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• W2042893247 abstract "Microbes are responsible for most of the chemical transformations that are crucial to sustaining life on Earth. Their ability to inhabit almost any environmental niche suggests that they possess an incredible diversity of physiological capabilities. However, we have little to no information on a majority of the millions of microbial species that are predicted to exist, mainly because of our inability to culture them in the laboratory.A growing discipline called metagenomics allows us to study these uncultured organisms by deciphering their genetic information from DNA that is extracted directly from their environment, thus effectively bypassing the laboratory culture step. Metagenomics allows us to address the questions “who's there?”, “what are they doing?”, and “how are they doing it?”, offering insights into the evolutionary history as well as previously unrecognized physiological abilities of uncultured communities.Studies such as the J. Craig Venter Institute's Global Ocean Sampling (GOS) expedition (in this issue) reveal a remarkable breadth and depth of microbial diversity in the oceans. To date, researchers have made significant but largely preliminary inroads into understanding the biogeography of microbial populations across ecosystems. We know even less about the dynamic physiological processes and complex interactions that impact global carbon cycles and ocean productivity. Marine microbes are thought to act as part of the biological conduit that transports carbon dioxide from the surface to the deep oceanic realms. By removing carbon from the atmosphere and sequestering it (in the form of organic matter), marine microorganisms may significantly affect global climate. Although we now have numerous global and real-time methods to measure physical and chemical parameters within the ocean, few methods or concepts have been developed to measure important microbial processes on a global scale. Even if the technology to make such measurements existed, we would presently not know what to measure or how to interpret those measurements.We invite the research community to submit its metagenomics data to CAMERA.We need a systematic way to explore the structure and function of ocean ecosystems, and their impact on global carbon processing and climate. Metagenomics has the potential to shed light on the genetic controls of these processes by investigating the key players, their roles, and community compositions that may change as a function of time, climate, nutrients, carbon dioxide, and anthropogenic factors. These studies include a substantial informatics component, requiring researchers to take on complex computational and mathematical challenges. Nonetheless, microbiologists have been quick to seize upon this modern technique, resulting in a deluge of sequence data, and an ever-widening gap between the rates of collecting data and interpreting it.The Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) project [1] is an important first step in attempting to bridge these gaps and in developing global methods for monitoring microbial communities in the ocean and their response to environmental changes. The aim is to create a rich, distinctive data repository and bioinformatics tools resource that will address many of the unique challenges of metagenomics and enable researchers to unravel the biology of environmental microorganisms (Figure 1). CAMERA's database includes environmental metagenomic and genomic sequence data, associated environmental parameters (“metadata”), precomputed search results, and software tools to support powerful cross-analysis of environmental samples.Figure 1Schematic of Intended Core Functions of the CAMERA ProjectThe initial release will include data and tools associated with the companion set of GOS expedition publications [2–4]; metagenome data from the Hawaii Ocean Time Series Station ALOHA [5] and marine viromes from four different oceanic regions[6]; standard nonredundant sequence databases (e.g., nrnt for nucleotides and nraa for amino acids[7]); and collections of microbial genome sequences, including a set of 155 marine microbial genomes funded by the Gordon and Betty Moore Foundation. The focal point for the CAMERA project is its Web site: http://camera.calit2.net. We invite the research community to submit its metagenomics data to CAMERA, and are establishing mechanisms to streamline this process. Here we describe some of the key challenges and features of the CAMERA project." @default.
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• W2042893247 date "2007-03-13" @default.
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• W2042893247 title "CAMERA: A Community Resource for Metagenomics" @default.
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• W2042893247 doi "https://doi.org/10.1371/journal.pbio.0050075" @default.
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