scholarly journals High-Throughput Sequencing Shows High Fungal Diversity and Community Segregation in the Rhizospheres of Container-Grown Conifer Seedlings

Forests ◽  
2016 ◽  
Vol 7 (2) ◽  
pp. 44 ◽  
Author(s):  
Audrius Menkis ◽  
Daiva Burokienė ◽  
Jan Stenlid ◽  
Elna Stenström
Keyword(s):  
High Throughput ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Conifer Seedlings ◽  
Community Segregation

scholarly journals Different Amplicon Targets for Sequencing-Based Studies of Fungal Diversity

2017 ◽  
Vol 83 (17) ◽  
Author(s):  
Francesca De Filippis ◽  
Manolo Laiola ◽  
Giuseppe Blaiotta ◽  
Danilo Ercolini
Keyword(s):  
Microbial Ecology ◽  
High Throughput ◽  
Biological Samples ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Amplicon Sequencing ◽  
Fungal Species ◽  
Fungal Communities ◽  
Its2 Region ◽  
Mock Community

ABSTRACT Target-gene amplicon sequencing is the most exploited high-throughput sequencing application in microbial ecology. The targets are taxonomically relevant genes, with 16S rRNA being the gold standard for bacteria. As for fungi, the most commonly used target is the internal transcribed spacer (ITS). However, the uneven ITS length among species may promote preferential amplification and sequencing and incorrect estimation of their abundance. Therefore, the use of different targets is desirable. We evaluated the use of three different target amplicons for the characterization of fungal diversity. After an in silico primer evaluation, we compared three amplicons (the ITS1-ITS2 region [ITS1-2], 18S ribosomal small subunit RNA, and the D1/D2 domain of the 26S ribosomal large subunit RNA), using biological samples and a mock community of common fungal species. All three targets allowed for accurate identification of the species present. Nevertheless, high heterogeneity in ITS1-2 length was found, and this caused an overestimation of the abundance of species with a shorter ITS, while both 18S and 26S amplicons allowed for more reliable quantification. We demonstrated that ITS1-2 amplicon sequencing, although widely used, may lead to an incorrect evaluation of fungal communities, and efforts should be made to promote the use of different targets in sequencing-based microbial ecology studies. IMPORTANCE Amplicon-sequencing approaches for fungi may rely on different targets affecting the diversity and abundance of the fungal species. An increasing number of studies will address fungal diversity by high-throughput amplicon sequencing. The description of the communities must be accurate and reliable in order to draw useful insights and to address both ecological and biological questions. By analyzing a mock community and several biological samples, we demonstrate that using different amplicon targets may change the results of fungal microbiota analysis, and we highlight how a careful choice of the target is fundamental for a thorough description of the fungal communities.

High-throughput sequencing analysis of endophytic fungal diversity in cynanchum sp.

2020 ◽  
Vol 134 ◽  
pp. 349-358
Author(s):  
W.-H. Chen ◽  
S.-J. Wu ◽  
X.-L. Sun ◽  
K.-M. Feng ◽  
K. Rahman ◽  
...  
Keyword(s):  
High Throughput ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Sequencing Analysis

scholarly journals Investigation of bacterial and fungal diversity in tarag using high-throughput sequencing

2014 ◽  
Vol 97 (10) ◽  
pp. 6085-6096 ◽  
Author(s):  
Zhihong Sun ◽  
Wenjun Liu ◽  
Qiuhua Bao ◽  
Jiachao Zhang ◽  
Qiangchuan Hou ◽  
...  
Keyword(s):  
High Throughput ◽  
Fungal Diversity ◽  
High Throughput Sequencing

scholarly journals High-throughput sequencing for the detection of the bacterial and fungal diversity in Mongolian naturally fermented cow’s milk in Russia

2015 ◽  
Vol 15 (1) ◽  
pp. 45 ◽  
Author(s):  
Wenjun Liu ◽  
Yi Zheng ◽  
Lai-Yu Kwok ◽  
Zhihong Sun ◽  
Jiachao Zhang ◽  
...  
Keyword(s):  
High Throughput ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Cow’S Milk ◽  
Cow's Milk

scholarly journals Fungal Composition and Diversity of the Tobacco Leaf Phyllosphere during Curing of Leaves

2020 ◽  
Author(s):  
Qian-Li Chen ◽  
Lin Cai ◽  
Hancheng Wang ◽  
Liu-Ti Cai ◽  
Paul Goodwin ◽  
...  
Keyword(s):  
High Throughput ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Rhizopus Oryzae ◽  
Curing Process ◽  
Leaf Lamina ◽  
Saprotrophic Fungi ◽  
Tobacco Leaves ◽  
Fungal Sequence ◽  
Abundant Genus

Abstract Background: Rhizopus oryzae causes tobacco pole rot in China during tobacco flue-curing. Flue-curing is a post-harvest process done to prepare tobacco leaves and involves three different stages: the yellowing stage has the lowest temperatures and highest humidity, then the color-fixing stage has higher temperatures and medium humidity, and finally the stem-drying stage has the highest temperatures and lowest humidity.Results: In this study, fungal culturing and IonS5TMXL high-throughput sequencing techniques were used to reveal the fungal community of the petioles and lamina of tobacco leaves infected with pole rot during flue-curing. A total of 108 fungal isolates belonging to 5 genera and 10 species were isolated on media. The most common fungi isolated was R. oryzae, most often found equally on petioles and laminas in the color-fixing stage, followed by saprotrophs, mostly Aspergillus fumigatus and Aspergillus flavus. High-throughput sequencing revealed saprotrophs, Alternaria being the most abundant genus, followed by Phoma, Cercospora and Aspergillus, whereas Rhizopus was the tenth most abundant genus, which was mostly found on petioles at the yellowing stage. Both culturable fungal diversity and fungal sequence diversity was higher at stem-drying stage than the yellowing and color-fixing stages, and diversity was higher with leaf lamina than petioles revealing that the changes in fungal composition and diversity during the curing process were similar with both methods.Conclusions: A better understanding of the saprotrophic fungi during curing of leaves with pole rot could result in the identification of highly competitive saproptrophs that may act as potential biocontrol agents of tobacco pole rot.

scholarly journals Assessment of Passive Traps Combined with High-Throughput Sequencing To Study Airborne Fungal Communities

2018 ◽  
Vol 84 (11) ◽  
Author(s):  
Jaime Aguayo ◽  
Céline Fourrier-Jeandel ◽  
Claude Husson ◽  
Renaud Ioos
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Linear Models ◽  
Environmental Dna ◽  
Illumina Miseq ◽  
Fungal Communities ◽  
Correct Identification ◽  
Spore Trap

ABSTRACTTechniques based on high-throughput sequencing (HTS) of environmental DNA have provided a new way of studying fungal diversity. However, these techniques suffer from a number of methodological biases which may appear at any of the steps involved in a metabarcoding study. Air is one of the most important environments where fungi can be found, because it is the primary medium of dispersal for many species. Looking ahead to future developments, it was decided to test 20 protocols, including different passive spore traps, spore recovery procedures, DNA extraction kits, and barcode loci. HTS was performed with the Illumina MiSeq platform targeting two subloci of the fungal internal transcribed spacer. Multivariate analysis and generalized linear models showed that the type of passive spore trap, the spore recovery procedure, and the barcode all impact the description of fungal communities in terms of richness and diversity when assessed by HTS metabarcoding. In contrast, DNA extraction kits did not significantly impact these results. Although passive traps may be used to describe airborne fungal communities, a study using specific real-time PCR and a mock community showed that these kinds of traps are affected by environmental conditions that may induce losses of biological material, impacting diversity and community composition results.IMPORTANCEThe advent of high-throughput sequencing (HTS) methods, such as those offered by next-generation sequencing (NGS) techniques, has opened a new era in the study of fungal diversity in different environmental substrates. In this study, we show that an assessment of the diversity of airborne fungal communities can reliably be achieved by the use of simple and robust passive spore traps. However, a comparison of sample processing protocols showed that several methodological biases may impact the results of fungal diversity when assessed by metabarcoding. Our data suggest that identifying these biases is of paramount importance to enable a correct identification and relative quantification of community members.

High-throughput sequencing view on the magnitude of global fungal diversity

2021 ◽  
Author(s):  
Petr Baldrian ◽  
Tomáš Větrovský ◽  
Clémentine Lepinay ◽  
Petr Kohout
Keyword(s):  
High Throughput ◽  
Fungal Diversity ◽  
High Throughput Sequencing
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