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.
Highlights
The end of the 19th century witnessed the development of the well known and long adopted culture-dependent approach which is used for the study of the structure of the bacterial communities in various environments
Molecular approaches which comprise among others the combination of DGGE fingerprinting with sequencing of 16S rDNA bands to identify the species present in the environmental samples (Fuhrman & Davies 1997; Nielsen et al 1999; Rölleke et al 1999), and correlating the banding patterns and band numbers on DGGE gels with environmental variables
The same environmental samples were used the same sampling day for total DNA extraction; the extracts were stored at −80°C and used in the current study
Summary
The end of the 19th century witnessed the development of the well known and long adopted culture-dependent approach which is used for the study of the structure of the bacterial communities in various environments. This approach drove advances in microbiology, in spite of its well known, serious limitations (Amann et al 1995; Jannasch & Jones 1959), mainly related to the selectivity of the nutrient media and culture conditions which lead to favoring only a fraction of the inhabiting bacterial community. Serious artifacts (Polz & Cavanaugh 1998; Sipos et al 2007) do arise viz preferential amplification of upcoming species, inadequate specificity of primers used for DNA amplification, production of single bands by multiple strains and others
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
