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

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

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

Agronomy ◽

10.3390/agronomy10101535 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1535

Author(s):

Kaire Loit ◽

Liina Soonvald ◽

Alar Astover ◽

Eve Runno-Paurson ◽

Maarja Öpik ◽

...

Keyword(s):

Fungal Diversity ◽

High Throughput Sequencing ◽

Solanum Tuberosum L ◽

Potato Cultivar ◽

Growing Season ◽

Sampling Time ◽

Fungal Communities ◽

Specific Effects ◽

Soil Fungal Community ◽

Soil Fungal Diversity

The soil fungal community plays an important role in determining plant growth and health. In this study, we investigated the fungal diversity and community composition in the roots and soil of 21 potato (Solanum tuberosum L.) cultivars using high-throughput sequencing at three different time points across the growing season. In soil and roots, the fungal richness and relative abundance of pathogens and saprotrophs were mainly affected by sampling time. While sampling time affected fungal composition in soil, root fungal communities were also significantly affected by cultivar. The cultivar had the strongest effect on diversity of pathogens and abundance of particular pathogen species. Our results demonstrate changes in soil and root fungal communities of potato over the growing season, as well as highlighting the importance of potato cultivar on root fungal communities and abundance of pathogens.

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

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

Site-Dependent Relationships Between Fungal Community Composition, Plant Genotypic Diversity and Environmental Drivers in a Salix Biomass System

Frontiers in Fungal Biology ◽

10.3389/ffunb.2021.671270 ◽

2021 ◽

Vol 2 ◽

Author(s):

Stefanie Hoeber ◽

Christel Baum ◽

Martin Weih ◽

Stefano Manzoni ◽

Petra Fransson

Keyword(s):

Community Composition ◽

Fungal Community ◽

Fungal Diversity ◽

Genotypic Diversity ◽

Fungal Communities ◽

Environmental Drivers ◽

Plant Genotype ◽

Fungal Community Composition ◽

Genotype Diversity ◽

Ecm Fungi

Soil fungi are strongly affected by plant species or genotypes since plants modify their surrounding environment, but the effects of plant genotype diversity on fungal diversity and function have not been extensively studied. The interactive responses of fungal community composition to plant genotypic diversity and environmental drivers were investigated in Salix biomass systems, posing questions about: (1) How fungal diversity varies as a function of plant genotype diversity; (2) If plant genotype identity is a strong driver of fungal community composition also in plant mixtures; (3) How the fungal communities change through time (seasonally and interannually)?; and (4) Will the proportion of ECM fungi increase over the rotation? Soil samples were collected over 4 years, starting preplanting from two Salix field trials, including four genotypes with contrasting phenology and functional traits, and genotypes were grown in all possible combinations (four genotypes in Uppsala, Sweden, two in Rostock, Germany). Fungal communities were identified, using Pacific Biosciences sequencing of fungal ITS2 amplicons. We found some site-dependent relationships between fungal community composition and genotype or diversity level, and site accounted for the largest part of the variation in fungal community composition. Rostock had a more homogenous community structure, with significant effects of genotype, diversity level, and the presence of one genotype (“Loden”) on fungal community composition. Soil properties and plant and litter traits contributed to explaining the variation in fungal species composition. The within-season variation in composition was of a similar magnitude to the year-to-year variation. The proportion of ECM fungi increased over time irrespective of plant genotype diversity, and, in Uppsala, the 4-mixture showed a weaker response than other combinations. Species richness was generally higher in Uppsala compared with that in Rostock and increased over time, but did not increase with plant genotype diversity. This significant site-specificity underlines the need for consideration of diverse sites to draw general conclusions of temporal variations and functioning of fungal communities. A significant increase in ECM colonization of soil under the pioneer tree Salix on agricultural soils was evident and points to changed litter decomposition and soil carbon dynamics during Salix growth.

Download Full-text

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

Plants ◽

10.3390/plants9050600 ◽

2020 ◽

Vol 9 (5) ◽

pp. 600

Author(s):

Qingqing Shen ◽

Junyu Yang ◽

Daifa Su ◽

Zhiying Li ◽

Wei Xiao ◽

...

Keyword(s):

Endangered Species ◽

Community Composition ◽

Fungal Community ◽

High Throughput Sequencing ◽

Fungal Communities ◽

Future Research ◽

Its2 Region ◽

Rhizospheric Soil ◽

Fungal Community Composition ◽

Opposite Pattern

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

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

Diversity and Structure of Soil Fungal Communities across Experimental Everglades Tree Islands

Diversity ◽

10.3390/d12090324 ◽

2020 ◽

Vol 12 (9) ◽

pp. 324

Author(s):

Brianna K. Almeida ◽

Michael S. Ross ◽

Susana L. Stoffella ◽

Jay P. Sah ◽

Eric Cline ◽

...

Keyword(s):

Water Level ◽

Fungal Community ◽

Plant Pathogen ◽

Fungal Diversity ◽

Fungal Communities ◽

Tree Islands ◽

Fungal Community Composition ◽

Everglades Tree Islands ◽

And Function ◽

Early Restoration

Fungi play prominent roles in ecosystem services (e.g., nutrient cycling, decomposition) and thus have increasingly garnered attention in restoration ecology. However, it is unclear how most management decisions impact fungal communities, making it difficult to protect fungal diversity and utilize fungi to improve restoration success. To understand the effects of restoration decisions and environmental variation on fungal communities, we sequenced soil fungal microbiomes from 96 sites across eight experimental Everglades tree islands approximately 15 years after restoration occurred. We found that early restoration decisions can have enduring consequences for fungal communities. Factors experimentally manipulated in 2003–2007 (e.g., type of island core) had significant legacy effects on fungal community composition. Our results also emphasized the role of water regime in fungal diversity, composition, and function. As the relative water level decreased, so did fungal diversity, with an approximately 25% decline in the driest sites. Further, as the water level decreased, the abundance of the plant pathogen–saprotroph guild increased, suggesting that low water may increase plant-pathogen interactions. Our results indicate that early restoration decisions can have long-term consequences for fungal community composition and function and suggest that a drier future in the Everglades could reduce fungal diversity on imperiled tree islands.

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