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

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.

Download Full-text

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

10.20944/preprints202007.0218.v1 ◽

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.

Download Full-text

Contrasting Patterns and Drivers of Soil Fungal Communities between Two Ecosystems Divided by the Treeline

Microorganisms ◽

10.3390/microorganisms9112280 ◽

2021 ◽

Vol 9 (11) ◽

pp. 2280

Author(s):

Xueying Wang ◽

Guixiang Li ◽

Yuxin Zhang ◽

Keming Ma

Keyword(s):

Climate Change ◽

Community Composition ◽

Fungal Community ◽

High Throughput Sequencing ◽

Montane Forest ◽

Fungal Communities ◽

Formation Mechanisms ◽

Fungal Community Composition ◽

Soil Fungal Community ◽

Soil Fungal Community Composition

The treeline is a sensitive region of the terrestrial ecosystem responding to climate change. However, studies on the composition and formation mechanisms of soil fungal communities across the treeline are still lacking. In this study, we investigated the patterns of soil fungal community composition and interactions among functional guilds above and below the treeline using Illumina high-throughput sequencing and ecological network analysis. The results showed that there were significant differences in the soil environment and soil fungal community composition between the two ecosystems above and below the treeline. At the local scale of this study, geographic distance and environmental factors affected the composition of the soil fungal community. Soil temperature was an important environmental predictor of soil fungal community composition. Species in soil fungal communities in the subalpine meadow were more closely related to each other compared to those in the montane forest. Furthermore, the soil fungal community in montane forest was more stable. Our findings contribute to a better understanding of how mountain ecological functions respond to global climate change.

Download Full-text

Vegetation Restoration Alters Fungal Community Composition and Functional Groups in a Desert Ecosystem

Frontiers in Environmental Science ◽

10.3389/fenvs.2021.589068 ◽

2021 ◽

Vol 9 ◽

Author(s):

Ying Zhang ◽

Hongyu Cao ◽

Peishan Zhao ◽

Xiaoshuai Wei ◽

Guodong Ding ◽

...

Keyword(s):

Community Composition ◽

Fungal Community ◽

Fungal Diversity ◽

High Throughput Sequencing ◽

Soil Depth ◽

Mycorrhizal Fungus ◽

Fungal Communities ◽

Desert Ecosystem ◽

Fungal Community Composition ◽

Soil Fungal Diversity

Revegetation is regarded as an effective means to improve the ecological environment in deserts and profoundly influences the potential ecological functions of the soil fungal community. Therefore, Illumina high-throughput sequencing was performed to characterize the soil fungal diversity and community composition at two soil depths (0–10 cm and 10–20 cm) with four revegetation durations (natural grassland, half-mature, nearly mature, and mature Pinus. sylvestris var. mongolica plantations) in the Mu Us Sandy Land, China. The effects of soil properties on soil fungal communities were also examined to reveal the connection between fungal function and soil environment. The results indicated that 1) soil nutrient content and enzyme activity showed significant differences through the restoration durations, 2) there was no significant effect of soil depth on soil fungal diversity, while the Shannon diversity index of all fungal communities was significantly different among different revegetation durations, 3) compared with grassland, ectomycorrhizal fungi (notably, Inocybe, Tuber, and Calostoma) were abundant in plantations. The endophyte fungus Mortierella was among the top 10 genera in all soil samples and arbuscular mycorrhizal fungus Diversispora was the indicator genus of the grassland, and 4) catalase and total nitrogen were the main factors affecting fungal community composition and were closely related to saprotrophs and pathotrophs, respectively. This new information indicates the variation of soil fungal communities along revegetation durations and highlights the interaction between fungal functions and desert ecosystems.

Download Full-text

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

Scientific Reports ◽

10.1038/s41598-021-95099-z ◽

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.

Download Full-text

Contrasting Patterns of Functional Diversity in Coffee Root Fungal Communities Associated with Organic and Conventionally Managed Fields

Applied and Environmental Microbiology ◽

10.1128/aem.00052-20 ◽

2020 ◽

Vol 86 (11) ◽

Cited By ~ 1

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.

Download Full-text

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

Applied and Environmental Microbiology ◽

10.1128/aem.03858-15 ◽

2016 ◽

Vol 82 (9) ◽

pp. 2632-2643 ◽

Cited By ~ 26

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.

Download Full-text

Limited Effects of Variable-Retention Harvesting on Fungal Communities Decomposing Fine Roots in Coastal Temperate Rainforests

Applied and Environmental Microbiology ◽

10.1128/aem.02061-17 ◽

2017 ◽

Vol 84 (3) ◽

Cited By ~ 2

Author(s):

Timothy J. Philpott ◽

Jason S. Barker ◽

Cindy E. Prescott ◽

Sue J. Grayston

Keyword(s):

Community Composition ◽

Fungal Community ◽

Fine Roots ◽

Fine Root ◽

Plant Litter ◽

Fungal Communities ◽

Decomposition Rates ◽

Fungal Community Composition ◽

Variable Retention ◽

Variable Retention Harvesting

ABSTRACT Fine root litter is the principal source of carbon stored in forest soils and a dominant source of carbon for fungal decomposers. Differences in decomposer capacity between fungal species may be important determinants of fine-root decomposition rates. Variable-retention harvesting (VRH) provides refuge for ectomycorrhizal fungi, but its influence on fine-root decomposers is unknown, as are the effects of functional shifts in these fungal communities on carbon cycling. We compared fungal communities decomposing fine roots (in litter bags) under VRH, clear-cut, and uncut stands at two sites (6 and 13 years postharvest) and two decay stages (43 days and 1 year after burial) in Douglas fir forests in coastal British Columbia, Canada. Fungal species and guilds were identified from decomposed fine roots using high-throughput sequencing. Variable retention had short-term effects on β-diversity; harvest treatment modified the fungal community composition at the 6-year-postharvest site, but not at the 13-year-postharvest site. Ericoid and ectomycorrhizal guilds were not more abundant under VRH, but stand age significantly structured species composition. Guild composition varied by decay stage, with ruderal species later replaced by saprotrophs and ectomycorrhizae. Ectomycorrhizal abundance on decomposing fine roots may partially explain why fine roots typically decompose more slowly than surface litter. Our results indicate that stand age structures fine-root decomposers but that decay stage is more important in structuring the fungal community than shifts caused by harvesting. The rapid postharvest recovery of fungal communities decomposing fine roots suggests resiliency within this community, at least in these young regenerating stands in coastal British Columbia. IMPORTANCE Globally, fine roots are a dominant source of carbon in forest soils, yet the fungi that decompose this material and that drive the sequestration or respiration of this carbon remain largely uncharacterized. Fungi vary in their capacity to decompose plant litter, suggesting that fungal community composition is an important determinant of decomposition rates. Variable-retention harvesting is a forestry practice that modifies fungal communities by providing refuge for ectomycorrhizal fungi. We evaluated the effects of variable retention and clear-cut harvesting on fungal communities decomposing fine roots at two sites (6 and 13 years postharvest), at two decay stages (43 days and 1 year), and in uncut stands in temperate rainforests. Harvesting impacts on fungal community composition were detected only after 6 years after harvest. We suggest that fungal community composition may be an important factor that reduces fine-root decomposition rates relative to those of above-ground plant litter, which has important consequences for forest carbon cycling.

Download Full-text

Landscape-level DNA metabarcoding study in the Pannonian forests reveals differential effects of slope aspect on taxonomic and functional groups of fungi

10.1101/281337 ◽

2018 ◽

Cited By ~ 1

Author(s):

József Geml

Keyword(s):

Functional Groups ◽

Community Composition ◽

Fungal Community ◽

Environmental Conditions ◽

Community Dynamics ◽

Fungal Communities ◽

Slope Aspect ◽

Fungal Community Composition ◽

Dna Metabarcoding ◽

Landscape Level

AbstractIn temperate regions, slope aspect is one of the most influential drivers of environmental conditions at landscape level. The effect of aspect on vegetation has been well studied, but virtually nothing is known about how fungal communities are shaped by aspect-driven environmental conditions. I carried out DNA metabarcoding of fungi from soil samples taken in a selected study area of Pannonian forests to compare richness and community composition of taxonomic and functional groups of fungi between slopes of predominantly southerly vs. northerly aspect and to assess the influence of selected environmental variables on fungal community composition. The deep sequence data presented here (i.e. 980 766 quality-filtered sequences) indicate that both niche (environmental filtering) and neutral (stochastic) processes shape fungal community composition at landscape level. Fungal community composition correlated strongly with aspect, with many fungi showing preference for either south-facing or north-facing slopes. Several taxonomic and functional groups showed significant differences in richness between north-and south-facing slopes and strong compositional differences were observed in all functional groups. The effect of aspect on fungal communities likely is mediated through contrasting mesoclimatic conditions, that in turn influence edaphic processes as well as vegetation. Finally, the data presented here provide an unprecedented insight into the diversity and landscape-level community dynamics of fungi in the Pannonian forests.

Download Full-text

The gut mycobiome of healthy mice is shaped by the environment and shapes metabolic outcomes in response to diet

10.1101/2020.06.25.158287 ◽

2020 ◽

Author(s):

Tahliyah S. Mims ◽

Qusai Al Abdullah ◽

Justin D. Stewart ◽

Sydney P. Watts ◽

Catrina T. White ◽

...

Keyword(s):

Community Composition ◽

Fungal Community ◽

Bacterial Communities ◽

Genetic Background ◽

Dietary Exposure ◽

Fungal Communities ◽

Metabolic Adaptation ◽

Fungal Community Composition ◽

Metabolic Outcomes ◽

Metabolic Biomarkers

ABSTRACTObjectiveAs an active interface between the host and their diet, the gut bacteriome influences host metabolic adaptation. However, the contribution of gut fungi to host metabolic outcomes is not yet understood. Therefore, we aimed to determine if host metabolic response to an ultra-processed diet reflects gut fungal community composition.DesignWe compared jejunal fungi and bacteria from 72 healthy mice with the same genetic background but different starting mycobiomes before and after 8 weeks on an ultra-processed or standardized diet using 16S and internal transcribed spacer region 2 ribosomal RNA sequencing. We measured host body composition using magnetic resonance imaging, examined changes in metabolically active host tissues and quantified serum metabolic biomarkers.ResultsGut fungal communities are highly variable between mice, differing by vendor, age and sex. After exposure to an ultra-processed diet for 8 weeks, persistent differences in fungal community composition strongly associate with differential deposition of body mass in male mice compared to mice on standardized diet. Fat deposition in the liver, genomic adaptation of metabolically active tissues and serum metabolic biomarkers are correlated with alterations in fungal diversity and community composition. Variation in fungi from the genera Thermomyces and Saccharomyces most strongly associate with increased weight gain.ConclusionsIn the gut of healthy mice, host-microbe metabolic interactions strongly reflect variability in fungal communities. Our results confirm the importance of luminal fungal communities to host metabolic adaptation to dietary exposure. Gut fungal communities may represent a therapeutic target for the prevention and treatment of metabolic disease.Graphical AbstractIn BriefWhat is already known about this subject?Gut bacterial communities have evolved to influence the metabolic outcomes of the host in mammals. Evidence from across the lifespan suggests that differences in composition of these communities is associated with energy consumption. However, gut microbial communities, while often equated to bacteria, are diverse, multi-kingdom ecologies and limited information is available for the role of other kingdoms of life, such as fungi.What are the new findings?Gut fungal communities, collectively termed the mycobiome, are less diverse and abundant than bacterial communities in the gastrointestinal tract. This study identifies the considerable influence of the environment and dietary exposure on the composition of jejunal fungal communities in healthy mice with the same genetic background. After exposure to processed diet, differences in fungal community composition in male mice were strongly correlated with persistent differences body composition and markers of metabolic tone.How might it impact on clinical practice in the foreseeable future?These results verify that the baseline metabolic tone of health mice strongly reflects the ecological complexity of the gastrointestinal mycobiome. Variation in the composition of gut fungal communities is likely an underappreciated source of experimental and clinical variability in metabolic studies. Gastrointestinal fungi are likely a target for prevention and treatment of metabolic disease.

Download Full-text

Tundra Type Drives Distinct Trajectories of Functional and Taxonomic Composition of Arctic Fungal Communities in Response to Climate Change – Results From Long-Term Experimental Summer Warming and Increased Snow Depth

Frontiers in Microbiology ◽

10.3389/fmicb.2021.628746 ◽

2021 ◽

Vol 12 ◽

Author(s):

József Geml ◽

Luis N. Morgado ◽

Tatiana A. Semenova-Nelsen

Keyword(s):

Climate Change ◽

Community Composition ◽

Fungal Community ◽

Snow Depth ◽

Fungal Communities ◽

The Arctic ◽

Fungal Community Composition ◽

Summer Warming ◽

Edaphic Variables

The arctic tundra is undergoing climate-driven changes and there are serious concerns related to the future of arctic biodiversity and altered ecological processes under possible climate change scenarios. Arctic land surface temperatures and precipitation are predicted to increase further, likely causing major transformation in terrestrial ecosystems. As a response to increasing temperatures, shifts in vegetation and soil fungal communities have already been observed. Little is known, however, how long-term experimental warming coupled with increased snow depth influence the trajectories of soil fungal communities in different tundra types. We compared edaphic variables and fungal community composition in experimental plots simulating the expected increase in summer warming and winter snow depth, based on DNA metabarcoding data. Fungal communities in the sampled dry and moist acidic tundra communities differed greatly, with tundra type explaining ca. one-third of compositional variation. Furthermore, dry and moist tundra appear to have different trajectories in response to climate change. Specifically, while both warming and increased snow depth had significant effects on fungal community composition and edaphic variables in dry tundra, the effect of increased snow was greater. However, in moist tundra, fungal communities mainly were affected by summer warming, while increased snow depth had a smaller effect and only on some functional groups. In dry tundra, microorganisms generally are limited by moisture in the summer and extremely low temperatures in winter, which is in agreement with the stronger effect of increased snow depth relative to warming. On the contrary, moist tundra soils generally are saturated with water, remain cold year-round and show relatively small seasonal fluctuations in temperature. The greater observed effect of warming on fungi in moist tundra may be explained by the narrower temperature optimum compared to those in dry tundra.

Download Full-text