In 1996, researchers from major genome sequencing centers around the world convened on the island of Bermuda and defined a finished genome as a gapless sequence with a nucleotide error rate of one or less in 10,000 bases. This effectively set the quality target for the human genome effort a ... more
Better sludge through metagenomics
Researchers seek to master wastewater treatment failures
28-09-2006: Wastewater treatment is the largest microbially-mediated biotechnology process on the planet. When it works, it is a microbial symphony in tune with humanity. When it fails, the consequences can be dire. Researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) and collaborators at the University of Wisconsin-Madison, and the Advanced Wastewater Management Centre, University of Queensland, Australia, have published the first metagenomic study of an activated sludge wastewater treatment process. The research appeared in Nature Biotechnology.
The metagenomic strategy entails generating DNA sequence information directly from samples of sewage sludge to provide a blueprint of the genes and hence the metabolic possibilities of the wastewater environment, with a view to understanding how the system works and predicting and averting failures or crashes.
"This is a first step in a much broader strategy employing a systems biology approach to the study of microbial communities with the goal of designing predictive models to understand how these communities function," said Hector Garcia Martin, lead author of the study and post-doctoral fellow in the DOE JGI's Microbial Ecology Program. "With this information now available, there are opportunities to bioengineer the process to make it more reliable."
Removing excess phosphorus from wastewater can be most economically accomplished by environmentally friendly biological means in a process known as enhanced biological phosphorus removal (EBPR). The researchers were able to obtain a nearly complete genetic blueprint for a key player in this process, the bacterial species Accumulibacter phosphatis.
Activated sludge wastewater treatment processes are used throughout the world to purify trillions of gallons of sewage annually. Many treatment plants employ specialized bacteria to remove the nutrient phosphorus, in an effort to protect lakes and rivers from eutrophication, a deterioration of water quality characterized by excessive algae blooms. Accumulibacter play a vital role in wastewater management, accumulating massive amounts of phosphorus inside their cells.
"Engineers and microbiologists have been trying for 35 years to grow this microbe, with no success," said Trina McMahon, Assistant Professor, Department of Civil and Environmental Engineering, University of Wisconsin, Madison, and one of the study's authors. "Remarkably, through metagenomic techniques, we were able to isolate and acquire the genome sequence of Accumulibacter phosphatis without a pure culture of the organism, which, like most microbes, eludes laboratory culture. We expect that clues hidden in the genome will lead to domestication of this mysterious organism, enabling further studies of its habits and lifestyle. The genome sequence will also enable biologists and engineers to understand why and how these organisms accumulate phosphorus, and it will lead to major advances in optimizing and controlling the EBPR wastewater treatment process," McMahon said. "In particular, it makes possible further research into why some wastewater treatment plants occasionally fail. These failures often result in serious pollution of lakes, rivers, and estuaries."
The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has selected 71 new genomic sequencing projects for its 2010 Community Sequencing Program (CSP) — a targeted sampling of the planet's biodiversity — to be characterized for bioenergy, climate, and environmental applications. ... more
Wastewater treatment is the largest microbially-mediated biotechnology process on the planet. When it works, it is a microbial symphony in tune with humanity. When it fails, the consequences can be dire. Researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) and col ... more
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When it comes to delivering genes to living human tissue, the odds of success come down the molecule. The entire therapy — including the tools used to bring new genetic material into a cell — must have predictable effects. Now, a new screening process will simplify non-viral transfection, p ... more
Researchers at the University of Wisconsin-Madison have found a new way to accelerate a workhorse instrument that identifies proteins. The high-speed technique could help diagnose cancer sooner and point to new drugs for treating a wide range of conditions.Proteins are not only numerous — h ... more
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Coat color of wild and domestic animals is a critical trait that has significant biological and economic impact. In a study published online in Genome Research, researchers have identified the genetic basis for black coat color, and white, in a breed of domestic sheep. In the wild, mammali ... more
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