Yue Lu

Name & affiliation
Yue Lu, Molecular Ecology, Laboratory of Microbiology, Wageningen University

PhD student

2006-2010, BS Resources and Environmental Science, China Agricultural University, China
2010-2012, MS Environmental Science, China Agricultural University, China
2012-present, PhD student, Microbiology, Wageningen University, The Netherlands

My research capitalizes on application of functional genomics methods for the research of organohalide respiring bacteria (OHRB) with special focus on Firmicutes such as members of the genera Desulfitobacterium and Dehalobacter. Transcriptomics and proteomics will be used for exploring the key components and regulatory networks associated with organohalide respiration (OHR) in OHRB such as Dehalobacter restrictus and Desulfitobacterium hafniense DCB-2. The response of these bacteria to environmental stresses such as corrinoid starvation, increasing concentrations of ortho- and meta-substituted chlorophenols and different chlorobenzenes will be studied. Next to pure culture studies, sediment-free stable enrichment cultures will be obtained from chlorobenzenes dechlorinating anaerobic sediment microcosms dominated by populations most closely related to Desulfitobacterium. Genome-wide gene expression patterns of Desulfitobacterium spp. will be assessed using a pan-genomic microarray specifically designed for the members of this genus based on known Desulfitobacterium genomes, as well as by direct RNA seq using next generation technology sequencing such as Illumina HiSeq. Next, the enrichments will be used for isolation of novel OHRB using a miniaturized cultivation platform developed at the Laboratory of Microbiology, the Microdish culture chip. The potential of the isolated strains for anaerobic respiration with different halogenated pollutants as terminal electron acceptor will be further studied. To sum up, my research mainly focuses on identification and elucidation of molecular mechanisms involved in OHR, by unravelling the relation between the genetic potential of OHRB and their actual functioning in vitro and in situ by downstream transcriptomics and proteomics study.