Literature DB >> 23209211

Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus sediminis" AR2, from Svalbard in the Arctic Circle.

Soo-Je Park1, Jong-Geol Kim, Man-Young Jung, So-Jeong Kim, In-Tae Cha, Rohit Ghai, Ana-Belén Martín-Cuadrado, Francisco Rodríguez-Valera, Sung-Keun Rhee.   

Abstract

Ammonia-oxidizing archaea (AOA) typically predominate over ammonia-oxidizing bacteria in marine sediments. We herein present the draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus sediminis" AR2, which was enriched in culture from a marine sediment obtained off Svalbard, within the Arctic Circle. The typical genes involved in archaeal ammonia oxidation and carbon fixation necessary for chemolithoautotrophic growth were observed. Interestingly, the AR2 genome sequence was revealed to possess, uniquely among cultivated AOA from marine environments, a capability for urea utilization.

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Year:  2012        PMID： 23209211      PMCID： PMC3510607          DOI： 10.1128/JB.01869-12

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


  16 in total

1.  Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine.

Authors:  Benjamin J Tully; William C Nelson; John F Heidelberg
Journal:  Environ Microbiol       Date:  2011-11-03       Impact factor: 5.491

2.  Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum.

Authors:  Steven J Hallam; Konstantinos T Konstantinidis; Nik Putnam; Christa Schleper; Yoh-ichi Watanabe; Junichi Sugahara; Christina Preston; José de la Torre; Paul M Richardson; Edward F DeLong
Journal:  Proc Natl Acad Sci U S A       Date:  2006-11-17       Impact factor: 11.205

3.  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

4.  Archaeal nitrification in the ocean.

Authors:  Cornelia Wuchter; Ben Abbas; Marco J L Coolen; Lydie Herfort; Judith van Bleijswijk; Peer Timmers; Marc Strous; Eva Teira; Gerhard J Herndl; Jack J Middelburg; Stefan Schouten; Jaap S Sinninghe Damsté
Journal:  Proc Natl Acad Sci U S A       Date:  2006-08-07       Impact factor: 11.205

5.  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

Review 6.  Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota.

Authors:  Céline Brochier-Armanet; Bastien Boussau; Simonetta Gribaldo; Patrick Forterre
Journal:  Nat Rev Microbiol       Date:  2008-03       Impact factor: 60.633

7.  A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea.

Authors:  Ivan A Berg; Daniel Kockelkorn; Wolfgang Buckel; Georg Fuchs
Journal:  Science       Date:  2007-12-14       Impact factor: 47.728

8.  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

9.  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

10.  Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota.

Authors:  Steven J Hallam; Tracy J Mincer; Christa Schleper; Christina M Preston; Katie Roberts; Paul M Richardson; Edward F DeLong
Journal:  PLoS Biol       Date:  2006-03-21       Impact factor: 8.029
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  20 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.  Urea uptake and carbon fixation by marine pelagic bacteria and archaea during the Arctic summer and winter seasons.

Authors:  Tara L Connelly; Steven E Baer; Joshua T Cooper; Deborah A Bronk; Boris Wawrik
Journal:  Appl Environ Microbiol       Date:  2014-07-25       Impact factor: 4.792

4.  Comparative Genomics of Thaumarchaeota From Deep-Sea Sponges Reveal Their Niche Adaptation.

Authors:  Peng Wang; Minchun Li; Liang Dong; Cheng Zhang; Wei Xie
Journal:  Front Microbiol       Date:  2022-07-04       Impact factor: 6.064

5.  Thaumarchaeotal signature gene distribution in sediments of the northern South China Sea: an indicator of the metabolic intersection of the marine carbon, nitrogen, and phosphorus cycles?

Authors:  Hongyue Dang; Haixia Zhou; Jinying Yang; Huangmin Ge; Nianzhi Jiao; Xiwu Luan; Chuanlun Zhang; Martin G Klotz
Journal:  Appl Environ Microbiol       Date:  2013-01-18       Impact factor: 4.792

6.  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

7.  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

8.  Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics.

Authors:  Linta Reji; Emily L Cardarelli; Kristin Boye; John R Bargar; Christopher A Francis
Journal:  ISME J       Date:  2021-12-06       Impact factor: 10.302

Review 9.  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

10.  Archaeal amoA and ureC genes and their transcriptional activity in the Arctic Ocean.

Authors:  Estelle Pedneault; Pierre E Galand; Marianne Potvin; Jean-Éric Tremblay; Connie Lovejoy
Journal:  Sci Rep       Date:  2014-04-11       Impact factor: 4.379
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