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The Gut(microbe)less Gribble – Biofuel Hero?

Behold the Gribble – a true gutless wonder. The Gribble (pictured here) is a marine wood-boring creature of around 2 millimeters in size. Scientists at the UK’s Biotechnology and Biological Sciences Research Council have been spending quality time with the Gribble because of its exceptional innards.

The Gribble lives in the sea and eats wood. Image: Laura Michie, University of Portsmouth

The Gribble lives in the sea and eats wood. Image: Laura Michie, University of Portsmouth

The tiny animal eats wood that finds its way into the sea. The wood can come from mangrove swamps or wash into estuaries from land. Gribbles, also called ship borers, have also been known to chow on wooden sailing vessels (including, rather famously, those of the Columbus voyages). “I’m sure they’ve taken down a few pirate ships, too” says Simon J McQueen-Mason a BBSRC researcher and materials biology professor at the University of York.

Most critters that eat wood or other lignocellulose plant material rely on symbiotic relationships with a diverse population of gut microbes – called the microbiome – to break down the tough-to-digest meal. When news reports suggest that pandas may hold the key to biofuels breakthroughs because they can live on tough bamboo, it’s really the microbes, and the enzymes made by the microbes, that are of interest.

(You can read a C&EN cover story about pandas, microbiomes and biofuels )

But the Gribble has no microbiome. And it doesn’t have the squishy, absorptive digestive system that most animals have. In fact, it digests its meals of wood in a sterile, hard-sided chamber in its hind gut. McQueen-Mason likens the environment to “a steel container you might use in an industrial lab.”

Instead of microbial helpers, the gribble has a separate organ where it produces the key enzyme itself. Termites do not do this (they have microbes). The gribble “must use quite aggressive chemistry; the enzyme is so harsh that it would kill any microbes” that might otherwise occupy the space, McQueen-Mason says.

The research team found the mystery organ and looked at the genes expressed there. Many of them encoded instructions for making what is called GH7 cellulase. This is a family of enzymes that are normally found in wood-degrading fungi. “These cellulases are abundant but were never reported in an animal before,” McQueen-Mason notes. “We were able to express the genes in a lab fungus and describe the properties.”

They also used X-ray crystallography to discover the structure of the enzyme and show how it binds cellulose chains and breaks them into small sugar molecules.

The GH7 cellulase, an enzyme made by the Gribble, breaks down cellulose into simpler sugars.

The GH7 cellulase, an enzyme made by the Gribble, breaks down cellulose into simpler sugars.

The Gribble’s enzyme appears to be very rugged and long-lasting, which is a good quality for an enzyme that might be used in an industrial setting to make biofuels from wood or straw, McQueen-Mason points out. It works very well in highly saline conditions and may also function well in ionic liquids. The use of salt water and ionic liquids for biofuels processing may cut down on the use of expensive, precious fresh water. And like a true catalyst, the enzyme may be reusable.
You can see a video of the Gribble  – which I highly recommend – it’s kind of cute.

For more on the enzyme, check out the journal paper: ‘Structural characterization of the first marine animal Family 7 cellobiohydrolase suggests a mechanism of cellulase salt tolerance’ www.pnas.org/cgi/doi/10.1073/pnas.1301502110.

Our Favorite Toxic Chemical: Nitrate

Today’s post is from guest blogger Melissae Fellet, a science writer based in Santa Cruz, California, and was written for the “Our Favorite Toxic Chemicals” blog carnival hosted by Sciencegeist.

Feeding my vegetable garden so it will feed me

I’m eager to grow some of my own food this summer, so I planted a vegetable garden in pots on my porch. Since my previous gardening experience consists of ignoring my plants, learning some gardening tips was a must.

I hope my plants look this healthy in a few weeks! (Image by flickr user despi88)

Like humans, plants need food, too. Those nutrients come from boosts of nitrogen, phosphorus and potassium-containing fertilizer. But plants need help getting their roots on some nutritious nitrogen when that fertilizer contains kelp, alfalfa, crushed bones, chicken poop and ground feathers, like the organic stuff I put in my garden.

Some of those ingredients contain nitrogen as ammonia, which plants can absorb directly. Proteins are another source of nitrogen. Bacteria in the soil separate proteins into amino acids. Other microbes chomp the nitrogen off the amino acids as ammonia. And super-specialized bacteria eat ammonia and release the nitrogen as nitrate (NO3-). Nitrate is great plant food, too, because it zips through the soil straight to a plant’s roots.

This biological nitrogen transformation is slow, so farmers may feed their plants a nitrate-containing fertilizer to speed growth. That’s a touchy subject in the agricultural areas near my home in California.

About 10 percent of 2500 public water wells tested in the Tulare Valley and Salinas Valley exceed the state limits of 45 mg nitrate per liter of water, according to a report prepared for the state water department last March. The majority of the nitrate in groundwater — about 96% — washes off cropland, the report found.

Nitrate takes time to trickle from a field into the groundwater, so most of that contamination is due to decades of past farming in the area. But if the nutrient pollution trend continues, 80% of the people living in those valleys could be drinking nitrate-laden water by 2050.

Nitrate becomes harmful when our bodies convert it to its chemical cousin, nitrite (NO2-). Nitrite transforms the iron in our blood so that it can no longer carry oxygen. Enough altered iron — 10 percent of the hemoglobin in your blood — causes breathing troubles especially in infants and pregnant women. Higher concentrations can lead to suffocation.

Still, it takes a lot of nitrate to harm a person. According to data from the World Health Organization [PDF], an average three-month old baby boy might have to drink about four liters of water contaminated with nitrate at twice the state limit to induce toxicity. An adult might drink up to 56 liters of the same water at once to get a fatal dose of nitrate.

Excess nitrate can be toxic to the environment, too. The nutrient washes into a Central Coast wetland, feeding microscopic algae until they grow into thick green mats that suffocate ponds and channels.

The UC Davis report says that fertilizer fees and improved groundwater monitoring can help protect drinking water. And policy changes are in the works for one part of the state. In March, the Central Coast Regional Water Control Board passed regulations to reduce nitrate-containing runoff from fields. These rules took three years to negotiate and they are still tangled in a lawsuit from growers.

Even without regulations, farmers can prevent nitrogen pollution by controlling the amount of fertilizer on the fields and feeding plants only what they can absorb. The state report also suggests using nitrate-laden ground water for irrigation. Plants absorb the nitrate from the water, and clean water returns to the aquifer.

Lacking a home nitrate test kit for my garden, I’ll choose organic fertilizer when it comes time to feed my plants again. That should give my plants a slow drip of nitrogen and hopefully prevent a build up of excess nutrients. I feed my plants nitrogen so they’ll be strong and healthy enough to produce food for me.

Bring on the orange carrots, yellow peppers and purple beans!

Hidden Chemistry at Solar Biggie BrightSource

We don’t have too many rules here in C&EN blogville, but we do try to maintain a chemistry connection.  I was worried that would be at risk if I were to post about BrightSource Energy, a mega solar tech firm that has filed for a $250 million IPO.

BrightSource Energy's solar mirrors. Credit: BrightSource

To generate energy from the sun, BrightSource puts thousands of big mirrors in the desert that track the sun and focus light on a tower with a boiler full of water. The steam generated cranks a turbine to create electricity. It sounds like what a technology firm would think up if someone forgot to invite a chemist or chemical engineer to the concept meeting.  [Note that in contrast, other solar thermal companies use nifty heat-transfer fluids like biphenyl and diphenyl oxide, as described by my colleague Alex Tullo.]

But there are at least two innovative uses of chemistry in the BrightSource system, one is basic CRC handbook stuff and one is rather mysterious. To extend the hours during which the water can be turned into steam, BrightSource is working to store some of the sun’s heat  in a blend of molten nitrate salts (sodium nitrate and potassium nitrate). To save you the Googling, the melting point of sodium nitrate is 308 C and potassium nitrate is 334 C. For some reason this nice detail is in the firm’s S1 filing but I did not see it on the website.

The more mysterious chemistry is alluded to on the company’s website. As you can imagine, the boiler tower has to withstand some unusual conditions. But worry not, because, “The boiler is designed to withstand the rigors of the daily cycling required in a solar power plant over the course of its lifetime, and is treated with a proprietary solar-absorptive coating

to ensure that maximum solar energy is absorbed in the steam. [emphasis mine]. Hmmmmm…. I wonder what is in that coating? Tell me what you think.

Gulf Clean-up: Breaking down oil with surfactants

Cleantech Chemistry will save for later the discussion of whether the environmental disaster in the Gulf of Mexico will put more attention on replacing petroleum in the U.S. economy. But in the meantime it is interesting to note the contribution that chemistry is making to clean-up efforts.

Water treatment firm Nalco released a statement confirming that it is supplying quantities of oil dispersants for the Gulf operation, but did not elaborate on how much of it the company was selling. Nevertheless, the announcement prompted Nalco’s stock to rise 18% to $29.25, hitting its highest point since October 2007. In the press release, Nalco thanks its suppliers for stepping up to the plate, which suggests the company is selling its dispersant as fast as it can be manufactured.

Though Nalco has not yet responded to a request for an interview, the company’s website describes its Corexit dispersant technology as designed specifically to protect and clean shorelines affected by oil spills at sea. The product is made with bio-degradable surfactants in a low-toxicity, de-aromatized hydrocarbon solvent system.

If the chemical dispersant works as designed, the solvent system distributes the surfactants into the oil slick. Then the surfactants go to work reducing the surface tension at the oil/water interface. With the oil film’s cohesion lessened, the action of the waves helps to break up the slick into small droplets of oil. The small drops sink from the surface of the sea and are further degraded by the ocean’s native bacteria.

BP CEO Tony Hayward has been reported as claiming the dispersants have had a significant impact keeping the oil from floating to the surface, but there is very little detail available about how successful the chemical treatment has been so far.

In addition to  Nalco, other producers of dispersants include BP, Croda, Dasic International, INEOS Chemical, Shell, Taiho, Total, and U.S. Polychemical, writes Laurence Alexander, chemicals analyst at Jefferies & Company. Alexander has been tracking reports that the operation is requiring around 10,000 gallons of dispersants a day.