VIRUSES IN THE DEEP

FROM:  NATIONAL SCIENCE FOUNDATION
The 'intraterrestrials': New viruses discovered in ocean depths

Viruses infect methane-eating archaea beneath the seafloor
The intraterrestrials, they might be called.

Strange creatures live in the deep sea, but few are odder than the viruses that inhabit deep ocean methane seeps and prey on single-celled microorganisms called archaea.

The least understood of life's three primary domains, archaea thrive in the most extreme environments on the planet: near hot ocean rift vents, in acid mine drainage, in the saltiest of evaporation ponds and in petroleum deposits deep underground.

Virus in the deep blue sea

While searching the ocean's depths for evidence of viruses, scientists have found a remarkable new one, a virus that seemingly infects archaea that live beneath the ocean floor.

The researchers were surprised to discover that the virus selectively targets one of its own genes for mutation, and that this capacity is also shared by archaea themselves.

The findings appear today in a paper in the journal Nature Communications.

The project was supported by a National Science Foundation (NSF) Dimensions of Biodiversity grant to characterize microbial diversity in methane seep ecosystems. Dimensions of Biodiversity is supported by NSF's Directorates for Biological Sciences and Geosciences.

New information about life in ocean depths

"Life far beneath the Earth's subsurface is an enigma," said Matt Kane, program director in NSF's Division of Environmental Biology. "By probing deep into our planet, these scientists have discovered new information about Earth's microbes and how they evolve."

"Our study uncovers mechanisms by which viruses and archaea can adapt in this hostile environment," said David Valentine, a geoscientist at the University of California Santa Barbara (UCSB) and co-author of the paper.

The results, he said, raise new questions about the evolution and interaction of the microbes that call the planet's interior home.

"It's now thought that there's more biomass inside the Earth than anywhere else, just living very slowly in this dark, energy-limited environment," said paper co-author Sarah Bagby of UCSB.

Using the submersible Alvin, Valentine and colleagues collected samples from a deep-ocean methane seep by pushing tubes into the ocean floor and retrieving sediments.

The contents were brought back to the lab and fed methane gas, helping the methane-eating archaea in the samples to grow.

When the team assayed the samples for viral infection, they discovered a new virus with a distinctive genetic fingerprint that suggested its likely host was methane-eating archaea.

Genetic sequence of new virus holds the key

The researchers used the genetic sequence of the new virus to chart other occurrences in global databases.

"We found a partial genetic match from methane seeps off Norway and California," said lead author Blair Paul of UCSB. "The evidence suggests that this viral type is distributed around the globe in deep ocean methane seeps."

Further investigation revealed another unexpected finding: a small genetic element, known as a diversity-generating retroelement, that accelerates mutation of a specific section of the virus's genome.

Such elements had been previously identified in bacteria and their viruses, but never among archaea or the viruses that infect them.

"These researchers have shown that cutting-edge genomic approaches can help us understand how microbes function in remote and poorly known environments such as ocean depths," said David Garrison, program director in NSF's Division of Ocean Sciences.

While the self-guided mutation element in the archaea virus resembles known bacterial elements, the researchers found that it has a divergent evolutionary history.

"The target of guided mutation--the tips of the virus that make first contact when infecting a cell--is similar," said Paul.

"But the ability to mutate those tips is an offensive countermeasure against the cell's defenses, a move that resembles a molecular arms race."

Unusual genetic adaptations

Having found guided mutation in a virus-infecting archaea, the scientists reasoned that archaea themselves might use the same mechanism for genetic adaptation.

In an exhaustive search, they identified parallel features in the genomes of a subterranean group of archaea known as nanoarchaea.

Unlike the deep-ocean virus that uses guided mutation to alter a single gene, the nanoarchaea target at least four distinct genes.

"It's a new record," said Bagby.

"Bacteria had been observed to target two genes with this mechanism. That may not seem like a huge difference, but targeting four is extraordinary."

According to Valentine, the genetic mutation that fosters these potential variations may be key to the survival of archaea beneath the Earth's surface.

"The cell is choosing to modify certain proteins," he said. "It's doing its own protein engineering. While we don't yet know what those proteins are being used for, learning about the process can tell us something about the environment in which these organisms thrive."

Viral DNA sequencing was provided through a Gordon and Betty Moore Foundation grant. The research team also included scientists from the University of California, Los Angeles; the University of California, San Diego; and the U.S. Department of Energy's Joint Genome Institute.

-NSF-
Media Contacts
Cheryl Dybas, NSF

NSF ARTICLE: TESTING FOR PATHOGENS

FROM:  NATIONAL SCIENCE FOUNDATION 

Testing for pathogens

Innovation Corps researchers focus on medical applications rather than food safety in response to customer needs

When Sunny Shah and his research colleagues at the University of Notre Dame developed a new diagnostic tool for detecting the presence of bacteria, viruses and other pathogens, they assumed that the food industry would be the perfect market.

It made sense, particularly amid ongoing concerns over food safety. The test could identify, among other things, E. coli 0157, which has caused a number of deadly outbreaks in the United States, as well as the bacterium responsible for brucellosis, a disease caused by eating undercooked meat or unpasteurized dairy products.

Their test was accurate and inexpensive. It just wasn't fast enough.

"Even though we could provide a cheaper test than what is already available, they said they would be willing to pay more for a faster test," Shah says, referring to his conversations with representatives from food processing plants, health agencies and food testing labs. "They said we needed to produce results within two hours, not two days, because they wouldn't be able to ship anything out, and had to pay for refrigeration, while waiting for test results."

So the National Science Foundation (NSF)-funded scientist switched his focus--he likes to call it a "pivot"--from food safety to medical applications. In addition to food-borne bacteria, the test also can recognize the virus that causes Dengue fever, potentially valuable for surveillance activities both here and abroad, and human papillomavirus (HPV), which is linked to cervical and oral cancers.

Shah, who also is assistant director for the ESTEEM graduate program, which exposes those with STEM (science, technology, engineering, and mathematics) backgrounds to business and entrepreneurial courses, received $50,000 in 2013 from NSF's Innovation Corps (I-Corps) program. I-Corps helps scientists assess how, and whether, they can translate their promising discoveries into viable commercial products.

The award supports a set of activities and programs that prepare scientists and engineers to extend their focus beyond the laboratory into the commercial world, with the idea of providing near-term benefits for the economy and society.

It is a public-private partnership program that teaches grantees to identify valuable product opportunities that can emerge from academic research, and offers entrepreneurship training to student participants.

Although things did not turn out as originally planned in this case, Shah's experience nevertheless actually embodies the I-Corps philosophy, since one of its major goals is to mentor scientists in ways that allow them to evaluate the commercial potential of their discoveries, and send them in different directions if necessary to ensure their research ends up in the best possible place to do the most good at an affordable price.

"It doesn't matter what we, as researchers, think is the value of our technology," Shah says. "It's what the customer thinks that is important and the only way to identify this customer need is by getting out and interviewing them."

NSF also earlier supported the research that developed the test in 2011. Shah's research colleagues on this project include Hsueh-Chia Chang, professor of chemical and biomolecular engineering, Satyajyoti Senapati, research assistant professor, and Zdenek Slouka, postdoctoral associate in the Chang group. For the I-Corps grant, Kerry Wilson, managing director of Springboard Engineers, played the role of the business mentor, while Shah was the entrepreneurial lead

The test uses a biochip that can detect the DNA or RNA of a particular pathogen.

"Every pathogen has a unique biomarker, and what we do is put a probe on our biochip that captures that biomarker," Shah says. "If the sample has that particular pathogen, then its biomarker will bind to this probe and give us a signal. There are changes in the electrical properties, so it gives us a visual electrical signal that can easily be translated into a target present/absent signal."

Each chip is programmed for a specific pathogen, "but in the future we hope to develop what we call a multiplex biochip that can detect numerous pathogens all on the same device," Shah adds.

The plan now is to develop the tool for future use by dentists to test their patients during office visits for early detection of HPV-related oral cancer before there are visible signs of disease.

"Usually dentists now just examine you visually for lesions, but this would be a sample swab that could give you advance warning," he says.

The test also might be useful as a diagnostic tool for food-borne disease after infection, that is, in testing an already ill patient's blood, he says.

The team recently received a National Institutes of Health grant to study a possible future surveillance role for the test in screening mosquitoes for the presence of Dengue Fever.

"This is not a huge problem for the United States, although there have been a number of cases in parts of Florida in recent years, but it is an issue in South America, Brazil and India, and other areas, " he says.

The impact of I-Corps allowed Shah to make the transition. "Knowing the market and the customer early is extremely important in the technology commercialization process," he says. The program helped him to "quickly assess a particular market to identify customer need and be ready to pivot from one market to another, if needed."

-- Marlene Cimons, National Science Foundation
Investigators
Sunny Shah
Li-Jing Cheng
Hsueh-Chia Chang
Satyajyoti Senapati
Related Institutions/Organizations
University of Notre Dame

COURT SHUTS DOWN TECH SUPPORT SCAMMERS WHO SOLD SOFTWARE AVAILABLE FOR FREE

FROM:  FEDERAL TRADE COMMISSION 

At FTC’s Request, Court Shuts Down New York-Based Tech Support Scam Business

At the request of the Federal Trade Commission, a federal court has shut down a company that scammed computer users by tricking them into paying hundreds of dollars for technical support services they did not need, as well as software that was otherwise available for free.

According to the FTC’s complaint, Pairsys, Inc., cold-called consumers masquerading as representatives of Microsoft or Facebook, and also purchased deceptive ads online that led consumers to believe they were calling the technical support line for legitimate companies.

“The defendants behind Pairsys targeted seniors and other vulnerable populations, preying on their lack of computer knowledge to sell ‘security’ software and programs that had no value at all,” said Jessica Rich, director of the FTC’s Bureau of Consumer Protection. “We are pleased that the court has shut down the company for now, and we look forward to getting consumers’ money back in their pockets.”

Whether consumers were cold-called by the company or drawn in by deceptive ads, the FTC’s complaint notes that what followed was a deceptive and high-pressure sales pitch conducted by scammers in an overseas call center. The scammers would convince a consumer to allow them to have remote control over the individual’s computer, in order to analyze the supposed issues.

Once they had access to a consumer’s computer, the FTC alleges, the scammers would lead the consumer to believe that benign portions of the computer’s operating system were in fact signs of viruses and malware infecting the consumer’s computer. In many cases, they implied that the computer was severely compromised and had to be “repaired” immediately.

At that point, consumers were pressured into paying for bogus warranty programs and software that was freely available, usually at a cost of $149 to $249, though in some cases, the defendants charged as much as $600 for the supposed products. The FTC’s filings in the case allege that the company made nearly $2.5 million since early 2012.

The defendants have agreed to the terms of a preliminary injunction issued by the court that prohibits the defendants in the case from making misrepresentations to consumers about what company they represent or whether consumers have viruses or spyware on their computer. They are also banned from deceptive telemarketing practices, and may not sell or rent their customer lists to any third party. The injunction requires that their websites and telephone numbers must be shut down and disconnected, and their assets be frozen.

The defendants in the case, Pairsys, Inc., Uttam Saha and Tiya Bhattacharya, are accused by the FTC of violating both the FTC Act and the Telemarketing Sales Rule. In its complaint, the FTC asks the court to permanently shut down the company and require the defendants to return their ill-gotten gains. The FTC previously brought cases against a number of tech support scammers in 2012 and has received settlements and judgments totaling more than $5 million in those cases.

The Commission vote authorizing the staff to file the complaint was 5-0. The complaint was filed in the U.S. District Court for the Northern District of New York. The stipulated preliminary injunction was entered by the court on Oct. 9. 2014.

NOTE: The Commission files a complaint when it has “reason to believe” that the law has been or is being violated and it appears to the Commission that a proceeding is in the public interest. The case will be decided by the court.

WASTEWATER GETS A COLD

FROM:  NATIONAL SCIENCE FOUNDATION 

Harnessing the power of viruses to improve wastewater treatment

Researcher developing a system to isolate and replicate a natural phenomenon 

that removes pollutants and other contaminants

Just as certain viruses infect humans, there also are viruses that infect only bacteria. Unlike human viruses, however, which are non-discriminatory and will infect any number of different people, these viruses, known as bacteriophages, are "host-specific,'' meaning each will attack only one particular bacteria.

"Wherever bacteria exist, there are bacteriophages,'' says Ramesh Goel, an associate professor of civil and environmental engineering at the University of Utah. "If we go to any wetland, or streams or wastewater treatment process, bacteria are there, and so are bacteriophages."

Goel believes he can put this phenomenon to good use.

The National Science Foundation (NSF)-funded scientist, who studies the microbial ecology of natural and engineered systems, particularly those that use microbes to remove pollutants and other contaminants from waste water, is trying to harness the power of bacteriophages to rid treated wastewater of problematic bacteria that cause operational problems during treatment.

The use of bacteria in wastewater treatment has become increasingly popular in recent years, but it is not without challenges. Certain bacteria involved in the process, for example, called filamentous bacteria, continue to float on the surface of the water when the treatment is complete, rather than settle on the bottom where they can be removed through a simple physical process known as gravity settling.

"On the one hand, we use the bacteria to treat the water, but some are not cooperating and create problems," Goel says. "We end up having bacteria in our final, treated water."

The problem-causing bacteria are non-toxic to humans, making them harmless, but can cause problems if the treated water is discharged into streams or rivers, where they will consume oxygen and pose a threat to aquatic life.

"The danger is in having them escape with the treated water,'' he says, adding that to otherwise kill the bacteria "requires a lot of chlorine,'' as well as other challenges.

Goel is developing a system to isolate and replicate the viruses that infect several filamentous bacteria known to cause settling problems in biological wastewater treatment processes.

"The idea is to use either single or a mixture of phages to kill unwanted filamentous bacteria up to their optimum concentration, a process we call phage therapy for filamentous bulking," he says. "We have been able to demonstrate phage therapy for filamentous bulking in laboratory scale reactors. The next challenge is to bring it into practice for full scale applications."

In a related project, Goel also is trying to use phages to solve the problem of biofilm formation in wastewater treatment systems that use membrane filtering, rather than gravity settling. During this process, which sends treated wastewater flowing through a membrane to separate it from bacteria, the bacteria often form biofilms on the surface of the membranes, which are substances that resemble slime, a problem known as biofouling. Goel hopes to use bacteriophages to eliminate biofilms, thus preventing biofouling, either by direct application of phages or by using intermediate chemicals produced by phages that are capable of degrading biofilm.

If successful in these water treatments, the use of bacteriophages "will have tremendous impact, unimaginable impact, since these are worldwide problems," he says.

Goel thinks there may be additional future practical applications for bacteriophages separate from wastewater treatment. He sees potential for them in the health field, for example, in drug delivery or in using them to treat external bacterial infections, such as on skin, or on medical devices, such as catheters, "which sometimes get biofilms," he says. "You end up using expensive chemicals. Could we use phages to remove these biofilms?

"Can we use phages to deliver drugs?" he adds. "There may be some antibiotics we want to deliver that aren't reaching the person--the phages will not only kill that particular bacteria, but deliver the drug. These are all new ideas we are exploring."

Goel is conducting this research under an NSF Faculty Early Career Development (CAREER) award, which he received in 2011. The award supports junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education, and the integration of education and research within the context of the mission of their organization.

As part of the grant's educational component, Goel is hosting a number of local K-12 students in his lab, exposing them to the field of wastewater engineering and microbiology. He also is working with three women undergraduates in his lab; one of them, from the computer science department, is creating computer animations for public outreach.

"The whole idea is to use animations to create a virtual lab, something that will go beyond our borders and that we can share with other countries," he says. "The animations will show how phages infect bacteria, and we think they will really help students better understand these concepts."

-- Marlene Cimons, National Science Foundation
Investigators
Ramesh Goel
Related Institutions/Organizations
University of Utah

NSF VIDEO: SCIENCE NATION - EVEN HEALTHY CORALS HAVE VIRUSES

EPA WARNS OF SWIMMING RELATED ILLNESSES

FROM:  U.S. ENVIRONMENTAL PROTECTION AGENCY 

Human Health

Most of the time when beaches are closed or advisories are issued, it's because the water has high levels of harmful microorganisms (or microbes) that come from untreated or partially treated sewage: bacteria, viruses, or parasites. We also use the word "pathogens" when they can cause disease in humans, animals, and plants.
Illnesses.

hildren, the elderly, and people with weakened immune systems are most likely to develop illnesses or infections after coming into contact with polluted water, usually while swimming. The most common illness is gastroenteritis, an inflammation of the stomach and the intestines that can cause symptoms like vomiting, headaches, and fever. Other minor illnesses include ear, eye, nose, and throat infections

Fortunately, while swimming-related illnesses are unpleasant, they are usually not very serious - they require little or no treatment or get better quickly upon treatment, and they have no long-term health effects. In very polluted water, however, swimmers can sometimes be exposed to more serious diseases like dysentery, hepatitis, cholera, and typhoid fever.

Most swimmers are exposed to waterborne pathogens when they swallow the water. People can get some infections simply from getting polluted water on their skin or in their eyes. In rare cases, swimmers can develop illnesses or infections if an open wound is exposed to polluted water.

Not all illnesses from a day at the beach are from swimming. Food poisoning from improperly refrigerated picnic lunches may also have some of the same symptoms as swimming-related illnesses, including stomachache, nausea, vomiting, and diarrhea.

It is also possible that people may come into contact with harmful chemicals in beach waters during or after major storms, especially if they swim near what we call “outfalls,” where sewer lines drain into the water. You can learn more about this by visiting our web site for stormwater.

Finally, the sun can hurt you if you're not careful. Overexposure can cause sunburn, and over time, it can lead to more serious problems like skin cancer. The sun can also dehydrate you and cause heat-related illnesses like heat exhaustion, muscle cramps, and heat stroke. Learn more about sun safety at our SunWise site or heat-related illnesses at the Centers for Disease Control and Prevention site.

How to Stay Safe

There are several things you can do to reduce the likelihood of getting sick from swimming at the beach. First, you should find out if the beach you want to go to is monitored regularly and posted for closures or swimming advisories. You are less likely to be exposed to polluted water at beaches that are monitored regularly and posted for health hazards.

In areas that are not monitored regularly, choose swimming sites in less developed areas with good water circulation, such as beaches at the ocean. If possible, avoid swimming at beaches where you can see discharge pipes or at urban beaches after a heavy rainfall.

To find out about the beaches you want to visit, contact the local beach manager.

Since most swimmers are exposed to pathogens by swallowing the water, you will be less likely to get sick if you wade or swim without putting your head under water.

NSF AND THE VIRUS PIRATES

FROM:  THE NATIONAL SCIENCE FOUNDATION 

Undersea warfare: Viruses hijack deep-sea bacteria at hydro-thermal vents

Unseen armies of viruses and bacteria battle in the deep

More than a mile beneath the ocean's surface, as dark clouds of mineral-rich water billow from seafloor hot springs called hydrothermal vents, unseen armies of viruses and bacteria wage war.

Like pirates boarding a treasure-laden ship, the viruses infect bacterial cells to get the loot: tiny globules of elemental sulfur stored inside the bacterial cells.

Instead of absconding with their prize, the viruses force the bacteria to burn their valuable sulfur reserves, then use the unleashed energy to replicate.

"Our findings suggest that viruses in the dark oceans indirectly access vast energy sources in the form of elemental sulfur," said University of Michigan marine microbiologist and oceanographer Gregory Dick, whose team collected DNA from deep-sea microbes in seawater samples from hydrothermal vents in the Western Pacific Ocean and the Gulf of California.

"We suspect that these viruses are essentially hijacking bacterial cells and getting them to consume elemental sulfur so the viruses can propagate themselves," said Karthik Anantharaman of the University of Michigan, first author of a paper on the findings published this week in the journal Science Express.

Similar microbial interactions have been observed in shallow ocean waters between photosynthetic bacteria and the viruses that prey upon them.

But this is the first time such a relationship has been seen in a chemosynthetic system, one in which the microbes rely solely on inorganic compounds, rather than sunlight, as their energy source.

"Viruses play a cardinal role in biogeochemical processes in ocean shallows," said David Garrison, a program director in the National Science Foundation's (NSF) Division of Ocean Sciences, which funded the research. "They may have similar importance in deep-sea thermal vent environments."

The results suggest that viruses are an important component of the thriving ecosystems--which include exotic six-foot tube worms--huddled around the vents.

"The results hint that the viruses act as agents of evolution in these chemosynthetic systems by exchanging genes with the bacteria," Dick said. "They may serve as a reservoir of genetic diversity that helps shape bacterial evolution."

The scientists collected water samples from the Eastern Lau Spreading Center in the Western Pacific Ocean and the Guaymas Basin in the Gulf of California.

The samples were taken at depths of more than 6,000 feet, near hydrothermal vents spewing mineral-rich seawater at temperatures surpassing 500 degrees Fahrenheit.

Back in the laboratory, the researchers reconstructed near-complete viral and bacterial genomes from DNA snippets retrieved at six hydrothermal vent plumes.

In addition to the common sulfur-consuming bacterium SUP05, they found genes from five previously unknown viruses.

The genetic data suggest that the viruses prey on SUP05. That's not too surprising, said Dick, since viruses are the most abundant biological entities in the oceans and are a pervasive cause of mortality among marine microorganisms.

The real surprise, he said, is that the viral DNA contains genes closely related to SUP05 genes used to extract energy from sulfur compounds.

When combined with results from previous studies, the finding suggests that the viruses force SUP05 bacteria to use viral SUP05-like genes to help process stored globules of elemental sulfur.

The SUP05-like viral genes are called auxiliary metabolic genes.

"We hypothesize that the viruses enhance bacterial consumption of this elemental sulfur, to the benefit of the viruses," said paper co-author Melissa Duhaime of the University of Michigan. The revved-up metabolic reactions may release energy that the viruses then use to replicate and spread.

How did SUP05-like genes end up in these viruses? The researchers can't say for sure, but the viruses may have snatched genes from SUP05 during an ancient microbial interaction.

"There seems to have been an exchange of genes, which implicates the viruses as an agent of evolution," Dick said.

All known life forms need a carbon source and an energy source. The energy drives the chemical reactions used to assemble cellular components from simple carbon-based compounds.

On Earth's surface, sunlight provides the energy that enables plants to remove carbon dioxide from the air and use it to build sugars and other organic molecules through the process of photosynthesis.

But there's no sunlight in the deep ocean, so microbes there often rely on alternate energy sources.

Instead of photosynthesis they depend on chemosynthesis. They synthesize organic compounds using energy derived from inorganic chemical reactions--in this case, reactions involving sulfur compounds.

Sulfur was likely one of the first energy sources that microbes learned to exploit on the young Earth, and it remains a driver of ecosystems found at deep-sea hydrothermal vents, in oxygen-starved "dead zones" and at Yellowstone-like hot springs.

Dick said the new microbial findings will help researchers understand how marine biogeochemical cycles, including the sulfur cycle, will respond to global environmental changes such as the ongoing expansion of dead zones.

SUP05 bacteria, which are known to generate the greenhouse gas nitrous oxide, will likely expand their range as oxygen-starved zones continue to grow in the oceans.

In addition to Anantharaman, Dick and Duhaime, co-authors of the Science Express paper are John Breir of the Woods Hole Oceanographic Institution, Kathleen Wendt of the University of Minnesota and Brandy Toner of the University of Minnesota.

The project was also funded by the Gordon and Betty Moore Foundation and the University of Michigan Rackham Graduate School Faculty Research Fellowship Program.

-NSF-
Media Contacts
Cheryl Dybas, NSF