TY - JOUR
T1 - Metagenomic analysis of planktonic microbial consortia from a non-tidal urbanimpacted segment of James River
AU - Brown, Bonnie L.
AU - LePrell, Rebecca V.
AU - Franklin, Rima B.
AU - Rivera, Maria C.
AU - Cabral, Francine M.
AU - Eaves, Hugh L.
AU - Gardiakos, Vicki
AU - Keegan, Kevin P.
AU - King, Timothy L.
N1 - Funding Information:
Acknowledgements This work was supported by the Virginia Commonwealth University Department of Biology and by GenEco, LLC, Richmond, Virginia. Partial funding for 16S sequencing was provided by the Aquatic Ecology Branch of the US Geological Survey's Leetown Science Center. This paper is contribution #56 from the VCU Rice Rivers Center. The Jeffress Trust Awards in Interdisciplinary Research partially supported the contribution of M.C. Rivera. The authors acknowledge Arthur Butt and Roger Stewart of Virginia Department of Environmental Quality for responding to our Freedom of Information Act request and providing data relating to James River and its uses, Blair Krusz of Virginia Department of Conservation and Recreation for assistance with mapping, and Robin Johnson of US Geological Survey Leetown Science Center for sequencing support. The authors thank Michael Sadowsky, Christopher Staley, and Trevor Gould for sharing Mississippi River sequence accessions. The authors also appreciate the valuable insight provided by two anonymous reviewers, and acknowledge John Miller and Aaron Aunins at the US Geological Survey, Leetown Science Center for critical review of this report. Use of trade, product, or firm names does not imply endorsement by the U.S. Government.
Funding Information:
This work was supported by the Virginia Commonwealth University Department of Biology and by GenEco, LLC, Richmond, Virginia. Partial funding for 16S sequencing was provided by the Aquatic Ecology Branch of the US Geological Survey’s Leetown Science Center. This paper is contribution #56 from the VCU Rice Rivers Center. The Jeffress Trust Awards in Interdisciplinary Research partially supported the contribution of M.C. Rivera. The authors acknowledge Arthur Butt and Roger Stewart of Virginia Department of Environmental Quality for responding to our Freedom of Information Act request and providing data relating to James River and its uses, Blair Krusz of Virginia Department of Conservation and Recreation for assistance with mapping, and Robin Johnson of US Geological Survey Leetown Science Center for sequencing support. The authors thank Michael Sadowsky, Christopher Staley, and Trevor Gould for sharing Mississippi River sequence accessions. The authors also appreciate the valuable insight provided by two anonymous reviewers, and acknowledge John Miller and Aaron Aunins at the US Geological Survey, Leetown Science Center for critical review of this report. Use of trade, product, or firm names does not imply endorsement by the U.S. Government.
Publisher Copyright:
© 2015 Brown et al.
PY - 2015/9/19
Y1 - 2015/9/19
N2 - 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.
AB - 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.
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U2 - 10.1186/s40793-015-0062-5
DO - 10.1186/s40793-015-0062-5
M3 - Article
C2 - 26388969
AN - SCOPUS:84941756052
SN - 1944-3277
VL - 10
JO - Standards in Genomic Sciences
JF - Standards in Genomic Sciences
IS - 1
M1 - 65
ER -