- Extended genome report
- Open Access
High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia
Standards in Genomic Sciencesvolume 12, Article number: 7 (2017)
Rhizobium mesoamericanum STM6155 (INSCD = ATYY01000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume Mimosa pudica L.. STM6155 was isolated in 2009 from a nodule of the trap host M. pudica grown in nickel-rich soil collected near Mont Dore, New Caledonia. R. mesoamericanum STM6155 was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) genome sequencing project. Here we describe the symbiotic properties of R. mesoamericanum STM6155, together with its genome sequence information and annotation. The 6,927,906 bp high-quality draft genome is arranged into 147 scaffolds of 152 contigs containing 6855 protein-coding genes and 71 RNA-only encoding genes. Strain STM6155 forms an ANI clique (ID 2435) with the sequenced R. mesoamericanum strain STM3625, and the nodulation genes are highly conserved in these strains and the type strain of Rhizobium grahamii CCGE501T. Within the STM6155 genome, we have identified a chr chromate efflux gene cluster of six genes arranged into two putative operons and we postulate that this cluster is important for the survival of STM6155 in ultramafic soils containing high concentrations of chromate.
The ability of legumes to engage in a dinitrogen fixing symbiosis with soil dwelling bacteria, collectively known as rhizobia, has contributed to their success in colonizing nitrogen deficient soils over a broad range of edaphic conditions. While legume crops and pastures make important contributions to agricultural productivity, invasive legume weeds such as Mimosa pudica L. have a negative impact on natural and agricultural ecological systems. M. pudica originates from America  and became a highly invasive pantropical weed. It has been identified as a pest species, associated with land degradation, biodiversity loss, and reduced agricultural and therefore economic productivity, with attendant social and health impacts . It requires resource-intensive chemical and mechanical control methods . Conversely, however, it has potential commercial value as a source of silver nanoparticles and pharmacologically active phytochemicals, and as a phytoremediant for arsenic-polluted soils [3–6]. Understanding the Mimosa symbiosis can therefore help to achieve outcomes such as preventing biodiversity loss and improving the use of terrestrial ecosystems, as well as promoting sustainable industry, which form part of the Sustainable Development Goals adopted in September 2015 as part of the UN’s development agenda ‘Transforming our world: the 2030 Agenda for Sustainable Development’ .
M. pudica has the unusual property of interacting with microsymbionts belonging to both alpha- and beta-rhizobia [8, 9]. Alpha-rhizobia are preferred symbionts of most legume species, but beta-rhizobia have a far narrower host range, with a particular affinity for the Mimosa genus in South America  and endemic papilionoid species in South Africa . Diversity studies have shown that alpha-rhizobia are found less frequently than beta-rhizobia in the nodules of M. pudica [12–17], and nodulating species exhibit different competitive and symbiotic characteristics [18, 19]. M. pudica thus represents an interesting legume species for comparative analyses of symbiotic traits and plant-infection genetic programs in the two categories of symbionts.
M. pudica was introduced to New Caledonia at the end of the 19th century . Rhizobium mesoamericanum STM6155 was isolated from nodules of M. pudica growing in soil characterized by neutral pH (6.8) and very high total nickel concentrations (10.1 g.kg−1) that was collected near the abandoned nickel mining site of Mont Dore (S3: 22°15’16.51”S and 166°36’44.27”E) in New Caledonia .
The 16S rRNA and recA house-keeping genes of STM6155 showed 100 and 97% nucleotide identity with their orthologs in Rhizobium mesoamericanum CCGE501T from Mexico , and STM6155 was thus tentatively included in the same species. Among described alpha-rhizobial symbionts of M. pudica ( R. etli bv. mimosae, R. tropici and R. mesoamericanum ), R. mesoamericanum is the most frequently detected species, with a distribution on different continents (Central & South America, Asia) [17, 20]. In Mexico, endemic Mimosa spp. growing in weakly acidic, neutral or slightly alkaline soil are preferentially nodulated by Alphaproteobacterial rhizobia, including strains of R. mesoamericanum , whereas acid-tolerant Burkholderia spp. are favoured microsymbionts of endemic Mimosa spp., including M. pudica, in acidic Brazilian soils [14, 22]. R. mesoamericanum is much less effective for nitrogen fixation on M. pudica than Burkholderia phymatum STM815 or Cupriavidus taiwanensis STM6070 [12, 15], and much less competitive in comparison to B. phymatum and B. tuberum . These data question how R. mesoamericanum can maintain itself as a symbiont of M. pudica despite its low competitiveness. Strain STM6155 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 [23, 24], to investigate the genome traits that enable this species to adapt to a symbiotic and saprophytic lifestyle. Here we present a summary classification and a set of general features for R. mesoamericanum STM6155, together with a description of its genome sequence and annotation.
Classification and features
Rhizobium mesoamericanum STM6155 is a motile, Gram-negative, non-spore forming strain in the order Rhizobiales of the class Alphaproteobacteria . The rod-shaped form has dimensions of 0.4–0.6 μm in width and 1.0–1.4 μm in length (Fig. 1 Left and Center). 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  at 28 °C. Colonies on ½LA are white-opaque, slightly domed and moderately mucoid with smooth margins (Fig. 1 Right).
Figure 2 shows the phylogenetic relationship of R. mesoamericanum STM6155 in a 16S rRNA sequence based tree. This strain is the most similar to R. mesoamericanum CCGE501T based on the 16S rRNA gene alignment, with sequence identities of 100% over 1362 bp, as determined using the EzTaxon-e database, which contains the sequences of validly published type strains . Minimum Information about the Genome Sequence for STM6155 is provided in Table 1 and Additional file 1: Table S1.
R. mesoamericanum STM6155 was isolated from nodules of M. pudica, as were others members of this species including STM3625, STM3629, tpud40a and tpud22.2 [12, 15, 17]. However, the type strain of the species, CCGE501T, originates from nodules of Phaseolus vulgaris L. . Strain STM6155 forms nodules and fixes N2 with several Mimosa species of American origin, including M. pudica and Mimosa acustipulata Benth. It forms white, ineffective nodules on Mimosa pigra L. and Mimosa caesalpinifolia Benth. but is unable to nodulate Mimosa scabrella Benth. STM6155 is also able to form nitrogen-fixing nodules on P. vulgaris and on a legume, Acacia spirorbis Labill., which grows in the same area from which STM6155 originates . The symbiotic characteristics of R. mesoamericanum STM6155 on a range of hosts are summarised in Additional file 1: Table S2. R. mesoamericanum STM6155 contains a full set of nodulation genes, and exhibits uncommon features, such as the presence of two alleles of the nodA gene in its genome, a feature that seems conserved in several strains of the species such as STM3625 [15, 17, 29].
Genome sequencing information
Genome project history
This organism was selected for sequencing at the U.S. Department of Energy funded Joint Genome Institute as part of the Genomic Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project [23, 24]. The root nodule bacteria in this project were selected on the basis of environmental and agricultural relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance. The genome project is deposited in the Genomes On-Line 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 2.
Growth conditions and genomic DNA preparation
Rhizobium mesoamericanum STM6155 was streaked onto TY solid medium  and grown at 28 °C for 3 days to obtain well grown, well separated colonies, 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 the cells were incubated at 28 °C on a gyratory shaker at 200 rpm until an OD600nm of 0.6 was reached. DNA was isolated from 60 ml of cells using a CTAB bacterial genomic DNA isolation method . Final concentration of the DNA was set to 0.5 mg ml-1.
Genome sequencing and assembly
The draft genome of R. mesoamericanum STM6155 was generated at the JGI using Illumina technology . An Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform which generated 14,034,164 reads totaling 2105 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 (Mingkun L, Copeland A, Han J. unpublished), providing 12,829,288 trimmed reads totaling 1924 Mbp. 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 r39750). Parameters for assembly steps were: 1) Velvet (velveth: --v --s 51 --e 71 --i 2 --t 1 --f “-shortPaired -fastq $FASTQ” --o “-ins_length 250 -min_contig_lgth 500”); 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 152 contigs in 147 scaffolds. The total size of the genome is 6.9 Mbp and the final assembly is based on 1924 Mbp of Illumina data, which provides an average 279x coverage of the genome.
Genes were identified using Prodigal  as part of the DOE-JGI annotation pipeline [39, 40]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, 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 platform  developed by the Joint Genome Institute, Walnut Creek, CA, USA. The annotated genome of R. mesoamericanum STM6155 is available in IMG (genome ID = 2513237088).
The genome is 6,927,906 nucleotides with 58.90% GC content (Table 3) and comprised of 147 scaffolds (selected scaffolds are shown in Fig. 3) of 152 contigs. The location of nodulation (Fig. 3a), nitrogenase (Fig. 3b) and chromate resistance (Fig. 3c) loci on genome scaffolds are shown. From a total of 6926 genes in the genome, 6855 were protein encoding and 71 RNA only encoding genes. The majority of genes (76.02%) 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.
Insights from the genome sequence
R. mesoamericanum STM6155 shares 100 and 99% sequence identity (over 1346 bp) to the 16S rRNA of the fully sequenced R. mesoamericanum type strain CCGE501T  and R. mesoamericanum strain STM3625 , respectively. Moreover the STM6155 genome shows 96.18% average nucleotide identity (ANI) (with 82% of conserved DNA), with the type strain of R. mesoamericanum CCGE501T , fitting with the species affiliation cut-off defined by Goris et al. (2007)  (Table 5).
We produced plasmid profiles of several R. mesoamericanum isolates by the Eckhardt method  to compare their plasmid content with genomic data. As shown in Fig. 4, the STM6155 plasmid profile differs from those of STM3625 and CCGE501T. Firstly, the STM6155 and STM3629 plasmid profiles suggested the absence of a 1.5 Mbp megaplasmid (P1) observed in CCGE501T and STM3625. The alignment of the megaplasmid P1 sequence of STM3625 with the draft genomes of STM6155 and CCGE501T (Fig. 5a) using progressive Mauve software  shows, however, the presence of P1 homologous regions in STM6155 and CCGE501T genomes. This suggests a putative integration of megaplasmid P1 into the bacterial chromosome in STM6155. This phenomenon was already reported in cell siblings of Ensifer fredii (formerly Rhizobium sp.) NGR234 . The STM6155 plasmid profile suggests thus a diversity of genome architectures at the intra-species level in R. mesoamericanum . This diversity is observed among isolates originating from different continents like STM6155 (New Caledonia) and STM3625 (French Guiana), but also among isolates from the same country like STM3625 and STM3629 (both from French Guiana) [15, 17]. Secondly, Fig. 4 shows that STM6155 harbors a ca. 500 Kbp symbiotic plasmid (pSym) of a slightly larger size than those of STM3625 and CCGE501T. The alignment of the STM3625 pSym with the draft genomes of STM6155 and CCGE501T (using progressive Mauve, Fig. 5b) confirms the observed pSym size difference, with the presence of additional genomic regions in the STM3625 pSym. Althabegoiti and colleagues  have previously observed that there is only 61.4% of conserved DNA (with ANI of 98.07%) between the pSyms of CCGE501T and STM3625. Here we can extend this observation to the STM6155 pSym, which differs from both STM3625 and CCGE501T pSyms.
Despite the sequence diversity of the pSyms within R. mesoamericanum isolates, the STM6155 symbiosis nodulation genes are highly conserved with those of STM3625 and CCGE501T. The STM6155 nodulation genes include nodA1BCSUIJHPQ, an additional nodA (nodA2) gene, three nodD (nodD1, 2 and 3) transcriptional regulator genes, nodM, and 2 nodO (nodO1, 2) genes. The gene order is also conserved in R. grahamii CCGE502T but this strain does not contain the nodA2 allele (Fig. 6).
Strain STM6155 was isolated from a nodule of M. pudica growing in ultramafic soil at a pH near neutral (pH 6.8) that contained high concentrations of heavy metals, and the highest concentrations of bioavailable chromate among four studied sites . This strain was identified as being resistant to chromate concentrations up to 0.3 mM, that is comparable with chromate tolerance of Cupriavidus metallidurans CH34 [15, 50, 51]. Chromate resistance loci (chr) have been identified in the heavy-metal-tolerant C. metallidurans CH34 and we have discovered orthologs to these genes in STM6155 (Fig. 3c), that were absent from the more chromate sensitive strain R. mesoamericanum STM3625. MaGe  analysis has revealed synteny of six of the C. metallidurans CH34 plasmid-borne chr loci in STM6155. However, in contrast to CH3, the loci in STM6155 are arranged into two putative operons, chrBAP (locus tags YY3DRAFT_04858 - YY3DRAFT_04860) and chrCFY (locus tags YY3DRAFT_04857 - YY3DRAFT_04855) located adjacent to one another on complementary strands.
R. mesoamericanum STM6155 is a microsymbiont of Mimosa pudica L. and Phaseolus vulgaris L. , both of which have centres of origin in central/south America. The genome size of STM6155 is 6.9 Mbp with 58.9% GC content. This strain forms a clique with the two other R. mesoamericanum strains STM3625 and CCGE501T based on average nucleotide identity comparisons (species cut-off above 95% on >69% of conserved DNA, as defined by Goris et al. . However, the genome of STM6155 has a different architecture compared with the genomes of STM3625 and CCGE501T, with STM6155 lacking a megaplasmid (P1) and containing a different sized pSym and small plasmid. Although STM6155 has a larger pSym, there is a notable symbiotic nod gene conservation between the three R. mesoamericanum strains, which is also shared with Rhizobium grahamii CCGE502T . However, the genomes of the R. mesoamericanum strains contain two nodA alleles whereas R. grahamii CCGE502T genome has only one. Within the STM6155 genome, we have identified a chr chromate efflux gene cluster of six genes arranged into two putative operons and we postulate that this cluster is important for the survival of STM6155 in ultramafic soils containing high concentrations of chromate. The availability of sequenced genomes of R. mesoamericanum should provide further insights into rhizobial biogeographic distribution and should enable free-living and symbiotic attributes to be compared with those Mimosa symbioses induced by beta-rhizobia.
Half strength lupin agar
Average nucleotide identity
Genomic encyclopedia for bacteria and Archaea-root nodule bacteria
Integrated microbial genomes
Tryptone-yeast extract agar
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We thank Gordon Thompson (Murdoch University) for the preparation of SEM and TEM photos.
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 gratefully acknowledge the funding received from the French National Agency of Research (Project BETASYM ANR-09-JCJ-0046), Curtin University Sustainability Policy Institute, and the funding received from Murdoch University Small Research Grants Scheme in 2016.
LM supplied the strain, AK and LM the background information for this project and AK, JA, LM, TR and WR drafted the manuscript. TR provided the DNA to the JGI and performed all imaging, MB and NB provided financial support and ALL, MG, DM, MH, TBKR, NV, TW, VM, NI, RS and NK were involved in sequencing the genome and/or editing the final paper. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
Associated MIGS record for STM6155. Table S2. Nodulation and N2 fixation properties of Rhizobium mesoamericanum STM6155 on selected legume hosts. (DOCX 50 kb)