Publication Details

Reference Category Book chapters
DOI / URL link
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.;
Journal Springer Protocols Handbooks
Year 2016
Department UMB;
Language englisch;
POF III (all) T41;
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.

ID 18197
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