scholarly journals Fungal communities in the biofilms colonizing the basalt sculptures of the Leizhou Stone Dogs and assessment of a conservation measure

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Yali Wang ◽  
Huan Zhang ◽  
Xiaobo Liu ◽  
Xiaoqing Liu ◽  
Wei Song
Keyword(s):  
High Throughput Sequencing ◽  
Antimicrobial Agents ◽  
Fungal Communities ◽  
Water Repellent ◽  
Sequencing Analysis ◽  
Fungal Community Structure ◽  
Conservation Measure ◽  
History Of ◽  
Effective Conservation ◽  
Microbial Attack

AbstractThe Leizhou Peninsula in China is very famous for its unique folk art creation, especially for the stonework, like the basalt sculptures of the Leizhou Stone Dogs, which have a history of more than two thousand years. Since these sculptures are usually exposed outdoors, many of them are suffering from severe damage by lichen and fungi. To protect them from microbial attack, we determined fungal communities in the biofilms colonizing the stone dogs and explored an effective conservation measure. Specifically, the micromorphology analysis of the biofilms on the stone dogs was performed through both on-site and laboratory-based microscopies in order to provide an overview of the fungal community structure. High-throughput sequencing analysis revealed that the predominant fungi in the biofilms belong to the following genera Caloplaca, Chaetomium, Clitopilus, Acanthostigma, Tolypocladium, Aspergillus, and Toxicocladosporium. The energy dispersive X-ray spectrometry (EDS) showed that the basalt is mainly composed of silica (53% by weight), followed by Al2O3 (14.4%), Fe2O3 (10.1%), CaO (8.4%), and MgO (7.4%) that are oxides susceptible to corrosion of biogenic acids. The EDS analysis of the hyphae provided the direct evidence on the leaching of the minerals of the sculptures. To control microbial attack, three kinds of antimicrobial agents were tested for 2 years. As a result, the mixture of biocide and water repellent showed the best effectiveness. Our findings provide an overview of fungi diversity in the biofilms on the stone dogs and help the investigation of fungi-induced biodeterioration and the exploration of specific conservation measure.

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 A case report of community-acquired Raoultella ornithinolytica infection in a healthy, young individual

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaonan Chen ◽  
Xinjian Zhou ◽  
Jun Cao ◽  
Ke Ma ◽  
Zhijie Xia
Keyword(s):  
Allergic Reaction ◽  
High Throughput Sequencing ◽  
Maculopapular Rash ◽  
Skin Condition ◽  
Sequencing Analysis ◽  
First Case ◽  
Lymph Node Enlargement ◽  
History Of ◽  
Tract Infections ◽  
Healthcare Associated

Abstract Background Raoultella ornithinolytica is a Gram-negative bacillus that resembles Klebsiella. This bacterium is present in many soil and aquatic environments and is a major causative agent of healthcare-associated infections (HAIs) in medical staff. Clinically, it has been reported to contribute to nosocomial infections in patients that include but are not limited to gastrointestinal, skin, and genitourinary tract infections. These complications are most common in hospitalized patients with underlying immunodeficiency, multiple comorbidities, or those receiving invasive surgery. Case presentation We present a case of a 25-year-old patient with a R. ornithinolytica infection. The patient had no history of any disease. Her main complaints were high fever, a scattered maculopapular rash, and superficial lymph node enlargement (SLNE). Peripheral blood samples were collected for high-throughput sequencing analysis to identify pathogenic microorganisms. The results confirmed a R. ornithinolytica infection, which was treated successfully using meropenem. Loratadine was also administered to treat the patient’s compromised skin condition caused by an allergic reaction. Conclusions To our knowledge, this is the first case of a systemic maculopapular rash and superficial lymphadenopathy caused by a R. ornithinolytica infection acquired at the community level. Based on this case, we recommend a combination of antibiotic and antiallergic drugs to treat a R. ornithinolytica infection and associated allergic reaction to the bacteria.

scholarly journals Managed and Unmanaged Pinus sylvestris Forest Stands Harbour Similar Diversity and Composition of the Phyllosphere and Soil Fungi

2020 ◽  
Vol 8 (2) ◽  
pp. 259 ◽  
Author(s):  
Jūratė Lynikienė ◽  
Diana Marčiulynienė ◽  
Adas Marčiulynas ◽  
Artūras Gedminas ◽  
Miglė Vaičiukynė ◽  
...  
Keyword(s):  
Pinus Sylvestris ◽  
National Parks ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Forest Stands ◽  
Forest Zone ◽  
The North ◽  
Study Sites

The aim was to assess fungal communities associated with living needles and soil of Pinus sylvestris in managed and unmanaged forest stands to get a better understanding of whether and how different intensities of forest management affects fungal diversity and community composition under the north temperate forest zone conditions. The study was carried out in three national parks in Lithuania. Each included five study sites in managed stands and five in unmanaged stands. At each site, three random soil cores and five random last-year needle samples were collected. Following DNA isolation, a DNA fragment of the ITS2 rRNA gene region of each sample was individually amplified and subjected to high-throughput sequencing. Analysis of 195,808 high-quality reads showed the presence of 1909 fungal taxa. Richness and composition of fungal taxa were similar in each substrate (needles and soil) in managed vs. unmanaged sites. The most common fungi in needles were Coleosporium campanulae (12.4% of all fungal sequences), Unidentified sp. 3980_1 (12.4%), Unidentified sp. 3980_4 (4.1%) and Sydowia polyspora (3.1%). In soil: Unidentified sp. 3980_21 (8.6%), Umbelopsis nana (8.2%), Archaeorhizomyces sp. 3980_5 (8.1%) and Penicillium spinulosum (6.3%). The results demonstrated that managed and unmanaged P. sylvestris stands support similar diversity and composition of fungal communities associated with living needles and soil.

scholarly journals Early Stage Root-Associated Fungi Show a High Temporal Turnover, but Are Independent of Beech Progeny

2020 ◽  
Vol 8 (2) ◽  
pp. 210 ◽  
Author(s):  
Kezia Goldmann ◽  
Silke Ammerschubert ◽  
Rodica Pena ◽  
Andrea Polle ◽  
Bin-Wei Wu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Early Stage ◽  
European Beech ◽  
Fungal Species ◽  
Fungal Communities ◽  
Transplant Experiment ◽  
Fungal Community Structure ◽  
Temporal Turnover ◽  
One Year ◽  
The Impact

The relationship between trees and root-associated fungal communities is complex. By specific root deposits and other signal cues, different tree species are able to attract divergent sets of fungal species. Plant intraspecific differences can lead to variable fungal patterns in the root’s proximity. Therefore, within the Beech Transplant Experiment, we analyzed the impact of three different European beech ecotypes on the fungal communities in roots and the surrounding rhizosphere soil at two time points. Beech nuts were collected in three German sites in 2011. After one year, seedlings of the different progenies were out-planted on one site and eventually re-sampled in 2014 and 2017. We applied high-throughput sequencing of the fungal ITS2 to determine the correlation between tree progeny, a possible home-field advantage, plant development and root-associated fungal guilds under field conditions. Our result showed no effect of beech progeny on either fungal OTU richness or fungal community structure. However, over time the fungal OTU richness in roots increased and the fungal communities changed significantly, also in rhizosphere. In both plant compartments, the fungal communities displayed a high temporal turnover, indicating a permanent development and functional adaption of the root mycobiome of young beeches.

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 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.

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.

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