Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi

Extreme environments simplify reassembly of communities of arbuscular mycorrhizal fungi

The ecological impacts of long-term (press) disturbance on mechanisms regulating the relative abundance (i.e., commonness or rarity) and temporal dynamics of species within a community remain largely unknown. This is particularly true for the functionally important arbuscular mycorrhizal (AM) fungi; obligate plant-root endosymbionts that colonize more than two-thirds of terrestrial plant species. Here, we use high-resolution amplicon sequencing to examine how AM fungal communities in a specific extreme ecosystem-mofettes or natural CO2 springs caused by geological CO2 exhalations-are affected by long-term stress. We found that in mofettes, specific and temporally stable communities form as a subset of the local metacommunity. These communities are less diverse and dominated by adapted, "stress tolerant" taxa. Those taxa are rare in control locations and more benign environments worldwide, but show a stable temporal pattern in the extreme sites, consistently dominating the communities in grassland mofettes. This pattern of lower diversity and high dominance of specific taxa has been confirmed as relatively stable over several sampling years and is independently observed across multiple geographic locations (mofettes in different countries). This study implies that the response of soil microbial community composition to long-term stress is relatively predictable, which can also reflect the community response to other anthropogenic stressors (e.g., heavy metal pollution or land use change). Moreover, as AM fungi are functionally differentiated, with different taxa providing different benefits to host plants, changes in community structure in response to long-term environmental change have the potential to impact terrestrial plant communities and their productivity.IMPORTANCEArbuscular mycorrhizal (AM) fungi form symbiotic relationships with more than two-thirds of plant species. In return for using plant carbon as their sole energy source, AM fungi improve plant mineral supply, water balance, and protection against pathogens. This work demonstrates the importance of long-term experiments to understand the effects of long-term environmental change and long-term disturbance on terrestrial ecosystems. We demonstrated a consistent response of the AM fungal community to a long-term stress, with lower diversity and a less variable AM fungal community over time under stress conditions compared to the surrounding controls. We have also identified, for the first time, a suite of AM fungal taxa that are consistently observed across broad geographic scales in stressed and anthropogenically heavily influenced ecosystems. This is critical because global environmental change in terrestrial ecosystems requires an integrative approach that considers both above- and below-ground changes and examines patterns over a longer geographic and temporal scale, rather than just single sampling events.

Plant Variety, Mycorrhization, and Herbivory Influence Induced Volatile Emissions and Plant Growth Characteristics in Tomato

Plants produce a range of volatile organic compounds (VOCs) that mediate vital ecological interactions between herbivorous insects, their natural enemies, plants, and soil dwelling organisms including arbuscular mycorrhizal fungi (AMF). The composition, quantity, and quality of the emitted VOCs can vary and is influenced by numerous factors such as plant species, variety (cultivar), plant developmental stage, root colonization by soil microbes, as well as the insect developmental stage, and level of specialization of the attacking herbivore. Understanding factors shaping VOC emissions is important and can be leveraged to enhance plant health and pest resistance. In this greenhouse study, we evaluated the influence of plant variety, mycorrhizal colonization, herbivory, and their interactions on the composition of emitted volatiles in tomato plants (Solanum lycopersicum L.). Four tomato varieties from two breeding histories (two heirlooms and two hybrids), were used. Tomato plants were inoculated with a commercial inoculum blend consisting of four species of AMF. Plants were also subjected to herbivory by Manduca sexta (Lepidoptera: Sphingidae L.) five weeks after transplanting. Headspace volatiles were collected from inoculated and non-inoculated plants with and without herbivores using solid phase-microextraction. Volatile profiles consisted of 21 different volatiles in detectable quantities. These included monoterpenes, sesquiterpenes, and alkane hydrocarbons. We documented a strong plant variety effect on VOC emissions. AMF colonization and herbivory suppressed VOC emissions. Plant biomass was improved by colonization of AMF. Our results show that mycorrhization, herbivory and plant variety can alter tomato plant VOC emissions and further shape volatile-mediated insect and plant interactions.

Species-area relationships in microbial-mediated mutualisms

Symbioses involving microorganisms prevail in nature and are key to regulating numerous ecosystem processes and in driving evolution. A major concern in understanding the ecology of symbioses involving microorganisms arises in the effectiveness of sampling strategies to capture the contrasting size of organisms involved. In many mutualisms, including mycorrhizas and gut systems, hosts interact simultaneously with multiple smaller sized mutualists, the identity of which determines success for the host. This complicates quantifying the diversity of mutualisms because sampling techniques fail to capture effectively the diversity of each partner. Here we propose the use of species-area relationships (SARs) to explicitly consider the spatial scale of microbial partners in symbioses, which we propose will improve our understanding of the ecology of mutualisms.

Testing the contribution of dispersal to microbial succession following a wildfire

IMPORTANCE

Identifying the mechanisms underlying microbial community succession is necessary for predicting how microbial communities, and their functioning, will respond to future environmental change. Dispersal is one mechanism expected to affect microbial succession, yet the difficult nature of manipulating microorganisms in the environment has limited our understanding of its contribution. Using a dispersal exclusion experiment, this study isolates the specific effect of environmental dispersal on bacterial and fungal community assembly over time following a wildfire. The work demonstrates the potential to quantify dispersal impacts on soil microbial communities over time and test how dispersal might further interact with other assembly processes in response to environmental change.

Paired Root-Soil Samples and Metabarcoding Reveal Taxon-Based Colonization Strategies in Arbuscular Mycorrhizal Fungi Communities in Japanese Cedar and Cypress Stands

Arbuscular mycorrhizal fungi (AMF) in the roots and soil surrounding their hosts are typically independently investigated and little is known of the relationships between the communities of the two compartments. We simultaneously collected root and surrounding soil samples from Cryptomeria japonica (Cj) and Chamaecyparis obtusa (Co) at three environmentally different sites. Based on molecular and morphological analyses, we characterized their associated AMF communities. Cj was more densely colonized than Co and that root colonization intensity was significantly correlated with soil AMF diversity. The communities comprised 15 AMF genera dominated by Glomus and Paraglomus and 1443 operational taxonomic units (OTUs) of which 1067 and 1170 were in roots and soil, respectively. AMF communities were significantly different among sites, and the root AMF communities were significantly different from those of soil at each site. The root and soil AMF communities responded differently to soil pH. At the genus level, Glomus and Acaulospora were abundant in roots while Paraglomus and Redeckera were abundant in soil. Our findings suggest that AMF colonizing roots are protected from environmental stresses in soil. However, the root-soil-abundant taxa have adapted to both environments and represent a model AMF symbiont. This evidence of strategic exploitation of the rhizosphere by AMF supports prior hypotheses and provides insights into community ecology.

Arbuscular mycorrhizal fungi associated with the rhizosphere of an endemic terrestrial bromeliad and a grass in the Brazilian neotropical dry forest

Arbuscular mycorrhizal fungi form symbiotic associations with 80-90% of all known plants, allowing the fungi to acquire plant-synthesized carbon, and confer an increased capacity for nutrient uptake by plants, improving tolerance to abiotic and biotic stresses. We aimed at characterizing the mycorrhizal community in the rhizosphere of Neoglaziovia variegata (so-called `caroa`) and Tripogonella spicata (so-called resurrection plant), using high-throughput sequencing of the partial 18S rRNA gene. Both plants are currently undergoing a bioprospecting program to find microbes with the potential of helping plants tolerate water stress. Sampling was carried out in the Caatinga biome, a neotropical dry forest, located in northeastern Brazil. Illumina MiSeq sequencing of 37 rhizosphere samples (19 for N. variegata and 18 for T. spicata) revealed a distinct mycorrhizal community between the studied plants. According to alpha diversity analyses, T. spicata showed the highest richness and diversity based on the Observed ASVs and the Shannon index, respectively. On the other hand, N. variegata showed higher modularity of the mycorrhizal network compared to T. spicata. The four most abundant genera found (higher than 10%) were Glomus, Gigaspora, Acaulospora, and Scutellospora, with Glomus being the most abundant in both plants. Nonetheless, Gigaspora, Diversispora, and Ambispora were found only in the rhizosphere of N. variegata, whilst Scutellospora, Paraglomus, and Archaeospora were exclusive to the rhizosphere of T. spicata. Therefore, the community of arbuscular mycorrhizal fungi of the rhizosphere of each plant encompasses a unique composition, structure and modularity, which can differentially assist them in the hostile environment.

AM fungal-bacterial relationships: what can they tell us about ecosystem sustainability and soil functioning?

Considering our growing population and our continuous degradation of soil environments, understanding the fundamental ecology of soil biota and plant microbiomes will be imperative to sustaining soil systems. Arbuscular mycorrhizal (AM) fungi extend their hyphae beyond plant root zones, creating microhabitats with bacterial symbionts for nutrient acquisition through a tripartite symbiotic relationship along with plants. Nonetheless, it is unclear what drives these AM fungal-bacterial relationships and how AM fungal functional traits contribute to these relationships. By delving into the literature, we look at the drivers and complexity behind AM fungal-bacterial relationships, describe the shift needed in AM fungal research towards the inclusion of interdisciplinary tools, and discuss the utilization of bacterial datasets to provide contextual evidence behind these complex relationships, bringing insights and new hypotheses to AM fungal functional traits. From this synthesis, we gather that interdependent microbial relationships are at the foundation of understanding microbiome functionality and deciphering microbial functional traits. We suggest using pattern-based inference tools along with machine learning to elucidate AM fungal-bacterial relationship trends, along with the utilization of synthetic communities, functional gene analyses, and metabolomics to understand how AM fungal and bacterial communities facilitate communication for the survival of host plant communities. These suggestions could result in improving microbial inocula and products, as well as a better understanding of complex relationships in terrestrial ecosystems that contribute to plant-soil feedbacks.

Composition and seasonal variation of the arbuscular mycorrhizal fungi spore community in litter, root mat, and soil from a subtropical rain forest

Community composition and seasonal variation of sporulation of arbuscular mycorrhizal fungi (AMF) have been studied in soils from many ecosystems including subtropical forest. Yet, AMF community composition has been surveyed only from the mineral soil but not from the litter layer and the root mat, and long-term variation in sporulation is not fully understood. We sampled a 75-m² plot from a subtropical forest to determine AMF community composition in the following habitats: the litter layer, the root mat, and the mineral soil. Moreover, samples were taken in fall, winter, spring, and summer over a 2-year period to follow the seasonal variation of AMF sporulation. We detected 47 AMF species belonging to six families and 14 genera, Glomeraceae and Acaulosporaceae being the most represented families. Sixteen species were common to all three habitats, five species were shared between two habitats, and 26 species were recovered exclusively from single habitats. While species richness was not significantly different among habitats, AMF total spore numbers were significantly higher in the litter and root mat compared to the soil. PERMANOVA did not detect a significant effect of habitats on community composition when species presence/absence was considered, but significant differences between litter versus soil and root mat versus soil were detected when spore abundance was considered. A seasonal pattern of spore abundance for species was not observed over the 2-year sampling period regardless of habitat. This study revealed that (i) different AMF species sporulate in the different habitats; thus, field surveys considering only the mineral soil might underestimate species richness and (ii) AMF species sporulate asynchronously in subtropical forest.

Improving Taxonomic Delimitation of Fungal Species in the Age of Genomics and Phenomics

Species concepts have long provided a source of debate among biologists. These lively debates have been important for reaching consensus on how to communicate across scientific disciplines and for advancing innovative strategies to study evolution, population biology, ecology, natural history, and disease epidemiology. Species concepts are also important for evaluating variability and diversity among communities, understanding biogeographical distributions, and identifying causal agents of disease across animal and plant hosts. While there have been many attempts to address the concept of species in the fungi, there are several concepts that have made taxonomic delimitation especially challenging. In this review we discuss these major challenges and describe methodological approaches that show promise for resolving ambiguity in fungal taxonomy by improving discrimination of genetic and functional traits. We highlight the relevance of eco-evolutionary theory used in conjunction with integrative taxonomy approaches to improve the understanding of interactions between environment, ecology, and evolution that give rise to distinct species boundaries. Beyond recent advances in genomic and phenomic methods, bioinformatics tools and modeling approaches enable researchers to test hypothesis and expand our knowledge of fungal biodiversity. Looking to the future, the pairing of integrative taxonomy approaches with multi-locus genomic sequencing and phenomic techniques, such as transcriptomics and proteomics, holds great potential to resolve many unknowns in fungal taxonomic classification.

Environmental identification of arbuscular mycorrhizal fungi using the LSU rDNA gene region: an expanded database and improved pipeline

Arbuscular mycorrhizal fungi (AMF; Glomeromycota) are difficult to culture; therefore, establishing a robust amplicon-based approach to taxa identification is imperative to describe AMF diversity. Further, due to low and biased sampling of AMF taxa, molecular databases do not represent the breadth of AMF diversity, making database matching approaches suboptimal. Therefore, a full description of AMF diversity requires a tool to determine sequence-based placement in the Glomeromycota clade. Nonetheless, commonly used gene regions, including the SSU and ITS, do not enable reliable phylogenetic placement. Here, we present an improved database and pipeline for the phylogenetic determination of AMF using amplicons from the large subunit (LSU) rRNA gene. We improve our database and backbone tree by including additional outgroup sequences. We also improve an existing bioinformatics pipeline by aligning forward and reverse reads separately, using a universal alignment for all tree building, and implementing a BLAST screening prior to tree building to remove non-homologous sequences. Finally, we present a script to extract AMF belonging to 11 major families as well as an amplicon sequencing variant (ASV) version of our pipeline. We test the utility of the pipeline by testing the placement of known AMF, known non-AMF, and Acaulospora sp. spore sequences. This work represents the most comprehensive database and pipeline for phylogenetic placement of AMF LSU amplicon sequences within the Glomeromycota clade.

Multiple Arbuscular Mycorrhizal Fungal Consortia Enhance Yield and Fatty Acids of Medicago sativa: A Two-Year Field Study on Agronomic Traits and Tracing of Fungal Persistence

Arbuscular mycorrhizal fungi are promoted as biofertilizers due to potential benefits in crop productivity, and macro- and microelement uptake. However, crop response to arbuscular mycorrhizal fungi (AMF) inoculation is context-dependent, and AMF diversity and field establishment and persistence of inoculants can greatly contribute to variation in outcomes. This study was designed to test the hypotheses that multiple and local AMF inoculants could enhance alfalfa yield and fatty acids (FA) compared to exotic isolates either single or in the mixture. We aimed also to verify the persistence of inoculated AMF, and which component of the AMF communities was the major driver of plant traits. Therefore, a field experiment of AMF inoculation of alfalfa (Medicago sativa L.) with three single foreign isolates, a mixture of the foreign isolates (FMix), and a highly diverse mixture of local AMF (LMix) was set up. We showed that AMF improved alfalfa yield (+ 68%), nutrient (+ 147% N content and + 182% P content in forage), and FA content (+ 105%). These positive effects persisted for at least 2 years post-inoculation and were associated with enhanced AMF abundance in roots. Consortia of AMF strains acted in synergy, and the mixture of foreign AMF isolates provided greater benefits compared to local consortia (+ 20% forage yield, + 36% forage N content, + 18% forage P content, + 20% total FA in forage). Foreign strains of Funneliformis mosseae and Rhizophagus irregularis persisted in the roots of alfalfa 2 years following inoculation, either as single inoculum or as a component of the mixture. Among inoculants, F. mosseae BEG12 and AZ225C and the FMix exerted a higher impact on the local AMF community compared with LMix and R. irregularis BEG141. Finally, the stimulation of the proliferation of a single-taxa (R. irregularis cluster1) induced by all inoculants was the main determinant of the host benefits. Crop productivity and quality as well as field persistence of inoculated AMF support the use of mixtures of foreign AMF. On the other hand, local mixtures showed a lower impact on native AMF. These results pave the way for extending the study on the effect of AMF mixtures for the production of high-quality forage for the animal diet.

Soil Bacterial Community Shifts Are Driven by Soil Nutrient Availability along a Teak Plantation Chronosequence in Tropical Forests in China

Simple Summary

Tropical forests play an important role in the global carbon cycle, especially in the context of global climate change. Soil microorganisms are essential to the functions, services, and productivity of terrestrial ecosystems as a link to maintain the connections and interactions between the aboveground and belowground ecosystems. The interactions between plants and the soil microbiome are crucial for plant growth, health, and resistance to stressors. However, information on the response of soil microbial communities to a chronosequence of woody plants is lacking, especially in tropical forests. This study compares the soil properties, diversity, composition, and co-occurrence patterns of bacterial communities in the rhizosphere and bulk soils along a teak plantation chronosequence. The results show that the composition and co-occurrence patterns of the bacterial communities are statistically different among the plantations, while stand age has no significant impact on soil bacterial alpha diversity. The results further show that soil nutrients play a key role in shaping the soil bacterial community. The study also provides information about the dynamics and characteristics of these soil bacterial communities and adds valuable information that may underpin new strategies for the management of teak plantations.

Abstract

Soil bacterial communities play crucial roles in ecosystem functions and biogeochemical cycles of fundamental elements and are sensitive to environmental changes. However, the response of soil bacterial communities to chronosequence in tropical ecosystems is still poorly understood. This study characterized the structures and co-occurrence patterns of soil bacterial communities in rhizosphere and bulk soils along a chronosequence of teak plantations and adjacent native grassland as control. Stand ages significantly shifted the structure of soil bacterial communities but had no significant impact on bacterial community diversity. Bacterial community diversity in bulk soils was significantly higher than that in rhizosphere soils. The number of nodes and edges in the bacterial co-occurrence network first increased and then decreased with the chronosequence. The number of strongly positive correlations per network was much higher than negative correlations. Available potassium, total potassium, and available phosphorus were significant factors influencing the structure of the bacterial community in bulk soils. In contrast, urease, total potassium, pH, and total phosphorus were significant factors affecting the structure of the bacterial community in the rhizosphere soils. These results indicate that available nutrients in the soil are the main drivers regulating soil bacterial community variation along a teak plantation chronosequence.

Alterations in Arbuscular Mycorrhizal Community Along a Chronosequence of Teak (Tectona grandis) Plantations in Tropical Forests of China

Arbuscular mycorrhizal (AM) fungi play a crucial role in promoting plant growth, enhancing plant stress resistance, and sustaining a healthy ecosystem. However, little is known about the mycorrhizal status of teak plantations. Here, we evaluated how the AM fungal communities of rhizosphere soils and roots respond to different stand ages of teak: 22, 35, 45, and 55-year-old from the adjacent native grassland (CK). A high-throughput sequencing method was used to compare the differences in soil and root AM fungal community structures. In combination with soil parameters, mechanisms driving the AM fungal community were revealed by redundancy analysis and the Mantel test. Additionally, spore density and colonization rates were analyzed. With increasing stand age, the AM fungal colonization rates and spore density increased linearly. Catalase activity and ammonium nitrogen content also increased, and soil organic carbon, total phosphorous, acid phosphatase activity, available potassium, and available phosphorus first increased and then decreased. Stand age significantly changed the structure of the AM fungal community but had no significant impact on the diversity of the AM fungal community. However, the diversity of the AM fungal community in soils was statistically higher than that in the roots. In total, nine and seven AM fungal genera were detected in the soil and root samples, respectively. The majority of sequences in soils and roots belonged to Glomus. Age-induced changes in soil properties could largely explain the alterations in the structure of the AM fungal community along a chronosequence, which included total potassium, carbon-nitrogen ratio, ammonium nitrogen, catalase, and acid phosphatase levels in soils and catalase, acid phosphatase, pH, and total potassium levels in roots. Soil nutrient availability and enzyme activity were the main driving factors regulating the shift in the AM fungal community structure along a chronosequence of the teak plantations.

Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples

Metabarcoding is an important tool for understanding fungal communities. The internal transcribed spacer (ITS) rDNA is the accepted fungal barcode but has known problems. The large subunit (LSU) rDNA has also been used to investigate fungal communities but available LSU metabarcoding primers were mostly designed to target Dikarya (Ascomycota + Basidiomycota) with little attention to early diverging fungi (EDF). However, evidence from multiple studies suggests that EDF comprise a large portion of unknown diversity in community sampling. Here, we investigate how DNA marker choice and methodological biases impact recovery of EDF from environmental samples. We focused on one EDF lineage, Zoopagomycota, as an example. We evaluated three primer sets (ITS1F/ITS2, LROR/LR3, and LR3 paired with new primer LR22F) to amplify and sequence a Zoopagomycota mock community and a set of 146 environmental samples with Illumina MiSeq. We compared two taxonomy assignment methods and created an LSU reference database compatible with AMPtk software. The two taxonomy assignment methods recovered strikingly different communities of fungi and EDF. Target fragment length variation exacerbated PCR amplification biases and influenced downstream taxonomic assignments, but this effect was greater for EDF than Dikarya. To improve identification of LSU amplicons we performed phylogenetic reconstruction and illustrate the advantages of this critical tool for investigating identified and unidentified sequences. Our results suggest much of the EDF community may be missed or misidentified with "standard" metabarcoding approaches and modified techniques are needed to understand the role of these taxa in a broader ecological context.

The Mycorrizal Status in Vineyards Affected by Esca

In this work we analyzed the relationship among native arbuscular mycorrhizal fungi (AMF) and vine roots affected by esca, a serious grapevine trunk disease. The AMF symbiosis was analyzed on the roots of neighboring plants (symptomatic and asymptomatic to esca) in 14 sites of three vineyards in Marche region (central–eastern Italy). The AMF colonization intensity, identified by non-vital staining, showed higher value in all esca symptomatic plants (ranging from 24.6% to 61.3%) than neighboring asymptomatic plants (from 17.4% to 57.6%). The same trend of Glomeromycota phylum abundance was detected by analyzing fungal operational taxonomic units (OTUs) linked to the AMF community, obtained by amplicon high throughput analysis of ITS 1 region. Overall, the highest amount of OTUs was detected on roots from symptomatic plants (0.42%), compared to asymptomatic roots (0.29%). Specific primer pairs for native Rhizophagus irregularis and Funneliformis mosseae AMF species, were designed in 28S rRNA and large subunit (LSU) ribosomal RNA, respectively, and droplet digital PCR protocol for absolute quantification was set up. A higher number of DNA copies of both fungal species were detected more frequently in symptomatic than asymptomatic vines. Our study suggests a relationship between esca and native AMF in grapevine. These results underline the importance of native rhizosphere microbial communities for a better knowledge of grapevine esca disease.

Temperate Forests Dominated by Arbuscular or Ectomycorrhizal Fungi Are Characterized by Strong Shifts from Saprotrophic to Mycorrhizal Fungi with Increasing Soil Depth

In temperate and boreal forests, competition for soil resources between free-living saprotrophs and ectomycorrhizal (EcM) fungi has been suggested to restrict saprotrophic fungal dominance to the most superficial organic soil horizons in forests dominated by EcM trees. By contrast, lower niche overlap with arbuscular mycorrhizal (AM) fungi could allow fungal saprotrophs to maintain this dominance into deeper soil horizons in AM-dominated forests. Here we used a natural gradient of adjacent forest patches that were dominated by either AM or EcM trees, or a mixture of both to determine how fungal communities characterized with high-throughput amplicon sequencing change across organic and mineral soil horizons. We found a general shift from saprotrophic to mycorrhizal fungal dominance with increasing soil depth in all forest mycorrhizal types, especially in organic horizons. Vertical changes in soil chemistry, including pH, organic matter, exchangeable cations, and extractable phosphorus, coincided with shifts in fungal community composition. Although fungal communities and soil chemistry differed among adjacent forest mycorrhizal types, variations were stronger within a given soil profile, pointing to the importance of considering horizons when characterizing soil fungal communities. Our results also suggest that in temperate forests, vertical shifts from saprotrophic to mycorrhizal fungi within organic and mineral horizons occur similarly in both ectomycorrhizal and arbuscular mycorrhizal forests.

Native AMF Communities in an Italian Vineyard at Two Different Phenological Stages of Vitis vinifera

Arbuscular mycorrhizal fungi (AMF) are beneficial soil microorganisms that can establish symbiotic associations with Vitis vinifera roots, resulting in positive effects on grapevine performance, both in terms of water use efficiency, nutrient uptake, and replant success. Grapevine is an important perennial crop cultivated worldwide, especially in Mediterranean countries. In Italy, Piedmont is one of the regions with the longest winemaking tradition. In the present study, we characterized the AMF communities of the soil associated or not with the roots of V. vinifera cv. Pinot Noir cultivated in a vineyard subjected to conventional management using 454 Roche sequencing technology. Samplings were performed at two plant phenological stages (flowering and early fruit development). The AMF community was dominated by members of the family Glomeraceae, with a prevalence of the genus Glomus and the species Rhizophagus intraradices and Rhizophagus irregularis. On the contrary, the genus Archaeospora was the only one belonging to the family Archaeosporaceae. Since different AMF communities occur in the two considered soils, independently from the plant phenological stage, a probable role of V. vinifera in determining the AMF populations associated to its roots has been highlighted.

PacBio sequencing of Glomeromycota rDNA: a novel amplicon covering all widely used ribosomal barcoding regions and its applicability in taxonomy and ecology of arbuscular mycorrhizal fungi

There is no consensus barcoding region for determination of arbuscular mycorrhizal fungal (AMF) taxa. To overcome this obstacle, we have developed an approach to sequence an AMF marker within the ribosome-encoding operon (rDNA) that covers all three widely applied variable molecular markers. Using a nested PCR approach specific to AMF, we amplified a part (c. 2.5 kb) of the rDNA spanning the majority of the small subunit rRNA (SSU) gene, the complete internal transcribed spacer (ITS) region and a part of the large subunit (LSU) rRNA gene. The PCR products were sequenced on the PacBio platform utilizing Single Molecule Real Time (SMRT) sequencing. Employing this method for selected environmental DNA samples, we were able to describe complex AMF communities consisting of various glomeromycotan lineages. We demonstrate the applicability of this new 2.5 kb approach to provide robust phylogenetic assignment of AMF lineages without known sequences from pure cultures and to consolidate information about AMF taxon distributions coming from three widely used barcoding regions into one integrative dataset.

Variation in hyphal production rather than turnover regulates standing fungal biomass in temperate hardwood forests

Soil fungi link above- and belowground carbon (C) fluxes through their interactions with plants and contribute to C and nutrient dynamics through the production, turnover, and activity of fungal hyphae. Despite their importance to ecosystem processes, estimates of hyphal production and turnover rates are relatively uncommon, especially in temperate hardwood forests. We sequentially harvested hyphal ingrowth bags to quantify the rates of Dikarya (Ascomycota and Basidiomycota) hyphal production and turnover in three hardwood forests in the Midwestern United States, where plots differed in their abundance of arbuscular (AM)- vs. ectomycorrhizal (ECM)-associated trees. Hyphal production rates increased linearly with the percentage of ECM trees and annual production rates were 66% higher in ECM- than AM-dominated plots. Hyphal turnover rates did not differ across the mycorrhizal gradient (plots varying in their abundance of AM vs. ECM trees), suggesting that the greater fungal biomass in ECM-dominated plots relates to greater fungal production rather than slower fungal turnover. Differences in hyphal production across the gradient aligned with distinctly different fungal communities and activities. As ECM trees increased in dominance, fungi inside ingrowth bags produced more extracellular enzymes involved in degrading nitrogen (N)-bearing relative to C-bearing compounds, suggesting greater fungal (and possibly plant) N demand in ECM-dominated soils. Collectively, our results demonstrate that shifts in temperate tree species composition that result in changes in the dominant type of mycorrhizal association may have strong impacts on Dikarya hyphal production, fungal community composition and extracellular enzyme activity, with important consequences for soil C and N cycling.

Dispersal of Arbuscular Mycorrhizal Fungi: Evidence and Insights for Ecological Studies

Dispersal is a critical ecological process that modulates gene flow and contributes to the maintenance of genetic and taxonomic diversity within ecosystems. Despite an increasing global understanding of the arbuscular mycorrhizal (AM) fungal diversity, distribution and prevalence in different biomes, we have largely ignored the main dispersal mechanisms of these organisms. To provide a geographical and scientific overview of the available data, we systematically searched for the direct evidence on the AM fungal dispersal agents (abiotic and biotic) and different propagule types (i.e. spores, extraradical hyphae or colonized root fragments). We show that the available data (37 articles) on AM fungal dispersal originates mostly from North America, from temperate ecosystems, from biotic dispersal agents (small mammals) and AM fungal spores as propagule type. Much lesser evidence exists from South American, Asian and African tropical systems and other dispersers such as large-bodied birds and mammals and non-spore propagule types. We did not find strong evidence that spore size varies across dispersal agents, but wind and large animals seem to be more efficient dispersers. However, the data is still too scarce to draw firm conclusions from this finding. We further discuss and propose critical research questions and potential approaches to advance the understanding of the ecology of AM fungi dispersal.

Contrasting fungal responses to wildfire across different ecosystem types

Wildfire affects our planet's biogeochemistry both by burning biomass and by driving changes in ecological communities and landcover. Some plants and ecosystem types are threatened by increasing fire pressure while others respond positively to fire, growing in local and regional abundance when it occurs regularly. However, quantifying total ecosystem response to fire demands consideration of impacts not only on aboveground vegetation, but also on soil microbes like fungi, which influence decomposition and nutrient mineralization. If fire-resistant soil fungal communities co-occur with similarly adapted plants, these above- and belowground ecosystem components should shift and recover in relative synchrony after burning. If not, fire might decouple ecosystem processes governed by these different communities, affecting total functioning. Here, we use a natural experiment to test whether fire-dependent ecosystems host unique, fire-resistant fungal communities. We surveyed burned and unburned areas across two California ecosystem types with differing fire ecologies in the immediate aftermath of a wildfire, finding that the soil fungal communities of fire-dependent oak woodlands differ from those of neighbouring mixed evergreen forests. We discovered furthermore that the latter are more strongly altered compositionally by fire than the former, suggesting that differences in fungal community structure support divergent community responses to fire across ecosystems. Our results thus indicate that fire-dependent ecosystems may host fire-resistant fungal communities.

Space and Vine Cultivar Interact to Determine the Arbuscular Mycorrhizal Fungal Community Composition

The interest in the use of microbes as biofertilizers is increasing in recent years as the demands for sustainable cropping systems become more pressing. Although very widely used as biofertilizers, arbuscular mycorrhizal (AM) fungal associations with specific crops have received little attention and knowledge is limited, especially in the case of vineyards. In this study, the AM fungal community associated with soil and roots of a vineyard on Mallorca Island, Spain was characterized by DNA sequencing to resolve the relative importance of grape variety on their diversity and composition. Overall, soil contained a wider AM fungal diversity than plant roots, and this was found at both taxonomic and phylogenetic levels. The major effect on community composition was associated with sample type, either root or soil material, with a significant effect for the variety of the grape. This effect interacted with the spatial distribution of the plants. Such an interaction revealed a hierarchical effect of abiotic and biotic factors in shaping the composition of AM fungal communities. Our results have direct implications for the understanding of plant-fungal assemblages and the potential functional differences across plants in vineyard cropping.

Moderate phosphorus additions consistently affect community composition of arbuscular mycorrhizal fungi in tropical montane forests in southern Ecuador

Anthropogenic atmospheric deposition can increase nutrient supply in the most remote ecosystems, potentially affecting soil biodiversity. Arbuscular mycorrhizal fungal (AMF) communities rapidly respond to simulated soil eutrophication in tropical forests. Yet the limited spatio-temporal extent of such manipulations, together with the often unrealistically high fertilization rates employed, impedes generalization of such responses. We sequenced mixed root AMF communities within a seven year-long fully factorial nitrogen (N) and phosphorus (P) addition experiment, replicated at three tropical montane forests in southern Ecuador with differing environmental characteristics. We hypothesized: strong shifts in community composition and species richness after long-term fertilization, site- and clade-specific responses to N vs P additions depending on local soil fertility and clade life history traits respectively. Fertilization consistently shifted AMF community composition across sites, but only reduced richness of Glomeraceae. Compositional changes were mainly driven by increases in P supply while richness reductions were observed only after combined N and P additions. We conclude that moderate increases of N and P exert a mild but consistent effect on tropical AMF communities. To predict the consequences of these shifts, current results need to be supplemented with experiments that characterize local species-specific AMF functionality.

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.

High-Throughput DNA Sequence-Based Analysis of AMF Communities

Arbuscular mycorrhizal fungi (AMF) are obligate symbionts of most land plants. They have great ecological and economic impacts as they support plant nutrition and water supply, soil structure, and plant resistance to pathogens. Investigating AMF presence and distribution at small and large scales is critical. Therefore, research requires standard protocols to be easily implemented. In this chapter, we describe a workflow for AMF identification by high-throughput sequencing through Illumina MiSeq platform of two DNA target regions: small subunit (SSU) and internal transcribed spacer (ITS). The protocol can apply to both soil and root AMF communities.

Arbuscular mycorrhizal fungi in roots and soil respond differently to biotic and abiotic factors in the Serengeti

This study explores the relationships of AM fungal abundance and diversity with biotic (host plant, ungulate grazing) and abiotic (soil properties, precipitation) factors in the Serengeti National Park, Tanzania. Soil and root samples were collected from grazed and ungrazed plots at seven sites across steep soil fertility and precipitation gradients. AM fungal abundance in the soil was estimated from the density of spores and the concentration of a fatty acid biomarker. Diversity of AM fungi in roots and soils was measured using DNA sequencing and spore identification. AM fungal abundance in soil decreased with grazing and precipitation and increased with soil phosphorus. The community composition of AM fungal DNA in roots and soils differed. Root samples had more AM fungal indicator species associated with biotic factors (host plant species and grazing), and soil samples had more indicator species associated with particular sample sites. These findings suggest that regional edaphic conditions shape the site-level species pool from which plant species actively select root-colonizing fungal assemblages modified by grazing. Combining multiple measurements of AM fungal abundance and community composition provides the most informed assessment of the structure of mycorrhizal fungal communities in natural ecosystems.

The relative importance of ecological drivers of arbuscular mycorrhizal fungal distribution varies with taxon phylogenetic resolution

The phylogenetic depth at which arbuscular mycorrhizal (AM) fungi harbor a coherent ecological niche is unknown, which has consequences for operational taxonomic unit (OTU) delineation from sequence data and the study of their biogeography. We tested how changes in AM fungi community composition across habitats (beta diversity) vary with OTU phylogenetic resolution. We inferred exact sequence variants (ESVs) to resolve phylotypes at resolutions finer than provided by traditional sequence clustering and analyzed beta diversity profiles up to order-level sequence clusters. At the ESV level, we detected the environmental predictors revealed with traditional OTUs or at higher genetic distances. However, the correlation between environmental predictors and community turnover steeply increased at a genetic distance of c. 0.03 substitutions per site. Furthermore, we observed a turnover of either closely or distantly related taxa (respectively at or above 0.03 substitutions per site) along different environmental gradients. This study suggests that different axes of AM fungal ecological niche are conserved at different phylogenetic depths. Delineating AM fungal phylotypes using DNA sequences should screen different phylogenetic resolutions to better elucidate the factors that shape communities and predict the fate of AM symbioses in a changing environment.

Sympatry and interference of divergent Microbotryum pathogen species

The impact of infectious diseases in natural ecosystems is strongly influenced by the degree of pathogen specialization and by the local assemblies of potential host species. This study investigated anther-smut disease, caused by fungi in the genus Microbotryum, among natural populations of plants in the Caryophyllaceae. A broad geographic survey focused on sites of the disease on multiple host species in sympatry. Analysis of molecular identities for the pathogens revealed that sympatric disease was most often due to co-occurrence of distinct, host-specific anther-smut fungi, rather than localized cross-species disease transmission. Flowers from sympatric populations showed that the Microbotryum spores were frequently moved between host species. Experimental inoculations to simulate cross-species exposure to the pathogens in these plant communities showed that the anther-smut pathogen was less able to cause disease on its regular host when following exposure of the plants to incompatible pathogens from another host species. These results indicate that multi-host/multi-pathogen communities are common in this system and they involve a previously hidden mechanism of interference between Microbotryum fungi, which likely affects both pathogen and host distributions.

Agroecological coffee management increases arbuscular mycorrhizal fungi diversity

Agroecology aims to maintain ecosystem services by minimizing the impact of agriculture and promoting the use of biological potential. Arbuscular mycorrhizal fungi (AMF) are elements which are key to improving crop productivity and soil quality. It is pertinent to understand how agricultural management in the tropics affects the AMF spatio-temporal community composition, especially in crops of global importance, such as coffee (Coffea arabica L.). Soil and root samples were collected from three localities under three management systems (agroecological, conventional and forest fragment), during the phenological stages of coffee (flowering, grain filling, harvesting). Spores were extracted for morphological identification and molecular community analysis by PCR-DGGE. Dendrograms were prepared and the bands were sequenced and analyzed by bioinformatics. No differences were observed in the richness of morphospecies between management systems, localities and period, but little is known about tropical species. Molecular analysis showed that the agroecological management system was similar to natural forest and with a higher diversity indices than conventional management. Locality and period of sample affect AMF community composition. It is necessary to associate classical taxonomic evaluations with molecular biological techniques because different approaches can lead to different outcomes. This study contributes to the understanding of the impact of agriculture management systems on AMF and provides evidence that agroecology is a management system applicable to sustainable coffee production.

Responses of arbuscular mycorrhizal fungi to long-term inorganic and organic nutrient addition in a lowland tropical forest

Improved understanding of the nutritional ecology of arbuscular mycorrhizal (AM) fungi is important in understanding how tropical forests maintain high productivity on low-fertility soils. Relatively little is known about how AM fungi will respond to changes in nutrient inputs in tropical forests, which hampers our ability to assess how forest productivity will be influenced by anthropogenic change. Here we assessed the influence of long-term inorganic and organic nutrient additions and nutrient depletion on AM fungi, using two adjacent experiments in a lowland tropical forest in Panama. We characterised AM fungal communities in soil and roots using 454-pyrosequencing, and quantified AM fungal abundance using microscopy and a lipid biomarker. Phosphorus and nitrogen addition reduced the abundance of AM fungi to a similar extent, but affected community composition in different ways. Nutrient depletion (removal of leaf litter) had a pronounced effect on AM fungal community composition, affecting nearly as many OTUs as phosphorus addition. The addition of nutrients in organic form (leaf litter) had little effect on any AM fungal parameter. Soil AM fungal communities responded more strongly to changes in nutrient availability than communities in roots. This suggests that the 'dual niches' of AM fungi in soil versus roots are structured to different degrees by abiotic environmental filters, and biotic filters imposed by the plant host. Our findings indicate that AM fungal communities are fine-tuned to nutrient regimes, and support future studies aiming to link AM fungal community dynamics with ecosystem function.

Seasonal variation in winter wheat field soil arbuscular mycorrhizal fungus communities after non-mycorrhizal crop cultivation

Intensive farming practices that implement deep and frequent tillage, high input inorganic fertilization, cultivation with non-host species, and pesticide use are widely reported to be detrimental for arbuscular mycorrhizal fungi (AMF), which are one of the most important plant biofertilizers. The effect of the reduction of agricultural input on AMF community dynamics following conversion from conventional non-mycorrhizal to lower input mycorrhizal crop cultivation has not yet been fully elucidated. We investigated the effect of the reduction of agricultural input, rotation, and season on AMF communities in winter wheat field soil after conversion from long-term (more than 20 years) non-mycorrhizal (sugar beet) crop cultivation. We described AMF communities from bulk soil samples by specifically targeting the 18S ribosomal gene using a combination of AMF specific primers and 454 pyrosequencing. No effect was found after 3 years' reduction of agricultural input, and only marginal effects were due to rotation with specific crops preceding winter wheat. Instead, season and year of sampling had the most appreciable influence on the AMF community. We suggest that, after conversion from long-term non-mycorrhizal to mycorrhizal crop cultivation, AMF diversity is low if compared to similar agroecosystems. Seasonal and successional dynamics play an important role as determinants of community structure.

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data

High-throughput amplicon sequencing (HTAS) of conserved DNA regions is a powerful technique to characterize microbial communities. Recently, spike-in mock communities have been used to measure accuracy of sequencing platforms and data analysis pipelines. To assess the ability of sequencing platforms and data processing pipelines using fungal internal transcribed spacer (ITS) amplicons, we created two ITS spike-in control mock communities composed of cloned DNA in plasmids: a biological mock community, consisting of ITS sequences from fungal taxa, and a synthetic mock community (SynMock), consisting of non-biological ITS-like sequences. Using these spike-in controls we show that: (1) a non-biological synthetic control (e.g., SynMock) is the best solution for parameterizing bioinformatics pipelines, (2) pre-clustering steps for variable length amplicons are critically important, (3) a major source of bias is attributed to the initial polymerase chain reaction (PCR) and thus HTAS read abundances are typically not representative of starting values. We developed AMPtk, a versatile software solution equipped to deal with variable length amplicons and quality filter HTAS data based on spike-in controls. While we describe herein a non-biological SynMock community for ITS sequences, the concept and AMPtk software can be widely applied to any HTAS dataset to improve data quality.

Morphological and molecular diversity of arbuscular mycorrhizal fungi in revegetated iron-mining site has the same magnitude of adjacent pristine ecosystems

Arbuscular mycorrhizal fungi (AMF) are important during revegetation of mining sites, but few studies compared AMF community in revegetated sites with pristine adjacent ecosystems. The aim of this study was to assess AMF species richness in a revegetated iron-mining site and adjacent ecosystems and to relate AMF occurrence to soil chemical parameters. Soil samples were collected in dry and rainy seasons in a revegetated iron-mining site (RA) and compared with pristine ecosystems of forest (FL), canga (NG), and Cerrado (CE). AMF species were identified by spore morphology from field and trap cultures and by LSU rDNA sequencing using Illumina. A total of 62 AMF species were recovered, pertaining to 18 genera and nine families of Glomeromycota. The largest number of species and families were detected in RA, and Acaulospora mellea and Glomus sp1 were the most frequent species. Species belonging to Glomeraceae and Acaulosporaceae accounted for 42%-48% of total species richness. Total number of spores and mycorrhizal inoculum potential tended to be higher in the dry than in the rainy season, except in RA. Sequences of uncultured Glomerales were dominant in all sites and seasons and five species were detected exclusively by DNA-based identification. Redundancy analysis evidenced soil pH, organic matter, aluminum, and iron as main factors influencing AMF presence. In conclusion, revegetation of the iron-mining site seems to be effective in maintaining a diverse AMF community and different approaches are complementary to reveal AMF species, despite the larger number of species being identified by traditional identification of field spores.

Poor plant performance under simulated climate change is linked to mycorrhizal responses in a semiarid shrubland

Warmer and drier conditions associated with ongoing climate change will increase abiotic stress for plants and mycorrhizal fungi in drylands worldwide, thereby potentially reducing vegetation cover and productivity and increasing the risk of land degradation and desertification. Rhizosphere microbial interactions and feedbacks are critical processes that could either mitigate or aggravate the vulnerability of dryland vegetation to forecasted climate change.We conducted a four-year manipulative study in a semiarid shrubland in the Iberian Peninsula to assess the effects of warming (~2.5ºC; W), rainfall reduction (~30%; RR) and their combination (W+RR) on the performance of native shrubs (Helianthemum squamatum) and their associated mycorrhizal fungi.Warming (W and W+RR) decreased the net photosynthetic rates of H. squamatum shrubs by ~31% despite concurrent increases in stomatal conductance (~33%), leading to sharp decreases (~50%) in water use efficiency. Warming also advanced growth phenology, decreased leaf nitrogen and phosphorus contents per unit area, reduced shoot biomass production by ~36% and decreased survival during a dry year in both W and W+RR plants. Plants under RR showed more moderate decreases (~10-20%) in photosynthesis, stomatal conductance and shoot growth.Warming, RR and W+RR altered ectomycorrhizal fungal (EMF) community structure and drastically reduced the relative abundance of EMF sequences obtained by high-throughput sequencing, a response associated with decreases in the leaf nitrogen, phosphorus and dry matter contents of their host plants. In contrast to EMF, the community structure and relative sequence abundances of other non-mycorrhizal fungal guilds were not significantly affected by the climate manipulation treatments.Synthesis: Our findings highlight the vulnerability of both native plants and their symbiotic mycorrhizal fungi to climate warming and drying in semiarid shrublands, and point to the importance of a deeper understanding of plant-soil feedbacks to predict dryland vegetation responses to forecasted aridification. The interdependent responses of plants and ectomycorrhizal fungi to warming and rainfall reduction may lead to a detrimental feedback loop on vegetation productivity and nutrient pool size, which could amplify the adverse impacts of forecasted climate change on ecosystem functioning in EMF-dominated drylands.

Biological invasions increase the richness of arbuscular mycorrhizal fungi from a Hawaiian subtropical ecosystem

Biological invasions can have various impacts on the diversity of important microbial mutualists such as mycorrhizal fungi, but few studies have tested whether the effects of invasions on mycorrhizal diversity are consistent across spatial gradients. Furthermore, few of these studies have taken place in tropical ecosystems that experience an inordinate rate of invasions into native habitats. Here, we examined the effects of plant invasions dominated by non-native tree species on the diversity of arbuscular mycorrhizal (AM) fungi in Hawaii. To test the hypothesis that invasions result in consistent changes in AM fungal diversity across spatial gradients relative to native forest habitats, we sampled soil in paired native and invaded sites from three watersheds and used amplicon sequencing to characterize AM fungal communities. Whether our analyses considered phylogenetic relatedness or not, we found that invasions consistently increased the richness of AM fungi. However, AM fungal species composition was not related to invasion status of the vegetation nor local environment, but stratified by watershed. Our results suggest that while invasions can lead to an overall increase in the diversity of microbial mutualists, the effects of plant host identity or geographic structuring potentially outweigh those of invasive species in determining the community membership of AM fungi. Thus, host specificity and spatial factors such as dispersal need to be taken into consideration when examining the effects of biological invasions on symbiotic microbes.

Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi

The arrival of 454 sequencing represented a major breakthrough by allowing deeper sequencing of environmental samples than was possible with existing Sanger approaches. Illumina MiSeq provides a further increase in sequencing depth but shorter read length compared with 454 sequencing. We explored whether Illumina sequencing improves estimates of arbuscular mycorrhizal (AM) fungal richness in plant root samples, compared with 454 sequencing. We identified AM fungi in root samples by sequencing amplicons of the SSU rRNA gene with 454 and Illumina MiSeq paired-end sequencing. In addition, we sequenced metagenomic DNA without prior PCR amplification. Amplicon-based Illumina sequencing yielded two orders of magnitude higher sequencing depth per sample than 454 sequencing. Initial analysis with minimal quality control recorded five times higher AM fungal richness per sample with Illumina sequencing. Additional quality control of Illumina samples, including restriction of the marker region to the most variable amplicon fragment, revealed AM fungal richness values close to those produced by 454 sequencing. Furthermore, AM fungal richness estimates were not correlated with sequencing depth between 300 and 30,000 reads per sample, suggesting that the lower end of this range is sufficient for adequate description of AM fungal communities. By contrast, metagenomic Illumina sequencing yielded very few AM fungal reads and taxa and was dominated by plant DNA, suggesting that AM fungal DNA is present at prohibitively low abundance in colonised root samples. In conclusion, Illumina MiSeq sequencing yielded higher sequencing depth, but similar richness of AM fungi in root samples, compared with 454 sequencing.

ITS fungal barcoding primers versus 18S AMF-specific primers reveal similar AMF-based diversity patterns in roots and soils of three mountain vineyards

ITS primers commonly used to describe soil fungi are flawed for AMF although it is unknown the extent to which they distort the interpretation of community patterns. Here, we focus on how the use of a specific ITS2 fungal barcoding primer pair biased for AMF changes the interpretation of AMF community patterns from three mountain vineyards compared to a novel AMF-specific approach on the 18S. We found that although discrepancies were present in the taxonomic composition of the two resulting datasets, the estimation of diversity patterns among AMF communities was similar and resulted in both primer systems being able to correctly assess the community-structuring effect of location, compartment (root vs. soil) and environment. Both methodologies made it possible to detect the same alpha-diversity trend among the locations under study but not between root and soil transects. We show that the ITS2 primer system for fungal barcoding provides a good estimate of both AMF community structure and relation to environmental variables. However, this primer system does not fit in with cross-compartment surveys (roots vs. soil) as it can underestimate AMF diversity in soil samples. When specifically focusing on AMF, the 18S primer system resulted in wide coverage and marginal non-target amplification.

Historical biome distribution and recent human disturbance shape the diversity of arbuscular mycorrhizal fungi

The availability of global microbial diversity data, collected using standardized metabarcoding techniques, makes microorganisms promising models for investigating the role of regional and local factors in driving biodiversity. Here we modelled the global diversity of symbiotic arbuscular mycorrhizal (AM) fungi using currently available data on AM fungal molecular diversity (small subunit (SSU) ribosomal RNA (rRNA) gene sequences) in field samples. To differentiate between regional and local effects, we estimated species pools (sets of potentially suitable taxa) for each site, which are expected to reflect regional processes. We then calculated community completeness, an index showing the fraction of the species pool present, which is expected to reflect local processes. We found significant spatial variation, globally in species pool size, as well as in local and dark diversity (absent members of the species pool). Species pool size was larger close to areas containing tropical grasslands during the last glacial maximum, which are possible centres of diversification. Community completeness was greater in regions of high wilderness (remoteness from human disturbance). Local diversity was correlated with wilderness and current connectivity to mountain grasslands. Applying the species pool concept to symbiotic fungi facilitated a better understanding of how biodiversity can be jointly shaped by large-scale historical processes and recent human disturbance.