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Analysis Of Actinomycete Communities By Specific Amplification Of Genes Encoding 16S RRNA And Gel-electrophoretic Separation In Denaturing Gradients.

H. Heuer, M. Krsek, P. Baker, K. Smalla, E. Wellington
Published 1997 · Biology, Medicine

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A group-specific primer, F243 (positions 226 to 243, Escherichia coli numbering), was developed by comparison of sequences of genes encoding 16S rRNA (16S rDNA) for the detection of actinomycetes in the environment with PCR and temperature or denaturing gradient gel electrophoresis (TGGE or DGGE, respectively). The specificity of the forward primer in combination with different reverse ones was tested with genomic DNA from a variety of bacterial strains. Most actinomycetes investigated could be separated by TGGE and DGGE, with both techniques giving similar results. Two strategies were employed to study natural microbial communities. First, we used the selective amplification of actinomycete sequences (E. coli positions 226 to 528) for direct analysis of the products in denaturing gradients. Second, a nested PCR providing actinomycete-specific fragments (E. coli positions 226 to 1401) was used which served as template for a PCR when conserved primers were used. The products (E. coli positions 968 to 1401) of this indirect approach were then separated by use of gradient gels. Both approaches allowed detection of actinomycete communities in soil. The second strategy allowed the estimation of the relative abundance of actinomycetes within the bacterial community. Mixtures of PCR-derived 16S rDNA fragments were used as model communities consisting of five actinomycetes and five other bacterial species. Actinomycete products were obtained over a 100-fold dilution range of the actinomycete DNA in the model community by specific PCR; detection of the diluted actinomycete DNA was not possible when conserved primers were used. The methods tested for detection were applied to monitor actinomycete community changes in potato rhizosphere and to investigate actinomycete diversity in different soils.



This paper is referenced by
10.1139/W11-032
Characterization of the bacterial community structure of Sydney Tar Ponds sediment
YeungC. William (2011)
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Maria Bernadete Amâncio Varesche (2013)
10.1002/9781118297674.CH18
Assessment of Rice Root‐Associated Bacteria
Pablo Rodrigo Hardoim (2013)
10.1007/s10482-011-9571-4
Genus-specific primers targeting the 16S rRNA gene for PCR detection of members of the genus Verrucosispora
Qingyi Xie (2011)
10.4172/2475-7675.1000110
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Reddy Gv (2016)
10.1016/j.sjbs.2020.01.003
Novel marine Nocardiopsis dassonvillei-DS013 mediated silver nanoparticles characterization and its bactericidal potential against clinical isolates
Suresh Dhanaraj (2020)
10.1016/j.jbiosc.2013.10.012
Evaluation of microbial diversity in sulfite-added and sulfite-free wine by culture-dependent and -independent methods.
Masayuki Takahashi (2014)
10.1088/1755-1315/107/1/012050
Influence of Biopreparations on the Bacterial Community of Oily Waste
Liliya Biktasheva (2018)
10.1016/J.SOILBIO.2005.04.021
Compositional shifts of bacterial groups in a solarized and amended soil as determined by denaturing gradient gel electrophoresis
A. Gelsomino (2006)
10.1046/J.1462-2920.2001.00164.X
In situ identification of polyphosphate- and polyhydroxyalkanoate-accumulating traits for microbial populations in a biological phosphorus removal process.
W. T. Liu (2001)
10.1371/journal.pone.0066019
Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents
C. Hoffmann (2013)
10.1016/j.scitotenv.2011.04.030
Antibiotic contamination and occurrence of antibiotic-resistant bacteria in aquatic environments of northern Vietnam.
Phan Thi Phuong Hoa (2011)
10.15517/RBT.V57I4.5451
Comunidades de hongos actinomicetos en tres tipos de vegetación de la Amazonia colombiana: abundancia, morfotipos y el gen 16s ADNr
Gladys I. Cardona (2008)
10.1016/S1001-0742(08)62216-0
Molecular characterization of bacterial community in aerobic granular sludge stressed by pentachlorophenol.
H. Liu (2008)
10.1007/s11104-007-9432-0
Rhizosphere microbial community and its response to plant species and soil history
P. Garbeva (2007)
10.1111/J.1574-6941.2000.TB00746.X
Polyphasic microbial community analysis of petroleum hydrocarbon-contaminated soils from two northern Canadian communities.
Juck (2000)
10.1007/s10532-017-9809-6
Biodegradation and chemotaxis of polychlorinated biphenyls, biphenyls, and their metabolites by Rhodococcus spp.
H. Wang (2017)
10.1007/8623_2015_158
Microbial Community Profiling: SSCP and T-RFLP Techniques
C. Tebbe (2015)
10.1007/s00253-004-1706-3
Studies on the production and purification of an antimicrobial compound and taxonomy of the producer isolated from the marine environment of the Sundarbans
M. Saha (2004)
10.1016/J.SOILBIO.2005.11.032
Microbial activity and community structure of a soil after heavy metal contamination in a model forest ecosystem
B. Frey (2006)
10.1002/ps.3491
Antagonistic bacterium Bacillus amyloliquefaciens induces resistance and controls the bacterial wilt of tomato.
S. Tan (2013)
10.1111/J.1095-8312.2006.00730.X
Bacterial microbiota associated with ants of the genus Tetraponera
S. Stoll (2007)
10.1016/B978-012369522-2/50016-6
CHAPTER 15 – EMERGING FORENSIC TECHNIQUES
Jean-Christophe Balouet (2007)
ffects of the herbicides acetochlor and metolachlor on antioxidant enzymes n soil bacteria
F. Martinsa (2011)
UNIVERSIDADE DE SÃO PAULO CENTRO DE ENERGIA NUCLEAR NA AGRICULTURA
E. Gomes (2013)
10.1111/j.1461-0248.2009.01424.x
Reduction of rare soil microbes modifies plant-herbivore interactions.
W. H. Gera Hol (2010)
10.1007/s00248-010-9752-0
Land Use Intensity Controls Actinobacterial Community Structure
P. Hill (2010)
10.1007/978-3-540-89621-0_17
The Environment and the Tools in Rhizo- and Bioremediation of Contaminated Soil
A. K. J. Surridge (2009)
10.1093/femsec/fix145
Soil texture‐depending effects of doxycycline and streptomycin applied with manure on the bacterial community composition and resistome
Khald Blau (2018)
10.1002/JPLN.200900267
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Antonio Gelsomino (2011)
10.4238/2012.February.8.3
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Lee Learn-han (2012)
10.7745/KJSSF.2012.45.5.822
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