The Importance of Marine Picoeukaryotes and the Search for Lost Time

submitted by: dougramsey
Unicellular eukaryotes are responsible for a massive amount of photosynthetic carbon fixation in marine systems. The smallest among these fall within the “pico” size fraction (<2 micrometers in diameter), are broadly distributed – from coastal to open-ocean environments – and are highly diverse. Picoeukaryotes contribute a significant proportion of the biomass and primary production within this size fraction, often rivaling their cyanobacterial counterparts Prochlorococcus and...

Deep-Ocean Metagenomics: Comparative Investigations of Microbes Inhabiting Hydrothermal Vents and the Cold Deep Ocean

submitted by: dougramsey
The deep-ocean accounts for the majority of the water on our planet. While the cold deep-ocean is the dominant nutrient-challenged ecosystem, hydrothermal vents represent oases along tectonically active areas of the seafloor. Hydrothermal vents and the surrounding cold deep-ocean each support unique communities of microbes and viruses that have become highly adapted to local conditions. Through cycles of infection and host cell lysis, bacteriophages (viruses that specifically infect...

Metagenomic Comparison of the Microbial Hindgut Communities in Drywood- and Grass-Feeding Termites

submitted by: dougramsey
Falk Warnecke, Microbial Ecology Program, Joint Genome Institute, DOE Co-authors: Natalia Ivanova, Martin Allgaier, Nikos Kyrpides, Rudolf Scheffrahn, and Phil Hugenholtz Termites are highly efficient in degrading lignocellulosic biomass. In a recent metagenomic study we showed for the first time that microbes inhabiting the termite hindgut encode hundreds of carbohydrate-active enzymes, e.g. glycosyl hydrolases (GHs) and tens of carbohydrate binding modules (CBMs) and by implication are...

International Soil Metagenome - Sequencing Project

submitted by: dougramsey
Soil is often considered to be one of the main reservoirs of microbial diversity on the planet. This diversity could provide a range of information about the origins of microbial functional diversity as well as novel genetic resources. However, our historical inability to cultivate the majority of soil bacteria has hampered our understanding and exploitation of this large diverse community (more than 95% are often considered inaccessible through traditional culture techniques). Over the last...

Metagenomic Analysis of Deep Subsurface Environments Hideto Takami, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)

submitted by: dougramsey
As a deep subsurface biosphere is thought to be the biggest biosphere in the earth, it is very interesting to know the phylogenetic and functional diversity in such environments. However, there is a little biological information for them because it is very hard to recover whole microbial community by only culture-base methods. In that sense, metagenomics is one of major useful methods to elucidate the microbial flora in unknown biosphere, which seems to be constructed by mainly unculturable...

Efficient Metagenomics Data Processing: Pitfalls and Solutions

submitted by: dougramsey
Nikos Kyrpides, Joint Genome Institute Co-authors: Kostas Mavrommatis, Natalia Ivanova Metagenomics has emerged as a powerful tool for exploration of the functional capabilities of microbial communities regardless of the ability of their members to grow in pure culture. However, little is known for the efficacy of the methods used to process these datasets. Further more, sequencing of environmental genomic DNA usually results in large, highly fragmented datasets representing a significant...