scholarly journals Identification, Phylogenetic Analysis, and Biological Characterization of Serratia marcescens Strains Causing Cucurbit Yellow Vine Disease

2003 ◽  
Vol 93 (10) ◽  
pp. 1233-1239 ◽  
Author(s):  
J. Rascoe ◽  
M. Berg ◽  
U. Melcher ◽  
F. L. Mitchell ◽  
B. D. Bruton ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Serratia Marcescens ◽  
16S Rdna ◽  
Acid Methyl Ester ◽  
Bacterial Strains ◽  
Metabolic Functions ◽  
Distinct Cluster ◽  
Cucurbit Yellow Vine Disease ◽  
Vine Decline ◽  
Reference Strains

A serious vine decline of cucurbits known as cucurbit yellow vine disease (CYVD) is caused by rod-shaped bacteria that colonize the phloem elements. Sequence analysis of a CYVD-specific polymerase chain reaction (PCR)-amplified 16S rDNA product showed the microbe to be a γ-proteobacterium related to the genus Serratia. To identify and characterize the bacteria, one strain each from watermelon and zucchini and several noncucurbit-derived reference strains were subjected to sequence analysis and biological function assays. Taxonomic and phylogenetic placement was investigated by analysis of the groE and 16S rDNA regions, which were amplified by PCR and directly sequenced. For comparison, eight other bacterial strains identified by others as Serratia spp. also were sequenced. These sequences clearly identified the CYVD strains as Serratia marcescens. However, evaluation of metabolic and biochemical features revealed that cucurbit-derived strains of S. marcescens differ substantially from strains of the same species isolated from other environmental niches. Cucurbit strains formed a distinct cluster, separate from other strains, when their fatty acid methyl ester profiles were analyzed. In substrate utilization assays (BIOLOG, Vitek, and API 20E), the CYVD strains lacked a number of metabolic functions characteristic for S. marcescens, failing to catabolize 25 to 30 compounds that were utilized by S. marcescens reference strains. These biological differences may reflect gene loss or repression that occurred as the bacterium adapted to life as an intracellular parasite and plant pathogen.

scholarly journals First Report of Brown Spot on White Button Mushroom (Agaricus bisporus) Caused by Cedecea neteri in Iran

Plant Disease ◽  
2021 ◽  
Author(s):  
Mozhde Hamidizade ◽  
Seied Mohsen Taghavi ◽  
Hamzeh Mafakheri ◽  
Rachel A Herschlag ◽  
Samuel Martins ◽  
...  
Keyword(s):  
16S Rdna ◽  
Agaricus Bisporus ◽  
Brown Spot ◽  
Bacterial Strains ◽  
Button Mushroom ◽  
First Report ◽  
Spot Disease ◽  
Brown Spot Disease ◽  
Brown Discoloration ◽  
Reference Strains

In autumn 2018, cap discoloration and browning symptoms (up to 20% incidence) were observed on commercially grown white button mushrooms (Agaricus bisporus) in two distinct farms located in Shiraz and Marvdasht Counties in Southern Iran. Symptomatic caps (13 and six caps from Shiraz and Marvdasht Counties, respectively) were characterized by visible brown discoloration with no blotch symptoms, bacterial sticky mass and cap wilting. Isolation of bacterial strains from infected cap tissues was performed on yeast-extract peptone glucose agar (YPGA) according to Hamidizade et al. (2020). The resulted bacterial colonies were oyster-white in color, non-fluorescent, domed convex circular with smooth margins 1-2 mm in diameter. A total of six bacterial strains (Shiraz: Ir1002, Ir1003, Ir1004, Ir1005, Ir1007 and Marvdasht: Ir1027) were isolated from distinct mushroom samples. Standard biochemical and phenotypic analyses (Schaad et al. 2001) showed that the bacterial strains were Gram and oxidase negative, catalase positive and facultatively anaerobic, while no capsule or endospore was observed. All strains were positive in urease production, arginine dihydrolase, hydrolysis of tween 80, and utilization of sucrose and D-sorbitol, while they were negative in amylase, cellulose, lecithinase, pectinase, and protease production as well as casein hydrolysis. Based on these phenotypic characteristics, the strains were supposed to be members of Enterobacteriaceae. They also did not induce hypersensitive reaction (HR) on tobacco (Nicotiana tabacum cv. Turkish) leaves nor did they produce tolaasin when streaked side-by-side with “Pseudomonas reactans” strains on King B medium (Osdaghi et al. 2019). Pathogenicity of the strains was evaluated (repeated twice) on fresh caps of white button mushroom using cut-cap method (Hamidizade et al. 2020). Reference strains of Pseudomonas tolaasii (CFBP 8707) and Mycetocola spp. (CFBP 8708) were used as positive controls, while sterile distilled water was used as a negative control. Brown discoloration appeared 24-36 hours post inoculation on cap surfaces while control caps remained asymptomatic. Koch’s postulates were accomplished by re-isolation and identification of bacterial strains from the symptomatic caps using colony morphology and Gram staining. For molecular identification, all initial as well as re-isolated strains were subjected to amplification and sequencing of 16S rDNA and gyrB (Yamamoto and Harayama 1995; Hamidizade et al. 2020). Obtained nucleotide sequences were deposited into NCBI GenBank (16S: MZ298620 to MZ298625; gyrB: MZ313184 to MZ313189). BLAST search using the 16S rDNA and gyrB sequences showed that the strains isolated in this study had 97-99% sequence similarity to the reference strains of Cedecea neteri. Phylogenetic analyses also confirmed close relationship of bacterial strains from this study to C. neteri strains. Pure cultures of representative strains Ir1004 (CFBP 8900) and Ir1027 (CFBP 8896) are deposited in CIRM-CFBP culture collection. This is the first report of C. neteri causing brown spot disease on button mushroom in Iran, while the bacterium has previously been reported to cause soft rot on Pholiota nameko (Yan et al. 2018), and yellow sticky disease on Flammulina velutipes (Yan et al. 2019) in China. Further comprehensive investigations will shed a light on the economic impact of the brown spot disease on mushroom industry in Iran.

scholarly journals First report of Stenotrophomonas maltophilia causing root soft rot of Sanqi (Panax notoginseng) in China

Plant Disease ◽  
2021 ◽  
Author(s):  
Kuan Yu Zheng ◽  
Xiaoxia Su ◽  
Xue Zheng ◽  
Lizhen Zhang ◽  
Yongdui Chen ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rdna ◽  
Genomic Dna ◽  
Stenotrophomonas Maltophilia ◽  
Panax Notoginseng ◽  
Soft Rot ◽  
Rdna Sequence ◽  
Bacterial Suspension ◽  
Bacterial Strains ◽  
First Report

Sanqi (Panax notoginseng (Burk.) F. H. Chen) is a traditional Chinese medicinal plant with a long planting cycle of 2-3 years that makes it vulnerable to root diseases caused by several pathogens, including Fusarium solani, Alternaria panax, Phytophthoracactorum, and Pseudomonas sp. In April 2019, root soft rot samples of Sanqi were collected from a plantation site in Songming, southwest of China. Typical symptoms included root softening and necrosis, yellow leaf, and stem wilting. Ten diseased roots samples were collected and sterilized with 0.1% HgCl2 for 1 min, 75% ethanol for 2min, and then rinsed thrice with sterile water. Sterilized roots were cut into small pieces of 5 × 5 mm and cultured on the nutrient agar (NA) medium for 48 h at 28°C. From the root cultures, a total of thirteen bacterial strains were obtained. Three strains, SM 2-5, SM 2-13, and SM 2-14 were selected for further study. These three strains were gram-negative, short rod-shaped (1～2×0.5～1μm), non-spore-forming and had polar tufted flagella as observed under a transmission electron microscope (TEM). Also, the strains were positive for oxidase, beta-galactosidase, arginine dihydrolase, and lysine decarboxylase while negative for amylase and urease tested by biochemical methods (Wang 2017). To further determine the pathogenic species, genomic DNA of these three strains was extracted using a Genomic DNA Kit (Tsing Ke, Beijing, China), to PCR amplify 16S rDNA using universal primers 27F/1492R (Wang et al. 2017). Also, S. maltophilia 23S rDNA specific primers SM1/SM4 (Whitby et al. 2000) were used for PCR amplification to confirm the species. 16S rDNA sequence analysis showed that SM 2-5 (GenBank Accession No. MW555227), SM 2-13 (GenBank Accession No. MW555228), and SM 2-14 (GenBank Accession No. MW555229) shared the highest identity (>99.9%) with the S. maltophilia strains (GenBank Accession No. MT323142, MH669295, MN826555). Furthermore, 23S rDNA sequence analysis of SM 2-5 (GenBank Accession No. MZ707732), SM 2-13 (GenBank Accession No. MZ645941) and SM 2-14 (GenBank Accession No. MZ707733) revealed their high identity (>99.8%) with the S. maltophilia species. 16S and 23S rDNA phylogenetic analysis (Mega6.06) using the neighbor-joining (NJ) method with 1,000 bootstrap replicates revealed the three strains clustering with the other S. maltophilia strains. Therefore, based on morphology, metabolic profile, and sequence analysis, the three strains were identified as Stenotrophomonas maltophilia. To test pathogenicity, the strains were grown in the nutrient broth (NB) medium for 48h at 28°C until bacterial suspension reached to OD600≈1.0 (2.0×109CFU/mL). Then, healthy roots of one-year-old Sanqi plants, pre-washed with sterilized water and -poked with a sterilized needle, were soaked in bacterial suspension (2.0×109CFU/mL) of the three strains separately for inoculation 10min. Sterilized water treatment was used as a control. Subsequently, bacteria-inoculated plants were planted in sterile soil pots and cultured in a greenhouse at 28°C with shading rate of 70%. Each treatment group included 3 plants with 3 replicates. Ten days post inoculation, symptoms similar to the ones in natural conditions were observed in the bacteria-inoculated plants. Based on the disease index (Li et al. 2020), we found that among the three strains, SM 2-13 displayed the highest virulence, while no symptoms were observed in the control plants. The same bacterial strains were re-isolated from these inoculated roots and identified by the methods described above. Previous studies showed that some Stenotrophomonas species cause plant diseases such as rice white stripe (Singh et al. 2001), strawberry leaf black spot (Wang et al. 2017), Cyclobalanopsis patelliformis leaf spot (Bian et al. 2020), and Jatropha curcas L. seed borne and stem necrosis (Wang et al. 2018). To our knowledge, this is the first report confirming Stenotrophomonas maltophilia causing root soft rot of Panax notoginseng in China.

scholarly journals Erratum to: Deodorization of pig slurry and characterization of bacterial diversity using 16S rDNA sequence analysis

2014 ◽  
Vol 52 (12) ◽  
pp. 1056-1056
Author(s):  
Ok-Hwa Hwang ◽  
Sebastian Raveendar ◽  
Young-Ju Kim ◽  
Ji-Hun Kim ◽  
Tae-Hun Kim ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Bacterial Diversity ◽  
16S Rdna ◽  
Rdna Sequence ◽  
Pig Slurry ◽  
16S Rdna Sequence ◽  
16S Rdna Sequence Analysis

scholarly journals Antibacterial Effects of Oregano Essential Oil (OEO) and Its Potential Applications

2020 ◽  
pp. 19-25
Author(s):  
R. Cabrera-Contreras ◽  
R. Morelos-Ramírez ◽  
J. P. Quiróz-Ríos ◽  
D. Muñoz-Quiróz
Keyword(s):  
Antibacterial Activity ◽  
Essential Oil ◽  
Essential Oils ◽  
Staphylococcus Epidermidis ◽  
Drug Resistant ◽  
Human Pathogens ◽  
Bacterial Strains ◽  
Methicillin Resistant ◽  
Reference Strains ◽  
Serial Dilutions

Essential oils (EOs) are commonly used in food industry, due that they possess antioxidative and antimicrobial properties. There are few essential oils that have been used in medicine, due to its potent antibacterial activity against intrahospital pathogens. OEO has experimentally shown potent antibacterial effect on nosocomial Gram-positive bacteria, therefore it can be very useful in hospital environments, where there are many bacterial pathogens, which are the etiological agents of nosocomial infections and most of them are resistant to several antibiotics. Objective: The aim of this study was to determine antimicrobial effect of OEO on most frequent bacterial intrahospital pathogens: MRSA, MRSE comparatively to selected ATCC bacterial reference strains. Methods: This experimental study investigates the antibacterial action of oregano (Origanum vulgare) essential oil (OvEO) on two human pathogens: Staphylococcus aureus (SA) and Staphylococcus epidermidis (SE) Here, we used OEO against one of the most prominent antibiotic-resistant bacterial strains: methicillin-resistant SA (MRSAmecA+ = Meticillin Resistant SA and mecA- = Meticillin Resistance SA ), methicillin-resistant SE (MRSEmecA+ = Meticillin Resistance Staphylococcus epidermidis mecA+) and reference strains: S. aureus ATCC 700699, S. epidermidis ATCC 359845 and E. coli ATCC 25922. Bactericidal effects of the OEO on these bacteria were mainly evaluated using undiluted and four serial dilutions in coconut oil (CCO) l: 1:10, 1:100, 1:200, 1:400. Results: OEO, undiluted and 4 serial dilutions showed potent antibacterial activity against all strains tested. In conclusion, this OEO could be used as an alternative in medicine. The ability of OEO to inhibit and kill clinical Multi-Drug-Resistant (MDR): MRSA and MRSE strains, highlights it´s potential for use in the management of drug-resistant MDR infections in hospitals wards.

scholarly journals Emergence of Bacterial Soft Rot in Cucumber Caused by Pectobacterium carotovorum subsp. brasiliense in China

Plant Disease ◽  
2017 ◽  
Vol 101 (2) ◽  
pp. 279-287 ◽  
Author(s):  
Xianglong Meng ◽  
Ali Chai ◽  
Yanxia Shi ◽  
Xuewen Xie ◽  
Zhanhong Ma ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Soft Rot ◽  
Economic Losses ◽  
Pectobacterium Carotovorum ◽  
Bacterial Soft Rot ◽  
Bacterial Strains ◽  
Phenotypic Properties ◽  
Gene Sequence Analysis ◽  
Wide Range ◽  
Carotovorum Subsp

During 2014 to 2015, a devastating bacterial soft rot on cucumber stems and leaves occurred in Shandong, Shanxi, Hebei, Henan, and Liaoning provinces of China, resulting in serious economic losses for cucumber production. The gummosis emerged on the surface of leaves, stems, petioles, and fruit of cucumber. The basal stem color was dark brown and the stem base turned to wet rot. Yellow spots and wet rot emerged at the edge of the infected cucumber leaves and gradually infected the leaf centers. In total, 45 bacterial strains were isolated from the infected tissues. On the basis of phenotypic properties of morphology, physiology, biochemistry, and 16S ribosomal RNA gene sequence analysis, the pathogen was identified as Pectobacterium carotovorum. Multilocus sequence analysis confirmed that the isolates were P. carotovorum subsp. brasiliense, and the pathogens fell in clade II. The pathogenicity of isolated bacteria strains was confirmed. The strains reisolated were the same as the original. The host range test confirmed that strains had a wide range of hosts. As far as we know, this is the first report of cucumber stem soft rot caused by P. carotovorum subsp. brasiliense in China as well as in the world, which has a significant economic impact on cucumber production.

scholarly journals Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries

1999 ◽  
Vol 29 (2) ◽  
pp. 159-169 ◽  
Author(s):  
Kiyoshi Tajima ◽  
Roustam I Aminov ◽  
Takafumi Nagamine ◽  
Koretsugu Ogata ◽  
Mutsumi Nakamura ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Bacterial Diversity ◽  
16S Rdna

scholarly journals Point mutations in the major outer membrane protein drive hypervirulence of a rapidly expanding clone of Campylobacter jejuni

2016 ◽  
Vol 113 (38) ◽  
pp. 10690-10695 ◽  
Author(s):  
Zuowei Wu ◽  
Balamurugan Periaswamy ◽  
Orhan Sahin ◽  
Michael Yaeger ◽  
Paul Plummer ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Membrane Protein ◽  
Outer Membrane ◽  
Campylobacter Jejuni ◽  
Outer Membrane Protein ◽  
Animal Health ◽  
Major Outer Membrane Protein ◽  
Whole Genome Sequence ◽  
Bacterial Strains ◽  
Zoonotic Pathogen

Infections due to clonal expansion of highly virulent bacterial strains are clear and present threats to human and animal health. Association of genetic changes with disease is now a routine, but identification of causative mutations that enable disease remains difficult. Campylobacter jejuni is an important zoonotic pathogen transmitted to humans mainly via the foodborne route. C. jejuni typically colonizes the gut, but a hypervirulent and rapidly expanding clone of C. jejuni recently emerged, which is able to translocate across the intestinal tract, causing systemic infection and abortion in pregnant animals. The genetic basis responsible for this hypervirulence is unknown. Here, we developed a strategy, termed “directed genome evolution,” by using hybridization between abortifacient and nonabortifacient strains followed by selection in an animal disease model and whole-genome sequence analysis. This strategy successfully identified SNPs in porA, encoding the major outer membrane protein, are responsible for the hypervirulence. Defined mutagenesis verified that these mutations were both necessary and sufficient for causing abortion. Furthermore, sequence analysis identified porA as the gene with the top genome-wide signal of adaptive evolution using Fu’s Fs, a population genetic metric for recent population size changes, which is consistent with the recent expansion of clone “sheep abortion.” These results identify a key virulence factor in Campylobacter and a potential target for the control of this zoonotic pathogen. Furthermore, this study provides general, unbiased experimental and computational approaches that are broadly applicable for efficient elucidation of disease-causing mutations in bacterial pathogens.

scholarly journals Presence and Persistence of Legionella spp. in Groundwater

2005 ◽  
Vol 71 (2) ◽  
pp. 663-671 ◽  
Author(s):  
Joana Costa ◽  
Igor Tiago ◽  
Milton S. da Costa ◽  
António Veríssimo
Keyword(s):  
Legionella Pneumophila ◽  
Random Amplified Polymorphic Dna ◽  
Acid Methyl Ester ◽  
Gene Exchange ◽  
Rapd Profile ◽  
Genetic Groups ◽  
Acid Methyl ◽  
Groundwater Samples ◽  
Rapd Pcr ◽  
Reference Strains

ABSTRACT Groundwater samples (111) from six different boreholes located in two geographical areas were examined for the presence of legionellae over a 7-year period. The number of Legionella isolates detected was generally low. The colonization of the aquifers was not uniform, and the persistence of Legionella was independent of the hydraulic pumps and the plumbing system present in the borehole. A total of 374 isolates identified by fatty acid methyl ester analysis belonged to Legionella pneumophila, L. oakridgensis, L. sainthelensi, and L. londiniensis. In area 1, L. oakridgensis constituted the major population detected, exhibiting only one random amplified polymorphic DNA (RAPD)-PCR profile. L. sainthelensi strains were less frequently isolated and also displayed a single RAPD profile, while L. pneumophila was only sporadically detected. In contrast, L. pneumophila comprised the vast majority of the isolates in area 2 and exhibited six distinct RAPD patterns, indicating the presence of different genetic groups; three L. londiniensis RAPD types were also detected. Two of the L. pneumophila and one of the L. londiniensis RAPD types were persistent in this environment for at least 12 years. The genetic structure of L. pneumophila groundwater populations, inferred from rpoB and dotA gene sequences, was peculiar, since the majority of the isolates were allied in a discrete group different from the lineages containing most of the type and reference strains of the three subspecies of L. pneumophila. Furthermore, gene exchange events related to the dotA allele could be envisioned.

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