Effect of Vineyard Floor Management on Seasonal Changes of Cultivable Fungal Diversity in the Rhizosphere

Vineyard floor management has been widely discussed for many decades, but it is still unclear how its intensity levels change the fungal community structure of grape rhizosphere. Our objective was to examine the density and rate of the habitats of fungi in three vineyards that differ only in the methods of tillage procedure applied, namely intensive, extensive and none (abandoned). The hypothesis was that in the cases of lower intensity or no soil tillage, there would be a higher level of fungal diversity with a lower ratio of pathogen strains in grape rhizosphere. In the course of this research, it has been determined that the level of fungal colonization of roots is the highest in the extensively managed vineyard, unrelated to season (spring and summer). Four of the five fungal genera detectable in all of the three sampled vineyards are registered as opportunist grape pathogens, however the fifth one, Trichoderma, is commonly used in biological plant protection. The diversity of fungal communities in grape rhizosphere, in accordance with the expectations, was the lowest in the intensively cultivated and highest in the abandoned vineyard, and it was not affected by seasons. The proportion of opportunist plant pathogen groups was higher in the intensive variant than in the other two (less-intensive variants); therefore, it is possible to conclude that soil under similar conditions but disturbed by intensive tillage methods tends to exhibit lower suppressivity.

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

Diversity ◽

10.3390/d12050172 ◽

2020 ◽

Vol 12 (5) ◽

pp. 172 ◽

Cited By ~ 3

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.

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Rock Surface Fungi in Deep Continental Biosphere—Exploration of Microbial Community Formation with Subsurface In Situ Biofilm Trap

Microorganisms ◽

10.3390/microorganisms9010064 ◽

2020 ◽

Vol 9 (1) ◽

pp. 64

Author(s):

Maija Nuppunen-Puputti ◽

Riikka Kietäväinen ◽

Lotta Purkamo ◽

Pauliina Rajala ◽

Merja Itävaara ◽

...

Keyword(s):

Significant Proportion ◽

Debaryomyces Hansenii ◽

Fungal Communities ◽

Fungal Colonization ◽

Rock Surface ◽

Mica Schist ◽

Deep Subsurface ◽

Bacterial Phyla ◽

In Situ Conditions

Fungi have an important role in nutrient cycling in most ecosystems on Earth, yet their ecology and functionality in deep continental subsurface remain unknown. Here, we report the first observations of active fungal colonization of mica schist in the deep continental biosphere and the ability of deep subsurface fungi to attach to rock surfaces under in situ conditions in groundwater at 500 and 967 m depth in Precambrian bedrock. We present an in situ subsurface biofilm trap, designed to reveal sessile microbial communities on rock surface in deep continental groundwater, using Outokumpu Deep Drill Hole, in eastern Finland, as a test site. The observed fungal phyla in Outokumpu subsurface were Basidiomycota, Ascomycota, and Mortierellomycota. In addition, significant proportion of the community represented unclassified Fungi. Sessile fungal communities on mica schist surfaces differed from the planktic fungal communities. The main bacterial phyla were Firmicutes, Proteobacteria, and Actinobacteriota. Biofilm formation on rock surfaces is a slow process and our results indicate that fungal and bacterial communities dominate the early surface attachment process, when pristine mineral surfaces are exposed to deep subsurface ecosystems. Various fungi showed statistically significant cross-kingdom correlation with both thiosulfate and sulfate reducing bacteria, e.g., SRB2 with fungi Debaryomyces hansenii.

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Are Wildfires a Threat to Fungi in European Pinus Forests? A Case Study of Boreal and Mediterranean Forests

Forests ◽

10.3390/f10040309 ◽

2019 ◽

Vol 10 (4) ◽

pp. 309 ◽

Cited By ~ 3

Author(s):

Iván Franco-Manchón ◽

Kauko Salo ◽

Juan Oria-de-Rueda ◽

José Bonet ◽

Pablo Martín-Pinto

Keyword(s):

Boreal Forests ◽

Fungal Diversity ◽

Community Dynamics ◽

Forest Products ◽

Climatic Conditions ◽

Fungal Communities ◽

Mediterranean Forests ◽

Natural Forests ◽

Edible Fungi ◽

Pinus Species

Natural forests and plantations of Pinus are ecologically and economically important worldwide, producing an array of goods and services, including the provision of non-wood forest products. Pinus species play an important role in Mediterranean and boreal forests. Although Pinus species seem to show an ecological adaptation to recurrent wildfires, a new era of mega fires is predicted, owing to climate changes associated with global warming. As a consequence, fungal communities, which are key players in forest ecosystems, could be strongly affected by these wildfires. The aim of this study was to observe the fungal community dynamics, and particularly the edible fungi, in maritime (Pinus pinaster Ait.), austrian pine (Pinus nigra J.F. Arnold), and scots pine (Pinus sylvestris L.) forests growing under wet Mediterranean, dry Mediterranean, and boreal climatic conditions, respectively, by comparing the mushrooms produced in severely burned Pinus forests in each area. Sporocarps were collected during the main sampling campaigns in non-burned plots, and in burned plots one year and five years after fire. A total of 182 taxa, belonging to 81 genera, were collected from the sampled plots, indicating a high level of fungal diversity in these pine forests, independent of the climatic conditions. The composition of the fungal communities was strongly affected by wildfire. Mycorrhizal taxa were impacted more severely by wildfire than the saprotrophic taxa, particularly in boreal forests—no mycorrhizal taxa were observed in the year following fire in boreal forests. Based on our observations, it seems that fungal communities of boreal P. sylvestris forests are not as adapted to high-intensity fires as the Mediterranean fungal communities of P. nigra and P. pinaster forests. This will have an impact on reducing fungal diversity and potential incomes in rural economically depressed areas that depend on income from foraged edible fungi, one of the most important non-wood forest products.

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Different Amplicon Targets for Sequencing-Based Studies of Fungal Diversity

Applied and Environmental Microbiology ◽

10.1128/aem.00905-17 ◽

2017 ◽

Vol 83 (17) ◽

Cited By ~ 40

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.

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Long Term Effects of Ploughing and Conservation Tillage Methods on Earthworm Abundance and Crumb Ratio

Agronomy ◽

10.3390/agronomy10101552 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1552 ◽

Cited By ~ 2

Author(s):

Igor Dekemati ◽

Barbara Simon ◽

Igor Bogunovic ◽

Ivica Kisic ◽

Katalin Kassai ◽

...

Keyword(s):

Water Content ◽

Water Conservation ◽

Conservation Tillage ◽

Soil Tillage ◽

Long Term Effects ◽

No Till ◽

Cover Ratio ◽

One Year ◽

Tillage Methods

In addition to the dry (D) and rainy (R) seasons, a combination of the two i.e., rainy-dry (RD) and dry-rainy (DR), can also be observed in one year. The effects of the dry (D) and rainy (R) on soil are known, hence we hypothesized that the effects of the rainy-dry (RD) and dry-rainy (DR) periods on soil may differ from the former assessments. The aim of the study is to investigate the effect of six tillage treatments (ploughing—P, disk tillage—DT, loosening—L, tine tillage (a deeper—T and a shallower—ST) and no-till—NT) on earthworm abundance and crumb ratio during a long-term research (16 years) on Chernozems. The results related to the four year-groups (D, R, RD, and DR) with different residue cover. Seven degrees of cover ratio (between 12.5% and 62.5%) were selected on stubbles. Higher cover ratio (≥52.5%) improved water conservation, increased earthworm abundance (31 and 41 ind m–2) and crumb (78 and 82%) ratio (p < 0.01). R year came first in the rank of water content and earthworm abundance and DR proved to be more favorable for crumb formation. Considering the rank of soil tillage treatments, ST takes first place in evaluation of soil water content (SWC) and crumb ratio, and NT for earthworm abundance.

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Effect of different soil tillage methods on rhizobial nodulation, biyomas and nitrogen content of second crop soybean

African Journal of Microbiology Research ◽

10.5897/ajmr11.165 ◽

2011 ◽

Vol 5 (20) ◽

pp. 3186-3194 ◽

Cited By ~ 9

Author(s):

Dogan Kemal ◽

Celik Ismail ◽

Gok Mustafa ◽

Coskan Ali

Keyword(s):

Nitrogen Content ◽

Soil Tillage ◽

Tillage Methods

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Water-Covered Depth with the Freeze–Thaw Cycle Influences Fungal Communities on Rice Straw Decomposition

Agriculture ◽

10.3390/agriculture11111113 ◽

2021 ◽

Vol 11 (11) ◽

pp. 1113

Author(s):

Xiaolong Lin ◽

Zongmu Yao ◽

Xinguang Wang ◽

Shangqi Xu ◽

Chunjie Tian ◽

...

Keyword(s):

Community Structure ◽

Rice Straw ◽

Fungal Community ◽

Fungal Communities ◽

Straw Decomposition ◽

Freeze Thaw ◽

Fungal Community Structure ◽

Thaw Cycle ◽

Freeze Thaw Cycle ◽

Rice Straw Decomposition

Rice is a staple food for the world’s population. However, the straw produced by rice cultivation is not used sufficiently. Returning rice straw to the field is an effective way to help reduce labor and protect the soil. This study focused on the effect of water-covered depth with the freeze–thaw cycle on rice straw decomposition and the soil fungal community structure in a field in Northeast China. The field and controlled experiments were designed, and the fungal ITS1 region was tested by high-throughput sequencing for analyzing the fungal communities in this study. The results showed that water coverage with the freeze–thaw cycle promoted the decomposition of rice straw and influenced the fungal community structure; by analyzing the network of the fungal communities, it was found that the potential keystone taxa were Penicillium, Talaromyces, Fusarium, and Aspergillus in straw decomposition; and the strains with high beta-glucosidase, carboxymethyl cellulase, laccase, lignin peroxidase, and manganese peroxidase could also be isolated in the treated experiment. Furthermore, plant pathogenic fungi were found to decrease in the water-covered treatment. We hope that our results can help in rice production and straw return in practice.

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Investigation and analysis of the fungal community structure in moldy Lonicerae japonicae Flos through ITS2 sequencing

E3S Web of Conferences ◽

10.1051/e3sconf/202123302031 ◽

2021 ◽

Vol 233 ◽

pp. 02031

Author(s):

Zhenying Liu ◽

Yan Zhao ◽

Lingna Wang ◽

Gaobin Pu ◽

Yongqing Zhang

Keyword(s):

Internal Transcribed Spacer ◽

Theoretical Basis ◽

Fungal Communities ◽

Mold Growth ◽

Fungal Contamination ◽

Fungal Community Structure ◽

Class Level ◽

First Time ◽

Comprehensive Characterization

Lonicerae japonicae Flos is a traditional Chinese medicine that has the effect is used for clearing away heat and detoxification. When stored improperly, this medicine is susceptible to mold growth, causing fungal contamination, reducing its safety and clinical efficacy. In order to understand the fungal contamination of Lonicerae japonicae Flos, we utilized the Illumina NovaSeq6000 platform to characterize fungal communities associated with five moldy Lonicerae japonicae Flos samples from warehouses in China via the sequencing of fungal internal transcribed spacer 2 regions. These analyses led us to identify 3 phyla, 5 classes, 7 orders, 9 families, 13 genera, and 20 species of fungi in these samples. Of these, Ascomycota was the dominant phylum, while Cysticomycetes, Ascomycetes, and Staphylococci were relatively dominant at the class level, and the most prevalent genera were Aspergillus, Penicillium, Xanthomonas, Microcystis, Talaromyces, and Erysiphe with relative abundance values of 79%, 21%, 94%, 100%, and 98%. In summary, in the present study we conducted the ITS-based comprehensive characterization of fungal communities associated with Lonicerae japonicae Flos for the first time. This approach aims to facilitate the early detection of fungal contamination in Lonicerae japonicae Flos, providing a theoretical basis for the study of anti-mold technologies.

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Fungal diversity in high Andean ecuadorian forest soil

10.22541/au.161546623.36028736/v1 ◽

2021 ◽

Author(s):

Adrian Valdez ◽

Sergio Covarrubias

Keyword(s):

Fungal Diversity ◽

High Performance ◽

Its Region ◽

Taxonomic Composition ◽

Soil Samples ◽

Fungal Communities ◽

Gallery Forest ◽

Volcanic Soils ◽

Altitudinal Gradients ◽

The Andes

The Andes range in Ecuador presents high biodiversity and characteristic altitudinal gradients, which are frequently threatened by deforestation and farming. In particular, forest have developed in the high inter-Andean alley on volcanic soils forming a unique ecoregion. Little is known on the fungal biodiversity of soil in such high Andean gallery forest submitted to strong degradation pressures. Therefore, in this study we evaluated wether the soil mycobiome was associated with altitudinal gradients during the dry season. Three representative locations were selected based on altitude: A (3,309 meters above the sea level, masl), B (3,809 masl) and C (4,409 masl). High performance sequencing (NGS) of the ITS region of ribosomal DNA genes with Illumina technology was used to explore the fungal taxonomic composition in the soil samples. Our results showed changes in the structure of fungal communities in the different locations, related to the relative abundance of Amplicon Sequence Variants (ASV). Higher fungal diversity was related with the altitudinal gradient with average taxa ranging from 675, 626 and 556 ASVs, respectively from location A to C. The results highlight the complexity and diversity of fungal communities in high Andean forest and the need to protect these unique mycobiomes. The findings in this ecosystem of Ecuador will improve our understanding of distribution, diversity, ecology, and biological perspectives for the restoration of terrestrial microbiomes.

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

10.21203/rs.3.rs-28393/v1 ◽

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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