Genetic Relationships of Soft Rot Bacteria Isolated from Konjac in China by Amplified Fragment Length Polymorphism (AFLP) and 16S rDNA Gene Sequences

Wu, Jinping; Yang, Chaozhu; Jiao, Zhenbiao; Hu, Zhongli; Ding, Zili; Qiu, Zhengming

doi:10.4236/as.2015.67069

Cited by 3 publications

(4 citation statements)

References 21 publications

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“…A nationwide survey in China indicated that konjac soft rot is caused by P. carotovora subsp. carotovora and P. chrysanthemi , with P. chrysanthemi acting as the major pathogen ( Wu et al, 2015 ). However, our study isolated 11 pathogenic strains from three sampling sites of two provinces (Yunnan and Shaanxi) in China, and proved that all these soft rot pathogens belong to P .…”

Section: Discussionmentioning

confidence: 99%

“…The konjac glucomannan (KGM), extracted from the corm, is a water-soluble polysaccharide (dietary fiber) with diverse applications in food science and nutrition, biotechnology, pharmacology and fine chemicals ( Behera and Ray, 2016 ; Zhu, 2018 ). However, bacterial sot rot is becoming a major threat to konjac production in China ( Wu et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

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Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics

Zhang

Chu

et al. 2022

Front. Microbiol.

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Bacterial soft rot is a devastating disease for a wide range of crops, vegetables, and ornamental plants including konjac (Amorphophallus konjac). However, the pangenome and genomic plasticity of the konjac soft rot pathogens is little explored. In this study, we reported the complete genome sequences of 11 bacterial isolates that can cause typical soft rot symptoms in konjac by in vitro and in vivo pathogenicity tests. Based on in silico DNA–DNA hybridization, average nucleotide identity and phylogenomic analysis, all 11 isolates were determined to be Pectobacterium aroidearum. In addition, synteny analysis of these genomes revealed considerable chromosomal inversions, one of which is triggered by homologous recombination of ribose operon. Pangenome analysis and COG enrichment analysis showed that the pangenome of P. aroidearum is open and that accessory genes are enriched in replication, recombination, and repair. Variations in type IV secretion system and type VI secretion system were found, while plant cell wall degrading enzymes were conserved. Furthermore, sequence analyses also provided evidence for the presence of a type V secretion system in Pectobacterium. These findings advance our understanding of the pathogenicity determinants, genomic plasticity, and evolution of P. aroidearum.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics

Zhang

Chu

et al. 2022

Front. Microbiol.

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“…Outbreaks of konjac soft rot disease have caused irreparable damage to the agroecosystem with serious economic losses and ecological destruction, including the added costs of labor management and disease control ( Wu et al, 2011a ). Therefore, many studies have been dedicated to identifying the pathogens of konjac soft rot and developing new control methods ( Wu et al, 2011b , 2012 , 2015 ; Chen, 2013 ). Biological control, for instance, using Paenibacillus polymyxa and Pseudomonas fluorescens , is considered to be a promising method for the control of konjac soft rot ( Helmy et al, 2008 ; Chen, 2013 ).…”

Section: Introductionmentioning

confidence: 99%

Response of Root-Associated Bacterial Communities to Different Degrees of Soft Rot Damage in Amorphophallus konjac Under a Robinia pseudoacacia Plantation

2021

Front. Microbiol.

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Bacterial soft rot is a destructive disease that restricts the development of the konjac (Amorphophallus konjac K. Koch ex N.E.Br) industry. The objective of this study was to investigate how soft rot disease affects bacterial communities associated with the roots of konjac plants growing under a pure Robinia pseudoacacia plantation. Three sampling sites affected by different degrees of soft rot damage were selected based on the disease incidence [0%, non-diseased (ND); 4.2%, moderately diseased (MD); and 18.6%, highly diseased (HD)]. The variation in soil and root bacterial diversity and community composition among the sampling sites was determined by Illumina HiSeq sequencing of the V3–V4 hypervariable regions of the bacterial 16S rRNA gene. The results showed that the contents of soil organic matter and available nutrients (N, P, and K) increased with increasing damage degree, whereas higher damage degree resulted in lower soil pH and enzymatic activity (sucrase, urease, catalase, and polyphenol oxidase). The composition of root-associated bacterial communities differed among the three sampling sites. Proteobacteria was the most dominant bacterial phylum in all soil and root samples. Pseudomonas, Bacillus, Rhizobium, and Streptomyces were the most abundant in all samples from the ND sites, whereas Pectobacterium carotovorum and Serratia were predominant in the samples from the MD and HD sites. The abundance and alpha diversity of root-associated bacteria were significantly higher (p < 0.05) in the ND sites than in the diseased sites. The results suggested pronounced differences in the abundance, alpha diversity, and community composition of bacteria associated with the roots of konjac plants affected by different degrees of soft rot damage. Such differences in bacterial community structure were related to dynamic changes in soil variables, especially soil available potassium content, sucrase activity, and urease activity. Analysis of the dominant root-associated bacterial taxa offers an approach to predict the damage degree due to soft rot in konjac and provides evidence for the prevention of this soil-borne disease via microecological regulation.

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“…In western Hubei province, bacterial soft rot is the most serious disease of konjac and generally causes a 30%–50% reduction in the corm yield. With continuous culture over several years, the loss of production can even exceed 80% in some plantings [5,6].…”

Section: Introductionmentioning

confidence: 99%

A Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Pectobacterium aroidearum that Causes Soft Rot in Konjac

Sun

Liu

Huang

et al. 2019

IJMS

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Bacterial soft rot caused by Pectobacterium species is a serious disease in konjac (Amorphophallus konjac), a healthy source of starch particularly in East Asia. An effective diagnostic method is crucial to control the disease and reduce losses in konjac production. In this study, we evaluated a loop-mediated isothermal amplification (LAMP) assay with a specific primer set for the rapid and accurate detection of P. aroidearum. A comparative genomics approach was used to identify the specific genes suitable for the design of LAMP primers. The candidate target genes were determined through a first-round comparison with a 50-genome nucleotide database, and subjected to a second-round screening with the GenBank NR database. As a result, nine specific genes of P. aroidearum were selected for LAMP primer design. After screening of the primers, the primer set 1675-1 was chosen for LAMP detection owing to its high specificity and sensitivity. The LAMP assay could detect the presence of P. aroidearum genomic DNA at a concentration as low as 50 fg and 1.2 × 104 CFU/g artificially infected soil within 40 min at 65 °C. Subsequently, this primer set was successfully used to specifically detect P. aroidearum in naturally infected and non-symptomatic plant samples or soil samples from the field. This study indicates that a comparative genomic approach may facilitate the development of highly specific primers for LAMP assays, and a LAMP diagnostic assay with the specific primer set 1675-1 should contribute to the rapid and accurate detection of soft-rot disease in konjac at an early stage.

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Genetic Relationships of Soft Rot Bacteria Isolated from Konjac in China by Amplified Fragment Length Polymorphism (AFLP) and 16S rDNA Gene Sequences

Cited by 3 publications

References 21 publications

Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics

Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics

Response of Root-Associated Bacterial Communities to Different Degrees of Soft Rot Damage in Amorphophallus konjac Under a Robinia pseudoacacia Plantation

A Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Pectobacterium aroidearum that Causes Soft Rot in Konjac

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