Arbuscular mycorrhizal fungal communities in plant roots are not random assemblages

Host preference and network properties in biotrophic plant-fungal associations

Analytical methods can offer insights into the structure of biological networks, but mechanisms that determine the structure of these networks remain unclear. We conducted a synthesis based on 111 previously published datasets to assess a range of ecological and evolutionary mechanisms that may influence the plant-associated fungal interaction networks. We calculated the relative host effect on fungal community composition and compared nestedness and modularity among different mycorrhizal types and endophytic fungal guilds. We also assessed how plant-fungal network structure was related to host phylogeny, environmental and sampling properties. Orchid mycorrhizal fungal communities responded most strongly to host identity, but the effect of host was similar among all other fungal guilds. Community nestedness, which did not differ among fungal guilds, declined significantly with increasing mean annual precipitation on a global scale. Orchid and ericoid mycorrhizal fungal communities were more modular than ectomycorrhizal and root endophytic communities, with arbuscular mycorrhizal fungi in an intermediate position. Network properties among a broad suite of plant-associated fungi were largely comparable and generally unrelated to phylogenetic distance among hosts. Instead, network metrics were predominantly affected by sampling and matrix properties, indicating the importance of study design in properly inferring ecological patterns.

Arbuscular mycorrhizal fungus responses to disturbance are context-dependent

Anthropogenic disturbance is one of the most important forces shaping soil ecosystems. While organisms that live in the soil, such as arbuscular mycorrhizal (AM) fungi, are sensitive to disturbance, their response is not always predictable. Given the range of disturbance types and differences among AM fungi in their growth strategies, the unpredictability of the responses of AM fungi to disturbance is not surprising. We investigated the role of disturbance type (i.e., soil disruption, agriculture, host perturbation, and chemical disturbance) and fungus identity on disturbance response in the AM symbiosis. Using meta-analysis, we found evidence for differential disturbance response among AM fungal species, as well as evidence that particular fungal species are especially susceptible to certain disturbance types, perhaps because of their life history strategies.

Arbuscular mycorrhizal fungi altered the hypericin, pseudohypericin, and hyperforin content in flowers of Hypericum perforatum grown under contrasting P availability in a highly organic substrate

St. John's Wort (Hypericum perforatum) is a perennial herb able to produce water-soluble active ingredients (a.i.), mostly in flowers, with a wide range of medicinal and biotechnological uses. However, information about the ability of arbuscular mycorrhizal fungi (AMF) to affect its biomass accumulation, flower production, and concentration of a.i. under contrasting nutrient availability is still scarce. In the present experiment, we evaluated the role of AMF on growth, flower production, and concentration of bioactive secondary metabolites (hypericin, pseudohypericin, and hyperforin) of H. perforatum under contrasting P availability. AMF stimulated the production of aboveground biomass under low P conditions and increased the production of root biomass. AMF almost halved the number of flowers per plant by means of a reduction of the number of flower-bearing stems per plant under high P availability and through a lower number of flowers per stem in the low-P treatment. Flower hyperforin concentration was 17.5% lower in mycorrhizal than in non-mycorrhizal plants. On the contrary, pseudohypericin and hypericin concentrations increased by 166.8 and 279.2%, respectively, with AMF under low P availability, whereas no effect of AMF was found under high P availability. These results have implications for modulating the secondary metabolite production of H. perforatum. However, further studies are needed to evaluate the competition for photosynthates between AMF and flowers at different nutrient availabilities for both plant and AM fungus.

Fungal-host diversity among mycoheterotrophic plants increases proportionally to their fungal-host overlap

The vast majority of plants obtain an important proportion of vital resources from soil through mycorrhizal fungi. Generally, this happens in exchange of photosynthetically fixed carbon, but occasionally the interaction is mycoheterotrophic, and plants obtain carbon from mycorrhizal fungi. This process results in an antagonistic interaction between mycoheterotrophic plants and their fungal hosts. Importantly, the fungal-host diversity available for plants is restricted as mycoheterotrophic interactions often involve narrow lineages of fungal hosts. Unfortunately, little is known whether fungal-host diversity may be additionally modulated by plant-plant interactions through shared hosts. Yet, this may have important implications for plant competition and coexistence. Here, we use DNA sequencing data to investigate the interaction patterns between mycoheterotrophic plants and arbuscular mycorrhizal fungi. We find no phylogenetic signal on the number of fungal hosts nor on the fungal hosts shared among mycoheterotrophic plants. However, we observe a potential trend toward increased phylogenetic diversity of fungal hosts among mycoheterotrophic plants with increasing overlap in their fungal hosts. While these patterns remain for groups of plants regardless of location, we do find higher levels of overlap and diversity among plants from the same location. These findings suggest that species coexistence cannot be fully understood without attention to the two sides of ecological interactions.

Temperature-mediated local adaptation alters the symbiotic function in arbuscular mycorrhiza

Variation in the symbiotic function of arbuscular mycorrhizal fungi (AM fungi) has been demonstrated among distinct biotic and abiotic interactions. However, there is little knowledge on how local temperature conditions influence the functional divergence of AM symbionts in alpine ecosystems. Here, we conduct a reciprocal inoculation experiment to explore the three-way interactions among plants, AM fungal inoculum and temperature at sites of contrasting elevation. Evidence of local adaptation of plant growth was found only under low temperature conditions, with no consistent local versus foreign effect found in AM fungal performance. The origin of either the plant or the inoculum relative to the temperature was important in explaining symbiotic function. Specifically, when inoculum and temperature were sympatric but allopatric to the plant, poor adaptation by the plant to the novel environment was clearly found under both temperature conditions. Further analysis found that the symbiotic function was inversely related to fungal diversity under high temperature conditions. These results suggest that local adaptation represents a powerful factor in the establishment of novel combinations of plant, inoculum and temperature, and confirms the importance of taking into account both biotic and abiotic interactions in the prediction of the response of symbionts to global environmental change.

The influence of environmental factors on communities of arbuscular mycorrhizal fungi associated with Chenopodium ambrosioides revealed by MiSeq sequencing investigation

Arbuscular mycorrhizal fungi (AMF) affect multiple ecosystem functions and processes, the assemblages of which vary across ecosystems. However, the influences of environmental factors on AMF communities which may shape these communities are still largely unknown. In this study, AMF communities from roots and rhizosphere soils of Chenopodium ambrosioides in different natural soils were investigated. The root habitat showed significantly smaller numbers of OTUs and lower community richness compared to the rhizosphere soil habitat. Most OTUs in the root habitat were shared by the soil habitat from the same sampling site, indicating that rhizosphere soils represent a pool of AMF species, a fraction of which is recruited by plants. Most of the AMF in root habitats were Glomeraceae, suggesting recruitment preferences of AMF by plants. The relative contributions of environmental factors to explain variations in AMF community composition and phylogenetic structure were assessed. The results revealed soil properties predominantly explained the variation, followed by geographic and climate parameters which explained a small fraction independently, while the host plant showed few explanations. Overall, our results indicated that soil and root habitats as well as soil characters, especially pH, nitrogen and micronutrients (Zn and Cu) affected AMF communities significantly.

Arbuscular mycorrhizal interactions of mycoheterotrophic Thismia are more specialized than in autotrophic plants

In general, plants and arbuscular mycorrhizal (AM) fungi exchange photosynthetically fixed carbon for soil nutrients, but occasionally nonphotosynthetic plants obtain carbon from AM fungi. The interactions of these mycoheterotrophic plants with AM fungi are suggested to be more specialized than those of green plants, although direct comparisons are lacking. We investigated the mycorrhizal interactions of both green and mycoheterotrophic plants. We used next-generation DNA sequencing to compare the AM communities from roots of five closely related mycoheterotrophic species of Thismia (Thismiaceae), roots of surrounding green plants, and soil, sampled over the entire temperate distribution of Thismia in Australia and New Zealand. We observed that the fungal communities of mycoheterotrophic and green plants are phylogenetically more similar within than between these groups of plants, suggesting a specific association pattern according to plant trophic mode. Moreover, mycoheterotrophic plants follow a more restricted association with their fungal partners in terms of phylogenetic diversity when compared with green plants, targeting more clustered lineages of fungi, independent of geographic origin. Our findings demonstrate that these mycoheterotrophic plants target more narrow lineages of fungi than green plants, despite the larger fungal pool available in the soil, and thus they are more specialized towards mycorrhizal fungi than autotrophic plants.

Arbuscular mycorrhizal fungi communities from tropical Africa reveal strong ecological structure

Understanding the distribution and diversity of arbuscular mycorrhizal fungi (AMF) and the rules that govern AMF assemblages has been hampered by a lack of data from natural ecosystems. In addition, the current knowledge on AMF diversity is biased towards temperate ecosystems, whereas little is known about other habitats such as dry tropical ecosystems. We explored the diversity and structure of AMF communities in grasslands, savannas, dry forests and miombo in a protected area under dry tropical climate (Gorongosa National Park, Mozambique) using 454 pyrosequencing. In total, 147 AMF virtual taxa (VT) were detected, including 22 VT new to science. We found a high turnover of AMF with ˂ 12% of VT present in all vegetation types. Forested areas supported more diverse AMF communities than savannas and grassland. Miombo woodlands had the highest AMF richness, number of novel VT, and number of exclusive and indicator taxa. Our data reveal a sharp differentiation of AMF communities between forested areas and periodically flooded savannas and grasslands. This marked ecological structure of AMF communities provides the first comprehensive landscape-scale evidence that, at the background of globally low endemism of AMF, local communities are shaped by regional processes including environmental filtering by edaphic properties and natural disturbance.

Aligning molecular studies of mycorrhizal fungal diversity with ecologically important levels of diversity in ecosystems

Arbuscular mycorrhizal fungi (AMF) occur in the roots of most plants and are an ecologically important component of the soil microbiome. Richness of AMF taxa is a strong driver of plant diversity and productivity, thus providing a rationale for characterizing AMF diversity in natural ecosystems. Consequently, a large number of molecular studies on AMF community composition are currently underway. Most published studies, at best, only address species or genera-level resolution. However, several experimental studies indicate that variation in plant performance is large among plants colonised by different individuals of one AMF species. Thus, there is a potential disparity between how molecular community ecologists are currently describing AMF diversity and the level of AMF diversity that may actually be ecologically relevant. We propose a strategy to find many polymorphic loci that can define within-species genetic variability within AMF, or at any level of resolution desired within the Glomermycota. We propose that allele diversity at the intraspecific level could then be measured for target AMF groups, or at other levels of resolution, in environmental DNA samples. Combining the use of such markers with experimental studies on AMF diversity would help to elucidate the most important level(s) of AMF diversity in plant communities. Our goal is to encourage ecologists who are trying to explain how mycorrhizal fungal communities are structured to take an approach that could also yield meaningful information that is relevant to the diversity, functioning and productivity of ecosystems.

Plant community, geographic distance and abiotic factors play different roles in predicting AMF biogeography at the regional scale in northern China

Arbuscular mycorrhizal fungi (AMF) are ubiquitous mutualists of terrestrial plants and play key roles in regulating various ecosystem processes, but little is known about AMF biogeography at regional scale. This study aims at exploring the key predictors of AMF communities across a 5000-km transect in northern China. We determined the soil AMF species richness and community composition at 47 sites representative of four vegetation types (meadow steppe, typical steppe, desert steppe and desert) and related them to plant community characteristics, abiotic factors and geographic distance. The results showed that soil pH was the strongest predictor of AMF richness and phylogenetic diversity. However, abiotic factors only have a low predictive effect on AMF community composition or phylogenetic patterns. By contrast, we found a significant relationship between community composition of AMF and plants, which was a surprising result given the extent of heterogeneity in the plant community across this transect. Moreover, the geographic distance predominantly explained the AMF phylogenetic structure, implying that history evolutionary may play a role in shaping AMF biogeographic patterns. This study highlighted the different roles of main factors in predicting AMF biogeography, and bridge landscape-scale studies to more recent global-scale efforts.

Prospects for arbuscular mycorrhizal fungi (AMF) to assist in phytoremediation of soil hydrocarbon contaminants

Arbuscular mycorrhizal fungi (AMF) form mutualistic associations with the roots of 80-90% of vascular plant species and may constitute up to 50% of the total soil microbial biomass. AMF have been considered to be a tool to enhance phytoremediation, as their mycelium create a widespread underground network that acts as a bridge between plant roots, soil and rhizosphere microorganisms. Abundant extramatrical hyphae extend the rhizosphere thus creating the hyphosphere, which significantly increases the area of a plant's access to nutrients and contaminants. The paper presents and evaluates the role and significance of AMF in phytoremediation of hydrocarbon contaminated sites. We focused on (1) an impact of hydrocarbons on arbuscular mycorrhizal symbiosis, (2) a potential of AMF to enhance phytoremediation, (3) determinants that influence effectiveness of hydrocarbon removal from contaminated soils. This knowledge may be useful for selection of proper plant and fungal symbionts and crucial to optimize environmental conditions for effective AMF-mediated phytoremediation. It has been concluded that three-component phytoremediation systems based on synergistic interactions between plant roots, AMF and hydrocarbon-degrading microorganisms demonstrated high effectiveness in dissipation of organic pollutants in soil.

Community assembly and coexistence in communities of arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi are asexual, obligately symbiotic fungi with unique morphology and genomic structure, which occupy a dual niche, that is, the soil and the host root. Consequently, the direct adoption of models for community assembly developed for other organism groups is not evident. In this paper we adapted modern coexistence and assembly theory to arbuscular mycorrhizal fungi. We review research on the elements of community assembly and coexistence of arbuscular mycorrhizal fungi, highlighting recent studies using molecular methods. By addressing several points from the individual to the community level where the application of modern community ecology terms runs into problems when arbuscular mycorrhizal fungi are concerned, we aim to account for these special circumstances from a mycocentric point of view. We suggest that hierarchical spatial structure of arbuscular mycorrhizal fungal communities should be explicitly taken into account in future studies. The conceptual framework we develop here for arbuscular mycorrhizal fungi is also adaptable for other host-associated microbial communities.

Land-use intensity and host plant simultaneously shape the composition of arbuscular mycorrhizal fungal communities in a Mediterranean drained peatland

Land-use change is known to be a major threat to biodiversity and ecosystem services in Mediterranean areas. However, the potential for different host plants to modulate the effect of land-use intensification on community composition of arbuscular mycorrhizal fungi (AMF) is still poorly understood. To test the hypothesis that low land-use intensity promotes AMF diversity at different taxonomic scales and to determine whether any response is dependent upon host plant species identity, we characterised AMF communities in the roots of 10 plant species across four land use types of differing intensity in a Mediterranean peatland system. AMF were identified using 454 pyrosequencing. This revealed an overall low level of AMF richness in the peaty soils; lowest AMF richness in the intense cropping system at both virtual taxa and family level; strong modulation by the host plant of the impact of land-use intensification on AMF communities at the virtual taxa level; and a significant effect of land-use intensification on AMF communities at the family level. These findings have implications for understanding ecosystem stability and productivity and should be considered when developing soil-improvement strategies in fragile ecosystems, such as Mediterranean peatlands.

Effect of vegetation types on soil arbuscular mycorrhizal fungi and nitrogen-fixing bacterial communities in a karst region

Arbuscular mycorrhizal (AM) fungi and nitrogen-fixing bacteria play important roles in plant growth and recovery in degraded ecosystems. The desertification in karst regions has become more severe in recent decades. Evaluation of the fungal and bacterial diversity of such regions during vegetation restoration is required for effective protection and restoration in these regions. Therefore, we analyzed relationships among AM fungi and nitrogen-fixing bacteria abundances, plant species diversity, and soil properties in four typical ecosystems of vegetation restoration (tussock (TK), shrub (SB), secondary forest (SF), and primary forest (PF)) in a karst region of southwest China. Abundance of AM fungi and nitrogen-fixing bacteria, plant species diversity, and soil nutrient levels increased from the tussock to the primary forest. The AM fungus, nitrogen-fixing bacterium, and plant community composition differed significantly between vegetation types (p < 0.05). Plant richness and pH were linked to the community composition of fungi and nitrogen-fixing bacteria, respectively. Available phosphorus, total nitrogen, and soil organic carbon levels and plant richness were positively correlated with the abundance of AM fungi and nitrogen-fixing bacteria (p < 0.05). The results suggested that abundance of AM fungi and nitrogen-fixing bacteria increased from the tussock to the primary forest and highlight the essentiality of these communities for vegetation restoration.

The Potential Role of Arbuscular Mycorrhizal Fungi in the Restoration of Degraded Lands

Experiences worldwide reveal that degraded lands restoration projects achieve little success or fail. Hence, understanding the underlying causes and accordingly, devising appropriate restoration mechanisms is crucial. In doing so, the ever-increasing aspiration and global commitments in degraded lands restoration could be realized. Here we explain that arbuscular mycorrhizal fungi (AMF) biotechnology is a potential mechanism to significantly improve the restoration success of degraded lands. There are abundant scientific evidences to demonstrate that AMF significantly improve soil attributes, increase above and belowground biodiversity, significantly improve tree/shrub seedlings survival, growth and establishment on moisture and nutrient stressed soils. AMF have also been shown to drive plant succession and may prevent invasion by alien species. The very few conditions where infective AMF are low in abundance and diversity is when the soil erodes, is disturbed and is devoid of vegetation cover. These are all common features of degraded lands. Meanwhile, degraded lands harbor low levels of infective AMF abundance and diversity. Therefore, the successful restoration of infective AMF can potentially improve the restoration success of degraded lands. Better AMF inoculation effects result when inocula are composed of native fungi instead of exotics, early seral instead of late seral fungi, and are consortia instead of few or single species. Future research efforts should focus on AMF effect on plant community primary productivity and plant competition. Further investigation focusing on forest ecosystems, and carried out at the field condition is highly recommended. Devising cheap and ethically widely accepted inocula production methods and better ways of AMF in situ management for effective restoration of degraded lands will also remain to be important research areas.

The effect of different land uses on arbuscular mycorrhizal fungi in the northwestern Black Sea Region

The object of the present research was to establish correlations between the status of root colonization of arbuscular mycorrhizal fungi (AMF) and different types of land use. In order to achieve this aim, rhizosphere soil samples from grassland crops were taken during June and July of 2013 in order to use for determining several soil characteristics. The 27 different taxa and 60 soil samples were collected from the rhizosphere level in the study areas. The existence of AMF was confirmed in 100 % of these plants with different rations of colonization (approximately 12-89 %). Bromus racemosus L. (pasture) was the most dense taxon with the percentage of AMF colonization of 88.9 %, and Trifolium pratense L. (forest) was the least dense taxon with the percentage of AMF colonization of 12.2 % (average 52.0 %). As a result of the statistical analysis, a positive relationship was found between the botanical composition of legumes and AMF colonization (r = 0.35; p = 0.006). However, a negative relationship was determined between botanical composition of other plant families and AMF colonization (r = -0.39; p = 0.002). In addition, a positive relationship was defined between soil pH (H2O) and the root colonization of AMF (r = 0.35; p = 0.005). The pasture had the highest mean value of AMF root colonization. However, the pasture and gap in the forest were in the same group, according to the results of the S-N-K test.

Soil Characteristics Driving Arbuscular Mycorrhizal Fungal Communities in Semiarid Mediterranean Soils

We investigated communities of arbuscular mycorrhizal fungi (AMF) in the roots and the rhizosphere soil of Brachypodium retusum in six different natural soils under field conditions. We explored phylogenetic patterns of AMF composition using indicator species analyses to find AMF associated with a given habitat (root versus rhizosphere) or soil type. We tested whether the AMF characteristics of different habitats or contrasting soils were more closely related than expected by chance. Then we used principal-component analysis and multivariate analysis of variance to test for the relative contribution of each factor in explaining the variation in fungal community composition. Finally, we used redundancy analysis to identify the soil properties that significantly explained the differences in AMF communities across soil types. The results pointed out a tendency of AMF communities in roots to be closely related and different from those in the rhizosphere soil. The indicator species analyses revealed AMF associated with rhizosphere soil and the root habitat. Soil type also determined the distribution of AMF communities in soils, and this effect could not be attributed to a single soil characteristic, as at least three soil properties related to microbial activity, i.e., pH and levels of two micronutrients (Mn and Zn), played significant roles in triggering AMF populations.

IMPORTANCE

Communities of arbuscular mycorrhizal fungi (AMF) are main components of soil biota that can determine the productivity of ecosystems. These fungal assemblages vary across host plants and ecosystems, but the main ecological processes that shape the structures of these communities are still largely unknown. A field study in six different soil types from semiarid areas revealed that AMF communities are significantly influenced by habitat (soil versus roots) and soil type. In addition, three soil properties related to microbiological activity (i.e., pH and manganese and zinc levels) were the main factors triggering the distribution of AMF. These results contribute to a better understanding of the ecological factors that can shape AMF communities, an important soil microbial group that affects multiple ecosystem functions.

Towards an Enhanced Understanding of Plant-Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism

Phytoremediation is a promising technology to clean-up contaminated soils based on the synergistic actions of plants and microorganisms. However, to become a widely accepted, and predictable remediation alternative, a deeper understanding of the plant-microbe interactions is needed. A number of studies link the success of phytoremediation to the plant-associated microbiome functioning, though whether the microbiome can exist in alternative, functional states for soil remediation, is incompletely understood. Moreover, current approaches that target the plant host, and environment separately to improve phytoremediation, potentially overlook microbial functions and properties that are part of the multiscale complexity of the plant-environment wherein biodegradation takes place. In contrast, in situ studies of phytoremediation research at the metaorganism level (host and microbiome together) are lacking. Here, we discuss a competition-driven model, based on recent evidence from the metagenomics level, and hypotheses generated by microbial community ecology, to explain the establishment of a catabolic rhizosphere microbiome in a contaminated soil. There is evidence to ground that if the host provides the right level and mix of resources (exudates) over which the microbes can compete, then a competitive catabolic and plant-growth promoting (PGP) microbiome can be selected for as long as it provides a competitive superiority in the niche. The competition-driven model indicates four strategies to interfere with the microbiome. Specifically, the rhizosphere microbiome community can be shifted using treatments that alter the host, resources, environment, and that take advantage of prioritization in inoculation. Our model and suggestions, considering the metaorganism in its natural context, would allow to gain further knowledge on the plant-microbial functions, and facilitate translation to more effective, and predictable phytotechnologies.

The Scion/Rootstock Genotypes and Habitats Affect Arbuscular Mycorrhizal Fungal Community in Citrus

Citrus roots have rare root hairs and thus heavily depend on arbuscular mycorrhizal fungi (AMF) for mineral nutrient uptake. However, the AMF community structure of citrus is largely unknown. By using 454-pyrosequencing of 18S rRNA gene fragment, we investigated the genetic diversity of AMF colonizing citrus roots, and evaluated the impact of habitats and rootstock and scion genotypes on the AMF community structure. Over 7,40,000 effective sequences were obtained from 77 citrus root samples. These sequences were assigned to 75 AMF virtual taxa, of which 66 belong to Glomus, highlighting an absolute dominance of this AMF genus in symbiosis with citrus roots. The citrus AMF community structure is significantly affected by habitats and host genotypes. Interestingly, our data suggests that the genotype of the scion exerts a greater impact on the AMF community structure than that of the rootstock where the physical root-AMF association occurs. This study not only provides a comprehensive assessment for the community composition of the AMF in citrus roots under different conditions, but also sheds novel insights into how the AMF community might be indirectly influenced by the spatially separated yet metabolically connected partner—the scion—of the grafted citrus tree.

Below-ground plant-fungus network topology is not congruent with above-ground plant-animal network topology

In nature, plants and their pollinating and/or seed-dispersing animals form complex interaction networks. The commonly observed pattern of links between specialists and generalists in these networks has been predicted to promote species coexistence. Plants also build highly species-rich mutualistic networks below ground with root-associated fungi, and the structure of these plant-fungus networks may also affect terrestrial community processes. By compiling high-throughput DNA sequencing data sets of the symbiosis of plants and their root-associated fungi from three localities along a latitudinal gradient, we uncovered the entire network architecture of these interactions under contrasting environmental conditions. Each network included more than 30 plant species and hundreds of mycorrhizal and endophytic fungi belonging to diverse phylogenetic groups. The results were consistent with the notion that processes shaping host-plant specialization of fungal species generate a unique linkage pattern that strongly contrasts with the pattern of above-ground plant-partner networks. Specifically, plant-fungus networks lacked a "nested" architecture, which has been considered to promote species coexistence in plant-partner networks. Rather, the below-ground networks had a conspicuous "antinested" topology. Our findings lead to the working hypothesis that terrestrial plant community dynamics are likely determined by the balance between above-ground and below-ground webs of interspecific interactions.

Arbuscular mycorrhizal fungi counteract the Janzen-Connell effect of soil pathogens

Soilborne pathogens can contribute to diversity maintenance in tree communities through the Janzen-Connell effect, whereby the pathogenic reduction of seedling performance attenuates with distance from conspecifics. By contrast, arbuscular mycorrhizal fungi (AMF) have been reported to promote seedling performance; however, it is unknown whether this is also distance dependent. Here, we investigate the distance dependence of seedling performance in the presence of both pathogens and AMF. In a subtropical forest in south China, we conducted a four-year field census of four species with relatively large phylogenetic distances and found no distance-dependent mortality for newly germinated seedlings. By experimentally separating the effects of AMF and pathogens on seedling performance of six subtropical tree species in a shade house, we found that soil pathogens significantly inhibited seedling survival and growth while AMF largely promoted seedling growth, and these effects were host specific and declined with increasing conspecific distance. Together, our field and experimental results suggest that AMF can neutralize the negative effect of pathogens and that the Janzen-Connell effect may play a less prominent role in explaining diversity of nondominant tree species than previously thought.

Altitudinal distribution patterns of AM fungal assemblages in a Tibetan alpine grassland

A better understanding of biogeography of Glomeromycota is essential for the conservation of arbuscular mycorrhizal (AM) fungal species and the ecosystem services that they provide worldwide. We examined the spatial dynamics of AM fungi along two slopes (4149 m a.s.l. to the summit at 5033 m a.s.l.) of Mount Mila on the Tibetan Plateau. Our hypothesis was that AM fungal communities at higher elevation would show distinct assemblages with lower diversity in conditions of increasing environmental harshness. A total of 52 operational taxonomic units (OTUs) spanning all four orders were detected and some OTUs were habitat specific. Nearly 30% of the OTUs were new phylotypes, including two family-like clades. Distinct communities of AM fungi were found at the higher elevation, demonstrating potential niche differentiation along the elevation gradient. Elevation patterns of taxon richness/diversity differed between the two transects, decreasing with increasing elevation on the eastern slope and being unimodal (or lacking a pattern) on the western slope. Taken together, our findings provide evidence of a significant spatial structure of AM fungi across the elevation gradient, with the distribution patterns of these fungi regulated simultaneously by the plant communities, soil properties and climatic conditions in this plateau montane ecosystem.

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

Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities.

Mycorrhizal networks and coexistence in species-rich orchid communities

Multispecies assemblages often consist of a complex network of interactions. Describing the architecture of these networks is a first step in understanding the stability and persistence of these species-rich communities. Whereas a large body of research has been devoted to the description of above-ground interactions, much less attention has been paid to below-ground interactions, probably because of difficulties to adequately assess the nature and diversity of interactions occurring below the ground. In this study, we used 454 amplicon pyrosequencing to investigate the architecture of the network between mycorrhizal fungi and 20 orchid species co-occurring in a species-rich Mediterranean grasslands. We found 100 different fungal operational taxonomic units (OTUs) known to be mycorrhizal in orchids, most of which were members related to the genera Ceratobasidium and Tulasnella. The network of interactions was significantly compartmentalized (M = 0.589, P = 0.001), but not significantly nested (N = 0.74, NODF = 10.58; P > 0.05). Relative nestedness was negative (N* = -0.014), also suggesting the existence of isolated groups of interacting species. Compartmentalization is a typical feature of ecological systems showing high interaction intimacy, and may reflect strong specialization between orchids and fungi resulting from physiological, physical or spatial constraints.

Quantification of arbuscular mycorrhizal fungal DNA in roots: how important is material preservation?

Monitoring populations of arbuscular mycorrhizal fungi (AMF) in roots is a pre-requisite for improving our understanding of AMF ecology and functioning of the symbiosis in natural conditions. Among other approaches, quantification of fungal DNA in plant tissues by quantitative real-time PCR is one of the advanced techniques with a great potential to process large numbers of samples and to deliver truly quantitative information. Its application potential would greatly increase if the samples could be preserved by drying, but little is currently known about the feasibility and reliability of fungal DNA quantification from dry plant material. We addressed this question by comparing quantification results based on dry root material to those obtained from deep-frozen roots of Medicago truncatula colonized with Rhizophagus sp. The fungal DNA was well conserved in the dry root samples with overall fungal DNA levels in the extracts comparable with those determined in extracts of frozen roots. There was, however, no correlation between the quantitative data sets obtained from the two types of material, and data from dry roots were more variable. Based on these results, we recommend dry material for qualitative screenings but advocate using frozen root materials if precise quantification of fungal DNA is required.

The composition of arbuscular mycorrhizal fungal communities differs among the roots, spores and extraradical mycelia associated with five Mediterranean plant species

Arbuscular mycorrhizal fungi (AMF) are essential constituents of most terrestrial ecosystems. AMF species differ in terms of propagation strategies and the major propagules they form. This study compared the AMF community composition of different propagule fractions - colonized roots, spores and extraradical mycelium (ERM) - associated with five Mediterranean plant species in Sierra de Baza Natural Park (Granada, Spain). AMF were identified using 454 pyrosequencing of the SSU rRNA gene. A total of 96 AMF phylogroups [virtual taxa (VT)] were detected in the study site, including 31 novel VT. After per-sample sequencing depth standardization, 71 VT were recorded from plant roots, and 47 from each of the spore and ERM fractions. AMF communities differed significantly among the propagule fractions, and the root-colonizing fraction differed among host plant species. Indicator VT were detected for the root (13 Glomus VT), spore (Paraglomus VT281, VT336, Pacispora VT284) and ERM (Diversispora VT62) fractions. This study provides detailed evidence from a natural system that AMF taxa are differentially allocated among soil mycelium, soil spores and colonized root propagules. This has important implications for interpreting AMF diversity surveys and designing applications of AMF in vegetation restoration.

Land-use intensity and host plant identity interactively shape communities of arbuscular mycorrhizal fungi in roots of grassland plants

We studied the effect of host plant identity and land-use intensity (LUI) on arbuscular mycorrhizal fungi (AMF, Glomeromycota) communities in roots of grassland plants. These are relevant factors for intraradical AMF communities in temperate grasslands, which are habitats where AMF are present in high abundance and diversity. In order to focus on fungi that directly interact with the plant at the time, we investigated root-colonizing communities. Our study sites represent an LUI gradient with different combinations of grazing, mowing, and fertilization. We used massively parallel multitag pyrosequencing to investigate AMF communities in a large number of root samples, while being able to track the identity of the host. We showed that host plants significantly differed in AMF community composition, while land use modified this effect in a plant species-specific manner. Communities in medium and low land-use sites were subsets of high land-use communities, suggesting a differential effect of land use on the dispersal of AMF species with different abundances and competitive abilities. We demonstrate that in these grasslands, there is a small group of highly abundant, generalist fungi which represent the dominating species in the AMF community.

Order of arrival structures arbuscular mycorrhizal colonization of plants

Priority effects - the impact of a species' arrival on subsequent community development - have been shown to influence species composition in many organisms. Whether priority effects among arbuscular mycorrhizal fungi (AMF) structure fungal root communities is not well understood. Here, we investigated whether priority effects influence the success of two closely related AMF species (Rhizophagus irregularis and Glomus aggregatum), hypothesizing that a resident AMF suppresses invader success, this effect is time-dependent and a resident will experience reduced growth when invaded. We performed two glasshouse experiments using modified pots, which permitted direct inoculation of resident and invading AMF on the roots. We quantified intraradical AMF abundances using quantitative PCR and visual colonization percentages. We found that both fungi suppressed the invading species and that this effect was strongly dependent on the time lag between inoculations. In contrast to our expectations, neither resident AMF was negatively affected by invasion. We show that order of arrival can influence the abundance of AMF species colonizing a host. These priority effects can have important implications for AMF ecology and the use of fungal inocula in sustainable agriculture.

Plant phosphorus acquisition in a common mycorrhizal network: regulation of phosphate transporter genes of the Pht1 family in sorghum and flax

In a preceding microcosm study, we found huge differences in phosphorus (P) acquisition in sorghum (Sorghum bicolor) and flax (Linum usitatissimum) sharing a common mycorrhizal network (CMN). Is the transcriptional regulation of arbuscular mycorrhizal (AM)-induced inorganic orthophosphate (Pi) transporters responsible for these differences? We characterized and analyzed the expression of Pi transporters of the Pht1 family in both plant species, and identified two new AM-inducible Pi transporters in flax. Mycorrhizal Pi acquisition was strongly affected by the combination of plant and AM fungal species. A corresponding change in the expression of two AM-inducible Pht1 transporters was noticed in both plants (SbPT9, SbPT10, LuPT5 and LuPT8), but the effect was very weak. Overall, the expression level of these genes did not explain why flax took up more Pi from the CMN than did sorghum. The post-transcriptional regulation of the transporters and their biochemical properties may be more important for their function than the fine-tuning of their gene expression.

The composition of arbuscular mycorrhizal fungal communities in the roots of a ruderal forb is not related to the forest fragmentation process

Land-use changes and forest fragmentation have strong impact on biodiversity. However, little is known about the influence of new landscape configurations on arbuscular mycorrhizal fungal (AMF) community composition. We used 454 pyrosequencing to assess AMF diversity in plant roots from a fragmented forest. We detected 59 virtual taxa (VT; phylogenetically defined operational taxonomic units) of AMF - including 10 new VT - in the roots of Euphorbia acerensis. AMF communities were mainly composed of members of family Glomeraceae and were similar throughout the fragmented landscape, despite variation in forest fragment size (i.e. small, medium and large) and isolation (i.e. varying pairwise distances). AMF communities in forest fragments were phylogenetically clustered compared with the global, but not regional and local AMF taxon pools. This indicates that non-random community assembly processes possibly related to dispersal limitation at a large scale, rather than habitat filtering or biotic interactions, may be important in structuring the AMF communities. In this system, forest fragmentation did not appear to influence AMF community composition in the roots of the ruderal plant. Whether this is true for AMF communities in soil and the roots of other ecological groups of host plants or in other habitats deserves further study.

Nitrogen and phosphorus additions impact arbuscular mycorrhizal abundance and molecular diversity in a tropical montane forest

Increased nitrogen (N) depositions expected in the future endanger the diversity and stability of ecosystems primarily limited by N, but also often co-limited by other nutrients like phosphorus (P). In this context a nutrient manipulation experiment (NUMEX) was set up in a tropical montane rainforest in southern Ecuador, an area identified as biodiversity hotspot. We examined impacts of elevated N and P availability on arbuscular mycorrhizal fungi (AMF), a group of obligate biotrophic plant symbionts with an important role in soil nutrient cycles. We tested the hypothesis that increased nutrient availability will reduce AMF abundance, reduce species richness and shift the AMF community toward lineages previously shown to be favored by fertilized conditions. NUMEX was designed as a full factorial randomized block design. Soil cores were taken after 2 years of nutrient additions in plots located at 2000 m above sea level. Roots were extracted and intraradical AMF abundance determined microscopically; the AMF community was analyzed by 454-pyrosequencing targeting the large subunit rDNA. We identified 74 operational taxonomic units (OTUs) with a large proportion of Diversisporales. N additions provoked a significant decrease in intraradical abundance, whereas AMF richness was reduced significantly by N and P additions, with the strongest effect in the combined treatment (39% fewer OTUs), mainly influencing rare species. We identified a differential effect on phylogenetic groups, with Diversisporales richness mainly reduced by N additions in contrast to Glomerales highly significantly affected solely by P. Regarding AMF community structure, we observed a compositional shift when analyzing presence/absence data following P additions. In conclusion, N and P additions in this ecosystem affect AMF abundance, but especially AMF species richness; these changes might influence plant community composition and productivity and by that various ecosystem processes.

Assembly of complex plant-fungus networks

Species in ecological communities build complex webs of interaction. Although revealing the architecture of these networks is fundamental to understanding ecological and evolutionary dynamics in nature, it has been difficult to characterize the structure of most species-rich ecological systems. By overcoming this limitation through next-generation sequencing technology, we herein uncover the network architecture of below-ground plant-fungus symbioses, which are ubiquitous to terrestrial ecosystems. The examined symbiotic network of a temperate forest in Japan includes 33 plant species and 387 functionally and phylogenetically diverse fungal taxa, and the overall network architecture differs fundamentally from that of other ecological networks. In contrast to results for other ecological networks and theoretical predictions for symbiotic networks, the plant-fungus network shows moderate or relatively low levels of interaction specialization and modularity and an unusual pattern of 'nested' network architecture. These results suggest that species-rich ecological networks are more architecturally diverse than previously recognized.

Where the wild things are: looking for uncultured Glomeromycota

Our knowledge of Glomeromycotan fungi rests largely on studies of cultured isolates. However, these isolates probably comprise one life-history strategy - ruderal. Consequently, our knowledge of arbuscular mycorrhizal (AM) fungi may be biased towards fungi that occur primarily in disturbed habitats and associate with disturbance-tolerant host plants. We can expect to see a signal for this in DNA-based community surveys: human-impacted habitats and cultivated plants should yield a higher proportion of AM fungal species that have been cultured compared with natural habitats and wild plants. Using the MaarjAM database (a curated open-access database of Glomeromycotan sequences), we performed a meta-analysis on studies that described AM fungal communities from a variety of habitats and host plants. We found a greater proportion of cultured AM fungal taxa in human-impacted habitats. In particular, undisturbed forests and grasslands/savannahs contained significantly fewer cultured taxa than human-impacted sites. We also found that wild plants hosted fewer cultured fungal taxa than cultivated plants. Our data show that natural communities of AM fungi are composed largely of uncultured taxa, and this is particularly pronounced in natural habitats and wild plants. We are better poised to understand the functioning of AM symbioses associated with cultivated plants and human-impacted habitats.

The interactions between plant life form and fungal traits of arbuscular mycorrhizal fungi determine the symbiotic community

Arbuscular mycorrhizal (AM) fungi have traditionally been considered generalist symbionts. However, an increasing number of studies are pointing out the selectivity potential of plant hosts. Plant life form, determined by plant life history traits, seems to drive the AM fungal community composition. The AM fungi also exhibit a wide diversity of functional traits known to be responsible for their distribution in natural ecosystems. However, little is known about the role of plant and fungal traits driving the resultant symbiotic assemblages. With the aim of testing the feedback relationship between plant and fungal traits on the resulting AM fungal community, we inoculated three different plant life forms, i.e. annual herbs, perennial herbs and perennial semi-woody plants, with AM fungal communities sampled in different seasons. We hypothesized that the annual climate variation will induce changes in the mean traits of the AM fungal communities present in the soil throughout the year. Furthermore, the association of plants with different life forms with AM fungi with contrasting life history traits will show certain preferences according to reciprocal traits of the plants and fungi. We found changes in the AM fungal community throughout the year, which were differentially disrupted by disturbance and altered by plant growth form and plant biomass. Both plant and fungal traits clearly contributed to the resultant AM fungal communities. The revealed process can have implications for the functioning of ecosystems since changes in dominant plant life forms or climatic variables could influence the traits of AM fungal communities in soil and hence ecosystem processes.

Anthropogenic land use shapes the composition and phylogenetic structure of soil arbuscular mycorrhizal fungal communities

Arbuscular mycorrhizal (AM) fungi play an important role in ecosystems, but little is known about how soil AM fungal community composition varies in relation to habitat type and land-use intensity. We molecularly characterized AM fungal communities in soil samples (n = 88) from structurally open (permanent grassland, intensive and sustainable agriculture) and forested habitats (primeval forest and spruce plantation). The habitats harboured significantly different AM fungal communities, and there was a broad difference in fungal community composition between forested and open habitats, the latter being characterized by higher average AM fungal richness. Within both open and forest habitats, intensive land use significantly influenced community composition. There was a broad difference in the phylogenetic structure of AM fungal communities between mechanically disturbed and nondisturbed habitats. Taxa from Glomeraceae served as indicator species for the nondisturbed habitats, while taxa from Archaeosporaceae, Claroideoglomeraceae and Diversisporaceae were indicators for the disturbed habitats. The distribution of these indicator taxa among habitat types in the MaarjAM global database of AM fungal diversity was in accordance with their local indicator status.