Cooperative Extension San Joaquin County
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Cooperative Extension San Joaquin County

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Biofilms: Friends or foes?

"Biofilms" surround us. They pervade our environment and our bodies. They form the dental plaque on our teeth and establish the chronic infections in our childrens' ear canals. They can spread on the watery surface of a contact lens.

Biofilms are now thought to be involved in 80 percent of human microbial infections, and are likely responsible for the resistance of chronic infections to antibiotics. Biofilms even form around "extremophiles" – such as the ancient blue-green cyanobacteria that thrive in extreme environments like the hot springs of Yellowstone National Park and the lake crusts of Antarctica. These microorganisms with fossil records going back 3.5 billion years also clog water pipes and create the slimy film on rocks in a pond.

A “biofilm” is a protective environment created by a microbial population. When microbes such as bacteria sense a “quorum” of their kind nearby, they begin to modify their genetic instructions to produce polysaccharides. The result is a sticky matrix that enables them to adhere to each other, and to surfaces.

This is the thin biofilm that first forms on the gravel in a constructed wetland.

But there is more to this story. Biofilms can also be employed for our benefit. Many sewage treatment plants include a stage where wastewater passes over biofilms, which “filter” — that is, extract and digest — organic compounds. Biofilms are integral to our current engineering processes for wastewater treatment.

Similarly, they play an essential role in constructed wetlands (CW), the artificial systems that approximate natural wetlands and that are used to treat wastewater or stormwater runoff.  Most constructed wetlands are planted with hydrophilic (water loving) plants, while others are simply a gravel “filter” media. Both involve biofilms at the water-solid interfaces.

Recent research has now shown that planted CW systems — with their associated biofilms — are significantly more effective in the first weeks and months of treating agricultural processing wastewater.

In greenhouse trials, the planted system removed approximately 80 percent of organic-loading oxygen demand from sugarcane process wastewater after only three weeks of plant growth. The unplanted system removed about 30 percent less.

“Every constructed wetland system has a 'ripening period' during which the biofilm is forming," said Mark Grismer, UC Davis biological engineer. "Ripening means the time it takes for bacteria or other microorganisms to become established and functioning with respect to organics removal. Results indicate this ripening period is shorter in planted CW systems, and can be as short as three weeks if fast-growing aquatic plants are involved in the constructed wetland. In systems without plants, it can continue for two to three years.”

Constructed wetland with plants.

“Plant roots provide the structure needed for biofilm bacteria to process wastewater. Also, because the surface area of plant roots is far greater than that of the sand, gravel, or rock substrate alone, and because roots have the ability to partially oxygenate their surfaces, they can support thicker and perhaps more robust biofilms,” he said.

Studies like this one are providing the field data needed to strengthen efforts to clean up agricultural processing wastewaters.

To read the complete article, go to the April-June edition of California Agriculture journal.

Posted on Wednesday, May 4, 2011 at 9:01 AM
  • Author: Janet L. White
Tags: biofilms (1), wastewater (1), water treatment (1), wetlands (1)

For the naturally curious

Adding a new observation on the iphone app for others to see and comment.Whether you are enjoying a family day at the beach or a hike through the woods, the pictures you take not only document your memories, but they also capture observations in nature. The relatively new website, iNaturalist, creates a forum for the public to be able to share those photos as a living record of our environment.

iNaturalist works in three different ways. You can post your own observations by creating a free account and uploading a picture of a beautiful patch of wildflowers or a type of bird you have never seen before. Other users can then comment on your photo and also help you identify the species you observed. You can also use the site to explore your neighborhood, community, or state by using the map to see where recent observations have been made or search by species to view the beautiful and strange creatures captured on camera. Lastly, you can create or join a project to pool your observations with others and help land managers and scientists track changes in biodiversity.

iNaturalist differs from other recent web-based resources out of the University of California to collect natural resource data from the public because it functions as a place for the public to learn about the environment around them through a collaborative social platform. It is also different in its environmental application since it does not focus specifically on invasive species, such as UC Berkeley’s Oakmapper and UCLA’s What’s Invasive, but all species of plant and wildlife.

First conceived as the Master's final project of Nate Agrin, Jessica Kline, and Ken-ichi Ueda at UC Berkeley's School of Information, iNaturalist was established in 2008. Currently Ken-ichi maintains the site in collaboration with Scott Loarie, a climate change researcher at the Carnegie Institution. An iphone app hit stores this past February so people can make photo observations on the go and upload pictures they take on their phone directly to the site.

“Having an app is important,” Ken-ichi notes. “We’re such a good platform for citizen science monitoring efforts and the app definitely enhances this ability.”

Two projects that stand out with regular contributors include the Pepperwood Monitoring Project on the Pepperwood Preserve and the Jasper Ridge Preserve Project on the Jasper Ridge Biological Reserve, both of which focus on tracking plant and animal data on their properties.

Currently the site has just under 1,000 registered users with an average of 100 to 150 unique users entering the site everyday and over 13,600 observations. So no matter if environmental science is your professional field, your passion, or you need help identifying the weeds that keep growing in your yard, iNaturalist is a helpful learning tool.

For more information or to join iNaturalist, please visit The iNaturalist app can be downloaded for free from the iTunes app store.

Posted on Wednesday, April 27, 2011 at 12:12 PM
  • Author: Jaime Adler
Tags: apps (2), iNaturalist (1), Oakmapper (1)

“Smart” orchard sprayers reduce pesticide use, protect waterways

Technology that allows orchard sprayers to skip the space between trees can protect the environment while saving growers money.

The idea is simple: when orchards receive dormant and in-season sprays of agricultural chemicals, the spray should only fall on the trees where it is needed, rather than on the ground, where it is not.

Orchard sprayers can be retrofit with target sensors that activate spray nozzles only when a tree is present.

A target-sensing smart sprayer travels between the rows of a Modesto almond orchard.
A review of research on this “smart” sprayer technology, published in the April-June 2011 issue of the University of California’s California Agriculture journal, found that the financial and environmental benefits of the technology are substantial.

“By reducing the application rate of the pesticide mix, each tank load of material covers a greater land area, effectively reducing the number or refills, ferry trips and time spent spraying each orchard,” wrote author Durham Giles, UC Davis professor of biological and agricultural engineering, in California Agriculture. “This provides additional economic return to growers by reducing labor and fuel costs.”

Based on field tests, the authors estimated that reductions in pesticide and operating costs with smart-sprayer technology ranged from $58 per acre for peaches grown in the San Joaquin Valley to $31 per acre for prunes grown in the Sacramento Valley.

At the same time, reductions in the total amounts of pesticide sprayed ranged from 15 percent for a mature prune orchard near Chico, to 22 percent for a mature almond orchard near Modesto, to 40 percent for a younger (more open) prune orchard near Oroville.

The trees themselves received the same amount of pesticide in the smart-sprayed orchards, but a lot less pesticide ended up on the ground than in the control. “For the almond and more open prune orchards, the reductions were 79 percent and 59 percent, respectively,” Giles and colleagues wrote.

Likewise, when the amount of pesticide in water running off from the younger prune orchard was measured, the reduction was 54% in the smart-sprayed orchard compared to the control.

Despite its obvious benefits, the study authors noted that “use of the smart-spray technology is growing but remains a small part of the spraying equipment market.” The retrofit spray sensor and control equipment cost about $15,000, with an estimated payback period of 2 years or less, given documented cost reductions.

Furthermore, the U.S. Department of Agriculture’s Environmental Quality Incentives Program (EQIP) can provide up to $30 per acre for a total of $15,000 per contract when the new equipment provides a 20% reduction in spray, which as been documented in peer-reviewed research such as the California Agriculture article.

“The amount is sufficient to adequately cover the cost of purchasing a typical target-sensing system for an orchard sprayer,” the authors note in California Agriculture journal.

Posted on Wednesday, April 20, 2011 at 8:31 AM
  • Author: Janet Byron

Keeping child care centers safe with integrated pest management techniques

With the early childhood eating habits of toddlers and young children, it is no surprise that preschools and child care centers often have problems with ants and cockroaches. Schools for the state’s youngest residents may also have concerns about black widow spiders, yellow jackets, mosquitos, rodents and other pests.

Many of the centers respond to the problem with pesticide sprays and foggers that could expose children and staff to residues on surfaces and in the air, a 2010 survey by the California Department of Pesticide Regulation revealed.

California’s Healthy Schools Act requires DPR to collect information about pesticide use and pest management in child care centers. The 2010 survey found that 55 percent of child care facilities use pesticides and 47 percent use foggers. One in five of the centers scheduled pesticide applications on a weekly or monthly basis, a strategy that is not recommended because applications may take place even when no pests are present.

The Healthy Schools Act also requires DPR to develop programs that encourage the facilities to voluntarily adopt integrated pest management practices, which emphasize pest monitoring, exclusion and safe treatment.

To help meet this requirement, DPR funded a Pest Management Alliance - including UC San Francisco’s School of Nursing, UC Berkeley’s Center for Children’s Environmental Research and the UC Statewide Integrated Pest Management Program - to develop a comprehensive pest management curriculum and outreach materials. The information is designed to help the centers minimize the risk of pesticide exposure and increase their use of safer pest management alternatives. This team created a detailed checklist that preschool directors can use to identify pest problems and find safe solutions, a 39-page curriculum, and four laminated posters:

  • Steps to a pest-free indoor environment
  • Steps to a pest-free outdoor environment
  • How to choose a safer pesticide to manage pests, with pictures of the best products to use and those that should be avoided
  • Clearly illustrated instructions for reading a pesticide label

The curriculum, which is available in English and Spanish, also includes 10 “health and safety” notes that detail pest problems and IPM strategies specific to common pests, plus a health and safety note that explains “green cleaning.”

The IPM strategy for ants, which pose the most common childcare center pest problem, begins with, “Don’t spray!”

“Spraying pesticides may kill ants, but spraying will expose staff and children to harmful chemicals and doesn’t eliminate ants in their nests,” the document says. “Pesticide residues can build up indoors where children spend a lot of time.”

Instead, users are advised to keep ants out by caulking cracks around foundations, removing plants and mulch that are within 12 inches of building foundations and removing ants’ food, water and shelter opportunities inside the facility. If other action must be taken to control the pest, IPM suggests the use of baits, not sprays, and as a last resort, hiring a pest management professional.

The curriculum can be downloaded for free from UCSF’s California Childcare Health Program website,

IPM techniques make child care centers a safer place for children.
IPM techniques make child care centers a safer place for children.

Posted on Wednesday, April 13, 2011 at 8:08 AM

Better living through green chemistry

We’ve all noticed the changed landscape on the grocery shelves: eco-friendly brands like Mrs. Meyers, Seventh Generation and even Clorox’s Sierra Club-endorsed Green Works sit next to conventional stalwarts like Tide, Cheer and those ferocious scrubbing bubbles. The new products are the consumers'-eye-view into a quiet “green chemistry” revolution taking shape in university and commercial labs across the country, and in education and public policy.

Even if the proliferation of green cleaning products, office supplies, packaging and appliances make the planet and its inhabitants healthier, the fact remains that more than 80,000 chemicals with uncertain health and environmental impacts currently are registered with the Environmental Protection Agency, with more discovered every day.

“Green chemistry involves discovering and implementing chemical processes and products that are safer, cleaner and more efficient,” said John Arnold, professor of chemistry at the University of California, Berkeley, and director of the campus’s Berkeley Center for Green Chemistry (BCGC).

Last month, the center hosted the sold-out event Green Chemistry: Collaborative Approaches and New Solutions,” the first national conference to take a multidisciplinary approach to this developing area of study. Speakers and panelists came from the EPA, California state government, private industry, departments across the Berkeley campus, and universities across the country, including the 2005 Nobel laureate Robert Grubbs of Cal Tech.

“The Berkeley Center for Green Chemistry has created a multidisciplinary team that represents all aspects of chemistry, from research and development to consumers and the environment,” Arnold said. “Through research, education and engagement, we aim to facilitate change by embedding the principles of green chemistry into science, markets and public policy.”

The BCGC already has begun redesigning undergraduate and graduate student education to include green chemistry by creating greener laboratory experiments and launching an interdisciplinary graduate course in green chemistry funded by California Environmental Protection Agency. But the center aims for a broader impact – on public policy as well as on the chemical industry. “We’re trying to promote activities that address more than one aspect of green chemistry, that also look at economics, business, law, toxicology or public health,” Arnold said.

Green chemistry programs are not new at universities or in the research labs of chemical companies, but most focus only on innovations in chemistry, such as developing catalysts or safer solvents, according to Alastair Iles, a UC Berkeley assistant professor of environmental science, policy and management and a center member. Iles said that these technical developments are critical to achieving sustainability, but they won’t be as effective or be widely used without also finding societal innovations in policy, law, environmental health and business.

“In contrast, BCGC has a vision of integrating multiple disciplinary fields with chemistry so that chemists can work with toxicologists, business experts, regulators and economic experts to develop technologies and products that are non-toxic and sustaining,” Iles said.

Center executive director Marty Mulvihill said that green chemistry is already being taken up by industry because it’s cheaper, it doesn't produce as much waste, it uses less energy, and it creates products that are safer, without the worry over what's going to happen at the end of a product's life.

“It just needs to be taken up by the entire industry in a transparent way that gives businesses and consumers the information they need to make choices,” said Mulvihill.

A key 2008 study led by UC Berkeley environmental health scientists and their UCLA colleagues, formed the technical basis for the state’s Green Chemistry Initiative and new legislation authored by Senator Joe Simitian (D-Palo Alto) and Assemblymember Mike Feuer (D-Los Angeles). Those new laws, and their implementing regulations, could improve public access to information on the sale of chemical products in the state and reductions in some uses of the most toxic chemicals, according to Michael Wilson, BCGC associate director for integrative sciences and an environmental health scientist at UC Berkeley's Center for Occupational and Environmental Health.

As members of the state’s Green Ribbon Science Panel, Wilson and his co-author Megan Schwarzman, the center’s associate director of health and environment, have worked with the DTSC to shape the Green Chemistry Initiative, with the hope that it will improve transparency and accountability in the chemicals market.

“Ultimately, in society, what we would like to see is the design of chemicals and products that don’t come at the expense of humans or the environment,” said Schwarzman. “That would mean creating chemicals that are short-lived and degrade in the environment so they don’t show up in breast milk 30 years after they have been banned, and industrial processes that use benign substances. I think we have the ingenuity and the know-how to do that, and we have to prioritize it as a society.”

Posted on Wednesday, April 6, 2011 at 7:28 AM
  • Author: Ann Brody Guy

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