Dataset: SPOT virus 3H peak abund

T4-like myovirus communities were analyzed by terminal restriction fragment length polymorphism (TRFLP) of g23, which encodes the major capsid protein (Chow and Fuhrman, 2012). Viral fingerprints were obtained from both terminal fragments (5’ and 3’). g23-TRFLP products were run in duplicate on non-adjacent lanes on an ABI377 by slab gel electrophoresis with internal size standards (Bioventures, Murfreesboro, TN, USA) every 25 bp (50–900 bp) or 50 bp (900–1400 bp). Peaks were identified in DAx (van Mierlo, Inc, Eindhoven, The Netherlands). Fragments (50–500 bp) were rounded to the nearest 0.1 bp and dynamically binned (Ruan, et al., 2006b; Chow and Fuhrman, 2012). The resulting bins were manually curated to merge bins <0.1 bp wide with the nearest neighbor. Terminal fragments from in silico analysis of publicly available T4-like viral genomes were used to assign identities to environmental g23-TRFLP OTUs. Unique fragment lengths were considered as individual OTUs. Relative abundance of each OTU was calculated by dividing a peak’s area by the total area within the monthly fingerprint. Viral OTUs <0.1% of the community were removed from further analysis, and the remaining peaks were normalized by sample to determine relative abundance per month; each community thus totaled to 100%.

Relevant References:

* Chow CET, Kim DY, Sachdeva R, Caron DA, and Fuhrman JA. (2014). Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists. ISME Journal, 8: 816-829

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 Chow C-ET, Fuhrman JA. (2012). Seasonality and monthly dynamics of marine myovirus communities. Environ Microbiol 14: 2171–2183.

 Chow C-ET, Sachdeva R, Cram JA, Steele JA, Needham DM, Patel A et al. (2013). Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight. ISME J; epub ahead of print 18 July 2013; doi:10.1038/ismej.2013.122.

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 Countway PD, Vigil PD, Schnetzer A, Moorthi SD, Caron DA. (2010). Seasonal analysis of protistan community structure and diversity at the USC Microbial Observatory (San Pedro Channel, North Pacific Ocean). Limnol Oceanogr 55: 2381–2396.

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