scholarly journals Stochastic and deterministic drivers of seasonal variation of fungal community in tobacco field soil

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6962
Author(s):  
Xing Li ◽  
Tianming Li ◽  
Delong Meng ◽  
Tianbo Liu ◽  
Yongjun Liu ◽  
...  
Keyword(s):  
Seasonal Variation ◽  
Fungal Community ◽  
Community Assembly ◽  
High Throughput Sequencing ◽  
Null Model ◽  
Dispersal Limitation ◽  
Community Diversity ◽  
Ecological Processes ◽  
Soil Fungal Community ◽  
Community Variation

Background The soil fungal community plays an important role in global carbon cycling and shows obvious seasonal variations, however, drivers, particularly stochastic drivers, of the seasonal variation in the fungal community have never been addressed in sufficient detail. Methods We investigated the soil fungal community variation between summer growing (SG) and winter fallow (WF) stage, through high throughput sequencing of internal transcribed spacer (ITS) amplicons. Subsequently, we assessed the contribution of different ecological processes to community assembly using null-model-based statistical framework. Results The results showed that the fungal community diversity decreased significantly after tobacco cropping in the SG stage and the composition showed a clear turnover between the WF and SG stages. The variation in community composition was largely attributable to the presence of a small portion of Dothideomycetes in the WF stage that dominated the soil fungal community in the SG stage. The organic matter, temperature, and water content were the main deterministic factors that regulated the fungal community; these factors explained 34.02% of the fungal community variation. Together with the result that the fungal community was mainly assembled by the dispersal process, our results suggested that the stochastic factors played important roles in driving the seasonal variation of fungal community. The dispersal limitation dominated the fungal community assembly during the WF stage when homogenizing dispersal was the main assembly process of the fungal community in the SG stage. Thus, we proposed that the dispersal processes are important drivers for seasonal variation of fungal community in tobacco planted soil.

scholarly journals Immediate and legacy effects of snow exclusion on soil fungal diversity and community composition

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Li Zhang ◽  
Yuzhi Ren ◽  
Kaijun Yang ◽  
Zhijie Li ◽  
Bo Tan ◽  
...  
Keyword(s):  
Snow Cover ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Community Diversity ◽  
Fungal Communities ◽  
Ecosystem Functions ◽  
Legacy Effects ◽  
Soil Microbial ◽  
Soil Fungal Community ◽  
Tibetan Forest

Abstract Background Soil fungi play crucial roles in ecosystem functions. However, how snow cover change associated with winter warming affects soil fungal communities remains unclear in the Tibetan forest. Methods We conducted a snow manipulation experiment to explore immediate and legacy effects of snow exclusion on soil fungal community diversity and composition in a spruce forest on the eastern Tibetan Plateau. Soil fungal communities were performed by the high throughput sequencing of gene-fragments. Results Ascomycota and Basidiomycota were the two dominant fungal phyla and Archaeorhizomyces, Aspergillus and Amanita were the three most common genera across seasons and snow manipulations. Snow exclusion did not affect the diversity and structure of soil fungal community in both snow-covered and snow-free seasons. However, the relative abundance of some fungal communities was different among seasons. Soil fungal groups were correlated with environmental factors (i.e., temperature and moisture) and soil biochemical variables (i.e., ammonium and enzyme). Conclusions These results suggest that the season-driven variations had stronger impacts on soil fungal community than short-term snow cover change. Such findings may have important implications for soil microbial processes in Tibetan forests experiencing significant decreases in snowfall.

scholarly journals Immediate and legacy effects of snow exclusion on soil fungal diversity and community composition

2020 ◽  
Author(s):  
Zhenfeng Xu ◽  
Li Zhang ◽  
Yuzhi Ren ◽  
Kaijun Yang ◽  
Zhijie Li ◽  
...  
Keyword(s):  
Snow Cover ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Community Diversity ◽  
Fungal Communities ◽  
Ecosystem Functions ◽  
Legacy Effects ◽  
Soil Microbial ◽  
Soil Fungal Community ◽  
Tibetan Forest

Abstract Background: Soil fungi play crucial roles in ecosystem functions. However, how snow cover change associated with winter warming affects soil fungal communities remains unclear in the Tibetan forest.Methods: We conducted a snow manipulation experiment to explore immediate and legacy effects of snow exclusion on soil fungal community diversity and composition in a spruce forest on the eastern Tibetan Plateau. Soil fungal communities were performed by the high throughput sequencing of gene-fragments.Results: Ascomycota and Basidiomycota were the two dominant fungal phyla and Archaeorhizomyces, Aspergillus and Amanita were the three most common genera across seasons and snow manipulations. Snow exclusion did not affect the diversity and structure of soil fungal community in both snow-covered and snow-free seasons. However, the relative abundance of some fungal communities was different among seasons. Soil fungal groups were correlated with environmental factors (i.e., temperature and moisture) and soil biochemical variables (i.e., ammonium and enzyme).Conclusions: These results suggest that the season-driven variations had stronger impacts on soil fungal community than short-term snow cover change. Such findings may have important implications for soil microbial processes in Tibetan forests experiencing significant decreases in snowfall.

scholarly journals Immediate and legacy effects of snow exclusion on soil fungal diversity and community composition

2020 ◽  
Author(s):  
Zhenfeng Xu ◽  
Li Zhang ◽  
Yuzhi Ren ◽  
Kaijun Yang ◽  
Zhijie Li ◽  
...  
Keyword(s):  
Snow Cover ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Community Diversity ◽  
Fungal Communities ◽  
Ecosystem Functions ◽  
Legacy Effects ◽  
Soil Dna ◽  
Soil Microbial ◽  
Soil Fungal Community

Abstract Background: Soil fungi play crucial roles in ecosystem functions. However, how snow cover change associated with winter warming affects soil fungal communities remains unclear in the Tibetan forest.Methods: We conducted a snow manipulation experiment to explore immediate and legacy effects of snow exclusion on soil fungal community diversity and composition in a spruce forest on the eastern Tibetan Plateau. SoilThe fungal communities were performed by the high throughput sequencing of gene-fragments amplified from forest soil DNA.Results: We found that the Ascomycota and Basidiomycota were the two dominant fungal phyla and Archaeorhizomyces, Aspergillus and Amanita were the three most common genera across seasons and snow manipulations. Snow exclusion did not affect the diversity and structure of soil fungal community in both snow-covered and snow-free seasons. However, the relative abundance of some fungal communities was different among seasons. Soil fungal groups were correlated with environmental factors (i.e., temperature and moisture) and soil biochemical variables (i.e., ammonium and enzyme).Conclusions: These results suggest that the season-driven variations had stronger impacts on soil fungal community than short-term snow cover change. Such findings may have important implications for soil microbial processes in Tibetan forests experiencing significant decreases in snowfall.

scholarly journals Different ecological processes drive the assembly of dominant and rare root-associated bacteria in a promiscuous legume

2020 ◽  
Author(s):  
Josep Ramoneda ◽  
Jaco Le Roux ◽  
Emmanuel Frossard ◽  
Beat Frey ◽  
Hannes Andres Gamper
Keyword(s):  
Community Assembly ◽  
Root Nodule ◽  
Regional Scale ◽  
Dispersal Limitation ◽  
System Size ◽  
Community Diversity ◽  
Plant Performance ◽  
Soil Conditions ◽  
Ecological Processes ◽  
Rhizobial Diversity

AbstractUnderstanding how plant-associated microbial communities assemble and the roles they play in plant performance are major goals in microbial ecology. For nitrogen-fixing rhizobia, assemblages are mostly determined by filtering by the host as well as abiotic soil conditions. However, for legumes adapted to highly variable environments and nutrient-poor soils, filtering out rhizobial partners may not be an effective strategy to ensure symbiotic benefits. As a consequence, this can lead to net increases in rhizobial diversity driven by stochastic (neutral) assembly processes. Here, we addressed whether symbiotic promiscuity of rooibos (Aspalathus linearis Burm. Dahlgren), reflects increases in rhizobial diversity that are independent of the environmental conditions, following a neutral assembly. We performed a common garden experiment to assess whether root system size and location- and habitat-specific rhizobial propagule pools of rooibos affected rhizobial community diversity and composition. We found a dominance of drift in driving taxonomic turnover in the root nodule communities, but operating at different scales in the dominant Mesorhizobium symbionts and the rest of bacterial taxa. Specifically, drift triggered differentiation between the core rhizobial symbionts of rooibos due to dispersal limitation on a regional scale, whereas it dominated the assembly of non-dominant rhizobial taxa at the root level. This suggests the existence of a significant neutral component in rhizobial community assembly when selectivity by the host plant is low. We conclude that in this promiscuous legume neutral processes govern bacterial community root nodule community assembly, but that these operate at different scales in dominant and rare rhizobial symbionts of the plant.

scholarly journals Immediate and Legacy Effects of Snow Exclusion on Soil Fungal Diversity and Community Composition

2020 ◽  
Author(s):  
Li Zhang ◽  
Yuzhi Ren ◽  
Kaijun Yang ◽  
Zhijie Li ◽  
Bo Tan ◽  
...  
Keyword(s):  
Snow Cover ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Community Diversity ◽  
Fungal Communities ◽  
Ecosystem Functions ◽  
Legacy Effects ◽  
Soil Dna ◽  
Soil Microbial ◽  
Soil Fungal Community

Abstract Background: Soil fungi play crucial roles in ecosystem functions. However, how snow cover change associated with winter warming affects soil fungal communities remains unclear in the Tibetan forest.Methods: We conducted a snow manipulation experiment to explore immediate and legacy effects of snow exclusion on soil fungal community diversity and composition in a spruce forest on the eastern Tibetan Plateau. The fungal communities were performed by the high throughput sequencing of gene-fragments amplified from forest soil DNA.Results: We found that the Ascomycota and Basidiomycota were the two dominant fungal phyla and Archaeorhizomyces, Aspergillus and Amanita were the three most common genera across seasons and snow manipulations. Snow exclusion did not affect the diversity and structure of soil fungal community in both snow-covered and snow-free seasons. However, the relative abundance of some fungal communities was different among seasons. Soil fungal groups were correlated with environmental factors (i.e., temperature and moisture) and soil biochemical variables (i.e., ammonium and enzyme).Conclusions: These results suggest that the season-driven variations had stronger impacts on soil fungal community than short-term snow cover change. Such findings may have important implications for soil microbial processes in Tibetan forests experiencing significant decreases in snowfall.

Soil fungal community variation by large-scale reclamation in Sanjiang plain, China

2017 ◽  
Vol 67 (10) ◽  
pp. 679-689 ◽  
Author(s):  
Fei Xu ◽  
Tijiu Cai ◽  
Xue Yang ◽  
Wenzhi Sui
Keyword(s):  
Fungal Community ◽  
Large Scale ◽  
Sanjiang Plain ◽  
Soil Fungal Community ◽  
Community Variation

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 Microbial diversity in raw milk and Sayram Ketteki from southern of Xinjiang, China

2021 ◽  
Author(s):  
Dongla Gao ◽  
Weihua Wang ◽  
Zhanjiang Han ◽  
Qian Xi ◽  
Ruicheng Guo ◽  
...  
Keyword(s):  
High Throughput ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Principal Component ◽  
Raw Milk ◽  
Fermented Milk ◽  
Community Diversity ◽  
Sampling Location ◽  
Fungal Community Structure ◽  
Microbial Resources

Raw milk and fermented milk are rich in microbial resources, which are essential for the formation of texture, flavor and taste. In order to gain a deeper knowledge of the bacterial and fungal community diversity in local raw milk and home-made yogurts from Sayram town, Baicheng county, Akesu area, southern of Xinjiang, China,30 raw milk and 30 home-made yogurt samples were collected and experiment of high-throughput sequencing was implemented.The results of experiments revealed the species of fungi in raw milk was the most, and the species of bacteria in fermented milk was the least.Based on principal component analysis (PCA), it was found that the bacterial and fungal community structure differed in samples from two types of dairy products.And the presence of 15 bacterial and 12 fungal phyla, comprising 218 bacterial and 495 fungal genera respectively, among all samples. Firmicutes and Ascomycota,Lactobacillus and Candida were the predominant phyla and genera of bacteria and fungi, respectively. The results indicated that the microbial community of raw milk differs from home-made yogurts due to sampling location and manufacturing process. The study suggested that high-throughput sequencing could provide a better understanding of microbiological diversity as well as lay a theoretical foundation for selecting beneficial microbial resources from this natural yogurt.

Assessing the Performance and the Microbial Dynamics of Co-composting System Using Recycled Cow Manure and Bedding Material Waste 

2021 ◽  
Author(s):  
Haiyan Duan ◽  
Minghua Ji ◽  
Ai Chen ◽  
Shiqiu Xie ◽  
Junsong Sun ◽  
...  
Keyword(s):  
Microbial Community ◽  
Fungal Community ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Agricultural Wastes ◽  
Community Diversity ◽  
Bedding Material ◽  
Cow Manure ◽  
Community Succession ◽  
Composting Systems

Abstract Co-composting of recycled cow manure and waste bedding material has been used to convert both agricultural wastes to biofertilizers. This study explored the succession of microbial community, metabolic function and substances conversion capacities during 60 days’ co-composting using high throughput sequencing technology. The study revealed that co-composting of cow manure and bedding material waste at a ratio of 1.32 (CM+B) had the highest efficiency among four treatments. The bacterial and fungal community diversity changed significantly during the co-composting of CM+B group, and the major phyla included Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria and Ascomycota. PICRUSt and FUNGuild analysis showed that carbohydrate, lipid metabolism and especially nitrogen fixation were enhanced in the thermophilic phase, while animal and plant pathogens were not detected after the co-composting. Wood saprotrophs became the dominant fungal group (89.1%) in the maturation phase. Canonical correlation analysis (CCA) and redundancy analysis (RDA) confirmed that temperature influenced bacterial community succession more than it influenced fungal community succession. Ruminiclostridium had a significantly positive relationship with temperature (p_value < 0.05), while pH and C/N had significant effect on the fungal (p_value < 0.05), and Penicillium and Mortierella were significantly related to moisture (p_value < 0.05). This work describes an efficient methodology to deal with co-composting systems that had been successfully applied in agricultural wastes treatment, enabling further understanding in mechanisms underlying the substance conversion and the involved microbial community succession in sophisticated composting system.

scholarly journals Detection of viable and total fungal community in zaopei of Chinese strong-flavor baijiu using PMA combined with qPCR and HTS based on ITS2 region

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Huanming Liu ◽  
Guangxun Tan ◽  
Qitong Chen ◽  
Weiwei Dong ◽  
Ping Chen ◽  
...  
Keyword(s):  
Fungal Community ◽  
High Throughput Sequencing ◽  
Raw Materials ◽  
Community Diversity ◽  
Its2 Region ◽  
Brewing Process ◽  
Total Fungi ◽  
Fermented Grains ◽  
Better Than

Abstract Background Chinese strong-flavor baijiu (CSFB), one of the three major baijiu types, is the most popular baijiu type among consumers in China. A variety of microbes are involved in metabolizing raw materials to produce ethanol and flavor substances during fermentation, which fundamentally determined the quality of baijiu. It is of great importance to study microbial community of fermented grains (zaopei) during baijiu brewing process for improving its quality. In this study, we firstly used propidium monoazide (PMA) to treat zaopei samples from 5-year pit and 20-year pit for removing the interference of non-viable fungi, and analyzed the diversity of total fungi and viable fungi by quantitative PCR (qPCR) and high-throughput sequencing (HTS) based on ITS2 gene. Results The results showed that total fungi and viable fungi displayed no significant differences at OTU, phylum, or genus levels during fermentation within two kinds of pits. A total of 6 phyla, 19 classes, and 118 genera in fungi were found based on OTUs annotation in zaopei samples from 5-year pit and 20-year pit. Besides, non-viable fungi had little effect on the fungal community diversity during the fermentation cycle. It was found that the most dominant viable fungi belonged to Saccharomyces, Kazachstania, Naumovozyma, and Trichosporon, and Naumovozyma was firstly detected in zaopei samples of CSFB. Moreover, based on the variation of flavor substances in zaopei samples, the quality of CSFB produced from older pit was better than that produced from younger pit. Conclusion The non-viable fungi had little effect on the fungal diversity, structure, and relative abundance in zaopei samples of CSFB, and Naumovozyma was firstly detected in zaopei samples of CSFB. Our findings can be applied as guidance for improving the quality and stability of CSFB.

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