Explore the videos below to learn more about our research efforts, technologies and facilities.

The Center for Root and Rhizosphere Biology at Penn State University

Here we provide an overview of ongoing research in the Center for Root and Rhizosphere Biology (CRRB) in the Huck Institute of Life Sciences at Penn State University. Special thanks to Cole Cullen, Creative Director at WPSU who directed and developed this video for the CRRB.

- [Speaker 1] So the Center itself is a group of faculty and I'm part of that. And our mission is really to improve plant health by focusing on roots in particular and root research and science.

- [Speaker 2] Currently we have over 850 million people around the world who are suffering from food insecurity. And as we gain another additional 2.3 billion people moving over the next 30 years, most of this growth is going to occur in regions that are already food insecure. And we're going to have to increase our food production by an estimated 50% to meet this increased demand from a growing population. So really the overall goal of this center is to address these issues of food insecurity in developing areas as well as to help agriculture. And the focus is really ultimately on root systems of major crop species.

- [Speaker 3] Roots are really hard to study. They're hidden, they're underground, and it's really hard to actually measure what matters to plants. But they're really important, because they're actually grabbing the resources, the water, the nutrients that are really essential for plant growth. And so this is a really sticky problem. It's an interdisciplinary problem. And so what we're trying to do is by bringing people from engineering and plant science and biological sciences and bringing all these scientists together, we're trying to create new methods and new paradigms to study that research at PSU.

- [Speaker 4] So in my work, I explore the natural diversity of maize landraces. These are corn varieties which are still grown and curated by indigenous communities around the world. So corn was first domesticated about 9,000 years ago in southwestern Mexico in a relatively restricted area. Very quickly, it diversified and it expanded out to this area as the efforts of the first farmers took corn and allowed it to adapt to many, many different environments, both into the highlands, up to the mountains of central Mexico, south into South America, up again into the mountains of the Andes and obviously up into North America, as far as Canada. Today corn is a global crop and it grows really across the world. And it's proved itself to be very, very adaptable. Understanding how this is possible and what corn has done in the past to adapt to new climatic challenges clearly can provide us lots of valuable lessons as we go forward and strive to continue to make this a crop that we can use in the future. So for any plant root system, the plant can invest either in the roots or in the leaves. Different plants will do this differently. With inside the root, the root effectively is functioning as a pipe, collecting the plant to the soil. And we can see differences in the internal plumbing of the root system. This gives differences in the way which water is taken up and used. In the field, we look to explore the diversity of such varieties, both in the way they look and they perform, directly looking at their root systems. But nowadays also looking at their genomes. By analyzing the DNA of these varieties, we can start to learn both how and why these plants are different and special.

- [Speaker 5] Plants are so important, especially as a food source for all of humanity, as we know. Food security is a big issue. And that basically means that not everybody has access to food or has access to food that's affordable. And some of the issues with growing plants is making sure the plants are healthy, that they grow fast, that farmers can grow them at a good price and that they're available for everyone. So I work really on trying to understand what little microbes, what bacteria, what fungi in particular, what viruses infect plants, make them sick and kill them. And I run experiments both in the field and also in the greenhouse and in the lab on understanding this question: Can we figure out early rapid diagnosis of diseases? Just like in humans, we want to know early on so we can treat something before it gets out of hand. Same thing with potatoes, with grapes, with all these different crops. We want to detect it early. One way that we do that is by using the DNA of the microbes to say are the microbes there and to create assays for detection.

- [Speaker 6] Our research in this lab, my research specifically, is focusing and trying to identify genetic variation for the root system in major crop species like maize or common bean. And just as there's genetic variation for all different traits in many different species, there's also genetic variation for the efficiency of root systems in acquire- in accessing and acquiring and taking up important resources for them to produce optimal yields. A lot of what my work involves is we'll grow a large variety of, say, maize, essentially trying to, in our field environments and greenhouse environments, replicate these stressful conditions that many crops are experiencing around the world in terms of drought or nutrient stress, and then excavate the root system and look at specific root traits, whether that be the architecture or placement of those roots within the soil profile or the anatomy of those roots, which can affect things like the acquisition and uptake of resources, or the metabolic efficiency of soil exploration, and characterize these different traits within the root system under stressful environments and see how these different traits relate to performance of important crop species under these stressful circumstances that we're simulating in our greenhouse or field trials. One tool that we use here at Penn State University is termed laser ablation tomography. This is a novel technology that's been developed here at Penn State university. And what we're able to do is it allows us as a research group to look at the anatomy or the different arrangement of cells within roots and characterize genetic variation for that anatomy and how that anatomy relates to performance in the field. And we can do this in a very high-throughput way, which allows us to screen hundreds and hundreds and hundreds of samples a day, which really then was previously a bottleneck to people within the breeding community and identifying genetic variation for anatomical traits.

- [Speaker 7] I come from a traditional evolutionary ecology background. I study how plants and microbes and climate interacts to determine how plants grow and what they do. And one of the reasons I came to PSU and into the Plant Science department is because I want to apply that fundamental research processes and questions to solving agricultural problems. And so in particular, I study legume-rhizobia interactions. And so these alfalfa behind me are an example of these legumes and rhizobia. And they're really special, because it's a plant-microbe interaction that actually fertilizes the plant. In this particular trial, these plants have been growing here for five full years. They have been putting out roots, they've been forming nodules and they've been enriching the soil for the rhizobia that actually fix nitrogen for them. And this happens over and over and over. And we know almost nothing about what's actually happening in the soil here. And I want to figure it out. I want to figure out if the 20 different varieties of alfalfa that are creating this alfalfa trial are actually selecting differently on the strains that are associating with them. And if this is actually an evolutionary mechanism that we can leverage to breed for alfalfa plants that are able to get better nitrogen out of their rhizobial partners. And we've actually developed new methods in the last four or five years where we can actually test this in the field and we can see if this is a new trait that we should be breeding for in agricultural systems. I'd really love if we could take these evolutionary principles that we've been studying for decades and apply them to solve our fundamental agricultural and plant health production problems of the future in ways that create sustainable agroecosystems that require less inputs and less resources to solve some of our problems.

- [Speaker 1] I'm not kidding when I say I wake up and I'm real excited to go to work, because I'm gonna be meeting with all these amazing experts and together we're gonna try to solve these problems in food security. And I'm not gonna do it alone. And that's why I'm part of this Center for Root and Rhizosphere Biology. There are multiple faculty who have different expertise. I'm one piece of that puzzle, but it's really wonderful to work with people who together, we can try to solve these questions.

- [Speaker 2] It's really fulfilling to see that there's actual impact to this work. And it's actually going to be improving the lives and food security of people around the world.

Novel application of lasers in plant science research at Penn State University

Developed in the Roots Lab at Penn State University, laser ablation tomography is a novel method that allows for rapid, three-dimensional quantitative and qualitative analysis of plant anatomy.

Hi everyone. Welcome to the laser ablation tomography facility that we have housed here in the Department of Plant Science at Penn State University. Behind me you can see the latest iteration of a tool that we use for visualizing plant anatomy. It’s a really interesting technique that generates a lot of interest whenever we present data generated from this methodology at meetings or in academic journals. We get a lot of questions about what it is, how it functions, and the capacities that it can be used for. So to address all of these questions, I thought it would be easiest to summarize all of this in a video that shows you how the system works and how it can be used.

 Our group is most interested in visualizing both the root and shoot anatomy of major crops like bean, maize, and rice. We are looking at different anatomical features, specifically in the root system, that can help these major crops in both acquiring and more efficiently utilizing important resources like water, especially under drought scenarios, as well as important macronutrients like nitrogen and phosphorus, which can often be limiting in many agricultural soils. 

 Here we can see a general schematic of the laser ablation tomography system. Its base is a UV laser source which is projected at 355 nm, and it occurs at a pulsed repetition rate somewhere between 25 kHz and 40 kHz, which is appropriate for most of our samples. This laser is directed through some beam shaping optics, and then into a galvanometer which is used to oscillate the beam over a linear distance to create a cutting sheet. We then have a biological sample that is moved into the path of the beam by a motorized stage, and as the sample is ablated by the beam, a digital camera that is fitted with a macro lens is imaging each illuminated slice in real time.

 Here we can see the laser source, with the beam path being directed by a series of mirrors and shielded from the user by these opaque tubes. The metallic box is the galvanometer which rapidly oscillates the beam back and forth to create a cutting sheet that ablates the sample positioned below at the focal plane of the camera.

 Another feature of the laser ablation tomography system is its capacity for differentiation of spectra from different tissues under UV excitation. Red, green, and blue channels can be measured from tissues illuminated by the UV laser, and dominant emission wavelength can then be determined from these data to provide some information on the composition of the tissue. For example, here we can differentiate between the chitinous cell wall of arbuscular mycorrhizae colonizing this maize root sample, which is highlighted in red, and the auto-fluorescent spectra emitted from the lignin and cellulose based walls of the plant tissue. 

Laser ablation tomography also allows for three-dimensional visualization and quantification of features in samples. Image stacks of a sample can be compiled into 3D reconstructions, similar to Z stacks in confocal microscopy. While Z stacks generated through confocal techniques are ideal for cellular level visualization, the depth that’s able to be visualized using traditional microscopy is limited by the opacity of the tissue. Although laser ablation tomography does not have the same resolution of a microscope, it is ideal for tissue level visualization on the scale from 0.1 mm to about 1 cm, and three-dimensional reconstruction of large opaque tissue samples is possible.

Studying Drought Stress in the Field at Penn State University

Here we provide an overview of our research on drought at Penn State University's Russell E. Larson Agricultural Research Center, including a brief explanation of some of methods used in our work.

Hi, welcome to the Russell E. Larson Agricultural Research Center out here at Rock Springs, Pennsylvania. We’re just a couple miles from Penn State University’s main campus, and this is the site where we perform a lot of our field-based studies to investigate some of the physiological adaptations in root and shoot tissue that help major field crops like corn and bean perform well under drought scenarios, as well as soils that are limiting in both nitrogen and phosphorus. 

Behind me here you can see some of these specially managed fields we have to mimic a terminal or intermittent drought scenario. These are what we refer to as “rainout shelters”, and they function as large greenhouses that can move over our experimental plots along these rails every time a rain event occurs. Then as that rain event terminates, these shelters will move back off of the plots and allow normal climatic conditions to exist above these fields. So, we get normal evapotranspiration rates occurring when these structures are off the plots, but we can move them over to inhibit rainfall.

The movement of these rainout shelters is automated by rain sensors, programmed to move the shelter over the field when they detect rainfall and off the field when it dries. 

To help us monitor soil moisture throughout our fields as we impose drought and as drought progresses throughout our field trials, we utilize what are called time-domain reflectometry probes or TDR probes. These function by hooking them into a computer system with software that sends an electrical pulse down these cables and into probes we have buried at various depths throughout the field, and the resistance of that waveform that goes down this cable and into the soil tells us something about soil moisture. Additionally, we use other methods like gravimetric soil moisture that we collect using these types of cores, where we can collect physical samples and bring them back to the lab and get information on gravimetric water content by weighing the fresh sample, drying that soil sample out, and then weighing it again to see how much water was in the original sample when it was freshly collected.

Estimates of aboveground shoot biomass can be determined from stem diameter, taken at the base of the shoot just above the emerging brace roots. For this measurement, we can use a caliper.

Similarly, record of plant height also correlates strongly with aboveground biomass.

Time of flowering and the anthesis silking interval can have significant effects on yield under drought stress. Consequently, diligent record of days to flowering and the time between pollen shed and silk emergence for all varieties being evaluated, is essential

To help us measure parameters like carbon assimilation, transpiration, stomatal conductance, and leaf temperature, we can utilize this instrument here, known as the Licor-6800.

To help us better understand the mechanisms of drought adaptation that may exist among the different varieties we are evaluating in our drought trials, we can utilize metrics like leaf relative water content. For this metric, we would take leaf punches throughout the newest, fully expanded leaf in the canopy of a given variety. We would take several of these punches and store them in these airtight containers, then take these back to the lab to get the fresh weight of these discs. We would then suspend these discs in deionized water so they can absorb additional water they may have expelled through transpiration, and then we will dry and re-weigh these samples so we will get the fresh weight, the turgid weight and dry weight of these samples. 

How efficiently different varieties utilize the water they take up through their root system is largely dependent upon the anatomy of their leaves. We collect leaf anatomy samples for evaluation back at the lab to explore different components like stomatal density and stomatal size on the surface of the leaf, as well as a lot of the anatomical features that can be visualized within the leaf. Leaf samples collected for anatomical analysis are cut to include part of the midrib as well as the leaf lamina and are preserved in 75% ethanol.

To help us understand the degree of stress that plants are experiencing in our drought trials, we utilize this tool which is known as a pressure bomb or Scholander bomb. To understand how this device works, you need to know something about how water is transported through plants. So just a brief overview, plants are acquiring water from the soil through their roots, and they are transporting that water through a series of hollow cells, or tubes, known as xylem vessels. That water is transported in a continuous column of these xylem vessels from the roots, to the stems, and into the leaves where that water is then transpired out of the stomates during photosynthesis. As water is transpired out of these leaves during photosynthesis, water needs to be continuously pulled out of the soil, through these xylem vessels in the roots, the stem, and the leaves. This negative tension that exists throughout the entire plant can be measured using this device. Under drought stress where there is less available water in the soil, that negative tension throughout the entire plant where they are trying to pull up that water from the soil through the roots, stems, and leaves, is more severe than under more well-watered scenarios where there is more available water in the soil and less negative tension that exists throughout this column of water where plants can more easily transport that water from the soils, to the roots, to the shoots, to the leaves.

This device is able to measure that negative tension by taking a leaf sample and placing it in a pressurized chamber. What we are measuring is the amount of pressure that it takes for xylem sap to be extruded out of a cut surface of that leaf. The amount of pressure it takes for that sample to extrude sap out of the cut surface is equal and opposite to the amount of tension that exists throughout that plant. 

Under circumstances of drought stress, shallow soil horizons are the first to dry and often plant available water can still exist at depth even as drought progresses through the season. Therefore, crop varieties that have deeper distribution of their roots can access these water reserves later in the season and can often perform better in term of yield, compared to varieties that have a shallower distribution of their root length within the soil. To help us understand the genotypic differences that exist among different varieties in terms of their root distribution by depth, we utilize soil coring. Here we can place one of these soil coring tubes into the soil and extract a soil core that is contained in this metal tube. That soil core sample is then transferred to one of these sample holders and we will take this back to our lab at Penn State, divide this into increments by depth, and wash away the soil from the root length that has been captured within the soil core. This helps us to understand how different crop varieties have differences in root length distribution by depth, and then we can relate that to how well these different varieties perform under drought scenarios in the field. 

Since roots are directly responsible for soil resource capture, our group is particularly interest in genetic variation for root traits that may affect how efficiently different crop varieties acquire and utilize water under drought. To measure different components of root architecture and collect samples for anatomical analysis, roots must be excavated and washed in the field.

After soil is washed from the root crowns, shoots are separated from the roots and subsequently dried for measurement of aboveground biomass.

Here we can see some of the genotypic variation that exists for maize root system architecture. The root crown on the left has a higher degree of gravitropism in its nodal roots, which can provide a benefit under scenarios of drought stress by placing roots in deeper soil domains where water is more available. The root crown on the right has a lower degree of gravitropism and consequently will have a shallower distribution of roots and less access to water at depth.

Here we have a fresh maize root crown that was just excavated from the field, and we’ve taken it back to the lab to collect root samples. We will subsequently look at the anatomy of these root samples to identify genetic variation for anatomical traits that may affect how efficiently different varieties acquire and utilize water under drought. For example, genetic variation for anatomical traits like xylem vessels may affect how well different varieties transport water through the plant, and ultimately may impact yield under drought stress

Maize Root Anatomy Sampling

In this video we provide an overview of our methodology for collecting samples from the maize root crown for anatomical analysis.

Since roots are directly responsible for soil resource capture, our group is particularly interested in genetic variation for root anatomy that may affect how efficiently different crop varieties acquire and utilize resources like water, nitrogen, and phosphorus. To collect samples for anatomical analysis, roots must first be excavated and washed in the field.

Here we have a fresh maize root crown that was just excavated from the field, and we’ve taken it back to the lab to collect root samples for anatomical analysis. At first glance this maize root crown may look like one big tangle of roots, but upon closer examination we can see how the root system is organized into distinct root classes. 

Here we can see the mesocotyl, where the seed initially existed, and the primary root which emerged from that germinating seed. The rest of the subterranean roots you see in this crown are referred to as nodal roots and upon closer examination we can see they are organized into distinct rings or “whorls”. 

Here we see the first whorl of nodal roots. These are the oldest nodal roots in the crown, and are the first nodals to emerge after germination. As the plant goes through its vegetative stage of growth, new, subsequently thicker, nodal roots are emerging above the older roots in the crown. 

So here is the second whorl, third whorl, forth whorl, and then fifth whorl nodal roots. These pigmented roots, which were emerging above the soil surface, are called brace roots. 

Because these nodal roots are developing over time while stresses like drought may be becoming more severe through plant growth, our group is interested in collecting anatomy samples from across these different whorls to look at how the anatomy may change from whorl to whorl. 

A sharp set of pruners are an ideal tool for removing roots from the crown. It is important to be consistent in sampling location from crown to crown and we typically focus on the basal-most 2 cm of each nodal root, right where they emerge from the crown.

Anatomy samples collected will be stored in 2 ml tubes filled with 75% ethanol. This will preserve the root samples until we can image the anatomy of these roots using our laser ablation tomography system at a later date. Using our laser system, no additional prep work to fix or stain samples will be needed, and they can be sectioned directly from storage in the ethanol solution.

Genetic variation in the anatomy of these maize roots may affect the metabolic efficiency of the roots in foraging soil resources, the ability of roots to penetrate strong soils, or the transport of soil resources through the roots to the shoot. Anatomical features of interest from these samples include the size and abundance of cortical cells, xylem vessels, and air pockets in the cortex known as aerenchyma.