scholarly journals Bacterial Canker Disease on Populus × euramericana Caused by Lonsdalea populi in Serbia

Forests ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1080
Author(s):  
Milica Zlatković ◽  
Imola Tenorio-Baigorria ◽  
Tamás Lakatos ◽  
Tímea Tóth ◽  
András Koltay ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Test Chamber ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
Bacterial Canker ◽  
Canker Disease ◽  
Populus Euramericana ◽  
First Report ◽  
Eastern Cottonwood

Populus × euramericana (Dode) Guinier clone (cl.) “I-214” is a fast-growing interspecific hybrid between Eastern cottonwood (P. deltoides Bartr. ex Marsh) and European black poplar (Populus nigra L.). Populus × euramericana was introduced into Serbia in the 1950s and has become one of the most widely grown poplar species. In September 2019, cankers were observed on stems and branches of P. × euramericana cl. “I-214” trees in a two-year-old poplar plantation in the province of Vojvodina, Serbia. The canker tissue was soft and watery, and a colorless fluid that smelled rotten flowed from the cracks in the bark, suggesting possible bacterial disease. After two weeks, diseased trees experienced crown die-back and oozing of foamy, odorous exudates and this study aimed to identify the causal agent of the disease. Canker margins and exudates were collected from 20 symptomatic trees. The associated bacterium was isolated and identified using biochemical characteristics, phylogenetic analyses based on 16S rRNA gene sequences, and multilocus sequence analyses (MLSA) based on partial sequencing of three housekeeping genes (gyrB, infB, and atpD). The pathogen was identified as Lonsdalea populi. Pathogenicity tests were conducted on rooted cuttings of P. × euramericana cl. “I-214” in an environmental test chamber and demonstrated that the isolated bacterial strain was able to reproduce symptoms of softened, water-soaked cankers and exudation. To the best of our knowledge, this is the first report of L. populi causing bacterial canker disease on P. × euramericana cl. “I-214” in Serbia and in southeastern Europe (SEE). It is also the first report of a bacterial disease on hybrid poplars, including P. × euramericana in this country and in SEE. If the disease spreads into new areas, selection for L. populi resistance may need to be integrated into future poplar breeding programs.

scholarly journals 'Candidatus Phytoplasma sacchari’, a novel taxon - associated with Sugarcane Grassy Shoot (SCGS) disease

2020 ◽  
Author(s):  
Kiran Kirdat ◽  
Bhavesh Tiwarekar ◽  
Vipool Thorat ◽  
Shivaji Sathe ◽  
Yogesh Shouche ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Indian Subcontinent ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Genome Sequences ◽  
Phytoplasma Strain ◽  
White Leaf

Sugarcane Grassy Shoot (SCGS) disease is known to be related to Rice Yellow Dwarf (RYD) phytoplasmas (16SrXI-B group) which are found predominantly in sugarcane growing areas of the Indian subcontinent and South-East Asia. The 16S rRNA gene sequences of SCGS phytoplasma strains belonging to the 16SrXI-B group share 98.07 % similarity with ‘Ca. Phytoplasma cynodontis’ strain BGWL-C1 followed by 97.65 % similarity with ‘Ca. P. oryzae’ strain RYD-J. Being placed distinctly away from both the phylogenetically related species, the taxonomic identity of SCGS phytoplasma is unclear and confusing. We attempted to resolve the phylogenetic positions of SCGS phytoplasma based on the phylogenetic analysis of 16S rRNA gene (>1500 bp), nine housekeeping genes (>3500 aa), core genome phylogeny (>10 000 aa) and OGRI values. The draft genome sequences of SCGS phytoplasma (strain SCGS) and Bermuda Grass White leaf (BGWL) phytoplasma (strain LW01), closely related to ‘Ca. P. cynodontis’, were obtained. The SCGS genome was comprised of 29 scaffolds corresponding to 505 173 bp while LW01 assembly contained 21 scaffolds corresponding to 483 935 bp with the fold coverages over 330× and completeness over 90 % for both the genomes. The G+C content of SCGS was 19.86 % while that of LW01 was 20.46 %. The orthoANI values for the strain SCGS against strains LW01 was 79.42 %, and dDDH values were 22. Overall analysis reveals that SCGS phytoplasma forms a distant clade in RYD group of phytoplasmas. Based on phylogenetic analyses and OGRI values obtained from the genome sequences, a novel taxon ‘Candidatus Phytoplasma sacchari’ is proposed.

scholarly journals Comparative Genomics and Phylogenetic Analyses Suggest Several Novel Species within the Genus Clavibacter, Including Nonpathogenic Tomato-Associated Strains

2020 ◽  
Vol 86 (6) ◽  
Author(s):  
Ebrahim Osdaghi ◽  
Touraj Rahimi ◽  
S. Mohsen Taghavi ◽  
Maryam Ansari ◽  
Sadegh Zarei ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Comparative Genomics ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Sensu Stricto ◽  
Bacterial Canker ◽  
Agricultural Crops ◽  
Content Type ◽  
Canker Disease

ABSTRACT Members of the genus Clavibacter are economically important bacterial plant pathogens infecting a set of diverse agricultural crops (e.g., alfalfa, corn, potato, tomato, and wheat). Tomato-associated Clavibacter sp. strains account for a great portion of the genetic diversity of the genus, and C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis), causing bacterial canker disease, is considered one of the most destructive seed-borne agents for the crop worldwide. However, current taxonomic descriptions of the genus do not reflect the existing diversity of the strains, resulting in unsatisfactory results in quarantine surveys for the pathogens. In this study, we used all the available genome sequences of Clavibacter sp. strains, including the type strains of newly described subspecies, to provide precise insight into the diversity of tomato-associated members of the genus and further clarify the taxonomic status of the strains using genotypic and phenotypic features. The results of phylogenetic analyses revealed the existence of nine hypothetical new species among the investigated strains. None of the three new subspecies (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) is included within the tomato-pathogenic C. michiganensis sensu stricto lineage. Although comparative genomics revealed the lack of chp and tomA pathogenicity determinant gene clusters in the nonpathogenic strains, a number of pathogenicity-related genes were noted to be present in all the strains regardless of their pathogenicity characteristics. Altogether, our results indicate a need for a formal taxonomic reconsideration of tomato-associated Clavibacter sp. strains to facilitate differentiation of the lineages in quarantine inspections. IMPORTANCE Clavibacter spp. are economically important bacterial plant pathogens infecting a set of diverse agricultural crops, such as alfalfa, corn, pepper, potato, tomato, and wheat. A number of plant-pathogenic members of the genus (e.g., C. michiganensis sensu stricto and C. sepedonicus, infecting tomato and potato plants, respectively) are included in the A2 (high-risk) list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Although tomato-associated members of Clavibacter spp. account for a significant portion of the genetic diversity in the genus, only the strains belonging to C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis) cause bacterial canker disease of tomato and are subjected to the quarantine inspections. Hence, discrimination between the pathogenic and nonpathogenic Clavibacter sp. strains associated with tomato seeds and transplants plays a pivotal role in the accurate detection and cost-efficient management of the disease. On the other hand, detailed information on the genetic contents of different lineages of the genus would lead to the development of genome-informed specific detection techniques. In this study, we have provided an overview of the phylogenetic and genomic differences between the pathogenic and nonpathogenic tomato-associated Clavibacter sp. strains. We also noted that the taxonomic status of newly introduced subspecies of C. michiganensis (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) should be reconsidered.

scholarly journals Characterization, Phylogenetic Analyses, and Pathogenicity of Enterobacter cloacae on Rice Seedlings in Heilongjiang Province, China

Plant Disease ◽  
2020 ◽  
Vol 104 (6) ◽  
pp. 1601-1609
Author(s):  
Peng Cao ◽  
Chenxu Li ◽  
Kefei Tan ◽  
Chuanzeng Liu ◽  
Xi Xu ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Enterobacter Cloacae ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
Heilongjiang Province ◽  
Rice Seedlings ◽  
Bacterial Strains ◽  
Gene Sequences

Rice is used as a staple food in different areas of world, especially in China. In recent years, rice seedlings have been affected seriously by symptoms resembling bacterial palea browning (BPB) in Heilongjiang Province. To isolate and identify the pathogenic bacteria responsible for the disease, 40 bacterial strains were isolated from diseased rice seedlings collected from the four major accumulative-temperature zones of rice fields cultivated in Heilongjiang Province, and these were identified as 13 species based on morphological characteristics and 16S ribosomal RNA (rRNA) gene sequences. Inoculation of all the isolates on healthy rice seedlings showed that the nine Enterobacter cloacae isolates were the pathogens causing typical symptoms of BPB, including yellowing to pale browning, stunting, withering, drying, and death. Moreover, the nine E. cloacae isolates could also cause symptoms of bacterial disease on the seedlings of soybean (Glycine max), maize (Zea mays L.), and tomato (Solanum lycopersicum). Phylogenetic analysis based on the 16S rRNA gene sequences and phenotypic and biochemical characteristics indicated that these nine pathogenic isolates were E. cloacae. In addition, analysis of the sequences of four housekeeping genes (rpoB, gyrB, infB, and atpD) from the selected strain SD4L also assigned the strain to E. cloacae. Therefore, E. cloacae is the pathogen causing disease of rice seedlings in Heilongjiang Province, which we propose to classify as a form of BPB. To the best of our knowledge, this is the first study to identify E. cloacae as a causal agent of BPB in rice.

Multi-locus phylogenetics of the Midichloria endosymbionts reveals variable specificity of association with ticks

Parasitology ◽  
2018 ◽  
Vol 145 (14) ◽  
pp. 1969-1978 ◽  
Author(s):  
M. Buysse ◽  
O. Duron
Keyword(s):  
Tick Species ◽  
Phylogenetic Analyses ◽  
High Specificity ◽  
Housekeeping Genes ◽  
Limited Range ◽  
Evolutionary Strategies ◽  
Rrna Gene ◽  
Typing Method ◽  
History Of ◽  
Horizontal Transfers

AbstractCandidatus Midichloria mitochondrii is a maternally inherited bacterium of ticks with a unique intra-mitochondrial lifestyle. Here, we investigate on the evolutionary history of these associations and the degree of Midichloria–tick specificity. While previous surveys used the 16S rRNA gene as an exclusive molecular marker, we rather developed a multi-locus typing method based on four more variable housekeeping genes (groEL, rpoB, dnaK and ftsZ) and on one flagellum gene (fliC) present in Midichloria genomes. Using this method, multi-locus phylogenetic analyses revealed the structuring of a wide Midichloria genetic diversity into three distinct lineages associated with ticks. Overall, two distinct evolutionary strategies are obvious depending on lineage: two Midichloria lineages are generalists with infections acquired through horizontal transfers between distantly related tick species but one other Midichloria lineage rather show a high specificity degree to the Ixodes tick genus. This pattern suggests a capacity of certain Midichloria strains to maintain infections in only limited range of related tick species. These different infection strategies of Midichloria highlight an unexpected variability in their dependency to their tick hosts. We further conjecture that this pattern is also likely to indicate variability in their effects on ticks.

scholarly journals First Report of Bacterial Stalk Rot of Maize Caused by Dickeya zeae in Mexico

Plant Disease ◽  
2014 ◽  
Vol 98 (9) ◽  
pp. 1267-1267 ◽  
Author(s):  
B. A. Martinez-Cisneros ◽  
G. Juarez-Lopez ◽  
N. Valencia-Torres ◽  
E. Duran-Peralta ◽  
M. Mezzalama
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Pathogenic Bacteria ◽  
The State ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
Sterile Water ◽  
First Report ◽  
Stalk Rot ◽  
Positive Controls

A bacterial disease of maize, bacterial stalk and top rot, was found in the state of Morelos in February 2011, and in the state of Puebla in July 2013, Mexico. In both cases, the incidence of diseased plants was lower than 0.5%. The typical symptoms were a soft rot and darkening of the tissues affecting the stalk and the top of the plant, causing breaking of the stalk. The lesions progressed from the top to below nodes, leaf sheaths and blades, and rotten tissues emitted an unpleasant odor. Eleven diseased plants were collected, and bacterial colonies were isolated from fragments detached from the edges of symptomatic tissues after sterilization with a 0.5% solution of NaClO for 30 s, rinsing three times in sterile water. The sterilized fragments were macerated in drops of distilled sterile water for 10 min and the extract was streaked on King's medium B (agar 15 g, distilled water 1,000 ml, proteose peptone 20 g, K2HPO4 1.5 g, MgSO4·7H2O 1.5 g, glycerol 10 ml). Eight representative strains from Morelos and five from Puebla were selected for identification. All strains were gram-negative, grew at 37°C, showed pectynolitic activity on potato tubers, were positive for indole production, utilized arabinose, galactose, glucose, glycerol, lactose, mannose, melibiose, rafinose, ribose, and sucrose but did not produce acid from arabitol, adonitol, and keto-methyl-glucoside (3,4). Pathogenicity tests were conducted with each strain by inoculating with a syringe four 25-day-old maize seedlings with 107 CFU ml–1 bacterial cells in the leaf collar. Plants were incubated in the greenhouse at 30°C during the day and 24°C during the night with a 12-h photoperiod, and relative humidity of 93%. The reference strains Erwinia chrysanthemi pv zeae ATTC29942 and Dickeya zeae CFBP 2052 were used as positive controls in laboratory and greenhouses tests. Sterile water was used as negative control. Two days after inoculation, soft stalk rot symptoms developed that were identical to those observed in the field. No symptoms were observed on the negative controls. Diagnostic amplification of DNA by conventional PCR was carried out and yielded the expected amplicon size of 420 bp of the Dickeya-specific pel gene with the ADE primers set (2). PCR was used to amplify the 16S rRNA gene with the universal primers 27f and 1495r (5) for molecular identification of the 13 strains (GenBank Accession Nos. KJ438941, KJ438942, KJ438943, KJ438944, KJ438945, KJ438946, KJ438947, KJ438948, KJ438949, KJ438950, KJ438951, KJ438952, and KJ438953). The strains D. zeae CFBP 2052 and E. chrysanthemi pv. zeae ATCC 29942 were sequenced as positive controls. A BLAST search with the 13 16S rRNA gene sequences of 1.4 kb were 99% identical to the sequence of D. zeae CFBP 2052 (NR_041923). D. zeae can be a major disease of maize in tropical and subtropical countries. It is particularly severe under conditions of high temperature and high humidity, but it occurs sporadically. Control of the vector, Chilo partellus, can aid disease management (1). To our knowledge, this is the first report of D. zeae causing maize stalk rot in Mexico. References: (1) CABI. Crop Prot. Compend. CAB International, Wallingford, UK, 2014. (2) A. Nassar et al. Appl. Environ. Microbiol. 62:2228, 1996. (3) R. Samson et al. Int. J. Syst. Evol. Microbiol. 55:1415, 2005. (4) N. W. Schaad et al. Laboratory Guide for Identification of Plant Pathogenic Bacteria. 3rd ed. APS Press, St. Paul, MN, 2001. (5) W. G. Weisburg. J. Bacteriol. 173:697, 1991.

scholarly journals First Report of Pear Blossom Blast Caused by Pseudomonas syringae pv. syringae in China

Plant Disease ◽  
2008 ◽  
Vol 92 (5) ◽  
pp. 832-832 ◽  
Author(s):  
L. H. Xu ◽  
G. L. Xie ◽  
B. Li ◽  
B. Zhu ◽  
F. S. Xu ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Similarity Index ◽  
Nutrient Agar ◽  
Identification System ◽  
Pyrus Pyrifolia ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
First Report ◽  
Microbial Identification ◽  
Microbial Identification System

In the spring of 2006, a new bacterial disease was noted in pear orchards near Hangzhou, Zhejiang Province, China. The disease caused severe blossom blast on pears (Pyrus pyrifolia; cv. Cuiguan). Early symptoms of the disease included blackening of the calyx end of developing fruit, blackening of blossom clusters while leaves of affected blossom clusters appeared normal, or death of clusters consisting of both blossoms and leaves. Later, tips of twigs turned dark brown and died. No bacterial ooze was observed. Twelve bacterial isolates were recovered from ten samples of buds and blossoms. Six isolates were selected for identification. They were similar to those of the reference strains of Pseudomonas syringae pv. syringae LMG5570 and LMG 2230 from Belgium in phenotypic tests on the basis of the Biolog Microbial Identification System (version 4.2; Biolog Inc., Hayward, CA), pathogenicity tests, gas chromatographic analysis of fatty acid methyl esters (FAMEs) using the Microbial Identification System (MIDI Inc., Newark, DE) with aerobic bacterial library (TABA50), and electron microscopy (TEM, KYKY-1000B, Japan). All isolates tested were gram-negative, aerobic rods measuring 1.5 to 2.4 × 0.5 to 0.6 μm with 2 to 4 polar flagella. Fluorescent green diffusible pigment was produced on King's Medium B. Colonies were gray-white and slightly raised with smooth margins on nutrient agar. They produced levan on sucrose nutrient agar. A hypersensitive reaction was observed on tobacco cv. Benshi 24 h after inoculation. All isolates were identified as P. syringae pv. syringae with Biolog similarity index of 0.57 to 0.86 and FAME similarity index of 0.58 to 0.81. Identification as P. syringae pv. syringae was confirmed using 16S rDNA universal primers (2,3): 5′-AGA GTT TGA TCA TGG CTC AG-3′ forward primer, 5′-ACG GTT ACC TTG TTA CGA CTT-3′ reverse primer. The PCR fragments of the three isolates were sequenced and compared with sequences in GenBank. They had 99% similiarity with P. syringae pv. syringae 16S rRNA gene strain NCPPB 3869. Koch's postulates were conducted on buds of the original pear cultivar growing in pots and detached pear blossoms in flasks by spray inoculation with cell suspensions containing 108 CFU/ml of the six isolates at 18 to 22°C with two replications. The bacteria induced symptoms on buds and blossoms similar to those observed in the field. The bacterium was reisolated from symptomatic pear buds and internal ovary tissues. P. syringae pv. syringae was first reported in England as the cause of pear blossom blast in 1914 (1). After searching all the Chinese agricultural databases and major journals (National Knowledge Infrastructure database, Vip Chinese periodical database, Chinese wanfang database, China InfoBank, Scientia Agricultura Sinica, Acta Phytopathologica Sinica, Acta Phytophylacica Sinica, and Journal of Fruit Science), to our knowledge, this is the first report of pear blossom blast caused by P. syringae pv. syringae in China. The disease cycle on pear trees and the control strategies in the regions are being further studied. References: (1) B. P. Barker et al. Ann. Appl. Biol. 1:85, 1914. (2) U. Edward et al. Nucleic Acids Res. 17:7843,1989. (3) B. Li et al. J. Phytopathol. 34:141, 2006.

scholarly journals Bradyrhizobium ingae sp. nov., isolated from effective nodules of Inga laurina grown in Cerrado soil

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3395-3401 ◽  
Author(s):  
Krisle da Silva ◽  
Sofie E. De Meyer ◽  
Luc F. M. Rouws ◽  
Eliane N. C. Farias ◽  
Marco A. O. dos Santos ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Slow Growth Rate ◽  
Link Type ◽  
Commercial Inoculant

Root-nodule bacteria were isolated from Inga laurina (Sw.) Willd. growing in the Cerrado Amazon region, State of Roraima, Brazil. The 16S rRNA gene sequences of six strains (BR 10250T, BR 10248, BR 10249, BR 10251, BR 10252 and BR 10253) showed low similarities with currently described species of the genus Bradyrhizobium . Phylogenetic analyses of sequences of five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed Bradyrhizobium iriomotense EK05T to be the closest type strain (97.4 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [with the major components C16 : 0 and summed feature 8 (C18 : 1ω6c/C18 : 1ω7c)], the slow growth rate and carbon compound utilization patterns supported the assignment of our strains to the genus Bradyrhizobium . Results from DNA–DNA hybridizations and physiological traits differentiated our strains from the closest related species of the genus Bradyrhizobium with validly published names. Sequences of symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) grouped together with those of B. iriomotense EK05T and Bradyrhizobium sp. strains BR 6610 (used as a commercial inoculant for Inga marginata in Brazil) and TUXTLAS-10 (previously observed in Central America). Based on these data, the six strains represent a novel species, for which the name Bradyrhizobium ingae sp. nov. is proposed. The type strain is BR 10250T ( = HAMBI 3600T).

scholarly journals Rhizobium vallis sp. nov., isolated from nodules of three leguminous species

2011 ◽  
Vol 61 (11) ◽  
pp. 2582-2588 ◽  
Author(s):  
Fang Wang ◽  
En Tao Wang ◽  
Li Juan Wu ◽  
Xin Hua Sui ◽  
Ying Li ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Root Nodules ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Bacterial Strains

Four bacterial strains isolated from root nodules of Phaseolus vulgaris, Mimosa pudica and Indigofera spicata plants grown in the Yunnan province of China were identified as a lineage within the genus Rhizobium according to the analysis of 16S rRNA gene sequences, sharing most similarity with Rhizobium lusitanum P1-7T (99.1 % sequence similarity) and Rhizobium rhizogenes IAM 13570T (99.0 %). These strains also formed a distinctive group from the reference strains for defined species of the genus Rhizobium in a polyphasic approach, including the phylogenetic analyses of the 16S rRNA gene and housekeeping genes (recA, atpD, glnII), DNA–DNA hybridization, BOX-PCR fingerprinting, phenotypic characterization, SDS-PAGE of whole-cell proteins, and cellular fatty acid profiles. All the data obtained in this study suggested that these strains represent a novel species of the genus Rhizobium, for which the name Rhizobium vallis sp. nov. is proposed. The DNA G+C content (mol%) of this species varied between 60.9 and 61.2 (T m). The type strain of R. vallis sp. nov. is CCBAU 65647T ( = LMG 25295T  = HAMBI 3073T), which has a DNA G+C content of 60.9 mol% and forms effective nodules on Phaseolus vulgaris.

scholarly journals Paracoccus aeridis sp. nov., an indole-producing bacterium isolated from the rhizosphere of an orchid, Aerides maculosa

2020 ◽  
Vol 70 (3) ◽  
pp. 1720-1728 ◽  
Author(s):  
Anusha Rai ◽  
Smita N ◽  
Suresh G ◽  
Shabbir A ◽  
Deepshikha G ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Western Ghats Of India

A Gram-stain-negative, non-motile, coccoid-shaped, catalase- and oxidase-positive, non-denitrifying, neutrophilic bacterium designated as strain JC501T was isolated from an epiphytic rhizosphere of an orchid, Aerides maculosa, growing in the Western Ghats of India. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that strain JC501T belonged to the genus Paracoccus and had the highest levels of sequence identity with Paracoccus marinus KKL-A5T (98.9 %), Paracoccus contaminans WPAn02T (97.3 %) and other members of the genus Paracoccus (<97.3 %). Strain JC501T produced indole-3 acetic acid and other indole derivatives from tryptophan. The dominant respiratory quinone was Q-10 and the major fatty acid was C18 : 1ω7c/C18 : 1ω6c, with significant quantities of C18 : 1ω9c, C17 : 0 and C16 : 0. The polar lipids of strain JC501T comprised phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an unidentified glycolipid, two unidentified aminolipids, two unidentified lipids and four unidentified phospholipids. The genome of strain JC501T was 3.3 Mbp with G+C content of 69.4 mol%. For the resolution of the phylogenetic congruence of the novel strain, the phylogeny was also reconstructed with the sequences of eight housekeeping genes. Based on the results of phylogenetic analyses, low (<85.9 %) average nucleotide identity, digital DNA–DNA hybridization (<29.8 %), chemotaxonomic analysis and physiological properties, strain JC501T could not be classified into any of the recognized species of the genus Paracoccus . Strain JC501T represents a novel species, for which the name Paracoccus aeridis sp. nov. is proposed. The type strain is JC501T (=LMG 30532T=NBRC 113644T).

scholarly journals First Report of Pectobacterium punjabense Causing Blackleg and Soft Rot on Potato in Hebei and Fujian Province, China

Plant Disease ◽  
2022 ◽  
Author(s):  
Utpal Handique ◽  
Yaning Cao ◽  
Dekang Wang ◽  
Ruofang Zhang ◽  
Wensi Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Housekeeping Genes ◽  
Soft Rot ◽  
Rrna Gene ◽  
Pectobacterium Carotovorum ◽  
Fujian Province ◽  
First Report ◽  
Potato Plants ◽  
Carotovorum Subsp

Pectobacterium spp. and Dickeya spp. cause blackleg and soft rot on potato worldwide (Charkowski, 2018). Potato plants (cv. Favorita or Jizhang 8#) with blackleg symptoms (vascular browning of crown stems, Fig. S1) were observed in the field in Zhangjiakou, Hebei province in 2018, and in Ningde, Fujian Province in 2019, in China. The disease incidence was around 50% and 10% in Zhangjiakou (5 ha) and Ningde (4 ha), respectively. Diseased plants (3 from each site) were collected to isolate the pathogen. Blackleg symptomatic stems were soaked in 75% ethanol for 2 min, rinsed and ground in sterile distilled water. Serial tenfold dilutions of the above solution were plated onto the crystal violet pectate agar (CVP) plate (Ge et al., 2018). Two to 3 days after incubation at 28°C, 4 bacterial colonies in total which digested pectin from the media and developed pit on CVP plates were purified and sequenced for identification using the universal 16S rRNA gene primer set 27F/1492R (Monciardini et al., 2002). Two colony sequences that showed more than 99% sequence identity to Pectobacterium punjabense type strain SS95 (MH249622) were submitted to the GenBank ( accession numbers: OK510280, MT242589). Additionally, six housekeeping genes proA (OK546205, OK546199), gyrA (OK546206, OK546200), icdA (OK546207, OK546201), mdh (OK546208, OK546202), gapA (OK546209, OK546203), and rpoS (OK546210, OK546204) of these two isolates were amplified and sequenced (Ma et al., 2007, Waleron et al., 2008). All strains show 99% to 100% identity with MH249622T . Phylogenetic trees based on 16S rRNA gene sequences (Fig. S2) and concatenated sequences of the housekeeping genes (Fig. S3) of the 2 isolates were constructed using MEGA 6.0 software (Tamura et al., 2013). Koch’s postulate was performed on potato seedlings and potato tubers (cv. Favorita) by injecting 100 μl bacterial suspension (105 CFU/ml) or sterile phosphate-buffered solution into the crown area of the stems or the tubers and kept at 100% humidity and 21°C for 1 day. Four days after inoculation, the infected area of the inoculated seedlings rotten and turned black, while the controls were symptomless (Fig. S4). Two days after inoculation, the infected tubers rotten and turned black, while the controls were symptomless (Fig. S4). Bacterial colonies were reisolated from these symptomatic tissues and identified using the same methods described above. Blackleg on potato plants or soft rot on potato has been reported to be caused by Pectobacterium atrosepticum, Pectobacterium carotovorum subsp. carotovorum, Pectobacterium carotovorum subsp. brasiliense, Pectobacterium parmentieri, Pectobacterium polaris in China (Zhao et al., 2018; Cao et al., 2021; Wang et al., 2021). To our knowledge, this is the first report of blackleg/soft rot of potato caused by Pectobacterium punjabense in China. We believe that this report will draw attention to the management of this pathogen in China.

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