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Stand Genomic Sci. 2015 Sep 19;10:65. doi: 10.1186/s40793-015-0062-5. eCollection 2015.

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River.

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Department of Biology, Virginia Commonwealth University, 1000 W Cary Street, Richmond, VA 23284 USA.
Environmental Epidemiology Division, Virginia Department of Health, 109 Governor Street, Richmond, VA 23219 USA.
Department of Microbiology and Immunology, Virginia Commonwealth University, 1101 East Marshall Street, Richmond, VA 23298 USA.
School of Life Sciences, Virginia Commonwealth University, 1000 W Cary Street, Richmond, VA 23284 USA.
Virginia Department of Conservation and Recreation, Soil and Water Conservation, 600 East Main Street, Richmond, VA 23219 USA.
Argonne National Laboratory, Biosciences Division, 9700 South Cass Avenue, Argonne, IL 60439 USA.
US Geological Survey, Aquatic Ecology Branch, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV 25430 USA.


Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 × 10(6) reads revealed >3 × 10(6) genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; MG-RAST:4631271.3; EMB:2184), 4 × 10(6) reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria, predominantly Comamonadaceae. The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads. Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax (biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3 % of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Taken together, these analyses exposed previously unknown aspects of microbial biodiversity, documented the ecological responses of microbes to urban effects, and revealed the noteworthy presence of 22 human-pathogenic bacterial genera (e.g., Enterobacteriaceae, pathogenic Pseudomonadaceae, and 'Vibrionales') and 6 pathogenic eukaryotic genera (e.g., Trypanosomatidae and Vahlkampfiidae). This information about pathogen diversity may be used to promote human epidemiological studies, enhance existing water quality monitoring efforts, and increase awareness of the possible health risks associated with recreational use of James River.


Industry; James River; Pathogen; Temperate urban river ecosystem; Virginia; Water-borne disease

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