scholarly journals Ginger Rhizome Rot caused by the Enterobacter cloacae in Tangshan, China

Plant Disease ◽  
2021 ◽  
Author(s):  
Na Zhao ◽  
Junyu Yang ◽  
He Liu ◽  
lingrui Li ◽  
Hongfei Yan ◽  
...  
Keyword(s):  
Solid Medium ◽  
Dark Period ◽  
Enterobacter Cloacae ◽  
Incidence Rates ◽  
Rrna Gene ◽  
Pathogenicity Test ◽  
Ginger Rhizome ◽  
And Control ◽  
Physiological And Biochemical ◽  
Rhizome Rot

Ginger (Zingiber officinale ROSC.) is an important economic crop in China, especially the rhizome tissue has a high medicinal value. In July 2019, the symptom of ginger rhizome rot appeared in Tangshan city of Hebei Province, with incidence rates of 15%. The diseased part of ginger rhizome became soft and presented light brown maceration. Serious internal all erosion, only have epidermis, gray-white juice overflowed the epidermis, and with foul smell. The surface of ginger rhizome was disinfected with 1% NaOCl, and colonies were isolated and purified on nutrient agar (NA) solid medium by streak plate method. Eight isolates were obtained from 15 diseased tissue samples. Further morphological, physiological and biochemical identification of the pure cultured bacteria were carried out. Two isolates of bacteria were picked for further analysis. The bacteria were gram-negative bacilli, which were milky white and round protuberances on NA solid medium. Physiological and biochemical test results showed that isolates were facultatively anaerobic, gelatin liquefaction; negative for indole, methyl red, hydrogen sulfide production and the Voges-Prauskauer test (V-P); positive for D-glucose, sucrose, sorbitol, inositol, mannitol and citrate utilization. A typical hypersensitive reaction was induced on 12-week-old tobacco (Nicotiana benthamiana) leaves, which were inoculated by injecting suspensions of the isolated strain (108 CFU/mL) at 25℃ after 24-h. These characteristics were consistent with Enterobacter spp. To further assess the identity of the species, the genomic DNA was extracted from one bacterium（SDXJ1）. The partial 16S rRNA gene and specific rpoB and gyrB genes were amplified and sequenced with primers 27F/1492R, CM7/CM31b and UP1f/UP2r (Brady et al. 2013, Mollet et al. 1997, Lane 1991). The obtained 16S and rpoB sequences (GenBank accession MK937637, MZ911902 and MZ911901) of the isolate showed 99.33%, 99.21% and 99.57% identity to the corresponding sequences of Enterobacter cloacae in GenBank (CP055458, AP022228 and AP022519). Maximum likelihood analysis was performed, and the phylogenetic tree clustered with E. cloacae (MEGAX, Bootstrap n=1000). The pathogenicity of the isolates was tested on ginger plants and rhizomes tissue. The bacterial suspensions (108 CFU/mL) of two isolates were injected into the basal stem and rhizomes center of 6 healthy ginger seedlings respectively, and control groups were treated with sterile water. The inoculated plants were kept in a moist chamber (28°C, 16-h light and 8-h dark period) and ginger rhizomes were placed in the incubator (30°C, 16-h light and 8-h dark period). Seven days after inoculation, the ginger tubers showed symptoms of decay, and 20 to 25 days later, the ginger plant leaves browned and died. The pathogenicity test was repeated 4 times and all controls were healthy. The pathogens of symptomatic plants and ginger rhizomes were studied. They were identified as E. cloacae by physiological, biochemical and molecular biological methods, fulfilling Koch's hypothesis. This is the first report of the ginger rhizome rot caused by the Enterobacter cloacae in Tangshan, China. The research results are of great significance for the prevention and control of the disease. Our laboratory has reported that Citrobacter freundii can cause Ginger Rot. (Zhao et al. 2021) Whether the two strains infect alone or compound in the field still needs to be further explored.

scholarly journals Citrobacter freundii causing Ginger (Zingiber officinale Rosc.) Rot in Tangshan, China

Plant Disease ◽  
2021 ◽  
Author(s):  
Na Zhao ◽  
Junyu Yang ◽  
Ping Wang ◽  
lingrui Li ◽  
Hongfei Yan ◽  
...  
Keyword(s):  
Dark Period ◽  
Zingiber Officinale ◽  
Hypersensitive Reaction ◽  
Incidence Rates ◽  
Pathogenicity Test ◽  
Citrobacter Freundii ◽  
Tissue Samples ◽  
Whole Plant ◽  
And Control ◽  
Physiological And Biochemical

Ginger (Zingiber officinale Rosc.) is an important economic crop and its rhizome can be used as seasoning agent and traditional medicine in China. During July 2018 and 2019, decay symptoms occurred in the ginger planting area of Tangshan City, Hebei Province, with incidence rates of 15%～20%. The pathogen infected the rhizomes and leaves. The symptoms included leaves chlorosis and gradually wilting, even the whole plant wilted, the rhizome became soft and presented light brown maceration. In serious cases, the interior of rhizome was completely eroded, gray-white juice overflowing the epidermis, and with foul smell. The rhizome surfaces of ginger plants were disinfected with 1% NaOCl, and colonies were isolated and purified on nutrient agar (NA) solid medium by streaking. Eight isolates were obtained from 15 diseased tissue samples. Further morphological, physiological and biochemical identification of the pure cultured bacteria were carried out. Three strains of bacteria were picked for further analysis. All of the three strains were gram-negative, short rod-shaped，nonmotile bacillus. Colonies were round and milky yellow, smooth raised, and moist after incubation at 28°C for 24h on NA. Physiological and biochemical test results showed that strains were facultatively anaerobic, negative for indole, methyl red, the Voges-Prauskauer test (V-P) and urease; positive for glucose, sucrose, sorbitol, inositol, mannitol, citrate utilization and hydrogen sulfide production; gelatin liquefaction. A typical hypersensitive reaction was induced on 12-week-old tobacco (Nicotiana benthamiana) leaves, which were inoculated by injecting suspensions of the isolated strain (108 CFU/mL) at 25 ℃ after 24h. These characteristics were consistent with Citrobacter freundii (Werkman and Gillen 1932). To further assess the identity of the strains, the genomic DNA was extracted from one bacterium（JXJ4）. The partial 16S rRNA region (Lane 1991) and specific rpoB and gyrB genes (Mollet et al. 1997, Brady et al. 2013) were amplified and sequenced with primers 27F/1492R, CM7/CM31b and UP1f/UP2r, respectively. The obtained 16S, rpoB and gyrB sequences (GenBank accession MN148645, MN158728 and MW199734) of the isolate showed 99.93%, 99.51% and 99.82% identity to the corresponding sequences of C. freundii in GenBank (CP024679.1, CP024677.1 and KM509081.1). Maximum likelihood analysis was performed, and the phylogenetic tree clustered with C. freundii (MEGAX, Bootstrap n=1000). The pathogenicity of the isolates was tested on ginger plants and rhizomes tissue. The bacterial suspensions (108 CFU/mL) of three isolates were injected into the basal stem and rhizomes center of 9 healthy ginger seedlings respectively, and Control groups were treated with sterile water. The inoculated plants were kept in a moist chamber (28°C, 16-h light and 8-h dark period) and ginger rhizomes were placed in the incubator (30°C, 16-h light and 8-h dark period). Seven days after inoculation, the ginger tubers showed symptoms of decay, and 20 to 25 days later, the ginger plant leaves browned and died. The pathogenicity test was repeated 4 times and all controls were healthy. Pathogens were reisolated from symptomatic plants and rhizomes and identified as C. freundii based on the morphological, biochemical and molecular methods described previously, fulfilling Koch's hypothesis. To our knowledge, this is the first report of ginger rot caused by C. freundii in China.

scholarly journals Association of Enterobacter cloacae with Rhizome Rot of Edible Ginger in Hawaii

Plant Disease ◽  
2004 ◽  
Vol 88 (12) ◽  
pp. 1318-1327 ◽  
Author(s):  
K. A. Nishijima ◽  
A. M. Alvarez ◽  
P. R. Hepperly ◽  
M. H. Shintaku ◽  
L. M. Keith ◽  
...  
Keyword(s):  
Enterobacter Cloacae ◽  
Host Susceptibility ◽  
Low Oxygen ◽  
Fresh Market ◽  
16S Rdna Sequence Analysis ◽  
Biochemical Assays ◽  
Spongy Texture ◽  
Ginger Rhizome ◽  
New Finding ◽  
Rhizome Rot

Edible ginger is a popular spice crop that is grown in Hawaii primarily for the fresh market, and as such, rhizome quality is of paramount importance. In our studies, a Gram-negative, facultative anaerobic, rod-shaped bacterium was consistently isolated from decayed as well as symptomless ginger rhizomes. The bacterium was identified as Enterobacter cloacae by biochemical assays and 16S rDNA sequence analysis. Rot symptoms, which usually occurred in the central cylinder of the rhizome, were characterized by yellowish-brown to brown discolored tissue and firm to spongy texture. In inoculation experiments, ginger strains of E. cloacae produced basal stem and root rot, with foliar chlorosis and necrosis in tissue-cultured ginger plantlets, and discolored and spongy tissue in mature ginger rhizome slices and whole segments. In other hosts, ginger strains of E. cloacae caused internal yellowing of ripe papaya fruit and internal rot of onion bulbs. All strains that caused symptoms in inoculated plants were reisolated and identified as E. cloacae. Our studies suggest that E. cloacae can exist as an endophyte of ginger rhizomes, and under conditions that are favorable for bacterial growth, or host susceptibility, including maturity of tissues, rhizome rot may occur. Rhizome quality may be impacted by the presence of E. cloacae under conditions such as high temperature, high relative humidity, and low oxygen atmosphere that may affect the development of decay, and such conditions should be avoided during post-harvest handling and storage. The association of E. cloacae with a rhizome rot of ginger is a new finding.

scholarly journals First Report of Enterobacter cloacae Causing Bulb Decay on Garlic in China

Plant Disease ◽  
2021 ◽  
Author(s):  
Erfeng Li ◽  
Xueliang Tian ◽  
Ruibian Zhao ◽  
Yuanhong Wang ◽  
Gang Wang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Enterobacter Cloacae ◽  
Chili Pepper ◽  
Rrna Gene ◽  
Gyra Gene ◽  
First Report ◽  
Brown Discoloration ◽  
Pathogenicity Tests ◽  
And Control

Enterobacter cloacae is a symbiotic bacterium, which is one of the species in intestinal microbiota in many humans and animals. In some cases, it causes harmful diseases in humans. More and more studies showed that E. cloacae caused disease on plants, such as macadamia, ginger, mulberry, onion, chili pepper and rice. Garlic (Allium sativum L.) is one of crops with economic importance in the world. It is also widely grown in China. During 2018 to 2020, the naturally infected garlic bulbs from garlic fields in Kaifeng of Henan Province (34.55° N; 114.78° E) showed dry brown discoloration and rot symptoms. The diseased garlic seriously affected its edible value. Voucher specimens collected on June, 2019 were deposited in Plant Disease Laboratory of Tianjin Agricultural University under accession no. PATAU190620. To identify the causal agent of this disease, the bulb tissues of infected garlic were surface-disinfested in 0.6% sodium hypochlorite, dipped in75% ethanol, and then dipped in sterile distilled water. These bulbs were plated on LB medium and incubated at 37℃. A number of white colonies grew on the medium after plating for 16 h. All colonies were round, white, opaque, smooth, and gram-negative, which is a typical characteristic of Enterobacter. To confirm the initial identification of the isolated bacterium, the fragments of 16S rRNA gene and gyrA gene of 6 colonies were amplified, respectively. The PCR products were purified and sequenced. All 16S rRNA and gyrA sequences were identical to each other. The sequences of 16S rRNA gene and gyrA gene were deposited in GenBank with accession numbers MW730711 and MW768876, respectively. BLAST searches were conducted using the sequences of 16S rRNA and gyrA. The results showed 99.72%, and 96.91% identity with the corresponding sequences of E. cloacae strain CBG15936 (CP046116.1), respectively. Phylogenetic trees were performed using the neighbor-joining (NJ) method of MAGA X based on the sequences of 16S rRNA gene and gyrA gene. Phylogenetic tree indicated that isolates are most likely E. cloacae. Pathogenicity tests were performed by puncturing garlic bulbs with a hypodermic needle, followed by dipping in bacterial suspension with the concentration of 2×108 CFU for 5 minutes. As control, the garlic bulbs were treated with sterile water. The inoculated and control were incubated at 30°C. 7 days after inoculation, brown discoloration and rot were developed on all inoculated garlic bulbs. No symptoms were observed in the control group.The symptoms were similar to that observed on the original diseased garlic bulbs. The garlic bulbs in inoculated and control were ten replicates in each independent biological experiments. The pathogenicity tests were conducted three times with similar results. The bacteria were re-isolated from the symptomatic diseased garlics and confirmed as E. cloacae by morphological and sequence analyses as above. The re-isolated bacteria were identified by biochemical and physiological characteristics using API 20E strips. The results of the identification were identical to those of the edible ginger strains and the chili pepper strains. As far as we know, this is the first report of bulb decay on garlic caused by E. cloacae. The results are of great significance not only for the management of garlic bulbs during postharvest handling and storage, but also for the further research of opportunistic human pathogens E. cloacae.

scholarly journals The dysbiosis of ovine foot microbiome during the development and treatment of contagious ovine digital dermatitis

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
J. S. Duncan ◽  
J. W. Angell ◽  
P. Richards ◽  
L. Lenzi ◽  
G. J. Staton ◽  
...  
Keyword(s):  
Antibiotic Treatment ◽  
Amplicon Sequencing ◽  
Strong Tendency ◽  
Rrna Gene ◽  
Digital Dermatitis ◽  
Healthy State ◽  
Foot Disease ◽  
End Stage ◽  
And Control ◽  
Interdigital Dermatitis

Abstract Background Contagious Ovine Digital Dermatitis (CODD) is an emerging and common infectious foot disease of sheep which causes severe welfare and economic problems for the sheep industry. The aetiology of the disease is not fully understood and control of the disease is problematic. The aim of this study was to investigate the polybacterial aetiopathogenesis of CODD and the effects of antibiotic treatment, in a longitudinal study of an experimentally induced disease outbreak using a 16S rRNA gene amplicon sequencing approach. Results CODD was induced in 15/30 experimental sheep. During the development of CODD three distinct phenotypic lesion stages were observed. These were an initial interdigital dermatitis (ID) lesion, followed by a footrot (FR) lesion, then finally a CODD lesion. Distinct microbiota were observed for each lesion in terms of microbial diversity, clustering and composition. Porphyromonadaceae, Family XI, Veillonellaceae and Fusobacteriaceae were significantly associated with the diseased feet. Veillonellaceae and Fusobacteriaceae were most associated with the earlier stages of ID and footrot rather than CODD. Following antibiotic treatment of the sheep, the foot microbiota showed a strong tendency to return to the composition of the healthy state. The microbiota composition of CODD lesions collected by swab and biopsy methods were different. In particular, the Spirochaetaceae family were more abundant in samples collected by the biopsy method, suggesting that these bacteria are present in deeper tissues of the diseased foot. Conclusion In this study, CODD presented as part of a spectrum of poly-bacterial foot disease strongly associated with bacterial families Porphyromonadaceae, Family XI (a family in Clostridiales also known as Clostridium cluster XI), Veillonellaceae and Fusobacteriaceae which are predominately Gram-negative anaerobes. Following antibiotic treatment, the microbiome showed a strong tendency to return to the composition of the healthy state. The composition of the healthy foot microbiome does not influence susceptibility to CODD. Based on the data presented here and that CODD appears to be the severest end stage of sheep infectious foot disease lesions, better control of the initial ID and FR lesions would enable better control of CODD and enable better animal welfare.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

scholarly journals Faecal bacterial composition in horses with and without free faecal liquid: a case control study

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Katrin M. Lindroth ◽  
Johan Dicksved ◽  
Erik Pelve ◽  
Viveca Båverud ◽  
Cecilia E. Müller
Keyword(s):  
Relative Abundance ◽  
Case Control Study ◽  
Sampling Period ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Clostridioides Difficile ◽  
Liquid Phases ◽  
And Control ◽  
The 16S Rrna Gene ◽  
Control Study

AbstractFree faecal liquid (FFL) is a condition in horses which manifests as differential defecation of solid and liquid phases of faeces. The etiology of FFL is currently unknown, but deviances in the hindgut microbiota has been suggested to be of importance. The present study aimed to compare the faecal bacterial composition of farm-matched horses with (case, n = 50) and without (control, n = 50) FFL. Samples were collected at three different occasions. The V3 and V4 regions of the 16S rRNA gene were amplified and sequenced using Illumina sequencing. Also, samples were cultivated for detection of Clostridioides difficile and Clostridium perfringens. Analysis revealed similar faecal bacterial composition between case and control horses, but an effect of sampling period (p = 0.0001). Within sampling periods, 14 genera were present in higher or lower proportions in case compared to control horses in at least one sampling period. Compared to controls, case horses had higher relative abundance of Alloprevotella (adjusted p < 0.04) and lower relative abundance of Bacillus spp. (adjusted p < 0.03) in at least two sampling periods. All horses tested negative for C. difficile and C. perfringens by culture of faeces. Further studies are required to establish the clinical relevance of specific bacterial taxa in FFL.

scholarly journals Halalkalicoccus jeotgali sp. nov., a halophilic archaeon from shrimp jeotgal, a traditional Korean fermented seafood

2007 ◽  
Vol 57 (10) ◽  
pp. 2296-2298 ◽  
Author(s):  
Seong Woon Roh ◽  
Young-Do Nam ◽  
Ho-Won Chang ◽  
Youlboong Sung ◽  
Kyoung-Ho Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Rrna Gene ◽  
Halophilic Archaeon ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Biochemical Tests ◽  
Extremely Halophilic Archaeon ◽  
Physiological And Biochemical

A novel, extremely halophilic archaeon B3T was isolated from shrimp-salted seafood. Its morphology, physiology, biochemical features and 16S rRNA gene sequence were characterized. Strain B3T is non-motile, Gram-variable, requires at least 10 % (w/v) NaCl for growth and grows in the ranges of 21–50 °C and pH 6.5–9.0. The DNA G+C content of strain B3T was 63.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain B3T belonged to the genus Halalkalicoccus and was phylogenetically closely related to the type strain Halalkalicoccus tibetensis (98.64 %). However, DNA–DNA hybridization experiments showed 7.0 % relatedness between strain B3T and a strain of a reference species of the genus Halalkalicoccus. Combined analysis of 16S rRNA gene sequences, DNA–DNA relatedness data, physiological and biochemical tests indicated that the genotypic and phenotypic characteristics differentiate strain B3T from other Halalkalicoccus species. On the basis of the evidence presented in this report, strain B3T represents a novel species of the genus Halalkalicoccus, for which the name Halalkalicoccus jeotgali. sp. nov. is proposed. The type strain is B3T (=KCTC 4019T=DSM 18796T=JCM 14584T=CECT 7217T).

scholarly journals Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Celiac Disease Patients and Controls

2017 ◽  
Author(s):  
Rahul Bodkhe ◽  
Sudarshan A. Shetty ◽  
Dhiraj P. Dhotre ◽  
Anil K. Verma ◽  
Khushbo Bhatia ◽  
...  
Keyword(s):  
Celiac Disease ◽  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sequence Variant ◽  
First Degree Relatives ◽  
Adult Celiac Disease ◽  
Disease Site ◽  
Rrna Gene Sequencing ◽  
And Control

AbstractRecent studies on celiac disease (CeD) have shown the role of gut microbiota alterations in CeD pathogenesis. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-disease state as FDRs are genetically susceptible to CeD. By using 16S rRNA gene sequencing, we observed between the disease condition (CeD), pre-disease (FDR) and control subjects. However, differences were observed at the level of amplicon sequence variant (ASV), suggesting alterations in specific taxa between pre-diseases and diseased condition. Duodenal biopsies showed higher differences in ASVs compared to faecal samples indicating larger disruption of microbiota at disease site. Increased abundance of specific Helicobacter ASVs were observed in duodenum of CeD when compared to FDR (p < 0.01). In case of fecal samples CeD microbiome and Actinomyces. In addition, predicted functional metagenome showed reduced ability of gluten that ecosystem level diversity measures (except in the duodenum) were not significantly different is characterized by reduced abundance of beneficial taxa such as Akkermansia, Ruminococcus degradation by CeD faecal microbiota in comparison to FDRs and controls.

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