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Complete genome sequence of Marinobacter adhaerens type strain (HP15), a diatom-interacting marine microorganism

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Standards in Genomic Sciences20103:3020097

https://doi.org/10.4056/sigs.922139

©  The Author(s) 2010

  • Published:

Abstract

Marinobacter adhaerens HP15 is the type strain of a newly identified marine species, which is phylogenetically related to M. flavimaris, M. algicola, and M. aquaeolei. It is of special interest for research on marine aggregate formation because it showed specific attachment to diatom cells. In vitro it led to exopolymer formation and aggregation of these algal cells to form marine snow particles. M. adhaerens HP15 is a free-living, motile, rod-shaped, Gram-negative gammaproteobacterium, which was originally isolated from marine particles sampled in the German Wadden Sea. M. adhaerens HP15 grows heterotrophically on various media, is easy to access genetically, and serves as a model organism to investigate the cellular and molecular interactions with the diatom Thalassiosira weissflogii. Here we describe the complete and annotated genome sequence of M. adhaerens HP15 as well as some details on flagella-associated genes. M. adhaerens HP15 possesses three replicons; the chromosome comprises 4,422,725 bp and codes for 4,180 protein-coding genes, 51 tRNAs and three rRNA operons, while the two circular plasmids are ∼187 kb and ∼42 kb in size and contain 178 and 52 protein-coding genes, respectively.

Keywords

  • marine heterotrophic bacteria
  • diatoms
  • attachment
  • marine aggregate formation

Introduction

Strain HP15 (DSM 23420) is the type strain of the newly established species Marinobacter adhaerens sp. nov. and represents one of 27 species currently assigned to the genus Marinobacter [1]. Strain HP15 was first described by Grossart et al. in 2004 [2] as a marine particle-associated, Gram-negative, gammaproteobacterium isolated from the German Wadden Sea. The organism is of interest because of its capability to specifically attach in vitro to the surface of the diatom Thalassiosira weissflogii-inducing exopolymer and aggregate formation and thus generating marine snow particles [3]. Marine snow formation is an important process of the biological pump, by which atmospheric carbon dioxide is taken up, recycled, and partly exported to the sediments. This sink of organic carbon plays a major role for marine biogeochemical cycles [4]. Several studies reported on the formation and properties of marine aggregates [5–8]. Although it was shown that heterotrophic bacteria control the development and aggregation of marine phytoplankton [3], specific functions of individual bacterial species on diatom aggregation have not been explored thus far.

A better understanding of the molecular basis of bacteria-diatom interactions that lead to marine snow formation is currently gained by establishing a bilateral model system, for which M. adhaerens sp. nov. HP15 serves as the bacterial partner of the easy-to-culture diatom, T. weissflogii [3]. Herein, we present a set of features for M. adhaerens sp. nov. HP15 (Table 1) together with its annotated complete genomic sequence, and a detailed analysis of its flagella-associated genes.
Table 1.

Classification and general features of M. adhaerens sp. nov. HP15 according to the MIGS recommendations [9]

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [10]

 

Phylum Proteobacteria

TAS [11]

 

Class Gammaproteobacteria

TAS [12,13]

 

Order Alteromonadales

TAS [12,14]

 

Family Alteromonadaceae

TAS [15–17]

 

Genus Marinobacter

TAS [1,18]

 

Species Marinobacter adhaerens

TAS [1]

 

Type strain HP15

TAS [1]

 

Gram stain

negative

IDA

 

Cell shape

rod-shaped

IDA

 

Motility

motile, single polar flagellum

IDA

 

Sporulation

non-sporulating

NAS

 

Temperature range

mesophilic

IDA

 

Optimum temperature

34–38°C

IDA

 

Salinity

0.4–10 g NaCl/l (optimum/growth within 1 day)

IDA

MIGS-22

Oxygen requirement

strictly aerobic

IDA

 

Carbon source

dextrin, Tween 40 and 80, pyruvic acid methyl ester, succinic acid mono-methyl-ester, cis-aconitic acid, β-hydroxybutyric acid, γ-hydroxybutyric acid, α-keto glutaric acid, α-keto valeric acid, D,L-lactic acid, bromosuccinic acid, L-alaninamide, D-alanine, L-alanine, L-glutamic acid, L-leucine and L-proline

IDA

 

Energy source

chemoorganoheterotrophic

IDA

MIGS-6

Habitat

sea water

IDA

MIGS-15

Biotic relationship

free-living and particle-associated

TAS [2]

MIGS-13

Culture deposition no.

DSM 23420

IDA

MIGS-14

Pathogenicity

none

NAS

 

Biosafety level

1

NAS

 

Isolation

marine aggregates (0.1–1 mm)

TAS [2]

MIGS-4

Geographic location

German Wadden Sea

TAS [2]

MIGS-4.1

Latitude

53°43′20″N

TAS [2]

MIGS-4.2

Longitude

07°43′20″E

TAS [2]

MIGS-4.3

Depth

surface waters

TAS [2]

MIGS-4.4

Altitude

sea level

TAS [2]

MIGS-5

Sample collection time

15 June 2000

TAS [2]

Evidence codes - IDA: inferred from Direct Assay (first time in publication); TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property of the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [19]. If evidence code is IDA, then the property was directly observed for a live isolate by one of the authors or an expert mentioned in the acknowledgements.

Classification and features

M. adhaerens sp. nov. strain HP15 is a motile, Gram-negative, non-spore-forming rod (Figure 1). Based on its 16S rRNA sequence, strain HP15 was assigned to the Marinobacter genus of Gammaproteobacteria. Two other Marinobacter species were identified based on their interactions with eukaryotes - M. algicola isolated from dinoflagellate cultures [20] and M. bryozoorum derived from Bryozoa [21]. The 16S rRNA gene of strain HP15 is most closely related to those of the type strains of M. flavimaris (99%), M. salsuginis (98%) and M. algicola (96%). These four type strains form a discrete cluster in the phylogenetic tree (Figure 2). In contrast, DNA-DNA hybridization experiments revealed that the genome of M. adhaerens sp. nov. HP15 showed about 64% binding to that of M. flavimaris [1], which is below the generally accepted species differentiation limit of 70% [25].
Figure 1.
Figure 1.

Transmission electron micrograph of M. adhaerens sp. nov. strain HP15.

Figure 2.
Figure 2.

Maximum likelihood phylogenetic tree based on 16S rRNA sequences of M. adhaerens type strain (HP15) plus all type strains of the genus Marinobacter and the type species of the neighbor order Pseudomonadales. Sequence selection and alignment improvements were carried out using the Living Tree Project database [22] and the ARB software package [23]. The tree was inferred from 1,531 alignment positions using RAxML [24] with GTRGAMMA model. Support values from 1,000 bootstrap replicates are displayed above branches if larger than 50%. The scale bar indicates substitutions per site.

Chemotaxonomy

Strain HP15 can grow in artificial sea water with a nitrogen-to-phosphorus ratio of 15:1 supplemented with glucose as the sole carbon source. In presence of diatom cells but without glucose, HP15 utilized diatom-produced carbohydrates as sole source of carbon. Furthermore, M. adhaerens sp. nov. HP15 differed from M. flavimaris and other Marinobacter species in a number of chemotaxonomic properties, such as utilization of glycerol, fructose, lactic acid, gluconate, alanine, and glutamate [1]. Additionally, strain HP15 showed a unique fatty acid composition pattern.

Genome sequencing and annotation

Genome project history

M. adhaerens HP15 was selected for sequencing because of its phylogenetic position, its particular feature as a diatom-interacting marine organism [3], and its feasible genetic accessibility to act as a model organism. The respective genome project is deposited in the Genome OnLine Database [19] and the complete genome sequence in GenBank. The main project information is summarized in Table 2.
Table 2.

Genome sequencing project information for M. adhaerens sp. nov. HP15

MIGS ID

Property

Term

MIGS-31

Finishing quality

Finished

MIGS-28

Library used

454 pyrosequencing standard library

MIGS-29

Sequencing platforms

454 FLX Ti

MIGS-31.2

Sequencing coverage

22.5× pyrosequencing

MIGS-30

Assemblers

Newbler version 2.0.00.22

MIGS-32

Gene calling method

GLIMMER v3.02, tRNAScan-SE

  

CP001978 (chromosome)

 

Genbank ID

CP001979 (pHP-42)

  

CP001980 (pHP-187)

 

Genbank Date of Release

September 18, 2010

 

GOLD ID

Gi06214

 

NCBI project ID

46089

 

Database: IMG

pending

 

Project relevance

Marine diatom-bacteria interactions

Growth conditions and DNA isolation

M. adhaerens sp. nov. HP15 was grown in 100 ml Marine Broth medium [26] at 28°C. A total of 23 µg DNA was isolated from the cell paste using a Qiagen DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

Genome sequencing and assembly

The Marinobacter adhaerens sp. nov. HP15 genome was sequenced at AGOWA (AGOWA GmbH, Berlin, Germany) using the 454 FLX Ti platform of 454 Life Sciences (Branford, CT, USA). The sequencing library was prepared according to the 454 instructions from genomic M. adhaerens sp. nov. HP15 DNA with a final concentration of 153 ng/µl. Sequencing was carried out on a quarter of a 454 picotiterplate, yielding 258.645 reads with an average length of 405 bp, totaling to almost 105 Mb. These reads were assembled using the Newbler assembler version 2.0.00.22 (Roche), resulting in 253.285 fully and 4.763 partially assembled reads, leaving 932 singletons, 226 repeats and 371 outliers. The assembly comprised 112 contigs, with 40 exceeding 500 bp. The latter comprised more than 4.6 Mb, with an average contig size of almost 116 kb and a longest contig of more than 1.2 Mb. Gaps between contigs were closed in a conventional PCR-based gap closure approach, resulting in a fully closed circular chromosome of 4.421.911 bp, and two plasmids of 187.465 bp and 42.349 bp, respectively. Together all sequences provided 22.5× coverage of the genome. The error rate of the completed genome sequence is about 3 in 1,000 (99.7%).

Genome annotation

Potential protein-coding genes were identified using GLIMMER v3.02 [27], transfer RNA genes were identified using tRNAScan-SE [28] and ribosomal RNA genes were identified via BLAST searches [29] against public nucleotide databases. The annotation of the genome sequence was performed with the GenDB v2.2.1 system [30]. For each predicted gene, similarity searches were performed against public sequence databases (nr, SwissProt, KEGG) and protein family databases (Pfam, InterPro, COG). Signal peptides were predicted with SignalP v3.0 [31,32] and transmembrane helices with TMHMM v2.0 [33]. Based on these observations, annotations were derived in an automated fashion using a fuzzy logic-based approach [34]. Finally, the predictions were manually checked with respect to missing genes in intergenic regions and putative sequencing errors, and the annotations were manually curated using the Artemis 11.3.2 program and refined for each putative gene [35].

Genome properties

The genome of strain HP15 comprises three circular replicons: the 4,422,725 bp chromosome and two plasmids of ∼187 kb and ∼42 kb, respectively (Table 3A and Figure 3). The genome possesses a 56.9% GC content (Table 3B). Of the 4,482 predicted genes, 4,422 were protein coding genes, and 60 RNAs; 391 pseudogenes were also identified. The majority of the protein-coding genes (67.5%) were assigned with a putative function, while those remaining were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4
Figure 3.
Figure 3.

Graphical circular maps of the genome and the two plasmids of HP15. 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 3A.

Genome composition for M. adhaerens HP15

Label

Size (Mb)

Topology

RefSeq ID

Chromosome§

4.423

circular

CP001978

Plasmid pHP-187

0.187

circular

CP001980

Plasmid pHP-42*

0.042

circular

CP001979

§Number of protein-coding genes: 4,180; Number of protein-coding genes: 178;

*Number of protein-coding genes: 52

Table 3B.

Genome statistics for M. adhaerens HP15

Attribute

Value

% of totala

Genome size (bp)

4,651,725

 

DNA Coding region (bp)

4,178,502

89.8

DNA G+C content (bp)

2,644,970

56.9

Number of replicons

3

 

Extrachromosomal elements

2

 

Total genesb

4,410

 

tRNA genes

51

1.16

5S rRNA genes

3

0.07

16S rRNA genes

3

0.07

23S rRNA genes

3

0.07

Protein-coding genes

4,355

98.66

Genes assigned to COGs

3,027

67.54

Genes with Pfam domains

2,918

65.1

1 Pfam domain

2,041

45.54

2 Pfam domains

598

13.34

3 Pfam domains

194

4.33

4 or more Pfam domains

85

1.9

Genes with signal peptides

765

17.07

Genes with transmembrane helices

1,043

23.27

1 transmembrane helix

341

7.61

2 transmembrane helices

154

3.44

3 transmembrane helices

72

1.61

4 or more transmembrane helices

476

10.62

Genes in paralogous clusters

570

12.72

Genes with 1 paralog

364

8.12

Genes with 2 paralogs

63

1.41

Genes with 3 paralogs

26

0.58

Genes with 4 or more paralogs

117

2.61

Pseudo/hypothetical genes

391

8.72

Conserved hypothetical genes

668

14.90

Genes for function prediction

3,363

75.03

a) The total is based on either the size of the genome in base pairs or the total number of protein coding genes in the annotated genome.

b) Also includes 54 pseudogenes and 5 other genes.

Table 4.

Number of genes associated with the 21 general COG functional categories

Code

Value

%agea

Description

J

162

3.7

Translation

A

0

0

RNA processing and modification

K

161

3.6

Transcription

L

132

3

Replication, recombination and repair

B

0

0

Chromatin structure and dynamics

D

32

0.7

Cell cycle control, mitosis and meiosis

Y

0

0

Nuclear structure

V

0

0

Defense mechanisms

T

199

4.5

Signal transduction mechanisms

M

151

3.4

Cell wall/membrane biogenesis

N

166

3.8

Cell motility

Z

0

0

Cytoskeleton

W

0

0

Extracellular structures

U

0

0

Intracellular trafficking and secretion

O

127

2.9

Posttranslational modification, protein turnover, chaperones

C

192

4.3

Energy production and conversion

G

82

1.9

Carbohydrate transport and metabolism

E

254

5.7

Amino acid transport and metabolism

F

51

1.1

Nucleotide transport and metabolism

H

97

2.2

Coenzyme transport and metabolism

I

141

3.2

Lipid transport and metabolism

P

138

3.1

Inorganic ion transport and metabolism

Q

76

1.7

Secondary metabolites biosynthesis, transport and catabolism

R

330

7.5

General function prediction only

S

251

5.7

Function unknown

-

285

6.4

multiple COGs

 

3,027

68.6

Total

-

1,383

31.4

Not in COGs

a) The total is based on the total number of protein coding genes in the annotated genome

Flagella-associated gene clusters of M. adhaerens HP15

Because M. adhaerens HP15 was experimentally shown to adhere to diatom cells, gene clusters coding for secretion, assembly, and mechanistic function of the polar flagellum were analyzed in detail (Figure 4). Besides several other chemotactic mechanisms and various cell surface interactions, bacterial flagella and other cell appendages had previously been shown to be instrumental for chemotactic movement towards and adhesion to biotic surfaces [36,37]. The amino acid sequences of proteins encoded by the three identified gene clusters showed significant similarities to orthologous and experimentally well-described gene products of P. aeruginosa PAO1 and various other bacterial species as determined by BLASTP algorithm comparison using the Blosum 62 substitution matrix [29]. Not surprisingly, hook and motor switch complex components were most conserved. However, gene products involved in flagellar filament formation encoded by Cluster II also showed 53 to 78% similarity to the respective PAO1 proteins. Mutagenesis of flagella-associated genes of M. adhaerens HP15 will be carried out in the near future to study the role of flagella in bacteria-diatom interactions and to further our understanding of the cell-to-cell communication between those organisms.
Figure 4.
Figure 4.

Schematic presentation of the three flagella-associated gene clusters of M. adhaerens HP15 coding for the basal body, the filament, and the hook and motor switch complex. Identities to the respective orthologs in the genome of P. aeruginosa PAO1 are indicated by gray-scale code. Numbers of CDS are shown below gene names.

Declarations

Acknowledgements

We thank Yannic Ramaye for help with TEM operation and Christian Quast for computer support. The work was financially supported by the Max Planck Society, the Helmholtz Foundation, and Jacobs University Bremen.

Authors’ Affiliations

(1)
School of Engineering and Science, Jacobs University Bremen, Bremen, Germany
(2)
Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
(3)
Marine Microbiology Group, Institut Mediterrani d’Estudis Avançats, Esporles, Spain
(4)
Dept. Limnology of Stratified Lakes, IGB-Neuglobsow, Stechlin, Germany

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