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

Abstract

© 2016 Kanukollu et al. 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 relatedmore » 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.« less

Authors:
; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1618955
Alternate Identifier(s):
OSTI ID: 1288270; OSTI ID: 1379156
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Published Article
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Name: Standards in Genomic Sciences Journal Volume: 11 Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; anaerobic metabolism; cell-connecting filaments; quorum quenching; flagella gene cluster; DMSP; DMSO reductase; denitrification; homoserine lactone acylase; escherichia-coli k-12; sp-nov.; emended description; rna genes; bacteria; system; clade; identification; annotation

Citation Formats

Kanukollu, Saranya, Voget, Sonja, Pohlner, Marion, Vandieken, Verona, Petersen, Jörn, Kyrpides, Nikos C., Woyke, Tanja, Shapiro, Nicole, Göker, Markus, Klenk, Hans-Peter, Cypionka, Heribert, and Engelen, Bert. Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment. United Kingdom: N. p., 2016. Web. doi:10.1186/s40793-016-0143-0.
Kanukollu, Saranya, Voget, Sonja, Pohlner, Marion, Vandieken, Verona, Petersen, Jörn, Kyrpides, Nikos C., Woyke, Tanja, Shapiro, Nicole, Göker, Markus, Klenk, Hans-Peter, Cypionka, Heribert, & Engelen, Bert. Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment. United Kingdom. https://doi.org/10.1186/s40793-016-0143-0
Kanukollu, Saranya, Voget, Sonja, Pohlner, Marion, Vandieken, Verona, Petersen, Jörn, Kyrpides, Nikos C., Woyke, Tanja, Shapiro, Nicole, Göker, Markus, Klenk, Hans-Peter, Cypionka, Heribert, and Engelen, Bert. 2016. "Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment". United Kingdom. https://doi.org/10.1186/s40793-016-0143-0.
@article{osti_1618955,
title = {Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment},
author = {Kanukollu, Saranya and Voget, Sonja and Pohlner, Marion and Vandieken, Verona and Petersen, Jörn and Kyrpides, Nikos C. and Woyke, Tanja and Shapiro, Nicole and Göker, Markus and Klenk, Hans-Peter and Cypionka, Heribert and Engelen, Bert},
abstractNote = {© 2016 Kanukollu et al. 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.},
doi = {10.1186/s40793-016-0143-0},
url = {https://www.osti.gov/biblio/1618955}, journal = {Standards in Genomic Sciences},
issn = {1944-3277},
number = 1,
volume = 11,
place = {United Kingdom},
year = {Sat Mar 12 00:00:00 EST 2016},
month = {Sat Mar 12 00:00:00 EST 2016}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at https://doi.org/10.1186/s40793-016-0143-0

Citation Metrics:
Cited by: 7 works
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