Pseudomonas rhizoryzae sp. nov., isolated from rice

Whole-genome sequence of Pseudomonas benzopyrenica MLY92: isolation from diseased leaves of tobacco in China

Here we present a sketch of the whole-genome sequence of Pseudomonas benzopyrenica. The strain comes from the leaf veins of a diseased tobacco plant. This study has significant research implications for gaining insights into the characteristics of microorganisms belonging to the genus Pseudomonas.

Expanding the Pseudomonas diversity of the wheat rhizosphere: four novel species antagonizing fungal phytopathogens and with plant-beneficial properties

Plant-beneficial Pseudomonas bacteria hold the potential to be used as inoculants in agriculture to promote plant growth and health through various mechanisms. The discovery of new strains tailored to specific agricultural needs remains an open area of research. In this study, we report the isolation and characterization of four novel Pseudomonas species associated with the wheat rhizosphere. Comparative genomic analysis with all available Pseudomonas type strains revealed species-level differences, substantiated by both digital DNA-DNA hybridization and average nucleotide identity, underscoring their status as novel species. This was further validated by the phenotypic differences observed when compared to their closest relatives. Three of the novel species belong to the P. fluorescens species complex, with two representing a novel lineage in the Pseudomonas phylogeny. Functional genome annotation revealed the presence of specific features contributing to rhizosphere colonization, including flagella and components for biofilm formation. The novel species have the genetic potential to solubilize nutrients by acidifying the environment, releasing alkaline phosphatases and their metabolism of nitrogen species, indicating potential as biofertilizers. Additionally, the novel species possess traits that may facilitate direct promotion of plant growth through the modulation of the plant hormone balance, including the ACC deaminase enzyme and auxin metabolism. The presence of biosynthetic clusters for toxins such as hydrogen cyanide and non-ribosomal peptides suggests their ability to compete with other microorganisms, including plant pathogens. Direct inoculation of wheat roots significantly enhanced plant growth, with two strains doubling shoot biomass. Three of the strains effectively antagonized fungal phytopathogens (Thielaviopsis basicola, Fusarium oxysporum, and Botrytis cinerea), demonstrating their potential as biocontrol agents. Based on the observed genetic and phenotypic differences from closely related species, we propose the following names for the four novel species: Pseudomonas grandcourensis sp. nov., type strain DGS24T ( = DSM 117501T = CECT 31011T), Pseudomonas purpurea sp. nov., type strain DGS26T ( = DSM 117502T = CECT 31012T), Pseudomonas helvetica sp. nov., type strain DGS28T ( = DSM 117503T = CECT 31013T) and Pseudomonas aestiva sp. nov., type strain DGS32T ( = DSM 117504T = CECT 31014T).

Pseudomonas flavocrustae sp. nov., an endophyte with plant growth promoting traits isolated from Passiflora incarnata

A polyphasic approach was applied to characterize taxonomically a novel endophytic bacterial strain, designated as EP178T, which was previously isolated from Passiflora incarnata leaves and characterized as plant-growth promoter. The strain EP178T forms Gram stain-negative and rod-shaped cells, and circular and yellow-pigmented colonies. Its growth occurs at 10-37 °C, at pH 6.0-8.0, and tolerates up to 7% (w/v) NaCl. The major cellular fatty acids found were summed feature 8 (C18:1 ω7c), summed feature 3 (C16:1 ω6c /C16:1 ω7c), and C16:0, and the predominant ubiquinone was Q-9. The phylogenetic and nucleotide-similarity analysis with 16S rRNA gene sequences showed that strain EP178T belongs to Pseudomonas genus. The genomic-based G + C content was 65.5%. The average nucleotide identity and digital DNA-DNA hybridization values between strains EP178T and the closest type strain, P. oryzihabitans DSM 6835T, were 92.6% and 52.2%, respectively. Various genes associated with plant-growth promoting mechanisms were annotated from genome sequences. Based on the phenotypic, genomic, phylogeny and chemotaxonomic data, strain EP178T represents a new species of the genus Pseudomonas, for which the name Pseudomonas flavocrustae sp. nov. was proposed. The type strain is EP178T (= CBMAI 2609T = ICMP 24844T = MUM 23.01T).

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.

Pseudomonas benzopyrenica sp. nov., isolated from soil, exhibiting high-efficiency degradation of benzo(a)pyrene

A Gram-negative, yellow-pigmented, aerobic and rod-shaped bacterium, designated as strain BaP3T, was isolated from the soil. Strain BaP3T grew at 16-37℃ (optimum, 30 °C) and pH 6.0-8.0 (optimum, pH 7.0). Additionally, strain BaP3T could tolerate NaCl concentrations in the range 0-6 % (optimum, 1%). Moreover, strain BaP3T was motile by flagella. The phylogenetic analysis of 16S rRNA sequences showed that strain BaP3T belonged to the genus Pseudomonas, and the sequence was most closely related to Pseudomonas oryzihabitans CGMCC 1.3392T and Pseudomonas psychrotolerans DSM 15758T, with 99.66 % sequence similarity. Pseudomonas rhizoryzae RY24T was the next closely related species, exhibiting 99.38 % 16S rRNA gene sequence similarity. The DNA-DNA hybridization and average nucleotide identity values between strain BaP3T and its closely related types were below 50 and 92 %, respectively. Both results were below the cut-off for species distinction. The genomic DNA G+C content of strain BaP3T was 65.30 mol%. The predominant quinone in strain BaP3T was identified as ubiquinone Q-9. The major cellular fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and C16 : 0. These results indicated that strain BaP3T represents a novel species in the genus Pseudomonas. The type strain is BaP3T (CCTCC AB 2022379T=JCM 35914T), for which the name Pseudomonas benzopyrenica sp. nov. is proposed.

Isolation and characterization of phosphate-solubilizing bacterium Pantoea rhizosphaerae sp. nov. from Acer truncatum rhizosphere soil and its effect on Acer truncatum growth

The Acer truncatum Bunge, widely distributed in North China, shows excellent tolerance to low-P soils. However, little information is available on potential phosphate-solubilizing bacterial (PSB) strains from the A. truncatum rhizosphere. The objectives of this work were to isolate and characterize PSB from A. truncatum rhizosphere soil and to evaluate the effect of inoculation with the selected strain on A. truncatum seedlings. The strains were characterized on the basis of phenotypic characteristics, carbon source utilization pattern, fatty acid methyl esters analysis, 16S rRNA gene and the whole-genome sequence. A Gram-negative and rod-shaped bacterium, designated MQR6^T, showed a high capacity to solubilize phosphate and produce indole-3-acetic acid (IAA) and siderophores. The strain can solubilize tricalcium phosphate (TCP) and rock phosphate (RP), and the solubilization of TCP was about 60% more effective than RP. Phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strain MQR6^T formed a distinct phyletic lineage as a new species within the genus Pantoea. The digital DNA-DNA hybridization value between strain MQR6^T and the closely related strains was 19.5-23.3%. The major cellular fatty acids were summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), summed feature 8 (C_18:1ω6c and/or C_18:1ω7c), C_14:0, C_16:0, and C_17:0 cyclo. Several genes related to IAA production, phosphonate transport, phosphate solubilization and siderophore biogenesis were found in the MQR6^T genome. Furthermore, inoculation with the strain MQR6^T significantly improved plant height, trunk diameter, dry weight and P accumulation in roots and shoot of A. truncatum seedlings compared to non-inoculated control. These plant parameters were improved even further in the treatment with both inoculation and P fertilization. Our results suggested that MQR6^T represented a new species we named Pantoea rhizosphaerae, as a plant growth-promoting rhizobacterium that can solubilize inorganic P and improve growth of A. truncatum seedlings, emerging as a potential strategy to improve A. truncatum cultivation.

The structure and diversity of microbial communities in Paederus fuscipes (Coleoptera: Staphylinidae): from ecological paradigm to pathobiome

BACKGROUND

Paederus fuscipes is medically the most famous rove beetle, which causes dermatitis or conjunctivitis in humans, as well as gastrointestinal toxicosis in livestock, via releasing toxic hemolymph containing pederin. Pedrin biosynthesis genes have been identified in uncultured Pseudomonas-like endosymbionts that are speculated to be acquired through a horizontal transfer. However, the composition of the P. fuscipes microbial community, especially of the gut and genital microbiome, remains unclear. This study was aimed to characterize the structure and diversity of P. fuscipes-associated bacterial communities in terms of gender, organ, and location using the Illumina HiSeq platform in the southern littorals of Caspian Sea.

RESULTS

The OTUs identified from P. fuscipes specimens were collapsed into 40 phyla, 112 classes, 249 orders, 365 families, 576 genera, and 106 species. The most abundant families were Pseudomonadaceae, Spiroplasmataceae, Weeksellaceae, Enterococcaceae, and Rhizobiaceae, respectively. Thirty top genera made up > 94% of the P. fuscipes microbiome, with predominating Pseudomonas, followed by the Spiroplasma, Apibacter, Enterococcus, Dysgonomonas, Sebaldella, Ruminococcus, and Wolbachia. Interesting dissimilarities were also discovered within and between the beetle microbiomes in terms of genders and organs. Analyses showed that Spiroplasma / Apibacter as well as Pseudomonas / Pseudomonas were the most abundant in the genitals / intestines of male and female beetles, respectively. Bacterial richness did not display any significant difference in the three provinces but was higher in male beetles than in females and more in the genitals than intestines.

CONCLUSIONS

The present study identified Pseudomonas-like endobacterium as a common symbiont of P. fuscipes beetles; this bacterium begins its journey from gut and genitalia of females to reach the male rove beetles. Additionally, male and female rove beetles were characterized by distinctive microbiota in different organs, likely reflecting different functions and/or adaptation processes. Evidence of the extension of P. fuscipes microbiome from the environmental paradigm to the pathobiome was also presented herein. A comprehensive survey of P. fuscipes microbiome components may eventually lead to ecological insights into the production and utilization of defensive compound of pederin and also the management of linear dermatitis with the use of available antibiotics against bacterial pathogens released by the beetles. Video Abstract.

Isolation of Pseudomonas aromaticivorans sp. nov from a hydrocarbon-contaminated groundwater capable of degrading benzene-, toluene-, m- and p-xylene under microaerobic conditions

Members of the genus Pseudomonas are known to be widespread in hydrocarbon contaminated environments because of their remarkable ability to degrade a variety of petroleum hydrocarbons, including BTEX (benzene, toluene, ethylbenzene and xylene) compounds. During an enrichment investigation which aimed to study microaerobic xylene degradation in a legacy petroleum hydrocarbon-contaminated groundwater, a novel Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated as MAP12T was isolated. It was capable of degrading benzene, toluene, meta- and para- xylene effectively under both aerobic and microaerobic conditions. The 16S rRNA gene sequence analysis revealed that strain MAP12T belongs to the genus Pseudomonas, with the highest 16S rRNA gene similarity to Pseudomonas linyingensis LYBRD3-7T (98.42%), followed by Pseudomonas sagittaria JCM 18195T (98.29%) and Pseudomonas alcaliphila JCM 10630T (98.08%). Phylogenomic tree constructed using a concatenated alignment of 92 core genes indicated that strain MAP12T is distinct from any known Pseudomonas species. The draft genome sequence of strain MAP12T is 4.36 Mb long, and the G+C content of MAP12T genome is 65.8%. Orthologous average nucleotide identity (OrthoANI) and digital DNA–DNA hybridization (dDDH) analyses confirmed that strain MAP12T is distinctly separated from its closest neighbors (OrthoANI < 89 %; dDDH < 36%). Though several members of the genus Pseudomonas are well known for their aerobic BTEX degradation capability, this is the first report of a novel Pseudomonas species capable of degrading xylene under microaerobic conditions. By applying genome-resolved metagenomics, we were able to partially reconstruct the genome of strain MAP12T from metagenomics sequence data and showed that strain MAP12T was an abundant member of the xylene-degrading bacterial community under microaerobic conditions. Strain MAP12T contains ubiquinone 9 (Q9) as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine as major polar lipids. The major cellular fatty acids of strain MAP12T are summed feature 3 (C16:1ω6c and/or C16:1ω7c), C16:0 and summed feature 8 (C18:1ω6c and/or C18:1ω7c). The results of this polyphasic study support that strain MAP12T represents a novel species of the genus Pseudomonas, hence the name of Pseudomonas aromaticivorans sp. nov. is proposed for this strain considering its aromatic hydrocarbon degradation capability. The type strain is MAP12T (=LMG 32466, =NCAIM B.02668).

Pseudomonas tumuqii sp. nov., isolated from greenhouse soil

A Gram-stain-negative, aerobic, rod-shaped and motile bacterium, named LAMW06^T, was isolated from greenhouse soil in Beijing, China. In the 16S rRNA gene sequence comparison, strain LAMW06^T had the highest similarity with Pseudomonas cuatrocienegasensis 1N^T. Phylogenetic analysis based on the 16S rRNA and three housekeeping gene sequences (gyrB, rpoB and rpoD) indicated that strain represented a member of the genus Pseudomonas. The genome sequence size of the isolate was 5.5 Mb, with a DNA G + C content of 63.5 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain LAMW06^T and closely related members of Pseudomonas borbori R-20821^T, Pseudomonas taeanensis MS-3^T and P. cuatrocienegasensis 1N^T were 90.9%, 82.4%, 81.5% and 43.0%, 25.9%, 24.6% respectively. The major fatty acids contained summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c), C_18:1 ω7c and C_16:0. The primary respiratory quinone was ubiquinone-9. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, six aminophospholipids, six phospholipids, one aminolipid and one glycolipid. According to the genotypic, phylogenetic and chemotaxonomic data, strain LAMW06^T represents a novel species within the genus Pseudomonas, for which the name Pseudomonas tumuqii sp. nov. is proposed. The type strain is LAMW06^T (= GDMCC 1.2003^T = KCTC 72829^T).

Diversity and Taxonomic Distribution of Endophytic Bacterial Community in the Rice Plant and Its Prospective

Endophytic bacterial communities are beneficial communities for host plants that exist inside the surfaces of plant tissues, and their application improves plant growth. They benefit directly from the host plant by enhancing the nutrient amount of the plant’s intake and influencing the phytohormones, which are responsible for growth promotion and stress. Endophytic bacteria play an important role in plant-growth promotion (PGP) by regulating the indirect mechanism targeting pest and pathogens through hydrolytic enzymes, antibiotics, biocontrol potential, and nutrient restriction for pathogens. To attain these benefits, firstly bacterial communities must be colonized by plant tissues. The nature of colonization can be achieved by using a set of traits, including attachment behavior and motility speed, degradation of plant polymers, and plant defense evasion. The diversity of bacterial endophytes colonization depends on various factors, such as plants’ relationship with environmental factors. Generally, each endophytic bacteria has a wide host range, and they are used as bio-inoculants in the form of synthetic applications for sustainable agriculture systems and to protect the environment from chemical hazards. This review discusses and explores the taxonomic distribution of endophytic bacteria associated with different genotypes of rice plants and their origin, movement, and mechanism of PGP. In addition, this review accentuates compressive meta data of endophytic bacteria communities associated with different genotypes of rice plants, retrieves their plant-growth-promoting properties and their antagonism against plant pathogens, and discusses the indication of endophytic bacterial flora in rice plant tissues using various methods. The future direction deepens the study of novel endophytic bacterial communities and their identification from rice plants through innovative techniques and their application for sustainable agriculture systems.