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Accolades Biodiversity Faculty Spotlight Food & Agriculture Grants News Research Sustainable Agriculture

Grant awarded to study how plants affect microbiomes

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VT News | October 6, 2020

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For centuries, scientists have worked above ground, studying plants and their effect on biodiversity. Lying below the scientists’ feet, though, is a world with even richer biodiversity — the soil.

There are an estimated 1 billion cells and thousands of species of microbes in a single gram of soil, making it an extremely complex microbiome.

To help understand the complexity of soil microbiomes and how cover crops can help manage them, a four-year $500,000 grant was awarded to a team of Virginia Tech interdisciplinary researchers by the United States Department of Agriculture National Institute of Food and Agriculture.

The project integrates key agricultural concepts of cover crops – the microbiome, biodiversity, yield, and soil health – to build a whole-system perspective. The project is being led by Brian Badgley, an associate professor of environmental microbiology, and Jacob Barney, associate professor of invasive plant ecology — both in the School of Plant and Environmental Sciences in the College of Agriculture and Life Sciences; and Brian Strahm, an associate professor of forest resources and environmental conservation in the College of Natural Resources and Environment. All three are affiliated faculty members of the Global Change Center and Fralin Life Sciences Institute.

The soil microbiome has strong effects on how ecosystems function but is difficult to directly alter. The team is researching whether or not crop mixtures can be designed to change it indirectly with predictable outcomes and benefits.

The team will conduct their work at the College of Agriculture and Life SciencesKentland Farm.

The underlying principle behind the work is to examine how plants affect soil microorganisms, which has mostly been researched looking at only how a single plant affects the soil.

The research team will conduct their work on soil microbiomes at Kentland Farm. Photo credit: Olivia Coleman
The research team will conduct their work on soil microbiomes at Kentland Farm. Photo credit: Olivia Coleman

 

“We don’t have a really good understanding of the aggregate effect on soil microorganisms when we combine multiple plant species,” Badgley said. “By investigating underlying rules about how that happens, we hope to better understand how those effects scale up as you add more plant diversity.”

Cover crops make an excellent model for that because a cover crop mixture could comprise up to five plant species, which, when compared to a giant field of nothing but corn, is quite a bit of diversity.

“On the other hand, cover crop systems are still relatively simple plant communities that will, hopefully, make it easier to see some of these important signals about which parts of the soil microbiome are changing,” Badgley said. “What we learn about cover crops and agricultural sustainability has the added benefit to farmers of direct application in the field. However, by identifying the underlying relationships, we hope that results will also have applied benefits in other contexts, such as ecosystem restoration and potentially even landscaping and gardening.”

Each of the researchers brings a unique perspective into the mix, allowing them to analyze the whole complex system.

“In the end, we want to design mixtures that maximize plant diversity in different ways – either plant characteristics or the diversity of soil microorganisms that they recruit – based on results from individual plants,” Badgley said. “We then hope to understand whether different types of plant diversity ultimately change how the whole system will function.”

If that’s achieved, the research team could mix plants in the field for particular effects on soil microorganisms.

To better support the research, the grant will fund two Ph.D. candidates during its four-year run.

— Written by Max Esterhuizen

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Suzanne Irby

Michael Stowe
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Categories
Disease Faculty Spotlight News Research

Linsey Marr shares airborne virus knowledge, COVID-19 tips during virtual conversation

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VT News | September 15, 2020

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Throughout much of her career, Linsey Marr found that her multi-disciplinary approach to science was more of a challenge than an asset.

“For the past 12 years I feel like I’ve toiled in total obscurity working on airborne viruses,” said Marr, the Charles P. Lunsford Professor of Civil and Environmental Engineering. “It’s an interdisciplinary topic that doesn’t fall neatly into one department or field of study. I’ve struggled at times to get funding and to get papers — except now over the period of a couple of months, it became one of the hottest topics around.”

When the COVID-19 pandemic erupted across the world, and as scientists collected evidence that the virus was transmitted through airborne aerosols, that “total obscurity” suddenly became a bright spotlight. As one of fewer than 12 worldwide experts on aerosol transmission of viruses, and one of only a few in America, Marr’s expertise and ability to communicate to the public became a hot commodity. Since March, she has given more than 300 interviews and been quoted more than 4,000 times in 79 countries.

 

 

“Most of us had never heard of aerosol science before the pandemic,” began a New York Times profile headlined, “The Scientist, the Air and the Virus.” “Then Virginia Tech’s Linsey Marr showed up and became our tour guide to the invisible world of airborne particles.”

“It’s been a bit of a spaceship ride,” Marr laughed in an hour-long conversation with Virginia Tech President Tim Sands on Tuesday.

Marr’s interdisciplinary background gives her a broad view of the COVID-19 pandemic, but also the ability to communicate knowledge through memorable analogies and visuals that help her students and the public to better understand the virus and how it moves through the air.

As Sands noted, Marr took an interdisciplinary approach from the beginning of her academic career, “and even broadened rather than narrowed down as you went forward.”

“I hated the idea of having to choose a major,” Marr said. “I loved and appreciated natural science and math and even social science. I tried to pick a major that was as broad as possible.”

Marr holds a B.S. in Engineering Science from Harvard College and a Ph.D. in Civil and Environmental Engineering from the University of California at Berkeley. At Virginia Tech, she leads the Applied Interdisciplinary Research in Air (AIR2) laboratory and teaches courses on air pollution and environmental engineering.

“Virginia Tech has a strong culture of promoting interdisciplinary research,” Marr said. “I felt free to pursue research that was interesting to me. I have great colleagues here. The culture of the university allows you to reach across departments. People are very friendly and open to collaboration. People aren’t trying to protect their turf as much.”

As COVID-19 emerged in Wuhan, China, and began to spread around the world, scientists debated how the virus was transmitted. Given her previous research on the spread of the flu and other diseases, as well as evidence that previous coronaviruses such as SARS spread through aerosols, Marr felt that COVID-19 would spread through aerosols as well.

In early March, Marr posted a thread on Twitter that began, “Let’s talk about #airborne transmission of #SARSCOV2 and other viruses. A discussion is needed to improve accuracy and reduce fear associated with the term.”

Marr told Sands she had posted that thread to bust some myths about airborne viruses and to replace them with more accurate information.

“As soon as people hear ‘airborne virus,’ there’s a tendency to panic,” Marr said. “I knew it was important to get the right information out there. We do know how this moves and there are things we can do to reduce transmission.”

The thread showcased Marr’s ability to communicate simply and effectively, and soon journalists came calling. She became an important voice in the public discourse. Marr used memorable images, describing large water droplets that are expelled by the mouth or nose as “cannonballs.” She compared the airborne transmission of the virus through clouds of microscopic droplets to being with a smoker: If one is indoors and the room is poorly ventilated, the smoke gets pretty thick, whereas if you’re in a car with the windows down, it’s not as bad.

Through the conversation, Sands leveraged Marr’s knowledge and descriptions to essentially walk through a how-to guide for students and the public to navigate this pandemic.

How to wear a mask:

Cover your nose and mouth, with no gaps around the edges.

How do masks work?

Marr described a horse and forest.

“What I like to think about is horse running full speed across a field, and at the edge of the field there’s a forest,” Marr said. “The trees are spaced closely, but they’re far enough apart that if the horse were moving slowly, the horse could get navigate through that forest. But the horse is going full speed, and it hits that the edge of the forest and it’s going to crash into the trees.

So that’s one way that the fibers in your mask trap particles that are coming at them. They [the particles] can’t make the turns that the airflow has to make around those fibers.”

Research shows that layering fabric improves a mask’s effectiveness. A single layer of fabric helps some, but two layers should block 95 percent of particles, Marr said.

How to gauge risk:

Remember the three Cs and the M.

  1. Avoid Close contact situations. Maintain distance from other people. Six feet doesn’t mark a magic barrier, but the particles do dilute with distance.
  2. Avoid Crowds. Being in large crowds increase the chances that one will be around someone infected with the virus, and that the virus will spread to others.
  3. Avoid Closed, poorly ventilated spaces. Imagine a cigarette smoker. In this room, will I take in any smoke?
  4. Wear Masks.

How to ride in a car:

Roll the windows down, even a few inches, and the air refreshes in a minute or two.

How to ride in an airplane:

The ventilation systems really help and are a point of pride for airlines. However, keep your mask on to reduce the risk of transmission from people in the row with you, in front of, and behind you.

How to socialize when it gets colder:

Marr suggested using blankets to tolerate cold temperatures outside, or indoors when all the windows are open. Another possibility for socializing outside would be to gather around a fire, if everyone is masked and keeping distance.

How to endure flu season:

Marr is optimistic.

“All the interventions that we’re taking for COVID-19 will also be effective for the flu, and so I expect we’ll see one of our mildest flu seasons ever,” Marr said. “The flu transmits largely in the in the same ways that COVID-19 transmits. There’s really a lot similarities, and I think we’ll see a lot fewer flus and other respiratory diseases this coming winter. But we need to remain vigilant.”

How to drink a beverage while wearing a mask:

Marr said she’d considered this at some length. Removing one’s mask to drink doesn’t really work. So she landed on the idea of combining a mask with a bendy straw — though Marr acknowledged with a laugh she hasn’t really tested this idea, either.

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CONTACT:

Suzanne Irby

Michael Stowe
540-392-4218

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Categories
Announcements Biodiversity Faculty Spotlight Global Change Research

Walking a fine line: How chemical diversity in plants facilitates plant-animal interactions

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VT News | September 9, 2020

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We aren’t the only beings who enjoy feasting on tasty fruits like apples, berries, peaches, and oranges. Species like bats, monkeys, bears, birds, and even fish consume fruits — and plants count on them to do so.

Wildlife disperse their seeds by eating the fruit and defecating the seed elsewhere, thus carrying the fruit farther away and spreading the next generation of that plant. But attracting wildlife might also mean attracting harmful organisms, like some species of fungi.

Plants walk a fine line between attraction and repulsion, and to do this, they evolved to become complex chemical factories. Chemical ecologists at the Whitehead Lab at Virginia Tech are working to uncover why plants have such diverse chemicals and to determine the functions of these chemicals in plant-microbe and plant-animal interactions.

“There is still so much we don’t know about the chemical compounds plants use to mediate these complicated interactions. As we continue to lose global biodiversity, we are also losing chemical diversity and the chance for discovery,” said Lauren Maynard, a Ph.D. candidate in the Department of Biological Sciences within the College of Science.

Piper sancti-felicis is a neotropical shrub related to Piper nigrum, which produces black peppercorn. Although P. sancti-felicis isn’t as economically important as its peppery cousin, it fulfills an important ecological role as one of the first plants to colonize a recently disturbed area. It also serves as an important food source for wildlife, especially bats and birds.

The research team on a Piper expedition in Barva Volcano National Park in Costa Rica. From left to right: Susan Whitehead, Lauren Maynard, Juan Pineda (Organization for Tropical Studies), Orlando Vargas Ramírez (Organization for Tropical Studies), Gerald Schneider (Virginia Tech), and Juan Chaves (Barva Volcano National Park).Photo courtesy of Lauren Maynard.
The research team on a Piper expedition in Barva Volcano National Park in Costa Rica. From left to right: Susan Whitehead, Lauren Maynard, Juan Pineda (Organization for Tropical Studies), Orlando Vargas Ramírez (Organization for Tropical Studies), Gerald Schneider (Virginia Tech), and Juan Chaves (Barva Volcano National Park). Photo courtesy of Lauren Maynard.

 

At La Selva Biological Station in Costa Rica, Maynard and a team of international ecologists worked to better understand the evolutionary ecology of P. sancti-felicis. Their findings were recently published in Ecology and serve as a step forward in understanding why plants have such great chemical diversity.

By analyzing the samples, the team discovered 10 previously undocumented alkenylphenol compounds in P. sancti-felicis. Alkenylphenols are rare in the plant kingdom, as they have been reported only in four plant families.

The alkenylphenol compounds were not distributed evenly across the plant, though. Maynard found that fruit pulp had the highest concentrations and diversity of alkenylphenol compounds, while leaves and seeds had only a few compounds at detectable levels. Later, a pattern emerged: Levels of alkenylphenol were highest as flowers developed into unripe pulp, but then decreased as the pulp ripened.

When Maynard and her collaborators tested alkenylphenols with different species of fruit fungi, they found that the alkenylphenols had antifungal properties. But those same compounds also made the fruits less tasty to bats, which are the plant’s main seed dispersers.

This is a delicate balance: high levels of alkenylphenols protected the fruit from harmful fungi as it developed, but when it ripened, alkenylphenol levels dwindled so that bats would be interested in eating it.

“Many fungal pathogens attack ripe fruits and can make fruits unattractive to dispersers, or worse, completely destroy the seeds. Our study suggests that these toxins represent a trade-off in fruits: They do deter some potential beneficial partners, but the benefits they provide in terms of protecting seeds outweigh those costs,” said Susan Whitehead, an assistant professor in the Department of Biological Sciences.

This study is the first to document an ecological role of alkenylphenols. Chemical interactions in the plant kingdom are not easy to see, but they play a crucial role in balancing trade-offs in various interactions. In the case of P. sancti-felicis, alkenylphenols help the plant walk the fine line between appealing to seed dispersers and repelling harmful fungi.

“Finding the nonlinear pattern of alkenylphenol investment across fruit development was really exciting. It suggests that the main function of the compounds is defense,” said Maynard, who is also an Interfaces of Global Change Fellow in the Global Change Center, housed in the Fralin Life Sciences Institute.

This discovery helps researchers understand the nuances of tropical forest ecology and how chemical diversity in plants helps maintain that delicate balance. Plant chemical defenses have mostly been studied in leaves of plants, so this new discovery furthers scientists’ understanding of how and why these compounds are crucial in fruits. And because fruits are the vehicle for seed dispersal, these chemicals play a significant ecological role.

“This study advanced our understanding of how tropical forests work by bringing together scientists and expertise from multiple fields of study: plant ecology, animal behavior, chemistry, and microbiology,” said Whitehead, who is also an affiliated faculty member of the Global Change Center and the Fralin Life Sciences Institute.

The Whitehead Lab has several ongoing projects focused on plant chemistry and seed dispersal at La Selva Biological Station. Since international travel is not possible at the moment, the team hopes to resume their research when it is safe to do so. 

 – Written by Rasha Aridi

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CONTACT:

Kristin Rose Jutras
(540) 231-6614

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Categories
Announcements Evolution Faculty Spotlight Global Change Research

A trans-Atlantic journey: how microbes and dust travel from Africa to the Americas

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VT News | September 1, 2020

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Each year, over 180 million tons of dust are swept up from the Sahara Desert, blown across the western edge of Africa, wisped across the Atlantic Ocean, and deposited throughout the Americas. These are called dust plumes, and they carry more than just sand.

In fact, dust plumes play a crucial role in the long-range transport of microorganisms. A team led by Virginia Tech researchers in collaboration with the U.S. Geological Survey and the University of La Laguna in the Canary Islands received a $1.1 million grant from NASA to study microbial diversity in dust plumes and the physics behind the transport of dust and microbes along superhighways in the sky.

“One of the less understood aspects of dust is that these particles could be a vehicle for microbes — viruses, bacteria, fungi that can come across the Atlantic, as if hitchhiking on these dust particles,” said Hosein Foroutan, the principal investigator on the grant and assistant professor in the Department of Civil and Environmental Engineering in the College of Engineering.

Foroutan and his collaborators will take a transdisciplinary approach to study the microbial biodiversity in dust plumes by analyzing collected samples, investigating satellite data, and creating transport models. Ultimately, this research will inform experts about which microbes are being transported to the Americas and what that could mean for the health of plants, domestic animals, and people.

 

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To do this, the team is operating on an intercontinental scale. They will analyze dust samples collected from various sites between the United States and Africa, including the middle of the Atlantic. Sampling at various locations on the “dust superhighway” will allow the team to study differences in microbial biodiversity. Using DNA sequencing, culturing, and other microbiological techniques, the team will be able to determine the types, concentrations, and viability of microbes in the dust samples.

“Little is known about the diversity and viability of microbes traveling on African dust. Could devastating plant and animal pathogens be riding on African dust? If so, we would like to know where they are going and when they might arrive there,” said David Schmale, professor in the School of Plant and Environmental Sciences in the College of Agriculture and Life Sciences. As a collaborator, Schmale will work to identify microorganisms in dust samples.

But microorganisms are especially sensitive to the environment — temperature, altitude, precipitation, humidity, and ultraviolet radiation can all affect the survival of microbes. Coupled with atmospheric and satellite data, the researchers will be able to use microbial diversity data to peer into the life of microorganisms traveling in dust plumes from one continent to another.

“We’re lucky we can associate microbes with dust, which we can detect using satellites because we have no way of continuously detecting these airborne microorganisms on this scale. You’re talking about a huge scale — a couple thousand kilometers apart — and up to five to six kilometers above the surface,” said Foroutan, who is also an affiliated faculty member of the Fralin Life Sciences Institute and the Global Change Center at Virginia Tech.

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esearch on the microbial diversity in dust plumes can help scientists understand what kind of microbes may be blown in from overseas and how to prepare for that. Since species in the Americas have not evolved to deal with microbes native to other parts of the world, an invasive microorganism can pose a significant threat to plants, animals, or people.

“Pathogens are not respecters of international boundaries. One of my main motivations is to help farmers and others manage the risk that dust-borne microorganisms may pose. With better tracking and prediction tools, stakeholders can make informed choices about precautions they can take to halt the spread of disease and ensure a secure food supply for all of us,” said Shane Ross, a collaborator on this grant and a professor in the Department of Aerospace and Ocean Engineering. Ross studies transport using observational and simulation data and will be applying his expertise to analyze dust transport.

Due to the scale and complexity of this study, Foroutan said “no one can tackle this problem by themselves” and that interdisciplinary collaboration is key. Other investigators include Dale Griffin from the U.S. Geological Survey and Cristina González Martín from the University of La Laguna in the Canary Islands, who helped collect dust samples to analyze for this project.

As the project progresses in the future, the team hopes to put out an open call for international collaborators to contribute their samples for a more global analysis of this phenomenon.

– Written by Rasha Aridi

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CONTACT:

Steven Mackay
540-231-5035

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Categories
Announcements Evolution Faculty Spotlight Global Change Research

Biological Science’s Josef Uyeda using NSF CAREER Award to capture big picture connection of macro- and micro-evolution

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VT News | August 27 2020

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Scientists know a lot about evolution. And like, evolution, this knowledge is always changing, growing, becoming stronger. But for all the work done during a span of two centuries and change, scientists mostly have pictures of evolution’s history, unsorted and scattered.

Snapshot photographs if you will, strewn across a table. Josef Uyeda, an assistant professor and evolutionary biologist in the Virginia Tech Department of Biological Sciences, seeks to take all those “photographs” and make them into a photomosaic – you’ve seen them, often in movie posters or jigsaw puzzles – where hundreds of photographs are assembled to form a larger image of its own. (Say, a man’s face, or the New York City skyline.) More simply, Uyeda is taking on a massive connect-the-dots project that spans millions of years of evolution, in its smallest and largest forms, with an eye toward the future.

“Studies of ‘evolution-in-action’ have revealed much about what causes evolutionary change, including why it sometimes fails. However, it is not always obvious when these causes are also responsible for extinction and adaptation over million-year timescales — the timescale primarily relevant to the evolution and maintenance of biodiversity,” said Uyeda, a faculty member in the Virginia Tech College of Science and an affiliated member of the Virginia Tech Global Change Center.

Uyeda will use a $778,000 five-year National Science Foundation (NSF) Faculty Early Career Development (CAREER) Program grant to carry out his study. The CAREER award is the NSF’s most prestigious awards in support of early-career faculty who have the potential to serve as academic role models in research and education.

“The goal of the grant is really to take how we study evolution across the tree of life from simply looking for patterns of how traits are related, to understanding what causes them to evolve,” Uyeda added. “How traits might evolve in response to the environment, how traits might respond to each other and trying to connect those to what we do at the microevolutionary scale, where we understand how variable traits are, the genetics underlying them, how natural selection works, and the driving processes of evolution. The goal is to bridge these together, making models smarter and allowing them to take data from both scales, rather than simply making more complicated models. If we unite those two sides together, we can get better answers to what’s happening.”

To take it a step further, Uyeda wants to predict future evolution much like meteorologist predict weather patterns hurricanes, and winter storms. This ties to climate change, and the survival of scores of fauna and flora. In weather, micro-actions in the atmosphere can lead to major- and macro-events, the butterfly effect. We know when the sunlight hits the Earth, certain parts are warmed, and where the sun does not reach as much, it is cold. It’s the predictability that Uyeda wants to bring to the study of evolution.

“With increasing rates of global change, it is vital to understand how and why species either adapt and survive, or fail to adapt and perish,” Uyeda said. “This project will build a bridge between the causes of evolution studied over short timescales and the long-term outcomes evident from existing evolutionary diversity with a new set of computational tools and resources for biology research and education. New models will integrate field, genetic, and experimental studies with patterns of trait change from across the tree of life.”

The bulk of the study will use statistics and data modeling. “It’s all based of what’s called the comparative method,” Uyeda added. “We can’t do experiments at million-year time scales, but we can look across species and see if all the species that live in a warm environment are evolving faster, or maybe all the warm-blooded organisms are evolving faster than the cold-blooded organisms. But how do we know those traits are actually related to one another? Well, we have to try and understand the entire evolutionary history through time to make sense of the patterns we see, and we have to use models to fill in the evolutionary history that we don’t see.”

This, of course, is difficult. The data sets of evolution from across the globe, the “tree of life” as Uyeda says, the fossil record, and in modern day studies of “evolution in action” are often disconnected. So, Uyeda and his team – which includes graduate students, a post-doc, and partner universities, will hit at the project in pieces.

“We’re going to take a page out of how we study DNA evolution, which borrows heavily from things like the theory of population genetics, and the understanding of how mutation and DNA actually evolves, to construct the tree of life.” To do the same for traits, they will look at what’s known from the evolution of biomechanics, the underlying genetics of mammal tooth evolution, and the millennia of fossil records and integrate these together to connect patterns from short to long timescales.

“I have not collected most of the data myself, and it would be impossible for me to do so alone. But I am trying to pull together existing datasets and bring them together in a single analysis. If we do so, then we can start to connect the big picture patterns of evolution to the short time scales we often use to study it, where we understand cause and effect,” Uyeda said.

“We want to look to the past to inform what we do in the future, as these are changes play out over millions of years. If we don’t understand how those processes work, then how can we understand what the future impacts will be of what we are doing today?”

 

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Categories
Biodiversity Blog Conservation Faculty Spotlight Global Change Science Communication Uncategorized Water

One fish, two fish: merging marine animal tracking with fishing fleet movements

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VT News | August 19, 2020

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The Food and Agriculture Organization of the United Nations estimated in 2018 that 34.2 percent of the world’s fish stocks were overfished, a worrying trend that has significant impacts on ocean environments and the fishing industries that utilize them.

Satellite technology has increased the capacities of researchers and scientists to collect data about marine animals while tracking the movements of commercial fishing vessels, two crucial drivers in the effort to maintain a healthy ocean ecosystem.

Virginia Tech collaborated with Stanford University and Global Fishing Watch to host “Fish and Ships,” an online workshop connecting researchers from around the world to discuss ways in which the merging of these two data sets might answer critical questions about human impacts on ocean biodiversity and sustainability. Participants brainstormed research approaches on overlapping species habitat maps with the data for national fishing fleet positions and discussed how emerging technologies can better model ocean dynamics.

“We’re in a new age in fisheries management,” said Assistant Professor Francesco Ferretti, of Virginia Tech’s College of Natural Resources and Environment, who coordinated the workshop. “Just a few years ago we had to rely mostly on what the fishers were telling us. Now we have a huge amount of data from satellites that track marine fishing vessels. From that data we can use models to track, predict, and characterize fishing operations around the world.”

Much of the fishing vessel data discussed was provided by Global Fishing Watch, which used the automatic identification system to track the movements of approximately 70,000 industrial fishing vessels from 2012 to 2016, resulting in the first “footprint map” of fishing fleet movement around the world. This map provides a crucial perspective on both the reach of commercial fishing and what drivers are potentially influencing the industry.

At the same time that fishing vessels are “pinging” data about where they are fishing, electronic tags on broad-ranging fish, such as tuna, swordfish, and sharks, are giving scientists new information about the movements of marine animals across the world’s oceans.

“We’re starting to do overlaps of these two data sets to see how much they cross paths,” explained Ferretti, a faculty member in the Department of Fish and Wildlife Conservation. “One goal is to develop a landscape of interactions so we can understand the ways that fishing impacts fish populations. From that information, we can go further, perhaps developing guidelines to help manage the fishing industry and provide data that will improve its efficiency while allowing ocean marine animal populations a chance to recover.”

Ferretti notes that workshop participants particularly enjoyed the opportunity to work collaboratively: “This first workshop has been a great success. We created a consortium of more than 70 scientists from academic institutions, national and international management bodies, and nongovernment organizations, all willing to play ball in making the ocean a more transparent place to use resources and benefit from its services.”

The July workshop served as the kickoff meeting; Virginia Tech is planning to host a second workshop to address the inventorying and integration of large data sets and ongoing analyses.

“We are currently taking steps to invite all these scientists to Virginia Tech,” Ferretti said. “While COVID will likely impact our plans, we are considering numerous hosting options, from our Innovation Campus in Washington, D.C., to our marine facilities on the Chesapeake Bay, to our beautiful campus in Blacksburg. The goal will be a full immersion into the technical aspects of the projects brainstormed during the kickoff meeting.”

Ferretti noted that Virginia Tech has a role to play in protecting and preserving our oceans and hopes that the Fish and Ships venture will prove to be a flagship project towards that effort. The Department of Fish and Wildlife Conservation is currently bolstering its research and educational opportunities in marine fisheries, ecology, and conservation.

“We are a technical university, and right now the ocean requires technical solutions,” said Ferretti, who is affiliated with the Global Change Center housed in Virginia Tech’s Fralin Life Sciences Institute. “There is a great deal of marine technology being developed to understand our oceans better, and Virginia Tech can play a big role in that domain.”

 

Written by David Fleming

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Categories
Blog Faculty Spotlight Global Change Water

VT researcher uses billions of data points to examine how increased flooding due to climate change impacts US waterways

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From CALS VT News  |  June 30, 2020

There’s a tendency in modern America to think of flooding as nothing but dangerous, a threat to homes, farms, roads, and bridges. But flooding — when the waters of a river rise above the banks and inundate the nearby land — is a natural phenomenon that benefits wildlife habitat and has been crucial for human civilizations ever since the first ones relied on the flooding of the Tigris, Euphrates, and Nile rivers to irrigate their crops.

Durelle Scott, an associate professor of Biological Systems Engineering affiliate of the Global Change Center at Virginia Tech, is the lead author of a paper recently published in the academic journal Nature Communicationsthat examines flooding in the continental United States in nearly unprecedented detail. Scott and his co-authors looked at what Scott calls “everyday” flooding in streams and rivers of all sizes, using data from 5,800 flood monitoring stations operated by the United States Geological Survey. With measurements typically taken every 15 minutes or every 30 minutes, that amounted to more than 2 billion individual measurements. For every station, the team performed 1,000 realizations of flooding thresholds to capture uncertainty, applying statistical techniques on a large computer server.

“The big picture is that flooding across the world is increasing with climate change, but not all flooding is bad and catastrophic,” said Scott, who is in both the College of Agriculture and Life Sciences and the College of Engineering. “We wanted to do an analysis where we captured the variability in annual flooding that occurs within small streams to larger rivers.”

Most flood studies are focused on single river basins or geographic regions, he said. By studying the entire lower 48 states, Scott and his team can examine flooding in both large and small rivers and conclude the entire nation could better manage its floodplains.

Among the paper’s findings: smaller streams flood more often than larger ones, but for shorter durations. The more frequent flooding means that smaller streams serve as a conduit between the landscape and the adjacent stream.

That’s a mixed blessing: “Delivery of nutrients and sediment to floodplain environments is partially why you have very rich soils and agriculture set up along river systems,” Scott said. But the movement of nutrients and sediment goes both ways, and when it moves from the floodplain into the river, it can be harmful to water users downstream.

“When excess nutrients get into a stream or river and are delivered downstream, you end up with algae blooms and the like, and that has implications whether it’s related to human health  or detrimental to commercial or recreational fisheries,” Scott said.

One of Scott’s findings is that the exchange of sediment and nutrients between rivers and floodplains depends not just on the levels of flooding, but on how long a flooding event lasts.

“If you have very short floods, you’ll end up having more net delivery from the floodplain into a river than removal of a specific nutrient or sediment,” Scott said. “That was unique in our study. We were able to quantify approximately how long water was on these floodplains and found for small streams the inundation is usually much less than a day, so there’s not usually an opportunity for removal of nutrients.”

This has implications for wetland restoration intended for water quality benefits. There has been much money and effort spent in recent decades to return rivers and floodplains to something resembling their natural state. This type of restoration, Scott said, must go beyond simply reconnecting a stream to a floodplain, by removing channels or levies that once contained the stream. If the water only tops the stream banks during high flows, flooding will be short and heavy, which could send more harmful material downstream. Instead, restoration within mid-sized rivers may produce more gradual flooding, to achieve what Scott called “the balance of optimal inundation time and nutrient supply for water quality benefits.”

Scott’s research could also have lessons for how we manage rivers to prevent catastrophic flooding. Serious flooding is certainly something to be prevented, but we may be over-protecting ourselves against moderate flooding to enable construction on low-lying floodplains.

“We’ve put in lots of levies to reduce infrastructure damage,” Scott said. “The flipside is if you put up a levy in a town and a town downstream doesn’t have as big of a levy, you’re making it worse for the downstream community. With more frequent flooding on the horizon, future water management needs to balance economic development within flood-prone areas relative to the societal costs of post-flood reconstruction.”

 

Written by Tony Biasotti

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Blog Drinking water Environmental Justice Faculty Spotlight Global Change Outreach Pollution Water

VT researcher working to provide clean water to Appalachia

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From CALS VT News  |  June 20, 2020

More than 2 million Americans live without access to safe drinking water or adequate sewer sanitation, according to a 2019 study by the U.S. Water Alliance. That includes around a quarter-million people in Puerto Rico and half a million homeless people in the United States. The biggest chunk, though — around 1.4 million people — are United States residents who live in homes that don’t have proper plumbing or tap water.

They are clustered in five areas: California’s Central Valley; predominantly Native American communities near the four corners of Utah, Colorado, Arizona, and New Mexico; the Texas-Mexico border; the Mississippi Delta region in Mississippi and Alabama; and central Appalachia. Virginia alone has around 20,000 homes without plumbing.

Leigh-Anne Krometis, an associate professor of biological systems engineering which is in both the College of Agriculture and Life Sciences and College of Engineering at Virginia Tech, is one of the foremost experts on water quality and availability in Appalachia. And while the basics of her work seem, well, basic — “I just spent a decade proving that not having sewers is a bad thing, which we’ve known for literally thousands of years,” she said — the implications are more complex.

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Often, the best minds in American civil and environmental engineering are looking abroad, at how to bring clean water to remote villages and slums in developing countries. The crisis over lead in the tap water in Flint, Michigan, was a reminder that all over the United States, people lack access to safe drinking water and adequate sanitation.

In the past three years, Krometis has authored a series of studies of water quality and availability in the Appalachian region. In 2017, she published “Tracking the Downstream Impacts of Inadequate Sanitation in Central Appalachia” in the “Journal of Water and Health.”

That article looked at what happens to streams when homes near them don’t have proper plumbing. Usually, that means a “straight pipe” that carries untreated sewage into an unlined hole in the ground, which drains either directly or indirectly into a stream. Krometis and her team found E. coli bacteria consistent with untreated human waste in those streams, in spots that were correlated with their proximity to homes without proper sewage systems. Sometimes the contamination carried as far as six miles downstream.

 

Image of Leigh-Anne Krometis

Krometis’ newest article on the subject, “Water Scavenging from Roadside Springs in Appalachia,” published in May 2019 in the “Journal of Contemporary Water Research and Education,” connects her earlier research on wastewater to the issue of drinking water. Some untold number of people in Appalachia drink untreated water from springs or streams — often the same streams that are close to straight sewage pipes. Krometis and her team tested the water at 21 springs used for drinking water, and more than 80 percent of them tested positive for E. coli.

Krometis also surveyed people who drink untreated spring water, and found that most of them do have running water in their homes, often from wells. They said they preferred the spring water because it tastes better than their tap water, or because they don’t trust the quality and reliability of the water in their homes.

Fixing these two interrelated problems, of wastewater and drinking water, isn’t easy. The homes that use straight pipes and roadsides springs tend to be far away from the nearest municipal sewer and water systems, and often separated by mountains and ravines. It could cost $50,000 or more to hook one of these homes up to a sewer system, even if there is one nearby, Krometis said. Septic tanks are usually unsuitable because the soil isn’t deep enough.

“These are legitimately challenging engineering problems, and they require a lot of money, and these places don’t have a lot of money,” she said. “We haven’t figured out ways to get water and sewer to extremely rural areas, and there are also huge issues with the homeless and the working poor in urban areas.”

There are cheaper and easier solutions, of the type used in developing countries. Public water kiosks for drinking water are one, and are already in use in some parts of Kentucky and West Virginia; small water or sewer treatment devices installed for each home or cluster of homes are another option. Krometis supports these tactics, though she sees the political and cultural obstacles to using them in the United States.

“The technologies that are best practices in Africa or Southeast Asia, we don’t use in the United States. They’re unacceptable because we’re a developed country,” she said. “But in my mind, if you have somebody who’s impoverished and doesn’t have access to clean water, that’s a problem that we need to address.”

People are hesitant to give residents of Appalachian mountain hollows or California’s dry and dusty farm town water and sewer systems that aren’t up to the standards of their fellow Americans in cities and suburbs. Krometis understands that hesitation, but she also understands that many of those poor Americans are going without any access to reliable, clean water.

“I see both sides of the coin,” she said. “The problem is, we’re not even having that debate.”

 

Written by Tony Biasotti

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Blog Disease Faculty Spotlight

VT researchers establish a reverse genetics system to facilitate COVID-19 research

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From VT News  |  June 4, 2020

The novel coronavirus, or SARS-CoV-2, is currently causing a worldwide pandemic that has infected more than 5 million human beings, and the number continues to climb. Vaccines and antivirals are urgently needed to combat this threat, and the viral genetics that resulted in this outbreak must be identified.

With funding from the Fralin Life Sciences Institute at Virginia Tech, researchers James Weger-Lucarelli and Nisha Duggal, from the Virginia-Maryland College of Veterinary Medicine, are establishing a reverse genetics system for SARS-CoV-2 that will serve as the basis for vaccine design and for studying viral mutations associated with COVID-19 severity and viral transmission.

“The reverse genetics system is the basis for all future studies, including vaccine studies. It will allow us to manipulate the SARS-CoV-2 viral genome so that we can discover weaknesses in the virus to exploit,” said Weger-Lucarelli, a research assistant professor in the Department of Biomedical Sciences and Pathobiology in the Virginia-Maryland College of Veterinary Medicine.

Having studied Zika and mosquito-borne viruses in the past using reverse genetics systems, Weger-Lucarelli and Duggal, who are both affiliated faculty of the Fralin Life Sciences Institute, will create a new reverse genetics system for SARS-CoV-2 that will provide a blueprint for making vaccines and reporter viruses.

SARS-CoV-2 stores its genetic material in ribonucleic acid (RNA), as opposed to deoxyribonucleic acid (DNA), making it difficult for scientists to study and manipulate the viral genome. With a reverse genetics system, scientists can convert the virus’s RNA back into DNA through a process called reverse transcription.

James Weger Lucarelli (left) and Nisha Duggal (right) conducting research in the lab. Lucarelli is wearing a rainbow colored mask while using a laptop. Duggal watches on with a yellow face mask. Ray Meese for Virginia Tech.
James Weger Lucarelli (left) and Nisha Duggal (right) conducting research in the lab. Ray Meese for Virginia Tech.

 

“With Zika virus, we were able to use a lot of the existing animal models that we already had, and we could use the templates from previous reverse genetics systems. This time, we are working with a novel respiratory pathogen; thus, there is a lack of available animal models, and we’re building a new reverse genetics system,” said Duggal, an assistant professor of molecular and cellular biology in the Department of Biomedical Sciences and Pathobiology.

Recent studies have shown that SARS-CoV-2 does not infect wild-type mice; the researchers will eventually study transgenic mice that are susceptible to the virus, but they are not readily available at this time. In the meantime, Weger-Lucarelli and Duggal will modify the virus to a mouse-adapted strain so that they can conduct research effectively. This model will recapitulate human disease for in vivo studies of vaccine efficacy and antiviral therapeutics.

However, Weger-Lucarelli and Duggal’s research won’t stop there. With the novelty of SARS-CoV-2, there are many factors that can contribute to the severity of COVID-19 disease that have yet to be explored in depth, such as obesity and the possibility of fetal transmission.

The Weger-Lucarelli lab is tasked with producing molecular tools to study SARS-CoV-2 and for testing antivirals. The lab is also working with Irving Coy Allen, an associate professor of inflammatory disease in the Department of Biomedical Sciences and Pathobiology, as they investigate the role of obesity and diabetes in COVID-19 severity.

According to estimates, around 43 percent of the United States population is obese, around 10 percent are diabetic, and 35 percent are pre-diabetic. Individuals with these conditions might be more prone to contracting severe diseases, such as COVID-19, because they have an irregular immune response.

“Obesity and diabetes limit a proper immune response to the virus,” said Weger-Lucarelli. “We are trying to figure out how and why the immune system is limited by these conditions so that we can produce therapeutics to prevent the severe disease that these individuals experience.”

Weger-Lucarelli’s $300,000 NSF proposal to study obesity, coronavirus disease, and transmission was just recommended for funding.

In addition to developing the mouse-adapted strain of SARS-CoV-2, the Duggal lab will study how COVID-19 infections differ in males and females and whether newborns of COVID-19 positive mothers may have an acquired immunity to infection through antibodies that are passed to the fetus in utero.

“With our Zika research, we have been looking at the transmission of the virus to fetuses. Based on the few reports that have been published so far for SARS-Cov-2, it looks like transmission of the virus to the fetus is unlikely to be happening. We want to find out how exposure can possibly protect the neonates from subsequent infections,” said Duggal.

Ultimately, Weger-Lucarelli and Duggal hope to share their genetic tools with researchers at Virginia Tech and at other universities around the country. They plan to submit a joint proposal on their reverse genetics system to the National Institutes of Health.

“I think we were lucky to get this COVID-19 seed funding. We are going to use it to help generate tools that everyone can use, which will be really helpful for anyone who wants to study any aspect of the virus or disease,” said Duggal.

In immediate response to the COVID-19 pandemic, Virginia Tech faculty, staff, and students have initiated numerous research projects with local and global salience. Learn more from the Office of the Vice President for Research and Innovation.

– Written by Kendall Daniels and Kristin Rose Jutras

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Accolades Announcements Faculty Spotlight

Five GCC affiliates receive 2020 promotions

[vc_row][vc_column][vc_column_text]June 8, 2020

Congratulations to five GCC affiliated faculty members who have earned tenure and promotion in June 2020 as a result of their outstanding achievements in teaching, research, and service. Tenure and promotion marks an important milestone in their academic careers, so please join us in congratulating our colleagues!

Zachary Easton, now professor, Biological Systems Engineering

Leah Johnson, now associate professor with tenure, Statistics

Ryan Stewart, now associate professor with tenure, School of Plant and Environmental Sciences

Kevin McGuire, now professor, Forest Resources and Environmental Conservation

Sterling Nesbitt, now associate professor with tenure, Geosciences

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