Bioinformatic analyses of marine microorganisms from contrasting habitats

  • Deep-sea hypersaline anoxic lakes (DHALs) are brine lakes found at the seafloor and harbor halophilic microorganisms that can withstand harsh physicochemical conditions. Various Eastern Mediterranean DHALs were investigated in the EU project MAMBA. It aimed at discovering extremophiles and their gene repertoires to elucidate the ecophysiological roles and enzymes with prospects in biotechnology. The interface-brine border of the DHAL Thetis was investigated and revealed a complex sulfur cycle. Halorhabdus tiamatea from the sediment of the Shaban Deep, a DHAL in the Red Sea, was analyzed by comparative genomics. I characterized it as potential polysaccharide degrader which was supported by proteomics and glucosidase activity measurements. H. tiamatea might not belong to the autochthonous community in DHALs. Still, it revealed different niche adaptations toward its isolation source, such as heavy metal transporters and polysaccharide-degrading enzymes. Such adaptations were also shown by the flavobacterium Formosa agariphila. Members of its genus were abundant during a phytoplankton bloom in the North Sea in 2009. The genome of F. agariphila was sequenced and analyzed with a focus on CAZymes. It revealed thirteen polysaccharide utilization loci, which show its capability to degrade polysaccharides from green, red and brown algae. The two major epibionts of the gill of the deep-sea shrimp Rimicaris exoculata were analyzed by metagenomics. They belong to the genera Sulfurovum and Leucothrix and deal with fluctuating conditions at hydrothermal vents. They share similar core metabolisms and might evade competition by niche-differentiation. The gene repertoire of extremophiles is widely unexploited. Despite the advances of NGS technologies, a large resource of enzyme candidates is untapped. I developed the software tool madeira which recognizes key motifs of protein sequences and allows a rapid screening of enzyme classes which constitute promising targets for biotechnology.

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Publishing Institution:IRC-Library, Information Resource Center der Jacobs University Bremen
Granting Institution:Jacobs Univ.
Author:Johannes Werner
Referee:Frank Oliver Glöckner, Matthias Ullrich, Rudolf I. Amann, Hanno Teeling
Advisor:Frank Oliver Glöckner
Persistent Identifier (URN):urn:nbn:de:gbv:579-opus-1003934
Document Type:PhD Thesis
Language:English
Date of Successful Oral Defense:2014/03/21
Date of First Publication:2014/03/25
PhD Degree:Bioinformatics
School:SES School of Engineering and Science
Other Organisations Involved:Max-Planck-Institut für Marine Mikrobiologie (marmic)
Library of Congress Classification:Q Science / QH Natural history - Biology / QH301-705.5 Biology (General) / QH324 Methods of research. Technique. Experimental biology / QH324.2 Data processing. Bioinformatics
Call No:Thesis 2014/06

$Rev: 13581 $