Illumina-based Analysis of Endophytic Bacterial Diversity of four Allium species

Huang, Yonghong

doi:10.1038/s41598-019-51707-7

Cited by 24 publications

(15 citation statements)

References 64 publications

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“…Recently, knowledge of composition and functions of microbial communities has increased significantly with the development of DNA sequencing and metagenomics [ 19 , 20 ]. For example, endophytic bacterial diversity of four Allium species was analyzed by Illumina MiSeq sequencing [ 21 ]. Flavobacterium species from rhizosphere soils of Allium plants suppressed Fusarium wilt were determined by Illumina MiSeq sequencing [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

High nitrogen concentration alter microbial community in Allium fistulosum rhizosphere

Zhao

et al. 2020

PLoS ONE

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Welsh onion (Allium fistulosum L.) constitutes an important plant species cultivated in China due the benefits and applications in different areas. Moreover, nitrogen is an essential nutrient during the growth and development of plant. Here, we present the effects of nitrogen on soil microbiome in welsh onion plants. We used High-throughput sequencing analysis to determine the diversity and abundances of microbes associated to soil rhizosphere in welsh onion under the influence of nitrogen application. Nitrogen application significantly influenced in the diversity of fungal community. The relative abundance of Orbiliomycetes increased with the nitrogen concentration. Nitrogen application did not affect the diversity of bacterial community, whereas the relative abundance of Acidobacteria_Gp2, Verrucomicrobiae and Sphingobacteriia decreased with the nitrogen condition. In this work, we introduced evidences of the effect of nitrogen fertilization on microbial community in welsh onion rhizosphere, and the change of microbial community may interfere the growth and development of welsh onion.

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Section: Introductionmentioning

confidence: 99%

High nitrogen concentration alter microbial community in Allium fistulosum rhizosphere

Zhao

et al. 2020

PLoS ONE

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“…Our results demonstrate that endophytic microbiome assembly in Ginkgo leaves was mainly influenced by leaf developmental stage regardless of individual species ( Figure 4 ). The regionality caused the formation of core members of endophytic bacteria in the host plant, but developmental stages caused substantial changes in endophytic bacterial diversity ( Figure 3 ) and community structure ( Figure 4 ) in Ginkgo leaves ( Huang, 2019 ). Because for individual species, the effect of time on endophytic bacterial community assembly was much stronger than spatial locations ( Figure 4 ), although spatial locations are well-known to make a great contribution to bacterial community composition ( Meyer and Leveau, 2012 ; Leff et al, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Endophytic Bacterial Communities of Ginkgo biloba Leaves During Leaf Developmental Period

et al. 2021

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Plant-specialized secondary metabolites have ecological functions in mediating interactions between plants and their entophytes. In this study, high-throughput gene sequencing was used to analyze the composition and abundance of bacteria from Ginkgo leaves at five different sampling times. The results indicated that the bacterial community structure varied during leaf developmental stage. Bacterial diversity was observed to be the highest at T2 stage and the lowest at T1 stage. Proteobacteria, Firmicutes, Actinobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes were found as the dominant phyla. The major genera also showed consistency across sampling times, but there was a significant variation in their abundance, such as Bacillus, Lysinibacillus, and Staphylococcus. Significant correlations were observed between endophytic bacteria and flavonoids. Especially, Staphylococcus showed a significant positive correlation with quercetin, and changes in the abundance of Staphylococcus also showed a strong correlation with flavonoid content. In order to determine the effect of flavonoids on endophytic bacteria of Ginkgo leaves, an extracorporeal culture of related strains (a strain of Staphylococcus and a strain of Deinococcus) was performed, and it was found that the effect of flavonoids on them remained consistent. The predicted result of Tax4Fun2 revealed that flavonoids might lead to a lower abundance of endophytic microorganisms, which further proved the correlation between bacterial communities and flavonoids. This study provided the first insight into the bacterial community composition during the development of Ginkgo leaves and the correlation between the endophytic bacteria and flavonoids.

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“…The taxonomy of the fungal sequence was analyzed by the RDP Classi er algorithm against the United States database (version 7.0/ its-fungi database) using a con dence threshold of 70%. Potential functional changes of the bacterial community in the soil samples were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) (Huang, 2019). The raw reads were deposited into the NCBI Sequence Read Archive (SRA) database (Accession Number: SRP313044).…”

Section: Measurement Of Plant Physiological Indicesmentioning

confidence: 99%

An emerging chemical fumigant: two-sided effects of dazomet on soil microbial environment and plant response

Chen

Jiang

et al. 2021

Environ Sci Pollut Res

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Methyl bromide has been banned worldwide because it causes damage to the ozone layer and the environment. To nd a substitute for methyl bromide, the relationships among fumigation, plant growth, and the microbial community in replant soil require further study. We performed pot and eld experiments to investigate the effects of dazomet fumigation on soil properties and plant performance. Changes in soil microbial community structure and diversity were assessed using high-throughput sequencing, and plant physiological performance and soil physicochemical properties were also measured. Dazomet fumigation enhanced photosynthesis and promoted plant growth in replant soil; it altered soil physical and chemical properties and reduced soil enzyme activities, although these parameters gradually recovered over time. After dazomet fumigation, the dominant soil phyla changed, microbial diversity decreased signi cantly, the relative abundance of biocontrol bacteria such as Mortierella increased, and the relative abundance of pathogenic bacteria such as Fusarium decreased. Over the course of the experiment, the soil microbial ora changed dynamically, and soil enzyme activities and other physical and chemical properties also recovered to a certain extent. This result suggested that the effect of dazomet on soil microorganisms was temporary. However, fumigation also led to an increase in some resistant pathogens, such as Trichosporon, that affect soil function and health. Therefore, it is necessary to consider potential negative impacts of dazomet on the soil environment and to perform active environmental risk management in China. HighlightsFumigation of apple replant soil with dazomet renewed the soil microbial environment, improved soil physical and chemical properties, and dynamically restored soil ecological function.The activities of several soil enzymes and the relative abundance of bene cial microorganisms increased after dazomet fumigation. These changes were accompanied by higher rates of apple photosynthesis and growth.Fumigation reduced the content of pathogenic fungi such as Fusarium and increased the abundance of bene cial bacteria in the soil. However, it also increased the abundance of pathogenic bacteria such as Trichosporon, indicating that it is important to perform active environmental risk management.

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Illumina-based Analysis of Endophytic Bacterial Diversity of four Allium species

Cited by 24 publications

References 64 publications

High nitrogen concentration alter microbial community in Allium fistulosum rhizosphere

High nitrogen concentration alter microbial community in Allium fistulosum rhizosphere

Endophytic Bacterial Communities of Ginkgo biloba Leaves During Leaf Developmental Period

An emerging chemical fumigant: two-sided effects of dazomet on soil microbial environment and plant response

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