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An rpoD gene sequence based evaluation of cultured Pseudomonas diversity on different growth media

Jonas Ghyselinck UGent, An Coorevits, Anita Van Landschoot UGent, EMLY SAMYN, Kim Heylen and Paul De Vos UGent (2013) MICROBIOLOGY-SGM. 159(10). p.2097-2108
abstract
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
BIOLOGICAL-CONTROL, 16S RIBOSOMAL-RNA, PROMOTING RHIZOBACTERIA, NUCLEOTIDE-SEQUENCES, RHIZOCTONIA-SOLANI, PHYLOGENETIC TREES, ALIGNMENT, BACTERIA, BIOCONTROL, SOFTWARE
journal title
MICROBIOLOGY-SGM
Microbiology-(UK)
volume
159
issue
10
pages
2097 - 2108
Web of Science type
Article
Web of Science id
000326910400009
JCR category
MICROBIOLOGY
JCR impact factor
2.835 (2013)
JCR rank
46/119 (2013)
JCR quartile
2 (2013)
ISSN
1350-0872
DOI
10.1099/mic.0.068031-0
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
4135096
handle
http://hdl.handle.net/1854/LU-4135096
date created
2013-09-18 09:09:31
date last changed
2016-12-19 15:43:01
@article{4135096,
  abstract     = {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.},
  author       = {Ghyselinck, Jonas and Coorevits, An and Van Landschoot, Anita and SAMYN, EMLY and Heylen, Kim and De Vos, Paul},
  issn         = {1350-0872},
  journal      = {MICROBIOLOGY-SGM},
  keyword      = {BIOLOGICAL-CONTROL,16S RIBOSOMAL-RNA,PROMOTING RHIZOBACTERIA,NUCLEOTIDE-SEQUENCES,RHIZOCTONIA-SOLANI,PHYLOGENETIC TREES,ALIGNMENT,BACTERIA,BIOCONTROL,SOFTWARE},
  language     = {eng},
  number       = {10},
  pages        = {2097--2108},
  title        = {An rpoD gene sequence based evaluation of cultured Pseudomonas diversity on different growth media},
  url          = {http://dx.doi.org/10.1099/mic.0.068031-0},
  volume       = {159},
  year         = {2013},
}

Chicago
Ghyselinck, Jonas, An Coorevits, Anita Van Landschoot, Emly Samyn, Kim Heylen, and Paul De Vos. 2013. “An rpoD Gene Sequence Based Evaluation of Cultured Pseudomonas Diversity on Different Growth Media.” Microbiology-sgm 159 (10): 2097–2108.
APA
Ghyselinck, J., Coorevits, A., Van Landschoot, A., Samyn, E., Heylen, K., & De Vos, P. (2013). An rpoD gene sequence based evaluation of cultured Pseudomonas diversity on different growth media. MICROBIOLOGY-SGM, 159(10), 2097–2108.
Vancouver
1.
Ghyselinck J, Coorevits A, Van Landschoot A, Samyn E, Heylen K, De Vos P. An rpoD gene sequence based evaluation of cultured Pseudomonas diversity on different growth media. MICROBIOLOGY-SGM. 2013;159(10):2097–108.
MLA
Ghyselinck, Jonas, An Coorevits, Anita Van Landschoot, et al. “An rpoD Gene Sequence Based Evaluation of Cultured Pseudomonas Diversity on Different Growth Media.” MICROBIOLOGY-SGM 159.10 (2013): 2097–2108. Print.