Biotechnology offers holistic approach to restoration of at-risk forest tree species

Solution depends on regulators, scientists and public support

Peer-Reviewed Publication

PURDUE UNIVERSITY

 

IMAGE: DOUGLASS JACOBS, THE FRED M. VAN ECK PROFESSOR OF FOREST BIOLOGY AT PURDUE UNIVERSITY, WITH A BUTTERNUT TREE THAT HAS BEEN INFECTED WITH STEM CANKER. BUTTERNUT IS ON THE LIST OF AT-RISK FOREST TREE SPECIES THAT WILL LIKELY NEED BIOTECHNOLOGY ALONG WITH TRADITIONAL TREE-BREEDING APPROACHES TO AVOID EXTINCTION. view more 

CREDIT: PURDUE AGRICULTURAL COMMUNICATIONS PHOTO/TOM CAMPBELL

WEST LAFAYETTE, Ind. – Many at-risk forest tree species will probably need biotechnology along with traditional tree-breeding approaches to survive, according to insights published in the July issue of the journal New Forests.

Purdue University’s Douglass Jacobs and Kasten Dumroese of the U.S. Forest Service led a team of 19 co-authors, including scientists, land managers and regulators, in presenting their findings on biotechnological risk assessment and forest tree restoration. Their New Forests paper, published in a special issue on threatened tree species, presents key outcomes of a 2021 virtual international conference on the issues. 

Among their conclusions: Society drives policy. If genetic engineering is the only way to save some species, its use will require public acceptance.

“Biotechnology is a diverse toolkit comprising different technologies that can be used to impart pest resistance – it could be bugs or pathogens – in our threatened forest trees,” said Jacobs, the Fred M. van Eck Professor of Forest Biology. But many people mistakenly equate biotechnology with genetic engineering. 

“Traditional tree breeding, whether you’re breeding different species or different varieties within species, has been going on for thousands of years. And the regulations on planting trees that have been traditionally bred are wide open,” he said. “Genetic engineering, on the other hand, is highly regulated, but all biotechnology is certainly not genetic engineering.”

Scientists often use genomics, for example, which involves working with the complete set of an organism’s genetic material, to learn more about what causes disease. Genomics also can help identify the genes responsible for useful traits such as pest resistance.

Blight began afflicting the American chestnut in the 1900s, killing billions of trees. Despite being the target of decades-long tree-breeding efforts, the chestnut’s prospects remain in doubt. The list of at-risk species also includes ash, butternut, and bristlecone pine among other members of the five-needle white pine family. 

“I feel a sense of urgency. We can’t take a hundred years like we’ve taken with chestnut to turn the page,” said Dumroese, a research plant physiologist at the Forest Service’s Rocky Mountain Research Station in Idaho.

“The species are becoming ecologically extinct,” Dumroese said. “They’re not able to provide their historic level of ecosystem function because often they don’t grow to maturity. And that’s happening at a faster and faster pace. Look at how rapidly we’ve lost ash trees from our forests and urban landscapes because of the introduced insect pest emerald ash borer.”

The western white pine is an example of how the Forest Service has, starting in the 1960s, effectively used traditional tree breeding to cope with white pine blister rust. The white pine population remains below its pre-blister-rust levels, however, and may never become fully restored.

“But we see a lot more western white pine on the landscape and being planted on the landscape every year because of those efforts,” Dumroese said. “That process only took a couple of decades where we come from a big problem to making improvements. We need that pace for all of the species that we’re calling at risk.”

Back in Indiana, the Hardwood Tree Improvement & Regeneration Center, a joint effort between Purdue and the Forest Service, for years has maintained a breeding program for pest resistance. Almost all of the center’s efforts to date have focused on traditional tree breeding and genomics. 

“The chance to work with chestnut and help reintroduce it back to the landscape was a big reason I took the Purdue job in the first place back in December of 2001,” Jacobs said. “Watching species disappear from the landscape provides me personally with a lot of motivation to contribute whatever I can toward helping to save some of these at-risk species.”

In the last 10 years, Jacobs has seen striking advancements in novel biotechnologies that use genomics and genetic engineering.

“For some species, traditional tree breeding doesn’t appear to be a viable long-term option to get disease-resistant trees. In those cases, it’s probably going to have to be genetic engineering if we want to save the species,” he said.

That applies even to a species like the blight-afflicted American chestnut, the target of a breeding program for 50 years. “Introducng enough chestnut and ash trees to bring us back to the pre-disturbance level is likely not possible in anyone’s lifetime, but you have to start somewhere,” Dumroese noted.

The participants of the 2021 conference came to a consensus on the applicability of biotechnology toward reintroducing some threatened forest tree species. They came from academia, the Forest Service, and organizations such as the American Chestnut Foundation and the Nature Conservancy.

“Societal perception and policy remain the weakest links,” Jacobs said. “There’s been this consistent one-way flow of information from scientists to the public with the idea of, ‘Hey, we’re scientists, trust us.’ Or ‘We’re the government, trust us.’ But you need a much more interactive dialogue to be successful in changing public opinion.”

Support for the conference and related work was provided by the U.S. Department of Agriculture Forest Service and National Institute of Food and Agriculture.

Writer: Steve Koppes

Kasten Dumroese, a research plant physiologist at the Forest Service’s Rocky Mountain Research Station in Idaho, stands in a crop of western white pine seedlings. These seedlings, the result of traditional tree breeding for enhanced resistance to white pine blister rust, are growing at the University of Idaho’s Pitkin Nursery.

CREDIT

Photo by USDA Forest Service/Anthony 

Among the at-risk native forest tree species in North America are the white ash (left), American chestnut (center), and butternut.

CREDIT

Photos provided by Douglass Jacobs

Douglass Jacobs, the Fred M. van Eck Professor of Forest Biology at Purdue University, Inspects a stand of butternut in Indiana’s John Wright Forest.

CREDIT

Purdue Agricultural Communications photo/Tom Campbell

JOURNAL

New Forests

DOI

10.1007/s11056-023-09980-y 

METHOD OF RESEARCH

Systematic review

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Reintroduction of at-risk forest tree species using biotechnology depends on regulatory policy, informed by science and with public support

Queensland native forestry can help achieve global environment goals

Peer-Reviewed Publication

UNIVERSITY OF QUEENSLAND

 

IMAGE: THIS NATIVE FOREST IN SOUTHERN QUEENSLAND HAS BEEN SELECTIVELY HARVESTED THREE TIMES SINCE THE 1950S AND IS ALMOST READY FOR ANOTHER HARVEST. view more 

CREDIT: DR TYRON VENN

Research conducted by The University of Queensland has revealed that Queensland native forestry, including timber harvesting, could actually help conserve biodiversity and mitigate climate risks.

Dr Tyron Venn from UQ’s School of Agriculture and Food Sustainability reviewed more than 350 publications, studying the ecological and economic impacts of Queensland native forest management, which includes everything from fire management to timber harvesting.

“Stopping forestry in Queensland’s native forests may sound like a positive outcome for the environment, but the research suggests that it would further shift our impacts offshore and increase carbon emissions, while generating little benefit for biodiversity conservation within Australia,” Dr Venn said.

Since the 1990s, Australia’s annual harvest of native hardwood sawlogs has dropped by 2.2 million cubic metres, as large areas of state-owned native forests have been declared National Parks or other types of conservation reserves in which harvesting is not allowed.

“Over the same time period, imports of hardwood products from less-well managed forests in Asia and the Pacific increased by a similar amount,” Dr Venn said.

“In many developing countries, large international timber companies operate with disregard for the environment and often have negative impacts on traditional forest communities.”

“Without realising it, many Australians buy products made with foreign timbers and threaten conservation efforts for the orangutan, Malayan tiger, Asian sun bear and Asian tapir.

The research found that Queensland’s low-intensity forestry management techniques are informed by science to minimise environmental impacts.

Queensland law allows selection harvesting in some of the state’s public and private native forests, which typically removes 10 to 20 trees per hectare every 20 to 40 years.

Strict rules regulate how this is conducted, such as by requiring minimum retention of trees of different sizes, including large old trees with hollows.

“Selection harvesting can restore wildlife habitat, promote and conserve floristic diversity and improve the resilience of large trees against climate change and bushfire,” Dr Venn said.

Dr Venn said forestry is the twenty-fifth most important threat to biodiversity in Australia, and forestry in Queensland impacts only 0.8 per cent of Australia’s 1,795 threatened species.

“There are 24 more important threats we should be focused on, including invasive weeds, invasive predators, urban development, and reduced fire frequency or intensity” he said.

Dr Venn said Queensland should continue to manage some of its forests for wood production, as recommended by the Intergovernmental Panel on Climate Change (IPCC).

“The IPCC has long argued that sustainably managing forests to produce timber, fibre and energy will generate the largest carbon sequestration benefit from forests,” he said.

“If Queensland reduced its native forestry in the near future, the knock-on effect would be negative impacts on global efforts to conserve biodiversity and reduce carbon emissions due to increased consumption of timber imports and carbon polluting substitutes.

“Queensland can maximise its contribution to global biodiversity and climate goals by continuing to manage some of the state’s native forests for timber production.”

The research has been published in Forest Policy and Economics.

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JOURNAL

Forest Policy and Economics

DOI

10.1016/j.forpol.2023.102979 

ARTICLE TITLE

Reconciling timber harvesting, biodiversity conservation and carbon sequestration in Queensland, Australia

Archaeology: The power of the Copper Age 'Ivory Lady' revealed

Peer-Reviewed Publication

SCIENTIFIC REPORTS

The highest status individual in ancient Copper Age society in Iberia, was a woman and not a man as previously thought, according to peptide analysis reported in Scientific Reports. 

The individual, now re-dubbed the 'Ivory Lady', was buried in a tomb filled with the largest collection of rare and valuable items in the region, including ivory tusks, high-quality flint, ostrich eggshell, amber, and a rock crystal dagger. These findings reveal the high status women could hold in this ancient society.

In 2008, an individual was discovered in a tomb in Valencia, Spain dating to the Copper Age between 3,200 and 2,200 years ago. As well as being a rare example of a single occupancy burial, the grave contained a large number of valuable goods, suggesting that this individual — originally thought to be a young male aged between 17 and 25 years.  — held a high status within society.

Marta Cintas‑Peña and colleagues used amelogenin peptide analysis to test for the presence of the sexually-dimorphic enamel-forming protein amelogenin in the teeth of the specimen. Analysis of a molar and an incisor detected the presence of the AMELX gene — which produces amelogenin and is located on the X chromosome — indicating that the individual was female rather than male. According to the authors, this means that the highest ranked person in Iberian Copper Age society was a woman. Additionally, the lack of grave goods in infant burials suggests that, in this period, individuals were not granted high status by birth rite. The authors therefore suggest that the Ivory Lady achieved her status through merit and achievements in life.

The authors report that no male of similarly high status has yet been found. As the only comparably lavish Copper Age tomb in the region, containing at least 15 women, was found next to the grave of the ‘Ivory Lady’ and is presumed to have been built by people who claimed descent from her. This suggests that women occupied positions of leadership in Iberian Copper Age society.

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JOURNAL

Scientific Reports

DOI

10.1038/s41598-023-36368-x 

ARTICLE TITLE

Amelogenin peptide analyses reveal female leadership in Copper Age Iberia (c. 2900–2650 BC)’

ARTICLE PUBLICATION DATE

6-Jul-2023

New Zealand kids spending one-third of after-school time on screens

Peer-Reviewed Publication

UNIVERSITY OF OTAGO

 

IMAGE: MOIRA SMITH view more 

CREDIT: UNIVERSITY OF OTAGO

Regulations are urgently needed to protect children from harm in the unregulated online world, researchers at the University of Otago, New Zealand, say.

The call comes as the researchers publish the results of their study into the after-school habits of 12-year-olds. Their research, published today in the New Zealand Medical Journal, finds children are spending a third of their after-school time on screens, including more than half their time after 8pm.

Senior researcher Dr Moira Smith from the University's Department of Public Health says this is considerably more than the current guidelines, which recommend less than two hours of screen time per day (outside school time) for school-aged children and adolescents.

The results are from the innovative Kids’Cam project, with the 108 children involved wearing cameras that captured images every seven seconds, offering a unique insight into their everyday lives in 2014 and 2015.

Children were mostly playing games and watching programmes. For ten per cent of the time the children were using more than one screen.

Screen use harms children’s health and wellbeing.

“It is associated with obesity, poor mental wellbeing, poor sleep and mental functioning and lack of physical activity,” Dr Smith says. “It also affects children’s ability to concentrate and regulate their behaviour and emotions.”

Screen use is now a regular part of children’s everyday lives and is likely to have increased since the Kids’Cam data was collected.

“Screen use rose rapidly during the COVID-19 pandemic, and children in 2023 are frequently spending time online, particularly on smartphones. According to the latest media use survey, YouTube and Netflix are the most popular websites for watching programmes, with one in three children under 14 using social media, most commonly TikTok, which is rated R13.”

She says children are being exposed to ads for vaping, alcohol, gambling and junk food, and experiencing sexism, racism and bullying while online.

“Cyberbullying is particularly high among children in Aotearoa, with one in four parents reporting their child has been subjected to bullying while online.”

Dr Smith says current New Zealand legislation is outdated and fails to adequately deal with the online world children are being exposed to.

“While screen use has many benefits, children need to be protected from harm in this largely unregulated space.”

She says the Government is to be applauded for proposing more regulation of social media in its recent consultation document from the Department of Internal Affairs (DIA), which notes concern about children accessing inappropriate content while online.

The Otago researchers are currently studying the online worlds of children in Aotearoa using screen capture technology, with the results expected to be published soon.

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METHOD OF RESEARCH

Observational study

SUBJECT OF RESEARCH

People

ARTICLE TITLE

Watching the watchers: assessing the nature and extent of children’s screen time using wearable cameras

ARTICLE PUBLICATION DATE

7-Jul-2023

Board games are boosting math ability in young children

Peer-Reviewed Publication

TAYLOR & FRANCIS GROUP

Board games based on numbers, like Monopoly, Othello and Chutes and Ladders, make young children better at math, according to a comprehensive review of research published on the topic over the last 23 years.

Board games are already known to enhance learning and development including reading and literacy.

Now this new study, published in the peer-reviewed journal Early Years, finds, for three to nine-year-olds, the format of number-based board games helps to improve counting, addition, and the ability to recognize if a number is higher or lower than another.

The researchers say children benefit from programs – or interventions – where they play board games a few times a week supervised by a teacher or another trained adult.

“Board games enhance mathematical abilities for young children,” says lead author Dr. Jaime Balladares, from Pontificia Universidad Católica de Chile, in Santiago, Chile.

“Using board games can be considered a strategy with potential effects on basic and complex math skills.

“Board games can easily be adapted to include learning objectives related to mathematical skills or other domains.”

Games where players take turns to move pieces around a board differ from those involving specific skills or gambling.

Board game rules are fixed which limits a player’s activities, and the moves on the board usually determine the overall playing situation.

However, preschools rarely use board games. This study aimed to compile the available evidence of their effects on children.

The researchers set out to investigate the scale of the effects of physical board games in promoting learning in young children.

They based their findings on a review of 19 studies published from 2000 onwards involving children aged from three to nine years. All except one study focused on the relationship between board games and mathematical skills.

All children participating in the studies received special board game sessions which took place on average twice a week for 20 minutes over one-and-a-half months. Teachers, therapists, or parents were among the adults who led these sessions.

In some of the 19 studies, children were grouped into either the number board game or to a board game that did not focus on numeracy skills. In others, all children participated in number board games but were allocated different types e.g. Dominoes.

All children were assessed on their math performance before and after the intervention sessions which were designed to encourage skills such as counting out loud.

The authors rated success according to four categories including basic numeric competency such as the ability to name numbers, and basic number comprehension e.g. ‘nine is greater than three’.

The other categories were deepened number comprehension – where a child can accurately add and subtract – and interest in mathematics.

In some cases, parents attended a training session to learn arithmetic that they could then use in the games.

Results showed that math skills improved significantly after the sessions among children for more than half (52%) of the tasks analyzed.

In nearly a third (32%) of cases, children in the intervention groups gained better results than those who did not take part in the board game intervention.

The results also show that from analyzed studies to date, board games on the language or literacy areas, while implemented, did not include scientific evaluation (i.e. comparing control with intervention groups, or pre and post-intervention) to evaluate their impact on children.

Designing and implementing board games along with scientific procedures to evaluate their efficacy, therefore, are “urgent tasks to develop in the next few years,” Dr. Balladares, who was previously at UCL, argues.

And this, now, is the next project they are investigating.

Dr. Balladares concludes: “Future studies should be designed to explore the effects that these games could have on other cognitive and developmental skills.

“An interesting space for the development of intervention and assessment of board games should open up in the next few years, given the complexity of games and the need to design more and better games for educational purposes.”

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DOI

10.1080/09575146.2023.2218598 

ARTICLE TITLE

The effects of board games on math skills in children attending prekindergarten and kindergarten: A systematic review

ARTICLE PUBLICATION DATE

7-Jul-2023

Team develops all-species coronavirus test

Peer-Reviewed Publication

UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN, NEWS BUREAU

 

IMAGE: ILLINOIS PATHOBIOLOGY PROFESSOR YING FANG AND HER COLLEAGUES DEVELOPED A RELIABLE CORONAVIRUS TEST THAT CAN BE USED TO DETECT AND MONITOR INFECTION IN WILD AND DOMESTICATED ANIMALS. view more 

CREDIT: PHOTO BY FRED ZWICKY

CHAMPAIGN, Ill. — In an advance that will help scientists track coronavirus variants in wild and domesticated animals, researchers report they can now detect exposure to the SARS-CoV-2 virus in any animal species. Most coronavirus antibody tests require specialized chemical reagents to detect host antibody responses against the virus in each species tested, impeding research across species.

The virus that causes COVID-19 in humans also infects a variety of animals, said University of Illinois Urbana-Champaign pathobiology professor and virologist Ying Fang, who led the new research. So far, the virus has been detected in cats, dogs, rodents, deer, apes and a variety of farm and zoo animals. The virus also mutates in these hosts, potentially leading to new variants that can endanger their – and human – health.

“Highly sensitive and specific diagnostic reagents and assays are urgently needed for rapid detection and implementation of strategies for prevention and control of the infection in animals,” the researchers wrote in the journal mSphere, where their findings are reported.

The new coronavirus test focuses on antibodies against a protein, called the N-protein, that is embedded in the virus’s nucleocapsid – a structure made up of proteins and nucleic acids contained within a viral membrane. The N-protein makes a better target than the membrane-bound viral proteins that are usually used in tests for antibody responses, Fang said.

“The N-protein is more abundant and it is more conserved than the proteins used in most tests,” she said. This means that the structure of the protein is more consistent across species, making it a good target for all-species antibody tests.

The team used an N-protein-based blocking ELISA protocol for their test. This method involves coating an ELISA plate with the N-protein, then adding a serum sample of whatever animal is being tested. If the animal has been infected with the coronavirus, its serum will contain anti-N-protein antibodies, which will bind to the N-protein-coated plate. The scientists then wash the plate and add a secondary biotin-tagged monoclonal antibody that targets the N-protein. If the animal is positive for coronavirus infection, its antibodies will block the secondary antibodies from binding to the N-protein. If the animal has not been infected, the monoclonal antibodies will attach to the coated plate and generate a color signal when specific chemicals are added to the plate.

The researchers validated their test using samples from various animals with known SARS-CoV-2 infection status, finding the tests had more than 97% sensitivity and 98% specificity. Further tests in domestic cats showed that the assay was able to detect infection within seven days of exposure to the virus.

 The development of accurate cross-species coronavirus tests provides a useful tool for SARS-CoV-2 field surveillance in animal populations, helping scientists identify potential new animal reservoirs to prevent future disease outbreaks, Fang said. 

The National Institutes of Health supported this research.

 

Editor’s note:  

To reach Ying Fang, email yingf@illinois.edu.  

The paper “Development of monoclonal antibody-based blocking ELISA for detecting SARS-CoV-2 exposure in animals” is available online or from the U. of I. News Bureau.

DOI: 10.1128/msphere.00067-23

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JOURNAL

mSphere

DOI

10.1128/msphere.00067-23 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Development of monoclonal antibody-based blocking ELISA for detecting SARS-CoV-2 exposure in animals

ARTICLE PUBLICATION DATE

6-Jul-2023

Village dogs match pet dogs in reading human facial expressions

Peer-Reviewed Publication

PEERJ

 

IMAGE: IMAGE OF VILLAGE DOGS view more 

CREDIT: PHOTO CREDIT: GIULIA CIMARELLI

A new study, published in PeerJ Life and Environment, conducted by Dr. Martina Lazzaroni (University of Veterinary Medicine, Vienna), Dr Joana Schar (University of Vienna) and colleagues, has shed light on the cognitive abilities of village dogs in understanding human communication. The research, which aimed to explore the impact of the domestication process on dogs' behavior and cognition, has yielded fascinating results, highlighting the importance of studying free-ranging dogs as representatives of the broader dog population. 

Previous studies examining dogs' cognitive skills in understanding human communication primarily focused on pet dogs. While pet dogs serve as valuable models, they represent only a small fraction of the global dog population. In contrast, free-ranging dogs, who continue to experience selective forces of domestication, offer valuable insights into the evolutionary impact on dogs' behavior and cognition. 

Despite the limited number of studies conducted on free-ranging dogs, particularly village dogs, the findings have been nothing short of intriguing. Researchers have discovered that village dogs exhibit a strong inclination towards social contact with humans and demonstrate an understanding of certain aspects of human communication. 

In this recent study, researchers sought to explore the ability of village dogs to decipher subtle human communicative cues, specifically focusing on human facial expressions. To compare their findings with those of pet dogs, who have already exhibited evidence of this social skill, researchers conducted a test mimicking a real-life scenario. 

During the experiment, the researchers repeatedly performed different facial expressions, such as neutral, happy, and angry, while in the presence of food. Eventually, the food was dropped on the ground. The results revealed that both village dogs and pet dogs were capable of distinguishing between subtle human communicative cues. Notably, the subjects exhibited a higher frequency of aversive gazes, such as looking away, in response to the angry facial expression compared to the happy expression. 

However, the study did not yield other significant behavioral effects across the different conditions, likely due to the low intensity of the emotional expressions used. Nevertheless, researchers posit that village dogs' ability to discern human facial expressions could provide them with a survival advantage in human-dominated environments. 

This research has opened new avenues of understanding regarding dogs' cognitive abilities and the effects of domestication on their behavior. By studying free-ranging dogs, scientists can gain valuable insights into the broader dog population's behavior and cognition, going beyond the limited scope of pet dogs. 

These findings hold implications for various fields, including animal behavior, evolutionary biology, and human-animal interactions. The research team anticipates that further exploration of free-ranging dogs will contribute to our knowledge of the intricate relationship between humans and dogs, ultimately enhancing our understanding of animal cognition.

 

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JOURNAL

PeerJ

DOI

10.7717/peerj.15601 

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Village dogs match pet dogs in reading human facial expressions

ARTICLE PUBLICATION DATE

6-Jul-2023

Unveiling the secret of viruses-bacteria interactions in man-made environments

CITY UNIVERSITY OF HONG KONG

 

IMAGE: PROFESSOR PATRICK LEE KWAN-HON (RIGHT) IN THE SCHOOL OF ENERGY AND ENVIRONMENT (SEE) AT CITYU, MISS DU SHICONG (LEFT), PHD STUDENT IN SEE AND THE TEAM COLLECTED SAMPLES FROM DIFFERENT TYPES OF MAN-MADE ENVIRONMENTS IN HONG KONG FOR THE RESEARCH. view more 

CREDIT: CITY UNIVERSITY OF HONG KONG

Viruses in man-made environments cause public health concerns, but they are generally less studied than bacteria. A recent study led by environmental scientists from City University of Hong Kong (CityU) provided the first evidence of frequent interactions between viruses and bacteria in man-made environments. It found that viruses can potentially help host bacteria adapt and survive in nutrient-depleted man-made environments through a unique gene insertion.

By understanding these virus–bacteria interactions and identifying the possible spread of antibiotic resistance genes, the research team hopes its latest findings can help derive effective control strategies to minimize human exposure to harmful microorganisms.

Virus–host interactions are central to the ecology and evolution of microbial communities in diverse ecosystems. However, the immune mechanisms of infection and the virus–host interactions that occur in man-made environments, including buildings, public space, transportation and infrastructure, have been poorly understood. 

“As more and more of the global population are living in urban areas, the importance of hygiene in man-made environments is growing, particularly indoor ones, as occupants inside are constantly exposed to diverse microorganisms, which have public health implications. However, most previous studies of man-made environments overlooked viruses,” said Professor Patrick Lee Kwan-Hon in the School of Energy and Environment (SEE) at CityU, who led the study.

“Therefore, in our study, we comprehensively investigated viruses in man-made environments, and we identified many novel molecular mechanisms in which viruses and bacteria interact with each other. These findings are important not only for basic microbial science, but also the management of man-made environments to protect residents’ health,” added Professor Lee. 

In the study, researchers collected 738 samples from different types of man-made environments, including public facilities and residences, in Hong Kong. They collected the samples mainly from the surfaces of handrails, bollards, floors, poles, doorknobs and skin of residents. Then they used the metagenomic sequencing technique for analysis.

The analysis resulted in many interesting discoveries. First, the data showed that viruses are integral members of microbial communities in man-made environments. Among them, bacteriophages, a kind of virus that infects and replicates within bacteria, are all over various surfaces in man-made environments. The team also identified many viruses that are distinct from those in other ecosystems.

Second, the team found evidence of viruses inserting genes that control a specific step in a metabolic pathway and even the entire metabolic pathway into bacteria hosts. This suggests that viruses could help bacteria adapt and coevolve to survive in nutrient-depleted man-made environments. 

The study also found diverse and novel immune systems against viruses in bacteria, and small proteins in viruses that can evade bacteria immune systems. These results suggest that viruses and bacteria hosts frequently interact with each other in man-made environments and that they each have mechanisms to defend against each other.

They also detected antibiotic resistance genes (ARGs) in viruses on human skin and frequently touched indoor surfaces. These ARG-carrying viruses might infect bacterial hosts, and ARGs might be horizontally transferred between bacterial species. Therefore, the role played by viruses in man-made environments in the development of antibiotic resistance in bacteria is crucial and warrants further investigation.

“Our study shows that the diversity, composition, metabolic functions and lifestyle of viruses vary, depending on the conditions of each man-made environment,” said Professor Lee. “Therefore, it is important to develop customized control strategies to minimize human exposure to harmful microorganisms and to better protect residents’ health. Our findings can contribute to this goal by enhancing the fundamental understanding of complex virus–bacteria interactions in man-made environments.” 

The findings were published in the scientific journal Nature Communications under the title “Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution”.

Network diagram illustrating viruses and their predicted bacterial hosts in various man-made environments. The circles and diamonds indicate the predicted bacterial hosts (at the family taxonomic level) and viruses, respectively, and the edges are coloured according to the prediction methods. The frequency of virus–host links occurring in a habitat is shown on the right

Schematic illustrating the insertion of genes by a virus into a bacteria host, disrupting the host genome or providing beneficial metabolic functions for the host.

CREDIT

Du, S. et al, https://www.nature.com/articles/s41467-023-38400-0

The first author is Miss Du Shicong, PhD student in SEE, and the corresponding author is Professor Lee. Other team members include Professor Alvin Lai Chi-Keung, Professor Chan Chak-Keung and Dr Tong Xinzhao, from SEE, and Professor Christopher E. Mason, from Weill Cornell Medicine.

The research is supported by the Research Grants Council’s Research Impact Fund and the General Research Fund in Hong Kong. 

https://www.cityu.edu.hk/research/stories/2023/07/06/unveiling-secret-viruses-bacteria-interactions-man-made-environments

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JOURNAL

Nature Communications

DOI

10.1038/s41467-023-38400-0 

METHOD OF RESEARCH

Data/statistical analysis

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution