Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses. (Q34792388)

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4 March 2020

editorial

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title

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses (English)

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4 March 2020

author name string

Steven J Blazewicz

series ordinal

1

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4 March 2020

Rebecca A Daly

series ordinal

3

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4 March 2020

publication date

4 July 2013

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4 March 2020

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4 March 2020

volume

7

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issue

11

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page(s)

2061-2068

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Responses of soil bacterial and fungal communities to extreme desiccation and rewetting

4 March 2020

cites work

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Soil microbe active community composition and capability of responding to litter addition after 12 years of no inputs

8 July 2018

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Thermal stress responses in the bacterial biosphere of the Great Barrier Reef sponge, Rhopaloeides odorabile

8 July 2018

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Acidobacteria dominate the active bacterial communities of Arctic tundra with widely divergent winter-time snow accumulation and soil temperatures

8 July 2018

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Relationship between abundance and specific activity of bacterioplankton in open ocean surface waters

8 July 2018

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Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient

8 July 2018

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Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups

8 July 2018

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Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse

8 July 2018

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Massive multiplication of genome and ribosomes in dormant cells (akinetes) of Aphanizomenon ovalisporum (Cyanobacteria).

8 July 2018

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Biodiversity of active and inactive bacteria in the gut flora of wood-feeding huhu beetle larvae (Prionoplus reticularis).

8 July 2018

1 reference

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Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

8 July 2018

1 reference

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Activity of abundant and rare bacteria in a coastal ocean

8 July 2018

1 reference

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PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip

8 July 2018

1 reference

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Analysis of bacterial core communities in the central Baltic by comparative RNA-DNA-based fingerprinting provides links to structure-function relationships.

8 July 2018

1 reference

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Ribosomal tag pyrosequencing of DNA and RNA from benthic coral reef microbiota: community spatial structure, rare members and nitrogen-cycling guilds.

8 July 2018

1 reference

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Microbial communities acclimate to recurring changes in soil redox potential status

8 July 2018

1 reference

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Clostridiaceae and Enterobacteriaceae as active fermenters in earthworm gut content.

8 July 2018

1 reference

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Dormancy contributes to the maintenance of microbial diversity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Activity profiles for marine sponge-associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, prochlorococcus

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Systems biology: Functional analysis of natural microbial consortia using community proteomics

8 July 2018

1 reference

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Permeabilization and hybridization protocols for rapid detection of Bacillus spores using fluorescence in situ hybridization.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Predictive behavior within microbial genetic networks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Microbial stress-response physiology and its implications for ecosystem function

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Microbial maintenance: a critical review on its quantification

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Study of bacterial communities in Antarctic coastal waters by a combination of 16S rRNA and 16S rDNA sequencing

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Estimating the growth rate of slowly growing marine bacteria from RNA content

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Comparison of Nucleic Acid Hybridization and Fluorometry for Measurement of the Relationship between RNA/DNA Ratio and Growth Rate in a Marine Bacterium.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Characterization of microbial community structure in Gulf of Mexico gas hydrates: comparative analysis of DNA- and RNA-derived clone libraries.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms

8 July 2018

1 reference

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Application of molecular tools for in situ monitoring of bacterial growth activity.

8 July 2018

1 reference

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Analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA.

8 July 2018

1 reference

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Bacterial activity in the rhizosphere analyzed at the single-cell level by monitoring ribosome contents and synthesis rates

8 July 2018

1 reference

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rRNA stability in heat-killed and UV-irradiated enterotoxigenic Staphylococcus aureus and Escherichia coli O157:H7.

8 July 2018

1 reference

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Growth rate regulation of rRNA content of a marine synechococcus (Cyanobacterium) strain

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

The concentrations of stable RNA and ribosomes in Rickettsia prowazekii

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

The regulation of ribosomal RNA synthesis and bacterial cell growth

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Regulation of the synthesis of ribosomes and ribosomal components

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Endogenous metabolism of Azotobacter agilis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Ribonucleic acid composition of bacteria as a function of growth rate

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Biochemical studies of bacterial sporulation and germination. IX. Ribonucleic acid and deoxyribonucleic acid polymerases in nuclear fractions of vegetative cells and spores of Bacillus megaterium

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Isolation and Characterization of Ribosomes from Bacillus subtilis Spores

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

The Adaptive Responses of Escherichia coli to a Feast and Famine Existence

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Overall controls on the biosynthesis of ribosomes in growing bacteria

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Chromosome replication and the division cycle of Escherichia coli B/r.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Role of ribosome degradation in the death of starved Escherichia coli cells

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Ribosomes exist in large excess over the apparent demand for protein synthesis during carbon starvation in marine Vibrio sp. strain CCUG 15956

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Variations in rRNA content of marine Vibrio spp. during starvation-survival and recovery

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Intermediates and time kinetics of the in vivo assembly of Escherichia coli ribosomes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Regulation of ribosome production in Escherichia coli: Synthesis and stability of ribosomal RNA and of ribosomal protein messenger RNA at different growth rates

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

rRNA-based profiling of bacteria in the axilla of healthy males suggests right-left asymmetry in bacterial activity

8 July 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.102

Inhibition of Escherichia coli precursor-16S rRNA processing by mouse intestinal contents

21 January 2018

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https://api.crossref.org/works/10.1038%2FISMEJ.2013.102

Turnover of protein and nucleic acid in soluble and ribosome fractions of non-growing Escherichia coli

21 January 2018

1 reference

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Adaptive prediction of environmental changes by microorganisms.

21 January 2018

1 reference

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Quantitation of the Population Size and Metabolic Activity of a Resin Acid Degrading Bacterium in Activated Sludge Using Slot-Blot Hybridization to Measure the rRNA:rDNA Ratio

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.102

Influence of growth rate and starvation on fluorescent in situ hybridization of Rhodopseudomonas palustris

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.102

16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.102

Effects of stress treatments on the detection of Salmonella typhimurium by in situ hybridization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.102

The distribution of ribosomal ribonucleic acids among subcellular fractions from bacteria and the adverse effect of the membrane fraction on the stability of ribosomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.102

Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria

21 January 2018

1 reference

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Dependency on medium and temperature of cell size and chemical composition during balanced grown of Salmonella typhimurium

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3806256

Ribonucleoprotein Particles from Escherichia Coli

26 October 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.102

Small ribosomal RNA content in marine Proteobacteria during non-steady-state growth

21 January 2018

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12 December 2020

RIBOSOMES IN GROWING AND NON-GROWING BACTERIAL CELLS

1 reference

12 December 2020

Studies on the role of ribonucleic acid in the growth of bacteria

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12 December 2020

Nucleic acid content of Synechococcus spp. during growth in continuous light and light/dark cycles

1 reference

12 December 2020

Unused protein synthetic capacity of Escherichia coli grown in phosphate-limited chemostats

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12 December 2020

Identifiers

DOI

10.1038/ISMEJ.2013.102

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23823491%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

4 March 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23823491%20AND%20SRC:MED&resulttype=core&format=json

4 March 2020

PubMed publication ID

23823491

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23823491%20AND%20SRC:MED&resulttype=core&format=json