scholarly journals DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors

2019 ◽  
Vol 7 (9) ◽  
pp. 341 ◽  
Author(s):  
Ali Nawaz ◽  
Witoon Purahong ◽  
Martina Herrmann ◽  
Kirsten Küsel ◽  
François Buscot ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Environmental Parameters ◽  
Fungal Communities ◽  
Its2 Region ◽  
Operational Taxonomic Units ◽  
Dna And Rna ◽  
Groundwater Aquifers ◽  
Groundwater Samples ◽  
Terrestrial Habitats ◽  
Total Dna

Recent advances in high-throughput sequencing (HTS) technologies have revolutionized our understanding of microbial diversity and composition in relation to their environment. HTS-based characterization of metabolically active (RNA-derived) and total (DNA-derived) fungal communities in different terrestrial habitats has revealed profound differences in both richness and community compositions. However, such DNA- and RNA-based HTS comparisons are widely missing for fungal communities of groundwater aquifers in the terrestrial biogeosphere. Therefore, in this study, we extracted DNA and RNA from groundwater samples of two pristine aquifers in the Hainich CZE and employed paired-end Illumina sequencing of the fungal nuclear ribosomal internal transcribed spacer 2 (ITS2) region to comprehensively test difference/similarities in the “total” and “active” fungal communities. We found no significant differences in the species richness between the DNA- and RNA-derived fungal communities, but the relative abundances of various fungal operational taxonomic units (OTUs) appeared to differ. We also found the same set of environmental parameters to shape the “total” and “active” fungal communities in the targeted aquifers. Furthermore, our comparison also underlined that about 30%–40% of the fungal OTUs were only detected in RNA-derived communities. This implies that the active fungal communities analyzed by HTS methods in the subsurface aquifers are actually not a subset of supposedly total fungal communities. In general, our study highlights the importance of differentiating the potential (DNA-derived) and expressed (RNA-derived) members of the fungal communities in aquatic ecosystems.

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 Fungal Community Analysis and Biodeterioration of Waterlogged Wooden Lacquerware from the Nanhai No. 1 Shipwreck

2020 ◽  
Vol 10 (11) ◽  
pp. 3797
Author(s):  
Yin Jia ◽  
Liuyu Yin ◽  
Fengyu Zhang ◽  
Mei Wang ◽  
Mingliang Sun ◽  
...  
Keyword(s):  
Fusarium Solani ◽  
High Throughput Sequencing ◽  
Environmental Parameters ◽  
Community Analysis ◽  
Fungal Species ◽  
Potato Dextrose Agar ◽  
Fungal Communities ◽  
Cellulolytic Enzymes ◽  
Biocidal Products

To avoid the lacquerware of the Nanhai No. 1 shipwreck from being corroded by microorganisms and to improve the knowledge on microbial ecology of the wood lacquers, we conducted a series of tests on the two water samples storing the lacquerware and colonies on the surface of the lacquerware. The high-throughput sequencing detected dominant fungal communities. After that, the fungal strains were isolated and then identified by amplification of ITS- 18S rRNA. Then the activity of ligninolytic and cellulolytic enzymes was detected on potato dextrose agar (PDA) plates with 0.04% (v/v) guaiacol and carboxymethyl cellulose (CMC) agar plates. Finally, we tested the biocide susceptibility of these fungi. Penicillium chrysogenum (NK-NH3) and Fusarium solani (NK- NH1) were the dominant fungi in the sample collected in April 2016 and June 2017. What is more, both showed activity of ligninolytic and cellulolytic enzymes. Four biocidal products (Preventol® D7, P91, BIT 20N, and Euxyl® K100) inhibited the growth of the fungal species in vitro effectively. In further research, the microbial community and environmental parameters in the museum should be monitored to assess the changes in the community and to detect potential microbial outbreaks.

scholarly journals Contrasting Patterns of Functional Diversity in Coffee Root Fungal Communities Associated with Organic and Conventionally Managed Fields

2020 ◽  
Vol 86 (11) ◽  
Author(s):  
Elizabeth C. Sternhagen ◽  
Katie L. Black ◽  
Eliza D. L. Hartmann ◽  
W. Gaya Shivega ◽  
Peter G. Johnson ◽  
...  
Keyword(s):  
Community Composition ◽  
Functional Diversity ◽  
Plant Pathogens ◽  
Trophic Structure ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Its2 Region ◽  
Organic Management ◽  
Rhizosphere Fungi ◽  
Calcium And Magnesium

ABSTRACT The structure and function of fungal communities in the coffee rhizosphere are influenced by crop environment. Because coffee can be grown along a management continuum from conventional application of pesticides and fertilizers in full sun to organic management in a shaded understory, we used coffee fields to hold host constant while comparing rhizosphere fungal communities under markedly different environmental conditions with regard to shade and inputs. We characterized the shade and soil environment in 25 fields under conventional, organic, or transitional management in two regions of Costa Rica. We amplified the internal transcribed spacer 2 (ITS2) region of fungal DNA from coffee roots in these fields and characterized the rhizosphere fungal community via high-throughput sequencing. Sequences were assigned to guilds to determine differences in functional diversity and trophic structure among coffee field environments. Organic fields had more shade, a greater richness of shade tree species, and more leaf litter and were less acidic, with lower soil nitrate availability and higher soil copper, calcium, and magnesium availability than conventionally managed fields, although differences between organic and conventionally managed fields in shade and calcium and magnesium availability depended on region. Differences in richness and community composition of rhizosphere fungi between organic and conventionally managed fields were also correlated with shade, soil acidity, and nitrate and copper availability. Trophic structure differed with coffee field management. Saprotrophs, plant pathogens, and mycoparasites were more diverse, and plant pathogens were more abundant, in organic than in conventionally managed fields, while saprotroph-plant pathogens were more abundant in conventionally managed fields. These differences reflected environmental differences and depended on region. IMPORTANCE Rhizosphere fungi play key roles in ecosystems as nutrient cyclers, pathogens, and mutualists, yet little is currently known about which environmental factors and how agricultural management may influence rhizosphere fungal communities and their functional diversity. This field study of the coffee agroecosystem suggests that organic management not only fosters a greater overall diversity of fungi, but it also maintains a greater richness of saprotrophic, plant-pathogenic, and mycoparasitic fungi that has implications for the efficiency of nutrient cycling and regulation of plant pathogen populations in agricultural systems. As well as influencing community composition and richness of rhizosphere fungi, shade management and use of fungicides and synthetic fertilizers altered the trophic structure of the coffee agroecosystem.

Temporal patterns in the interaction between photosynthetic picoeukaryotes and their attached fungi in Lake Chaohu

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Changqing Liu ◽  
Xiaoli Shi ◽  
Fan Wu ◽  
Min Zhang ◽  
Guang Gao ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Lake Chaohu ◽  
Operational Taxonomic Units ◽  
Flow Cytometric ◽  
Temporal Succession ◽  
Temperature Group ◽  
Flow Cytometric Sorting ◽  
Two Temperature ◽  
Molecular Ecological Network

ABSTRACT The combination of flow cytometric sorting and high-throughput sequencing revealed the broad existence of photosynthetic picoeukaryote attached fungi (PPE-attached fungi) in Lake Chaohu. The relative sequence abundance of attached fungi was negatively correlated with that of the photosynthetic picoeukaryotes (PPEs). PPE-attached fungal communities were mainly composed of Basidiomycota, Chytridiomycota and Ascomycota. Temperature, Si and PPE community structure are the most important driving factors for the temporal succession of PPE-attached fungal communities. In particular, PPE-attached fungi can be divided into three groups from high to low temperatures. Phylogenetic molecular ecological network results indicated that the connectivity and the total number of links in the network of the high-temperature group (> 21.82°C) are higher than those in the other two temperature groups (between  9.67 and  21.82°C, and < 9.67°C, respectively). Moreover, the interaction between PPE-attached fungi and the PPEs changed from antagonistic to cooperative, with the decline in temperature. The most abundant operational taxonomic units of PPE-attached fungi were affiliated with the Cladosporium, the most common saprophytic fungus, whereas most fungal hub taxa were Chytridiomycota, the main parasite fungi of phytoplankton.

scholarly journals Best practices in metabarcoding of fungi: from experimental design to results

2021 ◽  
Author(s):  
Leho Tedersoo ◽  
Mohammad Bahram ◽  
Lucie Zinger ◽  
Henrik Nilsson ◽  
Peter Kennedy ◽  
...  
Keyword(s):  
Experimental Design ◽  
Best Practices ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Its Region ◽  
Fungal Communities ◽  
Sequence Variants ◽  
Transcriptomic Data ◽  
Operational Taxonomic Units ◽  
Computational Analyses

The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview about current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By re-analysing published datasets, we find that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, which is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared with the ITS2 subregion. We conclude that metabarcoding analyses of fungi are especially promising for co-analyses with the functional metagenomic or transcriptomic data, integrating fungi in the entire microbiome, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.

scholarly journals Illumina-based analysis yields new insights into the diversity and composition of endophytic fungi in cultivated Huperzia serrata

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242258
Author(s):  
Shipeng Fan ◽  
Liyun Miao ◽  
Haodong Li ◽  
Aihua Lin ◽  
Fajun Song ◽  
...  
Keyword(s):  
Endophytic Fungi ◽  
High Throughput Sequencing ◽  
Comparative Sequence Analysis ◽  
Rrna Genes ◽  
Tissue Type ◽  
Size Analysis ◽  
Its2 Region ◽  
Huperzia Serrata ◽  
Operational Taxonomic Units ◽  
Composition And Structure

Endophytic fungi play an important role in plant growth. The composition and structure of endophytes vary in different plant tissues, which are specific habitats for endophyte colonization. To analyze the diversity and structural composition of endophytic fungi from toothed clubmoss (Huperzia serrata) that was artificially cultivated for 3 years, we investigated endophytic fungi from the roots, stems and leaves using comparative sequence analysis of the ITS2 region of the fungal rRNA genes sequenced with high-throughput sequencing technology. Seven fungal phyla were identified, and fungal diversity and structure varied across different tissues, with the most distinctive community features found in the roots. A total of 555 operational taxonomic units (OTUs) were detected, and 198 were common to all samples, and 43, 16, 16 OTUs were unique to the root, stem, leaf samples, respectively. Taxonomic classification showed that Ascomycota and Basidiomycota were dominant phyla, and Cladosporium, Oidiodendron, Phyllosticta, Sebacina and Ilyonectria were dominant genera. The relative abundance heat map at the genus level suggested that H. serrata had characteristic endophytic fungal microbiomes. Line discriminant analysis effect size analysis and principal coordinate analysis demonstrated that fungal communities were tissue-type and tissue-site specific. Overall, our study provides new insights into the complex composition of endophytic fungi in H. serrata.

scholarly journals Molecular characterization of endophytic fungal communities associated with Vitis vinifera L. at Taif region of Saudi Arabia

2021 ◽  
Vol 42 (2) ◽  
pp. 177-185
Author(s):  
S.M. Sayed ◽  
◽  
A.M. El-Shehawi ◽  
S.A. Elarnaouty ◽  
S.A. Al-Otaibi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Endophytic Fungi ◽  
Fungal Communities ◽  
Vitis Vinifera L ◽  
Next Generation ◽  
Operational Taxonomic Units ◽  
Grapevine Leaves ◽  
Total Dna ◽  
Generation Sequencing

Aim: The current study aimed to characterize the composition of endophytic fungal communities related to Taify grapevine leaves. Methodology: Taify grapevine leaves were collected from three different locations at Taif region. Total DNA was extracted and the endophytic fungal communities were investigated using next generation sequencing in a metagenomics approach. Results: The obtained data detected 26 fungal operational taxonomic units (OTUs) in all locations with variation in most taxa among three locations. The phylum Ascomycota dominated relative sequence abundance (90.83%), followed by Basidiomycota at 1.82%. Other unidentified fungi at phylum level dominated 7.35% abundance level. At genus level, Alternaria and Cladosporium genera were present at all locations, while Filobasidium and Didymella were detected in two locations. Most genera, Penicillium, Hanseniaspora, Fusarium, Chrysocorona and Quambalaria were detected in one location only. Interpretation: The present study confirmed the diversity of endophytic fungi in Taify grapevine, including pathogenic and non-pathogenic species. The detected species have potential to be used as biocontrol species against economically important pathogens such as Alternaria and Hanseniaspora. This will contribute to our understanding of grapevine-endophytic fungi interaction and their utilization to enhance grapevine production and quality. Key words: Endophytes, Fungi, Grapevine, Metagenomic, Next generation sequencing

Analysis of the structure of bacterial and fungal communities in disease suppressive and disease conducive tobacco-planting soils in China

Soil Research ◽  
2020 ◽  
Vol 58 (1) ◽  
pp. 35
Author(s):  
Lin Gao ◽  
Rui Wang ◽  
Jiaming Gao ◽  
Fangming Li ◽  
Guanghua Huang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Soil Samples ◽  
Fungal Communities ◽  
Sequencing Technology ◽  
Operational Taxonomic Units ◽  
Tobacco Cultivation ◽  
Bacteria And Fungi ◽  
Disease Suppressive Soil ◽  
Conducive Soil

To clarify the differences between microbial communities resident in disease suppressive soil (DSS) and disease conducive soil (DCS) in tobacco cultivation, representative soil samples were collected from tobacco plantations in Shengjiaba, China, and the structure and diversity of the resident bacterial and fungal communities were analysed using high-throughput sequencing technology. Our results showed a greater number of operational taxonomic units associated with bacteria and fungi in DSS than in DCS. At the phylum level, abundances of Chloroflexi, Saccharibacteria, Firmicutes, and Planctomycetes in DSS were lower than in DCS, but abundance of Gemmatimonadetes was significantly higher. Abundances of Zygomycota and Chytridiomycota were higher in DSS than DCS, but abundance of Rozellomycota was significantly lower. At the genus level, abundances of 18 bacterial and nine fungal genera varied significantly between DSS and DCS. Relative abundances of Acidothermus, Microbacterium, Curtobacterium, and Colletotrichum were higher in DCS than DSS. The Shannon and Chao1 indices of DSS microbial communities were higher than those of DCS communities. High microbial diversity reduces the incidence of soil-borne diseases in tobacco plantations and promotes the formation of DSSs.

scholarly journals Microbial community structure in rice, crops, and pastures rotation systems with different intensification levels in the temperate region of Uruguay

2021 ◽  
Author(s):  
Sebastian Martinez
Keyword(s):  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Fungal Community Composition ◽  
Bacterial Phyla ◽  
New Crops ◽  
Operational Taxonomic Units ◽  
Rotation System ◽  
Long Term Experiment ◽  
Well Differentiated ◽  
The Impact

Rice is an important crop in Uruguay associated mostly with livestock production in a rice and pasture rotation system since the 1920s. However, in recent years there has been interest in intensifying the production in some of these systems to satisfy market demands and increase income. Intensification occurs by augmenting the rice frequency in the rotation, including new crops like sorghum and soybean, or shortening the pasture phase. A long-term experiment was established in 2012 in the main rice producing area of Uruguay with the objective to study the impact of intensification in rice rotations. After the first cycle of rotation soils from seven rotation phases were sampled and microbial communities were studied by means of high-throughput sequencing of Illumina NovaSeq 6000. Archaeal/bacterial and fungal community composition were studied (16S rRNA and 18S gene regions) detecting 3662 and 807 bacterial and fungal Operational Taxonomic Units (OTUs), respectively. Actinobacteria, Firmicutes and Proteobacteria were the most common bacterial phyla. Among them, only Proteobacteria differed significantly between rotations. Although most fungal OTUs were unidentified, Ascomycota, Basidiomycota and Mucoromycota were the most abundant fungal classes within identified taxa. Bacterial communities differed between rotations forming three groups according to the percentage of rice in the system. Fungal communities clustered in four groups, although not well differentiated, and mostly associated with the antecessor crop. Only P and C:N varied between rotations among soil physicochemical variables after six years, and individual bacterial OTUs appeared weakly influenced by P, pH, Mg and fungal OTUs by P. The results suggest that after six years, bacteria/archaeal communities were influenced by the time with rice in the rotation, and fungal communities were more influenced by the antecessor crop. More studies are needed to associate fungal communities with certain rotational or environmental variables. Some taxa were associated with a particular rotation, and some bacterial taxa were identified as biomarkers. Fungal indicator taxa were not identified at the species level for any rotation.

scholarly journals Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244682
Author(s):  
Martino Adamo ◽  
Samuele Voyron ◽  
Matteo Chialva ◽  
Roland Marmeisse ◽  
Mariangela Girlanda
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Environmental Dna ◽  
Taxonomic Composition ◽  
Fungal Communities ◽  
Rna Sequences ◽  
Operational Taxonomic Units ◽  
Dna And Rna ◽  
Filamentous Microorganisms ◽  
Active Communities

In recent years, metabarcoding has become a key tool to describe microbial communities from natural and artificial environments. Thanks to its high throughput nature, metabarcoding efficiently explores microbial biodiversity under different conditions. It can be performed on environmental (e)DNA to describe so-called total microbial community, or from environmental (e)RNA to describe active microbial community. As opposed to total microbial communities, active ones exclude dead or dormant organisms. For what concerns Fungi, which are mostly filamentous microorganisms, the relationship between DNA-based (total) and RNA-based (active) communities is unclear. In the present study, we evaluated the consequences of performing metabarcoding on both soil and wood-extracted eDNA and eRNA to delineate molecular operational taxonomic units (MOTUs) and differentiate fungal communities according to the environment they originate from. DNA and RNA-based communities differed not only in their taxonomic composition, but also in the relative abundances of several functional guilds. From a taxonomic perspective, we showed that several higher taxa are globally more represented in either “active” or “total” microbial communities. We also observed that delineation of MOTUs based on their co-occurrence among DNA and RNA sequences highlighted differences between the studied habitats that were overlooked when all MOTUs were considered, including those identified exclusively by eDNA sequences. We conclude that metabarcoding on eRNA provides original functional information on the specific roles of several taxonomic or functional groups that would not have been revealed using eDNA alone.

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