dispersal and disassembly | journal = The ISME Journal | volume = 17 | issue = 8 | pages = 1290–1302 | date = August 2023 | pmid = 37270584 | pmc = 10356768 | doi = 10.1038/s41396-023-01446-5 | bibcode = 2023ISMEJ..17.1290M }}</ref> Biofilm dispersal induced bacteria to activate dispersal genes to actively depart from biofilms as single cells at consistent velocities but could not recolonize fresh surfaces. In contrast, biofilm disassembly by degradation of a biofilm exopolysaccharide released immotile aggregates at high initial velocities, enabling the bacteria to recolonize fresh surfaces and cause infections in the hosts efficiently. Hence, biofilm dispersal is more complex than previously thought, where bacterial populations adopting distinct behavior after biofilm departure may be the key to survival of bacterial species and dissemination of diseases.

[[File:Honors Option-MMG.svg|thumb|upright=2.5|center| {{center|'''Biofilm dispersal'''{{hsp}}}}]]

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== Properties ==
Biofilms are usually found on solid [[wikt:substrate|substrates]] submerged in or exposed to an [[aqueous solution]], although they can form as floating mats on liquid surfaces and also on the surface of leaves, particularly in high humidity climates. Given sufficient resources for growth, a biofilm will quickly grow to be macroscopic (visible to the naked eye). Biofilms can contain many different types of microorganism, e.g. bacteria, [[archaea]], [[protozoa]], [[fungus|fungi]] and [[algae]]; each group performs specialized [[metabolism|metabolic]] functions. However, some organisms will form single-species films under certain conditions. The social structure (cooperation/competition) within a biofilm depends highly on the different species present.<ref>{{cite journal | vauthors = Nadell CD, Xavier JB, Foster KR | title = The sociobiology of biofilms | journal = FEMS Microbiology Reviews | volume = 33 | issue = 1 | pages = 206–24 | date = January 2009 | pmid = 19067751 | doi = 10.1111/j.1574-6976.2008.00150.x | doi-access = free }}</ref>

=== Extracellular matrix ===
[[File:Mixed-culture biofilm.jpg|thumb|Scanning electron micrograph of mixed-culture biofilm, demonstrating in detail a spatially heterogeneous arrangement of bacterial cells and extracellular polymeric substances.]]
The EPS matrix consists of [[exopolysaccharides]], proteins and nucleic acids.<ref name="JMB"/><ref>{{cite journal | vauthors = Danese PN, Pratt LA, Kolter R | title = Exopolysaccharide production is required for development of Escherichia coli K-12 biofilm architecture | journal = Journal of Bacteriology | volume = 182 | issue = 12 | pages = 3593–6 | date = June 2000 | pmid = 10852895 | pmc = 101973 | doi = 10.1128/jb.182.12.3593-3596.2000 }}</ref><ref>{{cite journal | vauthors = Branda SS, Chu F, Kearns DB, Losick R, Kolter R | title = A major protein component of the Bacillus subtilis biofilm matrix | journal = Molecular Microbiology | volume = 59 | issue = 4 | pages = 1229–38 | date = February 2006 | pmid = 16430696 | doi = 10.1111/j.1365-2958.2005.05020.x | s2cid = 3041295 | doi-access = free }}</ref> A large proportion of the EPS is more or less strongly hydrated, however, hydrophobic EPS also occur; one example is cellulose<ref>{{cite journal | vauthors = Choong FX, Bäck M, Fahlén S, Johansson LB, Melican K, Rhen M, Nilsson KP, Richter-Dahlfors A | title = Salmonella biofilms using luminescent oligothiophenes | journal = npj Biofilms and Microbiomes | volume = 2 | page = 16024 | date = 23 November 2016 | pmid = 28721253 | pmc = 5515270 | doi = 10.1038/npjbiofilms.2016.24 }}</ref> which is produced by a range of microorganisms. This matrix encases the cells within it and facilitates communication among them through biochemical signals as well as gene exchange. The EPS matrix also traps extracellular enzymes and keeps them in close proximity to the cells. Thus, the matrix represents an external digestion system and allows for stable synergistic microconsortia of different species.<ref name="Wingender">{{cite journal | vauthors = Flemming HC, Wingender J, Szewzyk U, Steinberg P, Rice SA, Kjelleberg S | title = Biofilms: an emergent form of bacterial life | journal = Nature Reviews. Microbiology | volume = 14 | issue = 9 | pages = 563–75 | date = August 2016 | pmid = 27510863 | doi = 10.1038/nrmicro.2016.94 | s2cid = 4384131 }}</ref> Some biofilms have been found to contain water channels that help distribute [[nutrient]]s and signalling molecules.<ref>{{cite journal | vauthors = Stoodley P, Debeer D, Lewandowski Z | title = Liquid flow in biofilm systems | journal = Applied and Environmental Microbiology | volume = 60 | issue = 8 | pages = 2711–6 | date = August 1994 | pmid = 16349345 | pmc = 201713 | doi = 10.1128/aem.60.8.2711-2716.1994 | bibcode = 1994ApEnM..60.2711S }}</ref> This matrix is strong enough that under certain conditions, biofilms can become [[fossil]]ized ([[stromatolite]]s).

Bacteria living in a biofilm usually have significantly different properties from free-floating bacteria of the same species, as the dense and protected environment of the film allows them to cooperate and interact in various ways.<ref>{{cite journal | vauthors = Vlamakis H, Aguilar C, Losick R, Kolter R | title = Control of cell fate by the formation of an architecturally complex bacterial community | journal = Genes & Development | volume = 22 | issue = 7 | pages = 945–53 | date = April 2008 | pmid = 18381896 | pmc = 2279205 | doi = 10.1101/gad.1645008 }}</ref> One benefit of this environment is increased resistance to [[detergent]]s and [[antibiotic]]s, as the dense extracellular matrix and the outer layer of cells protect the interior of the community.<ref>{{cite journal | vauthors = Stewart PS, Costerton JW | title = Antibiotic resistance of bacteria in biofilms | journal = Lancet | volume = 358 | issue = 9276 | pages = 135–8 | date = July 2001 | pmid = 11463434 | doi = 10.1016/S0140-6736(01)05321-1 | s2cid = 46125592 | url = https://scholarworks.montana.edu/xmlui/handle/1/13570 }}</ref><ref name="Pandey">{{cite journal |vauthors=Pandey R, Mishra SK, Shrestha A |title=Characterisation of ESKAPE Pathogens with Special Reference to Multidrug Resistance and Biofilm Production in a Nepalese Hospital |journal=Infect Drug Resist |volume=14 |issue= |pages=2201–2212 |date=2021 |pmid=34163185 |pmc=8214009 |doi=10.2147/IDR.S306688 |url= |doi-access=free }}</ref> In some cases [[antibiotic resistance]] can be increased up to 5,000 times.<ref name="Del Pozo"/> [[Lateral gene transfer]] is often facilitated within bacterial and archaeal biofilms<ref name="Chimileski 65">{{cite journal | vauthors = Chimileski S, Franklin MJ, Papke RT | title = Biofilms formed by the archaeon Haloferax volcanii exhibit cellular differentiation and social motility, and facilitate horizontal gene transfer | journal = BMC Biology | volume = 12 | article-number = 65 | date = August 2014 | pmid = 25124934 | pmc = 4180959 | doi = 10.1186/s12915-014-0065-5 | doi-access = free }}</ref> and can lead to a more stable biofilm structure.<ref>{{cite journal | vauthors = Molin S, Tolker-Nielsen T | title = Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure | journal = Current Opinion in Biotechnology | volume = 14 | issue = 3 | pages = 255–61 | date = June 2003 | pmid = 12849777 | doi = 10.1016/S0958-1669(03)00036-3 }}</ref> Extracellular DNA is a major structural component of many different microbial biofilms.<ref name="Jakubovics">{{cite journal | vauthors = Jakubovics NS, Shields RC, Rajarajan N, Burgess JG | title = Life after death: the critical role of extracellular DNA in microbial biofilms | journal = Letters in Applied Microbiology | volume = 57 | issue = 6 | pages = 467–75 | date = December 2013 | pmid = 23848166 | doi = 10.1111/lam.12134 | s2cid = 206168952 | doi-access = free }}</ref> Enzymatic degradation of extracellular DNA can weaken the biofilm structure and release microbial cells from the surface.

However, biofilms are not always less susceptible to antibiotics. For instance, the biofilm form of ''[[Pseudomonas aeruginosa]]'' has no greater resistance to antimicrobials than do stationary-phase planktonic cells, although when the biofilm is compared to logarithmic-phase planktonic cells, the biofilm does have greater resistance to antimicrobials. This resistance to antibiotics in both stationary-phase cells and biofilms may be due to the presence of [[persister cell]]s.<ref>{{cite journal|vauthors=Spoering AL, Lewis K |title=Biofilms and planktonic cells of Pseudomonas aeruginosa have similar resistance to killing by antimicrobials |journal=Journal of Bacteriology |volume=183 |issue=23 |pages=6746–51 |date=December 2001 |pmid=11698361 |pmc=95513 |doi=10.1128/JB.183.23.6746-6751.2001}}</ref>

== Habitats ==
[[File:Bacteria mats near Grand Prismatic Spring in Yellowstone.JPG|thumb|Mats of bacterial biofilm color the hot springs in [[Yellowstone National Park]]. The longest raised mat area is about half a meter long.]]
[[File:Thermophilic bacteria.jpg|thumb|Thermophilic bacteria in the outflow of [[Mickey Hot Springs]], [[Oregon]], approximately 20&nbsp;mm thick.]]
Biofilms are ubiquitous in organic life. Nearly every species of microorganism have mechanisms by which they can adhere to surfaces and to each other. Biofilms will form on virtually every non-shedding surface in [[Asepsis|non-sterile]] aqueous or humid environments. Biofilms can grow in the most extreme environments: from, for example, the extremely hot, briny waters of [[hot spring]]s ranging from very acidic to very alkaline, to frozen [[glacier]]s.

Biofilms can be found on rocks and pebbles at the bottoms of most streams or rivers and often form on the surfaces of [[stagnant (water)|stagnant]] pools of water. Biofilms are important components of [[food chains]] in rivers and streams and are grazed by the aquatic [[invertebrate]]s upon which many fish feed. Biofilms are found on the surface of and inside plants. They can either contribute to crop disease or, as in the case of [[nitrogen-fixing]] [[rhizobia]] on [[root nodule]]s, exist [[symbiosome|symbiotically with the plant]].<ref>{{cite web|url=http://www.cs.montana.edu/ross/personal/intro-biofilms-s3.htm|title=Introduction to Biofilms: Desirable and undesirable impacts of biofilm|archive-url=https://web.archive.org/web/20080622002657/http://www.cs.montana.edu/ross/personal/intro-biofilms-s3.htm|archive-date=22 June 2008}} (primary source)</ref> Examples of crop diseases related to biofilms include citrus canker, [[Pierce's Disease|Pierce's disease]] of grapes, and bacterial spot of plants such as peppers and tomatoes.<ref>{{cite journal|date=September 2007|title=Influence of xylem fluid chemistry on planktonic growth, biofilm formation and aggregation of Xylella fastidiosa|journal=FEMS Microbiology Letters|volume=274|issue=2|pages=210–7|doi=10.1111/j.1574-6968.2007.00827.x|pmid=17610515|vauthors=Andersen PC, Brodbeck BV, Oden S, Shriner A, Leite B|doi-access=free}}</ref>

===Percolating filters===
[[Percolating filter]]s in sewage treatment works are highly effective removers of pollutants from settled sewage liquor. They work by trickling the liquid over a bed of hard material which is designed to have a very large surface area. A complex biofilm develops on the surface of the medium which absorbs, adsorbs and metabolises the pollutants. The biofilm grows rapidly and when it becomes too thick to retain its grip on the media it washes off and is replaced by newly grown film. The washed off ("sloughed" off) film is settled out of the liquid stream to leave a highly purified effluent.<ref>{{cite web|url=http://www.staffs.ac.uk/schools/sciences/consultancy/dladmin/zCIWEMWWT/Activity5/act5.html|title=Biological wastewater treatment processes; secondary treatment|access-date=13 December 2019|publisher=Staffordshire University|archive-url=https://web.archive.org/web/20110418060449/http://www.staffs.ac.uk/schools/sciences/consultancy/dladmin/zCIWEMWWT/Activity5/act5.html|archive-date=18 April 2011}}</ref>

===Slow sand filter===
[[Slow sand filter]]s are used in water purification for treating raw water to produce a potable product. They work through the formation of a biofilm called the [[hypogeal]] layer or ''[[Schmutzdecke]]'' in the top few millimetres of the fine sand layer. The ''Schmutzdecke'' is formed in the first 10–20 days of operation<ref name=cawst>Centre for Affordable Water and Sanitation Technology, Biosand Filter Manual: Design, Construction, & Installation," July 2007.</ref> and consists of [[bacterium|bacteria]], fungi, [[protozoa]], [[rotifera]] and a range of aquatic insect larvae. As an epigeal biofilm ages, more algae tend to develop and larger aquatic organisms may be present including some [[bryozoa]], [[Mollusca|snails]] and [[annelid]] worms. The surface biofilm is the layer that provides the effective purification in potable water treatment, the underlying sand providing the support medium for this biological treatment layer. As water passes through the hypogeal layer, particles of foreign matter are trapped in the mucilaginous matrix and soluble organic material is [[adsorbed]]. The contaminants are metabolised by the bacteria, fungi and protozoa. The water produced from an exemplary slow sand filter is of excellent quality with 90–99% bacterial cell count reduction.<ref name=ndwc>{{cite journal | publisher = National Drinking Water Clearinghouse (U.S.) | location = Morgantown, WV | url = http://www.nesc.wvu.edu/pdf/DW/publications/ontap/tech_brief/TB15_SlowSand.pdf | title = Slow Sand Filtration | archive-url = https://web.archive.org/web/20160406214558/http://www.nesc.wvu.edu/pdf/DW/publications/ontap/tech_brief/TB15_SlowSand.pdf | archive-date=6 April 2016 | journal = Tech Brief | volume = 14 | date = June 2000 }}</ref>

=== Rhizosphere ===
Plant-beneficial microbes can be categorized as [[Rhizobacteria#Plant growth-promoting rhizobacteria|plant growth-promoting rhizobacteria]].<ref>{{cite journal| vauthors = Kloepper JW |date=1988|title=Plant Growth-Promoting Rhizobacteria on Canola (Rapeseed)|journal=Plant Disease|volume=72|issue=1|page=42|doi=10.1094/pd-72-0042|bibcode=1988PlDis..72...42K |issn=0191-2917}}</ref> These plant growth-promoters colonize the roots of plants, and provide a wide range of beneficial functions for their host including nitrogen fixation, pathogen suppression, anti-fungal properties, and the breakdown of organic materials.<ref name="Nihorimbere_2012">{{cite journal | vauthors = Nihorimbere V, Cawoy H, Seyer A, Brunelle A, Thonart P, Ongena M | title = Impact of rhizosphere factors on cyclic lipopeptide signature from the plant beneficial strain Bacillus amyloliquefaciens S499 | journal = FEMS Microbiology Ecology | volume = 79 | issue = 1 | pages = 176–91 | date = January 2012 | pmid = 22029651 | doi = 10.1111/j.1574-6941.2011.01208.x | bibcode = 2012FEMME..79..176N | doi-access = free }}</ref> One of these functions is the defense against pathogenic, soil-borne bacteria and fungi by way of induced systemic resistance (ISR)<ref>{{cite journal | vauthors = Choudhary DK, Johri BN | title = Interactions of Bacillus spp. and plants—with special reference to induced systemic resistance (ISR) | journal = Microbiological Research | volume = 164 | issue = 5 | pages = 493–513 | date = September 2009 | pmid = 18845426 | doi = 10.1016/j.micres.2008.08.007 | doi-access = free }}</ref> or induced systemic responses triggered by pathogenic microbes (pathogen-induced systemic acquired resistance).<ref name="van Loon_2007">{{cite journal| vauthors = van Loon LC |date=5 June 2007|title=Plant responses to plant growth-promoting rhizobacteria|journal=European Journal of Plant Pathology|volume=119|issue=3|pages=243–254|doi=10.1007/s10658-007-9165-1|issn=0929-1873|doi-access=free|bibcode=2007EJPP..119..243V }}</ref> Plant exudates act as chemical signals for host specific bacteria to colonize.<ref name="Van Wees_2008">{{cite journal | vauthors = Van Wees SC, Van der Ent S, Pieterse CM | title = Plant immune responses triggered by beneficial microbes | journal = Current Opinion in Plant Biology | volume = 11 | issue = 4 | pages = 443–8 | date = August 2008 | pmid = 18585955 | doi = 10.1016/j.pbi.2008.05.005 | bibcode = 2008COPB...11..443V | hdl-access = free | hdl = 1874/30010 | s2cid = 25880745 }}</ref> Rhizobacteria colonization steps include attractions, recognition, adherence, colonization, and growth.<ref name="Nihorimbere_2012" /> Bacteria that have been shown to be beneficial and form biofilms include ''[[Bacillus]], [[Pseudomonas]],'' and ''[[Azospirillum]]''.<ref>{{cite journal| vauthors = Holguin G, Bashan Y |date=December 1996|title=Nitrogen-fixation by Azospirillum brasilense Cd is promoted when co-cultured with a mangrove rhizosphere bacterium (Staphylococcus sp.)|journal=Soil Biology and Biochemistry|volume=28|issue=12|pages=1651–1660|doi=10.1016/s0038-0717(96)00251-9|bibcode=1996SBiBi..28.1651H |issn=0038-0717}}</ref><ref>{{cite journal | vauthors = Babalola OO | title = Beneficial bacteria of agricultural importance | journal = Biotechnology Letters | volume = 32 | issue = 11 | pages = 1559–70 | date = November 2010 | pmid = 20635120 | doi = 10.1007/s10529-010-0347-0 | s2cid = 13518392 }}</ref> Biofilms in the rhizosphere often result in pathogen or plant induced systemic resistances. Molecular properties on the surface of the bacterium cause an immune response in the plant host.<ref name="Van Wees_2008" /> These microbe associated molecules interact with receptors on the surface of plant cells, and activate a biochemical response that is thought to include several different genes at a number of loci.<ref name="Van Wees_2008" /> Several other signaling molecules have been linked to both induced systemic responses and pathogen-induced systemic responses, such as jasmonic acid and ethylene.<ref name="Nihorimbere_2012"/> Cell envelope components such as bacterial flagella and lipopolysaccharides, which are recognized by plant cells as components of pathogens.<ref>{{cite journal | vauthors = Bakker PA, Pieterse CM, van Loon LC | title = Induced Systemic Resistance by Fluorescent Pseudomonas spp | journal = Phytopathology | volume = 97 | issue = 2 | pages = 239–43 | date = February 2007 | pmid = 18944381 | doi = 10.1094/phyto-97-2-0239 | bibcode = 2007PhPat..97..239B | doi-access = free }}</ref> Certain iron metabolites produced by ''Pseudomonas'' have also been shown to create an induced systemic response.<ref name="Van Wees_2008" /> This function of the biofilm helps plants build stronger resistance to pathogens.

Plants that have been colonized by PGPR forming a biofilm have gained systemic resistances and are primed for defense against pathogens. This means that the genes necessary for the production of proteins that work towards defending the plant against pathogens have been expressed, and the plant has a "stockpile" of compounds to release to fight off pathogens.<ref name="Van Wees_2008" /> A primed defense system is much faster in responding to pathogen induced infection, and may be able to deflect pathogens before they are able to establish themselves.<ref>{{cite book | vauthors = Bent E |chapter=Induced Systemic Resistance Mediated by Plant Growth-Promoting Rhizobacteria (PGPR) and Fungi (PGPF)|pages=225–258|publisher=Springer US|isbn=978-0-387-23265-2|doi=10.1007/0-387-23266-4_10|title=Multigenic and Induced Systemic Resistance in Plants|year=2006}}</ref> Plants increase the production of lignin, reinforcing cell walls and making it difficult for pathogens to penetrate into the cell, while also cutting off nutrients to already infected cells, effectively halting the invasion.<ref name="Nihorimbere_2012"/> They produce antimicrobial compounds such as phytoalexins, chitinases, and proteinase inhibitors, which prevent the growth of pathogens.<ref name="van Loon_2007" /> These functions of disease suppression and pathogen resistance ultimately lead to an increase in agricultural production and a decrease in the use of chemical pesticides, herbicides, and fungicides because there is a reduced amount of crop loss due to disease.<ref>{{Citation| vauthors = Lynch JM, Brimecombe MJ, De Leij FA |title=Rhizosphere|date=21 August 2001|work=eLS|publisher=John Wiley & Sons, Ltd|isbn=0-470-01617-5 |doi=10.1038/npg.els.0000403}}</ref> Induced systemic resistance and pathogen-induced systemic acquired resistance are both potential functions of biofilms in the rhizosphere, and should be taken into consideration when applied to new age agricultural practices because of their effect on disease suppression without the use of dangerous chemicals.

===Mammalian gut===
Studies in 2003 discovered that the immune system supports biofilm development in the large intestine. This was supported mainly with the fact that the two most abundantly produced molecules by the immune system also support biofilm production and are associated with the biofilms developed in the gut. This is especially important because the appendix holds a mass amount of these bacterial biofilms.<ref>{{cite journal | vauthors = Randal Bollinger R, Barbas AS, Bush EL, Lin SS, Parker W | title = Biofilms in the large bowel suggest an apparent function of the human vermiform appendix | journal = Journal of Theoretical Biology | volume = 249 | issue = 4 | pages = 826–31 | date = December 2007 | pmid = 17936308 | doi = 10.1016/j.jtbi.2007.08.032 | bibcode = 2007JThBi.249..826R }}</ref> This discovery helps to distinguish the possible function of the appendix and the idea that the appendix can help reinoculate the gut with good gut flora. However, modified or disrupted states of biofilms in the gut have been connected to diseases such as [[inflammatory bowel disease]] and [[colorectal cancer]].<ref>{{cite journal | vauthors = Buret AG, Motta JP, Allain T, Ferraz J, Wallace JL | title = Pathobiont release from dysbiotic gut microbiota biofilms in intestinal inflammatory diseases: a role for iron? | journal = Journal of Biomedical Science | volume = 26 | issue = 1 | article-number = 1 | date = January 2019 | pmid = 30602371 | pmc = 6317250 | doi = 10.1186/s12929-018-0495-4 | doi-access = free }}</ref>

===Human environment===
In the human environment, biofilms can grow in showers very easily since they provide a moist and warm environment for them to thrive. Mold biofilms on ceilings may form due to roof leaks.<ref>{{Cite web |date=2024-11-18 |title=Do You See Mold on the Ceiling Due to a Roof Leak? – Platinum Roofing and Construction |url=https://platinumroofingandconstruction.com/do-you-see-mold-on-the-ceiling-due-to-a-roof-leak/ |access-date=2024-11-26 |language=en-US |archive-date=8 December 2024 |archive-url=https://web.archive.org/web/20241208045205/https://platinumroofingandconstruction.com/do-you-see-mold-on-the-ceiling-due-to-a-roof-leak/ |url-status=live }}</ref> They can form inside water and [[Sanitary sewer|sewage]] [[pipe (material)|pipes]] and cause clogging and [[corrosion]]. On floors and counters, they can make sanitation difficult in food preparation areas. In soil, they can cause [[bioclogging]]. In cooling- or heating-water systems, they are known to reduce heat transfer.<ref>{{cite journal |doi=10.1080/01457638108939572 |title=Influence of Fouling Biofilms on Heat Transfer |year=1981 |vauthors=Characklis WG, Nevimons MJ, Picologlou BF |journal=Heat Transfer Engineering |volume=3 |issue=1 |pages=23–37 |bibcode=1981HTrEn...3...23C |url=https://scholarworks.montana.edu/xmlui/handle/1/13866 |access-date=19 December 2022 |archive-date=19 August 2022 |archive-url=https://web.archive.org/web/20220819231141/https://scholarworks.montana.edu/xmlui/handle/1/13866 |url-status=live }}</ref> Biofilms in marine engineering systems, such as pipelines of the offshore oil and gas industry,<ref>{{cite journal | vauthors = Schwermer CU, Lavik G, Abed RM, Dunsmore B, Ferdelman TG, Stoodley P, Gieseke A, de Beer D | title = Impact of nitrate on the structure and function of bacterial biofilm communities in pipelines used for injection of seawater into oil fields | journal = Applied and Environmental Microbiology | volume = 74 | issue = 9 | pages = 2841–51 | date = May 2008 | pmid = 18344353 | pmc = 2394879 | doi = 10.1128/AEM.02027-07 | bibcode = 2008ApEnM..74.2841S }}</ref> can lead to substantial corrosion problems. Corrosion is mainly due to abiotic factors; however, at least 20% of corrosion is caused by microorganisms that are attached to the metal subsurface (i.e., [[Microbial corrosion|microbially influenced corrosion]]).

===Ship fouling===
Bacterial adhesion to boat hulls serves as the foundation for [[biofouling]] of seagoing vessels. Once a film of bacteria forms, it is easier for other marine organisms such as barnacles to attach. Such fouling can reduce maximum vessel speed by up to 20%, prolonging voyages and consuming fuel. Time in dry dock for refitting and repainting reduces the productivity of shipping assets, and the useful life of ships is also reduced due to corrosion and mechanical removal (scraping) of marine organisms from ships' hulls.

===Stromatolites===
[[Stromatolites]] are layered accretionary structures formed in shallow water by the trapping, binding and cementation of sedimentary grains by microbial biofilms, especially of [[cyanobacteria]]. Stromatolites include some of the most ancient records of life on Earth, and are still forming today.

=== Dental plaque ===
Within the human body, biofilms are present on the [[teeth]] as [[dental plaque]], where they may cause [[tooth decay]] and [[gum disease]]. These biofilms can either be in an uncalcified state that can be removed by dental instruments, or a calcified state which is more difficult to remove. Removal techniques can also include [[antimicrobial]]s.<ref>{{cite journal | vauthors = Chandki R, Banthia P, Banthia R | title = Biofilms: A microbial home | journal = Journal of Indian Society of Periodontology | volume = 15 | issue = 2 | pages = 111–4 | date = April 2011 | pmid = 21976832 | pmc = 3183659 | doi = 10.4103/0972-124X.84377 | doi-access = free }}</ref>

Dental plaque is an oral biofilm that adheres to the teeth and consists of many species of both bacteria and fungi (such as ''[[Streptococcus mutans]]'' and ''Candida albicans''), embedded in salivary [[polymers]] and microbial extracellular products. The accumulation of microorganisms subjects the teeth and gingival tissues to high concentrations of bacterial [[metabolite]]s which results in dental disease.<ref name="RevistaOMF">{{cite journal |vauthors=Augustin M, Chifiriuc CB, Lazăr V, Stănescu R, Burlibașa M, Ispas DC |date=December 2010 |title=Microbial biofilms in dental medicine in reference to implanto-prostethic rehabilitation |url=http://www.revistaomf.ro/(8) |url-status=dead |journal=Revista de Chirurgie Oro-maxilo-facială și Implantologie |language=ro |volume=1 |issue=1 |pages=9–13 |issn=2069-3850 |id=8 |archive-url=https://web.archive.org/web/20170602060025/http://www.revistaomf.ro/(1)Colectia-pe-ani/(2)Anul-2010/(3)Numarul-1-2010/(8)Biofilme-microbiene-in-medicina-dentara-cu-referire-la-reabilitarea-implanto-protetica |archive-date=2 Jun 2017 |access-date=3 June 2012}}(webpage has a translation button)</ref> Biofilm on the surface of teeth is frequently subject to oxidative stress<ref name="pmid8519478">{{cite journal | vauthors = Marquis RE | title = Oxygen metabolism, oxidative stress and acid-base physiology of dental plaque biofilms | journal = Journal of Industrial Microbiology | volume = 15 | issue = 3 | pages = 198–207 | date = September 1995 | pmid = 8519478 | doi = 10.1007/bf01569826 | s2cid = 19959528 | doi-access = free }}</ref> and acid stress.<ref name="Lemos">{{cite journal | vauthors = Lemos JA, Abranches J, Burne RA | title = Responses of cariogenic streptococci to environmental stresses | journal = Current Issues in Molecular Biology | volume = 7 | issue = 1 | pages = 95–107 | date = January 2005 | pmid = 15580782 | url = http://www.horizonpress.com/cimb/v/v7/07.pdf | access-date = 3 April 2014 | archive-date = 7 April 2014 | archive-url = https://web.archive.org/web/20140407114140/http://www.horizonpress.com/cimb/v/v7/07.pdf }}</ref> Dietary carbohydrates can cause a dramatic decrease in pH in oral biofilms to values of 4 and below (acid stress).<ref name="Lemos" /> A pH of 4 at body temperature of 37&nbsp;°C causes [[depurination]] of DNA, leaving apurinic (AP) sites in DNA,<ref name="pmid14938354">{{cite journal | vauthors = Tamm C, Hodes ME, Chargaff E | title = The formation apurinic acid from the desoxyribonucleic acid of calf thymus | journal = The Journal of Biological Chemistry | volume = 195 | issue = 1 | pages = 49–63 | date = March 1952 | doi = 10.1016/S0021-9258(19)50874-2 | pmid = 14938354 | doi-access = free }}</ref> especially loss of guanine.<ref name="pmid13701660">{{cite journal | vauthors = Freese EB | title = Transitions and transversions induced by depurinating agents | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 47 | issue = 4 | pages = 540–5 | date = April 1961 | pmid = 13701660 | pmc = 221484 | doi = 10.1073/pnas.47.4.540 | bibcode = 1961PNAS...47..540B | doi-access = free }}</ref>

Dental plaque biofilm can result in [[Tooth decay|dental caries]] if it is allowed to develop over time. An ecologic shift away from balanced populations within the dental biofilm is driven by certain (cariogenic) microbiological populations beginning to dominate when the environment favors them. The shift to an [[acidogenic]], aciduric, and cariogenic microbiological population develops and is maintained by frequent consumption of fermentable dietary [[carbohydrate]]. The resulting activity shift in the biofilm (and resulting acid production within the biofilm, at the tooth surface) is associated with an imbalance of demineralization over remineralization, leading to net mineral loss within dental hard tissues ([[Tooth enamel|enamel]] and then [[dentin]]), the symptom being a [[carious lesion]], or cavity. By preventing the dental plaque biofilm from maturing or by returning it back to a non-cariogenic state, dental caries can be prevented and arrested.<ref name="Pennwell">Pennwell, "Toothbrush technology, dentifrices and dental biofilm removal." ''Dental Academy of CE'' Accessed 12 January 2022</ref><ref>{{cite book|title=Pathology of dental caries. In: Dental caries: the disease and its clinical management.| vauthors = Fejerskov O |publisher=Oxford (UK): Wiley Blackwell|year=2015|isbn=978-1-4051-3889-5|pages=7–9}}</ref> This can be achieved through the behavioral step of reducing the supply of fermentable carbohydrates (i.e. sugar intake) and frequent removal of the biofilm (i.e., [[Tooth brushing|toothbrushing]]).<ref name="Pennwell"/>

====Intercellular communication====
{{See also|Oral microbiology}}
A peptide pheromone quorum sensing signaling system in ''[[S. mutans]]'' includes the [[Oral microbiology#Intercellular communication|competence stimulating peptide]] (CSP) that controls genetic competence.<ref name="Li">{{cite journal|date=February 2001|title=Natural genetic transformation of Streptococcus mutans growing in biofilms|journal=J. Bacteriol.|volume=183|issue=3|pages=897–908|doi=10.1128/JB.183.3.897-908.2001|pmc=94956|pmid=11208787|vauthors=Li YH, Lau PC, Lee JH, Ellen RP, Cvitkovitch DG}}</ref><ref name="pmid18792689">{{cite book|year=2008|series=Advances in Experimental Medicine and Biology|volume=631|pages=[https://archive.org/details/bacterialsignalt0000unse/page/178 178–88]|doi=10.1007/978-0-387-78885-2_12|isbn=978-0-387-78884-5|pmid=18792689|vauthors=Senadheera D, Cvitkovitch DG|chapter=Quorum Sensing and Biofilm Formation by Streptococcus mutans |title=Bacterial Signal Transduction: Networks and Drug Targets|chapter-url=https://archive.org/details/bacterialsignalt0000unse/page/178}}</ref> Genetic competence is the ability of a cell to take up DNA released by another cell. Competence can lead to genetic transformation, a form of sexual interaction, favored under conditions of high cell density and/or stress where there is maximal opportunity for interaction between the competent cell and the DNA released from nearby donor cells. This system is optimally expressed when ''S. mutans'' cells reside in an actively growing biofilm. Biofilm grown ''S. mutans'' cells are genetically transformed at a rate 10- to 600-fold higher than ''S. mutans'' growing as free-floating planktonic cells suspended in liquid.<ref name="Li" />

When the biofilm, containing ''S. mutans'' and related oral streptococci, is subjected to acid stress, the competence regulon is induced, leading to resistance to being killed by acid.<ref name="Lemos" /> As pointed out by Michod et al., transformation in bacterial pathogens likely provides for effective and efficient recombinational repair of DNA damages.<ref name="Michod">{{cite journal|date=May 2008|title=Adaptive value of sex in microbial pathogens|journal=Infect. Genet. Evol.|volume=8|issue=3|pages=267–85|doi=10.1016/j.meegid.2008.01.002|pmid=18295550|vauthors=Michod RE, Bernstein H, Nedelcu AM|bibcode=2008InfGE...8..267M }}http://www.hummingbirds.arizona.edu/Faculty/Michod/Downloads/IGE%20review%20sex.pdf {{Webarchive|url=https://web.archive.org/web/20200511153411/http://www.hummingbirds.arizona.edu/Faculty/Michod/Downloads/IGE%20review%20sex.pdf |date=11 May 2020 }}</ref> It appears that ''S. mutans'' can survive the frequent acid stress in oral biofilms, in part, through the recombinational repair provided by competence and transformation.

'''Predator-prey interactions'''

{{See also|Lotka–Volterra equations|l1=Predator-prey interactions}}

[[Predation|Predator]]-[[Predation|prey]] interactions between biofilms and bacterivores, such as the soil-dwelling nematode ''[[Caenorhabditis elegans]],'' had been extensively studied. Via the production of sticky matrix and formation of aggregates, ''[[Yersinia pestis]]'' biofilms can prevent feeding by obstructing the mouth of ''C. elegans''.<ref>{{cite journal | vauthors = Atkinson S, Goldstone RJ, Joshua GW, Chang CY, Patrick HL, Cámara M, Wren BW, Williams P | title = Biofilm development on Caenorhabditis elegans by Yersinia is facilitated by quorum sensing-dependent repression of type III secretion | journal = PLOS Pathogens | volume = 7 | issue = 1 | article-number = e1001250 | date = January 2011 | pmid = 21253572 | pmc = 3017118 | doi = 10.1371/journal.ppat.1001250 | doi-access = free }}</ref> Moreover, ''[[Pseudomonas aeruginosa]]'' biofilms can impede the slithering motility of ''C. elegans'', termed as 'quagmire phenotype', resulting in trapping of ''C. elegans'' within the biofilms and preventing the exploration of nematodes to feed on susceptible biofilms.<ref>{{cite journal | vauthors = Chan SY, Liu SY, Seng Z, Chua SL | title = Biofilm matrix disrupts nematode motility and predatory behavior | journal = The ISME Journal | pages = 260–269 | date = September 2020 | volume = 15 | issue = 1 | pmid = 32958848 | doi = 10.1038/s41396-020-00779-9 | pmc = 7852553 | url = }}</ref> This significantly reduced the ability of predator to feed and reproduce, thereby promoting the survival of biofilms. ''Pseudomonas aeruginosa'' biofilms can also mask their chemical signatures, where they reduced the diffusion of quorum sensing molecules into the environment and prevented the detection of ''C. elegans''.<ref>{{cite journal | vauthors = Li S, Liu SY, Chan SY, Chua SL | title = Biofilm matrix cloaks bacterial quorum sensing chemoattractants from predator detection | journal = The ISME Journal | volume = 16 | issue = 5 | pages = 1388–1396 | date = May 2022 | pmid = 35034106 | pmc = 9038794 | doi = 10.1038/s41396-022-01190-2 | bibcode = 2022ISMEJ..16.1388L }}</ref>

== Taxonomic diversity ==
Many different bacteria form biofilms, including [[Gram-positive bacteria|gram-positive]] (e.g. ''[[Bacillus]]'' spp, ''[[Listeria monocytogenes]]'', ''[[Staphylococcus]]'' spp, and [[lactic acid bacteria]], including ''[[Lactobacillus plantarum]]'' and ''[[Lactococcus lactis]]'') and [[Gram-negative bacteria|gram-negative]] species (e.g. ''[[Escherichia coli]]'', or ''[[Pseudomonas aeruginosa]]'').<ref name="Abee">{{cite journal | vauthors = Abee T, Kovács AT, Kuipers OP, van der Veen S | title = Biofilm formation and dispersal in Gram-positive bacteria | journal = Current Opinion in Biotechnology | volume = 22 | issue = 2 | pages = 172–9 | date = April 2011 | pmid = 21109420 | doi = 10.1016/j.copbio.2010.10.016 | url = https://pure.rug.nl/ws/files/6762350/2011CurrOpinBiotechnolAbee2.pdf | hdl = 11370/999da2a4-d509-471b-bab5-085dac6ff681 | s2cid = 22024410 | hdl-access = free | access-date = 21 December 2018 | archive-date = 23 July 2018 | archive-url = https://web.archive.org/web/20180723094020/https://pure.rug.nl/ws/files/6762350/2011CurrOpinBiotechnolAbee2.pdf | url-status = live }}</ref> [[Cyanobacteria]] also form biofilms in aquatic environments.<ref>{{cite journal | vauthors = Rossi F, De Philippis R | title = Role of cyanobacterial exopolysaccharides in phototrophic biofilms and in complex microbial mats | journal = Life | volume = 5 | issue = 2 | pages = 1218–38 | date = April 2015 | pmid = 25837843 | pmc = 4500136 | doi = 10.3390/life5021218 | bibcode = 2015Life....5.1218R | doi-access = free }}</ref>

Biofilms are formed by bacteria that colonize plants, e.g. ''[[Pseudomonas putida]]'', ''[[Pseudomonas fluorescens]]'', and related pseudomonads which are common plant-associated bacteria found on leaves, roots, and in the soil, and the majority of their natural isolates form biofilms.<ref name="Danhorn">{{cite journal | vauthors = Danhorn T, Fuqua C | title = Biofilm formation by plant-associated bacteria | journal = Annual Review of Microbiology | volume = 61 | pages = 401–22 | year = 2007 | pmid = 17506679 | doi = 10.1146/annurev.micro.61.080706.093316 }}</ref> Several nitrogen-fixing symbionts of legumes such as ''[[Rhizobium leguminosarum]]'' and ''[[Sinorhizobium meliloti]]'' form biofilms on legume roots and other inert surfaces.<ref name="Danhorn" />

Along with bacteria, biofilms are also generated by [[archaea]]<ref name="Chimileski 65"/> and by a range of [[Eukaryote|eukaryotic]] organisms, including fungi e.g. ''Cryptococcus laurentii''<ref name="pmid16897306">{{cite journal | vauthors = Joubert LM, Wolfaardt GM, Botha A | title = Microbial exopolymers link predator and prey in a model yeast biofilm system | journal = Microb. Ecol. | volume = 52 | issue = 2 | pages = 187–97 | date = August 2006 | pmid = 16897306 | doi = 10.1007/s00248-006-9063-7 | bibcode = 2006MicEc..52..187J | s2cid = 20431229 }}</ref> and [[microalgae]]. Among microalgae, one of the main progenitors of biofilms are [[diatom]]s, which colonise both fresh and marine environments worldwide.<ref name="Van Colen 2014">{{cite journal | vauthors = Van Colen C, Underwood GC, Serôdio J, Paterson DM| year = 2014 | title = Ecology of intertidal microbial biofilms: Mechanisms, patterns and future research needs | journal = Journal of Sea Research | volume = 92 | pages = 2–5 | doi=10.1016/j.seares.2014.07.003| bibcode = 2014JSR....92....2V}}</ref><ref name="pmid27009999">{{cite journal | vauthors = Aslam SN, Cresswell-Maynard T, Thomas DN, Underwood GJ | title = Production and Characterization of the Intra- and Extracellular Carbohydrates and Polymeric Substances (EPS) of Three Sea-Ice Diatom Species, and Evidence for a Cryoprotective Role for EPS | journal = J. Phycol. | volume = 48 | issue = 6 | pages = 1494–509 | date = December 2012 | pmid = 27009999 | doi = 10.1111/jpy.12004 | s2cid = 9226690 | doi-access = free | bibcode = 2012JPcgy..48.1494A }}</ref>

For other species in disease-associated biofilms and biofilms arising from [[eukaryote]]s, see below.

== Infectious diseases ==
Biofilms have been found to be involved in a wide variety of microbial infections in the body, by one estimate 80% of all infections.<ref>{{cite web | title=Research on microbial biofilms (PA-03-047) | url=https://grants.nih.gov/grants/guide/pa-files/PA-03-047.html | date=20 December 2002 | publisher=NIH, National Heart, Lung, and Blood Institute | access-date=12 October 2006 | archive-date=10 December 2006 | archive-url=https://web.archive.org/web/20061210052551/http://grants.nih.gov/grants/guide/pa-files/PA-03-047.html | url-status=live }}</ref> Infectious processes in which biofilms have been implicated include common problems such as [[List of bacterial vaginosis microbiota|bacterial vaginosis]], [[urinary tract infections]], [[Urinary catheterization|catheter]] infections, [[otitis media|middle-ear infections]], formation of [[dental plaque]],<ref name=Rogers2008>{{cite book| vauthors = Rogers A |title=Molecular Oral Microbiology|date=2008|publisher=Caister Academic Press|isbn=978-1-904455-24-0|pages=88–91}}</ref> [[gingivitis]], coating [[contact lenses]],<ref>{{cite journal | vauthors = Imamura Y, Chandra J, Mukherjee PK, Lattif AA, Szczotka-Flynn LB, Pearlman E, Lass JH, O'Donnell K, Ghannoum MA | title = Fusarium and Candida albicans biofilms on soft contact lenses: model development, influence of lens type, and susceptibility to lens care solutions | journal = Antimicrobial Agents and Chemotherapy | volume = 52 | issue = 1 | pages = 171–82 | date = January 2008 | pmid = 17999966 | pmc = 2223913 | doi = 10.1128/AAC.00387-07 }}</ref> and less common but more lethal processes such as [[endocarditis]], infections in [[cystic fibrosis]], and infections of permanent indwelling devices such as joint [[prosthesis|prostheses]], [[Heart valve prosthesis|heart valves]], and intervertebral disc.<ref>{{cite journal | vauthors = Capoor MN, Ruzicka F, Schmitz JE, James GA, Machackova T, Jancalek R, Smrcka M, Lipina R, Ahmed FS, Alamin TF, Anand N, Baird JC, Bhatia N, Demir-Deviren S, Eastlack RK, Fisher S, Garfin SR, Gogia JS, Gokaslan ZL, Kuo CC, Lee YP, Mavrommatis K, Michu E, Noskova H, Raz A, Sana J, Shamie AN, Stewart PS, Stonemetz JL, Wang JC, Witham TF, Coscia MF, Birkenmaier C, Fischetti VA, Slaby O | title = Propionibacterium acnes biofilm is present in intervertebral discs of patients undergoing microdiscectomy | journal = PLOS ONE | volume = 12 | issue = 4 | article-number = e0174518 | date = 3 April 2017 | pmid = 28369127 | pmc = 5378350 | doi = 10.1371/journal.pone.0174518 | bibcode = 2017PLoSO..1274518C | doi-access = free }}</ref><ref>{{cite journal | vauthors = Lewis K | title = Riddle of biofilm resistance | journal = Antimicrobial Agents and Chemotherapy | volume = 45 | issue = 4 | pages = 999–1007 | date = April 2001 | pmid = 11257008 | pmc = 90417 | doi = 10.1128/AAC.45.4.999-1007.2001 }}</ref><ref>{{cite journal | vauthors = Parsek MR, Singh PK | title = Bacterial biofilms: an emerging link to disease pathogenesis | journal = Annual Review of Microbiology | volume = 57 | pages = 677–701 | year = 2003 | pmid = 14527295 | doi = 10.1146/annurev.micro.57.030502.090720 }}</ref> The first visual evidence of a biofilm was recorded after spine surgery.<ref name="Agarwal_2020">{{cite journal | vauthors = Agarwal A, Mooney M, Agarwal AG, Jayaswal D, Saakyan G, Goel V, Wang JC, Anand N, Garfin S, Shendge V, Elgafy H | title = High Prevalence of Biofilms on Retrieved Implants from Aseptic Pseudarthrosis Cases | journal = Spine Surgery and Related Research | volume = 5 | issue = 2 | pages = 104–108 | date = 2020 | pmid = 33842718 | pmc = 8026210 | doi = 10.22603/ssrr.2020-0147 | doi-access = free }}</ref> It was found that in the absence of clinical presentation of infection, impregnated bacteria could form a biofilm around an implant, and this biofilm can remain undetected via contemporary diagnostic methods, including swabbing. Implant biofilm is frequently present in "aseptic" pseudarthrosis cases.<ref name="Agarwal_2020" /><ref name="niamhcurran">{{Cite web|vauthors=Curran N|date=20 November 2020|title=New study first to visually capture biofilm architecture in retrieved implants from live patients|url=https://spinalnewsinternational.com/new-study-first-to-visually-capture-biofilm-architecture-in-retrieved-implants-from-live-patients/|access-date=24 November 2020|website=Spinal News International|language=en-GB|archive-date=23 November 2020|archive-url=https://web.archive.org/web/20201123193152/https://spinalnewsinternational.com/new-study-first-to-visually-capture-biofilm-architecture-in-retrieved-implants-from-live-patients/|url-status=live}}</ref><ref>{{Cite web|title=biofilm|date=22 December 2020|url=https://orthospinenews.com/2020/12/22/first-study-to-visually-capture-biofilm-structure-of-retrieved-implants-from-spine-patients-with-pseudarthrosis/|access-date=22 December 2020|archive-date=22 January 2021|archive-url=https://web.archive.org/web/20210122061753/https://orthospinenews.com/2020/12/22/first-study-to-visually-capture-biofilm-structure-of-retrieved-implants-from-spine-patients-with-pseudarthrosis/|url-status=live}}</ref> Furthermore, it has been noted that bacterial biofilms may impair cutaneous wound healing and reduce topical antibacterial efficiency in healing or treating infected skin wounds.<ref>{{cite journal | vauthors = Davis SC, Ricotti C, Cazzaniga A, Welsh E, Eaglstein WH, Mertz PM | title = Microscopic and physiologic evidence for biofilm-associated wound colonization in vivo | journal = Wound Repair and Regeneration | volume = 16 | issue = 1 | pages = 23–9 | year = 2008 | pmid = 18211576 | doi = 10.1111/j.1524-475X.2007.00303.x | s2cid = 205669081 }}</ref> The diversity of ''P. aeruginosa'' cells within a biofilm is thought to make it harder to treat the infected lungs of people with cystic fibrosis.<ref name="Labor"/> Early detection of biofilms in wounds is crucial to successful chronic wound management. Although many techniques have developed to identify planktonic bacteria in viable wounds, few have been able to quickly and accurately identify bacterial biofilms. Future studies are needed to find means of identifying and monitoring biofilm colonization at the bedside to permit timely initiation of treatment.<ref>{{cite journal | vauthors = Vyas KS, Wong LK | title = Detection of Biofilm in Wounds as an Early Indicator for Risk for Tissue Infection and Wound Chronicity | journal = Annals of Plastic Surgery | volume = 76 | issue = 1 | pages = 127–31 | date = January 2016 | pmid = 25774966 | doi = 10.1097/SAP.0000000000000440 | s2cid = 42078581 }}</ref>

It has been shown that biofilms are present on the removed tissue of 80% of patients undergoing surgery for chronic [[sinusitis]]. The patients with biofilms were shown to have been denuded of [[cilium|cilia]] and [[goblet cells]], unlike the controls without biofilms who had normal cilia and goblet cell morphology.<ref>{{cite journal|vauthors=Sanclement J, Webster P, Thomas J, Ramadan H |title=Bacterial biofilms in surgical specimens of patients with chronic rhinosinusitis |journal=The Laryngoscope |volume=115 |issue=4 |pages=578–82 |year=2005 |pmid=15805862 |doi=10.1097/01.mlg.0000161346.30752.18|s2cid=25830188 }}</ref> Biofilms were also found on samples from two of 10 healthy controls mentioned. The species of bacteria from intraoperative cultures did not correspond to the bacteria species in the biofilm on the respective patient's tissue. In other words, the cultures were negative though the bacteria were present.<ref>{{cite journal|vauthors=Sanderson AR, Leid JG, Hunsaker D |title=Bacterial biofilms on the sinus mucosa of human subjects with chronic rhinosinusitis |journal=The Laryngoscope |volume=116 |issue=7 |pages=1121–6 |date=July 2006 |pmid=16826045 |doi=10.1097/01.mlg.0000221954.05467.54|s2cid=24785016 |doi-access=free }}</ref> New staining techniques are being developed to differentiate bacterial cells growing in living animals, e.g. from tissues with allergy-inflammations.<ref>{{cite journal | vauthors = Leevy WM, Gammon ST, Jiang H, Johnson JR, Maxwell DJ, Jackson EN, Marquez M, Piwnica-Worms D, Smith BD | title = Optical imaging of bacterial infection in living mice using a fluorescent near-infrared molecular probe | journal = Journal of the American Chemical Society | volume = 128 | issue = 51 | pages = 16476–7 | date = December 2006 | pmid = 17177377 | pmc = 2531239 | doi = 10.1021/ja0665592 | bibcode = 2006JAChS.12816476L }}</ref>

Research has shown that sub-therapeutic levels of [[β-lactam antibiotics]] induce biofilm formation in ''[[Staphylococcus aureus]]''. This sub-therapeutic level of [[antibiotic]] may result from the use of antibiotics as growth promoters in agriculture, or during the normal course of antibiotic therapy. The biofilm formation induced by low-level methicillin was inhibited by DNase, suggesting that the sub-therapeutic levels of antibiotic also induce extracellular DNA release.<ref>{{cite journal | vauthors = Kaplan JB, Izano EA, Gopal P, Karwacki MT, Kim S, Bose JL, Bayles KW, Horswill AR | title = Low levels of β-lactam antibiotics induce extracellular DNA release and biofilm formation in Staphylococcus aureus | journal = mBio | volume = 3 | issue = 4 | article-number = e00198-12 | year = 2012 | pmid = 22851659 | pmc = 3419523 | doi = 10.1128/mBio.00198-12 }}</ref> 

=== ''Pseudomonas aeruginosa'' ===
''[[Pseudomonas aeruginosa|P. aeruginosa]]'' represents a commonly used biofilm [[model organism]] since it is involved in different types of biofilm-associated chronic infections.<ref name="JMB">{{cite journal | vauthors = Rybtke M, Hultqvist LD, Givskov M, Tolker-Nielsen T | title = Pseudomonas aeruginosa Biofilm Infections: Community Structure, Antimicrobial Tolerance and Immune Response | journal = Journal of Molecular Biology | volume = 427 | issue = 23 | pages = 3628–45 | date = November 2015 | pmid = 26319792 | doi = 10.1016/j.jmb.2015.08.016 }}</ref> Examples of such infections include chronic wounds, chronic otitis media, chronic prostatitis and chronic lung infections in [[cystic fibrosis]] (CF) patients. About 80% of CF patients have chronic lung infection, caused mainly by ''P. aeruginosa'' growing in a non-surface attached biofilms surround by [[Granulocyte|PMN]].<ref>{{cite journal | vauthors = Ciofu O, Tolker-Nielsen T, Jensen PØ, Wang H, Høiby N | title = Antimicrobial resistance, respiratory tract infections and role of biofilms in lung infections in cystic fibrosis patients | journal = Advanced Drug Delivery Reviews | volume = 85 | pages = 7–23 | date = May 2015 | pmid = 25477303 | doi = 10.1016/j.addr.2014.11.017 }}</ref> The infection remains present despite aggressive antibiotic therapy and is a common cause of death in CF patients due to constant inflammatory damage to the lungs.<ref name="JMB" /> In patients with CF, one therapy for treating early biofilm development is to employ [[DNase]] to structurally weaken the biofilm.<ref name="Aggarwal"/><ref>{{cite journal | vauthors = Whitchurch CB, Tolker-Nielsen T, Ragas PC, Mattick JS | title = Extracellular DNA required for bacterial biofilm formation | journal = Science | volume = 295 | issue = 5559 | page = 1487 | date = February 2002 | pmid = 11859186 | doi = 10.1126/science.295.5559.1487 }}</ref>

Biofilm formation of ''[[Pseudomonas aeruginosa|P. aeruginosa]]'', along with other bacteria, is found in 90% of chronic wound infections, which leads to poor healing and high cost of treatment estimated at more than US$25 billion every year in the [[United States]].<ref>{{cite journal | vauthors = Sen CK, Gordillo GM, Roy S, Kirsner R, Lambert L, Hunt TK, Gottrup F, Gurtner GC, Longaker MT | title = Human skin wounds: a major and snowballing threat to public health and the economy | journal = Wound Repair and Regeneration | volume = 17 | issue = 6 | pages = 763–771 | date = November 2009 | pmid = 19903300 | pmc = 2810192 | doi = 10.1111/j.1524-475X.2009.00543.x }}</ref> In order to minimize the ''[[Pseudomonas aeruginosa|P. aeruginosa]]'' [[infection]], host epithelial cells secrete [[antimicrobial peptides]], such as [[lactoferrin]], to prevent the formation of the biofilms.<ref>{{cite journal | vauthors = Singh PK, Parsek MR, Greenberg EP, Welsh MJ | title = A component of innate immunity prevents bacterial biofilm development | journal = Nature | volume = 417 | issue = 6888 | pages = 552–555 | date = May 2002 | pmid = 12037568 | doi = 10.1038/417552a | bibcode = 2002Natur.417..552S | s2cid = 4423528 }}</ref>

=== ''Streptococcus pneumoniae'' ===
''[[Streptococcus pneumoniae]]'' is the main cause of community-acquired pneumonia and meningitis in children and the elderly, and of sepsis in HIV-infected persons. When ''S. pneumoniae'' grows in biofilms, genes are specifically expressed that respond to oxidative stress and induce competence.<ref name="pmid16925554">{{cite journal | vauthors = Oggioni MR, Trappetti C, Kadioglu A, Cassone M, Iannelli F, Ricci S, Andrew PW, Pozzi G | title = Switch from planktonic to sessile life: a major event in pneumococcal pathogenesis | journal = Molecular Microbiology | volume = 61 | issue = 5 | pages = 1196–210 | date = September 2006 | pmid = 16925554 | pmc = 1618759 | doi = 10.1111/j.1365-2958.2006.05310.x }}</ref> Formation of a biofilm depends on [[competence stimulating peptide]] (CSP). CSP also functions as a quorum-sensing peptide. It not only induces biofilm formation, but also increases virulence in pneumonia and meningitis.

It has been proposed that competence development and biofilm formation is an adaptation of ''S. pneumoniae'' to survive the defenses of the host.<ref name=Michod /> In particular, the host's polymorphonuclear leukocytes produce an oxidative burst to defend against the invading bacteria, and this response can kill bacteria by damaging their DNA. Competent ''S. pneumoniae'' in a biofilm have the survival advantage that they can more easily take up transforming DNA from nearby cells in the biofilm to use for recombinational repair of oxidative damages in their DNA. Competent ''S. pneumoniae'' can also secrete an enzyme (murein hydrolase) that destroys non-competent cells (fratricide) causing DNA to be released into the surrounding medium for potential use by the competent cells.<ref name="pmid22706053">{{cite journal |vauthors=Wei H, Håvarstein LS |title=Fratricide is essential for efficient gene transfer between pneumococci in biofilms |journal=Appl. Environ. Microbiol. |volume=78 |issue=16 |pages=5897–905 |date=August 2012 |pmid=22706053 |pmc=3406168 |doi=10.1128/AEM.01343-12 |bibcode=2012ApEnM..78.5897W }}</ref>

The insect antimicrobial peptide [[Cecropin#Members|cecropin A]] can destroy planktonic and sessile biofilm-forming [[Uropathogenic Escherichia coli|uropathogenic ''E. coli'']] cells, either alone or when combined with the antibiotic [[nalidixic acid]], synergistically clearing infection in vivo (in the insect host ''[[Galleria mellonella]]'') without off-target cytotoxicity. The multi-target mechanism of action involves outer membrane permeabilization followed by biofilm disruption triggered by the inhibition of efflux pump activity and interactions with extracellular and intracellular nucleic acids.<ref>{{cite journal | vauthors = Kalsy M, Tonk M, Hardt M, Dobrindt U, Zdybicka-Barabas A, Cytrynska M, Vilcinskas A, Mukherjee K | title = The insect antimicrobial peptide cecropin A disrupts uropathogenic Escherichia coli biofilms | journal = npj Biofilms and Microbiomes | volume = 6 | issue = 1 | article-number = 6 | date = 2020 | pmid = 32051417 | doi = 10.1038/s41522-020-0116-3 | pmc = 7016129 | doi-access = free }}</ref>

=== ''Escherichia coli'' ===
''[[Escherichia coli]]'' biofilms are responsible for many intestinal infectious diseases.<ref>{{cite journal | vauthors = Sturbelle RT, de Avila LF, Roos TB, Borchardt JL, da Conceição R, Dellagostin OA, Leite FP | title = The role of quorum sensing in Escherichia coli (ETEC) virulence factors | journal = Veterinary Microbiology | volume = 180 | issue = 3–4 | pages = 245–252 | date = November 2015 | pmid = 26386492 | doi = 10.1016/j.vetmic.2015.08.015 }}</ref> The Extraintestinal group of ''E. coli'' (ExPEC) is the dominant bacterial group that attacks the [[urinary system]], which leads to [[urinary tract infection]]s.<ref>{{cite journal | vauthors = Vogeleer P, Tremblay YD, Mafu AA, Jacques M, Harel J | title = Life on the outside: role of biofilms in environmental persistence of Shiga-toxin producing Escherichia coli | journal = Frontiers in Microbiology | volume = 5 | page = 317 | date = 2014 | pmid = 25071733 | doi = 10.3389/fmicb.2014.00317 | pmc = 4076661 | doi-access = free }}</ref> The biofilm formation of these pathogenic ''[[Escherichia coli|E. coli]]'' is hard to eradicate due to the complexity of its aggregation structure, and it has a significant contribution to developing aggressive medical complications, increase in hospitalization rate, and cost of treatment.<ref>{{cite journal | vauthors = Danese PN, Pratt LA, Kolter R | title = Exopolysaccharide production is required for development of Escherichia coli K-12 biofilm architecture | journal = Journal of Bacteriology | volume = 182 | issue = 12 | pages = 3593–3596 | date = June 2000 | pmid = 10852895 | pmc = 101973 | doi = 10.1128/JB.182.12.3593-3596.2000 }}</ref><ref>{{cite journal | vauthors = Niranjan V, Malini A | title = Antimicrobial resistance pattern in Escherichia coli causing urinary tract infection among inpatients | journal = The Indian Journal of Medical Research | volume = 139 | issue = 6 | pages = 945–948 | date = June 2014 | pmid = 25109731 | pmc = 4165009 }}</ref> The development of ''E. coli'' biofilm is a common leading cause of [[Urinary tract infection|urinary tract infections (UTI)]] in hospitals through its contribution to developing [[Hospital-acquired infection|medical device-associated infections]]. [[Catheter-associated urinary tract infection|Catheter-associated urinary tract infections (CAUTI)]] represent the most common [[hospital-acquired infection]] due to the formation of the pathogenic ''E. coli biofilm'' inside the catheters.<ref>{{cite journal | vauthors = Reisner A, Maierl M, Jörger M, Krause R, Berger D, Haid A, Tesic D, Zechner EL | title = Type 1 fimbriae contribute to catheter-associated urinary tract infections caused by Escherichia coli | journal = Journal of Bacteriology | volume = 196 | issue = 5 | pages = 931–939 | date = March 2014 | pmid = 24336940 | pmc = 3957706 | doi = 10.1128/JB.00985-13 }}</ref>

=== ''Staphylococcus aureus'' ===
''[[Staphylococcus aureus]]'' pathogen can attack skin and lungs, leading to [[skin infection]] and [[pneumonia]].<ref>{{cite journal | vauthors = Kobayashi SD, Malachowa N, Whitney AR, Braughton KR, Gardner DJ, Long D, Bubeck Wardenburg J, Schneewind O, Otto M, Deleo FR | title = Comparative analysis of USA300 virulence determinants in a rabbit model of skin and soft tissue infection | journal = The Journal of Infectious Diseases | volume = 204 | issue = 6 | pages = 937–941 | date = September 2011 | pmid = 21849291 | pmc = 3156927 | doi = 10.1093/infdis/jir441 }}</ref><ref>{{cite journal | vauthors = Kitur K, Parker D, Nieto P, Ahn DS, Cohen TS, Chung S, Wachtel S, Bueno S, Prince A | title = Toxin-induced necroptosis is a major mechanism of Staphylococcus aureus lung damage | journal = PLOS Pathogens | volume = 11 | issue = 4 | article-number = e1004820 | date = April 2015 | pmid = 25880560 | pmc = 4399879 | doi = 10.1371/journal.ppat.1004820 | doi-access = free }}</ref> Moreover, the biofilm infections network of ''S. aureus'' plays a critical role in preventing immune cells, such as [[macrophage]]s from eliminating and destroying bacterial cells.<ref>{{cite journal | vauthors = Thurlow LR, Hanke ML, Fritz T, Angle A, Aldrich A, Williams SH, Engebretsen IL, Bayles KW, Horswill AR, Kielian T | title = Staphylococcus aureus biofilms prevent macrophage phagocytosis and attenuate inflammation in vivo | journal = Journal of Immunology | volume = 186 | issue = 11 | pages = 6585–6596 | date = June 2011 | pmid = 21525381 | pmc = 3110737 | doi = 10.4049/jimmunol.1002794 }}</ref> Furthermore, biofilm formation by bacteria, such as ''S. aureus'', not only develops [[Antimicrobial resistance|resistance against antibiotic]] medication but also develop internal resistance toward [[Antimicrobial peptides|antimicrobial peptides (AMPs)]], leading to preventing the inhibition of the pathogen and maintaining its survival.<ref>{{cite journal | vauthors = Craft KM, Nguyen JM, Berg LJ, Townsend SD | title = Methicillin-resistant ''Staphylococcus aureus'' (MRSA): antibiotic-resistance and the biofilm phenotype | journal = MedChemComm | volume = 10 | issue = 8 | pages = 1231–1241 | date = August 2019 | pmid = 31534648 | pmc = 6748282 | doi = 10.1039/c9md00044e }}</ref>

=== ''Serratia marcescens'' ===
''[[Serratia marcescens]]'' is a fairly common opportunistic pathogen that can form biofilms on various surfaces, including medical devices such as catheters and implants, as well as natural environments like soil and water. The formation of biofilms by ''S. marcescens'' is a serious concern because of its ability to adhere to and colonize surfaces, protecting itself from host immune responses and antimicrobial agents. This strength makes infections caused by ''S. marcescens'' challenging to treat, specifically in hospitals where the bacterium can cause severe, and specific, infections.

Research suggests that biofilm formation by S. marcescens is a process controlled by both nutrient cues and the quorum-sensing system.<ref>{{cite journal |vauthors=Rice SA, Koh KS, Queck SY, Labbate M, Lam KW, Kjelleberg S |date=2005 |title=Biofilm Formation and Sloughing in Serratia marcescens Are Controlled by Quorum Sensing and Nutrient Cues |journal=Journal of Bacteriology |volume=187 |issue=10 |pages=3477–3485 |doi=10.1128/JB.187.10.3477-3485.2005 |pmc=1111991 |pmid=15866935}}</ref> Quorum sensing influences the bacterium's ability to adhere to surfaces and establish mature biofilms, whereas the availability of specific nutrients can enhance or inhibit biofilm development.

''S. marcescens'' creates biofilms that ultimately develop into a highly porous, thread-like structure composed of chains of cells, filaments, and cell clusters. Research has shown that ''S. marcescens'' biofilms exhibit complex structural organization, including the formation of microcolonies and channels that facilitate nutrient and waste exchange. The production of extracellular polymeric substances (EPS) is a key factor in biofilm development, contributing to the bacterium's adhesion and resistance to antimicrobial agents. In addition to its role in healthcare-associated infections, ''S. marcescens'' biofilms have been implicated in the deterioration of industrial equipment and processes. For example, biofilm growth in cooling towers can lead to [[biofouling]] and reduced efficiency.

Efforts to control and prevent biofilm formation by ''S. marcescens'' involve the use of antimicrobial coatings on medical devices, the development of targeted biofilm disruptors, and improved sterilization protocols. Further research into the molecular mechanisms governing ''S. marcescens'' biofilm formation and persistence is crucial for developing effective strategies to combat its associated risks. The use of [[indole]] compounds has been studied to be used as protection against biofilm formation.<ref>{{cite journal |vauthors=Sethupathy S, Sathiyamoorthi E, Kim Y, Lee J, Lee J |date=2020 |title=Antibiofilm and Antivirulence Properties of Indoles Against Serratia marcescens |journal=Frontiers in Microbiology |volume=11 |article-number=584812 |doi=10.3389/fmicb.2020.584812 |pmc=7662412 |pmid=33193228 |doi-access=free}}</ref>

== Uses and impact ==
=== In medicine ===
It is suggested that around two-thirds of bacterial infections in humans involve biofilms.<ref name="Del Pozo"/><ref name="Lazar">{{cite journal | vauthors = Lazar V | title = Quorum sensing in biofilms—how to destroy the bacterial citadels or their cohesion/power? | journal = Anaerobe | volume = 17 | issue = 6 | pages = 280–5 | date = December 2011 | pmid = 21497662 | doi = 10.1016/j.anaerobe.2011.03.023 }}</ref> Infections associated with the biofilm growth usually are challenging to eradicate.<ref>{{cite book|title=Biofilm infections|date=2011|publisher=Springer| vauthors = Bjarnsholt T, Jensen PØ, Moser C, Høiby N |isbn=978-1-4419-6083-2|location=New York|oclc=682907381}}</ref> This is mostly due to the fact that mature biofilms display [[antimicrobial tolerance]], and immune response evasions.<ref name="medical biofilms" /><ref name="JMB"/> Biofilms often form on the inert surfaces of implanted devices such as catheters, prosthetic cardiac valves and intrauterine devices.<ref>{{cite journal | vauthors = Auler ME, Morreira D, Rodrigues FF, Abr Ao MS, Margarido PF, Matsumoto FE, Silva EG, Silva BC, Schneider RP, Paula CR | title = Biofilm formation on intrauterine devices in patients with recurrent vulvovaginal candidiasis | journal = Medical Mycology | volume = 48 | issue = 1 | pages = 211–6 | date = February 2010 | pmid = 20055746 | doi = 10.3109/13693780902856626 | doi-access = free }}</ref> Some of the most difficult infections to treat are those associated with the use of medical devices.<ref name="Del Pozo"/><ref name="niamhcurran"/>

The rapidly expanding worldwide industry for biomedical devices and tissue engineering related products is already at $180&nbsp;billion per year, yet this industry continues to suffer from microbial colonization. No matter the sophistication, microbial infections can develop on all medical devices and tissue engineering constructs.<ref name="medical biofilms">{{cite journal | vauthors = Bryers JD | title = Medical biofilms | journal = Biotechnology and Bioengineering | volume = 100 | issue = 1 | pages = 1–18 | date = May 2008 | pmid = 18366134 | pmc = 2706312 | doi = 10.1002/bit.21838 | bibcode = 2008BiotB.100....1B }}</ref> 60–70% of [[hospital-acquired infection]]s are associated with the implantation of a biomedical device.<ref name="medical biofilms" /> This leads to 2 million cases annually in the U.S., costing the healthcare system over $5&nbsp;billion in additional healthcare expenses.<ref name="medical biofilms" />

The level of antibiotic resistance in a biofilm is much greater than that of non-biofilm bacteria, and can be as much as 5,000 times greater.<ref name="Del Pozo">{{cite journal | vauthors = Del Pozo JL, Rouse MS, Patel R | title = Bioelectric effect and bacterial biofilms. A systematic review | journal = The International Journal of Artificial Organs | volume = 31 | issue = 9 | pages = 786–795 | date = September 2008 | pmid = 18924090 | pmc = 3910516 | doi = 10.1177/039139880803100906 }}</ref> The extracellular matrix of biofilm is considered one of the leading factors that can reduce the penetration of antibiotics into a biofilm structure and contributes to antibiotic resistance.<ref>{{cite journal | vauthors = Vuotto C, Longo F, Balice MP, Donelli G, Varaldo PE | title = Antibiotic Resistance Related to Biofilm Formation in Klebsiella pneumoniae | journal = Pathogens | volume = 3 | issue = 3 | pages = 743–758 | date = September 2014 | pmid = 25438022 | pmc = 4243439 | doi = 10.3390/pathogens3030743 | doi-access = free }}</ref> Further, it has been demonstrated that the evolution of resistance to antibiotics may be affected by the biofilm lifestyle.<ref>{{cite journal | vauthors = Santos-Lopez A, Marshall CW, Scribner MR, Snyder DJ, Cooper VS | title = Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle | journal = eLife | volume = 8 | article-number = e47612 | date = September 2019 | pmid = 31516122 | pmc = 6814407 | doi = 10.7554/eLife.47612 | doi-access = free }}</ref> [[Bacteriophage]] therapy can disperse the biofilm generated by antibiotic-resistant bacteria.<ref name="pmid38188636">{{cite journal |vauthors=Pai L, Patil S, Liu S, Wen F |title=A growing battlefield in the war against biofilm-induced antimicrobial resistance: insights from reviews on antibiotic resistance |journal=Front Cell Infect Microbiol |volume=13 |issue= |article-number=1327069 |date=2023 |pmid=38188636 |pmc=10770264 |doi=10.3389/fcimb.2023.1327069 |doi-access=free |url=}}</ref>

It has been shown that the introduction of a small current of electricity to the liquid surrounding a biofilm, together with small amounts of antibiotic can reduce the level of antibiotic resistance to levels of non-biofilm bacteria. This is termed the '''bioelectric effect'''.<ref name="Del Pozo"/><ref name="Kim">{{cite journal | vauthors = Kim YW, Subramanian S, Gerasopoulos K, Ben-Yoav H, Wu HC, Quan D, Carter K, Meyer MT, Bentley WE, Ghodssi R | title = Effect of electrical energy on the efficacy of biofilm treatment using the bioelectric effect | journal = npj Biofilms and Microbiomes | volume = 1 | article-number = 15016 | date = 2015 | pmid = 28721233 | pmc = 5515217 | doi = 10.1038/npjbiofilms.2015.16 }}</ref> The application of a small [[DC current]] on its own can cause a biofilm to detach from its surface.<ref name="Del Pozo"/> A study showed that the type of current used made no difference to the bioelectric effect.<ref name="Kim"/>

=== In industry ===
{{See also|Biofilms in industry}}
Biofilms can also be harnessed for constructive purposes. For example, many [[sewage treatment]] plants include a [[secondary treatment]] stage in which waste water passes over biofilms grown on filters, which extract and digest organic compounds. In such biofilms, bacteria are mainly responsible for removal of organic matter ([[Biochemical oxygen demand|BOD]]), while [[protozoa]] and [[rotifer]]s are mainly responsible for removal of suspended solids (SS), including pathogens and other microorganisms. [[Slow sand filter]]s rely on biofilm development in the same way to filter surface water from lake, spring or river sources for drinking purposes. What is regarded as clean water is effectively a waste material to these microcellular organisms. Biofilms can help eliminate petroleum oil from contaminated oceans or marine systems. The oil is eliminated by the [[microbial biodegradation|hydrocarbon-degrading]] activities of communities of [[hydrocarbonoclastic bacteria]] (HCB).<ref name="chapter9">{{cite book |title=Microbial Biodegradation: Genomics and Molecular Biology |vauthors=Martins dos Santos VA, Yakimov MM, Timmis KN, Golyshin PN |publisher=Horizon Scientific Press |year=2008 |isbn=978-1-904455-17-2 |pages=[https://archive.org/details/microbialbiodegr0000unse/page/1971 1971] |chapter=Genomic Insights into Oil Biodegradation in Marine Systems |chapter-url=https://books.google.com/books?id=wx6v3TIkzXUC&pg=PA1971 | veditors = Díaz E |url=https://archive.org/details/microbialbiodegr0000unse/page/1971}}</ref>
Biofilms are used in [[microbial fuel cells]] (MFCs) to generate electricity from a variety of starting materials, including complex organic waste and renewable biomass.<ref name="LearGLewisGD" /><ref>{{cite journal |vauthors = Wang VB, Chua SL, Cai Z, Sivakumar K, Zhang Q, Kjelleberg S, Cao B, Loo SC, Yang L |title = A stable synergistic microbial consortium for simultaneous azo dye removal and bioelectricity generation |journal = Bioresource Technology |volume = 155 |pages = 71–76 |date = March 2014 |pmid = 24434696 |doi = 10.1016/j.biortech.2013.12.078 |bibcode = 2014BiTec.155...71W }}</ref><ref>{{cite journal |vauthors = Wang VB, Chua SL, Cao B, Seviour T, Nesatyy VJ, Marsili E, Kjelleberg S, Givskov M, Tolker-Nielsen T, Song H, Loo JS, Yang L |title = Engineering PQS biosynthesis pathway for enhancement of bioelectricity production in pseudomonas aeruginosa microbial fuel cells |journal = PLOS ONE |volume = 8 |issue = 5 |article-number = e63129 |year = 2013 |pmid = 23700414 |pmc = 3659106 |doi = 10.1371/journal.pone.0063129 |doi-access = free |bibcode = 2013PLoSO...863129W }}</ref>
Biofilms are also relevant for the improvement of metal dissolution in [[bioleaching]] industry,<ref name="pmid23720034">{{cite journal |vauthors = Vera M, Schippers A, Sand W |title = Progress in bioleaching: fundamentals and mechanisms of bacterial metal sulfide oxidation—part A |journal = Appl. Microbiol. Biotechnol. |volume = 97 |issue = 17 |pages = 7529–41 |date = September 2013 |pmid = 23720034 |doi = 10.1007/s00253-013-4954-2 |s2cid = 17677624 }}</ref> and aggregation of microplastics pollutants for convenient removal from the environment.<ref>{{Cite journal | vauthors = Chan SY, Wong MW, Kwan BT, Fang JK, Chua SL |date=2022-10-12 |title=Microbial–Enzymatic Combinatorial Approach to Capture and Release Microplastics |journal=Environmental Science & Technology Letters |volume=9 |issue=11 |language=en |pages=975–982 |doi=10.1021/acs.estlett.2c00558 |bibcode=2022EnSTL...9..975C |s2cid=252892619 |issn=2328-8930}}</ref><ref>{{Cite journal | vauthors = Liu SY, Leung MM, Fang JK, Chua SL |date=2021-01-15 |title=Engineering a microbial 'trap and release' mechanism for microplastics removal |journal=Chemical Engineering Journal |language=en |volume=404 |article-number=127079 |doi=10.1016/j.cej.2020.127079 |bibcode=2021ChEnJ.40427079L |hdl=10397/88307 |s2cid=224972583 |issn=1385-8947|hdl-access=free }}</ref>

=== Food industry ===
Biofilms have become problematic in several food industries due to the ability to form on plants and during industrial processes.<ref name=ref1>{{cite journal | title = Biofilm formation in food industries: A food safety concern |journal=Food Control|volume=31|issue=2|date=June 2013| vauthors = Srey S, Jahid ID, Ha SD |pages =572–585|issn= 0956-7135|doi=10.1016/j.foodcont.2012.12.001 }}</ref> Bacteria can survive long periods of time in water, animal manure, and soil, causing biofilm formation on plants or in the processing equipment.<ref>T. Tarver, "Biofilms: A Threat to Food Safety – IFT.org", Ift.org, 2016.</ref> The buildup of biofilms can affect the heat flow across a surface and increase surface corrosion and frictional resistance of fluids.<ref name=ref2>{{cite journal | vauthors = Kumar CG, Anand SK | title = Significance of microbial biofilms in food industry: a review | journal = International Journal of Food Microbiology | volume = 42 | issue = 1–2 | pages = 9–27 | date = June 1998 | pmid = 9706794 | doi = 10.1016/s0168-1605(98)00060-9 }}</ref> These can lead to a loss of energy in a system and overall loss of products.<ref name=ref2 /> Along with economic problems, biofilm formation on food poses a health risk to consumers due to the ability to make the food more resistant to disinfectants<ref name=ref1 /> As a result, from 1996 to 2010 the [[Centers for Disease Control and Prevention]] estimated 48 million foodborne illnesses per year.<ref name=ref1 /> Biofilms have been connected to about 80% of bacterial infections in the United States.<ref name=ref1 />

In [[produce]], microorganisms attach to the surfaces and biofilms develop internally.<ref name=ref1 /> During the washing process, biofilms resist sanitization and allow bacteria to spread across the produce,<ref name=ref1 /> especially via kitchen utensils.<ref>{{cite journal | vauthors = Kwok TY, Ma Y, Chua SL | title = Biofilm dispersal induced by mechanical cutting leads to heightened foodborne pathogen dissemination | journal = Food Microbiology | volume = 102 | article-number = 103914 | date = April 2022 | pmid = 34809940 | doi = 10.1016/j.fm.2021.103914 | hdl = 10397/100037 | s2cid = 244234814 | hdl-access = free }}</ref> This problem is also found in ready-to-eat foods, because the foods go through limited cleaning procedures before consumption<ref name=ref1 /> Due to the perishability of dairy products and limitations in cleaning procedures, resulting in the buildup of bacteria, dairy is susceptible to biofilm formation and contamination.<ref name=ref1 /><ref name=ref2 /> The bacteria can spoil the products more readily and contaminated products pose a health risk to consumers. One species of bacteria that can be found in various industries and is a major cause of foodborne disease is ''[[Salmonella]]''.<ref name=ref3>{{cite journal | vauthors = Mizan F | year = 2015| title = Microbial biofilms in seafood: A food-hygiene challenge | journal = Food Microbiology| volume = 49| pages = 41–55| doi = 10.1016/j.fm.2015.01.009| pmid = 25846914}}</ref> Large amounts of Salmonella contamination can be found in the poultry processing industry as about 50% of ''Salmonella'' strains can produce biofilms on poultry farms.<ref name=ref1 /> ''Salmonella'' increases the risk of foodborne illnesses when the poultry products are not cleaned and cooked correctly. ''Salmonella'' is also found in the seafood industry where biofilms form from seafood borne pathogens on the seafood itself as well as in water.<ref name=ref3 /> Shrimp products are commonly affected by ''Salmonella'' because of unhygienic processing and handling techniques<ref name=ref3 /> The preparation practices of shrimp and other seafood products can allow for bacteria buildup on the products.<ref name=ref3 />

New forms of cleaning procedures are being tested to reduce biofilm formation in these processes which will lead to safer and more productive food processing industries. These new forms of cleaning procedures also have a profound effect on the environment, often releasing toxic gases into the groundwater reservoirs.<ref name=ref2 /> As a response to the aggressive methods employed in controlling biofilm formation, there are a number of novel technologies and chemicals under investigation that can prevent either the proliferation or adhesion of biofilm-secreting microbes. Latest proposed biomolecules presenting marked anti-biofilm activity include a range of metabolites such as bacterial [[rhamnolipid]]s<ref>{{cite journal| vauthors = De Araujo LV, Abreu F, Lins U, Santa Anna LM, Nitschke M, Freire DM |date=January 2011|title=Rhamnolipid and surfactin inhibit Listeria monocytogenes adhesion|journal=Food Research International|volume=44|issue=1|pages=481–488|doi=10.1016/j.foodres.2010.09.002}}</ref> and even plant-<ref>{{cite journal | vauthors = Wang X, Yao X, Zhu Z, Tang T, Dai K, Sadovskaya I, Flahaut S, Jabbouri S | title = Effect of berberine on Staphylococcus epidermidis biofilm formation | journal = International Journal of Antimicrobial Agents | volume = 34 | issue = 1 | pages = 60–6 | date = July 2009 | pmid = 19157797 | doi = 10.1016/j.ijantimicag.2008.10.033 }}</ref> and animal-derived [[alkaloid]]s.<ref>{{cite journal | vauthors = Carvalho DB, Fox EG, Santos DG, Sousa JS, Freire DM, Nogueira FC, Domont GB, Castilho LV, Machado EA | title = Fire Ant Venom Alkaloids Inhibit Biofilm Formation | journal = Toxins | volume = 11 | issue = 7 | page = 420 | date = July 2019 | pmid = 31323790 | pmc = 6669452 | doi = 10.3390/toxins11070420 | doi-access = free }}</ref>

=== In aquaculture ===
{{Further|Aquaculture}}
[[File:Screen Shot 2017-12-13 at 1.40.19 PM.png|thumb|A biofilm from the [[Dead Sea]]]]

In [[shellfish]] and [[algal]] [[aquaculture]], [[biofouling]] microbial species tend to block nets and cages and ultimately outcompete the farmed species for space and food.<ref>{{cite journal | vauthors = Braithwaite RA, McEvoy LA | title = Marine biofouling on fish farms and its remediation | journal = Advances in Marine Biology | volume = 47 | pages = 215–252 | year = 2004 | pmid = 15596168 | doi = 10.1016/S0065-2881(04)47003-5 | isbn = 978-0-12-026148-2 }}</ref> Bacterial biofilms start the colonization process by creating microenvironments that are more favorable for biofouling species. In the marine environment, biofilms could reduce the hydrodynamic efficiency of ships and propellers, lead to pipeline blockage and sensor malfunction, and increase the weight of appliances deployed in seawater.<ref name="pmid17497196">{{cite journal | vauthors = Qian PY, Lau SC, Dahms HU, Dobretsov S, Harder T | title = Marine biofilms as mediators of colonization by marine macroorganisms: implications for antifouling and aquaculture | journal = Marine Biotechnology | volume = 9 | issue = 4 | pages = 399–410 | date = 2007 | pmid = 17497196 | doi = 10.1007/s10126-007-9001-9 | bibcode = 2007MarBt...9..399Q | s2cid = 7614961 | url = http://scholarbank.nus.edu.sg/handle/10635/68293 | archive-date = 18 November 2024 | access-date = 1 September 2025 | archive-url = https://web.archive.org/web/20241118072341/https://scholarbank.nus.edu.sg/handle/10635/68293 | url-status = live }}</ref> Numerous studies have shown that biofilm can be a reservoir for potentially pathogenic bacteria in freshwater aquaculture.<ref name="pmid23851087">{{cite journal | vauthors = Cai W, De La Fuente L, Arias CR | title = Biofilm formation by the fish pathogen Flavobacterium columnare: development and parameters affecting surface attachment | journal = Applied and Environmental Microbiology | volume = 79 | issue = 18 | pages = 5633–42 | date = September 2013 | pmid = 23851087 | pmc = 3754160 | doi = 10.1128/AEM.01192-13 | bibcode = 2013ApEnM..79.5633C }}</ref><ref>{{cite journal|year=2004|title=Identification of bacterial pathogens in biofilms of recirculating aquaculture systems|journal=Journal of Aquatic Food Product Technology|volume=13|pages=125–133|doi=10.1300/j030v13n01_11|vauthors = King RK, Flick Jr GJ, Pierson D, Smith SA, Boardman GD, ((Coale Jr CW))|issue=1 |bibcode=2004JAFPT..13a.125K |s2cid=83791439}}</ref><ref>{{cite journal|year=2006|title=Biofilm development within a larval rearing tank of the tropical rock lobster, Panulirus ornatus|journal=Aquaculture|volume=260|issue=1–4|pages=27–38|doi=10.1016/j.aquaculture.2006.06.023|vauthors = Bourne DG, Høj L, Webster NS, Swan J, Hall MR|bibcode=2006Aquac.260...27B }}</ref><ref>{{cite journal | vauthors = Wietz M, Hall MR, Høj L | title = Effects of seawater ozonation on biofilm development in aquaculture tanks | journal = Systematic and Applied Microbiology | volume = 32 | issue = 4 | pages = 266–77 | date = July 2009 | pmid = 19446976 | doi = 10.1016/j.syapm.2009.04.001 | bibcode = 2009SyApM..32..266W }}</ref> Moreover, biofilms are important in establishing infections on the fish.<ref>{{cite journal | vauthors = Liu YS, Deng Y, Chen CK, Khoo BL, Chua SL | title = Rapid detection of microorganisms in a fish infection microfluidics platform | journal = Journal of Hazardous Materials | volume = 431 | article-number = 128572 | date = June 2022 | pmid = 35278965 | doi = 10.1016/j.jhazmat.2022.128572 | bibcode = 2022JHzM..43128572L | s2cid = 247136872 }}</ref> As mentioned previously, biofilms can be difficult to eliminate even when antibiotics or chemicals are used in high doses.<ref>{{cite journal|year=1994|title=Mass mortality of Penaeus monodon larvae due to antibiotic-resistant Vibrio harveyi infection|journal=Aquaculture|volume=128|issue=3–4|pages=203–209|doi=10.1016/0044-8486(94)90309-3|vauthors = Karunasagar I, Pai R, Malathi G|bibcode=1994Aquac.128..203K }}</ref><ref name="pmid1917879">{{cite journal | vauthors = Lawrence JR, Korber DR, Hoyle BD, Costerton JW, Caldwell DE | title = Optical sectioning of microbial biofilms | journal = Journal of Bacteriology | volume = 173 | issue = 20 | pages = 6558–67 | date = October 1991 | pmid = 1917879 | pmc = 208993 | doi = 10.1128/jb.173.20.6558-6567.1991 }}</ref> The role that biofilm plays as reservoirs of bacterial fish pathogens has not been explored in detail but it certainly deserves to be studied.

== Eukaryotic ==
{{See also|Phototrophic biofilms}}
Along with bacteria, biofilms are often initiated and produced by eukaryotic microbes. The biofilms produced by eukaryotes is usually occupied by bacteria and other eukaryotes alike, however the surface is cultivated and EPS is secreted initially by the eukaryote.<ref name="pmid16897306"/><ref name="Van Colen 2014" /><ref>{{cite journal | vauthors = Cooksey K, Wigglesworth-Cooksey B | year = 1995 | title = Adhesion of bacteria and diatoms to surfaces in the sea: a review | journal = Aquatic Microbial Ecology | volume = 9 | issue = 1| pages = 87–96 | doi=10.3354/ame009087| doi-access = free }}</ref> Both [[Fungus|fungi]] and [[microalgae]] are known to form biofilms in such a way. Biofilms of fungal origin are important aspects of human infection and fungal pathogenicity, as the fungal infection is more resistant to antifungals.<ref>{{cite journal | vauthors = Fanning S, Mitchell AP | year = 2012 | title = Fungal Biofilms | journal = PLOS Pathog | volume = 8 | issue = 4| article-number = e1002585 | doi = 10.1371/journal.ppat.1002585 | pmid = 22496639 | pmc = 3320593 | doi-access = free }}</ref><ref name="pmid11514524">{{cite journal | vauthors = Chandra J, Kuhn DM, Mukherjee PK, Hoyer LL, McCormick T, Ghannoum MA | title = Biofilm formation by the fungal pathogen Candida albicans: development, architecture, and drug resistance | journal = J. Bacteriol. | volume = 183 | issue = 18 | pages = 5385–94 | date = September 2001 | pmid = 11514524 | pmc = 95423 | doi =10.1128/jb.183.18.5385-5394.2001 }}</ref>

In the environment, fungal biofilms are an area of ongoing research. One key area of research is fungal biofilms on plants. For example, in the soil, plant associated fungi including [[mycorrhiza]] have been shown to decompose organic matter and protect plants from bacterial pathogens.<ref>{{cite book| vauthors = Burmølle M, Kjøller A, Sørenses S | veditors = Lear G, Gavin L, Lewis G |title=Microbial Biofilms: Current Research and Applications|date=2012|publisher=Horizon Scientific Press|isbn=978-1-904455-96-7|pages=61–71}}</ref>

Biofilms in aquatic environments are often founded by [[diatom]]s. The exact purpose of these biofilms is unknown, however there is evidence that the EPS produced by diatoms facilitates both cold and salinity stress.<ref name="pmid27009999"/><ref name="pmid25268215">{{cite journal | vauthors = Steele DJ, Franklin DJ, Underwood GJ | title = Protection of cells from salinity stress by extracellular polymeric substances in diatom biofilms | journal = Biofouling | volume = 30 | issue = 8 | pages = 987–98 | date = September 2014 | pmid = 25268215 | pmc = 4706044 | doi = 10.1080/08927014.2014.960859 | bibcode = 2014Biofo..30..987S }}</ref> These eukaryotes interact with a diverse range of other organisms within a region known as the [[phycosphere]], but importantly are the bacteria associated with diatoms, as it has been shown that although diatoms excrete EPS, they only do so when interacting with certain bacteria species.<ref name="pmid26986529">{{cite journal | vauthors = Windler M, Leinweber K, Bartulos CR, Philipp B, Kroth PG | title = Biofilm and capsule formation of the diatom Achnanthidium minutissimum are affected by a bacterium | journal = J. Phycol. | volume = 51 | issue = 2 | pages = 343–55 | date = April 2015 | pmid = 26986529 | doi = 10.1111/jpy.12280 | bibcode = 2015JPcgy..51..343W | s2cid = 1446573 | url = http://nbn-resolving.de/urn:nbn:de:bsz:352-0-289776 }}</ref><ref name="pmid23757240">{{cite journal | vauthors = Buhmann M, Kroth PG, Schleheck D | title = Photoautotrophic-heterotrophic biofilm communities: a laboratory incubator designed for growing axenic diatoms and bacteria in defined mixed-species biofilms | journal = Environ Microbiol Rep | volume = 4 | issue = 1 | pages = 133–40 | date = February 2012 | pmid = 23757240 | doi = 10.1111/j.1758-2229.2011.00315.x | bibcode = 2012EnvMR...4..133B | url = http://nbn-resolving.de/urn:nbn:de:bsz:352-177088 }}</ref>

== Horizontal gene transfer ==
[[Horizontal gene transfer]] is the lateral transfer of genetic material between cellular organisms. It happens frequently in prokaryotes, and less frequently in eukaryotes. In bacteria, horizontal gene transfer can occur through transformation (uptake of free floating DNA in the environment), transduction (virus mediated DNA uptake), or [[Bacterial conjugation|conjugation]] (transfer of DNA between pili structures of two adjacent bacteria).<ref>{{cite journal | vauthors = Thomas CM, Nielsen KM | title = Mechanisms of, and barriers to, horizontal gene transfer between bacteria | journal = Nature Reviews. Microbiology | volume = 3 | issue = 9 | pages = 711–721 | date = September 2005 | pmid = 16138099 | doi = 10.1038/nrmicro1234 | s2cid = 1231127 }}</ref> Recent studies have also uncovered other mechanisms, such as membrane vesicle transmission or gene transfer agents.<ref name="Luo_2022">{{cite journal | vauthors = Luo A, Wang F, Sun D, Liu X, Xin B | title = Formation, Development, and Cross-Species Interactions in Biofilms | journal = Frontiers in Microbiology | volume = 12 | article-number = 757327 | date = 2022 | pmid = 35058893 | pmc = 8764401 | doi = 10.3389/fmicb.2021.757327 | doi-access = free }}</ref> Biofilms promote horizontal gene transfer in a variety of ways.[[File:Escherichia coli forming biofilms via F-pilus.tif|thumb|396x396px|Transmission electron micrograph showing bacteria Escherichia coli that form extensive biofilms using a network of conjugative F-pili. Source: Jonasz Patkowski]]Bacterial conjugation has been shown to accelerate biofilm formation in difficult environment due to the robust connections established by the [[conjugative pili]].<ref>{{cite journal | vauthors = Patkowski JB, Dahlberg T, Amin H, Gahlot DK, Vijayrajratnam S, Vogel JP, Francis MS, Baker JL, Andersson M, Costa TR | title = The F-pilus biomechanical adaptability accelerates conjugative dissemination of antimicrobial resistance and biofilm formation | journal = Nature Communications | volume = 14 | issue = 1 | article-number = 1879 | date = April 2023 | pmid = 37019921 | pmc = 10076315 | doi = 10.1038/s41467-023-37600-y }}</ref> These connections can often foster cross-species transfer events due to the diverse heterogeneity of many biofilms. Additionally, biofilms are structurally confined by a polysaccharide matrix, providing the close spatial requirements for conjugation. Transformation is also frequently observed in biofilms. Bacterial autolysis is a key mechanism in biofilm structural regulation, providing an abundant source of competent DNA primed for transformative uptake.<ref>{{cite journal | vauthors = Thomas VC, Hancock LE | title = Suicide and fratricide in bacterial biofilms | journal = The International Journal of Artificial Organs | volume = 32 | issue = 9 | pages = 537–544 | date = September 2009 | pmid = 19851979 | doi = 10.1177/039139880903200902 | s2cid = 201969291 }}</ref><ref name="Luo_2022" /> In some instances, inter-biofilm [[quorum sensing]] can enhance the competence of free floating eDNA, further promoting transformation.<ref name="Luo_2022" /> Stx gene transfer through bacteriophage carriers has been witnessed within biofilms, which suggests that biofilms are also a suitable environment for transduction.<ref name="Luo_2022" /> Membrane vesicles HGT occurs when released membrane vesicles (containing genetic information) fuse with a recipient bacteria, and release genetic material into the bacteria's cytoplasm.<ref name="Luo_2022" /> Recent research has revealed that membrane vesicle HGT can promote single-strain biofilm formation, yet the role membrane vesicle HGT plays in the formation of multistrain biofilms is still unknown.<ref name="Luo_2022" /> GTAs, or gene transfer agents, are phage-like particles produced by the host bacteria and contain random DNA fragments from the host bacteria genome.<ref name="Luo_2022" /> HGT within biofilms can confer antibiotic resistance or increased pathogenicity across the biofilms' population, promoting biofilm homeostasis.<ref name="Luo_2022" />

=== Examples ===
Conjugative [[plasmid]]s may encode biofilm-associated proteins, such as PtgA, PrgB, or PrgC which promote cell adhesion (required for early biofilm formation).<ref name="Abe_2020">{{cite journal | vauthors = Abe K, Nomura N, Suzuki S | title = Biofilms: hot spots of horizontal gene transfer (HGT) in aquatic environments, with a focus on a new HGT mechanism | journal = FEMS Microbiology Ecology | volume = 96 | issue = 5 | date = May 2020 | article-number = fiaa031 | pmid = 32109282 | pmc = 7189800 | doi = 10.1093/femsec/fiaa031 }}</ref> Genes encoding type III fimbriae are found in pOLA52 (''[[Klebsiella pneumoniae]]'' plasmid) which promote conjugative-pilus-dependent biofilm formation.<ref name="Abe_2020" />

Transformation commonly occurs within biofilms. A phenomenon called fratricide can be seen among streptococcal species in which cell-wall degrading enzymes are released, lysing neighboring bacteria and releasing their DNA. This DNA can then be taken up by the surviving bacteria (transformation).<ref name="Abe_2020" /> Competence stimulating peptides may play an important role in biofilm formation among ''S. pneumoniae'' and ''S. mutans'' as well.<ref name="Abe_2020" /> Among ''V. cholerae'', the competence pilus itself promotes cell aggregation through pilus-pilus interactions at the beginning of biofilm formation.<ref name="Abe_2020" />

Phage invasion may play a role in biofilm life cycles, lysing bacteria and releasing their eDNA, which strengthens biofilm structures and can be taken up by neighboring bacteria in transformation.<ref name="Abe_2020" /> Biofilm destruction caused by the ''E. coli'' phage Rac and the ''P. aeruginosa'' prophage Pf4 causes detachment of cells from the biofilm.<ref name="Abe_2020" /> Detachment is a biofilm phenomenon which requires more study, but is hypothesized to proliferate the bacterial species that comprise the biofilm.

Membrane vesicle HGT has been witnessed occurring in marine environments, among ''[[Neisseria gonorrhoeae]]'', ''[[Pseudomonas aeruginosa]]'', ''[[Helicobacter pylori]]'', and among many other bacterial species.<ref name="Abe_2020" /> Even though membrane vesicle HGT has been shown as a contributing factor in biofilm formation, research is still required to prove that membrane vesicle mediated HGT occurs within biofilms.<ref name="Luo_2022" /><ref name="Abe_2020" /> Membrane vesicle HGT has also been shown to modulate phage-bacteria interactions in ''Bacillus subtilis'' SPP1 phage-resistant cells (lacking the SPP1 receptor protein). Upon exposure to vesicles containing receptors, transduction of pBT163 (a cat-encoding plasmid) occurs, resulting in the expression of the SPP1 receptor protein, opening the receptive bacteria to future phage infection.<ref name="Abe_2020" />

Recent research has shown that the archaeal species ''H. volcanii'' has some biofilm phenotypes similar to bacterial biofilms such as differentiation and HGT, which required cell-cell contact and involved formation of cytosolic bridges and cellular fusion events.<ref>{{cite journal | vauthors = Chimileski S, Franklin MJ, Papke RT | title = Biofilms formed by the archaeon Haloferax volcanii exhibit cellular differentiation and social motility, and facilitate horizontal gene transfer | journal = BMC Biology | volume = 12 | issue = 1 | article-number = 65 | date = August 2014 | pmid = 25124934 | pmc = 4180959 | doi = 10.1186/s12915-014-0065-5 | doi-access = free }}</ref>

== Cultivation devices ==
There is a wide variety of biofilm cultivation devices to mimic natural or industrial environments. Although it is important to consider that the particular experimental platform for biofilm research determines what kind of biofilm is cultivated and the data that can be extracted. These devices can be grouped into the following:<ref>{{cite journal | vauthors = Azeredo J, Azevedo NF, Briandet R, Cerca N, Coenye T, Costa AR, Desvaux M, Di Bonaventura G, Hébraud M, Jaglic Z, Kačániová M, Knøchel S, Lourenço A, Mergulhão F, Meyer RL, Nychas G, Simões M, Tresse O, Sternberg C | title = Critical review on biofilm methods | journal = Critical Reviews in Microbiology | volume = 43 | issue = 3 | pages = 313–351 | date = May 2017 | pmid = 27868469 | doi = 10.1080/1040841X.2016.1208146 | s2cid = 3991858 | doi-access = free | hdl = 1822/45004 | hdl-access = free }}</ref>
* microtiter plate (MTP) systems and MBEC Assay® [formerly the Calgary Biofilm Device (CBD)]
* BioFilm Ring Test {{Webarchive|url= |date=26 October 2021 }} (BRT) or clinical Biofilm Ring Test (cBRT)
* Robbins Device or modified Robbins Device (such as the MPMR-10PMMA or the Bio-inLine Biofilm Reactor)
* Drip Flow Biofilm Reactor®
* rotary devices (such as the CDC Biofilm Reactor®, the Rotating Disk Reactor, the Biofilm Annular Reactor, the Industrial Surfaces Biofilm Reactor, or the Constant Depth Film Fermenter)
* flow chambers or flow cells (such as the Coupon Evaluation Flow Cell, Transmission Flow Cell, and Capillary Flow Cell from BioSurface Technologies)
* microfluidic approaches, such as 3D-bacterial "biofilm-dispersal-then-recolonization" (BDR) microfluidic model <ref name="Ma 1–13"/>
== See also ==
{{Portal|Biology}}
{{div col}}
* {{annotated link|Amyloid}}
* {{annotated link|Bacterial nanowires}}
* {{annotated link|Biofilm factory}}
* {{annotated link|Biofilm prevention}}
* {{annotated link|Biomineralization}}
* {{annotated link|Center for Biofilm Engineering}}
* {{annotated link|Curli}}
* {{annotated link|Floc (biofilm)}}
* {{annotated link|Microbial intelligence}}
* {{annotated link|Microbial mat}}
* {{annotated link|Phage therapy}}
* {{annotated link|Phototrophic biofilm}}
* {{annotated link|Stromatolite}}
{{div col end}}

== References ==
{{Reflist|32em}}

== Further reading ==
{{refbegin|32em}}
* {{cite book| vauthors = Allison DG |title=Community structure and co-operation in biofilms |publisher=Cambridge University Press |location=Cambridge, UK |year=2000 |isbn=978-0-521-79302-5}}
* {{cite book| vauthors = Lynch JF, Lappin-Scott HM, Costerton JW |title=Microbial biofilms |publisher=Cambridge University Press |location=Cambridge, UK |year=2003 |isbn=978-0-521-54212-8}}
* {{cite book| vauthors = Fratamico M | title = Biofilms in the food and beverage industries | publisher = Woodhead Publishing Limited | year = 2009 | isbn = 978-1-84569-477-7}}
{{refend}}

== External links ==
* A TED-ED animation on basic biofilm biology: [https://www.youtube.com/watch?v=pHLP5CZMnL4 The microbial jungles all over the place (and you)] {{Webarchive|url=https://web.archive.org/web/20180807120656/https://www.youtube.com/watch?v=pHLP5CZMnL4 |date=7 August 2018 }} by Scott Chimileski and [[Roberto Kolter]]
* [https://web.archive.org/web/20141213132152/http://www.origalys.com/products/biofilm-monitor-legionella-risk-management Thickness analysis, organic and mineral proportion of biofilms in order to decide a treatment strategy]
<!-- 10 april 2016 not available: * [https://colloque4.inra.fr/biofilms5 Biofilms 5 International Conference, 10–12 december 2012, Paris] -->
* {{usurped|1=[https://web.archive.org/web/20101009045249/http://www.biofilmcommunity.org/ Biofilm Archive of Biofilm Research & News]}}
* [http://www.whyamistillsick.com/ "Why Am I Still Sick?" – The Movie, 2012: Documentary on Biofilms: The Silent Role of Biofilms in Chronic Disease] {{Webarchive|url=https://web.archive.org/web/20120805092943/http://www.whyamistillsick.com/ |date=5 August 2012 }}
* [https://www.youtube.com/user/ADRSupport/videos HD Video Interviews on biofilms, antibiotics, etc. with experts, youtube.com: ADRSupport/biofilm] {{Webarchive|url=https://web.archive.org/web/20151204053849/https://www.youtube.com/user/ADRSupport/videos |date=4 December 2015 }}

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[[Category:Bacteriology]]
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[[Category:Environmental microbiology]]
[[Category:Environmental soil science]]
[[Category:Membrane biology]]
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