Open Access

Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419

  • Wayne Reeve1,
  • Patrick Chain2, 3,
  • Graham O’Hara1,
  • Julie Ardley1,
  • Kemanthi Nandesena1,
  • Lambert Bräu1,
  • Ravi Tiwari1,
  • Stephanie Malfatti2, 3,
  • Hajnalka Kiss2, 3,
  • Alla Lapidus2,
  • Alex Copeland2,
  • Matt Nolan2,
  • Miriam Land2, 4,
  • Loren Hauser2, 4,
  • Yun-Juan Chang2, 4,
  • Natalia Ivanova2,
  • Konstantinos Mavromatis2,
  • Victor Markowitz5,
  • Nikos Kyrpides2,
  • Margaret Gollagher6,
  • Ron Yates1, 7,
  • Michael Dilworth1 and
  • John Howieson1, 7
Standards in Genomic Sciences20102:2010077

https://doi.org/10.4056/sigs.43526

Published: 28 February 2010

Abstract

Ensifer (Sinorhizobium) medicae is an effective nitrogen fixing microsymbiont of a diverse range of annual Medicago (medic) species. Strain WSM419 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from a M. murex root nodule collected in Sardinia, Italy in 1981. WSM419 was manufactured commercially in Australia as an inoculant for annual medics during 1985 to 1993 due to its nitrogen fixation, saprophytic competence and acid tolerance properties. Here we describe the basic features of this organism, together with the complete genome sequence, and annotation. This is the first report of a complete genome sequence for a microsymbiont of the group of annual medic species adapted to acid soils. We reveal that its genome size is 6,817,576 bp encoding 6,518 protein-coding genes and 81 RNA only encoding genes. The genome contains a chromosome of size 3,781,904 bp and 3 plasmids of size 1,570,951 bp, 1,245,408 bp and 219,313 bp. The smallest plasmid is a feature unique to this medic microsymbiont.

Keywords

microsymbiontnon-pathogenicaerobicGram-negative rodroot-nodule bacterianitrogen fixation Alphaproteobacteria

Introduction

Agricultural systems are nearly always nitrogen deficient, a factor which grossly limits their productivity. In fact, each year some 50 Tg of nitrogen is harvested globally in food crops [3], and must be replaced. External inputs of nitrogen to agriculture may come from mineral fertilizers, the production of which is heavily dependent on fossil fuels. Alternatively, nitrogen can be obtained from symbiotic nitrogen fixation (SNF) by root nodule bacteria (rhizobia) on nodulated legumes [4]. SNF is therefore considered a key biological process on the planet. The commonly accepted figure for global SNF in agriculture is 50–70 million metric tons annually, worth in excess of U.S. $10 billion [5]. Rhizobia associated with forage legumes contribute a substantial proportion of this fixed nitrogen across 400 million ha [5]. The amount fixed annually by the Ensifer (Sinorhizobium)-Medicago symbiosis is estimated to be worth $250 million.

A particular constraint to the formation of this symbiosis is acidity, due mainly to the acid-sensitive nature of the microsymbionts [6]. In laboratory culture, the medic microsymbionts fail to grow below pH 5.6 and are considered to be the most acid-sensitive of all the commercial root nodule bacteria [7]. Many agricultural regions have moderately acidic soils (typically in the pH range of 4.0 to 6.0) and this has prevented the Ensifer-Medicago symbiosis reaching its full potential [8]. Consequently, an effort was initiated in the 1980s to discover more acid-tolerant medic microsymbionts from world regions with acidic soils upon which annual medics had evolved. A particular suite of strains isolated from acidic soils on the Italian island of Sardinia proved to be acid soil tolerant [9], an attribute we now know is related to the presence of a unique set of genes required for acid adaptation [10]. Characterization of these acid-tolerant isolates revealed that they belonged to the species E. medicae and could be symbiotically distinguished from the related species E. meliloti by their unique capacity to fix nitrogen in association with annual acid soil adapted Medicago hosts of worldwide agronomic value [11], as well as with the perennial forage legume M. sativa (alfalfa) [12].

One of the acid-tolerant isolates, E. medicae strain WSM419, was isolated in 1981 from a nodule recovered from the roots of an annual medic (M. murex) growing south of Tempio in Sardinia. WSM419 is of particular interest because it is saprophytically competent in the acidic, infertile soils of southern Australia [9,13], and it is also a highly effective nitrogen fixing microsymbiont of a broad range of annual medics of Mediterranean origin [11,12]. These attributes contributed to the commercialization of the strain in Australia as an inoculant for acid soil medics between 1985 and 1993 [14,15]. Here we present a summary classification and a set of features (Table 1) for E. medicae strain WSM419, together with the description of a complete genome sequence and annotation.
Table 1.

Classification and general features of E. medicae WSM419 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 Rhizobiaceae

TAS [22,23]

 

Genus Ensifer

TAS [1,2,2427]

 

Species Ensifer medicae

TAS [1,2,11,2428]

 

strain WSM419

 
 

Gram stain

negative

TAS [29]

 

Cell shape

rod

TAS [29]

 

Motility

motile

TAS [29]

 

Sporulation

non-sporulating

TAS [29]

 

Temperature range

mesophile

TAS [29]

 

Optimum temperature

28°C

TAS [29]

 

Salinity

unknown

 

MIGS-22

Oxygen requirement

aerobic

TAS [29]

 

Carbon source

galactose, arabinose, glutamate

TAS [9,13]

 

Energy source

chemoorganotroph

TAS [9,13]

MIGS-6

Habitat

Soil, root nodule, host

TAS [9]

MIGS-15

Biotic relationship

Free living or symbiotic

TAS [9]

MIGS-14

Pathogenicity

none

TAS [16]

 

Biosafety level

1

TAS [30]

 

Isolation

Medicago murex root nodule

TAS [9]

MIGS-4

Geographic location

Forestry Station 7 km south of Tempio, Sardinia, Italy

TAS [9]

MIGS-5

Nodule collection date

May 1st, 1981

TAS [31]

MIGS-4.1

Longitude

9.101915

TAS [31]

MIGS-4.2

Latitude

40.888925

MIGS-4.3

Depth

<10 cm

TAS [31]

MIGS-4.4

Altitude

350m

TAS [31]

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 for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [32]. If the evidence code is IDA, then the property was directly observed for a living isolate by one of the authors or an expert mentioned in the acknowledgements.

Classification and features

E. medicae strain WSM419 forms mucoid colonies that may appear as donut shaped (Figure 1, left) on specific media such as YMA [13]. It is a Gram-negative, non-spore-forming rod (Figure 1, center) that has peritrichous flagellae (Figure 1, right).
Figure 1.

Unique colony morphology (Left) and scanning (Center) and transmission (Right) electron micrographs of E. medicae strain WSM419.

In minimal media E. medicae WSM419 has a mean generation time of 4.1 h when grown at 28°C [33]. It is a member of the Rhizobiaceae family of the class Alphaproteobacteria based on phylogenetic analysis. Figure 2 shows the phylogenetic neighborhood of E. medicae strain WSM419 inferred from a 16S rRNA based phylogenetic tree. An intragenic fragment of 1,440 bp was chosen since the 16S rRNA gene has not been completely sequenced in many type strains. A comparison of the entire 16S rRNA gene of WSM419 to completely sequenced 16S rRNA genes of other sinorhizoabia revealed 4 and 18 bp mismatches to the reported sequences of E. meliloti (Sm1021) and E. fredii (YcS2, 15067 and SjzZ4), respectively.
Figure 2.

Phylogenetic tree showing the relationships of E. medicae strain WSM419 to type strains in the Rhizobiaceae based on aligned sequences of the 16S rRNA gene (1,440 bp internal region). All sites were informative and there were no gap-containing sites. Phylogenetic analyses were performed using MEGA, version 3.1 [34]. Kimura two-parameter distances were derived from the aligned sequences [35] and a bootstrap analysis [36] as performed with 500 replicates in order to construct a consensus unrooted tree using the neighbor-joining method [37] for each gene alignment separately. Genera in this tree include Bradyrhizobium (B); Mesorhizobium (M); Rhizobium (R); Ensifer (Sinorhizobium) (S). Type strains are indicated with a superscript T. Strains with a genome sequencing project registered in GOLD [31] are in bold red print. Published genomes are designated with an asterisk.

Symbiotaxonomy

E. medicae and E. meliloti are traditionally separated on the basis of the effective nodulation (Nod+, Fix+) by E. medicae on M. polymorpha [38]. Specific symbiotic characteristics that further distinguish E. medicae WSM419 from E. meliloti include its ability to nodulate and fix nitrogen effectively with a wide range of annual Mediterranean medics, including M. polymorpha, M. arabica, M. murex and M. sphaerocarpos. WSM419 is symbiotically competent with these species when grown in acidic soils [39]. In contrast, WSM419 is Fix with the alkaline soil species of annual medics such as M. littoralis, M. tornata and hybrids of M. littoralis/M. truncatula [11,40]. WSM419 is also Nod+, Fix+ with the perennial forage legume M. sativa [11,12] but is less effective with this species than are some E. meliloti isolates. However, WSM419 is more effective at fixing nitrogen with M. truncatula than the previously sequenced E. meliloti Sm1021, making it an ideal candidate for inoculation of this model legume [12].

Genome sequencing and annotation

Genome project history

E. medicae WSM419 was selected for sequencing on the basis of its importance as a symbiotic nitrogen fixing bacterium in agriculture, and its tolerance for acidic soils [9,14].This strain was selected for sequencing as part of the Community Sequencing Program of the Joint Genome Institute (JGI) in 2005. The genome project is deposited in the Genomes OnLine Database [31] and the complete genome sequence in GenBank. A summary of the project information is shown in Table 2.
Table 2.

Genome sequencing project information of E. medicae WSM419.

MIGS ID

Property

Term

MIGS-31

Finishing quality

Finished

MIGS-28

Libraries used

Four Sanger libraries - 3 kb pUC18, 2 kb pTH1522, 8 kb pMCL200 and fosmid pCC1Fos

MIGS-29

Sequencing platforms

ABI3730xl; MegaBACE4500

MIGS-31.2

Sequencing coverage

~13× Sanger

MIGS-30

Assemblers

PHRED/PHRAP/CONSED

MIGS-32

Gene calling method

Critica, Generation and Glimmer

 

Genbank ID

CP000738 (Chromosome)a

 

CP000739 (pSMED01 or pSymB)b

 

CP000740 (pSMED02 or pSymA)c

 

CP000741 (pSMED03 or accessory plasmid)d

 

Genbank Date of Release

June 29, 2007

 

GOLD ID

Gc00590e

 

NCBI project ID

16304

 

Database: IMG

640753051ff

 

Project relevance

Symbiotic nitrogen fixation, agriculture

Growth conditions and DNA isolation

E. medicae strain WSM419 was grown to mid logarithmic phase in TY medium (a rich medium) [41] on a gyratory shaker at 28°C. DNA was isolated from 60 ml of cells using a CTAB (Cetyl trimethylammonium bromide) bacterial genomic DNA isolation method (JGI general information).

Genome sequencing and assembly

The genome was sequenced using a Sanger platform. All general aspects of library construction and sequencing performed at the JGI can be found at the JGI website (http://www.jgi.doe.gov/). Sequence data statistics from the trace archive for this project are presented in Table 3.
Table 3.

Production sequence data for the E. medicae WSM419 genome project (JGI project 4001622).

Library

Vector

Insert size(kb)

Reads

Mb

q20 (Mb)

BICH

pMCL200

5.9

37,091

36.3

25.7

BICG

pUC18c

2.6

33,520

36.8

26.1

BICI

pCC1Fos

38.8

13,929

13.9

8.9

FAUT

pTH1522

2.1

7,376

6.4

5.4

   

91,916

93.4

66.1

All reads were assembled using the phrap assembler. Possible mis-assemblies were corrected and gaps between contigs were closed by custom primer walks from sub-clones or PCR products. Processing of sequence traces and base calling and assessment of data quality and assembly were performed with the PHRED/PHRAP/CONSED package [4244]. The initial draft assembly was produced from 84,192 high-quality reads and consisted of 30 contigs (each with at least 20 reads per contig). Gaps in the sequence were primarily identified by mate-pair sequences and then closed by primer walking on gap-spanning library clones or genomic DNA amplified PCR products. True physical gaps were closed by combinatorial and multiplex PCR. All repeated sequences were addressed using mate-pair sequences and PCR data. Sequence finishing and polishing added 638 reads. The final assembly of the main chromosome and 3 plasmids from 84,830 reads produced approximately 13-fold coverage across the genome. Assessment of final assembly quality was completed as described previously [45].

Genome annotation

Automated gene prediction was completed by assessing congruence of gene call results from three independent programs, the Critica [46], Generation, and Glimmer [47] modeling packages, and by comparing the translations to the GenBank nonredundant database using the basic local alignment search tool for proteins (BLASTP). Product description annotations were obtained using searches against the KEGG, InterPro, TIGRFams, PROSITE, and Clusters of Orthologous Groups of protein (COGs) databases. The tRNAScanSE tool [48] was used to find tRNA genes, whereas ribosomal RNAs were found by using BLASTN vs. the 16S and 23S ribosomal RNA databases. Initial comparative analyses of bacterial genomes and gene neighborhoods were completed using the JGI Integrated Microbial Genomes web-based interface (http://img.jgi.doe.gov/cgi-bin/pub/main.cgi). Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes (IMG-ER) platform [49].

Genome properties

The genome is 6,817,576 bp long with 61.15% GC content and comprised of four replicons (Table 4); one circular chromosome of size 3,781,904 bp (Figure 3) and three plasmids of size 1,570,951 bp, 1,245,408 bp and 219,313 bp (Figure 4). Of the 6,599 genes predicted, 6,518 were protein-coding genes, and 81 RNA only encoding genes. In addition, 305 pseudogenes were identified. The majority of the genes (70.4%) were assigned a putative function while those remaining were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 5.
Figure 3.

Graphical circular map of the chromosome and plasmids of E. medicae WSM419. From outside to the center: Genes on forward strand (color by COG categories as denoted in the IMG platform), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, sRNAs red, other RNAs black), GC content, GC skew. The replicons are not drawn to scale.

Table 4.

Genome Statistics for E. medicae WSM419.

Attribute

Value

% of Total

Genome size (bp)

6,817,576

100.00

DNA coding region (bp)

6,001,805

88.03

DNA G+C content (bp)

4,168,935

61.15

Number of replicons

4

100.00

Extrachromosomal elements

3

75.00

Total genes

6,599

100.00

RNA genes

81

1.23

rRNA operons

3

 

Protein-coding genes

6,518

98.77

Pseudo genes

305

4.62

Genes with function prediction

4,646

70.40

Genes in paralog clusters

4,138

62.71

Genes assigned to COGs

4,999

75.75

Genes assigned Pfam domains

5,051

76.54

Genes with signal peptides

2,170

32.88

Genes with transmembrane helices

1,481

22.44

CRISPR repeats

0

 
Table 5.

Number of protein encoding genes of E. medicae WSM419 associated with the 21 general COG functional categories.

Code

value

% age

Description

J

182

2.79

Translation, ribosomal structure and biogenesis

A

0

0.00

RNA processing and modification

K

501

7.69

Transcription

L

250

3.84

Replication, recombination and repair

B

1

0.02

Chromatin structure and dynamics

D

36

0.55

Cell cycle control, mitosis and meiosis

Y

0

0.00

Nuclear structure

V

56

0.86

Defense mechanisms

T

247

3.79

Signal transduction mechanisms

M

287

4.40

Cell wall/membrane biogenesis

N

66

1.01

Cell motility

Z

0

0.00

Cytoskeleton

W

1

0.02

Extracellular structures

U

106

1.63

Intracellular trafficking and secretion

O

178

2.73

Posttranslational modification, protein turnover, chaperones

C

336

5.15

Energy production and conversion

G

582

8.93

Carbohydrate transport and metabolism

E

622

9.54

Amino acid transport and metabolism

F

109

1.67

Nucleotide transport and metabolism

H

196

3.01

Coenzyme transport and metabolism

I

209

3.21

Lipid transport and metabolism

P

296

4.54

Inorganic ion transport and metabolism

Q

159

2.44

Secondary metabolites biosynthesis, transport and catabolism

R

687

10.54

General function prediction only

S

528

8.10

Function unknown

-

1,519

23.30

Not in COGs

Notes

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 would like to gratefully acknowledge the funding received from Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI), and the Grains Research and Development Corporation (GRDC), to support the National Rhizobium Program (NRP) and the Centre for Rhizobium Studies (CRS) at Murdoch University.

Authors’ Affiliations

(1)
Centre for Rhizobium Studies, Murdoch University
(2)
DOE Joint Genome Institute
(3)
Lawrence Livermore National Laboratory
(4)
Oak Ridge National Laboratory
(5)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(6)
Institute for Sustainability and Technology Policy, Murdoch University
(7)
Department of Agriculture and Food

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