Literature DB >> 16376070

Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes.

Michael W Friedrich1.   

Abstract

Stable-isotope probing (SIP) of environmental genomic DNA allows populations in a natural microbial community to be identified through the incorporation of (13)C- or (15)N-labeled substrates into biomass. The isotopically labeled DNA is retrieved by density gradient centrifugation, and active microorganisms identified by molecular analysis of the DNA. Recent advances have set the stage for DNA-based SIP with higher sensitivities, shorter incubation times, and more relevant substrate concentrations than used previously. The first demonstration of a DNA-SIP-based metagenome analysis has paved the way for hypothesis-driven studies in environmental genomics.

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Year:  2006        PMID: 16376070     DOI: 10.1016/j.copbio.2005.12.003

Source DB:  PubMed          Journal:  Curr Opin Biotechnol        ISSN: 0958-1669            Impact factor:   9.740


  21 in total

Review 1.  Molecular ecology techniques for the study of aerobic methanotrophs.

Authors:  Ian R McDonald; Levente Bodrossy; Yin Chen; J Colin Murrell
Journal:  Appl Environ Microbiol       Date:  2007-12-28       Impact factor: 4.792

Review 2.  Anaerobic catabolism of aromatic compounds: a genetic and genomic view.

Authors:  Manuel Carmona; María Teresa Zamarro; Blas Blázquez; Gonzalo Durante-Rodríguez; Javier F Juárez; J Andrés Valderrama; María J L Barragán; José Luis García; Eduardo Díaz
Journal:  Microbiol Mol Biol Rev       Date:  2009-03       Impact factor: 11.056

3.  Identification of a toluene-degrading bacterium from a soil sample through H(2)(18)O DNA stable isotope probing.

Authors:  Angela Woods; Maribeth Watwood; Egbert Schwartz
Journal:  Appl Environ Microbiol       Date:  2011-07-08       Impact factor: 4.792

4.  Shotgun isotope array for rapid, substrate-specific detection of microorganisms in a microbial community.

Authors:  Tomohiro Tobino; Futoshi Kurisu; Ikuro Kasuga; Hiroaki Furumai
Journal:  Appl Environ Microbiol       Date:  2011-08-26       Impact factor: 4.792

5.  Active autotrophic ammonia-oxidizing bacteria in biofilm enrichments from simulated creek ecosystems at two ammonium concentrations respond to temperature manipulation.

Authors:  Sharon Avrahami; Zhongjun Jia; Josh D Neufeld; J Colin Murrell; Ralf Conrad; Kirsten Küsel
Journal:  Appl Environ Microbiol       Date:  2011-09-02       Impact factor: 4.792

Review 6.  Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation.

Authors:  Ondrej Uhlik; Mary-Cathrine Leewis; Michal Strejcek; Lucie Musilova; Martina Mackova; Mary Beth Leigh; Tomas Macek
Journal:  Biotechnol Adv       Date:  2012-09-26       Impact factor: 14.227

7.  Identification of acetate-assimilating microorganisms under methanogenic conditions in anoxic rice field soil by comparative stable isotope probing of RNA.

Authors:  Tomoyuki Hori; Matthias Noll; Yasuo Igarashi; Michael W Friedrich; Ralf Conrad
Journal:  Appl Environ Microbiol       Date:  2006-10-27       Impact factor: 4.792

8.  Diversity of anaerobic microorganisms involved in long-chain fatty acid degradation in methanogenic sludges as revealed by RNA-based stable isotope probing.

Authors:  Masashi Hatamoto; Hiroyuki Imachi; Yuto Yashiro; Akiyoshi Ohashi; Hideki Harada
Journal:  Appl Environ Microbiol       Date:  2007-05-04       Impact factor: 4.792

9.  Functional soil microbiome: belowground solutions to an aboveground problem.

Authors:  Venkatachalam Lakshmanan; Gopinath Selvaraj; Harsh P Bais
Journal:  Plant Physiol       Date:  2014-07-24       Impact factor: 8.340

10.  Decimal place slope, a fast and precise method for quantifying 13C incorporation levels for detecting the metabolic activity of microbial species.

Authors:  Nico Jehmlich; Ingo Fetzer; Jana Seifert; Jens Mattow; Carsten Vogt; Hauke Harms; Bernd Thiede; Hans-Hermann Richnow; Martin von Bergen; Frank Schmidt
Journal:  Mol Cell Proteomics       Date:  2010-01-11       Impact factor: 5.911

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