Thursday, 30 June 2011

on the algae trail - the most important plant in the world?

algae are important plants, are useful in the soil - some help fix nitrogen or make it bio-available, but of course one of the most interesting uses for algae would be in the production of biofuels.  We blogged here about algae being used in reactors (or living foundries) to create a biodiesel, for example.

So what is Algae?  Is it just seaweed?

want to know more?  here's a 50 minute in-depth seminar/presentation on algae:

but (if you survived that in-depth study) there are continuing developments in farming algae, reported just recently. Recall the algae bio-reactors?  Well in this news item here i spied a novel way of locating reactors with minimum land-use and greater efficiency of production - in bags at sea!

If you have been paying even the slightest attention to the algae industry, you probably have heard of companies like Solazyme or Synthetic Genomics, the big names that are making big public strides in the field. Algasol Renewables, on the other hand, is one name in the industry that you have probably never heard mentioned. However, Algasol looks to be on the brink of joining those big names as one of leaders in the algae industry with their photobioreactor system.

Photobioreactors (or PBR’s) come in many different shapes, sizes, and designs. Essentially, they consist of some clear material formed in a way that it can hold an algae-containing liquid. Typically, you will find them looking like long tubes, snaking back and forth, that allow sunlight to reach the algae-water concentration that is pumped through it. They work great for growing algae but have typically suffered from high initial and operating costs.

This is where Algasol comes into play. They have designed a photobioreactor system that can potentially cut costs by 90 percent. How have they done this? Well, their thinking has taken them outside the tube and placed them into a bag.

Basically, their system grows freshwater microalgae in large plastic bags that float on top of bodies of saltwater. There, as in any other bioreactor, nutrients and CO2 are pumped in to feed the algae.
This design led Frost & Sullivan to give Algasol their 2010 “Global Algae Biofuels Award.” According to them, “Algasol Renewables provides a critical and innovative method for micro algae biomass production. Its modular floating bag technology, a new variation of photobioreactors (PBRs), provides a low-cost design coupled with industrial scalability, optimal light exposure, high biomass concentration, low energy consumption, and efficient system control.”

The oceans of the world have a great potential to be the location for floating algae farms. First off, oceans cover around 70 percent of the world. With land (especially agricultural land) becoming a very precious commodity, moving production of fuel offshore is a major bonus.

Additionally, the ocean cuts out a lot of the energy costs associated with traditional PBR’s. For example, the water surrounding the bags acts as a temperature buffer, a process that would require spraying down the outsides of the photobioreactor in typical systems. Also, the wave action in the ocean helps to mix the algae in the bags, something that would otherwise take additional energy in land-based designs.

Now, some may be concerned about putting all this plastic into the ocean should a storm comes along or worried about what happens if these bags break. Luckily, engineers at Algasol have addressed both of these problems. If a storm comes along, the bags have been designed to be submerged beneath the water to levels up to 250 feet. There, they can wait out a tropical storm, hurricane, etc.

Researchers are also not too concerned if one of the bags breaks. Since the algae will be freshwater species, they will die when exposed to saltwater and there, researchers have concluded, they can become food for fish and other marine life.

Wednesday, 29 June 2011

the fascinating world of bacteria

here's Bonnie Bassler's take on the subject of bacteria:

in the last post, we saw how to make a compost tea (the 24 hour recipe) which is essentially a way of moving bacteria and other microbes from the contents of the compost pile into a liquid that can be applied to our precious plants.

but is that the only method of improving the bacterial content of our soils?  compost teas is but one route to take, as caretaker of the organic realm:

Compost Teas vs. Compost Extracts

First, it may be helpful to share some common terminology and practices associated with compost teas. How do compost teas differ from compost extracts or compost leachates?

Compost Leachate

Compost windrow leachate—the dark-colored solution that leaches out of the bottom of the compost pile—most likely will be rich in soluble nutrients; but, in the early stage of composting it may also contain pathogens. It would be viewed as a pollution source if allowed to run off-site. Compost leachate needs further bioremediation and is not suitable or recommended as a foliar spray.

Compost Extract

Compost watery extract—made from compost suspended in a barrel of water for 7 to 14 days, usually soaking in a burlap sack—a centuries-old technique. The primary benefit of the extract will be a supply of soluble nutrients, which can be used as a liquid fertilizer.

Compost Tea

Compost tea, in modern terminology, is a compost extract brewed with a microbial food source—molasses, kelp, rock dust, humic-fulvic acids. The compost-tea brewing technique, an aerobic process, extracts and grows populations of beneficial microorganisms.


Compost teas are distinguished from compost extracts both in method of production and in the way they are used. Teas are actively brewed with microbial food and catalyst sources added to the solution, and a sump pump bubbles and aerates the solution, supplying plenty of much-needed oxygen. The aim of the brewing process is to extract beneficial microbes from the compost itself, followed by growing these populations of microbes during the 24- to 36-hour brew period. The compost provides the source of microbes, and the microbial food and catalyst amendments promote the growth and multiplication of microbes in the tea. Some examples of microbial food sources: molasses, kelp powder, and fish powder. Some examples of microbial catalysts: humic acid, yucca extract, and rock dust.

Liquid Organic Extracts vs. Compost Teas

Building on the concept of compost teas as a liquid organic extract, what are some other common organic extracts used as a liquid drench or foliar spray?

Manure Tea

Manure-based extracts—a soluble nutrient source made from raw animal manure soaked in water. For all practical purposes, manure tea is prepared in the same way as the compost extracts described in the preceding section. The manure is placed in a burlap sack and suspended in a barrel of water for 7 to 14 days. The primary benefit of the tea will be a supply of soluble nutrients, which can be used as a liquid fertilizer.

Herbal Tea

Plant-based extracts—stinging nettle, horse tail, comfrey, clover. A common method is to stuff a barrel about three-quarters full of fresh green plant material, then top off the barrel with tepid water. The tea is allowed to ferment at ambient temperatures for 3 to 10 days. The finished product is strained, then diluted in portions of 1:10 or 1:5 and used as a foliar spray or soil drench. Herbal teas provide a supply of soluble nutrients as well as bioactive plant compounds.

Liquid Manures

Mixtures of plant and animal byproducts steeped as an extract—stinging nettle, comfrey, seaweed, fish wastes, fish meal. Liquid manures are a blend of marine products (local fish wastes, seaweed extract, kelp meal) and locally harvested herbs, soaked and fermented at ambient temperatures for 3 to 10 days. Liquid manures are prepared similarly to herbal tea—the material is fully immersed in the barrel during the fermenting period, then strained and diluted and used as a foliar spray or soil drench. Liquid manures supply soluble nutrients and bioactive compounds.


Compost teas and herbal teas are tools that can be made on the farm to enhance crop fertility and to inoculate the phyllosphere and rhizosphere with soluble nutrients, beneficial microbes, and the beneficial metabolites of microbes.


Wheareas raw animal manures are used as a compost windrow feedstock, the composting process—thermophyllic heating to 135-160° F for 10-15 days—assures pathogen reduction. The raw organic matter initially present in the compost windrow undergoes a complete transformation, with humus as an end product. Any pathogens associated with raw manures will be gone. So caution is extended: Manure teas are NOT the same thing as compost teas or compost extracts. Because of concerns over new pathogenic strains of E. coli, the author advises growers to reconsider manure teas and/or to work with a microbial lab to ensure a safe, worthwhile product.

references above are available from NCAT - National Centre Appropriate Technology

Friday, 24 June 2011

compost tea - the 24hr recipe

there's been a rare old hoo-har about compost tea, here in the uk, since Gardener's World broadcast their April 1st look at the RHS's experiments with this organic method of keeping our plants tip top and healthy.

Of course, the recent e-coli outbreak in mainland Europe shocked many folks into thinking about what goes on to our commercially grow veggies - whether manure-based feeds were robust enough to prevent the transmission of pathogens, or whether they were in part to blame for such a devastating pathogenic outbreak.

The issue of creating safe organic feeds is therefore a crucial one - the oldest form of compost tea comes from the Victorian country garden.

Simply put: a collection of dried "cow-pats" would be placed in a burlap sack, weighted down and placed into a water butt to steep for a few days, before the liquor would be watered into the veggies and flowers for the full fertilizer effect.

It worked well in that time, of course, as they had precious few petrochemicals which might upset the delicate food-chain in the soil food web ( fascinating subject we'll cover in more detail in later blog posts) and no long-lasting man-made compounds which might survive the journey through a cow's intestine and go on to mutate crops, as we had a few years ago with herbicides.

So, what with the concern over e-coli, pathogens from manure, i was reading through a couple of homesteading blogs and came across this recipe from the small measures blog.  It's a guest post by Indio of saving the big money blog in the states and gives a 24 hour recipe for compost tea:

I started out with a control group of plants that didn’t get the compost tea as a point of comparison. Eventually, I took pity on this group and one by one they got hooked on the delicious beverage. There is only one remaining anemic plant from my group of test plants.

This is my first year using compost tea and I quickly became a convert. It’s not a difficult process so I usually have a 5 gallon bucket of tea percolating daily. I alternate between my two vegetable beds and every other day they get a drink when it isn’t raining. With the recent ecoli outbreak in Europe, compost tea is one of the safest ways to add nutrients to soil instead of using animal manure. Rather than worrying about whether or not the manure has aged enough to be safe on root crops, or if it will splash on fruiting crops I’ve found that compost tea is a way to take the worry out of soil enhancement and organic nutritional supplements.

At its most basic, compost tea is made by soaking the compost in non-chlorinated water for twenty four hours to encourage the growth of bacteria, fungi, protozoa and beneficial microbes that will feed the plant either through the leaves or the root system. The tea can be either sprayed on the plants as a foliar spray or used to water the plants. If you soak the compost longer than 24 hours, you risk the microbes dying before they get to the plant so it’s important to use it as soon as it is ready.

The Four Step Process
1. Fill a large bucket with water (water temperature doesn’t matter). If you don’t have well water, then let the water sit for 24 hours prior to adding the compost to let the chlorine evaporate out of the treated water. Depending upon the size of your garden you may want to use something larger than a five gallon bucket, which is what I use for my two modest veg beds.

2. To encourage the microbe development, I add two tbsps of tea catalyst to the water and stir to dissolve it. This is not a mandatory step, but it does accelerate the development of the microbes.

3. An air pump, the kind that is typically used in an aquarium, with two air stones attached to the end of the pump tubing, are used to circulate the bucket water. The air stones are placed on the bottom of the bucket. The whole set up must be located near an electrical outlet because the pump will need to be higher than the bucket so that water doesn’t get sucked back into the pump and break it. The pump speeds up the process by circulating the water and organisms.

4. To make the tea, I use either worm castings or arctic humus. I usually run out of humus quickly, but worm castings I can dig out of the vermicompost bin in my basement. If you don’t have a worm bin, check with your local garden shop for bags of worm castings. Next put the compost in a mesh bag and hang that over the edges of the bucket. Stirring the compost every now and then helps distribute the organisms, rather than letting them get stuck in the compost.

In 24 hours, you can pour the tea into a watering can or use it as a foliar spray. Your plants will show their appreciation by being bountiful.

Now i'm not exactly sure what the tea catalyst might be, but i suspect it may be a commercially available additive from the varying compost tea suppliers in the States.

As we'll find out through the pages of this blog, there are a myriad of ways in which to make compost teas, wines, microbe brews and so on - with varying effects claimed and shown.  The main point that people are finding out, however, is that we don't need chemical or synthetic feeds to care for our plants - in fact these synthetic feeds may have done more harm than good since their introduction (in terms of damaging soil structure and allowing pathogenic species to flourish).

BUGS are part of the coming new understanding about how we can feed ourselves whilst taking care of nature, but remember -
the revolution will not be pasteurized*

* see the about this blog page for more 

Thursday, 23 June 2011

life on earth may not have evolved without microbes

another day, another post about microbes and this one from the "general" file drawer about the timeless importance of microbes to life on the earth, rather than the future...

As originally reported by Roger Highfield, the fact that microbes were instrumental in evolving complex life on planet Earth, may point us outwards, to the stars.

Are you feeling calm? Now listen carefully and don't panic. You are suffering from a serious crisis of identity. Scientists believe you are not entirely human. In fact, it's time to stop thinking of yourself as an individual, or even as a single living thing. You are a hybrid that consists of only about 10 per cent human cells. The rest of you is made up of microbes.

Anyone who has browsed through the latest research literature is left in no doubt: we should bury the traditional and comforting idea that Homo sapiens is somehow special, separate and "better" than the rest of life on the planet.

A study of remarkable rock formations in western Australia has provided a vivid reminder of our earliest forebears. These 3.4 billion-year-old features of the Pilbara region - some looking like egg cartons, others like crests, waves or upside-down ice-cream cones - are now thought to be the remains of ancient microbial communities that were among the first living things on Earth.

Abigail Allwood of Macquarie University, Sydney, one of the team that studied them, is convinced that these formations - stromatolites - are among the great-grandmothers of all life on our planet. But as DNA mutated and evolved over billions of years, it had been thought that we left our microbial origins far, far behind.
So far, in fact, that most people now regard our ancestors as worse than an embarrassing relative. They perceive bugs as alien, as a threat to our existence. When it comes to bacteria that lurk in hospitals, toilets and kitchens, we seem to be engaged in an endless war. They are germs that must be shown no mercy. They must be destroyed with chemicals, antibacterials and cleaning fluids.

But in the scientific world, there is a growing awareness that we are much more dependent on this "simpler" life than we realise. The best-known proponent of this view is Prof Lynn Margulis of the University of Massachusetts, Amherst, who developed the concept of "endosymbiosis", the idea that our complex cells depend on simpler microbial tenants.

Nature has mixed and matched simpler creatures for aeons. The plants in the window box, trees in the garden and the broccoli at the greengrocer's all date back to ancient ancestors that became verdant only around two billion years ago, when they abducted smaller green creatures that could capture sunbeams and turn them into food. Indeed, Noriko Okamoto and Isao Inouye of the University of Tsukuba, Japan, even discovered a tiny ocean creature on a beach - Hatena ("mysterious" in Japanese) - that seemed to be engaged in a similar process of becoming green.

Prof Margulis believes our senses evolved directly from bacterial ancestors that had found ways to swim toward food and away from noxious gases, or ascend to the well-lit waters at the surface of a pond. Our cells are also powered by the descendants of bacteria that traded chemical energy for a comfortable home, in the guise of structures called mitochondria. These are organelles (which divide up the task of cellular life as organs do for a body) that have their own DNA, passed down from mother to child to drive our muscles, our digestion, and our brains.

As if to underline how mitochondria complicate the human genetic recipe, the genome entrepreneur Dr Craig Venter made an odd discovery when he offered his facilities to identify the remains of those killed in the World Trade Centre on September 11, 2001. His efforts to create the world's biggest forensic laboratory to deal with the crisis had a surprising scientific spin-off: he found that each of us may be a home for more than one mitochondrial genome.

There is also evidence that other ancient unions of cells helped to make us human. Dr Mark Alliegro, of Louisiana State University Health Sciences Centre, and colleagues made a fascinating find when they studied centrosomes, organelles essential to cell division. The centrosome contains RNA, thought by many to be the most ancient genetic material, which helps to translate genes into proteins, among other things.

These structures could multiply independently of their host cells by passing RNA down to the next generation. Could centrosomes, like mitochondria, be the result of some kind of ancient union between the cells of our ancestors and a microbe long ago? "I like to kid around and say centrosomes may be the mother of all latent viral infections," he says.

Other passengers in the human super-organism are easier to distinguish from our cells. Scientists have long recognised that the number of human cells in the body is dwarfed by the 100 trillion or so bacteria living in and grazing on it.

This has been obscured by the fact that human cells are much bigger than bacterial cells. As a result, despite their incredible numbers, bacteria account for only about three pounds of the average person's weight.
Just how important those three pounds are, however, has been difficult to weigh up until now. Most bacteria are too fussy to grow in the lab. As a result, little was known about what these majority shareholders really are and what, exactly, they are doing to and for us.

At the Institute for Genomic Research in Maryland, Dr Steven Gill and colleagues decided to investigate the genetic recipe of our bacterial tenants - the "colon microbiome" - by collecting faeces from two anonymous, healthy adults: a man and a woman who had gone without antibiotics or other medications for a year (when faeces is unscathed by antibiotics, half of it is bacteria).

Dr Gill found that we depend on some ancient organisms from what is called the third domain of life. Using DNA screening methods, his team found a surprising number of archaea, also known as archaebacteria, which are genetically distinct from bacteria but are also one-celled organisms often found in extreme environments such as hot springs, or basking in salt and acid.

Overall, they found that the human genome - all the genes in our cells - is but a fraction of what it takes to make a human. The collective bacterial genome in the average person is so large that it contains between 60 and 100 times as many genes as the human genome.

Up to 100 trillion microbes, representing more than 1,000 species, make up a motley "microbiome" that allows humans to digest much of what we eat. We lack the means to break down the food we eat into energy essential for our survival and, while bacteria could survive perfectly well without us, we would be doomed without the toil of bacteria that graze in our guts.

"The GI tract has the most abundant, diverse population of bacteria in the human body," says Dr Gill, now at the State University of New York at Buffalo. "We're entirely dependent on this microbial population for our wellbeing. A shift within this population, often leading to the absence or presence of beneficial microbes, can trigger defects in metabolism and development of diseases such as inflammatory bowel disease."

Dr Gill suspects the ecology of the human gut is at least as complex as that in soils or seas. It teems with single-celled residents that can make vitamins, such as the B vitamins that we cannot synthesise, and can break down plant sugars, such as xylan and cellobiose (similar to cellulose), which humans could not otherwise digest because we lack the necessary enzymes. Our diet would be limited if we could not: cellobiose, for instance, is a key component of plant cell walls that is found in most edible plants, such as apples and carrots.

Some bacteria in the gut break down chemicals made by plants that could cause cancer or other illnesses if they were not neutralised. Others have the capacity to scavenge hydrogen gas from the gut - a byproduct of digestion that can kill helpful bacteria - and convert it into methane. That makes the intestines a more biologically friendly place, while contributing in sometimes embarrassing and smelly incidents to greenhouse emissions. Our intestinal residents even pay us a kind of rent: bacteria in the gut make generous quantities of an enzyme that facilitates the production of butyryl coenzyme A, a fatty acid that is a favourite food of the cells that line the colon.

In short, these gutsy little helpers keep us alive. You would be nothing without the trillions of microbial minions milling around your large intestine, performing crucial physiological functions that your fancy, complicated human cells wouldn't have a clue how to do. These fabulous bugs are part of our inheritance: babies acquire their gut flora as they pass down the birth canal and take a gulp of their mother's vaginal and faecal flora. It might not be the tastiest of first meals, but it could well be one of the healthiest.

This realisation that we are super-organisms gives real meaning to the hazy idea of holistic medicine. Awareness that we depend on "good" bacteria is increasingly being exploited by manufacturers of yogurts and "probiotic" dietary supplements. Soon, doctors will test for changes in the numbers and kinds of microbes in our guts as early indicators of disease. They may prescribe live bacterial supplements to bring certain physiological measures back into normal range. And drug companies will seek compounds that mimic or amplify the actions of beneficial bacteria.

The message of the latest research is clear: we must learn to love bacteria - they are our ancestors, our tenants and our saviours.

In the rust-red Pilbara desert of Western Australia, an international team of NASA and university researchers looks at ancient rocks to see if they offer unambiguous evidence of life on Earth as long ago as 3.5 billion years. Martin van Kranendonk, and Abby Allwood, show shapes they believe could only have been formed by living organisms. Others on the scientific field trip continue to be skeptical. The ongoing debate shows contemporary research as an exciting intellectual adventure, and looking for life in the Pilbara as a physical challenge. Forget to drink often, says Kranendonk, and you could be dead in less than a day! Life, everywhere on Earth, needs water to survive.

Wednesday, 22 June 2011

Microbial Inoculants: an Approach to Sustainable Agriculture

originally an article published here by Sunita Gaind, i thought i'd repost it, given there's a wealth of good information on the subject, which gives a broad overview:

The green revolution though made India self sufficient in food production, but at the cost of soil health. Persistent use of chemical fertilizers and low input of organic material in soil reduced its organic matter content, resulting in stagnation of food grain production by 1.5 %.

To restore the productivity of soil, efforts need to be focused on use of natural resources that can be an alternate to costly chemical fertilizers and restrict soil impoverishment. Current developments in sustainability involve the rationale exploitation of soil microbial activities and use of less available sources of plant nutrients. Nitrogen and phosphorus are the macronutrients that limit the plant growth. To meet the crop need, these are generally supplemented through chemical fertilizers. Soil inhabits microorganisms that possess the particular trait for nitrogen and phosphorus transformation. Their application to soil under crop cultivation can improve the nutrient availability; reduce the input of chemical fertilizer and a way to sustainable agriculture.

What are microbial inoculants?
Microbial inoculants are the formulations of beneficial living microorganisms that when added to soil, directly or indirectly, improve the nutrient availability to the host plant and promote plant growth. Microbial inoculants for biological nitrogen fixation are both strain and crop specific. However, phosphorus solubilization and mineralization can be mediated by potential isolates of bacteria and fungi. The latter being the key components of soil plant system can be developed as phosphate solubilizing microbial inoculants.

Fungi vs Bacteria as Phosphate solubilizeres
 Fungi maintain their P dissolving efficiency even on repeated sub culturing
 The extracellular production of phosphatase and organic acid is higher with fungi compared to bacteria. Therefore, fungi are more effective phosphate mineralizer/ solubilizers compared to bacteria.
 Their hyphae can travel long distance in soil more easily than bacteria and can prove more beneficial for solubilization of phosphorus in soil.
 They can tolerate low moisture, high temperature, heavy metals and agrochemicals.
 Their spore forming nature is an additional advantage for their survival under environmental stress.

How do microbes improve the availability of nutrients?
Soil microorganisms are involved in large number of processes that affect the P transformation and influence its availability to plant roots.
 By the excretion of hydrogen ions.
 By release of organic acids.
 By production of phosphatase enzymes that can mineralize soil organic P.
 Chelating metal ions that may be associated with complexed forms of P or may facilitate the release of adsorbed P through ligand exchange reactions.
 By displacement of sorption equilibria that results in increased net transfer of phosphate ions into soil solution or an increase in the mobility of organic forms of phosphorus.
 Growth stimulation through production of phytohormones.
 By production of siderophores.
 Phosphate dissolving fungi may also provide micronutrients for formation of polyphenol and other aspects of phenolic metabolism.
 Phosphate dissolving Trichoderma harzianum has shown the ability to accelerate the oxidative dissolution of metallic Zn.
 They also provide disease resistance to plants due to production of antibiotics and protection against soil borne pathogens.

Phosphate dissolving microorganisms used as microbial inoculants
Fungi: Aspergillus awamori, Aspergillus niger, Penicillium digitatum, Pencillium radicum, Penicillium bilaiae, Trichoderma koningii

Bacteria: Pseudomonas striata, Bacillus polymyxa, Bacillus megaterium, B.subtilis, B. circulans

Carriers: Charcoal- soil mixture, vermiculite, press mud, peat, cow dung cake powder, farm yard manure, wheat bran etc. Amendment of charcoal soil - mixture carrier with calcium alginate resulted in better retention of moisture.

Tuesday, 21 June 2011

living foundries - the new future with microbes?

As the name suggests, "Living Foundries" are the bacterial and fungal colonies which can produce a new generation of human resources, with a low environmental impact.

Aside from new uses in supplying phosphor and nitrogen for truly sustainable farming, one farming input which can't be solved with microbes is fuel.  Whether we like it or not, bacteria can't just eat sugars and secrete petroleum products into the tractors, combines and delivery trucks to supply us truly sustainable foods - or can they?

it seems they might just be able to.

for some time, research has been ongoing into the possibility of pressing oils from algae

but now bio-engineers in the USA are taking the idea of living foundries further - by engineering e-coli to excrete diesel directly.  A guardian interview asked Jay Keasling, a professor of bioengineering at the University of California, Berkeley and CEO of the US Department of Energy's Joint BioEnergy Institute (JBEI) about his previous successes manufacturing anti-malaria drugs using "living foundries" before asking him about his new biodiesel bugs:

How easy is it to make fuel from microbes?
About a year ago, we published a paper in Nature where we engineered E. coli to produce a diesel fuel. The beauty of it was that the E. coli took in the sugar, transformed it directly into diesel, and the diesel was secreted outside the cell. Because it's oily, the diesel floats to the top. So unlike ethanol, which you have to distil to get it pure enough to use in an engine, the diesel purifies itself. That reduces the cost and the amount of energy needed to make it.

Will your diesel be as good as the fuel at the pump?
It's as good, if not better. Fuel is incredibly complicated – it has many different components and it's optimised for different things. We can build the fuel from the most valuable molecules, so we don't have the unwanted components that existing fuels have. You get better gas mileage out of it and cleaner emissions. And we're talking about a substantial improvement for the environment. Our diesel reduces greenhouse gas emissions by 80%, which is pretty substantial.

The world uses around 90 million barrels of oil a day. How can bugs compete?
We're looking at replacing 30% of transportation fuel in, say, a 20- to 30-year period. That is a huge undertaking. We are going to develop the technology to make the fuels and license them out. In the next 10 to 20 years, we'll see a very diverse range of companies all working with different techniques to make fuels.

How will your work affect the giant oil companies?
The energy business is the biggest sector in the world, and the beauty about working in the biggest industry on the planet is that there is room for everybody. Exxon is the largest company in the US, but it has only 5% of the transportation fuel market. That alone tells you that anybody can play.

Will synthetic biology be used to make more than fuels?
As well as fuels, we are looking at everything else we produce from petroleum, including polymers and plastics, and asking: can we go in and replace those? I don't see any reason why we can't make almost any chemical we want from sugar, a renewable resource. It's a great time to be in biology and biotechnology, because we have so many more tools and it's so much more powerful than it used to be.

Jay Keasling
Jay Keasling believes he can create alternatives to diesel and jet fuel using synthetic biology.
Photograph: Roy Kaltschmidt/Lawrence Berkeley Nat'l Lab

a future-facing convention regarding living foundries is to be held soon.

in the mean-time, we wait with baited breath at what other uses bugs will be put to, in terms of the immense environmental service they can provide.

Monday, 20 June 2011

microbes and ancient egyptians

ok, so not really a post about how bacteria, fungi or other microbes can assist in higher-yield plant growing, but an interesting microbe-related news story, nonetheless.

abc news relates a scientific study into the brown splodges which Howard Carter noted, upon opening Tutankhamun's tomb, back in the 1920's.

"There are some marvellous objects here," Carter reported. The king's sarcophagus. His elaborate death mask and throne, all covered in gold. Jewelry, statues, great urns. And the spectacular hieroglyphs on the walls.

But why were there brown blotches all over everything? They are everywhere -- on paint, on plaster, on silver. Just look at the pictures. Tut's tomb was infested with something that Egypt's Supreme Council of Antiquities could not identify.

Close-up tomb painting of Tutankhamen.

Hathor, goddess of the west, in Tutankhamen's tomb.

Concerned that the endless stream of tourists over the years had potentially exacerbated the problem (what with the moisture from all that sweat, the tourists breathing over the walls, etc) the Egyptian Auuthorities contacted called the Getty Conservation Institute in Los Angeles, which called Ralph Mitchell, a microbiologist at the Harvard School of Engineering and Applied Sciences. After a year's research, they are now able to lay the original concern to rest.

Howard Carter

 Howard Carter, said Mitchell, was a good scientist. When he entered the tomb 90 years ago, he catalogued and photographed everything. He has been accused over the years of mishandling Tutankhamen's mummy, but he was nothing if not thorough. He noted the brown spots and photographed them back in 1922.

"They have not grown since then," said Mitchell.

But that, as they say in many a mystery story, is where the plot thickens. After DNA sequence analysis, modern researchers still cannot say what the ancient microbes were, other than that they may have been some sort of fungi. And beyond that, why was Tut's tomb -- just this one among the many from ancient Egypt that are less well preserved -- so blighted?

"The guessing, and it's only a guess," said Mitchell, "is that he died suddenly, and was buried quickly, before the plaster even had a chance to dry. The people finishing the tomb would have exhaled, lost flecks of dry skin -- there would have been enough organic matter in the tomb that microbes grew on the walls."

Thursday, 16 June 2011

bacteria may help improve one of the world’s most important food crop

Scientists in Canada are showing the way to a sustainable future for farming.  At the university of Guelph, research  is continuing into the beneficial role microbes may play in a post-peak oil world.

from: this page on their website

Inoculating corn seeds with “good” bacteria may help improve one of the world’s most important food crops, according to a University of Guelph professor.

Manish Raizada, Department of Plant Agriculture, says adding useful microbes to corn might be cheaper and more sustainable than expensive chemicals to help plants use nutrients or fight diseases or pests.

Raizada recently surveyed “good” bacteria living in ancestral and modern corn grown across North America. Completed with recent PhD graduate David Johnston-Monje, this study appeared in PLoS One. The research was supported by the Ontario Ministry of Agriculture, Food and Rural Affairs, the Ontario Ministry of Research and Innovation, and the Canada Foundation for Innovation, among others.

“We have found and cultured collections of microbes that might be providing different corn with beneficial functions,” said Raizada. “We will be determining if these microbes can be useful incoculants, or biofertilizers, for corn and other cereals.”

Raizada said breeders and agrifood companies might use the results to pack useful bacteria into corn and other cereal crops.

Scientists already knew that bacteria live in corn and other plants. Like the group of microbes in your gut that help digest and absorb food, certain types of bacteria in plants and seeds appear to help the plant survive by, say, making essential nutrients available, Raizada said.

Different corn types carry varying groups of beneficial microbes, but some of the good bacteria have been lost during 9,000 years of human cultivation in North America.

The Guelph researchers set out to determine what good bacteria remain, and where they are found. They looked at 10 kinds of corn and four teosintes (forerunners of domestic corn). They chose varieties between southern Mexico, where people began to cultivate the crop thousands of years ago, and Quebec’s GaspĂ© region, where First Nations people domesticated a type of corn only hundreds of years ago.
“As indigenous peoples have selected and bred corn plants, they unknowingly have also selected and cultivated microbes,” said Raizada.

They found some bacteria were conserved in all corn types. Others were found only in certain kinds of corn. One microbe in a giant Mexican variety makes a chemical known to promote plant growth. Another bacterium makes a hormone that stimulates roots, which might help a corn variety grow aerial roots to support and nurture itself in swampy conditions.

Raizada plans to test the effects of those bacteria, and that of another fungi-fighting microbe, in Guelph field trials. The researchers will also study such basic questions as how these bacteria move within plants and soil.
Reintroducing microbes into corn may be a good alternative to chemicals, Raizada said. Each year, Canadian farmers already use at least $100 million worth of biofertilizers to help corn plants use nitrogen.