Evidence map›Paper›PMID 25083935›Full record

ArticleThe ISME journal2015

Evidence of Geobacter-associated phage in a uranium-contaminated aquifer.

Dawn E Holmes, Ludovic Giloteaux, Akhilesh K Chaurasia, Kenneth H Williams, Birgit Luef, Michael J Wilkins, Kelly C Wrighton, Courtney A Thompson, Luis R Comolli, Derek R Lovley

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The ISME journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

14 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Dawn E Holmes1] Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA [2] Western New England University, Springfield, MA, USA.
Ludovic GiloteauxDepartment of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA.
Akhilesh K ChaurasiaDepartment of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA.
Kenneth H WilliamsLawrence Berkeley National Laboratory, Berkeley, CA, USA.
Birgit Luef1] Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA.
Michael J WilkinsPacific Northwest National Laboratory, Richland, WA, USA.
Kelly C WrightonDepartment of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA.
Courtney A ThompsonDepartment of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA.
Luis R ComolliLawrence Berkeley National Laboratory, Berkeley, CA, USA.
Derek R LovleyDepartment of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Geobacter species may be important agents in the bioremediation of organic and metal contaminants in the subsurface, but as yet unknown factors limit the in situ growth of subsurface Geobacter well below rates predicted by analysis of gene expression or in silico metabolic modeling. Analysis of the genomes of five different Geobacter species recovered from contaminated subsurface sites indicated that each of the isolates had been infected with phage. Geobacter-associated phage sequences were also detected by metagenomic and proteomic analysis of samples from a uranium-contaminated aquifer undergoing in situ bioremediation, and phage particles were detected by microscopic analysis in groundwater collected from sediment enrichment cultures. Transcript abundance for genes from the Geobacter-associated phage structural proteins, tail tube Gp19 and baseplate J, increased in the groundwater in response to the growth of Geobacter species when acetate was added, and then declined as the number of Geobacter decreased. Western blot analysis of a Geobacter-associated tail tube protein Gp19 in the groundwater demonstrated that its abundance tracked with the abundance of Geobacter species. These results suggest that the enhanced growth of Geobacter species in the subsurface associated with in situ uranium bioremediation increased the abundance and activity of Geobacter-associated phage and show that future studies should focus on how these phages might be influencing the ecology of this site.

Indexed as

BacteriophagesBiodegradation, EnvironmentalGenes, ViralGeobacterGroundwaterMetagenomeProteomicsTranscriptomeUraniumViral ProteinsWater Pollutants, RadioactiveUraniumViral ProteinsWater Pollutants, Radioactive

Identifiers

PMID25083935
PMCPMC4303627

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.