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Welcome to the Yuan Lab

Dr. Ze-Chun Yuan
Research Professor
Office/Lab: 1391 Sandford Street, Room 1017, London, Ontario
Phone: (519) 953-6641
Fax: (519) 457-3997

Email: zyuan27@uwo.ca


Education:
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
Our Research:
Environmental genomics and microbiology towards sustainable agriculture and environment: Plant Associated Bacteria, Bacterial Genetics and Genomics; Functional Genomics; Molecular Microbial Ecology, Microbiome, Metabolomics, Bioinformatics, Applied Microbiology and Biotechnology, with intensive bench work, greenhouse study and field trials.

1). Plant associated bacteria alleviating plant stresses. Plant associated bacteria play important roles in suppressing pathogens, managing disease, eliciting plant defense (induced systemic resistance) as well as enhancing tolerance to abiotic stresses. We are very interested in identifying and characterizing plant associated bacteria contributing to plant tolerance to biotic and abiotic stresses. One of the major interests from our lab is to identify microbial species, including bacteriophage and bacterium capable of producing antimicrobials for disease suppression (antagonism).

 

2). Molecular plant-microbe interactions and plant associated microbiomes. Beneficial microbes are able to promote plant health, enhance soil fertility, and enhance disease tolerance. Out of over 3,000 bacterial isolates, we identified and characterized numerous bacterial strains with multifaceted beneficial traits to plant hosts. These bacteria are able to fix nitrogen, produce plant growth hormone or solubilize inorganic phosphate. In line with the current demand for sustainable agriculture and environment, we are carrying out fundamental and applied researches for more detailed and predictive understanding of how plant associated microbiomes contribute to crop health and productivity, which involve microbial community (microbiome) analysis, microbe-plant co-cultivation, plant-microbe interaction and signaling (transcriptomics), plant-environment interactions at various organization levels (individual, population and community). We are elucidating the molecular signaling mechanism and symbiotic relationships between plant hosts and bacteria in their habitat and the ecological, genetic, and biochemical factors governing such symbiotic relationships (molecular microbial ecology and microbiomes).

 

3). Bioprospecting of microorganisms for sustainable agriculture, bioremediation, carbon sequestration, biodegradation and bioproducts from renewable source (also refer to the following section of microbial genomics, genetics and engineering). Lignocellulosic biomass, such as forestry and agricultural crop residues, are being considered as a very promising renewable source for biofuels and bio-products without threatening existing food supply chains. We are characterizing the genetic capability and regulatory mechanisms of biomass degradation. Another focus from our lab is herbicide biodegradation. Glyphosate (N-phosphonomethylglycine) (CAS No. 1071-83-6) is a broad-spectrum herbicide most widely used to control annual and perennial weeds in both agriculture and forestry and for aquatic system. However, massive use of glyphosate for decades has resulted in its ubiquitous presence in the environment, and poses a threat to humans and ecosystem. Bioremediation takes advantage of natural hydrocarbon-degrading bacteria in the environment and aims to optimize their metabolism, often by nutrient supplementation or biostimulation. We are isolating and characterizing glyphosate-degrading bacteria (bioremediation) for sustainable and resilient environment and ecosystem. In addition, we integrate environmental microbiology with civil and environmental engineering (electrokinetics) to promote diesel bioremediation.

 

 

4. Bacterial genomics, genetics and engineering (synthetic biology). Next-generation sequencing (NGS) known as the massively parallel sequencing technology, with its ultra-high throughput, scalability, and speed, has revolutionized the biological sciences, enabling researchers to perform a wide variety of applications and study biological systems at a level never before possible. To facilitate understanding the complex metabolic pathways and regulatory networks implicated in biodegradation and bioproduction, we are heavily involved in bacterial genome sequencing, assembly and analysis. In addition, we are using genetic tools such as transposon mutagenesis, loss of function analysis as well as several ‘omics’ approaches including transcriptomics (RNA-Seq), functional genomics, metabolomics and high throughput screening to identify and dissect bacterial metabolic pathway and regulatory mechanisms underpinning biodegradation and bioproductivity. We are also keen on using systems approaches, synthetic biology and genetic engineering to rewire bacterial metabolic flux in order to enhance bioegradation and bioproducts directly from lignocellulosic biomass, thereby making biorefinery cost efficient and bioproducts economically viable.

 

Current lab members:

Recent Graduate Students:
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, London, Ontario, Civil Project Engineer at Alfred Benesch & Company:
https://www.linkedin.com/in/ikremahassan/?originalSubdomain=ca
Editorial panel for Journal of Environmental Hazards: https://www.omicsonline.org/editor-profile/ikrema-hassan/

Open positions:
Occasionally, we are seeking highly motivated students at the BSc, MSc and PhD level as well as postdoctoral fellows. Please contact Dr. Ze-Chun Yuan for details on current projects and potential openings.

________________________________________
Recent Publications:

2019. Naeem Nathoo, Jacqueline MacDonald, Brian Weselowski and Ze-Chun Yuan. Comparative
transcriptomic analysis reveals different responses of Arabidopsis thaliana roots and shoots to
infection by Agrobacterium tumefaciens in a hydroponic co-cultivation system. Physiological and
Molecular Plant Pathology (in press).
2019. Ikrema Hassan, Eltayeb Mohamedelhassan, Ernest K. Yanful and Ze-Chun Yuan. Mitigation of soils
contaminated with diesel fuel using bioelectrokinetics. Journal of Environmental Science and
Health (in press).
2019. Elliot Grady; Jacqueline MacDonald; Margaret Ho; Brian Weselowski; Tim McDowell; Ori Solomon;
Justin Renaud; Ze-Chun Yuan. Characterization and complete genome analysis of the surfactin-
producing, plant-protecting bacterium Bacillus velezensis 9D-6. BMC Microbiology (in press).
2018. Munmun Nandi, Jacqueline MacDonald, Peng Liu, Brian Weselowski and Ze-Chun Yuan. Clavibacter
michiganensis subsp. michiganensis: Bacterial Canker of Tomato, Molecular Interactions and
Disease Management. Review. Molecular Plant Pathology. 2018 Mar 12. doi:
10.1111/mpp.12678.
2018. Ikrema Hassan, Eltayeb Mohamedelhassan, Ernest K. Yanful and Ze-Chun Yuan. Enhancement of
Bioremediation and Phytoremediation Using Electrokinetics. Chapter for book Advances in
Bioremediation and Phytoremediation. Published by InTech - open science.
2017. Margaret T. Ho, Filip Zekic, Brian Weselowski, Ze-Chun Yuan. Complete Genome Sequence of
Acinetobacter calcoaceticus CA16, a Bacterium Capable of Degrading Diesel and Lignin. Genome
Announcement. 2017. Jun 15;5(24). pii: e00494-17. doi: 10.1128/genomeA.00494-17.
2017. Filip Zekic, Brian Weselowski, Ze-Chun Yuan. Complete Genome Sequence of Burkholderia
cenocepacia CR318, a Phosphate-Solubilizing Bacterium Isolated from Corn Root. Genome
Announcement. 2017. Jun 8;5(23). pii: e00490-17. doi: 10.1128/genomeA.00490-17.
2017. Banyar Aung, Ruimin Gao, Margaret Y. Gruber, Ze-Chun Yuan, Mark Sumarah, Abdelali Hannoufa.
MsmiR156 affects global gene expression and promotes root regenerative capacity and nitrogen
fixation activity in alfalfa. Transgenic Research. 2017. 26(4):541-557. doi: 10.1007/s11248-017-
0024-3.
2017. Naeem Nathoo, Mark A. Bernards, Jacqueline MacDonald and Ze-Chun Yuan. A hydroponic co-
cultivation system for simultaneous and systematic analysis of plant-microbe molecular interactions
and signaling. 2017. Journal of Visualized Experiments. doi: 10.3791/55955. PMID: 28784965.
2017. Ikrema Hassan, Eltayeb Mohamedelhassan, Ernest K. Yanful and Ze-Chun Yuan. Solar power
enhancement of electrokinetic bioremediation of phenanthrene by Mycobacterium pallens.
Bioremediation Journal. 2017. 21:2, 53-70.
2016. Elliot Nicholas Grady, Jacqueline MacDonald, Linda Liu, Alex Richman, Ze-Chun Yuan. Current
Knowledge and Perspectives of Paenibacillus: A Review. BMC Microbial Cell Factories. 2016.
1;15(1):203.
2016. 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. BMC
Microbiology, 2016. Oct 18;16(1):244.
2016. Ikrema Hassan, Eltayeb Mohamedelhassan, Ernest K. Yanful, Ze-Chun Yuan. A Review Article:
Electrokinetic Bioremediation Current Knowledge and New Prospects. Advances in Microbiology,
Pub. Date: January 28, 2016. DOI: 10.4236/aim.2016.61006.
2015. 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. Genome
Announcements. genomeA01586-15).
2015. 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.
Journal of Environmental Chemical Engineering. 2015. Vol 3, 4: 2301–2310.
2015. 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. Frontier in Microbiology. 2015. 21;5:769.
2014. 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. BMC Genomics. 2014. Oct 3; 15(1):851.
2014. Sujatha Subramoni, Naeem Nathoo, Eugene Klimov, and Ze-Chun Yuan. Agrobacterium response
to plant-derived signaling molecules. Frontiers in Plant Science. 2014. 8; 5:322
2014. 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.
Genome Announcements. 2014. Jan. 23, 2(1). pii: e01218-13.
2012. Yuan, ZC., and Williams, M.E. A Really Useful Pathogen, Agrobacterium tumefaciens. Teaching
Tools in Plant Biology. The Plant Cell. doi/10.1105/ tpc.109.tt1109.


Other relevant publications: