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

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 x 106 reads revealed >3 x 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 x 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 polycyclicmore » 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. Altogether, 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.« less

Authors:
 [1];  [2];  [1];  [1];  [3];  [4];  [5];  [6];  [7]
  1. Virginia Commonwealth Univ., Richmond, VA (United States). Dept. of Biology
  2. Virginia Dept. of Health, Richmond, VA (United States). Environmental Epidemiology Div.
  3. Virginia Commonwealth Univ., Richmond, VA (United States). Dept. of Microbiology and Immunology
  4. Virginia Commonwealth Univ., Richmond, VA (United States). School of Life Sciences
  5. Virginia Dept. of Conservation and Recreation, Soil and Water Conservation, Richmond, VA (United States)
  6. Argonne National Lab. (ANL), Argonne, IL (United States). Biosciences Div.
  7. U.S. Geological Survey, Kearneysville, WV (United States). Aquatic Ecology Brance
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1224065
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; James River; Virginia; temperature urban river ecosystem; industry; pathogen; water-borne disease

Citation Formats

Brown, Bonnie L., LePrell, Rebecca V., Franklin, Rima B., Rivera, Maria C., Cabral, Francine M., Eaves, Hugh L., Gardiakos, Vicki, Keegan, Kevin P., and King, Timothy L. Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River. United States: N. p., 2015. Web. doi:10.1186/s40793-015-0062-5.
Brown, Bonnie L., LePrell, Rebecca V., Franklin, Rima B., Rivera, Maria C., Cabral, Francine M., Eaves, Hugh L., Gardiakos, Vicki, Keegan, Kevin P., & King, Timothy L. Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River. United States. https://doi.org/10.1186/s40793-015-0062-5
Brown, Bonnie L., LePrell, Rebecca V., Franklin, Rima B., Rivera, Maria C., Cabral, Francine M., Eaves, Hugh L., Gardiakos, Vicki, Keegan, Kevin P., and King, Timothy L. 2015. "Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River". United States. https://doi.org/10.1186/s40793-015-0062-5. https://www.osti.gov/servlets/purl/1224065.
@article{osti_1224065,
title = {Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River},
author = {Brown, Bonnie L. and LePrell, Rebecca V. and Franklin, Rima B. and Rivera, Maria C. and Cabral, Francine M. and Eaves, Hugh L. and Gardiakos, Vicki and Keegan, Kevin P. and King, Timothy L.},
abstractNote = {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 x 106 reads revealed >3 x 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 x 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. Altogether, 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.},
doi = {10.1186/s40793-015-0062-5},
url = {https://www.osti.gov/biblio/1224065}, journal = {Standards in Genomic Sciences},
issn = {1944-3277},
number = 1,
volume = 10,
place = {United States},
year = {Sat Sep 19 00:00:00 EDT 2015},
month = {Sat Sep 19 00:00:00 EDT 2015}
}

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Use of Barcoded Pyrosequencing and Shared OTUs To Determine Sources of Fecal Bacteria in Watersheds
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Application of Illumina next-generation sequencing to characterize the bacterial community of the Upper Mississippi River
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Works referencing / citing this record:

Rhizobacterial community structure differences among sorghum cultivars in different growth stages and soils
journal, July 2017


A meta-barcoding census of freshwater planktonic protists in Appalachia – Natural Tunnel State Park, Virginia, USA
journal, October 2018


MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach
journal, February 2017


Metagenomic Profiling of Microbial Pathogens in the Little Bighorn River, Montana
journal, March 2019