Open Access

Genome sequence of Ensifer medicae strain WSM1369; an effective microsymbiont of the annual legume Medicago sphaerocarpos

  • Jason Terpolilli1,
  • Giovanni Garau2,
  • Yvette Hill1,
  • Rui Tian1,
  • John Howieson1,
  • Lambert Bräu3,
  • Lynne Goodwin4,
  • James Han5,
  • Konstantinos Liolios5,
  • Marcel Huntemann5,
  • Amrita Pati5,
  • Tanja Woyke5,
  • Konstantinos Mavromatis6,
  • Victor Markowitz6,
  • Natalia Ivanova5,
  • Nikos Kyrpides5 and
  • Wayne Reeve1Email author
Standards in Genomic Sciences20139:9020420

DOI: 10.4056/sigs.4838624

Published: 20 December 2013

Abstract

Ensifer medicae WSM1369 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago. WSM1369 was isolated in 1993 from a nodule recovered from the roots of Medicago sphaerocarpos growing at San Pietro di Rudas, near Aggius in Sardinia (Italy). WSM1369 is an effective microsymbiont of the annual forage legumes M. polymorpha and M. sphaerocarpos. Here we describe the features of E. medicae WSM1369, together with genome sequence information and its annotation. The 6,402,557 bp standard draft genome is arranged into 307 scaffolds of 307 contigs containing 6,656 protein-coding genes and 79 RNA-only encoding genes. This rhizobial genome is one of 100 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 bacteria nitrogen fixation rhizobia Alphaproteobacteria

Introduction

One of the key nutritional constraints to plant growth and development is the availability of nitrogen (N) in nutrient deprived soils [1]. Although the atmosphere consists of approximately 80% N, the overwhelming proportion of this is present in the form of dinitrogen (N2) which is biologically inaccessible to most plants and other higher organisms. Before the development of the Haber-Bosch process, the primary mechanism for converting atmospheric N2 into a bioaccessible form was via biological nitrogen fixation (BNF) [2]. In BNF, N2 is made available by specialized microbes that possess the necessary molecular machinery to reduce N2 into NH3. Some plants, most of which are legumes, have harnessed BNF by evolving symbiotic relationships with specific N2-fixing microbes (termed rhizobia) whereby the host plant houses the bacteria in root nodules, supplying the microsymbiont with carbon and in return receives essential reduced N-containing products [3]. When BNF is exploited in agriculture, some of this N2 fixed into plant tissues is ultimately released into the soil following harvest or senescence, where it can then be assimilated by subsequent crops. Compared to industrially synthesized N-based fertilizers, BNF is a low energy, low cost and low greenhouse-gas producing alternative and hence its application is crucial to increasing the environmental and economic sustainability of farming systems [4].

Forage and fodder legumes play vital roles in sustainable farming practice, with approximately 110 million ha under production worldwide [5], a significant proportion of which is made up by members of the genus Medicago. Ensifer meliloti and E. medicae are known to nodulate and fix N2 with Medicago spp [6], although they have differences in host specificity. While E. meliloti strains do not nodulate M. murex, nodulate but do not fix N2 with M. polymorpha and nodulate but fix very poorly with M. arabica [7,8], they are able to nodulate and fix N2 with Medicago species originating from alkaline soils including the perennial M. sativa and the annuals M. littoralis and M. tornata [9,10]. In contrast, E. medicae strains can nodulate and fix N2 with annuals well adapted to acidic soils, such as M. murex, M. arabica and M. polymorpha [7,8].

The E. medicae strain WSM1369 was isolated from a nodule collected from M. sphaerocarpos growing at San Pietro di Rudas, near Aggius in Sardinia (Italy). This strain nodulates and fixes N2 effectively with M. polymorpha and M. sphaerocarpos [8]. Like M. murex and M. polymorpha, M. sphaerocarpos is an annual species which is tolerant of low pH soils [11], with studies suggesting that it only establishes N2-fixing associations with E. medicae strains [8,9]. However, owing to a paucity of symbiotic information, it is not yet clear whether M. sphaerocarpos fixes N2 with a wide range of E. medicae strains or if this ability is restricted to a smaller set of E. medicae accessions. Therefore, genome sequences of E. medicae strains effective with M. sphaerocarpos will provide a valuable genetic resource to further investigate the symbiotaxonomy of Medicago-nodulating rhizobia and will further enhance the existing available genome data for Ensifer microsymbionts [1215]. Here we present a summary classification and a set of general features for this microsymbiont together with a description of its genome sequence and annotation.

Classification and features

E. medicae WSM1369 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 0.25–0.5 µm in width and 1.0–1.5 µm in length (Figure 1 Left and 1 Center). It is fast growing, forming colonies within 3–4 days when grown on TY agar [16] or half strength Lupin Agar (½LA) [17] at 28°C. Colonies on ½LA are opaque, slightly domed and moderately mucoid with smooth margins (Figure 1 Right).
Figure 1.

Images of Ensifer medicae WSM1369 using scanning (Left) and transmission (Center) electron microscopy and the appearance of colony morphology on half strength lupin agar (Right).

Minimum Information about the Genome Sequence (MIGS) is provided in Table 1. Figure 2 shows the phylogenetic neighborhood of E. medicae WSM1369 in a 16S rRNA sequence based tree. This strain shares 100% sequence identity (over 1290 bp) to the 16S rRNA of E. medicae A321T and E. medicae WSM419 [13] and 99% sequence identity (1362/1366 bp) to the 16S rRNA of E. meliloti Sm1021 [12].
Figure 2.

Phylogenetic tree showing the relationship of Ensifer medicae WSM1369 (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 [31]. The tree was built using the Maximum-Likelihood method with the General Time Reversible model [32]. Bootstrap analysis [33] 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 [34]. Published genomes are indicated with an asterisk.

Table 1.

Classification and general features of Ensifer medicae WSM1369 according to the MIGS recommendations [18]

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [19]

 

Phylum Proteobacteria

TAS [20]

 

Class Alphaproteobacteria

TAS [21,22]

 

Order Rhizobiales

TAS [21,23]

 

Family Rhizobiaceae

TAS [24,25]

 

Genus Ensifer

TAS [2628]

 

Species Ensifer medicae

TAS [27]

 

Strain WSM1369

TAS [8]

 

Gram stain

Negative

IDA

 

Cell shape

Rod

IDA

 

Motility

Motile

IDA

 

Sporulation

Non-sporulating

NAS

 

Temperature range

Mesophile

NAS

 

Optimum temperature

28°C

IDA

 

Salinity

Non-halophile

NAS

MIGS-22

Oxygen requirement

Aerobic

TAS [8]

 

Carbon source

Varied

NAS

 

Energy source

Chemoorganotroph

NAS

MIGS-6

Habitat

Soil, root nodule, on host

NAS

MIGS-15

Biotic relationship

Free living, symbiotic

TAS [8]

MIGS-14

Pathogenicity

Non-pathogenic

NAS

 

Biosafety level

1

TAS [29]

 

Isolation

Root nodule

TAS [8]

MIGS-4

Geographic location

Sardinia, Italy

TAS [8]

MIGS-5

Soil collection date

28 April 1993

IDA

MIGS-4.1

Longitude

9.019167

IDA

MIGS-4.2

Latitude

40.971667

IDA

MIGS-4.3

Depth

0–10 cm

IDA

MIGS-4.4

Altitude

Not recorded

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 [30].

Symbiotaxonomy

E. medicae strain WSM1369 was isolated in 1993 from a nodule collected from the annual M. sphaerocarpos growing at San Pietro di Rudas, near Aggius, Sardinia in Italy (J. G. Howieson, pers. comm.). The site of collection was undulating grassland, with a soil derived from granite materials that had a depth of 20–40 cm and a pH of 6.0. The soil was a loamy-sand and Lathyrus and Trifolium spp. grew in association with M. sphaerocarpos. WSM1369 forms nodules (Nod+) and fixes N2 (Fix+) with M. polymorpha and M. sphaerocarpos [8].

Genome sequencing and annotation

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 [34] and a standard draft genome sequence in IMG. Sequencing, finishing and annotation were performed by the JGI. A summary of the project information is shown in Table 2.
Table 2.

Genome sequencing project information for E. medicae WSM1369

MIGS ID

Property

Term

MIGS-31

Finishing quality

Standard draft

MIGS-28

Libraries used

One Illumina fragment library

MIGS-29

Sequencing platforms

Illumina HiSeq 2000

MIGS-31.2

Sequencing coverage

Illumina: 321×

MIGS-30

Assemblers

Velvet version 1.1.04; Allpaths-LG version r39750

MIGS-32

Gene calling methods

Prodigal 1.4

 

GenBank

AQUS00000000

 

GenBank release date

August 28, 2013

 

GOLD ID

Gi08907

 

NCBI project ID

165337

 

Database: IMG

2513237156

 

Project relevance

Symbiotic N2 fixation, agriculture

Growth conditions and DNA isolation

E. medicae WSM1369 was cultured to mid logarithmic phase in 60 ml of TY rich medium on a gyratory shaker at 28°C [35]. DNA was isolated from the cells using a CTAB (Cetyl trimethyl ammonium bromide) bacterial genomic DNA isolation method [36].

Genome sequencing and assembly

The genome of Ensifer medicae WSM1369 was sequenced at the Joint Genome Institute (JGI) using Illumina technology [37]. An Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform which generated 13,712,318 reads totaling 2,057 Mbp.

All general aspects of library construction and sequencing performed at the JGI can be found at the JGI user home [36]. All raw Illumina sequence data was passed through DUK, a filtering program developed at JGI, which removes known Illumina sequencing and library preparation artifacts (Mingkun, L., Copeland, A. and Han, J., unpublished). The following steps were then performed for assembly: (1) filtered Illumina reads were assembled using Velvet [38] (version 1.1.04), (2) 1–3 Kbp simulated paired end reads were created from Velvet contigs using wgsim [39], (3) Illumina reads were assembled with simulated read pairs using Allpaths-LG [40] (version r39750). Parameters for assembly steps were: 1) Velvet (velveth: 63 -shortPaired and velvetg: -veryclean yes -exportFiltered yes -mincontiglgth 500 -scaffolding no-covcutoff 10) 2) wgsim (-e 0 -1 76 -2 76 -r 0 -R 0 -X 0) 3) Allpaths-LG (PrepareAllpathsInputs:PHRED64=1 PLOIDY=1 FRAGCOVERAGE=125 JUMPCOVERAGE=25 LONGJUMPCOV=50, RunAllpath-sLG: THREADS=8 RUN=stdshredpairs TARGETS=standard VAPIWARNONLY=True OVERWRITE=True). The final draft assembly contained 307 contigs in 307 scaffolds. The total size of the genome is 6.4 Mbp and the final assembly is based on 2,057 Mbp of Illumina data, which provides an average 321× coverage of the genome.

Genome annotation

Genes were identified using Prodigal [41] as part of the DOE-JGI annotation pipeline [42]. 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. The tRNAScanSE tool [43] was used to find tRNA genes, whereas ribosomal RNA genes were found by searches against models of the ribosomal RNA genes built from SILVA [44]. Other non-coding RNAs such as the RNA components of the protein secretion complex and the RNase P were identified by searching the genome for the corresponding Rfam profiles using INFERNAL [45]. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes (IMG-ER) platform [46].

Genome properties

The genome is 6,402,557 nucleotides with 61.13% GC content (Table 3) and comprised of 307 scaffolds (Figure 3) of 307 contigs. From a total of 6,735 genes, 6,656 were protein encoding and 79 RNA only encoding genes. The majority of genes (74.14%) were assigned a putative function while the remaining genes were annotated as hypothetical. The distribution of genes into COGs functional categories is presented in Table 4.
Figure 3.

Graphical map of the genome of Ensifer medicae WSM1369 showing the seven largest scaffolds. 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 3.

Genome Statistics for Ensifer medicae WSM1369

Attribute

Value

% of Total

Genome size (bp)

6,402,557

100.00

DNA coding region (bp)

5,536,774

86.48

DNA G+C content (bp)

3,913,921

61.13

Number of scaffolds

307

 

Number of contigs

307

 

Total gene

6,735

100.00

RNA genes

79

1.17

rRNA operons

1

0.01

Protein-coding genes

6,656

98.83

Genes with function prediction

4,993

74.14

Genes assigned to COGs

4,988

74.06

Genes assigned Pfam domains

5,185

76.99

Genes with signal peptides

508

7.54

Genes coding transmembrane proteins

1,424

21.14

CRISPR repeats

0

 
Table 4.

Number of protein coding genes of Ensifer medicae WSM1369 associated with the general COG functional categories.

Code

Value

% age

Description

J

193

3.48

Translation, ribosomal structure and biogenesis

A

0

0.00

RNA processing and modification

K

486

8.77

Transcription

L

275

4.96

Replication, recombination and repair

B

1

0.02

Chromatin structure and dynamics

D

40

0.72

Cell cycle control, mitosis and meiosis

Y

0

0.00

Nuclear structure

V

54

0.97

Defense mechanisms

T

241

4.35

Signal transduction mechanisms

M

267

4.82

Cell wall/membrane biogenesis

N

77

1.39

Cell motility

Z

0

0.00

Cytoskeleton

W

1

0.02

Extracellular structures

U

124

2.24

Intracellular trafficking and secretion

O

184

3.32

Posttranslational modification, protein turnover, chaperones

C

308

5.56

Energy production conversion

G

510

9.21

Carbohydrate transport and metabolism

E

613

11.06

Amino acid transport metabolism

F

108

1.95

Nucleotide transport and metabolism

H

196

3.54

Coenzyme transport and metabolism

I

193

3.48

Lipid transport and metabolism

P

280

5.05

Inorganic ion transport and metabolism

Q

158

2.85

Secondary metabolite biosynthesis, transport and catabolism

R

662

11.95

General function prediction only

S

569

10.27

Function unknown

-

1,747

25.94

Not in COGS

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.

Authors’ Affiliations

(1)
Centre for Rhizobium Studies, Murdoch University
(2)
Dipartimento di Agraria, S.T.A.A., University of Sassari
(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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