Abstract
Freshwater lakes are home to bacterial communities with 1000s of interdependent species. Numerous high-throughput 16S rRNA gene sequence surveys have provided insight into the microbial taxa found within these waters. Prior surveys of Lake Michigan waters have identified bacterial species common to freshwater lakes as well as species likely introduced from the urban environment. We cultured bacterial isolates from samples taken from the Chicago nearshore waters of Lake Michigan in an effort to look more closely at the genetic diversity of species found there within. The most abundant genus detected was Pseudomonas, whose presence in freshwaters is often attributed to storm water or runoff. Whole genome sequencing was conducted for 15 Lake Michigan Pseudomonas strains, representative of eight species and three isolates that could not be resolved with named species. These genomes were examined specifically for genes encoding functionality which may be advantageous in their urban environment. Antibiotic resistance, amidst other known virulence factors and defense mechanisms, were identified in the genome annotations and verified in the lab. We also tested the Lake Michigan Pseudomonas strains for siderophore production and resistance to the heavy metals mercury and copper. As the study presented here shows, a variety of pseudomonads have inhabited the urban coastal waters of Lake Michigan.
Highlights
Bacteria plays a critical role in the ecosystems of freshwater lakes driving global biogeochemical cycles
Water collected from the Chicago nearshore waters of Lake Michigan in the summer of 2009 and 2016 were plated on six different medias
The genera identified were representative of species which are known to be present within freshwaters and more critically are amenable to the conditions of culture used in this study
Summary
Bacteria plays a critical role in the ecosystems of freshwater lakes driving global biogeochemical cycles. Many bacterial groups within freshwaters have a global distribution: Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Verrucomicrobia (Zwart et al, 1998; Newton et al, 2011) Dominant members of these phyla include the Proteobacteria genus Acinetobacter (Lee et al, 2016), the acI cluster of Actinobacteria (Newton et al, 2007; Neuenschwander et al, 2018), and the Bacteroidetes genera Sphingobacteriales, Sediminibacterium, Fluviicola, and Flavobacterium (Salmaso et al, 2018). Bacteria can be introduced into a community via effluent from water treatment plants (e.g., Escherichia coli and Enterococcus) and stormwater runoff (e.g., Pseudomonas and Sphingomonas) Such introductions can include species harboring antibiotic resistance genes into the lake ecosystem (Drury et al, 2013; Marti et al, 2013; Fisher et al, 2015; Saarenheimo et al, 2017; Chu et al, 2018; Lorenzo et al, 2018)
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