Home > Publications database > Different influences of DNA purity indices and quantity on PCR-based DGGE and functional gene microarray in soil microbial community study > print

001     7048
005     20180208232148.0
024 7 _ |2 pmid
|a pmid:19247649
024 7 _ |2 DOI
|a 10.1007/s00253-009-1912-0
024 7 _ |2 WOS
|a WOS:000264460500020
024 7 _ |2 ISSN
|a 0175-7598
037 _ _ |a PreJuSER-7048
041 _ _ |a eng
082 _ _ |a 570
084 _ _ |2 WoS
|a Biotechnology & Applied Microbiology
100 1 _ |0 P:(DE-Juel1)VDB89160
|a Ning, J.
|b 0
|u FZJ
245 _ _ |a Different influences of DNA purity indices and quantity on PCR-based DGGE and functional gene microarray in soil microbial community study
260 _ _ |a Berlin
|b Springer
|c 2009
300 _ _ |a 983 - 993
336 7 _ |a Journal Article
|0 PUB:(DE-HGF)16
|2 PUB:(DE-HGF)
336 7 _ |a Output Types/Journal article
|2 DataCite
336 7 _ |a Journal Article
|0 0
|2 EndNote
336 7 _ |a ARTICLE
|2 BibTeX
336 7 _ |a JOURNAL_ARTICLE
|2 ORCID
336 7 _ |a article
|2 DRIVER
440 _ 0 |0 555
|a Applied Microbiology and Biotechnology
|v 82
|x 0175-7598
|y 5
500 _ _ |a The manuscript is a joint approach within the working group "Biodiversity" of the Helmholtz Association, Germany. The authors would like to thank Eva Mareike Seeger, Mareike Braeckevelt, and Heidrun Paschke in the group of the Department of Bioremediation (UFZ, Germany) for the help during the sampling at the SAFIRA plant in Bitterfeld and the group in the Institute for Environmental Genomics (Oklahoma, USA) for providing the microarray chips, as well as Dr. Naixin Li for the valuable discussion. The construction of microarray chips and its functional gene array predecessors is supported by the Environmental Stress Pathway Project (ESPP) of the Virtual Institute for Microbial Stress and Survival (http://vimss. lbl. gov) supported by the U. S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomics: GTL Program, through contract DE- AC0205CH11231 with Lawrence Berkeley National Laboratory.
520 _ _ |a Based on the comparative study of the DNA extracts from two soil samples obtained by three commercial DNA extraction kits, we evaluated the influence of the DNA quantity and purity indices (the absorbance ratios A260/280 and A260/230, as well as the absorbance value A320 indicating the amount of humic substances) on polymerase chain reaction (PCR)-based denaturing gradient gel electrophoresis (DGGE) and a functional gene microarray used in the study of microbial communities. Numbers and intensities of the DGGE bands are more affected by the A260/280 and A320 values than by the ratio A260/230 and conditionally affected by the DNA yield. Moreover, we demonstrated that the DGGE band pattern was also affected by the preferential extraction due to chemical agents applied in the extraction. Unlike DGGE, microarray is more affected by the A260/230 and A320 values. Until now, the successful PCR performance is the mostly used criterion for soil DNA purity. However, since PCR was more influenced by the A260/280 ratio than by A260/230, it is not accurate enough any more for microbial community assessed by non-PCR-based methods such as microarray. This study provides some useful hints on how to choose effective DNA extraction method for the subsequent assessment of microbial community.
536 _ _ |0 G:(DE-Juel1)FUEK407
|2 G:(DE-HGF)
|a Terrestrische Umwelt
|c P24
|x 0
588 _ _ |a Dataset connected to Web of Science, Pubmed
650 _ 2 |2 MeSH
|a Bacteriological Techniques: methods
650 _ 2 |2 MeSH
|a Biodiversity
650 _ 2 |2 MeSH
|a DNA, Bacterial: isolation & purification
650 _ 2 |2 MeSH
|a Electrophoresis, Gel, Two-Dimensional: methods
650 _ 2 |2 MeSH
|a Humic Substances: analysis
650 _ 2 |2 MeSH
|a Oligonucleotide Array Sequence Analysis: methods
650 _ 2 |2 MeSH
|a Polymerase Chain Reaction: methods
650 _ 2 |2 MeSH
|a Reagent Kits, Diagnostic: standards
650 _ 2 |2 MeSH
|a Reproducibility of Results
650 _ 2 |2 MeSH
|a Soil Microbiology
650 _ 7 |0 0
|2 NLM Chemicals
|a DNA, Bacterial
650 _ 7 |0 0
|2 NLM Chemicals
|a Humic Substances
650 _ 7 |0 0
|2 NLM Chemicals
|a Reagent Kits, Diagnostic
650 _ 7 |2 WoSType
|a J
653 2 0 |2 Author
|a DNA purity indices
653 2 0 |2 Author
|a DNA yield
653 2 0 |2 Author
|a DGGE
653 2 0 |2 Author
|a Functional gene microarray
653 2 0 |2 Author
|a Microbial community analyses
700 1 _ |0 P:(DE-Juel1)VDB940
|a Liebich, J.
|b 1
|u FZJ
700 1 _ |0 P:(DE-Juel1)VDB17717
|a Kästner, M.
|b 2
|u FZJ
700 1 _ |0 P:(DE-Juel1)VDB89161
|a Zhou, J. Z.
|b 3
|u FZJ
700 1 _ |0 P:(DE-Juel1)VDB1399
|a Schäffer, A.
|b 4
|u FZJ
700 1 _ |0 P:(DE-Juel1)VDB202
|a Burauel, P.
|b 5
|u FZJ
773 _ _ |0 PERI:(DE-600)1464336-4
|a 10.1007/s00253-009-1912-0
|g Vol. 82, p. 983 - 993
|p 983 - 993
|q 82<983 - 993
|t Applied Microbiology and Biotechnology
|v 82
|x 0175-7598
|y 2009
909 C O |o oai:juser.fz-juelich.de:7048
|p VDB
913 1 _ |0 G:(DE-Juel1)FUEK407
|a DE-HGF
|b Erde und Umwelt
|k P24
|l Terrestrische Umwelt
|v Terrestrische Umwelt
|x 0
914 1 _ |y 2009
915 _ _ |0 StatID:(DE-HGF)0010
|2 StatID
|a JCR/ISI refereed
915 _ _ |0 StatID:(DE-HGF)0100
|2 StatID
|a JCR
915 _ _ |0 StatID:(DE-HGF)0111
|2 StatID
|a WoS
|b Science Citation Index Expanded
915 _ _ |0 StatID:(DE-HGF)0150
|2 StatID
|a DBCoverage
|b Web of Science Core Collection
915 _ _ |0 StatID:(DE-HGF)0199
|2 StatID
|a DBCoverage
|b Thomson Reuters Master Journal List
915 _ _ |0 StatID:(DE-HGF)0300
|2 StatID
|a DBCoverage
|b Medline
920 1 _ |0 I:(DE-Juel1)VDB793
|d 31.10.2010
|g ICG
|k ICG-4
|l Agrosphäre
|x 1
970 _ _ |a VDB:(DE-Juel1)115556
980 _ _ |a VDB
980 _ _ |a ConvertedRecord
980 _ _ |a journal
980 _ _ |a I:(DE-Juel1)IBG-3-20101118
980 _ _ |a UNRESTRICTED
981 _ _ |a I:(DE-Juel1)IBG-3-20101118

LibraryCollectionCLSMajorCLSMinorLanguageAuthor
Marc 21