Analyses of microfungal diversity from a user's perspective

1995 ◽  
Vol 73 (S1) ◽  
pp. 33-41 ◽  
Author(s):  
Gerald F. Bills
Keyword(s):  
Species Diversity ◽  
Fungal Species ◽  
Rapid Expansion ◽  
Fungal Communities ◽  
Inventory Problem ◽  
Maximum Information ◽  
Rapid Isolation ◽  
Isolation Techniques ◽  
Biotic Diversity ◽  
Potential Methods

For microfungi, the understanding of the extent of their biotic diversity and of their ecological function remains underdeveloped. An insufficient number of specialists are available to collect and document the world's microfungi. Organizations that exploit microfungi as a source of chemical products or for biotechnological applications also may need to assess microfungal diversity to meet their specific objectives. During future inventories of biomes that are deemed of high biological interest or that may harbor species of commercial potential, methods for enumerating microfungi must be made more efficient, and fungal communities should be evaluated in such a way as to extract the maximum information. Rapid isolation techniques can be used to deliver high species diversity and obtain quantitative estimates of fungal species diversity and abundance. These methods, some previously developed by soil ecologists, rely heavily on selective media, dissection, physical and chemical elimination of contaminants, knowledge of spore behavior, and manipulation of incubation conditions. The rapid expansion of our knowledge of endophytes in woody plants exemplifies the success of this approach. Whenever rigorous isolation strategies have been applied to unstudied substrates, an unrealized depth of species diversity has been revealed. When methods are standardized, richness of different fungal communities, geographic variation within communities, or effectiveness of isolation procedures can be quickly and quantitatively compared. Exploration of complex substrata via indirect isolation expands the view of the fungal community in a way that complements traditional mycological collecting. However, fungi isolated into culture are often impossible to identify based on morphology. The utility of the rapid isolation approach to the inventory problem is illustrated with experiences with microfungi from rain-forest leaf litter.Key words: fungal metabolites, industrial microbiology, microbial diversity, natural products.

scholarly journals Artisanal and farmers bread making practices differently shape fungal species diversity in French sourdoughs

2019 ◽  
Author(s):  
Elisa Michel ◽  
Estelle Masson ◽  
Sandrine Bubbendorf ◽  
Léocadie Lapicque ◽  
Judith Legrand ◽  
...  
Keyword(s):  
Species Diversity ◽  
Microbial Diversity ◽  
Food Systems ◽  
Fungal Species ◽  
Fungal Communities ◽  
Research Approach ◽  
Fermented Foods ◽  
Bread Making ◽  
Sourdough Bread ◽  
Fungal Species Diversity

AbstractPreserving microbial diversity in food systems is one of the many challenges to be met to achieve food security and quality. However, there is still a lack of knowledge about the factors that may influence food microbial diversity, notably in fermented foods. Although industrialization led to the selection and spread of specific fermenting microbial strains, there are still ongoing artisanal processes that may allow the conservation of a wider diversity of microbial species. We examined whether the diversity of artisanal practices could lead to an increased level in fungal species diversity for bread making. We used an interdisciplinary participatory research approach including bakers, psycho-sociologists and microbiologists to analyse French bread making practices and describe fungal communities in naturally fermented sourdough. Bread making practices were clustered in a farmer practices’ group and an artisanal practices’ group. Surprisingly, the well-known bakery yeast, Saccharomyces cerevisiae, was dominant (i.e. with a relative abundance over 50%) in only 24% of sourdoughs and other yeast species of the closely related Kazachstania genus were frequent. Bread making practices were found to drive the distribution of these species. The differences in fungal communities were associated with variation in sourdough acidity, maltose concentration and hydration. Overall, our results showed that preserving bread making practices diversity allows the preservation of a higher taxonomic and functional diversity in microbial communities.

scholarly journals Fungal Diversity And Seasonal Succession Under Invasive Moss Campylopus Introflexus And Other Plants In Disturbed Peatlands

2015 ◽  
Vol 21 (1) ◽  
pp. 46-56 ◽  
Author(s):  
Jūratė Repečkienė ◽  
Ilona Jukonienė ◽  
Olga Salina
Keyword(s):  
Species Diversity ◽  
Species Composition ◽  
Vascular Plant ◽  
Seasonal Succession ◽  
Calluna Vulgaris ◽  
Fungal Species ◽  
Fungal Communities ◽  
Plant Residues ◽  
Campylopus Introflexus ◽  
Bare Peat

AbstractThe distribution of invasive moss Campylopus introflexus (Hedw.) Brid. may have negative influence on natural restoration of plant cover in peatlands due to the accumulation of heavy decomposing residues and suppression of the growth of microorganisms in peat. Species composition of fungal communities and seasonal succession under mosses C. introflexus and Polytrichum strictum, vascular plant Calluna vulgaris and bare peat were studied in two naturally regenerating disturbed peatlands in Lithuania. Cultivable fungi were isolated from peat and enumerated by applying the serial dilution plate technique. A total of 66 species of fungi ascribed to 21 genera (among these 30 species from 13 genera under moss C. introflexus) were identified. Fungus species of the genera Penicillium, Trichoderma, Mortierella and Paecilomyces dominated. The highest diversity of fungal species was found in Laukėsa under Calluna vulgaris. Differences in the structure of fungal communities were found in Mūšos Tyrelis in autumn and in Laukėsa in spring. Significant differences in species diversity under various plants were obtained only in summer. The Gleason species diversity index for peat under C. introflexus was not very high (1.77–2.58) in different seasons. Fungal species composition under moss C. introflexus did not show pronounced characteristic peculiarities compared to other plants and was similar to that in bare peat. The obtained data are important for the prediction of fungal community succession in peatlands and biodegradation level of plant residues.

The autumn communities of freshwater hyphomycetes in the tributaries of the River Neelum

1997 ◽  
Vol 75 (7) ◽  
pp. 1046-1060 ◽  
Author(s):  
Firdaus-e- Bareen ◽  
S. H. Iqbal
Keyword(s):  
Species Diversity ◽  
Riparian Vegetation ◽  
Stream Water ◽  
Significant Negative Correlation ◽  
Fungal Species ◽  
Fungal Communities ◽  
Deciduous Trees ◽  
Conidium Production ◽  
Ph Values ◽  
Percentage Similarity

Freshwater hyphomycete communities of autumn, based on data generated by three techniques used simultaneously, were richer than those detected by these techniques used singly. The fungal communities in the acidic streams were poorer (28–32 species) than in the circumneutral streams (39–64 species). No significant correlation was found between number of fungal species and pH of the stream water. Combining the data from this study with those of studies by other authors using the same techniques, linear correlation and regression analyses revealed the significant negative correlation between species composition of communities in a stream and its pH. The number of fungal species in assemblages detected by different techniques used singly (e.g., filtration of stream water or examination of foam concentrate) or communities based on data generated by these techniques used simultaneously versus pH values formed a unimodal curve with a maximum at a pH between 6 and 7, mostly at 6.7. The conidial dynamics were influenced by the riparian vegetation. Conidium production from submerged deciduous and conifer litter was determined under laboratory conditions. Generally conidium production per disc was higher for Anguillospora longissima (Sacc. & Syd) Ingold, Flagellospora cumula Ingold, Lunulospora curvula Ingold, and Tetracladium marchalianum de Wildeman in deciduous leaves than conifer leaves. Heliscus lugdunensis Sacc. & Therry, Alatospora acuminata Ingold, and Articulospora tetracladia Ingold produced more conidia per disc in conifer than in deciduous leaves. Percentage similarity between spora produced by submerged substrate and stream spora was higher for deciduous substratum than for coniferous substratum in five circumneutral streams with a riparian vegetation dominated by deciduous trees. This index was higher for coniferous substratum in three acidic streams in which coniferous and deciduous trees were evenly distributed. The fungal communities in the Nosehri, Pathika, and Jabbar Camp streams showed higher values of species diversity than in other streams. Key words: freshwater, hyphomycetes, species diversity.

scholarly journals Eutypella parasitica and Other Frequently Isolated Fungi in Wood of Dead Branches of Young Sycamore Maple (Acer pseudoplatanus) in Slovenia

Forests ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 467 ◽  
Author(s):  
Ana Brglez ◽  
Barbara Piškur ◽  
Nikica Ogris
Keyword(s):  
Species Diversity ◽  
Fungal Community ◽  
Sampling Site ◽  
Outer Part ◽  
Similarity Index ◽  
Asymptomatic Infection ◽  
Fungal Species ◽  
Acer Pseudoplatanus ◽  
Pure Cultures ◽  
Sycamore Maple

Eutypella parasitica R.W. Davidson and R.C. Lorenz is the causative agent of Eutypella canker of maple, a destructive disease of maples in Europe and North America. The fungus E. parasitica infects the trunk through a branch stub or bark wound. Because the fungal community may have an impact on infection and colonization by E. parasitica, the composition of fungi colonizing wood of dead branches of sycamore maple (Acer pseudoplatanus L.) was investigated in five sampling sites in Slovenia. Forty samples from each sampling site were collected between the November 2017 and March 2018 period. Isolations were made from the wood in the outer part of dead branches and from discoloured wood in the trunk that originated from a dead branch. Pure cultures were divided into morphotypes, and one representative culture per morphotype was selected for further molecular identification. From a total of 2700 cultured subsamples, 1744 fungal cultures were obtained, which were grouped into 212 morphotypes. The investigated samples were colonized by a broad spectrum of fungi. The most frequently isolated species were Eutypa maura (Fr.) Sacc., Eutypa sp. Tul. and C. Tul., Fusarium avenaceum (Fr.) Sacc., Neocucurbitaria acerina Wanas., Camporesi, E.B.G. Jones and K.D. Hyde and E. parasitica. In this study, we distinguished species diversity and the fungal community. There were no significant differences in the diversity of fungal species between the five sampling sites, and branch thickness did not prove to be a statistically significant factor in fungal species diversity. Nevertheless, relatively low Jaccard similarity index values suggested possible differences in the fungal communities from different sampling sites. This was confirmed by an analysis of similarities, which showed that the isolated fungal community distinctly differed between the five sampling sites and between the different isolation sources. Eutypella parasitica was isolated from all five investigated sampling sites, although Eutypella cankers were observed in only three sampling sites, indicating the possibility of asymptomatic infection.

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.

The Mycobiota of Speck, a Traditional Tyrolean Smoked and Cured Ham

2000 ◽  
Vol 63 (10) ◽  
pp. 1399-1403 ◽  
Author(s):  
URSULA PEINTNER ◽  
JOHANNES GEIGER ◽  
REINHOLD PÖDER
Keyword(s):  
Species Diversity ◽  
Fungal Species ◽  
Penicillium Canescens ◽  
Penicillium Verrucosum ◽  
South Tyrol ◽  
Cured Meat ◽  
Penicillium Commune ◽  
Penicillium Solitum ◽  
Penicillium Spp

Speck is a ham specialty product traditionally produced in South Tyrol (Italy) and North Tyrol (Austria) by farmers, butcheries, and meat industries. To date, nothing has been learned about fungi associated with this smoked and cured meat. Therefore, it was the main objective of this study to assess the typical mycobiota of Speck in relation to the different production types and the geographic provenance. A total of 121 Speck samples from North Tyrol and South Tyrol was analyzed. From 63 isolated fungal species, only a few can be regarded as typical colonizers: Eurotium rubrum and Penicillium solitum were the dominating species in all types and parts of Speck (crust, meat, and fat). Eight other Penicillium spp. were relatively frequent. The species diversity increased from industrially produced Speck to products from butcheries and farmers, and it was higher in all types of South Tyrolean products. Among the typical mycobiota, Penicillium verrucosum, Penicillium canescens, and Penicillium commune are known as potentially mycotoxigenic.

scholarly journals THE MACROFUNGI DIVERSITY AND THEIR POTENTIAL UTILIZATION IN TANGALE NATURE RESERVE GORONTALO PROVINCE

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Diah Irawati Dwi Arini ◽  
Margaretta Christita ◽  
Julianus Kinho
Keyword(s):  
Species Diversity ◽  
Nature Reserve ◽  
Edible Mushroom ◽  
Fungal Species ◽  
Conservation Area ◽  
Scleroderma Citrinum ◽  
Lenzites Betulina ◽  
The Veil ◽  
Decaying Wood ◽  
Potential Use

Tangale Nature reserve is a conservation area located in Gorontalo that have the biodiversity typical of Wallacea bioregion including macroscopic fungi. The purpose of this study was to identify the fungal species diversity found in the Tangale Nature reserve as well as its potential use, considering that the information on species diversity of fungi in the Wallacea region is very limited. This research was conducted using the cruise method by identifying macroscopic fungi along the hiking trail of Tangale Nature Reserve. The macroscopic fungi were observed for its morphological characteristic include the colour, diameter, surface of the veil, the shape of the stem, the length and diameter of the stem, the lamella, including ring and pore, type of lamella and the type of volva. The research recorded the substrates and the location where the fungus was found. Data were analyzed descriptively qualitative. The results of the research identified 28 species of macroscopic fungi that included to the division Ascomycota and Basidiomycota. It belongs to 16 families and 8 orders  are Pezizales, Agaricales, Auriculariales, Boletales, Cantharellales, Gomphales, Polyporales, dan Russulales. Based on place to grow as much as 57,14% were found growing on decaying wood and 42,86% found growing in the soil/litter. Based on the potential of use, it has identified four species of mushrooms potentially as edible mushroom are Pleurotus ostreatus,  Auricularia auricula, Ramaria formosa, and Polyporus arcularius. 11 species of mushrooms potentially as medicinal mushroom are Calvatia craniiformis, Scleroderma citrinum, Lenzites betulina, Microporus flabelliformis, Coriolus versicolor, Microporus xanthopus, and Albatrellus confluens.  

scholarly journals Diversity, host-specificity and stability of sponge-associated fungal communities of co-occurring sponges

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4965 ◽  
Author(s):  
Mary T.H.D. Nguyen ◽  
Torsten Thomas
Keyword(s):  
Host Specificity ◽  
Horizontal Transmission ◽  
Critical Role ◽  
Fungal Species ◽  
Fungal Communities ◽  
Sponge Species ◽  
Fungal Community Composition ◽  
Potential Core ◽  
Community Profiling ◽  
Surrounding Seawater

Fungi play a critical role in a range of ecosystems; however, their interactions and functions in marine hosts, and particular sponges, is poorly understood. Here we assess the fungal community composition of three co-occurring sponges (Cymbastela concentrica, Scopalina sp., Tedania anhelans) and the surrounding seawater over two time points to help elucidate host-specificity, stability and potential core members, which may shed light into the ecological function of fungi in sponges. The results showed that ITS-amplicon-based community profiling likely provides a more realistic assessment of fungal diversity in sponges than cultivation-dependent approaches. The sponges studied here were found to contain phylogenetically diverse fungi (eight fungal classes were observed), including members of the family Togniniaceae and the genus Acrostalagmus, that have so far not been reported to be cultured from sponges. Fungal communities within any given sponge species were found to be highly variable compared to bacterial communities, and influenced in structure by the community of the surrounding seawater, especially considering temporal variation. Nevertheless, the sponge species studied here contained a few “variable/core” fungi that appeared in multiple biological replicates and were enriched in their relative abundance compared to seawater communities. These fungi were the same or highly similar to fungal species detected in sponges around the world, which suggests a prevalence of horizontal transmission where selectivity and enrichment of some fungi occur for those that can survive and/or exploit the sponge environment. Our current sparse knowledge about sponge-associated fungi thus indicate that fungal communities may perhaps not play as an important ecological role in the sponge holobiont compared to bacterial or archaeal symbionts.

Distribution and occurrence of manglicolous marine fungi from eastern and southern Thailand

2017 ◽  
Vol 60 (4) ◽  
Author(s):  
Satinee Suetrong ◽  
Sita Preedanon ◽  
Anupong Klaysuban ◽  
Wunna Gundool ◽  
Panida Unagul ◽  
...  
Keyword(s):  
Species Diversity ◽  
Marine Fungi ◽  
Fungal Species ◽  
Mangrove Forests ◽  
Average Percentage ◽  
Percentage Occurrence ◽  
Southern Thailand ◽  
Asexual Fungi

AbstractThe species diversity of marine fungi was investigated in eastern and southern Thailand. Senescent and decaying woody substrata were collected from intertidal mangrove forests located in Trat, Prachuap Khiri Khan and Phetchaburi Provinces. A total of 99 fungal species was recorded. These included 84 Ascomycota (85%), two Basidiomycota (2%) and 13 asexual fungi (13%). The average percentage occurrence of the fungi recorded from each site ranged from 0.1% to 13.7%. Based on the percentage of samples in which a particular taxon was found, the most frequent fungi were

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