Root-Associated Mycobiome Differentiate between Habitats Supporting Production of Different Truffle Species in Serbian Riparian Forests

Balkan lowlands bordering with the Pannonia region are inhabited by diverse riparian forests that support production of different truffle species, predominantly the most prized white truffle of Piedmont (Tuber magnatum Pico), but also other commercial species (T.macrosporum Vitt., T. aestivum Vitt.). Surprisingly, little is known about the native root-associated mycobiome (RAM) of these lowland truffle-producing forests. Therefore, in this study we aim at exploring and comparing the RAMs of three different truffle-producing forests from Kolubara river plane in Serbia. Molecular methods based on next generation sequencing (NGS) were used to evaluate the diversity of root-associated fungal communities and to elucidate the influence of environmental factors on their differentiation. To our knowledge, this is the first study from such habitats with a particular focus on comparative analysis of the RAM in different truffle-producing habitats using a high-throughput sequencing approach. Our results indicated that the alpha diversity of investigated fungal communities was not significantly different between different truffle-producing forests and within a specific forest type, while the seasonal differences in the alpha diversity were only observed in the white truffle-producing forests. Taxonomic profiling at phylum level indicated the dominance of fungal OTUs belonging to phylum Ascomycota and Basidiomycota, with very minor presence of other phyla. Distinct community structures of root-associated mycobiomes were observed for white, mixed, and black truffle-producing forests. The core mycobiome analysis indicated a fair share of fungal genera present exclusively in white and black truffle-producing forest, while the core genera of mixed truffle-producing forests were shared with both white and black truffle-producing forests. The majority of detected fungal OTUs in all three forest types were symbiotrophs, with ectomycorrhizal fungi being a dominant functional guild. Apart from assumed vegetation factor, differentiation of fungal communities was driven by factors connected to the distance from the river and exposure to fluvial activities, soil age, structure, and pH. Overall, Pannonian riparian forests appear to host diverse root-associated fungal communities that are strongly shaped by variation in soil conditions.

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Early ecological succession patterns of bacterial, fungal and plant communities along a chronosequence in a recently deglaciated area of the Italian Alps

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa165 ◽

2020 ◽

Vol 96 (10) ◽

Author(s):

A Franzetti ◽

F Pittino ◽

I Gandolfi ◽

R S Azzoni ◽

G Diolaiuti ◽

...

Keyword(s):

High Throughput Sequencing ◽

Inorganic Compounds ◽

Alpha Diversity ◽

Ecological Succession ◽

Fungal Communities ◽

Rrna Gene ◽

Italian Alps ◽

Weathering Processes ◽

Pioneer Plants ◽

Heterotrophic Metabolism

ABSTRACT In this study, the early ecological succession patterns of Forni Glacier (Ortles-Cevedale group, Italian Alps) forefield along an 18-year long chronosequence (with a temporal resolution of 1 year) has been reported. Bacterial and fungal community structures were inferred by high-throughput sequencing of 16S rRNA gene and ITS, respectively. In addition, the occurrence of both herbaceous and arboreous plants was also recorded at each plot. A significant decrease of alpha-diversity in more recently deglaciated areas was observed for both bacteria and plants. Time since deglaciation and pH affected the structure of both fungal and bacterial communities. Pioneer plants could be a major source of colonization for both bacterial and fungal communities. Consistently, some of the most abundant bacterial taxa and some of those significantly varying with pH along the chronosequence (Polaromonas, Granulicella, Thiobacillus, Acidiferrobacter) are known to be actively involved in rock-weathering processes due to their chemolithotrophic metabolism, thus suggesting that the early phase of the chronosequence could be mainly shaped by the biologically controlled bioavailability of metals and inorganic compounds. Fungal communities were dominated by ascomycetous filamentous fungi and basidiomycetous yeasts. Their role as cold-adapted organic matter decomposers, due to their heterotrophic metabolism, was suggested.

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Factors Influencing the Fungal Diversity on Audio–Visual Materials

Microorganisms ◽

10.3390/microorganisms9122497 ◽

2021 ◽

Vol 9 (12) ◽

pp. 2497

Author(s):

Tereza Branysova ◽

Martina Kracmarova ◽

Michal Durovic ◽

Katerina Demnerova ◽

Hana Stiborova

Keyword(s):

High Throughput Sequencing ◽

Alpha Diversity ◽

Abundant Species ◽

Future Generations ◽

Fungal Communities ◽

Air Contamination ◽

Factors Influencing ◽

Significant Difference ◽

Visual Materials ◽

Cultural Heritage Objects

The biodeterioration of audio–visual materials is a huge problem, as it can cause incalculable losses. To preserve these cultural heritage objects for future generations, it is necessary to determine the main agents of biodeterioration. This study focuses on identifying fungi, both from the air and smears from photographs and cinematographic films that differ in the type of carrier and binder, using high-throughput sequencing approaches. The alpha diversity measures of communities present on all types of carriers were compared, and a significant difference between cellulose acetate and baryta paper was observed. Next, the locality, type of carrier, and audio–visual material seem to affect the structure of fungal communities. Additionally, a link between the occurrence of the most abundant classes and species on audio–visual materials and air contamination in the archives was proven. In both cases, the most abundant classes were Agariomycetes, Dothideomycetes, and Eurotiomycetes, and approximately half of the 50 most abundant species detected on the audio–visual materials and in the air were identical.

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Diet Induces the Difference of Gut Fungal Communities between Anser erythropus Wintering at Shengjin and Caizi Lakes, China

10.21203/rs.3.rs-795606/v1 ◽

2021 ◽

Author(s):

Gang Liu ◽

Zhizhong Gong ◽

Jiahui Feng ◽

Na Xu

Keyword(s):

High Throughput Sequencing ◽

Alpha Diversity ◽

Diversity Indices ◽

Fungal Communities ◽

Pathogenic Species ◽

Potential Pathogen ◽

Host Nutrition ◽

The Difference ◽

Serious Disease ◽

Anser Erythropus

Abstract The gut microbiota play major roles in host nutrition and metabolism, and even potential to cause serious disease for animals and human, however, the knowledge of waterbirds’ gut fungal communities are quite limited at present. In this paper, the gut fungal communities and infer the potential pathogens isolated from the feces of Anser erythropus wintering at Shengjin Lake (SJ) and Caizi Lake (CZ) were investigated based on ITS gene region by using high-throughput sequencing. 1,302,562 valid tags corresponding to 2,102 OTUs were retained from 20 fecal samples, including 10 samples per lake. The OTUs from SJ geese represented seven phyla and 27 classes, seven phyla and 28 classes were identified from CZ samples. Ascomycota, Basidiomycota, Zygomycota and Rozellomycota were the dominant gut fungal phyla in this study, accounted for 61.60%, 35.60%, 1.84%, and 0.30% of the OTUs, respectively. The alpha diversity indices showed significantly different between the geese from SJ and CZ. The Anser erythropus mainly ate Poaceae spp. at SJ, while Carex spp. component was identified at CZ, suggesting that the variations in fungal community between the two lake geese might be induced by different diets. We also observed a fungal pattern with a higher number of significant correlations to bacterial genus, and Ceratobasidium, Tomentella, Paurocotylis, Tuber, Podospora and Mortierella were core fungal genus in the two lake geese. Nine potential pathogenic species were identified in the guts across all samples of Anser erythropus at SJ and CZ, it also showed the relative abundance of potential pathogen was significantly higher from SJ samples than that from CZ samples. These findings expanded our knowledge on the gut fungi for waterbirds, indicating the fungi are highly sensitive to diet at two lakes and should pay more attention to the potential pathogenic species of Anser erythropus.

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

Journal of Fungi ◽

10.3390/jof7030194 ◽

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).

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Experimental infection with the hookworm, Necator americanus, is associated with stable gut microbial diversity in human volunteers with relapsing multiple sclerosis

BMC Biology ◽

10.1186/s12915-021-01003-6 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Timothy P. Jenkins ◽

David I. Pritchard ◽

Radu Tanasescu ◽

Gary Telford ◽

Marina Papaiakovou ◽

...

Keyword(s):

Multiple Sclerosis ◽

Experimental Infection ◽

High Throughput Sequencing ◽

Alpha Diversity ◽

Placebo Treatment ◽

Sequencing Data ◽

Faecal Microbiota ◽

Microbial Composition ◽

Necator Americanus ◽

Human Volunteers

Abstract Background Helminth-associated changes in gut microbiota composition have been hypothesised to contribute to the immune-suppressive properties of parasitic worms. Multiple sclerosis is an immune-mediated autoimmune disease of the central nervous system whose pathophysiology has been linked to imbalances in gut microbial communities. Results In the present study, we investigated, for the first time, qualitative and quantitative changes in the faecal bacterial composition of human volunteers with remitting multiple sclerosis (RMS) prior to and following experimental infection with the human hookworm, Necator americanus (N+), and following anthelmintic treatment, and compared the findings with data obtained from a cohort of RMS patients subjected to placebo treatment (PBO). Bacterial 16S rRNA high-throughput sequencing data revealed significantly decreased alpha diversity in the faecal microbiota of PBO compared to N+ subjects over the course of the trial; additionally, we observed significant differences in the abundances of several bacterial taxa with putative immune-modulatory functions between study cohorts. Parabacteroides were significantly expanded in the faecal microbiota of N+ individuals for which no clinical and/or radiological relapses were recorded at the end of the trial. Conclusions Overall, our data lend support to the hypothesis of a contributory role of parasite-associated alterations in gut microbial composition to the immune-modulatory properties of hookworm parasites.

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

International Journal of Food Microbiology ◽

10.1016/j.ijfoodmicro.2019.108496 ◽

2020 ◽

Vol 319 ◽

pp. 108496 ◽

Cited By ~ 1

Author(s):

Mengyue Guo ◽

Wenjun Jiang ◽

Meihua Yang ◽

Xiaowen Dou ◽

Xiaohui Pang

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Fungal Communities

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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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Vineyard ecosystems are structured and distinguished by fungal communities impacting the flavour and quality of wine

10.1101/2019.12.27.881656 ◽

2019 ◽

Author(s):

Di Liu ◽

Qinglin Chen ◽

Pangzhen Zhang ◽

Deli Chen ◽

Kate S. Howell

Keyword(s):

Regional Distribution ◽

Distribution Patterns ◽

Wine Fermentation ◽

Fungal Communities ◽

Soil Microbiome ◽

Soil Conditions ◽

Wine Aroma ◽

Wine Production ◽

Microbial Distribution

AbstractThe flavours of foods and beverages are formed by the agricultural environment where the plants are grown. In the case of wine, the location and environmental features of the vineyard site imprint the wine with distinctive aromas and flavours. Microbial growth and metabolism play an integral role in wine production from the vineyard to the winery, by influencing grapevine health, wine fermentation, and the flavour, aroma and quality of finished wines. The mechanism by which microbial distribution patterns drive wine metabolites is unclear and while flavour has been correlated with bacterial composition for red wines, bacterial activity provides a minor biochemical conversion in wine fermentation. Here, we collected samples across six distinct winegrowing areas in southern Australia to investigate regional distribution patterns of both fungi and bacteria and how this corresponds with wine aroma compounds. Results show that soil and must microbiota distinguish winegrowing regions and are related to wine chemical profiles. We found a strong relationship between microbial and wine metabolic profiles, and this relationship was maintained despite differing abiotic drivers (soil properties and weather/ climatic measures). Notably, fungal communities played the principal role in shaping wine aroma profiles and regional distinctiveness. We found that the soil microbiome is a potential source of grape- and must-associated fungi, and therefore the weather and soil conditions could influence the wine characteristics via shaping the soil fungal community compositions. Our study describes a comprehensive scenario of wine microbial biogeography in which microbial diversity responds to surrounding environments and ultimately sculpts wine aromatic characteristics. These findings provide perspectives for thoughtful human practices to optimise food and beverage flavour and composition through understanding of fungal activity and abundance.

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Effect of Periampullary Diverticulum on Biliary Flora and the Formation of Common Bile Duct Stone

10.21203/rs.3.rs-75499/v1 ◽

2020 ◽

Author(s):

Senlin Hou ◽

Hao Wang ◽

Lichao Zhang ◽

Tingting Yu ◽

Zhanying Qiao

Keyword(s):

Bile Duct ◽

Common Bile Duct ◽

High Throughput Sequencing ◽

Bile Duct Stone ◽

Stone Formation ◽

Intestinal Flora ◽

Alpha Diversity ◽

Intestinal Fluid ◽

Bacterial Gene ◽

Periampullary Diverticulum

Abstract Background: Bile duct stone is closely related to periampullary diverticulum, but it is not clear whether the formation of it was affected by the diverticulum through the biliary flora. To explore the diversity and correlation of biliary and intestinal flora in the patients with choledocholithiasis and the effects of periampullary diverticulum on the flora and bile duct stone. Methods: Bile and intestinal fluid were collected from patients with primary common bile duct stones, and then divided into diverticulum group and none- diverticulum group according to the presence or absence of paravertebral diverticula, DNA of these samples was extracted and a bacterial gene library was constructed, and related bioinformatics analysis was performed after high-throughput sequencing to obtain the bacterial components and community structure of the sample. Result: A total of 3001,613 valid sequences were obtained, with an average of 136436.95±3696.842 sequences, which were classified into 6021 ASV/OUT. Alpha diversity analysis showed that the species richness and diversity in the diverticulum group were lower than those in the nondiverticulum group. According to the species annotation results, the advantage bacterium group of the bile is Proteobacteria (BG 80.41%, Bg 70.95%), and advantage bacterium group of the intestinal fluid is Firmicutes and Proteobacteria (BG 89.39%, Bg 74.11%). A large proportion of Enterobacter was found in bile. Escherichia coli, Klebsiella, Streptococcus and other bacteria closely related to stone formation have been found. The proportion of E. coli in the diverticulum group was increased and due to the existence of the diverticulum Enterobacteria in the bile were increased and more complex. The bacteria that produce Betaglucuronidase are found to be increased in bile. Due to the influence of the periampullary diverticulum, the intestinal flora will be changed and then the biliary flora will also change. Conclusion: The existence of periampullary diverticulum will affect the biliary tract flora and lead to the increase of bacteria related to stone formation, which will affect the formation of choledocholithiasis and make it easier for choledocholithiasis to form.

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