Taxogenomics and Systematics of the Genus Pantoea

Phenazines are involved in the antagonism of a novel subspecies of Pseudomonas chlororaphis strain S1Bt23 against Pythium ultimum

Long-term use of chemical fungicides to control plant diseases caused by fungi and oomycetes has led to pathogen resistance and negative impacts on public health and environment. There is a global search for eco-friendly methods and antagonistic bacteria are emerging as alternatives. We isolated a potent antagonistic bacterial strain (S1Bt23) from woodland soil in Québec, Canada. Taxonomic characterization by 16S rRNA, multi-locus sequence analysis, pairwise whole-genome comparisons, phylogenomics and phenotypic data identified strain S1Bt23 as a novel subspecies within Pseudomonas chlororaphis. In dual culture studies, strain S1Bt23 exhibited potent mycelial growth inhibition (60.2-66.7%) against Pythium ultimum. Furthermore, strain S1Bt23 was able to significantly bioprotect potato tuber slices from the development of necrosis inducible by P. ultimum. Annotations of the whole genome sequence of S1Bt23 revealed the presence of an arsenal of secondary metabolites including the complete phenazine biosynthetic cluster (phzABCDEFG). Thin-layer (TLC) and high-performance liquid (HPLC) chromatographic analyses of S1Bt23 extracts confirmed the production of phenazines, potent antifungal compounds. CRISPR/Cas9-mediated deletion of phzB (S1Bt23ΔphzB) or phzF (S1Bt23ΔphzF) gene abrogated phenazine production based on TLC and HPLC analyses. Also, S1Bt23ΔphzB and S1Bt23ΔphzF mutants lost antagonistic activity and bioprotection ability of potato tubers against P. ultimum. This demonstrated that phenazines are involved in the antagonistic activity of S1Bt23 against P. ultimum. Finally, based on genotypic and phenotypic data, we taxonomically conclude that S1Bt23 represents a novel subspecies for which the name Pseudomonas chlororaphis subsp. phenazini is proposed.

Taxonogenomic analysis of the Xanthomonas translucens complex leads to the descriptions of Xanthomonas cerealis sp. nov. and Xanthomonas graminis sp. nov

The pathovar-based taxonomy of the Xanthomonas translucens group is very confusing due to an overlap of plant host ranges and level of host specificity. Here, whole-genome sequence-based parameters (digital DNA-DNA hybridization and blast-based average nucleotide identity), phylogenomic, biochemical and phenotypical data were used to taxonomically analyse the 11 known pathovars of the X. translucens complex. This polyphasic approach taxonomically assigned the 11 pathovars of X. translucens complex into three distinct species, two of which are new: X. translucens, X. cerealis sp. nov. and X. graminis sp. nov. X. translucens consists of three pathovars: pv. translucens (=pv. hordei), pv. pistaciae strain A ICMP 16316PT and pv. undulosa (=pv. secalis). X. cerealis sp. nov. encompasses the pv. cerealis strain LMG 679PT and pv. pistaciae strain B ICMP 16317PT with genome similarity of 92.7% (dDDH) and 99.0% (ANIb) suggesting taxonomically similar genotypes. The other new species, X. graminis sp. nov., consists of the remaining five designated pathovars (pv. graminis, pv. arrhenatheri, pv. poae, pv. phleipratensis and pv. phlei) with highly variable dDDH and ANIb values ranging from 74.5 to 93.0% and from 96.7 to 99.2%, respectively, an indication of a very divergent taxonomic group. Only strains of pvs. phlei and phleipratensis showed the highest genomic similarities of 93.0% (dDDH) and 99.2% (ANIb), suggesting synonymic pathovars as both infect the same plant hosts. The dDDH and ANI data were corroborated by phylogenomics clustering. The fatty acid contents were similar but the type strain of X. graminis sp. nov. exhibited 20% less C15 : 0 iso and 40% more C17 : 0 iso fatty acids than the other species. Based on phenotypic, biochemical and whole-genome sequence data, we propose two new species, Xanthomonas cerealis sp. nov. and Xanthomonas graminis sp. nov. with type strains LMG 679T (=NCPPB 1944T) and LMG 726T (=NCPPB 2700T), respectively.

In silico analysis of Ffp1, an ancestral Porphyromonas spp. fimbrillin, shows differences with Fim and Mfa

Background. Scant information is available regarding fimbrillins within the genus Porphyromonas, with the notable exception of those belonging to Porphyromonas gingivalis, which have been extensively researched for several years. Besides fim and mfa, a third P. gingivalis adhesin called filament-forming protein 1 (Ffp1) has recently been described and seems to be pivotal for outer membrane vesicle (OMV) production. Objective. We aimed to investigate the distribution and diversity of type V fimbrillin, particularly Ffp1, in the genus Porphyromonas. Methods. A bioinformatics phylogenomic analysis was conducted using all accessible Porphyromonas genomes to generate a domain search for fimbriae, using hidden Markov model profiles. Results. Ffp1 was identified as the sole fimbrillin present in all analysed genomes. After manual verification (i.e. biocuration) of both structural and functional annotations and 3D modelling, this protein was determined to be a type V fimbrillin, with a closer structural resemblance to a Bacteroides ovatus fimbrillin than to FimA or Mfa1 from P. gingivalis. Conclusion. It appears that Ffp1 is an ancestral fimbria, transmitted through vertical inheritance and present across all Porphyromonas species. Additional investigations are necessary to elucidate the biogenesis of Ffp1 fimbriae and their potential role in OMV production and niche adaptation.

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.

Discovery and characterization of a novel pathogen Erwinia pyri sp. nov. associated with pear dieback: taxonomic insights and genomic analysis

In 2022, a novel disease similar to pear fire blight was found in a pear orchard in Zhangye City, Gansu Province, China. The disease mainly damages the branches, leaves, and fruits of the plant. To identify the pathogen, tissue isolation and pathogenicity testing (inoculating the potential pathogen on healthy plant tissues) were conducted. Furthermore, a comprehensive analysis encompassing the pathogen's morphological, physiological, and biochemical characteristics and whole-genome sequencing was conducted. The results showed that among the eight isolates, the symptoms on the detached leaves and fruits inoculated with isolate DE2 were identical to those observed in the field. Verifying Koch's postulates confirmed that DE2 was the pathogenic bacterium that causes the disease. Based on a 16S rRNA phylogenetic tree, isolate DE2 belongs to the genus Erwinia. Biolog and API 20E results also indicated that isolate DE2 is an undescribed species of Erwinia. Isolate DE2 was negative for oxidase. Subsequently, the complete genome sequence of isolate DE2 was determined and compared to the complete genome sequences of 29 other Erwinia species based on digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses. The ANI and dDDH values between strain DE2 and Erwinia species were both below the species thresholds (ANI < 95-96%, dDDH<70%), suggesting that isolate DE2 is a new species of Erwinia. We will temporarily name strain DE2 as Erwinia pyri sp. nov. There were 548 predicted virulence factors in the genome of strain DE2, comprising 534 on the chromosome and 5 in the plasmids. The whole genome sequence of strain DE2 has been submitted to the NCBI database (ASM3075845v1) with accession number GCA_030758455.1. The strain DE2 has been preserved at the China Center for Type Culture Collection (CCTCC) under the deposit number CCTCC AB 2024080. This study represents the initial report of a potentially new bacterial species in the genus Erwinia that causes a novel pear dieback disease. The findings provide a valuable strain resource for the study of the genus Erwinia and establish a robust theoretical foundation for the prevention and control of emerging pear dieback diseases.

Genome-Scale Model of Rhizopus microsporus: Metabolic integration of a fungal holobiont with its bacterial and viral endosymbionts

Rhizopus microsporus often lives in association with bacterial and viral symbionts that alter its biology. This fungal model represents an example of the complex interactions established among diverse organisms in functional holobionts. We constructed a Genome-Scale Model (GSM) of the fungal-bacterial-viral holobiont (iHol). We employed a constraint-based method to calculate the metabolic fluxes to decipher the metabolic interactions of the symbionts with their host. Our computational analyses of iHol simulate the holobiont's growth and the production of the toxin rhizoxin. Analyses of the calculated fluxes between R. microsporus in symbiotic (iHol) versus asymbiotic conditions suggest that changes in the lipid and nucleotide metabolism of the host are necessary for the functionality of the holobiont. Glycerol plays a pivotal role in the fungal-bacterial metabolic interaction, as its production does not compromise fungal growth, and Mycetohabitans bacteria can efficiently consume it. Narnavirus RmNV-20S and RmNV-23S affected the nucleotide metabolism without impacting the fungal-bacterial symbiosis. Our analyses highlighted the metabolic stability of Mycetohabitans throughout its co-evolution with the fungal host. We also predicted changes in reactions of the bacterial metabolism required for the active production of rhizoxin. This iHol is the first GSM of a fungal holobiont.

Insights into the Potential Role of Plasmids in the Versatility of the Genus Pantoea

In the past two decades, 25 different species of the genus Pantoea within the Enterobacteriaceae family, have been isolated from different environmental niches. These species have a wide range of biological roles. Versatility in functions and hosts indicate that this genus has undergone extensive genetic diversification, which can be attributed to the different extra-chromosomal genetic elements or plasmids found across this genus. We have analyzed the functions of these plasmids and categorized them into four major groups for a better understanding of their future applications. The first and second group includes plasmids that contribute to genetic diversification and pathogenicity, respectively. The third group comprises cryptic plasmids of Pantoea. The last group includes plasmids that play a role in the metabolic versatility of the genus Pantoea. We have analyzed the data available up to May 2023 from two databases (viz; NCBI and PLSDB). In our analysis we have found a vast gap in knowledge. Complete gene annotations are available for only a few of the plasmids. This review highlights these challenges as an avenue for future research.

Genomic delineation and description of species and within-species lineages in the genus Pantoea

As the name of the genus Pantoea ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.

Diverse Virulence Attributes of Pantoea alfalfae sp. nov. CQ10 Responsible for Bacterial Leaf Blight in Alfalfa Revealed by Genomic Analysis

Alfalfa is widely grown worldwide for its excellent nutritional value. Pantoea species living in alfalfa seeds can easily spread over great distances with frequent trade. However, the pathogenic properties of this dangerous hitchhiker on alfalfa have not been evaluated. Here, we identified the taxonomic status of Pantoea strain CQ10 isolated from the interior of alfalfa seeds based on the whole genome sequence. The diverse virulence attributes of strain CQ10 during host infection were characterized through pathogenicity assays and functional and genomic analyses. We report that strain CQ10 belongs to a novel species in the genus Pantoea, which was phylogenetically close to Pantoea vagans and Pantoea agglomerans. Strain CQ10 caused bacterial leaf blight of alfalfa after inoculation from the roots. We found that strain CQ10 possesses a large number of pathogenic genes involved in shaping the virulence properties during bacteria-host interactions, including motility, biofilm, type VI secretion system, and nutrient acquisition. Compared with P. vagans and P. agglomerans, the unique virulence factors of strain CQ10 were mainly involved in motility and biofilm, which were confirmed by in vitro experiments. Taken together, our results suggest that strain CQ10 is the first Pantoea species to infect alfalfa, and it possesses diverse virulence attributes among which motility and biofilm may be the best weapons.

Genomic characterization of coexisting anatoxin-producing and non-toxigenic Microcoleus subspecies in benthic mats from the Wolastoq, New Brunswick, Canada

The presence of toxigenic benthic cyanobacteria in riverine ecosystems is an increasing concern around the world. In 2018, the death of three dogs along the Wolastoq (also known as the Saint John River) in New Brunswick, Canada, was attributed to anatoxin exposure after they ingested benthic microbial mats found along the shore. Here, we shotgun sequenced the DNA of 15 non-axenic cyanobacterial isolates derived from four anatoxin-containing benthic mat samples associated with the dog deaths. Anatoxins were produced by some of the isolates, but not all. We retrieved near-complete Microcoleus metagenome-assembled genomes (MAGs) from the isolates that are closely related to anatoxin-producing Microcoleus from the Cardrona River (New Zealand), although the Microcoleus MAGs from the Wolastoq varied in the presence/absence of the anatoxin-a biosynthesis cluster. Sequence similarity at the genomic level suggests that toxigenic and non-toxigenic Microcoleus MAGs from the Wolastoq belong to the same species but are separate subspecies. The toxigenic and nontoxic Wolastoq Microcoleus subspecies coexisted in the mat samples in similar relative abundance. Overall genomic comparisons revealed that toxigenic Microcoleus MAGs are longer and code for more accessory genes than their non-toxigenic relatives, suggesting a differential responsiveness to changing environments, stress conditions and nutrient availability.

Seeds of Stevia rebaudiana Bertoni as a Source of Plant Growth-Promoting Endophytic Bacteria with the Potential to Synthesize Rebaudioside A

In this study, a new strain of Pantoea vagans, SRS89, was isolated from surface-sterilized stevia seeds. The isolate was evaluated using morphological, molecular, and biochemical methods. The bacterium was 1.5 μm long, yellowish in color, and classified as Gram-negative. Whole genome sequencing of our strain revealed the presence of a 4,610,019 bp chromosome, and genome annotation resulted in the detection of 4283 genes encoding 4204 putative coding sequences. Phylogenic analysis classified the genome of our strain close to the MP7 and LMG 24199 strains of P. vagans. Functional analysis showed that the highest number of genes within the analyzed bacterium genome were involved in transcription, amino acid transport and metabolism, and carbohydrate transport and metabolism. We also identified genes for enzymes involved in the biosynthesis of carotenoids and terpenoids. Furthermore, we showed the presence of growth regulators, with the highest amount noted for gibberellic acid A₃, indole-3-acetic acid, and benzoic acid. However, the most promising property of this strain is its ability to synthesize rebaudioside A; the estimated amount quantified using reversed-phase (RP)-HPLC was 4.39 mg/g of the dry weight of the bacteria culture. The isolated endophytic bacterium may be an interesting new approach to the production of this valuable metabolite.

Effects of Isolated LAB on Chemical Composition, Fermentation Quality and Bacterial Community of Stipa grandis Silage

This study aimed to screen and identify lactic acid bacteria (LAB) strains from the Stipa grandis and naturally fermented silage, and assess their effects on the silage quality and bacterial community of Stipa grandis after 60 days of the fermentation process. A total of 38 LAB were isolated, and strains ZX301 and YX34 were identified as Lactiplantibacillus plantarum and Pediococcus pentosaceus using 16S rRNA sequences; they can normally grow at 10−30 °C, with a tolerance of pH and NaCl from 3.5 to 8.0 and 3 to 6.5%, respectively. Subsequently, the two isolated LAB and one commercial additive (Lactiplantibacillus plantarum) were added to Stipa grandis for ensiling for 60 days and recorded as the ZX301, YX34, and P treatments. The addition of LAB was added at 1 × 105 colony-forming unit/g of fresh weight, and the same amount of distilled water was sprayed to serve as a control treatment (CK). Compared to the CK treatment, the ZX301 and YX34 treatments exhibited a positive effect on pH reduction. The water-soluble carbohydrate content was significantly (p < 0.05) increased in ZX301, YX34, and P treatments than in CK treatment. At the genus level, the bacterial community in Stipa grandis silage involves a shift from Pantoea to Lactiplantibacillus. Compared to the CK treatment, the ZX301, YX34, and P treatments significantly (p < 0.05) increase the abundance of Pediococcus and Lactiplantibacillus, respectively. Consequently, the results indicated that the addition of LAB reconstructed microbiota and influenced silage quality. The strain ZX301 could improve the ensiling performance in Stipa grandis silage.

The interplay between the gut microbiota and metabolism during the third trimester of pregnancy

The gut microbiota undergoes dynamic changes during pregnancy. The gut microbial and metabolic networks observed in pregnant women have not been systematically analyzed. The primary purpose of this study was to explore the alterations in the gut microbiota and metabolism during late pregnancy and investigate the associations between the gut microbiota and metabolism. A total of thirty healthy pregnant women were followed from 30 to 32 weeks of gestation to full term. Fecal samples were collected for microbiome analysis and untargeted metabolomic analysis. The characteristics of the gut microbiota were evaluated by 16S ribosomal RNA gene sequencing of the V3-V4 regions. The plasma samples were used for untargeted metabolomic analysis with liquid chromatography-tandem mass spectrometry. The interplay between the gut microbiota and metabolism was analyzed further by bioinformatics approaches. We found that the relative abundances of Sellimonas and Megamonas were higher at full term, whereas that of Proteobacteria was lower. The correlation network of the gut microbiota tended to exhibit weaker connections from 32 weeks of gestation to the antepartum timepoint. Changes in the gut microbiota during late pregnancy were correlated with the absorbance and metabolism of microbiota-associated metabolites, such as fatty acids and free amino acids, thereby generating a unique metabolic system for the growth of the fetus. Decreasing the concentration of specific metabolites in plasma and increasing the levels of palmitic acid and 20-hydroxyarachidonic acid may enhance the transformation of a proinflammatory immune state as pregnancy progresses.

Characterization of Pantoea ananatis from rice planthoppers reveals a clade of rice-associated P. ananatis undergoing genome reduction

Pantoea ananatis is a bacterium that is found in many agronomic crops and agricultural pests. Here, we isolated a P. ananatis strain (Lstr) from the rice planthopper Laodelphax striatellus, a notorious pest that feeds on rice plant sap and transmits rice viruses, in order to examine its genome and biology. P. ananatis Lstr is an insect symbiont that is pathogenic to the host insect and appears to mostly inhabit the gut. Its pathogenicity thus raises the possibility of using the Lstr strain as a biological agent. To this end, we analysed the genome of the Lstr strain and compared it with the genomes of other Pantoea species. Our analysis of these genomes shows that P. ananatis can be divided into two mono-phylogenetic clades (clades one and two). The Lstr strain belongs to clade two and is grouped with P. ananatis strains that were isolated from rice or rice-associated samples. A comparative genomic analysis shows that clade two differs from clade one in many genomic characteristics including genome structures, mobile elements, and categories of coding proteins. The genomes of clade two P. ananatis are significantly smaller, have much fewer coding sequences but more pseudogenes than those of clade one, suggesting that clade two species are at the early stage of genome reduction. On the other hand, P. ananatis has a type VI secretion system that is highly variable but cannot be separated by clades. These results clarify our understanding of P. ananatis' phylogenetic diversity and provide clues to the interactions between P. ananatis, host insect, and plant that may lead to advances in rice protection and pest control.

Succession changes of fermentation parameters, nutrient components and bacterial community of sorghum stalk silage

To better understand the ensiling characteristics of sorghum stalk, the dynamic changes of fermentation parameters, nutrient components and bacterial community of sorghum stalk silage were analyzed by intermittently sampling on day 0, 1, 3, 7, 14, 28, and 56 of ensiling duration. The results showed that high-moisture sorghum stalk was well preserved during ensiling fermentation, with the DM loss of 4.10% and the little difference between the nutrients of sorghum stalk before and after ensiling. The pH value of silage declined to its lowest value of 4.32 by Day 7 of ensiling, and other fermentation parameters kept steady since Day 28 of ensiling. The amplicon sequencing analysis revealed that the alpha diversity parameters of silage bacterial community including Shannon index, observed features, Pielou evenness and Faith PD gradually declined (P < 0.01) with ensiling duration. Principal coordinate analysis (PCoA) revealed that bacterial profiles of raw material would experience a succession becoming a quite different community during ensiling fermentation. Taxonomic classification revealed a total of 10 and 173 bacterial taxa at the phylum and genus level, respectively, as being detected with relative abundances higher than 0.01% and in at least half samples. LEfSe analysis revealed that 26 bacterial taxa were affected by sampling timepoint (P < 0.05 and LDA score > 4). When focusing on the dynamic trend of silage bacterial taxa, lactic acid bacteria successfully dominated in the bacterial community on Day 1 of ensiling, and the bacterial community almost came to a plateau by Day 28 of ensiling, with Lactobacillus and Leuconostoc as the dominant genera. In a word, the succession of fermentation parameters, nutrient components and bacterial community indicate a successful dominance establishment of LAB and a fast advent of fermentation plateau, suggesting that high-moisture sorghum stalk can be ensiled directly, but the pH of mature silage is a little high.

Whole genome sequencing and taxonomic profiling of two Pantoea sp. isolated from environmental samples in Israel

OBJECTIVE

As part of a research aiming at the isolation of bacteria secreting growth inhibiting compounds, cultures of Francisella tularensis were implanted in environmental samples and monitored for inhibition zones on agar. Two antibiotic-like secreting bacteria were isolated, their genomic sequence was deciphered and taxonomic profiling analysis classified them as belonging to the Pantoea genus.

DATA DESCRIPTION

Two bacterial isolates exhibiting growth inhibition zones to F. tularensis (LVS) were analyzed using the Oxford Nanopore Technology (ONT). Preliminary de novo assembly of the reads was performed, followed by taxonomic profiling based on Multi Locus Sequence Analysis (MLSA) and implementation of the Average Nucleotide Identity (ANI) measure. The genomic sequences resulted in the identification of two different Pantoea species, denoted EnvD and EnvH. Subsequent de novo genome assembly generated 5 and 10 contigs for EnvD and EnvH, respectively. The largest contig (4,008,183 bps and 3,740,753 bps for EnvD and EnvH, respectively), overlaps to a major extent to the chromosome of closely related Pantoea species. ANI values calculated for both isolates revealed two apparently new species of the Pantoea genus. Our study deciphered the identity of two bacteria producing antibiotic-like compounds, and the genomic sequence revealed they represent distinct Pantoea species.

Phylogeny and Identification of Pantoea Species Associated with Bulb Rot and Bacterial Leaf Blight of Onion Crops in Uruguay

Onion is among the most consumed vegetables in Uruguay, grown in the northwestern and southern regions of the country. The onion supply presents interannual variations associated with significant postharvest losses, mainly caused by bacterial rots. Besides bulb rotting, onion leaf lesions as well as infections on seed-stalks during seed production may be devastating for some varieties under conducive conditions. This research aimed to identify the causal agents of bulb rots and leaf blight of onion crops in Uruguay. Symptomatic bulbs, seeds-stalks, and leaves were collected from commercial fields from 2015 to 2020. Bacterial colonies were isolated and identified at genera level using physiological tests and 16S rRNA gene sequence analysis. A collection of 59 Pantoea spp. isolates was obtained (11 from bulbs and 48 from leaves and seeds-stalks). Multilocus sequence analysis using four housekeeping genes (rpoB, gyrB, leuS, and fusA) allowed the assignment of the isolates to five Pantoea species: P. ananatis, P. agglomerans, P. allii, P. eucalypti, and P. vagans. The last two species were not previously reported as onion pathogens elsewhere. The ability to cause disease symptoms was tested by leaf inoculation and red onion scale assays. P. ananatis isolates showed the highest aggressiveness in both assays. Specific isolates from P. allii (MAI 6022), P. eucalypti (MAI 6036), P. vagans (MAI 6050), and Pantoea sp. (MAI 6049) ranked second in aggressiveness on onion leaves, whereas only three isolates belonging to P. eucalypti (MAI 6036 and MAI 6058) and P. agglomerans (MAI 6045) exhibited the same scale-clearing phenotype as P. ananatis. Leaf inoculation assays were also performed on a set of eight onion cultivars and breeding lines. Overall, P. ananatis MAI 6032 showed the highest aggressiveness in all tested cultivars, followed by P. eucalypti MAI 6036. The presence of new reported bacterial species leads to complex disease management and highlights the need for further studies on virulence factors and the epidemiology of these pathogens.

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.

Root-Derived Endophytic Diazotrophic Bacteria Pantoea cypripedii AF1 and Kosakonia arachidis EF1 Promote Nitrogen Assimilation and Growth in Sugarcane

Excessive, long-term application of chemical fertilizers in sugarcane crops disrupts soil microbial flora and causes environmental pollution and yield decline. The role of endophytic bacteria in improving crop production is now well-documented. In this study, we have isolated and identified several endophytic bacterial strains from the root tissues of five sugarcane species. Among them, eleven Gram-negative isolates were selected and screened for plant growth-promoting characteristics, i.e., production of siderophores, indole-3-acetic acid (IAA), ammonia, hydrogen cyanide (HCN), and hydrolytic enzymes, phosphorus solubilization, antifungal activity against plant pathogens, nitrogen-fixation, 1-aminocyclopropane-1-carboxylic acid deaminase activity, and improving tolerance to different abiotic stresses. These isolates had nifH (11 isolates), acdS (8 isolates), and HCN (11 isolates) genes involved in N-fixation, stress tolerance, and pathogen biocontrol, respectively. Two isolates Pantoea cypripedii AF1and Kosakonia arachidis EF1 were the most potent strains and they colonized and grew in sugarcane plants. Both strains readily colonized the leading Chinese sugarcane variety GT42 and significantly increased the activity of nitrogen assimilation enzymes (glutamine synthetase, NADH glutamate dehydrogenase, and nitrate reductase), chitinase, and endo-glucanase and the content of phytohormones gibberellic acid, indole-3-acetic acid, and abscisic acid. The gene expression analysis of GT42 inoculated with isolates of P. cypripedii AF1 or K. arachidis EF1 showed increased activity of nifH and nitrogen assimilation genes. Also, the inoculated diazotrophs significantly increased plant nitrogen content, which was corroborated by the 15N isotope dilution analysis. Collectively, these findings suggest that P. cypripedii and K. arachidis are beneficial endophytes that could be used as a biofertilizer to improve plant nitrogen nutrition and growth of sugarcane. To the best of our knowledge, this is the first report of sugarcane growth enhancement and nitrogen fixation by Gram-negative sugarcane root-associated endophytic bacteria P. cypripedii and K. arachidis. These strains have the potential to be utilized as sugarcane biofertilizers, thus reducing nitrogen fertilizer use and improving disease management.

Chryseobacterium lecithinasegens sp. nov., a siderophore-producing bacterium isolated from soil at the bottom of a pond

Bacterial strain PAGU 2197^T, which was isolated from soil collected from the bottom of a pond in Japan, is characterized in this study. Cells of strain PAGU 2197^T were aerobic, Gram-negative, short rod-shaped, non-motile, flexirubin-producing, oxidase-positive, catalase-positive and lecithinase-negative. A phylogenetic study based on 16S rRNA gene sequences and multilocus sequence analysis (gyrB, rpoB and rpoD) indicated that strain PAGU 2197^T belongs to the genus Chryseobacterium and is a member of an independent lineage including Chryseobacterium tructae CCUG 60111^T (sequence similarity, 95.9 %), Chryseobacterium lactis CCUG 60566^T (93.4 %) and Chryseobacterium viscerum CCUG 60103^T (91.6 %). The average nucleotide identity values were 80.83-85.04 %. Because average nucleotide identity values of 95-96 % exceed the 70 % DNA-DNA hybridization cutoff value for species discrimination, strain PAGU 2197^T represents a novel species in the genus Chryseobacterium. The genome of strain PAGU 2197^T was 4 967 738 bp with a G+C content of 35.5 mol%. The sole respiratory quinone of strain PAGU 2197^T was MK-6; the major cellular fatty acids were iso-C_15 : 0, iso-C_17 : 0 3OH, summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c) and summed feature 9 (iso-C_17 : 1  ω9c and/or C_16 : 0 10-methyl); and the major polar lipids were phosphoglycolipids and phosphatidylethanolamine. These results indicate that strain PAGU 2197^T should be classified as representing a novel species in the genus Chryseobacterium, for which the name Chryseobacterium lecithinasegens sp. nov. is proposed, with strain PAGU 2197^T (=NBRC 114264^T=CCUG 75150^T) as the type strain.

Genomics-Informed Multiplex PCR Scheme for Rapid Identification of Rice-Associated Bacteria of the Genus Pantoea

The genus Pantoea forms a complex of more than 25 species, among which several cause diseases of various crop plants, including rice. Notably, strains of Pantoea ananatis and P. stewartii have been repeatedly reported to cause bacterial leaf blight of rice, whereas other authors have observed that P. agglomerans can also cause bacterial leaf blight of rice. The contribution of these and perhaps other species of Pantoea to plant diseases and yield losses of crop plants is currently not well documented, partly due to the lack of efficient diagnostic tools. Using 32 whole-genome sequences of the three major plant-pathogenic Pantoea spp., a set of PCR primers that detect each of the three species P. agglomerans, P. ananatis, and P. stewartii was designed. A multiplex PCR scheme which can distinguish these three species and also detects members of other Pantoea spp. was further developed. Upon validation on a set of reference strains, 607 suspected Pantoea strains that were isolated from rice leaves or seed originating from 11 African countries were screened. In total, 41 P. agglomerans strains from 8 countries, 79 P. ananatis strains from 9 countries, 269 P. stewartii strains from 9 countries, and 218 unresolved Pantoea strains from 10 countries were identified. The PCR protocol allowed detection of Pantoea bacteria grown in vitro, in planta, and in rice seed. The detection threshold was estimated as total genomic DNA at 0.5 ng/µl and heated cells at 1 × 10⁴ CFU/ml. This new molecular diagnostic tool will help to accurately diagnose major plant-pathogenic species of Pantoea. Due to its robustness, specificity, sensitivity, and cost efficiency, it will be very useful for plant protection services and for the epidemiological surveillance of these important crop-threatening bacteria.

Phylogenetic study of rhizobia nodulating pea (Pisum sativum) isolated from different geographic locations in Tunisia

Nodulated Pisum sativum plants showed the presence of native rhizobia in 16 out of 23 soil samples collected especially in northern and central Tunisia. A total of 130 bacterial strains were selected and three different ribotypes were revealed after PCR-RFLP analysis. Sequence analyses of rrs and four housekeeping genes (recA, atpD, dnaK and glnII) assigned 35 isolates to Rhizobium laguerreae, R. ruizarguesonis, Agrobacterium radiobacter, Ensifer meliloti and two putative genospecies. R. laguerreae was the most dominant species nodulating P. sativum with 63%. The isolates 21PS7 and 21PS15 were assigned to R. ruizarguesonis, and this is the first report of this species in Tunisia. Two putative new lineages were identified, since strains 25PS6, 10PS4 and 12PS15 clustered distinctly from known rhizobia species but within the R. leguminosarum complex (Rlc) with the most closely related species being R. indicum with 96.4% sequence identity. Similarly, strains 16PS2, 3PS9 and 3PS18 showed 97.4% and 97.6% similarity with R. sophorae and R. laguerreae, respectively. Based on 16S-23S intergenic spacer (IGS) fingerprinting, there was no clear association between the strains and their geographic locations. According to nodC and nodA phylogenies, strains of Rlc species and, interestingly, strain 8PS18 identified as E. meliloti, harbored the symbiotic genes of symbiovar viciae and clustered in two different clades showing heterogeneity within the symbiovar. All these strains nodulated and fixed nitrogen with pea plants. However, the strains belonging to A. radiobacter and the two remaining strains of E. meliloti were unable to nodulate P. sativum, suggesting that they were non-symbiotic strains. The results of this study further suggest that the Tunisian Rhizobium community is more diverse than previously reported.

Relationship of the Pine Growth Promoting Pantoea eucalypti FBS135 with Type Strains P. eucalypti LMG 24197T and P. vagans 24199T

Endophytes in woody plants are much less understood. Pantoea strain FBS135 is an endophytic bacterium isolated from Pinus massoniana with the ability to promote pine growth significantly. In this study, we demonstrated that FBS135 has the astonishing ability of low nitrogen tolerance but no ability of nitrogen fixation. To exactly determine the phylogenetic status of FBS135, we sequenced the whole genomes of P. eucalypti LMG 24197^T and P. vagans 24199^T, type strains of two Pantoea species, which are evolutionarily closest to FBS135. P. eucalypti LMG 24197^T contained a single chromosome of 4,035,995 bp (C+G, 54.6%) plus three circular plasmids while LMG 24199^T comprises a single circular chromosome of 4,050,173 bp (C+G, 55.6%) and two circular plasmids. With the genomic information, FBS135 was finally identified as a P. eucalypti strain, although it showed some different physiological traits from the two type strains. Comparative genomic analyses were performed for the three strains, revealing their common molecular basis associated with plant lifecycle as well as the differences in their gene arrangements relating to nitrogen utilization.

Molecular Analysis of Bacterial Isolates From Necrotic Wheat Leaf Lesions Caused by Xanthomonas translucens, and Description of Three Putative Novel Species, Sphingomonas albertensis sp. nov., Pseudomonas triticumensis sp. nov. and Pseudomonas foliumensis sp. nov

Xanthomonas translucens is the etiological agent of the wheat bacterial leaf streak (BLS) disease. The isolation of this pathogen is usually based on the Wilbrink's-boric acid-cephalexin semi-selective medium which eliminates 90% of other bacteria, some of which might be novel species. In our study, a general purpose nutrient agar was used to isolate 49 bacterial strains including X. translucens from necrotic wheat leaf tissues. Maximum likelihood cluster analysis of 16S rRNA sequences grouped the strains into 10 distinct genera. Pseudomonas (32.7%) and Pantoea (28.6%) were the dominant genera while Xanthomonas, Clavibacter and Curtobacterium had 8.2%, each. Erwinia and Sphingomonas had two strains, each. BLAST and phylogenetic analyses of multilocus sequence analysis (MLSA) of specific housekeeping genes taxonomically assigned all the strains to validly described bacterial species, except three strains (10L4B, 12L4D and 32L3A) of Pseudomonas and two (23L3C and 15L3B) of Sphingomonas. Strains 10L4B and12L4D had Pseudomonas caspiana as their closest known type strain while strain 32L3A was closest to Pseudomonas asturiensis. Sphingomonas sp. strains 23L3C and 15L3B were closest to S. faeni based on MLSA analysis. Our data on MLSA, whole genome-based cluster analysis, DNA-DNA hybridization and average nucleotide identity, matrix-assisted laser desorption/ionization-time-of-flight, chemotaxonomy and phenotype affirmed that these 5 strains constitute three novel lineages and are taxonomically described in this study. We propose the names, Sphingomonas albertensis sp. nov. (type strain 23L3C^T = DOAB 1063^T = CECT 30248^T = LMG 32139^T), Pseudomonas triticumensis sp. nov. (type strain 32L3A^T = DOAB 1067^T = CECT 30249^T = LMG 32140^T) and Pseudomonas foliumensis sp. nov. (type strain 10L4B^T = DOAB 1069^T = CECT 30250^T = LMG 32142^T). Comparative genomics of these novel species, relative to their closest type strains, revealed unique repertoires of core secretion systems and secondary metabolites/antibiotics. Also, the detection of CRISPR-Cas systems in the genomes of these novel species suggests an acquired mechanism for resistance against foreign mobile genetic elements. The results presented here revealed a cohabitation, within the BLS lesions, of diverse bacterial species, including novel lineages.

Serratia rhizosphaerae sp. nov., a novel plant resistance inducer against soft rot disease in tobacco

A novel Gram-negative, facultatively anaerobic, non-spore-forming and rod-shaped bacterial strain (KUDC3025T) was isolated from rhizospheric soil of Artemisia japonica subsp. littoricola collected from the Dokdo Islands, Republic of Korea and bacterial strain MYb239 was isolated from compost from Kiel, Germany. Phylogenetic analysis based on 16S rRNA gene sequences, multilocus genes (atpD, gyrB, infB and rpoB), and whole-genome sequences indicated that both strains belonged to the genus Serratia and were most closely related to Serratia rubidaea KCTC 2927T. The average nucleotide identity values based on blast and MUMmer, tetranucleotide usage pattern and genome-based digital DNA-DNA hybridization values were all below the 95.0 %/95.0 %/0.998/70 % cutoff points. The genome G+C content was 58.0 mol%. The cellular quinone content contained ubiquinone-8 and the major components in the fatty acid profile were C16 : 0, C17 : 0 cyclo and C14 : 0. The polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unknown amino lipids, two unknown phospholipids and an unknown lipid. Based on phenotypic, chemotaxonomic and genotypic data, strain KUDC3025T (DSM 106578T=CGMCC 1.18473T) and MYb239 represents a novel species, for which the name Serratia rhizosphaerae sp. nov. is proposed. Furthermore, strain KUDC3025T was able to suppress disease symptoms by priming the plant defence system components, including the salicylic acid and ethylene pathways, furthering our understanding of Serratia as potential plant growth promoting bacteria.

Draft Genome Sequence of the Putative Endophytic Bacterium Pantoea agglomerans R6, Associated with Lactuca serriola from South Africa

Here, we present the draft genome sequence (∼4.7 Mb) of the endopyhtic bacterium Pantoea agglomerans strain R6, which was isolated from surface-sterilized roots of Lactuca serriola (prickly lettuce).

Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae

During a citywide microbiological screening project in Pavia (Italy) a bacterial strain isolated from the surface of an Automated Teller Machine was classified as a Klebsiella sp. by MALDI-TOF spectrometry, and shown to be susceptible to the most antimicrobial classes by phenotypic testing. After Illumina genome sequencing and subsequent assembly, a high-quality draft genome was obtained (size = 5,051,593 bp, N50 = 615,571 bp, largest contig = 1,328,029 bp, N_contig = 17, GC content = 51.58%, coverage = 141.42), absence of antimicrobial resistance genes was confirmed, but the strain resulted to be highly divergent from all Klebsiella, and more related to other Enterobacteriaceae. The higher values of 16S rRNA identity were with members of the genera Citrobacter, Salmonella, and “Superficieibacter.” An ortholog-based phylogenomic analysis indicated a sister group relationship with “Superficieibacter electus,” in a distinct clade from other members of the Enterobacteriaceae family. In order to evaluate whether the novel genome represents a new species of “Superficiebacter,” average nucleotide identity (ANI) and Hadamard analysis were performed on a dataset of 78 Enterobacteriaceae. The novel genome showed an ANI of 87.51% with S. electus, which compared on identity values between other members of the family, clearly indicates that the genome represents a new species within the genus “Superficieibacter.” We propose for the new species the name “Superficieibacter maynardsmithii.”

Yeast communities associated with cacti in Brazil and the description of Kluyveromyces starmeri sp. nov. based on phylogenomic analyses

Yeast communities associated with cacti were studied in three ecosystems of Southeast, Central and North Brazil. A total of 473 yeast strains belonging to 72 species were isolated from 190 samples collected. Cactophilic yeast species were prevalent in necrotic tissues, flowers, fruits and insects of cacti collected in Southeast and North Brazil. Pichia cactophila, Candida sonorensis and species of the Sporopachydermia complex were the most prevalent cactophilic species in Southeast and Central regions. Kodamaea nitidulidarum, Candida restingae and Wickerhamiella cacticola were frequently associated with cactus flowers and fruits. The diversity of yeasts associated with the substrates studied was high. Twenty-one novel species were found. One is described here as Kluyveromyces starmeri sp. nov. based on 21 isolates obtained from necrotic tissues, flowers, fruits and associated insects of the columnar cacti Cereus saddianus, Micranthocereus dolichospermaticus and Pilosocereus arrabidae in two different ecosystems in Brazil. Phylogenetic analyses of sequences encoding the gene of the small subunit (SSU) rRNA gene, the internal transcribed spacer, the 5.8S rRNA gene and the D1/D2 domains of the large subunit (LSU) rRNA showed that the species is related to Kluyveromyces dobzhanskii, Kluyveromyces lactis and Kluyveromyces marxianus. Phylogenomic analyses based on 1264 conserved genes shared among the new species and 19 other members of the Saccharomycetaceae confirmed this phylogenetic relationship. The holotype is K. starmeri sp. nov. CBS 16103^T (=UFMG-CM-Y3682^T ). The Mycobank number is MB 836817.