Author Archives: Lisa Hildebrand

The non-Ghostbusting Venkman: a virus that “eats” marine bacteria

Have you ever considered that a virus that eats bacteria could potentially have an effect on global carbon cycling? No? Me neither. Yet, our guest this week, Dr. Holger Buchholz, a postdoctoral researcher at OSU, taught me just that! Holger, who works with Drs. Kimberly Halsey and Stephen Giovannoni in OSU’s Department of Microbiology, is trying to understand how a bacteriophage (a bacteria-eating virus), called Venkman, impacts the metabolism of marine bacterial strains in a clade called OM43.

Bacteria that are part of the OM43 clade are methylotrophs, in other words, these bacteria eat methanol, a type of volatile organic compound. It is thought that the methanol that the OM43 bacteria consume are a by-product of photosynthesis by algae. In fact, OM43 bacteria are more abundant in coastal waters and are particularly associated with phytoplankton (algae) blooms. While this relationship has been shown in the marine environment before, there are still a lot of unknowns surrounding the exact dynamics. For example, how much methanol do the algae produce and how much of this methanol do the OM43 bacteria in turn consume? Is methanol in the ocean a sink or a source for methanol in the atmosphere? Given that methanol is a carbon compound, these processes likely affect global carbon cycles in some way. We just do not know how much yet. And methanol is just one of many different Volatile Organic Carbon (VOC) compounds that scientists think are important in the marine ecosystem, and they are probably consumed by bacteria too!

Depiction of the carbon cycle within the marine food web. DOM means Dissolved Organic Material, POM stands for Particulate Organic Material. This refers to all the things that are bound within cells that gets released when for example viruses destroy cells. 

All of this gets even more complicated by the fact that a bacteriophage, by the name of Venkman, infects the OM43 bacteria. If you are a fan of Ghostbusters and your mind is conjuring the image of Bill Murray in tan coveralls at the sound of the name Venkman, then you are actually not at all wrong. During his PhD, which he conducted at the University of Exeter, part of Holger’s research was to isolate the bacteriophage that consumes OM43 bacteria (which he successfully did). As a result, Holger and his advisor (Dr. Ben Temperton, who is a big Ghostbusters fan) were able to name the bacteriophage and called it Venkman. Holger’s current work at OSU is to try and figure out how the Venkman bacteriophage affects the metabolism of methanol in OM43 bacteria and the viral influence on methanol production in algae. Does the virus increase the bacteria’s methanol metabolism? Decrease it? Or does nothing happen at all? At this point, Holger is not entirely sure what he is going to find, but whatever the answer, there would be an effect on the amount of carbon in the oceans, which is why this work is being conducted.

Holger is currently in the process of setting up experiments to answer these questions. He has been at OSU since February 2022 and has funding to conduct this work for three years from the Simons Foundation. Join us live on Sunday at 7 pm PST on 88.7 KBVR FM or https://kbvrfm.orangemedianetwork.com/ to hear more about Holger’s research and how a chance encounter with a marine biologist in Australia set him on his current career path! Can’t make it live, catch the podcast after the episode on your preferred podcast platform!

The rigamarole of RNA, ribosomes, and machine learning

Basic biology and computer science is probably not an intuitive pairing to think of, when we think of pairs of scientific disciplines. Not as intuitive as say biology and chemistry (often referred to as biochem). However, for Joseph Valencia, a third year PhD student at OSU, the bridge between these two disciplines is a view of life at the molecular scale as a computational process in which cells store, transmit, and interpret the information necessary for survival. 

Think back to your 9th or 10th grade biology class content and you will (probably? maybe?) vaguely remember learning about DNA, RNA, proteins, and ribosomes, and much more. In case your memory is a little foggy, here is a short (and very simplified) recap of the basic biology. DNA is the information storage component of cells. RNA, which is the focus of Joseph’s research, is the messenger that carries information from DNA to control the synthesis of proteins. This process is called translation and ribosomes are required to carry out this process. Ribosomes are complex molecular machines and many of them can also be found in each of our cells. Their job is to interpret the RNA. The way this works is that they attach themselves to the RNA, they take the transcript of information that the RNA contains, interpret it and produce a protein. The proteins fold into a specific 3D shape and the shape determines the protein’s function. What do proteins do? Basically control everything in our bodies! Proteins make enzymes which control everything from muscle repair to eye twitching. The amazing thing about this process is that it is not specific to humans, but is a fundamental part of basic biology that occurs in basically every living thing!

An open reading frame (ORF) is a stretch of nucleotides beginning with a start codon and ending with a stop codon. Ribosomes bind to RNA transcripts and translate certain ORFs into proteins. The Kozak sequence (bottom right, from Wikipedia) depicts the nucleotides that commonly occur around the start codons of translated ORFs.

So now that you are refreshed on your high school biology, let us tie all of these ‘basics’ to what Joseph does for his research. Joseph’s research focuses on RNA, which can be broken down into two main groups: messenger  RNA (mRNA) and non-coding RNA. mRNA is what ends up turning into a protein following the translation by a ribosome, whereas with long non-coding RNA, the ribosome decides not to turn it into a protein. While we are able to distinguish between the two types of RNA, we do not  fully understand how a ribosome decides to turn one RNA (aka mRNA) into a protein, and not another (aka long non-coding RNA). That’s where Joseph and computer science come in – Joseph is building a machine learning model to try and better understand this ribosomal decision-making process.

Machine learning, a field within artificial intelligence, can be defined as any approach that creates an algorithm or model by using data rather than programmer specified rules. Lots of data. Modern machine learning models tend to  keep learning and improving when more data is fed to them. While there are many different types of machine-learning approaches, Joseph is interested in one called natural language processing . You are probably pretty familiar with an example of natural language processing at work – Google Translate! The model that Joseph is building is in fact not too dissimilar from Google Translate, or at least the idea behind it; except  that instead of taking English and translating it into Spanish, Joseph’s model is taking RNA and translating (or not translating) it into a protein. In Joseph’s own words, “We’re going through this whole rigamarole [aka his PhD] to understand how the ins [RNA & ribosomes] create the outs [proteins].”.

A high-level diagram of Joseph’s deep learning model architecture.

But it is not as easy as it sounds. There are a lot of complexities to the work because the thing that makes machine learning so powerful is that the exact complexities that gives these models the power that they have, also makes it hard to interpret why the model is doing what it is doing. Even a highly performing machine learning model may not capture the exact biological rules that govern translation, but successfully interpreting its learned patterns can help in formulating testable hypotheses about this fundamental life process.

To hear more about how Joseph is building this model, how it is going, and what brought him to OSU, listen to the podcast episode! Also, you can check out Joseph’s personal website to learn more about him & his work!

Imaging nuclear fallout with a camera and a scintillating crystal

Our guest this week, Dr. Ari Foley, is a recent (July 2021) OSU graduate from the School of Nuclear Science and Engineering. For her PhD research, she developed a rapid imaging method for post-detonation nuclear forensics. While methods to do this work already exist, a lot of them are time- and material-intensive. Therefore, the goal of Ari’s work was to develop a method that could inform optimized destructive analysis of samples after a detonation event of a nuclear weapon, with a particular focus on reducing the amount of imaging time required. Not only was Ari able to accomplish this task but the system she developed is able to take an image of the spatial distribution of radiation omitted from an object in the same exposure as taking a traditional photograph of the object being analyzed (see Image below). How in the world did Ari do this? Read below for a short synopsis or even better listen to the episode here!

A core component of Ari’s system was an electron-magnifying charged couple device, also known as an EMCCD. The CCD part of that is essentially a normal camera but the EM part magnifies the signal collected from whatever the camera is pointed at. Ari rigged an inorganic scintillation crystal to the EMCCD, which sits in a 3D-printed holder just in front of the camera. The purpose of the crystal is that once it is held in close proximity to radioactive fallout material from a detonation, the radiation interacts with the crystal, which leads to the emission of light. This light is proportional to the amount of energy that is imparted within the crystal. The EM part of the EMCCD kicks in as the image is taken as it allows for a high intensity image to be made that magnifies the light emitted from the crystal interacting with the radiation. This process needs to occur in light tight box, however it is mobile, meaning that it can easily be taken into the field and directly be used at a nuclear detonation site to measure the intensity of radiation of fallout material.

Ari spent the last three years of her PhD time in Idaho at the Idaho National Laboratory (INL), which is one of the leading nuclear research labs in the USA and has close ties with OSU. In fact, Ari was one of two students in the inaugural class of INL Graduate Fellows, which enabled her to conduct this work while working full-time at the lab. However, Ari’s career may have gone down a very different path because she had always wanted to be an Arts student or pursue a career in human rights. However, during a summer school experience during her high school years, Ari attended a class on Indigenous Peoples and the United Nations. During this class, the students took a trip to the United Nations General Assembly Building in New York, which hosts a statue from Hiroshima, Nagasaki. The statue is of a woman holding a lamb, which from the front, looks completely normal. However, when you walk around to the back of the statue, the statue is completed charred and scarred – a consequence of the atomic bomb. The same class presented case studies of radiation contamination on tribal reservations in the USA. Seeing and learning these things really riled Ari up at the time because while she had been interested by radiation in chemistry class, she was suddenly confronted by the fact that radiation contamination were actual ongoing world issues. 

Listen to the podcast episode here to learn more about the nitty-gritty of how Ari developed her nuclear forensic system, how she prevented from getting radiation in the lab, and her road to OSU!

How to help rusty plants

Plants can get rusty. No joke! There is a fungal pathogen called rust which can cover the leaves of plants. This is problematic given that leaves are the site where photosynthesis occurs, the process whereby plants use sunlight to synthesize foods from carbon dioxide and water in order to grow. While a plant may still be able to photosynthesize if the leaves contain just a little bit of rust, the more and more rust spreads across the leaves, the less and less surface area there is for photosynthesis to occur. When you get rust on a metallic item, there are several home remedies you can try to remove the rust, such as baking soda or a vinegar bath. But do plants have rust-removal options too? Possibly…and it’s what our guest this week, PhD student Maria-Jose Romero-Jimenez (or Majo), is trying to figure out.

Majo, who is in her second year of graduate school in the Department of Botany and Plant Pathology here at OSU, is using black cottonwood as her plant study species. Black cottonwood is a Pacific Northwest native which has many uses, including the paper industry in Oregon. Recently, the Department of Energy has also listed the black cottonwood as a plant of interest for its potential use as a biofuel. As you can imagine, with this much large-scale interest in black cottonwood, there is also huge interest in understanding how it is affected by disease and pathogens, and what can potentially be done to prevent pathogens, such as rust, from spreading.

Yeast diversity panel

Fortunately, it seems like black cottonwood has a natural ally that helps it fend off rust – yeast! Majo’s main research goal is to figure out what yeast colonies are able to prevent rust infestation of black cottonwood plants. While this task may sound relatively straightforward, it sure isn’t. Majo’s work involves both field and lab work and is started in the fall of 2020 when Majo had to isolate yeast colonies from a bunch of leaves that were collected in the PNW (primarily Washington and Oregon). This work resulted in isolating almost 400 yeast colonies, from which Majo had to select a subset to grow in the lab. Meanwhile, baby black cottonwood plants needed to be propagated, potted, and cared for to ensure that Majo would have enough grown plants for her first round of greenhouse experiments. These experiments involved a series of treatments with different combinations of yeast colonies that were applied to the black cottonwood plants before being sprayed with rust to see how plants in different yeast treatments would do.

Curious to know what the results of Majo’s first round of experiments was and what the next steps are? You can download the episode anywhere you get your podcasts! Also, check out Majo’s Instagram (@fungibrush) for some educational videos on how she conducts her research (as well as a lesson in Spanish!). 

Two ways of killing bacteria

You’re probably pretty familiar with a thing called antibiotics. You’ve most likely been prescribed them for a number of bacterial infections you may have had over the course of your life. Antibiotics are typically broad-spectrum, which can be good if the exact ailment a person is suffering from is uncertain. However, it can also be bad given that broad-spectrum antibiotics don’t just kill the bad bacteria, but they kill the good ones too. On top of this, antibiotic resistance is a pervasive issue. Alternatively, bacteriophages, which are viruses that attack bacteria, can be used to treat bacterial infections too. Bacteriophages are extremely effective at killing off a specific bacteria that you want to target. For example, there is a bacteriophage that specifically kills cholera, and nothing else. However, you have most likely never been treated with a bacteriophage for a bacterial infection. Why? Well, to understand that we’ve got to go back to the Cold War era (and even a little further). Enter Miriam Lipton, a PhD candidate in the College of Liberal Arts, whose research focuses on exactly this question.

There is speculation that the Cold War is the reason that there are these two ways to treat bacterial infections (antibiotics and bacteriophages), and Miriam is interested in this speculation as well as understanding how U.S. and Soviet scientists dealt with bacterial infections in real time during the Cold War period. To do this, Miriam is examining scientific papers and pharmaceutical trade journals from that time (1947-1991) to understand how scientists on either side thought about bacterial infections, their treatments, and antibiotic resistance. This quest has taken (or will take) Miriam to a number of different research institutions, including the Eliava Institute in Tbilisi, Georgia, Caltech in California, and the American Institute of the History of Pharmacy in Wisconsin. Reading scientific publications can be difficult enough as it is, however Miriam faces an added challenge of having to read many of the Soviet publications in Russian. Luckily, Miriam’s background lends itself quite well for this difficult task as one of her triple major’s during her Bachelor’s degree was Russian and she has a Master’s in Russian Studies from the University of Oregon, all of which have led to a good proficiency of the Russian language.

Miriam’s program at OSU is called History of Science and is quite rare. In fact, it is one of only four such programs in the country and Miriam is one of only four in her cohort at OSU. She is simultaneously a historian and a scientist on a mission to better understand past perceptions and thoughts of scientists about bacterial infections, to hopefully inform the present and future. Especially given the rise of antibiotic resistance across the globe.

Listen to the podcast episode of the show here to dive deep into the history of bacterial infection science!

Hearing is believing: characterizing ocean soundscapes and assessing noise impacts on whales

“I always loved science class and science questions, and I went to science camps – but as a kid I didn’t really put it together that being a scientist was a career or something other than sitting at a microscope in a lab coat,” Our guest this week, Dr. Samara Haver, has come a long way from not realizing the myriad of careers in science when she was a child. She now works as a marine acoustician, researching underwater soundscapes and ocean noise to understand the repercussions for marine ecosystems and animals, such as humpback and blue whales. 

Noise Reference Station deployment in Channel Islands National Marine Sanctuary (Near Santa Barbara/LA, CA). Source: S. Haver.

Samara is a recent graduate from Oregon State University (OSU) having completed both her Masters and PhD in the Department of Fisheries, Wildlife, and Conservation Sciences (FWCS). She is continuing at OSU as a postdoctoral scholar in FWCS, where she is advised by Dr. Scott Heppell and works within the OSU/National Oceanic and Atmospheric Administration (NOAA) Cooperative Institute for Marine Ecosystem and Resources Studies. Her dissertation research focused on underwater recordings from 12 diverse and widespread marine habitats in U.S. waters. Data from each site was recorded by stationary hydrophone (underwater microphones), a calibrated array collectively named the NOAA/National Park Service Ocean Noise Reference Station Network (NRS). The NRS is an ongoing multi-agency collaborative effort to record underwater sound throughout the U.S. to understand about the differences and similarities of soundscapes in U.S. waters, and provide information to managers about protected species. The 12 locations are deployed along west and east coasts of the U.S., as well as in the northern and southern hemispheres, and includes locations within U.S. National Marine Sanctuaries and U.S. National Parks. One of the primary objectives of this highly collaborative and nation-wide comparison was to quantify comparable baselines of ocean noise in U.S. waters. When the NRS was first established, there weren’t any other U.S. research groups collecting passive acoustic data in these widespread locations using identical time-aligned recorders. Thus, the NRS provided new and comparable information to NOAA and the NPS about the levels and sources that contributed to underwater sound.  

Prepping a Noise Reference Station, with concrete anchor, acoustic release, hydrophone, and float for deployment near Olympic Coast National Marine Sanctuary, near Washington state. Source: S. Haver.

Hence, Samara’s PhD research revolved around analyzing the recordings from the 12 NRSs to explore several questions regarding differences in U.S. soundscapes, including baleen whale presence which she was able to identify by their unique vocalizations. Many marine animals, including baleen whales, evolved to rely on sound as their primary sensory modality to survive in the dark environment of the ocean. Unlike humans, who rely heavily on sight, whales must find food, communicate, navigate, and avoid predators using sound. However, the ocean has become a noisy place, primarily because of increased anthropogenic (human-caused) activity, such as shipping, marine construction, and seismic surveys, to name a few. To best understand how noise is affecting the life history of baleen whales and their habitats, we need to understand how loud the ocean is, how much noisier it’s getting, and what is generating the noise.

Looking through the “big eye” binocular to search for marine mammals in the North Atlantic. Source: S. Haver.

Samara has become an expert in characterizing and understanding ocean soundscapes, uncovering a lot about the differences and similarities in U.S. soundscapes. To hear about what exactly she learned during her PhD and what management implications her results have on protected species and habitats, tune in on Sunday, November 7th at 7 PM on KBVR 88.7 FM, live stream the show, or download Samara’s episode on Apple Podcasts!

Don’t want to wait until then? You can check out Samara’s publications on her GoogleScholar or follow her on Twitter!

A blade of seagrass is a powerful thing

Even though seagrasses occupy less than 0.2% of the world’s oceans, they account for more than 10% of all carbon trapped in the sea. In a world and time where we are producing more carbon than we should be and can manage, making sure that seagrasses are healthy and abundant is extremely pertinent. Winni Wang is one such seagrass scientist working to understand the biology of seagrasses and what threatens them.

Winni is a 5th year PhD candidate in the Department of Microbiology working with Dr. Ryan Mueller. Winni specializes in studying the microbiome of different plants, which for her PhD happens to be seagrasses. The microbiome is the community of microorganisms in a particular environment, and therefore it is found on all living things. By studying the microbiome on different seagrasses, Winni hopes to determine how anthropogenic (human-induced) stressors affect seagrass plants as a whole through changes in the microbiome.

If you’re like me and you love marine megafauna, then when thinking about seagrass beds you most likely are picturing a big manatee slowly grazing on seagrass in tropical, warm waters. Well, then you might be surprised to know that seagrasses don’t only occur in warm, tropical waters. In fact, there are over 60 species of seagrass worldwide and they occur in all kinds of habitats and climates. As a matter of fact, there is a species of seagrass right off of our coast here in Oregon, in Yaquina Bay, which is one of Winni’s study sites for her thesis research.

Eelgrass at Yaquina Bay.
Winni with the experimental tanks at HMSC.

Her work in Yaquina Bay relates to understanding how seagrasses are affected by eutrophication. Eutrophication occurs when an excessive amount of nutrients enters an aquatic environment, often due to land run-off, which in extreme cases can lead to severe oxygen depletion in those habitats resulting in death of plant and animal life. Winni hypothesized that with increased nutrients in a seagrass habitat, the microbiome of the seagrass would change in a way that would have an effect on the overall plant. In order to test this hypothesis, Winni had to carry out controlled lab experiments but not without collecting her test species first. She collected over 200 seagrass individuals as well as buckets of mud from Yaquina Bay, which she took back to Hatfield Marine Science Center where she set up tanks for her experiment. The tanks housed seagrasses and the collected mud. Half of the tanks included added fertilizer to test the effects of nutrient addition, and the other half were left as controls. Over the course of the experiment, Winni tracked plant growth metrics and nitrogen concentrations of the tanks, as well as collecting root and leaf samples to look at the microbiomes on both of those parts of the seagrass. 

The mud buckets.

Winni found that the fertilizer affected the roots in such a way that it changed the microbiome community found there. This change resulted in enrichment for microbes that could cycle sulfur, which could potentially have quite detrimental effects on seagrasses. This is because seagrasses grow in anoxic, or oxygen-low, environments where sulfur is found in its reduced form, hydrogen sulfide. Usually, in environments without excessive nutrient input, seagrasses are able to deal with sulfide, which is typically toxic to plants and animals. However, with increased nutrients, the seagrasses may become overwhelmed by the amount of sulfur in the water as it gets converted into hydrogen sulfide. At certain thresholds, the sulfide ends up becoming toxic to seagrasses. Thus, Winni’s research shows that excessive fertilization to seagrass environments, potentially from land run-off, could have detrimental impacts on seagrasses.

Another chapter of her PhD takes Winni half way across the world to the Mediterranean. Well, it is not so much that it takes Winni to the Mediterranean, it is more that the Mediterranean comes to her! Through her advisor, Winni was able to obtain seagrass samples from the Mediterranean. What makes these samples unique is that they were taken from a site near a naturally occurring underwater volcano. You may be wondering how this is relevant to Winni’s research since she is trying to figure out how human-induced stressors impact seagrasses. Well, the underwater volcano spews carbon dioxide into the water, which makes the water more acidic. This phenomenon is essentially a natural experiment because it mimics the effects of human-induced ocean acidification, which is becoming a problem around the world’s oceans. The results are still underway but they will help fill some of the knowledge gaps concerning the effects of ocean acidification on organisms.

This blog started by emphasizing how important seagrasses are in sequestering carbon, however it is not the only thing that makes these small, unassuming plants so vital to our lives and the lives of many other organisms. Coastal waters with seagrass beds have been found to contain relatively less human pathogens than areas without seagrasses. This is because seagrasses filter the water and are able to remove a lot of pathogens. Furthermore, they are important in preventing coastal erosion and often make coastlines more resilient to storms. Not only are they also important habitats to some beloved marine megafauna (manatees, sharks, turtles) but they are also important for many smaller, but equally ecologically and economically important, species. For example, in Oregon, seagrass beds may actually be helping mitigate ocean acidification which is having a negative impact on oysters as it affects the strength of their shells. 

Winni’s life, both at Oregon State and before her arrival here, has not been all about seagrass science though. To hear more about her background and some of the struggles and lessons that she has had during her tenure here, tune in on Sunday, March 8 at 7 PM on KBVR Corvallis 88.7 FM or stream live. To follow Winni and her research, be sure to follow her on Twitter @ramenmicrobiome. Something that we weren’t able to cover on the blog but covered on the show, is that Winni is one of the founders of the Women of Color Caucus (WoCC) at OSU. Read about the origin story of WoCC here, follow their Instagram and Twitter pages and join their listserv here.

Not all robots are hard and made of metal…

Picture a robot. Seriously, close your eyes for 30 seconds and picture a robot in your head. Ok, most of you probably didn’t do it but if you had, my guess is that you would have pictured something very boxy, perhaps with pincher hands, quite awkward in its movements and perhaps with a weird robotic voice pre-Siri era. Or maybe something R2-D2 like. That’s definitely what comes to mind for me. Well, robots don’t all look like that. In fact, some robots aren’t hard and made of metal at all. Some are soft and pliable, and they’re the kind that Nick Bira studies.

Was a career in robotics always on the horizon for Nick? Perhaps…judging by this photo of him with his home-made robot, “Mr. Klanky”.

Nick is a 3rd year PhD student in the Department of Robotics working with Dr. Joseph Davidson. When asked to summarize his research into just a few words, Nick answered that he works on magnetism and soft robotics. What is soft robotics and why would we want a soft robot you may ask (I know I certainly did)? Well, soft robotics is exactly what the phrase implies – they’re robots that are soft, absolutely no hard parts (or very few) to them. Why would we want a soft robot? Well, imagine if you have a small space that you need a robot to fit through, like a small hole. A soft robot can mold into the shape that you need it to. Alternatively, soft robots are becoming more and more needed and used in medical robotics. After all, you don’t want some hard, klanky thing poking around inside of you and possibly causing damage. You’d much rather have something that’s soft, gentle, compliant and non-damaging. Another example is in instances of human-robot interactions and increasing the safety of such interactions. A big, metallic, hard robot on an assembly line could easily spin and injure a human. But a robot with arms designed like tentacles that are floppy and soft, will perhaps push you over and bruise you, but not lead to serious damage.

The utility of soft robotics is manifold. So why aren’t they used more or why haven’t you heard much of them before? Well, the challenge is how to keep the utility of a hard robot while making it soft and, by proxy, safe. In part, this is down to how the robot and its movements are controlled. Most soft robots to date are controlled by or pneumatics or hydraulics (using air or liquid pressure). The downside of these is that the soft robot has to be accompanied by bulky hard components, such as a pumps, electrical sources, batteries, or air tanks. So even though you may have this super soft, compliant robot, it comes with large apparatuses that are not soft. Kind of counter-intuitive. 

This is where the other half of Nick’s research phrase comes in – magnetism. Magnetism has very limited usage as a tool in soft robotics and Nick thinks it should be applied more. If you’re having a hard time picturing how a magnet could be used in soft robotics, then visualize this example Nick gave us. It could be used in a pincher – instead of using air pressure in inflate the pincers to open and close, you could have the fingers of the pincer be made out of stretch magnetic material that closes when exposed to a magnetic field. It seems pretty simple right? And yet, it doesn’t yet exist in soft robotics. This is why Nick is exploring this possibility because he believes ideas like this could be useful building blocks, and once we have them, we can build more complicated things. 

Now, you may be thinking, hang on, magnets are hard, I thought this was all about soft robotics? Good thought – here’s how Nick is planning to work around that. Nick is embedding iron particles, which are magnetically soft, into silicone rubber, which is a soft elastic material, to make a material that is soft and hyper elastic and when brought close to an ordinary magnet, will stick to it. However, this is only step 1. Nick is interested in creating magnetic fields within the robot rather than it only working if there is a big, hard magnet nearby. One core goal of soft robotics is to have them function on their own without needing some hard object nearby to ‘support’ it. He is still in the development and testing stages of this material, but Nick does have an application in mind. He wants to make a magneto-rheological fluid (MRF) valve that can be used in soft robots. Rather than have this valve open and shut with air pressure (which would require air tanks to accompany the robot), Nick wants the valve to open and close through a magnetic field generated by the elastic, soft magnetic material. This way everything would be compact, stretchy, and wouldn’t require any additional bulky parts.

To hear more about Nick’s research and also about his journey to OSU and more on his personal background, tune in on Sunday, February 16 at 7 PM on KBVR Corvallis 88.7 FM or stream live. Also, be sure to check out his Instagram (@nick_makes_stuff and @nick_bakes_stuff) and Twitter (@BiraNick) accounts. 

Climate change, carbon, roots vs shoots, and why soil is more than just dirt

For starters, soil and dirt are not the same thing (contrary to my own belief). First of all, dirt is in fact soil that has been removed from its intended location. For example, the stuff on your shoes after you go hiking in the forest or the grit under your fingernails after you go dig around in your garden, that’s all dirt. The stuff that is left untouched in the forest and in the garden, that’s all soil. Secondly, soil is super important for a number of reasons. One of the key reasons being that it has the potential to help us reduce the amount of carbon in our atmosphere on human timescales, and therefore, mitigate the effects of climate change. And Adrian Gallo is right in the nitty-gritty of it all. 

Adrian is a 4th year PhD student in the Department of Crops and Soil Sciences working with Dr. Jeff Hatten, who was also his Master’s advisor. While Adrian’s Master’s work was focused on understanding how carbon and water move in Oregon soils under intensive forest management, his PhD is looking at soils from a much wider and more diverse range of habitats and ecosystems. Specifically, the soil cores are from 43 different locations across North America spanning 20 different ecoclimatic zones, ranging from the Alaskan Arctic Tundra to the southern tip of Florida. By analyzing these samples, Adrian is making a continental-scale assessment of soil organic matter and how similar or different it is across these ecoclimatic zones. In particular, Adrian is looking at carbon. Carbon is unique to look at in soils because it is cycling in human timescales, unlike carbon in rocks and oceans, which cycles on geologic timescales. What this means is that essentially we can directly manage and influence the carbon on our landscapes. However, before we can do that, we need to understand why some carbon stays in soil much longer than other carbon (50,000 years vs 1 week) and how different microbes have different abilities to use these different kinds of carbon. 

While it may not sound like it to many of us, the work that Adrian is doing is soil-scientifically speaking quite ‘basic’. It is ‘basic’ because soil scientists today are only now realizing how little we actually know and understand about how carbon works and cycles within soil. The reason being that “we were using essentially the same analytical methods for more than 100 years, and our predictions and climate models were built using that data. It’s only in the last 25 years that we have had instruments sensitive enough to test some of these predictions, and in some cases we’ve found that our models are completely wrong.” (NEON Science). 

Many of us probably learned about how cycling of elements, such as nitrogen, calcium, and carbon, works in middle school. The terrestrial carbon cycle was likely explained in the following way; a tree grows, its leaves fall, the leaves decompose, the nutrients go back into the soil, the tree uses the nutrients, which includes carbon. However, what Adrian and many other soil scientists are finding is that the carbon cycle isn’t as cyclical as we thought it was, and as we perhaps wish it would. Additionally, our belief that most of the carbon that finds its way into soils is shoot-derived (aka from the leaves or from above the ground) is also being proven flawed, in some part by Adrian’s research. After analyzing the soil cores from his 43 sites, Adrian found that most of the carbon in soil is looking like it is in fact root-derived. 

You may be thinking to yourself, why should I care about how much carbon is in the soil and where it comes from and how long it stays there. Well, soil is actually the most important terrestrial carbon sink, storing an estimated 4,100 gigatons of carbon globally, which is more than the atmosphere (~590 Gt) and organisms (650 Gt) store. And the truth of the matter is that we want carbon in our soil. In fact, we want a whole lot more in there. Not only would having more carbon in our soil be beneficial to our climate (as we would be capturing and storing more of the atmospheric carbon in our soils rather than have it out in the atmosphere), but it is also beneficial from an agricultural perspective. If you put carbon in soil, it increases its water holding capacity, meaning farmers don’t have to irrigate as much, it increases the amount of nutrients in the soil, and as a consequence of both, it means that a more diverse range of crops can be planted. There are so many downstream benefits of putting carbon back into soil that is has the potential to make farmers much safer in bad drought or flood years.

Another really exciting component of Adrian’s research is how collaborative and interdisciplinary it is. One of the best examples of this is where he got his 43 soil cores from. You see, Adrian didn’t actually have to go to each of his 43 cross-continental sites (which would have been a nightmare temporally, logistically, financially, and many more words ending in -ally). Instead, he and his advisor were able to convince a team of researchers who were already going to these sites as part of an NSF-funded project called NEON (National Ecological Observatory Network), to send him the 1-m average length cores, which the NEON group were actually planning on not using and dumping. Furthermore, Adrian has joined forces with researchers from diverse backgrounds to look at these cores from totally different angles. While Adrian represents the role of chemist in the group, there is also an ecologist, mineralogist, and a statistician, who are all fitting different pieces of the puzzle together.

In Adrian’s own words, “it’s a really exciting time to be in the field of biogeochemistry because that’s basically what soil is – some mixture of biology, the chemistry that is involved, and the parent material– the rock itself–dictates a lot of the reactions that can occur. We have taken that for granted for a really long time but I really enjoy the complexity of it and having specialists come in to look at this problem from lots of different angles has been really great.”.

When Adrian is not in the lab breaking apart soil cores or in his office thinking about soil, you’ll probably find him speeding around in the woods on his bike…covered in soil. Source: Twitter.

To hear more about Adrian’s research and also about his journey to OSU and more on his personal background, tune in on Sunday, January 12 at 7 PM on KBVR Corvallis 88.7 FM or stream live. Also, make sure to follow Adrian on Twitter for updates on all things soil and check out a recording of a talk he recently gave at the American Society of Agronomy and Crop Science Society of America joined conference!

[Unfortunately due to a conflict with OSU Athletics schedule promoting a game, this on-air interview did not take place. The podcast/on-air interview will occur later in 2020]

Putting years and years of established theory to the test

A lot of the concepts that scientists use to justify why things are the way they are, are devised solely based on theory. Some theoretical concepts have been established for so long that they are simply accepted without being scrutinized very often. The umbrella species concept is one such example as it is a theoretical approach to doing conservation and although in theory it is thought to be an effective strategy for conserving ecosystems, it is actually very rarely empirically tested. Enter Alan Harrington, who is going to test its validity empirically.

Alan is a 2nd year Master’s student in the Department of Animal and Rangeland Sciences working with Dr. Jonathan Dinkins. Alan’s research and fieldwork focuses on three species of sagebrush- steppe habitat (SBSH) obligate songbirds: the Brewer’s sparrow, sagebrush sparrow, and sage thrasher. Being a SBSH obligate means that these three birds require sagebrush to fulfill a stage of their life-history needs, namely during their breeding season. However, by studying these three species, Alan is aiming to tackle a broad conservation shortcut as he is trying to figure out whether the umbrella species conservation approach has worked in the SBSH where conservation is guided by the biology of the greater sage-grouse (GSG), which has been termed an umbrella species for sagebrush habitat for many years.

An umbrella species, a close cousin to keystone or an indicator species, is a plant or animal used to represent other species or aspects of the environment to achieve conservation objectives. The GSG is such a species for the SBSH. However, the SBSH is an expansive habitat found across 11 western US states and two Canadian province that covers several millions acres of land. Hence, the question of whether one species alone can be used to manage this large habitat is a valid one. Furthermore, SBSH has been declining dramatically over the last decades. In fact, it is one of the fastest declining habitats in North America. This decrease in available sagebrush habitat has led to the decline in GSG populations since European settlement and the GSG requires SBSH to fulfill its life-history needs. Thus, populations of other birds that require the SBSH have been declining too, like sagebrush-obligate songbirds.

Alan using binoculars to survey for songbirds to determine their abundances.

The state of Oregon, like many other western US states, are concerned about protecting SBSH and GSG because they are both quickly declining and songbirds are extremely sensitive to changes in the environment responding quickly to them. Within the last 10 years, the GSG was petitioned to be listed under the Endangered Species Act by several expert groups due to the severity of the decline. Both times, the petitions were designated warranted however were precluded from listing. This issue of declining SBSH and declining GSG populations is made more complicated by the fact that most SBSH also doubles as rangeland for grazing cattle or SBSH is often used for agriculture. Thus, the petitioning for trying to get the GSG listed as endangered caused stakeholders in Oregon to get involved in this situation since the listing of the GSG as endangered could result in very radical management changes for the SBSH, limiting agricultural and land use of this habitat.

Map of Alan’s study area.

As you can see, the topic is not a simple, straightforward one, however Alan is already two years into getting the data to answer some of his questions. Alan’s fieldwork takes place in eastern Oregon in a study area that is 1.4 million acres big. Naturally, he doesn’t survey every single foot of that massive area. Instead he and his lab mates (three of them work together during the field season to collect data for all of their projects) have 147 random point locations, which are located within five Priority Areas of Conservation (PAC), designated by the Oregon Department of Fish & Wildlife as core conservation areas based on high densities of breeding GSG. The field season is from May to July and Alan often puts in 80-hour work weeks to get the job done. For his data collection, Alan does random nest transect surveys at each of the 147 locations for the three sagebrush obligate songbird species, as well as collecting abundance data on any songbird he sees at each random point location. These two methods are also done for GSG UTM locations so that Alan can compare data between them and the songbirds. On top of this, Alan received a grant from the Oregon Wildlife Foundation to purchase iButton temperature loggers to deploy into songbird nests. Along with trail cameras, these will help Alan identify events indicative of nest success or nest failure.

Alan will start his first round of analyses this winter and he’s looking forward to digging into the data that he and his lab mates have worked hard to collect. Ultimately, Alan hopes that his research will make a difference, not just for the sagebrush steppe habitat, his three songbird species, or the greater sage-grouse, but also within other ecosystems. The umbrella species concept is used in all aspects of ecology and so hopefully his findings will be applicable beyond his field of study. 

To hear more about Alan’s research and also about his journey to OSU and more on his personal background, tune in on Sunday, November 24 at 7 PM on KBVR Corvallis 88.7 FM or stream live

If you can’t wait until then, follow Alan’s lab on Twitter!

Also, check out this recent publication that Alan played a big role in devising and writing while he was at the University of Montana in the Avian Science Center. The project tested auditory survey methodologies and how methodology can help reduce survey issues like misidentification and double counting of bird calls/signals.