Table of Contents

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

Related Reference: Ankrah, N. Y. D., A. L. May, J. L., Middleton, D. R. Jones, M. Hadden, J. R. Gooding, G. R. LeCleir, S. W. Wilhelm, S. R. Campagna and A. Buchan. (2014 Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition. International Society for Microbial Ecology Journal (2014) 8, 1089-1100; doi:10.1038/ismej.2013.216; published online 5 December 2013

See also, Supplemental Material (PDF)

Phage DNA was submitted to the Broad Institute and sequenced under the Gordon and Betty Moore Foundation’s Marine Phage, Virus, and Virome Sequencing Project. The Broad Institute sequencing data were assembled using the Lasergene SeqMan Pro. The assemblies resulted in the generation of single contigs for each phage genome.

The genome of Sulfitobacter sp. strain CB2047was sequenced using Illumina technology with an average sequencing coverage of approximately 600 x. The genome was assembled into 12 contigs, ranging in size from 18 kb to 2.3 Mb, using CLC Assembly Cell (CLC bio, Cambridge, MA, USA). The genome of CB2047 was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm .nih.gov/genome/annotation_prok/) and the KAAS genome annotation and pathway reconstruction server. 

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date
- created a BCO-DMO servable table of accessions and associated metadata obtained from the GenBank source information.

Description from NSF award abstract:
Prokaryotic viruses (phage) have long been hypothesized to influence microbial community composition, nutrient biogeochemistry and both the flux and character of carbon in the world's oceans. Model estimates indicate that > 25% of the daily carbon production in marine surface waters is shunted to the dissolved organic matter (DOM) pool by viral activity. Through this process viruses redistribute nutrient elements from large biological particles (i.e., bacteria, algae) into biologically inactive (dead) particulate and dissolved pools of organic compounds. Many of these compounds contain macro- and micronutrients (e.g., P, N, Fe) that can be rapidly recycled back into the food web. While we now have a better (yet far from complete) appreciation of the role of viruses in the regeneration of nutrient elements, we remain almost completely ignorant to, and have almost no data for, the role of viruses in the regeneration of organic carbon, the subsequent partitioning of this carbon by size (e.g. dissolved vs particulate) and bioavailability (labile vs recalcitrant). Understanding the contribution of virus activity to the various carbon pools and the rates associated with this process is an absolute necessity if we are to develop accurate marine and global carbon models.

There is little doubt that the global-scale influence of viruses is determined by host-phage interactions, yet our understanding of these interactions and their quantitative effects on system processes is in its infancy. To address these questions, it is imperative that we examine ecologically relevant model systems. To that end, this project focuses on phage that infect the Roseobacter clade, a numerically abundant and biogeochemically active group of heterotrophic marine bacteria. Despite the recognized importance of lineage members to the global cycling of elements (particularly carbon), we know little of the viruses ("roseophage") that infect them, the influence viruses have on host processes and the effects of this interaction on other members of the marine microbial community. As such this project is transformative in that it will exploit recently characterized virus-host models for biogeochemical and molecular studies of a major heterotrophic bacterioplankton lineage that is truly ecologically relevant.

The overall objectives of the project are to: (i) examine the distribution, diversity and production of roseophage, (ii) assess the composition and bioavailability of Roseobacter cell lysis-derived DOM and (iii) to track the subsequent uptake and metabolism of Roseobacter-derived carbon and nitrogen by marine surface water microbial communities. These objectives will be achieved through a combination of lab and field-based experiments: molecular tools will be developed to quantify specific rates of roseophage production and Roseobacter mortality under three different environmental regimes (a naturally productive open ocean regime, a near shore to off-shore gradient and induced phytoplankton blooms from mesocosms). The PIs will specifically determine the character and biological availability of carbon from lysates of Roseobacter in lab trials with model microbes. They will examine the rates of assimilation of radiolabeled Roseobacter lysate by natural communities which, when coupled with data on the composition, bioavailability and fate of the DOM released, will form the baseline for a model of Roseobacter-phage C-cycling through the microbial foodweb. Finally, complementary metabolomics studies of lysate consuming populations (in the lab and field) will provide unprecedented insight into how microbes perceive and process viral-lysed material. Collectively, these data will provide critical information on the interplay of phage with a major marine bacterial lineage and the ensuing influence these interactions have on microbial food webs.