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Rapid screening for freshwater bacterial groups by using reverse line blot hybridization

Gabriel Zwart, Erik J van Hannen, Miranda P Kamst-van Agterveld, Katleen Van Der Gucht (UGent) , Eva S Lindström, Jeroen Van Wichelen (UGent) , Torben Lauridsen, Byron C Crump, Suk-Kyun Han and Steven Declerck
(2003) APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 69(10). p.5875-5883
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Abstract
The identification of phylogenetic clusters of bacteria that are common in freshwater has provided a basis for probe design to target important freshwater groups. We present a set of 16S ribosomal RNA gene-based oligonucleotide probes specific for 15 of these freshwater clusters. The probes were applied in reverse line blot hybridization, a simple method that enables the rapid screening of PCR products from many samples against an array of probes. The optimized assay was made stringent to discriminate at approximately the single-mismatch level. This made 10 of the probes highly specific, with at least two mismatches to the closest noncluster member in the global database. Screening of PCR products from bacterioplankton of 81 diverse lakes from Belgium, The Netherlands, Denmark, Sweden, and Norway showed that the respective probes were reactive against 5 to 100% of the lake samples. Positive reactivity of six highly specific probes showed that bacteria from actinobacterial clusters ACK-M1 and Sta2-30 and from verrucomicrobial cluster CLO-14 occurred in at least 90% of the investigated lakes. Furthermore, bacteria from alpha-proteobacterial cluster LD12 (closely related to the marine SAR11 cluster), beta-proteobacterial cluster LD28 and cyanobacterial cluster Synechococcus 6b occurred in more than 70% of the lakes. Reverse line blot hybridization is a new tool in microbial ecology that will facilitate research on distribution and habitat specificity of target species at relatively low costs.
Keywords
RIBOSOMAL-RNA SEQUENCES, BACTERIOPLANKTON COMMUNITY COMPOSITION, RALSTONIA-PICKETTII COLONIZATION, OLIGONUCLEOTIDE PROBES, GENE-SEQUENCES, DIVERSITY, LAKES, DNA, IDENTIFICATION, AMPLIFICATION

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Citation

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MLA
Zwart, Gabriel, et al. “Rapid Screening for Freshwater Bacterial Groups by Using Reverse Line Blot Hybridization.” APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 69, no. 10, 2003, pp. 5875–83, doi:10.1128/AEM.69.10.5875-5883.2003.
APA
Zwart, G., van Hannen, E. J., Kamst-van Agterveld, M. P., Van Der Gucht, K., Lindström, E. S., Van Wichelen, J., … Declerck, S. (2003). Rapid screening for freshwater bacterial groups by using reverse line blot hybridization. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 69(10), 5875–5883. https://doi.org/10.1128/AEM.69.10.5875-5883.2003
Chicago author-date
Zwart, Gabriel, Erik J van Hannen, Miranda P Kamst-van Agterveld, Katleen Van Der Gucht, Eva S Lindström, Jeroen Van Wichelen, Torben Lauridsen, Byron C Crump, Suk-Kyun Han, and Steven Declerck. 2003. “Rapid Screening for Freshwater Bacterial Groups by Using Reverse Line Blot Hybridization.” APPLIED AND ENVIRONMENTAL MICROBIOLOGY 69 (10): 5875–83. https://doi.org/10.1128/AEM.69.10.5875-5883.2003.
Chicago author-date (all authors)
Zwart, Gabriel, Erik J van Hannen, Miranda P Kamst-van Agterveld, Katleen Van Der Gucht, Eva S Lindström, Jeroen Van Wichelen, Torben Lauridsen, Byron C Crump, Suk-Kyun Han, and Steven Declerck. 2003. “Rapid Screening for Freshwater Bacterial Groups by Using Reverse Line Blot Hybridization.” APPLIED AND ENVIRONMENTAL MICROBIOLOGY 69 (10): 5875–5883. doi:10.1128/AEM.69.10.5875-5883.2003.
Vancouver
1.
Zwart G, van Hannen EJ, Kamst-van Agterveld MP, Van Der Gucht K, Lindström ES, Van Wichelen J, et al. Rapid screening for freshwater bacterial groups by using reverse line blot hybridization. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 2003;69(10):5875–83.
IEEE
[1]
G. Zwart et al., “Rapid screening for freshwater bacterial groups by using reverse line blot hybridization,” APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 69, no. 10, pp. 5875–5883, 2003.
@article{308338,
  abstract     = {{The identification of phylogenetic clusters of bacteria that are common in freshwater has provided a basis for probe design to target important freshwater groups. We present a set of 16S ribosomal RNA gene-based oligonucleotide probes specific for 15 of these freshwater clusters. The probes were applied in reverse line blot hybridization, a simple method that enables the rapid screening of PCR products from many samples against an array of probes. The optimized assay was made stringent to discriminate at approximately the single-mismatch level. This made 10 of the probes highly specific, with at least two mismatches to the closest noncluster member in the global database. Screening of PCR products from bacterioplankton of 81 diverse lakes from Belgium, The Netherlands, Denmark, Sweden, and Norway showed that the respective probes were reactive against 5 to 100% of the lake samples. Positive reactivity of six highly specific probes showed that bacteria from actinobacterial clusters ACK-M1 and Sta2-30 and from verrucomicrobial cluster CLO-14 occurred in at least 90% of the investigated lakes. Furthermore, bacteria from alpha-proteobacterial cluster LD12 (closely related to the marine SAR11 cluster), beta-proteobacterial cluster LD28 and cyanobacterial cluster Synechococcus 6b occurred in more than 70% of the lakes. Reverse line blot hybridization is a new tool in microbial ecology that will facilitate research on distribution and habitat specificity of target species at relatively low costs.}},
  author       = {{Zwart, Gabriel and van Hannen, Erik J and Kamst-van Agterveld, Miranda P and Van Der Gucht, Katleen and Lindström, Eva S and Van Wichelen, Jeroen and Lauridsen, Torben and Crump, Byron C and Han, Suk-Kyun and Declerck, Steven}},
  issn         = {{0099-2240}},
  journal      = {{APPLIED AND ENVIRONMENTAL MICROBIOLOGY}},
  keywords     = {{RIBOSOMAL-RNA SEQUENCES,BACTERIOPLANKTON COMMUNITY COMPOSITION,RALSTONIA-PICKETTII COLONIZATION,OLIGONUCLEOTIDE PROBES,GENE-SEQUENCES,DIVERSITY,LAKES,DNA,IDENTIFICATION,AMPLIFICATION}},
  language     = {{eng}},
  number       = {{10}},
  pages        = {{5875--5883}},
  title        = {{Rapid screening for freshwater bacterial groups by using reverse line blot hybridization}},
  url          = {{http://dx.doi.org/10.1128/AEM.69.10.5875-5883.2003}},
  volume       = {{69}},
  year         = {{2003}},
}
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