Open Access

Genome sequence of Ensifer medicae strain WSM1115; an acid-tolerant Medicago-nodulating microsymbiont from Samothraki, Greece

  • Wayne Reeve1Email author,
  • Ross Ballard2,
  • John Howieson1,
  • Elizabeth Drew2,
  • Rui Tian1,
  • Lambert Bräu3,
  • Christine Munk4,
  • Karen Davenport4,
  • Patrick Chain4,
  • Lynne Goodwin4,
  • Ioanna Pagani5,
  • Marcel Huntemann5,
  • Konstantinos Mavrommatis6,
  • Amrita Pati5,
  • Victor Markowitz6,
  • Natalia Ivanova5,
  • Tanja Woyke5 and
  • Nikos Kyrpides5
Standards in Genomic Sciences20149:9030514

https://doi.org/10.4056/sigs.4938652

Published: 15 June 2014

Abstract

Ensifer medicae strain WSM1115 forms effective nitrogen fixing symbioses with a range of annual Medicago species and is used in commercial inoculants in Australia. WSM1115 is an aerobic, motile, Gram-negative, non-spore-forming rod. It was isolated from a nodule recovered from the root of burr medic (Medicago polymorpha) collected on the Greek Island of Samothraki. WSM1115 has a broad host range for nodulation and N2 fixation capacity within the genus Medicago, although this does not extend to all medic species. WSM1115 is considered saprophytically competent in moderately acid soils (pH(CaCl2) 5.0), but it has failed to persist at field sites where soil salinity exceeded 10 ECe (dS/m). Here we describe the features of E. medicae strain WSM1115, together with genome sequence information and its annotation. The 6,861,065 bp high-quality-draft genome is arranged into 7 scaffolds of 28 contigs, contains 6,789 protein-coding genes and 83 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

Keywords

root-nodule bacterianitrogen fixationrhizobia Alphaproteobacteria

Introduction

The genus Medicago comprises 87 species of annual and perennial legumes, including some that were formerly recognized as Trigonella and Melilotus species [1]. A small number of annual Medicago species that have been domesticated are grown extensively in the sheep-wheat zone of southern Australia, particularly where pasture regeneration after a cropping phase is desirable. Annual Medicago species are grown on more than 20 M ha [2] and are particularly valued for their contribution to farming systems, in which Medicago fix around 25 kg of N per tonne of legume dry matter produced [3].

Medicago are nodulated by two species of root nodule bacteria (Ensifer medicae and Ensifer meliloti) that are recognized as being distinct based on their different nodulation and N2 fixation phenotypes in host interaction studies and more detailed analyses of their genetics [4,5].

Ensifer medicae strain WSM1115 is used in Australia to produce commercial peat cultures (referred to as Group AM inoculants) for the inoculation of several species of annual Medicago (predominantly M. truncatula, M. polymorpha, M. scutellata, M. sphaerocarpus, M. murex, M. rugosa and M. orbicularis). WSM1115 has been used commercially since 2002 [6], when it replaced strain WSM688. WSM1115 was isolated from a nodule from the roots of burr medic (Medicago polymorpha) collected by Prof. John Howieson (Murdoch University, Australia) on the island of Samothraki, Greece.

WSM1115 was selected for use in commercial inoculants having demonstrated good N2-fixation capacity with the relevant medic hosts and adequate saprophytic competence in moderately acidic soil (pH(CaCl2) 5).

Saprophytic competence in acidic soils is a requirement of strains used to inoculate Medicago because several species (M. murex, M. sphaerocarpus and M. polymorpha) are recommended and sown into soils below pH(CaCl2) 5.5, a level that is known to limit both survival of medic rhizobia and nodulation processes [710]. Useful variation in saprophytic competence occurs between strains of medic rhizobia [9] and valuable insights into the mechanisms that confer acidity tolerance have been provided by studies using strain WSM419 [11], which has been recently sequenced [12]. However, the complex nature of soil adaptation means that in-situ field studies still provide the most reliable means of selecting an inoculant strain and were used to select WSM1115 for commercial use. In a cross row experiment comparing 15 strains on acidic sand (pH(CaCl2) 5.0; Dowerin, West Australia), the nodulation of plants inoculated with WSM1115 was equal to or better than that of the other strains. This translated to better plant shoot weights, which were similar to those of plants inoculated with WSM688 (the incumbent inoculant strain at time of testing) and 48% greater when compared to former inoculant strain CC169 (J. G. Howieson unpublished data).

The nitrogen fixation capacity (effectiveness) of Medicago symbioses is characterized by strong interactions between the strain of rhizobia and species of Medicago [1316]. Hence, the ability to form effective symbiosis with the species recommended for inoculation is an important consideration in inoculant strain selection. WSM1115 satisfies this requirement. In greenhouse tests it formed effective symbiosis with 16 genotypes of Medicago and overall produced 48% more shoot dry matter compared to plants inoculated with WSM688, the strain that it replaced (R.A. Ballard and N. Charman, unpublished data).

A limitation of strain WSM1115 is its poor persistence in moderately saline soils (e.g. where summer salinity levels exceed 10 ECe (dS/m)). Poor nodulation of regenerating pasture was first noted in 2004 during the field evaluation and domestication of the salt tolerant annual pasture legume messina (Melilotus siculus syn. Melilotus messanensis). Subsequent studies [17] confirmed that although WSM1115 was able to nodulate and form effective symbiosis with messina, it did not persist as well as other strains (e.g. SRDI554) through the summer months when salinity levels increased.

Here we present a preliminary description of the general features of Ensifer medicae strain WSM1115 together with its genome sequence and annotation.

Classification and features

Ensifer medicae strain WSM1115 is a motile, non-sporulating, non-encapsulated, Gram-negative rod in the order Rhizobiales of the class Alphaproteobacteria. The rod-shaped form varies in size with dimensions of approximately 0.5 µm in width and 1.0 µm in length (Figure 1A). It is fast growing, forming colonies within 3–4 days when grown on TY [18] or half strength Lupin Agar (½LA) [19] at 28°C. Colonies on ½LA are opaque, slightly domed and moderately mucoid with smooth margins (Figure 1B).
Figure 1.

Images of Ensifer medicae strain WSM1115 using (A) scanning electron microscopy and (B) light microscopy to show the colony morphology on a solid medium.

Minimum Information about the Genome Sequence (MIGS) is provided in Table 1. Figure 2 shows the phylogenetic neighborhood of Ensifer medicae strain WSM1115 in a 16S rRNA gene sequence based tree. This strain has 100% sequence identity (1,366/1,366 bp) at the 16S rRNA sequence level to the fully sequenced Ensifer medicae strain WSM419 [12] and 99% 16S rRNA sequence (1362/1366 bp) identity to the fully sequenced E. meliloti Sm1021 [36].
Figure 2.

Phylogenetic tree showing the relationship of Ensifer medicae WSM1115 (shown in bold print) to other Ensifer spp. in the order Rhizobiales based on aligned sequences of the 16S rRNA gene (1,290 bp internal region). All sites were informative and there were no gap-containing sites. Phylogenetic analyses were performed using MEGA, version 5 [33]. The tree was built using the Maximum-Likelihood method with the General Time Reversible model [34]. Bootstrap analysis [35] with 500 replicates was performed to assess the support of the clusters. Type strains are indicated with a superscript T. Brackets after the strain name contain a DNA database accession number and/or a GOLD ID (beginning with the prefix G) for a sequencing project registered in GOLD [32]. Published genomes are indicated with an asterisk.

Table 1.

Classification and general features of Ensifer medicae strain WSM1115 according to the MIGS recommendations [20]

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [21]

 

Phylum Proteobacteria

TAS [22]

 

Class Alphaproteobacteria

TAS [23,24]

 

Order Rhizobiales

TAS [22,25]

 

Family Rhizobiaceae

TAS [26,27]

 

Genus Ensifer

TAS [2830]

 

Species Ensifer medicae

TAS [29]

 

Strain WSM1115

 
 

Gram stain

Negative

IDA

 

Cell shape

Rod

IDA

 

Motility

Motile

IDA

 

Sporulation

Non-sporulating

NAS

 

Temperature range

Mesophile

NAS

 

Optimum temperature

28°C

NAS

 

Salinity

Non-halophile

NAS

MIGS-22

Oxygen requirement

Aerobic

IDA

 

Carbon source

Varied

NAS

 

Energy source

Chemoorganotroph

NAS

MIGS-6

Habitat

Soil, root nodule, on host

IDA

MIGS-15

Biotic relationship

Free living, symbiotic

IDA

MIGS-14

Pathogenicity

Non-pathogenic

IDA

 

Biosafety level

1

TAS [31]

 

Isolation

Root nodule

IDA

MIGS-4

Geographic location

Samothraki, Greece

IDA

MIGS-5

Time of sample collection

May, 1987

IDA

MIGS-4.1

Latitude

40.4900

IDA

MIGS-4.2

Longitude

25.6500

IDA

MIGS-4.3

Depth

<10 cm

IDA

MIGS-4.4

Altitude

325 m

IDA

Evidence codes - IDA: Inferred from Direct Assay; 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). These evidence codes are from the Gene Ontology project [32].

Symbiotaxonomy

Ensifer medicae strain WSM1115 forms nodules (Nod+) and fixes N2 (Fix+) with a range of annual and perennial Medicago species and Melilotus species (Table 2). Levels of N2 fixation in combination with Medicago littoralis is suboptimal, that species generally forming more effective associations with strains of Ensifer meliloti including strain RRI128 [38]. The level of N2 fixation with Melilotus albus is also noted as positive, but has been observed to vary markedly with different plant accessions.
Table 2.

Compatibility of Ensifer medicae WSM1115 with various Medicago and allied genera for nodulation (Nod) and N2-fixation (Fix)

Species Name

Cultivar or line

Common Name

Growth Type

Nod

Fix

Reference

M. polymorpha

Santiago/Cavalier/Scimitar

Burr

Annual

+

+

IDA

M. truncatula

Caliph/Jester

Barrel

Annual

+

+

IDA

M. murex

Zodiac

Murex

Annual

+

+

IDA

M. sphaerocarpus

Orion

Sphere

Annual

+

+

IDA

M. scutellata

Sava/Silver/Essex

Snail

Annual

+

+

IDA

M. rugosa

Paraponto

Gama

Annual

+

+

IDA

M. littoralis

Herald/Harbinger

Strand

Annual

+

Poor

IDA

M. orbicularis

Estes

Button

Annual

+

+

[15]

M. rigiduloides

Accession PI 227850

Rigid

Annual

+(w)

[15]

M. rigidula

Accession PI 495552

Tifton

Annual

+(w)

[15]

M. arabica

Local ecotype

Spotted

Annual

+

+

[15]

M. minima

Devine

Woolly burr

Annual

+

+

[15]

M. sativa

SARDI Ten

Lucerne

Perennial

+

+

IDA

M. lupulina

“BEBLK”

Black

Perennial

+

+

[15]

Melilotus siculus

Accessions SA40006 & 39909

Messina

Annual

+

+

[17]

Melilotus albus

various accessions

Bokhara clover

Biennial

+

+

IDA

(w) indicates nodules present were white.

IDA: Inferred from Direct Assay from the Gene Ontology project [37].

Genome sequencing and annotation information

Genome project history

This organism was selected for sequencing on the basis of its environmental and agricultural relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the Community Sequencing Program at the U.S. Department of Energy, Joint Genome Institute (JGI) for projects of relevance to agency missions. The genome project is deposited in the Genomes OnLine Database [32] and a high-quality-draft genome sequence in IMG/GEBA. Sequencing, finishing and annotation were performed by the JGI. A summary of the project information is shown in Table 3.
Table 3.

Genome sequencing project information for Ensifer medicae strain WSM1115

MIGS ID

Property

Term

MIGS-31

Finishing quality

Permanent high quality draft

MIGS-28

Libraries used

2× Illumina libraries; Std short PE & CLIP long PE

MIGS-29

Sequencing platforms

Illumina HiSeq 2000

MIGS-31.2

Sequencing coverage

530× Illumina

MIGS-30

Assemblers

with Allpaths, version 38445, Velvet 1.1.05, phrap 4.24

MIGS-32

Gene calling methods

Prodigal 1.4, GenePRIMP

 

Genbank ID

AQZC01000000

 

Genbank Date of Release

April 22, 2013

 

GOLD ID

Gi08906

 

NCBI project ID

74391

 

Database: IMG-GEBA

2512875026

 

Project relevance

Symbiotic N2 fixation, agriculture

Growth conditions and DNA isolation

Ensifer medicae strain WSM1115 was cultured to mid logarithmic phase in 60 ml of TY rich medium on a gyratory shaker at 28°C [39]. DNA was isolated from the cells using a CTAB (Cetyl trimethyl ammonium bromide) bacterial genomic DNA isolation method [40].

Genome sequencing and assembly

The genome of Ensifer medicae strain WSM1115 was sequenced at the Joint Genome Institute (JGI) using Illumina [41] data. An Illumina standard paired-end library with a minimum insert size of 270 bp was used to generate 23,080,558 reads totaling 3,462 Mbp and an Illumina CLIP paired-end library with an average insert size of 9,584 + 2,493 bp was used to generate 2,163,668 reads totaling 324 Mbp of Illumina data (unpublished, Feng Chen).

All general aspects of library construction and sequencing performed at the JGI can be found at the JGI user home [40]. The initial draft assembly contained 57 contigs in 11 scaffolds. The initial draft data was assembled with Allpaths, version 38445, and the consensus was computationally shredded into 10 Kbp overlapping fake reads (shreds). The Illumina draft data was also assembled with Velvet, version 1.1.05 [42], and the consensus sequences were computationally shredded into 1.5 Kbp overlapping fake reads (shreds). The Illumina draft data was assembled again with Velvet using the shreds from the first Velvet assembly to guide the next assembly. The consensus from the second VELVET assembly was shredded into 1.5 Kbp overlapping fake reads. The fake reads from the Allpaths assembly and both Velvet assemblies and a subset of the Illumina CLIP paired-end reads were assembled using parallel phrap, version 4.24 (High Performance Software, LLC). Possible mis-assemblies were corrected with manual editing in Consed [4345]. Gap closure was accomplished using repeat resolution software (Wei Gu, unpublished), and sequencing of bridging PCR fragments. The estimated total size of the genome is 6.9 Mbp and the final assembly is based on 3,654 Mbp of Illumina draft data, which provides an average 530× coverage of the genome.

Genome annotation

Genes were identified using Prodigal [46] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [47]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. These data sources were combined to assert a product description for each predicted protein. Non-coding genes and miscellaneous features were predicted using tRNAscan-SE [48], RNAMMer [49], Rfam [50], TMHMM [51], and SignalP [52]. Additional gene prediction analyses and functional annotation were performed within the Integrated Microbial Genomes (IMG-ER) platform [53].

Genome properties

The genome is 6,861,065 nucleotides with 61.16% GC content (Table 4) and comprised of 7 scaffolds (Figures 3a,3b,3c,3d,3e,3f and Figure 3g) From a total of 6,872 genes, 6,789 were protein encoding and 83 RNA only encoding genes. The majority of genes (76.25%) were assigned a putative function whilst the remaining genes were annotated as hypothetical. The distribution of genes into COGs functional categories is presented in Table 5.
Figure 3a.

Graphical maps of SinmedDRAFT_Scaffold1.2 of the Ensifer medicae strain WSM1115 genome sequence. From bottom to the top of each scaffold: Genes on forward strand (color by COG categories as denoted by the IMG platform), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, sRNAs red, other RNAs black), GC content, GC skew.

Figure 3b.

Graphical maps of SinmedDRAFT_Scaffold2.1 of the Ensifer medicae strain WSM1115 genome sequence. From bottom to the top of each scaffold: Genes on forward strand (color by COG categories as denoted by the IMG platform), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, sRNAs red, other RNAs black), GC content, GC skew.

Figure 3c.

Graphical maps of SinmedDRAFT_Scaffold5.3 of the Ensifer medicae strain WSM1115 genome sequence. From bottom to the top of each scaffold: Genes on forward strand (color by COG categories as denoted by the IMG platform), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, sRNAs red, other RNAs black), GC content, GC skew.

Figure 3d.

Graphical maps of SinmedDRAFT_Scaffold3.7 of the Ensifer medicae strain WSM1115 genome sequence. From bottom to the top of each scaffold: Genes on forward strand (color by COG categories as denoted by the IMG platform), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, sRNAs red, other RNAs black), GC content, GC skew.

Figure 3e.

Graphical maps of SinmedDRAFT_Scaffold6.5 of the Ensifer medicae strain WSM1115 genome sequence. From bottom to the top of each scaffold: Genes on forward strand (color by COG categories as denoted by the IMG platform), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, sRNAs red, other RNAs black), GC content, GC skew.

Figure 3f.

Graphical maps of SinmedDRAFT_Scaffold4.6 of the Ensifer medicae strain WSM1115 genome sequence. From bottom to the top of each scaffold: Genes on forward strand (color by COG categories as denoted by the IMG platform), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, sRNAs red, other RNAs black), GC content, GC skew.

Figure 3g.

Graphical maps of SinmedDRAFT_Scaffold7.4 of the Ensifer medicae strain WSM1115 genome sequence. From bottom to the top of each scaffold: Genes on forward strand (color by COG categories as denoted by the IMG platform), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, sRNAs red, other RNAs black), GC content, GC skew.

Table 4.

Genome Statistics for Ensifer medicae strain WSM1115

Attribute

Value

% of Total

Genome size (bp)

6,861,065

100.00

DNA coding region (bp)

5,918,651

86.26

DNA G+C content (bp)

4,196,062

61.16

Number of scaffolds

7

 

Number of contigs

28

 

Total gene

6,872

100.00

RNA genes

83

1.21

rRNA operons

3

0.04

Protein-coding genes

6,789

98.79

Genes with function prediction

5,240

76.25

Genes assigned to COGs

5,168

75.20

Genes assigned Pfam domains

5,424

78.93

Genes with signal peptides

571

8.31

Genes coding membrane proteins

1,483

21.58

CRISPR repeats

0

 
Table 5.

Number of protein coding genes of Ensifer medicae strain WSM1115 associated with the general COG functional categories.

Code

Value

%age

COG Category

J

186

3.23

Translation, ribosomal structure and biogenesis

A

0

0.00

RNA processing and modification

K

527

9.16

Transcription

L

269

4.68

Replication, recombination and repair

B

3

0.05

Chromatin structure and dynamics

D

43

0.75

Cell cycle control, mitosis and meiosis

Y

0

0.00

Nuclear structure

V

55

0.96

Defense mechanisms

T

244

4.24

Signal transduction mechanisms

M

272

4.73

Cell wall/membrane biogenesis

N

68

1.18

Cell motility

Z

0

0.00

Cytoskeleton

W

1

0.02

Extracellular structures

U

112

1.95

Intracellular trafficking and secretion

O

195

3.39

Posttranslational modification, protein turnover, chaperones

C

335

5.82

Energy production conversion

G

575

10.00

Carbohydrate transport and metabolism

E

609

10.59

Amino acid transport metabolism

F

106

1.84

Nucleotide transport and metabolism

H

194

3.37

Coenzyme transport and metabolism

I

205

3.56

Lipid transport and metabolism

P

286

4.97

Inorganic ion transport and metabolism

Q

164

2.85

Secondary metabolite biosynthesis, transport and catabolism

R

726

12.62

General function prediction only

S

577

10.03

Function unknown

-

1,704

24.80

Not in COGS

-

5,752

 

Total

Declarations

Acknowledgements

This work was performed under the auspices of the US Department of Energy’s 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. We gratefully acknowledge the funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University and the GRDC National Rhizobium Program (Project UMU63).

Authors’ Affiliations

(1)
Centre for Rhizobium Studies, Murdoch University
(2)
South Australian Research and Development Institute
(3)
School of Life and Environmental Sciences, Deakin University
(4)
Bioscience Division, Los Alamos National Laboratory
(5)
DOE Joint Genome Institute
(6)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory

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