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Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic.
Metagenomic data sets were generated from samples collected along a coastal to open ocean transect between Southern California Bight and California Current waters during a seasonal upwelling event, providing an opportunity to examine the impact of episodic pulses of cold nutrient-rich water into surface ocean microbial communities. The data set consists of ~5.8 million predicted proteins across seven sites, from three different size classes: 0.1-0.8, 0.8-3.0 and 3.0-200.0 μm. Taxonomic and...
Functional tradeoffs underpin salinity-driven divergence in microbial community composition.
Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing...
Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities.
Transitions in community genomic features and biogeochemical processes were examined in surface and subsurface chlorophyll maximum (SCM) microbial communities across a trophic gradient from mesotrophic waters near San Diego, California to the oligotrophic Pacific. Transect end points contrasted in thermocline depth, rates of nitrogen and CO2 uptake, new production and SCM light intensity. Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and...
England, Here We Come!
In calm and clear conditions on May 11 Sorcerer II set sail for Plymouth, England. We enjoyed our brief stay in the Azores, but we were all excited to get to the U.K. and complete our North Atlantic crossing. As I mentioned in previous entries, we took samples near areas studied by the Department of Oceanography and Fisheries IMAR-University of the Azores (DOP/UAç). We sailed from Faial to the neighboring island of Pico to collect the first sample. On our second day...
In Memory of Dr. J. Robert Beyster
The JCVI family mourns the loss of a true friend and generous supporter, Dr. J. Robert Beyster. Dr. Beyster was a World War II Veteran, a nuclear engineer whose research propelled the Department of Defense's weapons systems and submarines into the future of war fighting, but most notably, he founded Science Applications International Corporation (SAIC), an employee-owned multi-billion dollar corporation. The Beyster Family have been generous supporters of science programs at the...
Complete genome sequence of Caulobacter crescentus.
The complete genome sequence of Caulobacter crescentus was determined to be 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes. This organism, which grows in a dilute aquatic environment, coordinates the cell division cycle and multiple cell differentiation events. With the annotated genome sequence, a full description of the genetic network that controls bacterial differentiation, cell growth, and cell cycle progression is within reach. Two-component signal...
The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples.
Viruses are the most abundant biological entities on our planet. Interactions between viruses and their hosts impact several important biological processes in the world's oceans such as horizontal gene transfer, microbial diversity and biogeochemical cycling. Interrogation of microbial metagenomic sequence data collected as part of the Sorcerer II Global Ocean Expedition (GOS) revealed a high abundance of viral sequences, representing approximately 3% of the total predicted proteins....
TIGR / HGS Funding Relationship Reaches Early Conclusion
June 24, 1997 ROCKVILLE, MD-- June 24, 1997 -- The Institute for Genomic Research (TIGR) and Human Genome Sciences, Inc. (HGS) (NASDAQ: HGSI) today announced that they have signed an agreement whereby HGS will cease future payments to TIGR in return for relinquishing rights to future work done by TIGR. While this ends the TIGR/HGS relationship, HGS will retain all rights to patents granted now or in the future on work by TIGR prior to this agreement. Additionally, TIGR agrees not to...
Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus.
We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of A1163 with the recently sequenced A. fumigatus isolate Af293 has identified core, variable and up to 2% unique genes in each genome. While the core genes are 99.8% identical at the nucleotide level, identity for variable genes...
Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.
Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5...