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

Overview of attention for article published in Standards in Genomic Sciences, September 2015
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  • Above-average Attention Score compared to outputs of the same age (61st percentile)
  • Good Attention Score compared to outputs of the same age and source (72nd percentile)

Mentioned by

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4 tweeters

Citations

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19 Dimensions

Readers on

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95 Mendeley
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Title
Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River
Published in
Standards in Genomic Sciences, September 2015
DOI 10.1186/s40793-015-0062-5
Pubmed ID
Authors

Bonnie L. Brown, Rebecca V. LePrell, Rima B. Franklin, Maria C. Rivera, Francine M. Cabral, Hugh L. Eaves, Vicki Gardiakos, Kevin P. Keegan, Timothy L. King

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 × 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.

Twitter Demographics

The data shown below were collected from the profiles of 4 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 95 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 3 3%
Italy 1 1%
Unknown 91 96%

Demographic breakdown

Readers by professional status Count As %
Student > Master 18 19%
Student > Ph. D. Student 15 16%
Researcher 15 16%
Student > Doctoral Student 13 14%
Student > Bachelor 7 7%
Other 14 15%
Unknown 13 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 31 33%
Biochemistry, Genetics and Molecular Biology 15 16%
Environmental Science 14 15%
Medicine and Dentistry 4 4%
Engineering 3 3%
Other 11 12%
Unknown 17 18%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 01 December 2015.
All research outputs
#2,383,374
of 6,632,903 outputs
Outputs from Standards in Genomic Sciences
#104
of 391 outputs
Outputs of similar age
#75,644
of 204,728 outputs
Outputs of similar age from Standards in Genomic Sciences
#8
of 29 outputs
Altmetric has tracked 6,632,903 research outputs across all sources so far. This one has received more attention than most of these and is in the 63rd percentile.
So far Altmetric has tracked 391 research outputs from this source. They receive a mean Attention Score of 1.9. This one has gotten more attention than average, scoring higher than 73% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 204,728 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 61% of its contemporaries.
We're also able to compare this research output to 29 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 72% of its contemporaries.