Substituting for Crude Oil: Bio-Feedstocks to Petrochemicals

One of the main themes of the Al Fin Energy blog is the development of substitute and alternative feedstocks to use in place of crude oil, in the production of fuels, high value chemicals, polymers, lubricants, fertilisers, and more.

For example, RheTech Inc. is developing a new high volume composite material derived from sugar cane feedstock, which will replace oil derived materials in automobiles, construction, and consumer products:

RheTech, Inc. has developed a new grade of biocomposite using sugarcane-based, high-density polyethylene supplied by Braskem, the largest thermoplastic resins producer in the Americas and a leader in biopolymers. The new grade adds to RheTech’s line of RheVision biocomposites for application in the automotive, consumer and construction industries.

... Braskem is the Americas’ top thermoplastic resins producer. With 35 industrial plants spread across Brazil, United States and Germany, the company produces more than 35 billion pounds of thermoplastic resins and other petrochemicals per year. Braskem is also the world’s leading biopolymers producer with its 440 million pound Green PE plant that produces polyethylene from sugarcane-based ethanol.

RheTech, Inc. is a leading producer of filled and reinforced polypropylenes and color concentrates and additives for the automotive, truck, electronics, construction, and consumer markets. RheVision is a line of bio-reinforced polyolefins that currently uses wood, rice hull, flax, agave and coconut shell waste as reinforcement. _GCC

Substitution of alternative materials in place of crude oil, frees up more crude oil for global oil markets. Another example from the US DOE's NREL:

Scientists at the US Department of Energy’s National Renewable Energy Laboratory (NREL) have developed a new photo-biological process for the sustained production of ethylene from CO2. The NREL team introduced a modified gene sequence encoding an ethylene-forming enzyme from Pseudomonas syringae pv. into a cyanobacterium—Synechocystis sp. PCC 6803—and demonstrated that the organism remained stable through at least four generations, producing ethylene gas that could be easily captured. Research results were published in the RSC journal Energy & Environmental Science.

Ethylene—a valuable commodity two-carbon chemical that can be oligomerized into transportation fuels—is the most widely produced petrochemical feedstock globally. The organism produced ethylene at a high rate and is still being improved. The laboratory demonstrated rate of 171 milligrams of ethylene per liter per day is greater than the rates reported for the photosynthetic production by microorganisms of ethanol, butanol or other algae biofuels. _GCC

Most crude oil being used today was originally created by micro-organisms, over geologic time scales. Humans are merely attempting to optimise microbes for much quicker, high volume production of fuels, high value chemicals, and other materials, so as to turn hydrocarbons into renewable chemicals and fuels, rather than "fossil fuels."

Neste Turns to Microbial Oil for Diesel & Aviation Fuel

GCC

Engineered microbes are capable of rapid exponential reproduction, and subsequent industrial-scale production of chemicals, fuels, pharmaceuticals, and more. The energy and feedstock needs of such microbes can be supplied by biomass-derived sugars, which are becoming more economical every year due to scientific progress in microbial engineering.

Neste Oil has completed the first phase of its project to build a pilot plant for producing microbial oil for use as a feedstock for NExBTL renewable diesel. Construction of the plant is on-schedule and on-budget. (Earlier post.) The first phase will enable the growth of oil-producing micro-organisms, and the following phases will concentrate on raw material pretreatment and oil recovery.

The technology is designed to produce feedstock for NExBTL renewable diesel by using yeast and fungi to convert sugars from waste and residues into oil highly efficiently. It utilizes bioreactors similar to those used in the biotech and brewing industries. Commercial-scale production is expected by 2015 at the earliest.

A wide range of different waste and residue materials can be used, such as straw and sidestreams from the pulp and paper industry, which makes feedstock optimization possible.

....Microbial oil technology represents an attractive option, both because of its efficiency and its sustainability. A number of partners have been involved in this work, including Aalto University. Neste Oil has been working on R&D in this area with Aalto University since 2007, and applied for various patents for technology that can produce microbial oil from waste using fungi in 2010. _GCC

More at the link.

Neste Oil has been one of the leaders in advanced biofuel and renewable diesel production. Up until now the profitability in this area has not been particularly high, but the numbers are improving with every new bioscientific breakthrough.

But in mainstream energy economics, the deluge of energy from tight oil & gas has altered the timetable for many advanced biofuels projects. It is likely that many of of the scheduled projects of Neste Oil and other companies, will be delayed -- in terms of actually coming to market.

Shortcuts to Custom Bio Production of Fuels and Chemicals

A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression.

Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism. _NatureCommunications

Nature Communications 3, Article number: 929 doi:10.1038/ncomms1928

UCSD researchers have taken an important step toward the ability to custom design the genome of organisms in order to produce synthetic fuels, chemicals, pharmaceuticals, and more, on a commercial scale.

"What you could hypothetically do with our model is simulate the total cost of producing a value-added product, such as a biofuel. That includes all the operating and maintenance costs," said Daniel Hyduke, a project scientist in Palsson's lab. Hyduke said the method has the potential to help streamline industrial metabolic engineering efforts by providing a near complete accounting of the minimal material and energy costs associated with novel strain designs for biofuel, commodity chemicals, and recombinant protein production.

Hyduke and Lerman prototyped the method on the minimal, yet metabolically versatile, hyperthermophile Thermotoga maritima. Because T. maritima is not currently ready for use in industrial applications, Hyduke and Lerman are working as part of a larger team to produce similar models for industrially relevant microorganisms, such as E. coli.

"We've built a virtual reality simulator of metabolism and gene expression for Thermotoga maritima, and shown that it much better approximates phenotypes of cells than modeling metabolism in isolation," said Lerman.

...Their method accounts, in molecular detail, for the material and energy required to keep a cell growing, the research team reported in the journal Nature Communications.

"This is a major advance in genome-scale analysis that accounts for the fundamental biological process of gene expression and notably expands the number of cellular phenotypes that we can compute," said Bernhard Palsson, Galetti Professor of Bioengineering, at the UC San Diego Jacobs School of Engineering.

"With this new method, it is now possible to perform computer simulations of systems-level molecular biology to formulate questions about fundamental life processes, the cellular impacts of genetic manipulation or to quantitatively analyze gene expression data," said Joshua Lerman, a Ph.D. candidate in Palsson's Systems Biology Research Group. _SD

This approach provides more useful information in advance, to researchers considering various approaches to the design of custom chemicals-producing organisms -- particularly microbes, but eventually plants and animals as well.

In summary, the development of this tool should streamline the design and development of organisms capable of producing commercially valuable chemicals and fuels in an economical manner. It should also prevent much wasted energy on the part of researchers, by pointing out dead-end research approaches in advance.

A World Bathed in the Glow of Bacterial Light

Scientists are becoming more clever at manipulating microbes to perform basic tasks. In this story, bacteria were taught to glow in synchrony, with the aim of creating microbial sensors to detect toxic gases. Similar technologies will soon be used to tweak microbes into producing valuable chemicals and fuels, and much more.

UCSD scientists have trained E. Coli bacteria to glow in synchrony, like a light chorus. The synchrony arises when colonies of bacteria on microfluidic chips communicate via gas channels. More:

Their achievement, detailed in this week’s advance online issue of the journal Nature, involved attaching a fluorescent protein to the biological clocks of the bacteria, synchronizing the clocks of the thousands of bacteria within a colony, then synchronizing thousands of the blinking bacterial colonies to glow on and off in unison.

...Using the same method to create the flashing signs, the researchers engineered a simple bacterial sensor capable of detecting low levels of arsenic. In this biological sensor, decreases in the frequency of the oscillations of the cells’ blinking pattern indicate the presence and amount of the arsenic poison.

Because bacteria are sensitive to many kinds of environmental pollutants and organisms, the scientists believe this approach could be also used to design low cost bacterial biosensors capable of detecting an array of heavy metal pollutants and disease-causing organisms. And because the senor is composed of living organisms, it can respond to changes in the presence or amount of the toxins over time unlike many chemical sensors.

...Hasty said he believes that within five years, a small hand-held sensor could be developed that would take readings of the oscillations from the bacteria on disposable microfluidic chips to determine the presence and concentrations of various toxic substances and disease-causing organisms in the field. _UCSD

"This development illustrates how basic, quantitative knowledge of cellular circuitry can be applied to the new discipline of synthetic biology," said James Anderson at the National Institutes of Health’s National Institute of General Medical Sciences, in a university statement.

The new chips can be used for the production of biochemicals, tissue engineering, and biosensors that continually monitor the environment, rather than offer a one-off test that must be replaced every time new readings are needed. Besides the obvious practical uses, the sensors offer good aesthetics: The new "biopixels" come in beautiful shades of blue. _FastCoexist

Imagine if all the microbes in the world were to glow in the dark. Should that happen, humans might begin to comprehend the real inhabitants of Earth, in terms of number and mass. At that point, these slightly advanced apes might begin to understand the promise of bio-technologies.

A Fruitful Collaboration Between Industry and University in Montana

Blue Marble Agate
Blue Marble Energy (BME) moved from Seattle to Missoula, Montana, in order to be close to its collaboration with the University of Montana. Together, UM and BME are working to solve a number of mundane but important problems that occur where energy, chemistry, economics, and the environment overlap.

Two geoscience faculty members at The University of Montana (UM) have started a partnership with Blue Marble Biomaterials to produce commercial products from algal biomass.

Potential products include organic fertilizers, natural pigments, food flavorings, fatty acids for biofuels, cholesterol-reducing compounds for food additives, and natural anti-inflammatory and anti-cancer drugs. Natural inputs and nontoxic production methods will give potential products a competitive advantage over similar products produced from petroleum and other nonrenewable sources.

...Stephens says UM’s favorable attitude toward industry partnerships was one factor in the decision to move the company from Seattle to Missoula in 2010.

Partnering with UM is key to our research and development program. Innovation happens at the nexus of science and market opportunity. This partnership combines Blue Marble’s expertise in chemistry, microbiology and industrial manufacturing with the University’s excellence in research methodology, geoscience and biology. By combining these strengths, we are able to take advantage of an existing market opportunity.

—James Stephens

Blank notes that such industry partnerships also offer educational opportunities for UM students. Since 2010 Blue Marble has hired six UM graduates, including four students from the College of Technology. Currently, Blue Marble hosts five interns from UM who gain broad experience in biology, chemistry, engineering and business operations. _GCC

Earlier article on BME

Blue Marble Energy’s AGATE (Acid, Gas, and Ammonia Targeted Extraction) technology utilizes modified anaerobic fermentation (like brewing beer) and non-GMO bacterial consortia to produce biochemicals, biomethane, biohydrogen, and nitrogen compounds. BME scientists encourage bacterial conjugation between select strains that specialize in the breakdown of different feedstocks. The conditioning of these consortia creates flexible and resilient bacterial cultures that perform well in high nitrogen environments and can withstand shocks to the system (such as changes in pH, temperature, and feedstock). This allows AGATE to process nearly any organic biomass: food waste, yard waste, spent brewery grain, algae, milfoil, corn silage, etc. AGATE can handle both fresh and wet feedstock, and can be adjusted to meet changing economic opportunities and market needs. _BME

This symbiotic multi-microbial approach would seem to be a more versatile way to deal with the conversion of biomass to useful materials and energy, and it reflects on a microbial level the symbiotic collaboration between BME and UM on the macro level.

Important Advances in Fuels & Chemicals from Bacteria, Biomass,

Exciting E. Coli Biorefinery from JBEI

GCC

E. coli bacteria normally cannot grow on switchgrass, but JBEI researchers engineered strains of the bacteria to express several enzymes that enable them to digest cellulose and hemicellulose and use one or the other for growth. These cellulolytic and hemicellulolytic strains of E. coli, which can be combined as co-cultures on a sample of switchgrass, were further engineered with three metabolic pathways that enabled the E. coli to produce the fuel substitute or precursor molecules.

The JEBI team chose to implement pathways that produce alcohols, linear hydrocarbons, or branched-chain hydrocarbons to test the integration of the biomass-consumption pathways with the “extensive” biosynthesis capabilities of E. coli. The team chose:

Biodiesel. Biodiesel can be made by E. coli in vivo in the form of fatty-acid ethyl esters (FAEE). They encoded a six-gene FAEE production pathway on a single plasmid and introduced the construct into a strain of E. coli. Using a co-culture of two strains grown in minimal medium containing 5.5% w∕vol IL-treated switchgrass, they produced 71 ± 43 mg∕L of FAEE. This corresponds to 80% of the estimated yield obtainable with this pathway from the amount of sugars anticipated to be released from 5.5% switchgrass by the Cel and Xyn10B enzymes.

Butanol. Butanol has been proposed as a gasoline replacement because it is fully compatible with existing internal combustion engines. Based in part on previous work, they constructed a heterologous butanol pathway encoded on a single plasmid. A co-culture yielded 28 ± 5 mg∕L butanol from defined rich medium containing 3.3% w∕vol IL-treated switchgrass. A control strain produced 8 ± 2 mg∕L butanol from pretreated switchgrass.

Pinene. The monoterpene pinene is an immediate chemical precursor to a potential jet fuel. The pinene synthesis pathway was encoded on a single plasmid. A co-culture yielded 1.7 ± 0.6 mg∕L pinene from pretreated switchgrass.

The pre-treatment of the switchgrass with ionic liquids was essential to this demonstration, according to Gregory Bokinsky, a post-doctoral researcher with JBEI’s synthetic biology group and lead author of the PNAS paper.

If properly optimized, I suspect you could use ionic liquid pre-treatment on any plant biomass and make it readily digestible by microbes. For us it was the combination of biomass from the ionic liquid pretreatment with the engineered E. coli that enabled our success.

—Gregory Bokinsky

The JBEI researchers also attribute the success of this work to the “unparalleled genetic and metabolic tractability” of E. coli, which over the years has been engineered to produce a wide range of chemical products. However, the researchers believe that the techniques used in this demonstration should also be readily adapted to other microbes. _GCC

Another significant advance from the JBEI is a beefing up of the starch content in switchgrass, which will make conventional fermentation of alcohols from switchgrass much easier.

The team of JBEI researchers, working with researchers at the U.S. Department of Agriculture’s Agricultural Research Service (ARS), has demonstrated that introducing a maize (corn) gene into switchgrass, a highly touted potential feedstock for advanced biofuels, more than doubles (250 percent) the amount of starch in the plant’s cell walls and makes it much easier to extract polysaccharides and convert them into fermentable sugars. _BrianWestenhaus

Amyris is raising the stakes in the biomass-to-chemicals market with a significant acceleration of its Biofene (farnesene) product, via expansion of its partnership with oil giant Total. Farnesene is an important precursor for the production of multiple high value chemicals, including fuels.

Amyris has developed advanced microbial engineering and screening technologies that modify the way microorganisms process sugars. Amyris is using this industrial synthetic biology platform to design microbes, primarily yeast, and use them as living factories in established fermentation processes to convert plant-sourced sugars into renewable chemical and transportation fuel products.

...Amyris is scaling its Biofene production in Brazil, Europe and the United States through various production arrangements; the company signed its sixth production agreement in October...

Farnesene is a 15-carbon isoprenoid hydrocarbon molecule that forms the basis for a wide range of products varying from specialty chemical applications to transportation fuels such as diesel. When used as a fuel precursor, farnesene can be hydrogenated to farnesane, which has a high cetane number (58). Amyris modifies farnesene to become renewable diesel. _GCC

The Ultimate Post-Apocalyptic Energy Source?

There are times when it is best to lower one's expectations. The post-apocalyptic setting might well be such a time. As the incompetent and corrupt governments of the world muddle their way toward global economic collapse, the thoughts of a wise and prudent observer might tend toward a post-apocalyptic energy source. An energy source which does not depend upon armies of engineers, technologists, and craftsmen. A vast source of energy which does not require an exorbitantly expensive high tech infrastructure to realise its potential. Where would one look for such a civ-saving source of power, when the chips are down?

Brian Westenhaus may have hit upon just the thing: The wastewater to hydrogen route, using exoelectrogenic bacteria as your electron source.

“This system could produce hydrogen anyplace that there is wastewater near seawater. It uses no grid electricity and is completely carbon neutral. It is an inexhaustible source of energy.”

Logan with postdoctoral fellow Younggy Kim use microbial electrolysis cells that produce hydrogen for the basis of the development whereas previously to produce hydrogen, the fuel cells required some electrical input.

The study results were published in the Sept. 19 issue of the Proceedings of the National Academy of Sciences. The team concludes the abstract by saying, “These results show that pure hydrogen gas can efficiently be produced from virtually limitless supplies of seawater and river water and biodegradable organic matter.” _BrianWestenhaus

PNAS Abstract

Interesting. All you need is a few simple bacterial electrolysis cells, salt water from the sea, and wastewater. The details might need a bit of ironing out, and the amount of hydrogen available might restrict the ambitions of your nascent new post-apocalyptic civilisation, but the idea has some promise.

More from gizmag:

...researchers at Pennsylvania State University have developed a way to produce hydrogen that uses no grid electricity and is carbon neutral and could be used anyplace that there is wastewater near sea water.

The researchers' work revolves around microbial electrolysis cells (MECs) - a technology related to microbial fuel cells (MFCs), which produce an electric current from the microbial decomposition of organic compounds. MECs partially reverse this process to generate hydrogen (or methane) from organic material but they require the some electrical input to do so.

Instead of relying on the grid to provide the electricity required for their MECs, Bruce E. Logan, Kappe Professor of Environmental Engineering, and postdoctoral fellow Younggy Kim, turned to reverse-electrodialysis (RED). _Gizmag

Advanced Biomass Pyrolysis vs. Advanced Bacterial Fermentation

GCCBiomass to liquid fuels (BTL) conversions will assume increasing importance as the technologies achieve greater yields and economies. Both thermochemical and fermentation approaches are capable of producing high quality substitute fuels and chemical feedstocks. And both technological approaches are receiving a lot of attention as the race for substitute fuels heats up.

UCSB researchers have developed an advanced pyrolytic method of biomass to fuels conversion, using methanol as a super-critical reaction medium.

Researchers at the University of California, Santa Barbara (UCSB) have developed a one-pot process for the catalytic conversions of wood and cellulosic solids to liquid and gaseous products in a reactor operating at 300–320 °C and 160-220 bar. Little or no char is formed during this process.

The reaction medium is supercritical methanol (sc-MeOH) and the catalyst—a copper-doped porous metal oxide—is composed of earth-abundant materials, they report in a paper published in the Journal of the American Chemical Society. The major liquid product is a mixture of C2–C6 aliphatic alcohols and methylated derivatives thereof that are, in principle, suitable for applications as liquid fuels.

There have been two types of approaches conventionally considered for the conversion of woody biomass to liquid fuels, Matson et al. note: (a) acid pretreatment and separation followed by fermentation or liquid phase processing, or (b) high temperature conversion such as gasification or pyrolysis to bio-oils. Each of these process has problems related to their efficiency. _GCC

Meanwhile, dozens of research centers around the world are tweaking the genomes of microbes in the attempt to create self-reproducing factories for the production of high value chemicals and fuels from cheap biomass feedstock.

A new microbe engineering trick could potentially make butanol, a promising biofuel, so cheaply that it could compete with ethanol. By tapping into a highly efficient metabolic pathway, scientists at Rice University engineered E. coli to convert sugars to butanol 10 times more efficiently than any other organism.

...Cobalt Biofuels, a biobutanol startup based in Mountainview, California, uses Clostridium bacteria to break down plant matter and convert the resulting sugars into a mix of butanol, acetone, and ethanol. Gevo, a company based in Englewood, Colorado is working with E. coli that are altered to divert some of their metabolites, which would otherwise be involved in synthesizing amino acids, toward alcohol production. And Butamax, a joint venture between Dupont and BP, is using genetically modified yeast.

...Gonzalez and his colleagues [Rice U.] outlined their new approach in a paper published online in the journal Nature. The researchers tapped into a pathway that microbes use to break down fatty acids, which are hydrocarbon molecules, to generate energy. They modified about a dozen genes in E. coli to reverse this beta-oxidation pathway so that the microbes build fatty acids.

The method is more efficient than others because it adds two carbon atoms at a time, rather than one, to the hydrocarbon molecules being formed. "What makes it really efficient is that the mechanism by which those two carbon atoms are added to the chain doesn't require [energy]," Gonzalez says.

By selectively manipulating genes, the researchers can program the microbes to synthesize many different fuels and chemicals. In addition to butanol, the bacteria can produce various useful fatty acids that existing processes derive from plant and animal oils. _TechnologyReview

Microbial fermentation produces chemicals and fuels at lower temperatures, saving energy. But living organisms are somewhat fragile compared to inorganic catalysts and methods. None of the approaches are ready to compete head to head with the petroleum industry just yet. But things are looking very promising for breakthroughs within the next 5 to 10 years in thermochemical fuels, and the next 10 to 15 years for advanced microbial fermentation, according to Al Fin analysts.

Direct Biomass to Alcohol: Boosting Yields from Clostridium Thermocellum

The discovery of the gene controlling ethanol production in a microorganism known as “Clostridium thermocellum” will mean that scientists can now experiment with genetically altering biomass plants to produce more ethanol. Current methods to make ethanol from a type of biomass found in switchgrass and agricultural waste require the addition of expensive enzymes to break down the plant’s barriers that guard energy-rich sugars. Scientists, including those at BESC, have been working to develop a more streamlined approach in which tailor-made microorganisms produce their own enzymes that unlock the plant’s sugars and ferment them into ethanol in a single step. Identifying this gene is a key step towards making the first tailor-made microorganism that produces more ethanol. _Energy.gov_via_GCC

Clostridium thermocellum is a promising bacterium capable of direct biomass to alcohol transformation. Oak Ridge National Labs scientists are learning how to make C. thermocellum more tolerant of higher ethanol concentrations, so that it can produce higher concentrations of ethanol. Such improved yields should reduce the overall costs of ethanol, and eventually the same approach will be used to achieve higher yields of other chemicals from biomass.

Ethanol intolerance is an important metric in terms of process economics, and tolerance has often been described as a complex and likely multigenic trait for which complex gene interactions come into play. Here, we resequence the genome of an ethanol-tolerant mutant, show that the tolerant phenotype is primarily due to a mutated bifunctional acetaldehyde-CoA/alcohol dehydrogenase gene (adhE), hypothesize based on structural analysis that cofactor specificity may be affected, and confirm this hypothesis using enzyme assays.

...Future determination of compounds resisted by these strains may reveal the selective pressures that led to evolution of altered cofactor specificity of AdhE and suggest further paths for metabolic engineering of this organism for industrial biofuel production. Finally, the ability to identify and characterize sets of biological components linked to desired phenotypes, such as the mutated AdhE gene in this study, or overexpression of endogenous genes offers the prospect for improved rational design of systems in the future that will be best suited to particular feedstocks and desired processes. _GCC

Another study on the metabolic analysis of C. thermocellum for improved bioethanol production

As mentioned many times here at AFE, the race is on between different approaches to produce high yields of biofuels and high yield chemicals directly from biomass and wastes.

• The above approach involves exhaustive genomic studies of promising organisms, with focused alterations of the genome.
• Another approach involves the attempt to "pack the genome" of a particular microbe with all the enzyme-genes it will need to carry out all the necessary reactions to produce the fuel or chemical from the inexpensive feedstock.
• Yet another approach involves the use of multiple micro-organisms working as a team, either in batch form, in stages, or separated by membranes which are permeable to the chemicals of interest.
• Still another approach will utilise biological enzymes packaged inside protective spheres which allow them to catalyse specific reactions but protect them from potentially harmful compounds in the broth.
• Finally, the use of nanotechnological catalysts, mimics of biological enzymes, is likely to be the ultimate winner of this contest -- given the greater hardiness of non-organic materials to potentially toxic alcohols and chemicals.

Al Fin has often joked about developing a strain of yeast which will let him brew 100 proof beer with a simple homebrew kit. While such an achievement may have to wait a while, if scientists can jazz up a microbe to achieve fermentation yields of 20% or more alcohol from cheap biomass or waste, the cost of biofuels is likely to take a nosedive.

Clever Reversal of Natural Cycle Yields Rapid Synthesis

"Rather than going with the process nature uses to build fatty acids, we reversed the process that it uses to break them apart," Gonzalez said. "It's definitely unconventional, but it makes sense because the routes nature has selected to build fatty acids are very inefficient compared with the reversal of the route it uses to break them apart."

The beta oxidation process is one of biology's most fundamental, Gonzalez said. Species ranging from single-celled bacteria to human beings use beta oxidation to break down fatty acids and generate energy.

In the Nature study, Gonzalez's team reversed the beta oxidation cycle by selectively manipulating about a dozen genes in the bacteria Escherichia coli. They also showed that selective manipulations of particular genes could be used to produce fatty acids of particular lengths, including long-chain molecules like stearic acid and palmitic acid, which have chains of more than a dozen carbon atoms.

"This is not a one-trick pony," Gonzalez said. "We can make many kinds of specialized molecules for many different markets. We can also do this in any organism. Some producers prefer to use industrial organisms other than E. coli, like algae or yeast. _Physorg

Nature abstract Reversed B Oxidation Cycle
Researchers at Rice University have engineered E. Coli bacteria to synthesise bio-butanol using a clever reversal of the natural beta oxidation cycle for fatty acids. By running oxidation enzymes in the reverse direction, the researchers achieved a far more rapid synthesis than was achievable from the normal fatty acid synthesis pathway.

In a biotechnological tour de force, Rice University engineering researchers this week unveiled a new method for rapidly converting simple glucose into biofuels and petrochemical substitutes. In a paper published online in Nature, Rice's team described how it reversed one of the most efficient of all metabolic pathways -- the beta oxidation cycle -- to engineer bacteria that produce biofuel at a breakneck pace.

...Just how fast are Rice's single-celled chemical factories? On a cell-per-cell basis, the bacteria produced the butanol, a biofuel that can be substituted for gasoline in most engines, about 10 times faster than any previously reported organism.

"That's really not even a fair comparison because the other organisms used an expensive, enriched feedstock, and we used the cheapest thing you can imagine, just glucose and mineral salts," said Ramon Gonzalez, associate professor of chemical and biomolecular engineering at Rice and lead co-author of the Nature study. _Physorg

Abstract from Nature

In other bioenergy news, the US DOE has released an updated Billion Ton report on biomass production for fuels. The updated report reaffirms the potential to replace up to 30% (or more) of the US petroleum consumption, using energy and fuels from biomass. The report also describes the best environmental approaches to biomass energy production, which could result in environmental benefits overall.

Once a bioenergy infrastructure has been built, it will be possible for the machinery of bioenergy to run on its own produced energy and fuels.

Microbes such as E. Coli tend to continue dividing as long as conditions allow them to do so. If you think of microbes as reproducing factories of high value products, you may begin to realise that as long as you feed them, provide the proper environment, and carry away their waste -- high value chemicals and fuels -- these little factories will keep producing.

Biomass itself will soon be the cheapest source for sugars, to feed the microbial factories. Other biomass will be used to produce chemicals and fuels via thermochemical methods. Some will be torrefied and mixed with coal, or gasified and the syngas burned with natural gas or by itself -- to produce combined heat and power.

The bottom line is that no scientist, engineer, or agriculturalist has any idea how much biomass the Earth can produce, when given the chance. Micro and macro algae appear to be the highest yielding crops -- capable of growing on over 80% of the planet's surface. But high yielding terrestrial biomass crops are being cooked up every day, along with the means of turning the biomass into sugars. And the microbes -- the microbes are getting a lot more sophisticated in terms of synthesis speed and yields.

As long as we understand that all of these converging efforts are in the pipeline, and should not be expected to replace petroleum right away, things will come together in time.

In the meantime we are floating in hydrocarbons. Time to get away from the dieoff.orgiasts and the carbon hysterics and set to work building a civilisation that feels at home in the larger universe.

LS9 Tests 2nd Generation Microbial Biodiesel in Brazil

Microbial biofuels and renewable chemicals company LS9 is working with Brazilian vehicle manufacturer and engineering firm, MAN Latin America to test LS9's 2nd generation biodiesel product.

LS9 UltraClean Diesel overcomes a number of the challenges of first-generation biodiesel, including high cost of production, poor oxidative stability, and/or poor cold flow. In April 2010, the fuel was officially registered with the United States Environmental Protection Agency (EPA) so it can be sold commercially in the United States.

LS9 modifies the ACP pathway in bacteria to produce renewable hydrocarbon fuels and chemicals with optimized properties, including UltraClean Diesel and surfactants, which LS9 is commercializing with one of its strategic partners, Procter and Gamble. _GCC

French startup Global Bioenergies is moving ahead with its microbial production of isobutene -- an important feedstock for high value chemical production. The product is made from plant sugars.

OPX Biotechnologies is developing the microbial production of renewable bio-acrylic. Acrylic from petroleum is an $8 billion annual market, globally. OPXBio is working with Dow chemical in developing microbially produced fuels and chemicals.

Choren Industries GmbH -- producer of 2nd generation biofuels from wood products via gasification -- has declared insolvency in connection with its German Freiberg plant. The company intends to consult with new investors soon.

A series of biofuel companies have declared insolvency in recent years after the German government changed course on biofuels, taxing the green fuels and scaling back previous incentives. _Reuters _ via _GSS

Choren's difficulties point out the danger of relying upon governmental incentives -- which are always subject to the whims of corrupt and small minded politicians.

Fuels markets are very volatile due to many factors, and newcomers such as biofuels -- lacking the huge infrastructure at all levels which petroleum fuels enjoy -- will have to swim against the current for a number of years yet. The high value chemicals markets, on the other hand, offer a ripe and juicy opportunity for clever and efficient companies in many sectors -- including biotechnology startups and more established industrial entities who wish to partner with renewable chemicals startups.

A. Niger Is an Industrial Slave and Workhorse, Other Microbes

GCC
Aspergillus Niger (A. Niger) is a fungus that contains industrial-strength enzymes capable of transforming much of modern industry. Global markets for potential products from A. Niger are priced well into the $billions. Improved capacity for breaking down polysaccharides into simple sugars alone -- for fermentation fuels and feedstock for sugar fuel cells -- can transform much of the world economy. Microbes have been around for over 3 billion years. They are hard workers with a lot of useful tools in their toolboxes.

A. niger is an industrial workhorse, with different strains efficient in producing polysaccharide-degrading enzymes (particularly amylases, pectinases, and xylanases) or organic acids (mainly citric acid) in high amounts. (As of 2007, the global market for citric acid was estimated to be approximately $1.2 billion with more than 500,000 tons produced annually by fermentation.) The production process involving A. niger is thus a well understood fungal fermentation process. _GCC

Japanese researchers aim to use synthetic biology to re-engineer protists, fungi, algae, and more, to overturn the established energy and industrial order. These scientists at the RIKEN Institute in Japan aim to give the Venter Institute a run for its money.

Most industrial uses of microbes utilise "pure cultures" of specific strains of microbe to avoid "contamination." But symbiotic groupings of microbes in the same reactor -- as well as "staged relays" of microbes using specific sequences of feedstock treatment -- may prove to be far more productive and economic than bioreactors built around isolated, pure strains.

Interestingly, symbiotic "microbial mats" may have been the prototypes for more complexed multi-cellular animals and plants which utilise specialised tissue types. Any industrial engineers contemplating the use of microbes in his industrial processes, would do well to consider the phenomenon of microbial symbiosis.

Joule Unlimited Calculates Cost as Low as $20 a Barrel Diesel

GCC
Joule Unlimited has signed a lease agreement for a site in New Mexico, for production of its Helioculture microbial fuel. As reported here earlier, Joule reckons it can achieve photosynthetic yields sufficient to produce renewable diesel at costs as low as $20 a barrel, when taking subsidies into account. (abstract and link to full text PDF supporting Joule's yield calculations, via GCC)

Joule’s process, called Helioculture, combines an engineered cyanobacterial organism supplemented with a product pathway and secretion system to produce and secrete a fungible alkane diesel product continuously in a SolarConverter designed to efficiently and economically collect and convert photonic energy. The process is closed and uses industrial waste CO2 at concentrations 50–100 times higher than atmospheric.

The diesel process yields long-chain alkanes, the majority component of diesel fuel, as opposed to a low-percentage blendstock like biodiesel. As a result it can immediately drop in to the existing diesel infrastructure with no need for refining or chemical processing.

Joule’s production facilities will employ the next generation of the company’s novel SolarConverter system, which manages the direct, continuous process from photon capture to product synthesis and separation with efficiencies that are up to 50X greater than those of biomass-dependent processes. At full-scale production, Joule expects to deliver diesel and ethanol for as little as $20/bble and $0.60/gallon respectively, including current subsidies. _GCC

It is possible that the theory supports Joule's assertions, but theoretical yields can be different from actual yields. While microbial fuels are likely to provide fuels and high value chemicals for the intermediate to distant futures, in the more near term, biomass approaches using thermochemical and clever fermentation and catalytic processes are likely to capture the field -- in terms of renewable fuels.

Biomass-derived sugars will be far cheaper than sugars from cane or corn (maize). Thermochemical approaches (gasification, pyrolysis, etc) are relatively quick and easy, and when combined with F-T and other advanced catalytic syntheses, can produce significan volumes of high grade fuels and chemicals -- as long as sufficient supplies of biomass are assured.

Joule is one of many microbial (including micro-algae) fuels startups combining world-class research talent with substantial financial backing. But it will take years to learn to get around what are currently seen as iron-clad limitations in yield from photosynthetic approaches. Eventually, they will succeed, and the world will change as a result.

Dyadic Lays Siege to Sugar Market: Sugars from Biomass

The worldwide market for sugars (cane, beets, maize) may exceed $100 billion annually, perhaps half used for food and half used for fuel. But recent achievements by Dyadic International Inc. may change the calculus of the world sugar market in ways impossible to anticipate. Here is more information on Dyadic's new product:

Dyadic International, Inc., a global biotechnology company focused on the discovery, development, manufacture and sale of enzyme and protein products for the bioenergy, industrial enzyme and biopharmaceutical industries, has introduced its most advanced biofuels enzyme, AlternaFuel CMAX. Dyadic says that AlternaFuel CMAX has proven to be effective in converting multiple forms of biomass into fermentable sugars.

Dyadic has developed an integrated technology platform to rapidly discover and express genes of both eukaryotic and prokaryotic origin, then efficiently and inexpensively manufacturing the products of those genes. The company uses a number of proprietary fungal strains to produce enzymes and other biomaterials, principally focused on a system for protein production based on the patented Chrysosporium lucknowense fungus, known as C1. Dyadic has recently completed its scale-up of AlternaFuel CMAX which was derived from Dyadic’s C1 platform technology. _GCC

There is no way of knowing whether Dyadic is "the guy" who will transform world sugar production by making the valuable substances cheaply out of agricultural and forestry waste. Someone will do it, sooner or later. When that happens, the entire economics of cane, beets, and maize will be transformed.

Even if the biomass sugars are not useful for food, the fermentable fuels market is quite likely to explode once the sugar feedstock achieves a relatively low and stable price point. When fed ample sugars of the proper type, microbes will work tirelessly -- producing valuable by-product 24 hours a day while multiplying exponentially.

There is no telling what cheap sugars will do to world markets. But those who continue to waste time (their own and others') fretting about "food vs fuels" will clearly be living in the past long before they are aware of the fact.

Synthetic Biology and the Future

Synthetic biology is one of the six world-changing basic sciences chosen by an expert panel at the US Department of Defense. Other than advanced cognitive science, it is difficult to conceive of any other science or technology which could have greater impact on the human future than synthetic biology.

Jay Keasling wants to use synth-bio to create jet fuel and diesel.

Here is a brief primer on synthetic biology, and a look at the quest for a "genetic transistor."

Here is a look at another ultra-rich investor (besides Khosla) who is investing big in synthetic biology.

A quick look at one of the powerful new tools of synthetic biology.

The sophisticated genetic modification of microbes, plants, and animals is likely to lead to a number of dramatic disruptive products and technologies -- going far beyond alleviating any conceivable fuel shortage.

While the bulk of energy journalists, pundits, and economists seem to be whining and obsessing over a temporary political peak oil accompanying political unrest in third world MENA countries, smarter people are looking past the insignificant speed bumpts toward longer term goals and technologies.

Off-Grid Local Power Generation Using Wastewater & Other Waste

Pilus Energy is converging digester, fermenter, scrubber, and other time-proven technologies into a single solution we call an electrogenic bioreactor (EBR). This transformative technology is the basis of the Pilus Cell™. The EBR harnesses genetically enhanced bacteria and harvests the direct current (DC) electricity, economically important biogases like hydrogen, isoprene, and methane from bacterial metabolism (cellular respiration) of organic molecules. _Pilus

Pilus Energy of Ohio is partnering with Horizon Fuel Cell Technologies of Singapore to provide a sustainable self-contained waste-to-electric power generation platform.

Ohio-based Pilus Energy has announced a strategic relationship with Horizon Fuel Cell Technologies in Singapore, to combine Horizon hydrogen fuel cells with Pilus Energy’s renewable hydrogen production platform.

The partnership will integrate Horizon’s PEM fuel cells with Pilus Energy's platform for renewable hydrogen production, to provide a unique turnkey, end-to-end solution to generate clean power at low cost.

Distributed or localized production of hydrogen can reduce reliance on external hydrogen supplies, and opens up the opportunity for self-sustainable power systems in remote, off-grid locations. Using waste or wastewater as feedstock for distributed bio-hydrogen production also offers a carbon-free solution for both urban and remote environments. _RenewableEnergyFocus

This combination of microbial hydrogen-from-waste plus fuel cell power generation, should allow for sustained power generation without need for relying on an outside source of fuel.

Converting Abundant Glycerol Waste into Useful Chemicals & Fuel

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A research student at U. Alabama Huntsville, is developing the capacity of cell bacterium Clostridium Pasteurianum to convert waste glycerol from biodiesel manaufacture into valuable fuels and chemicals.

A strain of bacteria found in soil is being studied for its ability to convert waste from a promising alternative fuel into several useful materials, including another alternative fuel.

A graduate student at The University of Alabama in Huntsville is developing biological tools to make products from crude glycerol -- a waste material from the production of biodiesel. The research is being funded by the National Science Foundation.

... About 100,000 gallons of glycerol is produced with every million gallons of biodiesel manufactured from animal fats or vegetable oils. (In 2009 more than 500 million gallons of biodiesel were produced in the U.S. while more than 2.75 billion gallons were produced in Europe.)

...The bacteria uses glycerol as a carbohydrate source. From that they produce three alcohol byproducts -- butanol, propanediol and ethanol -- plus acetic acid and butyric acid. Butanol is a particularly interesting byproduct.

"Butanol is a big alcohol molecule, twice as big as ethanol," Venkataramanan said. "You can use it as an industrial solvent and it can be used in cars, replacing gasoline with no modifications. It doesn't have some of the problems you have with ethanol, such as rapid evaporation. And ethanol is a two-carbon molecule, but butanol is a four-carbon molecule so its energy value is much higher. In fact, there are plans to use it for jet fuel.

...In their present form, the bacteria convert about 30 to 35 percent of their gylcerol meals into butanol and another 25 to 30 percent into a chemical used to make plastics. Venkataramanan is looking at different strategies to improve that yield. He is also studying the bacteria's genes to see if a more productive strain can be bioengineered. _Newswise_via_BiofuelsDigest

Similar approaches to microbial chemical synthesis are utilised at massive scale in the pharmaceutical and chemical industries. It is more difficult to produce fuels economically, given the much lower prices for fuels by weight or volume, compared to prices for pharmaceuticals, chemicals, foods, etc.

In Europe, planners are anticipating much higher utilisations of biofuels and sustainable fuels over the next 30 years. After taking a foolish and ruinous detour into wind and solar investments, some of the more intelligent energy analysts and planners of Europe are beginning to sober up and comprehend the gravity of their situation. Others -- particularly lefty-Luddites -- will never learn.

Do Fungal Fuels Foretell Endophytic Future?

Sandia National Lab researchers are zeroing in on production of fuels by endophytic fungi. According to Sandia scientists, the fungi in their lab can break down cellulose directly, and turn it into hydrocarbons.

The fungi grow on cellulose and digest it, forming fuel-type hydrocarbons as a by-product of their metabolic processes. Through genetic manipulation, the Sandia team hopes first to identify these pathways, and then to improve the yield and tailor the molecular structure of the hydrocarbons it produces.

Sandia’s bioscience team is using genetic sequencing to catalog the pathways and other molecular biology techniques to understand how changes in feedstock determine the type and amount of hydrocarbons the fungi make, with a long-term goal of engineering greater quantities of the desirable fuel species.


Meanwhile, Craig Taatjes and John Dec, both engine combustion researchers at Sandia, are experimenting with the main compounds produced by the fungi and are giving feedback to their bioresearch counterparts on the compounds’ ignition chemistry and engine performance. The ideal outcome, Dec said, is to “dial in” the right feedstocks combined with the right set of genes to produce the preferred blend of compounds to go into an engine.

The first step has been to learn what kinds of compounds the fungus makes naturally on its own. “We just don’t know much about some of the compounds, so we need to do research on their ignition chemistry and how they behave in an engine,” Taatjes said. The team, he says, is working with Professor William H. Green at the Massachusetts Institute of Technology to develop an ignition chemistry model that can predict the performance of the classes of compounds made by the fungus.

Hadi and his colleagues are contributing to building up the understanding of the distribution of molecules produced by the various fungi, at which point they can genetically tailor them to produce more of the optimal compounds to suit the needs of engine combustion. _GCC

The scientists and engineers are still working with very small quantities of product, and it will take some time before they will know if the project can be scaled to commercial levels.

Nevertheless, as a research project to expand the boundaries of basic science knowledge of what engineered endophytic fungi can achieve, the approach has potential to seed further projects and perhaps successful industrial ventures.

Endophytes can be injected directly into crops which themselves have been engineered to accept them and provide maximum surface area and biomass for conversion to hydrocarbon -- or any other high value chemical or substance the endophyte's enzymes can produce.

As plants are engineered to grow on marginal soils and to provide higher levels of more convertible biomass, they will provide yet one more piece of the larger interlocking puzzle. For microbial fuels it will take about ten years to proof of feasibility and proof of scalability. Ten more years to scale large enough to capture roughly 10% of the liquid fuels markets -- to microbial fuels alone (not counting alcohols).

Joule Unlimited Scores Loads of Free Publicity!

A synthetic biofuels company from Massachusetts called "Joule Unlimited" has managed to score tons of free publicity in newspapers, blogs, and news services -- without doing much at all! This is public relations at its finest, and the PR people at Joule have to be congratulated.

Joule is involved in the synthetic genomics of cyanobacteria -- having obtained patents to engineer the production of hydrocarbon fuels from bacteria using CO2 and sunlight. But in the news business, most journalists are always asking a potential news focus: "What have you done for me lately?" And in the case of Joule, the answer is "Not much at all."

It all started when the Globe & Mail had a story on Joule a few days ago which erroneously claimed that Joule's miracle bacterium was E. Coli -- after several people notified the paper of their error, they finally corrected it. But not before scores of blogs and other news sources repeated the G&M mistake verbatim. But the Globe & Mail story was about something that happened -- a patent approval -- in September 2010. So why did it take off in January 2011?

A respectable fusion energy forum -- Talk Polywell -- picked the story up, and it then spread. Respected blogger and engineer M. Simon picked up the story from Talk Polywell. Then Instapundit's Glenn Reynolds picked up the story from M. Simon. And from there the story spreads across the blogosphere...

But what has Joule Unlimited actually done lately to merit this new publicity?

Well, they elected John Podesta to their board of directors.

They somehow got dufus Senator John Kerry to call Joule's technology "a game changer."

Then, way back in September 2010 Joule is awarded a patent on its technology

Al Fin analysts can be heard muttering: "Not much progress for all of that free publicity."

Microbial bioenergy is indeed a game changer. But Joule Unlimited is only one of many fine companies with very fine research and development staffs who are working hard to bring large scale microbial fuels to reality. How did Joule's PR department trigger this isolated inflationary bubble of "news?"

Al Fin Energy Institute researchers are not complaining, mind you. Microbial fuels are set to be ready to start scaling up in roughly 10 years. In 20 years, microbial fuels will score at least 10% of the liquid fuels markets in advanced western countries. In 30 years, petroleum companies will be pushed to the wall to keep their costs down low enough to compete.

But premature ejaculations of gee whiz futurism can lead to wide-scale cynicism. In the case of microbial fuels, neither gee-whiz! optimism nor cynical pessimism are warranted. Synthetic genomics is pretty spectacular -- but it takes time to get results. Give it time.

Joule Unlimited patent applications

Proviso: In a fast-changing environment such as industrial synthetic genomics and synthetic fuels, breakthroughs can occur at any time. It is not always in a company's interest to reveal the state of its R&D progress. But all breakthroughs require time to develop into industrial processes, and much more time to scale up to actual commercial and industrial supply systems. As time goes on, we will hear about a lot of breakthroughs. Most of these newsreleases deserve to be taken with a tablespoon of magnesium sulfate and two glasses of water.

Update: Now Brian Wang has picked up the story at NextBigFuture. Brian featured the correct bacterial species in his posting and features some original material from the company's website -- proving once again that Brian's is the best of the technology blogs.

Watching this story getting picked up from site to site provides a dynamic portrait of blogospheric connections. In this case the Globe & Mail writer -- Neil Reynolds, who is one of my favourite mainstream press energy writers -- reported on a company that is no doubt doing some excellent work. But Reynolds was not actually reporting on recent news, he was merely highlighting ongoing work of one particular microbial fuels company. Just one out of many fine companies working on microbial fuels.

Biomass to Jet Fuel Using Microbial Lipid Fermentation

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The US military's DARPA has awarded Logos Technology with a $17.5 million phase 2 award to produce jet fuel from biomass, using microbial lipid fermentation.

This contract is to demonstrate an end-to-end Lipid Fermentation Process (LFP) at scale for the commercially viable production, from cellulosic biomass, of Hydrotreated Renewable Jet (HRJ) spec jet fuel—a near term surrogate for JP-8 that can be readily commercialized.

HRJ is produced from renewable oils (lipids) by methods common in petroleum refining. Fatty acids and triglycerides are hydrotreated to remove oxygen, and the resulting paraffinic hydrocarbons are processed to yield a mixture of straight-chain, branched-chain, and cyclic paraffinic hydrocarbons with collective properties that are similar to those of conventional jet fuel.

Oleaginous yeast can produce lipids from the sugars resulting from the pretreatment and hydrolysis of biomass; certain fungi can also produce lipids, either via solid-state fermentation of biomass or from the biomass hydrolyzate.

This primary program effort is to consist of optimized process development and engineering along with regionally specific economic modeling to produce fuel, demonstrate process energy efficiency and support commercialization.

...This phase of the BioJET program requires the delivery of larger quantities of jet fuel with a projected cost of production of JP-8 at commercial scale implementation (50Mgal/yr) at less than $3.00 per gallon. _GCC

Al Fin bio-synthesists believe that the greatest value of current advanced biofuels research is to put a rough ceiling on future prices of hydrocarbon fuels. Peak oil doomsayers claim that liquid fuels will have no price ceilings when "peak oil" truly hits the fan.

But that claim has already been falsified by the fact that shale gas cost per BTU is well less than half the cost of crude oil per BTU. As efficiencies of conversion from gas to liquids improve, we will see the "price ceiling" effect of shale gas begin to affect markets. Something similar will begin to happen in about ten years, as more efficient biomass to liquids processes begin to scale up.

Like everything associated with energy these days, oil futures markets are heavily politicised, and infiltrated by persons whose behaviour is -- shall we say -- somewhat less than ethical. The fluctuations of oil markets are highly profitable to those who know how to put their fingers on the scale in a reasonably surreptitious manner. But the conversion of alternative and unconventional fuels to liquid hydrocarbons: GTL, CTL, BTL, kerogensTL, BitumensTL, etc etc, provides a multiple bypass to the oil commodities markets. Such alternative routes to fuel makes the work of the energy mafias and faux environmentalists much harder -- unless they can use bribed politicians to stop the alternatives and unconventionals.

Cross-posted to Al Fin