Principal component analysis and discriminant analysis (PCA-DA) for discriminating profiles of terminal restriction fragment length polymorphism (T-RFLP) in soil bacterial communities

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Title
Principal component analysis and discriminant analysis (PCA-DA) for discriminating profiles of terminal restriction fragment length polymorphism (T-RFLP) in soil bacterial communities
Author(s)
S Park; Y K Ku; M J Seo; Do Young Kim; J E Yeon; K M Lee; Soon Chun JeongWoon Kee Yoon; C H Harn; Hwan Mook Kim
Bibliographic Citation
Soil Biology & Biochemistry, vol. 38, no. 8, pp. 2344-2349
Publication Year
2006
Abstract
To assess the impact of a transgenic crop on soil environment, we compared soil bacterial communities from the rhizospheres of cucumber green mottle mosaic virus (CGMMV)-resistant transgenic watermelon (Citrullus vulgaris [Twinser] cv. Gongdae) and non-transgenic parental line watermelon at an experimental farm in Miryang, Korea. Soil microbial community structure was studied using terminal restriction fragment length polymorphism (T-RFLP) using HaeIII and HhaI enzymes on products from polymerase chain amplification reactions (PCR) of total DNA from rhizosphere. We used principal component analyses (PCA) to reduce dimensionality of T-RFLP profiles before comparison. On these PCA scores, we conducted discrimination analyses to compare soil microbial communities from the rhizosphere of transgenic and non-transgenic. Discriminant analyses indicate that microbial communities from rhizosphere of transgenic and non-transgenic watermelon did not differ with significance at 95% level. Our study could be used as a model case to assess the environmental risk assessment of transgenic crops on soil microbial organisms.
Keyword
bacterial communitycitrullus vulgaris [Twinser] cv. gongdaediscriminant analysisPCArhizosphereT-RFLPtransgenic watermelon
ISSN
0038-0717
Publisher
Elsevier
DOI
http://dx.doi.org/10.1016/j.soilbio.2006.02.019
Type
Article
Appears in Collections:
Ochang Branch Institute > Division of Bioinfrastructure > Bio-Evaluation Center > 1. Journal Articles
Ochang Branch Institute > 1. Journal Articles
Ochang Branch Institute > Division of Bioinfrastructure > Laboratory Animal Resource Center > 1. Journal Articles
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