Literature DB >> 16000830

Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays.

Noah Fierer1, Jason A Jackson, Rytas Vilgalys, Robert B Jackson.   

Abstract

Here we describe a quantitative PCR-based approach to estimating the relative abundances of major taxonomic groups of bacteria and fungi in soil. Primers were thoroughly tested for specificity, and the method was applied to three distinct soils. The technique provides a rapid and robust index of microbial community structure.

Mesh:

Substances:

Year:  2005        PMID: 16000830      PMCID: PMC1169028          DOI: 10.1128/AEM.71.7.4117-4120.2005

Source DB:  PubMed          Journal:  Appl Environ Microbiol        ISSN: 0099-2240            Impact factor:   4.792


  24 in total

1.  A new mathematical model for relative quantification in real-time RT-PCR.

Authors:  M W Pfaffl
Journal:  Nucleic Acids Res       Date:  2001-05-01       Impact factor: 16.971

2.  Specific oligonucleotide probes for in situ detection of a major group of gram-positive bacteria with low DNA G + C content.

Authors:  H Meier; R Amann; W Ludwig; K H Schleifer
Journal:  Syst Appl Microbiol       Date:  1999-05       Impact factor: 4.022

3.  Specific detection of different phylogenetic groups of chemocline bacteria based on PCR and denaturing gradient gel electrophoresis of 16S rRNA gene fragments.

Authors:  J Overmann; M J Coolen; C Tuschak
Journal:  Arch Microbiol       Date:  1999-08       Impact factor: 2.552

4.  Prokaryotic diversity--magnitude, dynamics, and controlling factors.

Authors:  Vigdis Torsvik; Lise Øvreås; Tron Frede Thingstad
Journal:  Science       Date:  2002-05-10       Impact factor: 47.728

5.  Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning.

Authors:  J Dunbar; S Takala; S M Barns; J A Davis; C R Kuske
Journal:  Appl Environ Microbiol       Date:  1999-04       Impact factor: 4.792

6.  The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy.

Authors:  J R Cole; B Chai; T L Marsh; R J Farris; Q Wang; S A Kulam; S Chandra; D M McGarrell; T M Schmidt; G M Garrity; J M Tiedje
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

7.  Development of a real-time PCR method for quantification of the three genera Dehalobacter, Dehalococcoides, and Desulfitobacterium in microbial communities.

Authors:  Theo H M Smits; Christiane Devenoges; Katia Szynalski; Julien Maillard; Christof Holliger
Journal:  J Microbiol Methods       Date:  2004-06       Impact factor: 2.363

8.  Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays.

Authors:  Steffen Kolb; Claudia Knief; Stephan Stubner; Ralf Conrad
Journal:  Appl Environ Microbiol       Date:  2003-05       Impact factor: 4.792

9.  Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil.

Authors:  Yutaka Okano; Krassimira R Hristova; Christian M Leutenegger; Louise E Jackson; R Ford Denison; Binyam Gebreyesus; David Lebauer; Kate M Scow
Journal:  Appl Environ Microbiol       Date:  2004-02       Impact factor: 4.792

10.  Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species.

Authors:  R Vilgalys; M Hester
Journal:  J Bacteriol       Date:  1990-08       Impact factor: 3.490

View more
  285 in total

1.  Association of earthworm-denitrifier interactions with increased emission of nitrous oxide from soil mesocosms amended with crop residue.

Authors:  Lucas D Nebert; Jaap Bloem; Ingrid M Lubbers; Jan Willem van Groenigen
Journal:  Appl Environ Microbiol       Date:  2011-04-22       Impact factor: 4.792

2.  Acidobacteria in freshwater ponds at Doñana National Park, Spain.

Authors:  Johannes Zimmermann; M Carmen Portillo; Laura Serrano; Wolfgang Ludwig; Juan M Gonzalez
Journal:  Microb Ecol       Date:  2011-12-15       Impact factor: 4.552

3.  Microbial community succession during lactate amendment and electron acceptor limitation reveals a predominance of metal-reducing Pelosinus spp.

Authors:  Jennifer J Mosher; Tommy J Phelps; Mircea Podar; Richard A Hurt; James H Campbell; Meghan M Drake; James G Moberly; Christopher W Schadt; Steven D Brown; Terry C Hazen; Adam P Arkin; Anthony V Palumbo; Boris A Faybishenko; Dwayne A Elias
Journal:  Appl Environ Microbiol       Date:  2012-01-20       Impact factor: 4.792

4.  Vaginal microbial flora analysis by next generation sequencing and microarrays; can microbes indicate vaginal origin in a forensic context?

Authors:  Corina C G Benschop; Frederike C A Quaak; Mathilde E Boon; Titia Sijen; Irene Kuiper
Journal:  Int J Legal Med       Date:  2012-01-27       Impact factor: 2.686

5.  Archaeal abundance across a pH gradient in an arable soil and its relationship to bacterial and fungal growth rates.

Authors:  Per Bengtson; Anna E Sterngren; Johannes Rousk
Journal:  Appl Environ Microbiol       Date:  2012-06-15       Impact factor: 4.792

6.  Free tropospheric transport of microorganisms from Asia to North America.

Authors:  David J Smith; Daniel A Jaffe; Michele N Birmele; Dale W Griffin; Andrew C Schuerger; Jonathan Hee; Michael S Roberts
Journal:  Microb Ecol       Date:  2012-07-04       Impact factor: 4.552

7.  Microbial community shifts influence patterns in tropical forest nitrogen fixation.

Authors:  Sasha C Reed; Alan R Townsend; Cory C Cleveland; Diana R Nemergut
Journal:  Oecologia       Date:  2010-05-09       Impact factor: 3.225

8.  Evaluation of disease resistance and tolerance to elevated temperature stress of the selected tissue-cultured Kappaphycus alvarezii Doty 1985 under optimized laboratory conditions.

Authors:  Azhani Azizi; Nursyuhaida Mohd Hanafi; Mohd Nazir Basiran; Chee How Teo
Journal:  3 Biotech       Date:  2018-07-17       Impact factor: 2.406

9.  Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.

Authors:  Migun Shakya; Christopher Quince; James H Campbell; Zamin K Yang; Christopher W Schadt; Mircea Podar
Journal:  Environ Microbiol       Date:  2013-02-06       Impact factor: 5.491

10.  Seasonal variation of microbial populations and biomass in Tatachia grassland soils of Taiwan.

Authors:  Shine-Tsern Cho; Shu-Hsien Tsai; Anita Ravindran; Ammaiyappan Selvam; Shang-Shyng Yang
Journal:  Environ Geochem Health       Date:  2008-06       Impact factor: 4.609

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.