title: Survey of viral populations within Lake Michigan nearshore waters at four Chicago area beaches.
abstract: In comparison to the oceans, freshwater environments represent a more diverse community of microorganisms, exhibiting comparatively high levels of variability both temporally and spatially Maranger and Bird, Microb. Ecol. 31 (1996) 141-151. This level of variability is likely to extend to the world of viruses as well, in particular bacteria-infecting viruses (bacteriophages). Phages are known to influence bacterial diversity, and therefore key processes, in environmental niches across the globe Clokie et al., Bacteriophage 1 (2011) 31-45; Jacquet et al., Adv. Ocean Limn. 1 (2010) 97-141; Wilhelm and Suttle, Bioscience 49 (1999) 781-788; Bratback et al., Microb. Ecol. 28 (1994) 209-221. Despite their prevalence and likely critical role in freshwater environments, very few viral species have been characterized. Metagenomic approaches, however, have allowed for a glimpse into phage diversity. We collected surface water samples from four Chicago area beaches - Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach - every two weeks from May 13 through August 5, 2014. Sampling was conducted with four biological replicates for each sampling date and location, resulting in 112 samples. DNA isolated from each of the individual samples for a given collection date/location was pooled together, with one exception - Calumet Beach on August 5, 2014 - in which each biological replicate was sequenced individually. Raw sequence data is available via NCBI's SRA database (part of BioProject PRJNA248239).
authors.affiliation: Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA.
authors.forename: Emily
authors.initials: E
authors.lastname: Sible
authors.affiliation: Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA.
authors.forename: Alexandria
authors.initials: A
authors.lastname: Cooper
authors.affiliation: Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA.
authors.forename: Kema
authors.initials: K
authors.lastname: Malki
authors.affiliation: Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA.
authors.forename: Katherine
authors.initials: K
authors.lastname: Bruder
authors.affiliation: Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA.
authors.forename: Siobhan C
authors.initials: SC
authors.lastname: Watkins
authors.affiliation: Department of Pharmacology and Toxicology, University of Texas Medical Branch, 5.112 BSB, Galveston, TX 77555, USA.
authors.forename: Yuriy
authors.initials: Y
authors.lastname: Fofanov
authors.affiliation: Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA ; Bioinformatics Program, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA ; Department of Computer Science, Loyola University Chicago, 820 N Michigan Ave, Chicago, IL 60611, USA.
authors.forename: Catherine
authors.initials: C
authors.lastname: Putonti
keywords: Freshwater; Lake Michigan; Metagenomics; Viral community