scholarly journals Fungal Endophytic Communities in Grapevines (Vitis vinifera L.) Respond to Crop Management

2012 ◽  
Vol 78 (12) ◽  
pp. 4308-4317 ◽  
Author(s):  
Michael Pancher ◽  
Marco Ceol ◽  
Paola Elisa Corneo ◽  
Claudia Maria Oliveira Longa ◽  
Sohail Yousaf ◽  
...  
Keyword(s):  
Vitis Vinifera ◽  
Fungal Endophytes ◽  
Intergenic Spacer ◽  
Fungal Communities ◽  
Vitis Vinifera L ◽  
Multivariate Statistical ◽  
Content Type ◽  
Colony Pcr ◽  
Culture Independent ◽  
Culture Dependent

ABSTRACTWe studied the distribution of fungal endophytes of grapevine (Vitis viniferaL.) plants in a subalpine area of northern Italy, where viticulture is of high economic relevance. We adopted both cultivation-based and cultivation-independent approaches to address how various anthropic and nonanthropic factors shape microbial communities. Grapevine stems were harvested from several locations considering organic and integrated pest management (IPM) and from the cultivars Merlot and Chardonnay. Cultivable fungi were isolated and identified by internal-transcribed-spacer sequence analysis, using a novel colony-PCR method, to amplify DNA from fungal specimens. The composition of fungal communities was assessed using a cultivation-independent approach, automated ribosomal intergenic spacer analysis (ARISA). Multivariate statistical analysis of both culture-dependent and culture-independent data sets was convergent and indicated that fungal endophytic communities in grapevines from organically managed farms were different from those from farms utilizing IPM. Fungal communities in plants of cv. Merlot and cv. Chardonnay overlapped when analyzed using culture-dependent approaches but could be partially resolved using ARISA fingerprinting.

scholarly journals Endophytic fungal communities associated with field-grown soybean roots and seeds in the Huang-Huai region of China

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4713 ◽  
Author(s):  
Hongjun Yang ◽  
Wenwu Ye ◽  
Jiaxin Ma ◽  
Dandan Zeng ◽  
Zhenyang Rong ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Endophytic Fungi ◽  
Fungal Endophytes ◽  
Fungal Endophyte ◽  
Disease Suppression ◽  
Fungal Communities ◽  
Culture Independent ◽  
Soybean Roots ◽  
Abundant Genus ◽  
Culture Dependent

Plants depend on beneficial interactions between roots and fungal endophytes for growth, disease suppression, and stress tolerance. In this study, we characterized the endophytic fungal communities associated with the roots and corresponding seeds of soybeans grown in the Huang-Huai region of China. For the roots, we identified 105 and 50 genera by culture-independent and culture-dependent (CD) methods, respectively, and isolated 136 fungal strains (20 genera) from the CD samples. Compared with the 52 soybean endophytic fungal genera reported in other countries, 28 of the genera we found were reported, and 90 were newly discovered. Even though Fusarium was the most abundant genus of fungal endophyte in every sample, soybean root samples from three cities exhibited diverse endophytic fungal communities, and the results between samples of roots and seeds were also significantly different. Together, we identified the major endophytic fungal genera in soybean roots and seeds, and revealed that the diversity of soybean endophytic fungal communities was influenced by geographical effects and tissues. The results will facilitate a better understanding of soybean–endophytic fungi interaction systems and will assist in the screening and utilization of beneficial microorganisms to promote healthy of plants such as soybean.

scholarly journals Biodiversity of fungi on Vitis vinifera L. revealed by traditional and high-resolution culture-independent approaches

2018 ◽  
Vol 90 (1) ◽  
pp. 1-84 ◽  
Author(s):  
Ruvishika S. Jayawardena ◽  
Witoon Purahong ◽  
Wei Zhang ◽  
Tesfaye Wubet ◽  
XingHong Li ◽  
...  
Keyword(s):  
High Resolution ◽  
Vitis Vinifera ◽  
Vitis Vinifera L ◽  
Culture Independent

scholarly journals Comparison of DNA sequencing and morphological identification techniques to characterize environmental fungal communities

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Naohide Shinohara ◽  
Cheolwoon Woo ◽  
Naomichi Yamamoto ◽  
Kazuhiro Hashimoto ◽  
Hiroko Yoshida-Ohuchi ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Fungal Communities ◽  
Its2 Region ◽  
Morphological Identification ◽  
Ecological Studies ◽  
Culture Independent ◽  
Identification Technique ◽  
Relative Abundances ◽  
Identification Techniques ◽  
Culture Dependent

AbstractCulture-independent DNA sequencing of fungal internal transcribed spacer 2 (ITS2) region was compared to a culture-dependent morphological identification technique to characterize house dust-borne fungal communities. The abundant genera were Aspergillus, Wallemia, Cladosporium, and Penicillium. Statistically significant between-method correlations were observed for Wallemia and Cladosporium (Spearman’s ρ = 0.75 and 0.72, respectively; p < 0.001). Penicillium tended to be detected with much higher (averaged 26-times) relative abundances by the culture-based method than by the DNA-based method, although statistically significant inter-method correlation was observed with Spearman’s ρ = 0.61 (p = 0.002). Large DNA sequencing-based relative abundances observed for Alternaria and Aureobasidium were likely due to multicellularity of their spores with large number of per-spore ITS2 copies. The failure of the culture-based method in detectiing Toxicocladosporium, Verrucocladosporium, and Sterigmatomyces was likely due to their fastidiousness growth on our nutrient medium. Comparing between the two different techniques clarified the causes of biases in identifying environmental fungal communities, which should be amended and/or taken into consideration when the methods are used for future fungal ecological studies.

scholarly journals rpoDGene Pyrosequencing for the Assessment of Pseudomonas Diversity in a Water Sample from the Woluwe River

2014 ◽  
Vol 80 (15) ◽  
pp. 4738-4744 ◽  
Author(s):  
David Sánchez ◽  
Sandra Matthijs ◽  
Margarita Gomila ◽  
Catherine Tricot ◽  
Magdalena Mulet ◽  
...  
Keyword(s):  
Water Sample ◽  
Selection Criteria ◽  
Pseudomonas Stutzeri ◽  
Phylogenetic Groups ◽  
Content Type ◽  
Blast Analysis ◽  
Culture Independent ◽  
Total Dna ◽  
Culture Dependent ◽  
Criteria For Selection

ABSTRACTA water sample from a noncontaminated site at the source of the Woluwe River (Belgium) was analyzed by culture-dependent and -independent methods.Pseudomonasisolates were identified by sequencing and analysis of therpoDgene. Culture-independent methods consisted of cloning and pyrosequencing of aPseudomonasrpoDamplicon from total DNA extracted from the same sample and amplified with selectiverpoDgene primers. Among a total of 14,540 reads, 6,228 corresponded toPseudomonasrpoDgene sequences by a BLAST analysis in the NCBI database. The selection criteria for the reads were sequences longer than 400 bp, an averageQ40value greater than 25, and >85% identity with aPseudomonasspecies. Of the 6,228PseudomonasrpoDsequences, 5,345 sequences met the established criteria for selection. Sequences were clustered by phylogenetic analysis and by use of the QIIME software package. Representative sequences of each cluster were assigned by BLAST analysis to a knownPseudomonasspecies when the identity with the type strain was greater than or equal to 96%. Twenty-six species distributed among 12 phylogenetic groups or subgroups within the genus were detected by pyrosequencing.Pseudomonas stutzeri,P. moraviensis, andP. simiaewere the only cultured species not detected by pyrosequencing. The predominant phylogenetic group within thePseudomonasgenus was theP. fluorescensgroup, as determined by culture-dependent and -independent analyses. In all analyses, a high number of putative novel phylospecies was found: 10 were identified in the cultured strains and 246 were detected by pyrosequencing, indicating that the diversity ofPseudomonasspecies has not been fully described.

scholarly journals Genome Sequence of Methylobacterium sp. Strain GXF4, a Xylem-Associated Bacterium Isolated from Vitis vinifera L. Grapevine

2012 ◽  
Vol 194 (18) ◽  
pp. 5157-5158 ◽  
Author(s):  
Han Ming Gan ◽  
Teong Han Chew ◽  
André O. Hudson ◽  
Michael A. Savka
Keyword(s):  
Vitis Vinifera ◽  
Genome Sequence ◽  
Sequence Assembly ◽  
Vitis Vinifera L ◽  
Content Type ◽  
Shed Light

ABSTRACTMethylobacteriumsp. strain GXF4 is an isolate from grapevine. Here we present the sequence, assembly, and annotation of its genome, which may shed light on its role as a grapevine xylem inhabitant. To our knowledge, this is the first genome announcement of a plant xylem-associated strain of the genusMethylobacterium.

Direct comparison of culture-dependent and culture-independent molecular approaches reveal the diversity of fungal endophytic communities in stems of grapevine (Vitis vinifera)

2018 ◽  
Vol 90 (1) ◽  
pp. 85-107 ◽  
Author(s):  
Asha J. Dissanayake ◽  
Witoon Purahong ◽  
Tesfaye Wubet ◽  
Kevin D. Hyde ◽  
Wei Zhang ◽  
...  
Keyword(s):  
Vitis Vinifera ◽  
Molecular Approaches ◽  
Culture Independent ◽  
Culture Dependent

scholarly journals Genome Sequence of Novosphingobium sp. Strain Rr 2-17, a Nopaline Crown Gall-Associated Bacterium Isolated from Vitis vinifera L. Grapevine

2012 ◽  
Vol 194 (18) ◽  
pp. 5137-5138 ◽  
Author(s):  
Han Ming Gan ◽  
Teong Han Chew ◽  
André O. Hudson ◽  
Michael A. Savka
Keyword(s):  
Vitis Vinifera ◽  
Genome Sequence ◽  
Crown Gall ◽  
Draft Genome ◽  
Homoserine Lactone ◽  
Vitis Vinifera L ◽  
Acyl Homoserine Lactone ◽  
Content Type ◽  
Crown Gall Tumor

ABSTRACTNovosphingobiumsp. strain Rr 2-17 is anN-acyl homoserine lactone (AHL)-producing bacterium isolated from the crown gall tumor of a grapevine. To our knowledge, this is the first draft genome announcement of a plant-associated strain from the genusNovosphingobium.

Soil fungal communities are compositionally resistant to drought manipulations – Evidence from culture-dependent and culture-independent analyses

2021 ◽  
Vol 51 ◽  
pp. 101062
Author(s):  
Achala Narayanan ◽  
Kyle J. Ismert ◽  
Melinda D. Smith ◽  
Ari Jumpponen
Keyword(s):  
Fungal Communities ◽  
Culture Independent ◽  
Culture Dependent

scholarly journals Biodiversity in Oscypek, a Traditional Polish Cheese, Determined by Culture-Dependent and -Independent Approaches

2012 ◽  
Vol 78 (6) ◽  
pp. 1890-1898 ◽  
Author(s):  
Ángel Alegría ◽  
Pawel Szczesny ◽  
Baltasar Mayo ◽  
Jacek Bardowski ◽  
Magdalena Kowalczyk
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Starter Cultures ◽  
Rrna Gene ◽  
Content Type ◽  
Protected Designation Of Origin ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis ◽  
Microbial Groups ◽  
The Tatra Mountains ◽  
Culture Dependent

ABSTRACTOscypek is a traditional Polish scalded-smoked cheese, with a protected-designation-of-origin (PDO) status, manufactured from raw sheep's milk without starter cultures in the Tatra Mountains region of Poland. This study was undertaken in order to gain insight into the microbiota that develops and evolves during the manufacture and ripening stages of Oscypek. To this end, we made use of both culturing and the culture-independent methods of PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE) and pyrosequencing of 16S rRNA gene amplicons. The culture-dependent technique and PCR-DGGE fingerprinting detected the predominant microorganisms in traditional Oscypek, whereas the next-generation sequencing technique (454 pyrosequencing) revealed greater bacterial diversity. Besides members of the most abundant bacterial genera in dairy products, e.g.,Lactococcus,Lactobacillus,Leuconostoc,Streptococcus, andEnterococcus, identified by all three methods, other, subdominant bacteria belonging to the familiesBifidobacteriaceaeandMoraxellaceae(mostlyEnhydrobacter), as well as various minor bacteria, were identified by pyrosequencing. The presence of bifidobacterial sequences in a cheese system is reported for the first time. In addition to bacteria, a great diversity of yeast species was demonstrated in Oscypek by the PCR-DGGE method. Culturing methods enabled the determination of a number of viable microorganisms from different microbial groups and their isolation for potential future applications in specific cheese starter cultures.

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