An rpoD gene sequence based evaluation of cultured Pseudomonas diversity on different growth media.
The last decade has shown an increased interest in the utilization of bacteria for applications ranging from bioremediation to wastewater purification and promotion of plant growth. In order to extend the current number of micro-organism mediated applications, a continued quest for new agents is required. This study focused on the genus Pseudomonas, which is known to harbour strains with a very diverse set of interesting properties. The aim was to identify growth media that allow retrieval of a high Pseudomonas diversity, as such increasing the chance of isolating isolates with beneficial properties. Three cultivation media: trypticase soy agar (TSA), potato dextrose agar (PDA) and Pseudomonas isolation agar (PIA) were evaluated for their abilities to grow Pseudomonas strains. TSA and PDA were found to generate the largest Pseudomonas diversity. However, communities obtained with both media overlapped. Communities obtained with PIA, on the other hand, were unique. This indicated that the largest diversity is obtained by sampling from either PDA or TSA and from PIA in parallel. To evaluate biodiversity of the isolated Pseudomonas members on the media, an appropriate biomarker had to be identified. Hence, an introductory investigation of the taxonomic resolution of the 16S rRNA, rpoD, gyrB and rpoB genes was performed. The rpoD gene sequences not only had a high phylogenetic content and the highest taxonomic resolution amongst the genes investigated, it also had a gene phylogeny that related well with that of the 16S rRNA gene.
Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, Gent B-9000, Belgium.
Jonas
J
Ghyselinck
Faculty of Bioscience Engineering, Ghent University, Campus Schoonmeersen, Valentin Vaerwyckweg 1, Gent B-9000, Belgium.|Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, Gent B-9000, Belgium.
An
A
Coorevits
Faculty of Bioscience Engineering, Ghent University, Campus Schoonmeersen, Valentin Vaerwyckweg 1, Gent B-9000, Belgium.
Anita
A
Van Landschoot
Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, Gent B-9000, Belgium.
Emly
E
Samyn
Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, Gent B-9000, Belgium.
Kim
K
Heylen
BCCM/LMG Bacteria Collection, K.L. Ledeganckstraat 35, Gent B-9000, Belgium.|Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, Gent B-9000, Belgium.
Paul
P
De Vos
D044822:Biodiversity; D016000:Cluster Analysis; D003470:Culture Media / Q000737:chemistry*; D027081:DNA Gyrase / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D004783:Environmental Microbiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D011549:Pseudomonas / Q000145:classification* / Q000235:genetics / Q000254:growth & development* / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012808:Sigma Factor / Q000235:genetics*
D003470:Culture Media; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012808:Sigma Factor; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit; D027081:DNA Gyrase