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Genome Sequence of the Exopolysaccharide-Producing Salipiger Mucosus Type Strain (DSM 16094T), a Moderately Halophilic Member of the Roseobacter Clade

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Genome Sequence of the Exopolysaccharide-Producing Salipiger Mucosus Type Strain (DSM 16094T), a Moderately Halophilic Member of the Roseobacter Clade Riedel T, Spring S, Fiebig A, Petersen J, Kypides NC, Göker M, Klenk HP. Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (DSM 16094T), a moderately halophilic member of the Roseobacter clade. Standards in Genomic Sciences 2014, 9(3), 1333-1345. Copyright: © 2014 Standards in Genomic Sciences This is an open access article licensed under a Creative Commons License. DOI link to article: http://dx.doi.org/10.4056/sigs.4909790 Date deposited: 18/03/2015 This work is licensed under a Creative Commons Attribution 3.0 Unported License Newcastle University ePrints - eprint.ncl.ac.uk Standards in Genomic Sciences (2014) 9: 1331-1343 DOI:10.4056/sigs.4909790 Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (DSM 16094T), a moderately halophilic member of the Roseobacter clade Thomas Riedel1,2, Stefan Spring3, Anne Fiebig3, Jörn Petersen3, Nikos C. Kyrpides4, Markus Göker3*, Hans-Peter Klenk3 1Sorbonne Universités, UPMC Univ Paris 06, USR 3579, LBBM, Observatoire Océanologique, Banyuls/Mer, France 2 CNRS, USR 3579, LBBM, Observatoire Océanologique, Banyuls/Mer, France 3 Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany* Correspondence: Markus Göker ([email protected]) Keywords: aerobic, chemoheterotrophic, rod-shaped, photosynthesis, extrachromosomal el- ements, OmniLog phenotyping, Roseobacter clade, Rhodobacteraceae, Alphaproteobacteria. Salipiger mucosus Martínez-Cànovas et al. 2004 is the type species of the genus Salipiger, a moderately halophilic and exopolysaccharide-producing representative of the Roseobacter lineage within the alphaproteobacterial family Rhodobacteraceae. Members of this family were shown to be the most abundant bacteria especially in coastal and polar waters, but were also found in microbial mats and sediments. Here we describe the features of the S. mucosus strain DSM 16094T together with its genome sequence and annotation. The 5,689,389-bp genome sequence consists of one chromosome and several extrachromosomal elements. It contains 5,650 protein-coding genes and 95 RNA genes. The genome of S. mucosus DSM 16094T was sequenced as part of the activities of the Transregional Collabora- tive Research Center 51 (TRR51) funded by the German Research Foundation (DFG). Introduction be moderate halophiles, which are adapted to a The Roseobacter clade is a very heterogeneous wide range of salinities and were found to pro- group of marine Alphaproteobacteria that plays an duce special compounds like compatible solutes, important role in the global carbon cycle and oth- halophilic enzymes or exopolysaccharides [7-9]. er biogeochemical processes [1]. Members of this Strain A3T (= DSM 16094T = LMG 22090T = CECT group form an allegedly monophyletic, physiologi- 5855T) represents the type strain of S. mucosus cally heterogeneous, as well as metabolically ver- (initially proposed as ‘S. muscescens’) in the mono- satile group of bacterioplankton [1]. They are typic genus Salipiger [10] and was isolated from known to live in the open ocean, especially in saline soil bordering a saltern on the Mediterrane- coastal areas, where they have been found many an Sea coast at Calblanque (Spain) [7]. The genus times in symbiosis with algae, in microbial mats, name Salipiger was derived from the Latin noun sediments, or associated with invertebrates, but sal, salis (‘salt’) and the Latin adjective piger (‘la- representatives of this lineage were also isolated zy’) [10]. The species epithet mucosus refers to the from marine environments like polar waters or Latin adjective mucosus (‘slimy, mucous’) [10]. sea ice [1-4], which is also presented and reflected Current PubMed records do not indicate any fol- by their genome sequences [2]. Whereas some low-up research with strain A3T after the initial members of the Roseobacter clade contain the description of S. mucosus [7] and the characteriza- pigment bacteriochlorophyll a and are capable of tion of its exopolysaccharide [11]. aerobic anoxygenic photophosphorylation, other In this study we analyzed the genome sequence of members were found to transform S. mucosus DSM 16094T, which was selected for dimethylsulfonylpropionate into dimethylsulfide sequencing under the auspices of the German Re- [4-6]. search Foundation (DFG) Transregio-SFB51 Some representatives of the Roseobacter lineage Roseobacter grant because of its phylogenetic po- such as Salipiger mucosus A3T are also known to sition [12] and was also a candidate for the Ge- The Genomic Standards Consortium Salipiger mucosus sp. nov. nomic Encyclopedia of Archaea and Bacteria [13]. quence (AY527274), which contains two ambigu- We present a description of the genomic sequenc- ous base calls. ing and annotation and present a summary classi- fication together with a set of features for strain Morphology and physiology DSM 16094T, including novel aspects of its pheno- Cells of strain A3T are pleomorphic and stain type. Gram-negative (Figure 2). They are 1 µm in width and 2.0-2.5 µm in length. Motility was not ob- Classification and features served. They live a strictly aerobic and chemohet- erotrophic lifestyle. Colonies grown on MY solid 16S rRNA gene analysis medium are circular, convex, cream-colored and The single genomic 16S rRNA gene sequence of S. mucoid, whereas in liquid medium their growth is mucosus DSM 16094T was compared with the uniform. Cells are encapsulated. They are moder- Greengenes database for determining the ately halophilic, and capable of growth in a mix- weighted relative frequencies of taxa and (trun- ture of sea salts from 0.5 to 20% (w/v), whereas cated) keywords as previously described [14]. The the optimum is between 3 and 6% (w/v) sea salts. most frequently occurring genera were Salipiger When using NaCl instead of sea salts, optimal (21.2%), Pelagibaca (17.1%), Roseovarius growth occurs at a salt concentration of 9-10% (17.0%), Marinovum (13.1%) and Roseobacter (w/v). Cells of strain A3T grow within a tempera- (9.5%) (30 hits in total). Regarding the single hit ture range of 20-40°C and at a pH range between 6 to sequences from members of the species, the av- and 10. Growth does not occur under anaerobic erage identity within high scoring pairs (HSPs) conditions either by fermentation, fumarate or ni- was 100.0%, whereas the average coverage by trate reduction or photoheterotrophy. Cells are cy- HSPs was 97.2%. Regarding the two hits to se- tochrome oxidase and catalase positive. quences from other members of the genus, the av- Polyhydroxyalkanoates (PHA) are stored as re- erage identity within HSPs was 98.4%, whereas serve material within the cells. H2S is produced the average coverage by HSPs was 99.0%. Among from L-cysteine. Selenite reduction, gluconate oxi- all other species, the one yielding the highest dation and phosphatase were observed. Urea and score was 'Salipiger bermudensis' (DQ178660), Tween 20 are hydrolyzed. A variety of tested or- which corresponded to an identity of 96.8% and a ganic compounds were neither metabolized nor HSP coverage of 99.9%. (Note that the Greengenes sustained growth; for details see [7]. database uses the INSDC (= EMBL/NCBI/DDBJ) The utilization of carbon compounds by S. annotation, which is not an authoritative source mucosus DSM 16094T grown at 28°C was also de- for nomenclature or classification). The highest- termined for this study using Generation-III scoring environmental sequence was AB302369 microplates in an OmniLog phenotyping device (Greengenes short name 'Hydrocarbon-Degrading (BIOLOG Inc., Hayward, CA, USA). The microplates Indonesian Seawater seawater isolate B44-2B44-2 were inoculated with a cell suspension at a cell str. B44-2'), which showed an identity of 97.4% density of 95-96% turbidity and dye IF-A. Further and an HSP coverage of 95.4%. The most frequent- additives were vitamins, micronutrient and sea- ly occurring keywords within the labels of all en- salt solutions, which had to be added for dealing vironmental samples that yielded hits were 'aquat, with such marine bacteria [29]. The plates were rank' (4.9%), 'microbi' (3.7%), 'harbour, newport' sealed with parafilm to avoid a loss of fluid. The (3.3%), 'water' (2.7%) and 'seawat' (2.4%) (219 exported measurement data were further ana- hits in total) and in line with the habitat from lyzed with the opm package for R [30,31], using its which strain A3T was isolated. Environmental functionality for statistically estimating parame- samples that yielded hits of a higher score than ters from the respiration curves such as the max- the highest scoring species were not found. imum height, and automatically translating these Figure 1 shows the phylogenetic neighborhood of values into negative, ambiguous, and positive re- S. mucosus strain DSM 16094T in a 16S rRNA gene actions. The reactions were recorded in three in- sequence based tree. The sequence of the single dividual biological replicates. 16S rRNA gene copy in the genome does not differ from the previously published 16S rRNA gene se- 1332 Standards in Genomic Sciences Riedel et al. Figure 1. Phylogenetic tree highlighting the position of S. mucosus relative to the type strains of the type species of the other genera within the family Rhodobacteraceae. The tree was inferred from 1,331 aligned characters of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion as previously described [14]. Rooting was done initially using the midpoint method [15] and then checked for its agreement with the current classification (Table
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