Giant Virus Found in Sewage Blurs the Line Between Life and Non-Life

By Jeffrey Marlow | April 20, 2017 12:00 pm
An artist's rendition of the newly discovered Klosneuvirus (Image: NIH / Ella Maru studio)

An artist’s rendition of the newly discovered Klosneuvirus (Image: NIH / Ella Maru studio)

In most biology textbooks, there’s a clear separation between the three domains of cellular organisms – Bacteria, Archaea, and Eukaryotes – and viruses. This fault line is also typically accepted as the divider between life and non-life: since viruses rely on host machinery to enact metabolic transformations and to replicate, they are not self-sufficient, and generally not considered living entities.

But several discoveries of giant viruses over the last decade have blurred this distinction. Some viruses are even larger and contain more genes than typical microbes like E. coli. Ultra-small bacteria detected in filtered groundwater from Rifle, Colorado are moving the goalposts from the opposite end, leading to a virus-microbe continuum in which distinguishing one from the other isn’t so straightforward. Among the alluring interpretations: giant viruses could be indicative of a fourth domain of life.

A recent study led by Frederik Schulz at the Department of Energy’s Joint Genome Institute blurs the virus-microbe line even further. While assembling a metagenome from sewage sludge in Klosterneuburg, Austria, Schulz found several genes that all mapped back to the same unknown virus, genes that until now have only been associated with free-living cells.

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CATEGORIZED UNDER: environment, living world, top posts

“The First Green”: Ancient Life Inspires Modern Art

By Jeffrey Marlow | April 15, 2017 1:33 pm
"The First Green" at the Marianne Boesky Gallery.

“The First Green” at the Marianne Boesky Gallery. (Image: Ana Pantelic)

Every morning at Hamelin Pool, in Western Australia, the first rays of sunshine illuminate knobby reef-like structures, submerged or peeking just above the gentle waves, depending on the tide. On the crudely rounded surfaces of these rocks, microorganisms stir and begin the daily task of photosynthesizing, fighting against occluding sand grains to harvest the sunlight.

This scene, or something like it, has likely been occurring every morning, somewhere on Earth, for the last 3.7 billion years. To artist Thiago Rocha Pitta, the timelessness of these structures, known as stromatolites, makes them an important mirror of the human impact on the natural world. “Human history is just a little part of the history of our planet,” he explains. “I have no problems realizing how insignificant we are.”

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CATEGORIZED UNDER: environment, living world, top posts

Why Aren’t All Members of a Species the Same? Exploring the Pangenome

By Jeffrey Marlow | March 30, 2017 8:21 am
Individual microbes of the same species often have a lot of different genes. But why? (Image: NIAID)

Individual microbes of the same species often have a lot of different genes. But why? (Image: NIAID)

Prochlorococcus marinus are diminutive organisms. At less than a micrometer across, these photosynthesizing microbes may be small, but they’re plentiful – by many accounts one of the most abundant species on the planet.

But that’s not quite the full story: like any other member of the same species, no two P. marinus individuals are genetically identical. What’s remarkable is how different they may be. Take two different P. marinus cells from different parts of the ocean, sequence their genomes, and lay them side-by-side. Of the approximately 1900 genes that each genome contains, only about 62% are likely to be shared. What makes these two individuals members of the same species is the similarity of one particular gene – the 16S rRNA gene – but the rest of the genome isn’t so consistent.

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CATEGORIZED UNDER: environment, living world, top posts

The Slow Life Movement: A Microbial Perspective of the Subsurface Biosphere

By Jeffrey Marlow | March 23, 2017 11:59 am
Seafloor sediment is home to a vast repository of slow-growing, slow-evolving microbes. (Image: NOAA)

Seafloor sediment is home to a vast repository of slow-growing, slow-evolving microbes. (Image: NOAA)

On the seafloor, “marine snow” is constantly falling. Bits of dead plankton, decaying fecal material, biological remnants from shore – it all finds its way to the bottom of the ocean, delivering needed sources of organic molecules and energy to the microbial communities lying in wait.

Over time, this snow – along with sediment mineral grains – accumulates, burying previous layers. In Denmark’s Aarhus Bay, for example, digging ten meters down beneath the seafloor is like going 8,700 years back in time. The ability to see so much time in so compressed a space is a boon to evolutionary biologists, since it allows them to track genetic changes and community shifts in a relatively static environment. With no evidence of fluid flow or bioturbation to move microbes around or facilitate horizontal gene transfer, you’re stuck with the neighbors you’ve got at the surface – only evolutionary selection or death can change the cast of characters.

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CATEGORIZED UNDER: environment, living world, top posts

Could Life’s Earliest Stages Have Survived Without a Key Ingredient?

By Jeffrey Marlow | March 21, 2017 5:25 am
During the early Earth's heavy bombardment, could metabolism have started without phosphate, one of life's key ingredients? (Image: NASA/Simone Marchi)

During the early Earth’s heavy bombardment, could metabolism have started without phosphate, one of life’s key ingredients? (Image: NASA/Simone Marchi)

“CHNOPS” is one of science’s most revered acronyms, an amalgamation of letters that rolls of the tongues of high school biology students and practicing researchers alike. It accounts for the six elements that comprise most biological molecules: carbon, hydrogen, nitrogen, oxygen, phosphorous, and sulfur.

Biologists have traditionally assumed that all six elements were prerequisites, as each one is found in several of life’s most essential molecules. But what if earlier life forms weren’t quite so demanding? Could a sustainable metabolism actually exist without one of these seemingly essential elements? To explore this revolutionary possibility, Joshua Goldford, a graduate student in Boston University’s Bioinformatics Program, led a theoretical study taking aim at phosphorous and its most biologically utilitarian derivative, phosphate.

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The Forgotten Domain of the Gut Microbiome

By Jeffrey Marlow | February 28, 2017 12:36 pm
Which microbes could be helping this mountain gorilla digest its food? (Image: Jeffrey Marlow)

Which microbes could be helping this mountain gorilla digest its food? (Image: Jeffrey Marlow)

Over the last few years, the range of known organisms living in the human gut – that complex milieu of microbes known as the gut microbiome – has expanded dramatically. They influence your health, your appearance, and your behavior in largely unknown ways, and yet, despite the thousands of studies that have been published on the subject, the gut microbiome census may be woefully incomplete.

Most human microbiome studies go something like this: collect your fecal sample, extract the DNA, amplify representative genes from all available organisms using a “universal” set of primers, and wait for the sequences to roll in. The results typically reveal a vast zoo of bacteria sharing space in the gut with eukaryotic cells; the relative lack of the third domain of life – the Archaea – got Kasie Raymann, a postdoctoral fellow at the University of Texas, wondering if those “universal” primers were as promiscuous as advertised. And if the primers don’t bind to the DNA you’re trying to find, it won’t be exponentially amplified, and it won’t be sequenced.

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CATEGORIZED UNDER: Uncategorized

Lighter, Faster, Cheaper: Broadening Access to the Deep Sea

By Jeffrey Marlow | February 27, 2017 12:25 pm
Many island nations have deep water within an hour’s boat ride from shore; here, a view of Gatokae Island in the Solomon Islands is taken over water that is at least 1000 meters deep and known to be volcanically active. (Image: Brennan Phillips)

Many island nations have deep water within an hour’s boat ride from shore; here, a view of Gatokae Island in the Solomon Islands is taken over water that is at least 1000 meters deep and known to be volcanically active. (Image: Alex DeCiccio)

Most countries on Earth have no way to access vast portions of their sovereign territory. In a time when you can read street signs half a world a way on Google Earth, this fact may seem surprising, but these unreachable territories all have one thing in common: they’re underwater, hidden beneath the waves.

As dictated by the UN Convention on the Law of the Sea, a coastal country’s “exclusive economic zone” (EEZ) extends 200 nautical miles (370 km) into the open ocean. Everything from the sea surface on down is included – a bounty that can encompass abundant fish stocks, exotic marine habitats, and valuable mineral deposits.

Brennan Phillips, a postdoctoral fellow at Harvard University’s Wyss Institute for Biologially Inspired Engineering, sees this blindness as a major problem. In order to make decisions about resource use or conservation strategy, for example, you need to know what exactly you’re dealing with. When acquiring this information is prohibitively expensive, “you just don’t do it,” Phillips explains, “so you make a decision based on very little knowledge.” As seafloor mining efforts accelerate around metal-rich hydrothermal vent fields, resource-rich countries will be under increasing pressure to sell off mineral extraction rights. Most famously, the Canadian company Nautilus Minerals is moving forward with plans to mine the Solwara-1 vent field in Papua New Guinea, one of the world’s poorest countries. While the company has solicited input from well-respected scientists, government decision makers are almost entirely dependent upon outside counsel.

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MORE ABOUT: Exploration, ocean, robots

Scientists Narrow in on Landing Site for NASA’s Next Mars Rover

By Jeffrey Marlow | February 12, 2017 1:00 pm
A crater at Northeast Syrtis, one of the shortlisted landing sites for the Mars 2020 rover. (Image: NASA/HiRISE/University of Arizona)

A crater at Northeast Syrtis, one of the shortlisted landing sites for the Mars 2020 rover. (Image: NASA/HiRISE/University of Arizona)

The Curiosity Mars rover is in the prime of its robotic life, approaching dramatic layered deposits on the slopes of Mt. Sharp. But even as the four and a half year-old mission reaches the features it was initially sent to investigate, scientists and engineers are feverishly planning for the next rover mission, Mars 2020.

2020 is shaping up to be a busy year on the Mars exploration calendar: in addition to the NASA rover, the European Space Agency and China have missions slotted for the favorable launch window. But where to go? Making the decision is a complex process, as teams of scientists and engineers develop navigational software, optimize the payload, and establish the geologic context of potential landing sites.

The importance of site selection is magnified by the role of Mars 2020 as the first step in a sample return mission – a longtime grail of Mars scientists. In its current configuration, the rover can collect about 30 canisters of soil, air, or rock particles. A future, planned-but-not-yet-officially-on-the-books mission will return the cache to Earth, where a robust analytical arsenal will be waiting to conduct a battery of detailed tests.

For many scientists, one shift from previous missions is a tighter focus on investigating rocks that preserve signals from Mars’ active past – a period between about three and four billion years ago during which liquid water flowed across the surface, altered rocks, and may have created habitats for opportunistic organisms. And because the rover can only collect samples at the planet’s surface, researchers are avoiding places where more recent forces like craters or windswept sand have covered the ancient rocks.

At a meeting last week in Monrovia, California, hundreds of Mars scientists and mission engineers gathered to narrow the list of landing sites from eight to three. The selection process has been in full swing since 2014, and the final decision will be made in the next year or two, as the instrument teams finalize their flight-ready hardware and prepare for launch.

The workshop was a civil yet high-stakes environment, as proponents of the eight sites had a few hours each to make their case. Ken Farley, a professor of geochemistry at the California Institute of Technology, serves as the mission’s Project Scientist. “It’s hard to imagine any decisions on this mission that will be as impactful to the overall mission as selecting the landing site,” he told the attendees. “For decades to come, the decision we make will be important – it will drive a lot of science that gets done.”

In other words, no pressure.

After two days of presentations and debate, participants were polled on the sites, asked to consider the three main criteria: 1) Could the samples, if returned to Earth, lead to fundamental discoveries about Mars and the potential for extraterrestrial life? 2) Can the site be investigated over the course of the primary mission (roughly three Earth years)? 3) Are there significant water resources that may be advantageous for future, human-based exploration?

(The water issue is a double-edged sword, as the mission is also being steered away from water resources that are too active. A mandate of the planetary protection office is to avoid cross-contamination of Earth and Mars, so any habitats that could support hitchhiking terrestrial microbes need to be avoided. Sites with water ice within five meters of the surface are not being considered.)

And the winners – drumroll please – were, in some sort of preferential order, Jezero Crater, Northeast Syrtis, and the Columbia Hills. Jezero is an ancient lake – life may have taken hold in its waters, and the inflow of sediments from a wider watershed could concentrate compelling material. NE Syrtis maintains mineralogical signatures from water-rock interactions that could be similar to those powering rock-hosted life on Earth. The Columbia Hills site – which has been investigated by the Spirit rover – possesses an ancient hydrothermal spring. The idea of re-visiting a site with Mars 2020’s more powerful set of tools – at the expense of a geologically distinct portion of the planet – is a subject of heated debate.

In the coming weeks, the Extremo Files will profile each of the three sites still in the running. Astrobiology’s next great hope for transformative discovery may well hang in the balance.

Colliding Molecules in Mars’ Atmosphere May Solve an Ancient Climate Mystery

By Jeffrey Marlow | January 26, 2017 11:12 am
Features on Mars like this one, a likely river delta deposit, point to a warmer ancient past. (Image: NASA/JPL)

Features on Mars like this one, a likely river delta deposit, point to a warmer ancient past. (Image: NASA/JPL)

Climate change on Earth is a well-established phenomenon, but scientists have long struggled to explain an even more dramatic change of conditions, long ago in a far-off land.

Mars is a dry, frigid planet today, with an average ground temperature of about -60 °C. Liquid water seems to be possible only under a narrow range of circumstances, but for the most part, water sublimates directly from solid ice to gaseous water vapor. And yet, features on the surface of Mars tell a very different story. Dramatic river channels and canyons indicate that vast quantities of water once flowed from the southern highlands to northern plains.

Clearly, Mars must have been warmer to allow all of this liquid water to persist on its surface. But how were such distinct conditions created? What was different about the planet billions of years ago?

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Rogue Actors and the Coming Space Law Crisis

By Jeffrey Marlow | January 25, 2017 9:17 am
A night launch for SpaceX's Falcon 9 rocket. (Image: Flickr/SpaceX)

A night launch for SpaceX’s Falcon 9 rocket. (Image: Flickr/SpaceX)

Launching rockets into space has traditionally been the domain of nation states: only a handful of countries over the last several decades have mounted the technical expertise and financial resources to put payloads in orbit. With so few players, outer space was governed by the “Cold War principles” outlined in the Outer Space Treaty of 1967, which holds nation states accountable and reserves the use of space for scientific study and other peaceful purposes.

Today, space law needs an overhaul, according to James Gilley, an Instructor of International Studies at Louisiana State University. After all, some of the key assumptions that underlie the Outer Space Treaty no longer apply. A wide range of entities, from treaty non-signatories to private companies like SpaceX and Blue Origin, are charging into low Earth orbit and beyond, and their intentions are unlikely to be restricted to scientific research.

“We’ve kind of forgotten as an international community that we’ve written laws about this stuff,” says Gilley, “because nothing has truly upset the apple cart.” But that could change soon, and Gilley points to a few plausible cases where rogue actors could set off an international legal crisis.

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CATEGORIZED UNDER: space & physics, technology, top posts
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The Extremo Files

The Extremo Files traces the science that is pushing the boundaries of biology, from the deep sea to outer space to the brave new world of synthetic biology.
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