skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252T isolated from marine sediment

Journal Article · · Standards in Genomic Sciences
DOI:https://doi.org/10.4056/sigs.3828824· OSTI ID:1628662
 [1];  [2];  [3];  [2];  [2];  [4];  [5];  [5];  [5];  [6];  [2];  [6];  [7];  [3];  [5];  [5];  [1];  [3];  [3];  [1]
  1. Univ. of Oldenburg (Germany). Inst. for Chemistry and Biology of the Marine Environment
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Biosciences Division
  3. Leibniz Inst., Braunschweig (Germany). German Collection of Microorganisms and Cell Cultures (DSMZ)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biologival Data Management and Technology Center
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  6. Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Biosciences Division; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  7. HZI--Helmholtz Centre for Infection Research, Braunschweig (Germany)
+ Show Author Affiliations

Leisingera nanhaiensis DSM 24252T is a Gram-negative, motile, rod-shaped marine Alphaproteobacterium, isolated from sandy marine sediments. Here we present the noncontiguous genome sequence and annotation together with a summary of the organism's phenotypic features. The 4,948,550 bp long genome with its 4,832 protein-coding and 64 RNA genes consists of one chromosome and six extrachromosomal elements with lengths of 236 kb, 92 kb, 61 kb, 58 kb, 56 kb, and 35 kb, respectively. The analysis of the genome showed that DSM 24252T possesses all genes necessary for dissimilatory nitrite reduction, and the strain was shown to be facultatively anaerobic, a deviation from the original description that calls for an emendation of the species. Also present in the genome are genes coding for a putative prophage, for genetransfer agents and for the utilization of methylated amines. Phylogenetic analysis and intergenomic distances indicate that L. nanhaiensis might not belong to the genus Leisingera.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1628662
Journal Information:
Standards in Genomic Sciences, Vol. 9, Issue 3; ISSN 1944-3277
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

References (60)

Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide journal May 2002
Leisingera nanhaiensis sp. nov., isolated from marine sediment journal February 2010
Leisingera aquimarina sp. nov., isolated from a marine electroactive biofilm, and emended descriptions of Leisingera methylohalidivorans Schaefer et al. 2002, Phaeobacter daeponensis Yoon et al. 2007 and Phaeobacter inhibens Martens et al. 2006 journal December 2008
Comparative genomics of methylated amine utilization by marine Roseobacter clade bacteria and development of functional gene markers (tmm, gmaS): Methylamine utilization by Roseobacter journal April 2012
Complete genome sequence of Isosphaera pallida type strain (IS1BT) journal February 2011
Oceanicola nanhaiensis sp. nov., isolated from sediments of the South China Sea journal January 2007
Oceanicola marinus sp. nov., a marine alphaproteobacterium isolated from seawater collected off Taiwan journal July 2007
Roseobacter gallaeciensis sp. nov., a new marine bacterium isolated from rearings and collectors of the scallop Pecten maximus journal April 1998
Phaeobacter caeruleus sp. nov., a blue-coloured, colony-forming bacterium isolated from a marine electroactive biofilm journal April 2009
Seohaeicola saemankumensis gen. nov., sp. nov., isolated from a tidal flat journal July 2009
Phaeobacter daeponensis sp. nov., isolated from a tidal flat of the Yellow Sea in Korea journal April 2007
Oceanicola pacificus sp. nov., isolated from a deep-sea pyrene-degrading consortium journal April 2009
Phaeobacter arcticus sp. nov., a psychrophilic bacterium isolated from the Arctic journal June 2008
Oceanicola nitratireducens sp. nov., a marine alphaproteobacterium isolated from the South China Sea journal July 2010
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata journal December 2011
Genome sequence of the Leisingera aquimarina type strain (DSM 24565T), a member of the marine Roseobacter clade rich in extrachromosomal elements journal July 2013
Genome sequence of Phaeobacter caeruleus type strain (DSM 24564T), a surface-associated member of the marine Roseobacter clade journal July 2013
Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566T journal July 2013
Genome sequence of Phaeobacter inhibens type strain (T5T), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens journal December 2013
Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336T), a representative of the Roseobacter clade journal October 2013
Genome sequence of Phaeobacter daeponensis type strain (DSM 23529T), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis journal October 2013
The minimum information about a genome sequence (MIGS) specification journal May 2008
The Genomic Standards Consortium journal June 2011
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. journal June 1990
Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera journal June 2006
Gene Ontology: tool for the unification of biology journal May 2000
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation journal December 2012
The DNA Bank Network: The Start from a German Initiative journal March 2011
Solexa Ltd journal June 2004
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs journal February 2008
ALLPATHS: De novo assembly of whole-genome shotgun microreads journal February 2008
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities journal March 1998
Base-Calling of Automated Sequencer Traces Using Phred.  I. Accuracy Assessment journal March 1998
Consed: A Graphical Tool for Sequence Finishing journal March 1998
Prodigal: prokaryotic gene recognition and translation initiation site identification journal March 2010
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes journal July 2009
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes journal May 2010
IMG ER: a system for microbial genome annotation expert review and curation journal June 2009
Replication and Control of Circular Bacterial Plasmids journal June 1998
Bacterial flavin-containing monooxygenase is trimethylamine monooxygenase journal October 2011
The gene transfer agent of Rhodobacter capsulatus and "constitutive transduction" in prokaryotes journal April 2001
Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life journal June 2012
Molecular and phenotypic analyses reveal the non-identity of the Phaeobacter gallaeciensis type strain deposits CIP 105210T and DSM 17395 journal November 2013
Bemerkungen zu der Abhandlung der HH. Weselsky und Benedikt „Ueber einige Azoverbindungen” journal January 1879
Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs journal January 2010
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison journal January 2010
Genome sequence-based species delimitation with confidence intervals and improved distance functions journal January 2013
Origin and Evolution of a Novel DnaA-Like Plasmid Replication Type in Rhodobacterales journal November 2010
Diversity and evolution of repABC type plasmids in Rhodobacterales journal October 2009
Mechanisms of plasmid stable maintenance with special focus on plasmid addiction systems. journal December 2001
The versatile bacterial type IV secretion systems journal November 2003
Extrachromosomal, extraordinary and essential—the plasmids of the Roseobacter clade journal February 2013
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes journal March 2007
Growth yields of Desulfotomaculum orientis with hydrogen in chemostat culture journal January 1986
Phylogeny and compatibility: plasmid classification in the genomics era journal March 2011
The rhamnose pathway journal December 2000
Dietary palmitic acid promotes a prometastatic memory via Schwann cells journal November 2021
Multiplex profiling of serum proteins in solution using barcoded antibody fragments and next generation sequencing journal July 2020
Antibiotic Production by a Roseobacter Clade-Affiliated Species from the German Wadden Sea and Its Antagonistic Effects on Indigenous Isolates journal April 2004
Genome Sequences of Oceanicola granulosus HTCC2516T and Oceanicola batsensis HTCC2597T journal April 2010

Cited By (5)

Distinct compositions of free-living, particle-associated and benthic communities of the Roseobacter group in the North Sea journal November 2015
Complete Genome Sequence of Leisingera aquamixtae R2C4, Isolated from a Self-Regenerating Biocathode Consortium journal September 2019
Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment journal March 2016
Exemplar Abstract for Sedimentitalea nanhaiensis (Sun et al. 2010) Breider et al. 2014 and Leisingera nanhaiensis Sun et al. 2010 emend. Breider et al. 2013. dataset January 2013
Nomenclature Abstract for Leisingera nanhaiensis Sun et al. 2010 emend. Breider et al. 2013. dataset January 2013

Similar Records

Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336T), a representative of the Roseobacter clade
Journal Article · Fri Oct 04 00:00:00 EDT 2013 · Standards in Genomic Sciences · OSTI ID:1628662
+14 more
Genome sequence of Phaeobacter daeponensis type strain (DSM 23529T), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis
Journal Article · Thu Oct 03 00:00:00 EDT 2013 · Standards in Genomic Sciences · OSTI ID:1628662
+18 more
Genome sequence of Phaeobacter inhibens type strain (T5T), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens
Journal Article · Fri Dec 20 00:00:00 EST 2013 · Standards in Genomic Sciences · OSTI ID:1628662
+18 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
54 ENVIRONMENTAL SCIENCES
Genetics & Heredity
Microbiology
Marine
motile
facultative anaerobe
methylated compounds
Rhodobacteraceae
Roseobacter clade