scholarly journals Shifts in community composition and co-occurrence patterns of phyllosphere fungi inhabiting Mussaenda shikokiana along an elevation gradient

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5767 ◽  
Author(s):  
Xin Qian ◽  
Liang Chen ◽  
Xiaoming Guo ◽  
Dan He ◽  
Miaomiao Shi ◽  
...  
Keyword(s):  
Community Composition ◽  
Elevation Gradient ◽  
Taxonomic Diversity ◽  
Fungal Communities ◽  
Its2 Region ◽  
Mean Annual Temperature ◽  
Phyllosphere Fungi ◽  
Single Host ◽  
Fungal Assemblages ◽  
Occurrence Patterns

The altitudinal effects on the distributions of phyllosphere fungal assemblages in conspecific plants remain poorly elucidated. To address this, phyllosphere fungal communities associated with Mussaenda shikokiana were investigated at four sites across a 350 m elevation gradient in a subtropical forest by employing Illumina metabarcoding of the fungal internal transcribed spacer 2 (ITS2) region. Our results demonstrated that phyllosphere fungal assemblages with a single host possessed high taxonomic diversity and multiple trophic guilds. OTU richness was significantly influenced by elevation. The elevation gradient also entailed distinct shifts in the community composition of phyllosphere fungi, which was significantly related to geographical distance and mean annual temperature (MAT). Additionally, comparison of phyllosphere fungal networks showed reduced connectivity with increasing elevation. Our data provide insights on the distribution and interactions of the phyllosphere fungal community associated with a single host along a short elevation gradient.

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.

scholarly journals Ectomycorrhizal fungal communities associated with Larix gemelinii Rupr. in the Great Khingan Mountains, China

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11230
Author(s):  
Yonglong Wang ◽  
Yanling Zhao ◽  
Ying Xu ◽  
Jianjun Ma ◽  
Busayo Joshua Babalola ◽  
...  
Keyword(s):  
Fungal Community ◽  
Geographic Distance ◽  
Fungal Communities ◽  
Spatial Distance ◽  
Its2 Region ◽  
Mean Annual Temperature ◽  
Ecological Value ◽  
Abundant Otus ◽  
The Impact ◽  
Great Khingan Mountains

Larix gemelinii is an important tree species in the Great Khingan Mountains in Northeast China with a high economic and ecological value for its role in carbon sequestration and as a source of lumber and nuts. However, the ectomycorrhizal (EM) fungal diversity and community composition of this tree remain largely undefined. We examined EM fungal communities associated with L. gemelinii from three sites in the Great Khingan Mountains using Illumina Miseq to sequence the rDNA ITS2 region and evaluated the impact of spatial, soil, and climatic variables on the EM fungal community. A total of 122 EM fungal operational taxonomic units (OTUs) were identified from 21 pooled-root samples, and the dominant EM fungal lineages were /tricholoma, /tomentella-thelephora, /suillus-rhizopogon, and /piloderma. A high proportion of unique EM fungal OTUs were present; some abundant OTUs largely restricted to specific sites. EM fungal richness and community assembly were significantly correlated with spatial distance and climatic and soil variables, with mean annual temperature being the most important predictor for fungal richness and geographic distance as the largest determinant for community turnover. Our findings indicate that L. gemelinii has a rich and distinctive EM fungal community contributing to our understanding of the montane EM fungal community structure from the perspective of a single host plant that has not been previously reported.

scholarly journals Comparative Analysis of Fungal Diversity in Rhizospheric Soil from Wild and Reintroduced Magnolia sinica Estimated via High-Throughput Sequencing

Plants ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 600
Author(s):  
Qingqing Shen ◽  
Junyu Yang ◽  
Daifa Su ◽  
Zhiying Li ◽  
Wei Xiao ◽  
...  
Keyword(s):  
Endangered Species ◽  
Community Composition ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Future Research ◽  
Its2 Region ◽  
Rhizospheric Soil ◽  
Fungal Community Composition ◽  
Opposite Pattern

Magnolia sinica is a critically endangered species and considered a “plant species with extremely small populations” (PSESP). It is an endemic species in southeastern Yunnan Province, China, with reproductive barriers. Rhizosphere fungi play a crucial role in plant growth and health. However, the composition, diversity, and function of fungal communities in wild and reintroduced M. sinica rhizospheres remain unknown. In this study, Illumina sequencing of the internal transcribed spacer 2 (ITS2) region was used to analyze rhizospheric soil samples from wild and reintroduced M. sinica. Thirteen phyla, 45 classes, 105 orders, 232 families, and 433 genera of fungi were detected. Basidiomycota and Ascomycota were dominant across all samples. The fungal community composition was similar between the wild and reintroduced rhizospheres, but the fungal taxa relative abundances differed. The fungal community richness was higher in the reintroduced rhizosphere than in the wild rhizosphere, but the diversity showed the opposite pattern. Soil nutrients and leaf litter significantly affected the fungal community composition and functional diversity. Here, the composition, structure, diversity, and ecological functions of the fungal communities in the rhizospheres of wild and reintroduced M. sinica were elucidated for the first time, laying a foundation for future research and endangered species protection.

Temporal dynamics of mycorrhizal fungal communities and co-associations with grassland plant communities following experimental manipulation of rainfall

2019 ◽  
Author(s):  
Coline Deveautour ◽  
Sally Power ◽  
Kirk Barnett ◽  
Raul Ochoa-Hueso ◽  
Suzanne Donn ◽  
...  
Keyword(s):  
Community Composition ◽  
Plant Community ◽  
Plant Communities ◽  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
Temporal Dynamics ◽  
Arbuscular Mycorrhizal ◽  
Fungal Communities ◽  
Plant Responses ◽  
Rainfall Regimes

Climate models project overall a reduction in rainfall amounts and shifts in the timing of rainfall events in mid-latitudes and sub-tropical dry regions, which threatens the productivity and diversity of grasslands. Arbuscular mycorrhizal fungi may help plants to cope with expected changes but may also be impacted by changing rainfall, either via the direct effects of low soil moisture on survival and function or indirectly via changes in the plant community. In an Australian mesic grassland (former pasture) system, we characterised plant and arbuscular mycorrhizal (AM) fungal communities every six months for nearly four years to two altered rainfall regimes: i) ambient, ii) rainfall reduced by 50% relative to ambient over the entire year and iii) total summer rainfall exclusion. Using Illumina sequencing, we assessed the response of AM fungal communities sampled from contrasting rainfall treatments and evaluated whether variation in AM fungal communities was associated with variation in plant community richness and composition. We found that rainfall reduction influenced the fungal communities, with the nature of the response depending on the type of manipulation, but that consistent results were only observed after more than two years of rainfall manipulation. We observed significant co-associations between plant and AM fungal communities on multiple dates. Predictive co-correspondence analyses indicated more support for the hypothesis that fungal community composition influenced plant community composition than vice versa. However, we found no evidence that altered rainfall regimes were leading to distinct co-associations between plants and AM fungi. Overall, our results provide evidence that grassland plant communities are intricately tied to variation in AM fungal communities. However, in this system, plant responses to climate change may not be directly related to impacts of altered rainfall regimes on AM fungal communities. Our study shows that AM fungal communities respond to changes in rainfall but that this effect was not immediate. The AM fungal community may influence the composition of the plant community. However, our results suggest that plant responses to altered rainfall regimes at our site may not be resulting via changes in the AM fungal communities.

Do fungi and bacteria respond similar across a steep local pH gradient?

2021 ◽  
Author(s):  
Rasmus Kjoller ◽  
Carla Cruz-Paredes
Keyword(s):  
Community Composition ◽  
Soil Ph ◽  
Wood Ash ◽  
Ph Gradient ◽  
Fungal Communities ◽  
Ph Effects ◽  
Fungal Community Composition ◽  
Ph Gradients ◽  
Field Samples ◽  
Bacterial Richness

<p>Soil pH is consistently recorded as the single most important variable explaining bacterial richness and community composition locally as globally. Bacterial richness responds to soil pH in a bell-shaped pattern, highest in soils with near-neutral pH, while lower diversity is found in soil with pH >8 and <4.5. Also, community turnover is strongly determined by pH for bacteria. In contrast, pH effects on fungi is apparently less pronounced though also much less studied compared to bacteria. Still, pH appears to be a significant determinant for fungal communities but typically not the most important. Rarely are bacterial and fungal communities co-analyzed from the same field samples taken across pH gradients. Here we analyze the community responses of fungi and bacteria in parallel over an extreme pH gradient ranging from pH 4 to 8 established by applying strongly alkaline wood ash to replicated plots in a Picea abies plantation. Bacterial and fungal community composition were assessed by amplicon-based meta-barcoding. Bacterial richness were not significantly affected by pH, while fungal richness and a-diversity were stimulated with higher pH. We found that both, bacterial and fungal communities increasingly deviated from the untreated plots with increasing amount of wood ash though fungal communities were more resistant to changes than bacterial. Soil NH<sub>4</sub>, NO<sub>3</sub> and pH significantly correlated with the NMDS pattern for both bacterial and fungal communities. In the presentation we will discuss resistance versus sensitivity of different fungal functional guilds towards higher pH as well as the underlying factors explaining the community changes.</p>

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.

Elevational gradients of bryophyte diversity, life forms, and community assemblage in the southern Appalachian Mountains

2010 ◽  
Vol 40 (11) ◽  
pp. 2164-2174 ◽  
Author(s):  
Sarah E. Stehn ◽  
Christopher R. Webster ◽  
Janice M. Glime ◽  
Michael A. Jenkins
Keyword(s):  
Community Composition ◽  
Elevation Gradient ◽  
Light Availability ◽  
Basal Area ◽  
Life Forms ◽  
High Elevation ◽  
Canopy Openness ◽  
Fine Scale ◽  
Elevational Gradients ◽  
Community Assemblage

We investigated the influence of fine-scale elevational gradients and overstory disturbance on bryophyte distribution, diversity, and community composition. Bryophyte species cover and richness were sampled across 60 randomly selected plots within high-elevation spruce–fir ( Picea – Abies ) forests of Great Smoky Mountains National Park. Ordination and regression analyses revealed a fine-scale elevation gradient (700 m) in bryophyte community composition. Observed changes in bryophyte diversity and community composition were also associated with variation in deciduous basal area and thus litter composition, the prevalence of herbaceous plants, and the degree of canopy openness resulting from balsam woolly adelgid ( Adelges piceae Ratz.) infestation. Although overstory disturbances, such as those caused by the adelgid, create suitable substrate for bryophyte colonization, the corresponding increase in light availability and deciduous basal area may alter bryophyte diversity and community assemblages.

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