As scientists understand more about microbes, it seems that the miniscule life forms have the potential to contribute to a host of useful activities—making biofuels, fighting human disease, improving high tech, you name it!

Now, a feature article in the September issue of Scientific American looks at how soil microbes could revolutionize agriculture.

Soil microbes include everything from bacteria to fungi, and article author Richard Conniff likes to call the lot collectively “the agribiome.” These microscopic life forms have the potential to solve many crises facing agriculture today—everything from climate change and drought to Salmonella and other food-bourn illnesses, from the costs of man-made fertilizers to the GMO controversy.

Conniff’s article comes on the heels two other papers that highlight the importance of soil microbes. In a paper published last week in the Proceedings of the National Academy of Sciences, a team of British scientists emphasizes how important soil microbe diversity is for European crops. And two weeks ago, American researchers determined that soil microbes are responsible for controlling carbon in the soil—an important factor in retaining the important mineral in the dirt as temperatures rise and the climate warms.

The Scientific American article gives many examples of these crucial, unseen microbial workers. Bacteria found in soil on the United States West Coast can kill Salmonella, Conniff reports, so the USDA is looking at introducing the bacteria in East Coast soils to stop the occasionally deadly outbreaks.

And instead of genetically modifying actual crops to withstand drought conditions, Mexican scientists are looking at modifying bacteria to strengthen the plants in the soil at their roots.

Mycorrhizal fungi in the soil are heroes in both the SciAm article and the PNAS study. The fungi deliver much-needed phosphate to crops, an easier and cheaper way to get the important mineral to the plants to help them grow. Artificial fertilizers can be expensive, especially for farmers in developing countries, and harm the natural soil ecosystem. Run-off from these fertilizers also contaminates freshwater and marine environments. A simple animation of how the fungi works to help plants is available here.

(Mycorrhizal fungi also play a heroic role in the next Academy planetarium show! Currently in production and set for a fall 2014 opening date, the latest production from our visualization studio will highlight the complex relationships in ecosystems—and how humans fit into the picture.)

If farmers and scientists can acknowledge that collaborating with microbes can play a crucial role in farming, “we will have come a step closer to feeding a hungry world,” Conniff concludes.

The lead author of the PNAS paper, Franciska de Vries, says, “This research highlights the importance of soil organisms and demonstrates that there is a whole world beneath our feet, inhabited by small creatures that we can’t even see most of the time. By liberating nitrogen for plant growth and locking up carbon in the soil they play an important role in supporting life on Earth.”

Mycorrhizal fungi image: Nilsson et al. BMC Bioinformatics

What if the bacteria in your gut could produce a cleaner fuel for cars and trucks? It turns out, with a little fiddling, they can!

Researchers in the United Kingdom took the common gut bacteria, Escherichia coli, and added genes from the camphor tree, blue-green algae and two other bacteria (Photorhabdus luminescens and Bacillus subtilis). The addition of genes from blue-green algae and the two bacteria allow E.coli to make hydrocarbons from fatty acids; the camphor tree genes makes the hydrocarbons a similar length to those found in fossil fuels.

So when the scientists fed the glucose from plants to the souped-up E. coli, the gut bacteria turned the food into a fuel very similar to the diesel fuel derived from crude oil. Voilà! Gut Fuel!

The remarkable thing about this biofuel—a fuel derived directly from living matter— is that it can be pumped into current gas tanks with absolutely no modifications. Most other biofuels require vehicle owners to adjust their engines to operate with the more sustainable liquids, or involve mixing the biofuel with traditional fossil fuels.

John Love, of the University of Exeter, says this was a priority. “Producing a commercial biofuel that can be used without needing to modify vehicles has been the goal of this project from the outset. Replacing conventional diesel with a carbon neutral biofuel in commercial volumes would be a tremendous step towards meeting our target of an 80% reduction in greenhouse gas emissions by 2050.”

Well, not so fast… Producing this new biofuel en masse will take a lot more work. The scientists are hoping to wean the E. coli off plants and use animal or agriculture waste instead. Otherwise, they foresee a similar problem for their new biofuel as that faced by current biofuels—it’s tough to argue that we should be devoting our farmlands to growing fuels over growing food.

In addition, E. coli hydrocarbons cost more to produce than fossil fuel hydrocarbons. At least on paper. But in the long run, probably not.

The research is published in this week’s Proceedings of the National Academy of Sciences.

Image: Marian Littlejohn

What if you lived in a saltwater lake that was six times saltier than the ocean, and the water was buried under nearly 20 meters (65 feet) of ice? The temperature is a brisk -13°C and oh yeah, we forgot to mention that the lake lacks oxygen and contains high levels of organic carbon.

Sounds pleasant, right? You’re probably thinking nothing can live there. Wrong.

Lake Vida in Antarctica isn’t exactly teeming with life, but life does exist in its harsh environment. Diverse life, in fact. At least eight new species of bacteria call Lake Vida home according to a new study in the Proceedings of the National Academy of Sciences.

Researchers from the University of Illinois and the Desert Research Institute took samples from the lake in 2005 and 2010, using stringent protocols to avoid contaminating the pristine ecosystem. Scientists estimate that this lake has been isolated from outside influences (including the Sun’s energy!) for almost 3,000 years.

“This study provides a window into one of the most unique ecosystems on Earth,” says lead author Alison Murray. “[It] expands our understanding of the types of life that can survive in these isolated, cryoecosystems and how different strategies may be used to exist in such challenging environments.”

Strategies like food-supply. The researchers have a theory: “Geochemical analyses suggest that chemical reactions between the brine and the underlying sediment generate nitrous oxide and molecular hydrogen,” says co-author Fabien Kenig. “The hydrogen may provide some of the energy needed to support microbes.”

“If that’s the case,” says Murray, “This gives us an entirely new framework for thinking of how life can be supported in cryoecosystems on Earth and in other icy worlds of the Universe.” Think Mars or Europa, says New Scientist.

And also think Vostok and Ellsworth—two more Antarctic lakes that have been isolated millions of years longer than Vida. Scientists are studying those lakes this Antarctic summer. Perhaps they will find life in these harsh conditions, as well?

Image: Peter Glenday, University of Illinois

The experiment demonstrates natural selection at work. And because samples are frozen and available for later study, when something new emerges, scientists can go back to earlier generations to look for the steps that happened along the way.

Last month, Zachary Blount, Lenski and colleagues published a paper in Nature detailing a new evolution in E. coli—the ability to eat citrate.

Shannon Bennett, associate curator of the Academy’s Microbiology department, explains why this is so unusual.

E. coli doesn’t normally eat citrate unless it is desperate (there’s no glucose, no oxygen). But these E. coli did evolve the ability to eat citrate, in fact thrive on it, in the presence of both oxygen and glucose.

They were able to evolve to do this when certain individuals made mistakes and copied their citrate gene (which usually is turned on only under oxygen-poor conditions) to a different spot in the genome near a switch point that turns on in the presence of oxygen.

Blount was able to trace this new trait through generations and uncover a three-step process in which the bacteria developed this new ability.

The first stage was potentiation, when the E. coli accumulated at least two mutations that set the stage for later events (see Shannon’s explanation above). The second step, actualization, is when the bacteria first began eating citrate, but only just barely nibbling at it. The final stage, refinement, involved mutations that greatly improved the initially weak function. This allowed the citrate eaters to wolf down their new food source and to become dominant in the population.

“We were particularly excited about the actualization stage,” Blount says. “The actual mutation involved is quite complex. It re-arranged part of the bacteria’s DNA, making a new regulatory module that had not existed before. This new module causes the production of a protein that allows the bacteria to bring citrate into the cell when oxygen is present. That is a new trick for E. coli.

“It wasn’t a typical mutation at all, where just one base-pair, one letter, in the genome is changed,” he continues. “Instead, part of the genome was copied so that two chunks of DNA were stitched together in a new way. One chunk encoded a protein to get citrate into the cell, and the other chunk caused that protein to be expressed.”

Shannon explains why this study is so exciting:

This study is cool because it shows many of the important mechanisms in evolution, namely gene duplication and gene regulation (turning genes on and off at different times). It all went on in a series of test tubes, so it’s “artificial” evolution, but what’s nice about that is, they were able to freeze samples down at early time points through to the present, to trace the path of evolution, and that they used a model organism, Escherichia coli, that evolves very quickly (not as quick as viruses, but much faster that vertebrates). My work takes advantage of the same historical sampling and evolutionary speed, only I’ve focused on “natural” experiments in the viruses I work on.

Uncovering the human microbiome represents a new frontier in science. Thanks to new technology, we’re beginning to understand what these microscopic organisms do, how they do it, and why they exist inside of us.

Last Friday, the awesome Bay Area Science Festival presented “Gut Check: The Hidden World of Microbes.” The panel included two UC San Francisco researchers—our friend, Joe DeRisi, and Michael Fischbach—and science writer extraordinaire, Carl Zimmer. If you follow Zimmer’s Discover blog, The Loom, you know that he loves anything tiny and gross—parasites, bacteria, fungus, the like—so we knew it would be a juicy discussion.

DeRisi developed the ViroChip—a technology that allows scientists to scan samples for several different viruses—over 10,000 things at a time—and bacteria, fungi, and parasites. When Fischbach looks at us, he sees the 100 trillion microorganisms living inside us. These microorganisms make up 10% of our genes, so he uses genome-sequencing technology to study all of them at once.

The following are some of the topics discussed by the panel:

Antibiotics and other Good Bacteria

Fischbach got into human microbiome research looking for drugs. Your gut (and skin and oral) bacteria are natural antibiotics and statins (cholesterol-lowering drugs). They could also possibly control obesity and diabetes. Microbes support your immune system and metabolism, and many of the bacteria in your gut create neurotransmitters, fueling research about how our gut bacteria affect our brains.

Fischbach pointed out how current antibiotics take a “carpet bomb” approach—killing all bacteria in our bodies, good and bad. With more research, he believes that specific good bacteria could target specific bad bacteria—taking a more “scalpel” approach to antibiotics.

Tending the Garden

Among the microorganisms in our body, there are those that help us digest food and create energy and those that just feed themselves. Insoluble fiber may keep us healthy, but we’re not actually absorbing any of it—the microbes keep it all to themselves! As Zimmer said, “You’re not eating it for yourself, but rather tending the garden.” The garden of gut flora.

The Virome

Did you know we have seven trillion viruses in our body when we’re healthy? Some of these viruses attack us and some attack other viruses or bacteria. And, are you ready for this? DeRisi can’t “think of any example of a beneficial virus.” So what are they all doing there? DeRisi has no clue, and every time he sequences he finds new viruses, wondering what role they might play.  Bringing up the question, is there a virome in addition to the biome of the human body?

With trillions of viruses and new ones evolving, does DeRisi lay awake at night in a panic? No. (Phew!)

So whether riding BART or keeping your child in a germ-free environment, the message of the panel was don’t worry about these tiny organisms (at least, for now). More research is needed to find out exactly what kind of tug of war is going on inside of our bodies.

The animals are built like carnivores, too. A genomic study on the wild panda in 2009 proved that that the bears have none of the features that other herbivores (like cows) have to breakdown the tough cellulose fibers of bamboo.

In fact, of the 12.5 kg (27.5 lbs) of bamboo the pandas eat in a day, they’re only able to digest about 17% of it. According to National Geographic News:

This explains why pandas also evolved a sluggish, energy-conserving lifestyle.

Scientists from the Chinese Academy of Sciences decided to look at the microorganisms that live in the guts of these bears. So they grabbed some panda poop, or, rather, stool samples from seven wild pandas and eight captive pandas. (Their diets vary a bit.)

Analyzing the samples, the researchers found 13 different types of Clostridium-related bacteria, known to breakdown cellulose. Of those, seven were unique to the pandas compared to other mammals. The researchers conclude that these microbes allow the panda to gain extra energy from the bamboo stalks.

Nature News describes this extraordinary feat in context:

These microbes are part of a suite of evolutionary adaptations — alongside powerful jaws and teeth, and pseudo-thumbs, bones that allow them to grip plant stalks — that help pandas to live on bamboo, despite having a carnivore’s digestive system.

The new research is published in this week’s Proceedings of the National Academy of Sciences.

Image: Mfield, Matthew Field/Wikipedia

The squid are part of an experiment to see if, like some collegiate females on spring break, good bacteria “go wild” in the microgravity of space. Bobtail squid use bacteria called Vibrio fischeri to generate light. According to Discovery News:

That light helps the squid hunt for prey in dark waters. It also provides camouflage from any organisms trying to eat him, because the squid doesn’t cast a telltale shadow on the ocean floor as a result of the moon’s rays shining down into the water.

Previous shuttle experiments have shown what happens to harmful bacteria in space, but this will be the first experiment with beneficial bacteria.  Scientists are hoping that these results with squid will translate to beneficial bacteria with humans.

The NASA press kit reports that worms are part of the mission:

One NASA experiment known as Biology (Bio) will use, among other items, C. elegans worms, that are descendants of worms that survived the STS-107 space shuttle Columbia accident.

Haven’t these worms been through enough?!

Wired UK has a breakdown of other microbes joining STS134:

The microbes on-board Endeavour include the tardigrades (nicknamed Water Bears) which are large extremophiles that can withstand temperatures as biting as absolute zero, and as hot as 150 degrees Celsius. They’re joined by the Deinococcus radiodurans (which NASA dubbed “Conan the Bacterium“) which can survive upward of 15,000 Gy of radiation — 10 Gy is more than enough to kill an average human.

Haloarcula marismortui (Old Salty) loves salt, and lives in levels of high salinity that would kill other organisms. Pyrococcus furiosus (Fire Eater) is all about heat, and thrives in temperatures over 100 degrees Celsius. Cupriavidus metallidurans (which doesn’t have a nickname, unfortunately) plays a vital role in the formation of gold nuggets, thanks to its love of gold tetrachloride: a compound that is toxic to most other microorganisms.

Finally there’s Bacillus subtilis (The Average Joe), which is a model organism used in hundreds of biological experiments. It’s been into space many times before, so it’ll be a good comparison point for other studies.

You know, Dorothy only had lions and tigers and bears to face in Oz…

Image by Hans Hillewaert/Wikimedia

Hazen, on the other hand, believes that most of the oil is gone due to degradation and dilution. He is the lead author of a paper in Science about the amazing microbes that ate much of the oil. In his team’s continuous sampling of 120 sites in the Gulf from May through October 2010, he hasn’t seen much oil– only seven sites that have oil above EPA standards. He admits he may have missed some areas.

While they started the conference by saying they agreed about much, they seemed to disagree about everything brought up: the southeast plume that came out of the well; the oil on the surface, shore, sea floor and water column; the amount of oil that naturally seeps into the Gulf; what did or didn’t happen with the way the oil dispersed after the riser was removed on June 3rd.

Jane Lubchenco, head of NOAA, spoke after the conference and said that indeed, they were both right, “It’s not a contradiction to say that most of the oil is gone but some still lingers out there.”

(Her conference was actually an announcement of the next step of restoration in the Gulf– you can read more about that here.)

But remember, the press conference was supposed to be on “Deepwater Drilling: Worth the Risk?” Rao did address this issue. He thinks it’s worth it if there were better support onshore for these deepwater wells– with real time data available to experts and regulators, who would be perhaps monitoring several wells at the same time.

Lubchenco was not so certain it was worth the risk, “We must further evaluate the trade-off.”

Two smart reporters, trying to steer the original press conference back on course, asked Hazen if the oil-eating (and Gulf-saving) microbes were present near other sites of deepwater drilling. Some of the bacteria are found in the Arctic, and possibly the Atlantic, as well, Hazen said.

What do you think? Worth the risk? Oil there or gone? Share your thoughts.

(To learn more, you can check out the recent report on the monitoring of the Gulf or Samantha Joye’s blog. Science News also posted an interview with Joye over the weekend.)