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
© The Author(s) 2014
Published: 15 June 2014
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.
Keywordsroot-nodule bacteria nitrogen fixation rhizobia Alphaproteobacteria
The genus Medicago comprises 87 species of annual and perennial legumes, including some that were formerly recognized as Trigonella and Melilotus species . 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  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 .
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 , 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 [7–10]. Useful variation in saprophytic competence occurs between strains of medic rhizobia  and valuable insights into the mechanisms that confer acidity tolerance have been provided by studies using strain WSM419 , which has been recently sequenced . 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 [13–16]. 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  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
Classification and general features of Ensifer medicae strain WSM1115 according to the MIGS recommendations 
Species Ensifer medicae
Soil, root nodule, on host
Free living, symbiotic
Time of sample collection
Compatibility of Ensifer medicae WSM1115 with various Medicago and allied genera for nodulation (Nod) and N2-fixation (Fix)
Cultivar or line
Accession PI 227850
Accession PI 495552
Accessions SA40006 & 39909
Genome sequencing and annotation information
Genome project history
Genome sequencing project information for Ensifer medicae strain WSM1115
Permanent high quality draft
2× Illumina libraries; Std short PE & CLIP long PE
Illumina HiSeq 2000
with Allpaths, version 38445, Velvet 1.1.05, phrap 4.24
Gene calling methods
Prodigal 1.4, GenePRIMP
Genbank Date of Release
April 22, 2013
NCBI project ID
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 . DNA was isolated from the cells using a CTAB (Cetyl trimethyl ammonium bromide) bacterial genomic DNA isolation method .
Genome sequencing and assembly
The genome of Ensifer medicae strain WSM1115 was sequenced at the Joint Genome Institute (JGI) using Illumina  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 . 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 , 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 [43–45]. 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.
Genes were identified using Prodigal  as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline . 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 , RNAMMer , Rfam , TMHMM , and SignalP . Additional gene prediction analyses and functional annotation were performed within the Integrated Microbial Genomes (IMG-ER) platform .
Genome Statistics for Ensifer medicae strain WSM1115
% of Total
Genome size (bp)
DNA coding region (bp)
DNA G+C content (bp)
Number of scaffolds
Number of contigs
Genes with function prediction
Genes assigned to COGs
Genes assigned Pfam domains
Genes with signal peptides
Genes coding membrane proteins
Number of protein coding genes of Ensifer medicae strain WSM1115 associated with the general COG functional categories.
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, mitosis and meiosis
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Posttranslational modification, protein turnover, chaperones
Energy production conversion
Carbohydrate transport and metabolism
Amino acid transport metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolite biosynthesis, transport and catabolism
General function prediction only
Not in COGS
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).
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