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High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a microsymbiont isolated from Medicago polymorpha growing in alkaline soil

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Abstract

Ensifer medicae WSM244 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago species. WSM244 was isolated in 1979 from a nodule recovered from the roots of the annual Medicago polymorpha L. growing in alkaline soil (pH 8.0) in Tel Afer, Iraq. WSM244 is the only acid-sensitive E. medicae strain that has been sequenced to date. It is effective at fixing nitrogen with M. polymorpha L., as well as with more alkaline-adapted Medicago spp. such as M. littoralis Loisel., M. scutellata (L.) Mill., M. tornata (L.) Mill. and M. truncatula Gaertn. This strain is also effective with the perennial M. sativa L. Here we describe the features of E. medicae WSM244, together with genome sequence information and its annotation. The 6,650,282 bp high-quality permanent draft genome is arranged into 91 scaffolds of 91 contigs containing 6,427 protein-coding genes and 68 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.

Introduction

Root nodule bacteria that fix atmospheric nitrogen in association with annual and perennial pasture legumes have important roles in agriculture. Some of the most important associations in temperate and Mediterranean regions are the Ensifer ( Sinorhizobium Footnote 1) - Medicago symbioses that produce nutritious feed for animals. Medicago is a genus within tribe Trifolieae, which is included in the “temperate herbaceous papilionoid” Inverted Repeat Lacking Clade (IRLC) legumes [1, 2]. Species of Medicago are amongst the most extensively grown forage and pasture plants and have been cultivated ever since Medicago sativa L. (alfalfa, or lucerne) was first domesticated in the Near East and/or Central Asia in about 5000 BC. In addition to perennial M. sativa L., annual medic species used widely in agriculture include M. tornata (L.) Mill. (disc medic), the model legume M. truncatula Gaertn. (barrel medic) and M. littoralis Loisel. (strand medic), together with more recently commercialised species such as M. polymorpha L. (burr medic) and M. murex Willd. (murex medic) [3]. Medicago spp. are symbiotically specific: nearly all studied species are nodulated by strains of rhizobia belonging to either Ensifer medicae or the closely related species E. meliloti [4, 5]. E. medicae can be distinguished from E. meliloti by its ability to nodulate and fix nitrogen with M. polymorpha L. [5].

Ensifer medicae WSM244 was isolated in 1979 from a root nodule of M. polymorpha L. growing on alkaline soil (pH 8.0) near Tel Afer, Iraq [6]. This strain was superior in N2-fixation on a range of medics (M sativa L., M truncatula Gaertn., M. tornata L., M. polymorpha L., M. littoralis Loisel., M scutellata (L.) Mill.) in glasshouse tests in Australia and field trials in Iraq in 1980, and was recommended for development as an inoculant in Iraq (D. Chatel, pers com.). WSM244 has also been used in trials aimed at developing acid-tolerant inoculant strains for pasture medics, as the acid-sensitive nature of the microsymbiont is a constraint to the growth and persistence of Medicago spp. in agricultural regions with moderately acidic soils [7]. When field tested in an acidic soil (pH 5.0 CaCl2) in Western Australia, WSM244 survived at the site of inoculation for two years, but unlike several more acid tolerant strains it did not demonstrate saprophytic competence and was unable to colonize the soil [8]. This characteristic of WSM244 as an acid-soil sensitive strain correlates with its acid sensitive profile for growth in laboratory media and an inability to maintain a neutral intracellular pH when exposed to pH 6.0 or less [9]. This is in contrast to other E. medicae strains, which typically are the dominant microsymbiont partners of annual medics growing on acid soils, in contrast to the more acid-sensitive E. meliloti , which preferentially associates with alkaline-soil-adapted Medicago spp. [10]. The pH response phenotype of WSM244 is in marked contrast to the sequenced acid tolerant E. medicae strain WSM419 [11]. Sequencing the genome of WSM244 and comparing its attributes with an acid-tolerant strain such as WSM419 would provide a means of establishing the molecular determinants required for adaptation to acid soils. This strain was therefore selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project [12]. Here we present a summary classification and a set of general features for E. medicae strain WSM244, together with a description of its genome sequence and annotation.

Organism information

Classification and features

E. medicae WSM244 is a motile, Gram-negative rod (Fig. 1 Left and Center) in the order Rhizobiales of the class Alphaproteobacteria . It is fast growing, forming colonies within 3–4 days when grown on half strength Lupin Agar [13], tryptone-yeast extract agar [14] or a modified yeast-mannitol agar [15] at 28 °C. Colonies on ½LA are white-opaque, slightly domed and moderately mucoid with smooth margins (Fig. 1 Right).

Fig. 1
figure1

Images of Ensifer medicae WSM244 using scanning (Left) and transmission (Center) electron microscopy and the appearance of colony morphology on solid media (Right)

Figure 2 shows the phylogenetic relationship of E. medicae WSM244 in a 16S rRNA sequence based tree. This strain is the most phylogenetically related to Ensifer medicae WSM419 and Ensifer meliloti LMG 6133T based on the 16S rRNA gene alignment, with sequence identities of 100 % and 99.71 %, respectively, as determined using the EzTaxon-e database, which contains the sequences of validly published type strains [16]. Minimum Information about the Genome Sequence for WSM244 is provided in Table 1 and Additional file 1: Table S1.

Fig. 2
figure2

Phylogenetic tree showing the relationship of Ensifer medicae WSM244 (shown in bold blue print) to other type and non-type strains in the Ensifer genus and to other root nodule bacteria species in the order Rhizobiales, based on aligned sequences of the 16S rRNA gene (1,283 bp internal region). (The species name “Sinorhizobium chiapanecum” has not been validly published.) Azorhizobium caulinodans ORS 571T was used as an outgroup. All sites were informative and there were no gap-containing sites. Phylogenetic analyses were performed using MEGA, version 6 [37]. The tree was built using the Maximum-Likelihood method with the General Time Reversible model [38]. Bootstrap analysis [39] with 500 replicates was performed to assess the support of the clusters. Type strains are indicated with a superscript T. Strains with a genome sequencing project registered in GOLD [17] are in bold font and the GOLD ID is provided after the GenBank accession number. Finished genomes are indicated with an asterisk

Table 1 Classification and general features of Ensifer medicae WSM244 in accordance with the MIGS recommendations [40] published by the Genome Standards Consortium [41]

Symbiotaxonomy

WSM244 nodulates and is effective for nitrogen fixation with M. littoralis Loisel., M sativa L., M. tornata (L.) Mill. [3], M. murex Willd., M. polymorpha L., M truncatula Gaertn. [8] and M scutellata (L.) Mill. (D. Chatel per com). WSM244 nodulates and is partially effective for nitrogen fixation with M. rotata Boiss. and M. rugosa Desr., but does not nodulate M. blancheana Boiss. (D. Chatel per com). The symbiotic characteristics of E. medicae WSM244 on a range of selected hosts are summarised in Additional file 2: Table S2.

Genome sequencing 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 Genomic Encyclopedia of Bacteria and Archaea, The Root Nodulating Bacteria chapter project at the U.S. Department of Energy, Joint Genome Institute. The genome project is deposited in the Genomes OnLine Database [17] and a high-quality permanent draft genome sequence is deposited in IMG [18]. Sequencing, finishing and annotation were performed by the JGI [19]. A summary of the project information is shown in Table 2.

Table 2 Genome sequencing project information for E. medicae WSM244

Growth conditions and genomic DNA preparation

E. medicae WSM244 was grown on TY solid medium [14] for three days, then a single colony was selected and used to inoculate 5 ml TY broth medium. The culture was grown for 48 h on a gyratory shaker (200 rpm) at 28 °C. Subsequently 1 ml was used to inoculate 60 ml TY broth medium and grown on a gyratory shaker (200 rpm) at 28 °C until OD 0.6 was reached. DNA was isolated from 60 ml of cells using a CTAB bacterial genomic DNA isolation method (http://jgi.doe.gov/collaborate-with-jgi/pmo-overview/protocols-sample-preparation-information/). Final concentration of the DNA was 0.5 mg ml−1.

Genome sequencing and assembly

The draft genome of E. medicae WSM244 was generated at the DOE Joint genome Institute (JGI) using the Illumina technology [20]. An Illumina Std shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform which generated 22,576,268 reads totaling 3,386.4 Mbp. All general aspects of library construction and sequencing performed at the JGI can be found at the JGI website. 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, Han J. unpublished) . The following steps were then performed for assembly: (1) filtered Illumina reads were assembled using Velvet (version 1.1.04) [21], (2) 1–3 Kbp simulated paired end reads were created from Velvet contigs using wgsim (https://github.com/lh3/wgsim), (3) Illumina reads were assembled with simulated read pairs using Allpaths–LG (version r41043) [22]. Parameters for assembly steps were: 1) Velvet (velveth: 63 –shortPaired and velvetg: −very clean yes –export- Filtered yes –min contig lgth 500 –scaffolding no –cov cutoff 10) 2) wgsim (−e 0 –1 100 –2 100 –r 0 –R 0 –X 0) 3) Allpaths–LG (PrepareAllpathsInputs: PHRED 64 = 1 PLOIDY = 1 FRAG COVERAGE = 125 JUMP COVERAGE = 25 LONG JUMP COV = 50, RunAllpathsLG: THREADS = 8 RUN = std shredpairs TARGETS = standard VAPI WARN ONLY = True OVERWRITE = True) . The final draft assembly contained 91 contigs in 91 scaffolds. The total size of the genome is 6.7 Mbp and the final assembly is based on 789.1 Mbp of Illumina data, which provides an average 118.7x coverage of the genome.

Genome annotation

Genes were identified using Prodigal [23], as part of the DOE-JGI genome annotation pipeline [24, 25]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information nonredundant database, UniProt, TIGRFam, Pfam, KEGG, COG, and InterPro databases. The tRNAScanSE tool [26] was used to find tRNA genes, whereas ribosomal RNA genes were found by searches against models of the ribosomal RNA genes built from SILVA [27]. 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 [28]. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes (IMG) platform [29] developed by the Joint Genome Institute, Walnut Creek, CA, USA [30].

Genome properties

The genome is 6,650,282 nucleotides with 61.21 % GC content (Table 3) and comprised of 91 scaffolds of 91 contigs. From a total of 6,495 genes, 6,427 were protein encoding and 68 RNA only encoding genes. The majority of protein-coding genes (79.34 %) 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 4.

Table 3 Genome statistics for Ensifer medicae WSM244
Table 4 Number of genes of Ensifer medicae WSM244 associated with general COG functional categories

Insights from the genome sequence

WSM244 is one of six strains of E. medicae and one of 30 E. medicae or E. meliloti Medicago -nodulating strains that have been sequenced and whose genomes have been deposited in the IMG database. The genome of WSM244 falls within the expected size range of 6.4–7.2 Mbp for E. medicae . As observed in other E. medicae genomes, WSM244 possesses a large number of genes assigned to COG functional categories for: transport and metabolism of amino acids (12.15 %), carbohydrates (11.17 %), inorganic ions (5.3 %), lipids (3.91 %) and coenzymes (3.32 %), transcription (8.63 %) and signal transduction (3.66 %). The WSM244 genome contains only four pseudo genes, the numbers of which are highly variable in sequenced E. medicae strains and can be as high as 485 ( E. medicae WSM4191). All six E. medicae strains share high ANI values of 99.18–99.67 %, which is consistent with the low levels of genetic diversity found in E. medicae populations [31]. The six E. medicae strains share 5,425 core orthologous genes. WSM244 contains 202 unique genes, including those found in clusters encoding a putative polyketide synthase, phage proteins and a sulfonate transport system. Around 72 % of these unique genes encode hypothetical proteins. Strain WSM244 is particularly interesting, as it lacks the acid tolerance of other E. medicae strains. The genome of this strain does contain orthologs of acid response or acid tolerance genes that were initially discovered in E. medicae WSM419. These genes include actA (lnt), actP, actR, actS, phrR, lpiA and acvB [3235]. WSM244 also contains the tcsA-tcrA-fsrR- regulatory gene cluster which is required for the low-pH-activation of lpiA and acvB in E. medicae WSM419 [36]. This finding is in direct contrast to the absence of fsrR, tcsA and tcrA in the the acid-sensitive strain E. meliloti 1021. This suggests that either there may be differences in pH responsive gene expression in the WSM244 background, or that acid tolerant E. medicae strains possess other candidate genes that are required for low pH adaptation and have not yet been identified.

Conclusions

WSM244 is of particular interest as it was isolated from M. polymorpha growing in alkaline soil and it lacks the acid tolerance of E. medicae strains isolated from medics growing in acid Sardinian and Greek soils [9]. WSM244 is the only acid-sensitive E. medicae strain that has been sequenced to date. Analysis of its sequenced genome and comparison with other sequenced E. medicae and E. meliloti genomes will yield new insights into the molecular basis of acid tolerance in rhizobia and into the ecology and biogeography of the Ensifer-Medicago symbiosis.

Notes

  1. 1.

    Editorial note—Readers are advised that in Opinion 84 the Judicial Commission of the International Committee on Systematics of Prokaryotes ruled that the genus name Ensifer Casida 1982 has priority over Sinorhizobium Chen et al. 1988 and the names are synonyms [1]. It was further concluded that the transfer of members of the genus Sinorhizobium to the genus Ensifer, as proposed by Young [2] would not cause confusion.

Abbreviations

GEBA-RNB:

Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria

IRLC:

Inverted Repeat Lacking Clade

References

  1. 1.

    Steele KP, Ickert-Bond SM, Zarre S, Wojciechowski MF. Phylogeny and character evolution in Medicago (Leguminosae): Evidence from analyses of plastid trnK/matK and nuclear GA3ox1 sequences. Am J Bot. 2010;97:1142–55.

  2. 2.

    Steele KP, Wojciechowski MF. Phylogenetic systematics of tribes Trifolieae and Vicieae (Fabaceae), based on sequences of the plastid gene matK (Papilionoideae: Leguminosae). In: Klitgaard BB, Bruneau A, editors. Advances in Legume Systematics, part 10. Kew: Royal Botanic Garden; 2003. p. 355–70.

  3. 3.

    Howieson JG, Nutt B, Evans P. Estimation of host-strain compatibility for symbiotic N-fixation between Rhizobium meliloti, several annual species of Medicago and Medicago sativa. Plant Soil. 2000;219:49–55.

  4. 4.

    Béna G, Lyet A, Huguet T, Olivieri I. Medicago – Sinorhizobium symbiotic specificity evolution and the geographic expansion of Medicago. J Evol Biol. 2005;18:1547–58.

  5. 5.

    Rome S, Fernandez MP, Brunel B, Normand P, Cleyet-Marel JC. Sinorhizobium medicae sp. nov., isolated from annual Medicago spp. Int J Syst Bacteriol. 1996;46:972–80.

  6. 6.

    Materon LA, Danso SKA. Nitrogen fixation in two annual Medicago legumes, as affected by inoculation and seed density. Field Crops Res. 1991;26:253–62.

  7. 7.

    Howieson JG, Ewing MA, Thorn CW, Revell CK. Increased yield in annual species of Medicago grown in acidic soil in response to inoculation with acid tolerant Rhizobium meliloti. In: Wright RJ, Baligar VC, Murrmann RP, editors. Plant-Soil Interactions at Low pH, vol. 45. Dordrecht: Springer Netherlands; 1991. p. 589–95. Developments in Plant and Soil Sciences].

  8. 8.

    Howieson JG, Ewing MA. Acid tolerance in the Rhizobium meliloti-Medicago symbiosis. Aust J Agric Res. 1986;37:55–64.

  9. 9.

    O’Hara GW, Goss TJ, Dilworth MJ, Glenn AR. Maintenance of intracellular pH and acid tolerance in Rhizobium meliloti. Appl Environ Microb. 1989;55:1870–6.

  10. 10.

    Garau G, Reeve WG, Brau L, Deiana P, Yates RJ, James D, et al. The symbiotic requirements of different Medicago spp. suggest the evolution of Sinorhizobium meliloti and S. medicae with hosts differentially adapted to soil pH. Plant Soil. 2005;276:263–77.

  11. 11.

    Reeve W, Chain P, O’Hara G, Ardley J, Nandesena K, Brau L, et al. Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419. Stand Genomic Sci. 2010;2:77–86.

  12. 12.

    Reeve WG, Ardley JK, Tian R, Eshragi L, Yoon JW, Ngamwisetkun P, et al. A genomic encyclopedia of the root nodule bacteria: Assessing genetic diversity through a systematic biogeographic survey. Stand Genomic Sci. 2014;9:39.

  13. 13.

    Howieson JG, Ewing MA, D’antuono MF. Selection for acid tolerance in Rhizobium meliloti. Plant Soil. 1988;105:179–88.

  14. 14.

    Beringer JE. R factor transfer in Rhizobium leguminosarum. J Gen Microbiol. 1974;84:188–98.

  15. 15.

    Vincent JM. A manual for the practical study of the root-nodule bacteria. International Biological Programme. Oxford: Blackwell Scientific Publications; 1970.

  16. 16.

    Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M, Na H, et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol. 2012;62:716–21.

  17. 17.

    Reddy TBK, Thomas AD, Stamatis D, Bertsch J, Isbandi M, Jansson J, et al. The Genomes OnLine Database (GOLD) v. 5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res. 2015;43:D1099–D1106.

  18. 18.

    Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, Pillay M, et al. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 2014;42:D560–7.

  19. 19.

    Mavromatis K, Land ML, Brettin TS, Quest DJ, Copeland A, Clum A, et al. The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. PLoS One. 2012;7:e48837.

  20. 20.

    Bennett S. Solexa Ltd. Pharmacogenomics. 2004;5:433–8.

  21. 21.

    Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research. 2008;18:821–9.

  22. 22.

    Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A. 2011;108:1513–8.

  23. 23.

    Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.

  24. 24.

    Mavromatis K, Ivanova NN, Chen IMA, Szeto E, Markowitz VM, Kyrpides NC. The DOE-JGI Standard operating procedure for the annotations of microbial genomes. Stand Genomic Sci. 2009;1:63–7.

  25. 25.

    Chen IM, Markowitz VM, Chu K, Anderson I, Mavromatis K, Kyrpides NC, et al. Improving microbial genome annotations in an integrated database context. PLoS One. 2013;8:e54859.

  26. 26.

    Lowe TM, Eddy SR. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research. 1997;25:955–64.

  27. 27.

    Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007;35:7188–96.

  28. 28.

    Kamphuis LG, Williams AH, Küster H, Trengove RD, Singh KB, Oliver RP, et al. Phoma medicaginis stimulates the induction of the octadecanoid and phenylpropanoid pathways in Medicago truncatula. Molecular Plant Pathology. 2012. doi:10.1111/j.1364-3703.2011.00767.x.

  29. 29.

    The Integrated Microbial Genomes (IMG) platform. http://img.jgi.doe.gov

  30. 30.

    Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009;25:2271–8.

  31. 31.

    Epstein B, Branca A, Mudge J, Bharti AK, Briskine R, Farmer AD, et al. Population genomics of the facultatively mutualistic bacteria Sinorhizobium meliloti and S. medicae. PLoS Genet. 2012;8:e1002868.

  32. 32.

    Tiwari RP, Reeve WG, Dilworth MJ, Glenn AR. Acid tolerance in Rhizobium meliloti strain WSM419 involves a two-component sensor-regulator system. Microbiology. 1996;142(Pt 7):1693–704.

  33. 33.

    Tiwari RP, Reeve WG, Dilworth MJ, Glenn AR. An essential role for actA in acid tolerance of Rhizobium meliloti. Microbiology. 1996;142(Pt 3):601–10.

  34. 34.

    Reeve WG, Tiwari RP, Kale NB, Dilworth MJ, Glenn AR. ActP controls copper homeostasis in Rhizobium leguminosarum bv. viciae and Sinorhizobium meliloti preventing low pH-induced copper toxicity. Mol Microbiol. 2002;43:981–91.

  35. 35.

    Poole PS, Hynes MF, Johnston AWB, Tiwari RP, Reeve WG, Downie JA. Physiology of root-nodule bacteria. In: Dilworth MJ, James EK, Sprent JI, Newton WE, editors. Nitrogen-fixing Leguminous Symbioses, vol. 7. Dordrecht: Springer Netherlands; 2008. p. 241–92. Nitrogen Fixation: Origins, Applications, and Research Progress].

  36. 36.

    Reeve WG, Brau L, Castelli J, Garau G, Sohlenkamp C, Geiger O, et al. The Sinorhizobium medicae WSM419 lpiA gene is transcriptionally activated by FsrR and required to enhance survival in lethal acid conditions. Microbiology. 2006;152:3049–59.

  37. 37.

    Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol. 2011;28:2731–9.

  38. 38.

    Nei M, Kumar S. Molecular Evolution and Phylogenetics. New York: Oxford University Press; 2000.

  39. 39.

    Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39:783–91.

  40. 40.

    Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, et al. Towards a richer description of our complete collection of genomes and metagenomes “Minimum Information about a Genome Sequence” (MIGS) specification. Nat Biotechnol. 2008;26:541–7.

  41. 41.

    Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, et al. The Genomic Standards Consortium. PLoS Biology. 2011;9:e1001088.

  42. 42.

    Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87:4576–9.

  43. 43.

    Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol 2005, 55:2235–2238

  44. 44.

    Chen WX, Wang ET, Kuykendall LD. The Proteobacteria. New York: Springer - Verlag; 2005.

  45. 45.

    List of new names and new combinations previously effectively, but not validly, published. International Journal of Systematic and Evolutionary Microbiology 2006, 56:1–6.

  46. 46.

    Garrity GM, Bell JA, Lilburn T. Class I. Alphaproteobacteria class. nov. In: Garrity GM, Brenner DJ, Kreig NR, Staley JT, editors. Bergey’s Manual of Systematic Bacteriology. Secondth ed. New York: Springer; 2005.

  47. 47.

    Kuykendall LD. Order VI. Rhizobiales ord. nov. In: Garrity GM, Brenner DJ, Kreig NR, Staley JT, editors. Bergey’s Manual of Systematic Bacteriology. Secondth ed. New York: Springer; 2005. p. 324.

  48. 48.

    Kuykendall LD. Family I. Rhizobiaceae. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey’s Manual of Systematic Bacteriology. New York: Springer; 2005.

  49. 49.

    Kuykendall LD, Hashem FM, Wang ET. Genus VII. Sinorhizobium. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey’s Manual of Systematic Bacteriology, vol. 2. New York: Springer; 2005. p. 358–61.

  50. 50.

    Judicial Commission of the International Committee on Systematics of Prokaryotes. The genus name Sinorhizobium Chen et al. 1988 is a later synonym of Ensifer Casida 1982 and is not conserved over the latter genus name, and the species name ‘Sinorhizobium adhaerens’ is not validly published. Opinion 84. Int J Syst Evol Microbiol. 2008;58:1973.

  51. 51.

    Casida LE. Ensifer adhaerens gen. nov., sp. nov.: a bacterial predator of bacteria in soil. Int J Syst Bacteriol. 1982;32:339–45.

  52. 52.

    Biological Agents: Technical rules for biological agents. [http://www.baua.de/en/Topics-from-A-to-Z/Biological-Agents/TRBA/TRBA.html]

  53. 53.

    Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–9.

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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. We thank Gordon Thompson (Murdoch University) for the preparation of SEM and TEM photos.

Author information

Correspondence to Wayne Reeve.

Additional information

Competing interests

The authors declare that they have no competing interests.

Authors’ contributions

JH supplied the strain and background information for this project, TR supplied DNA to JGI and performed all imaging, JA and GOH drafted the paper, GOH provided financial support and all other authors were involved in sequencing the genome and/or editing the final paper. All authors read and approved the final manuscript.

Additional files

Additional file 1: Table S1.

Associated MIGS record for WSM244. (DOCX 19 kb)

Additional file 2: Table S2.

Nodulation and N2 fixation properties of E. medicae WSM244 on selected Medicago spp. Data compiled from [3, 6, 8]. Note that ‘+’ and ‘-’ denote presence or absence, respectively, of nodulation (Nod) or N2 fixation (Fix). (DOCX 15 kb)

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Ardley, J., Tian, R., O’Hara, G. et al. High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a microsymbiont isolated from Medicago polymorpha growing in alkaline soil. Stand in Genomic Sci 10, 126 (2015) doi:10.1186/s40793-015-0119-5

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Keywords

  • Root-nodule bacteria
  • Nitrogen fixation
  • Symbiosis
  • Alphaproteobacteria
  • Ensifer
  • GEBA-RNB