Eight noses are better than one
One bacterium’s devotion to finding its host plant is nothing to sniff at.
Thanks to years of evolution, Sinorhizobium meliloti bacteria have developed super-noses that allow them to sniff out alfalfa plants underground and swim to them through the soil.
Ben Webb, a Ph.D. student in the department of biological sciences in the College of Science, has devoted his graduate career to pinpointing exactly which molecules are involved in the underground union.
Without the bacteria, alfalfa plants—one of the most popular foraging crops for livestock in the United States—cannot fix nitrogen or grow very well. In turn, the bacteria rely on alfalfa for food and nourishment.
To attract the bacteria, the plant sends out attractants such as sugars, amino acids, betaines, and other undiscovered molecules underground, through its germinating seeds.
To determine which molecules play a crucial role, Webb—with guidance from his advisor Birgit Scharf—used liquid chromatography and mass spectrometry to analyze the alfalfa seed exudate. By observing molecule masses, they were able to identify the molecules and measure their relative abundance. Webb tested the most promising molecules with a chemotaxis assay to determine which are attractants for S. meliloti.
Webb also investigated the bacterial side of the connection. To identify which of the bacterium’s chemoreceptors are used to sense attractants, he knocked out single chemoreceptor genes creating ‘mutant’ bacterial strains. Each strain was tested for its ability to sense an attractant molecule.
Lastly, Webb purified the individual receptors, and then mixed the receptor and the attractant molecule together, watching for a change of heat that indicates a chemical reaction, and direct binding.
Based on this series of experiments, Webb concluded that certain betaines are the strongest attractants for the bacteria, and that the bacterial McpX chemoreceptor is most effective at sensing the attractant. This sort of scientific matchmaking and its resultant strong bond could greatly inform and benefit agricultural practices in the future.
“Matching the strong attractants with their cognate chemoreceptors will help us in designing S. meliloti strains with a more preferential chemotaxis towards the host alfalfa, which would propagate the symbiosis more efficiently,” said Webb, who defended his dissertation in August. “In essence, these chemoreceptors are to bacteria as noses are to humans, except S. melioti has eight of these noses,” said Webb.
Webb was a sophomore in college when he looked down a microscope and found his calling in the form of a plate full of bright, squirming bacteria.
“My mind was blown,” Webb said. “I couldn’t believe that there was this whole other universe under my nose this whole time, complete with a vast variety of species portraying similar ecological principles yet on a scale invisible to the naked eye.”
As an undergraduate at Virginia Tech, Webb was mentored by then-graduate student Sean Mury in the lab of David Popham, a professor of biological sciences in the College of Science. When Webb graduated with a bachelor’s degree in Biological Sciences in 2010, he entered the Interdepartmental Microbiology Graduate Program, where he rotated between three different labs, ultimately matching with Scharf, an assistant professor of biological sciences in the College of Science and a Fralin Life Science Institute affiliate.
“Ben contributed greatly to the success of my lab, not only because of his scholarly accomplishments, but also due to his engaging personality,” said Scharf. “I am extremely thankful that Ben shares my passion for mentoring. It was wonderful to watch the seed that I planted to germinate and fully develop, and I am looking forward to seeing Ben continuing our devotion for nurturing future seeds.”
Webb has five first author publications, and won the award for ‘Outstanding Talk by a Graduate Student’ at the Bacterial Locomotion and Signal Transduction meeting in 2015, according to Scharf.
“His excellent presentation skills are just one reflection of his dedication to teaching. Ben has advised seven undergraduate researchers in my lab by enabling them to grow and succeed,” said Scharf.
In 2015, Webb received the Noel Krieg Graduate Fellowship for excellence in teaching and research from the Department of Biological Sciences at Virginia Tech. He is one of the first recipients of the fellowship, which honors Noel Krieg, an Alumni Distinguished Professor Emeritus of Biological Sciences.
“Ben has the kind of teaching style that helps you grow as you learn. He helps you use the tools and abilities you already have to solve problems, which ends up yielding an understanding of both your work and yourself,” said Karl Compton, Webb’s former student. “He is exceptionally friendly and personable to everyone who comes into lab. If I had to use one word to describe him, it would be nurturing. In the future, it is my hope (though it may not necessarily be his own) that he does something that at least in part involves helping and teaching others - it is something of a gift he has.”
In 2016, Webb received the John Johnson Award for Excellence in Microbiology from the Fralin Life Science Institute at Virginia Tech. He is actively involved with the newly revised Integrated Microbiology Program (IMP) and the Translational Plant Sciences (TPS) program at Virginia Tech.
Posted September 8, 2016
By Lindsay Key
Q&A: Meet Ben
B.S., Biological Sciences with Biotechnology Concentration, Virginia Tech
Ph.D., Biological Sciences, Virginia Tech
Fralin Advisor: Birgit Scharf
Why do you want to be a scientist? When did you know?
There are many great reasons for me to be a scientist. One of the reasons I value the most is how being a scientist allows me to open my mind and understand new perspectives. Interestingly, I knew this about two years into my Ph.D. studies, not before I started my studies.
What attracted you to your particular field of science?
I was attracted by ability to actually see bacteria and watch them swim through their environment. This behavior was shown to me in Virginia Tech’s Microbiology laboratory class.
Your best Eureka! Moment (when something cool happened in your research):
This happens often… When I stay up late hypothesizing with colleagues. The ideas formed during those impromptu brain-storming events lead to great “Aha!” “of course!” “duh!” “Eureka!” moments. But then I get to test those ideas and if everything goes as planned, great. If not, then it’s back to hypothesizing.
What are your ultimate career goals?
Find ultimate freedom (a sign of the times, perhaps?)
Favorite hobby outside of school?
Exploring the woods
What's so great about the Fralin Life Science Institute?
Ooo, I don’t know that I have enough room here to answer that. There are many things that are great about FLSI. I’ll just list them here in no particular order…
The friendly vibes
Horace, the OG
The photos by Kristi
Lindsay and Cassandra**
The scientific amenities
The occasional free food
The climbing trees around Fralin Hall
**Bonus points for that one, Ben. Thanks for talking to us!