Overview

In this paper, we describe the viral diversity of Lake Michigan–one of the earliest studies of its kind (particularly for that of a populous urban environment). Notably, we show a high abundance of species of the Caudovirales class, which includes phages which infect environmental bacterial involved in basic ecological processes such as Planktothrix (photosynthetic cyanobacteria) and important to public health such as Escherichia and Enterobacteria. Further, we make use of multidimensional scaling (MDS) to compare the diversity of our samples to previously fresh and marine ecological samples which lie closest to freshwater samples, but form their own distinct grouping from either fresh or marine samples.

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Abstract

Bacteriophages are powerful ecosystem engineers. They drive bacterial mortality rates and genetic diversity, and affect microbially mediated biogeochemical processes on a global scale. This has been demonstrated in marine environments; however, phage communities have been less studied in freshwaters, despite representing a potentially more diverse environment. Lake Michigan is one of the largest bodies of freshwater on the planet, yet to date the diversity of its phages has yet to be examined. Here, we present a composite survey of viral ecology in the nearshore waters of Lake Michigan. Sequence analysis was performed using a web server previously used to analyse similar data. Our results revealed a diverse community of DNA phages, largely comprising the order Caudovirales. Within the scope of the current study, the Lake Michigan virome demonstrates a distinct community. Although several phages appeared to hold dominance, further examination highlighted the importance of interrogating metagenomic data at the genome level. We present our study as baseline information for further examination of the ecology of the lake. In the current study we discuss our results and highlight issues of data analysis which may be important for freshwater studies particularly, in light of the complexities associated with examining phage ecology generally.