Category: 7. Science

Study reveals why tomatoes and peppers can’t graft together

Grafting is a common agricultural practice to combine desirable traits by joining the rootstock of one plant with the scion of another. Compatibility is key—without successful vascular integration, the graft fails. While grafting works well within many plant families, cross-species combinations often result in unexplained failure. One well-documented example is the graft incompatibility between tomato (Solanum lycopersicum) and pepper (Capsicum spp.), two closely related species within the Solanaceae family. Past studies identified physical weakness and failed vascular reconnection, but lacked molecular explanation. The persistent presence of necrotic tissue at the graft site hinted at deeper cellular conflict. Due to these challenges, a comprehensive investigation of the biological underpinnings of graft incompatibility was needed.

Researchers from Cornell University and collaborators published a study (DOI: 10.1093/hr/uhae255) on September 11, 2024, in Horticulture Research, providing unprecedented insights into why grafts between tomato and pepper fail. Using anatomical inspection and high-resolution RNA sequencing, the team found that incompatible grafts triggered strong immune responses and sustained cell death at the junction site. The work identifies a novel mechanism of incompatibility based on autoimmunity, opening new directions for understanding plant-to-plant recognition and graft success.

The team performed reciprocal grafts between tomato and four pepper cultivars and found consistent failure across all combinations. Despite initial graft survival in some pairings, anatomical examination showed no vascular reconnection. Structural tests confirmed weakened stem stability. Using trypan blue staining, researchers observed high levels of nonviable tissue at the junction up to 21 days after grafting, in contrast to self-grafts that healed progressively. RNA-seq analysis revealed that incompatible grafts expressed significantly more differentially expressed genes—especially nucleotide-binding leucine-rich repeat receptors (NLRs)—than self-grafts. These NLRs, known for recognizing pathogenic threats, were upregulated without any pathogen presence, indicating a self-activated immune reaction. Moreover, markers of DNA damage and cell death, including BRCA1, BARD1, and programmed cell death genes, were highly expressed. Interestingly, the study also found that incompatible grafts shared transcriptional signatures with biotic stress responses like parasitism and fungal attack, suggesting that the plant perceived the other species as a biological invader. Shared orthologs between tomato and pepper—such as ERF114—further support that common genetic elements mediate this rejection. Overall, this is the first clear demonstration of autoimmunity being the molecular cause of interspecies graft incompatibility in crops.

“Our research reveals that incompatible grafts behave much like plants under attack,” said lead author Hannah Rae Thomas. “Tomato and pepper appear to mistake each other for invaders, activating immune pathways that lead to persistent cell death at the graft site. This immune-driven incompatibility offers a compelling explanation for why these species, despite their genetic closeness, cannot be successfully grafted. It’s a reminder that plant immune systems are remarkably discerning—even with their own family members.”

These findings have profound implications for plant breeding and agriculture. By identifying genetic markers and immune pathways responsible for graft failure, breeders may be able to screen for compatible scion-rootstock combinations or even engineer compatibility. The work also opens a new frontier in understanding how plants distinguish self from non-self—a process crucial not only in grafting but also in pathogen defense and hybrid breeding. Furthermore, this study lays the groundwork for predictive models of compatibility and may guide future development of interspecies grafting strategies across the Solanaceae family and beyond.

Source: NewsWise

Continue Reading

July 25, 2025
Millipedes make ants dizzy — and might soon treat human pain

Millipedes get a bad rap — their many legs put people off and could classify them as “creepy crawly.” But these anthropods’ secretions could hold the key to new drug discovery for the treatment of neurological diseases and pain.

Chemist Emily Mevers and her team recently discovered a new set of complex structures in millipede secretions that can modulate specific neuroreceptors in ant brains.

The newly discovered structures fall into a class of naturally occurring compounds called alkaloids. The Mevers team named them the andrognathanols and the andrognathines after the producing millipede, Andrognathus corticarius, found on Virginia Tech’s Blacksburg campus in Stadium Woods. These discoveries were recently published in the Journal of the American Chemical Society.

A new compound discovery

Mevers specializes in leveraging the chemistry of underexplored ecological niches, in this case the millipede, in the name of drug discovery.

After collecting millipedes from under leaf litter and fallen branches in Stadium Woods, Mevers and team members used a variety of analytical tools to identify the compounds contained in the millipedes’ defensive glands. They also learned that the millipedes release these compounds to ward off predators while also sharing their location with their kin.

Broader implications

Despite their pervasiveness, much about millipedes remains mysterious — including their specific habitats, numbers, diets, behaviors, and chemistry. Mevers, in collaboration with millipede expert Paul Marek in the entomology department, is working to fill in some of these gaps and see if what they uncover could be useful for future medications.

Previously, Mevers and Marek examined a millipede native to the Pacific Northwest, Ishcnocybe plicata, and discovered that related alkaloids potently and selectively interact with a single neuroreceptor called Sigma-1. The interaction suggested that this family of compounds may have useful pharmacology potential for the treatment of pain and other neurological disorders.

The Mevers group discovered that the new alkaloids are actively secreted from the Hokie millipede when it is physically disturbed. The secretions cause disorientation in ants, a presumed natural predator. A subset of these compounds possesses similar interactions with the Sigma-1 neuroreceptor.

Moving toward drug development

With the newfound complex compounds in hand, the next step is finding people to actually make them in larger quantities and evaluate their biomedical applications.

“These compounds are quite complex, so they’re going to take some time to synthesize in the lab,” said Mevers.

Once larger quantities are available, Mevers will be able to better study their properties and potential in drug development.

Continue Reading

July 25, 2025
‘You can zoom in to your country, your state, your city block’

NASA’s new web portal reveals ground movements across North America with precision that captures tiny shifts smaller than an inch, reported NASA’s Jet Propulsion Laboratory.

This tool helps people monitor the Earth’s movements, whether caused by natural phenomena such as earthquakes and volcanic activity or human activities such as the extraction of underground resources.

By converting complex satellite radar signals into user-friendly visual maps, NASA has made what was once specialist knowledge available to everyday users.

The project comes from NASA’s Observational Products for End-Users from Remote Sensing Analysis team working with the Alaska Satellite Facility. They’ve created a program that handles satellite information collected since 2014, with plans to include new data from another space mission launching this year.

“You can zoom in to your country, your state, your city block, and look at how the land there is moving over time,” said David Bekaert, OPERA project manager and radar scientist. “You can see that by a simple mouse click.”

Right now, you can explore data for areas such as the American Southwest, parts of Mexico’s northern region, and greater New York. The portal displays information for millions of spots on the map. When you click anywhere, you’ll see a chart showing that location’s movement history back to 2016.

Watch now: Giant snails invading New York City?

Water experts have already started using this mapping tool. Take Arizona, where tracking the gradual sinking of land helps manage precious groundwater supplies.

“It’s a great tool to say, ‘Let’s look at those areas more intensely with our own SAR processing,’” said Brian Conway, principal hydrogeologist at the Arizona Department of Water Resources.

The technology works by bouncing radar signals off Earth’s surface from satellites. When these signals return, special computer programs analyze them to determine if the land is rising or sinking. What once took specialists many days to calculate now happens automatically within seconds.

NASA plans to roll out coverage beyond its current regions. According to its timeline, people across North America will gain access as the map grows to include all U.S. states, neighboring areas in Canada, and countries throughout Central America before 2026 arrives.

Join our free newsletter for good news and useful tips, and don’t miss this cool list of easy ways to help yourself while helping the planet.

Continue Reading

July 25, 2025
NASA Just Snapped A Rare Solar Eclipse From Space — See The Photos

Topline

NASA’s Solar Dynamics Observatory has captured the moon eclipsing the sun in an event only observable from its position in space. At the height of the event on Friday, July 25, around 62% of the sun was covered by the moon. The SDO, which is solar-powered, coped with the drop in sunlight by having its batteries fully charged before the eclipse occurred.

NASA’s Solar Dynamic Observatory captured a rare solar eclipse from Earth orbit on July 25, 2025.

NASA SDO

Key Facts

The SDO sees several eclipses — or lunar transits — each year. This one was a deep partial eclipse, which lasted about 35 minutes. The SDO studies the sun’s atmosphere in various wavelengths of light.

The spacecraft is in a geosynchronous orbit around Earth, matching Earth’s rotation, and positioned 22,238 miles (35,789 kilometers) above a ground station in White Sands, New Mexico.

SDO has an almost constant but slightly different view of the sun than we do from Earth’s surface, but there are times when its orbit passes behind the Earth, causing an eclipse from its point of view. On July 25, SDO passed passed behind both the moon and the Earth on the same day, accotSDO.

The next solar eclipse visible from Earth will be a partial solar eclipse on Sept. 21, when up to 80% of the sun will be blocked by the moon as seen from New Zealand, Tasmania in Australia, the Indian Ocean, and Antarctica. Observers will need to wear solar eclipse glasses at all times, and all cameras and telescopes will need solar filters.

The next total solar eclipse visible from Earth will occur on Aug. 12, 2026, for parts of Greenland, western Iceland, and northern Spain. The maximum totality will be 2 minutes and 18 seconds off Iceland.

NASA’s Solar Dynamic Observatory captured a rare solar eclipse from Earth orbit on July 25, 2025.

NASA SDO

Europe’s ‘fake’ Total Solar Eclipses In Space

The European Space Agency’s Proba-3 mission — the world’s first precision formation flying mission — last month captured the first images of an artificial total solar eclipse from space. Proba-3 is a pair of satellites that fly in formation with millimeter precision, with one blocking the sun with an occulter disk and casting a shadow on a telescope on the satellite behind it. That allows it to image the sun’s corona — the sun’s outer, hotter but more tenuous atmosphere — which is only visible during a total solar eclipse. Although SDO can also see the corona, Proba-3 can see much farther into it, revealing what’s going on close to the Sun’s photosphere. That’s important because it’s there that the solar wind, solar flares and coronal mass ejections are produced. Proba-3 can produce a total solar eclipse lasting six hours once every 19.6-hour orbit.

The Sun’s inner corona appears greenish in this image taken on 23 May 2025 by the ASPIICS … More coronagraph aboard Proba-3, ESA’s formation-flying mission capable of creating artificial total solar eclipses in orbit. This image, captured in the visible light spectrum, shows the solar corona similarly to how a human eye would see it during an eclipse through a green filter. The hair-like structures were revealed using a specialised image processing algorithm.

ESA/Proba-3/ASPIICS/WOW algorithm

Apollo 11’s Solar Eclipse In Space

Exactly 56 years ago this week, the crew of NASA’s Apollo 11 mission — the first to put astronauts on the moon — saw a total solar eclipse. On Jul. 19, 1969, Neil Armstrong, Buzz Aldrin and Michael Collins photographed a total solar eclipse on their way to the moon. Aldrin had seen a total solar eclipse from space before, on Nov. 11, 1966, during the Gemini 12 mission with Jim Lovell. The crew of Apollo 12 — Pete Conrad, Alan Bean and Dick Gordon — also saw a total solar eclipse from space on Nov. 24, 1969.

AS11-42-6179 (19 July 1969) —- This photograph of the solar corona was taken from the Apollo 11 … More spacecraft during trans-lunar coast and prior to lunar orbit insertion.

NASA

When Is The Next Total Solar Eclipse In North America?

The next total solar eclipse in the contiguous U.S. will occur on Aug. 22, 2044. The path of totality will begin in Greenland, travel through Canada’s Northwest Territories (with maximum totality close to Great Bear Lake, at 2 minutes and 4 seconds) and finish with an eclipsed sunset from Montana, South Dakota and North Dakota. Another total solar eclipse will occur across the U.S. a lunar year later, on Aug 10, 2045.

Further Reading

ForbesIn Photos: First Ever ‘Fake’ Total Solar Eclipse Created In SpaceBy Jamie CarterForbesNASA Spacecraft ‘Touches Sun’ For Final Time In Defining Moment For HumankindBy Jamie CarterForbesNASA Urges Public To Leave The City As Milky Way Appears — 15 Places To GoBy Jamie Carter

Continue Reading

July 25, 2025
Moon, Mars, and meteors: Why July 28 is the best night for skywatching all summer

A beautiful crescent moon will appear close to Mars after dark on Monday, July 28. The dancing duo will make their debut about 45 minutes after sunset and will be visible from across the world — just as several meteor showers approach their peaks.

The conjunction between the 19%-illuminated waxing crescent moon and the Red Planet will take place above due west, making it visible to most people, although a park or open field will provide a better view. The gap between the moon and Mars will be about 1 degree — roughly the width of your little finger held at arm’s length.

Mars is well past its brightest point this year, but it remains a distinct, reddish dot in the twilight sky. The moon, meanwhile, will show Earthshine, a ghostly illumination of its night side caused by sunlight reflecting off Earth.

You may like

The spectacular sight of two of the brightest objects in the solar system alongside each other will come as meteor showers are beginning to dominate the sky. The peak of the Piscis Austrinid meteor shower will be in the early hours of July 28, when up to five meteors per hour will be visible under dark, clear skies. That makes it a minor affair, but it’s just one of four meteor showers approaching their peak.

Overnight on July 29-30 will be the peak of the Delta Aquariid and Alpha Capricornid meteor showers. While the former’s peak is known to be broad, up to 20 shooting stars per hour are possible. The latter adds another five per hour.

As a bonus, the crescent moon — together with Mars — will set a couple of hours after sunset, leaving the night skies dark and free of moonlight.

As if that weren’t enough, the Perseids — the year’s most prolific meteor shower — are arguably best viewed in late July. That’s because its peak night, Aug. 12-13, will be marred by a bright moon. August’s full Sturgeon Moon occurs on Saturday, Aug. 9, and on the peak night, an 84%-illuminated moon will shine brightly all night, making faint meteors hard to see.

Get the world’s most fascinating discoveries delivered straight to your inbox.

All of this makes July 28 arguably one of the best evenings for seeing “shooting stars” this summer. The best views will be from locations with low levels of light pollution, such as a Dark Sky Place or an area that appears dark on a light pollution map. Check local weather forecasts, allow your eyes to adjust to the darkness for at least 20 minutes, and avoid looking at smartphone screens or other artificial lights.

Continue Reading

July 25, 2025
The Southern Ocean Shift: A Warning Sign in Global Climate Circulation

A new scientific study sent a quiet but serious signal through the climate science community last week: researchers have detected a shift in the Southern Ocean’s circulation patterns. While the mainstream media barely registered the news, this finding could have significant implications for global climate dynamics and the resilience of Earth’s systems. The study, powered by satellite innovations, challenges longstanding climate model predictions and offers a fresh lens into one of the most remote yet critical regions on the planet.

Why does this matter? The ocean plays a key role in regulating global climate by distributing heat and storing carbon. Any change in the way its currents move or how its waters mix can ripple out to affect weather patterns, ice melt, and greenhouse gas release. In this post, we’ll unpack what this shift means, explore the risks, look at how ocean currents shape global climate, and highlight why ecosystem resilience may be our best ally in an era of accelerating change.

The risks of shifting waters

The core finding of the study is the detection of increased salinity at the surface of the Southern Ocean. This contradicts previous expectations that melting ice would make surface waters fresher. Saltier water is denser, and this density shift allows deep, warmer water to rise toward the surface — a process known as upwelling. That upwelling can, in turn, accelerate the melting of sea ice, releasing stored heat and CO2 (both dissolved in deeper waters and locked in the continental ice) into the atmosphere, which may intensify global warming.

These changes don’t operate in isolation. The Southern Ocean plays a crucial role in absorbing excess heat and carbon from the atmosphere. A disruption in its circulation could weaken this function, creating a feedback loop where warming leads to more warming. If these upwelling events become more frequent, they could destabilize not just regional systems but also larger-scale patterns like rainfall distribution and storm intensity across the Southern Hemisphere, and eventually, the rest of the planet.

The large-scale nature of climate

Earth’s climate is a vast, interconnected system shaped by interactions between the atmosphere, oceans, land, ice, and ecosystems. Solar radiation is distributed unevenly across the planet, warming the equator more than the poles. This temperature imbalance sets air and water in motion, creating the engine behind weather and climate. The ocean and atmosphere are tightly coupled: winds drive surface currents, while the ocean stores and redistributes heat, shaping pressure systems and wind patterns in return.

One of the most critical components of this system is the global ocean circulation, often called the Ocean Conveyor Belt<. Near the equator, warm, less dense water rises and fuels the atmosphere with moisture. At the poles, colder, denser water sinks, making space for warm water to flow in. This movement creates a planetary-scale conveyor that transports heat, nutrients, and carbon around the world. A shift in any part of this system, such as shifts in the Antarctic Ocean, could have far-reaching consequences for global climate stability.

The overturning circulation of the global ocean. Throughout the Atlantic Ocean, the circulation carries warm waters (red arrows) northward near the surface and cold deep waters (blue arrows) southward. Image credit: NASA, via Wikimedia Commons https://commons.wikimedia.org/wiki/File:Overturning_circulation_of_the_global_ocean.jpg. File is in the Public Domain.

Reading the signs

Although the detection of increased salinity and upwelling in the Southern Ocean is concerning, it doesn’t yet signal a full-scale breakdown of global circulation. Climate and ocean systems operate on seasonal, decadal, and even multidecadal cycles. The observed changes may be part of natural variability rather than a permanent shift. What matters now is monitoring how often these events occur, and whether their frequency is increasing compared to the past.

This is where ecosystem resilience becomes essential. Healthy marine ecosystems can absorb some of the shocks from climate variability, helping to stabilize key processes even as conditions shift. But their ability to do so depends on the pressures we place on them. As warming accelerates and ocean circulation patterns change, safeguarding ecosystem resilience becomes a critical line of defense. Investing in science, policy, and conservation isn’t just prudent, it’s urgent. For now, the study serves as a powerful reminder: the Earth is speaking. It’s up to us to listen and respond.

Teaser image credit: Antarctica Melts Under Its Hottest Days on Record. Credit NASA, Public Domain.

Continue Reading

July 25, 2025
How To See Monday’s Rare Moon-Mars Conjunction — Then ‘Shooting Stars’

Topline

Skywatchers across the globe can witness a stunning conjunction of the moon and Mars shortly after sunset on Monday, July 28. Visible low in the west, the striking pair will be visible during twilight in the western sky before setting a few hours later. That evening, shooting stars are expected as both the Southern delta Aquariids and the alpha Capricornids meteor showers peak.

Close up earth view with moon and mars in view

getty

Key Facts

The conjunction of the moon and Mars will be best seen about 45 minutes after sunset and be visible for around an hour before setting in the west.

A clear view of the western horizon is recommended. Although it will be easily visible to the naked eye as twilight takes hold, binoculars will make it easier to scan the sky. The moon will be below and slightly to the left of Mars.

The waxing crescent moon will be 19%-illuminated, with its night side bathed in Earthshine — sunlight reflected from Earth’s ice caps, clouds and oceans onto the lunar surface,

Mars won’t be at its peak brightness — that happened last January — but its distinct reddish hue will be obvious as it gets darker.

If Clouds Block Your View

Although the conjunction will only be visible for one night, if it’s cloudy, it’s worth looking again the next night. On Tuesday, July 29, the waxing crescent moon will be 27%-illuminated and still be displaying Earthshine. Instead of being beneath Mars, it will be alongside it. The moon will be on the left and Mars on the right above due west.

Observing Mars In 2025

Mars reached opposition on Jan. 16, when it made its closest approach to Earth since 2022. It’s been prominent for most of the year and will continue to be visible shortly after sunset for a few months, eventually becoming lost in the sun’s glare in late November. Mars will next come to opposition on Feb. 19, 2027.

Three Meteor Showers Peak

Just hours after observing the moon-Mars conjunction, two meteor showers will peak — the Southern delta Aquariids and the alpha Capricornids. Expect up to 25 shooting stars per hour from the Southern delta Aquariid meteor shower. Although the Alpha Capricornids contribute just five shooting stars per hour at their peak, they tend to include bright and colorful fireballs, according to the American Meteor Society. The Piscis Austrinid meteor shower will peak the previous night, in the early hours of July 28, with about five meteors per hour possible, according to In-The-Sky.org. With the crescent moon and Mars setting a few hours after sunset, July 28-29 will be an excellent night for stargazing and looking for shooting stars if the skies are clear.

Further Reading

ForbesWhen To See June’s ‘Strawberry Moon,’ The Lowest Full Moon Since 2006By Jamie CarterForbesNASA Urges Public To Leave The City As Milky Way Appears — 15 Places To GoBy Jamie CarterForbesGet Ready For The Shortest Day Since Records Began As Earth Spins FasterBy Jamie Carter

Continue Reading

July 25, 2025
Tiny, pea-sized dinosaur bone discovered in Mongolia’s Gobi Desert has scientists gobsmacked at what it means

The wrists of birds are incredibly complex and functionally crucial in both flight and the folding of wings at rest, says Will Newton.

To stabilise their wings during flight, birds rely on a tiny bone known as the pisiform. This bone was long thought to have been lost in the early ancestors of birds, only returning as they started to take to the skies and evolve into the birds we know today.

However, CT scans of two small, flightless theropod dinosaurs – an unnamed troodontid and an oviraptor known as Citipati from the Late Cretaceous (75 to 71 million years ago) – have revealed the presence of pisiforms in their wrists. These dinosaurs were discovered in Mongolia’s Gobi Desert and recently prepared for close examination.

“Wrist bones are small and even when they are preserved, they are not in the positions they would occupy in life, having shifted during decay and preservation,” said Alex Ruebenstahl, a co-author of the new study, in an associated press release. “Seeing this little bone in the right position cracked it wide open and helped us interpret the wrists of fossils we had on hand and other fossils described in the past.”

Prior to this study, pisiforms were only identified in the earliest theropod dinosaurs – a group of meat-eating dinosaurs that includes famous species such as T.rex and Velociraptor.

The discovery of pisiforms in the wrists of the aforementioned theropod dinosaurs suggests the bone ‘re-appeared’ a lot earlier than first thought. It also established its presence in Oviraptorosauria and Troodontidae, in addition to later birds.

Based on their discovery, Ruebenstahl, lead author James Napoli, and co-authors Matteo Fabbri, Jingmai O’Connor, Bhart-Anjan Bhullar, and Mark Norell examined fossils from a wide range of theropod species, including Microraptor,Ambopteryx, and Caudipteryx. Knowing what to look for, the team found pisiforms in all three of these dinosaurs and more.

A key change in the transformation of forelimbs to wings was the replacement of another wrist bone – the ulnare – with the pisiform. “The pisiform, in living birds, is an unusual wrist bone in that it initially forms within a muscle tendon, as do bones like your kneecap – but it comes to occupy the position of a ‘normal’ wrist bone called the ulnare,” said co-author Bhullar.

The results of this new study indicate the pisiform replaced the ulnare before the origin of the clade Pennaraptora – a group of raptor-like dinosaurs who can trace their roots all the way back to the Late Jurassic, roughly 160 million years ago.

This pushes back one of the key mechanisms in the origin of bird flight by tens of millions of years. It also quashes the previous assumption that flight-stabilising pisiform bones were a novelty restricted to just birds; they were also present in near-bird dinosaurs who were just starting to experiment with the power of flight.

This study is published in the journal Nature and is a collaboration by palaeontologists from Stony Brook University, Yale University, the American Museum of Natural History, and the Mongolian Academy of Sciences.

Main image: A life reconstruction of the specimen of Citipati, a dinosaur closely related to birds, analyzed with an x-ray cutaway of the specimen’s wrist. The small and rounded pisiform is highlighted in blue.

Credit: A life reconstruction of the specimen of Citipati, a dinosaur closely related to birds, analyzed with an x-ray cutaway of the specimen’s wrist. The small and rounded pisiform is highlighted in blue. © Henry S. Sharpe/University of Alberta

Continue Reading

July 25, 2025
Identification and profiling of novel metagenome assembled uncultivated virus genomes from human gut | Virology Journal
Páez-Espino D, et al. Uncovering Earth’s Virome. Nature. 2016;536:425–30.

PubMed

Google Scholar
Shi M, et al. Redefining the invertebrate RNA virosphere. Nature. 2016;540:539–43.

CAS
PubMed

Google Scholar
Dayaram A, et al. Diverse circular replication-associated protein encoding viruses Circulating in invertebrates within a lake ecosystem. Infect Genet Evol. 2016;39:304–16.

CAS
PubMed

Google Scholar
Roux S, et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature. 2016;537:689–93.

CAS
PubMed

Google Scholar
Arkhipova K, et al. Temporal dynamics of uncultured viruses: a new dimension in viral diversity. ISME J. 2018;12:199–211.

PubMed

Google Scholar
Wilson WH, et al. Genomic exploration of individual giant ocean viruses. ISME J. 2017;11:1736–45.

PubMed
PubMed Central

Google Scholar
Simmonds P, Adams M, Benkő M, et al. Virus taxonomy in the age of metagenomics. Nat Rev Microbiol. 2017;15:161–8. https://doi.org/10.1038/nrmicro.2016.177.

Article
CAS
PubMed

Google Scholar
Krupovic M, Ghabrial SA, Jiang D, Varsani A. Genomoviridae: a new family of widespread single-stranded DNA viruses. Arch Virol. 2016;161(9):2633–43. https://doi.org/10.1007/s00705-016-2943-3.

Article
CAS
PubMed

Google Scholar
Shi M, Lin XD, Tian JH, et al. Redefining the invertebrate RNA virosphere. Nature. 2016;540:539–43. https://doi.org/10.1038/nature20167.

Article
CAS
PubMed

Google Scholar
Labonté JM, Suttle CA. Previously unknown and highly divergent SsDNA viruses populate the oceans. ISME J. 2013;7(11):2169–77. https://doi.org/10.1038/ismej.2013.110.

Article
CAS
PubMed
PubMed Central

Google Scholar
Dayaram A, Goldstien S, Argüello-Astorga GR, Zawar-Reza P, Gomez C, Harding JS, Varsani A. Diverse small circular DNA viruses Circulating amongst estuarine molluscs. Infect Genet Evol. 2015;31:284–95. https://doi.org/10.1016/j.meegid.2015.02.010.

Article
CAS
PubMed

Google Scholar
Dayaram A, Galatowitsch ML, Argüello-Astorga GR, van Bysterveldt K, Kraberger S, Stainton D, Harding JS, Roumagnac P, Martin DP, Lefeuvre P, Varsani A. Diverse circular replication-associated protein encoding viruses Circulating in invertebrates within a lake ecosystem. Infect Genet Evol. 2016;39:304–16. https://doi.org/10.1016/j.meegid.2016.02.011.

Article
CAS
PubMed

Google Scholar
Rosario K, Schenck RO, Harbeitner RC, Lawler SN, Breitbart M. Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins. Front Microbiol. 2015;6:696.

PubMed
PubMed Central

Google Scholar
Yutin N, Shevchenko S, Kapitonov V, Krupovic M, Koonin EV. A novel group of diverse Polinton-like viruses discovered by metagenome analysis. BMC Biol. 2015;13:95. https://doi.org/10.1186/s12915-015-0207-4.

Article
CAS
PubMed
PubMed Central

Google Scholar
Zhou J, Zhang W, Yan S, Xiao J, Zhang Y, Li B, Pan Y, Wang Y. Diversity of virophages in metagenomic data sets. J Virol. 2013;87(8):4225. https://doi.org/10.1128/JVI.03398-12.

Article
CAS
PubMed
PubMed Central

Google Scholar
Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GG, Boling L, Barr JJ, Speth DR, Seguritan V, Aziz RK, Felts B, Dinsdale EA, Mokili JL, Edwards RA. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun. 2014;5:4498. https://doi.org/10.1038/ncomms5498.

Article
CAS
PubMed

Google Scholar
Yutin N, Kapitonov VV, Koonin EV. A new family of hybrid virophages from an animal gut metagenome. Biol Direct. 2015;10:19. https://doi.org/10.1186/s13062-015-0054-9.

Article
CAS
PubMed
PubMed Central

Google Scholar
Zhang W, Zhou J, Liu T, Yu Y, Pan Y, Yan S, Wang Y. Four novel algal virus genomes discovered from Yellowstone lake metagenomes. Sci Rep. 2015;5:15131. https://doi.org/10.1038/srep15131.

Article
CAS
PubMed
PubMed Central

Google Scholar
Yau S, Lauro FM, DeMaere MZ, Brown MV, Thomas T, Raftery MJ, Andrews-Pfannkoch C, Lewis M, Hoffman JM, Gibson JA, Cavicchioli R. Virophage control of Antarctic algal host-virus dynamics. Proc Natl Acad Sci U S A. 2011;108(15):6163. https://doi.org/10.1073/pnas.1018221108.

Article
PubMed
PubMed Central

Google Scholar
Schmidtke DT, Hickey AS, Liachko I, Sherlock G, Bhatt AS. Analysis and culturing of [preprint].e [preprint].ototypic crassphage [preprint].veals a [preprint].age-plasmid lifestyle. BioRxiv [Preprint]. 2024 Mar 20:2024.03.20.585998. https://doi.org/10.1101/2024.03.20.585998
Roux S, Hawley AK, Beltran MT, Scofield M, Schwientek P, Stepanauskas R, Woyke T, Hallam SJ, Sullivan MB. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. eLife Sci. 2014;3:e03125.

Google Scholar
Mojica FJM, Díez-Villaseñor C, García-Martínez J, Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol. 2005;60:174.

CAS
PubMed

Google Scholar
Pourcel C, Salvignol G, Vergnaud GY. CRISPR elements in Yersinia pestis acquire new repeats by Preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology. 2005;151:653.

CAS
PubMed

Google Scholar
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339:819.

CAS
PubMed
PubMed Central

Google Scholar
Bragg JG, Chisholm SW. Modeling the fitness consequences of a Cyanophage-Encoded photosynthesis gene. PLoS ONE. 2008;3:e3550.

PubMed
PubMed Central

Google Scholar
Mann NH, Cook A, Millard A, Bailey S, Clokie M. Bacterial photosynthesis genes in a virus. Nature. 2003;424:741.

CAS
PubMed

Google Scholar
Trubl G, Jang HB, Roux S, Emerson JB, Solonenko N, Vik DR, Solden L, Ellenbogen J, Runyon AT, Bolduc B, et al. Soil viruses are underexplored players in ecosystem carbon processing. mSystems. 2018;3:e00076–18.

CAS
PubMed
PubMed Central

Google Scholar
Chen L-X, Méheust R, Crits-Christoph A, McMahon KD, Nelson TC, Slater GF, Warren LA, Banfield JF. Large freshwater phages with the potential to augment aerobic methane oxidation. Nat Microbiol. 2020;5:1504.

CAS
PubMed
PubMed Central

Google Scholar
Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature. 2016;537:689.

CAS
PubMed

Google Scholar
Kieft K, Breister AM, Huss P, Linz AM, Zanetakos E, Zhou Z, Rahlff J, Esser SP, Probst AJ, Raman S, et al. Virus-associated organosulfur metabolism in human and environmental systems. Cell Rep. 2021;36:109471.

CAS
PubMed

Google Scholar
Kieft K, Zhou Z, Anderson RE, Buchan A, Campbell BJ, Hallam SJ, Hess M, Sullivan MB, Walsh DA, Roux S, et al. Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. Nat Commun. 2021;12:3503.

CAS
PubMed
PubMed Central

Google Scholar
Fujimoto K, Kimura Y, Shimohigoshi M, Satoh T, Sato S, Tremmel G, Uematsu M, Kawaguchi Y, Usui Y, Nakano Y, et al. Metagenome data on intestinal phage-Bacteria associations aids the development of phage therapy against pathobionts. Cell Host Microbe. 2020;28:380.

CAS
PubMed

Google Scholar
Mangalea MR, Paez-Espino D, Kieft K, Chatterjee A, Chriswell ME, Seifert JA, Feser ML, Demoruelle MK, Sakatos A, Anantharaman K, et al. Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential. Cell Host Microbe. 2021;29:726.

CAS
PubMed
PubMed Central

Google Scholar
Clooney AG, Sutton TDS, Shkoporov AN, Holohan RK, Daly KM, O’Regan O, Ryan FJ, Draper LA, Plevy SE, Ross RP, et al. Whole-Virome analysis sheds light on viral dark matter in inflammatory bowel disease. Cell Host Microbe. 2019;26:764.

CAS
PubMed

Google Scholar
Bhardwaj K, Garg A, Pandey AD, Sharma H, Kumar M, Vrati S. Insights into the human gut Virome by sampling a population from the Indian Subcontinent. J Gen Virol. 2022;103(8). https://doi.org/10.1099/jgv.0.001774.
Nayfach S, Camargo AP, Schulz F, et al. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat Biotechnol. 2021;39:578. https://doi.org/10.1038/s41587-020-00774-7.

Article
CAS
PubMed

Google Scholar
Schackart KE 3rd, Graham JB, Ponsero AJ, Hurwitz BL. Evaluation of computational phage detection tools for metagenomic datasets. Front Microbiol. 2023;14:1078760. https://doi.org/10.3389/fmicb.2023.1078760.

Article
PubMed
PubMed Central

Google Scholar
Menzel P, Ng K, Krogh A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun. 2016;7:11257.

CAS
PubMed
PubMed Central

Google Scholar
Bin Jang H, Bolduc B, Zablocki O, et al. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat Biotechnol. 2019;37:632. https://doi.org/10.1038/s41587-019-0100-8.

Article
CAS
PubMed

Google Scholar
Cook R, Brown N, Redgwell T, Rihtman B, Barnes M, Clokie M, Stekel DJ, Hobman J, Jones MA, Millard A. INfrastructure for a phage reference database: identification of Large-Scale biases in the current collection of cultured phage genomes. Phage (New Rochelle). 2021;2(4):214. https://doi.org/10.1089/phage.2021.0007.

Article
PubMed

Google Scholar
Turner D, Shkoporov AN, Lood C, Millard AD, Dutilh BE, Alfenas-Zerbini P, van Zyl LJ, Aziz RK, Oksanen HM, Poranen MM, Kropinski AM, Barylski J, Brister JR, Chanisvili N, Edwards RA, Enault F, Gillis A, Knezevic P, Krupovic M, Kurtböke I, Kushkina A, Lavigne R, Lehman S, Lobocka M, Moraru C, Moreno Switt A, Morozova V, Nakavuma J, Reyes Muñoz A, Rūmnieks J, Sarkar BL, Sullivan MB, Uchiyama J, Wittmann J, Yigang T, Adriaenssens EM. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee. Arch Virol. 2023;168(2):74. https://doi.org/10.1007/s00705-022-05694-2.

Article
CAS
PubMed
PubMed Central

Google Scholar
Moraru C, Varsani A, Kropinski AM. VIRIDIC-A novel tool to calculate the intergenomic similarities of Prokaryote-Infecting viruses. Viruses. 2020;12(11):1268. https://doi.org/10.3390/v12111268.

Article
CAS
PubMed
PubMed Central

Google Scholar
Turner D, Adriaenssens EM, Tolstoy I, Kropinski AM. Phage annotation guide: guidelines for assembly and High-Quality annotation. Phage (New Rochelle). 2021;2(4):170. https://doi.org/10.1089/phage.2021.0013.

Article
PubMed

Google Scholar
Ramsey J, Rasche H, Maughmer C, Criscione A, Mijalis E, Liu M, et al. Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation. PLoS Comput Biol. 2020;16(11):e1008214. https://doi.org/10.1371/journal.pcbi.1008214.

Article
CAS
PubMed
PubMed Central

Google Scholar
Bouras G, Nepal R, Houtak G, Psaltis AJ, Wormald P-J. Sarah Vreugde, Pharokka: a fast scalable bacteriophage annotation tool. Bioinformatics. 2023;39. https://doi.org/10.1093/bioinformatics/btac776.
McNair K, Zhou C, Dinsdale EA, Souza B, Edwards RA. PHANOTATE: a novel approach to gene identification in phage genomes. Bioinformatics. 2019;35(22):4537. https://doi.org/10.1093/bioinformatics/btz265.

Article
CAS
PubMed
PubMed Central

Google Scholar
Skennerton CT, Soranzo N, Angly F. MinCED. https://github.com/ctSkennerton/minced
Patricia P, Chan, Brian Y, Lin AJ, Mak, Todd M, Lowe. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res. 2021;49:9077.

Google Scholar
Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and TmRNA genes in nucleotide sequences. Nucleic Acids Res. 2004;32(1):11–6. https://doi.org/10.1093/nar/gkh152.

Article
CAS
PubMed
PubMed Central

Google Scholar
Brian P, Alcock AR, Raphenya, Tammy TY, Lau KK, Tsang Mégane, Bouchard A, Edalatmand W, Huynh, Anna-Lisa V, Nguyen AA, Cheng S, Liu, Sally Y, Min A, Miroshnichenko H-K, Tran RE, Werfalli JA, Nasir M, Oloni DJ, Speicher N, Sharma E, Bordeleau AC, Pawlowski HL, Zubyk D, Dooley E, Griffiths F, Maguire GL, Winsor RG, Beiko, Fiona SL, Brinkman WWL, Hsiao GV, Domselaar, Andrew G, McArthur. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database, Nucleic Acids Research, 48, D517, (2020). https://doi.org/10.1093/nar/gkz935
Liu B, Zheng D, Zhou S, Chen L, Yang J. VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res. 2022;50(D1):D912–7. https://doi.org/10.1093/nar/gkab1107.

Article
CAS
PubMed

Google Scholar
Paul Terzian EO, Ndela C, Galiez J, Lossouarn. Rubén Enrique Pérez Bucio, robin mom, Ariane Toussaint, Marie-Agnès Petit, François Enault, PHROG: families of prokaryotic virus proteins clustered using remote homology. NAR Genomics Bioinf. 2021;3. https://doi.org/10.1093/nargab/lqab067.
Bonnie L, Hurwitz, Jana M, U’Ren. Viral metabolic reprogramming in marine ecosystems. Curr Opin Microbiol. 2016;31:161. https://doi.org/10.1016/j.mib.2016.04.002.

Article
CAS

Google Scholar
Kieft K, Zhou Z, Anantharaman K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome. 2020;8(1):90. https://doi.org/10.1186/s40168-020-00867-0.

Article
CAS
PubMed
PubMed Central

Google Scholar
Luo XQ, Wang P, Li JL, et al. Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts. Microbiome. 2022;10:190. https://doi.org/10.1186/s40168-022-01384-y.

Article
PubMed
PubMed Central

Google Scholar
Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol. 2016;428(4):726. https://doi.org/10.1016/j.jmb.2015.11.006.

Article
CAS
PubMed

Google Scholar
Enault F, Briet A, Bouteille L, Roux S, Sullivan MB, Petit MA. Phages rarely encode antibiotic resistance genes: a cautionary Tale for Virome analyses. ISME J. 2017;11(1):237–47. https://doi.org/10.1038/ismej.2016.90.

Article
CAS
PubMed

Google Scholar
Lu C, Zhang Z, Cai Z, et al. Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics. BMC Biol. 2021;19:5. https://doi.org/10.1186/s12915-020-00938-6.

Article
CAS
PubMed
PubMed Central

Google Scholar
Liang G, Cobián-Güemes AG, Albenberg L, et al. The gut Virome in inflammatory bowel diseases. Curr Opin Virol. 2021;51:190. https://doi.org/10.1016/j.coviro.2021.10.005.

Article
CAS
PubMed

Google Scholar
Székely AJ, Breitbart M. Single-strandedDNAphages: from early molecular biology tools to recent revolutions in environmental microbiology. FEMS Microbiol Lett 363, fnw027 (2016).

PubMed

Google Scholar
Kirchberger PC, Martinez ZA, Ochman H. Organizing the global diversity of microviruses. mBio. 2022;13(3):e0058822. https://doi.org/10.1128/mbio.00588-22.

Article
PubMed

Google Scholar
Krupovic M, Forterre P. Microviridae goes temperate: Microvirus-related proviruses reside in the genomes of bacteroidetes. PLoS ONE. 2011;6:e19893.

CAS
PubMed
PubMed Central

Google Scholar
Liang G, Bushman FD. The human Virome: assembly, composition and host interactions. Nat Rev Microbiol. 2021;19:514–27.

CAS
PubMed
PubMed Central

Google Scholar
Turner D, Kropinski AM, Adriaenssens EM. A Roadmap for Genome-Based Phage Taxonomy. Viruses 13, 506 (2021).
Casjens SR, Gilcrease EB. Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions. Methods Mol Biol. 2009;502:91.

CAS
PubMed
PubMed Central

Google Scholar
Merrill BD, Ward AT, Grose JH, Hope S. Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies. BMC Genom. 2016;17:679.

Google Scholar
Meijer WJ, Horcajadas JA, Salas M. Phi29 family of phages. Microbiol Mol Biol Rev. 2001;65:261–87.

CAS
PubMed
PubMed Central

Google Scholar
Iranzo J, Krupovic M, Koonin EV. The Double-Stranded DNA virosphere as a modular hierarchical network of gene sharing. mBio. 2016;7:e00978–16.

CAS
PubMed
PubMed Central

Google Scholar
Adriaenssens EM. Phage diversity in the human gut microbiome: A taxonomist’s perspective. mSystems. 2021;6:e0079921.

PubMed

Google Scholar
Mantynen S, Laanto E, Oksanen HM, Poranen MM, Diaz-Munoz SL. Black box of phage-bacterium interactions: exploring alternative phage infection strategies. Open Biol. 2021;11:210188.

CAS
PubMed
PubMed Central

Google Scholar
Howard-Varona C, Hargreaves KR, Abedon ST, Sullivan MB. Lysogeny in nature: mechanisms, impact and ecology of temperate phages. ISME J. 2017;11:1511.

PubMed
PubMed Central

Google Scholar
Veses-Garcia M, Liu X, Rigden DJ, Kenny JG, McCarthy AJ, Allison HE. Transcriptomic analysis of Shiga-toxigenic bacteriophage carriage reveals a profound regulatory effect on acid resistance in Escherichia coli. Appl Environ Microbiol. 2015;81:8118. https://doi.org/10.1128/AEM.02034-15.

Article
CAS
PubMed
PubMed Central

Google Scholar
Mai-Prochnow A, Hui JG, Kjelleberg S, Rakonjac J, McDougald D, Rice SA. Big things in small packages: the genetics of filamentous phage and effects on fitness of their host’. FEMS Microbiol Rev. 2015;39:465. https://doi.org/10.1093/femsre/fuu007).

Article
PubMed

Google Scholar
Jahn MT, Arkhipova K, Markert SM, et al. A phage protein aids bacterial symbionts in eukaryote immune evasion. Cell Host Microbe. 2019;26. https://doi.org/10.1016/j.chom.2019.08.019. 542– 50 e5.
Aktories K, Schwan C, Jank T. Clostridium difficile toxin biology. Annu Rev Microbiol. 2017;71:281. https://doi.org/10.1146/annurev-micro-090816-093458.

Article
CAS
PubMed

Google Scholar
Wu R, Smith CA, Buchko GW, et al. Structural characterization of a soil viral auxiliary metabolic gene product– a functional Chitosanase. Nat Commun. 2022;13:5485. https://doi.org/10.1038/s41467-022-32993-8.

Article
CAS
PubMed
PubMed Central

Google Scholar
Coutinho FH, Silveira CB, Gregoracci GB, Thompson CC, Edwards RA, Brussaard CPD, et al. Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans. Nat Commun. 2017;8:15955.

CAS
PubMed
PubMed Central

Google Scholar
Hurwitz BL, Brum JR, Sullivan MB. Depth-stratified functional and taxonomic niche specialization in the core and flexible Pacific ocean Virome. ISME J. 2015;9:472.

CAS
PubMed

Google Scholar
Jurėnas D, Fraikin N, Goormaghtigh F, et al. Biology and evolution of bacterial toxin–antitoxin systems. Nat Rev Microbiol. 2022;20:335. https://doi.org/10.1038/s41579-021-00661-1.

Article
CAS
PubMed

Google Scholar
Thomas C, Tampé R. Structural and mechanistic principles of ABC transporters. Annu Rev Biochem. 2020;89:605. https://doi.org/10.1146/annurev-biochem-011520-105201.

Article
CAS
PubMed

Google Scholar
Cannon RD, Lamping E, Holmes AR, Niimi K, Baret PV, Keniya MV, et al. Efflux-mediated antifungal drug resistance. Clin Microbiol Rev. 2009;22:291.

CAS
PubMed
PubMed Central

Google Scholar
Sá-Correia I, Santos SC, Teixeira MC, Cabrito TR, Mira NM. Drug:H⁺ antiporters in chemical stress response in yeast. Trends Microbiol. 2009;17:22.

PubMed

Google Scholar
Morschhäuser J. Regulation of multidrug resistance in pathogenic fungi. Fungal Genet Biol. 2010;47(2):94. https://doi.org/10.1016/j.fgb.2009.08.002.

Article
CAS
PubMed

Google Scholar
Mann E, Ovchinnikova OG, King JD, Whitfield C. Bacteriophage-mediated glucosylation can modify lipopolysaccharide O-Antigens synthesized by an ATP-binding cassette (ABC) Transporter-dependent assembly mechanism. J Biol Chem. 2015;290(42):25561. https://doi.org/10.1074/jbc.M115.660803.

Article
CAS
PubMed
PubMed Central

Google Scholar
Nakayashiki T, Mori H. Genome-Wide screening with hydroxyurea reveals a link between nonessential ribosomal proteins and reactive oxygen species production. J Bacteriol. 2013;195:1226. https://doi.org/10.1128/JB.02145-12.

Article
CAS
PubMed
PubMed Central

Google Scholar
Soule T, Gao Q, Stout V, Garcia-Pichel F. The global response of Nostoc punctiforme ATCC 29133 to UVA stress, assessed in a Temporal DNA microarray study. Photochem Photobiol. 2013;89:415. https://doi.org/10.1111/php.12014.

Article
CAS
PubMed

Google Scholar