scholarly journals Dispersal Limitation Plays Stronger Role in the Community Assembly of Fungi Relative to Bacteria in Rhizosphere Across the Arable Area of Medicinal Plant

2021 ◽  
Vol 12 ◽  
Author(s):  
Guozhuang Zhang ◽  
Guangfei Wei ◽  
Fugang Wei ◽  
Zhongjian Chen ◽  
Mingjun He ◽  
...  
Keyword(s):  
Community Assembly ◽  
Large Scale ◽  
Panax Notoginseng ◽  
Dispersal Limitation ◽  
Fungal Communities ◽  
Ecosystem Functions ◽  
Biogeographic Patterns ◽  
Ecological Patterns ◽  
Bacteria And Fungi ◽  
Occurrence Patterns

Understanding the ecological patterns of rhizosphere microbial communities is critical for propelling sustainable agriculture and managing ecosystem functions by exploiting microorganisms. However, this knowledge is still unclear, especially under host-associated large-scale and regarding the comparison between bacteria and fungi. We examined community assembly processes and community characters including environmental thresholds and co-occurrence patterns across the cultivatable area of Panax notoginseng for bacteria and fungi. Both are vital members of the rhizosphere but differ considerably in their life history and dispersal potentiality. Edaphic factors drove the parallel variations of bacterial and fungal communities. Although bacterial and fungal communities exhibited similar biogeographic patterns, the assembly of fungi was more driven by dispersal limitation than selection compared with bacteria. This finding supported the ‘size-dispersal’ hypothesis. pH and total nitrogen respectively mediated the relative importance of deterministic and stochastic processes in shaping bacterial and fungal communities. In addition, fungal communities exhibited potentially broader environmental thresholds and more modular co-occurrence patterns than bacteria (bacteria: 0.67; fungi: 0.78). These results emphasized the importance of dispersal limitation in structuring rhizosphere microbiota and shaping community features of ecologically distinct microorganisms. This study provides insights into the improved prediction and management of the key functions of rhizosphere microbiota.

Distinct large-scale biogeographic patterns of fungal communities in bulk soil and soybean rhizosphere in China

2018 ◽  
Vol 644 ◽  
pp. 791-800 ◽  
Author(s):  
Jun Zhang ◽  
Baogang Zhang ◽  
Yao Liu ◽  
Yanqing Guo ◽  
Peng Shi ◽  
...  
Keyword(s):  
Large Scale ◽  
Fungal Communities ◽  
Bulk Soil ◽  
Biogeographic Patterns

Community Structure and Co-Occurrence Network Analysis of Bacteria and Fungi in Wheat Fields vs Fruit Orchards

2021 ◽  
Author(s):  
Xinyu Cui ◽  
Huan He ◽  
Fengxiao Zhu ◽  
Xiaobo Liu ◽  
You Ma ◽  
...  
Keyword(s):  
Community Structure ◽  
Amplicon Sequencing ◽  
Yangtze River Delta ◽  
Vital Role ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Network Analyses ◽  
Planting Methods ◽  
Bacteria And Fungi ◽  
Occurrence Patterns

Abstract Soil microorganisms play a vital role in biogeochemical processes and nutrient turnover in agricultural ecosystems. However, the information on how the structure and co-occurrence patterns of microbial communities respond to the change of planting methods is still limited. In this study, a total of 34 soil samples were collected from 17 different fields of two planting types (wheat and orchards) along the Taige Canal in Yangtze River Delta. The distribution and diversity of bacterial and fungal communities in soil were determined using amplicon sequencing targeting the 16S rRNA gene and ITS gene, respectively. The dominated bacteria were Proteobacteria, Acidobacteriota, Actinobacteriota, Chloroflexi, Bacteroidota, and Firmicutes. The relative abundance of Actinobacteriota and Firmicutes was higher in the orchards, while Chloroflexi and Nitrospirota were more abundant in wheat fields. Ascomycota, Mortierellomycota, and Basidiomycota were the predominant fungi in both types of soils. The diversity of bacterial and fungal communities was greater in the wheat fields than in the orchards. The statistical analyses showed that pH was the main factor shaping the community structure. Moreover, high co-occurrence patterns of bacteria and fungi were confirmed in both wheat fields and orchards. Network analyses showed that both the wheat fields and orchards occurred modular structure, which mainly contained nodes of Acidobacteriota, Chloroflexi, Gemmatimonadota, Nitrospirota and Ascomycota. In summary, our work showed the co-occurrence network and the convergence/divergence of microbial community structure in wheat fields and orchards, giving a comprehensive understanding of the microbe-microbe interaction during planting methods changes.

scholarly journals Assembly processes lead to divergent soil fungal communities within and among twelve forest ecosystems along a latitudinal gradient

2021 ◽  
Author(s):  
Yong Zheng ◽  
Liang Chen ◽  
Niu-Niu Ji ◽  
Yong-Long Wang ◽  
Cheng Gao ◽  
...  
Keyword(s):  
Ectomycorrhizal Fungi ◽  
Fungal Community ◽  
Community Assembly ◽  
Large Scale ◽  
Spatial Scales ◽  
Geographic Distance ◽  
Latitudinal Gradients ◽  
Fungal Communities ◽  
Environmental Drivers ◽  
Natural Forests

Latitudinal gradients provide opportunities to better understand soil fungal community assembly and its relationship with vegetation, climate, soil and ecosystem function. We quantified the relative importance of stochastic and deterministic processes in structuring soil fungal communities using patterns of community dissimilarity observed within and between twelve natural forests. The results revealed that whole fungal communities and communities of arbuscular and ectomycorrhizal fungi consistently exhibited divergent patterns but with less divergence for ectomycorrhizal fungi at most sites. Within those forests, no clear relationships were observed between the degree of divergence within fungal and plant communities. When comparing communities at larger spatial scales, among the twelve forests, we observed distinct separation in all three fungal groups among tropical, subtropical and temperate biomes. Soil fungal β-diversity patterns between forests were greater when comparing forests exhibiting high habitat turnover, with these patterns being driven to a greater extent in each fungal group by temperature, soil pH, soil carbon and plant community composition than by geographic distance. Taken together, although large-scale community turnover could be attributed to specific environmental drivers, strong divergence during community assembly in forest soils at local scales limits the predictability of fungal community assembly outcomes.

scholarly journals Vertical stratification of microbial communities in woody plants

2021 ◽  
Author(s):  
Mohammad Bahram ◽  
Kati Kings ◽  
Mari Pent ◽  
Sergei Polme ◽  
Daniyal Gohar ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Community Assembly ◽  
Boreal Forests ◽  
Fungal Endophytes ◽  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Distribution Patterns ◽  
Fungal Communities ◽  
Spatial Distance ◽  
Related Factors

Bacterial and fungal endophytes form diverse communities and contribute to the performance and health of their host plants. Recent evidence suggests that both host related factors and environmental conditions determine the community structure of plant endophytes. Yet, we know little about their distribution patterns, and underlying community assembly mechanisms across plant compartments. Here we analysed the structure of bacterial and fungal communities associated with tree compartments as well as their underlying soils across 12 tree individuals in boreal forests. We found that the structure of bacterial and fungal communities depends more strongly on the vertical location of tree compartments rather than the locality, species, and individuals of host trees. Microbial communities showed much stronger host specificity in aboveground than belowground compartments. While having lower compartment community variability compared to fungi, bacterial communities were markedly more distinct between below- and aboveground components but not between hosts, reflecting the greater importance of environmental filtering rather than dispersal limitation and host identity in their community assembly. Our data suggest that spatial distance from soil as a major microbiome source contributes to the formation of microbiomes in plants, and that bacterial and fungal communities may follow contrasting assembly processes.

scholarly journals Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Pengfa Li ◽  
Weitao Li ◽  
Alex J. Dumbrell ◽  
Ming Liu ◽  
Guilong Li ◽  
...  
Keyword(s):  
Spatial Variation ◽  
Fungal Community ◽  
Community Assembly ◽  
Soil Depth ◽  
Environmental Filtering ◽  
Its Region ◽  
Dispersal Limitation ◽  
Fungal Communities ◽  
Subtropical China ◽  
Soil Layers

ABSTRACT Fungi underpin almost all terrestrial ecosystem functions, yet our understanding of their community ecology lags far behind that of other organisms. Here, red paddy soils in subtropical China were collected across a soil depth profile, comprising 0-to-10-cm- (0-10cm-), 10-20cm-, and 20-40cm-deep layers. Using Illumina MiSeq amplicon sequencing of the internal transcribed spacer (ITS) region, distance-decay relationships (DDRs), and ecological models, fungal assemblages and their spatial patterns were investigated from each soil depth. We observed significant spatial variation in fungal communities and found that environmental heterogeneity decreased with soil depth, while spatial variation in fungal communities showed the opposite trend. DDRs occurred only in 0-10cm- and 10-20cm-deep soil layers, not in the 20-40cm layer. Our analyses revealed that the fungal community assembly in the 0-10cm layer was primarily governed by environmental filtering and a high dispersal rate, while in the deeper layer (20-40cm), it was primarily governed by dispersal limitation with minimal environmental filtering. Both environmental filtering and dispersal limitation controlled fungal community assembly in the 10-20cm layer, with dispersal limitation playing the major role. Results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Effectively, “everything is everywhere, but the environment selects,” although only in shallower soils that are easily accessible to dispersive fungal propagules. This work highlights that perceived drivers of fungal community assembly are dependent on sampling depth, suggesting that caution is required when interpreting diversity patterns from samples that integrate across depths. IMPORTANCE In this work, Illumina MiSeq amplicon sequencing of the ITS region was used to investigate the spatial variation and assembly mechanisms of fungal communities from different soil layers across paddy fields in subtropical China, and the results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Therefore, the results of this study highlight that perceived drivers of fungal community assembly are dependent on sampling depth and suggest that caution is required when interpreting diversity patterns from samples that integrate across depths. This is the first study focusing on assemblages of fungal communities in different soil layers on a relatively large scale, and we thus believe that this study is of great importance to researchers and readers in microbial ecology, especially in microbial biogeography, because the results can provide sampling guidance in future studies of microbial biogeography.

scholarly journals High diversity of basal fungal lineages and stochastic processes controlled fungal community assembly in mangrove sediments

2021 ◽  
Author(s):  
Zhi-Feng Zhang ◽  
Yue-Ping Pan ◽  
Yue Liu ◽  
Meng Li
Keyword(s):  
Fungal Community ◽  
Large Scale ◽  
Southern China ◽  
Dispersal Limitation ◽  
Driving Factors ◽  
Minor Role ◽  
Mangrove Sediments ◽  
A Minor ◽  
Occurrence Patterns

Fungi are key components of microbial community in mangrove wetlands, with important roles in the transformation of nutrients and energy. However, existing studies typically focus on cultivable fungi, and seldomly on the structure and driving factors of the entire fungal communities. The compositions, community assembly and interaction patterns of mangrove fungal community on large scale remain elusive. Here, biogeography, assembly and co-occurrence patterns of fungal communities in mangrove across Eastern to Southern China were systematically analyzed by targeting the entire ITS region with high-throughput Pacific Biosciences single-molecule real-time sequencing. The analysis recovered a high level of fungal diversity, including a number of basal fungal lineages not previously reported in mangroves, such as Rozellomycota and Chytridiomycota . Beta nearest-taxon index analyses suggested a determinant role of dispersal limitation on fungal community in overall and most individual mangroves, with supporting from the strong distance-decay patterns of community similarity. Further, nonmetric multidimensional scaling analyses revealed a similar biogeography of dominant and rare fungal community. A minor role of environmental selection on the fungal community was noted, with geographical location and sediment depth as crucial factors driving the distribution of both, the dominant and rare taxa. Finally, network analysis revealed high modularized co-occurrence patterns of fungal community in mangrove sediments, and the keystone taxa might play important roles in microbial interactions and ecological functions. The investigation expands our understanding of biogeography, assembly patterns, driving factors, and co-occurrence relationships of mangrove fungi, and will spur the further functional exploration and protection of fungal resources in mangrove. IMPORTANCE As key components of microbial community in mangroves, fungi have important ecological functions. However, fungal community in mangrove on large scale is generally elusive, and mangroves are declining rapidly due to climate change and anthropogenic activities. This work provided an overview of fungal community structure and biogeography in mangrove wetlands along an over-9000 km coastline across Eastern to Southern China. Our study observed a high number of basal fungal lineages in mangrove sediments, such as Rozellomycota and Chytridiomycota . In addition, our results highlighted a crucial role of dispersal limitation and a minor role of environmental selections on fungal community in mangrove sediments. These novel findings add important knowledge about the structure, assembly processes, and driving factors of fungal community in mangrove sediments.

scholarly journals Leaf δ15N, δ13C and Their Associations with Soil Fungal Biodiversity, Ectomycorrhizal and Plant Pathogenic Abundance in Forest Ecosystems of China

2020 ◽  
Author(s):  
Wenchen Song
Keyword(s):  
Relative Abundance ◽  
Plant Pathogen ◽  
Large Scale ◽  
Plant Pathogens ◽  
Forest Ecosystems ◽  
Fungal Communities ◽  
Factors Affecting ◽  
Biogeographic Patterns ◽  
Fungal Biodiversity ◽  
Temperature And Precipitation

Abstract Leaf δ15N and δ13C are important functional traits in biogeographic studies of forest ecosystems. However, little is known about their relationships with soil fungal biodiversity, ectomycorrhizal, and plant pathogen abundance at large scales. In this study, leaf and soil samples were collected from 33 forest reserves along a large range across China to explore the associations between leaf δ15N and δ13C and soil fungal biodiversity, ectomycorrhizal, and plant pathogen relative abundance using molecular and stable isotope techniques. We found large-scale biogeographic patterns for leaf δ15N, δ13C, soil fungal biodiversity, and ectomycorrhizal relative abundance. The soil-plant-microbial interaction may contribute to the variations in leaf δ15N, δ13C, and soil fungal communities across different types of forest ecosystems. Temperature and precipitation were the main factors affecting large-scale biogeographic patterns of latitude and longitude. Leaf δ15N was mainly affected by the relative abundance of ectomycorrhizal fungi and leaf δ13C was affected by the relative abundance of plant pathogens. Leaf δ15N and δ13C may be indicators reflecting soil fungal communities in forest ecosystems.

scholarly journals Microbial phylogenetic relatedness links to distinct successional patterns of bacterial and fungal communities

2021 ◽  
Author(s):  
Qiang Lin ◽  
Francisco Dini-Andreote ◽  
Travis B Meador ◽  
Roey Angel ◽  
Lenka Meszarosov ◽  
...  
Keyword(s):  
Microbial Community ◽  
Resource Availability ◽  
Community Assembly ◽  
Ecological Succession ◽  
Fungal Communities ◽  
Ecological Processes ◽  
Soil Age ◽  
Successional Stages ◽  
Occurrence Patterns ◽  
Microbial Community Assembly

Development of soil microbial communities along ecological succession is crucial for ecosystem functioning and maintenance. However, ecological processes mediating microbial community assembly and microbial co-occurrence patterns along ecological succession remain unclear. Here, we explored community phylogenetic structures, ecological processes driving community phylogenetic turnover, and taxa co-occurrence patterns in bacterial and fungal communities across a well-established chronosequence of post-mining lands spanning 54 years of recovery. Meanwhile, by synthesizing prior studies of microbial phylogeny in community assembly, we proposed two conceptual models to better explain our results. At early successional stages, the significantly increasing phylogenetic clustering of bacterial communities with soil age was co-determined by the environmental selection from soil vegetation cover and by bacterial heterogeneous responses that less phylogenetically similar bacteria differently expanded their population in response to the increasing resource availability in soil along succession. At later successional stages, bacterial community phylogenetic structures displayed progressively lower variability. The fungal community phylogenetic structures varied relatively less and were independent of soil age, soil properties and vegetation cover, which was attributed to the dominance of stochastic processes in community structure turnover along succession. Network analysis revealed a decrease in bacterial co-occurrence complexity along succession, which aligned with a decrease in average pairwise phylogenetic distances between co-occurring bacteria. These patterns together implied a decrease in potential bacterial cooperation that was probably mediated by increasing resource availability along succession. The increased complexity of fungal co-occurrence along succession was independent of the phylogeny between co-occurring fungi. This study provides new sights into ecological processes and mechanisms underlying bacterial and fungal community dynamics along ecological succession, thereby boosting our understanding of the interactions between microbial community assembly and soil environment gradients.

Experimentally altered rainfall regimes and host root traits affect grassland arbuscular mycorrhizal fungal communities

2019 ◽  
Author(s):  
Coline Deveautour ◽  
Suzanne Donn ◽  
Sally Power ◽  
Kirk Barnett ◽  
Jeff Powell
Keyword(s):  
Fungal Community ◽  
Community Assembly ◽  
Root Length ◽  
Specific Root Length ◽  
Root Traits ◽  
Arbuscular Mycorrhizal ◽  
Fungal Communities ◽  
Rainfall Regime ◽  
Precipitation Regimes ◽  
Rainfall Regimes

Future climate scenarios predict changes in rainfall regimes. These changes are expected to affect plants via effects on the expression of root traits associated with water and nutrient uptake. Associated microorganisms may also respond to these new precipitation regimes, either directly in response to changes in the soil environment or indirectly in response to altered root trait expression. We characterised arbuscular mycorrhizal (AM) fungal communities in an Australian grassland exposed to experimentally altered rainfall regimes. We used Illumina sequencing to assess the responses of AM fungal communities associated with four plant species sampled in different watering treatments and evaluated the extent to which shifts were associated with changes in root traits. We observed that altered rainfall regimes affected the composition but not the richness of the AM fungal communities, and we found distinctive communities in the increased rainfall treatment. We found no evidence of altered rainfall regime effects via changes in host physiology because none of the studied traits were affected by changes in rainfall. However, specific root length was observed to correlate with AM fungal richness, while concentrations of phosphorus and calcium in root tissue and the proportion of root length allocated to fine roots were correlated to community composition. Our study provides evidence that climate change and its effects on rainfall may influence AM fungal community assembly, as do plant traits related to plant nutrition and water uptake. We did not find evidence that host responses to altered rainfall drive AM fungal community assembly in this grassland ecosystem.

scholarly journals Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China

mSystems ◽  
2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Bin Ma ◽  
Zhongmin Dai ◽  
Haizhen Wang ◽  
Melissa Dsouza ◽  
Xingmei Liu ◽  
...  
Keyword(s):  
Eastern China ◽  
Soil Microbial Communities ◽  
Natural Forest ◽  
Community Diversity ◽  
Biogeographic Patterns ◽  
Soil Microbial ◽  
Continental Scale ◽  
Forest Sites ◽  
Vegetation Gradient ◽  
Bacteria And Fungi

ABSTRACT Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem’s decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change. The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China. The distance decay relationships demonstrated the distinct biogeographic patterns of archaeal, bacterial, and fungal communities. While historical processes mainly influenced bacterial community variations, spatially autocorrelated environmental variables mainly influenced the fungal community. Archaea did not display a distance decay pattern along the vegetation gradient. Bacterial community diversity and structure were correlated with the ratio of acid oxalate-soluble Fe to free Fe oxides (Feo/Fed ratio). Fungal community diversity and structure were influenced by dissolved organic carbon (DOC) and free aluminum (Ald), respectively. The role of these environmental variables was confirmed by the correlations between dominant operational taxonomic units (OTUs) and edaphic variables. However, most of the dominant OTUs were not correlated with the major driving variables for the entire communities. These results demonstrate that soil archaea, bacteria, and fungi have different biogeographic patterns and driving processes along this continental-scale natural vegetation gradient, implying different community assembly mechanisms and ecological functions for archaea, bacteria, and fungi in soil ecosystems. IMPORTANCE Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem’s decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change. Author Video: An author video summary of this article is available.

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