Preferences for core microbiome composition and function by different definition methods: Evidence for the core microbiome of Eucommia ulmoides bark

Dong, Chunbo; Shao, Qiuyu; Zhang, Qingqing; Yao, Ting; Huang, Jianzhong; Liang, Zong-Qi; Han, Yan-Feng

doi:10.1016/j.scitotenv.2021.148091

Cited by 24 publications

(31 citation statements)

References 63 publications

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“…Venn diagram analysis showed that 690 genera, such as Enterobacter , Sphingomonas , and Lactobacillus ( Figure 3A ), were shared between soil and bark communities. These genera were also found in previous studies on E. ulmoid es ( Dong et al, 2020 , 2021a ) and are beneficial microorganisms with potential ecological functions for medicinal plants ( Quijada et al, 2018 ; Asaf et al, 2020 ; Webster et al, 2020 ). Highly abundant unique bacteria of the rhizosphere soil samples included Bacteroidia, Clostridiales, Saccharibacillus , Spirochaeta , and Erysipelotrichaceae , which have specific selective effects on the soil, predominantly exist in the soil, and play an important role in geo-biological-chemical circulation ( Wilms et al, 2006 ; Namirimu et al, 2019 ).…”

Section: Discussionsupporting

confidence: 76%

“…Core microbiota was defined with reference to the method of Dong et al (2021a) . The operational taxonomic units (OTUs) with all samples were screened out to construct a co-occurrence network.…”

Section: Methodsmentioning

confidence: 99%

“…Moreover, the gutta percha from E. ulmoides rubber is an excellent polymer material that contributes to the supply of rubber resources and the sustainable development of the rubber industry ( Wei et al, 2021 ). Previous studies revealed that E. ulmoides bark harbored members of the microbial genera Cladosporium , Sphingomonas , Alternaria , Devosia , Marmoricola , Rhodococcu s, and Teratosphaeria , which were affected by climatic conditions, altitude, and secondary metabolites ( Dong et al, 2020 , 2021a , c ). However, most of the related studies mainly considered one or a few aspects.…”

Section: Introductionmentioning

confidence: 99%

“…Particular microbes, termed “hub microbes or core microbes” due to their central position in a microbial network, are disproportionally important in shaping microbial communities on plant hosts ( Agler et al, 2016 ). The core microbiota of medicinal plants may be instrumental in determining the quality of medicinal materials ( Huang et al, 2018 ; Dong et al, 2021a ; Xu et al, 2021 ). The core microbiota not only directly play a beneficial role ( Chen et al, 2018 ) but can also influence the wider microbial community through the community cascade effect, thereby driving evolution and function of the microbial community ( Agler et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

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Assembly, Core Microbiota, and Function of the Rhizosphere Soil and Bark Microbiota in Eucommia ulmoides

et al. 2022

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Medicinal plants are inhabited by diverse microbes in every compartment, and which play an essential role in host growth and development, nutrient absorption, synthesis of secondary metabolites, and resistance to biological and abiotic stress. However, the ecological processes that manage microbiota assembly and the phenotypic and metabolic characteristics of the core microbiota of Eucommia ulmoides remain poorly explored. Here, we systematically evaluated the effects of genotypes, compartment niches, and environmental conditions (climate, soil nutrition, and secondary metabolites) on the assembly of rhizosphere soil and bark associated bacterial communities. In addition, phenotypic and metabolic characteristics of E. ulmoides core microbiota, and their relationship with dominant taxa, rare taxa, and pharmacologically active compounds were deciphered. Results suggested that microbiota assembly along the two compartments were predominantly shaped by the environment (especially pH, relative humidity, and geniposide acid) and not by host genotype or compartment niche. There were 690 shared genera in the rhizosphere soil and bark, and the bark microbiota was mainly derived from rhizosphere soil. Core microbiota of E. ulmoides was a highly interactive “hub” microbes connecting dominant and rare taxa, and its phenotypic characteristics had a selective effect on compartment niches. Metabolic functions of the core microbiota included ammonia oxidation, nitrogen fixation, and polyhydroxybutyrate storage, which are closely related to plant growth or metabolism. Moreover, some core taxa were also significantly correlated with three active compounds. These findings provide an important scientific basis for sustainable agricultural management based on the precise regulation of the rhizosphere soil and bark microbiota of E. ulmoides.

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Section: Discussionsupporting

confidence: 76%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Assembly, Core Microbiota, and Function of the Rhizosphere Soil and Bark Microbiota in Eucommia ulmoides

et al. 2022

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“…The network was constructed using only positive and signi cant correlations (r > 0.6, P < 0.05) [24]. For both samples, the complexity of interaction networks of later aging stage was higher than that of early aging stage, which was concluded based on more edges, higher average degrees, and more complex network relationships in later aging stage (Table 1).…”

Section: Microbial Interaction Network and Key Microbesmentioning

confidence: 99%

Microbial communities changes across aging process of tobacco leaves

Wang

Jin

Zhang

et al. 2022

Preprint

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Background: Microbial communities that inhabit aging tobacco leaves play a key role in improving quality by interactions with themselves and tobacco leaves to release tannins, increase sugar levels, promote aromatic taste and degrade harmful compounds. A better understanding of microbial communities on the aging of tobacco leaves could provide an important microbial repository for the industrial applications. Results: Here, we examined the structural and compositional changes of microbial communities and identified the potential metabolic pathways of bacteria and fungi throughout the aging process. The results showed that the diversity and structure of the microbial communities keep changing along with the aging process went on. The richness and diversity of bacterial community decreased, while the richness of fungal community was in an inverse trend. At the phylum level, the bacterial community was dominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidete, while Ascomycota and Basidiomycota were the dominant species in the fungal community. In the bacterial community, metabolic functions related to the carbon and nitrogen cycles which response to the degradation of harmful components, and the metabolism of aromatic hydrocarbons showed extremely dynamic at different aging periods. The change of the main nutritional mode of the fungal community also led to an increase in the abundance of saprophytic fungi. Conclusion: These results provide information on the succession of microbial community structure and function in the whole process of tobacco aging and suggest that the aging process of tobacco leaves can be a natural microbial collection for target microorganism and their metabolites. It also enables the further investigation of coordination mechanisms between beneficial microbial regulation and pathogenicity during aging process.

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Unraveling endophytic diversity in dioecious Siraitia grosvenorii: implications for mogroside production

Tamang,

Kaur,

Thakur

et al. 2024

Appl Microbiol Biotechnol

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Host and tissue-specificity of endophytes are important attributes that limit the endophyte application on multiple crops. Therefore, understanding the endophytic composition of the targeted crop is essential, especially for the dioecious plants where the male and female plants are different. Here, efforts were made to understand the endophytic bacterial composition of the dioecious Siraitia grosvenorii plant using 16S rRNA amplicon sequencing. The present study revealed the association of distinct endophytic bacterial communities with different parts of male and female plants. Roots of male and female plants had a higher bacterial diversity than other parts of plants, and the roots of male plants had more bacterial diversity than the roots of female plants. Endophytes belonging to the phylum Proteobacteria were abundant in all parts of male and female plants except male stems and fruit pulp, where the Firmicutes were most abundant. Class Gammaproteobacteria predominated in both male and female plants, with the genus Acinetobacter as the most dominant and part of the core microbiome of the plant (present in all parts of both, male and female plants). The presence of distinct taxa specific to male and female plants was also identified. Macrococcus, Facklamia, and Propionibacterium were the distinct genera found only in fruit pulp, the edible part of S. grosvenorii. Predictive functional analysis revealed the abundance of enzymes of secondary metabolite (especially mogroside) biosynthesis in the associated endophytic community with predominance in roots. The present study revealed bacterial endophytic communities of male and female S. grosvenorii plants that can be further explored for monk fruit cultivation, mogroside production, and early-stage identification of male and female plants. Key points • Male and female Siraitia grosvenorii plants had distinct endophytic communities • The diversity of endophytic communities was specific to different parts of plants • S. grosvenorii-associated endophytes may be valuable for mogroside biosynthesis and monk fruit cultivation

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Preferences for core microbiome composition and function by different definition methods: Evidence for the core microbiome of Eucommia ulmoides bark

Cited by 24 publications

References 63 publications

Assembly, Core Microbiota, and Function of the Rhizosphere Soil and Bark Microbiota in Eucommia ulmoides

Assembly, Core Microbiota, and Function of the Rhizosphere Soil and Bark Microbiota in Eucommia ulmoides

Microbial communities changes across aging process of tobacco leaves

Unraveling endophytic diversity in dioecious Siraitia grosvenorii: implications for mogroside production

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