Draft genome sequences of Chryseobacterium sp. MHB01, Rhodococcus qingshengii MHB02, and Agrobacterium tumefaciens MHB03 isolated from superabsorbent polymer granules inoculated with an arbuscular mycorrhizal fungus

Chryseobacterium sp. MHB01, Rhodococcus qingshengii MHB02, and Agrobacterium tumefaciens MHB03 were isolated from superabsorbent polymer granules cultured with an arbuscular mycorrhizal fungus. Whole-genome sequencing of these three strains revealed genome sizes of 4.57 Mb, 7.13 Mb, and 5.49 Mb with G + C contents of 36.9%, 62.5%, and 58.2%, respectively.

Fern mycorrhizae do not respond to fertilization in a tropical montane forest

Ferns are known to have a lower incidence of mycorrhization than angiosperms. It has been suggested that this results from carbon being more limiting to fern growth than nutrient availability, but this assertion has not been tested yet. In the present study, we took advantage of a fertilization experiment with nitrogen and phosphorus on cloud forest plots of the Ecuadorean Andes for 15 years. A previous analysis revealed changes in the abundances of fern species in the fertilized plots compared to the control plots and hypothesized that this might be related to the responses of the mycorrhizal relationships to nutrient availability. We revisited the plots to assess the root-associated fungal communities of two epiphytic and two terrestrial fern species that showed shifts in abundance. We sampled and analyzed the roots of 125 individuals following a metabarcoding approach. We recovered 1382 fungal ASVs, with a dominance of members of Tremellales (Basidiomycota) and Heliotales (Ascomycota). The fungal diversity was highly partitioned with little overlap between individuals. We found marked differences between terrestrial and epiphytic species, with the latter fundamentally missing arbuscular mycorrhizal fungi (AMF). We found no effect of fertilization on the diversity or relative abundance of the fungal assemblages. Still, we observed a direct impact of phosphorus fertilization on its concentration in the fern leaves. We conclude that fern-fungi relationships in the study site are not restricted by nutrient availability and suggest the existence of little specificity on the fungal partners relative to the host fern species.

Heterogeneous landscape promotes distinct microbial communities in an imperiled scrub ecosystem

Habitat heterogeneity is a key driver of biodiversity of macroorganisms, yet how heterogeneity structures belowground microbial communities is not well understood. Importantly, belowground microbial communities may respond to any number of abiotic, biotic, and spatial drivers found in heterogeneous environments. Here, we examine potential drivers of prokaryotic and fungal communities in soils across the heterogenous landscape of the imperiled Florida scrub, a pyrogenic ecosystem where slight differences in elevation lead to large changes in water and nutrient availability and vegetation composition. We employ a comprehensive, large-scale sampling design to characterize the communities of prokaryotes and fungi associated with three habitat types and two soil depths (crust and subterranean) to evaluate (i) differences in microbial communities across these heterogeneous habitats, (ii) the relative roles of abiotic, biotic, and spatial drivers in shaping community structure, and (iii) the distribution of fungal guilds across these habitats. We sequenced soils from 40 complete replicates of habitat × soil depth combinations and sequenced the prokaryotic 16S and fungal internal transcribed spacer (ITS) regions using Illumina MiSeq. Habitat heterogeneity generated distinct communities of soil prokaryotes and fungi. Spatial distance played a role in structuring crust communities, whereas subterranean microbial communities were primarily structured by the shrub community, whose roots they presumably interacted with. This result helps to explain the unexpected transition we observed between arbuscular mycorrhiza-dominated soils at low-elevation habitats to ectomycorrhiza-dominated soils at high-elevation habitats. Our results challenge previous notions of environmental determinism of microbial communities and generate new hypotheses regarding symbiotic relationships across heterogeneous environments.

Plant productivity response to inter- and intra-symbiont diversity: Mechanisms, manifestations and meta-analyses

Symbiont diversity can have large effects on plant growth but the mechanisms generating this relationship remain opaque. We identify three potential mechanisms underlying symbiont diversity-plant productivity relationships: provisioning with complementary resources, differential impact of symbionts of varying quality and interference between symbionts. We connect these mechanisms to descriptive representations of plant responses to symbiont diversity, develop analytical tests differentiating these patterns and test them using meta-analysis. We find generally positive symbiont diversity-plant productivity relationships, with relationship strength varying with symbiont type. Inoculation with symbionts from different guilds (e.g. mycorrhizal fungi and rhizobia) yields strongly positive relationships, consistent with complementary benefits from functionally distinct symbionts. In contrast, inoculation with symbionts from the same guild yields weak relationships, with co-inoculation not consistently generating greater growth than the best individual symbiont, consistent with sampling effects. The statistical approaches we outline, along with our conceptual framework, can be used to further explore plant productivity and community responses to symbiont diversity, and we identify critical needs for additional research to explore context dependency in these relationships.

Structurally distinct mitoviruses: are they an ancestral lineage of the Mitoviridae exclusive to arbuscular mycorrhizal fungi (Glomeromycotina)?

Mitoviruses in the family Mitoviridae are the mitochondria-replicating "naked RNA viruses" with genomes encoding only the replicase RNA-dependent RNA polymerase (RdRp) and prevalent across fungi, plants, and invertebrates. Arbuscular mycorrhizal fungi in the subphylum Glomeromycotina are obligate plant symbionts that deliver water and nutrients to the host. We discovered distinct mitoviruses in glomeromycotinian fungi, namely "large duamitovirus," encoding unusually large RdRp with a unique N-terminal motif that is endogenized in some host genomes. More than 400 viral sequences similar to the large duamitoviruses are present in metatranscriptome databases. They are globally distributed in soil ecosystems, consistent with the cosmopolitan distribution of glomeromycotinian fungi, and formed the most basal clade of the Mitoviridae in phylogenetic analysis. Given that glomeromycotinian fungi are the only confirmed hosts of these viruses, we propose the hypothesis that large duamitoviruses are the most ancestral lineage of the Mitoviridae that have been maintained exclusively in glomeromycotinian fungi.

Adaptative Strategies in Gymnocalycium Species (Cactaceae) and the Presence of Ectomycorrhizae Associated with Survival in Arid Environments

The Cactaceae family makes use of different strategies, both physiological and biochemical, for anatomical adjustments that allow them to grow and reproduce in arid environments. Morphological studies of Gymnocalycium have been scarce, and the anatomy and phytochemistry are still largely unknown. The aim of the present work was to analyze the structural, physiological, and biochemical features of Gymnocalycium marianae and G. oenanthemum, two endemic species of arid regions in Argentina. The anatomic structure, biomass, and photosynthetic pigments, as well as phenolic compound contents, were analyzed in the stem, spine, and root of both species. G. marianae showed stems with deeper substomatal chambers and a more developed photosynthetic tissue than G. oenanthemum. The spines of G. oenanthemum showed higher biomass, thicker epidermal and subepidermal cell walls, and a higher content of phenolic compounds than those of G. marianae. Ectomycorrhizae were observed for the first time in roots in both species. Roots of G. marianae showed high colonization, biomass, and content of phenolic compounds. Both species showed abundant mucilaginous fibers in the stem and root. Finally, these results show the strategies associated with the survival in xeric environments of two cacti species at risk of extinction. They could be useful for the development of ex situ conservation programs.

Comparative genomics and phylogenomic investigation of the class Geoglossomycetes provide insights into ecological specialization and the systematics of Pezizomycotina

Despite their global presence and ubiquity, members of the class Geoglossomycetes (Pezizomycotina, Ascomycota) are understudied systematically and ecologically. These fungi have long been presumed saprobic due to their occurrence in or near leaf litter and soils. Additionally, they lack an apparent association with other organisms, reinforcing this perception. However, observations of sporocarps near ericaceous shrubs have given rise to an alternative hypothesis that members of Geoglossomycetes may form ericoid mycorrhizae or ectomycorrhizae. This claim, however, has yet to be confirmed via microscopy or amplicon-based studies examining root communities. As a result, our current understanding of their ecology is based on cursory observations. This study presents a comparative analysis of genomic signatures related to ecological niche to investigate the hypothesis of an ericoid mycorrhizal or ectomycorrhizal ecology in the class. We compared the carbohydrate-active enzyme (CAZyme) and secondary metabolite contents of six newly sequenced Geoglossomycetes genomes with those of fungi representing specific ecologies across Pezizomycotina. Our analysis reveals CAZyme and secondary metabolite content patterns consistent with ectomycorrhizal (EcM) members of Pezizomycotina. Specifically, we found a reduction in CAZyme-encoding genes and secondary metabolite clusters that suggests a mutualistic ecology. Our work includes the broadest taxon sampling for a phylogenomic study of Pezizomycotina to date. It represents the first functional genomic and genome-scale phylogenetic study of the class Geoglossomycetes and improves the foundational knowledge of the ecology and evolution of these understudied fungi.

Spore traits mediate disturbance effects on arbuscular mycorrhizal (AM) fungal community composition and mutualisms

Trait-based approaches in ecology are powerful tools for understanding how organisms interact with their environment. These approaches show particular promise in disturbance and community ecology contexts for understanding how disturbances like prescribed fire and bison grazing influence interactions between mutualist like arbuscular mycorrhizal (AM) fungi and their plant hosts. In this work we examined how disturbance effects on AM fungal spore community composition and mutualisms were mediated by selection for specific functional spore traits at both the species and community level. We tested these questions by analyzing AM fungal spore communities and traits from a frequently burned and grazed (bison) tallgrass prairie system and using these spores to inoculate a plant growth response experiment. Selection for darker, pigmented AM fungal spores, changes in the abundance and volume of individual AM fungal taxa, and altered sporulation, were indicators of fire and grazing effects on AM fungal community composition. Disturbance associated changes in AM fungal community composition were then correlated with altered growth responses of Schizachyrium scoparium grass. Our work shows that utilization of trait-based approaches in ecology can clarify the mechanisms that underly belowground responses to disturbance, and provide a useful framework for understanding interactions between organisms and their environment. This article is protected by copyright. All rights reserved.

Grassland ecosystem type drives AM fungal diversity and functional guild distribution in North American grasslands

Nutrient exchange forms the basis of the ancient symbiotic relationship that occurs between most land plants and arbuscular mycorrhizal (AM) fungi. Plants provide carbon (C) to AM fungi and fungi provide the plant with nutrients such as nitrogen (N) and phosphorous (P). Nutrient addition can alter this symbiotic coupling in key ways, such as reducing AM fungal root colonization and changing the AM fungal community composition. However, environmental parameters that differentiate ecosystems and drive plant distribution patterns (e.g., pH, moisture), are also known to impact AM fungal communities. Identifying the relative contribution of environmental factors impacting AM fungal distribution patterns is important for predicting biogeochemical cycling patterns and plant-microbe relationships across ecosystems. To evaluate the relative impacts of local environmental conditions and long-term nutrient addition on AM fungal abundance and composition across grasslands, we studied experimental plots amended for 10 years with N, P, or N and P fertilizer in different grassland ecosystem types, including tallgrass prairie, montane, shortgrass prairie, and desert grasslands. Contrary to our hypothesis, we found ecosystem type, not nutrient treatment, was the main driver of AM fungal root colonization, diversity, and community composition, even when accounting for site-specific nutrient limitations. We identified several important environmental drivers of grassland ecosystem AM fungal distribution patterns, including aridity, mean annual temperature, root moisture, and soil pH. This work provides empirical evidence for niche partitioning strategies of AM fungal functional guilds and emphasizes the importance of long-term, large scale research projects to provide ecologically relevant context to nutrient addition studies.

Zutano under Salt Stress Conditions

In Peru, almost 50% of the national agricultural products come from the coast, highlighting the production of avocado. Much of this area has saline soils. Beneficial microorganisms can favorably contribute to mitigating the effect of salinity on crops. Two trials were carried out with var. Zutano to evaluate the role of native rhizobacteria and two Glomeromycota fungi, one from a fallow (GFI) and the other from a saline soil (GWI), in mitigating salinity in avocado: (i) the effect of plant growth promoting rhizobacteria, and (ii) the effect of inoculation with mycorrhizal fungi on salt stress tolerance. Rhizobacteria P. plecoglissicida, and B. subtilis contributed to decrease the accumulation of chlorine, potassium and sodium in roots, compared to the uninoculated control, while contributing to the accumulation of potassium in the leaves. Mycorrhizae increased the accumulation of sodium, potassium, and chlorine ions in the leaves at a low saline level. GWI decreased the accumulation of sodium in the leaves compared to the control (1.5 g NaCl without mycorrhizae) and was more efficient than GFI in increasing the accumulation of potassium in leaves and reducing chlorine root accumulation. The beneficial microorganisms tested are promising in the mitigation of salt stress in avocado.

Can Microbial Consortium Applications Affect Yield and Quality of Conventionally Managed Processing Tomato?

Three commercial microbial-based biostimulants containing fungi (arbuscular mycorrhizae and Trichoderma spp.) and other microrganisms (plant growth-promoting bacteria and yeasts) were applied on a processing tomato crop in a two-year field experiment in southern Italy. The effects of the growing season and the microorganism-based treatments on the yield, technological traits and functional quality of the tomato fruits were assessed. The year of cultivation affected yield (with a lower fruit weight, higher marketable to total yield ratio and higher percentage of total defective fruits in 2020) and technological components (higher dry matter, titratable acidity, total soluble solids content in 2020). During the first year of the trial, the consortia-based treatments enhanced the soluble solids content (+10.02%) compared to the untreated tomato plants. The sucrose and lycopene content were affected both by the microbial treatments and the growing season (greater values found in 2021 with respect to 2020). The year factor also significantly affected the metabolite content, except for tyrosine, essential (EAA) and branched-chain amino acids (BCAAs). Over the two years of the field trial, FID-consortium enhanced the content of proteins (+53.71%), alanine (+16.55%), aspartic acid (+31.13%), γ-aminobutyric acid (GABA) (+76.51%), glutamine (+55.17%), glycine (+28.13%), monoethanolamine (MEA) (+19.57%), total amino acids (TAA) (+33.55), EAA (+32.56%) and BCAAs (+45.10%) compared to the control. Our findings highlighted the valuable effect of the FID microbial inoculant in boosting several primary metabolites (proteins and amino acids) in the fruits of the processing tomato crop grown under southern Italian environmental conditions, although no effect on the yield and its components was appreciated.

Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes

Ascomycota account for about two-thirds of named fungal species.1 Over 98% of known Ascomycota belong to the Pezizomycotina, including many economically important species as well as diverse pathogens, decomposers, and mutualistic symbionts.2 Our understanding of Pezizomycotina evolution has until now been based on sampling traditionally well-defined taxonomic classes.3,4,5 However, considerable diversity exists in undersampled and uncultured, putatively early-diverging lineages, and the effect of these on evolutionary models has seldom been tested. We obtained genomes from 30 putative early-diverging lineages not included in recent phylogenomic analyses and analyzed these together with 451 genomes covering all available ascomycete genera. We show that 22 of these lineages, collectively representing over 600 species, trace back to a single origin that diverged from the common ancestor of Eurotiomycetes and Lecanoromycetes over 300 million years BP. The new clade, which we recognize as a more broadly defined Lichinomycetes, includes lichen and insect symbionts, endophytes, and putative mycorrhizae and encompasses a range of morphologies so disparate that they have recently been placed in six different taxonomic classes. To test for shared hidden features within this group, we analyzed genome content and compared gene repertoires to related groups in Ascomycota. Regardless of their lifestyle, Lichinomycetes have smaller genomes than most filamentous Ascomycota, with reduced arsenals of carbohydrate-degrading enzymes and secondary metabolite gene clusters. Our expanded genome sample resolves the relationships of numerous "orphan" ascomycetes and establishes the independent evolutionary origins of multiple mutualistic lifestyles within a single, morphologically hyperdiverse clade of fungi.

Environmental interference of plant-microbe interactions

Environmental stresses can compromise the interactions of plants with beneficial microbes. In the present review, experimental results showing that stresses negatively affect the abundance and/or functionality of plant beneficial microbes are summarized. It is proposed that the environmental interference of these plant-microbe interactions is explained by the stress-mediated induction of plant signalling pathways associated with defence hormones and reactive oxygen species. These plant responses are recognized to regulate beneficial microbes within plants. The direct negative effect of stresses on microbes may also contribute to the environmental regulation of these plant mutualisms. It is also posited that, in stress situations, beneficial microbes harbour mechanisms that contribute to maintain the mutualistic associations. Beneficial microbes produce effector proteins and increase the antioxidant levels in plants that counteract the detrimental effects of plant stress responses on them. In addition, they deliver specific stress-protective mechanisms that assist to their plant hosts to mitigate the negative effects of stresses. Our study contributes to understanding how environmental stresses affect plant-microbe interactions and highlights why beneficial microbes can still deliver benefits to plants in stressful environments.

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.

Parametarhizium hingganense, a Novel Ectomycorrhizal Fungal Species, Promotes the Growth of Mung Beans and Enhances Resistance to Disease Induced by Rhizoctonia solani

The mutualistic interactions between mycorrhizae and plants first occurred along with the terrestrialization of plants. The majority of vascular plants are in symbiosis with mycorrhizal fungi. Due to their importance to the economy and ecology, arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi emerge as the most popular ones. However, the mechanism underlying the beneficial function of ECM fungi is not as clear as AM fungi. Here, the interaction between Parametarhizium hingganense, a novel fungal species isolated from forest litter, and mung bean (Vigna radiata) was studied. P. hingganense demonstrated P solubilization ability in vitro. Treatment of P. hingganense on the seeds resulted in promoted growth with enhanced P content. The hyphae of green fluorescence protein (GFP)-tagged P. hingganense were found to surround the roots and develop between cells, suggesting the establishment of an ectomycorrhizal symbiosis. Upon symbiosis with P. hingganense, the levels of jasmonic acid (JA) and gibberellin (GA₁) and total phenolic and flavonoid content elevated. Meanwhile, damping off caused by Rhizoctonia solani in mycorrhizal plants was alleviated. Taken together, the above findings suggested that symbiosis with P. hingganense conferred growth promotion and priming of defense responses to host plants which should be associated with facilitated P uptake and increased JA and GA₁ levels.

Modeling Global Carbon Costs of Plant Nitrogen and Phosphorus Acquisition

Most Earth system models (ESMs) do not explicitly represent the carbon (C) costs of plant nutrient acquisition, which leads to uncertainty in predictions of the current and future constraints to the land C sink. We integrate a plant productivity-optimizing nitrogen (N) and phosphorus (P) acquisition model (fixation & uptake of nutrients, FUN) into the energy exascale Earth system (E3SM) land model (ELM). Global plant N and P uptake are dynamically simulated by ELM-FUN based on the C costs of nutrient acquisition from mycorrhizae, direct root uptake, retranslocation from senescing leaves, and biological N fixation. We benchmarked ELM-FUN with three classes of products: ILAMB, a remotely sensed nutrient limitation product, and CMIP6 models; we found significant improvements in C cycle variables, although the lack of more observed nutrient data prevents a comprehensive level of benchmarking. Overall, we found N and P co-limitation for 80% of land area, with the remaining 20% being either predominantly N or P limited. Globally, the new model predicts that plants invested 4.1 Pg C yr-1 to acquire 841.8 Tg N yr-1 and 48.1 Tg P yr-1 (1994-2005), leading to significant downregulation of global net primary production (NPP). Global NPP is reduced by 20% with C costs of N and 50% with C costs of NP. Modeled and observed nutrient limitation agreement increases when N and P are considered together (r 2 from 0.73 to 0.83).

Arbuscular Mycorrhizal Fungi and Fertilization Influence Yield, Growth and Root Colonization of Different Tomato Genotype

Arbuscular mycorrhizal fungi (AMF) are beneficial for plant development and help absorb water and minerals from the soil. The symbiosis between these fungi and plant roots is extremely important and could limit crop dependence on fertilizers. The aim of this study was to evaluate the influence of AMF on tomatoes (Solanum lycopersicum L.), based on important agronomic traits of vegetative biomass, production, and fruits. The experiment was conducted in high tunnels, using 12 tomato genotypes under three different treatments: T1, control, without fertilizer and mycorrhizae colonization; T2, fertigation, without mycorrhizae colonization; and T3, arbuscular mycorrhizal fungi (AMF), seedling roots being inoculated with specialized soil-borne fungi. Plant growth, yield and fruit parameters indicated better results under mycorrhizal treatment. Root colonization with fungi varied significantly depending on the treatment and genotype, with a variation of 6.0-80.3% for frequency and 2.6-24.6% for intensity. For a majority of characteristics, the mycorrhization (T3) induced significant differences compared with the T1 and T2 treatments. In addition, AMF treatment induced a different response among the genotypes. Among the elements analyzed in the soil, significant differences were observed in phosphorous levels between planting the seedlings and after tomato harvesting and clearing of the plants. The results suggest that reducing fertilizers and promoting the symbiotic relationships of plants with soil microorganisms may have beneficial consequences for tomato crops.

Does Shift in Vegetation Abundance After Nitrogen and Phosphorus Additions Play a Key Role in Regulating Fungal Community Structure in a Northern Peatland?

Soil fungal communities are key players in biogeochemical processes of peatlands, which are important carbon stocks globally. Although it has been elucidated that fungi are susceptible to environmental changes, little is known about the intricate and interactive effect of long-term nitrogen (N) and phosphorus (P) enrichment on fungal community structure in northern peatlands. In this study, we compared a short- (2 years) with a long-term (10 years) fertilization experiment in a peatland complex in northeastern China to assess how N and/or P additions influence fungal community structure. The results showed that fungal community composition and diversity were altered by N addition, without a significant interactive effect with P addition. Not only the long-term but also the short-term nutrient addition could change the abundance of different plant functional types. However, there were no strong cascading effects on the fungal community in any of the fertilization experiments. Long-term nutrient addition showed a stronger effect on the relative abundance of different fungal functional guilds; an increase in the relative abundance of saprotrophs after fertilization did not jeopardize mycorrhizal fungi. Moreover, the decline in Sphagnum cover after long-term N addition did not parallel changes in the relative abundance of Sphagnum-associated fungi (Clavaria sphagnicola, Galerina tibiicystis, G. sphagnicola, and G. paludosa). Given that short- and long-term fertilization showed strongly contrasting effects on fungal community structure, our study highlights the necessity of assessing the long-term effects of nutrient enrichment on the association between vegetation and fungal community in peatland ecosystems. Future research priorities should emphasize the connection between the community structure of fungal functional guilds and their functionality, which is of paramount importance to better understand their influences on C storage in the face of uncertain N and P deposition regimes.

When does mutualism offer a competitive advantage? A game-theoretic analysis of host-host competition in mutualism

Due to their non-motile nature, plants rely heavily on mutualistic interactions to obtain resources and carry out services. One key mutualism is the plant-microbial mutualism in which a plant trades away carbon to a microbial partner for nutrients like nitrogen and phosphorous. Plants show much variation in the use of this partnership from the individual level to entire lineages depending upon ecological, evolutionary and environmental context. We sought to determine how this context dependency could result in the promotion, exclusion or coexistence of the microbial mutualism by asking if and when the partnership provided a competitive advantage to the plant. To that end, we created a 2 × 2 evolutionary game in which plants could either be a mutualist and pair with a microbe or be a non-mutualist and forgo the partnership. Our model includes both frequency dependence and density dependence, which gives us the eco-evolutionary dynamics of mutualism evolution. As in all models, mutualism only evolved if it could offer a competitive advantage and its net benefit was positive. However, surprisingly the model reveals the possibility of coexistence between mutualist and non-mutualist genotypes due to competition between mutualists over the microbially obtained nutrient. Specifically, frequency dependence of host strategies can make the microbial symbiont less beneficial if the microbially derived resources are shared, a phenomenon that increasingly reduces the frequency of mutualism as the density of competitors increases. In essence, ecological competition can act as a hindrance to mutualism evolution. We go on to discuss basic experiments that can be done to test and falsify our hypotheses.

Phylogenetic Signal, Root Morphology, Mycorrhizal Type, and Macroinvertebrate Exclusion: Exploring Wood Decomposition in Soils Conditioned by 13 Temperate Tree Species

Woodlands are pivotal to carbon stocks, but the process of cycling C is slow and may be most effective in the biodiverse root zone. How the root zone impacts plants has been widely examined over the past few decades, but the role of the root zone in decomposition is understudied. Here, we examined how mycorrhizal association and macroinvertebrate activity influences wood decomposition across diverse tree species. Within the root zone of six predominantly arbuscular mycorrhizal (AM) (Acer negundo, Acer saccharum, Prunus serotina, Juglans nigra, Sassafras albidum, and Liriodendron tulipfera) and seven predominantly ectomycorrhizal (EM) tree species (Carya glabra, Quercus alba, Quercus rubra, Betula alleghaniensis, Picea rubens, Pinus virginiana, and Pinus strobus), woody litter was buried for 13 months. Macroinvertebrate access to woody substrate was either prevented or not using 0.22 mm mesh in a common garden site in central Pennsylvania. Decomposition was assessed as proportionate mass loss, as explained by root diameter, phylogenetic signal, mycorrhizal type, canopy tree trait, or macroinvertebrate exclusion. Macroinvertebrate exclusion significantly increased wood decomposition by 5.9%, while mycorrhizal type did not affect wood decomposition, nor did canopy traits (i.e., broad leaves versus pine needles). Interestingly, there was a phylogenetic signal for wood decomposition. Local indicators for phylogenetic associations (LIPA) determined high values of sensitivity value in Pinus and Picea genera, while Carya, Juglans, Betula, and Prunus yielded low values of sensitivity. Phylogenetic signals went undetected for tree root morphology. Despite this, roots greater than 0.35 mm significantly increased woody litter decomposition by 8%. In conclusion, the findings of this study suggest trees with larger root diameters can accelerate C cycling, as can trees associated with certain phylogenetic clades. In addition, root zone macroinvertebrates can potentially limit woody C cycling, while mycorrhizal type does not play a significant role.

Seed Treatments with Microorganisms Can Have a Biostimulant Effect by Influencing Germination and Seedling Growth of Crops

Seed quality is an important aspect of the modern cultivation strategies since uniform germination and high seedling vigor contribute to successful establishment and crop performance. To enhance germination, beneficial microbes belonging to arbuscular mycorrhizal fungi, Trichoderma spp., rhizobia and other bacteria can be applied to seeds before sowing via coating or priming treatments. Their presence establishes early relationships with plants, leading to biostimulant effects such as plant-growth enhancement, increased nutrient uptake, and improved plant resilience to abiotic stress. This review aims to highlight the most significant results obtained for wheat, maize, rice, soybean, canola, sunflower, tomato, and other horticultural species. Beneficial microorganism treatments increased plant germination, seedling vigor, and biomass, as well as overcoming seed-related limitations (such as abiotic stress), both during and after emergence. The results are generally positive, but variable, so more scientific information needs to be acquired for different crops and cultivation techniques, with considerations to different beneficial microbes (species and strains) and under variable climate conditions to understand the effects of seed treatments.

The ectomycorrhizal fungus Pisolithus microcarpus encodes a microRNA involved in cross-kingdom gene silencing during symbiosis

Plant genomes encode hundreds of genes controlling the detection, signaling pathways, and immune responses necessary to defend against pathogens. Pathogens, in turn, continually evolve to evade these defenses. Small RNAs, such as microRNAs (miRNAs), are one mechanism used by pathogens to overcome plant defenses and facilitate plant colonization. Mounting evidence would suggest that beneficial microbes, likewise, use miRNAs to facilitate symbiosis. Here, we demonstrate that the beneficial fungus Pisolithus microcarpus encodes a miRNA that enters plant cells and stabilizes the symbiotic interaction. These results demonstrate that beneficial fungi may regulate host gene expression through the use of miRNAs and sheds light on how beneficial microbes have evolved mechanisms to colonize plant tissues.

Small RNAs (sRNAs) are known to regulate pathogenic plant–microbe interactions. Emerging evidence from the study of these model systems suggests that microRNAs (miRNAs) can be translocated between microbes and plants to facilitate symbiosis. The roles of sRNAs in mutualistic mycorrhizal fungal interactions, however, are largely unknown. In this study, we characterized miRNAs encoded by the ectomycorrhizal fungus Pisolithus microcarpus and investigated their expression during mutualistic interaction with Eucalyptus grandis. Using sRNA sequencing data and in situ miRNA detection, a novel fungal miRNA, Pmic_miR-8, was found to be transported into E. grandis roots after interaction with P. microcarpus. Further characterization experiments demonstrate that inhibition of Pmic_miR-8 negatively impacts the maintenance of mycorrhizal roots in E. grandis, while supplementation of Pmic_miR-8 led to deeper integration of the fungus into plant tissues. Target prediction and experimental testing suggest that Pmic_miR-8 may target the host NB-ARC domain containing transcripts, suggesting a potential role for this miRNA in subverting host signaling to stabilize the symbiotic interaction. Altogether, we provide evidence of previously undescribed cross-kingdom sRNA transfer from ectomycorrhizal fungi to plant roots, shedding light onto the involvement of miRNAs during the developmental process of mutualistic symbioses.

Elucidating the Mechanisms Underlying Enhanced Drought Tolerance in Plants Mediated by Arbuscular Mycorrhizal Fungi

Plants are often subjected to various environmental stresses during their life cycle, among which drought stress is perhaps the most significant abiotic stress limiting plant growth and development. Arbuscular mycorrhizal (AM) fungi, a group of beneficial soil fungi, can enhance the adaptability and tolerance of their host plants to drought stress after infecting plant roots and establishing a symbiotic association with their host plant. Therefore, AM fungi represent an eco-friendly strategy in sustainable agricultural systems. There is still a need, however, to better understand the complex mechanisms underlying AM fungi-mediated enhancement of plant drought tolerance to ensure their effective use. AM fungi establish well-developed, extraradical hyphae on root surfaces, and function in water absorption and the uptake and transfer of nutrients into host cells. Thus, they participate in the physiology of host plants through the function of specific genes encoded in their genome. AM fungi also modulate morphological adaptations and various physiological processes in host plants, that help to mitigate drought-induced injury and enhance drought tolerance. Several AM-specific host genes have been identified and reported to be responsible for conferring enhanced drought tolerance. This review provides an overview of the effect of drought stress on the diversity and activity of AM fungi, the symbiotic relationship that exists between AM fungi and host plants under drought stress conditions, elucidates the morphological, physiological, and molecular mechanisms underlying AM fungi-mediated enhanced drought tolerance in plants, and provides an outlook for future research.

Enriched CO2 and Root-Associated Fungi (Mycorrhizae) Yield Inverse Effects on Plant Mass and Root Morphology in Six Asclepias Species

While milkweeds (Asclepias spp.) are important for sustaining biodiversity in marginal ecosystems, CO2 flux may afflict Asclepias species and cause detriment to native communities. Negative CO2-induced effects may be mitigated through mycorrhizal associations. In this study, we sought to determine how mycorrhizae interacts with CO2 to influence Asclepias biomass and root morphology. A broad range of Asclepias species (n = 6) were chosen for this study, including four tap-root species (A. sullivantii, A. syriaca, A. tuberosa, and A. viridis) and two fibrous root species (A. incarnata and A. verticillata). Collectively, the six Asclepias species were manipulated under a 2 × 2 full-factorial design that featured two mycorrhizal levels (-/+ mycorrhizae) and two CO2 levels (ambient and enriched (i.e., 3.5× ambient)). After a duration of 10 months, Asclepias responses were assessed as whole dry weight (i.e., biomass) and relative transportive root. Relative transportive root is the percent difference in the diameter of highest order root (transportive root) versus that of first-order absorptive roots. Results revealed an asymmetrical response, as mycorrhizae increased Asclepias biomass by ~12-fold, while enriched CO2 decreased biomass by about 25%. CO2 did not impact relative transportive roots, but mycorrhizae increased root organ's response by more than 20%. Interactions with CO2 and mycorrhizae were observed for both biomass and root morphology (i.e., relative transportive root). A gene associated with CO2 fixation (rbcL) revealed that the two fibrous root species formed a phylogenetic clade that was distant from the four tap-root species. The effect of mycorrhizae was most profound in tap-root systems, as mycorrhizae modified the highest order root into tuber-like structures. A strong positive correlation was observed with biomass and relative transportive root. This study elucidates the interplay with roots, mycorrhizae, and CO2, while providing a potential pathway for mycorrhizae to ameliorate CO2 induced effects.

Composted Municipal Green Waste Infused with Biocontrol Agents to Control Plant Parasitic Nematodes-A Review

The last few years have witnessed the emergence of alternative measures to control plant parasitic nematodes (PPNs). We briefly reviewed the potential of compost and the direct or indirect roles of soil-dwelling organisms against PPNs. We compiled and assessed the most intensively researched factors of suppressivity. Municipal green waste (MGW) was identified and profiled. We found that compost, with or without beneficial microorganisms as biocontrol agents (BCAs) against PPNs, were shown to have mechanisms for the control of plant parasitic nematodes. Compost supports a diverse microbiome, introduces and enhances populations of antagonistic microorganisms, releases nematicidal compounds, increases the tolerance and resistance of plants, and encourages the establishment of a "soil environment" that is unsuitable for PPNs. Our compilation of recent papers reveals that while the scope of research on compost and BCAs is extensive, the role of MGW-based compost (MGWC) in the control of PPNs has been given less attention. We conclude that the most environmentally friendly and long-term, sustainable form of PPN control is to encourage and enhance the soil microbiome. MGW is a valuable resource material produced in significant amounts worldwide. More studies are suggested on the use of MGWC, because it has a considerable potential to create and maintain soil suppressivity against PPNs. To expand knowledge, future research directions shall include trials investigating MGWC, inoculated with BCAs.

Shared friends counterbalance shared enemies in old forests

Mycorrhizal mutualisms are nearly ubiquitous across plant communities. Yet, it is still unknown whether facilitation among plants arises primarily from these mycorrhizal networks or from physical and ecological attributes of plants themselves. Here, we tested the relative contributions of mycorrhizae and plants to both positive and negative biotic interactions to determine whether plant-soil feedbacks with mycorrhizae neutralize competition and enemies within multitrophic forest community networks. We used Bayesian hierarchical generalized linear modeling to examine mycorrhizal-guild-specific and mortality-cause-specific woody plant survival compiled from a spatially and temporally explicit data set comprising 101,096 woody plants from three mixed-conifer forests across western North America. We found positive plant-soil feedbacks for large-diameter trees: species-rich woody plant communities indirectly promoted large tree survival when connected via mycorrhizal networks. Shared mycorrhizae primarily counterbalanced apparent competition mediated by tree enemies (e.g., bark beetles, soil pathogens) rather than diffuse competition between plants. We did not find the same survival benefits for small trees or shrubs. Our findings suggest that lower large-diameter tree mortality susceptibility in species-rich temperate forests resulted from greater access to shared mycorrhizal networks. The interrelated importance of aboveground and belowground biodiversity to large tree survival may be critical for counteracting increasing pathogen, bark beetle, and density threats.

How Tillage and Crop Rotation Change the Distribution Pattern of Fungi

Massive sequencing of fungal communities showed that climatic factors, followed by edaphic and spatial variables, are feasible predictors of fungal richness and community composition. This study, based on a long-term field experiment with tillage and no-tillage management since 1995 and with a crop rotation introduced in 2009, confirmed that tillage practices shape soil properties and impact soil fungal communities. Results highlighted higher biodiversity of saprotrophic fungi in soil sites with low disturbance and an inverse correlation between the biodiversity of ectomycorrhizal and saprotrophic fungi. We speculated how their mutual exclusion could be due to a substrate-mediated niche partitioning or by space segregation. Moreover, where the soil was ploughed, the species were evenly distributed. There was higher spatial variability in the absence of ploughing, with fungal taxa distributed according to a small-scale pattern, corresponding to micro-niches that probably remained undisturbed and heterogeneously distributed. Many differentially represented OTUs in all the conditions investigated were unidentified species or OTUs matching at high taxa level (i.e., phylum, class, order). Among the fungi with key roles in all the investigated conditions, there were several yeast species known to have pronounced endemism in soil and are also largely unidentified. In addition to yeasts, other fungal species emerged as either indicator of a kind of management or as strongly associated with a specific condition. Plant residues played a substantial role in defining the assortment of species.

Plant-associated fungal biofilms-knowns and unknowns

Nearly all microbes, including fungi, grow firmly attached to surfaces as a biofilm. Yet, attention toward fungal interactions with plants and the environment is dedicated to free-floating (planktonic) cells. Fungal biofilms are generally thought to configure interactions across and among plant populations. Despite this, plant fungal biofilm research lags far behind the research on biofilms of medically important fungi. The deficit in noticing and exploring this research avenue could limit disease management and plant improvement programs. Here, we provide the current state of knowledge of fungal biofilms and the different pivotal ecological roles they impart in the context of disease, through leveraging evidence across medically important fungi, secondary metabolite production, plant beneficial functions and climate change. We also provide views on several important information gaps potentially hampering plant fungal biofilm research, and propose a way forward to address these gaps.

Endophytic Fungi and Ecological Fitness of Chestnuts

Chestnuts (Castanea spp.) are plants of relevant economic interest in the agro-sylvicultural contexts of mountain regions throughout the temperate zone, particularly in the northern hemisphere. In recent years, several biological adversities have repeatedly endangered species belonging to this genus, calling for coordinated actions addressed to contrast their decline. These actions have mainly focused on the control of key pests/pathogens and the improvement of resistance/tolerance by the plant host, while the role of microorganisms as mediators of interactions between plants and the noxious agents has been less considered, essentially by reason of a limited knowledge on their ecological impact. In line with the increasing awareness of the basic importance of microbial symbionts in regulating plant fitness in both natural and crop contexts, this paper offers an overview on the occurrence and effects of endophytic fungi of chestnuts.

Plant-Soil-Microbiota Combination for the Removal of Total Petroleum Hydrocarbons (TPH): An In-Field Experiment

The contamination of soil with total petroleum hydrocarbons (TPH) may result in dramatic consequences and needs great attention, as soil rehabilitation would need more effort from a sustainability perspective. However, there is still no known general method since the remediation technology is strictly site-specific. Adaptive biological system dynamics can play a key role in understanding and addressing the potential of situ-specific biological combinations for soil pollutants removal. The potential worst-case of TPH contamination reflects soil affected by heavy industrial activities, such as oil refineries. Therefore, the experimental trial was conducted on a 2,000 m2 area from a contaminated site located in northern Italy. We evaluated the remediation potential over time (270 days) assessing (i) the phytoremediation efficiency of two species of Poaceae (Festuca arundinacea Schreb. and Dactylis glomerata L.) and two species of Fabaceae (Medicago sativa L. and Lotus corniculatus L.) and (ii) the role of the indigenous bacteria flora and endo-mycorrhizae consortium addition in plant growth promotion. We also induced resistance to contamination stress in a field experiment. Thirty-three indigenous bacteria selected from the contaminated soils showed marked plant growth promotion. Moreover, functional metagenomics confirmed the metabolic capability of hydrocarbon-degrading microorganisms living in the polluted soil. Our data showed that soil enzymatic activities increased with hydrocarbon degradation rate after 60 days. Both Poaceae and Fabaceae resulted in remarkable remediation potential. Stress markers and antioxidant activity indicated that the selected plant species generally need some time to adapt to TPH stress. In conclusion, our evaluation implied both the rhizosphere effects and functional features of the plant and suggested that plants should (i) have marked tolerance to specific contaminants, (ii) be characterized by an extensive root system, and (iii) be susceptible to arbuscular mycorrhizal fungi (AMF) infection.

Potential for Mycorrhizae-Assisted Phytoremediation of Phosphorus for Improved Water Quality

During this 6th Great Extinction, freshwater quality is imperiled by upland terrestrial practices. Phosphorus, a macronutrient critical for life, can be a concerning contaminant when excessively present in waterways due to its stimulation of algal and cyanobacterial blooms, with consequences for ecosystem functioning, water use, and human and animal health. Landscape patterns from residential, industrial and agricultural practices release phosphorus at alarming rates and concentrations threaten watershed communities. In an effort to reconcile the anthropogenic effects of phosphorus pollution, several strategies are available to land managers. These include source reduction, contamination event prevention and interception. A total of 80% of terrestrial plants host mycorrhizae which facilitate increased phosphorus uptake and thus removal from soil and water. This symbiotic relationship between fungi and plants facilitates a several-fold increase in phosphorus uptake. It is surprising how little this relationship has been encouraged to mitigate phosphorus for water quality improvement. This paper explores how facilitating this symbiosis in different landscape and land-use contexts can help reduce the application of fertility amendments, prevent non-point source leaching and erosion, and intercept remineralized phosphorus before it enters surface water ecosystems. This literature survey offers promising insights into how mycorrhizae can aid ecological restoration to reconcile humans' damage to Earth's freshwater. We also identify areas where research is needed.

Nitrogen cycling microbiomes are structured by plant mycorrhizal associations with consequences for nitrogen oxide fluxes in forests

Volatile nitrogen oxides (N2 O, NO, NO2 , HONO, …) can negatively impact climate, air quality, and human health. Using soils collected from temperate forests across the eastern United States, we show microbial communities involved in nitrogen (N) cycling are structured, in large part, by the composition of overstory trees, leading to predictable N-cycling syndromes, with consequences for emissions of volatile nitrogen oxides to air. Trees associating with arbuscular mycorrhizal (AM) fungi promote soil microbial communities with higher N-cycle potential and activity, relative to microbial communities in soils dominated by trees associating with ectomycorrhizal (ECM) fungi. Metagenomic analysis and gene expression studies reveal a 5 and 3.5 times greater estimated N-cycle gene and transcript copy numbers, respectively, in AM relative to ECM soil. Furthermore, we observe a 60% linear decrease in volatile reactive nitrogen gas flux (NOy  ≡ NO, NO2 , HONO) as ECM tree abundance increases. Compared to oxic conditions, gas flux potential of N2 O and NO increase significantly under anoxic conditions for AM soil (30- and 120-fold increase), but not ECM soil-likely owing to small concentrations of available substrate ( NO 3 - ) in ECM soil. Linear mixed effects modeling shows that ECM tree abundance, microbial process rates, and geographic location are primarily responsible for variation in peak potential NOy flux. Given that nearly all tree species associate with either AM or ECM fungi, our results indicate that the consequences of tree species shifts associated with global change may have predictable consequences for soil N cycling.

Low phosphorus supply constrains plant responses to elevated CO2 : A meta-analysis

Phosphorus (P) is an essential macro-nutrient required for plant metabolism and growth. Low P availability could potentially limit plant responses to elevated carbon dioxide (eCO₂ ), but consensus has yet to be reached on the extent of this limitation. Here, based on data from experiments that manipulated both CO₂ and P for young individuals of woody and non-woody species, we present a meta-analysis of P limitation impacts on plant growth, physiological, and morphological response to eCO₂ . We show that low P availability attenuated plant photosynthetic response to eCO₂ by approximately one-quarter, leading to a reduced, but still positive photosynthetic response to eCO₂ compared to those under high P availability. Furthermore, low P limited plant aboveground, belowground, and total biomass responses to eCO₂ , by 14.7%, 14.3%, and 12.4%, respectively, equivalent to an approximate halving of the eCO₂ responses observed under high P availability. In comparison, low P availability did not significantly alter the eCO₂ -induced changes in plant tissue nutrient concentration, suggesting tissue nutrient flexibility is an important mechanism allowing biomass response to eCO₂ under low P availability. Low P significantly reduced the eCO₂ -induced increase in leaf area by 14.3%, mirroring the aboveground biomass response, but low P did not affect the eCO₂ -induced increase in root length. Woody plants exhibited stronger attenuation effect of low P on aboveground biomass response to eCO₂ than non-woody plants, while plants with different mycorrhizal associations showed similar responses to low P and eCO₂ interaction. This meta-analysis highlights crucial data gaps in capturing plant responses to eCO₂ and low P availability. Field-based experiments with longer-term exposure of both CO₂ and P manipulations are critically needed to provide ecosystem-scale understanding. Taken together, our results provide a quantitative baseline to constrain model-based hypotheses of plant responses to eCO₂ under P limitation, thereby improving projections of future global change impacts.

Interactive Impact of Arbuscular Mycorrhizal Fungi and Elevated CO2 on Growth and Functional Food Value of Thymus vulgare

Arbuscular mycorrhizal fungi (AMF) and elevated CO₂ (eCO₂) have been effectively integrated to the agricultural procedures as an ecofriendly approach to support the production and quality of plants. However, less attention has been given to the synchronous application of AMF and eCO₂ and how that could affect the global plant metabolism. This study was conducted to investigate the effects of AMF and eCO₂, individually or in combination, on growth, photosynthesis, metabolism and the functional food value of Thymus vulgare. Results revealed that both AMF and eCO₂ treatments improved the photosynthesis and biomass production, however much more positive impact was obtained by their synchronous application. Moreover, the levels of the majority of the detected sugars, organic acids, amino acids, unsaturated fatty acids, volatile compounds, phenolic acids and flavonoids were further improved as a result of the synergistic action of AMF and eCO₂, as compared to the individual treatments. Overall, this study clearly shows that co-application of AMF and eCO₂ induces a synergistic biofertilization impact and enhances the functional food value of T. vulgare by affecting its global metabolism.

Calligonum polygonoides L. Shrubs Provide Species-Specific Facilitation for the Understory Plants in Coastal Ecosystem

Plant facilitation has a pivotal role in regulating species coexistence, particularly under arid environments. The present study aimed to evaluate the facilitative effect of Calligonum polygonoides L. on its understory plants in coastal habitat. Forty Calligonum shrubs were investigated and the environmental data (soil temperature, moisture, pH, salinity, carbon and nitrogen content, and light intensity), vegetation composition, and diversity of associated species were recorded under- and outside canopies. Eight of the most frequent understory species were selected for evaluating their response to the facilitative effect of C. polygonoides. Bioactive ingredients of Calligonum roots were analyzed using gas chromatography-mass spectrometry (GC-MS), and mycorrhizal biodiversity in their rhizosphere soil was also assessed. The effect of Calligonum on understory plants ranged between facilitation and inhibition in an age-dependent manner. Old shrubs facilitated 18 and inhibited 18 associated species, while young shrubs facilitated 13 and inhibited 9 species. Calligonum ameliorated solar radiation and high-temperature stresses for the under canopy plants. Moreover, soil moisture was increased by 509.52% and 85.71%, while salinity was reduced by 47.62% and 23.81% under old and young shrubs, respectively. Soil contents of C and N were increased under canopy. This change in the microenvironment led to photosynthetic pigments induction in the majority of understory species. However, anthocyanin, proline contents, and antioxidant enzyme activities were reduced in plants under canopy. Thirteen mycorrhizal fungal species were identified in the rhizospheric soil of Calligonum with the predominance of Funneliformis mosseae. Thirty-one compounds were identified in Calligonum root extract in which pyrogallol and palmitic acid, which have antimicrobial and allelopathic activities, were the major components. The obtained results demonstrated that facilitation provided by Calligonum is mediated with multiple mechanisms and included a set of interrelated scenarios that took place in a species-specific manner.

Glomus ibericum, Septoglomus mediterraneum, and Funneliformis pilosus, three new species of arbuscular mycorrhizal fungi

Three new arbuscular mycorrhizal fungal species-Glomus ibericum, Septoglomus mediterraneum, and Funneliformis pilosus-are described and illustrated. In the field, the three species were associated with roots of Ammophila arenaria (Poaceae), Elymus farctus (Poaceae), Otanthus maritimus (Asteraceae), and Echinophora spinosa (Apiaceae) colonizing maritime dunes located along the Mediterranean coast in eastern Spain. The novelty of these species is supported by morphological, molecular, and phylogenetic analyses. Single-species cultures of S. mediterraneum and F. pilosus were obtained using Trifolium repens as a host plant, both forming arbuscular mycorrhizae, whereas single-species cultures from G. ibericum could not be obtained. Spores of G. ibericum usually occur in sporocarps, rarely singly in soil or inside roots. In contrast, S. mediterraneum only forms single spores in soil and F. pilosus occurs in sporocarps and singly in soil or inside roots. The respective small subunit, internal transcribed spacer, and large subunit (SSU-ITS1-5.8S-ITS2-LSU) nrDNA sequences placed the new species in the genera Glomus, Septoglomus, and Funneliformis, all of them separated from previously described species.

Secret lifestyles of pyrophilous fungi in the genus Sphaerosporella

PREMISE

Pyrophilous fungi form aboveground fruiting structures (ascocarps) following wildfires, but their ecology, natural history, and life cycles in the absence of wildfires are largely unknown. Sphaerosporella is considered to be pyrophilous. This study explores Sphaerosporella ascocarp appearance following a rare 2016 wildfire in the Great Smoky Mountains National Park (GSMNP), compares the timing of ascocarp formation with recovery of Sphaerosporella DNA sequences in soils, and explores the association of Sphaerosporella with post-fire Table Mountain pine (Pinus pungens) seedlings.

METHODS

Burned sites in the GSMNP were surveyed for pyrophilous fungal ascocarps over 2 years. Ascocarps, mycorrhizae, and endophyte cultures were evaluated morphologically and by Sanger sequencing of the nuclear ribosomal ITS gene region (fungal barcode; Schoch et al., 2012). DNA from soil cores was subjected to Illumina sequencing.

RESULTS

The timing and location of post-fire Sphaerosporella ascocarp formation was correlated with recovery of Sphaerosporella DNA sequences in soils. Genetic markers (fungal barcode) of Sphaerosporella were also recovered from mycorrhizal root tips and endophyte cultures from seedlings of Pinus pungens.

CONCLUSIONS

This study demonstrates that Sphaerosporella species, in the absence of fire, are biotrophic, forming both mycorrhizal and endophytic associations with developing Pinus pungens seedlings and may persist in nature in the absence of wildfire as a conifer symbiont. We speculate that Sphaerosporella may fruit only after the host plant is damaged or destroyed and that after wildfires, deep roots, needle endophytes, or heat-resistant spores could serve as a source of soil mycelium.

Natural Products as Fungicide and Their Role in Crop Protection

Seeking solutions from nature for solving one and all problems is the age-old practice for mankind, and natural products are proved to be the most effective one for keeping up the balance of development as well as the “healthy, wealthy, and well” condition of mother nature. Fungal pathogens are proved to be a common and popular contaminant of agroecosystem that approximately causes 70–80% of total microbial crop loss. To meet the proper global increasing need of food products as a result of population explosion, managing agricultural system in an eco-friendly and profitable manner is the prime target; thus the word “sustainable agriculture” plays it part, and this package is highly effective when coupled with nature-derived fungicidal products that can minimize the event of fungal infections in agrarian ecosystem. Present study enlists the most common and effective natural products that might be of plant or microbial origin, their mode of action, day-by-day development of phytopathogenic resistance against the prevailing fungicides, and also their role in maintenance of sustainability of agricultural practices with special emphasis on their acceptance over the synthetic or chemical one. A large number of bioactive compounds ranging from direct plant (both cryptogams algae and moss and phanerogams)-derived natural extracts, essential oil of aromatic plants, and low-molecular-weight antimicrobial compounds known as phytoalexins to secondary metabolites that are both volatile and nonvolatile organic compounds of microbes (fungal and actinobacterial members) residing inside the host tissue, called endophyte, are widely used as agricultural bioweapons. The rhizospheric partners of plant, mycorrhizae, are also a prime agent of this chemical warfare and protect their green partners from fungal invaders and emphasize the concept of “sustainable agriculture.”

Impact of Irrigation Strategies on Tomato Root Distribution and Rhizosphere Processes in an Organic System

Root exploitation of soil heterogeneity and microbially mediated rhizosphere nutrient transformations play critical roles in plant resource uptake. However, how these processes change under water-saving irrigation technologies remains unclear, especially for organic systems where crops rely on soil ecological processes for plant nutrition and productivity. We conducted a field experiment and examined how water-saving subsurface drip irrigation (SDI) and concentrated organic fertilizer application altered root traits and rhizosphere processes compared to traditional furrow irrigation (FI) in an organic tomato system. We measured root distribution and morphology, the activities of C-, N-, and P-cycling enzymes in the rhizosphere, the abundance of rhizosphere microbial N-cycling genes, and root mycorrhizal colonization rate under two irrigation strategies. Tomato plants produced shorter and finer root systems with higher densities of roots around the drip line, lower activities of soil C-degrading enzymes, and shifts in the abundance of microbial N-cycling genes and mycorrhizal colonization rates in the rhizosphere of SDI plants compared to FI. SDI led to 66.4% higher irrigation water productivity than FI, but it also led to excessive vegetative growth and 28.3% lower tomato yield than FI. Our results suggest that roots and root-microbe interactions have a high potential for coordinated adaptation to water and nutrient spatial patterns to facilitate resource uptake under SDI. However, mismatches between plant needs and resource availability remain, highlighting the importance of assessing temporal dynamics of root-soil-microbe interactions to maximize their resource-mining potential for innovative irrigation systems.

Digging Deeper: In Search of the Mechanisms of Carbon and Nitrogen Exchange in Ectomycorrhizal Symbioses

Symbiosis with ectomycorrhizal (ECM) fungi is an advantageous partnership for trees in nutrient-limited environments. Ectomycorrhizal fungi colonize the roots of their hosts and improve their access to nutrients, usually nitrogen (N) and, in exchange, trees deliver a significant portion of their photosynthetic carbon (C) to the fungi. This nutrient exchange affects key soil processes and nutrient cycling, as well as plant health, and is therefore central to forest ecosystem functioning. Due to their ecological importance, there is a need to more accurately understand ECM fungal mediated C and N movement within forest ecosystems such that we can better model and predict their role in soil processes both now and under future climate scenarios. There are a number of hurdles that we must overcome, however, before this is achievable such as understanding how the evolutionary history of ECM fungi and their inter- and intra- species variability affect their function. Further, there is currently no generally accepted universal mechanism that appears to govern the flux of nutrients between fungal and plant partners. Here, we consider the current state of knowledge on N acquisition and transport by ECM fungi and how C and N exchange may be related or affected by environmental conditions such as N availability. We emphasize the role that modern genomic analysis, molecular biology techniques and more comprehensive and standardized experimental designs may have in bringing cohesion to the numerous ecological studies in this area and assist us in better understanding this important symbiosis. These approaches will help to build unified models of nutrient exchange and develop diagnostic tools to study these fungi at various scales and environments.

Extended cognition in plants: is it possible?

Plants do not possess brains or neurons. However, they present astonishingly complex behaviors such as information acquisition, memory, learning, decision making, etc., which helps these sessile organisms deal with their ever-changing environments. As a consequence, they have been proposed to be cognitive and intelligent, an idea which is becoming increasingly accepted. However, how plant cognition could operate without a nervous central system remains poorly understood and new insights on this topic are urgently needed. According to the Extended Cognition hypothesis, cognition may also occur beyond the limits of the body, encompassing objects from the environment. This was shown possible in humans and spiders, who actively manipulate their external environment to extend their cognitive capacity. Here, we propose that extended cognition may also be found in plants and could partly explain the complexity of plant behavior. We suggest that plants can extend their cognitive abilities to the environment they manipulate through the root influence zone and the mycorrhizal fungi that associate with them. The possibility of a cognitive process involving organisms from different kingdoms is exciting and worthwhile exploring as it may provide key insights into the origin and evolution of cognition.

Fungal functional ecology: bringing a trait-based approach to plant-associated fungi

Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (Fun^Fun ). Fun^Fun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.

Root cortical anatomy is associated with differential pathogenic and symbiotic fungal colonization in maize

Root anatomical phenotypes vary among maize (Zea mays) cultivars and may have adaptive value by modifying the metabolic cost of soil exploration. However, the microbial trade-offs of these phenotypes are unknown. We hypothesized that nodal roots of maize with contrasting cortical anatomy have different patterns of mutualistic and pathogenic fungal colonization. Arbuscular mycorrhizal colonization in the field and mesocosms, root rots in the field, and Fusarium verticillioides colonization in mesocosms were evaluated in maize genotypes with contrasting root cortical anatomy. Increased aerenchyma and decreased living cortical area were associated with decreased mycorrhizal colonization in mesocosm and field experiments with inbred genotypes. In contrast, mycorrhizal colonization of hybrids increased with larger aerenchyma lacunae; this increase coincided with larger root diameters of hybrid roots. F. verticillioides colonization was inversely correlated with living cortical area in mesocosm-grown inbreds, and no relation was found between root rots and living cortical area or aerenchyma in field-grown hybrids. Root rots were positively correlated with cortical cell file number and inversely correlated with cortical cell size. Mycorrhizae and root rots were inversely correlated in field-grown hybrids. We conclude that root anatomy is associated with differential effects on pathogens and mycorrhizal colonization of nodal roots in maize.

Laser ablation tomography for visualization of root colonization by edaphic organisms

Soil biota have important effects on crop productivity, but can be difficult to study in situ. Laser ablation tomography (LAT) is a novel method that allows for rapid, three-dimensional quantitative and qualitative analysis of root anatomy, providing new opportunities to investigate interactions between roots and edaphic organisms. LAT was used for analysis of maize roots colonized by arbuscular mycorrhizal fungi, maize roots herbivorized by western corn rootworm, barley roots parasitized by cereal cyst nematode, and common bean roots damaged by Fusarium. UV excitation of root tissues affected by edaphic organisms resulted in differential autofluorescence emission, facilitating the classification of tissues and anatomical features. Samples were spatially resolved in three dimensions, enabling quantification of the volume and distribution of fungal colonization, western corn rootworm damage, nematode feeding sites, tissue compromised by Fusarium, and as well as root anatomical phenotypes. Owing to its capability for high-throughput sample imaging, LAT serves as an excellent tool to conduct large, quantitative screens to characterize genetic control of root anatomy and interactions with edaphic organisms. Additionally, this technology improves interpretation of root-organism interactions in relatively large, opaque root segments, providing opportunities for novel research investigating the effects of root anatomical phenes on associations with edaphic organisms.

Plant facilitation through mycorrhizal symbiosis is stronger between distantly related plant species

The tendency of closely related plant species to share natural enemies has been suggested to limit their co-occurrence and performance, but we lack a deep understanding on how mutualistic interactions such as the mycorrhizal symbiosis affect plant-plant interactions depending on the phylogenetic relatedness of the interacting plants. We hypothesise that the effect of the mycorrhizal symbiosis on plant-plant facilitative interactions depends on the phylogenetic distance between the nurse and facilitated plants. A recently published meta-analysis compiled the strength of plant facilitative interactions in the presence or absence (or reduced abundance) of mycorrhizal fungi. We use phylogenetically informed Bayesian linear models to test whether the effect size is influenced by the phylogenetic distance between the plant species involved in each plant facilitative interaction. Conspecific facilitative interactions are more strongly enhanced by mycorrhizal fungi than interactions between closely related species. In heterospecific interactions, the effect of the mycorrhizal symbiosis on plant facilitation increases with the phylogenetic distance between the nurse and facilitated plant species. Our result showing that the effect of mycorrhizal symbiosis on the facilitation interactions between plants depends on their phylogenetic relatedness provides new mechanisms to understand how facilitation is assembling ecological communities.

From plant fungi to bee parasites: mycorrhizae and soil nutrients shape floral chemistry and bee pathogens

Bee populations have experienced declines in recent years, due in part to increased disease incidence. Multiple factors influence bee-pathogen interactions, including nectar and pollen quality and secondary metabolites. However, we lack an understanding of how plant interactions with their environment shape bee diet quality. We examined how plant interactions with the belowground environment alter floral rewards and, in turn, bee-pathogen interactions. Soil-dwelling mycorrhizal fungi are considered plant mutualists, although the outcome of the relationship depends on environmental conditions such as nutrients. In a 2 × 2 factorial design, we asked whether mycorrhizal fungi and nutrients affect concentrations of nectar and pollen alkaloids (anabasine and nicotine) previously shown to reduce infection by the gut pathogen Crithidia in the native bumble bee Bombus impatiens. To ask how plant interactions affect this common bee pathogen, we fed pollen and nectar from our treatment plants, and from a wildflower pollen control with artificial nectar, to bees infected with Crithidia. Mycorrhizal fungi and fertilizer both influenced flowering phenology and floral chemistry. While we found no anabasine or nicotine in nectar, high fertilizer increased anabasine and nicotine in pollen. Arbuscular mycorrhizal fungi (AMF) decreased nicotine concentrations, but the reduction due to AMF was stronger in high than low-nutrient conditions. AMF and nutrients also had interactive effects on bee pathogens via changes in nectar and pollen. High fertilizer reduced Crithidia cell counts relative to low fertilizer in AMF plants, but increased Crithidia in non-AMF plants. These results did not correspond with effects of fertilizer and AMF on pollen alkaloid concentrations, suggesting that other components of pollen or nectar were affected by treatments and shaped pathogen counts. Our results indicate that soil biotic and abiotic environment can alter bee-pathogen interactions via changes in floral rewards, and underscore the importance of integrative studies to predict disease dynamics and ecological outcomes.

Poor nutrition as a potential cause of divergent tree growth near the Arctic treeline in northern Alaska

Trees growing near the Arctic treeline have long been used to reconstruct past climates. However, recent studies have shown deterioration of historically strong positive correlations between air temperature and tree growth (known as "divergence"). Divergence has important implications for confidence in paleoclimate reconstructions and ecosystem-atmosphere carbon exchange. Studies in the Brooks Range of northern Alaska showed that white spruce in the west increased growth in response to late 20th century warming, whereas those in the east failed to show a growth increase. In an earlier study across four watersheds in the Brooks Range, we tested and rejected the hypothesis that divergence in the easternmost watershed reflects moisture limitation of growth. Here, using 16 sites distributed across the same four watersheds, we tested an alternative hypothesis, that greater nutrient limitation in the east may have impeded positive growth responses to warming. Climate comparison across the four Brooks Range study watersheds revealed that, although the easternmost watershed generally had a drier growing-season climate, the most consistent difference was that winter air temperature and both winter and summer soil temperatures were much colder in the central and eastern watersheds. Soil nutrient availability, foliar nutrient concentrations, and tree growth were all generally lower in the central and eastern than in the western watersheds. Foliar phosphorus concentration was the best predictor of spatial variation in branch extension growth-a finding that is somewhat inconsistent with the theory that forest productivity on young, glacially derived soils should be strongly nitrogen limited. Experimental fertilization yielded the greatest growth increase in the eastern, an intermediate response in the central, and the smallest growth increase in the western watershed, generally mirroring trends in soil temperature, soil nutrient availability, foliar nutrient concentrations, and growth of control trees. Our results confirm that growth in the easternmost watershed is more nutrient limited and suggest that phosphorus limitation may be at least as important as nitrogen limitation of growth. We hypothesize that cold soil effects on tree access to nutrients might explain divergence in the eastern Brooks Range and elsewhere near the Arctic treeline, particularly in areas with cold winters and widespread permafrost.

Drought soil legacy overrides maternal effects on plant growth

Maternal effects (i.e. trans-generational plasticity) and soil legacies generated by drought and plant diversity can affect plant performance and alter nutrient cycling and plant community dynamics. However, the relative importance and combined effects of these factors on plant growth dynamics remain poorly understood.We used soil and seeds from an existing plant diversity and drought manipulation field experiment in temperate grassland to test maternal, soil drought and diversity legacy effects, and their interactions, on offspring plant performance of two grassland species (Alopecurus pratensis and Holcus lanatus) under contrasting glasshouse conditions.Our results showed that drought soil legacy effects eclipsed maternal effects on plant biomass. Drought soil legacy effects were attributed to changes in both abiotic (i.e. nutrient availability) and biotic soil properties (i.e. microbial carbon and enzyme activity), as well as plant root and shoot atom 15N excess. Further, plant tissue nutrient concentrations and soil microbial C:N responses to drought legacies varied between the two plant species and soils from high and low plant diversity treatments. However, these diversity effects did not affect plant root or shoot biomass.These findings demonstrate that while maternal effects resulting from drought occur in grasslands, their impacts on plant performance are likely minor relative to drought legacy effects on soil abiotic and biotic properties. This suggests that soil drought legacy effects could become increasingly important drivers of plant community dynamics and ecosystem functioning as extreme weather events become more frequent and intense with climate change. A plain language summary is available for this article.