Literature DB >> 19011059

Characterization of denitrification gene clusters of soil bacteria via a metagenomic approach.

Sandrine Demanèche1, Laurent Philippot, Maude M David, Elisabeth Navarro, Timothy M Vogel, Pascal Simonet.   

Abstract

We characterized operons encoding enzymes involved in denitrification, a nitrogen-cycling process involved in nitrogen losses and greenhouse gas emission, using a metagenomic approach which combines molecular screening and pyrosequencing. Screening of 77,000 clones from a soil metagenomic library led to the identification and the subsequent characterization of nine denitrification gene clusters.

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Year:  2008        PMID： 19011059      PMCID： PMC2620714          DOI： 10.1128/AEM.01706-08

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


  17 in total

1.  Presence of two different active nirS nitrite reductase genes in a denitrifying Thauera sp. from a high-nitrate-removal-rate reactor.

Authors:  Claudia Etchebehere; James Tiedje
Journal:  Appl Environ Microbiol       Date:  2005-09       Impact factor: 4.792

Review 2.  Finding the missing link between diversity and activity using denitrifying bacteria as a model functional community.

Authors:  Laurent Philippot; Sara Hallin
Journal:  Curr Opin Microbiol       Date:  2005-06       Impact factor: 7.934

3.  Accurate phylogenetic classification of variable-length DNA fragments.

Authors:  Alice Carolyn McHardy; Héctor García Martín; Aristotelis Tsirigos; Philip Hugenholtz; Isidore Rigoutsos
Journal:  Nat Methods       Date:  2006-12-10       Impact factor: 28.547

4.  Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE.

Authors:  Ingela Noredal Throbäck; Karin Enwall; Asa Jarvis; Sara Hallin
Journal:  FEMS Microbiol Ecol       Date:  2004-09-01       Impact factor: 4.194

5.  Multiple transcription factors of the FNR family in denitrifying Pseudomonas stutzeri: characterization of four fnr-like genes, regulatory responses and cognate metabolic processes.

Authors:  K U Vollack; E Härtig; H Körner; W G Zumft
Journal:  Mol Microbiol       Date:  1999-03       Impact factor: 3.501

6.  Quantitative detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils.

Authors:  S Henry; D Bru; B Stres; S Hallet; L Philippot
Journal:  Appl Environ Microbiol       Date:  2006-08       Impact factor: 4.792

Review 7.  Cell biology and molecular basis of denitrification.

Authors:  W G Zumft
Journal:  Microbiol Mol Biol Rev       Date:  1997-12       Impact factor: 11.056

8.  Characterization of nirV and a gene encoding a novel pseudoazurin in Rhodobacter sphaeroides 2.4.3.

Authors:  Roshan Jain; James P Shapleigh
Journal:  Microbiology (Reading)       Date:  2001-09       Impact factor: 2.777

9.  Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification.

Authors:  Christopher M Jones; Blaz Stres; Magnus Rosenquist; Sara Hallin
Journal:  Mol Biol Evol       Date:  2008-07-08       Impact factor: 16.240

10.  Evaluation of functional gene enrichment in a soil metagenomic clone library.

Authors:  Sandrine Demanèche; Maude M David; Elisabeth Navarro; Pascal Simonet; Timothy M Vogel
Journal:  J Microbiol Methods       Date:  2008-09-17       Impact factor: 2.363
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  9 in total

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

Authors:  Petr Baldrian; Miroslav Kolařík; Martina Stursová; Jan Kopecký; Vendula Valášková; Tomáš Větrovský; Lucia Zifčáková; Jaroslav Snajdr; Jakub Rídl; Cestmír Vlček; Jana Voříšková
Journal:  ISME J       Date:  2011-07-21       Impact factor: 10.302

2.  Four PCR primers necessary for the detection of periplasmic nitrate reductase genes in all groups of Proteobacteria and in environmental DNA.

Authors:  Tobias Klatte; Laura Evans; Rebekah N Whitehead; Jeffrey A Cole
Journal:  Biochem Soc Trans       Date:  2011-01       Impact factor: 5.407

3.  Denitrification activity of a remarkably diverse fen denitrifier community in finnish lapland is N-oxide limited.

Authors:  Katharina Palmer; Marcus A Horn
Journal:  PLoS One       Date:  2015-04-10       Impact factor: 3.240

4.  Back to the Future of Soil Metagenomics.

Authors:  Joseph Nesme; Wafa Achouak; Spiros N Agathos; Mark Bailey; Petr Baldrian; Dominique Brunel; Åsa Frostegård; Thierry Heulin; Janet K Jansson; Edouard Jurkevitch; Kristiina L Kruus; George A Kowalchuk; Antonio Lagares; Hilary M Lappin-Scott; Philippe Lemanceau; Denis Le Paslier; Ines Mandic-Mulec; J Colin Murrell; David D Myrold; Renaud Nalin; Paolo Nannipieri; Josh D Neufeld; Fergal O'Gara; John J Parnell; Alfred Pühler; Victor Pylro; Juan L Ramos; Luiz F W Roesch; Michael Schloter; Christa Schleper; Alexander Sczyrba; Angela Sessitsch; Sara Sjöling; Jan Sørensen; Søren J Sørensen; Christoph C Tebbe; Edward Topp; George Tsiamis; Jan Dirk van Elsas; Geertje van Keulen; Franco Widmer; Michael Wagner; Tong Zhang; Xiaojun Zhang; Liping Zhao; Yong-Guan Zhu; Timothy M Vogel; Pascal Simonet
Journal:  Front Microbiol       Date:  2016-02-10       Impact factor: 5.640

5.  Nitric Oxide Accumulation: The Evolutionary Trigger for Phytopathogenesis.

Authors:  Margarida M Santana; Juan M Gonzalez; Cristina Cruz
Journal:  Front Microbiol       Date:  2017-10-10       Impact factor: 5.640

Review 6.  Targeted metagenomics unveils the molecular basis for adaptive evolution of enzymes to their environment.

Authors:  Hikaru Suenaga
Journal:  Front Microbiol       Date:  2015-09-22       Impact factor: 5.640

Review 7.  Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils.

Authors:  Silvia Pajares; Brendan J M Bohannan
Journal:  Front Microbiol       Date:  2016-07-05       Impact factor: 5.640

8.  Genomic organization, gene expression and activity profile of Marinobacter hydrocarbonoclasticus denitrification enzymes.

Authors:  Cíntia Carreira; Olga Mestre; Rute F Nunes; Isabel Moura; Sofia R Pauleta
Journal:  PeerJ       Date:  2018-09-21       Impact factor: 2.984

9.  The Structure and Species Co-Occurrence Networks of Soil Denitrifying Bacterial Communities Differ Between A Coniferous and A Broadleaved Forests.

Authors:  Jie Chen; Jiajia Li; Weijun Shen; Han Xu; Yide Li; Tushou Luo
Journal:  Microorganisms       Date:  2019-09-18
  9 in total

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