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This chimp may look innocent, but he may harbor any of dozens of diseases that infect humans. Photo by AfrikaForce

Anyone who has read a Richard Preston book, such as The Hot Zone or Panic in Level 4, knows the danger of tampering with wildlife. The story usually goes something like this: Intrepid explorers venture into a dark, bat infested cave in the heart of East Africa, only to encounter something unseen and living, which takes up residence in their bodies. Unknowingly infected, the happy travelers jump on a plane back to Europe or the States, spreading their deadly pathogen willy-nilly to every human they encounter upon the way. Those people, in turn, bring the novel virus or bacterium back home to strangers and loved ones alike. Before the world knows it, a pandemic has arrived.

This scenario may sound like fiction, but it’s exactly what infectious disease experts fear most. Most emerging infectious diseases in humans have indeed arisen from animals–think swine and bird flu (poultry and wild birds), SARS (unknown animals in Chinese markets), Ebola (probably bats) and HIV (non-human primates). Therefore, experts prioritize the task of figuring out which animals in which regions of the world are most prone to delivering the latest novel pathogen to hapless humanity.

With this in mind, researchers at Harvard University, the University of Granada and the University of Valencia set out to develop a new strategy for predicting the risk and rise of new diseases transmitted from animals before they happen, describing their efforts in the journal Proceedings of the National Academy of Sciences.

To narrow the hypothetical disease search down, the team chose to focus on non-human primates. Because monkeys and great apes are so closely related to us, their potential for developing and transmitting a pathogen suited to the human body is greater than the equivalent risk from animals such as birds or pigs. As a general rule, the more related species are, the greater the chances they can share a disease. The researchers gathered data from 140 species of primates. They overlaid that information with more than 6,000 infection records from those various primate species, representing 300 different pathogens, including viruses, bacteria, parasitic worms, protozoa, insects and fungus. This way, they could visualize which pathogens infect which species and where.

Like mapping links between who-knows-who in a social network, primates that shared pathogens were connected. This meant that the more pathogens an animal shared with other species, the more centrally located it was on the tangled web of the disease diagram.    

A diagram depicting shared parasites among primate species. Each bubble represents one species, with lines connecting species by shared pathogens. The larger the bubble, the more emerging infectious diseases that species harbors. The dark blue bubbles represent the top 10 primates that share the most emerging infectious diseases with humans. Photo by Gomez et al., via PNAS

From studying these charts, a few commonalities emerged. Animals at the center of the diagram tended to be those that lived in dense social groups and also covered a wide geographic range (yes, similar to humans). These species also tended to harbor parasites that are known to infect humans, including more pathogens identified as emerging infectious diseases. In other words, those species that occurred in the center of the diagram are the best positioned to kick off the next pandemic or horrific infectious disease, and thus should be the ones that experts should keep the closest watch on.

Such animals could qualify as “superspreaders,” or those that receive and transmit pathogens very often to other species.”The identification of species that behave as superspreaders is crucial for developing surveillance protocols and interventions aimed at preventing future disease emergence in human populations,” the authors write.

Apes appeared in the heart of the disease diagram and are among the species we should be most worried about, which is not surprising considering that diseases such as malaria and HIV first emerged from these animals. On the other hand, some non-ape primates, including baboons and vervet monkeys, also popped up in the center of the diagram and turn out to harbor many human emerging disease parasites. 

Currently, our ability to predict where, when and how new emerging infectious diseases might arise is “remarkably weak,” they continue, but if we can identify those sources before they become a problem we could prevent a potential health disaster on a regional or even global scale. This new approach for identifying animal risks, the authors write, could also be applied to other wildlife groups, such as rodents, bats, livestock and carnivores. “Our findings suggest that centrality may help to detect risks that might otherwise go unnoticed, and thus to predict disease emergence in advance of outbreaks—an important goal for stemming future zoonotic disease risks,” they conclude. 

Image via NASA/NOAA/GSFC/Suomi NPP/VIIRS/Norman Kuring

Last year, to celebrate the 42nd Earth Day, we took a look at 10 of the most surprising, disheartening, and exciting things we’d learned about our home planet in the previous year—a list that included discoveries about the role pesticides play in bee colony collapses, the various environmental stresses faced by the world’s oceans and the millions of unknown species are still out in the environment, waiting to be found.

This year, in time for Earth Day on Monday, we’ve done it again, putting together another list of 10 notable discoveries made by scientists since Earth Day 2012—a list that ranges from specific topics (a species of plant, a group of catfish) to broad (the core of planet Earth), and from the alarming (the consequences of climate change) to the awe-inspiring (Earth’s place in the universe).

Even the supposedly pristine Antarctic landscape is marred by trash heaps. Image via Germany Federal Environment Agency Report (PDF)

1. Trash is accumulating everywhere, even in Antarctica. As we’ve explored the most remote stretches of the planet, we’ve consistently left behind a trail of one supply in particular: garbage. Even in Antarctica, a February study found (PDF), abandoned field huts and piles of trash are mounting. Meanwhile, in the fall, a new research expedition went to study the Great Pacific Garbage Patch, counting nearly 70,000 pieces of garbage over the course of a month at sea.

2. Climate change could erode the ozone layer. Until recently, atmospheric scientists viewed climate change and the disintegration of the ozone layer as entirely distinct problems. Then, in July, Harvard researcher Jim Anderson (who won a Smithsonian Ingenuity Award for his work) led a team that published the troubling finding that the two might be linked. Some warm summer storms, they discovered, can pull moisture up into the stratosphere, an atmospheric layer 6 miles up. Through a chain of chemical reactions, this moisture can lead to the disintegration of ozone, which is crucial for protecting us from ultraviolet (UV) radiation. Climate change, unfortunately,  is projected to cause more of these sorts of storms.

3. This flower lives on exactly two cliffs in Spain. In September, Spanish scientists told us about one of the most astounding survival stories in the plant kingdom: Borderea chouardii, an extremely rare flowering plant that is found on only two adjacent cliffs in the Pyrenees. The species is believed to be a relic of the Tertiary Period, which ended more than 2 million years ago, and relies on several different local ant species to spread pollen between its two local populations.

4. Some catfish have learned to kill pigeons. In December, a group of French scientists revealed a phenomenon they’d carefully been observing over the previous year: a group of catfish in Southwestern France had learned how to leap onto shore, briefly strand themselves, and swim back into the water to consume their prey. With more than 2,000,000 Youtube views so far, this is clearly one of the year’s most widely enjoyed scientific discoveries.

5. Fracking for natural gas can trigger moderate earthquakes. Scientists have known for a while that whenever oil and gas are extracted from the ground at a large scale, seismic activity can be induced. Over the past few years, evidence has mounted that injecting water, sand and chemicals into bedrock to cause gas and oil to flow upward—a practice commonly known as fracking—can cause earthquakes by lubricating pre-existing faults in the ground. Initially, scientists found correlations between fracking sites and the number of small earthquakes in particular areas. Then, in March, other researchers found evidence that a medium-sized 2011 earthquake in Oklahoma(which registered a 5.7 on the moment magnitude scale) was likely caused by injecting wastewater into wells to extract oil.

6. Our planet’s inner core is more complicated than we thought. Despite decades of research, new data on the iron and nickel ball 3,100 miles beneath our feet continue to upset our assumptions about just how the earth’s core operates. A paper published last May showed that iron in the outer parts of the inner core is losing heat much more quickly than previously estimated, suggesting that it might hold more radioactive energy than we’d assumed, or that novel and unknown chemical interactions are occurring. Ideas for directly probing the core are widely regarded as pipe dreams, so our only options remains studying it from afar, largely by monitoring seismic waves.

The berries of Pollia condensata were found to produce the most intense color in the natural world. Image via PNAS

7. The world’s most intense natural color comes from an African fruit. When a team of researchers looked closely at the blue berries of Pollia condensata, a wild plant that grows in East Africa, they found something unexpected: it uses an uncommon structural coloration method to produce the most intense natural color ever measured. Instead of pigments, the fruit’s brilliant blue results from nanoscale-size cellulose strands layered in twisting shapes, which which interact with each other to scatter light in all directions.

8. Climate change will let ships cruise across the North Pole. Climate change is sure to create countless problems for many people around the world, but one specific group is likely to see a significant benefit from it: international shipping companies. A study published last month found that rising temperatures make it probable that during summertime, reinforced ice-breaking ships will be able to sail directly across the North Pole—an area currently covered by up to 65 feet of ice—by the year 2040. This dramatic shift will shorten shipping routes from North America and Europe to Asia.

9. One bacteria species conducts electricity. In October, a group of Danish researchers revealed that the seafloor mud of Aarhus’ harbor was coursing with electricity due to an unlikely source: mutlicellular bacteria that behave like tiny electrical cables. The organisms, the team found, built structures that traveled several centimeters down into the sediment and conduct measurable levels of electricity. The researchers speculate that this seemingly strange behavior is a byproduct of the way of the bacteria harvests energy from the nutrients buried in the soil.

Kepler 62f, discovered yesterday, is the most promising exoplanet candidate yet in terms of its potential to harbor life. Image via NASA/Ames/JPL-Caltech

10. Our Earth isn’t alone. Okay, this one might not technically be a discovery about Earth, but over the past year we have learned a tremendous amount about what our Earth isn’t: the only habitable planet in the visible universe. The pace of exoplanet detection has accelerated rapidly, with a total of 866 planets in other solar systems discovered so far. As our methods have become more refined, we’ve been able to detect smaller and smaller planets, and just yesterday, scientists finally discovered a pair of distant planets in the habitable zone of their stars that are relatively close in size to Earth, making it more likely than ever that we might have spied an alien planet that actually supports life.

Lashed to a spear made in the Gilbert Islands, researchers found a tooth from a dusky shark, a species previously unknown in the area. Image via PLOS ONE/Drew et. al.

For decades, a total of 124 swords, tridents and spears taken from the Pacific Ocean’s Gilbert Islands in the mid-1800s sat untouched in vaults in Chicago’s Field Museum. The weapons—each made up of dozens of individual shark teeth that islanders lashed to a wooden core with coconut fibers—were primarily considered artifacts of anthropological value.

Then, Joshua Drew, a marine conservation biologist at the museum, had an unusual idea: that the shark teeth lining the serrated blades could also serve as an ecological snapshot of the reefs that lined the islands more than a century ago. Sharks can be clearly identified solely by their teeth, so the teeth that islanders had harvested and used for their weapons might reflect historical biodiversity in the reefs that’s since been lost due to environmental degradation.

When Drew and others closely examined the hundreds of teeth on the weapons, they found that they came from eight different shark species, six of which were known to commonly swim in the Gilbert Islands’ waters. Two species, though—the dusky shark (Carcharhinus obscurus) and the spottail shark (Carcharhinus sorrah)—were something of a surprise. When the researchers looked at the scientific literature and various museum holdings of fish collected in the area, they found that these two species had never been documented within thousands of miles of the islands.

A trident lined with shark teeth, used in the study. Image via PLOS ONE/Drew et. al.

Drew calls this “shadow biodiversity”—a reflection of the life that lived in an ecosystem before we even started studying what was there. “[These are] hints and whispers of what these reefs used to be like,” he said in a press statement accompanying the paper documenting his team’s find, published today in PLOS ONE. “It’s our hope that by understanding how reefs used to look we’ll be able to come up with conservation strategies to return them to their former vivid splendor.”

Working with Mark Westneat, the museum’s curator of fishes, and Christopher Philipp, who manages the anthropology collections, Drew classified each tooth on every weapon by shark species, primarily using field guides and photos. In cases where the tooth’s identity was ambiguous, he made use of the Museum’s own ichthyological holdings, comparing it to preserved specimens from each shark species.

Because dusky and spottail shark teeth were found on the weapons—crafted sometime between the 1840s and 1860s, shortly before they were collected—the researchers believe these two species were once part of the ecosystem and have since been eradicated. There is the possibility that the teeth were harvested elsewhere and came to the Gilbert Islands via trade, but the team says it’s unlikely.

For one, sharks figure largely in the islanders’ traditional culture, and it’s well-known that they had effective shark-fishing techniques, making it unlikely that they’d go to the trouble of exporting teeth from afar. The two species’ teeth were among the most common found on the weapons, so it also stands to reason that they were fairly abundant nearby. Secondly, there is no historical or archaeological evidence that trade occurred between the extremely remote Gilbert Islands and either the Solomon Islands (the closest known location of spottail sharks) or Fiji (for dusky sharks).

It’s impossible to know for sure, but given the environmental degradation that’s occurred over the past century in the Pacific’s coral reefs, the researchers suspect that humans played a role in these sharks’ local eradication. Because sharks mature slowly and have a small number of offspring per individual, they can be wiped out quickly by moderate levels of fishing, and the commercial shark fishing industry started up in the area as early as 1910.

Rigorous fish surveys of the Pacific didn’t begin for a few more decades, so these weapons—and perhaps other human artifacts that incorporate biological specimens—serve as a valuable time capsule of the ecosystems that predated scientific study. Drew thinks that the “shadow diversity” we’ve since lost should inspire people in the marine conservation field to recreate the biodiversity that predates the Industrial Age.

“When we set up modern conservation plans, we shouldn’t sell ourselves short,” he told Nature last year, when he revealed his preliminary results at a conference. “We might not recapture the vivid splendor of those super-rich levels, but this information argues for setting up management plans to protect what sharks are there.”

Roosters have an internal circadian rhythm, which keeps them crowing on schedule even when the lights are turned off. Image via Wikimedia Commons/Muhammad Mahdi Karim

Some scientists investigate the universe’s biggest mysteries, like the Higgs boson, the mysterious particle that endows all other subatomic particles with mass.

Other researchers look into questions that are, well, a bit humbler—like the age-old puzzle of whether roosters simply crow when they see light of any kind, or if they truly know to crow when the morning sun arrives.

Lofty or not, it’s the goal of science to answer all questions that arise from the natural world, from roosters to bosons and everything in between. And a new study by Japanese researchers published today in Current Biology resolves the rooster question once and for all: The birds truly do have an inner circadian rhythm that tells when to crow.

The research team, from Nagoya University, investigated via a fairly straightforward route: They put several groups of four roosters in a room for weeks at a time, turned the lights off, and let a video camera running. Although roosters can occasionally crow at any time of day, the majority of their crowing was like clockwork, peaking in frequency at time intervals roughly 24 hours apart—the time their bodies knew to be morning based on the sunlight they’d last seen before entering the experiment.

This consistency continued for about 2 weeks, then gradually began to die out. The roosters were left in the room for 4 weeks in total, and during the second half of the experiment, their crowing began occurring less regularly, at any time of day, suggesting that they do need to see the sun on a regular basis for their circadian rhythms to function properly.

In the experiment’s second part, the researchers also subjected the roosters to alternating periods of 12 hours of light and 12 hours of darkness, while using bright flashes of light and the recorded crowing of roosters (since crowing is known to be contagious) to induce crowing at different times of day. When they activated these stimuli near at or near the dawn of the roosters’ 12-hour day, crowing rates increased significantly. At other times of day, though, exposing them to sudden flashes of light or playing the sound of crowing had virtually no effect, showing that the underlying circadian cycle played a role in the birds’ response to the stimuli.

Of course, many people who live in close proximity to roosters note that they often crow in response to a random light source turning on, like a car’s headlights, no matter what time of day it is. While this may be true, the experiment shows that the odds of a rooster responding to a car’s headlights depend on how close the current time is to dawn—at some level, the rooster’s body knows whether it should be crowing or not, and responding to artificial stimuli based on this rhythm.

For the research team, all this is merely a prelude to their bigger, more complex questions: Why do roosters have a biological clock that controls crowing in the first place, and how does it work? They see the simple crowing patterns of the rooster as an entry point into better understanding the vocalizations of a range of animals. “We still do not know why a dog says ‘bow-wow’ and a cat says ‘meow,’” Takashi Yoshimura, one of the co-authors, said in a press statement. “We are interested in the mechanism of this genetically controlled behavior and believe that chickens provide an excellent model.”

At the bottom of the Mariana Trench, nearly eight miles below the ocean’s surface, abundant communities of bacteria thrive. Image via PNAS/Yayanos et. al.

The Challenger Deep, the deepest point on the entire seafloor, lies in the Mariana Trench off the coast of the Pacific Ocean’s Mariana Islands. It is nearly 36,000 feet—6.8 miles—below the ocean’s surface. If you were to stand at this remarkable depth, the column of water above your head would exert 1000 times the amount of pressure you normally experience at the surface, crushing you instantly.

Even in this extreme environment, though, organisms can survive. One type, it turns out, can even prosper: bacteria. A new study, published today in Nature Geoscience, finds that unexpectedly abundant bacteria communities grow in the depths of the Mariana Trench, with organisms living at densities ten times greater than in the much shallower ocean floor at the trench’s rim.

To probe the ultra-deep ecosystem, the international research team, led by Ronnie Glud of the University of Southern Denmark, sent a specially-designed, 1300-pound robot down to the bottom of the trench in 2010. The robot was equipped with thin sensors that can slice into the seafloor sediments to help measure the organic consumption of oxygen. Because living things consume oxygen as they respire, tallies on how much ambient oxygen is missing from the sediments can be used as a proxy for the amount of microorganisms living in that area.

The research team’s specialized robot, designed to take samples under extremely high pressure. Photo by Anni Glud

When the team used the device to sample the sediments at a pair of sites with depths of 35,476 and 35,488 feet, they found surprisingly high amounts of oxygen consumption—levels that indicated there were ten times more bacteria present at the ultra-deep site than at another, shallower site they sampled for reference about 37 miles away, at a depth of just 19,626 feet.

The robot also collected a total of 21 sediment cores from the two sites, and these cores were hauled up and analyzed in the lab. Although many of the microorganisms died when they were brought up to the surface—after all, the creatures are adapted for the high pressure and low temperature of the ocean floor—the finding was confirmed: Cores from the Mariana Trench had much higher densities of bacterial cells than those from the reference site.

The team also remotely recorded video of the ocean floor, using lights to illuminate the pitch-black environment, and found a few life forms much larger than bacteria scurrying around on top of the sediment. When they used baited traps to recover a few of the specimens and bring them to the surface, they determined they were Hirondellea gigas, a species of amphipods—small crustaceans typically less than an inch in length.

A video still from the seafloor reveals an amphipod (left) scurrying across the bacteria-filled sediment. Image via Nature Geoscience/Glud et. al.

The discovery of such abundant bacterial life is particularly surprising because conventional wisdom would suggest that not enough nutrients are present at such depths to support much growth. Photosynthetic plankton serve as the nutrient base for nearly any ocean food chain, but they’re unable to survive on the lightless seafloor. The waste products (such as dead animals and microorganisms) of ecosystems higher up in the shallow light-filled waters do filter down and feed deeper food webs, but typically, less and less organic matter makes it down as depths increase.

In this case, though, the scientists seem to have found an exception to the rule, since the ultra-deep trench was home to so much more bacterial activity than the nearby shallower reference site. Their explanation is that the trench acts as a natural sediment trap, gradually collecting nutrients that filter down and land at shallower locations on the ocean floor nearby, then are dislodged by earthquakes or other perturbations.

In the years since the 2010 exploration, the research team has sent the same robot down to sample the Japan Trench (roughly 29,500 feet deep) and plans to sample the Kermadec-Tonga Trench (35,430 feet deep) later this year. “The deep sea trenches are some of the last remaining ‘white spots’ on the world map,” Glud, the lead author, said in a press statement. “We know very little about what is going on down there.”