scholarly journals Rolling a mycobiome down a hill: endophytes in the Taiwanese Cloud Forest

2017 ◽  
Author(s):  
Dan Thomas ◽  
Roo Vandegrift ◽  
Yu-Ming Ju ◽  
Monica Hsieh ◽  
Bitty Roy
Keyword(s):  
Tree Species ◽  
Spatial Scales ◽  
Cloud Forest ◽  
Fungal Endophytes ◽  
Amplicon Sequencing ◽  
Fungal Endophyte ◽  
Core Microbiome ◽  
The Core ◽  
Host Tree Species ◽  
Ecological Importance

AbstractFungal endophytes of plants are ubiquitous and important to host plant health. Despite their ecological importance, landscape-level patterns of microbial communities in plant hosts are not well-characterized. Fungal wood-inhabiting and foliar endophyte communities from multiple tree hosts were sampled at multiple spatial scales across a 25 ha subtropical research plot in northern Taiwan, using culture-free, community DNA amplicon sequencing methods. Fungal endophyte communities were distinct between leaves and wood, but the mycobiomes were highly variable across and within tree species. Of the variance that could be explained, host tree species was the most important driver of mycobiome community-composition. Within a single tree species, “core” mycobiomes were characterized using cooccurrence analysis. These core groups of endophytes in leaves and wood show divergent spatial patterns. For wood endophytes, a more consistent, “minimal” core mycobiome coexisted with the host across the extent of the study. For leaf endophytes, the core fungi resembled a more dynamic, “gradient” model of the core microbiome, changing across the topography and distance of the study.

scholarly journals Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment

Diversity ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 234 ◽  
Author(s):  
Eric A. Griffin ◽  
Joshua G. Harrison ◽  
Melissa K. McCormick ◽  
Karin T. Burghardt ◽  
John D. Parker
Keyword(s):  
Phylogenetic Diversity ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Spatial Scales ◽  
Fungal Endophytes ◽  
Fungal Endophyte ◽  
Tree Diversity ◽  
Trophic Levels ◽  
Community Diversity ◽  
And Function

Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.

scholarly journals 21 Profiling sow vaginal and fecal and piglet gastrointestinal microbiome and the passage of sow microbiome to their progeny from birth to weaning

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 21-21
Author(s):  
Huyen Tran ◽  
Brenda de Rodas ◽  
Manohar M Lahoti ◽  
Timothy J Johnson
Keyword(s):  
Alpha Diversity ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Gastrointestinal Microbiome ◽  
Core Microbiome ◽  
Linear Discriminant ◽  
Fecal Microbiome ◽  
The Core ◽  
Vaginal Swabs ◽  
Sampling Points

Abstract The objectives of this study were 1) to profile the sow vaginal and fecal microbiome and the corresponding piglet gastrointestinal microbiome from birth to weaning, and 2) to identify the core microbiome shared between sows and piglets. A total of 226 samples collected from sows (vaginal swabs pre-farrow; fecal samples at farrow, d 3, 7, 10, 17 post-farrow) and their progenies (stomach, ileum, and colon digesta at birth, d 2, and 14 after birth) were used for the analyses of microbial community structure using 16S rRNA V4 amplicon sequencing with Illumina MiSeq. Our data indicated that the piglet and sow microbiome were quite distinct. Piglets had lower bacterial alpha diversity (chao1, richness, Shannon, Simpson indices; P < 0.01) than sows across all timepoints. Beta diversity of piglets by sample types was significantly different (P < 0.001) than sows by sample types when averaged across all timepoints or separation by timepoints. Feature selection by the Linear discriminant analysis effect size (LEfSe) indicated that the genera associated with piglets included those classified as Lactobacillus, unclassified Micrococcaceae, and Rothia when averaged across sampling points and sample types. Genera associated with sows included those classified as Treponema, YRC22, Unclassified RF39, Unclassified Christensenellaceae, Turicibacter, Unclassified RFP12, Unclassified F16, Collinsella, Coprococcus, Unclassified Coriobacteriaceae, and Unclassified Mogibacteriaceae. The genera shared between sow vaginal samples and piglets included those classified as Bacteroides, Fusobacterium, Haemophilus, Prevotella, Veillonella, and unclassified Clostridiadiaceae. The genera shared between sow fecal and piglet samples included those classified as Bacteroides, Lactobacillus, unclassified Clostridiadiaceae, unclassified Ruminococceae, and Prevotella. Overall, there are evidences that bacterial genera were passed from sows to piglets and influenced the microbial communities of piglets later in life.

scholarly journals Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7744 ◽  
Author(s):  
Gian Maria Niccolò Benucci ◽  
Reid Longley ◽  
Peng Zhang ◽  
Qi Zhao ◽  
Gregory Bonito ◽  
...  
Keyword(s):  
16S Rdna ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Human Consumption ◽  
Fruiting Bodies ◽  
Core Microbiome ◽  
Microbial Indicators ◽  
The Core ◽  
History Of ◽  
Body Production

Morels (Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter, Pseudomonas, Stenotrophomonas, and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella, Phialophora, and Mortierella. This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production.

Fungal endophyte diversity in table grapes

2021 ◽  
Vol 67 (1) ◽  
pp. 29-36
Author(s):  
Champa Wijekoon ◽  
Zoe Quill
Keyword(s):  
Internal Transcribed Spacer ◽  
Fungal Endophytes ◽  
Pathogenic Fungi ◽  
Amplicon Sequencing ◽  
Fungal Endophyte ◽  
Table Grape ◽  
Fungal Communities ◽  
Table Grapes ◽  
Pharmaceutical Applications ◽  
Microbial Sources

Plant fungal endophytes are diverse microbial sources that reside inside plants. Grapes (Vitis vinifera) are rich in polyphenols that have beneficial health effects, and recent research has shown that fungal endophytes in grapes may contribute to the production of these polyphenols and may serve as biocontrol agents. In this study, we determined the fungal microbial endophyte diversity in North American table grapes found at a Winnipeg, Manitoba, market. The amplicon internal transcribed spacer (ITS) metagenomics approach was used to profile the fungal communities of the fruit endophyte microbiome of three table grape types. The data supported endophyte diversity in different table grapes, including possible bioactive, saprophytic, and pathogenic fungi. Culturable endophytes were isolated and identified by morphology and ITS amplicon sequencing. The majority of the isolated culturable strains included Alternaria spp. and Cladosporium spp. The results provided evidence of the existence of diverse fungal endophytes isolated and identified from the fruit of the table grapes. These fungal endophytes may have potential in agricultural, industrial, and pharmaceutical applications.

scholarly journals Agroforestry Management Systems Drive the Composition, Diversity, and Function of Fungal and Bacterial Endophyte Communities in Theobroma Cacao Leaves

2020 ◽  
Vol 8 (3) ◽  
pp. 405 ◽  
Author(s):  
Franziska Wemheuer ◽  
Dirk Berkelmann ◽  
Bernd Wemheuer ◽  
Rolf Daniel ◽  
Stefan Vidal ◽  
...  
Keyword(s):  
Theobroma Cacao ◽  
Fungal Endophytes ◽  
Alpha Diversity ◽  
Fungal Endophyte ◽  
Management Systems ◽  
Home Garden ◽  
Bacterial Endophytes ◽  
Core Microbiome ◽  
Fungal Phytopathogens ◽  
And Function

Cacao (Theobroma cacao L.) is one of the most economically important crops worldwide. Despite the important role of endophytes for plant growth and health, very little is known about the effect of agroforestry management systems on the endophyte communities of T. cacao. To close this knowledge gap, we investigated the diversity, community composition, and function of bacterial and fungal endophytes in the leaves of T. cacao trees growing in five major cacao-growing regions in the central region of Cameroon using DNA metabarcoding. Fungal but not bacterial alpha diversity measures differed significantly between the agroforestry management systems. Interestingly, less managed home-garden cacao forests harbored the lowest fungal richness and diversity. Our results suggest that the composition of bacterial and fungal endophyte communities is predominantly affected by agroforestry management systems and, to a lesser extent, by environmental properties. The core microbiome detected comprised important fungal phytopathogens, such as Lasiodiplodia species. Several predicted pathways of bacterial endophytes and functional guilds of fungal endophytes differed between the agroforest systems which might be attributed to bacteria and fungi specifically associated with a single agroforest. Our results provide the basis for future studies on foliar fungal and bacterial endophytes of T. cacao and their responsiveness towards agroforestry management systems.

scholarly journals Core of the saliva microbiome: an analysis of the MG-RAST data

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Simone G. Oliveira ◽  
Rafaela R. Nishiyama ◽  
Claudio A. C. Trigo ◽  
Ana Luiza Mattos-Guaraldi ◽  
Alberto M. R. Dávila ◽  
...  
Keyword(s):  
Statistical Tests ◽  
Principal Component ◽  
Amplicon Sequencing ◽  
Health Condition ◽  
Oral Microbiota ◽  
Oral Diseases ◽  
Core Microbiome ◽  
Shotgun Metagenomics ◽  
The Core ◽  
Spearman’S Correlation

Abstract Background Oral microbiota is considered as the second most complex in the human body and its dysbiosis can be responsible for oral diseases. Interactions between the microorganism communities and the host allow establishing the microbiological proles. Identifying the core microbiome is essential to predicting diseases and changes in environmental behavior from microorganisms. Methods Projects containing the term “SALIVA”, deposited between 2014 and 2019 were recovered on the MG-RAST portal. Quality (Failed), taxonomic prediction (Unknown and Predicted), species richness (Rarefaction), and species diversity (Alpha) were analyzed according to sequencing approaches (Amplicon sequencing and Shotgun metagenomics). All data were checked for normality and homoscedasticity. Metagenomic projects were compared using the Mann–Whitney U test and Spearman's correlation. Microbiome cores were inferred by Principal Component Analysis. For all statistical tests, p < 0.05 was used. Results The study was performed with 3 projects, involving 245 Amplicon and 164 Shotgun metagenome datasets. All comparisons of variables, according to the type of sequencing, showed significant differences, except for the Predicted. In Shotgun metagenomics datasets the highest correlation was between Rarefaction and Failed (r =  − 0.78) and the lowest between Alpha and Unknown (r =  − 0.12). In Amplicon sequencing datasets, the variables Rarefaction and Unknown (r = 0.63) had the highest correlation and the lowest was between Alpha and Predicted (r =  − 0.03). Shotgun metagenomics datasets showed a greater number of genera than Amplicon. Propionibacterium, Lactobacillus, and Prevotella were the most representative genera in Amplicon sequencing. In Shotgun metagenomics, the most representative genera were Escherichia, Chitinophaga, and Acinetobacter. Conclusions Core of the salivary microbiome and genera diversity are dependent on the sequencing approaches. Available data suggest that Shotgun metagenomics and Amplicon sequencing have similar sensitivities to detect the taxonomic level investigated, although Shotgun metagenomics allows a deeper analysis of the microorganism diversity. Microbiome studies must consider characteristics and limitations of the sequencing approaches. Were identified 20 genera in the core of saliva microbiome, regardless of the health condition of the host. Some bacteria of the core need further study to better understand their role in the oral cavity.

scholarly journals Highly restricted dispersal in habitat-forming seaweed may impede natural recovery of disturbed populations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Florentine Riquet ◽  
Christiane-Arnilda De Kuyper ◽  
Cécile Fauvelot ◽  
Laura Airoldi ◽  
Serge Planes ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Spatial Scales ◽  
Mediterranean Ecosystems ◽  
Dispersal Distance ◽  
Genetic Connectivity ◽  
Restricted Gene Flow ◽  
Isolated Populations ◽  
Natural Recovery ◽  
Limited Dispersal ◽  
Ecological Importance

AbstractCystoseira sensu lato (Class Phaeophyceae, Order Fucales, Family Sargassaceae) forests play a central role in marine Mediterranean ecosystems. Over the last decades, Cystoseira s.l. suffered from a severe loss as a result of multiple anthropogenic stressors. In particular, Gongolaria barbata has faced multiple human-induced threats, and, despite its ecological importance in structuring rocky communities and hosting a large number of species, the natural recovery of G. barbata depleted populations is uncertain. Here, we used nine microsatellite loci specifically developed for G. barbata to assess the genetic diversity of this species and its genetic connectivity among fifteen sites located in the Ionian, the Adriatic and the Black Seas. In line with strong and significant heterozygosity deficiencies across loci, likely explained by Wahlund effect, high genetic structure was observed among the three seas (ENA corrected FST = 0.355, IC = [0.283, 0.440]), with an estimated dispersal distance per generation smaller than 600 m, both in the Adriatic and Black Sea. This strong genetic structure likely results from restricted gene flow driven by geographic distances and limited dispersal abilities, along with genetic drift within isolated populations. The presence of genetically disconnected populations at small spatial scales (< 10 km) has important implications for the identification of relevant conservation and management measures for G. barbata: each population should be considered as separated evolutionary units with dedicated conservation efforts.

Multi-level social-ecological networks in a payments for ecosystem services programme in central Veracruz, Mexico

2020 ◽  
pp. 1-7
Author(s):  
Alfonso Langle-Flores ◽  
Adriana Aguilar Rodríguez ◽  
Humberto Romero-Uribe ◽  
Julia Ros-Cuéllar ◽  
Juan José Von Thaden
Keyword(s):  
Ecosystem Services ◽  
Spatial Scales ◽  
Payments For Ecosystem Services ◽  
Collaboration Network ◽  
Governmental Organizations ◽  
Social Ecological ◽  
Non Governmental Organizations ◽  
Conservation Activity ◽  
Ecological Importance ◽  
Hydrological Services

Summary Payments for ecosystem services (PES) programmes have been considered an important conservation mechanism to avoid deforestation. These environmental policies act in social and ecological contexts at different spatial scales. We evaluated the social-ecological fit between stakeholders and ecosystem processes in a local PES programme across three levels: social, ecological and social-ecological. We explored collaboration among stakeholders, assessed connectivity between forest units and evaluated conservation activity links between stakeholders and forest units. In addition, to increase programme effectiveness, we classified forest units based on their social and ecological importance. Our main findings suggest that non-governmental organizations occupy brokerage positions between landowners and government in a dense collaboration network. We also found a partial spatial misfit between conservation activity links and the forest units that provide the most hydrological services to Xalapa. We conclude that conservation efforts should be directed towards the middle and high part of the Pixquiac sub-watershed and that the role of non-governmental organizations as mediators should be strengthened to increase the efficiency and effectiveness of the local PES programme.

scholarly journals Impact of Harvest Conditions and Host Tree Species on Chemical Composition and Antioxidant Activity of Extracts from Viscum album L.

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3741
Author(s):  
Wioleta Pietrzak ◽  
Renata Nowak
Keyword(s):  
Antioxidant Activity ◽  
Biological Activity ◽  
Chemical Composition ◽  
Tree Species ◽  
Plant Material ◽  
Plant Secondary Metabolites ◽  
Host Tree ◽  
Host Tree Species ◽  
High Antioxidant Activity ◽  
Mistletoe Extracts

The content of plant secondary metabolites is not stable, and factors such as the region/location effect and seasonal variations have an impact on their chemical composition, especially in parasitic plants. Research in this area is an important step in the development of quality parameter standards of medicinal plants and their finished products. The effects of the time and place of harvest and the host tree species on the chemical composition and antioxidant activity of mistletoe extracts were investigated. Statistical tools were used to evaluate the results of the spectrophotometric and LC-ESI-MS/MS studies of the phenolic composition and antioxidant activity. The investigations indicate that the qualitative and quantitative composition, influencing the biological activity of mistletoe extracts, largely depends on the origin of the plant. The mistletoe extracts exhibited a rich phenol profile and high antioxidant activity. The chemometric analysis indicated that mistletoe collected from conifers (Viscum abietis and Viscum austriacum) had the most advantageous chemical composition and antioxidant activity. Moreover, the chemical profile and biological activity of the plant material were closely related to the climatic conditions and location of the harvested plant. Higher levels of phenolic compounds and high antioxidant activity were found in extracts obtained from plant material collected in cold weather with the presence of snow and less sunshine (autumn–winter period).

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