title: Bias problems in culture-independent analysis of environmental bacterial communities: a representative study on hydrocarbonoclastic bacteria.
abstract: Culture-dependent methods for bacterial community analysis are currently considered obsolete; therefore, molecular techniques are usually used instead. The results of the current study on hydrocarbonoclastic bacteria in various oily habitats in Kuwait showed however, that the bacterial identities varied dramatically according to the analytical approach used. For six desert and six seawater samples used in this study, the culture-independent and culture-dependent techniques each led to a unique bacterial composition. Problems related to the culture-dependent technique are well known. The results of the current study highlighted bias problems other than those already recorded in the literature for the molecular approaches. Thus, for example, in contrast to the culture-dependent technique, the primers used in the molecular approach preferentially amplified the 16S rDNAs of hydrocarbonoclastic bacteria in total genomic DNAs of all the studied environmental samples, and in addition, failed to reveal in any environmental sample members of the Actinobacteria. The primers used in the molecular approach also amplified certain "pure" 16S rDNAs, but failed to do so when these DNAs were in mixture. In view of these results, it is recommended that the two analytical approaches should be used simultaneously because their combined results would reflect the bacterial community composition more precisely than either of them can do alone.
authors.affiliation: Department of Biological Sciences, Faculty of Science, Kuwait University, P.O. Box 5969, Safat, 13060 Kuwait.
authors.forename: Husain
authors.initials: H
authors.lastname: Al-Awadhi
authors.forename: Narjis
authors.initials: N
authors.lastname: Dashti
authors.forename: Majida
authors.initials: M
authors.lastname: Khanafer
authors.forename: Dina
authors.initials: D
authors.lastname: Al-Mailem
authors.forename: Nidaa
authors.initials: N
authors.lastname: Ali
authors.forename: Samir
authors.initials: S
authors.lastname: Radwan
references.citation: Appl Environ Microbiol. 2006 May;72(5):3531-42
references.pmid: 16672500
references.citation: Appl Environ Microbiol. 2000 Aug;66(8):3376-80
references.pmid: 10919794
references.citation: FEMS Microbiol Ecol. 2007 Feb;59(2):342-55
references.pmid: 17026513
references.citation: Appl Environ Microbiol. 1999 Jun;65(6):2478-84
references.pmid: 10347030
references.citation: Int J Syst Evol Microbiol. 2004 Jan;54(Pt 1):141-148
references.pmid: 14742471
references.citation: Microbiology (Reading). 2009 Oct;155(Pt 10):3362-3370
references.pmid: 19541999
references.citation: Microb Ecol. 1998 Jan;35(1):1-21
references.pmid: 9459655
references.citation: Appl Environ Microbiol. 1999 Feb;65(2):422-30
references.pmid: 9925563
references.citation: FEMS Microbiol Ecol. 2007 May;60(2):341-50
references.pmid: 17343679
references.citation: Int J Syst Evol Microbiol. 2007 May;57(Pt 5):911-915
references.pmid: 17473232
references.citation: Environ Sci Pollut Res Int. 2013 May;20(5):3252-62
references.pmid: 23089957
references.citation: Appl Environ Microbiol. 1999 Feb;65(2):795-801
references.pmid: 9925618
references.citation: Appl Environ Microbiol. 2012 Nov;78(21):7626-37
references.pmid: 22923391
references.citation: Appl Microbiol Biotechnol. 2011 Mar;89(6):2019-25
references.pmid: 21052991
references.citation: Appl Environ Microbiol. 1999 Mar;65(3):982-8
references.pmid: 10049851
references.citation: Appl Environ Microbiol. 1998 Oct;64(10):3724-30
references.pmid: 9758791
references.citation: J Biotechnol. 2012 Feb 20;157(4):564-72
references.pmid: 21939698
references.citation: Antonie Van Leeuwenhoek. 1998 Jan;73(1):127-41
references.pmid: 9602286
references.citation: Appl Environ Microbiol. 1999 Sep;65(9):3834-42
references.pmid: 10473383
references.citation: Curr Opin Biotechnol. 2007 Jun;18(3):257-66
references.pmid: 17493798
references.citation: Appl Environ Microbiol. 1999 Mar;65(3):1251-8
references.pmid: 10049891
references.citation: Arch Microbiol. 2012 Aug;194(8):689-705
references.pmid: 22398928
references.citation: Appl Microbiol Biotechnol. 2007 Dec;77(4):935-45
references.pmid: 17943279
references.citation: J Bacteriol. 1997 Jan;179(1):115-21
references.pmid: 8981987
references.citation: J Microbiol Methods. 1999 May;36(1-2):107-14
references.pmid: 10353804
references.citation: Microbiol Rev. 1995 Mar;59(1):143-69
references.pmid: 7535888
references.citation: Environ Sci Technol. 2010 Oct 1;44(19):7266-71
references.pmid: 20707373