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High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris
Standards in Genomic Sciences volume 10, Article number: 34 (2015)
Ensifer meliloti 4H41 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of common bean (Phaseolus vulgaris). Strain 4H41 was isolated in 2002 from root nodules of P. vulgaris grown in South Tunisia from the oasis of Rjim-Maatoug. Strain 4H41 is salt- and drought-tolerant and highly effective at fixing nitrogen with P. vulgaris. Here we describe the features of E. meliloti 4H41, together with genome sequence information and its annotation. The 6,795,637 bp high-quality permanent draft genome is arranged into 47 scaffolds of 47 contigs containing 6,350 protein-coding genes and 72 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.
Common bean ( Phaseolus vulgaris ) represents a very valuable source of proteins for low-income populations in Latin America and Africa . However, this legume is considered to be a poor nitrogen-fixing pulse in comparison to other grain legumes . This problem is generally attributed to the ineffectiveness of the native rhizobia, which is typically linked to the nodulation promiscuity of P. vulgaris [3-6] or to adverse abiotic conditions [7,8]. Salinity and drought are considered to be the major abiotic constraints that affect legumes in Tunisia and other countries. The selection of superior strains of rhizobia capable of assuring optimal nitrogen fixation under these adverse conditions is of high interest. Attention has therefore been directed to the isolation and characterization of rhizobial strains from various marginal areas that are subject to adverse climatic and edaphic conditions. In this context, Ensifer meliloti (formerly ‘ Sinorhizobium meliloti ’) strain 4H41 was isolated from root nodules of common bean grown in sandy, slightly alkaline soil from the oasis of Rjim-Maatoug in South Tunisia .
E. meliloti is classically considered to be a specific microsymbiont of the genera Medicago , Melilotus and Trigonella , however, recent studies have identified strains of E. meliloti that effectively nodulate P. vulgaris or several other legume species in northern Africa, South Africa and the Canary Islands [11-14]. Strain 4H41 induced nitrogen-fixing nodules on P. vulgaris but failed to nodulate Medicago spp. The phylogenetic analysis of nifH and nodC genes showed that strain 4H41 should be classified in a novel symbiovar (sv. mediterranense) . The symbiovar mediterranense has also been used to describe Ensifer fredii and Ensifer americanum strains that can nodulate and fix nitrogen with P. vulgaris , species of Mexican Acacia (now reclassified as Vachellia and Senegalia ) and Leucaena leucocephala . Strain 4H41 was able to grow in 4.4% NaCl (750 mM), while the P. vulgaris commercial inoculant Rhizobium tropici CIAT899T did not grow in salt concentrations higher than 1.8% . Inoculationwater deficiency showed that strain 4H41 was more competitive and more effective than strain experiments under CIAT899T . In field trials, P. vulgaris inoculated with strain 4H41 showed a significant increase in nodule number, shoot dry weight and grain yield even in non-irrigated fields. Under these conditions of water deficiency, nodulation by indigenous rhizobia was totally absent. However, when common bean was grown in adequately irrigated soil samples from these fields, numerous nodules could be observed, suggesting that, in contrast to 4H41, the native rhizobia were not tolerant of water deficiency . Because of its effectiveness and high salt tolerance, strain 4H41 is considered to be an elite candidate for inoculant formulation in order to promote cultivation of common bean under salt and drought constraints. This strain has therefore been selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project . Here we present a summary classification and a set of general features for E. meliloti strain 4H41, together with a description of its genome sequence and annotation.
Classification and features
E. meliloti 4H41 is a motile, Gram-negative strain in the order Rhizobiales of the class Alphaproteobacteria . The rod shaped form (Figure 1 Left and Center) has dimensions of approximately 0.25-0.5 μm in width and 0.75-1.0 μm in length. It is fast growing, forming colonies within 3–4 days when grown on half strength Lupin Agar (½LA) , tryptone-yeast extract agar (TY)  or a modified yeast-mannitol agar (YMA)  at 28°C. Colonies on ½LA are white-opaque, slightly domed and moderately mucoid with smooth margins (Figure 1 Right).
Figure 2 shows the phylogenetic relationship of E. meliloti 4H41 in a 16S rRNA sequence based tree. This strain is the most similar to Ensifer meliloti LMG 6133T and Ensifer numidicus ORS 1407T based on the 16S rRNA gene alignment with sequence identities of 99.85% and 99.63%, respectively, as determined using the EzTaxon-e server . Minimum Information about the Genome Sequence (MIGS) for 4H41 is provided in Table 1 and Additional file 1: Table S1.
E. meliloti strain 4H41 is highly effective for nitrogen fixation with P. vulgaris , but is unable to nodulate several legume species that have previously been identified as E. meliloti hosts . The symbiotic characteristics of E. meliloti strain 4H41 on a range of selected phylogenetically diverse hosts are provided in Table 2.
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 (GEBA-RNB) project at the U.S. Department of Energy, Joint Genome Institute (JGI). The genome project is deposited in the Genomes OnLine Database  and a high-quality permanent draft genome sequence is deposited in IMG . Sequencing, finishing and annotation were performed by the JGI . A summary of the project information is shown in Table 3.
Growth conditions and genomic DNA preparation
E. meliloti 4H41 was cultured to mid logarithmic phase in 60 ml of TY rich media  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 draft genome of E. meliloti 4H41 was generated at the DOE Joint Genome Institute (JGI) using the Illumina technology . An Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform which generated 17,481,364 reads totaling 2,622.2 Mbp. All general aspects of library construction and sequencing performed at the JGI can be found on 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 . The following steps were then performed for assembly: (1) filtered Illumina reads were assembled using Velvet (version 1.1.04) , (2) 1–3 Kbp simulated paired end reads were created from Velvet contigs using wgsim , (3) Illumina reads were assembled with simulated read pairs using Allpaths–LG (version r41043) . 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 47 contigs in 47 scaffolds. The total size of the genome is 6.8 Mbp and the final assembly is based on 830.5 Mbp of Illumina data, which provides an average 122.2x coverage of the genome.
Genes were identified using Prodigal  as part of the DOE-JGI genome annotation pipeline [35,36]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, KEGG, COG, and InterPro databases. The tRNAScanSE tool  was used to find tRNA genes, whereas ribosomal RNA genes were found by searches against models of the ribosomal RNA genes built from SILVA . 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 . Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes Expert Review (IMG-ER)  developed by the Joint Genome Institute, Walnut Creek, CA, USA.
The genome is 6,795,637 nucleotides with 62.01% GC content (Table 4) and comprised of 47 scaffolds of 47 contigs. From a total of 6,422 genes, 6,350 were protein encoding and 72 RNA only encoding genes. The majority of protein-coding genes (82.01%) 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.
Based on the 16S rRNA gene alignment, 4H41 is most closely related to Ensifer meliloti LMG 6133T , a Medicago microsymbiont  and Ensifer numidicus ORS 1407T , which effectively nodulates Argyrolobium uniflorum . In contrast to these two strains, 4H41 is unable to nodulate either of these hosts. Strain 4H41 is one of 27 strains of E. meliloti with sequenced genomes deposited in the IMG database. Of these, 4H41 and strain GVPV12  are the only two E. meliloti strains that have been isolated from, and are able to nodulate and fix nitrogen with, P. vulgaris . As the other sequenced E. meliloti strains are microsymbionts of Medicago spp., 4H41 is therefore a useful strain for comparing the molecular determinants of symbiosis in rhizobia with similar chromosomal backgrounds but which nodulate different legume hosts.
The genome size of the E. meliloti strains ranges from 6.6 – 8.9 Mbp; at 6.80 Mbp, the 4H41 genome is at the lower end of this range. It contains one pseudo gene, the numbers of which are highly variable in the sequenced E. meliloti genomes and can be up to 444 ( E. melilotiAK83). In common with the other E. meliloti genomes, 4H41 possesses a large number of genes assigned to COG functional categories for transport and metabolism of amino acids (12.22%), carbohydrates (11.03%), inorganic ions (5.3%), lipids (3.97%) and coenzymes (3.59%), and involved in transcription (8.78%), and signal transduction (3.58%). Genome analysis has revealed three distinct nodA genes, two coding for NodA proteins composed of 196 amino acids while the third encodes a NodA protein of 141 amino acids that lacks a 55 amino acid segment at the C-terminus. All three nodA copies are harboured within a symbiotic region of the genome and have highest sequence identity at the protein level with the common bean-nodulating strains Ensifer fredii GR64  and E. meliloti GVPV12. Three distinct nodA genes are also found in the P. vulgaris commercial inoculant strains Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 .
4H41 is salt- and drought-tolerant and highly effective for nitrogen fixation with P. vulgaris , and as such is a valuable inoculant strain. Analysis of its sequenced genome and comparison with the genomes of other sequenced E. meliloti and with RNB that nodulate the common bean will yield new insights into the molecular basis of salt- and drought-tolerance in rhizobia and into the molecular determinants of symbiotic specificity and nitrogen fixation in the important pulse legume P. vulgaris .
Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria
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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.
The authors declare that they have no competing interests.
RM supplied the strain, DNA and background information for this project, TR supplied DNA to JGI and performed all imaging, JA drafted the paper, RM 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.