Microbial Genomics

Microbial genomics

Jeff Chang | Professor | Department of Botany and Plant Pathology | Chang Lab

Bacteria Backstory

My research program studies the evolutionary, ecological, and mechanistic bases for how bacteria interact and affect the health of plants. We use methods in molecular biology, biochemistry, genomics, ecology, and evolutionary biology. We study bacteria that interact closely in beneficial ways and provide fixed nitrogen, those that interact loosely to promote plant health or suppress pathogenic bacteria, and those that are pathogens and cause disease to plants.

A Seed Planted

My story is defined by the many people who have influenced the way I think and the many opportunities I have had in working at the forefront of research on plant-microbe interactions. I began my academic career as a pre-architecture major. An introductory biology course gave me a new direction and my academic advisor helped me find a position as a dishwasher in a research laboratory. The graduate students, postdocs, and laboratory technicians in the lab and department taught me so much, showed confidence in me, and transitioned me into a researcher. The ability to investigate life at the molecular level was so intriguing.

The start of my PhD coincided with the cloning of the first disease resistance gene from plants. It was an exciting time in molecular plant pathology, and I was able to work in a new area of research and make discoveries on the molecular mechanisms of plant disease resistance. The start of my postdoc was concurrent with two emerging areas of research in pathogen genomics and pathogen virulence. I used genome-enabled and molecular methods to screen pathogens for genes that encode for secreted virulence proteins. Lastly, my arrival at Oregon State University coincided with a revolutionary change in genome sequencing technology. Since then, our use of whole genome sequencing has greatly diversified my research program at OSU. I am fortunate to have students and postdocs as well as colleagues who think about host-microbe interactions in diverse ways. They are constantly making me think and approach research on plant-microbe interactions in a variety of ways.

Picking up the Trail

Plant-microbe research has many positive outcomes. We are given opportunities to satisfy curiosities on how the living world works, but our pursuits are not merely academic. The knowledge we generate has direct--and indirect--impacts on farmers and growers. We study how pathogens evolve and use this framework to understand how those pathogens are transmitted across this world. Our findings provide important clues as to how we can slow the spread of disease. Similarly, we study how mutualistic nitrogen-fixing bacteria evolve and the data provide important insights into how we can use these types of bacteria more effectively to promote sustainable agriculture. Additionally, we study the mechanisms that pathogens use to incite disease and the mechanisms that bio-control bacteria employ to suppress these pathogens.

Research is also a powerful teaching tool. My laboratory is a classroom for students and postdocs alike. While working to address important needs in plant health, food security, and ecosystem health, researchers in the lab learn important thinking, technical, and social skills. They quickly learn how their research can be translated to help society at large.

Pathogen Detectives

One recent study exemplifies how our research addresses both fundamental and applied aspects of plant-microbe research: We sequenced the genomes of hundreds of strains from a genus of plant pathogenic bacteria; carefully analyzing the genome sequences to model the evolution of the bacteria as well as “accessory” DNA elements called plasmids. We then used this evolutionary framework to identify--with high resolution--global transmission patterns and the processes that influenced their spread. This work was done in collaboration with numerous OSU researchers. These include Dr. Joyce Loper of the College of Agricultural Sciences; Dr. Niklaus Grunwald, a USDA-ARS scientist and courtesy member of the Department of Botany and Plant Pathology; and Melodie Putnam, the director of the Plant Clinic. Last but not least, we relied extensively on bacteria collected by Dr. Larry Moore and Marilyn Miller, both of whom are retired from the Department of Botany and Plant Pathology.