Analysis of Bacterial Community in the Ginseng Soil Using Denaturing Gradient Gel Electrophoresis (DGGE)

Vendan, R. Thamizh; Lee, Sun Hee; Yu, Young Joon; Rhee, Young Ha

doi:10.1007/s12088-011-0193-3

Cited by 16 publications

(18 citation statements)

References 5 publications

(4 reference statements)

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“…The BIOLOG profiles, which could not separately represent the activity of bacterial or fungal communities, were the total values of microbial communities. The main finding in this study was that the cultivation of P. ginseng , especially cultivation ages, exerted the most profound influence on the genetic and functional diversity in P. ginseng rhizosphere soil, which is consistent with the results of previous studies [21] , [30] , [31] .…”

Section: Discussionsupporting

confidence: 92%

“…Soil samples were collected from five replicate plots randomly distributed over the fields. The entire root system along with rhizosphere soil was collected by digging at a depth of 20 cm from five healthy plants, and sampling was performed as described previously [21] , [22] . Soil samples of different cultivation ages and modes of P. ginseng were used directly for DNA extraction using the UltraClean Soil DNA Isolation Kit (Mo Bio Laboratories Inc., Bohemia, NY, USA) according to the manufacturer's instructions [23] .…”

Section: Methodsmentioning

confidence: 99%

“…Recently, a variety of culture-independent approaches—including random amplified polymorphic DNA, PCR-DGGE, and BIOLOG—have been applied for the investigation of bacterial diversity and metabolic function diversity of P. ginseng soil [4] , [21] , [22] . However, only a few trials have reported on the microbial community diversity of P. ginseng soil among different cultivation ages using both PCR-DGGE and BIOLOG.…”

Section: Introductionmentioning

confidence: 99%

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Effects of cultivation ages and modes on microbial diversity in the rhizosphere soil of Panax ginseng

Xiao

Yang

Zhang

et al. 2016

Journal of Ginseng Research

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BackgroundPanax ginseng cannot be cultivated on the same land consecutively for an extended period, and the underlying mechanism regarding microorganisms is still being explored.MethodsPolymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) and BIOLOG methods were used to evaluate the microbial genetic and functional diversity associated with the P. ginseng rhizosphere soil in various cultivation ages and modes.ResultsThe analysis of microbial diversity using PCR-DGGE showed that microbial communities were significantly variable in composition, of which six bacterial phyla and seven fungal classes were detected in P. ginseng soil. Among them, Proteobacteria and Hypocreales dominated. Fusarium oxysporum, a soilborne pathogen, was found in all P. ginseng soil samples except R0. The results from functional diversity suggested that the microbial metabolic diversity of fallow soil abandoned in 2003 was the maximum and transplanted soil was higher than direct-seeding soil and the forest soil uncultivated P. ginseng, whereas the increase in cultivation ages in the same mode led to decreases in microbial diversity in P. ginseng soil. Carbohydrates, amino acids, and polymers were the main carbon sources utilized. Furthermore, the microbial diversity index and multivariate comparisons indicated that the augmentation of P. ginseng cultivation ages resulted in decreased bacterial diversity and increased fungal diversity, whereas microbial diversity was improved strikingly in transplanted soil and fallow soil abandoned for at least one decade.ConclusionThe key factors for discontinuous P. ginseng cultivation were the lack of balance in rhizosphere microbial communities and the outbreak of soilborne diseases caused by the accumulation of its root exudates.

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Section: Discussionsupporting

confidence: 92%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Effects of cultivation ages and modes on microbial diversity in the rhizosphere soil of Panax ginseng

Xiao

Yang

Zhang

et al. 2016

Journal of Ginseng Research

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“…He et al [23] reported a significant impact from 8 years of reclamation and cultivation on the structure and taxonomic composition, and TN and CEC were noted to be potentially important factors for soil microbial composition and function. Furthermore, other studies indicated that the long-term effect of reclamation was essential for improving soil TN content and soil fertility, which are the major factors responsible for shifts in soil community structures [57]. In general, the shifts in bacterial community structure under different environments may not only be ascribed to some significant changes in the soil properties, but also to soil fertility and TN change caused by reclamation measure amendment.…”

Section: Impact Of Soil Properties On the Relative Abundances Of Bactmentioning

confidence: 99%

454 Pyrosequencing Analysis of Bacterial Diversity Revealed by a Comparative Study of Soils from Mining Subsidence and Reclamation Areas

Li¹,

Chen²,

Wen³

et al. 2014

Journal of Microbiology and Biotechnology

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Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coalmining reclamation areas was suggested.

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“…Additionally, relatively few studies have evaluated the relationship between rusty root and changes in the microbial community of the rhizosphere of P. ginseng. Most investigations on rusty root have only considered one microbial species, while not all predominant microbial groups can be detected due to the limitations of traditional molecular methods, such as polymorphic DNA amplification [31] and denaturing gradient gel electrophoresis [32], and the results obtained using these methods have been inconsistent. erefore, whether rusty root is caused by multiple pathogenic microorganisms, rather than just one, remains unknown.…”

Section: Introductionmentioning

confidence: 99%

Microbial Community Changes in the Rhizosphere Soil of Healthy and Rusty Panax ginseng and Discovery of Pivotal Fungal Genera Associated with Rusty Roots

Wei

Wang

Cao

et al. 2020

BioMed Research International

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Panax ginseng Meyer, a valuable medicinal plant, is severely threatened by rusty root, a condition that greatly affects its yield and quality. Studies investigating the relationship between soil microbial community composition and rusty roots are vital for the production of high-quality ginseng. Here, high-throughput sequencing was employed to systematically characterize changes in the soil microbial community associated with rusty roots. Fungal diversity was lower in the soils of rusty root-affected P. ginseng than in those of healthy plants. Importantly, principal coordinate analysis separated the fungal communities in the rhizosphere soils of rusty root-affected ginseng from those of healthy plants. The dominant bacterial and fungal genera differed significantly between rhizosphere soils of healthy and rusty root-affected P. ginseng, and linear discriminant analysis effect size (LEfSe) further indicated a strong imbalance in the soil microbial community of diseased plants. Significantly enriched bacterial genera (including Rhodomicrobium, Knoellia, Nakamurella, Asticcacaulis, and Actinomadura) were mainly detected in the soil of rusty root-affected P. ginseng, whereas significantly enriched fungal genera (including Xenopolyscytalum, Arthrobotrys, Chalara, Cryptococcus, and Scutellinia) were primarily detected in the soil of healthy plants. Importantly, five fungal genera (Cylindrocarpon, Acrophialophora, Alternaria, Doratomyces, and Fusarium) were significantly enriched in the soil of rusty root-affected plants compared with that of healthy plants, suggesting that an increase in the relative abundance of these pathogenic fungi (Cylindrocarpon, Alternaria, and Fusarium) may be associated with ginseng rusty roots. Additionally, this study is the first to report that an increase in the relative abundances of Acrophialophora and Doratomyces in the rhizosphere of P. ginseng may be associated with the onset of rusty root symptoms in this plant. Our findings provide potentially useful information for developing biological control strategies against rusty root, as well as scope for future screening of fungal pathogens in rusty roots of P. ginseng.

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Analysis of Bacterial Community in the Ginseng Soil Using Denaturing Gradient Gel Electrophoresis (DGGE)

Cited by 16 publications

References 5 publications

Effects of cultivation ages and modes on microbial diversity in the rhizosphere soil of Panax ginseng

Effects of cultivation ages and modes on microbial diversity in the rhizosphere soil of Panax ginseng

454 Pyrosequencing Analysis of Bacterial Diversity Revealed by a Comparative Study of Soils from Mining Subsidence and Reclamation Areas

Microbial Community Changes in the Rhizosphere Soil of Healthy and Rusty Panax ginseng and Discovery of Pivotal Fungal Genera Associated with Rusty Roots

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