Publication Details

Category Text Publication
Reference Category Book chapters
DOI 10.1007/8623_2014_9
Title (Primary) Identification of microorganisms in hydrocarbon-contaminated aquifer samples by fluorescence in situ hybridization (CARD-FISH)
Title (Secondary) Hydrocarbon and lipid microbiology protocols. Ultrastructure and imaging
Author Schattenhofer, M.; Hubalek, V.; Wendeberg, A.
Publisher McGenity, T.J.; Timmis, K.N.; Nogales, B.
Source Titel Springer Protocols Handbooks
Year 2016
Department UMB
Page From 103
Page To 113
Language englisch
Keywords Aquifer; CARD-FISH; Cell quantification; Hydrocarbon contamination; Microbial community
UFZ wide themes RU3;
Abstract

High loads of petroleum hydrocarbons in contaminated soils and sediments make these ecosystems difficult to study with molecular techniques. Among these sites, aquifers – environments with low turnover rates and, hence, slow-growing microbial communities–pose a great challenge for microbial ecologists.

Fluorescence produced by petroleum hydrocarbons coating sediment particles can be so strong that microscopic techniques are made impossible. Low microbial cell numbers pose further limitations for molecular analyses such as fluorescence in situ hybridization (FISH).

Here, we present a protocol for the separation of microbial cells from sediment samples of highly petroleum-contaminated aquifers. By excluding the strongly autofluorescing sediment particles, by concentrating microbial cells on membrane filters, and by using signal amplification in combination with FISH (CARD-FISH), we were able to quantify various microbial populations in this intriguing ecosystem.

Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=18197
Schattenhofer, M., Hubalek, V., Wendeberg, A. (2016):
Identification of microorganisms in hydrocarbon-contaminated aquifer samples by fluorescence in situ hybridization (CARD-FISH)
In: McGenity, T.J., Timmis, K.N., Nogales, B. (eds.)
Hydrocarbon and lipid microbiology protocols. Ultrastructure and imaging
Springer Protocols Handbooks
Springer, Berlin, Heidelberg, p. 103 - 113 10.1007/8623_2014_9