An interdisciplinary team of researchers from the Georgia Institute of Technology has received a $2 million federal grant to create tools that will provide the clearest three-dimensional images yet of the chemical and biomolecular interactions between plants and the soil in which they grow.

At just a few inches underground, the rhizosphere — the thin strip of earth that includes the soil-root interface — has so far been difficult to visualize on site. If scientists can build instruments that capture in real-time clearer images of the physical associations of microbes attached to roots, along with the oxygen-carbon-nitrogen chemical exchanges they mediate, it could help mitigate the effects of climate change and lead to the development of more sustainable fuels and fertilizers.

“From a microbiological perspective, we have catalogued what microbes are in the root zone and how abundant they are,” said Joel Kostka, professor in the School of Biological Sciences and School of Earth and Atmospheric Sciences at Georgia Tech. “But there's been very little work to understand their dynamics under real soil conditions.”

Kostka, who also serves as associate chair for Research in Biological Sciences, joins Marcus Cicerone, professor in the School of Chemistry and Biochemistry and principal investigator for the new grant from the U.S. Department of Energy’s Office of Biological and Environmental Research. The research team also includes Francisco Robles, assistant professor in the Wallace H. Coulter Department of Biomedical Engineering, and Lily Cheung, assistant professor in the School of Chemical and Biomolecular Engineering in the College of Engineering.

Together, the researchers plan to produce a new optical instrument that will provide 3D images of dynamic metabolic processes with chemical specificity — meaning it will be able to identify carbon sources (sugars, organic acids) exuded by plant roots and nitrogen-rich compounds provided to the root by nitrogen-fixing (diazotrophic) microbes. The instrument will be built with commercially available components, and with an eye towards simplicity so that it can be easily leveraged by Department of Energy (DOE) Bioenergy Research Centers and field sites.

A ‘hotspot for microbes’ in 3D

Understanding more about the metabolic processes happening in the rhizosphere will help the DOE develop a wider range of sustainable products like new types of biofertilizers and biofuels. The research will also help create practices for better crop management — and will help researchers use plants and soil as more effective carbon traps that sequester greenhouse gases from the atmosphere into the soil.

“The problem is that we don’t know much about the free-living bacteria in the soil, because we can’t get in there and look,” Cicerone said. “The DOE wanted somebody to build an instrument that would allow them to image or gather information about the metabolic processes, the interaction — the metabolic interactions between the microbes and the plants, in real time.”

Kostka adds that the rhizosphere is “a hotspot for microbes.”

“It’s often where the plant is communicating with the outside world,” he explained. “Our goal is to develop an instrument that they (the DOE) can use to better understand those interactions between plants and microbes and how those can be tweaked, say, to optimize plant production, crop production, biofuels and biomass production. And that's the long-term goal for us.”

How light gets scattered, smothered, and covered in soil

Cicerone says the visibility issue with soil involves how photons — or particles of light — scatter once they hit the soil. He likens it to someone putting a red light up to the back of their thumb.

“You turn your thumb around, your thumb glows red, right? So, the light comes through, but most of it scatters. The unscattered light contains the spatial information, but it is so weak that you can’t detect it by eye, and you lose the spatial information. The same thing happens with the soils. You get a lot of light scattering, and you lose spatial information,” Cicerone said.

Cicerone and Robles will build instrumentation that will focus light into the soil and that is “exquisitely sensitive to the minuscule amount of light that only scatters when it reaches its target.” Evaluating that light will help scientists learn even more about the chemical processes in the rhizosphere.

The visibility enhancements will be implemented in optical techniques with names like coherent Raman scattering and optical coherence tomography, which are commonly used for non-invasive imaging of thin biological material, like the retina of the eye — or the tiniest of plant roots.

“We learn two things from the light coming out of the sample. The amount of light coming out tells you about the refractive index of the material, and the light’s frequency change tells you about the chemical composition of the material,” Cicerone explained.

It’s through imaging and then optimizing those microbe-plant interactions that the DOE aims to design more sustainable products and practices, based on the chemistry to be learned from the team’s new optical instruments.

“This is a three-year funded project, and we hope at the end of the three years to have an experimental system, where we can do something that nobody else can do,” Cicerone added. “And that is that we can follow the biochemistry under the soil, in situ, in real time, to clearly see what's going on there and find out what the microbes really are doing in natural conditions. At that point, we can start manipulating the biology, start doing the experiments that the DOE is primarily interested in.”

Award Number: DE-SC0022121
Title: Deep Chemical Imaging of the Rhizosphere
Institution: Georgia Tech Research Corporation, Atlanta, GA
Principal Investigator: Cicerone, Marcus

About Georgia Institute of Technology

The Georgia Institute of Technology, or Georgia Tech, is a top 10 public research university developing leaders who advance technology and improve the human condition. The Institute offers business, computing, design, engineering, liberal arts, and sciences degrees. Its nearly 40,000 students representing 50 states and 149 countries, study at the main campus in Atlanta, at campuses in France and China, and through distance and online learning. As a leading technological university, Georgia Tech is an engine of economic development for Georgia, the Southeast, and the nation, conducting more than $1 billion in research annually for government, industry, and society.

By Frida Carrera

As one of the nation’s leading research institutions, Georgia Tech has always emphasized the pursuit of progress and service in its research endeavors. With such a strong focus on research, it is only right that many students at Tech have seized their opportunities to make an impact on the real world and solve complex problems. Taking initiative, asking the right questions, and being passionate about making a positive impact are innate characteristics that make a researcher, and Georgia Tech has in no way come short of giving rise to many exemplary researchers. The following undergraduate student researchers are serving as catalysts for innovation and development in their respective fields and are representative of Georgia Tech’s mission in developing leadership and improving the human condition. 

Prahathishree (Premi) Mohanavelu is a 5^th-year Computer Science major with a Pre-Health concentration. She conducts research with Dr. Cassie Mitchell in Biomedical Engineering on informatics-based literature mapping to personalize therapy for Chronic Myeloid Leukemia. 

“I was really looking for a way to apply the concepts I was learning in my computer science classes to the field of healthcare, and I felt this position was the perfect fit for that.” 

One of her main reasons for conducting this research was her interest in medical innovation. Premi believes the future of medicine will rely on preventative care and says her research position has also helped her with oral presentation and communication skills. Premi also serves as president of the Undergraduate Research Ambassadors and utilizes her research role and experience to teach prospective research students the ins and outs of obtaining research knowledge.

Yiyang (Diana) Wang is a 4^th-year Computer Science major conducting research with Dr. Jennifer Kim on contact tracing visualization tool design and implementation. Her research is applicable to easily contracted illnesses including COVID-19. Yiyang believes her research will help people understand the importance of contact tracing and how data collection, for contact tracing purposes, could be beneficial. Yiyang’s goal is to become a software engineer and wants to focus on improving technology for the benefit of the user. Yiyang thanks the Undergraduate Research Opportunities Program (UROP) for obtaining her position as it was a major resource for her in finding and landing her current research position. 

Milan Riddick is currently a 5^th-year Biomedical Engineering major with a minor in Health, Medicine, and Society conducting research with Dr. Jennifer Singh in the area of History, Technology, and Society on the mistrust of the COVID-19 vaccine among black citizens of Georgia. Milan has been the primary lead in her own research and has combined her passions for medical sociology and research to do what she loves. From proposing, securing funding, recruiting, and interviewing, Milan had a vision from the start and hopes to understand and improve the trust disparity between black Georgia citizens and the COVID-19 vaccine. Milan hopes her current research will aid with the trust between people and medicine as well as securing her path to graduate school.

William York is a 4^th-year Biomedical Engineering major with a concentration in Pre-Health. He is currently conducting research with Dr. Edward Botchwey on using biomaterials to immunomodulate muscular defects for tissue regeneration. He believes his research is important because it will aid in the initiative in potentially replacing stem cells with exosomes in stem cell research while retaining the same regenerative effects and creating fewer risks. William wasn’t sure about research when he first arrived at Tech, but after learning the opportunities and resources UROP had for undergraduate students, he quickly became involved. William is now currently in the Research Option program and is also an Undergraduate Research Ambassador providing guidance to students also interested in research. 

Hannah Shin is a 3^rd-year Biology major with a concentration in Physiology and is conducting research with Dr. Colin Harrison on measuring the organization of biological knowledge around experimental design utilizing a card sorting task. Hannah’s research uses its results to identify the weak areas in biology programs and make the necessary revisions to instruct students more effectively. Hannah believes her research will also aid her in future endeavors. 

 “My career goal is medical school and I believe my research will advance both my academic and career goals because it exposes me to real-world applications of data analysis and allows me to dive into the differences in knowledge organization among people of different backgrounds.” 

 Hannah is also a participant in the Research Option program and is the executive vice president of the Undergraduate Research Ambassadors. She uses her research and personal experience to help students gain confidence in pursuing research they are passionate about. 

Read more about Undergraduate Research opportunities by going to http://urop.gatech.edu. 

Atlanta is often called the “city in a forest” because of its lush canopy of trees, uncommon for a major city. In the heart of that forest sits Georgia Tech’s 400-acre campus. And within campus lies a variety of wildlife that has made Georgia Tech its home.

“I don’t think most people are aware of wildlife on campus,” said Emily Weigel, senior academic professional in the School of Biological Sciences. “They might see a feral cat here or there, but they don’t really think about all the other animals that live on campus. Georgia Tech is the animals’ home base, and they probably don’t know anything other than they were born in this area. They don’t know they’re in the middle of a city.”

Included in the biodiversity surveys of the area are squirrels, possums, raccoons, rats, and birds. Several months ago a couple of coyotes were spotted, but they were just passing through campus. At least two foxes live in the glade, a densely forested area behind the president’s residence on the north side of campus.

Ben Seleb, a Ph.D. student in quantitative biosciences, is developing an open source camera for studying the foxes and other wildlife. He and his colleagues at Tech4Wildife, a course and campus organization devoted to the conservation of wildlife, have been monitoring the foxes.

“We had some suspicions that foxes were in the glade,” Seleb said. “It’s a very secluded area with dense vegetation, so it’s a great spot for campus wildlife to hide during the day and then come out at night.”

To confirm their suspicions, they set up cameras inside the glade and left them for a couple of weeks. When they reviewed the images, they had captured two foxes on camera at the same time.

“We know there could be more, but we’ve only seen two foxes at one time. They’re difficult to tell apart, but we’re working on identifying individuals,” he said. “There are a number of other animals on campus, and the glade is where many of them live. We have seen raccoons, possums, and a couple of feral cats that travel in and out of the glade.”

The glade connects to Tech’s new EcoCommons, a lush 8-acre woodland area near the center of campus, providing a pathway for wildlife to travel into campus at night, while still giving them the cover of vegetation. Georgia Tech generally offers a handful of classes related to wildlife or ecology, but the amount of wildlife on campus is creating new research opportunities.

“I’m happy to see programs giving students opportunities that they may not have been aware of,” Seleb said.

For his latest research on motor skills, visual learning, and their effects on human physiology, School of Biological Sciences associate professor Lewis Wheaton and his team went all the way back to the Paleolithic Era to study a very retro skill: stone toolmaking.

“One of the cool things about this particular study,” Wheaton says, “is this opportunity to look at a completely novel motor task, something most people have no idea how to do, and that’s making a stone tool.”

The new research, published today in Communications Biology, attempts to fill in the gaps when it comes to the science of how we learn complex motor skills — and what may be required to relearn them. 

Wheaton says there are studies researching the behavioral changes that are involved with learning complex skills. But research is still thin on how people adapt their visuomotor skills (how vision and movements combine) to carry out a complex task. Wheaton’s current study sought to quantify and evaluate the changes and relationship in action perception processes – how we understand actions, then select, organize, and interpret what needs to be done for a particular task. 

“The overall motivation was to determine if we could see any kind of emerging relationship between the perceptual system and the motor system, as somebody is really trying to learn to do this skill,” Wheaton says. Those are important processes to understand, he adds, not just for how people attain complex motor skills learning, but what would be needed for motor relearning, as in a rehabilitation setting.

Wheaton conducted the research with graduate students Kristel Yu Tiamco Bayani and Nikhilesh Natraj, plus three researchers from Emory University’s Department of Anthropology.

Tracking the eyes to learn about learning 

The test subjects in the study watched videos of paleolithic stone toolmaking for more than 90 hours of training. The subjects’ visual gaze patterns and motor performance were checked at three different training time points: the first time they watched the video, at 50 hours of training, and at approximately 90 hours. Everybody was able to make a stone tool (with varying degrees of success) at 90 hours, but some picked up the skills at 50 hours.

Wheaton says there was a lot of information to pay attention to in the videos. “There’s a lot of physics in (making stone tools). You’re hitting a rock which is made up of all different kinds of material. There could be a fissure or fault lines, and if you hit it the wrong way it could crumble. When you’re doing it at first, you don’t know that.”

As the video training went on, the participants started to pick up cues about how to strike the rock, along with other aspects of toolmaking. “At first you’re watching from curiosity, then you’re watching with intent.”

That was the exciting part for Wheaton and his team: Being able to see the different phases of learning during the training — which they actually could see by monitoring gaze tracking, or where the subjects’ eyes landed on the video screen as they watched (see photo.)

“Part of the study was to understand the variability where they are visually focused as they get better at the task,” he says.

That’s how Wheaton’s team found there are certain parts of the skills learning that connect better to gaze, but others that connect better to the physical act of making a stone tool. “As you’re going through time, your motor abilities are changing, and at some point that allows you to watch somebody else perform the same task differently, suggesting you’re able to follow the action better, and pull more information from the video in a much clearer way.”

The study not only found a connection between gaze and motor skills learning, but that the connection evolved as the learning went on. The next step in this research, Wheaton says, should include brain imaging “heat maps” to determine where learning takes place with this process. 

That could also help Wheaton’s team apply these lessons for rehabilitation purposes.

“That’s the link between that and some of the other work we’ve done in a rehab context,” he says. “If you’re watching somebody perform a task, if you’re undergoing rehab, there are different ways you’re watching the task. You’re not always watching it the same way. Maybe it depends on how good you are, or how you’re impaired, but all those variables play a role into what you’re visually pulling out” of the rehab training.

DOI: doi.org/10.1038/s42003-021-02768-w

Tara Holdampf is the new College of Sciences satellite counselor, and will provide consultation services and support for students from an office at the Molecular Science and Engineering Building (MoSE). 

“I'm excited to join the incredibly welcoming and talented group at the College of Sciences at Georgia Tech as a satellite counselor,” Holdampf says, “to continue the process of breaking down barriers between students and mental health services.”

Satellite counselor locations improve accessibility for students by providing counseling in places where students spend most of their time. Placing a counselor in an academic department helps to destigmatize mental health and may serve those who might hesitate to go to the Georgia Tech Counseling Center. A primary goal is to reach students who might not have otherwise sought out services. 

Holdampf will provide a wide variety of services such as individual counseling, group counseling, psycho-educational workshops, and walk-in hours for brief consultations (available to students, or faculty/staff who need to consult about a student). 

Holdampf issues a reminder that “as stress levels increase, and the fall semester continues, please know that GT CARE and GTCC are here to offer confidential support and services to students in need of mental healthcare.”

Currently enrolled interested students can reach out to GT CARE at (404) 894-3498 to schedule an initial assessment, and to be connected to health and wellness services. Current clients can continue to reach their GTCC counselor via email.

Holdampf will be offering consultation hours during which students, faculty, and staff can meet to learn more about mental health resources on campus, and/or to discuss a specific non-emergency student concern. These consults typically last 15 minutes. Those interested can email Holdampf at tara.holdampf@studentlife.gatech.edu to request a meeting. Holdampf will respond with a date/time and link/location for the consultation.

Find Tara's consultation hours and more resources here.

Students in need of mental health support after hours can call the GTCC main number at 404-894-2575, and follow the prompts to speak with an after-hours counselor.  Please visit the GTCC website for upcoming workshops, Let’s Talk sessions, and online offerings.

Holdampf, who has practiced in a higher education setting for seven years, has an M.S. in Clinical Mental Health Counseling and is a Licensed Professional Counselor in Georgia. Holdampf is also a Certified Clinical Trauma Professional and serves on the council of the Georgia College Counseling Association.