A huge spike in the Earth’s atmospheric oxygen about 800 million years ago, the story goes, paved the way for the Cambrian explosion a couple hundred million years later, and with it the rise of complex life. But a new study out in Nature says that picture is incomplete. Researchers found evidence of substantial oxygen 1.2 billion years ago, meaning that the conditions needed for complex life appeared much earlier than scientists knew, and that perhaps something else was required to set off the explosion of biodiversity.
The geologists led by John Parnell hunted in the Scottish Highlands for clues in ancient rocks, where evidence of ancient bacteria could reveal how much oxygen was around 1.2 billion years ago.
Before there was a useful amount of free oxygen around, these bacteria used to get energy by converting sulfate, a molecule with one sulfur atom and four oxygens, to sulfide, a sulfur atom that is missing two electrons. Geologists can get a glimpse of how efficient the bacteria were by looking at two different sulfur isotopes, versions of the same element that have different atomic masses. Converting sulfate to sulfide leaves the rock with a lot more of the isotope sulfur-32 than would be there without the bacteria’s help. [Wired.com]
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From Ed Yong:
Imagine taking a course of antibiotics and suddenly finding that your sexual preferences have changed. Individuals who you once found attractive no longer have that special allure. That may sound far-fetched, but some fruit flies at Tel Aviv University have just gone through that very experience. They’re part of some fascinating experiments by Gil Sharon, who has shown that the bacteria inside the flies’ guts can actually shape their sexual choices.
The guts of all kinds of animals, from flies to humans, are laden with bacteria and other microscopic passengers. This ‘microbiome’ acts as a hidden organ. It includes trillions of genes that outnumber those of their hosts by hundreds of times. They affect our health, influencing the risk of obesity and chronic diseases. They affect our digestion, by breaking down chemicals in our food that we wouldn’t normally be able to process. And, at least in flies, they can alter sexual preferences, perhaps even contributing to the rise of new species.
For more about how Sharon altered the flies‘ microbiome—and therefore their love interests—check out the rest of the post at Not Exactly Rocket Science.
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Image: Wikimedia Commons
Three times the plague has appeared in deadly force. And all three times, scientists have found, the disease-bearing bacteria originated in China and spread across the world through different routes.
The plague’s most famous appearance came as the Black Death in 14th century Europe, when it wiped out nearly a third of the population. But it also struck as the Justinian Plague in the Byzantine Empire of the 6th century, and a less severe outbreak spread around the world and reached the American mainland in 1900 (see map above). This week in the journal Nature Genetics, Mark Achtman and colleagues rebuilt the evolutionary history of the bacterium Yersinia pestis, the cause of bubonic plague, and traced all three major waves of plague back to a starting point in China.
By looking at genetic variations in living strains of Yersinia pestis, Dr. Achtman’s team has reconstructed a family tree of the bacterium. By counting the number of genetic changes, which clock up at a generally steady rate, they have dated the branch points of the tree, which enables the major branches to be correlated with historical events. [The New York Times]
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Illness-inducing bacteria, meet nano-engineered cotton–and a quick death. Researchers have created a new “filter” that zaps bacteria with electric fields to clean drinking water. They say their system may find use in developing countries since it requires only a small amount of voltage (a couple of car batteries, a stationary bike, or a solar panel could do the job) and cleans water an estimated 80,000 times faster than traditional devices.
Instead of trapping bacteria in small pores like many slow-going traditional filters, the cotton and silver nanowire combo uses small electric currents running through the nanowires to kill the bacteria outright. In a paper to appear in the journal Nano Letters researchers say that 20 volts and 2.5 inches worth of the material killed 98 percent of Escherichia coli in the water they tested in their lab setup.
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Beer: Some people think it’s proof that God loves us and wants us to be happy. Others value it as a great source of antibiotics—of course, those people lived nearly 1,700 years ago.
For much of the last three decades, anthropologist George Armelagos has been trying to explain how mummies that date from an ancient kingdom in Nubia—the area south of Egypt that’s located in present-day Sudan—got so much of the antibiotic tetracycline in their bones. Since scientists didn’t synthesize antibiotics like that one until the 20th century (and these bones date back to between 350 to 550 A.D.), finding a buildup in ancient bones screams out “contamination.”
Armelagos and his colleagues longed to prove that it wasn’t, and in a study out in American Journal of Physical Anthropology, the team argues that the find is no fluke. Nubians got antibiotics into their systems by drinking beer, and lots of it, and from an early age.
How? Thanks to the help of a kind of bacteria called Streptomyces.
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We knew that bacteria could stink, but new research asks if bacteria can smell. A study published today argues that Bacillus licheniformis found in soil can sense ammonia given off by neighboring bacteria. Though we might turn our noses when we smell the gases given off by neighbors, the bacteria respond to ammonia by building a thick biofilm coating.
The research appears today in Biotechnology Journal. Previous studies have shown that bacteria can sense gases such as oxygen, but this is the first study to argue that bacteria can smell, since ammonia has a scent. Lead author Reindert Nijland explains that bacteria break the pungent gas down for its useful nitrogen, so an ammonia-detector and biofilm response might be a useful survival tool. He even suggests that this might be the earliest example of olfaction in evolutionary history.
“Ammonia is the simplest available nitrogen source,” Nijland said. “All organisms need nitrogen to produce their proteins.” The ammonia is thought to signal both the presence of nutrients and the presence of other bacteria, since the biofilms Bacillus species produce in response to ammonia contain antibiotics that can kill competing bacteria. And the ability to “smell” ammonia “gives bacteria a way to sense nutrients where nutrients are and then migrate towards them,” he said. [The Scientist]
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The antibiotics-resistant superbug that emerged in South Asia appears to have claimed its first life. According to doctors who treated a man in Belgium, he went to a hospital in Pakistan after a car accident, and there he picked up the bacterial infection. While the man died back in June, his doctors announced today that he carried the superbug.
This new health scare intensified this week after researchers published a study in The Lancet Infectious Diseases characterizing “a new antibiotic resistance mechanism” in the U.K., India, and Pakistan. How bad is this “mechanism?”
It’s bad:
The problem isn’t a particular kind of bacteria. It’s a gene that encodes an enyzme called New Delhi metallo-lactamase-1 (NDM-1). Bacteria that carry it aren’t bothered by traditional antibiotics, or even the drugs known as carbapenems deployed against antibiotic-resistant microbes.
The NDM-1 gene is a special worry because it is found in plasmids — DNA structures that can easily be copied and then transferred promiscuously among different types of bacteria. These include Escherichia coli, the commonest cause of urinary tract infections, and Klebsiella pneumoniae, which causes lung and wound infections and is generated mainly in hospitals [AFP].
It’s no worse than what we had before:
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The health detriments of a Western diet—eating foods high in fat, sugar, and animal protein—are now well known. However, according to a group of studies out in this week’s Proceedings of the National Academy of Sciences, how you eat when you’re just a kid can have a great impact, influencing the gut microbes you’ll carry your entire life.
Researchers led by Carlotta de Filippo studied the gut microbes of African children raised in Burkina Faso versus those in European children from Italy. According to the team’s findings, the kids’ diet had a dramatic effect on what bacteria they harbored in their guts to help them with digestion. The Burkina Faso children, who grew up eating a lot of fiber, had gut bacteria that help to break down that tough material. Meanwhile the Italian children, who grew up on a Western diet, had guts dominated by a kind of bacteria that’s more common in obese people, and they had less bacterial diversity overall.
Two other PNAS papers this week took on the formation and evolution of a human’s gut microbiome. One showed how a nursing infant gets its first helpful gut microbes from mother’s milk, and the other followed the same baby for two and a half years—collecting “samples” from diapers—to show how its population of gut bacteria changed and developed.
For an in-depth take on these studies and insight on how they fit together, check out Ed Yong’s post at Not Exactly Rocket Science.
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Image: Wikimedia Commons
Identical twins don’t share everything. The mix of viruses in a person’s gut, a new study says, is unique to each of us, even if we share nearly all our DNA with another person. That is, at least according to our poop.
This year scientists have been working to decode the genetics of the beneficial microbes that live inside us, like the bacteria that help us digest food. But those trillions of bacteria have partners of their own—beneficial viruses. Jeffrey Gordon and colleagues wanted to see what those viruses were like, and how they differed from person to person. To do it, they studied fecal samples that came from four sets of identical twins, as well as their mothers.
Each identical twin had virus populations that didn’t resemble those of their sibling—or anybody else, for that matter.
Remarkably, more than 80 percent of the viruses in the stool samples had not been previously discovered. “The novelty of the viruses was immediately apparent,” Gordon said. The intestinal viromes of identical twins were about as different as the viromes of unrelated individuals [MSNBC].
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Some like it hot. The bacteria Francisella tularensis is among them. It likes to live at the temperatures present inside human bodies, and give us the disease tularaemia. But Barry Duplantis figured out a way to make the body an unattractive destination for the bacteria: He injected it with the genes of a cold-lover.
In a study in this week’s Proceedings of the National Academy of Sciences, Duplantis brought in Colwellia psycherythraea, a bacteria that can survive in the icy temperatures of the Arctic, but would die at a temperature like the nearly 100 degrees inside our bodies. By transferring genes responsible for that temperature sensitivity into F. tularensis, he created versions of that bacteria with lower heat tolerances.
When he injected these microbes into mice, they couldn’t migrate to warm areas like the lungs and do damage. Plus, the presence of the incapacitated bacteria acted as a sort of vaccine, putting the animals’ immune systems at the ready. When the researchers later gave the mice large exposures to unaltered F. tularensis, they didn’t get as sick as control mice.
For plenty more on this study, check out Ed Yong’s post at Not Exactly Rocket Science.
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DNA may dictate your development, but you also wouldn’t be you without the unique mix of bacteria that make their home on your body. This week in the Proceedings of the National Academy of Sciences, researchers say that the very moment of your birth can decide for a lifetime what kind bacteria live in your body, and even whether you’ll be at a higher risk for conditions like asthma.
The uterus is a sterile environment. So, in the womb, babies don’t have any bacteria to call their own. It’s only once they enter the world that they begin to collect the microbes that will colonize their bodies and help shape their immunity [Scientific American].
How babies enter the world is the key, the team says. The studied surveyed the bacterial colonies of 10 mothers just before birth; four of those women gave birth traditionally and six did through cesarean section. When the scientists then checked up on the bacteria living in the newborns, they found that the difference in birth method decided what microbes the baby would get. Those born vaginally tended to pick up the bacteria from their mother’s vagina, while those born via C-section harbored bacterial colonies that tend to come from skin.
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This is not an “eat dirt for your health and happiness” study. You don’t need to shovel soil in your mouth. Just go outside.
Biologist Dorothy Matthews and company wanted to test a particular bacteria, Mycobacterium vaccae. It’s found commonly in the soil and carried widely through the air, so if you take a walk in the park you’ll probably breathe it in. Previous studies have shown that the bacterium increases serotonin in the brain, and have even suggested that the bacterium has antidepressant qualities. Since the neurotransmitter serotonin is also involved in cognition, the team wanted to see if the bacterium could have a direct effect on learning. Indeed it did, Matthews’ team announced at the General Meeting of the American Society for Microbiology in San Diego.
In a classic test of learning ability, Matthews gave mice a treat – white bread with peanut butter – as a reward to encourage them to learn to run through a maze. When she laced the treat with a tiny bit of Mycobacterium vaccae, she found that the mice ran through the maze twice as fast as mice that were given plain peanut butter [New Scientist].
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Kaleidoscopic. Delightfully odd. And too numerous to truly grasp.
There are many more words one could deploy to describe the worlds unknown under the sea. An international group of scientists has been scouring them for life for the last decade, and later this year, on October 4, the Census of Marine Life will release it catalog of marine inhabitants. “The number could be astonishingly large, perhaps a million or more, if all small animals and protists are included,” the organization says.
Octopuses, jellyfish, and other sprawling sea creatures dominated the census’ prior reports. But this time they’ve dived even deeper, surveying tiny life. Remotely operated deep-sea vehicles discovered that roundworms dominate the deepest, darkest abyss. Sometimes, more than 500,000 can exist in just over a square yard of soft clay [AP].
And then there are the microbes. The scientists conservatively estimate that there must be at least 20 million kinds of microbe in the oceans. The true number may even be billions or trillions [Nature]. Individual microbes reach even more astronomical number. There are probably a nonillion of them in the sea, the scientists estimate. That’s a billion cubed, and then times 1,000. Or, if you prefer your measurements given in the weight of African elephants, it’d be 240 billion of them.
Take a peek through this quick slideshow of some of the weirdest ocean life seen so far.
Image: David Patterson et. al.
Here’s a new way to prove the maxim that we are what we eat: Take a peek into the teeming universe of bacteria that thrive in a Japanese person’s gut. Trillions of microbes in the gut help digest the foods we eat, and researchers have found that the “gut microbiomes” of Japanese people have adapted over the centuries to help digest seaweed–an integral part of sushi. Remarkably, they adapted by taking in genetic material found in that very sushi.
The new study, published in Nature, reveals that these gut bacteria engaged in a gene swap, grabbing algae-digesting genes from marine bacteria that live on red algae like nori, the seaweed used to wrap sushi. The marine bacteria traveled on the seaweed into human digestive systems, where the crucial genes were transferred to bacteria in the gut.
Scientists stumbled on this swap when they identified a new group of enzymes from the algae-chomping marine bacteria that help the microbes break down the unique carbohydrates in seaweed. When they searched for other organisms that had the same enzymes, they found one match that, oddly, came from a species of bacteria that lived in the gut of a Japanese volunteer. Further study revealed that this species of gut bacteria is seen only in Japanese individuals.
For an in-depth look at what the horizontal gene transfer means and how this could affect your sushi-chomping habits, turn to the new DISCOVER blog Not Exactly Rocket Science and Ed Yong’s illuminating post, “Gut bacteria in Japanese people borrowed sushi-digesting genes from ocean bacteria.”
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Image: Flickr/johndmelo
If you thought that fingerprints or DNA fragments were the only bits of forensic evidence that could pin you to a scene of a crime, then think again. Researchers at the University of Colorado, Boulder have found preliminary evidence suggesting that you can be identified from the unique mix of bacteria that lives on you.
Each person, they say, is a teeming petri dish of bacteria, but the composition varies from person to person. Every place a person goes and each thing he touches is smudged with his unique “microbial fingerprint.” The bacterial mixes are so specific to individuals that researchers found that they could pair up individual computer keyboards with their owners–just by matching the bacteria found on the keyboard to the bacteria found on the person’s fingertips. Describing their findings in the journal Proceedings of the National Academy of Sciences, scientists write that that if this bacterial fingerprint technique is refined, it could one day help in forensic investigations.
The Human Microbiome Project has already found that different body parts harbor different kinds of microbes. Study coauthors Noah Fierer and Rob Knight note that these colonies don’t change much over time. No amount of hand-washing will change a person’s microbial make-up, they say.
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