Editing Biofilm (section)

=== 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|pages=42|doi=10.1094/pd-72-0042|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 | 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.