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The discovery of mysterious microbes brings a new perspective to marine ecosystem research
The discovery of mysterious microbes brings a new perspective to marine ecosystem research
The first paper published in the 454 Sequencing System's new GS FLX Titanium reagent focuses on metagenomics
An unusual microbe found in the high seas forced scientists to rethink their understanding of the carbon-nitrogen cycle in marine ecosystems. A team from the University of California, USA, used the new GS FLX Titanium series of reagents from Roche's 454 Life Sciences to sequence the metagenomics of marine samples and discovered a new species of cyanobacteria. The long-length, highly accurate technique of this sequencing system provides a comprehensive view of the long-neglected bacterial species and its surprising genetic makeup. The study was published in the November 14, 2008 issue of Science and details the discovery process of the new cyanobacteria. Cyanobacteria are a class of bacteria that can be used for photosynthesis and were formerly known as blue-green algae. Unlike other known free-living cyanobacteria, this species lacks a fixed carbon source and a gene for photosynthesis - photosynthesis is a process of light energy dependence that converts carbon dioxide and water into sugar and by-product oxygen. Importantly, this mysterious microbe is another expert in key ecological functions. It “fixes†the nitrogen in the atmosphere into a form that can be used by other organisms to provide a natural fertilizer for the ocean.
“It’s so exciting to have such an extraordinary metabolic process,†said lead researcher Jonathan Zehr. “We are trying to understand how organisms like this can survive and grow in the absence of so many factors.†Early research by the Zehr team found a surprisingly large number of nitrogen-fixing cyanobacteria in the offshore and high seas. Although 80% of the air is nitrogen, most of the organisms cannot be used directly unless the nitrogen is fixed to molecules such as ammonia and nitrate. Since nitrogen is very important for all life forms, nitrogen fixation is a major factor in regulating total biomass in the ocean. “New bacteria are one of the most abundant nitrogen-fixing organisms in many seas,†Zehr said. “From an ecological point of view, it is important to understand its role in ecosystems and how it affects carbon and nitrogen balance.â€
The new cyanobacteria were discovered using a new GS FLX Titanium series of reagents for rapid, high-throughput genomic DNA sequencing of enriched marine water samples. In fact, this study was the first article published after the upgrade of the reagent series. The upgraded reagents produce more than 1 million independent fragment readings per run, and reading lengths greater than 400 are shocking to get data and analysis results. We have been trying to cultivate this for many years.
Microorganisms, but not successful, with the data generated by a single run of GS FLX Titanium, we performed a single sequencing run in a few days and obtained valuable genomic information directly from environmental samples. Zehr explains that the long read length of this system is critical for identifying and analyzing this unique bacterial genome from complex microbial populations. â€
“This study clearly demonstrates the importance and usefulness of the long and highly accurate read lengths that can be produced by the new GS FLX Titanium series of reagents. The sequence read length and the result of the stitching are exactly what the Zehr team has done for this attractive long term. A missing link in the research," said Jason Affourtit, project leader for the 454 Advanced Technology Integration Division of Life Sciences. He is also a collaborator of this research.
The research team hopes to continue their research, locate the location of new bacteria in the ocean, and determine its global abundance. They will also focus on the differences between the metabolism of this species and other known cyanobacteria. Although the cultivation of this bacterium has not been successful, new genomic information opens up a potential way to explore the application of its unusual metabolic mechanisms in biotechnology.
The title of the paper is "Globally distributed Uncultivated Oceanic N2-Fixing Cyanobacteria Lack Oxygenic Photosystem II", published in the November 14 issue of Science. 454 Life Sciences is one of Roche's Centers of Excellence in Applied Science, developing and commercializing the innovative 454 Sequencing System for ultra-high throughput DNA sequencing. Specific applications include de novo sequencing and resequencing of genomes, metagenomics, RNA analysis, and directed sequencing of DNA target regions. The 454 sequencing system features simple sample preparation and no
Bias, the read length includes the paired end read length is long and the accuracy is high. The technology of the 454 Sequencing System has spawned hundreds of peer-reviewed studies in various research areas, such as cancer and infectious disease research, drug screening, marine biology, anthropology, and paleontology.