Category Archives: Crop and Soil Science

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. 

  • Organizing cores from his 43 NEON sites. Source: Twitter.
  • These soils from Klemme field site (OAES) were likely the most red soils Adrian has documented in 2.5 years. Source: Twitter.

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. 

  • Photos from 24-Jun-2018 when Adrian had to haul his samples across campus to get them from freezers to incubators. Source: Twitter.

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.”.

https://twitter.com/adriancgallo/status/964185681500110848?s=21
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]

Zebrafish sentinels: studying the effects of cadmium on biology and behavior

Cadmium exposure is on the rise

There’s a good chance you might have touched cadmium today. A heavy metal semi-conductor used in industrial manufacturing, cadmium is found in batteries and in some types of solar panels. Fertilizers and soil also contain cadmium because it is present in small levels in the Earth’s crust. The amount of cadmium in the environment is increasing because of improper disposal of cell phone batteries, contaminating groundwater and soil. This is a problem that impacts people all over the world, particularly in developing countries.

Plants take up cadmium from the soil, which is how exposure through food can occur. Leafy greens like spinach and lettuce can contain high levels of cadmium. From the soil, cadmium can leach into groundwater, contaminating the water supply. Cadmium is also found in a variety of other foods, including chocolate, grains and shellfish, as well as drinking water.

Cadmium has a long half-life, reaching decades, which means that any cadmium you are exposed to will persist in your body for a long time. Once in the body, cadmium ends up in the eyes or can displace minerals with similar chemical properties, such as zinc, copper, iron, and calcium. Displacement can cause grave effects related to the metabolism of those minerals. Cadmium accumulation in the eyes is linked to age-related macular degeneration, and for people in the military and children, elevated cadmium is linked to psychosocial and neurological disorders.

Read more about cadmium in the food supply:



Using zebrafish to study the effects of cadmium

Delia Shelton, a National Science Foundation post-doctoral fellow in the Department of Environmental and Molecular Toxicology, uses zebrafish to investigate how cadmium exposure in an individual affects the behavior of the group. Exposing a few individuals to cadmium changes how the group interacts and modifies their response to novel stimuli and environmental landmarks, such as plants. For example, poor vision in a leader might lead a group closer to predators, resulting in the group being more vulnerable to predation.

Zebrafish

As part of her post-doctoral research, Delia is asking questions about animal behavior in groups: how does a zebrafish become a leader, how do sick zebrafish influence group behavior, and what are the traits of individuals occupying different social roles? These specific questions are born from larger inquiries about what factors lead to individual animals wielding inordinately large influence on a group’s social dynamic. Can we engineer groups that are resilient to anthropogenic influences on the environment and climate change?

Zebrafish

Zebrafish are commonly used in biomedical research because they share greater than 75% similarity with the human genome. Because zebrafish are closely related to humans, we can learn about human biology by studying biological processes in zebrafish. Zebrafish act as a monitoring system for studying the effects of compounds and pollution on development. It is possible to manipulate their vision, olfactory system, level of gene expression, size, and aggression level to study the effects of pollutants, drugs, or diseases. As an added benefit, zebrafish are small and adapt easily to lab conditions. Interestingly, zebrafish are transparent, so they are great for imaging. Zebrafish have the phenomenal ability to regenerate their fins, heart and brain. What has Delia found? Zebrafish exposed to cadmium are bolder and tend to be attracted more to novel stimuli, and they have heightened aggression.

Read more about zebrafish:

ZFIN- Zebrafish Information Network – https://zfin.org/
Zebrafish International Research Center in Eugene Or – http://zebrafish.org/home/guide.php



What led Delia to study cadmium toxicity in zebrafish?

As a child, Delia was fascinated by animals and wanted to understand why they do the things they do. As an undergrad, she enjoyed research and pursued internships at Merck pharmaceutical, a zoo consortium, and Indiana University where she worked with Siamese fighting fish. She became intrigued by social behavior, social roles, and leadership. Delia studied the effects of cadmium in grad school at Indiana University, and decided to delve into this area of research further.

Delia began her post-doctoral work after she finished her PhD in 2016. She was awarded an NSF Postdoctoral Fellowship to complete a tri-institute collaboration: Oregon State University, Leibniz Institute for Freshwater Ecology and Inland Fisheries in Berlin, Germany, and University of Windsor in Windsor, Ontario. She selected the advisors she wanted to work with by visiting labs and interviewing past students. She wanted to find advisors she would work well with and who would help her to accomplish her goals. Delia also outlined specific goals heading into her post-doc about what she wanted to accomplish: publish papers, identify collaborators, expand her funding portfolio, learn about research institutes, and figure out if she wanted to stay in academia.

Research commercialization and future endeavors

During her time at OSU, Delia developed a novel assay to screen multiple aspects of vision, and saw an opportunity to explore commercialization of the assay. She was awarded a grant through the NSF Innovation Corps and has worked closely with OSU Accelerator to pursue commercialization of her assay. Delia is now wrapping up her post-doc, and in the fall, she will begin a tenure track faculty position at University of Tennessee in the Department of Psychology, where she will be directing her lab, Environmental Psychology Innovation Center (E.P.I.C) and teaching! She is actively recruiting graduate students, postdocs, and other ethnusiatic individuals to join her at EPIC.

Please join us tonight as we speak with Delia about her research and navigation of the transition from PhD student to post-doc and onwards to faculty. We will be talking to her about her experience applying for the NSF Postdoctoral Fellowship, how she selected the labs she wanted to join as a post-doc, and her experience working and traveling in India to collect zebrafish samples.

Tune in to KBVR Corvallis 88.7 FM or stream the show live on Sunday, April 7th at 7 PM. You can also listen to the episode on our podcast.

Stream ecosystems and a changing climate

Examining the effect of climate change on stream ecosystems

Oak Creek near McDonald Dunn research lab. The salamander and trout in the experiments were collected along this stretch of creek.

As a first year Master’s student in the lab of Ivan Arismendi, Francisco Pickens studies how the changing, warming climate impacts animals inhabiting stream ecosystems. A major component of stream ecosystem health is rainfall. In examining and predicting the effects of climate change on rainfall, it is important to consider not only the amount of rainfall, but also the timing of rainfall. Although a stream may receive a consistent amount of rain, the duration of the rainy season is projected to shrink, leading to higher flows earlier in the year and a shift in the timing of the lowest water depth. Currently, low flow and peak summer temperature are separated by time. With the shortening and early arrival of the rainy season, it is more likely that low flow and peak summer temperature will coincide.

A curious trout in one of the experimental tanks.

Francisco is trying to determine how the convergence of these two events will impact the animals inhabiting streams. This is an important question because the animals found in streams are ectothermic, meaning that they rely on their surrounding environment to regulate their body temperature. Synchronization of the peak summer temperature with the lowest level of water flow could raise the temperature of the water, profoundly impacting the physiology of the animals living in these streams.

 

 

How to study animals in stream ecosystems?

Salamander in its terrestrial stage.

Using a simulated stream environment in a controlled lab setting, Francisco studies how temperature and low water depth impact the physiology and behavior of two abundant stream species – cutthroat trout and the pacific giant salamander. Francisco controls the water temperature and depth, with depth serving as a proxy for stream water level.

Blood glucose level serves as the experimental readout for assessing physiological stress because elevated blood glucose is an indicator of stress. Francisco also studies the animals’ behavior in response to changing conditions. Increased speed, distance traveled, and aggressiveness are all indicators of stress. Francisco analyzes their behavior by tracking their movement through video. Manual frame-by-frame video analysis is time consuming for a single researcher, but lends itself well to automation by computer. Francisco is in the process of implementing a computer vision-based tool to track the animals’ movement automatically.

The crew that assisted in helping collect the animals: From left to right: Chris Flora (undergraduate), Lauren Zatkos (Master’s student), Ivan Arismendi (PI).

Why OSU?

Originally from a small town in Washington state, Francisco grew up in a logging community near the woods. He knew he wanted to pursue a career involving wild animals and fishing, with the opportunity to work outside. Francisco came to OSU’s Department of Fisheries and Wildlife for his undergraduate studies. As an undergrad, Francisco had the opportunity to explore research through the NSF REU program while working on a project related to algae in the lab of Brooke Penaluna. After he finishes his Master’s degree at OSU, Francisco would like to continue working as a data scientist in a federal or state agency.

Tune in on Sunday, June 24th at 7pm PST on KBVR Corvallis 88.7 FM, or listen live at kbvr.com/listen.  Also, check us out on Apple Podcasts!

Dirt: It’s under all of us!

We depend on the humble soil beneath our feet to grow the cotton in our shirts, feed the world with fruits and vegetables, and growing all the commodities necessary to make beer and whisky alike! Given the range of functions soils have on earth it’s no surprise soils themselves have very different colors, sizes, and even smells! If we look closely at soils, especially their horizons resembling layers of a cake, they can be read to ascertain how nutrients got there, how long those nutrients can last for the plants above, and what to do if an area needs to be remediated.

Great soil profile showing the burial of an old soil (reddish-grey) formed on a basalt flow. The soil surface was buried by volcanic ash ejected during the cataclysmic eruption of Mt.Mazama (Crater lake. Photo taken near Cougar Ridge, Eagle Cap Wilderness,Summer 2015.

Great soil profile showing the burial of an old soil (reddish-grey) formed on a basalt flow. The soil surface was buried by volcanic ash ejected during the cataclysmic eruption of Mt. Mazama which is now Crater lake. (Eagle Cap Wilderness, Summer 2015)

12cm is of soil is precariously protected from alpine winds by a thin gravel mulch (Summer 2015).

12cm is of soil is precariously protected from alpine winds by a thin gravel mulch (Summer 2015).

 

 

 

 

 

 

 

 

 

Even though humans rely on soils for our health and comfort, we too often take soil for granted. But our guest reminds us exactly how essential soils are to life! Vance Almquist is a PhD student joining us from the Crops and Soil Science Department, in the College of Agricultural Sciences, and focuses on how soils develop in wildland environments, as well as how to read soils in order to understand its historical record keeping. Vance is also known as a soil pedologist, or someone who studies soil genesis, its transformations, and specializes in how to read the language of soil horizons. You might ask, ‘why do we need to know the history of a soil in order to use it?’

Human society developed in the ‘Cradle of Civilization’, an area known as the Fertile Crescent because (as you guessed it) the soils were extraordinary fertile! To practice higher-level agriculture, early settlers built levees to block the floodwaters. But when they prevented the annual floods soils were no longer getting enough nutrients, salts started to build up, and eventually it lead to a collapse of civilizations. If only they understood the soils’ history, they would’ve know the annual floods are essential to maintaining their prosperous way of life. If we know how soils develop, and how to read them, these are the kinds of problems we can avoid in the future.

Hiking toward China Cap in the Eagle Cap Wilderness to describe and map soils (Summer 2016)

Hiking toward China Cap in the Eagle Cap Wilderness to describe and map soils (Summer 2016)

Vance grew up in Utah and before yearning to be a soil scientist he worked at a brewery, trained dogs, and is a master forklift driver. High school was never terribly fun because nothing really challenged him, but he continued to enroll in classes at the local community college. He was really turned onto botany because he always went mushroom hunting as a kid and he saw the practical application of knowing which plants we share the world with. Then he realized how soil science was at the intersection of biology, chemistry, and physics. Here he found his calling because he also noticed how much our economy was overlooking the usefulness of soils and wanted to continue to explore this idea further in graduate school.

Not only can understanding soils avert disasters, but ranges of scientific disciplines are dependent on soils. A botanist can be interested in finding rare flowers, a hydrologist is interested in finding out how much sediment is mucking up the streams, and a meteorologist wants to know how much CO2 is released into atmosphere. Specific soil properties are needed for certain plants to grow, some soils erode faster than others, and soils can become a source, instead of a sink, of CO2 emissions! Soils are integrators of many scientific disciplines and I hope you join us to discuss this with Vance. You can tune in on Sunday November 20th at 7PM on 88.7FM or listen live here.

Mosquito soup in the Brazilian rainforest

Fieldwork in the Brazilian Amazonia meant continuously trying to outsmart their savviest opponents…ants!

Fieldwork in the Brazilian Amazonia meant continuously trying to outsmart their savviest opponents…ants!

Deforestation in Brazil due to cultivation of monoculture crops, such as soybean, has profoundly impacted wildlife populations. In the lab of Taal Levi in the Department of Fisheries and Wildlife, wildlife biologist Aimee Massey has adopted a quantitative approach to studying this impact. During her first and second year of graduate school, Aimee traveled to Brazil for fieldwork and data collection, collaborating with researchers from Brazil and the UK. During this trip, she collected 70,000 biting flies, including mosquitoes and sandflies, by engineering 200 fly traps constructed from 2-liter soda bottles, netting, and rotting beef. Aimee installed biting traps throughout 40 individual forest patches, which are regions delineated by their physical characteristics, ranging approximately in size from the OSU campus to the state of Rhode Island.

Who knew fieldwork could be such a balancing act?!…especially when trying to avoid poisonous insects and thorns. Let’s hope the next branch Aimee reaches for is not of the slithering snake kind!

Who knew fieldwork could be such a balancing act?!…especially when trying to avoid poisonous insects and thorns. Let’s hope the next branch Aimee reaches for is not of the slithering snake kind!

Subsequent DNA analysis on biting flies provides a relatively unbiased source of wildlife tracking, since mosquitoes serve as a repository of DNA for the wildlife they have feasted upon. DNA analysis also provides information regarding diseases that may be present in a particular patch, based on the bacterial and viral profile. For example, sandflies are carriers of protozoa such as leishmania, which cause the disease leishmaniasis. To analyze DNA, Aimee uses bioinformatics and metabarcoding, which is a technique for assessing biodiversity from an environmental sample containing DNA. Different species of animals possess characteristic DNA sequences that can be compared to a known sequence in an online database. By elucidating the source of the DNA, it is possible to determine the type of wildlife that predominates in a specific patch, and whether that animal may be found preferentially in patches featuring deforestation or pristine, primary rain forest.

Learning about human/wildlife interactions while drinking tea with camel’s milk in Laikipia, Kenya.

Learning about human/wildlife interactions while drinking tea with camel’s milk in Laikipia, Kenya.

Aimee completed her undergraduate studies at University of Maine, where she quickly discovered she wanted to study biology and chemistry in greater depth. She planned to attend med school, and was even accepted to a school in her junior year; however, an introductory fieldwork course in Panama spent exploring, doing fieldwork, and trekking made a deep impression on her, so she decided to apply to graduate school instead. Aimee completed a Masters degree in environmental studies at the University of Michigan, during which time she spent 4 months at the Mpala Research Centre in the middle of the Kenyan plateau, just north of the Masai Mara. Following completion of her Masters degree, Aimee spent a year as a research assistant at the University of New Hampshire working with small mammals. Before beginning her PhD studies at OSU, Aimee spent two months in Haines, Alaska doing fieldwork with her future PI, Taal Levi. After she finishes her PhD, Aimee plans to focus on conservation work in New England where she is originally from.

Having fun after fieldwork; Aimee’s eulachon fish catch of the day in Haines, Alaska. One is better than none!

Having fun after fieldwork; Aimee’s eulachon fish catch of the day in Haines, Alaska. One is better than none!

Tune in on October 23rd, 2016 at 7PM on the radio at 88.7FM KBVR, or stream live, to hear more about Aimee’s adventures in Brazil, and why her graduate work is shaping our understanding of how deforestation impacts biodiversity.

 

Go play in the dirt!

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Shannon harvesting potatoes in Corvallis, OR

Over the last five years the modern agricultural economy has become a hot topic to debate. As the population continues to grow, so to will the need to produce more food to feed the world. There are many ideas about how to meet this demand including organic farming, GMOs, hydroponics, among others. When most people discuss the pros and cons of different farming practices, the conversation usually centers around human health. How much pesticide is making it into my body? Are there more nutrients in organically grown produce? Was Monsanto involved? These are just some of the questions you’ve probably heard at your grocery store or local farmer’s market. Shannon Andrews has spent the last ten years working and researching in many disciplines within the agriculture industry and she’s asking a different question; how can we increase agronomic value and reduce the negative environmental impacts of agricultural production?

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Corn harvest crew in Klamath Falls, OR

As it turns out, that is a very important question to be asking. Many of the farming practices that have enabled improvements in crop yield are also detrimental to the environment, specifically the soil. In an attempt to combat these ill effects, soil scientists are studying the effects of tilling, organic vs conventional farming, and nutrient retention in the soil, among other things. If we can better understand the impact of our farming practices, then we can potentially change or curtail them to generate a more sustainable agricultural economy. Shannon, and other soil scientists, are hoping to make further improvements to sustainable agriculture by creating recycled fertilizers that have reduced environmental impact and don’t affect crop yield.

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Potatoes growing in Madras, OR. Crops in the front are growing without Nitrogen added, while the crops in the back are growing in algae fertilizer

With a diverse background of undergraduate studies in marine biology, wildlife biology, agricultural studies, and animal science, as well as work experience on a beef ranch and with trading commodities in the feedstock industry, Shannon has the knowledge to create these fertilizers of the future. All of these different experiences have led to a trifecta of exciting new ideas on how to improve the fertilizers used in farming. Through her master’s work, and now into her doctoral research, Shannon is working to optimize the soil chemistry for maximum crop growth and minimal environmental impact. Her early graduate school work with Dr. Dan Sullivan, studying soil pH showed that the use of sulfur in compost fertilizer makes it possible to grow blueberries, which turn out to be quite a fickle fruit. Shannon then turned her attention to another recycled fertilizer, algal meal, a waste product from algae-based biodiesel production. During her work in Dr. David Myrold’s lab, Shannon showed that algae based fertilizer has a reduced environmental impact while maintaining corn yields. Shannon is now finishing up her doctoral research by studying the water absorption properties of soil with Dr. Marcus Kleber and Dr. Maria Dragila.

After all her research and work experience, Shannon is uniquely positioned to study the agriculture industry. It will be important to consider perspectives from people like Shannon so that we can quantify and improve farming practices as we move forward in the 21st century. After all, agriculture is one of the most important industries in the world and that’s not about to change as the global population, and the need for food, increases.

We’ll talk with Shannon about her crop soil research and how she got into this field, Sunday May 22nd at 7pm PST on 88.7 KBVR-FM.

When you can’t see the soil for the forest

Did you know that December 5th is World Soil Day? It’s only fitting that we would feature Kris Osterloh, a 3rd year Ph. D. student of Jay Noller in the department of Crop and Soil Science.

A soil core is carefully measured in the field. The data from this core and the surrounding ecology will help construct a model to understand the soils in the Willamette Valley National Forest

A soil core is carefully measured in the field. The data from this core and the surrounding ecology will help construct a model to map the soils in the Willamette Valley National Forest

Soil is more than just dirt in the ground, it’s rich and vibrant with life, and there are many, many different types of soil on this planet. Our soil is the reason civilization can exist, or as FDR so eloquently put it:

The Nation that destroys its soil destroys itself.

– Franklin D Roosevelt, 1937

Tonight at 7PM, Kris Osterloh will talk about his passion for soils and his research using computer models to rapidly map and understand the development of soils in the Willamette National Forest. With this knowledge in hand, we can understand how we can better manage the land to protect the soil and everything that comes from it.

Tune in Sunday, December 6th at 7PM Pacific on 88.7FM or stream at http://kbvr.com/listen to hear Kris’ tale of adventure, leadership, and science!

Kris Osterloh pauses for reflection in the field

Kris Osterloh pauses for reflection.