scholarly journals Root-associated endophytic fungal community composition and structure of three medicinal licorices in Xinjiang

2020 ◽  
Author(s):  
Hanli Dang ◽  
Zhongke Wang ◽  
Guifang Li ◽  
Yudi Mu ◽  
Xinhua Lv ◽  
...  
Keyword(s):  
Fungal Community ◽  
High Throughput Sequencing ◽  
Ammonium Nitrogen ◽  
Shannon Index ◽  
Glycyrrhiza Uralensis ◽  
Root Depth ◽  
Contributing Factors ◽  
Fungal Community Composition ◽  
Composition And Structure ◽  
Glycyrrhiza Inflata

Abstract The purpose of this study was to explore the diversity and composition of endophytic fungal community in the root of three medicinal licorices, and learn more about its biological characteristics by analyzing its interaction with soil and root factors. A total of 2,118,633 effective sequences and 1,063 effective operational taxonomic units (OTUs) with 97% identity were obtained by high-throughput sequencing among 27 samples. In this study, a total of 8 phyla and 140 genera were annotated, among them, the phylum Ascomycota and Basidiomycota, and the genera Fusarium, Paraphoma and Helminthosporium were significantly dominant in the 27 samples. Wilcoxon rank sum test showed that the Shannon index was significantly different distribution between Glycyrrhiza uralensis and Glycyrrhiza inflata, especially 0-20cm at the root depth, the Chao1 index in Glycyrrhiza inflate was significantly affected by root depth, and there were significant differences in beta diversity between Glycyrrhiza uralensis and Glycyrrhiza inflata. Distance-based redundancy analysis (db-RDA) showed that soil physicochemical properties (available potassium and ammonium nitrogen), and the root factor (liquiritin and water content) were the main contributing factors to the variations in the overall structure of endophytic fungal community in this study. This study provides useful information for formulating strategies to improve the quantity and quality of medicinal licorices.

scholarly journals Differences in the endophytic fungal community and effective ingredients in root of three Glycyrrhiza species in Xinjiang, China

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11047
Author(s):  
Hanli Dang ◽  
Tao Zhang ◽  
Zhongke Wang ◽  
Guifang Li ◽  
Wenqin Zhao ◽  
...  
Keyword(s):  
Physicochemical Properties ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Soil Samples ◽  
Glycyrrhiza Glabra ◽  
Glycyrrhiza Uralensis ◽  
Fungal Communities ◽  
Depth Range ◽  
Fungal Community Composition ◽  
Glycyrrhiza Inflata

Background Endophytic fungi influence the quality and quantity of the medicinal plant’s bioactive compounds through specific fungus-host interactions. Nevertheless, due to the paucity of information, the composition of endophytic fungal communities and the mechanism by which effective ingredients regulate endophytic fungal communities in roots remains unclear. Methods In this study, we collected root and soil samples (depth range: 0–20, 20–40, and 40–60 cm) of three Glycyrrhiza species (Glycyrrhiza uralensis, Glycyrrhiza inflata, and Glycyrrhiza glabra). Glycyrrhizic acid and liquiritin content were determined using high-performance liquid chromatography (HPLC), and total flavonoid content was determined using ultraviolet spectrophotometry. High-throughput sequencing technology was employed to explore the composition and diversity of the endophytic fungal community in different root segments of three Glycyrrhiza species. Furthermore, soil samples were subjected to physicochemical analyses. Results We observed that the liquiritin content was not affected by the root depth (0–20 cm, 20–40 cm, and 40–60 cm). Still, it was significantly affected by the Glycyrrhiza species (Glycyrrhiza uralensis, Glycyrrhiza inflata, Glycyrrhiza glabra) (P < 0.05). In Glycyrrhiza root, a total of eight phyla and 140 genera were annotated so far, out of which Ascomycota and Basidiomycota phyla, and the Fusarium, Paraphoma, and Helminthosporium genera were found to be significantly dominant. Spearman correlation analysis revealed that liquiritin content was accountable for the differences in the diversity of the endophytic fungal community. Furthermore, distance-based redundancy analysis (db-RDA) showed that physicochemical properties of the soil (available potassium and ammonium nitrogen) and the root factors (liquiritin and water content) were the main contributing factors for the variations in the overall structure of the endophytic fungal community. Our results showed that the effective ingredients of Glycyrrhiza root and physicochemical properties of the soil regulated the endophytic fungal community composition and medicinal licorice diversity.

scholarly journals Earthworms drastically change fungal and bacterial communities during vermicomposting of sewage sludge

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jorge Domínguez ◽  
Manuel Aira ◽  
Keith A. Crandall ◽  
Marcos Pérez-Losada
Keyword(s):  
Sewage Sludge ◽  
Community Composition ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Wastewater Treatment Plants ◽  
Agricultural Practices ◽  
Fungal Community Composition ◽  
Earthworm Casts ◽  
Composition And Structure ◽  
Sustainable Agricultural Practices

AbstractWastewater treatment plants produce hundreds of million tons of sewage sludge every year all over the world. Vermicomposting is well established worldwide and has been successful at processing sewage sludge, which can contribute to alleviate the severe environmental problems caused by its disposal. Here, we utilized 16S and ITS rRNA high-throughput sequencing to characterize bacterial and fungal community composition and structure during the gut- and cast-associated processes (GAP and CAP, respectively) of vermicomposting of sewage sludge. Bacterial and fungal communities of earthworm casts were mainly composed of microbial taxa not found in the sewage sludge; thus most of the bacterial (96%) and fungal (91%) taxa in the sewage sludge were eliminated during vermicomposting, mainly through the GAP. Upon completion of GAP and during CAP, modified microbial communities undergo a succession process leading to more diverse microbiotas than those found in sewage sludge. Consequently, bacterial and fungal community composition changed significantly during vermicomposting. Vermicomposting of sewage resulted in a stable and rich microbial community with potential biostimulant properties that may aid plant growth. Our results support the use of vermicompost derived from sewage sludge for sustainable agricultural practices, if heavy metals or other pollutants are under legislation limits or adequately treated.

scholarly journals Earthworms drastically change fungal and bacterial communities during vermicomposting of sewage sludge

2021 ◽  
Author(s):  
Jorge Domínguez ◽  
Manuel Aira ◽  
Keith A. Crandall ◽  
Marcos Pérez-Losada
Keyword(s):  
Sewage Sludge ◽  
Community Composition ◽  
Fungal Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Wastewater Treatment Plants ◽  
Agricultural Practices ◽  
Fungal Community Composition ◽  
Composition And Structure ◽  
Sustainable Agricultural Practices

Abstract Wastewater treatment plants produce hundreds of million tons of sewage sludge every year all over the world. Vermicomposting is well established worldwide and has been successful in processing sewage sludge, which can contribute to alleviate the severe environmental problems caused by their disposal. Here, we utilized 16S and ITS rRNA high-throughput sequencing to characterize bacterial and fungal community composition and structure during the gut- and cast-associated processes (GAP and CAP, respectively) of vermicomposting of sewage sludge. Bacterial and fungal community composition and diversity changed significantly during both vermicomposting processes. Most of the bacterial and fungal taxa in the sewage sludge were eliminated during vermicomposting, mainly through the GAP. Vermicomposting of sewage resulted in a stable and rich microbial community with potential biostimulant properties that may aid plant growth. Our results support the use of vermicompost derived from sewage sludge for sustainable agricultural practices.

scholarly journals Global diversity and biogeography of the Zostera marina mycobiome

2021 ◽  
Author(s):  
Cassandra L. Ettinger ◽  
Laura E. Vann ◽  
Jonathan A. Eisen
Keyword(s):  
Fungal Community ◽  
Community Assembly ◽  
Zostera Marina ◽  
High Throughput Sequencing ◽  
Marine Fungi ◽  
Marine Ecosystem ◽  
Fungal Community Composition ◽  
Functional Roles ◽  
Functional Guilds ◽  
The Many

Seagrasses are marine flowering plants that provide critical ecosystem services in coastal environments worldwide. Marine fungi are often overlooked in microbiome and seagrass studies, despite terrestrial fungi having critical functional roles as decomposers, pathogens or endophytes in global ecosystems. Here we characterize the distribution of fungi associated with the seagrass, Zostera marina, using leaves, roots, and rhizosphere sediment from 16 locations across its full biogeographic range. Using high throughput sequencing of the ribosomal internal transcribed spacer (ITS) region and 18S ribosomal RNA gene, we first measured fungal community composition and diversity. We then tested hypotheses of neutral community assembly theory and the degree to which deviations suggested amplicon sequence variants (ASVs) were plant-selected or dispersal-limited. Finally, we identified a core mycobiome and investigated the global distribution of differentially abundant ASVs. We found that the fungal community is significantly different between sites and that the leaf mycobiome follows a weak, but significant pattern of distance decay in the Pacific Ocean. Generally, there was evidence for both deterministic and stochastic factors contributing to community assembly of the mycobiome, with most taxa assembling through stochastic processes. The Z. marina core leaf and root mycobiomes were dominated by unclassified Sordariomycetes spp., unclassified Chytridiomycota lineages (including Lobulomycetaceae spp.), unclassified Capnodiales spp. and Saccharomyces sp. It is clear from the many unclassified fungal ASVs and fungal functional guilds, that knowledge of marine fungi is still rudimentary. Further studies characterizing seagrass-associated fungi are needed to understand the roles of these microorganisms generally and when associated with seagrasses. Importance Fungi have important functional roles when associated with land plants, yet very little is known about the roles of fungi associated with marine plants, like seagrasses. In this study, we report the results of a global effort to characterize the fungi associated with the seagrass, Zostera marina, across its full biogeographic range. Although we defined a putative global core fungal community, it is apparent from the many fungal sequences and predicted functional guilds that had no matches to existing databases, that general knowledge of seagrass-associated fungi and marine fungi generally is lacking. This work serves as an important foundational step towards future work investigating the functional ramifications of fungi in the marine ecosystem.

scholarly journals Dominant Tree Species and Soil Type Affect the Fungal Community Structure in a Boreal Peatland Forest

2016 ◽  
Vol 82 (9) ◽  
pp. 2632-2643 ◽  
Author(s):  
Hui Sun ◽  
Eeva Terhonen ◽  
Andriy Kovalchuk ◽  
Hanna Tuovila ◽  
Hongxin Chen ◽  
...  
Keyword(s):  
Community Structure ◽  
Community Composition ◽  
High Throughput ◽  
Fungal Community ◽  
Tree Species ◽  
High Throughput Sequencing ◽  
Soil Layer ◽  
Fungal Community Composition ◽  
Content Type ◽  
Boreal Peatlands

ABSTRACTBoreal peatlands play a crucial role in global carbon cycling, acting as an important carbon reservoir. However, little information is available on how peatland microbial communities are influenced by natural variability or human-induced disturbances. In this study, we have investigated the fungal diversity and community structure of both the organic soil layer and buried wood in boreal forest soils using high-throughput sequencing of the internal transcribed spacer (ITS) region. We have also compared the fungal communities during the primary colonization of wood with those of the surrounding soils. A permutational multivariate analysis of variance (PERMANOVA) confirmed that the community composition significantly differed between soil types (P< 0.001) and tree species (P< 0.001). The distance-based linear models analysis showed that environmental variables were significantly correlated with community structure (P< 0.04). The availability of soil nutrients (Ca [P= 0.002], Fe [P= 0.003], and P [P= 0.003]) within the site was an important factor in the fungal community composition. The species richness in wood was significantly lower than in the corresponding soil (P< 0.004). The results of the molecular identification were supplemented by fruiting body surveys. Seven of the genera ofAgaricomycotinaidentified in our surveys were among the top 20 genera observed in pyrosequencing data. Our study is the first, to our knowledge, fungal high-throughput next-generation sequencing study performed on peatlands; it further provides a baseline for the investigation of the dynamics of the fungal community in the boreal peatlands.

scholarly journals Temporal and Cultivar-Specific Effects on Potato Root- and Rhizosphere Fungal Diversity

2020 ◽  
Author(s):  
Kaire Loit ◽  
Liina Soonvald ◽  
Alar Astover ◽  
Eve Runno-Paurson ◽  
Maarja Öpik ◽  
...  
Keyword(s):  
Community Composition ◽  
Fungal Community ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Solanum Tuberosum L ◽  
Potato Cultivar ◽  
Substantial Effect ◽  
Sampling Time ◽  
Fungal Communities ◽  
Fungal Community Composition

The rhizosphere fungal community can play an important role in determining plant growth and health. In this study, using high-throughput sequencing, we investigated the fungal diversity and community composition in the roots and rhizosphere soil of 21 potato (Solanum tuberosum L.) cultivars. The samples were collected at three different sampling points. Furthermore, we assessed the differences in both diversity and composition of pathogen and saprotroph communities. In soil and roots, the fungal richness and relative abundance of pathogens and saprotrophs were mainly affected by sampling time. However, root fungal communities were also significantly affected by cultivar. The most substantial effect of cultivar was on root pathogen diversity. Moreover, the occurrence of most pathogens strongly varied among cultivars. Soil fungal community composition was primarily determined by sampling time; whereas in roots, the primary determinant was cultivar. Our results demonstrate changes in fungal communities over the potato growing season, as well as highlight the importance of potato cultivar on root fungal communities, and emphasise their importance in plant breeding.

scholarly journals Drivers of Ectomycorrhizal Fungal Community Structure Associated with Pinus sylvestris var. mongolica Differ at Regional vs. Local Spatial Scales in Northern China

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 323
Author(s):  
Mishan Guo ◽  
Guanglei Gao ◽  
Guodong Ding ◽  
Ying Zhang
Keyword(s):  
Community Composition ◽  
Fungal Community ◽  
Phosphorus Content ◽  
Regional Scale ◽  
Northern China ◽  
Local Scale ◽  
Stand Age ◽  
Organic Carbon Content ◽  
Fungal Community Composition ◽  
Composition And Structure

Pinus sylvestris var. mongolica, a widely planted tree species, is facing long-lasting, unresolved degradation in desertified Northern China. Ectomycorrhizal fungi (EMF) are closely related to the stand status, because they substantially participate in ecological processes of terrestrial forest ecosystems. EMF may be key to solving the introduction recession. Therefore, we performed DNA sequencing of P. sylvestris root samples from plantations and natural forests as control to characterize the EMF from semi-arid and dry sub-humid regions, using ITS Illumina sequencing and conventional soil physicochemical index determination. The results indicated that (1) the dominant EMF genera were Suillus, Rhizopogon, and Wilcoxina in the Hulunbuir, Mu Us, and Horqin Sandy Lands, respectively. Their dominance retained with stand ageing. (2) Plantation EM fungal diversity differs significantly among the three sandy lands and was significantly lower than in natural forest. The diversity varied with stand age, showing distinct trends at the local scale. (3) At the regional scale, the mean annual sunshine times and the soil organic carbon content affect EMF diversity. The community composition and structure were more characterized by temperature and precipitation. At the local scale, besides the soil organic carbon content, the EM fungal community composition and structure were correlated with total nitrogen and phosphorus content (Hulunbuir), the total phosphorus content (Mu Us), and the pH and total soil porosity (Horqin). The EM fungal community composition and structure have the obvious geographical distribution variation; they were strongly correlated with the meteorological elements and soil nutrients at the regional scale. At the local scale, they were jointly driven by stand age and soil properties. This improved information contributes to increasing the understanding of the interaction between EMF and forest ecosystems and guides sustainable forest management of degraded P. sylvestris plantations.

Rhizospheric soil fungal community patterns of Duchesnea indica in response to altitude gradient in Yunnan, southwest China

2020 ◽  
Vol 66 (5) ◽  
pp. 359-367
Author(s):  
Arslan Jamil ◽  
Jun-Yu Yang ◽  
Dai-Fa Su ◽  
Jiang-Yun Tong ◽  
Shan-Yan Chen ◽  
...  
Keyword(s):  
Community Composition ◽  
Fungal Community ◽  
Altitudinal Gradient ◽  
Rhizosphere Soil ◽  
Fungal Community Composition ◽  
Altitude Gradient ◽  
Community Patterns ◽  
Composition And Structure ◽  
Soil Fungal Community ◽  
Duchesnea Indica

The magnitude of the impact of altitude gradient on microbial community and diversity has been studied in recent decades. Whereas bacteria have been the focus of most studies, fungi have been given relatively less attention. As a vital part of the macro- and microscopic ecosystem, rhizosphere fungi play a key role in organic matter decomposition and relative abundance of plant species and have an impact on plant growth and development. Using Duchesnea indica as the host plant, we examined the rhizosphere soil fungal community patterns across the altitude gradient in 15 sites of Yunnan province by sequencing the fungal ITS2 region with the Illumina MiSeq platform. We determined the fungal community composition and structure. We found that, surprisingly, rhizosphere soil fungal diversity of D. indica increased with altitudinal gradient. There was a slight difference in diversity between samples from high- and medium-altitude sites, with medium-altitude sites having the greater diversity. Furthermore, the rhizosphere soil fungal community composition and structure kept changing along the altitudinal gradient. Taxonomic results showed that the extent of phylum diversity was greatest at high-altitude sites, with Ascomycota, Basidiomycota, Zygomycota, and Glomeromycota as the most dominant fungal phyla.

Plant traits and taxonomy drive host associations in tropical phyllosphere fungal communities

Botany ◽  
2014 ◽  
Vol 92 (4) ◽  
pp. 303-311 ◽  
Author(s):  
Steven W. Kembel ◽  
Rebecca C. Mueller
Keyword(s):  
Host Plant ◽  
Tropical Forests ◽  
Fungal Community ◽  
Tree Species ◽  
High Throughput Sequencing ◽  
Plant Traits ◽  
Fungal Species ◽  
Fungal Communities ◽  
Fungal Community Composition ◽  
Individual Tree

The aerial surface of plants, known as the phyllosphere, represents a widespread and diverse habitat for microbes, but the fungal communities colonizing the surface of leaves are not well characterized, and how these communities are assembled on hosts is unknown. We used high-throughput sequencing of fungal communities on the leaves of 51 tree species in a lowland tropical rainforest in Panama to examine the influence of host plant taxonomy and traits on the fungi colonizing the phyllosphere. Fungal communities on leaves were dominated by the phyla Ascomycota (79% of all sequences), Basidiomycota (11%), and Chytridiomycota (5%). Host plant taxonomic identity explained more than half of the variation in fungal community composition across trees, and numerous host functional traits related to leaf morphology, leaf chemistry, and plant growth and mortality were significantly associated with fungal community structure. Differences in fungal biodiversity among hosts suggest that individual tree species support unique fungal communities and that diverse tropical forests also support a large number of fungal species. Similarities between phyllosphere and decomposer communities suggest that fungi inhabiting living leaves may have significant roles in ecosystem functioning in tropical forests.

scholarly journals Differential mechanisms underlying responses of soil bacterial and fungal communities to nitrogen and phosphorus inputs in a subtropical forest

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7631 ◽  
Author(s):  
Yong Li ◽  
Dashuan Tian ◽  
Jinsong Wang ◽  
Shuli Niu ◽  
Jing Tian ◽  
...  
Keyword(s):  
Species Richness ◽  
Bacterial Community ◽  
Community Composition ◽  
Fungal Community ◽  
Bacterial Community Composition ◽  
Shannon Index ◽  
Subtropical Forest ◽  
Fungal Community Composition ◽  
Soil Bacterial ◽  
P Addition

Atmospheric nitrogen (N) deposition and phosphorus (P) addition both can change soil bacterial and fungal community structure with a consequent impact on ecosystem functions. However, which factor plays an important role in regulating responses of bacterial and fungal community to N and P enrichments remains unclear. We conducted a manipulative experiment to simulate N and P inputs (10 g N · m−2 · yr−1 NH4NO3 or 10 g P · m−2 · yr−1 NaH2PO4) and compared their effects on soil bacterial and fungal species richness and community composition. The results showed that the addition of N significantly increased NH4+ and Al3+ by 99.6% and 57.4%, respectively, and consequently led to a decline in soil pH from 4.18 to 3.75 after a 5-year treatment. P addition increased Al3+ and available P by 27.0% and 10-fold, respectively, but had no effect on soil pH. N addition significantly decreased bacterial species richness and Shannon index and resulted in a substantial shift of bacterial community composition, whereas P addition did not. Neither N nor P addition changed fungal species richness, Shannon index, and fungal community composition. A structural equation model showed that the shift in bacterial community composition was related to an increase in soil acid cations. The principal component scores of soil nutrients showed a significantly positive relationship with fungal community composition. Our results suggest that N and P additions affect soil bacterial and fungal communities in different ways in subtropical forest. These findings highlight how the diversity of microbial communities of subtropical forest soil will depend on future scenarios of anthropogenic N deposition and P enrichment, with a particular sensitivity of bacterial community to N addition.

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