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Bachelor/ Master Thesis
The role of viruses in contaminant biodegradation
Background:
Bacteria exposed to pollutants can adapt to them by mutating or acquiring derivative
genes as a result of the selective pressure created by pollutants. The latter process,
termed horizontal gene transfer (HGT), typically involves large-scale DNA shuffle between
microbes. Direct and indirect evidences have provided indications that HGTs play a major
role in the worldwide horizontal spread of existing biodegradation pathways, as well as in
the natural construction of novel ones, enabling bacteria to rapidly adapt to new pollutant
compounds entering their habitats (termed ‘evolution of biodegrading pathways). Among
all mechanisms of horizontally transferred biodegradation genes, plasmids have been
rather well-studied, with dozens of plasmids being described along with the biodegradation
genes they carry, as well as the donor and recipient bacterial strains. Such plasmids,
however, have been rarely observed in obligate anaerobes that again indicate that an
important piece of the puzzle is missing.
In this project, I hypothesize that viral-mediated HGT greatly impact critical metabolic
processes of key degraders. In addition, I hypothesize that viruses significantly take
influence on dynamics of bacterial contaminant transformation by shifting or even breaking
down degrader populations. Viruses hence may play central ecological and evolutionary
roles in groundwater similar to those that have been demonstrated in the surface and deep
marine ecosystems (1).
Project:
Attempts will be made to isolate viruses
capable of infecting selected microbial
degraders, applying the plaque assay and/or
the serials dilution and transfer approach,
combining with the newly developed highthroughput ‘Viral Tagging’ method (2). Purified
isolations will be prepared for viral genomes
sequencing. Expression of both viral-encoded
host metabolic genes of interest and their host
homologs will be followed over the period of
infection using RT-PCR.
Unveiling viral–host interactions
Qualifications:
Interested applicants should have a background in microbiology and laboratory
experience. He/she will work in a motivated, young and friendly working group at the
institute of groundwater ecology at the Helmholtz Zentrum Muenchen.
For application or further information please contact:
Dr. Li Deng ([email protected])
References:
1. Suttle, C.A. (2005). Viruses in the sea. Nature 437, 356-361.
2. Deng, L., Ignacio-Espinoza, J.C., Gregory, A.C., Poulos, B.T., Weitz, J.S., Hugenholtz, P., and Sullivan, M.B. (2014). Viral tagging
reveals discrete populations in Synechococcus viral genome sequence space. Nature 513, 242-245.