Welcome to the Yuan Lab
Dr. Ze-Chun Yuan
Office/Lab: 1391 Sandford Street, Room 1017, London, Ontario
Phone: (519) 953-6641
Fax: (519) 457-3997
B.Sc. (Biology), Henan University, P. R. China 1992
M. Sc (Microbiology) McMaster University, Canada 2001
Ph.D. (Microbiology) McMaster University, Canada 2006
Postdoctoral (Microbiology), University of Washington at Seattle, 2005-2009
Major research interests: Plant Associated Bacteria, Bacterial Genetics; Environmental Genomics; Functional Genomics; Molecular Microbiology Ecology, Microbiome, Applied Microbiology and Biotechnology.
I obtained my M.Sc and Ph.D from Dr. Turlough M. Finan’s lab at McMaster University, Canada, where I started my research of plant associated bacteria. My graduate study focused on understanding how phosphate limitation affects biological nitrogen fixation and Rhizobium-alfalfa symbiosis (Yuan et al. Journal of Bacteriology, 2006; Yuan et al. Nucleic Acid Research. 2006; Yuan et al. Molecular Microbiology, 2005). I did my postdoctoral work with Dr. Eugene W. Nester at the University of Washington (Seattle), where I studied Agrobacterium tumefaciens and crown gall disease (plant tumor), which is a chronic and resurgent problem for many important plants in agriculture and horticulture.
Current and future researches in my lab focus on environmental genomics and microbial ecology towards sustainable agriculture and environment: 1) we are elucidating complex interactions and molecular mechanism of microorganisms, from single organisms to complex communities, within their environmental niches including plant root, insect, soil or water (molecular microbial ecology); 2) using high-throughput technologies including Illumina MiSeq and a variety of ‘omics’ approaches to explore the structure, dynamics and functioning of microorganisms (microbiome) pertinent to crop health; 3) bioprospecting of microorganisms for sustainable agriculture, bioremediation, carbon sequestration, biodegradation and bioproducts from renewable source (microbial genetics and engineering).
The recent achievements from my team (lab) include: A) identified several bacterial species capable of disease suppression (antagonism), production of plant hormone, lignin degradation, bioremediation, carbon sequestration, phosphate solubilisation and biological nitrogen fixation (Microbial Cell Factories 2016; BMC Microbiology 2016; BMC Genomics 2014); B) complete genome sequencing of Paenibacillus polymyxa CR1 (Frontier in Microbiology 2015; Genome Announcements 2014) and Arthrobacter sp. LS16, a bioremediation bacterium (Genome Announcements 2015); C) integrated environmental microbiology with engineering for enhanced bioremediation and bioengineering (Advances in Microbiology 2016; Journal of Environmental Chemical Engineering. 2015); D) microbial community analysis and applied microbiology (develop inoculants) to enhance crop health; E) developed a microbe-plant co-cultivation system in hydroponics to study plant associated microbiome, plant-microbe or plant-environment interactions at various organization levels (individual, population and community).
Current lab members:
Dr. Jacqueline MacDonald (postdoc)
Elliot Nicholas Grady (thesis student)
Margaret Truc Ho (thesis student)
Ke Ding (undergraduate researcher)
Filip Zekic (undergraduate researcher)
Brian Weselowski (Lab manager and technician)Recent Graduates:
Alexander W. Eastman, M. Sc Graduate, Technology Officer at Cistech Ltd. https://www.linkedin.com/in/alexandereastman
Naeem Nathoo. M. Sc Graduate, Account Manager - Massachusetts and Rhode Island https://www.linkedin.com/in/naeemnathoo
Ikrema Hassan, Ph.D. graduate, Professional consultant and freelancer, London, Ontario. https://www.linkedin.com/in/ikrema-hassan-ph-d-0327bb23
Selected recent publications:
- Elliot Nicholas Grady, Jacqueline MacDonald, Linda Liu, Alex Richman, Ze-Chun Yuan. Current Knowledge and Perspectives of Paenibacillus: A Review. 2016. Microbial Cell Factories (in press).
- Brian Weselowski, Naeem Amirali Nathoo, Alexander Eastman, Jacqueline MacDonald and Ze-Chun Yuan. Isolation, Identification and characterization of Paenibacillus polymyxa CR1 with potentials for biopesticide, biofertilization, biomass degradation and biofuel production. 2016. BMC Microbiology, Oct 18;16(1):244.
- Ikrema Hassan, Eltayeb Mohamedelhassan, Ernest K. Yanful, Ze-Chun Yuan. A Review Article: Electrokinetic Bioremediation Current Knowledge and New Prospects. 2016. Advances in Microbiology. DOI: 10.4236/aim.2016.61006.
- Ikrema Hassan, Eltayeb Mohamedelhassan, Ernest K. Yanful, and Ze-Chun Yuan. Sorption of Phenanthrene by kaolin and efficacy of hydraulic versus electroosmotic flow to stimulate desorption. 2015. Journal of Environmental Chemical Engineering. Vol 3, 4: 2301–2310.
- Ikrema Hassan, Alexander W. Eastman, Brian Weselowski, Eltayeb Mohamedelhassan, Ernest K. Yanful, Ze-Chun Yuan. Complete genome sequence of Arthrobacter sp. LS16, isolated from agricultural soils with potential applications in bioremediation and bioproducts. 2015. Genome Announcements. genomeA01586-15).
- Alexander W. Eastman and Ze-Chun Yuan. Second-generation sequencing, assembly and finishing of Paenibacillus polymyxa CR1 genome using a novel and expedited strategy based on repetitive rDNA operons and primer walking. 2015. Frontier in Microbiology 21;5:769.
- Alexander W. Eastman, David E. Heinrichs and Ze-Chun Yuan. Comparative and genetic analysis of four sequenced Paenibacillus polymyxa genomes reveals high genome plasticity but conservation of genes relevant to host interaction and competitiveness. 2014. BMC Genomics. Oct 3; 15(1):851.
- Sujatha Subramoni, Naeem Nathoo, Eugene Klimov, and Ze-Chun Yuan. Agrobacterium response to plant-derived signaling molecules. 2014. Frontiers in Plant Science. 8; 5:322
- Alexander W. Eastman, Brian Weselowski, Naeem Nathoo, Ze-Chun Yuan. Complete genome sequence of Paenibacillus polymyxa CR1, a plant growth-promoting bacterium isolated from corn rhizosphere exhibiting potential for biocontrol, biomass degradation, and biofuel production. 2014. Genome Announcements. Jan. 23, 2(1). pii: e01218-13.
- Yuan, ZC., and Williams, M.E. A Really Useful Pathogen, Agrobacterium tumefaciens. Teaching Tools in Plant Biology. 2012. Plant Cell. doi/10.1105/ tpc.109.tt1109.
- Full PubMed publication: http://www.ncbi.nlm.nih.gov/pubmed/?term=Ze-Chun+Yuan
- Yuan ZC, Haudecoeur E, Faure D, Kerr KD and Nester EW. Comparative transcriptome analysis of Agrobacterium tumefaciens in response to plant signals salicylic acid, indole-3-acetic acid, and Gamma-amino butyric acid reveals signaling crosstalk and Agrobacterium-plant co-evolution. 2008. Cellular Microbiology. 10: 2339-2354.
- Yuan ZC, Liu P, Saenkham P, Kerr KD and Nester EW. Transcriptome profiling and functional analysis of Agrobacterium tumefaciens reveals a general conserved response to acidic condition (pH5.5) and a complex acid-mediated signaling involved in Agrobacterium-plant interactions. 2008. Journal of Bacteriology. 190: 494-507.
- Yuan ZC, Edlind MP, Liu P, Saenkham P, Banta L, Wise AA, Ronzone E, Binns AN, Nester EW. The plant signal salicylic acid shuts down expression of the vir regulon and activates quormone-quenching genes in Agrobacterium. 2007. Proceedings of the National Academy of Sciences. 104: 11790-11795.
- Yuan ZC, Zaheer R, Morton R, Finan TM. Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria. 2006. Nucleic Acids Research. 34: 2686-2697.
- Yuan ZC, Zaheer R, Finan TM. Regulation and properties of PstSCAB, a highaffinity, high-velocity phosphate transport system of Sinorhizobium meliloti. 2006. Journal of Bacteriology. 188: 1089-1102. Yuan ZC, Zaheer R, Finan TM. Phosphate limitation induces catalase expression in Sinorhizobium meliloti, Pseudomonas aeruginosa and Agrobacterium tumefaciens. 2005. Molecular Microbiology. 58: 877-894.