If bacteria can’t grow in a Petri dish, sequencing them is difficult.

What’s the News: Want the genome of a bacterium you found in your belly button? Or, for that matter, of a bacterium producing a promising new antibiotic? Well, unless you can get it to thrive in a Petri dish and create a billion sister cells for analysis, you’re out of luck.

But sequencing the genomes of notoriously finicky bacteria, like those on skin, could be on the horizon with a new procedure that bypasses the Petri dish step. Pairing a new algorithm with an earlier technique, scientists from the Venter Institute and their collaborators can now get all that information from a single cell.

(more…)

Elkhorn coral infected with white pox.

What’s the News: Over the past decade, diseases, pollution, and warming waters have put coral populations across the globe in a dramatic decline. In an extreme case, the population of elkhorn coral, considered one of the most important reef-building corals in the Caribbean, has decreased by 90–95 percent since 1980, partly due to a disease called white pox.

Now, scientists have traced this lethal disease back to humans. Human feces, which seep into the Florida Keys and the Caribbean from leaky septic tanks, transmit a white pox-causing bacterium to elkhorn coral, researchers report in the journal PLoS ONE. “It is the first time ever that a human disease has been shown to kill an invertebrate,” ecologist James Porter told Livescience. “This is unusual because we humans usually get disease from wildlife, and this is the other way around.”

(more…)

What’s the News: Biologists have discovered an eel so bizarre that they didn’t initially know if it was an eel or some other kind of fish. The strange creature, dubbed Protoanguilla palau after a researcher found it in an undersea cavern off the coast of Palau, has very few of the anatomic features of modern eels, but displays many hallmarks of primitive eels from the Mesozoic era. It appears that the eel’s last common ancestor with any other living creature existed 200 million years ago, the researchers report in the journal Proceedings of the Royal Society B.

(more…)

From Ed Yong:

In 1996, a loggerhead turtle called Adelita swam across 9,000 miles from Mexico to Japan, crossing the entire Pacific on her way. Wallace J. Nichols tracked this epic journey with a satellite tag. But Adelita herself had no such technology at her disposal. How did she steer a route across two oceans to find her destination?

Nathan Putman has the answer. By testing hatchling turtles in a special tank, he has found that they can use the Earth’s magnetic field as their own Global Positioning System (GPS). By sensing the field, they can work out both their latitude and longitude and head in the right direction.

By testing turtle hatchlings in a tank surrounded by magnets he could control, Putman showed turtles could sense it if he reversed the magnetic field around them and would begin heading in the opposite direction.

For more about the experiment—and how turtles can travel so far at such high stakes with just magnetism to guide them—check out the rest of Ed’s post at Not Exactly Rocket Science.

Related Content:
Not Exactly Rocket Science: Foxes use the Earth’s magnetic field as a targeting system
Not Exactly Rocket Science: Robins can literally see magnetic fields, but only if their vision is sharp
80beats: Did Earth’s Magnetic Field Have a Fast Flip-Flop?

Image: Wikimedia Commons

Yesterday we reported on a new study that showed shining a laser on certain neurons in mice brains could make them angry and aggressive. But with squid, you don’t need a laser to make the males get mean. All you need is to expose them to a particular chemical. From DISCOVER blogger Ed Yong:

In a flash, schools of male longfin squid can turn from peaceful gatherings to violent mobs. One minute, individuals are swimming together in peace; the next, they’re attacking one another. The males give chase, ramming each other in the sides and grappling with their tentacles.

These sudden bouts of violence are the doing of the female squid. Males are attracted to the sight of eggs, and females lace the eggs with a chemical that transforms the males into aggressive brutes.

For plenty more about how this chemical whips the males into an angry frenzy—and why—check out the rest of Ed’s post at Not Exactly Rocket Science.

Related Content:
Not Exactly Rocket Science: A Squid’s Beak is a Marvel of Biological Engineering
Not Exactly Rocket Science: Tears as chemical signals – smell of female tears affects sexual behaviour of men
80beats: A Blast of Light to the Brain Can Make Mice Mean

The oil stopped spilling from the Deepwater Horizon wellhead months ago, but the Gulf of Mexico’s environmental saga continues. Researchers have investigated the chemicals used to disperse the oil flow in the first place, and found that these “dispersants” didn’t disperse. The effects of this massive chemistry experiment, however, are still unknown.

“The dispersants got stuck in deep water layers around 3,000 feet [915 meters] and below,” said study leader David Valentine, a microbial geochemist at the University of California, Santa Barbara…. “We were seeing it three months after the well had been capped. We found that all of that dispersant added at depth stayed in the deepwater plumes. Not only did it stay, but it didn’t get rapidly biodegraded as many people had predicted.” [National Geographic]

In total, the response team pumped over 800,000 gallons of dispersants into the oil flow; dispersants break down oil into smaller droplets that can degrade more quickly. But the impact of the dispersants themselves has been up for debate. For the new study, scientists tracked the dispersants by following one of its ingredients: dioctyl sodium sulfosuccinate (DOSS).

(more…)

If you’ve ever wondered why the seahorse has its elegantly curved body (aside from luring snorkelers into the water), wonder no more: it helps them hunt.

Researchers at the University of Antwerp in Belgium, led by biomechanicist Sam Van Wassenbergh, analyzed video footage of seahorses on the hunt and used mathematical models to come to the conclusion that a seahorse’s curvy neck lets it strike at more distant prey.

“They rotate their heads upward to bring their mouth close to the prey [passing above],” explained Dr Wassenbergh…. The creatures’ curved bodies mean that when they do this, their mouths also moved forward, helping to bring passing small crustaceans within sucking distance of their snouts. [BBC News]

He even has an evolutionary theory to back up his observations.

“My theory is that you have this ancestral pipefish-like fish and they evolved a more cryptic lifestyle,” said Dr Wassenbergh. [BBC News]

Unlike the seahorse, the related pipefish has a straight body and swims while attacking its prey. Seahorses, on the other hand, tend to hide out and wait for the prey to come to them. And according to this study, published in the journal Nature Communications, a longer striking distance is a big advantage for a couch-potato creature.

“Once this shift in foraging behavior is made, natural selection will favor animals that can increase the strike distance, which according to our study puts a selective pressure to increase the angle between head and trunk and to become what we now know as sea horses,” [said] researcher Sam Van Wassenbergh. [LiveScience]

Related Content:
Not Exactly Rocket Science: Pregnant male pipefish abort babies from unattractive females
Science Not Fiction: Electric Fish “Plug in” and Turn Their Zapping Into Music
The Loom: Dawn of the Picasso Fish
DISCOVER: Your Inner Fish

Image: flickr / oscar alexander

When you’re nature’s ideal killing machine, perhaps color vision is merely an unnecessary affection. New research argues that sharks could be completely colorblind.

An Australian team led by Nathan Scott Hart investigated 17 shark species, peeking at the structure of their rod and cone photoreceptor cells in the retina. Human eyes come with red, green, and blue cone variations, allowing us to see in color. But not shark eyes. They appear to have just one kind of cone.

“Our study shows that contrast against the background, rather than color per se, may be more important for object detection by sharks,” Hart said. [CNN]

That, Hart says, may explain the common wisdom that sharks love yellow (and therefore you ought to avoid sunny swimsuits). It may be the reflective quality of yellow that catches a shark’s eye, not the hue itself.

“Bright yellow is supposed to be attractive to some sharks, presumably because it appears to the sharks as a very bright target against the water,” said Dr Hart. “So perhaps it is best to avoid those fluoro-yellow shorts next time you are in the surf.” [BBC News]

(more…)

Oil wasn’t the only thing seeping into the Gulf of Mexico after the Deepwater Horizon disaster. The explosion of BP’s oil rig also triggered a leak a methane.

From Ed Yong:

With the well unsealed, substantial amounts of the gas were released into the gulf. This plume of dissolved methane should have lurked in the water for years, hanging around like a massive planetary fart. But by August, it had disappeared. On three separate trips through the gulf, John Kessler from Texas A&M University couldn’t find any traces of the gas above background levels. He thinks he knows why – the methane was eaten by bacteria.

The gas pouring out of the broken well spurred the growth of bacteria called methanotrophs, which can break down methane as their only source of energy. They made short work of the gas. By the time that Kessler reached the gulf, just four months after the initial blowout, he found plenty of bacteria and precious little methane.

Check out the rest of Ed’s post on this discovery at Not Exactly Rocket Science.

As for BP itself: The petroleum giant now finds itself in the legal arena, but the company may avoid a worst-case scenario there. A presidential commission established to investigate the affair has found the brunt of liability to be BP’s, but also found the root cause of the disaster to be widespread, systematic mismanagement by everyone, and not rogue behavior by any one player. That is, BP will skate without being charged with “gross negligence” because everybody else made mistakes, too.

Commission co-chair William K Reilly said: “So a key question posed from the outset by this tragedy is, do we have a single company, BP, that blundered with fatal consequences, or a more pervasive problem of a complacent industry? Given the documented failings of both Transocean and Halliburton, both of which serve the offshore industry in virtually every ocean, I reluctantly conclude we have a system-wide problem.” [The Guardian]

Related Content:
80beats: Massive Coral Die-Off Found Just 7 Miles from BP Oil Spill Site
80beats: BP’s Oil Well of Doom Is Declared Officially, Permanently Dead
80beats: BP Report on Gulf Disaster Spreads the Blame Around
80beats: Scientists Find 22-Mile-Long Oily Plume Drifting in the Gulf of Mexico
80beats: Gulf Coast Turtle News: No More Fiery Death; Relocating 70,000 Eggs

Image: U.S. Coast Guard

About 540 million years ago, things were looking pretty rosy for complex life on Earth. Conditions were favorable, and the diversity of multicellular organisms took off during the so-called Cambrian Explosion. Trilobites frolicked. Brachiopods abounded. And then, things went south.

Between 490 million and 520 million years ago, a swift extinction event wiped out many of the Cambrian lifeforms. Geologists Benjamin Gill and Graham Shields-Zhou thinks they have found the trigger right in the midst of that era. According to their study in this week’s Nature, the ocean’s oxygen level plunged and the sulfur levels rose sharply 499 million years ago, killing off species that could not quickly adapt. That included some, but not all, of the trilobites that ruled the seas of the time.

Gill’s team decided to look at a specific subset of Cambrian extinctions that began 499 million years ago and lasted for 2 million to 4 million years. Other researchers had proposed that low oxygen levels — a condition known as anoxia — could be involved. But no one had marshaled enough evidence to prove that. [Science News]

The key to showing it in this case is in the chemical compositions of the samples the team collected, which hold clues to the ocean conditions of the time.

Gill and his colleagues took samples of 500-million-year-old rock from six locations around the world and measured the amounts of various isotopes of carbon and sulphur. Both were significantly different from the norm, suggesting that enormous amounts of carbon and sulphur were being buried. In modern oceans, this only occurs in low-oxygen waters like the Black Sea. [New Scientist]

The next question is, what drove down the oxygen levels so quickly? To that, Gill doesn’t have an answer. But such cyclical dramatic changes driving extinction is the rule, not the exception—there were several events during the latter Cambrian when many species were wiped out, and anoxia could have been at play in some of those, too.

Related Content:
DISCOVER: Just One Bite And Life Took Off
80beats: Ancient Rocks Show Oxygen Was Abundant Long Before Complex Life Arose
80beats: How “Snowball Earth” Could Have Triggered the Rise of Life
80beats: One of the Earth’s Earliest Animals Left Behind “Chemical Fossils”

Image: Wikimedia Commons

Leatherback turtles are the wandering type, undertaking far-flung ocean migrations of thousands of miles. What scientists who follow these long-lived creatures didn’t know, though, was just how many different routes they travel, and how far they journey before returning home. These are critical pieces of information for protecting the turtles, whose numbers are dropping. So Matthew Witt says he and his international team affixed trackers to the turtles and revealed the routes of their great sea voyages:

“What we’ve shown is that there are three clear migration routes as they head back to feeding grounds after breeding in Gabon, although the numbers adopting each strategy varied each year. We don’t know what influences that choice yet, but we do know these are truly remarkable journeys.” [The Guardian]

Gabon, in West Africa, is the home base for this largest breeding group of leatherbacks—it’s where they nest and lay their eggs. Witt’s team tracked 25 female turtles, all of whom followed one of those three general routes: out to the middle of the Atlantic and then back, down the African coast to the temperate South, or even all the way across the ocean to South America.

One female was tracked making a 7,563 kilometer (4,699 mile) journey traveling in a straight line across the South Atlantic from Africa to South America, said [Witt]. At a pace of 50 kilometers a day, that trip took about 150 days of consistent swimming, he said. [AP]

(more…)

Some of the consequences of ocean acidification appear obvious: The shells of mollusks, for instance, could dissolve as the pH of ocean water drops thanks to the ocean pulling out some of the excess carbon dioxide humans put into the atmosphere. But what about more subtle effects of seawater growing more acidic?

In the Proceedings of the National Academy of Sciences this week, researchers set up an experiment to see whether the growing acidity of the ocean could disrupt the marine cycle of nitrogen, which provides key nutrients for plant life. Indeed it can, J. Michael Beman’s team found, and that’s another potentially dangerous side effect of the ocean as a carbon sink.

The authors of the study examined a specific step in the marine nitrogen cycle, called nitrification, in which microorganisms convert one form of nitrogen, ammonium, into nitrate, a form plants and other marine microorganisms require to survive. Previous research studies on experimentally acidified freshwater … in the laboratory have suggested that reduced pH slows nitrification, and one study in coastal ocean waters showed that large pH decreases did the same. [Scientific American]

So Beman sought to test the ocean by gathering samples of seawater from locations around the world and adding CO2 to simulate what will be happening to the oceans in the coming decades. Just decreasing the pH from 8.1 to 8.0 resulted in about 20 percent less nitrate creation, the team wrote. In their experiments that lowered pH between .05 and .14, the nitrate production dropped between 8 and 38 percent.

(more…)

New sea creatures, humongous stars, and cockroach antibiotics: Those are just a few reader favorites from this year in science. As 2010 comes to a close, we bring you a dozen of the most popular 80beats posts of the year.

---

For more great stories from the year in science, check out DISCOVER’s Top 100 Stories of the Year.

The wild pink salmon of western Canada are in trouble: In the early 2000s, their numbers in some locations swiftly dropped by 90 percent or more. One explanation put forth for this steep population decline is that sea lice, parasites ubiquitous on farmed salmon, jumped to the wild variety of the fish. But this week in the Proceedings of the National Academy of Sciences, a new study casts doubt on that idea and says the sea lice are not to blame.

When Gary Marty of the University of California, Davis, and his colleagues looked at that aspect for the Broughton Archipelago of western Canada, they found that salmon survival was not lower in years when the juveniles passed by louse-infested farms. This, they say, suggests that something other than sea lice must be reducing survival rates. [New Scientist]

Marty’s team checked up on a decade worth of data dating back to before the 2002 crash, and found a few interesting things. First, they say, the predominance of the lice in wild populations appears to predict the number found in farms a little later, suggesting the parasites travel from wild salmon to farmed ones and not the other way around. Second, they argue, it does appear that a high number of lice in the farmed fish predicts higher than normal exposure for the juveniles of the wild variety, but that increased exposure can’t account for the huge population drop in the wild salmon.

(more…)

It takes a tremendous amount of energy to move the largest animal on Earth from a standstill to chasing food in a fierce dive. Could the krill that a blue whale catches in its gargantuan mouth really provide a high enough calorie count to make all this effort worthwhile? To find out, Jeremy Goldbogen tagged whales with data recorders and monitored hundreds of their dives. It can take 770 to 1900 calories to get the whale moving, but it’s worth it.

From Ed Yong:

When Goldbogen plugged the data from his recorders into a simulation of a feeding whale, he found that the lunge is staggeringly efficient. Despite the massive outlay in energy, the whale easily recoups anywhere from 6 to 240 times that amount, depending on how big it is and how tightly packed its krill targets are.

If a big whale attacks a particularly dense swarm, it can swallow up to 500 kilograms of krill, eating 457,000 calories in a single monster mouthful and getting back almost 200 times the amount it burned in the attempt. A smaller whale lunging at a sparse collection of krill would only get around 8,000 calories, but that’s still 8 times more than what it burned. Even when Goldbogen accounted for the energy needed to dive in search of prey, the whales still regained 3 to 90 times as much energy as they spent.

Check out the rest of this post at Not Exactly Rocket Science.

Related Content:
Not Exactly Rocket Science: Across an ocean, round a continent – the epic 10,000km voyage of a humpback whale
Not Exactly Rocket Science: Behold Livyatan: the sperm whale that killed other whales
80beats: Climate Scientists Enlist Narwhals to Study the Arctic Ocean

Image: Wikimedia Commons