Host Phylogenetic Relatedness and Soil Nutrients Shape Ectomycorrhizal Community Composition in Native and Exotic Pine Plantations

Exotic non-native Pinus species have been widely planted or become naturalized in many parts of the world. Pines rely on ectomycorrhizal (ECM) fungi mutualisms to overcome barriers to establishment, yet the degree to which host specificity and edaphic preferences influence ECM community composition remains poorly understood. In this study, we used high-throughput sequencing coupled with soil analyses to investigate the effect of host plant identity, spatial distance and edaphic factors on ECM community composition in young (30-year-old) native (Pinus massoniana Lamb.) and exotic (Pinus elliottii Engelm.) pine plantations in China. The ECM fungal communities comprised 43 species with the majority belonging to the Thelephoraceae and Russulaceae. Most species were found associated with both host trees while certain native ECM taxa (Suillus) showed host specificity to the native P. massoniana. ECM fungi that are known to occur exclusively with Pinus (e.g., Rhizopogon) were uncommon. We found no significant effect of host identity on ECM communities, i.e., phylogenetically related pines shared similar ECM fungal communities. Instead, ECM fungal community composition was strongly influenced by site-specific abiotic factors and dispersal. These findings reinforce the idea that taxonomic relatedness might be a factor promoting ECM colonization in exotic pines but that shifts in ECM communities may also be context-dependent.

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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.

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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.

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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.

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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.

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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.

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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.

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Assessing Genotypic and Environmental Effects on Endophyte Communities of Fraxinus (Ash) Using Culture Dependent and Independent DNA Sequencing

Journal of Fungi ◽

10.3390/jof7070565 ◽

2021 ◽

Vol 7 (7) ◽

pp. 565

Author(s):

Anindita Lahiri ◽

Brian R. Murphy ◽

Trevor R. Hodkinson

Keyword(s):

Community Composition ◽

Environmental Effects ◽

High Throughput Sequencing ◽

Fungal Community Composition ◽

Species Identity ◽

Ash Dieback ◽

Hymenoscyphus Fraxineus ◽

Culture Independent ◽

The Impact ◽

Culture Dependent

Fraxinus excelsior populations are in decline due to the ash dieback disease Hymenoscyphus fraxineus. It is important to understand genotypic and environmental effects on its fungal microbiome to develop disease management strategies. To do this, we used culture dependent and culture independent approaches to characterize endophyte material from contrasting ash provenances, environments, and tissues (leaves, roots, seeds). Endophytes were isolated and identified using nrITS, LSU, or tef DNA loci in the culture dependent assessments, which were mostly Ascomycota and assigned to 37 families. Few taxa were shared between roots and leaves. The culture independent approach used high throughput sequencing (HTS) of nrITS amplicons directly from plant DNA and detected 35 families. Large differences were found in OTU diversity and community composition estimated by the contrasting approaches and these data need to be combined for estimations of the core endophyte communities. Species richness and Shannon index values were highest for the leaf material and the French population. Few species were shared between seed and leaf tissue. PCoA and NMDS of the HTS data showed that seed and leaf microbiome communities were highly distinct and that there was a strong influence of Fraxinus species identity on their fungal community composition. The results will facilitate a better understanding of ash fungal ecology and are a step toward identifying microbial biocontrol systems to minimize the impact of the disease.

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Do fungi and bacteria respond similar across a steep local pH gradient?

10.5194/egusphere-egu21-5720 ◽

2021 ◽

Author(s):

Rasmus Kjoller ◽

Carla Cruz-Paredes

Keyword(s):

Community Composition ◽

Soil Ph ◽

Wood Ash ◽

Ph Gradient ◽

Fungal Communities ◽

Ph Effects ◽

Fungal Community Composition ◽

Ph Gradients ◽

Field Samples ◽

Bacterial Richness

Soil pH is consistently recorded as the single most important variable explaining bacterial richness and community composition locally as globally. Bacterial richness responds to soil pH in a bell-shaped pattern, highest in soils with near-neutral pH, while lower diversity is found in soil with pH >8 and <4.5. Also, community turnover is strongly determined by pH for bacteria. In contrast, pH effects on fungi is apparently less pronounced though also much less studied compared to bacteria. Still, pH appears to be a significant determinant for fungal communities but typically not the most important. Rarely are bacterial and fungal communities co-analyzed from the same field samples taken across pH gradients. Here we analyze the community responses of fungi and bacteria in parallel over an extreme pH gradient ranging from pH 4 to 8 established by applying strongly alkaline wood ash to replicated plots in a Picea abies plantation. Bacterial and fungal community composition were assessed by amplicon-based meta-barcoding. Bacterial richness were not significantly affected by pH, while fungal richness and a-diversity were stimulated with higher pH. We found that both, bacterial and fungal communities increasingly deviated from the untreated plots with increasing amount of wood ash though fungal communities were more resistant to changes than bacterial. Soil NH4, NO3 and pH significantly correlated with the NMDS pattern for both bacterial and fungal communities. In the presentation we will discuss resistance versus sensitivity of different fungal functional guilds towards higher pH as well as the underlying factors explaining the community changes.

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Diversity, host-specificity and stability of sponge-associated fungal communities of co-occurring sponges

PeerJ ◽

10.7717/peerj.4965 ◽

2018 ◽

Vol 6 ◽

pp. e4965 ◽

Cited By ~ 7

Author(s):

Mary T.H.D. Nguyen ◽

Torsten Thomas

Keyword(s):

Host Specificity ◽

Horizontal Transmission ◽

Critical Role ◽

Fungal Species ◽

Fungal Communities ◽

Sponge Species ◽

Fungal Community Composition ◽

Potential Core ◽

Community Profiling ◽

Surrounding Seawater

Fungi play a critical role in a range of ecosystems; however, their interactions and functions in marine hosts, and particular sponges, is poorly understood. Here we assess the fungal community composition of three co-occurring sponges (Cymbastela concentrica, Scopalina sp., Tedania anhelans) and the surrounding seawater over two time points to help elucidate host-specificity, stability and potential core members, which may shed light into the ecological function of fungi in sponges. The results showed that ITS-amplicon-based community profiling likely provides a more realistic assessment of fungal diversity in sponges than cultivation-dependent approaches. The sponges studied here were found to contain phylogenetically diverse fungi (eight fungal classes were observed), including members of the family Togniniaceae and the genus Acrostalagmus, that have so far not been reported to be cultured from sponges. Fungal communities within any given sponge species were found to be highly variable compared to bacterial communities, and influenced in structure by the community of the surrounding seawater, especially considering temporal variation. Nevertheless, the sponge species studied here contained a few “variable/core” fungi that appeared in multiple biological replicates and were enriched in their relative abundance compared to seawater communities. These fungi were the same or highly similar to fungal species detected in sponges around the world, which suggests a prevalence of horizontal transmission where selectivity and enrichment of some fungi occur for those that can survive and/or exploit the sponge environment. Our current sparse knowledge about sponge-associated fungi thus indicate that fungal communities may perhaps not play as an important ecological role in the sponge holobiont compared to bacterial or archaeal symbionts.

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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.

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