Dataset Information

Metagenomic characterization of Chesapeake Bay virioplankton.

ABSTRACT: Viruses are ubiquitous and abundant throughout the biosphere. In marine systems, virus-mediated processes can have significant impacts on microbial diversity and on global biogeocehmical cycling. However, viral genetic diversity remains poorly characterized. To address this shortcoming, a metagenomic library was constructed from Chesapeake Bay virioplankton. The resulting sequences constitute the largest collection of long-read double-stranded DNA (dsDNA) viral metagenome data reported to date. BLAST homology comparisons showed that Chesapeake Bay virioplankton contained a high proportion of unknown (homologous only to environmental sequences) and novel (no significant homolog) sequences. This analysis suggests that dsDNA viruses are likely one of the largest reservoirs of unknown genetic diversity in the biosphere. The taxonomic origin of BLAST homologs to viral library sequences agreed well with reported abundances of cooccurring bacterial subphyla within the estuary and indicated that cyanophages were abundant. However, the low proportion of Siphophage homologs contradicts a previous assertion that this family comprises most bacteriophage diversity. Identification and analyses of cyanobacterial homologs of the psbA gene illustrated the value of metagenomic studies of virioplankton. The phylogeny of inferred PsbA protein sequences suggested that Chesapeake Bay cyanophage strains are endemic in that environment. The ratio of psbA homologous sequences to total cyanophage sequences in the metagenome indicated that the psbA gene may be nearly universal in Chesapeake Bay cyanophage genomes. Furthermore, the low frequency of psbD homologs in the library supports the prediction that Chesapeake Bay cyanophage populations are dominated by Podoviridae.

SUBMITTER: Bench SR

PROVIDER: S-EPMC2168038 | biostudies-literature | 2007 Dec

REPOSITORIES: biostudies-literature

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Metagenomic characterization of Chesapeake Bay virioplankton.

Bench Shellie R SR Hanson Thomas E TE Williamson Kurt E KE Ghosh Dhritiman D Radosovich Mark M Wang Kui K Wommack K Eric KE

Applied and environmental microbiology 20071005 23

Viruses are ubiquitous and abundant throughout the biosphere. In marine systems, virus-mediated processes can have significant impacts on microbial diversity and on global biogeocehmical cycling. However, viral genetic diversity remains poorly characterized. To address this shortcoming, a metagenomic library was constructed from Chesapeake Bay virioplankton. The resulting sequences constitute the largest collection of long-read double-stranded DNA (dsDNA) viral metagenome data reported to date. ...[more]

PMID: 17921274

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Project description:Vibrio parahaemolyticus naturally-occurs in brackish and marine waters and is one of the leading causes of seafood-borne illness. Previous work studying the ecology of V. parahaemolyticus is often limited in geographic extent and lacking a full range of environmental measures. This study used a unique, large dataset of surface water samples in the Chesapeake Bay (n=1,385) collected from 148 monitoring stations from 2007 to 2010. Water was analyzed for over 20 environmental parameters with additional meteorological and surrounding land use data. V. parahaemolyticus-specific genetic markers thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and tdh-related hemolysin (trh) were assayed using quantitative PCR (qPCR), and interval-censored regression models with non-linear effects were estimated to account for limits of detection and quantitation. tlh was detected in 19.6% of water samples; tdh or trh markers were not detected. Results confirmed previously reported positive associations for V. parahaemolyticus abundance with temperature and turbidity and negative associations with high salinity (> 10-23‰). Furthermore, the salinity relationship was determined to be a function of both low temperature and turbidity, with an increase of either nullifying the high salinity effect. Associations with dissolved oxygen and phosphate also appeared stronger when samples were taken nearby human developments. Renewed focus on the V. parahaemolyticus ecological paradigm is warranted to protect public health.ImportanceVibrio parahaemolyticus is one of the leading causes of seafood-borne illness in the United States and across the globe. Exposure is often through consuming raw or undercooked shellfish. Given the natural presence of the bacterium in the marine environment, improved understanding of its environmental determinants is necessary for future preventative measures. This analysis of environmental Vibrio parahaemolyticus is one of only a few that utilize a large dataset measured over a wide geographic and temporal range. The analysis also includes a large number of environmental parameters for Vibrio modeling, many of which have previously only been tested sporadically, and some of which have not been considered before. The results of the analysis revealed previously unknown relationships between salinity, turbidity, and temperature that provide significant insight into the abundance and persistence of V.parahaemolyticus bacterium in the environment. This information will be essential for developing environmental forecast models for the bacterium.

Dataset Information

Metagenomic characterization of Chesapeake Bay virioplankton.

Publications

Metagenomic characterization of Chesapeake Bay virioplankton.

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