Friday, June 02, 2023

Ancient viruses discovered in coral symbionts’ DNA

Researchers surprised to find fragments of RNA viruses in coral partners’ genomes

RICE UNIVERSITY

Veglia and Correa in lab — IMAGE: RICE GRADUATE STUDENT ALEX VEGLIA AND MARINE BIOLOGIST ADRIENNE CORREA CO-LED A STUDY THAT FOUND FRAGMENTS OF NON-RETROVIRUSES IN THE GENOMES OF CORAL SYMBIONTS. view more
CREDIT: CREDIT: RICE UNIVERSITY

HOUSTON – (June 1, 2023) – An international team of marine biologists has discovered the remnants of ancient RNA viruses embedded in the DNA of symbiotic organisms living inside reef-building corals.

The RNA fragments are from viruses that infected the symbionts as long ago as 160 million years. The discovery is described in an open-access study published this week in the Nature journal Communications Biology, and it could help scientists understand how corals and their partners fight off viral infections today. But it was a surprising find because most RNA viruses are not known for embedding themselves in the DNA of organisms they infect.

The research showed that endogenous viral elements, or EVEs, appear widely in the genomes of coral symbionts. Known as dinoflagellates, the single-celled algae live inside corals and provide them with their dramatic colors. The EVE discovery underscores recent observations that viruses other than retroviruses can integrate fragments of their genetic code into their hosts’ genomes.

“So why did it get in there?” asked study co-author Adrienne Correa of Rice University. “It could just be an accident, but people are starting to find that these ‘accidents’ are more frequent than scientists had previously believed, and they’ve been found across all kinds of hosts, from bats to ants to plants to algae.”

That an RNA virus appears at all in coral symbionts was also a surprise.

“This is what made this project so interesting to me,” said study lead author Alex Veglia, a graduate student in Correa’s research group. “There’s really no reason, based on what we know, for this virus to be in the symbionts’ genome.”

The study was supported by the Tara Ocean Foundation and the National Science Foundation and led by Correa, Veglia and two scientists from Oregon State University, postdoctoral scholar Kalia Bistolas and marine ecologist Rebecca Vega Thurber. The research provides clues that can help scientists better understand the ecological and economic impact of viruses on reef health.

The researchers did not find EVEs from RNA viruses in samples of filtered seawater or in the genomes of dinoflagellate-free stony corals, hydrocorals or jellyfish. But EVEs were pervasive in coral symbionts that were collected from dozens of coral reef sites, meaning the pathogenic viruses were — and probably remain — picky about their target hosts.

“There’s a huge diversity of viruses on the planet,” said Correa, an assistant professor of biosciences. “Some we know a lot about, but most viruses haven't been characterized. We might be able to detect them, but we don’t know who serves as their hosts.”

She said viruses, including retroviruses, have many ways to replicate by infecting hosts. “One reason our study is cool is because this RNA virus is not a retrovirus,” Correa said. “Given that, you wouldn’t expect it to integrate into host DNA.

“For quite a few years, we’ve seen a ton of viruses in coral colonies, but it’s been hard to tell for sure what they were infecting,” Correa said. “So this is likely the best, most concrete information we have for the actual host of a coral colony-associated virus. Now we can start asking why the symbiont keeps that DNA, or part of the genome. Why wasn’t it lost a long time ago?”

The discovery that the EVEs have been conserved for millions of years suggests they may somehow be beneficial to the coral symbionts and that there is some kind of mechanism that drives the genomic integration of the EVEs.

“There are a lot of avenues we can pursue next, like whether these elements are being used for antiviral mechanisms within dinoflagellates, and how they are likely to affect reef health, especially as oceans warm,” Veglia said.

“If we’re dealing with an increase in the temperature of seawater, is it more likely that Symbiodiniaceae species will contain this endogenous viral element? Does having EVEs in their genomes improve their odds of fighting off infections from contemporary RNA viruses?” he said.

“In another paper, we showed there was an increase in RNA viral infections when corals underwent thermal stress. So there are a lot of moving parts. And this is another good piece of that puzzle.”

Correa said, “We can’t assume that this virus has a negative effect. But at the same time, it does look like it’s becoming more productive under these temperature stress conditions.”

Thurber is the Emile F. Pernot Distinguished Professor in Oregon State’s Department of Microbiology.

The study included more than 20 co-authors from the University of Konstanz, Germany; the Institute of Microbiology and Swiss Institute of Bioinformatics, Zürich; the University of Perpignan, France; the Scientific Center of Monaco; the Université Paris-Saclay, Evry, France; the Tara Ocean Foundation, Paris; the University of Maine; Sorbonne University, France; the University of Tsukuba, Japan; Paris Science and Letters University, France; the University of Paris-Saclay; the Weizmann Institute of Science, Rehovot, Israel; Côte d’Azur University, Nice, France; the European Bioinformatics Institute, University of Cambridge, England; Ohio State University; and the National University of Ireland, Galway.

National Science Foundation support was provided by three grants (2145472, 2025457, 1907184).

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Marine biologists sample reefs of Pocillopora corals. Researchers at Rice University and Oregon State University studied corals and found fragments of non-retroviruses in the genomes of their symbionts, perhaps the result of infections millions of years ago. (Credit: Andrew Thurber/Oregon State University)

CREDIT

Credit: Andrew Thurber/Oregon State University

Rice University graduate student Alex Veglia samples a coral for a study by researchers at Rice and Oregon State that found fragments of non-retroviruses in the genomes of coral symbionts. Rice marine biologist Adrienne Correa is in the background.

CREDIT

Credit: Courtesy of the Correa Lab/Rice University

Peer-reviewed paper:

“Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes” | Communications Biology | DOI: 10.1038/s42003-023-04917-9

Authors: Alex J. Veglia, Kalia S.I. Bistolas, Christian R, Voolstra, Benjamin C. C. Hume, Hans-Joachim Ruscheweyh, Serge Planes, Denis Allemand, Emilie Boissin, Patrick Wincker, Julie Poulain, Clémentine Moulin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Varga, Eric Douville, Michel Flores, Didier Forcioli, Paola Furla, Pierre Galand, Eric Gilson, Fabien Lombard, Stéphane Pesant, Stéphanie Reynaud, Matthew B. Sullivan, Shinichi Sunagawa, Olivier Thomas, Romain Troublé, Didier Zoccola, Adrienne M.S. Correa, and Rebecca L. Vega Thurber

https://doi.org/10.1038/s42003-023-04917-9

VIDEO is available at:

https://youtu.be/0Kvlnaqg738
CAPTION: Symbiotic dinoflagellates, viewed from a dissecting microscope, are key to the health of reef-building corals. (Credit: Carsten Grupstra/Boston University)

Image downloads:

https://news-network.rice.edu/news/files/2022/12/1205_CORAL-1-WEB.jpg
CAPTION: Rice graduate student Alex Veglia and marine biologist Adrienne Correa co-led a study that found fragments of non-retroviruses in the genomes of coral symbionts. (Credit: Rice University)

https://news-network.rice.edu/news/files/2022/12/1205_CORAL-2-WEB.jpg
CAPTION: Marine biologists sample reefs of Pocillopora corals. Researchers at Rice University and Oregon State University studied corals and found fragments of non-retroviruses in the genomes of their symbionts, perhaps the result of infections millions of years ago. (Credit: Andrew Thurber/Oregon State University)

https://news-network.rice.edu/news/files/2022/12/1205_CORAL-3-WEB.jpg
CAPTION: Rice University graduate student Alex Veglia samples a coral for a study by researchers at Rice and Oregon State that found fragments of non-retroviruses in the genomes of coral symbionts. Rice marine biologist Adrienne Correa is in the background. (Credit: Courtesy of the Correa Lab/Rice University)

JOURNAL

Communications Biology

DOI

10.1038/s42003-023-04917-9

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

ARTICLE PUBLICATION DATE

1-Jun-2023

I NEEDED THIS IN GRADE 2

Eye drops slow nearsightedness progression in kids, study finds

Clinical trial suggests low-dose atropine is effective myopia treatment

Peer-Reviewed Publication

OHIO STATE UNIVERSITY

COLUMBUS, Ohio – The results of a new clinical trial suggest that the first drug therapy to slow the progression of nearsightedness in kids could be on the horizon.

The three-year study found that a daily drop in each eye of a low dose of atropine, a drug used to dilate pupils, was better than a placebo at limiting eyeglass prescription changes and inhibiting elongation of the eye in nearsighted children aged 6 to 10.

That elongation leads to myopia, or nearsightedness, which starts in young kids and continues to get worse into the teen years before leveling off in most people. In addition to requiring life-long vision correction, nearsightedness increases the risk for retinal detachment, macular degeneration, cataracts and glaucoma later in life – and most corrective lenses don’t do anything to stop myopia progression.

“The idea of keeping eyeballs smaller isn’t just so people’s glasses are thinner – it would also be so that in their 70s they don’t suffer visual impairment,” said lead study author Karla Zadnik, professor and dean of the College of Optometry at The Ohio State University.

“This is exciting work for the myopia research community, which I’ve been part of for 35 years. We’ve talked about treatment and control for decades,” she said. “And it’s exciting to think that there could be options in the future for millions of children we know are going to be myopic.”

The results of the CHAMP (Childhood Atropine for Myopia Progression) trial are published today (June 1, 2023) in JAMA Ophthalmology.

About one in three adults worldwide is nearsighted, and the global prevalence of myopia is predicted to increase to 50% by 2050. Though one federally approved contact lens can slow progression of nearsightedness, no pharmaceutical products are approved in the United States or Europe to treat myopia.

Animal studies years ago hinted at atropine’s ability to slow the growth of the eye, but the full-strength drug’s interference with near vision and concerns about pupil dilation hindered early considerations of its potential as a human therapy for myopia. More recent research has suggested a low dose of atropine might be the ticket.

This new double-masked, randomized phase 3 trial assessed the safety and effectiveness of two low-dose solutions, with atropine concentrations of either .01% or .02%, versus placebo. Treatment for each of the 489 children aged 6 to 10 assessed for the drug’s effectiveness consisted of one daily drop per eye at bedtime, which minimized the disruption of any blurring effects atropine might have on vision.

Researchers were a bit surprised to find that the most significant improvements at all time points compared to placebo resulted from the solution containing .01% of atropine. Though the .02% atropine formulation was also better at slowing progression of myopia than placebo, the results were less consistent.

“The .01% story is clearer and more obvious in terms of significantly slowing both the growth of the eye as well as then resulting in a lower glasses prescription,” Zadnik said.

Including a measure of the eye’s growth was a key component of the study because “the field is actually moving toward axial elongation being as important as, or more important than, the glasses prescription in terms of the most meaningful outcome,” she said. “If we’re trying to slow eye growth to prevent bad outcomes for people in their 80s, measuring the eye growth directly is really important.”

The drugs’ safety was assessed in a larger sample of 573 participants that also included children as young as 3 and up to age 16. Both low-dose formulations were safe and well tolerated. The most common side effects were sensitivity to light, allergic conjunctivitis, eye irritation, dilated pupils and blurred vision, although reports of these side effects were few.

The CHAMP trial was the first study of low-dose atropine to include placebo controls for three years and to involve a large, diverse population recruited from 26 clinical sites in North America and five countries in Europe. In a second section of the trial, researchers are evaluating how the eyes respond when the treatment is over.

The experimental drug is made without preservatives and, if federally approved as a therapy, would be distributed in single-use packaging for convenience and to prevent contamination. Off-label low-dose atropine that can currently be obtained at compounding pharmacies may contain preservatives that can lead to dry eye and corneal irritation, researchers noted.

The experimental product studied in the CHAMP trial is manufactured by Vyluma, a New Jersey development-stage biopharmaceutical company with a focus on pharmaceutical treatments for refractive errors of the eye. A subsidiary of Nevakar Inc., Vyluma sponsored the trial, has submitted a New Drug Application to the FDA to seek approval in the U.S. and has partnered with two companies to commercialize the product outside the United States..

Zadnik led the study as a paid expert consultant to Vyluma. Jennifer Fogt, assistant professor at Ohio State, also worked on the trial. Additional co-authors Erica Schulman of SUNY College of Optometry; Ian Flitcroft of the Center for Eye Research in Dublin, Ireland; Louis Blumenfeld of Eye Physicians of Central Florida; and Tung Fong, Eric Lang, Houman Hemmati and Simon Chandler of Vyluma represented the CHAMP trial group investigators.

Contact: Karla Zadnik, Zadnik.4@osu.edu

Written by Emily Caldwell, Caldwell.151@osu.edu

JOURNAL

JAMA Ophthalmology

DOI

10.1001/jamaophthalmol.2023.2097

METHOD OF RESEARCH

Randomized controlled/clinical trial

SUBJECT OF RESEARCH

People

ARTICLE TITLE

Efficacy and Safety of 0.01% and 0.02% Atropine for the Treatment of Pediatric Myopia Progression Over 3 Years

ARTICLE PUBLICATION DATE

1-Jun-2023

New LUX search tool offers unprecedented access to Yale’s vast collections

Reports and Proceedings

YALE UNIVERSITY

New Haven, Conn. — Yale University’s museums, libraries, and archives contain vast troves of cultural and scientific heritage that fire curiosity and fuel research worldwide. Now there’s a simple new way to make astonishing connections among millions of objects.

Starting today, anyone can explore the university’s unparalleled holdings online through LUX: Yale Collections Discovery — a groundbreaking discovery and research platform that provides single-point access to more than 17 million items, including defining specimens of dinosaur fossils, illuminated medieval manuscripts, paintings by Vincent van Gogh and J.M.W. Turner, and the archives of Langston Hughes, Gertrude Stein, and other renowned literary figures.

Free and easy to use, the platform — a powerful kind of database that maps relationships — helps users find clear pathways through the collections and uncover links between objects that might otherwise seem unconnected, such as a fish fossil and an 18th-century sketch of a young woman. Previously there was no easy way to search multiple collections at once or discern associations among the objects within them.

Developed by Yale over the past five years, LUX encompasses the collections of the Yale Center for British Art (YCBA), the Yale University Art Gallery, the Yale Peabody Museum, and Yale University Library, which includes the Beinecke Rare Book and Manuscript Library, the Lewis Walpole Library, and specialized collections devoted to the arts, music, film, history of medicine, and religion. The Mellon Foundation, the nation’s largest funder of the arts and humanities, funded key aspects of the project and was instrumental in its completion.

“LUX is designed to open the breadth of Yale’s cultural and natural history collections, connecting our wide range of extraordinary objects, specimens, and works from across our libraries, archives, and museums,” said Susan Gibbons, vice provost for collections and scholarly communication. “We are committed to fostering curiosity and illuminating the hidden threads within the collections at Yale, from rare books and manuscripts to sculptures and fossils, to highlight unexpected avenues for collaboration and new research opportunities.”

Through the platform, she said, “we hope to build on Yale’s mission to improve our world for future generations through the pursuit of innovation in research, scholarship, and education.”

Holdings relating to Benjamin Silliman, a pioneering Yale professor whose teaching in the early 1800s established scientific education at the university, offer a case study in the kinds of unexpected connections researchers can uncover through LUX:

A fossilized fish skeleton collected by Silliman in Italy is housed in the Yale Peabody Museum. An 1857 letter he wrote to philanthropist George Peabody, who would provide the funding for establishing the Peabody Museum, is housed in Silliman’s archives at the Yale University Library. The scientist’s wife, Harriet Trumbull, was the subject of a graphite and watercolor sketch now owned by the Yale University Art Gallery. Her uncle, the artist John Trumbull, was mentored by the artist Benjamin West and helped complete his painting of the Battle of La Hogue, which is housed at the Yale Center for British Art. A search of “Benjamin Silliman” in the LUX search bar unearthed all these items and tied them together.

In short, LUX enables researchers and other inquiring minds to use simple language to discover — and easily sort — art, cultural, and scientific heritage objects, and to explore the connections among them and with people, places, and events, without prior knowledge that those ties exist.

“The power of LUX comes from its ability to allow users to uncover hidden relationships between objects, from shared concepts to famous figures in Yale’s collections,” Robert Sanderson, Yale’s senior director for digital cultural heritage, said. “This groundbreaking tool brings together all the university’s collections through modern technology that will enrich discovery opportunities for users, making it easier for them to find what they’re looking for and explore new objects.

“We think LUX is game-changing for the cultural heritage domain,” he added. “No other institution has a system with this level of capability.”

LUX is designed to allow individuals with little experience searching databases (this type is known as a “knowledge graph”) to conduct fine-grained intellectual explorations.

For instance, a search for “John Trumbull” (the artist who rendered many of revolutionary America’s defining moments and established the Yale University Art Gallery in 1832) pulls up, from across Yale’s different collections, 680 objects he created or owned or are otherwise related to him, including his acclaimed painting “The Declaration of Independence,” which he worked on for more than three decades. Tabs located above the primary search field direct the user to “works,” “people and groups,” “places,” “concepts,” and “events” relating to Trumbull, each revealing new avenues to explore.

A series of filters listed on the left of the screen allows users to refine searches by, for example, sorting exclusively for objects for which there are already digital images. (Yale is a global leader in digitizing museum and library collections. Extensive portions of the holdings at the art gallery, YCBA, and Peabody are fully digitized, as are a significant number of objects in the Beinecke Library and other Yale Library collections.)

An advanced search function for targeted queries allows users to go deeper. The record pages for individual objects contain basic information, such as when and where an object was produced, the materials used to create it, and its physical size, among other metadata. The pages also include relevant information drawn from non-Yale institutions and databases, such as the Library of Congress, with links to those sources at the lower right of the screen.

Ayesha Ramachandran, associate professor of comparative literature in Yale’s Faculty of Arts and Sciences, has experimented with LUX, and calls it a “terrific tool” for teaching and conducting research.

“I was struck by the way LUX is constructed to be a tool of exploration and not just a database,” Ramachandran said. “It is extremely intuitive and conceptually organized to allow you to drill down to learn more about the object of your search.”

To begin exploring Yale’s collection through LUX, visit lux.collections.yale.edu.

Bremen researchers cultivate archaea that break down crude oil in novel ways

How microorganisms deep in the seabed render crude oil harmless

Peer-Reviewed Publication

MARUM - CENTER FOR MARINE ENVIRONMENTAL SCIENCES, UNIVERSITY OF BREMEN

U.S. deep-sea submersible ALVIN in the deep-sea at the Guaymas Basin — IMAGE: IN THE SPOTLIGHT OF THE U.S. DEEP-SEA SUBMERSIBLE ALVIN, A SMALL REDDISH-BROWN VENT MASSIF CAN BE SEEN ON THE SEAFLOOR OF THE GUAYMAS BASIN. THIS FORMATION IS SURROUNDED BY ABUNDANT HYDROTHERMALLY HEATED OIL-RICH SEDIMENTS COVERED BY WHITE AND ORANGE BACTERIAL MATS. THE CORE FROM WHICH THE CANDIDATUS ALKANOPHAGA ARCHAEA ULTIMATELY ORIGINATED WAS COLLECTED BY THE TEAM OF THE MANNED DEEP-SEA SUBMERSIBLE. PHOTO: WOODS HOLE OCEANOGRAPHIC INSTITUTION. view more
CREDIT: WOODS HOLE OCEANOGRAPHIC INSTITUTION

Microbial communities are especially active near hydrothermal seeps like those in the Guaymas Basin in the Gulf of California. The team of researchers has been working on understanding these communities for many years. Organic material deposited in the Guaymas Basin is cooked by heat sources from within the Earth, which breaks it down into crude oil and natural gas. Their components provide the primary source of energy for microorganisms in an otherwise hostile environment. In their latest study, the researchers have demonstrated that archaea use a previously unknown mechanism to degrade liquid petroleum alkanes at high temperatures without the presence of oxygen.

Alkanes are highly stable compounds of carbon and hydrogen. They are natural components of natural gas and crude oil. The latter is refined by humans into fuels like gasoline and kerosene. Environmental catastrophes occur repeatedly due to accidents during the extraction of crude oil. A prime example was the accident on the Deepwater Horizon drilling platform, which caused severe environmental damage in the Gulf of Mexico due to the toxic effects of crude oil compounds like liquid alkanes. In the presence of oxygen, microorganisms can rapidly break down many components of crude oil, among others alkanes. Without the reactive oxygen, however, degradation is considerably more difficult. Organisms that can perform this task have not been extensively researched. In recent years, however, evidence has been found that archaea are able to employ a surprising mechanism to do this. It is based on newly discovered variants of the key enzyme of methanogenesis and anaerobic methane degradation, methyl-coenzyme M reductase (MCR). The genes that encode these enzymes have been found in many environmental samples. However, laboratory cultures of the microbes that could illustrate the function of these enzymes were still lacking. This is where the laboratory study of Hanna Zehnle and her colleagues becomes significant.

The team used sediments from the 2000-meter-deep Guaymas Basin in the Gulf of California. The special geological conditions that exist here include high temperatures, liquid crude-oil components, and an anaerobic environment at shallow sediment depths, all of which are normally only found in deep-lying oil reservoirs which are difficult for scientists to access.

In the Bremen laboratories the researchers prepared cultures with liquid alkanes and allowed them to grow anaerobically, i.e., without oxygen, at high temperatures (70 degrees Celsius). “After a time,” explains first author Hanna Zehnle, “sulfide forms in the cultures. This provides evidence that they are active.” The composition of the cultures is studied using DNA and RNA samples. “With this method we can find out what organisms are living in this system and which metabolic pathways they are using,” says Zehnle. These include the chemical reactions in which substances are metabolized. They found archaea of the genus Candidatus Alkanophaga in the cultures. These archaea use variants of the MCR for breaking down the alkanes. The researchers verified this by transcriptome data, measurement of the enzyme products, and by demonstrating inactivity of the cultures when the enzyme was inhibited. But the organisms are not able to degrade the crude oil alone. Respiration, in the form of sulfate reduction in this case (because no oxygen is present), is carried out by bacteria of the genus Thermodesulfobacterium, which form dense consortia with the archaea.

Methanogenesis is one of the oldest known metabolic processes and is a part of the global carbon cycle. The laboratory study by Hanna Zehnle and her colleagues shows that the enzymes involved in this process can also utilize liquid (and thus toxic) hydrocarbons which highlights the relevance of this pathway for the global carbon cycle.

“Thanks to their newly discovered capabilities, Alkanophaga and their relatives are targeting hydrocarbons in oil reservoirs. The remaining oil becomes more and more solid and therefore tends to remain in the seafloor,” explains corresponding author Gunter Wegener. “We still have not been able to investigate any deep oil reservoirs, but the archaea are certainly annoying the oil industry with their activity. But they also make an important contribution to the fact that natural oil seeps are rare.”

This study is a part of the research within the Cluster of Excellence “The Ocean Floor – Earth’s Uncharted Interface”, which is housed at MARUM. Among other research areas, investigations are being conducted here to determine which microorganisms and environmental conditions provide the ocean floor with the qualities required to function as a reactor that has been balancing the Earth's carbon cycle since time immemorial. Questions relating to what the organisms in the deep biosphere in higher temperature ranges live from is one of the core themes of the Cluster.

Participating Institutes:

MARUM – Center for Marine Environmental Sciences at the University of Bremen, Bremen, Germany
Max Planck Institute for Marine Microbiology, Bremen, Germany
Faculty of Geosciences, University of Bremen, Bremen, Germany
Department of Systems Biology, National Centre for Biotechnology – CSIC, Madrid, Spain
Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, NC, USA

MARUM produces fundamental scientific knowledge about the role of the ocean and the seafloor in the total Earth system. The dynamics of the oceans and the seabed significantly impact the entire Earth system through the interaction of geological, physical, biological and chemical processes. These influence both the climate and the global carbon cycle, resulting in the creation of unique biological systems. MARUM is committed to fundamental and unbiased research in the interests of society, the marine environment, and in accordance with the sustainability goals of the United Nations. It publishes its quality-assured scientific data to make it publicly available. MARUM informs the public about new discoveries in the marine environment and provides practical knowledge through its dialogue with society. MARUM cooperation with companies and industrial partners is carried out in accordance with its goal of protecting the marine environment.

JOURNAL

Nature Microbiology

DOI

10.1038/s41564-023-01400-3

ARTICLE TITLE

Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes.

ARTICLE PUBLICATION DATE

1-Jun-2023

Researchers develop new detection tool for beech leaf disease’s nematode pest

Researchers at the Holden Arboretum developed an improved, effective way to monitor and detect the presence of a disease-causing nematode in beech leaf tissue.

Peer-Reviewed Publication

HOLDEN FORESTS & GARDENS

North American Beech Leaf Disease Nematodes under a microscope — IMAGE: EVEN UNDER A MICROSCOPE, THE NEMATODE LITYLENCHUS CRENATAE SUBSP. MCCANNII DOESN’T LOOK LIKE MUCH. BUT IT CAN BRING A LOT OF DAMAGE: RESEARCHERS FIND IT LIVING IN THE BUDS OF BEECH TREES SUFFERING FROM BEECH LEAF DISEASE. NOW, SCIENTISTS HAVE DEVELOPED A NEW TOOL THAT FOREST HEALTH PROFESSIONALS CAN USE TO MORE EASILY IDENTIFY AND QUANTIFY THE DISEASE-CAUSING NEMATODES AS THEY SPREAD ACROSS THE NORTH AMERICAN LANDSCAPE. view more
CREDIT: MARY C. PITTS, HOLDEN FORESTS & GARDENS

Beech leaf disease is an emerging threat to North American forest ecosystems. It was first discovered in northeastern Ohio in 2012, and has already spread to 12 additional U.S. states and Canadian provinces. At first the cause of the disease was unknown, and the sick and dying trees were diagnosed on symptoms alone: Dark banding along the leaf veins and shriveled, leathery leaves. But in 2017, nematodes were found in diseased leaves, and by 2020 we had the answer: A newly recognized subspecies of the wormlike creature, Litylenchus crenatae mccannii, was definitely associated with the symptoms.

In order to monitor the spread of the disease, to understand the nemotode’s presence among both symptomatic and possibly asymptomatic trees, and to begin to develop control measures, forestry professionals will need a rapid, accurate method for detecting the nematodes. Before now, forest health professionals hoping to diagnose a tree would have to undertake a slow process that involves soaking leaves for twelve hours, further preparing samples and then looking for nematodes under a microscope. It’s a fine method for one expert to study one tree, but not one that can be readily used on a large scale.

In a new report, published by forest health researchers at the Holden Arboretum, the Ontario Forest Research Institute, and the U.S. Forest Service, the team outlines a new tool for detecting these nematodes. Their work appeared in the journal Plant Disease.

The new nematode detection tool utilizes a long-standing laboratory method that can be used to detect DNA specific to a certain organism. In this method, researchers use a short DNA sequence that is specific to the species of interest, called a primer, to identify and then amplify on-target DNA in a sample. The amplification step is a relatively basic laboratory technique, PCR, but the real challenge lies in developing the primer in the first place — which is exactly what the researchers have done.

“The new primer will make detection of the North American beech leaf nematode faster and easier, allowing forest health professionals across the U.S. and Canada to keep better tabs on this emerging disease,” says David Burke, Vice President for Science and Conservation at Holden Forests & Gardens, who led the work. “Better detection will mean more accurate monitoring and improved research on treatment.”

The new primer can be used to differentiate L. crenatae from other nematodes that might be found in areas affected by BLD, and also allows researchers to estimate the relative degree of nematode infestation between samples.

“We need all the forest professionals we can get working on BLD if we want to nip it in the bud,” says Burke. “Our forests may depend on it.”

—

Citation: Burke, David, et al. "Development of primers specific for detection of Litylenchus crenatae, the causal agent of beech leaf disease, in plant tissue." Plant Disease (2023). DOI: 10.1094/PDIS-12-22-2911-SR

About Holden Forests & Gardens: Holden Forests & Gardens is made up of two of Northeast Ohio’s most important environmental and cultural institutions — the Holden Arboretum and Cleveland Botanical Garden — whose mission is to connect people with the wonder, beauty, and value of trees and plants, to inspire action for healthy communities. One of the largest public gardens in the country, Holden Forests & Gardens has 18,000 member households and an annual attendance of nearly 350,000 for whom we strive to provide inspirational and educational visitor experiences. For more information, visit holdenfg.org.

Media Contact:
Anna Funk
Science Communications Specialist
Holden Forests & Gardens
afunk@holdenfg.org

Corresponding Author:
David Burke
Vice President for Science and Conservation
Holden Forests & Gardens
dburke@holdenfg.org
440-602-3858

Why we need to fall out of love with flaky white fish - study

The UK’s growing mismatch between the fish we catch and the fish we want to eat has clear implications for our future food security, according to new research

Peer-Reviewed Publication

UNIVERSITY OF ESSEX

The UK’s growing mismatch between the fish we catch and the fish we want to eat has clear implications for our future food security, according to new research.

Led by the University of Essex and the Centre for Environment Fisheries and Aquaculture Science (Cefas), the study, published in the international peer-reviewed journal Reviews in Fish Biology and Fisheries, for the first time offers a comprehensive, long-term analysis of how major policy changes in the past 120 years have influenced patterns in UK seafood production, trade and consumption.

It shows that even if we changed our fish-eating habits away from choosing flaky white fish such as cod and haddock - that are largely imported from other countries - to the species more common to our own waters, like herring and mackerel, UK seafood production would still be unable to meet domestic demand or the Government’s healthy eating recommendations.

Luke Harrison, who led the study while at Essex’s School of Life Sciences, explained: “Our research highlighted that policy changes in the mid-1970s, particularly the introduction of Exclusive Economic Zones (EEZ) and the UK joining the European Union, drove a growing mismatch between the seafood produced in the UK and what we ate domestically.

“Exacerbated by stock declines caused by fishing, climate change and habitat loss, this growing disconnect far out-scales any previous mismatches between availability and consumption - including those seen during both world wars - and we have seen an increasing reliance on seafood imports and a decrease in domestic landings.”

Fish is now one of the most traded food products in the world and there has been a rapid increase in the UK’s seafood imports, which were relatively low before the 1970s. The UK currently imports most of the fish it eats and exports most of the fish it produces from fisheries and aquaculture. The UK’s love of large, flaky fish began in the early 1900s when the UK had a thriving distant-water fishery.

However, today these species are landed in low quantities in UK waters, while cheap, nutritious, bony species, particularly mackerel and herring, are landed in high quantities but primarily exported to the Netherlands and France.

“The increasing popularity of tuna, shrimps and prawns highlights how UK consumers have largely not changed their eating habits to reflect changes in local seafood availability over the years,” added Cefas co-author Dr Georg Engelhard.

Since the forming of EEZs and the UK joining the EU in the mid-1970s, UK domestic landings declined rapidly from 869 thousand tonnes in 1975 to 349 thousand tonnes in 2020.

The UK public currently eats 31% less seafood than is recommended by government guidelines, and even if local species were more popular, all domestic fisheries and aquaculture production would still be 73% below recommended levels without the inclusion of imports.

Senior author Dr Anna Sturrock, from Essex’s School of Life Sciences, added: “In the face of climate change, global overfishing and potentially restrictive trade barriers, it is important that we promote locally sourced seafood and provide clearer guidance on non-seafood alternatives. Ultimately this will help meet national food security demands as well as health and environmental targets.”

JOURNAL

Reviews in Fish Biology and Fisheries

DOI

10.1007/s11160-023-09776-5

METHOD OF RESEARCH

Data/statistical analysis

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Widening mismatch between UK seafood production and consumer demand: a 120 year perspective

ARTICLE PUBLICATION DATE

2-Jun-2023

Below the surface: Researchers uncover reasons to rethink how mountains are built

Peer-Reviewed Publication

COLORADO STATE UNIVERSITY

Calabrian marine terrace — IMAGE: CALABRIAN LANDSCAPE OVERLOOKING THE TYRRHENIAN SEA WITH A MARINE TERRACE IN THE FOREGROUND (FLAT AREA). view more
CREDIT: SEAN GALLEN

A study led by Colorado State University suggests that the answers to how and why mountains form are buried deeper than once thought.

"Mountain building is a fundamental process of how Earth behaves,” said Sean Gallen, lead author and CSU assistant professor of geosciences, “and this study suggests that we may not understand that as well as we thought we did.”

Gallen and his team generated new data sets and techniques to use landscapes to reconstruct long-term histories of mountain building in southern Italy. Their novel approach yielded some “confounding” results, according to Gallen.

In subduction zones, like the one in Calabria in southern Italy, one tectonic plate dives beneath another plate. Mountains in these settings are believed to have formed through the crumpling and thickening of Earth’s crust.

The team combined measurements that recorded geologically short and long timescales, from thousands of years to tens of millions of years. Like a “geologic tape recorder” of the tectonic history, the landscape filled in the rest.

"In southern Italy, the landscape actually is the bridge between these different methods that we typically use,” Gallen said.

The flat, high-elevation patches of the landscape along the “toe” of the Italian peninsula represent a time when mountain formation was slow, and a steep transition below marks a rapid acceleration. These clues in the landscape allowed the researchers to produce a long-term, continuous record of rock uplift, the longest and most complete record of its kind.

"We would expect to see a correlation between the rate at which the plate is diving down beneath the other plate through time and our rock uplift history, and we don't see that," Gallen said.

Crumpling and thickening of the crust appears to be secondary to another process in the formation of the Calabrian mountains. Data points to descension of the lower plate through the Earth's mantle and its alteration of the mantle flow field as the primary factor controlling rock uplift.

"The results suggest that the typical way we view mountain building doesn't hold for southern Italy,” Gallen said. “It appears to be controlled by things that are much deeper within the Earth system. This behavior has been seen in models but never in nature. This is the first time we think we've observed it.”

Gallen cautioned that more data is needed to confirm whether their interpretation is correct, but it is backed by existing numerical models. Scientists have previously connected mountain height to tectonic plate interactions within Earth’s plastically flowing mantle, but this research indicates for the first time that this mechanism is the dominant force in mountain building in subduction zones.

“The records we have produced imply that deep earth signals appear to dominate what's happening at the surface," Gallen said. “I've been working in the Mediterranean for 15 years, and this result has profoundly changed the way I think about these subduction zones.”

Transformative, transparent research

The new techniques developed for this study offer a breakthrough in constructing long-term rock uplift histories.

The team created a unified framework based on a collection of standard geomorphology measurements – thermochronology, cosmogenic nuclides, bedrock river profiles and the record of past sea levels found in marine terraces. The novel approach goes back further in time than other methods and uses different data sets to constrain modeling in a unique way.

The method is best applied to active systems, where the modern landscape offers clues to its history. The further back in geologic time a system was active, the harder it is to reconstruct its history with confidence.

Software developed for the study, published in Nature Geoscience, is freely available for other researchers to use. Gallen hopes the new techniques will stimulate research and discoveries in other areas.

Co-authors on the study are Nikki M. Seymour, Christoph Glotzbach, Daniel F. Stockli and Paul O’Sullivan. The Department of Geosciences is in the Warner College of Natural Resources.

View of the Calabrian landscape overlooking the Ionian Sea.

CSU graduate students sample bedrock for thermochronology in Calabria, Italy. From left, Nikki Seymour, second author on the study, Johanna Eidmann and Eyal Marder.
CREDIT
Sean Gallen

JOURNAL

Nature Geoscience

DOI

10.1038/s41561-023-01185-4

METHOD OF RESEARCH

Data/statistical analysis

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Below the surface: Researchers uncover reasons to rethink how mountains are built

ARTICLE PUBLICATION DATE

1-Jun-2023

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Friday, June 02, 2023

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Bremen researchers cultivate archaea that break down crude oil in novel ways

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