Temperature and pH define the realised niche space of arbuscular mycorrhizal fungi

Biochar is colonized by select arbuscular mycorrhizal fungi in agricultural soils

Arbuscular mycorrhizal fungi (AMF) colonize biochar in soils, yet the processes governing their colonization and growth in biochar are not well characterized. Biochar amendment improves soil health by increasing soil carbon, decreasing bulk density, and improving soil water retention, all of which can increase yield and alleviate environmental stress on crops. Biochar is often applied with nutrient addition, impacting mycorrhizal communities. To understand how mycorrhizas explore soils containing biochar, we buried packets of non-activated biochar in root exclusion mesh bags in contrasting agricultural soils. In this greenhouse experiment, with quinoa (Chenopodium quinoa) as the host plant, we tested impacts of mineral nutrient (as manure and fertilizer) and biochar addition on mycorrhizal colonization of biochar. Paraglomus appeared to dominate the biochar packets, and the community of AMF found in the biochar was a subset (12 of 18) of the virtual taxa detected in soil communities. We saw differences in AMF community composition between soils with different edaphic properties, and while nutrient addition shifted those communities, the shifts were inconsistent between soil types and did not significantly influence the observation that Paraglomus appeared to selectively colonize biochar. This observation may reflect differences in AMF traits, with Paraglomus previously identified only in soils (not in roots) pointing to predominately soil exploratory traits. Conversely, the absence of some AMF from the biochar implies either a reduced tendency to explore soils or an ability to avoid recalcitrant nutrient sources. Our results point to a selective colonization of biochar in agricultural soils.

Mycorrhizal effects on crop yield and soil ecosystem functions in a long-term tillage and fertilization experiment

It is well understood that agricultural management influences arbuscular mycorrhizal (AM) fungi, but there is controversy about whether farmers should manage for AM symbiosis. We assessed AM fungal communities colonizing wheat roots for three consecutive years in a long-term (> 14 yr) tillage and fertilization experiment. Relationships among mycorrhizas, crop performance, and soil ecosystem functions were quantified. Tillage, fertilizers and continuous monoculture all reduced AM fungal richness and shifted community composition toward dominance of a few ruderal taxa. Rhizophagus and Dominikia were depressed by tillage and/or fertilization, and their abundances as well as AM fungal richness correlated positively with soil aggregate stability and nutrient cycling functions across all or no-tilled samples. In the field, wheat yield was unrelated to AM fungal abundance and correlated negatively with AM fungal richness. In a complementary glasshouse study, wheat biomass was enhanced by soil inoculum from unfertilized, no-till plots while neutral to depressed growth was observed in wheat inoculated with soils from fertilized and conventionally tilled plots. This study demonstrates contrasting impacts of low-input and conventional agricultural practices on AM symbiosis and highlights the importance of considering both crop yield and soil ecosystem functions when managing mycorrhizas for more sustainable agroecosystems.

A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists

Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.

Local Community Assembly Mechanisms and the Size of Species Pool Jointly Explain the Beta Diversity of Soil Fungi

Fungi play vital regulatory roles in terrestrial ecosystems. Local community assembly mechanisms, including deterministic and stochastic processes, as well as the size of regional species pools (gamma diversity), typically influence overall soil microbial community beta diversity patterns. However, there is limited evidence supporting their direct and indirect effects on beta diversity of different soil fungal functional groups in forest ecosystems. To address this gap, we collected 1606 soil samples from a 25-ha subtropical forest plot in southern China. Our goal was to determine the direct effects and indirect effects of regional species pools on the beta diversity of soil fungi, specifically arbuscular mycorrhizal (AM), ectomycorrhizal (EcM), plant-pathogenic, and saprotrophic fungi. We quantified the effects of soil properties, mycorrhizal tree abundances, and topographical factors on soil fungal diversity. The beta diversity of plant-pathogenic fungi was predominantly influenced by the size of the species pool. In contrast, the beta diversity of EcM fungi was primarily driven indirectly through community assembly processes. Neither of them had significant effects on the beta diversity of AM and saprotrophic fungi. Our results highlight that the direct and indirect effects of species pools on the beta diversity of soil functional groups of fungi can significantly differ even within a relatively small area. They also demonstrate the independent and combined effects of various factors in regulating the diversities of soil functional groups of fungi. Consequently, it is crucial to study the fungal community not only as a whole but also by considering different functional groups within the community.

Nitrogen fertilization reduces plant diversity by changing the diversity and stability of arbuscular mycorrhizal fungal community in a temperate steppe

Nitrogen (N) deposition resulting from anthropogenic activities poses threats to ecosystem stability by reducing plant and microbial diversity. However, the role of soil microbes, particularly arbuscular mycorrhizal fungi (AMF), as mediators of N-induced shifts in plant diversity remains unclear. In this study, we conducted 6 and 11 years of N addition field experiments in a temperate steppe to investigate AMF richness and network stability and their associations with plant species richness in response to N deposition. The N fertilization, especially in the 11 years of N addition, profoundly decreased the AMF richness and plant species richness. Furthermore, N fertilization significantly decreased the AMF network complexity and stability, with these effects becoming more enhanced with the increase in N addition duration. AMF richness and network stability showed positive associations with plant diversity, and these associations were stronger after 11 than 6 years of N addition. Our findings suggest that N deposition may lead to plant diversity loss via a reduction of AMF richness and network stability, with these effects strengthened over time. This study provides a better understanding of plant-AMF interactions and their response to the prevailing global N deposition.

Extreme environments simplify reassembly of communities of arbuscular mycorrhizal fungi

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

Distinct biogeographic patterns in Glomeromycotinian and Mucoromycotinian arbuscular mycorrhizal fungi across China: A meta-analysis

Fine root endophytes, recently reclassified as Mucoromycotinian arbuscular mycorrhizal fungi (M-AMF), are now recognized as functionally important as Glomeromycotinian AMF (G-AMF). However, little is known about the biogeography and ecology of M-AMF and G-AMF communities, particularly on a large scale, preventing a systematic assessment of ecosystem diversity and functioning. Here, we investigated the biogeographic assemblies and ecological diversity patterns of both G-AMF and M-AMF, using published 18S rDNA amplicon datasets and associated metadata from 575 soil samples in six ecosystems across China. Contrasting with G-AMF, putative M-AMF were rare in natural/semi-natural sites, where their communities were a subset of those in agricultural sites characterized by intensive disturbances, suggesting different ecological niches that they could occupy. Spatial and environmental factors (e.g., vegetation type) significantly influenced both fungal communities, with soil total‑nitrogen and mean-annual-precipitation being the strongest predictors for G-AMF and M-AMF richness, respectively. Both groups exhibited a strong spatial distance-decay relationship, shaped more by environmental filtering than spatial effects for M-AMF, and the opposite for G-AMF, presumably because stochasticity (e.g., drift) dominantly structured G-AMF communities; while the narrower niche breadth (at community-level) of M-AMF compared to G-AMF suggested its more susceptibility to environmental differences. Furthermore, co-occurrence network links between G-AMF and M-AMF were prevalent across ecosystems, and were predicted to play a key role in stabilizing overall communities harboring both fungi. Based on the macroecological spatial scale datasets, this study provides solid evidence that the two AMF groups have distinct ecological preferences at the continental scale in China, and also highlights the potential impacts of anthropogenic activities on distributions of AMF. These results advance our knowledge of the ecological differences between the two fungal groups in terrestrial ecosystems, suggesting the need for further field-based investigation that may lead to a more sophisticated understanding of ecosystem function and sustainable management.

Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe

Trees interact with a multitude of microbes through their roots and root symbionts such as mycorrhizal fungi and root endophytes. Here, we explore the role of fungal root symbionts as predictors of the soil and root-associated microbiomes of widespread broad-leaved trees across a European latitudinal gradient. Our results suggest that, alongside factors such as climate, soil, and vegetation properties, root colonization by ectomycorrhizal, arbuscular mycorrhizal, and dark septate endophytic fungi also shapes tree-associated microbiomes. Notably, the structure of root and soil microbiomes across our sites is more strongly and consistently associated with dark septate endophyte colonization than with mycorrhizal colonization and many abiotic factors. Root colonization by dark septate endophytes also has a consistent negative association with the relative abundance and diversity of nutrient cycling genes. Our study not only indicates that root-symbiotic interactions are an important factor structuring soil communities and functions in forest ecosystems, but also that the hitherto less studied dark septate endophytes are likely to be central players in these interactions.

Niche types and community assembly

Studies of niche differentiation and biodiversity often focus on a few niche dimensions due to the methodological challenge of describing hyperdimensional niche space. However, this may limit our understanding of community assembly processes. We used the full spectrum of realized niche types to study arbuscular mycorrhizal fungal communities: distinguishing abiotic and biotic, and condition and resource, axes. Estimates of differentiation in relation to different niche types were only moderately correlated. However, coexisting taxon niches were consistently less differentiated than expected, based on a regional null model, indicating the importance of habitat filtering at that scale. Nonetheless, resource niches were relatively more differentiated than condition niches, which is consistent with the effect of a resource niche-based coexistence mechanism. Considering niche types, and in particular distinguishing resource and condition niches, provides a more complete understanding of community assembly, compared with studying individual niche axes or the full niche.

Diversity of Arbuscular Mycorrhizal Fungi in Distinct Ecosystems of the North Caucasus, a Temperate Biodiversity Hotspot

BACKGROUND

Investigations that are focused on arbuscular mycorrhizal fungus (AMF) biodiversity is still limited. The analysis of the AMF taxa in the North Caucasus, a temperate biodiversity hotspot, used to be limited to the genus level. This study aimed to define the AMF biodiversity at the species level in the North Caucasus biotopes.

METHODS

The molecular genetic identification of fungi was carried out with ITS1 and ITS2 regions as barcodes via sequencing using Illumina MiSeq, the analysis of phylogenetic trees for individual genera, and searches for operational taxonomic units (OTUs) with identification at the species level. Sequences from MaarjAM and NCBI GenBank were used as references.

RESULTS

We analyzed >10 million reads in soil samples for three biotopes to estimate fungal biodiversity. Briefly, 50 AMF species belonging to 20 genera were registered. The total number of the AM fungus OTUs for the "Subalpine Meadow" biotope was 171/131, that for "Forest" was 117/60, and that for "River Valley" was 296/221 based on ITS1/ITS2 data. The total number of the AM fungus species (except for virtual taxa) for the "Subalpine Meadow" biotope was 24/19, that for "Forest" was 22/13, and that for "River Valley" was 28/24 based on ITS1/ITS2 data. Greater AMF diversity, as well as number of OTUs and species, in comparison with that of forest biotopes, characterized valley biotopes (disturbed ecosystems; grasslands). The correlation coefficient between "Percentage of annual plants" and "Glomeromycota total reads" r = 0.76 and 0.81 for ITS1 and ITS2, respectively, and the correlation coefficient between "Percentage of annual plants" and "OTUs number (for total species)" was r = 0.67 and 0.77 for ITS1 and ITS2, respectively.

CONCLUSION

High AMF biodiversity for the river valley can be associated with a higher percentage of annual plants in these biotopes and the active development of restorative successional processes.

GlobalAMFungi: a global database of arbuscular mycorrhizal fungal occurrences from high-throughput sequencing metabarcoding studies

Arbuscular mycorrhizal (AM) fungi are crucial mutualistic symbionts of the majority of plant species, with essential roles in plant nutrient uptake and stress mitigation. The importance of AM fungi in ecosystems contrasts with our limited understanding of the patterns of AM fungal biogeography and the environmental factors that drive those patterns. This article presents a release of a newly developed global AM fungal dataset (GlobalAMFungi database, https://globalamfungi.com) that aims to reduce this knowledge gap. It contains almost 50 million observations of Glomeromycotinian AM fungal amplicon DNA sequences across almost 8500 samples with geographical locations and additional metadata obtained from 100 original studies. The GlobalAMFungi database is built on sequencing data originating from AM fungal taxon barcoding regions in: i) the small subunit rRNA (SSU) gene; ii) the internal transcribed spacer 2 (ITS2) region; and iii) the large subunit rRNA (LSU) gene. The GlobalAMFungi database is an open source and open access initiative that compiles the most comprehensive atlas of AM fungal distribution. It is designed as a permanent effort that will be continuously updated by its creators and through the collaboration of the scientific community. This study also documented applicability of the dataset to better understand ecology of AM fungal taxa.

Above- and belowground fungal biodiversity of Populus trees on a continental scale

Understanding drivers of terrestrial fungal communities over large scales is an important challenge for predicting the fate of ecosystems under climate change and providing critical ecological context for bioengineering plant-microbe interactions in model systems. We conducted an extensive molecular and microscopy field study across the contiguous United States measuring natural variation in the Populus fungal microbiome among tree species, plant niche compartments and key symbionts. Our results show clear biodiversity hotspots and regional endemism of Populus-associated fungal communities explained by a combination of climate, soil and geographic factors. Modelling climate change impacts showed a deterioration of Populus mycorrhizal associations and an increase in potentially pathogenic foliar endophyte diversity and prevalence. Geographic differences among these symbiont groups in their sensitivity to environmental change are likely to influence broader forest health and ecosystem function. This dataset provides an above- and belowground atlas of Populus fungal biodiversity at a continental scale.

Connecting the multiple dimensions of global soil fungal diversity

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.

Environmental modulation of plant mycorrhizal traits in the global flora

Mycorrhizal symbioses are known to strongly influence plant performance, structure plant communities and shape ecosystem dynamics. Plant mycorrhizal traits, such as those characterising mycorrhizal type (arbuscular (AM), ecto-, ericoid or orchid mycorrhiza) and status (obligately (OM), facultatively (FM) or non-mycorrhizal) offer valuable insight into plant belowground functionality. Here, we compile available plant mycorrhizal trait information and global occurrence data (∼ 100 million records) for 11,770 vascular plant species. Using a plant phylogenetic mega-tree and high-resolution climatic and edaphic data layers, we assess phylogenetic and environmental correlates of plant mycorrhizal traits. We find that plant mycorrhizal type is more phylogenetically conserved than plant mycorrhizal status, while environmental variables (both climatic and edaphic; notably soil texture) explain more variation in mycorrhizal status, especially FM. The previously underestimated role of environmental conditions has far-reaching implications for our understanding of ecosystem functioning under changing climatic and soil conditions.

Species-area relationships in microbial-mediated mutualisms

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

Arbuscular Mycorrhizal Fungi Associated with Maize (Zea mays L.) in the Formation and Stability of Aggregates in Two Types of Soil

Knowledge of native Arbuscular Mycorrhizal Fungi (AMF) and their relationship with the edaphic characteristics where they live is important to establish the influence of allochthonous AMF, which were inoculated, on the development and stability of soil aggregates. The objectives of this research were to know the composition of native AMF species from two contrasting soils, and to establish the development and stability of aggregates in those soils with corn plants after inoculating them with allochthonous AMF. The experiment had three factors: Soil (two levels [S1 and S2]), HMA (three levels: without application [A0], with the application of Claroideoglomus claroideum [A1] and with the application of a consortium [A2]) and Fertilization (two levels (without fertilization [f0] and with fertilization [f1])). Twelve treatments were generated, with five replicates (60 experimental units [EU]). The EU consisted of a pot with a corn plant and the distribution was completely random. The results demonstrated that the Typic Ustifluvent presented nine species of native AMF, while the Typic Dystrustert had three; the native AMF in each soil influenced the activity of allochthonous AMF, such as their colonization and sporulation. Likewise, differences were found in the stability of macro-sized aggregates (0.5 to 2.0 mm).

Stochastic Processes Derive Gut Fungi Community Assembly of Plateau Pikas (Ochotona curzoniae) along Altitudinal Gradients across Warm and Cold Seasons

Although fungi occupy only a small proportion of the microbial community in the intestinal tract of mammals, they play important roles in host fat accumulation, nutrition metabolism, metabolic health, and immune development. Here, we investigated the dynamics and assembly of gut fungal communities in plateau pikas inhabiting six altitudinal gradients across warm and cold seasons. We found that the relative abundances of Podospora and Sporormiella significantly decreased with altitudinal gradients in the warm season, whereas the relative abundance of Sarocladium significantly increased. Alpha diversity significantly decreased with increasing altitudinal gradient in the warm and cold seasons. Distance-decay analysis showed that fungal community similarities were significantly and negatively correlated with elevation. The co-occurrence network complexity significantly decreased along the altitudinal gradients as the total number of nodes, number of edges, and degree of nodes significantly decreased. Both the null and neutral model analyses showed that stochastic or neutral processes dominated the gut fungal community assembly in both seasons and that ecological drift was the main ecological process explaining the variation in the gut fungal community across different plateau pikas. Homogeneous selection played a weak role in structuring gut fungal community assembly during the warm season. Collectively, these results expand our understanding of the distribution patterns of gut fungal communities and elucidate the mechanisms that maintain fungal diversity in the gut ecosystems of small mammals.

Specificity in plant-mycorrhizal fungal relationships: prevalence, parameterization, and prospects

Species interactions exhibit varying degrees of specialization, ranging from generalist to specialist interactions. For many interactions (e.g., plant-microbiome) we lack standardized metrics of specialization, hindering our ability to apply comparative frameworks of specificity across niche axes and organismal groups. Here, we discuss the concept of plant host specificity of arbuscular mycorrhizal (AM) fungi and ectomycorrhizal (EM) fungi, including the predominant theories for their interactions: Passenger, Driver, and Habitat Hypotheses. We focus on five major areas of interest in advancing the field of plant-mycorrhizal fungal host specificity: phylogenetic specificity, host physiology specificity, functional specificity, habitat specificity, and mycorrhizal fungal-mediated plant rarity. Considering the need to elucidate foundational concepts of specificity in this globally important symbiosis, we propose standardized metrics and comparative studies to enhance our understanding. We also emphasize the importance of analyzing global mycorrhizal data holistically to draw meaningful conclusions and suggest a shift toward single-species analyses to unravel the complexities underlying these associations.

Into the microbial niche

The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.

Fungal Fight Club: phylogeny and growth rate predict competitive outcomes among ectomycorrhizal fungi

Ectomycorrhizal fungi are among the most prevalent fungal partners of plants and can constitute up to one-third of forest microbial biomass. As mutualistic partners that supply nutrients, water, and pathogen defense, these fungi impact host plant health and biogeochemical cycling. Ectomycorrhizal fungi are also extremely diverse, and the community of fungal partners on a single plant host can consist of dozens of individuals. However, the factors that govern competition and coexistence within these communities are still poorly understood. In this study, we used in vitro competitive assays between five ectomycorrhizal fungal strains to examine how competition and pH affect fungal growth. We also tested the ability of evolutionary history to predict the outcomes of fungal competition. We found that the effects of pH and competition on fungal performance varied extensively, with changes in growth media pH sometimes reversing competitive outcomes. Furthermore, when comparing the use of phylogenetic distance and growth rate in predicting competitive outcomes, we found that both methods worked equally well. Our study further highlights the complexity of ectomycorrhizal fungal competition and the importance of considering phylogenetic distance, ecologically relevant traits, and environmental conditions in predicting the outcomes of these interactions.

Nutrient conditions mediate mycorrhizal effects on biomass production and cell wall chemistry in poplar

Large-scale biofuel production from lignocellulosic feedstock is limited by the financial and environmental costs associated with growing and processing lignocellulosic material and the resilience of these plants to environmental stress. Symbiotic associations with arbuscular (AM) and ectomycorrhizal (EM) fungi represent a potential strategy for expanding feedstock production while reducing nutrient inputs. Comparing AM and EM effects on wood production and chemical composition is a necessary step in developing biofuel feedstocks. Here, we assessed the productivity, biomass allocation and secondary cell wall (SCW) composition of greenhouse-grown Populus tremuloidesMichx. inoculated with either AM or EM fungi. Given the long-term goal of reducing nutrient inputs for biofuel production, we further tested the effects of nutrient availability and nitrogen:phosphorus stoichiometry on mycorrhizal responses. Associations with both AM and EM fungi increased plant biomass by 14-74% depending on the nutrient conditions but had minimal effects on SCW composition. Mycorrhizal plants, especially those inoculated with EM fungi, also allocated a greater portion of their biomass to roots, which could be beneficial in the field where plants are likely to experience both water and nutrient stress. Leaf nutrient content was weakly but positively correlated with wood production in mycorrhizal plants. Surprisingly, phosphorus played a larger role in EM plants compared with AM plants. Relative nitrogen and phosphorus availability were correlated with shifts in SCW composition. For AM associations, the benefit of increased wood biomass may be partially offset by increased lignin content, a trait that affects downstream processing of lignocellulosic tissue for biofuels. By comparing AM and EM effects on the productivity and chemical composition of lignocellulosic tissue, this work links broad functional diversity in mycorrhizal associations to key biofuel traits and highlights the importance of considering both biotic and abiotic factors when developing strategies for sustainable biofuel production.

Multidimensional specialization and generalization are pervasive in soil prokaryotes

Habitat specialization underpins biological processes from species distributions to speciation. However, organisms are often described as specialists or generalists based on a single niche axis, despite facing complex, multidimensional environments. Here, we analysed 236 environmental soil microbiomes across the United States and demonstrate that 90% of >1,200 prokaryotes followed one of two trajectories: specialization on all niche axes (multidimensional specialization) or generalization on all axes (multidimensional generalization). We then documented that this pervasive multidimensional specialization/generalization had many ecological and evolutionary consequences. First, multidimensional specialization and generalization are highly conserved with very few transitions between these two trajectories. Second, multidimensional generalists dominated communities because they were 73 times more abundant than specialists. Lastly, multidimensional specialists played important roles in community structure with ~220% more connections in microbiome networks. These results indicate that multidimensional generalization and specialization are evolutionarily stable with multidimensional generalists supporting larger populations and multidimensional specialists playing important roles within communities, probably stemming from their overrepresentation among pollutant detoxifiers and nutrient cyclers. Taken together, we demonstrate that the vast majority of soil prokaryotes are restricted to one of two multidimensional niche trajectories, multidimensional specialization or multidimensional generalization, which then has far-reaching consequences for evolutionary transitions, microbial dominance and community roles.

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.

Plant-symbiotic fungal diversity tracks variation in vegetation and the abiotic environment along an extended elevational gradient in the Himalayas

Arbuscular mycorrhizal (AM) fungi can benefit plants under environmental stress, and influence plant adaptation to warmer climates. However, very little is known about the ecology of these fungi in alpine environments. We sampled plant roots along a large fraction (1941-6150 m asl (above sea level)) of the longest terrestrial elevational gradient on Earth and used DNA metabarcoding to identify AM fungi. We hypothesized that AM fungal alpha and beta diversity decreases with increasing elevation, and that different vegetation types comprise dissimilar communities, with cultured (putatively ruderal) taxa increasingly represented at high elevations. We found that the alpha diversity of AM fungal communities declined linearly with elevation, whereas within-site taxon turnover (beta diversity) was unimodally related to elevation. The composition of AM fungal communities differed between vegetation types and was influenced by elevation, mean annual temperature, and precipitation. In general, Glomeraceae taxa dominated at all elevations and vegetation types; however, higher elevations were associated with increased presence of Acaulosporaceae, Ambisporaceae, and Claroideoglomeraceae. Contrary to our expectation, the proportion of cultured AM fungal taxa in communities decreased with elevation. These results suggest that, in this system, climate-induced shifts in habitat conditions may facilitate more diverse AM fungal communities at higher elevations but could also favour ruderal taxa.

Changes of root AMF community structure and colonization levels under distribution pattern of geographical substitute for four Stipa species in arid steppe

The establishment of symbiotic relationship between arbuscular mycorrhizal fungi (AMF) and roots is a mutually beneficial process and plays an important role in plant succession in ecosystems. However, there is less understanding of information about the AMF community in roots under vegetation succession on a large regional scale, especially the spatial variation in the AMF community and its potential ecological functions. Here, we elucidated the spatial variations in root AMF community structure and root colonization along a distribution pattern of four zonal Stipa species in arid and semiarid grassland systems and explored key factors regulating AMF structure and mycorrhizal symbiotic interactions. Four Stipa species established a symbiosis with AMF, and annual mean temperature (MAT) and soil fertility were the main positive and negative driving factors of AM colonization, respectively. The Chao richness and Shannon diversity of AMF community in the root system of Stipa species tended to increase firstly from S. baicalensis to S. grandis and then decreased from S. grandis to S. breviflora. While evenness of root AMF and root colonization showed a trend of increasing from S. baicalensis to S. breviflora, and biodiversity was principally affected by soil total phosphorus (TP), organic phosphorus (Po) and MAT. It is emphasized that Stipa species have certain dependence on AMF, especially in a warming environment, and the root AMF community structure among the four Stipa taxa was different. Additionally, the composition and spatial distribution of root AMF in host plants varied with MAT, annual mean precipitation (MAP), TP and host plant species. These results will broaden our understanding of the relationship between plant and AMF communities and their ecological role, and provide basic information for the application of AMF in the conservation and rehabilitation of forage plants in degraded semiarid grasslands.

Niche differentiation of Mucoromycotinian and Glomeromycotinian arbuscular mycorrhizal fungi along a 2-million-year soil chronosequence

Current literature suggests ecological niche differentiation between co-occurring Mucoromycotinian arbuscular mycorrhizal fungi (M-AMF) and Glomeromycotinian AMF (G-AMF), but experimental evidence is limited. We investigated the influence of soil age, water availability (wet and dry), and plant species (native Microlaena stipoides and exotic Trifolium subterraneum) on anatomical root colonisation and DNA profiles of M-AMF and G-AMF under glasshouse conditions. We grew seedlings of each species in soils collected from the four stages of a soil chronosequence, where pH decreases from the youngest to oldest stages, and phosphorus (P) is low in the youngest and oldest, but high in the intermediate stages. We scored the percentage of root length colonised and used DNA metabarcoding to profile fungal richness and community composition associated with treatment combinations. Soil age, water availability, and plant species were important influencers of root colonisation, although no M-AMF were visible following staining of M. stipoides roots. Soil age and host plant influenced fungal richness and community composition. However, response to soil age, potential host species, and water availability differed between M-AMF and G-AMF. Root colonisation of T. subterraneum by M-AMF and G-AMF was inversely correlated with soil P level. Community composition of M-AMF and G-AMF was structured by soil age and, to a lesser extent, plant species. Richness of M-AMF and G-AMF was negatively, and positively, correlated with available P, respectively. These findings are experimental evidence of ecological niche differentiation of M-AMF and G-AMF and invite further exploration into interactive effects of abiotic and biotic factors on their communities along successional trajectories.

Vegetation as a key driver of the distribution of microbial generalists that in turn shapes the overall microbial community structure in the low Arctic tundra

Understanding the variability of microbial niches and their interaction with abiotic and biotic factors in the Arctic can provide valuable insights into microbial adaptations to extreme environments. This study investigates the structure and diversity of soil bacterial communities obtained from sites with varying vegetation coverage and soil biogeochemical properties in the low Arctic tundra and explores how bacteria interact under different environmental parameters. Our findings reveal differences in bacterial composition and abundance among three bacterial niche breadths (specialists, common taxa, and generalists). Co-occurrence network analysis revealed Rhizobiales and Ktedonobacterales as keystone taxa that connect and support other microbes in the habitat. Low-elevation indicators, such as vascular plants and moisture content, were correlated with two out of three generalist modular hubs and were linked to a large proportion of generalists' distribution (18%). Structural equation modeling revealed that generalists' distribution, which influenced the remaining microbial communities, was mainly regulated by vegetation coverage as well as other abiotic and biotic factors. These results suggest that elevation-dependent environmental factors directly influence microbial community structure and module formation through the regulation of generalists' distribution. Furthermore, the distribution of generalists was mainly affected by macroenvironment filtering, whereas the distribution of specialists was mainly affected by microenvironment filtering (species-engineered microbial niche construction). In summary, our findings highlight the strong top-down control exerted by vegetation on generalists' distribution, which in turn shapes the overall microbial community structure in the low Arctic tundra.

Building a genome-based understanding of bacterial pH preferences

The environmental preferences of many microbes remain undetermined. This is the case for bacterial pH preferences, which can be difficult to predict a priori despite the importance of pH as a factor structuring bacterial communities in many systems. We compiled data on bacterial distributions from five datasets spanning pH gradients in soil and freshwater systems (1470 samples), quantified the pH preferences of bacterial taxa across these datasets, and compiled genomic data from representative bacterial taxa. While taxonomic and phylogenetic information were generally poor predictors of bacterial pH preferences, we identified genes consistently associated with pH preference across environments. We then developed and validated a machine learning model to estimate bacterial pH preferences from genomic information alone, a model that could aid in the selection of microbial inoculants, improve species distribution models, or help design effective cultivation strategies. More generally, we demonstrate the value of combining biogeographic and genomic data to infer and predict the environmental preferences of diverse bacterial taxa.

Forest microbiome and global change

Forests influence climate and mitigate global change through the storage of carbon in soils. In turn, these complex ecosystems face important challenges, including increases in carbon dioxide, warming, drought and fire, pest outbreaks and nitrogen deposition. The response of forests to these changes is largely mediated by microorganisms, especially fungi and bacteria. The effects of global change differ among boreal, temperate and tropical forests. The future of forests depends mostly on the performance and balance of fungal symbiotic guilds, saprotrophic fungi and bacteria, and fungal plant pathogens. Drought severely weakens forest resilience, as it triggers adverse processes such as pathogen outbreaks and fires that impact the microbial and forest performance for carbon storage and nutrient turnover. Nitrogen deposition also substantially affects forest microbial processes, with a pronounced effect in the temperate zone. Considering plant-microorganism interactions would help predict the future of forests and identify management strategies to increase ecosystem stability and alleviate climate change effects. In this Review, we describe the impact of global change on the forest ecosystem and its microbiome across different climatic zones. We propose potential approaches to control the adverse effects of global change on forest stability, and present future research directions to understand the changes ahead.

Grass-microbial inter-domain ecological networks associated with alpine grassland productivity

Associations between grasses and soil microorganisms can strongly influence plant community structures. However, the associations between grass productivity and diversity and soil microbes, as well as the patterns of co-occurrence between grass and microbes remain unclear. Here, we surveyed grass productivity and diversity, determined soil physicochemical, and sequenced soil archaea, bacteria and fungi by metabarcoding technology at 16 alpine grasslands. Using the Distance-decay relationship, Inter-Domain Ecological Network (IDEN), and Mantel tests, we investigated the relationship between grass productivity, diversity and microbial diversity, and the patterns of co-occurrence between grass and microbial inter-domain network in alpine grassland. We found the archaea richness, bacteria richness and Shannon, and fungi α-diversity were significantly negatively correlation with grass diversity, but archaea and bacteria diversity were positively correlation with grass productivity. Moreover, an increase in microbial β-diversity was observed along with increased discrepancy in grass diversity and productivity and soil variables. Variance partitioning analysis suggested that the contribution of grass productivity on microbial community was higher than that of soil variables and grass diversity, which implies that microbial community was more related to grass productivity. Inter-Domain Ecological Network showed that the grass species formed complex and stable ecological networks with some bacterial, archaeal, and fungal species, and the grass-fungal ecological networks showed the highest robustness, which indicated that soil fungi could better co-coexist with aboveground grass in alpine grasslands. Besides, the connectivity degrees of the grass-microbial network were significantly positively correlated with grass productivity, suggesting that the coexistence pattern of grasses and microbes had a positive feedback effect on the grass productivity. The results are important for establishing the regulatory mechanisms between plants and microorganisms in alpine grassland ecosystems.

Multidimensional analysis reveals environmental factors that affect community dynamics of arbuscular mycorrhizal fungi in poplar roots

INTRODUCTION

Poplar is a tree species with important production and application value. The symbiotic relationship between poplar and arbuscular mycorrhizal fungi (AMF) has a key role in ecosystem functioning. However, there remain questions concerning the seasonal dynamics of the AMF community in poplar roots, the relationship between AMF and the soil environment, and its ecological function.

METHOD

Poplar roots and rhizosphere soil were sampled at the end of April and the end of October. The responses of AMF communities to season, host age, and host species were investigated; the soil environmental factors driving community changes were analyzed.

RESULTS

The diversity and species composition of the AMF community were higher in autumn than in spring. Season, host age, host species, and soil environmental factors affected the formation of the symbiotic mycorrhizal system and the AMF community. Differences in the communities could be explained by soil pH, total nitrogen, total phosphorus, total potassium, available potassium, and glomalin content.

DISCUSSION

The AMF community was sensitive to changes in soil physicochemical properties caused by seasonal dynamics, particularly total potassium. The change in the mycorrhizal symbiotic system was closely related to the growth and development of poplar trees.

Accuracy of mutual predictions of plant and microbial communities vary along a successional gradient in an alpine glacier forefield

Receding glaciers create virtually uninhabited substrates waiting for initial colonization of bacteria, fungi and plants. These glacier forefields serve as an ideal ecosystem for studying transformations in community composition and diversity over time and the interactions between taxonomic groups in a dynamic landscape. In this study, we investigated the relationships between the composition and diversity of bacteria, fungi, and plant communities as well as environmental factors along a successional gradient. We used random forest analysis assessing how well the composition and diversity of taxonomic groups and environmental factors mutually predict each other. We did not identify a single best indicator for all taxonomic and environmental properties, but found specific predictors to be most accurate for each taxon and environmental factor. The accuracy of prediction varied considerably along the successional gradient, highlighting the dynamic environmental conditions along the successional gradient that may also affect biotic interactions across taxa. This was also reflected by the high accuracy of predictions of plot age by all taxa. Next to plot age, our results indicate a strong importance of pH and temperature in structuring microbial and plant community composition. In addition, taxonomic groups predicted the community composition of each other more accurately than environmental factors, which may either suggest that these groups similarly respond to other not measured environmental factors or that direct interactions between taxa shape the composition of their communities. In contrast, diversity of taxa was not well predicted, suggesting that community composition of one taxonomic group is not a strong driver of the diversity of another group. Our study provides insights into the successional development of multidiverse communities shaped by complex interactions between taxonomic groups and the environment.

Modeling geographic distribution of arbuscular mycorrhizal fungi from molecular evidence in soils of Argentinean Puna using a maximum entropy approach

The biogeographic region of Argentinean Puna mainly extends at elevations higher than 3,000 m within the Andean Plateau and hosts diverse ecological communities highly adapted to extreme aridity and low temperatures. Soils of Puna are typically poorly evolved and geomorphology is shaped by drainage networks, resulting in highly vegetated endorheic basins and hypersaline basins known as salar or salt flats. Local communities rely on soil fertility for agricultural practices and on pastures for livestock rearing. From this perspective, investigating the scarcely explored microbiological diversity of these soils as indicators of ecosystems functioning might help to predict the fragility of these harsh environments. In this study we collected soil samples from 28 points, following a nested design within three different macro-habitats, i.e., Puna grassland, hypersaline salar and family-run crop fields. Total fungi and arbuscular mycorrhizal fungi (AMF) occurrence were analyzed using eDNA sequencing. In addition, the significance of soil salinity and organic matter content as significant predictors of AMF occurrence, was assessed through Generalized Linear Mixed Modeling. We also investigated whether intensive grazing by cattle and lama in Puna grasslands may reduce the presence of AMF in these highly disturbed soils, driving or not major ecological changes, but no consistent results were found, suggesting that more specific experiments and further investigations may address the question more specifically. Finally, to predict the suitability for AMF in the different macro-habitats, Species Distribution Modeling (SDM) was performed within an environmental coherent area comprising both the phytogeographic regions of Puna and Altoandino. We modeled AMF distribution with a maximum entropy approach, including bioclimatic and edaphic predictors and obtaining maps of environmental suitability for AMF within the predicted areas. To assess the impact of farming on AMF occurrence, we set a new series of models excluding the cultivated Chaupi Rodeo samples. Overall, SDM predicted a lower suitability for AMF in hypersaline salar areas, while grassland habitats and a wider temperature seasonality range appear to be factors significantly related to AMF enrichment, suggesting a main role of seasonal dynamics in shaping AMF communities. The highest abundance of AMF was observed in Vicia faba crop fields, while potato fields yielded a very low AMF occurrence. The models excluding the cultivated Chaupi Rodeo samples highlighted that if these cultivated areas had theoretically remained unmanaged habitats of Puna and Altoandino, then large-scale soil features and local bioclimatic constraints would likely support a lower suitability for AMF. Using SDM we evidenced the influence of bioclimatic, edaphic and anthropic predictors in shaping AMF occurrence and highlighted the relevance of considering human activities to accurately predict AMF distribution.

Stochastic processes dominate soil arbuscular mycorrhizal fungal community assembly along an elevation gradient in central Japan

Arbuscular mycorrhizal (AM) fungi play an important role in facilitating ecosystem function and stability. Yet, their community response patterns and ecological assembly processes along elevational gradients which cross a range of climates and soil conditions remain elusive. We used Illumina MiSeq sequencing to examine trends in soil AM fungal community along an elevational gradient from 100 m to 2300 m in central Japan. A total of 750 operational taxonomic units (OTUs) affiliated to 12 AM fungal genera were identified from soil samples, and the AM fungal community composition differed strongly with elevation, with variance explained more by climate, followed by soil and plant factors. The AM fungal α-diversity, network connectivity and complexity between AM fungal taxa and also with plant communities all exhibited a maximum at the mid-elevation of 800 m and then declined, principally influenced by soil pH and precipitation. Stochastic processes dominated AM fungal community assembly across the whole elevation gradient, with homogenizing dispersal being the main process. Only when AM fungal communities were contrasted across a relatively broad range of elevations, did variable selection (deterministic process) became significant, and even then in a mixed role with stochasticity. While OTUs of AM fungi are clearly adapted to particular environmental ranges, stochasticity due to rapid dispersal has a major role in determining their occurrence, suggesting that AM fungi may possess generalized and interchangeable niches, and can adjust their distribution rapidly - at least on the scale of a single mountain. This finding emphasizes that the roles of AM fungi in plant ecology may be non-specific and easily substituted, and furthermore that there is rapid local scale dispersal, which may allow plants to maintain effective AM associations under environmental change.

Identifying thresholds of nitrogen enrichment for substantial shifts in arbuscular mycorrhizal fungal community metrics in a temperate grassland of northern China

Nitrogen (N) enrichment poses threats to biodiversity and ecosystem stability, while arbuscular mycorrhizal (AM) fungi play important roles in ecosystem stability and functioning. However, the ecological impacts, especially thresholds of N enrichment potentially causing AM fungal community shifts have not been adequately characterized. Based on a long-term field experiment with nine N addition levels ranging from 0 to 50 g N m^-2  yr^-1 in a temperate grassland, we characterized the community response patterns of AM fungi to N enrichment. Arbuscular mycorrhizal fungal biomass continuously decreased with increasing N addition levels. However, AM fungal diversity did not significantly change below 20 g N m^-2  yr^-1 , but dramatically decreased at higher N levels, which drove the AM fungal community to a potentially unstable state. Structural equation modeling showed that the decline in AM fungal biomass could be well explained by soil acidification, whereas key driving factors for AM fungal diversity shifted from soil nitrogen : phosphorus (N : P) ratio to soil pH with increasing N levels. Different aspects of AM fungal communities (biomass, diversity and community composition) respond differently to increasing N addition levels. Thresholds for substantial community shifts in response to N enrichment in this grassland ecosystem are identified.

Glomerales Dominate Arbuscular Mycorrhizal Fungal Communities Associated with Spontaneous Plants in Phosphate-Rich Soils of Former Rock Phosphate Mining Sites

Arbuscular mycorrhizal fungi (AMF) are key drivers of soil functioning. They interact with multiple soil parameters, notably, phosphorus (P). In this work, AMF communities of native plants grown spontaneously on former mining sites either enriched (P sites) or not enriched with P (nP sites) by mining cuttings of rock phosphate (RP) were studied. No significant differences were observed in the root mycorrhizal rates of the plants when comparing P and nP sites. The assessment of AMF diversity and community structure using Illumina MiSeq metabarcoding and targeting 18S rDNA in roots and rhizospheric soils showed a total of 318 Amplicon Sequence Variants (ASVs) of Glomeromycota phylum. No significant difference in the diversity was found between P and nP sites. Glomeraceae species were largely dominant, formed a fungal core of 26 ASVs, and were persistent and abundant in all sites. In the P soils, eight ASVs were identified by indicator species analysis. A trend towards an increase in Diversisporaceae and Claroideoglomeraceae and a reduction in Paraglomeraceae and Glomeraceae were noticed. These results provide new insights into AMF ecology in former RP mining sites; they document that P concentration is a driver of AMF community structures in soils enriched in RP long term but also suggest an influence of land disturbance, ecosystem self-restoration, and AMF life history strategies as drivers of AMF community profiles.

Integrating plant and fungal quantitative genetics to improve the ecological and agricultural applications of mycorrhizal symbioses

Finding and targeting genes that quantitatively contribute to agricultural and ecological processes progresses food production and conservation efforts. Typically, quantitative genetic approaches link variants in a single organism's genome with a trait of interest. Recently, genome-to-genome mapping has found genome variants interacting between species to produce the result of a multiorganism (including multikingdom) interaction. These were plant and bacterial pathogen genome interactions; plant-fungal coquantitative genetics have not yet been applied. Plant-mycorrhizae symbioses exist across most biomes, for a majority of land plants, including crop plants, and manipulate many traits from single organisms to ecosystems for which knowing the genetic basis would be useful. The availability of Rhizophagus irregularis mycorrhizal isolates, with genomic information, makes dual-genome methods with beneficial mutualists accessible and imminent.

Environmental response of arbuscular mycorrhizal fungi under soybean cultivation at a regional scale

Climate change, the shortage of fertilizers and reduced land for cultivation have drawn attention to the potential aid provided by soil-borne organisms. Arbuscular mycorrhizal fungi (AMF) offer a wide range of ecosystem benefits and hence, understanding the mechanisms that control AMF occurrence and maintenance is essential for resilient crop production. We conducted a survey of 123 soybean fields located across a 75,000-km² area of Argentina to explore AMF community composition and to quantify the impact of soil, climate, and geographical distance on these key soil organisms. First, based upon morphological identification of spores, we compiled a list of the AMF species found in the studied area and identified Acaulospora scrobiculata and Glomus fuegianum as the most frequent species. G. fuegianum abundance was negatively correlated with precipitation seasonality and positively correlated with mean annual precipitation as well as mycorrhizal colonisation of soybean roots. Second, we observed that species richness was negatively correlated with soil P availability (Bray I), clay content and mean annual precipitation. Finally, based on partitioning variation analysis, we found that AMF exhibited spatial patterning at a broad scale. Therefore, we infer that geographical distance was positively associated with spore community composition heterogeneity across the region. Nevertheless, we highlight the importance of precipitation sensitivity of frequent species, overall AMF richness and community composition, revealing a crucial challenge to forthcoming agriculture considering an expected change in global climate patterns.

Global patterns in endemicity and vulnerability of soil fungi

Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.

Legacy Effects of Biochar and Compost Addition on Arbuscular Mycorrhizal Fungal Community and Co-Occurrence Network in Black Soil

Compost and biochar are beneficial soil amendments which derived from agricultural waste, and their application was proven to be effective practices for promoting soil fertility. Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most crop plant species, and are recognized as one group of the most important soil microorganisms to increase food security in sustainable agriculture. To understand the legacy effects of compost and biochar addition on AM fungal communities, a field study was conducted on the Songnen Plain, Northeast China. Two years after application, compost addition improved soil aggregate stability, but we did not detect a legacy effect of compost addition on AM fungal community. Our results indicated that AM fungal Shannon diversity and Pielou evenness indices were significantly increased by one-time biochar addition, but unaffected by compost addition after two year’s application. PERMANOVA analysis also revealed a legacy effect of biochar addition on AM fungal community. Network analysis revealed a dramatically simplified AM fungal co-occurrence network and small network size in biochar added soils, demonstrated by their topological properties (e.g., low connectedness and betweenness). However, AM fungal community did not differ among aggregate fractions, as confirmed by the PERMANOVA analysis as well as the fact that only a small number of AM fungal OTUs were shared among aggregate fractions. Consequently, the current study highlights a stronger legacy effect of biochar than compost addition on AM fungi, and have implications for agricultural practices.

Changes of Arbuscular Mycorrhizal Fungal Community and Glomalin in the Rhizosphere along the Distribution Gradient of Zonal Stipa Populations across the Arid and Semiarid Steppe

Arbuscular mycorrhizal fungi (AMF) have been reported to have a wide distribution in terrestrial ecosystems and to play a vital role in ecosystem functioning and symbiosis with Stipa grasses. However, exactly how AMF communities in the rhizosphere change and are distributed along different Stipa population with substituted distribution and their relationships remain unclear. Here, the changes and distribution of the rhizosphere AMF communities and their associations between hosts and the dynamic differences in the glomalin-related soil protein (GRSP) in the rhizosphere soil of seven Stipa species with spatial substitution distribution characteristics in arid and semiarid grasslands were investigated. Along with the substituted distribution of the Stipa populations, the community structures, taxa, species numbers, and alpha diversity index values of AMF in the rhizosphere changed. Some AMF taxa appeared only in certain Stipa species, but there was no obvious AMF taxon turnover. When the Stipa baicalensis population was replaced by the Stipa gobica population, the GRSP tended to decline, whereas the carbon contribution of the GRSP tended to increase. Stipa grandis and Stipa krylovii had a great degree of network modularity of the rhizosphere AMF community and exhibited a simple and unstable network structure, while the networks of Stipa breviflora were complex, compact, and highly stable. Furthermore, with the succession of zonal populations, the plant species, vegetation coverage, and climate gradient facilitated the differentiation of AMF community structures and quantities in the rhizospheres of different Stipa species. These findings present novel insights into ecosystem functioning and dynamics correlated with changing environments. IMPORTANCE This study fills a gap in our understanding of the soil arbuscular mycorrhizal fungal community distribution, community composition changes, and diversity of Stipa species along different Stipa population substitution distributions and of their adaptive relationships; furthermore, the differences in the glomalin-related soil protein (GRSP) contents in the rhizospheres of different Stipa species and GRSP's contribution to the grassland organic carbon pool were investigated. These findings provide a theoretical basis for the protection and utilization of regional biodiversity resources and sustainable ecosystem development.

Genotype, mycorrhizae, and herbivory interact to shape strawberry plant functional traits

Arbuscular mycorrhizal fungi (AMF) and herbivores are ubiquitous biotic agents affecting plant fitness. While individual effects of pairwise interactions have been well-studied, less is known about how species interactions above and belowground interact to influence phenotypic plasticity in plant functional traits, especially phytochemicals. We hypothesized that mycorrhizae would mitigate negative herbivore effects by enhancing plant physiology and reproductive traits. Furthermore, we expected genotypic variation would influence functional trait responses to these biotic agents. To test these hypotheses, we conducted a manipulative field-based experiment with three strawberry (Fragaria x ananassa) genotypes to evaluate plant phenotypic plasticity in multiple functional traits. We used a fully-crossed factorial design in which plants from each genotype were exposed to mycorrhizal inoculation, herbivory, and the combined factors to examine effects on plant growth, reproduction, and floral volatile organic compounds (VOCs). Genotype and herbivory were key determinants of phenotypic variation, especially for plant physiology, biomass allocation, and floral volatiles. Mycorrhizal inoculation increased total leaf area, but only in plants that received no herbivory, and also enhanced flower and fruit numbers across genotypes and herbivory treatments. Total fruit biomass increased for one genotype, with up to 30-40% higher overall yield depending on herbivory. Herbivory altered floral volatile profiles and increased total terpenoid emissions. The effects of biotic treatments, however, were less important than the overall influence of genotype on floral volatile composition and emissions. This study demonstrates how genotypic variation affects plant phenotypic plasticity to herbivory and mycorrhizae, playing a key role in shaping physiological and phytochemical traits that directly and indirectly influence productivity.

Defending Earth's terrestrial microbiome

Microbial life represents the majority of Earth's biodiversity. Across disparate disciplines from medicine to forestry, scientists continue to discover how the microbiome drives essential, macro-scale processes in plants, animals and entire ecosystems. Yet, there is an emerging realization that Earth's microbial biodiversity is under threat. Here we advocate for the conservation and restoration of soil microbial life, as well as active incorporation of microbial biodiversity into managed food and forest landscapes, with an emphasis on soil fungi. We analyse 80 experiments to show that native soil microbiome restoration can accelerate plant biomass production by 64% on average, across ecosystems. Enormous potential also exists within managed landscapes, as agriculture and forestry are the dominant uses of land on Earth. Along with improving and stabilizing yields, enhancing microbial biodiversity in managed landscapes is a critical and underappreciated opportunity to build reservoirs, rather than deserts, of microbial life across our planet. As markets emerge to engineer the ecosystem microbiome, we can avert the mistakes of aboveground ecosystem management and avoid microbial monocultures of single high-performing microbial strains, which can exacerbate ecosystem vulnerability to pathogens and extreme events. Harnessing the planet's breadth of microbial life has the potential to transform ecosystem management, but it requires that we understand how to monitor and conserve the Earth's microbiome.

Elevation and plant species identity jointly shape a diverse arbuscular mycorrhizal fungal community in the High Arctic

Knowledge about the distribution and local diversity patterns of arbuscular mycorrhizal (AM) fungi are limited for extreme environments such as the Arctic, where most studies have focused on spore morphology or root colonization. We here studied the joint effects of plant species identity and elevation on AM fungal distribution and diversity. We sampled roots of 19 plant species in 18 locations in Northeast Greenland, using next generation sequencing to identify AM fungi. We studied the joint effect of plant species, elevation and selected abiotic conditions on AM fungal presence, richness and composition. We identified 29 AM fungal virtual taxa (VT), of which six represent putatively new VT. Arbuscular mycorrhizal fungal presence increased with elevation, and as vegetation cover and the active soil layer decreased. Arbuscular mycorrhizal fungal composition was shaped jointly by elevation and plant species identity. We demonstrate that the Arctic harbours a relatively species-rich and nonrandomly distributed diversity of AM fungi. Given the high diversity and general lack of knowledge exposed herein, we encourage further research into the diversity, drivers and functional role of AM fungi in the Arctic. Such insight is urgently needed for an area with some of the globally highest rates of climate change.

Mechanisms of stress tolerance and their effects on the ecology and evolution of mycorrhizal fungi

Stress is ubiquitous and disrupts homeostasis, leading to damage, decreased fitness, and even death. Like other organisms, mycorrhizal fungi evolved mechanisms for stress tolerance that allow them to persist or even thrive under environmental stress. Such mechanisms can also protect their obligate plant partners, contributing to their health and survival under hostile conditions. Here we review the effects of stress and mechanisms of stress response in mycorrhizal fungi. We cover molecular and cellular aspects of stress and how stress impacts individual fitness, physiology, growth, reproduction, and interactions with plant partners, along with how some fungi evolved to tolerate hostile environmental conditions. We also address how stress and stress tolerance can lead to adaptation and have cascading effects on population- and community-level diversity. We argue that mycorrhizal fungal stress tolerance can strongly shape not only fungal and plant physiology, but also their ecology and evolution. We conclude by pointing out knowledge gaps and important future research directions required for both fully understanding stress tolerance in the mycorrhizal context and addressing ongoing environmental change.

Agricultural management and pesticide use reduce the functioning of beneficial plant symbionts

Phosphorus (P) acquisition is key for plant growth. Arbuscular mycorrhizal fungi (AMF) help plants acquire P from soil. Understanding which factors drive AMF-supported nutrient uptake is essential to develop more sustainable agroecosystems. Here we collected soils from 150 cereal fields and 60 non-cropped grassland sites across a 3,000 km trans-European gradient. In a greenhouse experiment, we tested the ability of AMF in these soils to forage for the radioisotope ³³P from a hyphal compartment. AMF communities in grassland soils were much more efficient in acquiring ³³P and transferred 64% more ³³P to plants compared with AMF in cropland soils. Fungicide application best explained hyphal ³³P transfer in cropland soils. The use of fungicides and subsequent decline in AMF richness in croplands reduced ³³P uptake by 43%. Our results suggest that land-use intensity and fungicide use are major deterrents to the functioning and natural nutrient uptake capacity of AMF in agroecosystems.

The effects of arbuscular mycorrhizal fungal species and taxonomic groups on stressed and unstressed plants: a global meta-analysis

The great majority of plants gain access to soil nutrients and enhance their performance under stressful conditions through symbiosis with arbuscular mycorrhizal fungi (AMF). The benefits that AMF confer vary among species and taxonomic groups. However, a comparative analysis of the different benefits among AMF has not yet been performed. We conducted a global meta-analysis of recent studies testing the benefits of individual AMF species and main taxonomic groups in terms of plant performance (growth and nutrition). Separately, we examined AMF benefits to plants facing biotic (pathogens, parasites, and herbivores) and abiotic (drought, salinity, and heavy metals) stress. AMF had stronger positive effects on phosphorus nutrition than on plant growth and nitrogen nutrition and the effects on the growth of plants facing biotic and abiotic stresses were similarly positive. While the AMF taxonomic groups showed positive effects on plant performance either with or without stress, Diversisporales were the most beneficial to plants without stress and Gigasporales to plants facing biotic stress. Our results provide a comprehensive analysis of the benefits of different AMF species and taxonomic groups on plant performance and useful insights for their management and use as bio-inoculants for agriculture and restoration.

The Costs and Benefits of Plant-Arbuscular Mycorrhizal Fungal Interactions

The symbiotic interaction between plants and arbuscular mycorrhizal (AM) fungi is often perceived as beneficial for both partners, though a large ecological literature highlights the context dependency of this interaction. Changes in abiotic variables, such as nutrient availability, can drive the interaction along the mutualism-parasitism continuum with variable outcomes for plant growth and fitness. However, AM fungi can benefit plants in more ways than improved phosphorus nutrition and plant growth. For example, AM fungi can promote abiotic and biotic stress tolerance even when considered parasitic from a nutrient provision perspective. Other than being obligate biotrophs, very little is known about the benefits AM fungi gain from plants. In this review, we utilize both molecular biology and ecological approaches to expand our understanding of the plant-AM fungal interaction across disciplines.

Dominance, diversity, and niche breadth in arbuscular mycorrhizal fungal communities

Classical theory identifies resource competition as the major structuring force of biotic communities and predicts that: (i) levels of dominance and richness in communities are inversely related, (ii) narrow niches allow dense 'packing' in niche space and thus promote diversity, and (iii) dominants are generalists with wide niches, such that locally abundant taxa also exhibit wide distributions. Current empirical support, however, is mixed. We tested these expectations using published data on arbuscular mycorrhizal (AM) fungal community composition worldwide. We recorded the expected negative relationship between dominance and richness and, to a degree, the positive association between local and global dominance. However, contrary to expectation, dominance was pronounced in communities where more specialists were present; and, conversely, richness was higher in communites with more generalists. Thus, resource competition and niche packing appear of limited importance in AM fungal community assembly; rather patterns of dominance and diversity seem more consistent with habitat filtering and stochastic processes. This article is protected by copyright. All rights reserved.