Literature DB >> 21398538

Genome sequence of the verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems.

Mark W J van Passel1, Ravi Kant, Airi Palva, Alex Copeland, Susan Lucas, Alla Lapidus, Tijana Glavina del Rio, Sam Pitluck, Eugene Goltsman, Alicia Clum, Hui Sun, Jeremy Schmutz, Frank W Larimer, Miriam L Land, Loren Hauser, Nikolaos Kyrpides, Natalia Mikhailova, P Paul Richardson, Peter H Janssen, Willem M de Vos, Hauke Smidt.   

Abstract

Bacteria of the deeply branching phylum Verrucomicrobia are rarely cultured yet commonly detected in metagenomic libraries from aquatic, terrestrial, and intestinal environments. We have sequenced the genome of Opitutus terrae PB90-1, a fermentative anaerobe within this phylum, isolated from rice paddy soil and capable of propionate production from plant-derived polysaccharides.

Entities:  

Mesh：

Year:  2011        PMID： 21398538      PMCID： PMC3133072          DOI： 10.1128/JB.00228-11

Source DB:  PubMed          Journal:  J Bacteriol        ISSN： 0021-9193            Impact factor:   3.490


  19 in total

1.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.

Authors:  A Krogh; B Larsson; G von Heijne; E L Sonnhammer
Journal:  J Mol Biol       Date:  2001-01-19       Impact factor: 5.469

2.  Rfam: an RNA family database.

Authors:  Sam Griffiths-Jones; Alex Bateman; Mhairi Marshall; Ajay Khanna; Sean R Eddy
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

3.  Improved prediction of signal peptides: SignalP 3.0.

Authors:  Jannick Dyrløv Bendtsen; Henrik Nielsen; Gunnar von Heijne; Søren Brunak
Journal:  J Mol Biol       Date:  2004-07-16       Impact factor: 5.469

4.  GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes.

Authors:  Amrita Pati; Natalia N Ivanova; Natalia Mikhailova; Galina Ovchinnikova; Sean D Hooper; Athanasios Lykidis; Nikos C Kyrpides
Journal:  Nat Methods       Date:  2010-05-02       Impact factor: 28.547

5.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.

Authors:  T M Lowe; S R Eddy
Journal:  Nucleic Acids Res       Date:  1997-03-01       Impact factor: 16.971

6.  Propionate formation by Opitutus terrae in pure culture and in mixed culture with a hydrogenotrophic methanogen and implications for carbon fluxes in anoxic rice paddy soil.

Authors:  Kuk-Jeong Chin; Peter H Janssen
Journal:  Appl Environ Microbiol       Date:  2002-04       Impact factor: 4.792

7.  Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell.

Authors:  M R Lindsay; R I Webb; M Strous; M S Jetten; M K Butler; R J Forde; J A Fuerst
Journal:  Arch Microbiol       Date:  2001-06       Impact factor: 2.552

8.  Novel anaerobic ultramicrobacteria belonging to the Verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil.

Authors:  P H Janssen; A Schuhmann; E Mörschel; F A Rainey
Journal:  Appl Environ Microbiol       Date:  1997-04       Impact factor: 4.792

9.  Opitutus terrae gen. nov., sp. nov., to accommodate novel strains of the division 'Verrucomicrobia' isolated from rice paddy soil.

Authors:  K J Chin; W Liesack; P H Janssen
Journal:  Int J Syst Evol Microbiol       Date:  2001-11       Impact factor: 2.747

10.  Phylum Verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum Planctomycetes.

Authors:  Kuo-Chang Lee; Richard I Webb; Peter H Janssen; Parveen Sangwan; Tony Romeo; James T Staley; John A Fuerst
Journal:  BMC Microbiol       Date:  2009-01-08       Impact factor: 3.605
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  12 in total

1.  Impacts of Arsenic and Antimony Co-Contamination on Sedimentary Microbial Communities in Rivers with Different Pollution Gradients.

Authors:  Xiaoxu Sun; Baoqin Li; Feng Han; Enzong Xiao; Tangfu Xiao; Weimin Sun
Journal:  Microb Ecol       Date:  2019-02-06       Impact factor: 4.552

2.  Horticoccus luteus gen. nov., sp. nov., A Novel Member of the Phylum Verrucomicrobia Isolated from a Dichlorodiphenyltrichloroethane (DDT)-Contaminated Orchard Soil.

Authors:  Joon-Hui Chung; Ja-Yeon Lee; Geun-Hyung Choi; Miyoung Won; Jehyeong Yeon; Younggun Yoon; Si-Hyun An; Da-Yeon Kim; InCheol Park; Ye-Eun Kim; Jae-Hyung Ahn
Journal:  Curr Microbiol       Date:  2022-10-08       Impact factor: 2.343

3.  Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apple plantlets grown in soils affected by replant disease.

Authors:  Viviane Radl; Jana Barbro Winkler; Susanne Kublik; Luhua Yang; Traud Winkelmann; Gisle Vestergaard; Peter Schröder; Michael Schloter
Journal:  Environ Microbiome       Date:  2019-11-07

4.  Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of Bacteria Provide Insights into Their Evolutionary Relationships.

Authors:  Radhey S Gupta; Vaibhav Bhandari; Hafiz Sohail Naushad
Journal:  Front Microbiol       Date:  2012-09-17       Impact factor: 5.640

5.  Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus).

Authors:  Andrew H Loudon; Douglas C Woodhams; Laura Wegener Parfrey; Holly Archer; Rob Knight; Valerie McKenzie; Reid N Harris
Journal:  ISME J       Date:  2013-12-12       Impact factor: 10.302

6.  Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities.

Authors:  Eric R Hester; Sarah F Harpenslager; Josepha M H van Diggelen; Leon L Lamers; Mike S M Jetten; Claudia Lüke; Sebastian Lücker; Cornelia U Welte
Journal:  mSystems       Date:  2018-01-30       Impact factor: 6.496

7.  Methylacidiphilum fumariolicum SolV, a thermoacidophilic 'Knallgas' methanotroph with both an oxygen-sensitive and -insensitive hydrogenase.

Authors:  Sepehr Mohammadi; Arjan Pol; Theo A van Alen; Mike Sm Jetten; Huub Jm Op den Camp
Journal:  ISME J       Date:  2016-12-09       Impact factor: 10.302

8.  Three Novel Species with Peptidoglycan Cell Walls form the New Genus Lacunisphaera gen. nov. in the Family Opitutaceae of the Verrucomicrobial Subdivision 4.

Authors:  Patrick Rast; Ines Glöckner; Christian Boedeker; Olga Jeske; Sandra Wiegand; Richard Reinhardt; Peter Schumann; Manfred Rohde; Stefan Spring; Frank O Glöckner; Christian Jogler; Mareike Jogler
Journal:  Front Microbiol       Date:  2017-02-13       Impact factor: 5.640

9.  16S rDNA Profiling to Reveal the Influence of Seed-Applied Biostimulants on the Rhizosphere of Young Maize Plants.

Authors:  Giovanna Visioli; Anna Maria Sanangelantoni; Teofilo Vamerali; Cristian Dal Cortivo; Massimo Blandino
Journal:  Molecules       Date:  2018-06-15       Impact factor: 4.411

10.  Active microbiome structure and its association with environmental factors and viruses at different aquatic sites of a high-altitude wetland.

Authors:  Yoanna Eissler; María-Jesús Gálvez; Cristina Dorador; Martha Hengst; Verónica Molina
Journal:  Microbiologyopen       Date:  2018-07-30       Impact factor: 3.139
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