The El Yunque National Forest in Puerto Rico is a tropical rainforest where a strain of the microbe Enterobacter lignolyticus was found that can tolerate an ionic liquid used to dissolve cellulosic biomass for microbial-based biofuel production. (Credit: Photo by Kristen DeAngelis)

In the search for technology by which economically competitive biofuels can be produced from cellulosic biomass, the combination of sugar-fermenting microbes and ionic liquid solvents looks to be a winner save for one major problem: the ionic liquids used to make cellulosic biomass more digestible for microbes can also be toxic to them. A solution to this conundrum, however, may be in the offing.

Researchers with the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI), a multi-institutional partnership led by Berkeley Lab, have identified a tropical rainforest microbe that can endure relatively high concentrations of an ionic liquid used to dissolve cellulosic biomass. The researchers have also determined how the microbe is able to do this, a discovery that holds broad implications beyond the production of advanced biofuels.

“Our findings represent an important first step in understanding the mechanisms of ionic liquid resistance in bacteria and provide a basis for engineering ionic liquid tolerance into strains of fuel-producing microbes for a more efficient biofuel production process,” says Blake Simmons, a chemical engineer who heads JBEI’s Deconstruction Division and one of the senior investigators for this research.

Adds Michael Thelen, the principal investigator and a member of JBEI’s Deconstruction Division, “Our study also demonstrates that vigorous efforts to discover and analyze the unique properties of microorganisms can provide an important basis for understanding microbial stress and adaptation responses to anthropogenic chemicals used in industry.”

Thelen is the corresponding author and Simmons a co-author of a paper reporting the results of this research in the Proceedings of the National Academy of Sciences (PNAS). Other co-authors are Jane Khudyakov, Patrik D’haeseleer, Sharon Borglin, Kristen DeAngelis, Hannah Wooa, Erika Lindquist and Terry Hazen.

The burning of fossil fuels releases nearly 9 billion metric tons of excess carbon into the atmosphere each year. Meanwhile the global demand for gasoline and other petroleum-based fuels continues to rise. Clean, green and renewable fuels that won’t add excess carbon to the atmosphere are sorely needed. Among the best candidates are advanced biofuels synthesized from the cellulosic biomass in non-food plants. Such fuels could displace petroleum-based fuels on a gallon-for-gallon basis and be incorporated into today’s vehicles and infrastructures with no impact on performance.

To this end, researchers at JBEI have already engineered a strain of E. coli bacteria to digest the cellulosic biomass of switchgrass, a perennial grass that thrives on land not suitable for food crops, and convert its sugars into biofuel replacements for gasoline, diesel and jet fuels. A key to this success was the pretreatment of the switchgrass with an ionic liquid to dissolve it.

“Unlike the starch sugars in grains, the complex polysaccharides in cellulosic biomass are semicrystalline and deeply embedded within a tough woody material called lignin,” Simmons says. “Lignin can be removed and cellulose crystallinity can be reduced if the biomass is pretreated with ionic liquids, environmentally benign organic salts often used as green chemistry substitutes for volatile organic solvents.”

Current strategies for processing cellulosic biomass into biofuels involve multiple production steps in which the bulk of ionic liquids used to pretreat biomass can be washed out before the microbes are added. However, to cut production costs, a “one pot” strategy in which processing steps take place in a single vat would be highly desirable. This strategy requires microbes that can tolerate and grow in ionic liquids used to pretreat cellulosic biomass.

In search of such microbes, a team of JBEI researchers led by microbiologist and PNAS paper co-author Kristen DeAngelis ventured into the El Yunque National Forest in Puerto Rico, a tropical rain forest where microbial communities have demonstrated exceptionally high rates of biomass decomposition, and a tolerance to high osmotic pressures of the sort generated by exposure to ionic liquids. They returned with a prime candidate in the SCF1 strain of Enterobacter lignolyticus.

“We first determined that the SCF1 strain of Enterobacter lignolyticus grows in the presence of the ionic liquid [C2mim]Cl at concentrations comparable to the concentrations that remain in the cellulose after pretreatment and recovery,” Thelen says. “Next, through a combination of phenotypic growth assays, phospholipid fatty acid analysis, and RNA sequencing technologies, we investigated the mechanisms by which SCF1 tolerates this ionic liquid.”

Working in collaboration with researchers at DOE’s Joint Genome Institute, another multi-institutional partnership led by Berkeley Lab, Thelen and Simmons and their JBEI colleagues developed a preliminary model of ionic liquid tolerance for SCF1.

“Our model suggests that SCF1 bacteria resist the toxic effect of the [C2mim]Cl ionic liquid by altering the permeability of their cell membrane and pumping the toxic chemical out of the cell before damage occurs,” Thelen says. “These detoxifying mechanisms are known to be involved in bacterial responses to stress, but not in a coordinated manner as we have shown for the response of SCF1 to ionic liquid.”

Thelen says the information gained from this study will be used at JBEI to help engineer new fuel-producing microbes that can tolerate ionic liquid pretreatments. Beyond biofuels, the techniques developed in this study should also be applicable to the screening of microbial responses to other chemical compounds, such as antibiotics.

This work was supported by the DOE Office of Science.

Blake Simmons, in addition to his JBEI appointment, is also a scientist with the Sandia National Laboratories. Michael Thelen, in addition to his JBEI appointment, is also a scientist with the Lawrence Livermore National Laboratory.

via Rainforest microbe can handle ionic liquids: New find could help reduce biofuel production costs.

Having large tracts of natural habitat surrounding fields increase ladybug populations and help farmers reduce insecticide use. (Credit: G.L. Kohuth)

Ladybugs and other predatory insects eat crop pests, saving farmers an estimated $4.6 billion a year on insecticides. Non-crop plants provide these predatory insects with food and shelter, helping them to survive and thrive in areas where they are needed. In an attempt to increase benefits from predatory insects, researchers have often planted strips of flowers along the edges of crop fields.

However, natural habitats also provide vital food and shelter resources and may be more important for pest control, said Megan Woltz, MSU doctoral student and co-author of the study that appears in the current issue of Agriculture, Ecosystems and Environment.

“Creating predator-attracting habitats next to crops is only a partial solution,” said Woltz, who co-authored the study with MSU entomologists Doug Landis and Rufus Isaacs. “Ladybugs and many other pest-eating insects travel long distances throughout the growing season, sometimes flying or crawling over many miles as they search for food and shelter. So we also have to consider what resources are available to these predators at larger scales.”

Ladybugs are heralded as a natural, effective killer of soybean aphids, the most-destructive soybean pest in the northern United States. To determine the best way to attract ladybugs to soybean fields, researchers planted buckwheat strips next to soybean fields and also examined the amount of natural habitat within 1.5 miles of the fields.

“Ladybugs loved our buckwheat strips,” Woltz said. “We always found way more ladybugs in the buckwheat than are usually in field edges. Unfortunately, all of the ladybugs in the buckwheat did little to change their populations in the soybean fields.”

Ultimately, natural habitat proved to be more important. The amount of grasslands and forests within 1.5 miles of the soybean fields determined how many ladybugs ended up in the field, she added.

Such large areas typically encompass multiple farms, suggesting that rural neighbors may need to work together. In other studies, landscapes with at least 20 percent of non-crop habitat showed good pest control. Providing some habitat on every farm and the properties that surround them would add up to a lot of habitat at the landscape scale — the scale that matters to ladybugs.

via Increasing predator-friendly land can help farmers reduce costs.

Image from bagitmovie.wordpress.com

A 100-fold upsurge in human-produced plastic garbage in the ocean is altering habitats in the marine environment, according to a new study led by a graduate student researcher at Scripps Institution of Oceanography at UC San Diego.

In 2009 an ambitious group of graduate students led the Scripps Environmental Accumulation of Plastic Expedition (SEAPLEX) to the North Pacific Ocean Subtropical Gyre aboard the Scripps research vessel New Horizon. During the voyage the researchers, who concentrated their studies a thousand miles west of California, documented an alarming amount of human-generated trash, mostly broken down bits of plastic the size of a fingernail floating across thousands of miles of open ocean.

At the time the researchers didn’t have a clear idea of how such trash might be impacting the ocean environment, but a new study published in the May 9 online issue of the journal Biology Letters reveals that plastic debris in the area popularly known as the “Great Pacific Garbage Patch” has increased by 100 times over in the past 40 years, leading to changes in the natural habitat of animals such as the marine insect Halobates sericeus. These “sea skaters” or “water striders”—relatives of pond water skaters—inhabit water surfaces and lay their eggs on flotsam (floating objects). Naturally existing surfaces for their eggs include, for example: seashells, seabird feathers, tar lumps and pumice. In the new study researchers found that sea skaters have exploited the influx of plastic garbage as new surfaces for their eggs. This has led to a rise in the insect’s egg densities in the North Pacific Subtropical Gyre.

Such an increase, documented for the first time in a marine invertebrate (animal without a backbone) in the open ocean, may have consequences for animals across the marine food web, such as crabs that prey on sea skaters and their eggs.

“This paper shows a dramatic increase in plastic over a relatively short time period and the effect it’s having on a common North Pacific Gyre invertebrate,” said Scripps graduate student Miriam Goldstein, lead author of the study and chief scientist of SEAPLEX, a UC Ship Funds-supported voyage. “We’re seeing changes in this marine insect that can be directly attributed to the plastic.”

The new study follows a report published last year by Scripps researchers in the journal Marine Ecology Progress Series showing that nine percent of the fish collected during SEAPLEX contained plastic waste in their stomachs. That study estimated that fish in the intermediate ocean depths of the North Pacific Ocean ingest plastic at a rate of roughly 12,000 to 24,000 tons per year.

The Goldstein et al. study compared changes in small plastic abundance between 1972-1987 and 1999-2010 by using historical samples from the Scripps Pelagic Invertebrate Collection and data from SEAPLEX, a NOAA Ship Okeanos Explorer cruise in 2010, information from the Algalita Marine Research Foundation as well as various published papers.

In April, researchers with the Instituto Oceanográfico in Brazil published a report that eggs of Halobates micans, another species of sea skater, were found on many plastic bits in the South Atlantic off Brazil.

“Plastic only became widespread in late ’40s and early ’50s, but now everyone uses it and over a 40-year range we’ve seen a dramatic increase in ocean plastic,” said Goldstein. “Historically we have not been very good at stopping plastic from getting into the ocean so hopefully in the future we can do better.”

via Plastic trash altering ocean habitats, Scripps study shows.

The coop is made up of two 4′ by 8′ pallets, a salvaged tin roof purchased at a flea market, assorted lumber, and shingles made from empty beer cans. Matt bought the chicken wire and the latches for the gates, and spent less than $40 on the whole shebang, which he built in less than ten hours.

Follow the link for pix and more.

via Homemade Chicken Coop with Beer Can Shingles Was Built in 10 Hours for $40 : TreeHugger.

via Sleepy Brains Think More Freely: Scientific American.

I shot this video as part of a larger project for Seely Family Farm in Clatskanie, Oregon. You can get their real-peppermint mint confections at Whole Foods and other stores that sell real food.

We are people. People eat. And even though we go to the grocery store all the time, I never really stop to look at how many different foods exist (acknowledging, of course, that so much of it is the same: modified corn). That is, until my aunt and I took a pit stop at Safeway last night. While browsing through gefilte fish, she inspired me to start What does it taste like Wednesday. No, it isn’t about the flavor of the actual week day, but instead the opportunity to embrace delicious, odd, never- before-tasted-in-my-life “cuisine.” Two rules: 1) I can’t have eaten or remember ever eating the item. 2) No purchases over $5.

Her first foray was into something called “DONA MARIA, NOPALITOS TENDER CACTUS”:

After duking it out with can openers, oven mitts and finally a corkscrew, I popped open the yellow lid to smell vinegar and what I think would be okay to describe here as tangy. What does it taste like? Like a light kick to the back of my throat leaving a lingering spice–like the tequila of edible plants. A crossbreed between a pickle and a hot pepper in the texture and shape of the green bean and length of a worm… And like many things in life, once you get through the spikes, it isn’t so bad.

Great pics, too!