Ching-Hong Yang Associate Professor Ph. D. University of California, Riverside Postdoctoral fellow University of California, Riverside University of California, Davis	Office: Lapham 131D Phone: 414-229-6331 FAX: 414-229-3926 Email: chyang@uwm.edu
Genomics, Functional Genomics and Host-Microbe Interactions

Research Interests

1) Application of functional genomic tools to investigate microbial gene expression in different environments With the availability of the complete sequences of the genomes of different microorganisms, functional genomic tools provide a powerful approach for identifying microbial genes that are expressed during association of bacteria with hosts and or in response to various environmental factors. In my current research, I am working on a project to sequence the complete genome of Erwinia chrysanthemi 3937. E. chrysanthemi is a common colonist of aerial plant surfaces and causes soft-rot, wilts and blight diseases on a wide range of plant species. Infection of plants by E. chrysanthemi serves as a model for studying the mechanism of bacterial infection. My students and I are using complementary approaches to look at gene expression in this model organism. The first involves a custom designed microarray for E. chrysanthemi that will enable us to look at sets of genes that are regulated over time during the infection process. Secondly, we are using in vivo expression techniques (IVET) to investigate specific genes of E. chrysanthemi that are up-regulated in plant hosts. Thirdly, by hrp functional cloning technology, we explore genes of E. chrysanthemi 3937 that are involved in pathogenesis. Using bioinformatic tools, the known hrp regulated genes and DNA clones identified in hrp functional screening are used as a training set for a genomewide identification of potential virulence genes in E. chrysanthemi. 2) Developing novel approaches for microbial diversity profiling The quantitative description of microbial communities is one of the most promising areas of research in microbial ecology. Classical culture based techniques recover only a small proportion of microorganisms from environmental samples, but have provided us with a wide array of products that have benefited humanity. New techniques in molecular ecology have now opened the door for a revolutionary advance in our understanding of microbial communities in nature and identification of new microorganisms and microbial products that can be harnessed for biotechnology. My students and I have been especially interested in developing novel approaches to analyze microbial diversity that is associated with plants. Going beyond these initial descriptions of microbial communities, my most recent work has begun to focus on interactions between plants and microorganisms using genome profiling. In addition, I would like to further explore how plant pathogens are influenced by the microbial communities with which they are associated and how gene expression is modified by environmental factors that influence both the pathogen and leaf bacterial communities. This research may lead to improved understanding of disease and methods for biocontrol by promoting disease suppressive bacterial communities on plant leaf surfaces.

Selected Publications

Yap, M.-N., C. Rojas, C.-H. Yang, and A. O. Charkowski. 2008. The response regulator HrpY of Dickeya dadantii 3937 regulates virulence genes not linked to the hrp cluster. Mol. Plant-Microbe Interact. 21: 304-314. Yang, S., Q. Peng, Q. Zhang, X. Yi, C. J. Choi, R. M. Reedy, A. O. Charkowski, and C.-H. Yang. 2008. Dynamic regulation of GacA in type III secretion system, pectinase gene expression, pellicle formation, and pathogenicity of Dickeya dadantii. Mol. Plant-Microbe Interact. 21:133-142. Yang L., C.-H. Yang, and J. Li. 2008. Adhesion and Retention of a Bacterial Phytopathogen Erwinia Chrysanthemi in Biofilm-Coated Porous Media. Environ. Sci. Technol. 42: 159-165. Wang, Y.; H. Wang, C.-H. Yang, Q. Wang, and R. Mei. 2007. Two distinct manganese-containing superoxide dismutase genes in Bacillus cereus: their physiological characterizations and roles in surviving in wheat rhizosphere. FEMS Microbiol. Lett. 272:206-213. Yang, S., Q. Zhang, J. Guo, A. O. Charkowski, B. R. Glick, A. M. Ibekwe, D. A. Cooksey, and C.-H. Yang. 2007. Global effect of Indole-3-acetic acid (IAA) biosynthesis on multiple virulence factors of Erwinia chrysanthemi 3937. Appl. Environ. Microbiol. 73: 1079-1088. Yang L., C.-H. Yang, and J. Li. 2007. Influence of extracellular polymeric substances (EPS) on Pseudomonas aeruginosa transport and deposition profiles in porous media. Environ. Sci. Technol. 41:198-205. Ibekwe, A. M., C. M. Grieve, and C.-H. Yang. 2007. Survival of E. coli O157:H7 in soil and on lettuce after soil fumigation. Can. J. Microbiol. 53:623-635. Ahn, S.-J., C.-H. Yang, and D. A. Cooksey. 2007. Pseudomonas putida 06909 genes expressed during colonization on mycelial surfaces and phenotypic characterization of mutants. J. Appl. Microbiol. 103: 120-132. Ibekwe, A. M., A.C. Kennedy, J. J. Halvorson, and C.-H. Yang. 2007. Characterization of developing microbial communities in Mount St. Helens pyroclastic substrate. Soil Biol. Biochem. 39:2496-2507. Peng Q., S. Yang, A. O. Charkowski, M.-N. Yap, D. A. Steeber, N. T. Keen, and C.-H. Yang. 2006. Population behavior analysis of dspE and pelD regulation in Erwinia chrysanthemi 3937. Mol. Plant-Microbe Interact. 19:451-457. Okinaka, Y., N. T. Perna, S. Yang, N. T. Keen, and C.-H. Yang. 2006. Identification of potential virulence genes in Erwinia chrysanthemi 3937: transposon insertion into plant-upregulated genes J. Gen. Plant Pathology 72: 360-368. Yap, M.-N., C. Rojas, C.-H., Yang, and A. O. Charkowski. 2006. Harpin mediates cell aggregation in Erwinia chrysanthemi 3937. J. Bacteriol. 188:2280-2284. Yang, L., Y.-H. Zhaoa, B.-X. Zhang,  C.-H. Yang, and X. Zhang. 2005. Isolation and characterization of a chlorpyrifos and 3,5,6-trichloro-2-pyridionol degrading bacterium. FEMS Microbiol. Lett. 251:67-73. Kawai T., C.-H. Yang, M. R. Matsumoto, D. E. Crowley, and J. D. Sheppard. 2005. Comparison of PCR-DGGE and selective plating methods for monitoring the dynamics of a mixed culture population in synthetic brewery wastewater. Biotechnol. Prog. 21:712–719. Yap, M.-N., C.-H. Yang, J. D. Barak, and A. O. Charkowski. 2005. The Erwinia chrysanthemi type III secretion system is required for multicellular behavior. J. Bacteriol. 187:639-648. Yang, S., N. T. Perna, D. A. Cooksey, Y. Okinaka, S. E. Lindow, A. M. Ibekwe, N. T. Keen, and C.-H Yang. 2004. Genome-wide identification of plant-upregulated genes of Erwinia chrysanthemi 3937 using a GFP-based IVET leaf array.  Mol. Plant-Microbe Interact. 17:999-1008.  http://www.apsnet.org/mpmi/search/2004/0701-01r.asp Marschner, P., D. Crowley and C.-H. Yang. 2004. Development of specific rhizosphere bacterial communities in relation to plant species, nutrition and soil type. Plant and Soil. 261: 199-208. Ibekwe, A. M., S. K. Papiernik, C.-H. Yang. 2004. Enrichment and molecular characterization of chloropicrin- and metam-sodium-degrading microbial communities. Appl. Microbiol. Biotechnol.  66:325-332. Alvey, S., C.-H. Yang, A. Buerkert, and D. E. Crowley. 2003. Cereal/legume rotation effects on rhizosphere bacterial community structure in West African soils. Biol Fert. Soils 37:73-82.  http://www.wiz.uni-kassel.de/ink/pub/2003buerkert02.pdf Yang, C.-H., M. Gavilanes-Ruiz, Y. Okinaka, R. Vedel, I. Bethuy, M. Boccara, J. W. Chen, N. T. Perna, and N. T. Keen. 2002. hrp genes of Erwinia chrysanthemi 3937 are important virulence factors. Mol. Plant-Microbe Interact. 15:472-480.  http://www.apsnet.org/mpmi/search/2002/0329-01r.asp Okinaka, Y., C.-H. Yang, N. T. Perna and N. T. Keen. 2002. Microarray profiling of Erwinia chrysanthemi 3937 genes that are regulated during plant infection. Mol. Plant-Microbe Interact. 15:619-629.  http://www.apsnet.org/mpmi/search/2002/0506-02r.asp Okinaka, Y., C.-H. Yang, E. Herman, A. Kinney, and N. T. Keen. 2002. The P34 elicitor interacts with a soybean photorespiration enzyme, NADH-dependent hydroxypyruvate reductase. Mol. Plant-Microbe Interact. 15:1213-1218.  http://www.apsnet.org/mpmi/search/2002/1001-01r.asp Ibekwe A. M., A. C. Kennedy, P. S. Frohne, S. K. Papiernik, C.-H. Yang, and D. E. Crowley. 2002. Microbial diversity along a transect of agronomic zones. FEMS Microbial. Ecol. 39:183-191. Luepromchai, E., A. C. Singer, C.-H. Yang, and D. E. Crowley. 2002. Interactions of earthworms with indigenous and bioaugmented PCB-degrading bacteria. FEMS Microbial. Ecol. 41:191-197. Yang, C.-H., D. E. Crowley, J., Borneman, and N. T. Keen. 2001. Microbial phyllosphere populations are more complex than previously realized. Proc. Natl. Acad. Sci. USA 98:3889-3894.  http://www.pnas.org/cgi/reprint/98/7/3889.pdf Yang, C.-H., D. E. Crowley, and J. A. Mange. 2001. 16S rDNA fingerprinting of rhizosphere bacterial communities associated with healthy and phytophthora infected avocado roots. FEMS Microbial. Ecol. 35:129-136. Marschner, P., C.-H. Yang, R. Lieberei, D. E. Crowley. 2001. Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol. Biochem. 33:1437-1445. Ibekwe A. M., S. K. Papiernik, J. Gan, S. R. Yate, D. E. Crowley, and C.-H. Yang. 2001. Microcosm enrichment of 1, 3-Dichloropropene-degrading microbial communities. J. of Appl. Microbiol. 91:668-676.  http://www.pw.ucr.edu/textfiles/13D_Mark.pdf Ibekwe A. M., S. K. Papiernik, J. Gan, S. R. Yate, C.-H. Yang, and D. E. Crowley. 2001. Impact of fumigants on soil microbial community. Appl. Environ. Microbiol. 67:3245-3257.   http://aem.asm.org/cgi/reprint/67/7/3245.pdf Yang, C.-H., D. E. Crowley, G. H. Anthony, and N. T. Keen. 2000. Strain level identification of Pseudomonas using denaturing gradient gel electrophoresis of 16S-23S spacer region rDNA. J. Gen. Plant Pathology 66:225-233. Yang, C.-H., and D. E. Crowley. 2000. Rhizosphere microbial community structure in relation to root location and plant iron nutritional status. Appl. Environ. Microbiol. 66:345-351.   http://aem.asm.org/cgi/reprint/66/1/345.pdf Yang, C.-H., H. R. Azad, and D. A. Cooksey. 1996. A chromosomal locus required for copper resistance, competitive fitness, and cytochrome c biogenesis in Pseudomonas fluorescens. Proc. Natl. Acad. Sci. USA 93:7315-7320.  http://www.pnas.org/cgi/reprint/93/14/7315.pdf Yang, C.-H., J. A. Menge, and D. A. Cooksey. 1994. Mutation affecting hyphal colonization and pyoverdine production in pseudomonads toward Phytophthora parasitica. Appl. Environ. Microbiol. 60:473-481.  Yang, C.-H., J. A. Menge, and D. A. Cooksey. 1993. Role of copper resistance in competitive survival of Pseudomonas fluorescens in soil. Appl. Environ. Microboil. 59:580-584.  http://aem.asm.org/cgi/content/abstract/59/2/580 Book Chapters: Yang, C.-H. and S.-H. Yang. Managing bacterial plant diseases by modulating quorum sensing and Type III secretory systems. 2008. In: Z.K. Punja, S.H. De Boer and H. Sanfacon (eds.) Biotechnology and Plant Disease Management. CABI Publishing. Oxfordshire. UK. P. 16-57. Crowley, D.E., E.S. Gilbert, A. Singer, D. Newcombe, and C.-H. Yang. 1999. Bioremediation of organic contaminants using repeated applications of xenobiotic degrading bacteria. In:  R. Fass, Y Flashner, and S. Reuveny (eds.) Novel Methods for Bioremediation of Organic Pollution. Plenum Press. NY. p. 273-284. Minireview Keen, N. T., C. K. Dumenyo, C.-H. Yang, and D. A Cooksey. 2000. From rags to riches: insights from the first genomic sequence of a plant pathogenic bacterium. Genome Biology 1: 1019.1-1019.4.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11178244 Keen, N. T. and C.-H. Yang. 1999. Functional genomics: Plant-Microbe interactions gingerly puts a foot in the water. Physiol. and Mol. Plant Pathology 55:313-315.