Examining phylogenetic relationships of Erwinia and Pantoea species using whole genome sequence data

Insights from a Genome-Wide Study of Pantoea agglomerans UADEC20: A Promising Strain for Phosphate Solubilization and Exopolysaccharides Production

The genome sequence of Pantoea agglomerans UADEC20 is presented, which is a strain isolated from agricultural fields in northeast Mexico. The genome was assembled into 13 scaffolds, constituting a total chromosome size of 4.2 Mbp, with two of the scaffolds representing closed plasmids. The strain exhibits activity in phosphate solubilization and exopolysaccharide (EPS) production and secretion; therefore, we explored its biotechnological potential via its genome sequencing and annotation. Genomic analyses showed that a total of 57 and 58 coding sequences (CDSs) related to phosphate solubilization and EPS production were identified within its genome, in addition to a reduced number of CDSs related to drug resistance and phages. The comprehensive set of genes supporting phosphate solubilization, EPS synthesis, and secretion, along with its low virulence and antibiotic resistance levels, justify further research for its potential biotechnological application and possible use as a plant growth-promoting agent in the field. These findings suggest a unique genetic background in the P. agglomerans UADEC20 strain.

Paramixta manurensis gen. nov., sp. nov., a novel member of the family Erwiniaceae producing indole-3-acetic acid isolated from mushroom compost

There are numerous species in the Erwiniaceae family that are important for agricultural and clinical purposes. Here we described the Erwiniaceae bacterium PD-1 isolated from mushroom (Pleurotus eryngii) compost. Comparative genomic and phylogenetic analyses showed that the strain PD-1 was assigned to a new genus and species, Paramixta manurensis gen. nov., sp. nov. in the family Erwiniaceae. From the average amino acid index, we identified the five AroBEKAC proteins in the shikimate pathway as a minimal set of molecular markers to reconstruct the phylogenetic tree of the Erwiniaceae species. The strain PD-1 containing annotated genes for ubiquinone and menaquinone produced a higher level of ubiquinone (Q8) than demethylmenaquinone (DMK8) and menaquinone (MK8) in anaerobic condition compared to aerobic condition, as similarly did the reference strains from the genera Mixta and Erwinia. Results from fatty acid methyl ester and numerical analyses of strain PD-1 showed a similarity to species of the genera Mixta and Winslowiella. This study revealed that the strain's ability to utilize polyols, such as glycerol, erythritol, and D-arabitol, distinguished the strain PD-1 from the nearest relative and other type strains. The analyzed genetic markers and biochemical properties of the strain PD-1 suggest its potential role in the process of mushroom compost through the degradation of carbohydrates and polysaccharides derived from fungi and plants. Additionally, it can produce a high concentration of indole-3-acetic acid as a plant growth-promoting agent.

Microcystis pangenome reveals cryptic diversity within and across morphospecies

Microcystis, a common harmful algal bloom (HAB) taxon, threatens water supplies and human health, yet species delimitation is contentious in this taxon, leading to challenges in research and management of this threat. Historical and common morphology-based classifications recognize multiple morphospecies, most with variable and diverse ecologies, while DNA sequence-based classifications indicate a single species with multiple ecotypes. To better delimit Microcystis species, we conducted a pangenome analysis of 122 genomes. Core- and non-core gene phylogenetic analyses placed 113 genomes into 23 monophyletic clusters containing at least two genomes. Overall, genome-related indices revealed that Microcystis contains at least 16 putative genospecies. Fifteen genospecies included at least one Microcystis aeruginosa morphospecies, and 10 genospecies included two or more morphospecies. This classification system will enable consistent taxonomic identification of Microcystis and thereby aid in resolving some of the complexities and controversies that have long characterized eco-evolutionary research and management of this important HAB taxon.

Tardigrade Community Microbiomes in North American Orchards Include Putative Endosymbionts and Plant Pathogens

The microbiome of tardigrades, a phylum of microscopic animals best known for their ability to survive extreme conditions, is poorly studied worldwide and completely unknown in North America. An improved understanding of tardigrade-associated bacteria is particularly important because tardigrades have been shown to act as vectors of the plant pathogen Xanthomonas campestris in the laboratory. However, the potential role of tardigrades as reservoirs and vectors of phytopathogens has not been investigated further. This study analyzed the microbiota of tardigrades from six apple orchards in central Iowa, United States, and is the first analysis of the microbiota of North American tardigrades. It is also the first ever study of the tardigrade microbiome in an agricultural setting. We utilized 16S rRNA gene amplicon sequencing to characterize the tardigrade community microbiome across four contrasts: location, substrate type (moss or lichen), collection year, and tardigrades vs. their substrate. Alpha diversity of the tardigrade community microbiome differed significantly by location and year of collection but not by substrate type. Our work also corroborated earlier findings, demonstrating that tardigrades harbor a distinct microbiota from their environment. We also identified tardigrade-associated taxa that belong to genera known to contain phytopathogens (Pseudomonas, Ralstonia, and the Pantoea/Erwinia complex). Finally, we observed members of the genera Rickettsia and Wolbachia in the tardigrade microbiome; because these are obligate intracellular genera, we consider these taxa to be putative endosymbionts of tardigrades. These results suggest the presence of putative endosymbionts and phytopathogens in the microbiota of wild tardigrades in North America.

Curtobacterium spp. and Curtobacterium flaccumfaciens: Phylogeny, Genomics-Based Taxonomy, Pathogenicity, and Diagnostics

The genus of Curtobacterium, belonging to the Microbacteriaceae family of the Actinomycetales order, includes economically significant pathogenic bacteria of soybeans and other agricultural crops. Thorough phylogenetic and full-genome analysis using the latest genomic data has demonstrated a complex and contradictory taxonomic picture within the group of organisms classified as the Curtobacterium species. Based on these data, it is possible to delineate about 50 new species and to reclassify a substantial part of the Curtobacterium strains. It is suggested that 53 strains, including most of the Curtobacterium flaccumfaciens pathovars, can compose a monophyletic group classified as C. flaccumfaciens. A genomic analysis using the most recent inventory of bacterial chromosomal and plasmid genomes deposited to GenBank confirmed the possible role of Microbacteriaceae plasmids in pathogenicity and demonstrated the existence of a group of related plasmids carrying virulence factors and possessing a gene distantly related to DNA polymerase found in bacteriophages and archaeal and eukaryotic viruses. A PCR diagnostic assay specific to the genus Curtobacterium was developed and tested. The presented results assist in the understanding of the evolutionary relations within the genus and can lay the foundation for further taxonomic updates.

Phylogenomic analysis of the Erwiniaceae supports reclassification of Kalamiella piersonii to Pantoea piersonii comb. nov. and Erwinia gerundensis to the new genus Duffyella gen. nov. as Duffyella gerundensis comb. nov

To better understand the taxonomy of Erwinia in the context of the Erwiniaceae family, we carried out a taxogenomic analysis of the Erwiniaceae, a family that was created following the taxonomic revision of the family, Enterobacteriaceae. There has been no systematic analysis of this family, including the agriculturally relevant genus, Erwinia. Our analyses focused on 80 strains of Erwinia along with 37 strains representing 7 other genera in the family. We identified 308 common proteins, generated a genome-level phylogeny and carried out Average Nucleotide Identity, Average Amino Acid Identity and Percentage of Conserved Protein analyses. We show that multiple strains of Erwinia cannot be assigned to established species groups and that both Erwinia gerundensis and "Erwinia mediterraneensis" are not members of Erwinia. We propose the creation of the genus Duffyella gen. nov. and the reclassification of Erwinia gerundensis to this genus as the type species, Duffyella gerundensis comb. nov. Furthermore, divergence between other species within Erwinia as measured by Average Amino Acid Identity is greater than the divergence between Erwinia and other genera, supporting the possible subdivision of the genus Erwinia into at least two genera. Our analyses also suggest that there is no basis for the establishment of the genus Kalamiella within the Erwiniaceae or the taxonomic revision of the Pantoea septica lineage. Therefore, we propose reclassifying Kalamiella piersonii as Pantoea piersonii comb. nov. Our study provides new insight into the diversity of the Erwiniaceae and provides a solid foundation for advancing taxonomic revision of this broadly relevant family.

Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant-Bacteria Interactions

Plant growth-promoting bacteria can improve host plant traits including nutrient uptake and metabolism and tolerance to biotic and abiotic stresses. Understanding the molecular basis of plant–bacteria interactions using dual RNA-seq analyses provides key knowledge of both host and bacteria simultaneously, leading to future enhancements of beneficial interactions. In this study, dual RNA-seq analyses were performed to provide insights into the early-stage interactions between barley seedlings and three novel bacterial strains (two Paenibacillus sp. strains and one Erwinia gerundensis strain) isolated from the perennial ryegrass seed microbiome. Differentially expressed bacterial and barley genes/transcripts involved in plant–bacteria interactions were identified, with varying species- and strain-specific responses. Overall, transcriptome profiles suggested that all three strains improved stress response, signal transduction, and nutrient uptake and metabolism of barley seedlings. Results also suggested potential improvements in seedling root growth via repressing ethylene biosynthesis in roots. Bacterial secondary metabolite gene clusters producing compounds that are potentially associated with interactions with the barley endophytic microbiome and associated with stress tolerance of plants under nutrient limiting conditions were also identified. The results of this study provided the molecular basis of plant growth-promoting activities of three novel bacterial strains in barley, laid a solid foundation for the future development of these three bacterial strains as biofertilisers, and identified key differences between bacterial strains of the same species in their responses to plants.

Jekyll or Hyde? The genome (and more) of Nesidiocoris tenuis, a zoophytophagous predatory bug that is both a biological control agent and a pest

Nesidiocoris tenuis (Reuter) is an efficient predatory biological control agent used throughout the Mediterranean Basin in tomato crops but regarded as a pest in northern European countries. From the family Miridae, it is an economically important insect yet very little is known in terms of genetic information and no genomic or transcriptomic studies have been published. Here, we use a linked-read sequencing strategy on a single female N. tenuis. From this, we assembled the 355 Mbp genome and delivered an ab initio, homology-based and evidence-based annotation. Along the way, the bacterial "contamination" was removed from the assembly. In addition, bacterial lateral gene transfer (LGT) candidates were detected in the N. tenuis genome. The complete gene set is composed of 24 688 genes; the associated proteins were compared to other hemipterans (Cimex lectularis, Halyomorpha halys and Acyrthosiphon pisum). We visualized the genome using various cytogenetic techniques, such as karyotyping, CGH and GISH, indicating a karyotype of 2n = 32. Additional analyses include the localization of 18S rDNA and unique satellite probes as well as pooled sequencing to assess nucleotide diversity and neutrality of the commercial population. This is one of the first mirid genomes to be released and the first of a mirid biological control agent.

A Re-evaluation of the Taxonomy and Classification of the Type III Secretion System in a Pathogenic Bacterium Causing Soft Rot Disease of Pleurotus eryngii

Pantoea beijingensis, a gram-negative pathogenic bacterium, causes soft rot disease in the fungus Pleurotus eryngii in China. However, the taxonomic classification of this pathogen is controversial due to close relationships between bacteria of the genera Pantoea and Erwinia. This study aimed to resolve the identity of P. beijingensis using phylogenomic and systematic analyses of Pantoea and Erwinia by whole-genome sequencing. Single-copy orthologs identified from the Erwinia/Pantoea core genomes were used to delineate Erwinia/Pantoea phylogeny. P. beijingensis LMG27579^T clustered within a single Erwinia clade. A whole-genome-based phylogenetic tree and average nucleotide and amino-acid identity values indicate that P. beijingensis LMG27579^T should be renamed Erwinia beijingensis. The hrp/hrc genes encoding type III secretion system (T3SS) proteins in Erwinia and Pantoea were divided into five groups according to gene contents and organization. Neighbor-joining-inferred phylogenetic trees based on concatenated HrcU, HrcN, and HrcR in the main hrp/hrc cluster showed that E. beijingensis T3SS proteins are closely related to those in Ewingella americana, implying that E. beijingensis and E. americana have a recent common hrp/hrc gene ancestor. Furthermore, T3SS proteins of Erwinia and Pantoea were clustered in different clades separated by other bacterial T3SS proteins. Thus, T3SS genes in Pantoea and Erwinia strains might have been acquired by horizontal gene transfer. Overall, our findings clarify the taxonomy of the bacterium causing soft rot in P. eryngii, as well as the genetic structure and classification of the hrp/hrc T3SS virulence factor. We propose that T3SS acquisition is important for E. beijingensis emergence and pathogenesis.

Metabolites Secreted by a Plant-Growth-Promoting Pantoea agglomerans Strain Improved Rooting of Pyrus communis L. cv Dar Gazi Cuttings

Strains belonging to Pantoea agglomerans species are known for their ability to produce metabolites that can act in synergy with auxins to induce the adventitious root (AR) formation. The latter is critically important in the agamic propagation of several woody species, including pear (Pyrus communis L.), playing a considerable role in the commercial nursery farms including those using micropropagation techniques. When grown on a medium amended with tryptophan, the plant-growth-promoting (PGP) strain P. agglomerans C1 produces a cocktail of auxin and auxin-like molecules that can be utilized as biostimulants to improve the rooting of vegetable (Solanum lycopersicum L.) and woody crop species (Prunus rootstock GF/677 and hazelnut). In this study, we evaluated the morphological and molecular responses induced by strain C1 exometabolites in microcuttings of P. communis L. cv Dar Gazi and the potential benefits arising from their application. Results showed that exometabolites by P. agglomerans C1 induced a direct and earlier emergence of roots from stem tissues and determined modifications of root morphological parameters and root architecture compared to plants treated with the synthetic hormone indole-3-butyric acid (IBA). Transcription analysis revealed differences in the temporal expression pattern of ARF17 gene when IBA and C1 exometabolites were used alone, while together they also determined changes in the expression pattern of other key auxin-regulated plant genes. These results suggest that the phenotypic and molecular changes triggered by P. agglomerans C1 are dependent on different stimulatory and inhibitory effects that auxin-like molecules and other metabolites secreted by this strain have on the gene regulatory network of the plant. This evidence supports the hypothesis that the strategies used to harness the metabolic potential of PGP bacteria are key factors in obtaining novel biostimulants for sustainable agriculture. Our results demonstrate that metabolites secreted by strain C1 can be successfully used to increase the efficiency of micropropagation of pear through tissue culture techniques.

Genetic diversity of Pantoea stewartii subspecies stewartii causing jackfruit-bronzing disease in Malaysia

Jackfruit-bronzing is caused by bacteria Pantoea stewartii subspecies stewartii (P. stewartii subsp. stewartii), showing symptoms of yellowish-orange to reddish discolouration and rusty specks on pulps and rags of jackfruit. Twenty-eight pure bacterial strains were collected from four different jackfruit outbreak collection areas in Peninsular Malaysia (Jenderam, Maran, Muadzam Shah and Ipoh). Positive P. stewartii subsp. stewartii verification obtained in the study was based on the phenotypic, hypersensitivity, pathogenicity and molecular tests. Multilocus sequence analysis (MLSA) was performed using four housekeeping genes (gyrB, rpoB, atpD and infB) on all 28 bacterial strains. Single gyrB, rpoB, atpD and infB phylogenetic trees analyses revealed the bootstrap value of 99-100% between our bacterial strains with P. stewartii subsp. stewartii reference strains and P. stewartii subsp. indologenes reference strains. On the other hand, phylogenetic tree of the concatenated sequences of the four housekeeping genes revealed that our 28 bacterial strains were more closely related to P. stewartii subsp. stewartii (99% similarities) compared to its close relative P. stewartii subsp. indologenes, although sequence similarity between these two subspecies were up to 100%. All the strains collected from the four collection areas clustered together, pointing to no variation among the bacterial strains. This study improves our understanding and provided new insight on the genetic diversity of P. stewartii subsp. stewartii associated with jackfruit-bronzing in Malaysia.

Species Diversity of Dickeya and Pectobacterium Causing Potato Blackleg Disease in Pakistan

Potato blackleg is caused by a diverse species of pectinolytic bacteria. In Pakistan, approximately 90% of the pathogens involved belong to Pectobacterium atrosepticum. Survey (2014 to 2017), sampling, and isolation from different potato growing areas of Punjab, Pakistan depicted an overall disease incidence of approximately 15%. Thirty-six pectinolytic strains confirmed through biochemical and pathogenicity testing were characterized via gapA gene to identify them at the species level. To further validate the identification, one strain from each species SS26 (P. atrosepticum), SS28 (Pectobacterium polaris), SS70 (Dickeya dianthicola), SS90 (Pectobacterium parmentieri), SS95 (Pectobacterium punjabense), and SS96 (Pectobacterium versatile) were selected for draft genome sequencing and multilocus sequence analysis of 13 housekeeping genes (fusA, rpoD, acnA, purA, gyrB, recA, mdh, mtlD, groEL, secY, glyA, gapA, and rplB). Phylogenetic analysis revealed considerable genetic diversity in the genus Pectobacterium. In silico DNA-DNA hybridization and average nucleotide identity values of the strains selected for genome sequencing were determined with other reference Pectobacterium and Dickeya strains. Moreover, all six representative strains were also phenotypically characterized on the basis of metabolism of different carbon sources. Overall, on the basis of genotypic and phenotypic characteristics, these 36 isolates were grouped into six species: P. atrosepticum, P. versatile, P. parmentieri, P. polaris, P. punjabense, and D. dianthicola.

Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status

Background

Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed.

Methods

We compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Using the available whole genome sequences of BCC, we inferred a species tree based on estimated single-copy orthologous genes and demarcated species of BCC using dDDH/ANI clustering.

Results

We showed that 16S rRNA, recA, hisA and MLSA have limited resolutions in the taxonomic study of closely related bacteria such as BCC. Our estimated species tree and dDDH/ANI clustering clearly separated 116 BCC strains into 36 clusters. With the appropriate reclassification of misidentified strains, these clusters corresponded to 22 known species as well as 14 putative novel species.

Conclusions

This is the first large-scale and systematic study of the taxonomic status of the BCC and could contribute to further insights into BCC taxonomy. Our study suggested that conjunctive use of core phylogeny based on single-copy orthologous genes, as well as pangenome-based dDDH/ANI clustering would provide a preferable framework for demarcating closely related species.

Reviewer

This article was reviewed by Dr. Xianwen Ren.

Genome Sequencing of Pantoea agglomerans C1 Provides Insights into Molecular and Genetic Mechanisms of Plant Growth-Promotion and Tolerance to Heavy Metals

Distinctive strains of Pantoea are used as soil inoculants for their ability to promote plant growth. Pantoea agglomerans strain C1, previously isolated from the phyllosphere of lettuce, can produce indole-3-acetic acid (IAA), solubilize phosphate, and inhibit plant pathogens, such as Erwinia amylovora. In this paper, the complete genome sequence of strain C1 is reported. In addition, experimental evidence is provided on how the strain tolerates arsenate As (V) up to 100 mM, and on how secreted metabolites like IAA and siderophores act as biostimulants in tomato cuttings. The strain has a circular chromosome and two prophages for a total genome of 4,846,925-bp, with a DNA G+C content of 55.2%. Genes related to plant growth promotion and biocontrol activity, such as those associated with IAA and spermidine synthesis, solubilization of inorganic phosphate, acquisition of ferrous iron, and production of volatile organic compounds, siderophores and GABA, were found in the genome of strain C1. Genome analysis also provided better understanding of the mechanisms underlying strain resistance to multiple toxic heavy metals and transmission of these genes by horizontal gene transfer. Findings suggested that strain C1 exhibits high biotechnological potential as plant growth-promoting bacterium in heavy metal polluted soils.

Systematic Identification of Pathogenic Streptomyces sp. AMCC400023 That Causes Common Scab and Genomic Analysis of Its Pathogenicity Island

Potato scab, a serious soilborne disease caused by Streptomyces spp., occurs in potato-growing areas worldwide and results in severe economic losses. In this paper, the pathogenicity of Streptomyces strain AMCC400023, isolated from potato scabs in Hebei Province, China, was verified systematically by the radish seedling test, the potato tuber slice assay, the potted back experiment, and the detection of phytotoxin thaxtomin A. Morphological, physiological, and biochemical characteristics were determined, and the 16S ribosomal RNA analyses of Streptomyces sp. AMCC400023 were carried out. To obtain the accurate taxonomic status of the pathogen strain, the whole genome was sequenced, and the phylogenetic tree among 31 Streptomyces genomes was formed. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) were analyzed, and at the same time, the toxicity-related genes between Streptomyces sp. AMCC400023 and Streptomyces scabiei were compared, all based on the whole-genome level. All of the data supported that, instead of a member of S. scabiei, test strain Streptomyces sp. AMCC400023 was a distinct phytopathogen of potato common scab, which had a relatively close relationship with S. scabiei while separating clearly from S. scabiei at least in the species level of taxonomic status. The complete pathogenicity island (PAI) composition of Streptomyces sp. AMCC400023 was identified, which contained a toxin region and a colonization region. It was conjectured that the PAI of Streptomyces sp. AMCC400023 might be directly or indirectly acquired from S. scabiei 87-22 by horizontal gene transfer, or at the very least, there was a very close homologous relationship between the two pathogens as indicated by a series of analyses, such as phylogenetic relationships among 31 Streptomyces species, ANI and isDDH analyses, PAI structure mapping, thaxtomin A synthetic gene cluster tree construction, and most important, the collinearity analysis at the genome level.

Characterization and Control of Erwinia spp. and Pluralibacter sp. in Tuna Salad Preparations

HIGHLIGHTS

Metagenome and Culture-Based Methods Reveal Candidate Bacterial Mutualists in the Southern House Mosquito (Diptera: Culicidae)

Mosquitoes are intensely studied as vectors of disease-causing pathogens, but we know relatively less about microbes that naturally reside in mosquitoes. Profiling resident bacteria in mosquitoes can help identify bacterial groups that can be exploited as a strategy of controlling mosquito populations. High-throughput 16S rRNA gene sequencing and traditional culture-based methods were used to identify bacterial assemblages in Culex quinquefasciatus Say (Diptera: Culicidae) in a tissue- and stage-specific design. In parallel, wild host Cx. quinquefasciatus was compared with our domestic strain. 16S rRNA genes survey finds that Cx. quinquefasciatus has taxonomically restricted bacterial communities, with 90% of its bacterial microbiota composed of eight distinctive bacterial groups: Nocardioidaceae (Actinomycetales), Microbacteriaceae (Actinomycetales), Flavobacteriaceae, Rhizobiales, Acetobacteraceae, Rickettsiaceae, Comamondaceae (Burkholderiales), and Enterobacteriaceae. Taking into account both metagenome- and culture-based methods, we suggest three bacterial groups, Acetobacteraceae, Flavobacteriaceae, and Enterobacteriaceae, as candidates for mutualists in Cx. quinquefasciatus. Members of these three bacterial families have been studied as mutualists, or even as symbionts, in other insect groups, so it is quite possible they play similar roles in mosquitoes.

Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella

Investigation of the evolutionary relationships between related bacterial species and genera with a variety of lifestyles have gained popularity in recent years. For analysing the evolution of specific traits, however, a robust phylogeny is essential. In this study we examined the evolutionary relationships among the closely related genera Erwinia, Tatumella and Pantoea, and also attempted to resolve the species relationships within Pantoea. To accomplish this, we used the whole genome sequence data for 35 different strains belonging to these three genera, as well as nine outgroup taxa. Multigene datasets consisting of the 1039 genes shared by these 44 strains were then generated and subjected to maximum likelihood phylogenetic analyses, after which the results were compared to those using conventional multi-locus sequence analysis (MLSA) and ribosomal MLSA (rMLSA) approaches. The robustness of the respective phylogenies was then explored by considering the factors typically responsible for destabilizing phylogenetic trees. We found that the nucleotide datasets employed in the MLSA, rMLSA and 1039-gene datasets contained significant levels of homoplasy, substitution saturation and differential codon usage, all of which likely gave rise to the observed lineage specific rate heterogeneity. The effects of these factors were much less pronounced in the amino acid dataset for the 1039 genes, which allowed reconstruction of a fully supported and resolved phylogeny. The robustness of this amino acid tree was also supported by different subsets of the 1039 genes. In contrast to the smaller datasets (MLSA and rMLSA), the 1039 amino acid tree was also not as sensitive to long-branch attraction. The robust and well-supported evolutionary hypothesis for the three genera, which confidently resolved their various inter- and intrageneric relationships, represents a valuable resource for future studies. It will form the basis for studies aiming to understand the forces driving the divergence and maintenance of lineages, species and biological traits in this important group of bacteria.

Promiscuous Pathogenicity Islands and Phylogeny of Pathogenic Streptomyces spp

Approximately 10 Streptomyces species cause disease on underground plant structures. The most economically important of these is potato scab, and the most studied of these pathogens is Streptomyces scabiei (syn. S. scabies). The main pathogenicity determinant of scab-causing Streptomyces species is a nitrated diketopiperazine, known as thaxtomin A (ThxA). In the pathogenic species Streptomyces turgidiscabies, ThxA biosynthetic genes reside on a mobile pathogenicity island (PAI). However, the mobilization of PAIs in other Streptomyces species remains uncharacterized. Here, we investigated the mobilization of the PAI of S. scabiei 87-22. Based on whole genome sequences, we inferred the evolutionary relationships of pathogenic Streptomyces species and discovered that Streptomyces sp. strain 96-12, a novel pathogenic species isolated from potatoes in Egypt, was phylogenetically grouped with nonpathogenic species rather than with known pathogenic species. We also found that Streptomyces sp. strain 96-12 contains a PAI that is almost identical to the PAI in S. scabiei 87-22, despite significant differences in their genome sequences. This suggested direct or indirect in vivo mobilization of the PAI between S. scabiei and nonpathogenic Streptomyces species. To test whether the S. scabiei 87-22 PAI could, indeed, be mobilized, S. scabiei 87-22 deletion mutants containing antibiotic resistance markers in the PAI were mated with Streptomyces diastatochromogenes, a nonpathogenic species. The PAI of S. scabiei was site-specifically inserted into the aviX1 gene of S. diastatochromogenes and conferred pathogenicity in radish seedling assays. Our results demonstrated that S. scabiei, the earliest described Streptomyces pathogen, could be the source of a PAI responsible for the emergence of novel pathogenic species.

Draft genome sequences of Pantoea agglomerans and Pantoea vagans isolates associated with termites

The genus Pantoea incorporates many economically and clinically important species. The plant-associated species, Pantoea agglomerans and Pantoea vagans, are closely related and are often isolated from similar environments. Plasmids conferring certain metabolic capabilities are also shared amongst these two species. The genomes of two isolates obtained from fungus-growing termites in South Africa were sequenced, assembled and annotated. A high number of orthologous genes are conserved within and between these species. The difference in genome size between P. agglomerans MP2 (4,733,829 bp) and P. vagans MP7 (4,598,703 bp) can largely be attributed to the differences in plasmid content. The genome sequences of these isolates may shed light on the common traits that enable P. agglomerans and P. vagans to co-occur in plant- and insect-associated niches.

Phylogenomic analysis of the genus Ralstonia based on 686 single-copy genes

The genus Ralstonia contains species that are devastating plant pathogens, opportunistic human pathogens, and/or important degraders of xenobiotic and recalcitrant compounds. However, significant nomenclature problems exist, especially for the Ralstonia solanacearum species complex which consists of four phylotypes. Phylogenomics of the Ralstonia genus was investigated via a comprehensive analysis of 39 Ralstonia genomes as well as four genomes of Cupriavidus necator (more commonly known by its previous name Ralstonia eutropha). These data revealed 686 single-copy orthologs that could be extracted from the Ralstonia core-genome and used to reconstruct the phylogeny of the genus Ralstonia. The generated tree has strong bootstrap support for almost all branches. We also estimated the in silico DNA-DNA hybridization (isDDH) and the average nucleotide identity (ANI) values between each genome. Our data confirmed that whole genome sequence data provides a powerful tool to resolve the complex taxonomic questions of the genus Ralstonia, e.g. strains of Ralstonia solanacearum phylotype IIA and IIB may represent two subspecies of R. solanacearum, and strains of R. solanacearum phylotype I and III may be classified into two subspecies of Ralstonia pseudosolanacearum. Recently, strains of R. solanacearum phylotype IV were proposed to be reclassified into different subspecies of Ralstonia syzygii; our study, however, showed that phylotype IV strains had high isDDH values (83.8-96.1 %), indicating it may be not appropriate to classify these closely related strains into different subspecies. We also evaluated the performance of six chromosomal housekeeping genes (gdhA, mutS, adk, leuS, rplB and gyrB) used in Ralstonia phylogenetic inference. The multilocus sequence analysis of these six marker genes was able to reliably infer the phylogenetic relationships of the genus Ralstonia.