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:

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

Publication Date:

Sat Mar 12 00:00:00 EST 2016

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:

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