Reclassification of Burkholderia insecticola as Caballeronia insecticola comb. nov. and reliability of conserved signature indels as molecular synapomorphies

Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera

Genus Pseudomonas is a large assemblage of diverse microorganisms, not sharing a common evolutionary history. To clarify their evolutionary relationships and classification, we have conducted comprehensive phylogenomic and comparative analyses on 388 Pseudomonadaceae genomes. In phylogenomic trees, Pseudomonas species formed 12 main clusters, apart from the "Aeruginosa clade" containing its type species, P. aeruginosa. In parallel, our detailed analyses on protein sequences from Pseudomonadaceae genomes have identified 98 novel conserved signature indels (CSIs), which are uniquely shared by the species from different observed clades/groups. Six CSIs, which are exclusively shared by species from the "Aeruginosa clade," provide reliable demarcation of this clade corresponding to the genus Pseudomonas sensu stricto in molecular terms. The remaining 92 identified CSIs are specific for nine other Pseudomonas species clades and the genera Azomonas and Azotobacter which branch in between them. The identified CSIs provide strong independent evidence of the genetic cohesiveness of these species clades and offer reliable means for their demarcation/circumscription. Based on the robust phylogenetic and molecular evidence presented here supporting the distinctness of the observed Pseudomonas species clades, we are proposing the transfer of species from the following clades into the indicated novel genera: Alcaligenes clade - Aquipseudomonas gen. nov.; Fluvialis clade - Caenipseudomonas gen. nov.; Linyingensis clade - Geopseudomonas gen. nov.; Oleovorans clade - Ectopseudomonas gen. nov.; Resinovorans clade - Metapseudomonas gen. nov.; Straminea clade - Phytopseudomonas gen. nov.; and Thermotolerans clade - Zestomonas gen. nov. In addition, descriptions of the genera Azomonas, Azotobacter, Chryseomonas, Serpens, and Stutzerimonas are emended to include information for the CSIs specific for them. The results presented here should aid in the development of a more reliable classification scheme for Pseudomonas species.

Large effect of phosphate-solubilizing bacteria on the growth and gene expression of Salix spp. at low phosphorus levels

Phosphorus is one of the most important nutrients required for plant growth and development. However, owing to its low availability in the soil, phosphorus is also one of the most difficult elements for plants to acquire. Phosphorus released into the soil from bedrock quickly becomes unavailable to plants, forming poorly soluble complexes. Phosphate-solubilizing bacteria (PSB) can solubilize unavailable phosphorus-containing compounds into forms in which phosphorus is readily available, thus promoting plant growth. In this study, two willow species, Salix dasyclados cv. Loden and Salix schwerinii × Salix viminalis cv. Tora, were inoculated with two selected bacterial strains, Pantoea agglomerans and Paenibacillus spp., to evaluate the plant growth parameters and changes in gene expression in the presence of different concentrations of tricalcium phosphate: 0 mM (NP), 1 mM (LP), and 2 mM (HP). Inoculation with PSB increased root, shoot and leaf biomass, and for the HP treatment, significant changes in growth patterns were observed. However, the growth responses to plant treatments tested depended on the willow species. Analysis of the leaf transcriptomes of the phosphate-solubilizing bacterium-inoculated plants showed a large variation in gene expression between the two willow species. For the Tora willow species, upregulation of genes was observed, particularly for those involved in pathways related to photosynthesis, and this effect was strongly influenced by bacterial phosphate solubilization. The Loden willow species was characterized by a general downregulation of genes involved in pathway activity that included ion transport, transcription regulation and chromosomes. The results obtained in this study provide an improved understanding of the dynamics of Salix growth and gene expression under the influence of PSB, contributing to an increase in yield and phosphorus-use efficiency.

Specialized acquisition behaviors maintain reliable environmental transmission in an insect-microbial mutualism

Understanding how horizontally transmitted mutualisms are maintained is a major focus of symbiosis research.^1,2,3,4 Unlike vertical transmission, hosts that rely on horizontal transmission produce symbiont-free offspring that must find and acquire their beneficial microbes from the environment. This transmission strategy is inherently risky since hosts may not obtain the right symbiont every generation. Despite these potential costs, horizontal transmission underlies stable mutualisms involving a large diversity of both plants and animals.^5,6,7,8,9 One largely unexplored way horizontal transmission is maintained is for hosts to evolve sophisticated mechanisms to consistently find and acquire specific symbionts from the environment. Here, we examine this possibility in the squash bug Anasa tristis, an insect pest that requires bacterial symbionts in the genus Caballeronia¹⁰ for survival and development.¹¹ We conduct a series of behavioral and transmission experiments that track strain-level transmission in vivo among individuals in real-time. We demonstrate that nymphs can accurately find feces from adult bugs in both the presence and absence of those adults. Once nymphs locate the feces, they deploy feeding behavior that results in nearly perfect symbiont acquisition success. We further demonstrate that nymphs can locate and feed on isolated, cultured symbionts in the absence of feces. Finally, we show this acquisition behavior is highly host specific. Taken together, our data describe not only the evolution of a reliable horizontal transmission strategy, but also a potential mechanism that drives patterns of species-specific microbial communities among closely related, sympatric host species.

AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species

Taxon-specific conserved signature indels (CSIs) in genes/proteins provide reliable molecular markers (synapomorphies) for unambiguous demarcation of taxa of different ranks in molecular terms and for genetic, biochemical and diagnostic studies. Because of their predictive abilities, the shared presence of known taxon-specific CSIs in genome sequences has proven useful for taxonomic purposes. However, the lack of a convenient method for identifying the presence of known CSIs in genome sequences has limited their utility for taxonomic and other studies. We describe here a web-based tool/server (AppIndels.com) that identifies the presence of known and validated CSIs in genome sequences and uses this information for predicting taxonomic affiliation. The utility of this server was tested by using a database of 585 validated CSIs, which included 350 CSIs specific for ≈45 Bacillales genera, with the remaining CSIs being specific for members of the orders Neisseriales, Legionellales and Chlorobiales, family Borreliaceae, and some Pseudomonadaceae species/genera. Using this server, genome sequences were analysed for 721 Bacillus strains of unknown taxonomic affiliation. Results obtained showed that 651 of these genomes contained significant numbers of CSIs specific for the following Bacillales genera/families: Alkalicoccus, 'Alkalihalobacillaceae', Alteribacter, Bacillus Cereus clade, Bacillus Subtilis clade, Caldalkalibacillus, Caldibacillus, Cytobacillus, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Mesobacillus, Metabacillus, Neobacillus, Niallia, Peribacillus, Priestia, Pseudalkalibacillus, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sporosarcina, Sutcliffiella, Weizmannia and Caryophanaceae. Validity of the taxon assignment made by the server was examined by reconstructing phylogenomic trees. In these trees, all Bacillus strains for which taxonomic predictions were made correctly branched with the indicated taxa. The unassigned strains likely correspond to taxa for which CSIs are lacking in our database. Results presented here show that the AppIndels server provides a useful new tool for predicting taxonomic affiliation based on shared presence of the taxon-specific CSIs. Some caveats in using this server are discussed.

Phylogenomic Analyses and Molecular Signatures Elucidating the Evolutionary Relationships amongst the Chlorobia and Ignavibacteria Species: Robust Demarcation of Two Family-Level Clades within the Order Chlorobiales and Proposal for the Family Chloroherpetonaceae fam. nov

Evolutionary relationships amongst Chlorobia and Ignavibacteria species/strains were examined using phylogenomic and comparative analyses of genome sequences. In a phylogenomic tree based on 282 conserved proteins, the named Chlorobia species formed a monophyletic clade containing two distinct subclades. One clade, encompassing the genera Chlorobaculum, Chlorobium, Pelodictyon, and Prosthecochloris, corresponds to the family Chlorobiaceae, whereas another clade, harboring Chloroherpeton thalassium, Candidatus Thermochlorobacter aerophilum, Candidatus Thermochlorobacteriaceae bacterium GBChlB, and Chlorobium sp. 445, is now proposed as a new family (Chloroherpetonaceae fam. nov). In parallel, our comparative genomic analyses have identified 47 conserved signature indels (CSIs) in diverse proteins that are exclusively present in members of the class Chlorobia or its two families, providing reliable means for identification. Two known Ignavibacteria species in our phylogenomic tree are found to group within a larger clade containing several Candidatus species and uncultured Chlorobi strains. A CSI in the SecY protein is uniquely shared by the species/strains from this “larger Ignavibacteria clade”. Two additional CSIs, which are commonly shared by Chlorobia species and the “larger Ignavibacteria clade”, support a specific relationship between these two groups. The newly identified molecular markers provide novel tools for genetic and biochemical studies and identification of these organisms.

Phylogenomic and comparative genomic analyses of Leuconostocaceae species: identification of molecular signatures specific for the genera Leuconostoc, Fructobacillus and Oenococcus and proposal for a novel genus Periweissella gen. nov

The genera Convivina, Fructobacillus, Leuconostoc, Oenococcus and Weissella, which formed the family Leuconostocaceae, have recently been merged within the family Lactobacillaceae. Using genome sequences for 47 of the 52 named species from these genera, we report here comprehensive phylogenomic and comparative analyses on protein sequences from these species using multiple approaches. In a phylogenomic tree based on concatenated sequences of 498 core proteins from these five genera, and in a 16S rRNA gene tree, members of the genera Fructobacillus, Leuconostoc and Oenococcus formed distinct strongly supported clades. In contrast, Weissella species grouped into two distinct unrelated clades designated as the ‘Weissella main clade’ and ‘Weissella clade 2’. The presence of these clades is also seen in a matrix of pairwise average amino acid identity based on core protein sequences. In parallel, comparative genomic studies on protein sequences from Leuconostocaceae genomes have identified 46 conserved signature indels (CSIs) in diverse proteins that are unique characteristics of the different observed species clades. Of these identified CSIs, five, five and 13 CSIs are uniquely present in members of the genera Fructobacillus, Leuconostoc and Oenococcus, respectively. We also report here six and five CSIs that are exclusively present in the species from the Weissella main clade and Weissella clade 2, respectively, providing independent evidence supporting their distinctness from each other. The remaining 12 identified CSIs are commonly shared by some or all of the species from the genera Convivina, Fructobacillus and Leuconostoc, clarifying their interrelationships. The identified CSIs provide novel and reliable means for the identification/circumscription of members of the genera Fructobacillus, Leuconostoc and Oenococcus as well as the two Weissella species clades in molecular terms. Based on the strong phylogenetic and molecular evidence presented here, we propose that the genus Weissella be limited to only the species from the Weissella main clade, whereas the species forming Weissella clade 2 should be transferred to a new genus Periweissella gen. nov.

Pangenome inventory of Burkholderia sensu lato, Burkholderia sensu stricto, and the Burkholderia cepacia complex reveals the uniqueness of Burkholderia catarinensis

Here the pangenome analysis of Burkholderia sensu lato (s.l.) was performed for the first time, together with an updated analysis of the pangenome of Burkholderia sensu stricto, and Burkholderia cepacia complex (Bcc) focusing on the Bcc B. catarinensis specific features of its re-sequenced genome. The pangenome of Burkholderia s.l., Burkholderia s.s., and of the Bcc are open, composed of more than 96% of accessory genes, and more than 62% of unknown genes. Functional annotations showed that secondary metabolism genes belong to the variable portion of genomes, which might explain their production of several compounds with varied bioactivities. Taken together, this work shows the great variability and uniqueness of these genomes and reveals an underexplored unknown potential in poorly characterized genes. Regarding B. catarinensis 89^T, its genome harbors genes related to hydrolases production and plant growth promotion. This draft genome will be valuable for further investigation of its biotechnological potentials.

The Importance of Environmentally Acquired Bacterial Symbionts for the Squash Bug (Anasa tristis), a Significant Agricultural Pest

Most insects maintain associations with microbes that shape their ecology and evolution. Such symbioses have important applied implications when the associated insects are pests or vectors of disease. The squash bug, Anasa tristis (Coreoidea: Coreidae), is a significant pest of human agriculture in its own right and also causes damage to crops due to its capacity to transmit a bacterial plant pathogen. Here, we demonstrate that complete understanding of these insects requires consideration of their association with bacterial symbionts in the family Burkholderiaceae. Isolation and sequencing of bacteria housed in the insects’ midgut crypts indicates that these bacteria are consistent and dominant members of the crypt-associated bacterial communities. These symbionts are closely related to Caballeronia spp. associated with other true bugs in the superfamilies Lygaeoidea and Coreoidea. Fitness assays with representative Burkholderiaceae strains indicate that the association can significantly increase survival and decrease development time, though strains do vary in the benefits that they confer to their hosts, with Caballeronia spp. providing the greatest benefit. Experiments designed to assess transmission mode indicate that, unlike many other beneficial insect symbionts, the bacteria are not acquired from parents before or after hatching but are instead acquired from the environment after molting to a later developmental stage. The bacteria do, however, have the capacity to escape adults to be transmitted to later generations, leaving the possibility for a combination of indirect vertical and horizontal transmission.

Competitive exclusion of phytopathogenic Serratia marcescens from squash bug vectors by the gut endosymbiont Caballeronia

Many insects harbor microbial symbiotic partners that offer protection against pathogens, parasitoids, and other natural enemies. Mounting evidence suggests that these symbiotic microbes can play key roles in determining infection outcomes in insect vectors, making them important players in the quest to develop novel vector control strategies. Using the squash bug Anasa tristis, we investigated how the presence of Caballeronia symbionts affected the persistence and intensity of phytopathogenic Serratia marcescens within the insect vector. We reared insects aposymbiotically and with different Caballeronia isolates, infected them with S. marcescens, then sampled the insects periodically to assess the intensity and persistence of pathogen infection. Squash bugs harboring Caballeronia consistently had much lower-intensity infections and cleared S. marcescens significantly faster than their aposymbiotic counterparts. These patterns held even when we reversed the timing of exposure to symbiont and pathogen. Taken together, these results indicate that Caballeronia symbionts play an essential role in S. marcescens infection outcomes in squash bugs and could be used to alter vector competence to enhance agricultural productivity in the future. Importance Insect-microbe symbioses have repeatedly been shown to profoundly impact an insect's ability to vector pathogens to other hosts. The use of symbiotic microbes to control insect vector populations is of growing interest in agricultural settings. Our study examines how symbiotic microbes affect the dynamics of a plant pathogen infection within the squash bug vector Anasa tristis-a well-documented pest of squash and other cucurbit plants and vector of Serratia marcescens, causative agent of Cucurbit Yellow Vine Disease. We provide evidence that the symbiont Caballeronia prevents successful, long-term establishment of S. marcescens in the squash bug. These findings give us insight into symbiont-pathogen dynamics within the squash bug that could ultimately determine its ability to transmit pathogens and be leveraged to interrupt disease transmission in this system.

Phylogenomics and molecular signatures support division of the order Neisseriales into emended families Neisseriaceae and Chromobacteriaceae and three new families Aquaspirillaceae fam. nov., Chitinibacteraceae fam. nov., and Leeiaceae fam. nov

The order Neisseriales contains 37 genera harboring 122 species with validly published names, which are placed into two families, Neisseriaceae and Chromobacteriaceae. Genome sequences are now available for 35 of the 37 Neisseriales genera for reliably determining their evolutionary relationships and taxonomy. We report here comprehensive phylogenomic and comparative analyses on protein sequences from 110 Neisseriales genomes plus 3 Chitinimonas genomes using multiple approaches. In a phylogenomic tree based on 596 core proteins, Neisseriales species formed 5 strongly supported clades. In addition to the clades for Neisseriaceae and Chromobacteriaceae families, three novel species clades designated as the "Chitinibacteraceae", "Aquaspirillaceae", and "Leeiaceae" were observed. The genus Chitinimonas grouped reliably with members of the "Chitinibacteraceae" clade. The major clades within the order Neisseriales can also be distinguished based on average amino acid identity analysis. In parallel, our comparative genomic studies have identified 30 conserved signature indels (CSIs) that are specific for members of the order Neisseriales or its five main clades. One of these CSIs is uniquely shared by all Neisseriales, whereas 8, 4, 9, 3 and 5 CSIs are distinctive characteristics of the Neisseriaceae, Chromobacteriaceae, "Chitinibacteraceae", "Aquaspirillaceae" and "Leeiaceae" clades, respectively. Based on the strong phylogenetic and molecular evidence presented here, we are proposing that the three newly identified clades should be recognized as novel families (Chitinibacteraceae fam. nov., Aquaspirillaceae fam. nov. and Leeiaceae fam. nov.) within the order Neisseriales. In addition, we are also emending descriptions of the families Neisseriaceae and Chromobacteriaceae regarding their constituent genera and other distinguishing characteristics.

Phylogenomic and comparative genomic analyses of species of the family Pseudomonadaceae: Proposals for the genera Halopseudomonas gen. nov. and Atopomonas gen. nov., merger of the genus Oblitimonas with the genus Thiopseudomonas, and transfer of some misclassified species of the genus Pseudomonas into other genera

The evolutionary relationships among species of the family Pseudomonadaceae were examined based on 255 available genomes representing >85 % of the species from this family. In a phylogenetic tree based on concatenated sequences of 118 core proteins, most species of the genus Pseudomonas grouped within one large cluster which also included members of the genera Azotobacter and Azomonas. Within this large cluster 18-30 clades/subclades of species of the genus Pseudomonas consisting of between 1 and 36 species, were observed. However, a number of species of the genus Pseudomonas branched outside of this main cluster and were interspersed among other genera of the family Pseudomonadaceae. This included a strongly supported clade (Pertucinogena clade) consisting of 19 mainly halotolerant species. The distinctness of this clade from all other members of the family Pseudomonadaceae is strongly supported by 24 conserved signature indels (CSIs) in diverse proteins that are exclusively found in all members of this clade. Nine uncharacterized members of the genus Pseudomonas also shared these CSIs and they branched within the Pertucinogena clade, indicating their affiliation to this clade. On the basis of the strong evidence supporting the distinctness of the Pertucinogena clade, we are proposing transfer of species from this clade into a novel genus Halopseudomonas gen. nov. Pseudomonas caeni also branches outside of the main cluster and groups reliably with Oblitimonas alkaliphila and Thiopseudomonas denitrificans. Six identified CSIs are uniquely shared by these three species and we are proposing their integration into the emended genus Thiopseudomonas, which has priority over the name Oblitimonas. We are also proposing transfer of the deep-branching Pseudomonas hussainii, for which 22 exclusive CSIs have been identified, into the genus Atopomonas gen. nov. Lastly, we present strong evidence that the species Pseudomonas cissicola and Pseudomonas geniculata are misclassified into the genus Pseudomonas and that they are specifically related to the genera Xanthomonas and Stenotrophomonas, respectively. In addition, we are also reclassifying 'Pseudomonas acidophila' as Paraburkholderia acidicola sp. nov. (Type strain: G-6302=ATCC 31363=BCRC 13035).

Phylogenomic analysis supports the reclassification of Burkholderia novacaledonica as Caballeronia novacaledonica comb. nov

Burkholderia novacaledonica is a Betaproteobacterial species isolated from ultramafic soils in New Caledonia. The characterization and classification of this species into the Burkholderia genus was done simultaneously with the proposal of the new genus Caballeronia, initially composed of closely related Burkholderia glathei-like species. Thereafter, some reports based on the use of phylogenetic marker genes suggested that B. novacaledonica forms part of Caballeronia genus. Lacking a formal validation, and with the availability of its genome sequence, a genome-based phylogeny of B. novacaledonica was obtained to unravel its taxonomic position in Burkholderia sensu lato. A partial gyrB gene phylogeny, extended multilocus sequence typing on homologous protein sequences, and genomic distance-based phylogeny, all support the placement of this species in the Caballeronia genus. Therefore, the reclassification of B. novacaledonica to Caballeronia novacaledonica comb. nov. is proposed.

Genome-Wide Metabolic Reconstruction of the Synthesis of Polyhydroxyalkanoates from Sugars and Fatty Acids by Burkholderia Sensu Lato Species

Burkholderia sensu lato (s.l.) species have a versatile metabolism. The aims of this review are the genomic reconstruction of the metabolic pathways involved in the synthesis of polyhydroxyalkanoates (PHAs) by Burkholderia s.l. genera, and the characterization of the PHA synthases and the pha genes organization. The reports of the PHA synthesis from different substrates by Burkholderia s.l. strains were reviewed. Genome-guided metabolic reconstruction involving the conversion of sugars and fatty acids into PHAs by 37 Burkholderia s.l. species was performed. Sugars are metabolized via the Entner-Doudoroff (ED), pentose-phosphate (PP), and lower Embden-Meyerhoff-Parnas (EMP) pathways, which produce reducing power through NAD(P)H synthesis and PHA precursors. Fatty acid substrates are metabolized via β-oxidation and de novo synthesis of fatty acids into PHAs. The analysis of 194 Burkholderia s.l. genomes revealed that all strains have the phaC, phaA, and phaB genes for PHA synthesis, wherein the phaC gene is generally present in ≥2 copies. PHA synthases were classified into four phylogenetic groups belonging to class I II and III PHA synthases and one outlier group. The reconstruction of PHAs synthesis revealed a high level of gene redundancy probably reflecting complex regulatory layers that provide fine tuning according to diverse substrates and physiological conditions.

A robust phylogenetic framework for members of the order Legionellales and its main genera (Legionella, Aquicella, Coxiella and Rickettsiella) based on phylogenomic analyses and identification of molecular markers demarcating different clades

The order Legionellales contains several clinically important microorganisms. Although members of this order are well-studied for their pathogenesis, there is a paucity of reliable characteristics distinguishing members of this order and its constituent genera. Genome sequences are now available for 73 Legionellales species encompassing ≈90% of known members from different genera. With the aim of understanding evolutionary relationships and identifying reliable molecular characteristics that are specific for this order and its constituent genera, detailed phylogenetic and comparative analyses were conducted on the protein sequences from these genomes. A phylogenomic tree was constructed based on 393 single copy proteins that are commonly shared by the members of this order to delineate the evolutionary relationships among its members. In parallel, comparative analyses were performed on protein sequences from Legionellales genomes to identify novel molecular markers consisting of conserved signature indels (CSIs) that are specific for different clades and genera. In the phylogenomic tree and in an amino acid identity matrix based on core proteins, members of the genera Aquicella, Coxiella, Legionella and Rickettsiella formed distinct clades confirming their monophyly. In these studies, Diplorickettsia massiliensis exhibited a close relationship to members of the genus Rickettsiella. The results of our comparative genomic analyses have identified 59 highly specific molecular markers consisting of CSIs in diverse proteins that are uniquely shared by different members of this order. Four of these CSIs are specific for all Legionellales species, except the two deeper-branching "Candidatus Berkiella" species, providing means for identifying members of this order in molecular terms. Twenty four, 7 and 6 CSIs are uniquely shared by members of the genera Legionella, Coxiella and Aquicella, respectively, identifying these groups in molecular terms. The descriptions of these three genera are emended to include information for their novel molecular characteristics. We also describe 12 CSIs that are uniquely shared by D. massiliensis and different members of the genus Rickettsiella. Based on these results, we are proposing an integration of the genus Diplorickettsia with Rickettsiella. Three other CSIs suggest that members of the genera Coxiella and Rickettsiella shared a common ancestor exclusive of other Legionellales. The described molecular markers, due to their exclusivity for the indicated taxa/genera, provide important means for the identification of these clinically important microorganisms and for discovering novel properties unique to them.

Neobacillus endophyticus sp. nov., an endophytic bacterium isolated from Selaginella involvens roots

A Gram-stain-positive, facultatively anaerobic, rod-shaped, endospore-forming, oxidase-positive, and catalase-negative strain designated as BRMEA1^T was isolated from the surface-sterilized Selaginella involvens roots. Growth of strain BRMEA1^T was found to occur at pH 6.0-8.0 (optimum, pH 7.0), 15-50 °C (optimum, 25-30 °C) and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BRMEA1^T formed a lineage within the genus Neobacillus (family Bacillaceae) and showed the highest sequence similarity to Neobacillus drentensis DSM 15600^T (98.3 %) and Neobacillus fumarioli KCTC 13885^T (98.2 %), and less than 98.2 % 16S rRNA gene sequence similarity to the other members of the genus Neobacillus. Whole-genome analysis of strain BRMEA1^T comprised a circular chromosome (5 632 809 bp in size) with 38.5 mol% G+C content. Digital DNA-DNA hybridization analyses revealed that strain BRMEA1^T showed 20.5 and 22.0% genomic DNA relatedness with the closest species, N. drentensis DSM 15600^T and N. fumarioli KCTC 13885^T, respectively. The whole-genome sequence of strain BRMEA1^T showed the presence of 11 specific conserved signature indels for the genus Neobacillus. The major cellular fatty acids (>10 %) of strain BRMEA1^T were found to be iso-C_15 : 0 and anteiso-C_15 : 0, while the major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Polyphasic analysis results revealed that BRMEA1^T represents a novel species of the genus Neobacillus, with the proposed name Neobacillus endophyticus sp. nov. The type strain is BRMEA1^T (=KCTC 43208^T=CCTCC AB 2020071^T).

Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species

To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium. The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer 'Bacillus kyonggiensis' to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569^T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis) or the Cereus clade (containing B. anthracis and B. cereus). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.

The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia sp. Msb3 Is a Potent Growth Promotor in Tomato

The genus Paraburkholderia includes a variety of species with promising features for sustainable biotechnological solutions in agriculture through increasing crop productivity. Here, we present a novel Paraburkholderia isolate, a permanent and predominant member of the Dioscoreae bulbifera (yam family, Dioscoreaceae) phyllosphere, making up to 25% of the microbial community on leaf acumens. The 8.5 Mbp genome of isolate Msb3 encodes an unprecedented combination of features mediating a beneficial plant-associated lifestyle, including biological nitrogen fixation (BNF), plant hormone regulation, detoxification of various xenobiotics, degradation of aromatic compounds and multiple protein secretion systems including both T3SS and T6SS. The isolate exhibits significant growth promotion when applied to agriculturally important plants such as tomato, by increasing the total dry biomass by up to 40%. The open question about the “beneficial” nature of this strain led us to investigate ecological and generic boundaries in Burkholderia sensu lato. In a refined phylogeny including 279 Burkholderia sensu lato isolates strain Msb3 clusters within Clade I Paraburkholderia, which also includes few opportunistic strains that can potentially act as pathogens, as revealed by our ecological meta-data analysis. In fact, we demonstrate that all genera originating from the “plant beneficial and environmental” (PBE) Burkholderia species cluster include opportunists. This indicates that further functional examinations are needed before safe application of these strains in sustainable agricultural settings can be assured.