Open Access

Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1T)

  • Marcel Huntemann1,
  • Hazuki Teshima1, 2,
  • Alla Lapidus1,
  • Matt Nolan1,
  • Susan Lucas1,
  • Nancy Hammon1,
  • Shweta Deshpande1,
  • Jan-Fang Cheng1,
  • Roxanne Tapia1, 2,
  • Lynne A. Goodwin1, 2,
  • Sam Pitluck1,
  • Konstantinos Liolios1,
  • Ioanna Pagani1,
  • Natalia Ivanova1,
  • Konstantinos Mavromatis1,
  • Natalia Mikhailova1,
  • Amrita Pati1,
  • Amy Chen3,
  • Krishna Palaniappan3,
  • Miriam Land1, 4,
  • Loren Hauser1, 4,
  • Chongle Pan1, 4,
  • Evelyne-Marie Brambilla5,
  • Manfred Rohde6,
  • Stefan Spring5,
  • Markus Göker5,
  • John C. Detter1, 2,
  • James Bristow1,
  • Jonathan A. Eisen1, 7,
  • Victor Markowitz3,
  • Philip Hugenholtz1, 8,
  • Nikos C. Kyrpides1,
  • Hans-Peter Klenk5Email author and
  • Tanja Woyke1
Standards in Genomic Sciences20126:6020185

DOI: 10.4056/sigs.2786069

Published: 25 May 2012

Abstract

Muricauda ruestringensis Bruns et al. 2001 is the type species of the genus Muricauda, which belongs to the family Flavobacteriaceae in the phylum Bacteroidetes. The species is of interest because of its isolated position in the genomically unexplored genus Muricauda, which is located in a part of the tree of life containing not many organisms with sequenced genomes. The genome, which consists of a circular chromosome of 3,842,422 bp length with a total of 3,478 protein-coding and 47 RNA genes, is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

facultatively anaerobic non-motile Gram-negative mesophilic marine chemoheterotrophic Flavobacteriaceae GEBA

Introduction

Strain B1T (= DSM 13258 = LMG 19739 = KCTC 12928) is the type strain of the species Muricauda ruestringensis, which is the type species of the currently six species containing genus Muricauda [1,2]. The genus name was derived from the Latin words muris, of the mouse, and cauda, the tail; Muricauda, tail of the mouse, referring to the cellular appendages observed on some cells [1]. The species epithet is derived from the Neo-Latin word ruestringensis, pertaining to the former village of Rüstringen, which was destroyed by a tidal wave in 1362 [1]. Stain B1T was isolated from a seawater sediment suspension from intertidal sediment at the German North Sea coast, which contained hexadecane as the sole carbon source during the initial cultivation. Later, the organism either turned out to be unable to degrade hexadecane or lost its ability to do so [1]. Other isolates belonging to the species are not known, nor was strain B1T used for scientific work other than the description of the species M. ruestringensis. Here we present a summary classification and a set of features for M. ruestringensis strain B1T, together with the description of the complete genomic sequencing and annotation.

Classification and features

A representative genomic 16S rRNA sequence of M. ruestringensis B1T was compared using NCBI BLAST [3,4] under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database [5] and the relative frequencies of taxa and keywords (reduced to their stem [6]) were determined, weighted by BLAST scores. The most frequently occurring genera were Muricauda (24.7%), Maribacter (24.0%), Cytophaga (12.3%), Zobellia (9.6%) and Flavobacterium (7.1%) (118 hits in total). Regarding the two hits to sequences from members of the species, the average identity within HSPs was 99.7%, whereas the average coverage by HSPs was 93.8%. Regarding the six hits to sequences from other members of the genus, the average identity within HSPs was 97.9%, whereas the average coverage by HSPs was 97.9%. Among all other species, the one yielding the highest score was Muricauda aquimarina (EU440979), which corresponded to an identity of 98.7% and an HSP coverage of 98.4%. (Note that the Greengenes database uses the INSDC (= EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification.) The highest-scoring environmental sequence was HQ326265 (‘Microbial structure biofilm on SWRO membranes clone SBS-FW-047’), which showed an identity of 98.5% and a HSP coverage of 98.0%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were ‘microbi’ (4.7%), ‘sediment’ (4.1%), ‘sea’ (2.9%), ‘marin’ (2.4%) and ‘biofilm’ (2.4%), (132 hits in total). Environmental samples which yielded hits of a higher score than the highest scoring species were not found.

Figure 1 shows the phylogenetic neighborhood of M. ruestringensis in a 16S rRNA based tree. The sequences of the two identical 16S rRNA gene copies in the genome differ by one nucleotide from the previously published 16S rRNA sequence (AF218782).
Figure 1.

Phylogenetic tree highlighting the position of M. ruestringensis relative to the type strains of the other species within the genus Muricauda. The tree was inferred from 1,481 aligned characters [7,8] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [9]. Flavobacterium aquatile was included in the dataset for use as outgroup taxa. The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 850 ML bootstrap replicates [10] (left) and from 1,000 Maximum-Parsimony bootstrap replicates [11] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [12] are labeled with one asterisk, those also listed as ‘Complete and Published’ with two asterisks.

Cells of strain B1T are rod-shaped with rounded ends, 0.3–0.6 µm wide and 1.1–2.7 µm long (Figure 2 and Table 1) [1]. Cells of older cultures are characterized by mainly polar appendages with vesicle-like structures (blebs) at the end (Figure 2), which were discussed in detail by Bruns et al. in [1] and probably serve to contact cells to each other or for colonization of a substratum [1]. The non-motile cells (see missing genes in the motility category in COGs table) stain Gram-negative and grow as facultative anaerobes in seawater. The temperature range for growth is between 8°C and 40°C, with an optimum between 20 and 30°C [1]. The pH range for growth is 6.0–8.0, with an optimum at pH 6.5–7.5 [1]. Physiology and metabolism are discussed in detail in [1], with the surprising discovery that although strain B1T was isolated from a continuous-flow culture containing hexadecane as a sole carbon source, the strain was unable to degrade hexadecane (even if it was offered as cosubstrate along with other carbon sources); nor could it use acetate or pyruvate as sole carbon sources, but required a wide spectrum of amino acids as carbon and energy sources in addition to some carbohydrates [1].
Figure 2.

Scanning electron micrograph of M. ruestringensis B1T

Table 1.

Classification and general features of M. ruestringensis B1T according to the MIGS recommendations [13].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [14]

 

Phylum Bacteroidetes

TAS [15,16]

 

Class Flavobacteria

TAS [17,18]

 

Order Flavobacteriales

TAS [19,20]

 

Family Flavobacteriaceae

TAS [2124]

 

Genus Muricauda

TAS [1,25,26]

 

Species Muricauda ruestringensis

TAS [1]

 

Type strain B1

TAS [1]

 

Gram stain

negative

TAS [1]

 

Cell shape

rod-shaped

TAS [1]

 

Motility

non-motile

TAS [1]

 

Sporulation

not reported

 
 

Temperature range

mesophile, 20°C–30°C

TAS [1]

 

Optimum temperature

30°C

TAS [1]

 

Salinity

slightly halophilic, optimum 3% NaCl (w/v)

TAS [1]

MIGS-22

Oxygen requirement

facultatively anaerobic

TAS [1]

 

Carbon source

various sugars and amino acids

TAS [1]

 

Energy metabolism

chemoheterotroph

TAS [1]

MIGS-6

Habitat

marine

TAS [1]

MIGS-15

Biotic relationship

free-living

TAS [1]

MIGS-14

Pathogenicity

none

NAS

 

Biosafety level

1

TAS [27]

 

Isolation

seawater sediment suspension

TAS [1]

MIGS-4

Geographic location

Jadebusen Bay, coast of North Sea, Germany

TAS [1]

MIGS-5

Sample collection time

1998 or earlier

NAS

MIGS-4.1

Latitude

53.45

NAS

MIGS-4.2

Longitude

8.20

NAS

MIGS-4.3

Depth

not reported

 

MIGS-4.4

Altitude

about 0 m, sea level

NAS

Evidence codes - NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [28].

Chemotaxonomy

The spectrum of whole-cell fatty acids represents the only chemotaxonomical data published thus far for strain B1T. The spectrum of fatty acids was dominated by branched-chain acids (72%): iso-C17:0 3OH (28.7%), iso-C15:1 (16.3%), iso-C15:0 (15.5%), iso-C15:0 3OH (4.9%), iso-C16:0 3OH (2.9%), iso-C17:0 2OH (2.8%), iso -C15:0 2OH (2.5%), C16:1 ω7c (2.5%), anteiso-C15:0(2.4%), other acids below 2% [1].

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [29], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [30]. The genome project is deposited in the Genomes On Line Database [12] and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.
Table 2.

Genome sequencing project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

Finished

MIGS-28

Libraries used

Four genomic libraries: one 454 pyrosequence standard library, two 454 PE libraries (4 kb and 8 kb insert size), one Illumina library

MIGS-29

Sequencing platforms

Illumina GAii, 454 GS FLX Titanium

MIGS-31.2

Sequencing coverage

996.4 × Illumina; 36.4 × pyrosequence

MIGS-30

Assemblers

Newbler version 2.3, Velvet version 0.7.63, phrap version SPS - 4.24

MIGS-32

Gene calling method

Prodigal 1.4, GenePRIMP

 

INSDC ID

CP002999

 

Genbank Date of Release

August 19, 2011

 

GOLD ID

Gc01927

 

NCBI project ID

52467

 

Database: IMG-GEBA

2505679007

MIGS-13

Source material identifier

DSM 13258

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

M. ruestringensis strain B1T, DSM 13258, was grown in DSMZ medium 917 (Modified Sea Water Agar) [31] at 30°C. DNA was isolated from 0.5–1 g of cell paste using Jetflex Genomic DNA Purification Kit (GENOMED 600100) following the manufacturer’s instructions, with a modified procedure for cell lysis: incubation with 40 εl proteinase K for 40 minutes at 58°C. DNA is available through the DNA Bank Network [32].

Genome sequencing and assembly

The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website [33]. Pyrosequencing reads were assembled using the Newbler assembler (Roche). The initial Newbler assembly consisting of 26 contigs in one scaffold was converted into a phrap [34] assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (3,847 Mb) was assembled with Velvet [35] and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 268.3 Mb 454 draft data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The Phred/Phrap/Consed software package [34] was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution [33], Dupfinisher [36], or sequencing cloned bridging PCR fragments with subcloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Chang, unpublished). A total of 46 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using a software Polisher developed at JGI [37]. The error rate of the completed genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 1,032.9 × coverage of the genome. The final assembly contained 422,407 pyrosequence and 49,819,141 Illumina reads.

Genome annotation

Genes were identified using Prodigal [38] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [39]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes – Expert Review (IMG-ER) platform [40].

Genome properties

The genome consists of a 3,842,422 bp long circular chromosome with a G+C content of 41.4% (Table 3 and Figure 3). Of the 3,525 genes predicted, 3,478 were protein-coding genes, and 47 RNAs; 46 pseudogenes were also identified. The majority of the protein-coding genes (66.6%) were assigned with a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.
Figure 3.

Graphical map of the chromosome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Table 3.

Genome Statistics

Attribute

Value

% of Total

Genome size (bp)

3,842,422

100.00%

DNA coding region (bp)

3,479,569

90.56%

DNA G+C content (bp)

1,589,148

41.36%

Number of replicons

1

 

Extrachromosomal elements

0

 

Total genes

3,525

100.00%

RNA genes

47

1.33%

rRNA operons

2

 

tRNA genes

38

1.08%

Protein-coding genes

3,478

98.67%

Pseudo genes

46

1.30%

Genes with function prediction

2,349

66.64%

Genes in paralog clusters

1,644

46.64%

Genes assigned to COGs

2,433

69.02%

Genes assigned Pfam domains

2,500

70.92%

Genes with signal peptides

970

27.52%

Genes with transmembrane helices

809

22.95%

CRISPR repeats

0

 
Table 4.

Number of genes associated with the general COG functional categories

Code

value

%age

Description

J

151

5.8

Translation, ribosomal structure and biogenesis

A

0

0.0

RNA processing and modification

K

206

7.9

Transcription

L

130

5.0

Replication, recombination and repair

B

2

0.1

Chromatin structure and dynamics

D

23

0.9

Cell cycle control, cell division, chromosome partitioning

Y

0

0.0

Nuclear structure

V

77

2.9

Defense mechanisms

T

145

5.5

Signal transduction mechanisms

M

186

7.1

Cell wall/membrane/envelope biogenesis

N

7

0.3

Cell motility

Z

1

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

50

1.9

Intracellular trafficking, secretion, and vesicular transport

O

106

4.0

Posttranslational modification, protein turnover, chaperones

C

129

4.9

Energy production and conversion

G

136

5.2

Carbohydrate transport and metabolism

E

220

8.4

Amino acid transport and metabolism

F

65

2.5

Nucleotide transport and metabolism

H

138

5.3

Coenzyme transport and metabolism

I

86

3.3

Lipid transport and metabolism

P

141

5.4

Inorganic ion transport and metabolism

Q

49

1.9

Secondary metabolites biosynthesis, transport and catabolism

R

339

12.9

General function prediction only

S

236

9.0

Function unknown

-

1,092

31.0

Not in COGs

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Maren Schröder (DSMZ) for growing M. ruestringensis cultures. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2.

Authors’ Affiliations

(1)
DOE Joint Genome Institute
(2)
Bioscience Division, Los Alamos National Laboratory
(3)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(4)
Oak Ridge National Laboratory
(5)
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures
(6)
HZI - Helmholtz Centre for Infection Research
(7)
University of California Davis Genome Center
(8)
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland

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