Literature DB >> 21498748

Novel biphenyl-oxidizing bacteria and dioxygenase genes from a korean tidal mudflat.

Tae Kwon Lee1, Jaejin Lee, Woo Jun Sul, Shoko Iwai, Benli Chai, James M Tiedje, Joonhong Park.   

Abstract

Gene-targeted FLX titanium pyrosequencing integrated with stable isotope probing (SIP) using [(13)C]biphenyl substrate revealed that tidal mudflat sediments harbor novel aromatic ring hydroxylating dioxygenases (ARHD). More than 80% of the detected ARHD genes comprise four clades (0.5 distance) with 49 to 70% amino acid identity to sequences in public databases. The 16S rRNA sequences enriched in the (13)C fraction were from the Betaproteobacteria, bacilli (primarily Paenibacillus-like), and unclassified phyla.

Mesh：

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Year:  2011        PMID： 21498748      PMCID： PMC3127585          DOI： 10.1128/AEM.00023-11

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


  20 in total

1.  MUSCLE: multiple sequence alignment with high accuracy and high throughput.

Authors:  Robert C Edgar
Journal:  Nucleic Acids Res       Date:  2004-03-19       Impact factor: 16.971

2.  Discovery of commonly existing anode biofilm microbes in two different wastewater treatment MFCs using FLX Titanium pyrosequencing.

Authors:  Tae Kwon Lee; Tuan Van Doan; Kyuseon Yoo; Soojung Choi; Changwon Kim; Joonhong Park
Journal:  Appl Microbiol Biotechnol       Date:  2010-06-08       Impact factor: 4.813

3.  Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.

Authors:  T Z DeSantis; P Hugenholtz; N Larsen; M Rojas; E L Brodie; K Keller; T Huber; D Dalevi; P Hu; G L Andersen
Journal:  Appl Environ Microbiol       Date:  2006-07       Impact factor: 4.792

4.  Extensive degradation of Aroclors and environmentally transformed polychlorinated biphenyls by Alcaligenes eutrophus H850.

Authors:  D L Bedard; R E Wagner; M J Brennan; M L Haberl; J F Brown
Journal:  Appl Environ Microbiol       Date:  1987-05       Impact factor: 4.792

5.  Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea.

Authors:  Marc Mussmann; Kousuke Ishii; Ralf Rabus; Rudolf Amann
Journal:  Environ Microbiol       Date:  2005-03       Impact factor: 5.491

6.  Directed evolution of biphenyl dioxygenase: emergence of enhanced degradation capacity for benzene, toluene, and alkylbenzenes.

Authors:  H Suenaga; M Mitsuoka; Y Ura; T Watanabe; K Furukawa
Journal:  J Bacteriol       Date:  2001-09       Impact factor: 3.490

7.  Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters.

Authors:  Reinhard Wilms; Henrik Sass; Beate Köpke; Jürgen Köster; Heribert Cypionka; Bert Engelen
Journal:  Appl Environ Microbiol       Date:  2006-04       Impact factor: 4.792

8.  Isolation and characterization of a novel polychlorinated biphenyl-degrading bacterium, Paenibacillus sp. KBC101.

Authors:  M Sakai; S Ezaki; N Suzuki; R Kurane
Journal:  Appl Microbiol Biotechnol       Date:  2005-01-28       Impact factor: 4.813

9.  DNA stable-isotope probing.

Authors:  Josh D Neufeld; Jyotsna Vohra; Marc G Dumont; Tillmann Lueders; Mike Manefield; Michael W Friedrich; J Colin Murrell
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

10.  Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs).

Authors:  Mary Beth Leigh; Vivian H Pellizari; Ondrej Uhlík; Robin Sutka; Jorge Rodrigues; Nathaniel E Ostrom; Jizhong Zhou; James M Tiedje
Journal:  ISME J       Date:  2007-05-24       Impact factor: 10.302
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  8 in total

1.  Biofilms constructed for the removal of hydrocarbon pollutants from hypersaline liquids.

Authors:  D M Al-Mailem; M Eliyas; M Khanafer; S S Radwan
Journal:  Extremophiles       Date:  2014-10-08       Impact factor: 2.395

Review 2.  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

3.  Bacterial degradation of Aroclor 1242 in the mycorrhizosphere soils of zucchini (Cucurbita pepo L.) inoculated with arbuscular mycorrhizal fungi.

Authors:  Hua Qin; Philip C Brookes; Jianming Xu; Youzhi Feng
Journal:  Environ Sci Pollut Res Int       Date:  2014-06-28       Impact factor: 4.223

4.  Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil.

Authors:  Ondrej Uhlik; Jiri Wald; Michal Strejcek; Lucie Musilova; Jakub Ridl; Miluse Hroudova; Cestmir Vlcek; Erick Cardenas; Martina Mackova; Tomas Macek
Journal:  PLoS One       Date:  2012-07-13       Impact factor: 3.240

5.  Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities.

Authors:  Y Verastegui; J Cheng; K Engel; D Kolczynski; S Mortimer; J Lavigne; J Montalibet; T Romantsov; M Hall; B J McConkey; D R Rose; J J Tomashek; B R Scott; T C Charles; J D Neufeld
Journal:  MBio       Date:  2014-07-15       Impact factor: 7.867

6.  Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta.

Authors:  Xiaofei Lv; Bin Ma; Junbao Yu; Scott X Chang; Jianming Xu; Yunzhao Li; Guangmei Wang; Guangxuan Han; Guan Bo; Xiaojing Chu
Journal:  Sci Rep       Date:  2016-11-08       Impact factor: 4.379

7.  DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil.

Authors:  Julian Yu; Michael J Pavia; Lauren M Deem; Susan E Crow; Jonathan L Deenik; Christopher Ryan Penton
Journal:  Front Microbiol       Date:  2020-11-17       Impact factor: 5.640

8.  Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses.

Authors:  Song-Can Chen; Rohit Budhraja; Lorenz Adrian; Federica Calabrese; Hryhoriy Stryhanyuk; Niculina Musat; Hans-Hermann Richnow; Gui-Lan Duan; Yong-Guan Zhu; Florin Musat
Journal:  ISME J       Date:  2021-06-11       Impact factor: 10.302
  8 in total

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