Abstract
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 × 106 reads revealed >3 × 106 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 × 106 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.
Highlights
James River is an historical, cultural, and economic icon in North America [1] and one of the largest tributaries of the Chesapeake Bay
Bacterial groups that accounted for ≈ 1 % of assigned reads in either the WGS or the 16S data sets included Deltaproteobacteria, Curvibacter (1 % of bacterial reads: a symbiont of Hydra which was the most abundant of all eukaryote reads), Delftia, Comamonas, Alicycliphilus, and Verminephrobacter
Rivers provide numerous ecosystem services for humans and we are especially dependent on them for fresh water supply and sanitation purposes. This metagenome analysis illustrates that the core freshwater planktonic bacterio- and eukaryoplankton communities of this non-tidal portion of James River closely mirror the upper Mississippi River [22, 25], both of which differ from lake systems studied in a similar manner
Summary
James River is an historical, cultural, and economic icon in North America [1] and one of the largest tributaries of the Chesapeake Bay. Bacterial groups that accounted for ≈ 1 % of assigned reads in either the WGS or the 16S data sets included Deltaproteobacteria (some of which have recently been identified as pathogens), Curvibacter (1 % of bacterial reads: a symbiont of Hydra which was the most abundant of all eukaryote reads), Delftia (non-fermentative, Gram-negative bacteria from soil, activated sludge, crude oil, oil brines, and water [27], and recently observed in association with the use of medically invasive devices such as endotracheal tubes [28] and intravascular-catheters [29]), Comamonas (a soil bacterium utilized to treat the industrial by-product 3-chloroaniline [30]; one strain has been observed to be the cause of bacteremic infections [31]), Alicycliphilus (degrades alicyclic and aromatic hydrocarbons), and Verminephrobacter (earthworm symbionts).
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