RNA based research development, application and analysis within the MIMAS project

  • Every prokaryotic cell contains different sorts of ribonucleic acid (RNA) molecules, which are mainly dedicated to processing and regulating gene expression. The wide palette of functions is reflected by distinct RNA types, and each of them is represented by a complex and comprehensive research field. In particular, different culture-independent applications have attracted attention recently because the majority of microbes still resists cultivation until today. For example, the standard approach for microbial diversity studies is based on the comparative analysis of the evolutionarily conserved 16S ribosomal RNA gene (16S rDNA), and messenger RNA (mRNA) based metatranscriptomics allows culture independent gene expression analysis without prior knowledge of the present microbes or transcripts. 16S rDNA biodiversity studies, metatranscriptomics and other ‘omic’ applications play a central role within the MIMAS project, which aims at characterizing a bacterioplankton community at the long-term ecological research site Helgoland Roads. However, culture-independent applications have their limitations, and a careful design of experimental procedures is crucial to assure that these limitations do not overtly bias the results. Therefore, this thesis outlines the development and application of an improved pipeline for the analysis of metatranscriptomic data and the evaluation of PCR primers used to amplify 16S rRNA. In particular, the outcome of the latter serves as a guideline for enhanced research to find the most suitable primer pair for 16S rDNA biodiversity analysis in any habitat using any currently available sequencing technology. The methods developed were used in a multi ‘omic’ study to characterize the phylogenetic and functional potential of the microbial community. The results identified the key players of an observed bacterioplankton bloom at Helgoland Roads and provided the first insights into taxonomically distinct nutrient strategies. They indicated that Flavobacteria, Gammaproteobacteria and Alphaproteobacteria are specialized for successive degradation of different algal primary products. This provided a series of ecological niches, allowing certain community members to grow. The results helped to uncover the secret of how members of the bacterioplankton can evade extinction despite the limited resources in the habitat. The work accomplished allows future follow-up studies and furnishes scientific society with guidelines to perform accurate diversity studies. Moreover the outcome serves as basis for future ecosystem monitoring.

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Publishing Institution:IRC-Library, Information Resource Center der Jacobs University Bremen
Granting Institution:Jacobs Univ.
Author:Anna Klindworth
Referee:Frank Oliver Glöckner, Matthias Ullrich, Jack Gilbert
Advisor:Frank Oliver Glöckner
Persistent Identifier (URN):urn:nbn:de:101:1-201305294928
Document Type:PhD Thesis
Language:English
Date of Successful Oral Defense:2012/10/08
Date of First Publication:2012/11/06
PhD Degree:Biology
School:SES School of Engineering and Science
Other Organisations Involved:Max-Planck-Institut für Marine Mikrobiologie (marmic)
Other Countries Involved:United States of America
Library of Congress Classification:Q Science / QH Natural history - Biology / QH301-705.5 Biology (General) / QH426-470 Genetics / QH434 Microbial genetics
Call No:Thesis 2012/36

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