Literature DB >> 23209206

Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" AR1, from marine sediment.

Soo-Je Park1, Jong-Geol Kim, Man-Young Jung, So-Jeong Kim, In-Tae Cha, Kaekyoung Kwon, Jung-Hyun Lee, Sung-Keun Rhee.   

Abstract

Ammonia-oxidizing archaea (AOA) are ubiquitous in various marine environments and play important roles in the global nitrogen and carbon cycles. We here present a high-quality draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" AR1, which was found to dominate an ammonia-oxidizing enrichment culture in marine sediment off Svalbard, the Arctic Circle. Despite a significant number of nonoverlapping genes (ca. 30%), similarities of this strain to "Candidatus Nitrosopumilus maritimus" were revealed by core genes for archaeal ammonia oxidation and carbon fixation, G+C content, and extensive synteny conservation.

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Year:  2012        PMID: 23209206      PMCID: PMC3510587          DOI: 10.1128/JB.01857-12

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


  12 in total

1.  Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria.

Authors:  Byoung-Joon Park; Soo-Je Park; Dae-No Yoon; Stefan Schouten; Jaap S Sinninghe Damsté; Sung-Keun Rhee
Journal:  Appl Environ Microbiol       Date:  2010-09-24       Impact factor: 4.792

2.  Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling.

Authors:  Alexander H Treusch; Sven Leininger; Arnulf Kletzin; Stephan C Schuster; Hans-Peter Klenk; Christa Schleper
Journal:  Environ Microbiol       Date:  2005-12       Impact factor: 5.491

3.  Genomic insights that advance the species definition for prokaryotes.

Authors:  Konstantinos T Konstantinidis; James M Tiedje
Journal:  Proc Natl Acad Sci U S A       Date:  2005-02-08       Impact factor: 11.205

4.  Isolation of an autotrophic ammonia-oxidizing marine archaeon.

Authors:  Martin Könneke; Anne E Bernhard; José R de la Torre; Christopher B Walker; John B Waterbury; David A Stahl
Journal:  Nature       Date:  2005-09-22       Impact factor: 49.962

5.  Comparative analysis of archaeal 16S rRNA and amoA genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments.

Authors:  Soo-Je Park; Byoung-Joon Park; Sung-Keun Rhee
Journal:  Extremophiles       Date:  2008-05-09       Impact factor: 2.395

6.  Archaea predominate among ammonia-oxidizing prokaryotes in soils.

Authors:  S Leininger; T Urich; M Schloter; L Schwark; J Qi; G W Nicol; J I Prosser; S C Schuster; C Schleper
Journal:  Nature       Date:  2006-08-17       Impact factor: 49.962

7.  The COG database: new developments in phylogenetic classification of proteins from complete genomes.

Authors:  R L Tatusov; D A Natale; I V Garkavtsev; T A Tatusova; U T Shankavaram; B S Rao; B Kiryutin; M Y Galperin; N D Fedorova; E V Koonin
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

8.  The Pfam protein families database.

Authors:  Robert D Finn; Jaina Mistry; John Tate; Penny Coggill; Andreas Heger; Joanne E Pollington; O Luke Gavin; Prasad Gunasekaran; Goran Ceric; Kristoffer Forslund; Liisa Holm; Erik L L Sonnhammer; Sean R Eddy; Alex Bateman
Journal:  Nucleic Acids Res       Date:  2009-11-17       Impact factor: 16.971

9.  The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.

Authors:  F Meyer; D Paarmann; M D'Souza; R Olson; E M Glass; M Kubal; T Paczian; A Rodriguez; R Stevens; A Wilke; J Wilkening; R A Edwards
Journal:  BMC Bioinformatics       Date:  2008-09-19       Impact factor: 3.169

10.  MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes.

Authors:  Hideki Noguchi; Takeaki Taniguchi; Takehiko Itoh
Journal:  DNA Res       Date:  2008-10-21       Impact factor: 4.458

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  14 in total

1.  Single-cell genomics shedding light on marine Thaumarchaeota diversification.

Authors:  Haiwei Luo; Bradley B Tolar; Brandon K Swan; Chuanlun L Zhang; Ramunas Stepanauskas; Mary Ann Moran; James T Hollibaugh
Journal:  ISME J       Date:  2013-11-07       Impact factor: 10.302

2.  "Candidatus Nitrosotenuis aquarius," an Ammonia-Oxidizing Archaeon from a Freshwater Aquarium Biofilter.

Authors:  Laura A Sauder; Katja Engel; Chien-Chi Lo; Patrick Chain; Josh D Neufeld
Journal:  Appl Environ Microbiol       Date:  2018-09-17       Impact factor: 4.792

3.  Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea.

Authors:  David Kamanda Ngugi; Jochen Blom; Intikhab Alam; Mamoon Rashid; Wail Ba-Alawi; Guishan Zhang; Tyas Hikmawan; Yue Guan; Andre Antunes; Rania Siam; Hamza El Dorry; Vladimir Bajic; Ulrich Stingl
Journal:  ISME J       Date:  2014-08-08       Impact factor: 10.302

4.  A mesophilic, autotrophic, ammonia-oxidizing archaeon of thaumarchaeal group I.1a cultivated from a deep oligotrophic soil horizon.

Authors:  Man-Young Jung; Soo-Je Park; So-Jeong Kim; Jong-Geol Kim; Jaap S Sinninghe Damsté; Che Ok Jeon; Sung-Keun Rhee
Journal:  Appl Environ Microbiol       Date:  2014-06       Impact factor: 4.792

Review 5.  Archaeal diversity in biofilm technologies applied to treat urban and industrial wastewater: recent advances and future prospects.

Authors:  Kadiya Calderón; Alejandro González-Martínez; Cinta Gómez-Silván; Francisco Osorio; Belén Rodelas; Jesús González-López
Journal:  Int J Mol Sci       Date:  2013-09-09       Impact factor: 5.923

6.  Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea.

Authors:  Kateryna V Zhalnina; Raquel Dias; Michael T Leonard; Patricia Dorr de Quadros; Flavio A O Camargo; Jennifer C Drew; William G Farmerie; Samira H Daroub; Eric W Triplett
Journal:  PLoS One       Date:  2014-07-07       Impact factor: 3.240

7.  Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments.

Authors:  Soo-Je Park; Rohit Ghai; Ana-Belén Martín-Cuadrado; Francisco Rodríguez-Valera; Won-Hyong Chung; KaeKyoung Kwon; Jung-Hyun Lee; Eugene L Madsen; Sung-Keun Rhee
Journal:  PLoS One       Date:  2014-05-05       Impact factor: 3.240

8.  Bacterial and archaeal communities in Lake Nyos (Cameroon, Central Africa).

Authors:  Rosine E Tiodjio; Akihiro Sakatoku; Akihiro Nakamura; Daisuke Tanaka; Wilson Y Fantong; Kamtchueng B Tchakam; Gregory Tanyileke; Takeshi Ohba; Victor J Hell; Minoru Kusakabe; Shogo Nakamura; Akira Ueda
Journal:  Sci Rep       Date:  2014-08-21       Impact factor: 4.379

9.  Metagenomics of an Alkaline Hot Spring in Galicia (Spain): Microbial Diversity Analysis and Screening for Novel Lipolytic Enzymes.

Authors:  Olalla López-López; Kamila Knapik; Maria-Esperanza Cerdán; María-Isabel González-Siso
Journal:  Front Microbiol       Date:  2015-11-20       Impact factor: 5.640

10.  Microbial Communities on Seafloor Basalts at Dorado Outcrop Reflect Level of Alteration and Highlight Global Lithic Clades.

Authors:  Michael D Lee; Nathan G Walworth; Jason B Sylvan; Katrina J Edwards; Beth N Orcutt
Journal:  Front Microbiol       Date:  2015-12-23       Impact factor: 5.640

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