2012
DOI: 10.1016/j.syapm.2012.01.004
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Fluorescence in situ hybridization (CARD-FISH) of microorganisms in hydrocarbon contaminated aquifer sediment samples

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Cited by 35 publications
(28 citation statements)
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“…In the case of sediments, cells have to be detached from the substratum by sonication or other methods and diluted in buffer before being brought onto a filter (26,27). Additionally, Bižić-Ionescu and coworkers (28) successfully adapted the autonomous cell enumeration system to quantify specific cell types after FISH in aggregate samples.…”
Section: Discussionmentioning
confidence: 99%
“…In the case of sediments, cells have to be detached from the substratum by sonication or other methods and diluted in buffer before being brought onto a filter (26,27). Additionally, Bižić-Ionescu and coworkers (28) successfully adapted the autonomous cell enumeration system to quantify specific cell types after FISH in aggregate samples.…”
Section: Discussionmentioning
confidence: 99%
“…The CARD-FISH protocol we present here has been developed and optimized for hydrocarbon-contaminated aquifers, in particular heavily polluted aquifers containing large plumes of methyl tertiary butyl ether (MTBE) and benzene, toluene, ethylbenzene, and xylenes (BTEX) [38]. We obtained considerable improved permeabilization and hybridization efficiency (2-to 20-fold) by applying a laboratory microwave.…”
Section: Hybridization Of Target Cells With Specific Oligonucleotidementioning
confidence: 99%
“…As mentioned earlier, fluorescent in situ hybridization (FISH), similar to other hybridization methods, uses specific fluorescently labeled oligoprobes binding to their complementary DNA sequence. FISH along with its different variations, such as catalyzed reporter deposition fluorescent in situ hybridization (CARD-FISH) or MAR-FISH, the combination of FISH with microautoradiography (MAR), have proven invaluable for the detection and enumeration of specific bacterial taxa and the investigation of microbial activities in complex communities, as well as for imaging their spatial association with mineral phases (Edwards et al 2003;Okabe et al 2004;Peplies et al 2006;Norlund et al 2009;Tischer et al 2012). Like other molecular biological methods, the standard FISH technique has its limitations.…”
Section: Coupling Molecular Based With Microscopic and Isotopic Appromentioning
confidence: 99%
“…Some of those have been reviewed by Wagner et al (2003) along with new trends in the use of FISH techniques to identify and analyze functional groups of microorganisms (Wagner and Haider 2012). (Shokralla et al 2012) CARD-FISH has proven valuable for assessing complexities of microbial communities associated with hydrocarbon contaminated aquifer environments (Tischer et al 2012). To investigate both bacteria and archaea simultaneously, the authors used a dual hybridization approach followed by two consecutive stainings.…”
Section: Coupling Molecular Based With Microscopic and Isotopic Appromentioning
confidence: 99%
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