scholarly journals Antibacterial activity and mode of action of potassium tetraborate tetrahydrate against soft-rot bacterial plant pathogens

Microbiology ◽  
2020 ◽  
Vol 166 (9) ◽  
pp. 837-848
Author(s):  
Yingyu Liu ◽  
Melanie J. Filiatrault
Keyword(s):  
Type Species ◽  
Plant Pathogens ◽  
Point Mutations ◽  
Resistant Mutant ◽  
Soft Rot ◽  
Alternative Methods ◽  
Management Options ◽  
Content Type ◽  
Link Type ◽  
Resistant Mutants

Bacterial soft rot caused by the bacteria Dickeya and Pectobacterium is a destructive disease of vegetables, as well as ornamental plants. Several management options exist to help control these pathogens. Because of the limited success of these approaches, there is a need for the development of alternative methods to reduce losses. In this study, we evaluated the effect of potassium tetraborate tetrahydrate (PTB) on the growth of six Dickeya and Pectobacterium spp. Disc diffusion assays showed that Dickeya spp. and Pectobacterium spp. differ in their sensitivity to PTB. Spontaneous PTB-resistant mutants of Pectobacterium were identified and further investigation of the mechanism of PTB resistance was conducted by full genome sequencing. Point mutations in genes cpdB and supK were found in a single Pectobacterium atrosepticum PTB-resistant mutant. Additionally, point mutations in genes prfB (synonym supK) and prmC were found in two independent Pectobacterium brasiliense PTB-resistant mutants. prfB and prmC encode peptide chain release factor 2 and its methyltransferase, respectively. We propose the disruption of translation activity due to PTB leads to Pectobacterium growth inhibition. The P. atrosepticum PTB-resistant mutant showed altered swimming motility. Disease severity was reduced for P. atrosepticum -inoculated potato stems sprayed with PTB. We discuss the potential risk of selecting for bacterial resistance to this chemical.

scholarly journals Proposal for the creation of a new genus Musicola gen. nov., reclassification of Dickeya paradisiaca (Samson et al. 2005) as Musicola paradisiaca comb. nov. and description of a new species Musicola keenii sp. nov.

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Nicole Hugouvieux-Cotte-Pattat ◽  
Cécile Jacot des-Combes ◽  
Jérôme Briolay ◽  
Leighton Pritchard
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Plant Pathogens ◽  
Phenotypic Analysis ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
A New Species ◽  
Laboratory Collection

The Pectobacteriaceae family of important plant pathogens includes the genus Dickeya . There are currently 12 described species of Dickeya , although some are poorly characterized at the genomic level. Only two genomes of Dickeya paradisiaca , the type strain CFBP 4178T and strain Ech703, have previously been sequenced. Members of this species are mostly of tropical or subtropical origin. During an investigation of strains present in our laboratory collection we sequenced the atypical strain A3967, registered as CFBP 722, isolated from Solanum lycopersicum (tomato) in the South of France in 1965. The genome of strain A3967 shares digital DNA–DNA hybridization and average nucleotide identity (ANI) values of 68 and 96 %, respectively, with the D. paradisiaca type strain CFBP 4178T. However, ANI analysis showed that D. paradisiaca strains are significantly dissimilar to the other Dickeya species, such that less than one third of their genomes align to any other Dickeya genome. On phenotypic, phylogenetic and genomic grounds, we propose a reassignment of D. paradisiaca to the genus level, for which we propose the name Musicola gen. nov., with Musicola paradisiaca as the type species and CFBP 4178T (NCPPB 2511T) as the type strain. Phenotypic analysis showed differences between strain A3967T and CFBP 4178T, such as for the assimilation of melibiose, raffinose and myo-inositol. These results support the description of two novel species, namely Musicola paradisiaca comb. nov. and Musicola keenii sp. nov., with CFBP 4178T (NCPPB 2511T=LMG 2542T) and A3967T (CFBP 8732T=LMG 31880T) as the type strains, respectively.

scholarly journals Pseudomonas allii sp. nov., a pathogen causing soft rot of onion in Japan

2020 ◽  
Author(s):  
Hiroyuki Sawada ◽  
Takashi Fujikawa ◽  
Mizue Tsuji ◽  
Mamoru Satou
Keyword(s):  
Fatty Acids ◽  
Type Species ◽  
Soft Rot ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Content Type ◽  
Link Type ◽  
Total Fatty Acids ◽  
Phylogenomic Analyses

Six phytopathogenic bacterial strains, MAFF 301512, MAFF 301513, MAFF 301514T, MAFF 301515, MAFF 301516 and MAFF 301517, were isolated from soft rot lesions of onion (Allium cepa L.) in Japan. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella and rod-shaped. Analysis of their 16S rRNA gene sequences showed that they belong to the genus Pseudomonas , with the highest similarities to Pseudomonas poae DSM 14936T (99.86 %), Pseudomonas simiae OLiT (99.85 %), Pseudomonas trivialis DSM 14937T (99.79 %) and Pseudomonas extremorientalis KMM 3447T (99.79 %). Their genomic DNA G+C content was 60.9 mol% and the major fatty acids (>5 % of the total fatty acids) present were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c /C18 : 1 ω6c) and C17 : 0 cyclo. Phylogenetic and phylogenomic analyses based on the rpoD gene and whole genome sequences, respectively, demonstrated that the strains belong to the Pseudomonas fluorescens subgroup, but form a monophyletic and robust clade, with Pseudomonas azotoformans as their neighbour. Between the strains and P. azotoformans , the average nucleotide identity scores were 95.63–95.70 %, whereas the digital DNA–DNA hybridization scores of the strains against their closest relatives, including P. azotoformans , were 65.4 % or less, which are lower than the 70 % cut-off for prokaryotic species delineation. The strains were differentiated from their closest relatives by phenotypic characteristics, pathogenicity in onion and cellular fatty acid composition. The phenotypic, chemotaxonomic and genotypic data showed that the strains represent a novel Pseudomonas species, proposed to be named Pseudomonas allii sp. nov., with MAFF 301514T (=ICMP 23680T) being the type strain.

scholarly journals Comparative genomic insights into the epidemiology and virulence of plant pathogenic pseudomonads from Turkey

2021 ◽  
Vol 7 (7) ◽  
Author(s):  
Marcus M. Dillon ◽  
Tatiana Ruiz-Bedoya ◽  
Cedoljub Bundalovic-Torma ◽  
Kevin M. Guttman ◽  
Haejin Kwak ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Type Species ◽  
Plant Pathogens ◽  
Molecular Mechanisms ◽  
Comparative Genomic ◽  
Complex Nature ◽  
Growth Promoter ◽  
Content Type ◽  
Link Type ◽  
Species Complexes

Pseudomonas is a highly diverse genus that includes species that cause disease in both plants and animals. Recently, pathogenic pseudomonads from the Pseudomonas syringae and Pseudomonas fluorescens species complexes have caused significant outbreaks in several agronomically important crops in Turkey, including tomato, citrus, artichoke and melon. We characterized 169 pathogenic Pseudomonas strains associated with recent outbreaks in Turkey via multilocus sequence analysis and whole-genome sequencing, then used comparative and evolutionary genomics to characterize putative virulence mechanisms. Most of the isolates are closely related to other plant pathogens distributed among the primary phylogroups of P. syringae , although there are significant numbers of P. fluorescens isolates, which is a species better known as a rhizosphere-inhabiting plant-growth promoter. We found that all 39 citrus blast pathogens cluster in P. syringae phylogroup 2, although strains isolated from the same host do not cluster monophyletically, with lemon, mandarin orange and sweet orange isolates all being intermixed throughout the phylogroup. In contrast, 20 tomato pith pathogens are found in two independent lineages: one in the P. syringae secondary phylogroups, and the other from the P. fluorescens species complex. These divergent pith necrosis strains lack characteristic virulence factors like the canonical tripartite type III secretion system, large effector repertoires and the ability to synthesize multiple bacterial phytotoxins, suggesting they have alternative molecular mechanisms to cause disease. These findings highlight the complex nature of host specificity among plant pathogenic pseudomonads.

Rapid typing of carbapenem-resistant Acinetobacter baumannii and Acinetobacter nosocomialis by multiplex Pan- and OXA-PCR assays

2021 ◽  
Vol 70 (7) ◽  
Author(s):  
Hsing-Yu Chen ◽  
Chuan-Chung Chuang ◽  
Yu-Ching Chou ◽  
Wei-Jane Hsu ◽  
I-Chieh Lin ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Molecular Typing ◽  
Type Species ◽  
Alternative Methods ◽  
Promising Alternative ◽  
Content Type ◽  
Link Type ◽  
Healthcare Settings ◽  
Carbapenem Resistant ◽  
Pcr Assays

Introduction. Outbreaks of carbapenem-resistant A. baumannii and A. nosocomialis have occurred worldwide in healthcare settings. Rapid and reliable molecular typing of bacterial isolates is vital for the effective surveillance of institutional outbreaks. The Pan-PCR and OXA-PCR assays are two multiplex PCR-based assays for the molecular typing of Acinetobacter species. Gap statement. However, few studies have investigated the discriminatory power of two multiplex PCR assays in in the genotyping of Acinetobacter species. Aim. We aimed to evaluate the efficacies of the Pan-PCR and OXA-PCR assays for molecular typing of A. baumannii and A. nosocomialis . Methodology. A total of 105 carbapenem-resistant A. baumannii isolates (CRABs) and 93 carbapenem-resistant A. nosocomialis isolates (CRANs) obtained from blood cultures were used for molecular typing by the Pan-PCR and OXA-PCR assays and two multilocus sequence typing (MLST) schemes. Results. The isolates were individually divided into 12 and 21 different sequence types via the Pasteur and Oxford MLST schemes, respectively. Additionally, these isolates were distinguished into 18 different types by the Pan-PCR and OXA-PCR assays. The results of the Pan-PCR and OXA-PCR assays distinguished CRABs and CRANs with a sensitivity of 98.13 % and a specificity of 100 %. Conclusion. The Pan-PCR and OXA-PCR assays are promising alternative methods for rapid molecular typing of CRABs and CRANs in a routine laboratory setting.

scholarly journals Sequence analysis of 16S rDNA, gyrB and alkB genes of plant-associated Rhodococcus species from Tunisia

2020 ◽  
Vol 70 (12) ◽  
pp. 6491-6507
Author(s):  
Sabrine Dhaouadi ◽  
Amira H. Mougou ◽  
Chao J. Wu ◽  
Mark L. Gleason ◽  
Ali Rhouma
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rdna ◽  
Type Species ◽  
Plant Pathogens ◽  
Species Level ◽  
Plant Growth Promoting Bacteria ◽  
Content Type ◽  
Link Type ◽  
Rhodococcus Species ◽  
Type Strains

The genus Rhodococcus contains several species with agricultural, biotechnological and ecological importance. Within this genus, many phyllosphere, rhizosphere and endosphere strains are plant growth promoting bacteria, whereas strains designated as R. fascians are plant pathogens. In this study, we isolated 47 Rhodococcus strains from a range of herbaceous and woody plant species. Phylogenetic analysis based on 16S rDNA, gyrB and alkB genes was used to compare our strains with type strains of Rhodococcus . For most of our strains, sequence similarity of the 16S rDNA, gyrB and alkB regions to type strains ranged from 98–100 %. Results of the concatenated gene sequence comparisons identified 18 strains of R. fascians and three strains of R. kroppenstedtii . The remaining strains were unclassified, and may represent novel species of Rhodococcus . Phylogenetic analysis based on gyrB sequences provided a more precise classification of our strains to species level than 16S rDNA sequences, whereas analysis of alkB sequences was unable to identify strains with orange-coloured colonies to species level.

scholarly journals Rapid molecular evolution of Spiroplasma symbionts of Drosophila

2021 ◽  
Vol 7 (2) ◽  
Author(s):  
Michael Gerth ◽  
Humberto Martinez-Montoya ◽  
Paulino Ramirez ◽  
Florent Masson ◽  
Joanne S. Griffin ◽  
...  
Keyword(s):  
Type Species ◽  
Plant Pathogens ◽  
Evolutionary Ecology ◽  
Structural Genomic ◽  
Substitution Rates ◽  
Content Type ◽  
Link Type ◽  
Insect Symbionts ◽  
Peculiar Nature

Spiroplasma is a genus of Mollicutes whose members include plant pathogens, insect pathogens and endosymbionts of animals. Spiroplasma phenotypes have been repeatedly observed to be spontaneously lost in Drosophila cultures, and several studies have documented a high genomic turnover in Spiroplasma symbionts and plant pathogens. These observations suggest that Spiroplasma evolves quickly in comparison to other insect symbionts. Here, we systematically assess evolutionary rates and patterns of Spiroplasma poulsonii , a natural symbiont of Drosophila. We analysed genomic evolution of sHy within flies, and sMel within in vitro culture over several years. We observed that S. poulsonii substitution rates are among the highest reported for any bacteria, and around two orders of magnitude higher compared with other inherited arthropod endosymbionts. The absence of mismatch repair loci mutS and mutL is conserved across Spiroplasma , and likely contributes to elevated substitution rates. Further, the closely related strains sMel and sHy (>99.5 % sequence identity in shared loci) show extensive structural genomic differences, which potentially indicates a higher degree of host adaptation in sHy, a protective symbiont of Drosophila hydei. Finally, comparison across diverse Spiroplasma lineages confirms previous reports of dynamic evolution of toxins, and identifies loci similar to the male-killing toxin Spaid in several Spiroplasma lineages and other endosymbionts. Overall, our results highlight the peculiar nature of Spiroplasma genome evolution, which may explain unusual features of its evolutionary ecology.

Martelella endophytica sp. nov., an antifungal bacterium associated with a halophyte

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2914-2919 ◽  
Author(s):  
Fehmida Bibi ◽  
Eu Jin Chung ◽  
Ajmal Khan ◽  
Che Ok Jeon ◽  
Young Ryun Chung
Keyword(s):  
Type Species ◽  
Plant Pathogens ◽  
Biochemical Characterization ◽  
Endophytic Bacterium ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Hybridization Data ◽  
Gram Staining

A Gram-staining-negative, non-spore-forming endophytic bacterium, designated strain YC6887T, was isolated from a root sample of a halophyte, Rosa rugosa, collected from a tidal flat area of Namhae Island, located at the southern end of Korea. Strain YC6887T was found to exhibit inhibitory activity against oomycete plant pathogens. The cells were non-motile and aerobic rods. The strain was able to grow at 4–40 °C (optimum 28–30 °C) and at pH 5.0–9.0 (optimum pH 7.0–8.5). Strain YC6887T was able to grow at NaCl concentrations of 0–9 % (w/v) with optimum growth at 4–5 % (w/v) NaCl, but NaCl is not essential for growth. Comparison of 16S rRNA gene sequences showed that the strain was a member of the genus Martelella , a member of order Rhizobiales , exhibiting highest similarity with Martelella mediterranea (98.6 %). The DNA–DNA relatedness between strain YC6887T and M. mediterranea MACL11T was 19.8±6.8. Chemotaxonomically, strain YC6887T contained C19 : 0 cyclo ω8c (28.0 %) and C18 : 1ω7c (17.9 %) as predominant fatty acids, confirming the affiliation of strain YC6887T with the genus Martelella . The major respiratory quinone was Q-10 and the DNA G+C content was 62.1 mol%. On the basis of phylogenetic analysis, physiological and biochemical characterization and DNA–DNA hybridization data, strain YC6887T should be classified as representing a novel species of the genus Martelella , for which the name Martelella endophytica sp. nov. is proposed. The type strain is YC6887T ( = KCCM 43011T = NBRC 109149T).

scholarly journals From cloning to mutant in 5 days: rapid allelic exchange in Staphylococcus aureus

2021 ◽  
Author(s):  
Ian R. Monk ◽  
Timothy P. Stinear
Keyword(s):  
Staphylococcus Aureus ◽  
Type Species ◽  
Point Mutations ◽  
Site Specific ◽  
Content Type ◽  
Allelic Exchange ◽  
Link Type ◽  
Foreign Dna ◽  
Time Required ◽  
A Site

In the last 10 years, the barriers preventing the uptake of foreign DNA by clinical Staphylococcus aureus isolates have been identified and powerful mutagenesis techniques such as allelic exchange are now possible in most genotypes. However, these targeted approaches can still be cumbersome, and the construction of unmarked deletions/point mutations may take many weeks or months. Here, we introduce a streamlined allelic exchange protocol using IMxxB Escherichia coli and the plasmid pIMAY-Z. With this optimized approach, a site-specific mutation can be introduced into S. aureus in 5 days, from the start of cloning to isolation of genomic DNA for confirmatory whole-genome sequencing. This streamlined protocol considerably reduces the time required to introduce a specific, unmarked mutation in S. aureus and should dramatically improve the scalability of gene-function studies.

Clostridium fungisolvens sp. nov., a new β-1,3-glucan-decomposing bacterium isolated from anoxic soil subjected to biological soil disinfestation

2021 ◽  
Author(s):  
Atsuko Ueki ◽  
Akio Tonouchi ◽  
Nobuo Kaku ◽  
Katsuji Ueki
Keyword(s):  
Genome Analysis ◽  
Type Species ◽  
Plant Pathogens ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Soil Disinfestation ◽  
Link Type ◽  
Biological Soil Disinfestation

Biological soil disinfestation (BSD) or reductive soil disinfestation (RSD) is a bioremediation method used to suppress or eliminate soil-borne plant pathogens by stimulating activities of indigenous anaerobic bacteria of the soil. An anaerobic bacterial strain (TW1T) was isolated from an anoxic soil sample subjected to the BSD treatment and comprehensively characterized. Cells of the strain were Gram-stain-positive, slightly curved and motile rods producing terminal spores. The strain was aerotolerant. Strain TW1T was saccharolytic and produced acetate, butyrate, H2 and CO2 as fermentation end products. Strain TW1T decomposed β-1,3-glucan (curdlan and laminarin) and degraded mycelial cells of an ascomycete Fusarium plant pathogen. Major cellular fatty acids of strain TW1T were C14 : 0, C14 : 0 dimethylacetal (DMA), C16 : 0 aldehyde and C16 : 0 DMA. Strain TW1T made a group on the phylogenetic tree constructed based on 16S rRNA gene sequences with species such as Clostridium fallax (96.3 %) and Clostridium polyendosporum (96.0 %). Whole genome analysis of strain TW1T showed that the total length of the genome was 5.28 Mb with the DNA G+C content of 31.3 mol%. The average nucleotide identity (ANIb) between strain TW1T and C. fallax was 71.2 %. Presence of the genes encoding laminarinase or GH16 β-glucosidase was confirmed from the genome analysis of strain TW1T. Based on the genomic, phylogenetic and phenotypic properties obtained, we propose strain TW1T should be assigned in the genus Clostridium in the family Clostridiaceae as Clostridium fungisolvens sp. nov. The type strain TW1T (=NBRC 112097T=DSM 110791T).

scholarly journals Friend or foe? Exploring the fine line between Pseudomonas brassicacearum and phytopathogens

2020 ◽  
Vol 69 (3) ◽  
pp. 347-360 ◽  
Author(s):  
April S. Gislason ◽  
Teri R. de Kievit
Keyword(s):  
Type Species ◽  
Plant Pathogens ◽  
Growth Promotion ◽  
Physiological State ◽  
Content Type ◽  
Fine Line ◽  
Link Type ◽  
Fitness Advantage ◽  
Single Organism ◽  
Pseudomonas Brassicacearum

Pseudomonas brassicacearum is one of over fifty species of bacteria classified into the P. fluorescens group. Generally considered a harmless commensal, these bacteria are studied for their plant-growth promotion (PGP) and biocontrol characteristics. Intriguingly, P. brassicacearum is closely related to P. corrugata , which is classified as an opportunistic phytopathogen. Twenty-one P. brassicacearum genomes have been sequenced to date. In the current review, genomes of P. brassicacearum and strains from the P. corrugata clade were mined for regions associated with PGP, biocontrol and pathogenicity. We discovered that ‘beneficial’ bacteria and those classified as plant pathogens have many genes in common; thus, only a fine line separates beneficial/harmless commensals from those capable of causing disease in plants. The genotype and physiological state of the plant, the presence of biotic/abiotic stressors, and the ability of bacteria to manipulate the plant immune system collectively contribute to how the bacterial-plant interaction plays out. Because production of extracellular metabolites is energetically costly, these compounds are expected to impart a fitness advantage to the producer. P. brassicacearum is able to reduce the threat of nematode predation through release of metabolites involved in biocontrol. Moreover this bacterium has the unique ability to form biofilms on the head of Caenorhabditis elegans, as a second mechanism of predator avoidance. Rhizobacteria, plants, fungi, and microfaunal predators have occupied a shared niche for millions of years and, in many ways, they function as a single organism. Accordingly, it is essential that we appreciate the dynamic interplay among these members of the community.

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