Abstract
Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has been increased in the last few years, the vast majority of marine diversity is rather unexplored. Moreover, most studies focused on the entire bacterial community and thus disregarded active microbial community players. Here, we describe a detailed protocol for the simultaneous extraction of DNA and RNA from marine water samples and for the generation of cDNA from the isolated RNA which can be used as a universal template in various marker gene studies.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Wemheuer B, Wemheuer F, Daniel R (2012) RNA-based assessment of diversity and composition of active archaeal communities in the German Bight. Archaea 2012:695826
Schneider D, Arp G, Reimer A, Reitner J, Daniel R (2013) Phylogenetic analysis of a microbialite-forming microbial mat from a hypersaline lake of the Kiritimati Atoll, Central Pacific. PLoS One 8:e66662
Wemheuer B, Wemheuer F, Hollensteiner J, Meyer F-D, Voget S, Daniel R (2015) The green impact: bacterioplankton response towards a phytoplankton spring bloom in the southern North Sea assessed by comparative metagenomic and metatranscriptomic approaches. Front Microbiol 6:805
Wemheuer B, Güllert S, Billerbeck S, Giebel H-A, Voget S, Simon M et al (2014) Impact of a phytoplankton bloom on the diversity of the active bacterial community in the southern North Sea as revealed by metatranscriptomic approaches. FEMS Microbiol Ecol 87:378–389
Schneider D, Reimer A, Hahlbrock A, Arp G, Daniel R (2015) Metagenomic and metatranscriptomic analyses of bacterial communities derived from a calcifying karst water creek biofilm and tufa. Geophys J 32:316–331
Weinbauer MG, Fritz I, Wenderoth DF, Höfle MG (2002) Simultaneous extraction from bacterioplankton of total RNA and DNA suitable for quantitative structure and function analyses. Appl Environ Microbiol 68:1082–1087
Voget S, Wemheuer B, Brinkhoff T, Vollmers J, Dietrich S, Giebel H-A et al (2015) Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses. ISME J 9:371–384
Miteva VI, Sheridan PP, Brenchley JE (2004) Phylogenetic and physiological diversity of microorganisms isolated from a deep greenland glacier ice core. Appl Environ Microbiol 70:202–213
Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700
Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169
Heuer H, Krsek M, Baker P, Smalla K, Wellington EM (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63:3233–3241
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Schneider, D., Wemheuer, F., Pfeiffer, B., Wemheuer, B. (2017). Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a cDNA as Universal Template for Marker Gene Studies. In: Streit, W., Daniel, R. (eds) Metagenomics. Methods in Molecular Biology, vol 1539. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6691-2_2
Download citation
DOI: https://doi.org/10.1007/978-1-4939-6691-2_2
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-6689-9
Online ISBN: 978-1-4939-6691-2
eBook Packages: Springer Protocols