Shady Amin and coauthors published a new study on the copper requirements of ammonia-oxidizing archaea (AOA), a major group of prokaryotes that are believed to dominate ammonia oxidation in the oceans. The few publicly available AOA genomes suggested these organisms have a Cu requirement due to the presence of a high number of Cu metalloenzymes. Indeed, this study finds that the only marine AOA available in pure culture is Cu-limited at copper concentrations that are commonly found in the marine environment.
Silicification in Coastal Diatom Communities
Colleen A. Durkin and co-authors published a new study on diatom silicification. The authors used in situ incubation experiments, along with laboratory culturing experiments, to demonstrate that variation in silicic acid supply alters the silicification of coastal diatom blooms and diatom sinking rates. Click here to read more in Limnology and Oceanography: Silicic acid supplied to coastal diatom communities influences cellular silicification and the potential export of carbon
SEAStAR Software for Metagenome Analysis Released
SEAStAR is an open-source package of software tools for the analysis of environmental next-generation (Illumina®, SOLiD™) sequence data. Prototype versions of these tools were used to analyze the metagenomic data in our publication: Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota. You can learn more by visiting the SEAStAR Home Page.
Positive Gene Selection in Diatoms
Julie Koester and co-authors published new findings on positive selection in diatoms. The authors were able to connect positively selected genes to the selective pressures of nutrient limitation and temperature, successfully integrating genotype with phenotype in diatoms. Click here to read more in Molecular Biology and Evolution: Positive Selection within a Diatom Species Acts on Putative Protein Interactions and Transcriptional Regulation
Investigating Silica Precipitation in Diatoms
Colleen Durkin and co-authors published on the role of diatom community composition and the transcription of key, frustule-related genes on silica precipitation in the environment. Click here to read more in Limnology and Oceanography: Frustule-related gene transcription and the influence of diatom community composition on silica precipitation in an iron-limited environmentt
Genome of an uncultured class of Euryarchaeota assembled from a metagenomic sample of Puget Sound seawater
Vaughn Iverson and colleagues published "Untangling Genomes from Metagenomes" in Science recently. Synopses of the study may be found at Nature News, Biotechniques, Genome Web, and the New York Times.