title: Assessing the diversity of bacterial communities associated with plants.
abstract: Plant-bacteria interactions result from reciprocal recognition between both species. These interactions are responsible for essential biological processes in plant development and health status. Here, we present a review of the methodologies applied to investigate shifts in bacterial communities associated with plants. A description of techniques is made from initial isolations to culture-independent approaches focusing on quantitative Polymerase Chain Reaction in real time (qPCR), Denaturing Gradient Gel Electrophoresis (DGGE), clone library construction and analysis, the application of multivariate analyses to microbial ecology data and the upcoming high throughput methodologies such as microarrays and pyrosequencing. This review supplies information about the development of traditional methods and a general overview about the new insights into bacterial communities associated with plants.
authors.affiliation: Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo , Piracicaba, SP , Brasil ; Laboratório de Microbiologia Ambiental, Embrapa Meio Ambiente , Jaguariúna, SP , Brasil.
authors.forename: Fernando Dini
authors.initials: FD
authors.lastname: Andreote
authors.forename: João Lúcio
authors.initials: JL
authors.lastname: Azevedo
authors.forename: Welington Luiz
authors.initials: WL
authors.lastname: Araújo
keywords: Plant–bacteria interactions; endophytes; molecular techniques; multivariate analysis; rhizosphere
references.citation: Antonie Van Leeuwenhoek. 1998 Jan;73(1):127-41
references.pmid: 9602286
references.citation: Int Microbiol. 2007 Dec;10(4):253-60
references.pmid: 18228222
references.citation: FEMS Microbiol Ecol. 2008 Aug;65(2):179
references.pmid: 18713129
references.citation: Curr Opin Plant Biol. 2008 Apr;11(2):135-43
references.pmid: 18329329
references.citation: Nat Rev Microbiol. 2007 May;5(5):384-92
references.pmid: 17435792
references.citation: Phytopathology. 2002 Oct;92(10):1048-54
references.pmid: 18944214
references.citation: Appl Environ Microbiol. 1998 Aug;64(8):2770-9
references.pmid: 9687429
references.citation: FEMS Microbiol Ecol. 2006 May;56(2):219-35
references.pmid: 16629752
references.citation: Environ Microbiol. 2006 Dec;8(12):2136-49
references.pmid: 17107555
references.citation: Appl Environ Microbiol. 2000 Aug;66(8):3376-80
references.pmid: 10919794
references.citation: Res Microbiol. 2000 Apr;151(3):167-77
references.pmid: 10865943
references.citation: Appl Environ Microbiol. 2005 Mar;71(3):1501-6
references.pmid: 15746353
references.citation: Appl Environ Microbiol. 1995 Jan;61(1):116-21
references.pmid: 7887594
references.citation: Curr Opin Microbiol. 2003 Jun;6(3):288-94
references.pmid: 12831906
references.citation: Appl Environ Microbiol. 2002 May;68(5):2391-6
references.pmid: 11976113
references.citation: ISME J. 2007 May;1(1):67-77
references.pmid: 18043615
references.citation: Science. 2006 Jun 30;312(5782):1917
references.pmid: 16809531
references.citation: Nature. 2006 Aug 17;442(7104):806-9
references.pmid: 16915287
references.citation: Curr Opin Microbiol. 2001 Jun;4(3):285-9
references.pmid: 11378480
references.citation: Antonie Van Leeuwenhoek. 2001 Jun;79(2):209-17
references.pmid: 11520007
references.citation: FEMS Microbiol Ecol. 2008 May;64(2):175-86
references.pmid: 18336555
references.citation: Microb Ecol. 1998 Jan;35(1):1-21
references.pmid: 9459655
references.citation: BMC Genomics. 2006 Mar 20;7:57
references.pmid: 16549033
references.citation: Appl Environ Microbiol. 2005 Nov;71(11):7271-8
references.pmid: 16269768
references.citation: Appl Environ Microbiol. 1997 Aug;63(8):3233-41
references.pmid: 9251210
references.citation: J Microbiol Methods. 2003 Aug;54(2):213-31
references.pmid: 12782377
references.citation: Microb Ecol. 2001 Apr;41(3):252-263
references.pmid: 11391463
references.citation: Appl Environ Microbiol. 2008 May;74(9):2717-27
references.pmid: 18310425
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12115-20
references.pmid: 16880384
references.citation: Appl Environ Microbiol. 2004 Aug;70(8):4748-55
references.pmid: 15294811
references.citation: Appl Environ Microbiol. 1997 Nov;63(11):4516-22
references.pmid: 9361437
references.citation: Microb Ecol. 2007 Nov;54(4):587-97
references.pmid: 17851710
references.citation: FEMS Microbiol Ecol. 2007 Nov;62(2):142-60
references.pmid: 17892477
references.citation: Appl Environ Microbiol. 2006 Nov;72(11):7286-93
references.pmid: 16980418
references.citation: Appl Environ Microbiol. 1998 Jul;64(7):2545-53
references.pmid: 9647828
references.citation: Appl Environ Microbiol. 1999 May;65(5):1980-90
references.pmid: 10223989
references.citation: Appl Environ Microbiol. 2000 Jul;66(7):3044-51
references.pmid: 10877804
references.citation: Nature. 2005 Sep 15;437(7057):376-80
references.pmid: 16056220
references.citation: New Phytol. 2006;171(4):719-35
references.pmid: 16918544
references.citation: Appl Environ Microbiol. 2002 Apr;68(4):1595-603
references.pmid: 11916673
references.citation: Annu Rev Phytopathol. 1999;37:81-125
references.pmid: 11701818
references.citation: Appl Environ Microbiol. 2005 Sep;71(9):5544-50
references.pmid: 16151147
references.citation: Appl Environ Microbiol. 1997 Dec;63(12):4704-12
references.pmid: 9406389
references.citation: J Microbiol Methods. 2007 Jun;69(3):470-9
references.pmid: 17407797
references.citation: Adv Microb Physiol. 1999;41:93-137
references.pmid: 10500845
references.citation: Trends Microbiol. 2008 Oct;16(10):463-71
references.pmid: 18789693
references.citation: Appl Environ Microbiol. 1993 Mar;59(3):695-700
references.pmid: 7683183
references.citation: FEMS Microbiol Ecol. 2004 Jan 1;47(1):51-64
references.pmid: 19712346
references.citation: Appl Environ Microbiol. 2004 Jul;70(7):4012-20
references.pmid: 15240277
references.citation: Trends Microbiol. 2007 Mar;15(3):135-41
references.pmid: 17289390
references.citation: Appl Environ Microbiol. 2006 Aug;72(8):5547-55
references.pmid: 16885308
references.citation: Appl Microbiol Biotechnol. 2006 Apr;70(3):281-9
references.pmid: 16470363
references.citation: Lett Appl Microbiol. 2002;35(4):316-20
references.pmid: 12358695
references.citation: FEMS Microbiol Ecol. 2008 May;64(2):297-306
references.pmid: 18336554
references.citation: J Microbiol Methods. 2006 Jun;65(3):535-41
references.pmid: 16266765
references.citation: FEMS Microbiol Lett. 1992 Dec 15;100(1-3):59-65
references.pmid: 1282488
references.citation: J Biosci Bioeng. 2005 May;99(5):485-92
references.pmid: 16233821
references.citation: Phytopathology. 2004 May;94(5):463-9
references.pmid: 18943764
references.citation: Science. 1998 Jul 17;281(5375):363, 365
references.pmid: 9705713
references.citation: Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14683-8
references.pmid: 16186488
references.citation: ISME J. 2007 Aug;1(4):283-90
references.pmid: 18043639
references.citation: EMBO Rep. 2001 Sep;2(9):770-4
references.pmid: 11559589
references.citation: FEMS Microbiol Ecol. 1999 Oct 1;30(2):137-145
references.pmid: 10508938
references.citation: Trends Microbiol. 2005 Sep;13(9):411-5
references.pmid: 16043355
references.citation: Microbiol Rev. 1994 Mar;58(1):1-9
references.pmid: 8177167
references.citation: Appl Environ Microbiol. 1998 Dec;64(12):4870-6
references.pmid: 9835576
references.citation: Anal Biochem. 1996 Nov 1;242(1):84-9
references.pmid: 8923969
references.citation: Environ Microbiol. 2007 Sep;9(9):2260-73
references.pmid: 17686023
references.citation: Appl Environ Microbiol. 2001 Sep;67(9):4374-6
references.pmid: 11526051