Table of Contents

• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

This datasest links to accessions at the iMicrobe data repository containing fasta formatted nucleic acid sequences. Samples are from Surface waters of Kaneohe Bay, a tropical embayment on eastern shore of Oahu, HI, 21° 25’ 46.80” N, 157° 47’ 31.51” W.

Sample Name: CAM_SMPL_000815 (collected Aug 1, 2009)
Link: http://data.imicrobe.us/sample/view/333

Sample Name: CAM_SMPL_000824 (collected Jun 3, 2010)
Link: http://data.imicrobe.us/sample/view/324

Related References:

Culley AI, JA Mueller, M Belcaid, EM Wood-Charlson, G Poisson, GF Steward (2104). The characterization of RNA viruses in tropical seawater using targeted PCR and metagenomics. mBio 5(3):e01210-14. doi:10.1128/mBio.01210-14.

Steward GF, AI Culley, JA Mueller, EM Wood-Charlson, M Belcaid, G Poisson (2013). Are we missing half the viruses in the sea? ISME Journal 7(3) 627-679.

454 Pyrosequencing on the GS FLX Titanium platform (Roche Diagnostics Corporation) was used to generate the sequence data. 

Sequences were processed though the quality control pipeline of the RAST metagenomics server (http://metagenomics.anl.gov/?page=Home) to remove short and low-quality reads as well as artificial replicates.

Viruses are an integral component of the marine food web contributing to the disease and mortality of essentially every type of marine life, yet the diversity of marine viral assemblages remains very poorly characterized. This is especially true of the RNA-containing viruses. There are several reports of isolations of RNA-containing viruses that infect marine protists, but the number of isolates and the number of cultivation-independent surveys of RNA viral diversity are still very limited. Previous studies in coastal British Columbia and in coastal Oahu have shown RNA viruses are diverse and persistent in both temperate and tropical waters. Many of these novel gene sequences appear to derive from viruses of marine protists and their high diversity suggests that viral infections are a persistent force shaping protistan community composition in the sea. It is now clear that the few available isolates of marine RNA viruses are just the tip of the iceberg; novel RNA viruses are still being discovered with each new sample analyzed and the cultivated representatives are not adequately representative. Quantifying the abundance, diversity, and dynamics of these viruses, and obtaining additional representative isolates are some of the important first steps we need to take to incorporate the RNA viruses into the ecology of the sea. Our tasks in this project were to 1) determine the diversity of RNA viruses in coastal and offshore seawater 2) determine whether the RNA viruses make a significant numerical contribution to the total virus pool and 3) isolate and characterize new RNA viruses that infect phytoplankton.