Semi-Nested PCR Approach to Amplify Large 18S rRNA Gene Fragments for PCR-DGGE Analysis of Soil Fungal Communities

Oros-Sichler, Miruna; Smalla, Kornelia

doi:10.1007/978-1-4614-2356-0_23

Cited by 7 publications

(3 citation statements)

References 28 publications

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“…Relatively few fungi have been isolated using traditional culture methods. Sequence analysis on 18S rDNA [20][21][22] and internal transcribed spacer (ITS) regions [23][24][25] is widely used in classification and identification of fungi. Further, high-throughput sequencing of amplicons has been used in studies on fungal community diversity [26,27].…”

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confidence: 99%

Temporal and spatial pattern of endophytic fungi diversity of Camellia sinensis (cv. Shu Cha Zao)

Cui

et al. 2020

BMC Microbiol

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Background: The experimental materials were a 60-year-old tea tree (Camellia sinensis cv. Shu Cha Zao; SCZ) (the mother plant) and 1-year-old and 20-year-old plants of SCZ that originated as mother plant cuttings. The aim of this study was to use high-throughput sequencing to study the spatial and dynamic distribution of endophytic fungi in different leaf niches (upper leaves, middle leaves, lower leaves) and rhizosphere soil on tea plants of different ages in the same garden. Results: Ascomycota (83.77%), Basidiomycota (11.71%), and Zygomycota (3.45%) were the dominant fungal phyla in all samples. Cladosporium (12.73%), Zymoseptoria (9.18%), and Strelitziana (13.11%) were the dominant genera in the leaf. Alpha diversity analysis revealed that endophytic communities in leaves differed from those in rhizosphere soil and different leaf niches had similar fungal diversity. Shannon's indices and NMDS analysis indicated significant differences in fungal diversity and composition among the SCZ trees of different ages (p ≤ 0.01). The abundance of Cladosporium and Zymoseptoria decreased with increasing SCZ age, whereas the abundance of Strelitziana increased. Conclusions: The results illustrate variation in endophytic fungi among different niches on tea plants of different ages. The distribution of endophytic fungi in leaves of C. sinensis shows spatiotemporal variation.

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confidence: 99%

Temporal and spatial pattern of endophytic fungi diversity of Camellia sinensis (cv. Shu Cha Zao)

Cui

et al. 2020

BMC Microbiol

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“…Although there have been several studies that focused on analyzing the changes in the diversity, structure, and quantity of intestinal flora Ling et al 2010;Oros-Sichler and Smalla 2013;Ding et al 2013) by PCR-DGGE, the overall structure and composition of intestinal microbiota still cannot be comprehensively demonstrated and the method is heavy and time-consuming mainly because of the DGGE stage.…”

Section: Discussionmentioning

confidence: 98%

Oral administration ofBifidobacterim bifidumfor modulating microflora, acid and bile resistance, and physiological indices in mice

Wang

Wei

et al. 2015

Can. J. Microbiol.

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Bifidobacteria are generally acknowledged as major gut microflora used as probiotics, which promote human health. In this study, the effects of the administration of Bifidobacterim bifidum on modulating gastrointestinal (GI) tract microflora, acid and bile resistance, and physiological indices in BALB/c mice were investigated. Results showed that B. bifidum can significantly improve the ecosystem of the GI tract by increasing the amount of probiotics and reducing the populations of pathogenic bacteria, as measured by plate count and real-time PCR. After exposure to simulated GI tract conditions, the growth of gut microflora in the B. bifidum group was higher than that in the control group when incubated for 12 h in MRS or nutrient broth adjusted to pH 2.0 or 3.0 or in the presence of a concentration of bile salt (0.45% m/v). The blood biochemical index was examined, and the physiological effect of the cell-free extract of gut microflora was evaluated by measuring the activity of various enzymes, including α-glucosidases, esterase, and lactate dehydrogenase. This study suggested that a B. bifidum strain can stabilize blood sugar, lower cholesterol levels in serum, and improve metabolic activity. Moreover, B. bifidum was a promising enhancer of microbial diversity in mouse intestine and played a vital role in human physiological processes, which can benefit the health of a host.

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“…In those studies, fungi were isolated using traditional culture methods. While with the development of molecular biology, sequence analysis on 18S rDNA [22,23,24] and internal transcribed spacer (ITS) region [25,26,27] have been widely used in classification and identification of fungi. And based on the advantages of high throughput sequencing, this method has been the core choice in studies on fungal community diversity [28,29].…”

Section: Shu Cha Zao Endophytic Fungi Spatial and Dynamic Distributmentioning

confidence: 99%

Temporal and spatial pattern of endophytic fungi diversity of Camellia Sinensis (cv. Shu Cha Zao)

Cui

et al. 2020

Preprint

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Background: The experimental materials were a 60-year-old tea tree (cv. Shu Cha Zao; SCZ) (the mother plant), and 1-year-old and 20-year old plants of SCZ that originated as cuttings from the mother plant. The aim of this study was to explore the spatial and dynamic distribution of endophytic fungi in different leaf niches (upper leaves, middle leaves, lower leaves) and rhizosphere soil on tea plants (Camellia sinensis) which with different ages in the same garden by high-throughput sequencing.Results: In this study, Ascomycota (83.77%), Basidiomycota (11.71%), and Zygomycota (3.45%) were the three dominant fungal phyla in all samples. Cladosporium (12.73%), Zymoseptoria (9.18%), and Strelitziana (13.11%) were the dominant genera in the leaf. Alpha diversity analysis revealed that endophytic communities in leaves differed from those in rhizosphere soil and different leaf niches had similar fungal diversity. Shannon’s indices and NMDS analysis indicated significant differences in fungal diversity and composition among the SCZ trees of different ages (p≤0.01). The abundance of Cladosporium and Zymoseptoria decreased with increasing SCZ age, whereas the abundance of Strelitziana increased.Conclusions: Our results illustrate the variation in endophytic fungi among different niches on tea plants of different ages. The distribution of endophytic fungi in leaves of C. Sinensis (cv. Shu Cha Zao) has a certain spatiotemporal variation.

show abstract

Semi-Nested PCR Approach to Amplify Large 18S rRNA Gene Fragments for PCR-DGGE Analysis of Soil Fungal Communities

Cited by 7 publications

References 28 publications

Temporal and spatial pattern of endophytic fungi diversity of Camellia sinensis (cv. Shu Cha Zao)

Temporal and spatial pattern of endophytic fungi diversity of Camellia sinensis (cv. Shu Cha Zao)

Oral administration ofBifidobacterim bifidumfor modulating microflora, acid and bile resistance, and physiological indices in mice

Temporal and spatial pattern of endophytic fungi diversity of Camellia Sinensis (cv. Shu Cha Zao)

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