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...

Setting the Stage: Mobilizing the Metagenomics Community

submitted by: dougramsey

About 250 leaders in the emerging science of metagenomics converged at the UC San Diego division of the California Institute for Telecommunications and Information Technology (Calit2) earlier this month for the third Annual International Conference on Metagenomics. The conference was a week-long opportunity to share data and discuss the latest research, explore how advances in computing and sequencing technologies might be of benefit, and build or strengthen collaborations in the field.

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...

Towards Transparency of Computational Analyses: A Central SOP Repository

submitted by: dougramsey
The methodologies used to generate genome and metagenome annotations are diverse and vary between groups and laboratories. Descriptions of the annotation process are helpful in interpreting genome annotation data. Some groups have produced Standard Operating Procedures (SOPs) that describe the annotation process, but standards are lacking for structure and content of these descriptions. A general structure for SOP documents that are relevant to genome annotation, metagenomics, environmental...

Towards an Open Access Gazetteer

submitted by: dougramsey
The Gazetteer (Gaz) is a community-based project of the EnvO Consortium for describing instances of organism environments and biological samples supporting consistent annotation of locations and environments. The Gazetteer describes places and place names, and the relations between them. The Gaz, with 130,000 plus terms (over 50 % of terms defined) and relations, is being utilizing in scientific investigations such as applying Gaz terms to organisms based on free-text from the Encyclopedia...

Challenges in Ecological Metagenomics

submitted by: dougramsey
Since the first metagenomics study was published 17 years ago, the ability to make ecological inferences has been limited by sequencing throughput and the ability to analyze the data. Yet, if the potential of metagenomics to help us decipher the structure and function of microbial ecosystems is to be realized, it is essential that our bioinformatics tools motivate our sequencing efforts. This is analogous to the bioinformatics advances that were made to accelerating the sequencing of the...