Author Archives: Lisa Hildebrand

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!

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. 

What ties the Panama Canal, squeaky swing sets, and the Smithsonian together? Birds of course!

Have you ever wondered why you see birds in some places and not in others? Or why you see a certain species in one place and not in a different one? Birds have wings enabling them to fly so surely we should see them everywhere and anywhere because their destination options are technically limitless. However, this isn’t actually the case. Different bird species are in fact limited to where they can and/or want to go and so the question of why do we see certain birds in certain areas is a real research question that Jenna Curtis has been trying to get to the bottom of for her PhD research.

Jenna is a 4th year PhD candidate working with Dr. Doug Robinson in the Department of Fisheries & Wildlife. Jenna studies bird communities to figure out which species occur within those communities, and where and why they occur there. To dial in on these big ecological questions, Jenna focuses on tropical birds along the Panama Canal (PC). PC is a unique area to study because there is a large man-made feature (the canal) mandating what the rest of the landscape looks and behaves like. Additionally, it’s short, only about 50 miles long, however, it is bookended by two very large cities, Panama City (which has a population over 1 million people) and Colón. Despite the indisputable presence and impact of humans in this area, PC is still flanked by wide swaths of pristine rainforest that occur between these two large cities as well as many other types of habitat.

Barro Colorado Island can be seen in the centre of the Panama Canal.

A portion of Jenna’s PhD research focuses on the bird communities found on an island in the PC called Barro Colorado Island (BCI), which is the island smack-dab in the middle of the canal. To put Jenna’s research into context, we need to dive a little deeper into the history of the PC. When it was constructed by the USA (1904-1914), huge areas of land were flooded. In this process, some hills on the landscape did not become completely submerged and so areas that used to be hilltops became islands in the canal. BCI is one such island and it is the biggest one of them in the PC. In the 1920s, the Smithsonian acquired administrative rights for BCI from the US government and started to manage the island as a research station. This long-term management of the island is what makes BCI so unique to study as we have studies dating back to 1923 from the island but it has also been managed by the Smithsonian since 1946 so that significant development of infrastructure and urbanization never occurred here.

Large cargo vessels pass next to BCI on their transit of the Panama Canal

Now back to Jenna. Over time, researchers on the island noticed that fewer bird species were occurring on the island. There are now less species on the island than would be expected based on the amount of available habitat. Therefore, Jenna’s first thesis chapter looks at which bird species went extinct on BCI after the construction of PC and why these losses occurred. She found that small, ground-dwelling, insectivore species were the group to disappear first. Jenna determined that this group was lost because BCI has started to “dry out”, ecologically speaking, since the construction of PC. This is because after the PC was built, the rainforest on BCI was subjected to more exposure from the sun and wind, and over time BCI’s rainforest has no longer been able to retain as much moisture as it used to. Therefore, many of the bird species that like shady, cool, wet areas weren’t able to persist once the rainforest started becoming more dry and consequently disappeared from BCI.

Another chapter of Jenna’s thesis considers on a broader scale what drives bird communities to be how they are along the entire PC, and what Jenna found was that urbanization is the number one factor that affects the structure and occurrence of bird communities there. The thing that makes Jenna’s research and findings even more impactful is that we have very little information on what happens to bird communities in tropical climates under urbanization pressure. This phenomenon is well-studied in temperate climates, however a gap exists in the tropics, which Jenna’s work is aiming to fill (or at least a portion of it). In temperate cities, urban forests tend to look the same and accommodate the same bird communities. For example, urban forest A in Corvallis will have pigeons, house sparrows, and starlings, and this community of birds will also be found in urban forest B, C, D, etc. Interestingly, Jenna’s research revealed that this trend was not the case in Panama. She found that bird communities within forest patches that were surrounded by urban areas were significantly different to one another. She believes that this finding is driven by the habitat that each area may provide to the birds. 

Jenna has loved birds her entire life. To prove to you just how much she loves birds, on her bike ride to the pre-interview with us, she stopped on the road to smash walnuts for crows to eat. Surprisingly though, Jenna didn’t start to follow her passion for birds as a career until her senior year of her undergraduate degree. The realization occurred while she was in London to study abroad for her interior design program at George Washington University in D.C. where on every walk to school in the morning she would excitedly be pointing out European bird species to her friends and classmates, while they all excitedly talked about interior design. It was seeing this passion among her peers for interior design that made her realize that interior design wasn’t the passion she should be pursuing (in fact, she realized it wasn’t a passion at all), but that birds were the thing that excited her the most. After completely changing her degree track, picking up an honor’s thesis project in collaboration with the Smithsonian National Zoo on Kori bustard’s behavior, an internship at the Klamath Bird Observatory after graduating, Jenna started her Master’s degree here at OSU with her current PhD advisor, Doug Robinson in 2012. Now in her final term of her PhD, Jenna hopes to go into non-profit work, something at the intersection of bird research and conservation, and public relations and citizen science. But until then, Jenna will be sitting in her office (which houses a large collection of bird memorabilia including a few taxidermized birds) and working towards tying all her research together into a thesis.

To hear more about Jenna’s research, tune in on Sunday, October 6th at 7 PM on KBVR 88.7 FM, live stream the show at http://www.orangemedianetwork.com/kbvr_fm/, or download our podcast on iTunes!

Proteins run the show (except when they unfold and cause cataracts)

Your eye lenses host one of the highest concentrated proteins in your entire body. The protein under investigation is called crystallin and the investigator is called Heather Forsythe.

Heather is a 4th year PhD candidate working with Dr. Elisar Barbar in the Department of Biochemistry and Biophysics. The Barbar lab conducts work in structural biology and biophysics. Specifically, they are trying to understand molecular processes that dictate protein networks involving disordered proteins and disordered protein regions. To do this work, the lab uses a technique called nuclear magnetic resonance (NMR). NMR is essentially the same technology as an MRI, the big difference being the scale at which these two technologies measure. MRIs are for big things (like a human body) whereas NMR instruments are for tiny things (like the bonds between amino acids which are the building blocks of proteins). Heather employed OSU’s NMR facility (which has an 800 megahertz magnet and is on the higher end of the NMR magnetic field strength range) to investigate what the eye lens protein crystallin has to do with cataracts.

Your eye completely forms before birth, and the lens of the eye that helps us see is made of a protein called crystallin. This protein is essential to the structure and function of the eye, but it cannot be regenerated by the body so whatever you have at birth is all you will ever have. However, in the eye lens of someone affected by cataracts, the crystallin proteins become unfolded and then aggregate together. They stack on top of each other in a way that they are not supposed to. A person with cataracts will suffer from blurry vision, almost like you’re looking through a frosty or fogged-up window. While the surgery to fix cataracts (which basically takes out the old lens and puts in a new, artificial one) is pretty straight-forward and not very invasive, it isn’t easily accessible or affordable to a lot of people all over the world. Cataracts is attributed to causing ~50% of blindness worldwide, likely due to the fact that not everyone is able to take advantage of the simple surgery to fix it. Therefore, understanding the molecular, atomic basis of how cataracts happens could result in more accessible treatments (say a type of eye drop) for it worldwide.

This is where Heather comes in. There are different types of crystallin proteins and Heather zeroed in on one of them – gamma-S. Gamma-S is one of the most highly conserved proteins (meaning it hasn’t changed much over a long time) among all mammals, which tells us that it’s super important for it to remain just the way it is. Gamma-S makes up the eye lens by stacking on top of itself, making a brick wall of sorts ensuring that the eye lens retains its structure. However, research prior to Heather’s found that with increased age there is an increase in a modification called deamidation, which occurs in the unstructured loops of the gamma-S protein. Deamidation is a pretty minor change and is common in proteins all over the body, however in the eye lens if too much of it happens it no longer is a minor issue since it starts to disrupt the structure and protein-protein interactions of the eye lens. Heather’s collaborators at Oregon Health Sciences University found that there are two sites on the gamma-S protein (sites 14 and 76) where these deamidation events increase the most in cataracts-stricken eyes. It’s been known for a while that this deamidation is associated with cataracts however we never knew why it is associated with cataract formation because the changes caused by this modification were seemingly minor. This is how the Barbar Lab, and Heather specifically, became connected to this work since they specialize in studying unstructured proteins and protein regions, such as the loops present in gamma-S.

An example of an “1H(x-axis) 15N(y-axis) HSQC” spectra, aka, the fingerprint of a protein. This spectra is of WT gamma-S crystallin.

These deamidation changes are mimicked in the lab by creating two different mutants of the gamma-S protein’s DNA. Heather then compared the two mutants with the normal DNA by putting them through a series of experiments using the trusty NMR. The NMR is basically a large magnet that can make use of the magnetic fields around an atom’s nucleus to determine protein structure and motions. When Heather puts a protein sample into the NMR, the spins of the atomic nuclei will either align with or against the magnetic field of the NMR’s magnet. The NMR spits out spectra, which look like a square with lots of polka dots. This is essentially the fingerprint of the protein, unique to each one and extremely replicable. Heather can analyze this protein fingerprint since the different polka dots represent different amino acids in the gamma-s protein. Heather can compare spectra of the two mutants to the spectra of the normal protein to see whether any of the dots have moved, which would signal a change in the position of the amino acids.

After running experiments which measure protein motions at various timescales, from days to picoseconds, Heather discovered significant changes in protein dynamics when either site 14 or 76 was deamidated, however at different timescales. What this discovery means is that if both of these mutations are associated with cataracts and they are changing the same regions of the gamma-S protein, then these regions are likely central to changes resulting in cataracts. Therefore, research could be directed to target these regions to perhaps come up with solution to prevent and/or solve cataracts in a non-surgical way. The results of Heather’s study were recently published in Biochemistry.

Heather with her dog Piper.

Heather is from Arkansas where she completed her high school and undergraduate education. Living in a single-parent, non-academic home at this time, it took Heather a long time to figure out how to navigate the scientific and college-application scene, as well as even coming to the realization that science was something she was good at and could pursue. Despite receiving scholarships for college, she still had to work multiple jobs while in high school and college to have enough money for car-payments and gas to get to extra-curricular activities and volunteer jobs in the science field; things critical for graduate school applications. As a result, Heather is a strong advocate for inclusivity, striving to make things like science and college in general more accessible to low-income and diverse students. Heather’s decision to leave Arkansas and come to the PNW was inspired by advice she received from her undergraduate advisor who told her “not to go anywhere where you wouldn’t want to live. You will learn to love research, whatever it ends up being, but if you live in an environment that you don’t find fulfilling, then you are going to suffocate.”. Following this advice has lead Heather to where she is now – the senior in her lab where she has become a mentor to undergraduates, makes Twitter-famous Tik Tok videos (see below), goes on adventures with her dog Piper, and publishes cutting edge structural biology research.

Heather and her undergraduate mentee performing The Git Up in the lab.

To learn more you can check out the Barbar Lab website and Twitter page.

To hear more about Heather’s research, tune in on Sunday, September 29th at 7 PM on KBVR 88.7 FM, live stream the show at http://www.orangemedianetwork.com/kbvr_fm/, or download our podcast on iTunes!