Chlorine-eating bacteria can consume a lot of waste clogging landfills and waterways. So can bacteria that love eating plastic bags. In fact, bags of empty plastic bottles have piled up before they can be recycled at Sure We Can, a non-profit bottle redemption center in Bushwick, Brooklyn that is pushing to become a cooperative for the canning community on February 16, 2013 in New York City.
Sure We Can, which was partly started by homeless canners in 2007 is run by one of its founders Sister Ana Martinez de Luco. The organization looks to give the diverse members of the canning community a safe and fraternal place to redeem cans, store their carriages and become members of an association that encourages self-dependence and responsibility.
Many of New York's canners are non-English-speaking elderly immigrants who live a marginalized existence and are vulnerable to dishonest business practices. Sure We Can currently serves around 50 canners per day and recycles over 6 million bottles and cans per year. You can recycle the aluminum soda cans. But then what do you do with the plastic unless you have the type of bacteria that eats plastic?
That's what a variety of scientists, students, and researchers are working on, including developing bacteria that eats cellulose waste products, tires, plastic bags, and oil spill waste. Each area of the U.S.A. has its own group focused on finding out how to get rid of waste that takes centuries or more to degrade. In Sacramento, check out the sites, "Too Valuable To Waste. Recycle. Plastics," and "Read, Write, Recycle! Partners Reward Sacramento Area School for Recycling."
Sacramento elementary public school recycled plastics, aluminum, glass, and paper
Recycling is now a competition, a contest among Sacramento's school children. What Sacramento has now is a school that teaches kids how to recycle plastic bags and other items that don't degrade naturally when thrown in landfills or worse yet, dumped into the waterways.
For example, on Wednesday, November 28, 2012, Assemblymember Dr. Richard Pan, the American Chemistry Council (ACC) and the Sacramento Regional Conservation Corps (SRCC) teamed up to award the grand prize to the winning school of the five-week Read, Write, Recycle! Challenge in Greater Sacramento. Recycling competitions also can help kids learn more about science, chemistry, biology, and good habits about how to properly dispose of waste for future generations, waste that simply can't be thrown in garbage cans and forgotten. Recycling also teaches kids more about concern for the future of the environment and people as well as wildlife who are harmed by plastic bottles, bags, and fast-food plastic 'rings' that hold cans in containers that often get around the necks of wildlife.
Whitney Avenue Elementary School in San Juan Unified School District won the competition by recycling 1,124 pounds of plastics, aluminum, glass and paper. During a school assembly, program partners and school staff conducted a surprise awards ceremony honoring the hard work of Whitney Avenue Elementary’s 320 kindergarten through fifth grade students.
Each student was given a recognition certificate from Dr. Pan, as well as a free pizza coupon donated by Round Table Pizza. The American Chemistry Council presented Whitney Avenue Elementary with a $1,500 prize check, which included its $1,000 grand prize award and $500 award for winning at the school district level. The event culminated with a celebratory pizza party for the entire school.
Read, Write, Recycle! (RWR) is a recycling competition offering schoolchildren the opportunity to recycle material on their campus and be rewarded for it. The Sacramento area challenge pitted students in San Juan Unified against students in Natomas Unified School Districts. Participating schools included Natomas Park Elementary, Witter Ranch Elementary, Heron School, H. Allen Hight Elementary, Greer Elementary and Whitney Avenue Elementary.
Students and researchers around the world are trying out various types of garbage-eating bacteria to clean up toxic waste, and some students compete to discover the type of bacteria that eat plastic bags
At Cornell University researchers hope to learn how certain bacteria that break down pollutants do their job and then to make them more effective in cleaning up toxic wastes. Bacteria called Dehalococcoides ethenogenes, discovered in Ithaca sewage sludge in 1997 by James Gossett, Cornell professor of civil and environmental engineering, and isolated and studied by Stephen Zinder, Cornell professor of microbiology, are now in wide use to detoxify such carcinogenic chemicals as perchloroethylene (PCE) and trichloroethylene (TCE). They do this by removing chlorine atoms from molecules and leaving less-toxic compounds behind.
But D. ethenogenes strains work well at some sites and not so well at others, and nobody knows for sure why. In fact, very little is understood about how these organisms live and breathe. Normal laboratory procedures haven't provided enough answers, because the bacteria are hard to grow in a petri dish, said Ruth Richardson, Cornell assistant professor of civil and environmental engineering, who is following up on Gossett's and Zinder's work, in continued collaboration with them.
She is partnering with Gene Network Sciences (GNS), a firm specializing in computer simulation of biochemical processes, to create computer models of the inner workings of the bacterium. The project is funded by a three-year, $381,000 grant from the Department of Defense, which has some 6,000 toxic-dump sites of its own to clean up.
Chlorine-eating bacteria
Richardson explained, according to the news release, "Helping chlorine-eating bacteria clean up toxic waste," that in the field "the bacteria sometimes start and then stop. We might improve conditions for the organisms." For example, she said, it has been found that Dehalococcoides needs vitamin B-12, so the vitamin is added to cultures that are injected into cleanup sites. The bacterium also grows better in a mixed community with other kinds of bacteria. "There are some factors it needs from other organisms, and we don't know yet what they are," she said in the news release.
Her laboratory tested the D. ethenogenes strains under a variety of different conditions, such as exposing them to different chlorinated compounds one at a time, varying the environment or the nutrients supplied, and then observing which genes are expressed and what proteins are manufactured. The data was sent to GNS, which will try to build computer models of how the bacteria's proteins work together under each condition and whether the pathway for each condition is the same for PCE and TCE, and if not, what steps they have in common.
It will be an "iterative process," Richardson said. If a model shows that changing a particular condition produces a particular result, the lab will try it out and see if the result matches the model. Eventually, Richardson said, some commonalities should appear.
"There will be a suite of models, and we can highlight features that are common across several models," she said. "As we develop the model, we can begin to look at the genomes of other strains of Dehalococcoides. If genes that are important in our strain are found in others ... then we can do the same experiments with the others." Finding which genes are at work with which pollutants might lead to understanding how to remediate other kinds of pollutants, such as PCBs, dioxins, chlorobenzenes or chlorophenols.
Richardson, who grew up in the Hudson River Valley, notes that such pollutants are common in the river's harbors. "There are still thousands of sites around the country that need to be cleaned up," she said. "Ithaca has three or four, and that's not atypical."
Oil-eat bacteria may show the environmental impact of Gulf Oil
Microbes to the rescue is the motto for bacteria that eats oil spills and similar garbage, according to news from the American Chemical Society. The environmental impact of millions of gallons of oil still in the Gulf of Mexico from the Deepwater Horizon incident may depend on microscopic helpers: Bacteria that consume oil and other hydrocarbons and could break down the spilled crude, making it disappear. That's the topic of an article in the August 2010 issue of Chemical & Engineering News (C&EN), ACS' weekly newsmagazine.
It points out that the oil-eating bacteria are beneficial in helping to clear away the oil. Their activity, however, could eventually pose risks to the Gulf's ecosystem, particularly in the deep ocean. The oil acts as a huge source of food and could produce bacteria 'blooms' or massive population explosions. As the blooms die and decay, they remove oxygen from the Gulf water, jeopardizing the health of fish and other aquatic animals, according to the news release, "Oil-eating bacteria may determine environmental impact of Gulf oil."
The article discusses scientific research underway to shed light on the bacteria's effects. It notes that the oxygen depletion so far is not as serious as the Gulf of Mexico's infamous "dead zone," an 8,000 square mile area — about the size of New Jersey — with oxygen levels too low for fish to survive. The Gulf's oil plumes cause nearly a 35 percent oxygen drop compared to a 90 percent drop in that dead zone.
Paper-eating bacteria being developed
DNA detective work with paper-eating bacteria that 'glide' allows scientists to explore how bacteria use these cellulose parts from trees and other plants. Paper can be recycled. But why develop cellulose-eating bacteria? And what if it got into the food chain? Scientists have found that a specific genome shows a possible link between cellulose digestion and motility, the ability of bacteria to move around and eat up paper pulp waste such as sawdust. Yet some people compost sawdust to feed to plants in gardens.
Grain and the ethanol made from it can be turned into a fuel to use in cars instead of gasoline. But what about renewable materials made as bacteria break down cellulose that comes from plants such as trees and forestry by-products such as paper? After all sawdust and grain hulls as well as paper pulp can be recycled, composted to become fertilizer for plants, or eaten by bacteria.
You may want to check out a news release, "McBride shows DNA detective work with paper-eating bacteria that 'glide'," based on a study from the University of Wisconsin - Milwaukee. The eco-friendly fuel ethanol is usually made from grain, but the U.S. Department of Energy (DOE) would like to find other renewable materials that will be cost-effective alternatives, such as paper pulp, sawdust, straw and grain hulls.
A UWM professor recently helped DOE do just that by analyzing the DNA of a bacterium that can break down cellulose, the major structural component of plants that is also found in forestry by-products (including paper) and waste feedstocks.
Mark McBride, a professor of biological sciences, worked with DOE's Joint Genome Institute and scientists at Los Alamos National Laboratory to examine the genes of Cytophaga hutchinsonii that are responsible for the organism's ability to digest cellulose – the first step in the carbohydrate's conversion into ethanol.
Sequencing the genome of C. hutchinsonii provides what McBride calls a "parts list" for the microbe, allowing scientists to explore how bacteria use these parts to build and run their key functions – some of which have potential uses in bioenergy.
The genome has revealed surprises, he says in the news release, "McBride shows DNA detective work with paper-eating bacteria that 'glide'." "Microorganisms typically require two kinds of enzymes to efficiently break down cellulose," he says. "One type cuts the long carbohydrate molecule through the middle, while another chews small pieces from the ends."
Not so with C. hutchinsonii. Although it efficiently digests cellulose, in DNA analysis it appears to be lacking one of the usual enzymes, suggesting that it may use either a novel strategy or novel enzymes. The information McBride reports could help DOE devise mixtures of microorganisms or enzymes that will more efficiently convert cellulose into glucose, and finally into ethanol.
McBride's interest in C. hutchinsonii goes beyond its possible value in bioenergy
What really intrigues him is that it's a "gliding bacterium," able to crawl rapidly over surfaces by an unknown mechanism, which is the main subject of McBride's research with another glider called Flavobacterium johnsoniae. The two microbes are not closely related.
"You are more closely related to a fruit fly than these two organisms are to each other," he says in the news release, "McBride shows DNA detective work with paper-eating bacteria that 'glide'." However, from analysis of genes from the two bacteria, McBride suspects that they use the same basic machinery to move.
And there may be another connection. F. johnsoniae doesn't eat cellulose, but it is able to digest a similar carbohydrate polymer, chitin. Like cellulose, chitin, which is found in the hard shells of lobsters and insects, is also difficult to break down.
McBride hypothesizes that digestion of cellulose and chitin may also be linked to cell movement, or motility
"Loss of motility results in loss of ability to digest chitin," he says in the news release. "This suggests that motility and digestion of some carbohydrate polymers may be connected in both gliding microbes."
McBride and his students have used F. johnsoniae to study the motility of gliding bacteria for more than a decade. They cloned "mutants" of F. johnsoniae that are unable to move, and then attempted to "repair" them by inserting certain pieces of DNA.
In this way, they have uncovered nearly all the genetic components that propel the cells. It has been a long process. A decade ago, his lab had found one protein involved. He now knows of 24, and he doesn't expect to find many more.
Until recently, McBride was not able to image the bacteria closely enough to see the structures involved in movement. Instead, he bonded latex spheres to the surface of F. johnsoniae cells and observed that they moved in all directions around the cell's perimeter. "The cell wall appears to have a series of moving conveyer belts," he says, according to the news release.
He also has learned that some of the motility proteins ("parts") act at the surface of the cell, and he thinks some are involved in forming nearly invisible filaments around the perimeter of the cell. These filaments were recently imaged in collaboration with Sriram Subramaniam and Jun Liu at the National Institutes of Health by cryo-electron tomography.
"The filaments may be the cell's 'tires,' and there are different kinds," McBride says in the news release. "They are designed to help the organism move over a variety of surfaces, like an all-terrain vehicle."
Besides providing movement, McBride says the filaments also may be needed to move the cellulose and chitin molecules to certain sites where they can be digested or taken into the cell. McBride hopes the complete genome for C. hutchinsonii will yield other clues to the interconnections among gliding bacteria. He is now collaborating with DOE to sequence the entire genome of F. johnsoniae, which will allow a full comparison of the genes of the two microorganisms. DNA detective work with paper-eating bacteria that 'glide' allows scientists to explore how bacteria use these parts.
Sacramento and Davis college students at the University of California are creating bacteria that eats plastic waste
Will it help clear out plastic bags and plastic fast-food litter or plastic bottles dumped in some of the landfills, vacant lands, or floating in the oceans, streams, lakes, and rivers? College students in Sacramento at the University of California, Davis are working and competing to solve one of the biggest problems of this century, creating bacteria that eats plastic garbage.
Can simple biological systems be built from standard, interchangeable parts and operated in living cells? Or is biology so complicated that every case is unique? Students have to find an answer to that question posed on the iGEM website which stands for the UC Davis International Genetically Engineered Machine.
The field is called synthetic biology. And students are competing against one another in teams to develop a genetically-engineered bacteria that degrades plastics so the landfills won't be overflowing in plastic refuse such as bags and soda bottles.
Every weekday this summer, 10 students from different departments at the University of California, Davis work at the university's Genome Center to genetically engineer a type of bacteria that will biodegrade and eat up plastic trash that clogs our landfills and oceans.
The goal is to cleaning up the world's landfills by developing a type of plastic-devouring bacteria that thrives on plastic bags and other plastic material found in landfills or tossed into the oceans. For more details you can check out the August 28, 2012 Sacramento Bee article by Ravali Reddy, "UC Davis students work to engineer plastic-degrading bacteria." Or follow the team as it progresses in its research at the university's iGEM (International Genetically Engineered Machine) website.
UC Davis International Genetically Engineered Machine: The Synthetic Biology Competition
These students are members are of the UC Davis International Genetically Engineered Machine, or iGEM, team. For months the students have been competing in the world's premiere collegiate synthetic biology competition.
The push to develop plastic-degrading bacteria to clean out the landfills of the world from discarded plastic garbage first began at MIT back in 2003. How the competition works is that student teams across the world receive a kit of biology parts from the Registry of Standard Biological Parts.
During the summer the students work with fellow undergraduates to create a biological system that includes those parts they have received with the kit of biology parts and the added new parts the students can design themselves or as a team. The end product is supposed to operate in a living cell. That means, a living cell from some organism gets implanted with some type of bacteria that likes to eat, degrade, or devour plastic garbage such as soda bottles and bags.
If you check out the official iGEM website, the competition has to answer that one question, " Can simple biological systems be built from standard, interchangeable parts and operated in living cells?" The iGEM website is about synthetic biology based on standard parts.
There's also a high-school division of iGEM, a college division, and an entrepreneurial division. Check out the iGem videos from around the world. This is one positive way students in high school and at the university level can compete to make the world a cleaner place.
Tackling plastic phthalates pollution in Sacramento: Can bacteria biodegrade polyethylene terephtalate (PET)?
Locally, the University of California, Davis team is tackling the problem of plastic pollution and is working to create a bacteria that can biodegrade polyethylene terephthalate, or PET, a commonly used plastic that's in such items as soda bottles and food trays.
You read in medical journals how toxic phthalates from plastics are when they get into the human body, that even infants are found with phthalates in their bodies. So students need to find a way to engineer bacteria that can eat up or degrade plastic in such a form that the bacteria can use the product as a food source to live.
This is the fourth year that UC Davis is competing at iGEM
Last year's successful four-person team placed in the top 16 at the world championship and received the Best Foundational Advancement Award. What will happen this year? Will one student or a team find a way to engineer a type of bacteria that degrades plastic that otherwise would take thousands of years to fall apart?
The local team is preparing for another regional round to be held next month at Stanford University. Look for the North America West Jamboree regional qualification round to be held October 12-14 at Stanford. Teams presenting their projects will give 20-minute presentations on what they're developing. Then they'll answer a few minutes of questions from judges. The students will have poster displays on their research.
Then it's on to MIT for the few finalists from this round as the world championship will be held at MIT in Cambridge, Massachusetts, November 2-5, 2012. There's a new Entrepreneurship Division. This business-oriented division will be tyring to develop a business plan that works well for marketing its project. The UC Davis team also will enter the Entrepreneurship Division.
Entrepreneurship in iGEM focuses on developing a business plan for synthetic biology projects
The goal of the business entrepreneurship division at iGEM is about fostering the development of a new industry where Synthetic Biology is the underlying technological platform. As with any new industry, it is not clear which business plans will be the most successful.
There are also more fundamental questions: What business models will succeed, how will intellectual property affect company formation and funding, what skills are required at each stage of company’s life cycle, how will government policies promote or hinder new companies, what will be the social contract with Synthetic Biology companies? Or you can ask your own questions about business models for synthetic biology product development and use.
For this first year the iGEM project will be considering at least four tracks examining critical business, regulatory and market issues that will determine the path of the Synthetic Biology industry:
* Business Plans
* Economic and Business Models
* Industry Development
* Business and Regulation
The iGEM website asks that if you have an idea for a project that does not fit in any of these tracks, let the iGEM website contacts know, and they will figure out how to make it work.
UC Davis will try to come up with a successful business plan for marketing synthetic biology in the world
You have a team of University of California, Davis students working on the science end, and at the same time also entering the new Entrepreneurship Division, trying to come up with a successful business plan for marketing its project in the real world. The project is not easy, trying to develop a bacteria that degrades plastics.
It's a full-time commitment with team members working 40 hours a week on the project, mostly in a laboratory as well as on their website as they prepare their presentation. Students don't get any money for their summer full-time work. However, their travel to regional and foreign competitions are paid for, and the funding they do get goes to pay the costs of the project.
If your child is science or business-oriented, let the person know about such projects open to high-school and college students. It could mean some great experience in making the world a cleaner and healthier place, or at least making a difference.
Resources
iGEM Entrepreneurship
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