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Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment

Overview of attention for article published in Environmental Microbiome, March 2016
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Title
Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment
Published in
Environmental Microbiome, March 2016
DOI 10.1186/s40793-016-0143-0
Pubmed ID
Authors

Saranya Kanukollu, Sonja Voget, Marion Pohlner, Verona Vandieken, Jörn Petersen, Nikos C. Kyrpides, Tanja Woyke, Nicole Shapiro, Markus Göker, Hans-Peter Klenk, Heribert Cypionka, Bert Engelen

Abstract

Shimia strain SK013 is an aerobic, Gram-negative, rod shaped alphaproteobacterium affiliated with the Roseobacter group within the family Rhodobacteraceae. The strain was isolated from surface sediment (0-1 cm) of the Skagerrak at 114 m below sea level. The 4,049,808 bp genome of Shimia str. SK013 comprises 3,981 protein-coding genes and 47 RNA genes. It contains one chromosome and no extrachromosomal elements. The genome analysis revealed the presence of genes for a dimethylsulfoniopropionate lyase, demethylase and the trimethylamine methyltransferase (mttB) as well as genes for nitrate, nitrite and dimethyl sulfoxide reduction. This indicates that Shimia str. SK013 is able to switch from aerobic to anaerobic metabolism and thus is capable of aerobic and anaerobic sulfur cycling at the seafloor. Among the ability to convert other sulfur compounds it has the genetic capacity to produce climatically active dimethyl sulfide. Growth on glutamate as a sole carbon source results in formation of cell-connecting filaments, a putative phenotypic adaptation of the surface-associated strain to the environmental conditions at the seafloor. Genome analysis revealed the presence of a flagellum (fla1) and a type IV pilus biogenesis, which is speculated to be a prerequisite for biofilm formation. This is also related to genes responsible for signalling such as N-acyl homoserine lactones, as well as quip-genes responsible for quorum quenching and antibiotic biosynthesis. Pairwise similarities of 16S rRNA genes (98.56 % sequence similarity to the next relative S. haliotis) and the in silico DNA-DNA hybridization (21.20 % sequence similarity to S. haliotis) indicated Shimia str. SK013 to be considered as a new species. The genome analysis of Shimia str. SK013 offered first insights into specific physiological and phenotypic adaptation mechanisms of Roseobacter-affiliated bacteria to the benthic environment.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 33 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 3%
Unknown 32 97%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 8 24%
Student > Master 8 24%
Researcher 5 15%
Student > Bachelor 3 9%
Professor 2 6%
Other 1 3%
Unknown 6 18%
Readers by discipline Count As %
Agricultural and Biological Sciences 12 36%
Environmental Science 6 18%
Biochemistry, Genetics and Molecular Biology 4 12%
Immunology and Microbiology 2 6%
Earth and Planetary Sciences 2 6%
Other 2 6%
Unknown 5 15%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 05 April 2016.
All research outputs
#22,759,452
of 25,374,647 outputs
Outputs from Environmental Microbiome
#720
of 786 outputs
Outputs of similar age
#271,542
of 315,306 outputs
Outputs of similar age from Environmental Microbiome
#12
of 15 outputs
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