Complete Genome Sequence of \u3ci\u3eBurkholderia phymatum\u3c/i\u3e STM815T , a Broad Host Range and Efficient Nitrogen-Fixing Symbiont of \u3ci\u3eMimosa\u3c/i\u3e Species

Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815T , was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp)

Characterization of symbiotic specificities between beta-rhizobia and Mimosa pudica by microbial ecology and functional genomic studies.

Les béta-rhizobia sont des symbiotes de légumineuses retrouvées principalement associés au genre Mimosa. Les études des symbiotes de Mimosa pudica révèlent différents profils de diversité au sein des alpha (Rhizobium spp) et béta-rhizobia (Burkholderia, Cupriavidus) le long de la ceinture tropicale, les béta-rhizobia étaient toujours majoritaires dans les nodosités de cette plante hôte. Dans ce travail de thèse, nous avons étudié cette spécificité d'association béta-rhizobia/Mimosa pudica, par une approche couplant l'étude des traits symbiotiques bactériens à l'analyse des profils d'expression de leurs génomes dans les premières étapes de la symbiose, et en comparaison avec les alpha-rhizobia. Nous avons analysé les traits symbiotiques (compétitivité pour la nodulation, efficience symbiotique) au niveau intra et interspécifique de 4 espèces de béta-rhizobia et 4 d'alpha-rhizobia. Si l'efficience symbiotique est similaire parmi toutes les souches testées, différents niveaux de compétitivité ont été trouvés selon l'espèce, B. phymatum et B. tuberum étant les plus compétitives. Les tests effectués sur différentes variétés de M. pudica montrent un effet variétal sur la compétitivité de C. taiwanensis. Les traits symbiotiques mesurés expliquent en partie les profils de diversité des symbiotes de M. pudica dans les zones d'origine (Amérique du Sud) ou en zone introduite (Taiwan). Les transcriptomes de trois bactéries ayant des traits symbiotiques différents (B. phymatum STM815, C. taiwanensis LMG19424 et R. mesoamericanum STM3625) ont été comparés (par RNAseq), pour relier les différentes réponses induites par les exsudats racinaires aux traits symbiotiques de chaque rhizobium. Chaque bactérie développe une stratégie spécifique liée à ses traits symbiotiques et à l'origine de la symbiose dans son groupe bactérien.Beta-rhizobia are legume symbionts mainly found associated to the Mimosa genus. Diversity studies of Mimosa pudica symbionts in native and introduced areas reveal different diversity patterns of alpha (Rhizobium spp) and beta-rhizobia (Burkholderia, Cupriavidus), with beta-rhizobia being always the main symbionts in the nodules of this legumes species. In this thesis we have studied the symbiotic specificity between beta-rhizobia and M. pudica (and the comparison with alpha-rhizobia) by a dual approach combining the study of bacterial symbiotic traits and the analysis of their transcriptomes in the first steps of symbiosis. We analysed symbiotic traits (nodulation competitiveness, symbiotic efficiency) at intra and interspecific levels on four species of beta-rhizobia and four of alpha-rhizobia. If symbiotic efficiency is similar among all strains, different levels of competitiveness were measured with a strong strain effect largely explained by the species affiliation, B. phymatum and B. tuberum being the most competitive species. Tests on different M. pudica varieties showed an impact on the competitiveness of C. taiwanensis. Symbiotic traits explained in part the symbiont patterns observed in diversity studies in French Guiana (M. pudica native area) and Taiwan (introduced). Root-exudates induced transcriptomes of three bacteria (two beta--rhizobia: B. phymatum STM815, C. taiwanensis LMG19424 and one alpha, R. mesoamericanum STM3625) with contrasted symbiotic traits were compared (by RNAseq). Each bacterium develops a specific strategy linked to its symbiotic traits and the origin of symbiosis in its bacterial group

Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history

Abstract Background Rhizobial symbionts belong to the classes Alphaproteobacteria and Betaproteobacteria (called “alpha” and “beta”-rhizobia). Most knowledge on the genetic basis of symbiosis is based on model strains belonging to alpha-rhizobia. Mimosa pudica is a legume that offers an excellent opportunity to study the adaptation toward symbiotic nitrogen fixation in beta-rhizobia compared to alpha-rhizobia. In a previous study (Melkonian et al., Environ Microbiol 16:2099–111, 2014) we described the symbiotic competitiveness of M. pudica symbionts belonging to Burkholderia, Cupriavidus and Rhizobium species. Results In this article we present a comparative analysis of the transcriptomes (by RNAseq) of B. phymatum STM815 (BP), C. taiwanensis LMG19424 (CT) and R. mesoamericanum STM3625 (RM) in conditions mimicking the early steps of symbiosis (i.e. perception of root exudates). BP exhibited the strongest transcriptome shift both quantitatively and qualitatively, which mirrors its high competitiveness in the early steps of symbiosis and its ancient evolutionary history as a symbiont, while CT had a minimal response which correlates with its status as a younger symbiont (probably via acquisition of symbiotic genes from a Burkholderia ancestor) and RM had a typical response of Alphaproteobacterial rhizospheric bacteria. Interestingly, the upregulation of nodulation genes was the only common response among the three strains; the exception was an up-regulated gene encoding a putative fatty acid hydroxylase, which appears to be a novel symbiotic gene specific to Mimosa symbionts. Conclusion The transcriptional response to root exudates was correlated to each strain nodulation competitiveness, with Burkholderia phymatum appearing as the best specialised symbiont of Mimosa pudica

Caractérisation des protéines codées par l'opéron yoxA-dacC de Bacillus subtilis

Abstract In Bacillus subtilis, the yoxA and dacC genes were proposed to form an operon. The yoxA gene was overexpressed in Escherichia coli and its product fused to a polyhistidine tag was purified. An aldose-1-epimerase or mutarotase activity was measured with the YoxA protein that we propose to rename as GalM by analogy with its counterpart in E. coli. The peptide d-Glu-delta-m-A(2)pm-d-Ala-m-A(2)pm-d-Ala mimicking the B. subtilis and E. coli interpeptide bridge was synthesized and incubated with the purified dacC product, the PBP4a. A clear dd-endopeptidase activity was obtained with this penicillin-binding protein, or PBP. The possible role of this class of PBP, present in almost all bacteria, is discussed.PAI, ARC et EUR-INTAFA

Additional file 1: Figure S1. of Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history

Venn diagram of gene orthologs across the 3 bacteria. Figure S2. Symbiotic plasmids syntenies and differentially regulated genes. Figure S3. Summary of RNAseq results per replicate and condition. Figure S4. Comparison of pVal and Fold Change values on the number of DEG. Figure S5. Genes targeted 5 for qPCR (A) & primers used (B). Figure S6. Comparison of gene expression between RNAseq counts and qPCR. Table S1. Excel tables of all DEG data shared or specific. Figure S8. Myo-inositol catabolism operons in BP, RM and CT. Figure S9. Biolog GN20 API galleries results for BP, CT and RM. Figure S10. Annotation of the putative rhizobitoxine biosynthesis operon in BP. Figure S11. Up-regulated (A) and down-regulated (B) T6SS in B. phymatum (BP). Figure S12. T4SS of B. phymatum STM815. Figure S13. Elution profiles of C. taiwanensis RNA samples. Figure S14. Scatter plots (A) & Volcano plot (B) of RNAseq data. (ZIP 15222 kb

Biodiversity of Mimosa pudica rhizobial symbionts (Cupriavidus taiwanensis, Rhizobium mesoamericanum) in New Caledonia and their adaptation to heavy metal-rich soils

Rhizobia are soil bacteria able to develop a nitrogen-fixing symbiosis with legumes. They are taxonomically spread among the alpha and beta subclasses of the Proteobacteria. Mimosa pudica, a tropical invasive weed, has been found to have an affinity for beta-rhizobia, including species within the Burkholderia and Cupriavidus genera. In this study, we describe the diversity of M. pudica symbionts in the island of New Caledonia, which is characterized by soils with high heavy metal content, especially of Ni. By using a plant-trapping approach on four soils, we isolated 96 strains, the great majority of which belonged to the species Cupriavidus taiwanensis (16S rRNA and recA gene phylogenies). A few Rhizobium strains in the newly described species Rhizobium mesoamericanum were also isolated. The housekeeping and nod gene phylogenies supported the hypothesis of the arrival of the C. taiwanensis and R. mesoamericanum strains together with their host at the time of the introduction of M. pudica in New Caledonia (NC) for its use as a fodder. The C. taiwanensis strains exhibited various tolerances to Ni, Zn and Cr, suggesting their adaptation to the specific environments in NC. Specific metal tolerance marker genes were found in the genomes of these symbionts, and their origin was investigated by phylogenetic analyses. (Résumé d'auteur

Spirochaetes dominate the microbial community associated with the red coral Corallium rubrum on a broad geographic scale

Mass mortality events in populations of the iconic red coral Corallium rubrum have been related to seawater temperature anomalies that may have triggered microbial disease development. However, very little is known about the bacterial community associated with the red coral. We therefore aimed to provide insight into this species' bacterial assemblages using Illumina MiSeq sequencing of 16S rRNA gene amplicons generated from samples collected at five locations distributed across the western Mediterranean Sea. Twelve bacterial species were found to be consistently associated with the red coral, forming a core microbiome that accounted for 94.6% of the overall bacterial community. This core microbiome was particularly dominated by bacteria of the orders Spirochaetales and Oceanospirillales, in particular the ME2 family. Bacteria belonging to these orders have been implicated in nutrient cycling, including nitrogen, carbon and sulfur. While Oceanospirillales are common symbionts of marine invertebrates, our results identify members of the Spirochaetales as other important dominant symbiotic bacterial associates within Anthozoans.publishe

The geographical patterns of symbiont diversity in the invasive legume Mimosa pudica can be explained by the competitiveness of its symbionts and by the host genotype

Variations in the patterns of diversity of symbionts have been described worldwide on Mimosa pudica, a pan-tropical invasive species that interacts with both alpha and beta-rhizobia. In this study, we investigated if symbiont competitiveness can explain these variations and the apparent prevalence of beta- over alpha-rhizobia. We developed an indirect method to measure the proportion of nodulation against a GFP reference strain and tested its reproducibility and efficiency. We estimated the competitiveness of 54 strains belonging to four species of beta-rhizobia and four of alpha-rhizobia, and the influence of the host genotype on their competitiveness. Our results were compared with biogeographical patterns of symbionts and host varieties. We found: (i) a strong strain effect on competitiveness largely explained by the rhizobial species, with Burkholderia phymatum being the most competitive species, followed by B. tuberum, whereas all other species shared similar and reduced levels of competitiveness; (ii) plant genotype can increase the competitiveness of Cupriavidus taiwanensis. The latter data support the likelihood of the strong adaptation of C. taiwanensis with the M. pudica var. unijuga and help explain its prevalence as a symbiont of this variety over Burkholderia species in some environments, most notably in Taiwan