Open Access

Genome of the marine alphaproteobacterium Hoeflea phototrophica type strain (DFL-43T)

  • Anne Fiebig1,
  • Silke Pradella1,
  • Jörn Petersen1,
  • Victoria Michael1,
  • Orsola Päuker1,
  • Manfred Rohde2,
  • Markus Göker1,
  • Hans-Peter Klenk1Email author and
  • Irene Wagner-Döbler2
Standards in Genomic Sciences20137:7030440

https://doi.org/10.4056/sigs.3486982

Published: 25 February 2013

Abstract

Hoeflea phototrophica Biebl et al. 2006 is a member of the family Phyllobacteriaceae in the order Rhizobiales, which is thus far only partially characterized at the genome level. This marine bacterium contains the photosynthesis reaction-center genes pufL and pufM and is of interest because it lives in close association with toxic dinoflagellates such as Prorocentrum lima. The 4,467,792 bp genome (permanent draft sequence) with its 4,296 protein-coding and 69 RNA genes is a part of the Marine Microbial Initiative.

Keywords

aerobic rod-shaped motile photoheterotroph Phenotype MicroArray bacteriochlorophyll a symbiosis dinoflagellates Prorocentrum lima Phyllobacteriaceae

Introduction

Strain DFL-43T (= DSM 17068 = NCIMB 14078) is the type strain of Hoeflea phototrophica, a marine member of the Phyllobacteriaceae (Rhizobiales, Alphaproteobacteria) [1]. The genus, which was named in honor of the German microbiologist Manfred Höfle [2], contains four species, with H. marina as type species [2]; the name of a fifth member of the genus, ‘Hoeflea siderophila’, is until now only effectively published [3]. H. phototrophica DFL-43T and strain DFL-44 were found in the course of a screening program for marine bacteria containing the photosynthesis reaction-center genes pufL and pufM [4]. The species epithet ‘phototrophica’ refers to the likely ability of H. phototrophica strains to use light as an additional energy source [1]. Strain DFL-43T was isolated from single cells of a culture of the toxic dinoflagellate Prorocentrum lima maintained at the Biological Research Institute of Helgoland, Germany [1]. Here we present a summary classification and a set of features for H. phototrophica DFL-43T including so far undiscovered aspects of its phenotype, together with the description of the complete genomic sequencing and annotation.

This work is part of the Marine Microbial Initiative (MMI) which enabled the J. Craig Venter Institute (JCVI) to sequence the genomes of approximately 165 marine microbes with funding from the Gordon and Betty Moore Foundation. These microbes were contributed by collaborators worldwide, and represent an array of physiological diversity, including carbon fixers, photoautotrophs, photoheterotrophs, nitrifiers, and methanotrophs. The MMI was designed to complement other ongoing research at JCVI and elsewhere to characterize the microbial biodiversity of marine and terrestrial environments through metagenomic profiling of environmental samples.

Classification and features

16S rRNA analysis

A representative genomic 16S rRNA sequence of H. phototrophica DFL-43T was compared using NCBI BLAST [5,6] 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 [7] and the relative frequencies of taxa and keywords (reduced to their stem [8]) were determined, weighted by BLAST scores. The most frequently occurring genera were Rhizobium (53.7%), Sinorhizobium (24.0%), Hoeflea (4.5%), Bartonella (4.5%) and Ahrensia (3.7%) (132 hits in total). Regarding the two hits to sequences from members of the species, both, the average identity within HSPs and the average coverage by HSPs were 100.0%. Regarding the single hit to sequences from other members of the genus, the average identity within HSPs was 98.2%, whereas the average coverage by HSPs was 100.0%. Among all other species, the one yielding the highest score was H. marina (AY598817), which corresponded to an identity of 98.2% and an HSP coverage of 100.0%. (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 AY922224 (Greengenes short name ‘whalefall clone 131720’), which showed an identity of 98.1% and an HSP coverage of 97.5%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were ‘bee’ (3.1%), ‘singl’ (3.0%), ‘abdomen, bumbl, distinct, honei, microbiota, simpl’ (2.9%), ‘microbi’ (2.8%) and ‘structur’ (1.8%) (118 hits in total). Environmental samples which yielded hits of a higher score than the highest scoring species were not found, indicating that H. phototrophica is rarely found in environmental samples.

Figure 1 shows the phylogenetic neighborhood of H. phototrophica 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 (AJ582088)
Figure 1.

Phylogenetic tree highlighting the position of H. phototrophica relative to the type strains of the other species within the family Phyllobacteriaceae. The tree was inferred from 1,362 aligned characters [9,10] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [11]. Rooting was done initially using the midpoint method [12] and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 1,000 ML bootstrap replicates [13] (left) and from 1,000 maximum-parsimony bootstrap replicates [14] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [15] are labeled with one asterisk, those also listed as ‘Complete and Published’ (CP002279 for Mesorhizobium opportunistum) with two asterisks.

Morphology and physiology

Cells of H. phototrophica are small rods of 0.3–0.5 µm in width and 0.7–2.0 µm length [1] (Figure 2) and motile by means of single, polar flagellum [1] (not visible in Figure 2). Depending on the availability of light, colonies are opaque to beige (grown in the dark) on marine agar 2216 [1]. The cultures are strictly aerobic and prefer microaerobic conditions. Good growth was detectable within a range of 25–33°C (1/5 limited growth rate below this value), concentration of sea salt from 0.5–7.0% and pH values from 6.0–9.0 [1]. Acetate and malate were accepted as carbon sources, whereas ethanol and methanol were not used for growth [1]. No hydrolysis of gelatin, starch, alginate or Tween 8 was observed [1].
Figure 2.

Scanning electron micrograph of H. phototrophica DFL-43T

The utilization of carbon compounds by H. phototrophica DFL-43T was also determined for this study using PM01 microplates in an OmniLog phenotyping device (BIOLOG Inc., Hayward, CA, USA). The microplates were inoculated at 28°C with a cell suspension at a cell density of 85% Turbidity and dye D. Further additives were artificial sea salts, vitamins, trace elements and NaHCO3. The exported measurement data were further analyzed with the opm package for R [25], using its functionality for statistically estimating parameters from the respiration curves such as the maximum height, and automatically translating these values into negative, ambiguous, and positive reactions. The strain was studied in two independent biological replicates, and reactions with a different behavior between the two repetitions were regarded as ambiguous and are not listed below.

H. phototrophica DFL-43T was positive for D,L-malic acid, D-cellobiose, D-fructose, D-galactonic acid-γ-lactone, D-galactose, D-galacturonic acid, D-gluconic acid, D-glucuronic acid, D-malic acid, D-mannitol, D-melibiose, D-sorbitol, D-trehalose, D-xylose, L-alanine, L-arabinose, L-glutamic acid, L-glutamine, L-lactic acid, L-lyxose, L-malic acid, L-proline, L-serine, acetic acid, adonitol, α-D-glucose, α-keto-glutaric acid, α-methyl-D-galactoside, β-methyl-D-glucoside, bromo-succinic acid, citric acid, ethanolamine, fumaric acid, m-inositol, maltose, maltotriose, mono-methyl succinate, propionic acid, pyruvic acid, succinic acid, sucrose and uridine. The strain was negative for 1,2-propanediol, 2′-deoxy-adenosine, D,L-α-glycerol-phosphate, D-alanine, D-aspartic acid, D-fructose-6-phosphate, D-glucosaminic acid, D-glucose-1-phosphate, D-glucose-6-phosphate, D-mannose, D-psicose, D-serine, D-threonine, L-alanyl-glycine, L-aspartic acid, L-fucose, L-galactonic acid-γ-lactone, L-rhamnose, L-threonine, N-acetyl-D-glucosamine, N-acetyl-β-D-mannosamine, acetoacetic acid, adenosine, α-D-lactose, α-hydroxy-butyric acid, α-hydroxy-glutaric acid-γ-lactone, α-keto-butyric acid, β-phenylethylamine, dulcitol, glycolic acid, glycyl-L-aspartic acid, glyoxylic acid, inosine, m-hydroxy-phenylacetic acid, m-tartaric acid, mucic acid, thymidine, tricarballylic acid, tween 40, tween 80 and tyramine.

Chemotaxonomy

Phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine were the predominant polar lipids of the membrane. The most frequent cellular fatty acids in strain DFL-43T are the mono-unsaturated straight chain acids C18:1 ω7 (62.8%) and its methylated form C18:1 ω7 11Me (21%), followed by C16:0 (6.3%) and C19:1 (3.4%) [1]. The absorption spectrum of an acetone/methanol extract showed the presence of bacteriochlorophyll a and an additional carotenoid (possibly spheroidenone) in small amounts [1]. Further experiments indicated that the pigment production depends on the concentration of sea salts in the medium [1].

Genome sequencing and annotation

Genome project history

The genome was sequenced within the MMI supported by the Gordon and Betty Moore Foundation. Initial Sequencing was performed by the J. Craig Venter Institute, JCVI (Rockville, MD, USA), and a high-quality draft sequence was deposited at INSDC. The number of scaffolds and contigs was reduced and the assembly improved by a subsequent round of manual gap closure at HZI/DSMZ. A summary of the project information is shown in Table 2.
Table 1.

Classification and general features of H. phototrophica DFL-43T according to the MIGS recommendations [16].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [17]

 

Phylum Proteobacteria

TAS [18]

 

Class Alphaproteobacteria

TAS [19,20]

 

Order Rhizobiales

TAS [20,21]

 

Family Phyllobacteriaceae

TAS [20,22]

 

Genus Hoeflea

TAS [2]

 

Species Hoeflea phototrophica

TAS [1]

MIGS-7

Subspecific genetic lineage (strain)

DFL-43T

TAS [1]

MIGS-12

Reference for biomaterial

Biebl et al. 2006

TAS [1]

 

Gram stain

Gram-negative

TAS [1]

 

Cell shape

rod-shaped

TAS [1]

 

Motility

motile

TAS [1]

 

Sporulation

not reported

 
 

Temperature range

mesophile, 25–33°C

TAS [1]

 

Optimum temperature

31°C

TAS [1]

 

Salinity

0.5–7.0% NaCl

TAS [1]

MIGS-22

Relationship to oxygen

aerobe

TAS [1]

 

Carbon source

acetate, malate

TAS [1]

 

Energy metabolism

photoheterotroph

TAS [1]

MIGS-6

Habitat

marine

TAS [1]

MIGS-6.2

pH

6–9.0

TAS [1]

MIGS-15

Biotic relationship

host-associated

TAS [1]

MIGS-14

Known pathogenicity

none

TAS [1]

MIGS-16

Specific host

Prorocentrum lima ME130

TAS [1]

MIGS-18

Health status of Host

not reported

 
 

Biosafety level

1

TAS [23]

MIGS-19

Trophic level

not reported

 

MIGS-23.1

Isolation

from a culture of Prorocentrum lima ME130

TAS [1]

MIGS-4

Geographic location

not reported

 

MIGS-5

Time of sample collection

April 1, 2002

TAS [1]

MIGS-4.1

Latitude

54.133

TAS [1]

MIGS-4.2

Longitude

7.867

TAS [1]

MIGS-4.3

Depth

not reported

 

MIGS-4.4

Altitude

not reported

 

Evidence codes 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 for the species, or anecdotal evidence). Evidence codes are from the Gene Ontology project [24].

Table 2.

Genome sequencing project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

High quality draft

MIGS-28

Libraries used

Two genomic libraries: 40 kb fosmid library and 3 kb pUC18 plasmid library

MIGS-29

Sequencing platform

ABI3730

MIGS-31.2

Sequencing coverage

10.3 × Sanger

MIGS-30

Assemblers

Consed 20.0

MIGS-31.3

Contig count

5

MIGS-32

Gene calling method

Prodigal 2.0, Infernal 1.0.2

 

INSDC ID

Final ID pending; previous version ABIA00000000

 

Genbank Date of Release

final version not yet available

 

GOLD ID

Gi01415

 

NCBI project ID

19311

 

Database: IMG

2509276008

MIGS-13

Source Material Identifier

DSM 17068

 

Project relevance

Environmental, Marine Microbial Initiative

Growth conditions and DNA extractions

Cells of strain DFL-43T were grown for two to three days on a LB & sea-salt agar plate, containing (l-1) 10 g tryptone, 5 g yeast extract, 10 g NaCl, 17 g sea salt (Sigma-Aldrich S9883) and 15 g agar. A single colony was used to inoculate LB & sea-salt liquid medium and the culture was incubated at 28°C on a shaking platform. The genomic DNA was isolated using the Qiagen Genomic 500 DNA Kit (Qiagen 10262) as indicated by the manufacturer. DNA quality and quantity were in accordance with the instructions of the genome sequencing center. DNA is available through the DNA Bank Network [26].

Genome sequencing and assembly

The genome was sequenced with the Sanger technology using a combination of two libraries. All general aspects of library construction and sequencing performed at the JCVI can be found on the JCVI website. Base calling of the sequences were performed with the phredPhrap script using default settings. The reads were assembled and assemblies analyzed using the phred/phrap/consed pipeline [27]. The last gaps were closed by adding new reads produced by recombinant PCR and PCR primer walks. In total 21 Sanger reads were required for gap closure and improvement of low quality regions. The final consensus sequence was built from 46,086 Sanger reads (10.3 × coverage).

Genome annotation

Gene prediction was carried out using GeneMark as part of the genome annotation pipeline in the Integrated Microbial Genomes Expert Review (IMG-ER) system [28]. To identify coding genes, Prodigal [29] was used, while ribosomal RNA genes within the genome were identified using RNAmmer [30]. Other non-coding genes were predicted using Infernal [31]. Manual functional annotation was performed within the IMG platform [28] and the Artemis Genome Browser [32].

Genome properties

The draft genome consists of one circular scaffold with a total length of 4,467,822 bp containing five large contigs with a total length of 4,467,792 bp and a G+C content of 59.8%. Contig lengths vary from 133,683 bp to 2,215,172 bp (Figure 3); genome statistics are provided in Table 3. Of the 4,296 genes predicted, 4,227 were protein-coding genes, and 69 RNAs; pseudogenes were not identified. The majority of the protein-coding genes (83.1%) were assigned 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 centerp: Genes on forward 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)

4,467,832

100.00

DNA coding region (bp)

4,006,040

89.66

DNA G+C content (bp)

2,671,973

59.81

Number of replicons

1

 

Extrachromosomal elements

0

 

Total genes

4,296

100.00

RNA genes

69

1.61

rRNA operons

2

 

tRNA genes

47

1.09

Protein-coding genes

4,227

98.39

Pseudo genes

0

 

Genes with function prediction

3,574

83.19

Genes in paralog clusters

1,423

33.12

Genes assigned to COGs

3,525

82.05

Genes assigned Pfam domains

3,580

83.33

Genes with signal peptides

927

21.58

Genes with transmembrane helices

994

24.57

CRISPR repeats

0

 
Table 4.

Number of genes associated with the general COG functional categories

Code

Value

%age

Description

J

178

4.58

Translation, ribosomal structure and biogenesis

A

0

0.00

RNA processing and modification

K

274

7.05

Transcription

L

162

4.17

Replication, recombination and repair

B

2

0.05

Chromatin structure and dynamics

D

27

0.69

Cell cycle control, cell division, chromosome partitioning

Y

-

-

Nuclear structure

V

39

1.00

Defense mechanisms

T

175

4.50

Signal transduction mechanisms

M

205

5.27

Cell wall/membrane/envelope biogenesis

N

60

1.54

Cell motility

Z

0

0.00

Cytoskeleton

W

-

-

Extracellular structures

U

66

1.70

Intracellular trafficking, secretion, and vesicular transport

O

135

3.47

Posttranslational modification, protein turnover, chaperones

C

226

5.81

Energy production and conversion

G

325

8.36

Carbohydrate transport and metabolism

E

405

10.41

Amino acid transport and metabolism

F

80

2.06

Nucleotide transport and metabolism

H

157

4.04

Coenzyme transport and metabolism

I

188

4.83

Lipid transport and metabolism

P

178

4.58

Inorganic ion transport and metabolism

Q

130

3.34

Secondary metabolites biosynthesis, transport and catabolism

R

524

13.47

General function prediction only

S

353

9.08

Function unknown

-

773

18.00

Not in COGs

Declarations

Acknowledgements

Sequencing, assembly, annotation and data analysis for the first draft version were supported by the Gordon and Betty Moore Foundation Marine Microbiology Initiative, as part of its Marine Microbial Sequencing Project (http://www.moore.org/marinemicro). Support for the subsequent gap closure and analysis via the German Research Foundation (DFG) SFB/TRR 51 is gratefully acknowledged. We also thank the European Commission which supported phenotyping via the Microme project 222886 within the Framework 7 program.

Authors’ Affiliations

(1)
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures
(2)
HZI - Helmholtz Center for Infection Research

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Copyright

© The Author(s) 2013