Plant traits determine the phylogenetic structure of arbuscular mycorrhizal fungal communities

Accumulation of pathogens in soil microbiome can explain long-term fluctuations of legumes in a grassland community

All plant populations fluctuate in time. Apart from the dynamics imposed by external forces such as climate, these fluctuations can be driven by endogenous processes taking place within the community. In this study, we aimed to identify potential role of soil-borne microbial communities in driving endogenous fluctuations of plant populations. We combined a unique, 35-yr long abundance data of 11 common plant species from a species-rich mountain meadow with development of their soil microbiome (pathogenic fungi, arbuscular mycorrhizal fungi and oomycetes) observed during 4 yr of experimental cultivation in monocultures. Plant species which abundance fluctuated highly in the field (particularly legumes) accumulated plant pathogens in their soil mycobiome. We also identified increasing proportion of mycoparasitic fungi under highly fluctuating legume species, which may indicate an adaptation of these species to mitigate the detrimental effects of pathogens. Our study documented that long-term fluctuations in the abundance of plant species in grassland communities can be explained by the accumulation of plant pathogens in plant-soil microbiome. By contrast, we found little evidence of the role of mutualists in plant population fluctuations. These findings offer new insights for understanding mechanisms driving both long-term vegetation dynamics and patterns of species coexistence and richness.

Arbuscular mycorrhizal fungi attenuate negative impact of drought on soil functions

Although positive effects of arbuscular mycorrhizal (AM) fungi on plant performance under drought have been well documented, how AM fungi regulate soil functions and multifunctionality requires further investigation. In this study, we first performed a meta-analysis to test the potential role of AM fungi in maintaining soil functions under drought. Then, we conducted a greenhouse experiment, using a pair of hyphal ingrowth cores to spatially separate the growth of AM fungal hyphae and plant roots, to further investigate the effects of AM fungi on soil multifunctionality and its resistance against drought. Our meta-analysis showed that AM fungi promote multiple soil functions, including soil aggregation, microbial biomass and activities of soil enzymes related to nutrient cycling. The greenhouse experiment further demonstrated that AM fungi attenuate the negative impact of drought on these soil functions and thus multifunctionality, therefore, increasing their resistance against drought. Moreover, this buffering effect of AM fungi persists across different frequencies of water supply and plant species. These findings highlight the unique role of AM fungi in maintaining multiple soil functions by mitigating the negative impact of drought. Our study highlights the importance of AM fungi as a nature-based solution to sustaining multiple soil functions in a world where drought events are intensifying.

Measuring leaf and root functional traits uncovers multidimensionality of plant responses to arbuscular mycorrhizal fungi

PREMISE

While many studies have measured the aboveground responses of plants to mycorrhizal fungi at a single time point, little is known about how plants respond belowground or across time to mycorrhizal symbiosis. By measuring belowground responses and growth over time in many plant species, we create a more complete picture of how mycorrhizal fungi benefit their hosts.

METHODS

We grew 26 prairie plant species with and without mycorrhizal fungi and measured 14 functional traits to assess above- and belowground tissue quality and quantity responses and changes in resource allocation. We used function-valued trait (FVT) modeling to characterize changes in species growth rate when colonized.

RESULTS

While aboveground biomass responses were positive, the response of traits belowground were much more variable. Changes in aboveground biomass accounted for 60.8% of the variation in mycorrhizal responses, supporting the use of aboveground biomass response as the primary response trait. Responses belowground were not associated with aboveground responses and accounted for 18.3% of the variation. Growth responses over time were highly variable across species. Interestingly, none of the measured responses were phylogenetically conserved.

CONCLUSIONS

Mycorrhizal fungi increase plant growth in most scenarios, but the effects of these fungi belowground and across time are more complicated. This study highlights how differences in plant allocation priorities might affect how they utilize the benefits from mycorrhizal fungi. Identifying and characterizing these differences is a key step to understanding the effects of mycorrhizal mutualisms on whole plant physiology.

Prairie restoration promotes the abundance and diversity of mutualistic arbuscular mycorrhizal fungi

Predicting how biological communities assemble in restored ecosystems can assist in conservation efforts, but most research has focused on plants, with relatively little attention paid to soil microbial organisms that plants interact with. Arbuscular mycorrhizal (AM) fungi are an ecologically significant functional group of soil microbes that form mutualistic symbioses with plants and could therefore respond positively to plant community restoration. To evaluate the effects of plant community restoration on AM fungi, we compared AM fungal abundance, species richness, and community composition of five annually cultivated, conventionally managed agricultural fields with paired adjacent retired agricultural fields that had undergone prairie restoration 5-9 years prior to sampling. We hypothesized that restoration stimulates AM fungal abundance and species richness, particularly for disturbance-sensitive taxa, and that gains of new taxa would not displace AM fungal species present prior to restoration due to legacy effects. AM fungal abundance was quantified by measuring soil spore density and root colonization. AM fungal species richness and community composition were determined in soils and plant roots using DNA high-throughput sequencing. Soil spore density was 2.3 times higher in restored prairies compared to agricultural fields, but AM fungal root colonization did not differ between land use types. AM fungal species richness was 2.7 and 1.4 times higher in restored prairies versus agricultural fields for soil and roots, respectively. The abundance of Glomeraceae, a disturbance-tolerant family, decreased by 25% from agricultural to restored prairie soils but did not differ in plant roots. The abundance of Claroideoglomeraceae and Diversisporaceae, both disturbance-sensitive families, was 4.6 and 3.2 times higher in restored prairie versus agricultural soils, respectively. Species turnover was higher than expected relative to a null model, indicating that AM fungal species were gained by replacement. Our findings demonstrate that restoration can promote a relatively rapid increase in the abundance and diversity of soil microbial communities that had been degraded by decades of intensive land use, and community compositional change can be predicted by the disturbance tolerance of soil microbial taxonomic and functional groups.

Host plant height explains the effect of nitrogen enrichment on arbuscular mycorrhizal fungal communities

Nitrogen (N) enrichment is widely known to affect the root-associated arbuscular mycorrhizal fungal (AMF) community in different ways, for example, via altering soil properties and/or shifting host plant functional structure. However, empirical knowledge of their relative importance is still lacking. Using a long-term N addition experiment, we measured the AMF community taxonomic and phylogenetic diversity at the single plant species (roots of 15 plant species) and plant community (mixed roots) levels. We also measured four functional traits of 35 common plant species along the N addition gradient. We found divergent responses of AMF diversity to N addition for host plants with different innate heights (i.e. plant natural height under unfertilized treatment). Furthermore, our data showed that species-specific responses of AMF diversity to N addition were negatively related to the change in maximum plant height. When scaling up to the community level, N addition affected AMF diversity mainly through increasing the maximum plant height, rather than altering soil properties. Our results highlight the importance of plant height in driving AMF community dynamics under N enrichment at both species and community levels, thus providing important implications for understanding the response of AMF diversity to anthropogenic N deposition.

Ecological drivers of fine-scale distribution of arbuscular mycorrhizal fungi in a semiarid Mediterranean scrubland

BACKGROUND AND AIMS

Arbuscular mycorrhizal (AM) fungi enhance the uptake of water and minerals by the plant hosts, alleviating plant stress. Therefore, AM fungal-plant interactions are particularly important in drylands and other stressful ecosystems. We aimed to determine the combined and independent effects of above- and below-ground plant community attributes (i.e. diversity and composition), soil heterogeneity and spatial covariates on the spatial structure of the AM fungal communities in a semiarid Mediterranean scrubland. Furthermore, we evaluated how the phylogenetic relatedness of both plants and AM fungi shapes these symbiotic relationships.

METHODS

We characterized the composition and diversity of AM fungal and plant communities in a dry Mediterranean scrubland taxonomically and phylogenetically, using DNA metabarcoding and a spatially explicit sampling design at the plant neighbourhood scale.

KEY RESULTS

The above- and below-ground plant community attributes, soil physicochemical properties and spatial variables explained unique fractions of AM fungal diversity and composition. Mainly, variations in plant composition affected the AM fungal composition and diversity. Our results also showed that particular AM fungal taxa tended to be associated with closely related plant species, suggesting the existence of a phylogenetic signal. Although soil texture, fertility and pH affected AM fungal community assembly, spatial factors had a greater influence on AM fungal community composition and diversity than soil physicochemical properties.

CONCLUSIONS

Our results highlight that the more easily accessible above-ground vegetation is a reliable indicator of the linkages between plant roots and AM fungi. We also emphasize the importance of soil physicochemical properties in addition to below-ground plant information, while accounting for the phylogenetic relationships of both plants and fungi, because these factors improve our ability to predict the relationships between AM fungal and plant communities.

Nitrogen Addition Does Not Change AMF Colonization but Alters AMF Composition in a Chinese Fir (Cunninghamia lanceolata) Plantation

Aims: Our aim was to investigate how N addition affects arbuscular mycorrhizal fungal (AMF) growth in Chinese fir plantations. Methods: A Chinese fir plantation was treated with four different N addition treatments for one and half years starting in April 2019. AMF colonization, hyphal length density, community composition, and soil properties were under measurement. Results: N addition caused inapparent effects on AMF colonization, hyphal length density, and functional guilds (rhizophilic, edaphophilic, and ancestral). The predominant AMF species in the soil was Septoglomus viscosum. N addition altered AMF community and some rare species (e.g., Entrophospora infrequens) disappeared with N addition. Conclusion: AMF community structure was more sensitive to short-time N deposition than the symbiotic relationship between AMF and host plants.

Climate warming promotes deterministic assembly of arbuscular mycorrhizal fungal communities

Arbuscular mycorrhizal fungi (AMF) significantly contribute to plant resource acquisition and play important roles in mediating plant interactions and soil carbon (C) dynamics. However, it remains unclear how AMF communities respond to climate change. We assessed impacts of warming and precipitation alterations (30% increase or decrease) on soil AMF communities, and examined major ecological processes shaping the AMF community assemblage in a Tibetan alpine meadow. Our results showed that warming significantly increased root biomass, and available nitrogen (N) and phosphorus (P) in soil. While precipitation alterations increased AMF abundances, they did not significantly affect the composition or diversity of AMF communities. In contrast, warming altered the composition of AMF communities and reduced their Shannon-Wiener index and Pielou's evenness. In particular, warming shifted the AMF community composition in favor of Diversisporaceae over Glomeraceae, likely through its impact on soil N and P availability. In addition, AMF communities were phylogenetically random in the unwarmed control but clustered in warming plots, implying more deterministic community assembly under climate warming. Warming enhancement of root growth, N and P availability likely reduced plant C-allocation to AMF, imposing stronger environmental filtering on AMF communities. We further proposed a conceptual framework that integrates biological and geochemical processes into a mechanistic understanding of warming and precipitation changes' effects on AMF. Taken together, these results suggest that soil AMF communities may be more sensitive to warming than expected, highlighting the need to monitor their community structure and associated functional consequences on plant communities and soil C dynamics under the future warmer climate.

Host age and surrounding vegetation affect the community and colonization rates of arbuscular mycorrhizal fungi in a temperate grassland

Arbuscular mycorrhizal fungi (AMF) are important symbionts for the majority of terrestrial vascular plants, yet the drivers of the compositional variation in AMF communities need to be better understood. What effects does the ontogenetic stage of host plants have and do these effects differ between plant functional groups? Are the AMF communities modified by the properties of surrounding vegetation, such as the proportion of different functional groups or nonmycorrhizal plants ? We addressed these questions in a temperate grassland and studied AMF communities using next-generation sequencing and light microscopy, evaluating their composition, taxonomic, phylogenetic and functional diversity, functional traits and root colonization levels. We found important differences between AMF communities and their diversity between seedlings and adults which are larger than the differences among host species or between functional groups. The proportion of nonmycorrhizal plants in the surrounding affected AMF community composition and increased its richness. Our results highlight the need for further investigating the existence of a common mycelial networks. The decision to use seedlings for experimental work can affect the results more than the chosen host species.

Legacy effects of pre-crop plant functional group on fungal root symbionts of barley

Arbuscular mycorrhizal (AM) fungi, a group of widespread fungal symbionts of crops, could be important in driving crop yield across crop rotations through plant-soil feedbacks (PSF). However, whether preceding crops have a legacy effect on the AM fungi of the subsequent crop is poorly known. We set up an outdoor mesocosm crop rotation experiment that consisted of a first phase growing either one of four pre-crops establishing AM and/or rhizobial symbiosis or not (spring barley, faba bean, lupine, canola), followed by an AM crop, winter barley. After the pre-crop harvest, carbon-rich organic substrates were applied to test whether it attenuated, accentuated or modified the effect of pre-crops. The pre-crop mycorrhizal status, but not its rhizobial status, affected the richness and composition of AM fungi, and this difference, in particular community composition, persisted and increased in the roots of winter barley. The effect of a pre-crop was driven by its single symbiotic group, not its mixed symbiotic group and/or by a crop-species-specific effect. This demonstrates that the pre-crop symbiotic group has lasting legacy effects on the AM fungal communities and may steer the AM fungal community succession across rotation phases. This effect was accentuated by sawdust amendment, but not wheat straw. Based on the previous observation of decreased crop yield after AM pre-crops, our findings suggest negative PSF at the level of the plant symbiotic group driven by a legacy effect of crop rotation history on AM fungal communities, and that a focus on crop symbiotic group offers additional understanding of PSF.

How Mycorrhizal Associations Influence Orchid Distribution and Population Dynamics

Orchid distribution and population dynamics are influenced by a variety of ecological factors and the formation of holobionts, which play key roles in colonization and ecological community construction. Seed germination, seedling establishment, reproduction, and survival of orchid species are strongly dependent on orchid mycorrhizal fungi (OMF), with mycorrhizal cheating increasingly observed in photosynthetic orchids. Therefore, changes in the composition and abundance of OMF can have profound effects on orchid distribution and fitness. Network analysis is an important tool for the study of interactions between plants, microbes, and the environment, because of the insights that it can provide into the interactions and coexistence patterns among species. Here, we provide a comprehensive overview, systematically describing the current research status of the effects of OMF on orchid distribution and dynamics, phylogenetic signals in orchid-OMF interactions, and OMF networks. We argue that orchid-OMF associations exhibit complementary and specific effects that are highly adapted to their environment. Such specificity of associations may affect the niche breadth of orchid species and act as a stabilizing force in plant-microbe coevolution. We postulate that network analysis is required to elucidate the functions of fungal partners beyond their effects on germination and growth. Such studies may lend insight into the microbial ecology of orchids and provide a scientific basis for the protection of orchids under natural conditions in an efficient and cost-effective manner.

Hierarchical spatial sampling reveals factors influencing arbuscular mycorrhizal fungus diversity in Côte d'Ivoire cocoa plantations

While many molecular studies have documented arbuscular mycorrhizal fungi (AMF) communities in temperate ecosystems, very few studies exist in which molecular techniques have been used to study tropical AMF communities. Understanding the composition of AMF communities in tropical areas gains special relevance as crop productivity in typically low fertility tropical soils can be improved with the use of AMF. We used a hierarchical sampling approach in which we sampled soil from cocoa (Theobroma cacao L.) plantations nested in localities, and in which localities were nested within each of three regions of Côte d'Ivoire. This sampling strategy, combined with 18S rRNA gene sequencing and a dedicated de novo OTU-picking model, allowed us to study AMF community composition and how it is influenced at different geographical scales and across environmental gradients. Several factors, including pH, influenced overall AMF alpha diversity and differential abundance of specific taxa and families of the Glomeromycotina. Assemblages and diversity metrics at the local scale did not reliably predict those at regional scales. The amount of variation explained by soil, climate, and geography variables left a large proportion of the variance to be explained by other processes, likely happening at smaller scales than the ones considered in this study. Gaining a better understanding of processes involved in shaping tropical AMF community composition and AMF establishment are much needed and could allow for the development of sustainable, productive tropical agroecosystems.

Potential Use of Beneficial Microorganisms for Soil Amelioration, Phytopathogen Biocontrol, and Sustainable Crop Production in Smallholder Agroecosystems

Smallholder agroecosystems play a key role in the world's food security providing more than 50% of the food produced globally. These unique agroecosystems face a myriad of challenges and remain largely unsupported, yet they are thought to be a critical resource for feeding the projected increasing human population in the coming years. The new challenge to increase food production through agricultural intensification in shrinking per capita arable lands, dwindling world economies, and unpredictable climate change, has led to over-dependence on agrochemical inputs that are often costly and hazardous to both human and animal health and the environment. To ensure healthy crop production approaches, the search for alternative ecofriendly strategies that best fit to the smallholder systems have been proposed. The most common and widely accepted solution that has gained a lot of interest among researchers and smallholder farmers is the use of biological agents; mainly plant growth promoting microorganisms (PGPMs) that provide essential agroecosystem services within a holistic vision of enhancing farm productivity and environmental protection. PGPMs play critical roles in agroecological cycles fundamental for soil nutrient amelioration, crop nutrient improvement, plant tolerance to biotic and abiotic stresses, biocontrol of pests and diseases, and water uptake. This review explores different research strategies involving the use of beneficial microorganisms, within the unique context of smallholder agroecosystems, to promote sustainable maintenance of plant and soil health and enhance agroecosystem resilience against unpredictable climatic perturbations.

Spatial factors and plant attributes influence soil fungal community distribution patterns in the lower reaches of the Heihe River Basin, Northwest China

Inland river basins include critical habitats and provide various ecosystem services in extremely arid lands. However, we know little about the distribution patterns of soil fungal communities in these river basins. We investigated the distribution patterns of soil fungal communities from the riparian oasis zone (ROZ) to the circumjacent desert zone (CDZ) at the lower reaches of the Heihe River. The results indicated that soil fungal communities were mainly dominated by the phyla Ascomycota and Basidiomycota across all samples. The dominant soil fungi taxa were significantly different between ROZ and CDZ habitats at both the phylum and genus levels. Fungal alpha diversity was mainly affected by spatial factors and plant functional traits, and Pearson correlation analysis revealed that fungal alpha diversity was more closely related to plant functional traits than soil properties. Furthermore, fungal community structure was best explained by spatial factors and plant attributes (including plant diversity and plant functional traits). Together, our findings provide new insights into the significance of spatial factors and plant attributes for predicting distributions of fungal communities in arid inland river basins, which will help us better understand the functions and services of these ecosystems.

Analysis of Arbuscular Mycorrhizal Fungal Communities by Terminal Restriction Fragment Length Polymorphism (TRFLP)

Terminal restriction fragment length polymorphism (TRFLP) approaches enable the detection and identification of microbial taxa into samples coming from root or soil material DNA extraction. The low taxonomic diversity of arbuscular mycorrhizal (AM) fungi makes this technique a cheap and adequate method for fingerprinting their communities. Here, I describe the TRFLP database approach, a version of the technique in which the AM fungal taxa present in the sample pool is identified for, later, match their presence in the different samples contained in the experiment. A final AM fungal operational taxonomic unit x sample presence-absence matrix is obtained, which allows the subsequent multivariate statistical analysis of the experimental results.

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.

Plant health status effects on arbuscular mycorrhizal fungi associated with Lavandula angustifolia and Lavandula intermedia infected by Phytoplasma in France

We investigated root communities of arbuscular mycorrhizal fungi (AMF) in relation to lavender (Lavandula angustifolia) and lavandin (Lavandula intermedia) health status from organic and conventional fields affected by Phytoplasma infection. The intensity of root mycorrhizal colonization was significantly different between diseased and healthy plants and was higher in the latter regardless of agricultural practice. This difference was more pronounced in lavender. The root AMF diversity was influenced by the plant health status solely in lavender and only under the conventional practice resulting in an increase in the AMF abundance and richness. The plant health status did not influence the distribution of root AMF communities in lavandin unlike its strong impact in lavender in both agricultural practices. Finally, among the most abundant molecular operational taxonomic units (MOTUs), four different MOTUs for each plant species were significantly abundant in the roots of healthy lavender and lavandin in either agricultural practice. Our study demonstrated that the plant health status influences root colonization and can influence the diversity and distribution of root AMF communities. Its effects vary according to plant species, can be modified by agricultural practices and allow plants to establish symbiosis with specific AMF species.

Influence of Citrus Scion/Rootstock Genotypes on Arbuscular Mycorrhizal Community Composition under Controlled Environment Condition

Citrus is vegetatively propagated by grafting for commercial production, and most rootstock cultivars of citrus have scarce root hairs, thus heavily relying on mutualistic symbiosis with arbuscular mycorrhizal fungi (AMF) for mineral nutrient uptake. However, the AMF community composition, and its differences under different citrus scion/rootstock genotypes, were largely unknown. In this study, we investigated the citrus root-associated AMF diversity and richness, and assessed the influence of citrus scion/rootstock genotypes on the AMF community composition in a controlled condition, in order to exclude interferences from environmental factors and agricultural practices. As a result, a total of 613,408 Glomeromycota tags were detected in the citrus roots, and 46 AMF species were annotated against the MAARJAM database. Of these, 39 species belonged to Glomus, indicating a dominant role of the Glomus AMF in the symbiosis with citrus. PCoA analysis indicated that the AMF community’s composition was significantly impacted by both citrus scion and rootstock genotypes, but total samples were clustered according to rootstock genotype rather than scion genotype. In addition, AMF α diversity was significantly affected merely by rootstock genotype. Thus, rootstock genotype might exert a greater impact on the AMF community than scion genotype. Taken together, this study provides a comprehensive insight into the AMF community in juvenile citrus plants, and reveals the important effects of citrus genotype on AMF community composition.

Plant functional groups associate with distinct arbuscular mycorrhizal fungal communities

The benefits of the arbuscular mycorrhizal (AM) symbiosis between plants and fungi are modulated by the functional characteristics of both partners. However, it is unknown to what extent functionally distinct groups of plants naturally associate with different AM fungi. We reanalysed 14 high-throughput sequencing data sets describing AM fungal communities associating with plant individuals (2427) belonging to 297 species. We examined how root-associating AM fungal communities varied between plants with different growth forms, photosynthetic pathways, CSR (competitor, stress-tolerator, ruderal) strategies, mycorrhizal statuses and N-fixing statuses. AM fungal community composition differed in relation to all studied plant functional groups. Grasses, C₄ and nonruderal plants were characterised by high AM fungal alpha diversity, while C₄ , ruderal and obligately mycorrhizal plants were characterised by high beta diversity. The phylogenetic diversity of AM fungi, a potential surrogate for functional diversity, was higher among forbs than other plant growth forms. Putatively ruderal (previously cultured) AM fungi were disproportionately associated with forbs and ruderal plants. There was phylogenetic correlation among AM fungi in the degree of association with different plant growth forms and photosynthetic pathways. Associated AM fungal communities constitute an important component of plant ecological strategies. Functionally different plants associate with distinct AM fungal communities, linking mycorrhizal associations with functional diversity in ecosystems.

Plant functional traits regulate soil bacterial diversity across temperate deserts

Despite the known influence of plant diversity on soil microbial diversity, the potential role of plant functional traits in regulating soil bacterial diversity remains largely unclear. There is a lack of strong empirical evidence for the relative effects of plant diversity and functional traits on soil bacterial diversity across large-scale deserts. Here, we simultaneously explore the internal links among plant diversity, functional traits and soil bacterial diversity across 90 temperate deserts habitat of China, after accounting for confounding abiotic and spatial factors. The results showed that soil bacterial alpha and beta diversities were mainly determined by abiotic and spatial factors, follow by plant factors. However, plant diversity and functional traits played diverse roles in shaping soil bacterial alpha and beta diversities. Plant diversity exerted a substantial influence on soil bacterial beta diversity, but not on alpha diversity. In contrast, plant functional traits still directly influenced soil bacterial alpha and beta diversity, after accounting for other confounding key drivers. More precisely, plant functional traits surpass plant diversity in affecting soil bacterial alpha diversity. These results provide robust evidence that plant functional traits can effectively regulate soil bacterial diversity across temperate deserts. Taken together, we highlight the importance and irreplaceability of plant functional traits in predicting soil biodiversity under current and future global environmental changes.

Contrasting effects of host identity, plant community, and local species pool on the composition and colonization levels of arbuscular mycorrhizal fungal community in a temperate grassland

Arbuscular mycorrhizal fungi (AMFs) are important plant symbionts, but we know little about the effects of plant taxonomic identity or functional group on the AMF community composition. To examine the effects of the surrounding plant community, of the host, and of the AMF pool on the AMF community in plant roots, we manipulated plant community composition in a long-term field experiment. Within four types of manipulated grassland plots, seedlings of eight grassland plant species were planted for 12 wk, and AMFs in their roots were quantified. Additionally, we characterized the AMF community of individual plots (as their AMF pool) and quantified plot abiotic conditions. The largest determinant of AMF community composition was the pool of available AMFs, varying at metre scale due to changing soil conditions. The second strongest predictor was the host functional group. The differences between grasses and dicotyledonous forbs in AMF community variation and diversity were much larger than the differences among species within those groups. High cover of forbs in the surrounding plant community had a strong positive effect on AMF colonization intensity in grass hosts. Using a manipulative field experiment enabled us to demonstrate direct causal effects of plant host and surrounding vegetation.

Plant Taxonomic Diversity Better Explains Soil Fungal and Bacterial Diversity than Functional Diversity in Restored Forest Ecosystems

Plant attributes have direct and indirect effects on soil microbes via plant inputs and plant-mediated soil changes. However, whether plant taxonomic and functional diversities can explain the soil microbial diversity of restored forest ecosystems remains elusive. Here, we tested the linkage between plant attributes and soil microbial communities in four restored forests (Acacia species, Eucalyptus species, mixed coniferous species, mixed native species). The trait-based approaches were applied for plant properties and high-throughput Illumina sequencing was applied for fungal and bacterial diversity. The total number of soil microbial operational taxonomic units (OTUs) varied among the four forests. The highest richness of fungal OTUs was found in the Acacia forest. However, bacterial OTUs were highest in the Eucalyptus forest. Species richness was positively and significantly related to fungal and bacterial richness. Plant taxonomic diversity (species richness and species diversity) explained more of the soil microbial diversity than the functional diversity and soil properties. Prediction of fungal richness was better than that of bacterial richness. In addition, root traits explained more variation than the leaf traits. Overall, plant taxonomic diversity played a more important role than plant functional diversity and soil properties in shaping the soil microbial diversity of the four forests.

Effects of host phylogeny, habitat and spatial proximity on host specificity and diversity of pathogenic and mycorrhizal fungi in a subtropical forest

Soil plant-pathogenic (PF) and mycorrhizal fungi (MF) are both important in maintaining plant diversity, for example via host-specialized effects. However, empirical knowledge on the degree of host specificity and possible factors affecting the fungal assemblages is lacking. We identified PF and MF in fine roots of 519 individuals across 45 subtropical tree species in southern China in order to quantify the importance of host phylogeny (including via its effects on functional traits), habitat and space in determining fungal communities. We also compared host specificity in PF and MF at different host-phylogenetic scales. In both PF and MF, host phylogeny independently accounted for > 19% of the variation in fungal richness and composition, whereas environmental and spatial factors each explained no more than 4% of the variation. Over 77% of the variation explained by phylogeny was attributable to covariation in plant functional traits. Host specificity was phylogenetically scale-dependent, being stronger in PF than in MF at low host-phylogenetic scales (e.g. within genus) but similar at larger scales. Our study suggests that host-phylogenetic effects dominate the assembly of both PF and MF communities, resulting from phylogenetically clustered plant traits. The scale-dependent host specificity implies that PF were specialized at lower-level and MF at higher-level host taxa.

Local abiotic conditions are more important than landscape context for structuring arbuscular mycorrhizal fungal communities in the roots of a forest herb

Due to human influence, large tracts of natural vegetation have been cleared and replaced by other types of land use, resulting in highly fragmented landscapes consisting of small fragments of well-conserved habitat scattered within a matrix of intensively managed land. Changes in land use and associated fragmentation have important consequences for biodiversity in the remaining fragments. Most studies so far have investigated the impact of land use change on macro-organisms, but little is known about how landscape fragmentation affects microbial communities. Here, we studied how changes in land use and abiotic conditions affected the arbuscular mycorrhizal fungal (AMF) communities in the roots of the forest herb Stachys sylvatica. Root samples were collected from 40 populations occurring in fragmented forest patches of varying age and size embedded within an agricultural landscape. Our results showed that forest age and isolation did not affect AMF diversity or community composition, suggesting that AMF disperse easily throughout the landscape and that AMF communities reassemble fast in recently established forest patches. On the other hand, AMF richness increased with increasing forest area, indicating that small forest sizes limit AMF richness. Additionally, AMF richness increased with increasing soil pH and decreased with soil nitrate content, while AMF community composition was affected plant-available phosphorus. Overall, these results show that landscape context is less important than local abiotic conditions for structuring AMF communities. However, the significant area effect indicates that further reductions in forest area will lead to impoverished AMF communities, potentially affecting long-term plant fitness and community structure.

Temperature-mediated phylogenetic assemblage of fungal communities and local adaptation in mycorrhizal symbioses

Recent work demonstrates that habitat conditions exert striking effects on symbiont performance by mediating trade-offs in plants, AM fungi and environmental interactions. However, how local temperature conditions influence the functional diversity of mycorrhizal symbioses and the genetics of coexisting AM fungi at the local scale remain unclear. In the present study, we conducted a reciprocal inoculation experiment to explore the performance of sympatric associations against allopatric associations under contrasting temperatures and the AM fungal community in colonized roots. No local adaptation of plant biomass was found under both temperature conditions investigated, but a consistent local versus foreign effect was found in AM fungal performance. The temperature and the origin of the inoculum relative to the plant origin were important in explaining symbiotic function. Correspondingly, the community structure and Nearest Relatedness Index of the AM fungal community of the root symbiont varied with inoculum source, and assemblages with more closely related taxa led to a decline in plant biomass and stronger disequilibrium among AM fungi in roots. Our findings suggest that functional divergence exists in naturally coexisting communities of AM fungi from contrasting climatic origins, and fungal relatedness is an important driver of plant growth.

Land-Use Intensity Rather Than Plant Functional Identity Shapes Bacterial and Fungal Rhizosphere Communities

The rhizosphere encompasses the soil surrounding the surface of plants’ fine roots. Accordingly, the microbiome present is influenced by both soil type and plant species. Furthermore, soil microbial communities respond to land-use intensity due to the effects on soil conditions and plant performance. However, there is limited knowledge about the impact of grassland management practices under field conditions on the composition of both bacteria and fungi in the rhizosphere of different plant functional groups. In spring 2014 we planted four phytometer species, two forbs (Plantago lanceolata, Achillea millefolium) and two grasses (Dactylis glomerata, Arrhenatherum elatius) into 13 permanent experimental grassland plots, differing in management. After 6 months, rhizosphere and bulk soil associated with the phytometer plants were sampled, microbial genomic DNA was extracted and bacterial 16S and fungal ITS rDNA were sequenced using Illumina MiSeq. Our study revealed that the rhizosphere microbial community was more diverse than the bulk soil community. There were no differences in microbial community composition between the two plant functional groups, but a clear impact of root traits and edaphic conditions. Land-use intensity strongly affected plant productivity, neighboring plant richness and edaphic conditions, especially soil C/N ratio, which in turn had a strong influence on root traits and thereby explained to large extent microbial community composition. Rhizosphere microbes were mainly affected by abiotic factors, in particular by land-use intensity, while plant functional type had only subordinate effects. Our study provides novel insights into the assembly of rhizosphere bacterial and fungal communities in response to land-use intensity and plant functional groups in managed grassland ecosystems.

Ectomycorrhizal Fungal Communities and Their Functional Traits Mediate Plant-Soil Interactions in Trace Element Contaminated Soils

There is an increasing consensus that microbial communities have an important role in mediating ecosystem processes. Trait-based ecology predicts that the impact of the microbial communities on ecosystem functions will be mediated by the expression of their traits at community level. The link between the response of microbial community traits to environmental conditions and its effect on plant functioning is a gap in most current microbial ecology studies. In this study, we analyzed functional traits of ectomycorrhizal fungal species in order to understand the importance of their community assembly for the soil-plant relationships in holm oak trees (Quercus ilex subsp. ballota) growing in a gradient of exposure to anthropogenic trace element (TE) contamination after a metalliferous tailings spill. Particularly, we addressed how the ectomycorrhizal composition and morphological traits at community level mediate plant response to TE contamination and its capacity for phytoremediation. Ectomycorrhizal fungal taxonomy and functional diversity explained a high proportion of variance of tree functional traits, both in roots and leaves. Trees where ectomycorrhizal fungal communities were dominated by the abundant taxa Hebeloma cavipes and Thelephora terrestris showed a conservative root economics spectrum, while trees colonized by rare taxa presented a resource acquisition strategy. Conservative roots presented ectomycorrhizal functional traits characterized by high rhizomorphs formation and low melanization which may be driven by resource limitation. Soil-to-root transfer of TEs was explained substantially by the ectomycorrhizal fungal species composition, with the highest transfer found in trees whose roots were colonized by Hebeloma cavipes. Leaf phosphorus was related to ectomycorrhizal species composition, specifically higher leaf phosphorus was related to the root colonization by Thelephora terrestris. These findings support that ectomycorrhizal fungal community composition and their functional traits mediate plant performance in metal-contaminated soils, and have a high influence on plant capacity for phytoremediation of contaminants. The study also corroborates the overall effects of ectomycorrhizal fungi on ecosystem functioning through their mediation over the plant economics spectrum.

Plant host habitat and root exudates shape fungal diversity

The rhizospheric microbiome is clearly affected by plant species and certain of their functional traits. These functional traits allow plants to adapt to their environmental conditions by acquiring or conserving nutrients, thus defining different ecological resource-use plant strategies. In the present study, we investigated whether plants with one of the two nutrient-use strategies (conservative versus exploitative) could influence fungal communities involved in soil organic matter degradation and root exudate assimilation, as well as those colonizing root tissues. We applied a DNA-based, stable-isotope probing (DNA-SIP) approach to four grass species distributed along a gradient of plant nutrient resource strategies, ranging from conservative to exploitative species, and analyzed their associated mycobiota composition using a fungal internal transcribed spacer (ITS) and Glomeromycotina 18S rRNA gene metabarcoding approach. Our results demonstrated that fungal taxa associated with exploitative and conservative plants could be separated into two general categories according to their location: generalists, which are broadly distributed among plants from each strategy and represent the core mycobiota of soil organic matter degraders, root exudate consumers in the root-adhering soil, and root colonizers; and specialists, which are locally abundant in one species and more specifically involved in soil organic matter degradation or root exudate assimilation on the root-adhering soil and the root tissues. Interestingly, for arbuscular mycorrhizal fungi analysis, all plant roots were mainly colonized by Glomus species, whereas an increased diversity of Glomeromycotina genera was observed for the exploitative plant species Dactylis glomerata.

Plant attributes explain the distribution of soil microbial communities in two contrasting regions of the globe

We lack strong empirical evidence for links between plant attributes (plant community attributes and functional traits) and the distribution of soil microbial communities at large spatial scales. Using datasets from two contrasting regions and ecosystem types in Australia and England, we report that aboveground plant community attributes, such as diversity (species richness) and cover, and functional traits can predict a unique portion of the variation in the diversity (number of phylotypes) and community composition of soil bacteria and fungi that cannot be explained by soil abiotic properties and climate. We further identify the relative importance and evaluate the potential direct and indirect effects of climate, soil properties and plant attributes in regulating the diversity and community composition of soil microbial communities. Finally, we deliver a list of examples of common taxa from Australia and England that are strongly related to specific plant traits, such as specific leaf area index, leaf nitrogen and nitrogen fixation. Together, our work provides new evidence that plant attributes, especially plant functional traits, can predict the distribution of soil microbial communities at the regional scale and across two hemispheres.

Phosphorus Acquisition Efficiency Related to Root Traits: Is Mycorrhizal Symbiosis a Key Factor to Wheat and Barley Cropping?

Wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) are major crops cultivated around the world, thus playing a crucial role on human diet. Remarkably, the growing human population requires a significant increase in agricultural production in order to feed everybody. In this context, phosphorus (P) management is a key factor as it is component of organic molecules such as nucleic acids, ATP and phospholipids, and it is the most abundant macronutrient in biomass after nitrogen (N), although being one of the scarcest elements in the lithosphere. In general, P fertilization has low efficiency, as only a fraction of the applied P is acquired by roots, leaving a substantial amount to be accumulated in soil as not readily available P. Breeding for P-efficient cultivars is a relatively low cost alternative and can be done through two mechanisms: i) improving P use efficiency (PUE), and/or ii) P acquisition efficiency (PAE). PUE is related to the internal allocation/mobilization of P, and is usually represented by the amount of P accumulated per biomass. PAE relies on roots ability to acquire P from the soil, and is commonly expressed as the relative difference of P acquired under low and high P availability conditions. In this review, plant adaptations related to improved PAE are described, with emphasis on arbuscular mycorrhizal (AM) symbiosis, which is generally accepted to enhance plant P acquisition. A state of the art (1980-2018) of AM growth responses and P uptake in wheat and barley is made to discuss about the commonly accepted growth promoting effect and P increased uptake by AM fungi and the contrasting evidence about the generally accepted lack of positive responses in both plant species. Finally, the mechanisms by which AM symbiosis can affect wheat and barley PAE are discussed, highlighting the importance of considering AM functional diversity on future studies and the necessity to improve PAE definition by considering the carbon trading between all the directly related PAE traits and its return to the host plant.