Ph.D. student Carl Wepking and his team research the effects of added antibiotics in local farming soil ecosystems.
Research endeavors of all types are constantly ongoing in the labs across Virginia Tech’s campus. Walking up to the lab and office of Carl Wepking in Derring Hall provided an interesting first impression and one of mild displeasure: the room smelled like cow manure.
After meeting Wepking and discussing his current research, I realized it was indeed the smell of cow feces circulating through the air via the soil samples being analyzed on the table in front of us.
Wepking, a Ph.D student in biological sciences in the College of Science and an Interfaces of Global Change Fellow, currently studies the effect of antibiotic use in livestock production on soil microbes and the ecosystem functions that they regulate. This research mainly focuses on the effects of antibiotics on the environment. Specifically, Wepking works to determine the effects on soils and how antibiotics can influence microbes, which can therefore effect the greater cycling of important nutrients like carbon and nitrogen.
The project is a timely endeavor as the science for the research only started roughly 5 years ago because of regulations created by the FDA and CDC. A call for stricter legislation led to these regulations to protect the families and individuals living near antibiotic-fueled agricultural sites.
In order to bring greater attention to the issue of antibiotic resistance, Wepking has published a nationwide study on soil from areas with large cattle presence versus those with none. This study addresses one of the largest problems the team is facing in their research: understanding the effect of the manure itself separately from the effect of the antibiotics. High input sites, such as those observed in their local farm collections, versus low input sites used as the control in the study, helps to decipher the outcomes of the various elements of this microbial ecology research.
These communities, similar to those found in the greater Blacksburg community, can experience antibiotic resistance and additional major health concerns. Wepking and his team are working to learn more about the role the antibiotics play and trying to document the effects that agricultural antibiotics are having on soils in this region.
“This project is important from two angles,” Wepking explained. “It’s worrisome from a human health perspective but also the microbes in the soil have to work harder, which causes them to burn through soil organic matter inefficiently. This can have negative effects on the long term sustainability of soils.”
The team, comprised of Wepking along with a handful of undergraduate researchers and advisor Mike Strickland, a soil biologist now at the University of Idaho, performs field work locally at Kentland Farm.
Along with collecting soil samples, Wepking and his team must also evaluate the ecosystems in the spring during peak plant growth season. The project has been ongoing for two years and is projected to conclude within the next academic year.
“Ultimately, we need to ask ourselves what effect these antibiotics can have on the ecosystems as a whole,” Wepking said. “Antibiotics in general are a pretty modern tool but their role in soils and the idea of antibiotic resistance as a result isn’t always thought of right away. Through our research, I’m hoping to come to some concrete conclusions of how this cycle can have a longstanding impact on the natural and agricultural systems.”
Article written by Ali Marhefka while participating in ENGL 4824: Science Writing in Spring 2017 as part of a collaboration between Fralin and the Department of English at Virginia Tech. Learn more.
Arizona’s Petrified Forest National Park is known for its stunning views and beautifully preserved petrified wood. The trees here are Late Triassic in age (230-200 million years ago) and are preserved in agate, an often multicolored form of granular quartz. These fossil trees are what bring people from all over the world to the park each year but the petrified wood is not the only thing of significance to a paleontologist. The park is also an important source of vertebrate fossils from the Triassic.
The bones that are preserved here are weathering out of what’s left of local exposures of the Chinle formation. Most of the fossil-bearing rock here has long ago weathered away leaving the petrified trees scattered around the area. The bones tend to be less resilient than the wood so paleontologists rely primarily on the remaining outcrops of Triassic mudstone to find vertebrate fossils still in place in the mudstone.
As part of a month-long expedition across the Midwest, Virginia Tech’s paleobiology group visited PEFO (Petrified Forest) over the last week in order to collect fossils and/or help out as needed with work in the preparation labs on site. The weather has not been cooperating however (it is monsoon season after all) and this has limited our time in the field. We were only able to spend a few days out on the bone beds but we didn’t come out empty handed!
A day of prospecting in the canyons around our target site yielded lots of phytosaur (large extinct croc-like reptiles) bone fragments too damaged to keep and some teeth and osteoderms (bony armor plates) worth retrieving. Because of the weather during the days leading up to our arrival, we were cut off from the target locality but by the next day, the road out to the site had dried up enough for us to drive all the way in and actually start excavating there. The site, called “the green layer,” is a thin layer of greenish-grey mudstone that contains abundant vertebrate fossils including those of phytosaurs, aetosaurs (large armor plated reptiles), and dinosaurs.
We recovered several bone fragments and osteoderms that had to be jacketed as well as several hundred pounds of sediment from the layer. The extra sediment we collected can be screen washed for microfossils back at Tech. Altogether, it was a productive few days of collecting (despite the weather) and an incredible experience working in the park! Some of the specimens we collected could potentially help with reconstructing the fauna and ecosystems of the Triassic of what is now the American Midwest!
We managed to catch a lizard (Holbrookia maculata). The local wildlife is beautiful and quick!
Some of the crew looking at calcified root casts in the mudstone. These formed as a result of calcium carbonate precipitating inside the voids left by plant roots that, at one point in the distant past, infiltrated the sediment.
Over the past week, the VT Paleobiology group, led by Drs. Michelle Stocker and Sterling Nesbitt, headed out to Wyoming to find fossil bones from the Triassic (~199 to 252 million years ago) as a part of a month-long expedition to do field work across the Midwest. The area around Lander Wyoming is home to several exposures of Triassic sedimentary rocks, exactly the kind of place you want to look to find vertebrate fossils from that time. We spent the week prospecting several localities and weren’t disappointed!
The main focus of the trip has been to uncover a large (~8 foot long) fossil phytosaur that was found in 2015 on a previous expedition. These creatures looked superficially like crocodiles but are distantly related. They had armor plating all over their bodies and long snouts filled to the brim with sharp, serrated teeth. The fossil in question lies on a ridge of exposed sedimentary rock that happens to be incredibly difficult to reach. The hike is roughly a mile from start to finish and the elevation change is over 1000 feet. We had to haul tools, personal supplies, and eventually fossils up and down this path twice a day for 6 days!
The first day on site was mostly spent scoping out the area around the phytosaur fossil which had been capped (coated in plaster and burlap to protect it) and buried at the end of the 2015 expedition. The goal for this day was to prospect for new fossils and new sites in the Chugwater formation, the formation that contains the phytosaur skeleton. We found lots of phytosaur teeth and some small fragments of miscellaneous bone from the first site that was located in 2015 but nothing new.
On the way back from the quarry, we found the bones of a horse that had died shortly before the 2015 expedition. The 2015 team dubbed it DH (dead horse) and left it to skeletonize in the desert. Two years in the elements has certainly done the trick! We collected the skull and lower jaw, the sacrum (fused pelvic vertebrae), half of the pelvis, and some of the limb bones for use as a reference in the paleobiology lab at Tech.
The first hike was a challenge but by the next day we were getting the hang of it. We arrived on site a little earlier and were able to do some more thorough prospecting in a larger area around the phytosaur fossil. A few of us found several large fossil amphibian bones in a productive layer of purplish rock near the phytosaur! These amphibians, called metoposaurids, were enormous, reaching lengths up to 6 feet. In addition to prospecting, we were able to uncover the phytosaur and begin working on excavating it further.
We spent the whole rest of the week excavating the phytosaur but it just keeps getting bigger! There’s no sign of it ending so we couldn’t get it out this trip but hey, plans change. After capping what we uncovered, the whole fossil was then buried just like last time. It’s too big to move at this point and still well encased in rock. We’ll have to come back next year!
We finished off our stay in Wyoming with some prospecting at different sites down the road from the phytosaur locality. We ended up finding a crazy new locality that’s just overflowing with fossil bones! This could be another place to quarry in the future.
The Great Barrier Reef is like a sick trauma patient. It is suffering from mass coral bleaching, excessive seaweed or macroalgae, poor water quality, runoff, and other ailments. In many places, it is degraded and dying. However, it is not dead yet.
So, what are people doing to breathe new life into this patient?
University students from Virginia Tech and The College at Brockport, State University of New York, in collaboration with Reef Ecologic and Bungalow Bay, experienced firsthand how to restore the Great Barrier Reef and learn why coral reef restoration is important.
The Great Barrier Reef is a living, diverse ecosystem that provides many significant services to humans, similar to other ecosystems across the globe. It is important to learn about and conserve these ecosystems, so that we can conserve them.
The Great Barrier Reef is the largest coral reef ecosystem on the planet. It is a living organism that provides a home for a diversity of plant and animal species. The Great Barrier Reef is a network of coral reefs located off of Australia’s east coast.
Coral is an animal that has a symbiotic relationship with algae called zooxanthellae. These tiny organisms live in coral structures and harvest sunlight, much like plants on land, to create energy for themselves and the coral. Coral and zooxanthellae work together to keep the reef healthy.
The following video details some of our efforts and experiences in our Hokies Abroad course, during which we worked with Reef Ecologic on a citizen science project focused on coral reef restoration.
So what does the Great Barrier Reef do for us? The reef protects the beautiful beaches of Australia by breaking waves and slowing them. The reef can also absorb excess carbon in the atmosphere, providing oxygen for the colorful life that inhabits it. There are roughly 6,000 species of marine life that call this reef home. It is the unique and diverse aquatic community that draws many people to Australia, contributing significantly to Australia’s economy. According to Nathan Cook, a scientist from Reef Ecologic, the Great Barrier Reef’s net worth is estimated at $900 billion.
What is happening now? Currently, there are several threats to the reef, which include climate change and nutrient runoff. Our project focused on removing excess macroalgae from the reef associated with runoff from coastal development. These macroalgae outcompete coral for space.
By removing small sections of macroalgae, we provided the coral with more room to colonize and grow. Even though we only removed a relatively small amount of macroalgae, the continuation of reef restoration projects like this can give the Great Barrier Reef a second chance at life.
Our experience with the Hokies Abroad Australia and New Zealand program gave us the opportunity to give back to our environment in a way we never thought possible. In the spirit of Ut Prosim, we participated in a citizen science project to help restore a degraded part of the Great Barrier Reef.
Students from Virginia Tech and The College at Brockport, State University of New York, are working with Reef Ecologic and Bungalow Bay on a citizen science Great Barrier Reef restoration project.[/caption]
[Written by Virginia Tech students Rebecca Brassfield of Department of Biochemistry in the College of Science; Tyvanté Gillison of the Department of Fish and Wildlife Conservation in the College of Natural Resources and Environment; Norah Hopkins of the Department of Forest Resources and Environmental Conservation in the College of Natural Resources and Environment; Irene Jenkins of the Department of Biochemistry, College of Science; Jillian Kazmierczak of the Department of Animal and Poultry Sciences in the College of Agriculture and Life Sciences; and Alex Mansueto of the Department of Department of Human Nutrition, Foods, and Exercise in the College of Agriculture and Life Sciences.]
By Gifty Anane-Taabeah, a Ph.D. student in fish and wildlife conservation, College of Natural Resources and Environment, and an Interfaces of Global Change Fellow with the Global Change Center at Virginia Tech
[About the blogger: My Ph.D. research focuses on quantifying the genetic variability within and differentiation between natural populations of Nile tilapia Oreochromis niloticus in different river basins in Ghana. We have very little information on the genetic diversity of O. niloticus outside the Volta system. Furthermore, O. niloticus populations in major river basins in Ghana including the Pra, Ankobra, and Tano currently face diverse threats including habitat destruction from illegal small-scale gold mining activities, overfishing, and pollution. Using a population genetics approach, my research seeks to generate baseline data that will aid in conserving the species’ genetic diversity and local adaptation.]
Today is Wednesday June 7, 2017. I am currently lodging in Half-Assini, a border town between Ghana and our western neighboring country, Ivory Coast. I spent most of my day at Elubo, another border town about 45 minutes-drive from Half-Assini, in search of O. niloticus samples. Wednesdays are market days in Elubo and an opportune time to scout for wild-caught O. niloticus. This is especially important because Ghana shares the Tano River with Ivory Coast and the data generated will be useful for conserving the species in both countries.
I have successfully collected samples from the Pra and Ankobra Rivers, and I am amazed about the morphological differences I have observed among individuals within each river. I am already excited about what I will discover after my genetic analysis. I am hopeful that my research will provide the much needed baseline information about O. niloticus genetic diversity in Ghana, and add to the body of knowledge on the population genetics of O. niloticus in West Africa.
My research also seeks to identify wild populations of O. niloticus with a natural local adaptation to future climate conditions in Ghana. The average water temperatures in rivers vary along the latitudinal gradient of Ghana. Our previous experimental studies using different populations from the Volta River basin have revealed that some northern populations of O. niloticus may already be adapted to high temperature conditions, similar to the future climate conditions expected for southern Ghana.
Given this background, I have spent the last four months setting up and running three separate experiments to quantify the adaptation of different wild populations to varying temperature conditions both under laboratory and outdoor conditions, as well as to quantify the heritability of the growth rate trait from parents to their young.
I have a great local team comprising local fishers, government scientists and graduate students who have helped me with the collection of adult fish, monitoring of their growth and reproduction, and selection of their young for the experiments. I am hopeful that the data obtained from this research will be useful in selecting suitable populations and developing them for aquaculture in Ghana and sub-Saharan Africa.
I am chugging café con leche and downing a whole plate of fresh papaya and pineapple while I wait for Dani to pick me up at the hotel. It was a late night, with a delayed flight from Atlanta to Panama City, but I am anxious to get out to the field with Dani and Angie today. Dani arrives and we weave our way through crazy traffic heading east out of the city. Every bus stop has a fruit stand and I implore Dani to stop for guanabana, my favorite tropical fruit, but he says it is too dangerous to pull over at the bus stops, and after watching a few buses pull in and out, I have to admit he is probably right.* We eventually leave the highway at a small town and stop to buy a few giant avocados en route to the field station. A few river and stream crossings later, and we arrive in a tropical paradise.
Dani and I are waiting in the open air “comedor” for Angie to return from scouting out a field site. When she gets there, she immediately starts cooking. We have a great lunch of tortillas and chorizo, with some of our recently acquired avocado. After lunch, Dani and Angie start packing for the hike to the field site. They are doing an important conservation project here—seeing if endangered toads that have been raised in captivity can survive at a site where they used to live. The hardest part of the project, hauling all the enclosures to the site (one per toad) and putting in the toads, was done a few days ago. Today we are going to go check on the toads and swab them, so we can monitor potential infection by chytrid fungus, the skin pathogen that likely drove this species to the brink of extinction in the first place. That swab will also allow us to assess the other microbes on their skin, so we can see how their symbiotic skin microbes change following re-introduction. We think these microbes might play a role in disease resistance, and so we want to track how they might change over time in the field in these toads that are so susceptible to chytrid fungus.
We are hiking up a very steep trail, just outside of the station. I stop to look at a frog (or maybe just to catch my breath). There is so much life in the lowland tropics– so many things to see. Hiking in a tropical forest, as a lover of biodiversity, is like no other experience. Every step brings something new to see… a frog leaping from underfoot, a giant caterpillar, a gorgeous orchid on a branch overhead, an amazing mushroom growing out of a stump, a flock of birds that make a ridiculous amount of noise but can’t be seen, the slightly eery sound of howler monkeys in the distance. We stop to watch two pied puff birds that look like small black and white kingfishers. They are sitting on a branch right next to the trail, near a termite mound and they seem as curious about us as we are about them. We keep moving and are headed downhill now, to a stream. We walk down this stream, on slippery boulders and large cobbles. Dani points out a small frog carrying tadpoles on her back, looking for a place to put them in the stream. It seems a precarious venture for such a small creature in a big stream, and I wish her well. We climb down the edge of a small waterfall that looks like it should be on a postcard, and soon we arrive at a larger stream, where the enclosures are, and the toads. It took an hour to get here and we have a lot to do, so we find the first enclosure downstream and get to work. Dani and Angie carefully check and swab each toad. Most are hiding in the leaf litter inside the enclosures, which is damp to the touch. I watch my students, trying to help a little where I can, and listen to the sounds of the forest—I am reminded of how much I love being in the field, and how that used to be a much bigger part of my job.
“Does everyone have extra batteries for their headlamps?” Angie asks. Dusk is rapidly approaching and we still have about 10 frogs left to swab. We are walking upstream to the next set of enclosures, which are spaced out along the banks as the stream topography allows. I pause momentarily, and Angie says, “Keep walking, please”, with a bit of urgency. I move forward as my brain ticks off the things that might have produced that tone in her voice. Fer-de-lance, bullet ants, jaguar…That is as far as I get on my list before Angie points out the coral snake climbing through some short palms to our right at about shoulder height. It is beautiful with its bands of red, yellow and black, and they aren’t aggressive snakes, so I stop to enjoy it for a moment.** When we arrive at the next enclosure it is nearly dark, and the loud squawking of blue-headed parrots is filling the dusky jungle. Soon it is completely dark, and we are working by headlamp to the plinking calls of hopeful male glassfrogs. The toads are sleeping on top of the palm fronds in their enclosures now that it is dark, so they are easier to find as we finish up our work.
It took us 90 minutes to get back to the field station from the end of the enclosure transect. We walked very carefully, eyes staring for vipers in the leaf litter on the trail as if it was a magic eyes illusion that would spring to life at any instant. At one point, Angie stopped to point out a large tree with a sparse line of bullet ants climbing it, and a few seconds later we all skirted around a bullet ant crossing the trail. We have nothing but respect for the insects given a “4+” for the pain of their sting on a 4-point scale. After shockingly cold showers, we had peanut butter, bananas and crackers for dinner, and maybe a little rum. I climb into my hammock for the night, feeling grateful that I have the opportunity to be here for a few days with these two amazing graduate students in this incredible forest.
*A few days later, Dani found me a guanabana at a city market, and I ate the whole thing, essentially all by myself. It was so good.
**We saw the snake again on the way out, and Dani determined it was a false coral snake, actually a colubrid, but still beautiful.
David Millican has a nickname around the community he lives in when he is in Namibia: Bird Man. He’s unique in that he is one of only a handful of people in the community studying birds; most are there to work with the cheetahs at the Cheetah Conservation Fund (CCF).
We arrived to CCF about a day ahead of David, who was held up in the capital city of Windhoek having repairs made to his vehicle.
“Oh you’re here to hang out with Bird Man,” said one CCF volunteer with a chuckle. “Although,” he added, “we’ve decided that maybe we should start calling him Bird Boy. Because Mark is the original Bird Man.”
Dr. Mark Stanback is a biology professor at Davidson College and a long-time mentor to David. He was one of the main reasons David got into birding: his enthusiasm and passion is contagious.
Mark began conducting research in Namibia in the 1990s. Two years ago, after an extended time away from Africa, he returned to launch a new set of experiments with the help of CCF and invited David to help.
Two years ago, he and David set up nest boxes around Otjiwarongo and Windhoek in hopes of attracting as many cavity nesting birds as possible so that he could study multiple aspects of their lives including mating, nest site competition and feeding habits.
But when Mark came back to monitor the boxes, he did not find birds but a disturbing new resident: honeybees, also known as African killer bees! The bees were highly aggressive in taking over the bird holes and also messy tenants— they left tree holes chock full of wax in their wake and birds can’t nest in the used cavities.
“I was not happy– it was ruining my nest-site competition experiment,” explained Mark. “But eventually I decided to study them instead of fighting them. And it got me thinking about honeyguides.”
Honeyguides are the only kind of bird that eats beeswax for a living.
“My hypothesis is that the honeyguide can act as a keystone species, having a greater impact on the community than their numbers would indicate,” said Mark. “I’ve never seen one here, but I know that when I arrived a year ago, 25 boxes that had had bees in 2015 had been picked clean of wax. So I want to know how quickly they can find wax and how quickly they can eat it.”
Mark generously invited us to go out with him to inspect next boxes. We drive down a dirt road, and get out every kilometer to check the boxes, which he has expertly tied to trees. We soon find that the African bees can’t be bought—there are no hives in the boxes.
Instead, we find a much more pleasing site: hornbills.
If you’re more familiar with Disney movies than exotic bird species like I am, it will help to picture Zazu from the Lion King to get a good idea of what a hornbill looks like. The birds are shockingly prehistoric-looking and beautiful, with black and white plumage and long curved beaks that are perfect for digging in the dirt and crushing lizards and millipedes.
In the first box we check, we find a mother and two half-grown nestlings. Mark predicts that they will fledge soon. The mom spends more than two months in the box, with most of that time spent incubating the eggs. When the biggest nestling is about two thirds grown, the mother breaks out, and the nestling then seals up the hole until it’s ready to leave. When the oldest leaves, the next chick will seal up the hole until it’s ready to leave, and so on.
About an hour later, we find another hornbill family (a mom, two babies, and un-hatched egg) in another box. The mother seems to glower at us as we observe and record our findings. But she does not move.
In another box, we find only remnants of a hornbill nest: grass, poop, and crushed millipedes. Another project Mark is working on involves trying to determine what purpose millipedes may serve in the hornbill home.
“People have known for a long time that hornbills smash millipedes and incorporate them into their nests and nest plugs,” said Mark. “And people have known for a long time that millipedes release cyanide. So people have kind of assumed that the hornbills are using the millipedes to cut down on pests in their nests. But no one has tested it.”
To test this, Mark will find multiple hornbill nests, and wait until the eggs start to hatch. Then he will replace all of the nests with new nest material, with half receiving smashed millipedes as well. After the nestlings fledge, he will monitor the parasite load in the control and experimental nests to determine any positive correlation between millipedes and number of parasites.
Mark will also collect data on egg size and egg production rate in one particular species: the Monteiro hornbill.
“I have a lot of projects going on right now,” says Mark with a chuckle. In addition to his own projects, he is on David’s thesis committee, serving as an adjunct professor at Virginia Tech.
Together, the two “Bird Men” have their work cut out for them over the next few months.
Written by Lindsay Key; Photos by Jelena Djakovic.
The sky is bright blue and a cool breeze blows across the savannah as we load into the field rover for a morning’s fieldwork session. Last night’s electric rain shower brought a renewed sense of prosperity to the land, and the air is thrumming with joy and thumb-sized African beetles. Like tiny helicopters, they attempt to land on our shoulders and heads, attracted to the bright colored ties we wear in our hair.
They’re harmless enough, but our guide warns that the insect’s nickname, ‘blister beetle’ is well earned for the welt it can deliver.
“Just duck, it’s cool—it’s like Jedi training,” says David Millican, our guide and researcher extraordinaire.
We’ve followed him to what could be considered the middle of nowhere—just outside of Otjiwarongo, Namibia. But the truth is, despite the low human population it’s quite definitely a somewhere: a beautiful rocky and sandy landscape brimming with biodiversity. Some of the world’s most rare and unique animals—cheetahs, giraffes, jackals, aardwolves, leopards, hornbills, and much, much more— call this harsh climate home.
Today, we’re accompanying David on a trip to check for cavities—and not the painful trip-to-the-dentist kind. We’re looking for bird homes: holes and rips in tree trunks and branches that are used by bird species within the local cavity guild. While the guild consists of bird, mammals, and reptile species, we’re most interested in the feathered ones.
As a bird biologist, David has a nagging question: which types of tree cavities are the birds using? By recording the species of birds that reside in different types of cavities, we can also determine who may be in competition. Finding the answer to these questions will help him answer larger ones about the structure and dynamics of the guild community.
David has established 20 sites across four adjacent farms that he believes could harbor a significant amount of tree cavities. During this season’s fieldwork he will repeatedly visit the sites, which are 16 hectares, to monitor cavities he’s discovered and search for new ones.
Acacia trees—which are abundant in these parts—are a favorite nesting spot. Some of the cavities we will visit were created by lightning, broken limbs, and insects or fungal decay. But others—known as excavated cavities—are pecked and created by the birds themselves. The birds that create the holes are known as primary excavators and the birds that live in the holes another bird created are known as secondary nesters, according to David.
“Some cavities can take a while to excavate, especially in live trees,” says David.
David’s tools today are a ladder, a peeping camera, a handheld GPS system, and a notebook for recording our findings.
He uses the GPS to navigate through his seventh site— a scrubby grassland of fallen brush and thorny plants, littered with a few antelope skulls.
Using the ladder to climb up to the first cavity resting high in the tree, David sticks the long cord of the peeping camera into the hole and is able to see on his monitor what awaits inside. This time, it’s nothing.
However, a few cavities later, we see signs of a former nest: feathers and grass. David’s hopes are lifted.
On the way to the next cavity, a cacophony of peeps arises from a tree ahead.
“Those are alarm calls,” says David, pointing in that direction. “That means there is likely a predator is nearby—could be a black mamba, boomslang, or mongoose. It’s best for us to go around that area.”
Working our way around the commotion, we come to a beautiful old camel thorn tree with a long slivered cavity in the trunk, about eye level . David inspects the hole with delight. Part of it is caked over with a thick mud: the telltale signs of a hornbill nest.
When female hornbills are ready to nest, they will enter a cavity and caulk themselves in, closing up the hole with mud, millipede shells, grass, and other vegetation. This is to prevent predators from entering and disturbing the nest when both babies and mom are vulnerable: moms lose their wing and tail feathers when incubating eggs and cannot fly.
Carefully and quietly, David sticks his cord into the small opening that remains and watches his monitor. Three timid faces stare back at him. Nestlings! And not very old at all, judging by their pink, featherless alien bodies.
David points the cord upwards into the hole and sees a fluff of feathers that he determines to be the mother, a yellow-billed hornbill. Often the mother will move to an area with more space above the cavity floor, allowing her to climb above the cavity entrance if a predator tries to break in.
David quickly retracts the cord. We will leave this nest alone for now, tiptoeing away quietly to avoid upsetting the sweet family.
By Casey Lowe, a Virginia Tech senior majoring in Humanities, Science, and the Environment in the College of Liberal Arts and Human Sciences
Between 1845 and 1849, the Irish Potato Famine destroyed crops and ultimately killed more than 2 million people in Ireland. The culprit? A highly destructive oomycete pathogen called Phytophthora infestans. Oomycete pathogens are a class of eukaryotic microbes that are similar to fungi and are well known for their destructive history.
Relatives of the oomycete pathogen that destroyed Ireland’s main food source in the 19th century are being studied at Virginia Tech today. Unlocking their genetic secrets could provide powerful benefits to agriculture worldwide. Plant disease causes a 15-20% yearly reduction in global crop productivity, and in today’s growing world food stability is volatile. By 2050 the world’s population is projected to have risen by 30% indicating the rising importance of food production efficiency and stability. That’s where plant pathologists come in.
Kasia Dinkeloo of Delaware, a fourth-year Ph.D. student in the department of plant pathology, physiology, and weed science in the College of Agriculture and Life Sciences, is working with John McDowell and Guillaume Pilot, both professors in the department, as well as four fellow graduate students, to analyze the manner in which oomycete plant pathogens invade plant hosts and extract nutrients.
Kasia found her interest in plants as a high school student. Her original plan was to attend art school, but after reading many books on plants for an art project she found a new passion to become a scientist, a route she also believed would be much more beneficial for her life. While completing her undergrad at the University of Delaware, Kasia took a class on plant pathology and immediately knew it was the direction she wanted to take.
She and her team, directed by McDowell and Pilot, operate in two different labs in Latham Hall investigating the mechanisms by which oomycetes alter the host plants metabolism to fit their nutrient requirements. Some oomycetes are challenging to study because they are biotrophic, meaning the organism must remain in the living host to complete its life cycle, and therefore cannot be cultured or grown away from the plant in order to be studied.
Much like humans, plants have complex and efficient immune systems consisting of a network of thousands of proteins working together. However, plant pathogens can still successfully invade and extract resources from the host plant by overcoming the plants immune responses. The mechanism by which oomycetes suppress plant immune responses is well studied and increasingly understood, but little research or knowledge exists that explains how pathogens trick the plant into giving away its nutrients. For Kasia, this unknown is the most exciting part of her graduate research, but also the most challenging.
For the past three years, Kasia has been developing a method which will eventually allow the team to isolate the specific cells that contain the oomycetes feeding structures from the bulk plant tissue. Once Kasia’s molecular technology is complete, the team will have access to RNA data that should contain genetic evidence of how oomycetes are capable of their takeovers. This information will bring the team much closer to their end goal: to create genetically modified versions of these plants that will resist nutrient extraction by the pathogen.
The test subject is a plant known as Arabidopsis thaliana, a commonly used model organism for pathology studies. The oomycete Hyaloperonospora arabidopsidis is a natural pathogen to Arabidopsis thaliana, making it a perfect candidate for the studies. By understanding how oomycetes successfully hijack nutrients from Arabidopsis, Kasia will be able to isolate the enabling traits and then create modified plants that suppress or are unaffected by the pathogen interference. This will help create plants that won’t give up their nutrient sources, cutting the supply line to the pathogen.
Kasia is well aware of the economic value of her research beyond its scientific implementations. “The value of our science is a dollar value,” said Kasia. “If we can create healthier plants with a higher yield, it will decrease food prices, something the consumer will see in the grocery store and directly benefit from.”
Using pesticides for the chemical control of pathogens has been successful in some ways, but they have caused irreversible environmental damage as well as generated new pathogens resistant to pesticides. By creating modified plants with a genetic defense against oomycetes, the need for pesticides could be eliminated altogether.
According to Kasia, genetically modified plants will be essential for feeding our growing population. She believes creating more food on less land will only be accomplished by working on the plants themselves, not just the environments in which they are grown and produced.
“I’m going to feed the world, that’s the dream! Food is security,” she said.
Q&A: Meet Kasia
Hometown: Wilmington, Delaware
Major/Year: Fourth-year Ph.D. student
Fralin Advisors: John McDowell and Guillaume Pilot
Other Degrees: Bachelor of Science from the University of Delaware
Why do you want to be a scientist?
I really enjoy plant science because it’s a really beautiful way to see the world. I like knowing that the work I do is not only very fulfilling to me as a person, but can be used to help feed our population.
What created your interest in plant pathology?
I knew that plant science/plant pathology was for me after a freshman year course at U.D. called “People and plants: feast or famine.” I loved learning about how plant pathogens and plant growth shaped so much of history, and how understanding plant disease is a key part of food security for the future. After that class, I guess I was hooked.
Career goals after graduate school?
As far as ultimate career goals after the Ph.D., it’s hard to give a clear answer since I am so undecided. But whether I am in academia or industry, I would really love to keep exploring different aspects of plant-pathogen interactions and stay as close to a research lab setting as possible.
Favorite hobby outside of school?
I have a dog; he’s the best ever. I really like having a dog because it reminds me to go home and not spend all day in the lab. I love hiking and outdoor activities as well as powerlifting.
Favorite thing about Blacksburg?
People here are so nice! I thought I was nice when I moved here, but I was just nice for Delaware. There is such a good sense of community here.
This past year, a new undergraduate course was successfully introduced at Virginia Tech: Phage Hunters, BIOL 1135 and 1136.
Housed in the department of biological sciences in the College of Science, the two-semester course, offered beginning each fall, gives students the chance to undertake a genomics project from start to finish, while gaining experience beyond the typical coursework in introductory laboratory classes.
During the fall semester, students were tasked with finding bacteriophage, or viruses that infect bacteria, using wet lab isolation techniques.
Bacteriophage, or phage for short, are often studied in clinical research settings for their ability to target bacteria. While in the class, the students cultured the phage using Mycobacterium smegmatis, which is similar (though non-pathogenic) to the strain of bacteria that causes tuberculosis.
After the phage were isolated, they were sent for genomic sequencing at the University of Pittsburgh, which works in tandem with the Howard Hughes Medical Institute’s Science Education division to administer the SEA-PHAGES program, in which Virginia Tech is now a part.
Once in Pittsburgh, the genomes of the phages were sequenced and then sent back to Virginia Tech to be annotated – or in layman’s terms, thoroughly described – during the spring semester.
From there, the students had to describe each genome, and argue for each gene’s location based on outside research. Finally, they had to present the function of each gene as they understood it based on their research of gene functioning in other phages, as well as what they had learned with their instructor, Stephanie Voshell, and in other biology courses.
“The annotating was incredibly difficult to grasp at first,” said Tetyana Senchyshyn, an undergraduate majoring in biological sciences who took the second semester of the course first.
“Once you get the hang of the software and the annotating, it’s not as hard as I thought it might be. It’s actually a lot of fun. Every gene is a new puzzle piece you’re trying to fit into the genome and the entire phage as a whole.”
Initially, the students got a feel for the techniques used to annotate genes. They then spent the rest of the semester working in teams to annotate the genomes of the three sequenced phages, with each having 89-112 genes.
Using computer software designed at the University of Pittsburgh, they began identifying the genes in order to identify their location on the phage genome and, ultimately, each gene’s function.
“The students had to look at each site where the computer thought a gene was, and use logic to reason through and take all the pieces of evidence into consideration to decide if that was the correct call,” said Voshell, an instructor of biological sciences who teaches the two-semester sequence along with Kristi DeCourcy, a research associate at the Fralin Life Science Institute, in the fall.
“You want to find the genes so you can determine the amino acid sequence, because if you don’t know what the specific start and stop sites are, you can’t study the translations to learn about their structure and function,” said Voshell.
By the end of the semester, the students fine-tuned their descriptions for every single gene for each of these three genomes. Their work culminated in a final report that will be published in the Actinobacteriophage database, which is run and maintained by the Pittsburgh Bacteriophage Institute at the University of Pittsburgh, and GenBank, a genetic sequence database at the National Institutes of Health. Both include annotated sequences from other participating students and scientists so others can reference them in future research. This includes when scientists are studying bacteria that cause disease.
“Because their work builds on what others have done, the students always had to be thinking, is this logical or could someone have perpetuated a mistake?” said Voshell. “They really had to think about what’s happening in the phage, what it’s doing in the host when it’s replicating itself, and use that knowledge to decide what functions these genes might have.”
In addition to Voshell and DeCourcy, Kyle Szwetkowski, a master’s student in biological sciences who studies mycobacteria, and Holly Packard, a graduate student also in biological sciences, joined the students. Both served as the course’s graduate teaching assistants, with Packard helping guide the students in the fall, and Szwetkowski helping throughout the entire yearlong process.