scholarly journals Patterns of Fungal Diversity in Needles, Rootlets and Soil of Endemic Pinus Peuce

2021 ◽  
Author(s):  
Jelena Lazarević ◽  
Ana Topalović ◽  
Audrius Menkis
Keyword(s):  
High Altitude ◽  
High Throughput Sequencing ◽  
Dna Amplification ◽  
Fungal Communities ◽  
The Balkans ◽  
Functional Capabilities ◽  
Forest Sites ◽  
Substrate Properties ◽  
Host Tree Species ◽  
Pinus Peuce

Abstract Pinus peuce Griseb is five-needle pine native in high-altitude montane habitats of the Balkans. The aim was to assess the diversity and composition of fungal communities associated with the soil, rootlets and living needles of P. peuce at three high-altitude forest sites with different edaphic conditions and stand characteristics in southeastern Montenegro. In total, 90 needle, 90 rootlet and 90 soil samples were sampled. DNA amplification using ITS2 rDNA as a marker and high-throughput sequencing resulted in 17,620 high-quality reads, representing 825 fungal taxa. There were 52.5% Basidiomycota, 43.9% Ascomycota and 3.6% Mucoromycotina. There were 118 unique fungal taxa in the rootlets, 230 in the soil and 113 in the needles, with 8 taxa were shared. The most common fungi in rootlets were Rhizopogon mohelensis (11.0%), Suillus sibiricus (8.4%), R. fallax (6.9%), in the soil – Phlebiopsis gigantea (5.1%), Tylospora asterophora (2.9%), Sollicocossima terricola (2.7%), and in the needles – Dothideomycetes sp. 3360_7 (17.6%), Dothideomycetes sp. 3360_10 (10.7%), Leotiomycetes sp. 3360_16 (6.5%). The results showed that the functional tissues and the rhizosphere soil of P. peuce were inhabited by a high diversity of fungi, which were largely specific to each particular substrate, while. the site conditions had only limited effect on associated fungal communities. Associated fungal communities were largely determined by the host tree species, substrate properties and functional capabilities of associated fungi.

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 Host tree organ is the primary driver of endophytic fungal community structure in a hemiboreal forest

2019 ◽  
Vol 96 (2) ◽  
Author(s):  
Kati Küngas ◽  
Mohammad Bahram ◽  
Kadri Põldmaa
Keyword(s):  
Community Structure ◽  
High Throughput Sequencing ◽  
Dispersal Limitation ◽  
Fungal Communities ◽  
Species Identity ◽  
Fungal Community Structure ◽  
Forest Sites ◽  
Primary Driver ◽  
Main Determinants ◽  
Individual Trees

ABSTRACT Despite numerous studies on plant endophytes, little is known about fungal communities associated with different aboveground tissues of living trees. We used high-throughput sequencing to compare the diversity and community structure of fungi inhabiting leaves, branches and trunks of Alnus incana and Corylus avellana growing at three hemiboreal forest sites. Our analysis revealed that tree organs are the main determinants of the structure of fungal communities, whereas the effects of host species and locality remained secondary and negligible, respectively. The structure of fungal communities in trunks was the most distinct compared to that in leaves and branches. The foliar fungal communities were more similar within than between individual trees, implying that certain fungi may grow through parts of the tree crown. The weak effect of locality compared to host organs and species identity suggests that the structural variation of fungal communities in the aboveground parts of trees depends mainly on deterministic factors rather than dispersal limitation.

scholarly journals The Banana Root Endophytome: Differences between Mother Plants and Suckers and Evaluation of Selected Bacteria to Control Fusarium oxysporum f.sp. cubense

2021 ◽  
Vol 7 (3) ◽  
pp. 194
Author(s):  
Carmen Gómez-Lama Cabanás ◽  
Antonio J. Fernández-González ◽  
Martina Cardoni ◽  
Antonio Valverde-Corredor ◽  
Javier López-Cepero ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Canary Islands ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Phenological Stage ◽  
Mother Plants ◽  
Fusarium Wilt Of Banana ◽  
Identification And Characterization

This study aimed to disentangle the structure, composition, and co-occurrence relationships of the banana (cv. Dwarf Cavendish) root endophytome comparing two phenological plant stages: mother plants and suckers. Moreover, a collection of culturable root endophytes (>1000) was also generated from Canary Islands. In vitro antagonism assays against Fusarium oxysporum f.sp. cubense (Foc) races STR4 and TR4 enabled the identification and characterization of potential biocontrol agents (BCA). Eventually, three of them were selected and evaluated against Fusarium wilt of banana (FWB) together with the well-known BCA Pseudomonas simiae PICF7 under controlled conditions. Culturable and non-culturable (high-throughput sequencing) approaches provided concordant information and showed low microbial diversity within the banana root endosphere. Pseudomonas appeared as the dominant genus and seemed to play an important role in the banana root endophytic microbiome according to co-occurrence networks. Fungal communities were dominated by the genera Ophioceras, Cyphellophora, Plecosphaerella, and Fusarium. Overall, significant differences were found between mother plants and suckers, suggesting that the phenological stage determines the recruitment and organization of the endophytic microbiome. While selected native banana endophytes showed clear antagonism against Foc strains, their biocontrol performance against FWB did not improve the outcome observed for a non-indigenous reference BCA (strain PICF7).

scholarly journals Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Feng Chen ◽  
Min Bai ◽  
Xiaowen Cao ◽  
Jing Xue ◽  
Yue Zhao ◽  
...  
Keyword(s):  
Fluorescence Imaging ◽  
Spatial Organization ◽  
High Throughput Sequencing ◽  
Dna Amplification ◽  
Chromatin Modifications ◽  
Dynamic Changes ◽  
Recognition Mechanism ◽  
Cell Cycles ◽  
Dna Modifications ◽  
Relationship Of

AbstractExploring spatial organization and relationship of diverse biomolecules within cellular nanoenvironments is important to elucidate the fundamental processes of life. However, it remains methodologically challenging. Herein, we report a molecular recognition mechanism cellular macromolecules-tethered DNA walking indexing (Cell-TALKING) to probe the nanoenvironments containing diverse chromatin modifications. As an example, we characterize the nanoenvironments of three DNA modifications around one histone posttranslational modification (PTM). These DNA modifications in fixed cells are labeled with respective DNA barcoding probes, and then the PTM site is tethered with a DNA walking probe. Cell-TALKING can continuously produce cleavage records of any barcoding probes nearby the walking probe. New 3’-OH ends are generated on the cleaved barcoding probes to induce DNA amplification for downstream detections. Combining fluorescence imaging, we identify various combinatorial chromatin modifications and investigate their dynamic changes during cell cycles. We also explore the nanoenvironments in different cancer cell lines and clinical specimens. In principle, using high-throughput sequencing instead of fluorescence imaging may allow the detection of complex cellular nanoenvironments containing tens of biomolecules such as transcription factors.

scholarly journals Wood-inhabiting fungal responses to forest naturalness vary among morpho-groups

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Purhonen Jenna ◽  
Abrego Nerea ◽  
Komonen Atte ◽  
Huhtinen Seppo ◽  
Kotiranta Heikki ◽  
...  
Keyword(s):  
Tree Species ◽  
Boreal Forests ◽  
Negative Impact ◽  
Important Variable ◽  
Host Tree ◽  
Conservation Areas ◽  
Fungal Community Composition ◽  
Forest Sites ◽  
Protected Forests ◽  
Host Tree Species

AbstractThe general negative impact of forestry on wood-inhabiting fungal diversity is well recognized, yet the effect of forest naturalness is poorly disentangled among different fungal groups inhabiting dead wood of different tree species. We studied the relationship between forest naturalness, log characteristics and diversity of different fungal morpho-groups inhabiting large decaying logs of similar quality in spruce dominated boreal forests. We sampled all non-lichenized fruitbodies from birch, spruce, pine and aspen in 12 semi-natural forest sites of varying level of naturalness. The overall fungal community composition was mostly determined by host tree species. However, when assessing the relevance of the environmental variables separately for each tree species, the most important variable varied, naturalness being the most important explanatory variable for fungi inhabiting pine and aspen. More strikingly, the overall species richness increased as the forest naturalness increased, both at the site and log levels. At the site scale, the pattern was mostly driven by the discoid and pyrenoid morpho-groups inhabiting pine, whereas at the log scale, it was driven by pileate and resupinate morpho-groups inhabiting spruce. Although our study demonstrates that formerly managed protected forests serve as effective conservation areas for most wood-inhabiting fungal groups, it also shows that conservation planning and management should account for group- or host tree -specific responses.

Characterizing fungal communities in medicinal and edible Cassiae Semen using high-throughput sequencing

2020 ◽  
Vol 319 ◽  
pp. 108496 ◽  
Author(s):  
Mengyue Guo ◽  
Wenjun Jiang ◽  
Meihua Yang ◽  
Xiaowen Dou ◽  
Xiaohui Pang
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Fungal Communities

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.

scholarly journals Broad-leaved plants of the Southern Urals broad-leaved-conifer forests (some results of the studies)

2018 ◽  
Vol 7 (2) ◽  
pp. 16-20
Author(s):  
Yuriy Petrovich Gorichev ◽  
Ildar Ravilevich Yusupov ◽  
Alexander Nikolaevich Davydychev ◽  
Aleksey Yurievich Kulagin
Keyword(s):  
High Altitude ◽  
Plant Communities ◽  
Southern Urals ◽  
Conifer Forests ◽  
The South ◽  
The Southern Urals ◽  
Standard Methods ◽  
Forest Sites ◽  
Natural Reserve ◽  
Different Types

The paper deals with the study of broad-leaved plants of the Southern Urals broad-leaved-conifer forests. Stationary studies were conducted on the territory of the South Ural state natural reserve, where 9 forest sites in different types of broad-leaved forests were laid. The research used standard methods while microclimatic observations used digital thermometers-recorders Thermochron. The authors have obtained some data on the structure and composition of the characteristic types of broad-leaved forests with oak and maple domination. The authors have classified ecosystems and plant communities, selected 3 types of biogeocenoses and 4 types of phytocoenoses. Studies have established that selected types of broad-leaved forests are associated to certain elements of relief and high-altitude levels. The obtained materials provide the basis for further monitoring of forests.

scholarly journals Hairpin structure facilitates high-fidelity DNA amplification reactions in both qPCR and high-throughput sequencing

2021 ◽  
Author(s):  
Kerou Zhang ◽  
Alessandro Pinto ◽  
Peng Dai ◽  
Michael Wang ◽  
Lauren Yuxuan Cheng ◽  
...  
Keyword(s):  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Limit Of Detection ◽  
Dna Polymerases ◽  
Dna Amplification ◽  
Cost Effective ◽  
High Fidelity ◽  
Resistance Mutations ◽  
Chain Reactions ◽  
Early Cancer Diagnosis

Effective polymerase chain reactions (PCR) are important in bio-laboratories. It is essential to detect rare DNA-sequence variants for early cancer diagnosis or for drug-resistance mutations identification. Some of the common detection quantitative PCR (qPCR) methods are restricted in the limit of detection (LoD) because of the high polymerase misincorporation rate in Taq DNA polymerases. High-fidelity (HiFi) DNA polymerases have a 50- to 250-fold higher fidelity. Yet, there are currently no proper designs for multiplexed HiFi qPCR reactions. Moreover, the popularity of targeting highly multiplex DNA sequences requires minimizing PCR side products, as the potential of dimerization grows quadratically as the plexes of primers increases. Efforts tried before were either an add-on step, or technology-specific, or requiring high-level computing skills. There lacks an easy-to-apply and cost-effective method for dimerization reduction. Here, we presented the Occlusion System, composed of a 5'-overhanged primer and a probe with a short-stem hairpin. We demonstrated that it allowed multiplexing high-fidelity qPCR reaction, it was also compatible with the current variant-enrichment method to improve the LoD by 10-fold. Further, we found that the Occlusion System reduced the dimerization up to 10-fold in highly multiplexed PCR. Thus, the Occlusion System satisfactorily improved both qPCR sensitivity and PCR efficiency.

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.

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