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Start Over Descriptor "16S rDNA PCR-DGGE" Publisher south african water research commission
2 results on '"16S rDNA PCR-DGGE"'

1. The impact of physico–chemical water quality parameters on bacterial diversity in the Vaal River, South Africa

Author

Karen Jordaan, Cornelius Carlos Bezuidenhout, and 12540110 - Bezuidenhout, Cornelius Carlos

Subjects
biology, Ecology, Firmicutes, Bacteroidetes, high-throughput sequencing, 16S rDNA PCR-DGGE, Management, Monitoring, Policy and Law, biology.organism_classification, Applied Microbiology and Biotechnology, Vaal River, bacterial community structures, 16S rDNA PCR-DGGE, high-throughput sequencing, multivariate analysis, multivariate analysis, Fibrobacteres, Vaal River, Gammaproteobacteria, bacterial community structures, Water quality, Waste Management and Disposal, Betaproteobacteria, Temperature gradient gel electrophoresis, Water Science and Technology, Acidobacteria
Abstract

This study aimed to identify bacterial community structures in the Vaal River using PCR-DGGE (polymerase chain reaction denaturing gradient gel electrophoresis) and high-throughput sequencing. The impact of physico-chemical characteristics on bacterial structures was investigated through multivariate analysis. Samples were collected from 4 sampling stations along the Upper Vaal River during winter (June 2009) and summer (December 2010). Physico-chemical analysis was conducted on-site. Additional physico-chemical data were obtained from statutory bodies. DNA was directly isolated from water samples and PCR amplified using universal bacterial primer pairs. PCR products were subjected to DGGE fingerprinting and high-throughput sequencing, followed by Shannon-Weaver diversity calculations, cluster analysis and multivariate analysis. Physico-chemical parameters did not exceed the prescribed South African water quality standards for domestic use, aquatic ecosystems, livestock watering and irrigation. DGGE banding patterns revealed similar bacterial community structures for 3 of the 4 sampling stations. PCA and RDA indicated that pH, water temperature and inorganic nutrient concentrations could be used to explain changes in bacterial community structures. High-throughput sequencing data showed that bacterial assemblages were dominated by common freshwater groups: Cyanobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria. Other freshwater phyla such as Deltaproteobacteria, Epsilonbacteria, Acidobacteria, Verrucomicrobia, Firmicutes, Fusobacteria, Flavobacteria and Fibrobacteres were found in low proportions. This study provides an overview of the dominant bacterial groups in the Upper Vaal River and the impact of environmental changes on bacterial diversity Water Research Commission (WRC) and North-West University http://www.wrc.org.za/Pages/KH_WaterSA.aspx?dt=5&L0=1&L1=4 http://www.wrc.org.za/Pages/DisplayItem.aspx?ItemID=10288&FromURL=%2fPages%2fKH_WaterSA.aspx%3fdt%3d5%26ms%3d%26d%3dVolume%26e%3d39+No.+3%2c+WISA+2012+Special+Edition+2013%26start%3d1 http://dx.doi.org/10.4314/wsa.v39i3.7

Published
2013

2. The impact of physico–chemical water quality parameters on bacterial diversity in the Vaal River, South Africa

Author

12540110 - Bezuidenhout, Cornelius Carlos, Jordaan, Karen, Bezuidenhout, Cornelius Carlos, 12540110 - Bezuidenhout, Cornelius Carlos, Jordaan, Karen, and Bezuidenhout, Cornelius Carlos

Abstract

This study aimed to identify bacterial community structures in the Vaal River using PCR-DGGE (polymerase chain reaction denaturing gradient gel electrophoresis) and high-throughput sequencing. The impact of physico-chemical characteristics on bacterial structures was investigated through multivariate analysis. Samples were collected from 4 sampling stations along the Upper Vaal River during winter (June 2009) and summer (December 2010). Physico-chemical analysis was conducted on-site. Additional physico-chemical data were obtained from statutory bodies. DNA was directly isolated from water samples and PCR amplified using universal bacterial primer pairs. PCR products were subjected to DGGE fingerprinting and high-throughput sequencing, followed by Shannon-Weaver diversity calculations, cluster analysis and multivariate analysis. Physico-chemical parameters did not exceed the prescribed South African water quality standards for domestic use, aquatic ecosystems, livestock watering and irrigation. DGGE banding patterns revealed similar bacterial community structures for 3 of the 4 sampling stations. PCA and RDA indicated that pH, water temperature and inorganic nutrient concentrations could be used to explain changes in bacterial community structures. High-throughput sequencing data showed that bacterial assemblages were dominated by common freshwater groups: Cyanobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria. Other freshwater phyla such as Deltaproteobacteria, Epsilonbacteria, Acidobacteria, Verrucomicrobia, Firmicutes, Fusobacteria, Flavobacteria and Fibrobacteres were found in low proportions. This study provides an overview of the dominant bacterial groups in the Upper Vaal River and the impact of environmental changes on bacterial diversity

Published
2013

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