scholarly journals Epibiotic Fungal Communities of Three Tomicus spp. Infesting Pines in Southwestern China

2019 ◽  
Vol 8 (1) ◽  
pp. 15
Author(s):  
Hui-Min Wang ◽  
Fu Liu ◽  
Su-Fang Zhang ◽  
Xiang-Bo Kong ◽  
Quan Lu ◽  
...  
Keyword(s):  
Fungal Community ◽  
Bark Beetles ◽  
Yunnan Province ◽  
High Throughput Sequencing ◽  
Sequence Similarity ◽  
Illumina Miseq ◽  
Fungal Communities ◽  
Southwestern China ◽  
Community Structures ◽  
Baseline Knowledge

The association between insects and fungi has evolved over millions of years and is ubiquitous in nature. This symbiotic relationship holds critical implications for both partners, the insects and the associated microbes. Numerous fungi are externally allied with bark beetles and form a close symbiosis, but the community structures of these fungi are largely unknown. In Yunnan Province in southwestern China, the beetles Tomicus yunnanensis, T. minor, and T. brevipilosus are major forest pests that cause large losses of two indigenous pines, Pinus yunnanensis and P. kesiya. In this study, we used the Illumina MiSeq PE300 platform to process 48 samples of epibiotic fungal communities pooled from 1348 beetles; the beetles were collected during both the branch- and trunk-infection sections from five locations across Yunnan Province. Considerably greater species richness was detected using high-throughput sequencing of amplified internal transcribed spacer 1 (ITS1) ribosomal DNA (rDNA) libraries than previously documented by using culture-dependent methods. In total, 1,413,600 reads were generated, and a 97% sequence-similarity cutoff produced eight phyla, 31 classes, 83 orders, 181 families, 331 genera, 471 species, and 1157 operational taxonomic units (OTUs), with 659, 621, and 609 OTUs being confined to T. yunnanensis, T. minor, and T. brevipilosus, respectively. Tomicus yunnanensis, T. minor, and T. brevipilosus had the similar OTUs richness and evenness of fungal communities in Yunnan Province; nevertheless, the two fungal community compositions associated with T. yunnanensis and T. minor were structurally similar to each other but distinct from that associated with T. brevipilosus. Lastly, the results of principal co-ordinates analysis suggested that epibiotic fungal community structures of the three Tomicus spp. were conditioned strongly by the locations and pine hosts but weakly by beetle species and infection sections. Our findings provide baseline knowledge regarding the epibiotic fungal communities of three major Tomicus spp. in southwestern China.

scholarly journals Analysis of the Fungal Community in Ziziphi Spinosae Semen through High-Throughput Sequencing

Toxins ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 494 ◽  
Author(s):  
Mengyue Guo ◽  
Wenjun Jiang ◽  
Jiaoyang Luo ◽  
Meihua Yang ◽  
Xiaohui Pang
Keyword(s):  
Fungal Community ◽  
High Throughput Sequencing ◽  
Drug Efficacy ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Fungal Communities ◽  
Consumer Health ◽  
Efficacy And Safety ◽  
Fungal Contamination ◽  
New Approach

Ziziphi Spinosae Semen (ZSS) has been widely used in traditional Chinese medicine system for decades. Under proper humidity and temperature, ZSS is easily contaminated by fungi and mycotoxins during harvest, storage, and transport, thereby posing a considerable threat to consumer health. In this study, we first used the Illumina MiSeq PE250 platform and targeted the internal transcribed spacer 2 sequences to investigate the presence of fungi in moldy and normal ZSS samples collected from five producing areas in China. Results showed that all 14 samples tested were contaminated by fungi. Ascomycota was the dominant fungus at the phylum level, accounting for 64.36–99.74% of the fungal reads. At the genus level, Aspergillus, Candida, and Wallemia were the most predominant genera, with the relative abundances of 13.52–87.87%, 0.42–64.56%, and 0.06–34.31%, respectively. Meanwhile, 70 fungal taxa were identified at the species level. Among these taxa, three potential mycotoxin-producing fungi, namely, Aspergillus flavus, A. fumigatus, and Penicillium citrinum that account for 0.30–36.29%, 0.04–7.37%, and 0.01–0.80% of the fungal reads, respectively, were detected in all ZSS samples. Moreover, significant differences in fungal communities were observed in the moldy and normal ZSS samples. In conclusion, our results indicated that amplicon sequencing is feasible for the detection and analysis of the fungal community in the ZSS samples. This study used a new approach to survey the fungal contamination in herbal materials. This new approach can provide early warning for mycotoxin contamination in herbal materials, thereby ensuring drug efficacy and safety.

scholarly journals Fungal Diversity in the Phyllosphere of Pinus heldreichii H. Christ—An Endemic and High-Altitude Pine of the Mediterranean Region

Diversity ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 172 ◽  
Author(s):  
Jelena Lazarević ◽  
Audrius Menkis
Keyword(s):  
High Altitude ◽  
Bark Beetles ◽  
Fungal Pathogens ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
High Quality ◽  
The Balkans ◽  
Fungal Community Structure ◽  
Growing Conditions ◽  
Coniferous Tree Species

Pinus heldreichii is a high-altitude coniferous tree species naturaly occurring in small and disjuncted populations in the Balkans and southern Italy. The aim of this study was to assess diversity and composition of fungal communities in living needles of P. heldreichii specifically focusing on fungal pathogens. Sampling was carried out at six different sites in Montenegro, where 2-4 year-old living needles of P. heldreichii were collected. Following DNA isolation, it was amplified using ITS2 rDNA as a marker and subjected to high-throughput sequencing. Sequencing resulted in 31,831 high quality reads, which after assembly were found to represent 375 fungal taxa. The detected fungi were 295 (78.7%) Ascomycota, 79 (21.0%) Basidiomycota and 1 (0.2%) Mortierellomycotina. The most common fungi were Lophodermium pinastri (12.5% of all high-quality sequences), L. conigenum (10.9%), Sydowia polyspora (8.8%), Cyclaneusma niveum (5.5%), Unidentified sp. 2814_1 (5.4%) and Phaeosphaeria punctiformis (4.4%). The community composition varied among different sites, but in this respect two sites at higher altitudes (harsh growing conditions) were separated from three sites at lower altitudes (milder growing conditions), suggesting that environmental conditions were among major determinants of fungal communities associated with needles of P. heldreichii. Trees on one study site were attacked by bark beetles, leading to discolouration and frequent dieback of needles, thereby strongly affecting the fungal community structure. Among all functional groups of fungi, pathogens appeared to be an important component of fungal communities in the phyllosphere of P. heldreichii, especially in those trees under strong abiotic and biotic stress.

scholarly journals Uncovering fungal community composition in natural habitat of Ophiocordyceps sinensis using high-throughput sequencing and culture-dependent approaches

2020 ◽  
Author(s):  
Chuanbo Zhang ◽  
Chao-Hui Ren ◽  
Yan-Li Wang ◽  
Qi-Qi Wang ◽  
Yun-Sheng Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
High Throughput ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Bioactive Metabolites ◽  
Fungal Community Structure ◽  
Ophiocordyceps Sinensis ◽  
Culturable Fungi ◽  
Culture Dependent

Abstract Background The fungal communities inhabiting natural Ophiocordyceps sinensis play critical ecological roles in alpine meadow ecosystem, contribute to infect host insect, influence the occurrence of O. sinensis, and are repertoire of potential novel metabolites discovery. However, a comprehensive understanding of fungal communities of O. sinensis remain elusive. Therefore, the present study aimed to unravel fungal communities of natural O. sinensis using combination of high-throughput sequencing and culture-dependent approach. Results A total of 280,519 high-quality sequences, belonging to 5 fungal phyla, 15 classes, 41 orders, 79 families, 112 genera, and 352 putative operational taxonomic units (OTUs) were obtained from natural O. sinensis using high-throughput sequencing. Among of which, 43 genera were identified in external mycelial cortices (EMC), Ophiocordyceps, Sebacinia, Archaeorhizomyces were predominant genera with the abundance of 95.86%, 1.14%, 0.85%, respectively. Total 66 genera were identified from soil microhabitat, Inocybe, Archaeorhizomyces, Unclassified Thelephoraceae, Tomentella, Thelephora, Sebacina, Unclassified Ascomycota, Unclassified Fungi were predominant genera with an average abundance of 53.32%, 8.69%, 8.12%, 8.12%, 7.21%, 4.6%, 3.08% and 3.05%, respectively. The fungal communities in external mycelial cortices (EMC) were significantly distinct from the soil microhabitat (Soil). Meanwhile, seven culture media that benefit for the growth of O. sinensis were used to isolate culturable fungi at 16 °C, resulted in 77 fungal strains isolated for rDNA ITS sequence analysis, belonging to 33 genera, including Ophiocordyceps, Trichoderma, Cytospora, Truncatella, Dactylonectria, Isaria, Cephalosporium, Fusarium, Cosmospora, Paecilomyces, etc.. Among all culturable fungi, Mortierella and Trichoderma were predominant genera of total isolates. Conclusions The significantly distinction and overlap in fungal community structure between two approaches highlight that integration of approaches would generate more information than either of them. Our finding is the first investigation of fungal community structure of natural O. sinensis by two approachs, provide new insight into O. sinensis associated fungi, and support that microbiota of O. sinensis is an untapped source for novel bioactive metabolites discovery.

scholarly journals Temporal and Cultivar-Specific Effects on Potato Root- and Rhizosphere Fungal Diversity

2020 ◽  
Author(s):  
Kaire Loit ◽  
Liina Soonvald ◽  
Alar Astover ◽  
Eve Runno-Paurson ◽  
Maarja Öpik ◽  
...  
Keyword(s):  
Community Composition ◽  
Fungal Community ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Solanum Tuberosum L ◽  
Potato Cultivar ◽  
Substantial Effect ◽  
Sampling Time ◽  
Fungal Communities ◽  
Fungal Community Composition

The rhizosphere fungal community can play an important role in determining plant growth and health. In this study, using high-throughput sequencing, we investigated the fungal diversity and community composition in the roots and rhizosphere soil of 21 potato (Solanum tuberosum L.) cultivars. The samples were collected at three different sampling points. Furthermore, we assessed the differences in both diversity and composition of pathogen and saprotroph communities. In soil and roots, the fungal richness and relative abundance of pathogens and saprotrophs were mainly affected by sampling time. However, root fungal communities were also significantly affected by cultivar. The most substantial effect of cultivar was on root pathogen diversity. Moreover, the occurrence of most pathogens strongly varied among cultivars. Soil fungal community composition was primarily determined by sampling time; whereas in roots, the primary determinant was cultivar. Our results demonstrate changes in fungal communities over the potato growing season, as well as highlight the importance of potato cultivar on root fungal communities, and emphasise their importance in plant breeding.

scholarly journals Uncovering fungal community composition in natural habitat of Ophiocordyceps sinensis using high-throughput sequencing and culture-dependent approaches

2020 ◽  
Author(s):  
Chuanbo Zhang ◽  
Chao-Hui Ren ◽  
Yan-Li Wang ◽  
Qi-Qi Wang ◽  
Yun-Sheng Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
High Throughput ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Comprehensive Understanding ◽  
Fungal Community Structure ◽  
Ophiocordyceps Sinensis ◽  
Culturable Fungi ◽  
Culture Dependent

Abstract Background: The fungal communities inhabiting natural Ophiocordyceps sinensis play critical ecological roles in alpine meadow ecosystem, contribute to infect host insect, influence the occurrence of O. sinensis, and are repertoire of potential novel metabolites discovery. However, a comprehensive understanding of fungal communities of O. sinensis remain elusive. Therefore, the present study aimed to unravel fungal communities of natural O. sinensis using combination of high-throughput sequencing and culture-dependent approaches. Results: A total of 280,519 high-quality sequences, belonging to 5 fungal phyla, 15 classes, 41 orders, 79 families, 112 genera, and 352 putative operational taxonomic units (OTUs) were obtained from natural O. sinensis using high-throughput sequencing. Among of which, 43 genera were identified in external mycelial cortices, Ophiocordyceps, Sebacinia, Archaeorhizomyces were predominant genera with the abundance of 95.86%, 1.14%, 0.85%, respectively. A total of 66 genera were identified from soil microhabitat, Inocybe, Archaeorhizomyces, unclassified Thelephoraceae, Tomentella, Thelephora, Sebacina, unclassified Ascomycota, unclassified Fungi were predominant genera with an average abundance of 53.32%, 8.69%, 8.12%, 8.12%, 7.21%, 4.6%, 3.08% and 3.05%, respectively. The fungal communities in external mycelial cortices were significantly distinct from the soil microhabitat. Meanwhile, seven types of culture media were used to isolate culturable fungi at 16°C, resulted in 77 fungal strains isolated by rDNA ITS sequence analysis, belonging to 33 genera, including Ophiocordyceps, Trichoderma, Cytospora, Truncatella, Dactylonectria, Isaria, Cephalosporium, Fusarium, Cosmospora and Paecilomyces, etc.. Among all culturable fungi, Mortierella and Trichoderma were predominant genera. Conclusions: The significantly differences and overlap in fungal community structure between two approaches highlight that the integration of high-throughput sequencing and culture-dependent approaches would generate more information. Our result reveal a comprehensive understanding of fungal community structure of natural O. sinensis, provide new insight into O. sinensis associated fungi, and support that microbiota of natural O. sinensis is an untapped source for novel bioactive metabolites discovery.

scholarly journals Uncovering fungal community composition in natural habitat of Ophiocordyceps sinensis using high-throughput sequencing and culture-dependent approaches

2020 ◽  
Author(s):  
Chuanbo Zhang ◽  
Chao-Hui Ren ◽  
Yan-Li Wang ◽  
Qi-Qi Wang ◽  
Yun-Sheng Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
High Throughput ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Comprehensive Understanding ◽  
Fungal Community Structure ◽  
Ophiocordyceps Sinensis ◽  
Culturable Fungi ◽  
Culture Dependent

Abstract Background: The fungal communities inhabiting natural Ophiocordyceps sinensis play critical ecological roles in alpine meadow ecosystem, contribute to infect host insect, influence the occurrence of O. sinensis, and are repertoire of potential novel metabolites discovery. However, a comprehensive understanding of fungal communities of O. sinensis remain elusive. Therefore, the present study aimed to unravel fungal communities of natural O. sinensis using combination of high-throughput sequencing and culture-dependent approaches. Results: A total of 280,519 high-quality sequences, belonging to 5 fungal phyla, 15 classes, 41 orders, 79 families, 112 genera, and 352 putative operational taxonomic units (OTUs) were obtained from natural O. sinensis using high-throughput sequencing. Among of which, 43 genera were identified in external mycelial cortices (EMC), Ophiocordyceps, Sebacinia, Archaeorhizomyces were predominant genera with the abundance of 95.86%, 1.14%, 0.85%, respectively. A total of 66 genera were identified from soil microhabitat (Soil), Inocybe, Archaeorhizomyces, unclassified Thelephoraceae, Tomentella, Thelephora, Sebacina, unclassified Ascomycota, unclassified Fungi were predominant genera with an average abundance of 53.32%, 8.69%, 8.12%, 8.12%, 7.21%, 4.6%, 3.08% and 3.05%, respectively. The fungal communities in external mycelial cortices were significantly distinct from the soil microhabitat. Meanwhile, seven types of culture media were used to isolate culturable fungi at 16°C, resulted in 77 fungal strains isolated by rDNA ITS sequence analysis, belonging to 33 genera, including Ophiocordyceps, Trichoderma, Cytospora, Truncatella, Dactylonectria, Isaria, Cephalosporium, Fusarium, Cosmospora and Paecilomyces, etc.. Among all culturable fungi, Mortierella and Trichoderma were predominant genera. Conclusions: The significantly differences and overlap in fungal community structure between two approaches highlight that the integration of high-throughput sequencing and culture-dependent approaches would generate more information. Our result reveal a comprehensive understanding of fungal community structure of natural O. sinensis, provide new insight into O. sinensis associated fungi, and support that microbiota of natural O. sinensis is an untapped source for novel bioactive metabolites discovery.

scholarly journals The Diversity Analysis and Functional Prediction of Endophytic Fungi Community of Gymnadenia Conopsea from Different Altitudes in Tibet

2021 ◽  
Author(s):  
Xiu Yin ◽  
Erhao Zhang ◽  
Yazhou Lu ◽  
Hong Quan ◽  
Lianqiang Li ◽  
...  
Keyword(s):  
Community Structure ◽  
Endophytic Fungi ◽  
Fungal Community ◽  
Diversity Index ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Fungal Communities ◽  
Reproduction Rate ◽  
Gymnadenia Conopsea ◽  
Different Altitudes

Abstract Gymnadenia conopsea has high economic value, and can be used as a medicinal and ornamental plant. Due to its low natural reproduction rate and overexploitation, the extinction of this plant is gradually accelerating. Understanding the composition and diversity of endophytic fungi is of great significance in promoting its propagation and the utilization of beneficial fungal strains. In this study, the diversity of fungal communities from roots, stems, leaves, fruits, and soils at four different elevations was studied with Illumina MiSeq sequencing. A total of 3,707,871 sequences were detected from all samples, and the number of clustering OTUs was 14,800. The OTUs were assigned to 4 phyla, 17 classes, 41 orders, 73 families, and 99 genera. The predominant fungal groups included Ascomycota and Basidiomycota, accounting for 33.71%-86.38% and 6.98%-58.30% of the total species, respectively. According to the alpha diversity index analysis, the diversity and richness of endophytic fungal communities in plant tissues at low altitudes were higher than those at high altitudes, while the diversity and richness of soil fungi were the opposite. In addition, principal coordinate analysis (PCoA) not only showed that the fungal community structure was correlated with altitude but also indicated tissue specificity of the community structure. Our study explored the composition of the endophytic fungal community among different tissues from different altitudes and included functional analysis, which might provide new ideas for saving the endangered species G. conopsea.

scholarly journals Non-symbiotic soil microbes are more strongly influenced by altered tree biodiversity than arbuscular mycorrhizal fungi during initial forest establishment

2019 ◽  
Vol 95 (10) ◽  
Author(s):  
Jake J Grossman ◽  
Allen J Butterfield ◽  
Jeannine Cavender-Bares ◽  
Sarah E Hobbie ◽  
Peter B Reich ◽  
...  
Keyword(s):  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
High Throughput Sequencing ◽  
Arbuscular Mycorrhizal ◽  
Tree Diversity ◽  
Fungal Communities ◽  
Juniperus Virginiana ◽  
Lipid Fatty Acid ◽  
Neutral Lipid Fatty Acid ◽  
Fungal Abundance

ABSTRACT While the relationship between plant and microbial diversity has been well studied in grasslands, less is known about similar relationships in forests, especially for obligately symbiotic arbuscular mycorrhizal (AM) fungi. To assess the effect of varying tree diversity on microbial alpha- and beta-diversity, we sampled soil from plots in a high-density tree diversity experiment in Minnesota, USA, 3 years after establishment. About 3 of 12 tree species are AM hosts; the other 9 primarily associate with ectomycorrhizal fungi. We used phospho- and neutral lipid fatty acid analysis to characterize the biomass and functional identity of the whole soil bacterial and fungal community and high throughput sequencing to identify the species-level richness and composition of the AM fungal community. We found that plots of differing tree composition had different bacterial and fungal communities; plots with conifers, and especially Juniperus virginiana, had lower densities of several bacterial groups. In contrast, plots with a higher density or diversity of AM hosts showed no sign of greater AM fungal abundance or diversity. Our results indicate that early responses to plant diversity vary considerably across microbial groups, with AM fungal communities potentially requiring longer timescales to respond to changes in host tree diversity.

scholarly journals Response of soil fungal communities to continuous cropping of flue-cured tobacco

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shengnan Wang ◽  
Jiangke Cheng ◽  
Tong Li ◽  
Yuncheng Liao
Keyword(s):  
Community Structure ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Cropping Systems ◽  
Quantitative Polymerase Chain Reaction ◽  
Fungal Communities ◽  
Continuous Cropping ◽  
Fungal Community Structure ◽  
Soil Variables ◽  
Fungal Abundance

AbstractFungal communities are considered to be critically important for crop health and soil fertility. However, our knowledge of the response of fungal community structure to the continuous cropping of flue-cured tobacco is limited, and the interaction of soil fungal communities under different cropping systems remains unclear. In this study, we comparatively investigated the fungal abundance, diversity, and community composition in the soils in which continuous cropping of flue-cured tobacco for 3 years (3ys), 5 years (5ys), and cropping for 1 year (CK) using quantitative polymerase chain reaction and high-throughput sequencing technology. The results revealed that continuous cropping of flue-cured tobacco changed the abundance of soil fungi, and caused a significant variation in fungal diversity. In particular, continuous cropping increased the relative abundance of Mortierellales, which can dissolve mineral phosphorus in soil. Unfortunately, continuous cropping also increased the risk of potential pathogens. Moreover, long-term continuous cropping had more complex and stabilize network. This study also indicated that available potassium and available phosphorous were the primary soil factors shifting the fungal community structure. These results suggested that several soil variables may affect fungal community structure. The continuous cropping of flue-cured tobacco significantly increased the abundance and diversity of soil fungal communities.

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