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Studying Protistan Communities in Hydrocarbon-Contaminated Environments

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Hydrocarbon and Lipid Microbiology Protocols

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Abstract

Protists represent mostly unicellular eukaryotic microorganisms which are crucial for the microbial food webs in virtually all ecosystems. Until recently, much of our knowledge regarding the distribution, taxonomic diversity, and activity of protists relied on classical observation and cultivation methods. The application of molecular biological approaches which are based on the analysis of phylogenetic marker genes, such as the 18S ribosomal RNA gene, has greatly advanced protistan diversity studies in the environment. This development has contributed to a better understanding of how protistan communities – in particular in aquatic systems – relate to other microbial groups and ecosystem processes. However, microbial ecologists have largely neglected the role of protists in hydrocarbon-polluted sites which stands in sharp contrast to the number of studies on prokaryotic communities in these habitats. The protocols collected in this chapter provide detailed descriptions of cultivation-independent methods which we consider highly useful to study protistan communities in polluted habitats. We start with protocols for DNA and RNA extraction from environmental samples, followed by methods which allow the acquisition of qualitative (via terminal restriction fragment length polymorphism (T-RFLP) analysis) as well as quantitative (via quantitative PCR or fluorescence in situ hybridization (FISH)) information.

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Authors and Affiliations

  1. Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Permoserstr. 15, 04318, Leipzig, Germany

    Julia Johnke & Antonis Chatzinotas

  2. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany

    Antonis Chatzinotas

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  1. Julia Johnke
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  2. Antonis Chatzinotas
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Correspondence to Antonis Chatzinotas .

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Editors and Affiliations

  1. University of Essex Dept. Biological Sciences, Colchester, Essex, United Kingdom

    Terry J. McGenity

  2. Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany

    Kenneth N. Timmis

  3. Dept. Biologia, Univ de les Illes Balears, Palma de Mallorca, Spain

    Balbina Nogales

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Johnke, J., Chatzinotas, A. (2015). Studying Protistan Communities in Hydrocarbon-Contaminated Environments. In: McGenity, T., Timmis, K., Nogales , B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2015_169

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  • DOI: https://doi.org/10.1007/8623_2015_169

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