Multiple mutualist effects on genomewide expression in the tripartite association between Medicago truncatula, nitrogen‐fixing bacteria and mycorrhizal fungi

Transfer from ciliate to zebrafish: Unveiling mechanisms and combined effects of microplastics and heavy metals

The impacts and toxicological mechanisms of microplastics (MPs) or heavy metals on aquatic ecosystems have been the subject of extensive research and initial understanding. However, the combined toxicity of co-pollutants on organisms and cumulative toxic effects along the food chain are still underexplored. In this study, the ciliate protozoan Paramecium caudatum and zebrafish Danio rerio were used to represent the microbial loop and the higher trophic level, respectively, to illustrate the progressive exposure of MPs and cadmium (Cd2+). The findings indicate that MPs (ca. 1 ×105 items/L) containing with Cd2+ (below 0.1 µg/L) could permeate the bodies of zebrafish through trophic levels after primary ingestion by ciliates. This could cause adverse effects on zebrafish, including alterations in bioindicators (total sugar, triglycerides, lactate, and glycogen) associated with metabolism, delayed hepatic development, disruption of intestinal microbiota, DNA damage, inflammatory responses, and abnormal cellular apoptosis. In addition, the potential risks associated with the transfer of composite pollutants through the microbial loop into traditional food chain were examined, offering novel insights on the evaluation of the ecological risks associated with MPs. As observed, understanding the bioaccumulation and toxic effects of combined pollutants in zebrafish holds crucial implications for food safety and human health.

The Defective in Autoregulation (DAR) gene of Medicago truncatula encodes a protein involved in regulating nodulation and arbuscular mycorrhiza

BACKGROUND

Legumes utilize a long-distance signaling feedback pathway, termed Autoregulation of Nodulation (AON), to regulate the establishment and maintenance of their symbiosis with rhizobia. Several proteins key to this pathway have been discovered, but the AON pathway is not completely understood.

RESULTS

We report a new hypernodulating mutant, defective in autoregulation, with disruption of a gene, DAR (Medtr2g450550/MtrunA17_Chr2g0304631), previously unknown to play a role in AON. The dar-1 mutant produces ten-fold more nodules than wild type, similar to AON mutants with disrupted SUNN gene function. As in sunn mutants, suppression of nodulation by CLE peptides MtCLE12 and MtCLE13 is abolished in dar. Furthermore, dar-1 also shows increased root length colonization by an arbuscular mycorrhizal fungus, suggesting a role for DAR in autoregulation of mycorrhizal symbiosis (AOM). However, unlike SUNN which functions in the shoot to control nodulation, DAR functions in the root.

CONCLUSIONS

DAR encodes a membrane protein that is a member of a small protein family in M. truncatula. Our results suggest that DAR could be involved in the subcellular transport of signals involved in symbiosis regulation, but it is not upregulated during symbiosis. DAR gene family members are also present in Arabidopsis, lycophytes, mosses, and microalgae, suggesting the AON and AOM may use pathway components common to other plants, even those that do not undergo either symbiosis.

Genotype-by-genotype interkingdom cross-talk between symbiotic nitrogen fixing Sinorhizobium meliloti strains and Trichoderma species

In the understanding of the molecular interaction between plants and their microbiome, a key point is to identify simplified models of the microbiome including relevant bacterial and fungal partners which could also be effective in plant growth promotion. Here, as proof-of-concept, we aim to identify the possible molecular interactions between symbiotic nitrogen-fixing rhizobia and soil fungi (Trichoderma spp.), hence shed light on synergistic roles rhizospheric fungi could have in the biology of symbiotic nitrogen fixation bacteria. We selected 4 strains of the model rhizobium Sinorhizobium meliloti and 4 Trichoderma species (T. velutinum, T. tomentosum, T. gamsii and T. harzianum). In an experimental scheme of 4 ×4 strains x species combinations, we investigated the rhizobia physiological and transcriptomic responses elicited by fungal spent media, as well as spent media effects on rhizobia-host legume plant (alfalfa, Medicago sativa L.) symbiosis. Fungal spent media had large effects on rhizobia, specific for each fungal species and rhizobial strains combination, indicating a generalized rhizobia genotype x fungal genotype interaction, including synergistic, neutral and antagonistic effects on alfalfa symbiotic phenotypes. Differential expression of a high number of genes was shown in rhizobia strains with up to 25% of total genes differentially expressed upon treatment of cultures with fungal spent media. Percentages over total genes and type of genes differentially expressed changed according to both fungal species and rhizobial strain. To support the hypothesis of a relevant rhizobia genotype x fungal genotype interaction, a nested Likelihood Ratio Test indicated that the model considering the fungus-rhizobium interaction explained 23.4% of differentially expressed genes. Our results provide insights into molecular interactions involving nitrogen-fixing rhizobia and rhizospheric fungi, highlighting the panoply of genes and genotypic interactions (fungus, rhizobium, host plant) which may concur to plant symbiosis.

Arbuscular mycorrhizal fungi alleviate erosional soil nitrogen loss by regulating nitrogen cycling genes and enzymes in experimental agro-ecosystems

Nutrient losses from agricultural ecosystems are increasingly threatening global environmental and human health. Although arbuscular mycorrhizal (AM) fungi have the potential to regulate soil nitrogen (N) loss by enhancing plant uptake and soil particle immobilization, the microbial mechanism behind such mycorrhizal effect is unknown. Herein, by conducting a simulated erosion experiment, we compared the effects of exogenous AM fungal inoculation (Funneliformis mosseae) on the gene abundances and enzyme activities of N-cycling processes, and associated such effect to N uptake and loss. The experiment was composed of combinations of two AM fungal treatments (control vs. AM fungal inoculation), two crops (maize vs. soybean) and two slopes of the plots (6° vs. 20°). The experimental plots subjected to natural rainfalls to simulate the erosion events. We showed that the effects of AM fungi were greater in the maize soils than in the soybean soils. In the maize soils, AM fungi increased the abundances of N-fixing (+81.1 %) and nitrifying genes (+200.7 %) and N cycling enzyme activity (+22.3 %). In the soybean soils, AM fungi increased the N-fixing gene abundance (+36.9 %) but decreased the abundance of nitrifying genes (-18.9 %). The abundance of N-fixing gene was positively correlated with N uptake but negatively correlated with N loss. Additionally, AM fungi enhanced the effects of mycorrhizal colonization and moisture but decreased the effects of nutrients on soil microbial metrics related to N-cycling processes. Therefore, AM fungal inoculation enhanced N uptake and reduced N loss by increasing N-fixing gene abundance, and that AM fungi should be preferably used for the low N environments or for the ecosystems highly limited by or competing for N.

Generalized mutualisms promote range expansion in both plant and ant partners

Mutualism improves organismal fitness, but strong dependence on another species can also limit a species' ability to thrive in a new range if its partner is absent. We assembled a large, global dataset on mutualistic traits and species ranges to investigate how multiple plant-animal and plant-microbe mutualisms affect the spread of legumes and ants to novel ranges. We found that generalized mutualisms increase the likelihood that a species establishes and thrives beyond its native range, whereas specialized mutualisms either do not affect or reduce non-native spread. This pattern held in both legumes and ants, indicating that specificity between mutualistic partners is a key determinant of ecological success in a new habitat. Our global analysis shows that mutualism plays an important, if often overlooked, role in plant and insect invasions.

Positive interactions between mycorrhizal fungi and bacteria are widespread and benefit plant growth

Bacteria, ectomycorrhizal (EcM) fungi, and land plants have been coevolving for nearly 200 million years, and their interactions presumably contribute to the function of terrestrial ecosystems. The direction, stability, and strength of bacteria-EcM fungi interactions across landscapes and across a single plant host, however, remains unclear. Moreover, the genetic mechanisms that govern them have not been addressed. To these ends, we collected soil samples from Bishop pine forests across a climate-latitude gradient spanning coastal California, fractionated the soil samples based on their proximity to EcM-colonized roots, characterized the microbial communities using amplicon sequencing, and generated linear regression models showing the impact that select bacterial taxa have on EcM fungal abundance. In addition, we paired greenhouse experiments with transcriptomic analyses to determine the directionality of these relationships and identify which genes EcM-synergist bacteria express during tripartite symbioses. Our data reveal that ectomycorrhizas (i.e., EcM-colonized roots) enrich conserved bacterial taxa across climatically heterogeneous regions. We also show that phylogenetically diverse EcM synergists are positively associated with plant and fungal growth and have unique gene expression profiles compared with EcM-antagonist bacteria. In sum, we identify common mechanisms that facilitate widespread and diverse multipartite symbioses, which inform our understanding of how plants develop in complex environments.

Mutualisms in a warming world: How increased temperatures affect the outcomes of multi-mutualist interactions

In nature, plant species simultaneously interact with many different mutualistic partners. These mutualists may influence one another through direct interference or indirectly by competing for shared reward resources or through alteration of plant traits. Together, these mutualists also may combine to affect plant hosts in ways that may not be predictable based on pairwise interactions. Given that the outcome of mutualistic interactions often depends on environmental conditions, multi-mutualist effects on one another, and their plant hosts may be affected by global changes. Here, we grew focal plants under simulated global warming conditions and manipulated the presence of partner mutualists to test how warming affects the outcome of interactions between focal plants and their partners (nitrogen-fixing rhizobia, ant defenders, and pollinators) and interactions among these partner mutualists. We find that warming alters the fitness benefits plants receive from rhizobium resource mutualists but not ant mutualists and that warming altered plant investment in all mutualists. We also find that mutualist partners interact, often by altering the availability of plant-produced rewards that facilitate interactions with other partners. Our work illustrates that global changes may affect some but not all mutualisms, often asymmetrically (e.g., affecting investment in the mutualist partner but not plant host benefits) and also highlights the ubiquity of interactions between the multiple mutualists associating with a shared host.

Differential responses and mechanistic controls of soil phosphorus transformation in Eucalyptus plantations with N fertilization and introduced N2 -fixing tree species

Introducing N₂ -fixing tree species into Eucalyptus plantations could replace nitrogen (N) fertilization to maintain high levels of N consumption and productivity. However, N enrichment may exacerbate phosphorus (P) limitation as Eucalyptus robusta Smith is extensively planted in P-poor tropical and subtropical soils. We conducted a field experiment in a pure plantation of Eucalyptus urophylla × grandis to investigate the impacts of N fertilization and introduced an N₂ -fixing tree of Dalbergia odorifera T. Chen on soil P transformation. Nitrogen fertilization significantly enhanced soil occluded P pool and reduced the other P pools due to acidification-induced pH-sensitive geochemical processes, lowering Eucalyptus leaf P concentration with higher N : P ratio. By contrast, introduced N₂ -fixing tree species did not change soil pH, labile inorganic P pool, and Eucalyptus leaf N : P ratio, even enhanced organic P pools and reduced occluded P pool probably due to altering microbial community composition particularly stimulating arbuscular mycorrhiza fungal abundance. Our results revealed differential responses and mechanistic controls of soil P transformation in Eucalyptus plantations with N fertilization and introduced N₂ -fixing tree species. The dissolution of occluded P pool along with organic P accumulation observed in the mixed plantations may represent a promising future to better manage soil P availability.

Cooperative virulence via the collective action of secreted pathogen effectors

Although virulence is typically attributed to single pathogenic strains, here we investigated whether effectors secreted by a population of non-virulent strains could function as public goods to enable the emergence of collective virulence. We disaggregated the 36 type III effectors of the phytopathogenic bacterium Pseudomonas syringae strain PtoDC3000 into a 'metaclone' of 36 coisogenic strains, each carrying a single effector in an effectorless background. Each coisogenic strain was individually unfit, but the metaclone was collectively as virulent as the wild-type strain on Arabidopsis thaliana, suggesting that effectors can drive the emergence of cooperation-based virulence through their public action. We show that independently evolved effector suits can equally drive this cooperative behaviour by transferring the effector alleles native to the strain PmaES4326 into the conspecific but divergent strain PtoDC3000. Finally, we transferred the disaggregated PtoDC3000 effector arsenal into Pseudomonas fluorescens and show that their cooperative action was sufficient to convert this rhizosphere-inhabiting beneficial bacterium into a phyllosphere pathogen. These results emphasize the importance of microbial community interactions and expand the ecological scale at which disease may be attributed.

Genetic architecture of multiple mutualisms and mating system in Turnera ulmifolia

Plants often associate with multiple arthropod mutualists. These partners provide important services to their hosts, but multiple interactions can constrain a plant's ability to respond to complex, multivariate selection. Here, we quantified patterns of genetic variance and covariance among rewards for pollination, biotic defence and seed dispersal mutualisms in multiple populations of Turnera ulmifolia to better understand how the genetic architecture of multiple mutualisms might influence their evolution. We phenotyped plants cultivated from 17 Jamaican populations for several mutualism and mating system-related traits. We then fit genetic variance-covariance (G) matrices for the island metapopulation and the five largest individual populations. At the metapopulation level, we observed significant positive genetic correlations among stigma-anther separation, floral nectar production and extrafloral nectar production. These correlations have the potential to significantly constrain or facilitate the evolution of multiple mutualisms in T. ulmifolia and suggest that pollination, seed dispersal and defence mutualisms do not evolve independently. In particular, we found that positive genetic correlations between floral and extrafloral nectar production may help explain their stable coexistence in the face of physiological trade-offs and negative interactions between pollinators and ant bodyguards. Locally, we found only small differences in G among our T. ulmifolia populations, suggesting that geographic variation in G may not shape the evolution of multiple mutualisms.

Nitrogen-fixing symbiotic bacteria act as a global filter for plant establishment on islands

Island biogeography has classically focused on abiotic drivers of species distributions. However, recent work has highlighted the importance of mutualistic biotic interactions in structuring island floras. The limited occurrence of specialist pollinators and mycorrhizal fungi have been found to restrict plant colonization on oceanic islands. Another important mutualistic association occurs between nearly 15,000 plant species and nitrogen-fixing (N-fixing) bacteria. Here, we look for evidence that N-fixing bacteria limit establishment of plants that associate with them. Globally, we find that plants associating with N-fixing bacteria are disproportionately underrepresented on islands, with a 22% decline. Further, the probability of N-fixing plants occurring on islands decreases with island isolation and, where present, the proportion of N-fixing plant species decreases with distance for large, but not small islands. These findings suggest that N-fixing bacteria serve as a filter to plant establishment on islands, altering global plant biogeography, with implications for ecosystem development and introduction risks.

Priming of rhizobial nodulation signaling in the mycosphere accelerates nodulation of legume hosts

The simultaneous symbiosis of leguminous plants with two root mutualists, endophytic fungi and rhizobia is common in nature, yet how two mutualists interact and co-exist before infecting plants and the concomitant effects on nodulation are less understood. Using a combination of metabolic analysis, fungal deletion mutants and comparative transcriptomics, we demonstrated that Bradyrhizobium and a facultatively biotrophic fungus, Phomopsis liquidambaris, interacted to stimulate fungal flavonoid production, and thereby primed Bradyrhizobial nodulation signaling, enhancing Bradyrhizobial responses to root exudates and leading to early nodulation of peanut (Arachis hypogaea), and such effects were compromised when disturbing fungal flavonoid biosynthesis. Stress sensitivity assays and reactive oxygen species (ROS) determination revealed that flavonoid production acted as a strategy to alleviate hyphal oxidative stress during P. liquidambaris-Bradyrhizobial interactions. By investigating the interactions between P. liquidambaris and a collection of 38 rhizobacteria, from distinct bacterial genera, we additionally showed that the flavonoid-ROS module contributed to the maintenance of fungal and bacterial co-existence, and fungal niche colonization under soil conditions. Our results demonstrate for the first time that rhizobial nodulation signaling can be primed by fungi before symbiosis with host plants and highlight the importance of flavonoid in tripartite interactions between legumes, beneficial fungi and rhizobia.

Legume germination is delayed in dry soils and in sterile soils devoid of microbial mutualists: Species-specific implications for upward range expansions

Climate change is affecting species and their mutualists and can lead to the weakening or loss of important interspecific interactions. Through independent shifts in partner phenology and distribution, climatic stress can separate mutualists temporally or spatially, leading to alterations in partner functional traits and fitness. Here, we explored the effects of the loss of microbial mutualists on legume germination success and phenology. In particular, we assessed the effects of mutualism loss via soil sterilization, increased drought, and introduction to novel soils found beyond the current distributions of two focal legume species in subalpine environments. Through common garden experiments in controlled environments, we found evidence that soil sterilization (and consequent microbial absence) and dry soils caused species-specific phenological delays of 2-5 weeks in germination, likely as a result of interaction loss between legumes and specialized germination-promoting soil microbes, such as mutualistic rhizobia. Delays in germination caused by a mismatch between legumes and beneficial microbes could negatively affect legume fitness through increased plant-plant competition later in the season. Additionally, we found evidence of the presence of beneficial microbes beyond the current elevational range of one of our focal legumes, which may allow for expansion of the leading edge, although harsh abiotic factors in the alpine may hinder this. Alterations in the strength of soil microbe-legume mutualisms may lead to reduced fitness and altered demography for both soil microbes and legumes.

Commensal Pseudomonas strains facilitate protective response against pathogens in the host plant

The community structure in the plant-associated microbiome depends collectively on host–microbe, microbe–microbe and host–microbe–microbe interactions. The ensemble of interactions between the host and microbial consortia may lead to outcomes that are not easily predicted from pairwise interactions. Plant–microbe–microbe interactions are important to plant health but could depend on both host and microbe strain variation. Here we study interactions between groups of naturally co-existing commensal and pathogenic Pseudomonas strains in the Arabidopsis thaliana phyllosphere. We find that commensal Pseudomonas prompt a host response that leads to selective inhibition of a specific pathogenic lineage, resulting in plant protection. The extent of protection depends on plant genotype, supporting that these effects are host-mediated. Strain-specific effects are also demonstrated by one individual Pseudomonas isolate eluding the plant protection provided by commensals. Our work highlights how within-species genetic differences in both hosts and microbes can affect host–microbe–microbe dynamics.

The authors conduct competition experiments with multiple strains of Pseudomonas (some pathogenic and some commensal) in the phylosphere microbiome of Arabidopsis plants, showing that both the host and the commensal strains interact to inhibit the pathogenic strains.

Molecular-Based Diversity Studies and Field Surveys Are Not Mutually Exclusive: On the Importance of Integrated Methodologies in Mycological Research

Understanding and describing the diversity of living organisms is a great challenge. Fungi have for a long time been, and unfortunately still are, underestimated when it comes to taxonomic research. The foundations were laid by the first mycologists through field observations. These important fundamental works have been and remain vital reference works. Nevertheless, a non-negligible part of the studied funga escaped their attention. Thanks to modern developments in molecular techniques, the study of fungal diversity has been revolutionized in terms of tools and knowledge. Despite a number of disadvantages inherent to these techniques, traditional field-based inventory work has been increasingly superseded and neglected. This perspective aims to demonstrate the central importance of field-based research in fungal diversity studies, and encourages researchers not to be blinded by the sole use of molecular methods.

Roles of Arbuscular Mycorrhizal Fungi on Soil Fertility: Contribution in the Improvement of Physical, Chemical, and Biological Properties of the Soil

Many of the world's soils are experiencing degradation at an alarming rate. Climate change and some agricultural management practices, such as tillage and excessive use of chemicals, have all contributed to the degradation of soil fertility. Arbuscular Mycorrhizal Fungi (AMFs) contribute to the improvement of soil fertility. Here, a short review focusing on the role of AMF in improving soil fertility is presented. The aim of this review was to explore the role of AMF in improving the chemical, physical, and biological properties of the soil. We highlight some beneficial effects of AMF on soil carbon sequestration, nutrient contents, microbial activities, and soil structure. AMF has a positive impact on the soil by producing organic acids and glomalin, which protect from soil erosion, chelate heavy metals, improve carbon sequestration, and stabilize soil macro-aggregation. AMF also recruits bacteria that produce alkaline phosphatase, a mineralization soil enzyme associated with organic phosphorus availability. Moreover, AMFs influence the composition, diversity, and activity of microbial communities in the soil through mechanisms of antagonism or cooperation. All of these AMF activities contribute to improve soil fertility. Knowledge gaps are identified and discussed in the context of future research in this review. This will help us better understand AMF, stimulate further research, and help in sustaining the soil fertility.

Split down the middle: studying arbuscular mycorrhizal and ectomycorrhizal symbioses using split-root assays

Most land plants symbiotically interact with soil-borne fungi to ensure nutrient acquisition and tolerance to various environmental stressors. Among these symbioses, arbuscular mycorrhizal and ectomycorrhizal associations can be found in a large proportion of plants, including many crops. Split-root assays are widely used in plant research to study local and systemic signaling responses triggered by local treatments, including nutrient availability, interaction with soil microbes, or abiotic stresses. However, split-root approaches have only been occasionally used to tackle these questions with regard to mycorrhizal symbioses. This review compiles and discusses split-root assays developed to study arbuscular mycorrhizal and ectomycorrhizal symbioses, with a particular emphasis on colonization by multiple beneficial symbionts, systemic resistance induced by mycorrhizal fungi, water and nutrient transport from fungi to colonized plants, and host photosynthate allocation from the host to fungal symbionts. In addition, we highlight how the use of split-root assays could result in a better understanding of mycorrhizal symbioses, particularly for a broader range of essential nutrients, and for multipartite interactions.

The soil microbiome increases plant survival and modifies interactions with root endosymbionts in the field

Evidence is accumulating that the soil microbiome-the community of microorganisms living in soils-has a major effect on plant traits and fitness. However, most work to date has taken place under controlled laboratory conditions and has not experimentally disentangled the effect of the soil microbiome on plant performance from the effects of key endosymbiotic constituents. As a result, it is difficult to extrapolate from existing data to understand the role of the soil microbiome in natural plant populations. To address this gap, we performed a field experiment using the black medick Medicago lupulina to test how the soil microbiome influences plant performance and colonization by two root endosymbionts (the mutualistic nitrogen-fixing bacteria Ensifer spp. and the parasitic root-knot nematode Meloidogyne hapla) under natural conditions. We inoculated all plants with nitrogen-fixing bacteria and factorially manipulated the soil microbiome and nematode infection. We found that plants grown in microbe-depleted soil exhibit greater mortality, but that among the survivors, there was no effect of the soil microbiome on plant performance (shoot biomass, root biomass, or shoot-to-root ratio). The soil microbiome also impacted parasitic nematode infection and affected colonization by mutualistic nitrogen-fixing bacteria in a plant genotype-dependent manner, increasing colonization in some plant genotypes and decreasing it in others. Our results demonstrate the soil microbiome has complex effects on plant-endosymbiont interactions and may be critical for survival under natural conditions.

Perennial, but not annual legumes synergistically benefit from infection with arbuscular mycorrhizal fungi and rhizobia: a meta-analysis

Many plant species simultaneously interact with multiple symbionts, which can, but do not always, generate synergistic benefits for their host. We ask if plant life history (i.e. annual vs perennial) can play an important role in the outcomes of the tripartite symbiosis of legumes, arbuscular mycorrhizal fungi (AMF), and rhizobia. We performed a meta-analysis of 88 studies examining outcomes of legume-AMF-rhizobia interactions on plant and microbial growth. Perennial legumes associating with AMF and rhizobia grew larger than expected based on their response to either symbiont alone (i.e. their response to co-inoculation was synergistic). By contrast, annual legume growth with co-inoculation did not differ from additive expectations. AMF and rhizobia differentially increased phosphorus (P) and nitrogen (N) tissue concentration. Rhizobium nodulation increased with mycorrhizal fungi inoculation, but mycorrhizal fungi colonization did not increase with rhizobium inoculation. Microbial responses to co-infection were significantly correlated with synergisms in plant growth. Our work supports a balanced plant stoichiometry mechanism for synergistic benefits. We find that synergisms are in part driven by reinvestment in complementary symbionts, and that time-lags in realizing benefits of reinvestment may limit synergisms in annuals. Optimization of microbiome composition to maximize synergisms may be critical to productivity, particularly for perennial legumes.

Diversity and Functionalities of Unknown Mycorrhizal Fungal Microbiota

Beneficial ecosystem services provided by arbuscular mycorrhizal fungi (AMF) are the outcome of their synergistic actions with diverse bacterial communities (AMF-associated bacteria; AAB) living in strict association with AMF hyphae and spores. Herein, bacterial diversity associated with 6 AMF species from 33 different co-cultures belonging to order Glomerales and Diversisporales were identified, using a combination of culture-dependent functional analyses and amplicon sequencing. Overall, 231 bacterial strains were isolated from the AMF spores and hyphae which covered 30 bacterial genera and 52 species. Hierarchical clustering based on plant growth promoting traits identified 9 clades comprising diverse bacterial genera with clades 7, 8 and 9 representing the most functionally rich AAB. High-throughput amplicon sequencing across a small subset of 8 AMF co-cultures spread across 3 AMF genera identified Operational Taxonomic Units belonging to 118 bacterial genera. The study revealed a greater diversity of AAB from spores of in vitro transformed AMF root co-cultures rather than in situ, pot AMF cultures. Functionally active, culturable AABs with multiple plant growth promoting traits such as phosphate solubilisation, nitrogen fixation, biofilm formation, enzyme and plant growth regulator production along with biocontrol activity were identified. These properties could be utilized individually and/or as consortia with AMF, as biological growth enhancers.

Co-inoculation with arbuscular mycorrhizal fungi differing in carbon sink strength induces a synergistic effect in plant growth

Arbuscular mycorrhizal (AM) fungi play a key role in determining ecosystem functionality. Understanding how diversity in the fungal community affects plant productivity is therefore an important question in ecology. Current research has focused on understanding the role of functional complementarity in the fungal community when the host plant faces multiple stress factors. Fewer studies, however, have investigated how variation in traits affecting nutrient exchange can impact the plant growth dynamics, even in the absence of environmental stressors. Combining experimental data and a mathematical model based on ordinary differential equations, we investigate the role played by carbon sink strength on plant productivity. We simulate and measure plant growth over time when the plant is associated with two fungal isolates with different carbon sink strength, and when the plant is in pairwise association with each of the isolates alone. Overall, our theoretical as well as our experimental results show that co-inoculation with fungi with different carbon sink strength can induce positive non-additive effects (or synergistic effects) in plant productivity. Fungi with high carbon sink strength are able to quickly establish a fungal community and increase the nutrient supply to the plant, with a consequent positive impact on plant growth rate. On the other side, fungi with low carbon sink strength inflict lower carbon costs to the host plant, and support maximal plant productivity once plant biomass is large. As AM fungi are widely used as organic fertilizers worldwide, our findings have important implications for restoration ecology and agricultural management.

Multiple Mutualism Effects generate synergistic selection and strengthen fitness alignment in the interaction between legumes, rhizobia and mycorrhizal fungi

Nearly all organisms participate in multiple mutualisms, and complementarity within these complex interactions can result in synergistic fitness effects. However, it remains largely untested how multiple mutualisms impact eco-evolutionary dynamics in interacting species. We tested how multiple microbial mutualists-N-fixing bacteria and mycorrrhizal fungi-affected selection and heritability of traits in their shared host plant (Medicago truncatula), as well as fitness alignment between partners. Our results demonstrate for the first time that multiple mutualisms synergistically affect the selection and heritability of host traits and enhance fitness alignment between mutualists. Specifically, we found interaction with multiple microbial symbionts doubled the strength of natural selection on a plant architectural trait, resulted in 2- to 3-fold higher heritability of plant reproductive success, and more than doubled fitness alignment between N-fixing bacteria and plants. These findings show synergism generated by multiple mutualisms extends to key components of microevolutionary change, emphasising the importance of multiple mutualism effects on evolutionary trajectories.

Multi-species relationships in legume roots: From pairwise legume-symbiont interactions to the plant - microbiome - soil continuum

Mutualistic relationships of legume plants with, either bacteria (like rhizobia) or fungi (like arbuscular mycorrhizal fungi), have been investigated intensively, usually as bi-partite interactions. However, diverse symbiotic interactions take place simultaneously or sequentially under field conditions. Their collective, but not additive, contribution to plant growth and performance remains hard to predict, and appears to be furthermore affected by crop species and genotype, non-symbiotic microbial interactions and environmental variables. The challenge is: (i) to unravel the complex overlapping mechanisms that operate between the microbial symbionts as well as between them, their hosts and the rhizosphere (ii) to understand the dynamics of the respective mechanisms in evolutionary and ecological terms. The target for agriculture, food security and the environment, is to use this insight as a solid basis for developing new integrated technologies, practices and strategies for the efficient use of beneficial microbes in legumes and other plants. We review recent advances in our understanding of the symbiotic interactions in legumes roots brought about with the aid of molecular and bioinformatics tools. We go through single symbiont-host interactions, proceed to tripartite symbiont-host interactions, appraise interactions of symbiotic and associative microbiomes with plants in the root-rhizoplane-soil continuum of habitats and end up by examining attempts to validate community ecology principles in the legume-microbe-soil biosystem.

Mycorrhizal symbiosis modulates the rhizosphere microbiota to promote rhizobia-legume symbiosis

Plants establish symbioses with mutualistic fungi, such as arbuscular mycorrhizal (AM) fungi, and bacteria, such as rhizobia, to exchange key nutrients and thrive. Plants and symbionts have coevolved and represent vital components of terrestrial ecosystems. Plants employ an ancestral AM signaling pathway to establish intracellular symbioses, including the legume-rhizobia symbiosis, in their roots. Nevertheless, the relationship between the AM and rhizobial symbioses in native soil is poorly understood. Here, we examined how these distinct symbioses affect root-associated bacterial communities in Medicago truncatula by performing quantitative microbiota profiling (QMP) of 16S rRNA genes. We found that M. truncatula mutants that cannot establish AM or rhizobia symbiosis have an altered microbial load (quantitative abundance) in the rhizosphere and roots, and in particular that AM symbiosis is required to assemble a normal quantitative root-associated microbiota in native soil. Moreover, quantitative microbial co-abundance network analyses revealed that AM symbiosis affects Rhizobiales hubs among plant microbiota and benefits the plant holobiont. Through QMP of rhizobial rpoB and AM fungal SSU rRNA genes, we revealed a new layer of interaction whereby AM symbiosis promotes rhizobia accumulation in the rhizosphere of M. truncatula. We further showed that AM symbiosis-conditioned microbial communities within the M. truncatula rhizosphere could promote nodulation in different legume plants in native soil. Given that the AM and rhizobial symbioses are critical for crop growth, our findings might inform strategies to improve agricultural management. Moreover, our work sheds light on the co-evolution of these intracellular symbioses during plant adaptation to native soil conditions.

Population-level variation in host plant response to multiple microbial mutualists

PREMISE

Multipartite mutualisms are widespread in nature, but population-level variation in these interactions is rarely quantified. In the model multipartite mutualism between legumes, arbuscular mycorrhizal (AM) fungi and rhizobia bacteria, host responses to microbial partners are expected to be synergistic because the nutrients provided by each microbe colimit plant growth, but tests of this prediction have not been done in multiple host populations.

METHODS

To test whether plant response to associations with AM fungi and rhizobia varies among host populations and whether synergistic responses to microbial mutualists are common, we grew 34 Medicago truncatula populations in a factorial experiment that manipulated the presence or absence of each mutualist.

RESULTS

Plant growth increased in response to each mutualist, but there were no synergistic effects. Instead, plant response to inoculation with AM fungi was an order of magnitude higher than with rhizobia. Plant response to AM fungi varied among populations, whereas responses to rhizobia were relatively uniform. There was a positive correlation between plant host response to each mutualist but no correlation between AM fungal colonization and rhizobia nodulation of plant roots.

CONCLUSIONS

The greater population divergence in host response to AM fungi relative to rhizobia, weak correlation in host response to each microbial mutualist, and the absence of a correlation between measures of AM fungal and rhizobia performance suggests that each plant-microbe mutualism evolved independently among M. truncatula populations.

Tripartite mutualisms as models for understanding plant-microbial interactions

All plants host diverse microbial assemblages that shape plant health, productivity, and function. While some microbial effects are attributable to particular symbionts, interactions among plant-associated microbes can nonadditively affect plant fitness and traits in ways that cannot be predicted from pairwise interactions. Recent research into tripartite plant-microbe mutualisms has provided crucial insight into this nonadditivity and the mechanisms underlying plant interactions with multiple microbes. Here, we discuss how interactions among microbial mutualists affect plant performance, highlight consequences of biotic and abiotic context-dependency for nonadditive outcomes, and summarize burgeoning efforts to determine the molecular bases of how plants regulate establishment, resource exchange, and maintenance of tripartite interactions. We conclude with four goals for future tripartite studies that will advance our overall understanding of complex plant-microbial interactions.

Transcriptomic analysis reveals the possible roles of sugar metabolism and export for positive mycorrhizal growth responses in soybean

To elucidate molecular mechanisms controlling differential growth responses to root colonization by arbuscular mycorrhizal (AM) fungi varying in colonization and cooperative behavior, a pot experiment was carried out using two soybean genotypes and three AM inocula. The results showed that inoculation by cooperative Rhizophagus irregularis (Ri) or less cooperative Glomus aggregatum with high AM colonization (Ga-H) significantly promoted plant growth compared with inoculation by G. aggregatum with low AM colonization (Ga-L). A comparative RNA sequencing analysis of the root transcriptomes showed that fatty acid synthesis pathway was significantly enriched in all three AM inoculation roots. However, sugar metabolism and transport were significantly enriched only in Ri and Ga-H inoculation, which was consistent with positive growth responses in these two inoculation treatments. Accordingly, the expression levels of the key genes related to sugar metabolism and transport were also upregulated in Ri and Ga-H roots compared with Ga-L roots. Of them, two sugars will eventually be exported transporters (SWEET) transporter genes, GmSWEET6 (Glyma.04G198600) and GmSWEET15 (Glyma.06G166800), and one invertase (Glyma.17G227900) gene were exclusively induced only in Ri and Ga-H roots. Promoter analyses in transgenic soybean roots further demonstrated that GUS driven by the GmSWEET6 promoter was highly expressed in arbuscule-containing cortical cells. Additionally, Ri and Ga-H inoculation increased the contents of sucrose, glucose and fructose in both shoots and roots compared with those of Ga-L and non-mycorrhizal. These results imply that positive mycorrhizal growth responses in plants might mostly be due to the stimulation of photosynthate metabolism and transport by AM fungal inoculum with high colonization capabilities.

A window into the transcriptomic basis of genotype-by-genotype interactions in the legume-rhizobia mutualism

The maintenance of genetic variation in the benefits provided by mutualists is an evolutionary puzzle (Heath & Stinchcombe, ). Over time, natural selection should favour the benefit strategy that confers the highest fitness, eroding genetic variation in partner quality. Yet abundant genetic variation in partner quality exists in many systems (Heath & Stinchcombe, ). One possible resolution to this puzzle is that the genetic identity of both a host and its partner affects the benefits each mutualist provides to the other, a pattern known as a genotype-by-genotype interaction (Figure ). Mounting evidence suggests that genotype-by-genotype interactions between partners are pervasive at the phenotypic level (Barrett, Zee, Bever, Miller, & Thrall, ; Heath, ; Hoeksema & Thompson, ). Ultimately, however, to link these phenotypic patterns to the maintenance of genetic variation in mutualisms we need to answer two questions: How much variation in mutualism phenotypes is attributable to genotype-by-genotype interactions, and what mutualistic functions are influenced by each partner and by the interaction between their genomes? In this issue of Molecular Ecology, Burghardt et al. (2017) use transcriptomics to address both questions in the legume-rhizobia mutualism.

Profiling of Seed Proteome in Pea (Pisum sativum L.) Lines Characterized with High and Low Responsivity to Combined Inoculation with Nodule Bacteria and Arbuscular Mycorrhizal Fungi

Legume crops represent the major source of food protein and contribute to human nutrition and animal feeding. An essential improvement of their productivity can be achieved by symbiosis with beneficial soil microorganisms-rhizobia (Rh) and arbuscular mycorrhizal (AM) fungi. The efficiency of these interactions depends on plant genotype. Recently, we have shown that, after simultaneous inoculation with Rh and AM, the productivity gain of pea (Pisum sativum L) line K-8274, characterized by high efficiency of interaction with soil microorganisms (EIBSM), was higher in comparison to a low-EIBSM line K-3358. However, the molecular mechanisms behind this effect are still uncharacterized. Therefore, here, we address the alterations in pea seed proteome, underlying the symbiosis-related productivity gain, and identify 111 differentially expressed proteins in the two lines. The high-EIBSM line K-8274 responded to inoculation by prolongation of seed maturation, manifested by up-regulation of proteins involved in cellular respiration, protein biosynthesis, and down-regulation of late-embryogenesis abundant (LEA) proteins. In contrast, the low-EIBSM line K-3358 demonstrated lower levels of the proteins, related to cell metabolism. Thus, we propose that the EIBSM trait is linked to prolongation of seed filling that needs to be taken into account in pulse crop breeding programs. The raw data have been deposited to the ProteomeXchange with identifier PXD013479.

Harnessing Soil Microbes to Improve Plant Phosphate Efficiency in Cropping Systems

Phosphorus is an essential macronutrient required for plant growth and development. It is central to many biological processes, including nucleic acid synthesis, respiration, and enzymatic activity. However, the strong adsorption of phosphorus by minerals in the soil decreases its availability to plants, thus reducing the productivity of agricultural and forestry ecosystems. This has resulted in a complete dependence on non-renewable chemical fertilizers that are environmentally damaging. Alternative strategies must be identified and implemented to help crops acquire phosphorus more sustainably. In this review, we highlight recent advances in our understanding and utilization of soil microbes to both solubilize inorganic phosphate from insoluble forms and allocate it directly to crop plants. Specifically, we focus on arbuscular mycorrhizal fungi, ectomycorrhizal fungi, and phosphate-solubilizing bacteria. Each of these play a major role in natural and agroecosystems, and their use as bioinoculants is an increasing trend in agricultural practices.

Nutrient demand and fungal access to resources control the carbon allocation to the symbiotic partners in tripartite interactions of Medicago truncatula

Legumes form tripartite interactions with arbuscular mycorrhizal fungi and rhizobia, and both root symbionts exchange nutrients against carbon from their host. The carbon costs of these interactions are substantial, but our current understanding of how the host controls its carbon allocation to individual root symbionts is limited. We examined nutrient uptake and carbon allocation in tripartite interactions of Medicago truncatula under different nutrient supply conditions, and when the fungal partner had access to nitrogen, and followed the gene expression of several plant transporters of the Sucrose Uptake Transporter (SUT) and Sugars Will Eventually be Exported Transporter (SWEET) family. Tripartite interactions led to synergistic growth responses and stimulated the phosphate and nitrogen uptake of the plant. Plant nutrient demand but also fungal access to nutrients played an important role for the carbon transport to different root symbionts, and the plant allocated more carbon to rhizobia under nitrogen demand, but more carbon to the fungal partner when nitrogen was available. These changes in carbon allocation were consistent with changes in the SUT and SWEET expression. Our study provides important insights into how the host plant controls its carbon allocation under different nutrient supply conditions and changes its carbon allocation to different root symbionts to maximize its symbiotic benefits.

On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics

Understanding the quantitative genetics of crops has been and will continue to be central to maintaining and improving global food security. We outline four stages that plant breeding either has already achieved or will probably soon achieve. Top-of-the-line breeding programs are currently in Breeding 3.0, where inexpensive, genome-wide data coupled with powerful algorithms allow us to start breeding on predicted instead of measured phenotypes. We focus on three major questions that must be answered to move from current Breeding 3.0 practices to Breeding 4.0: ( a) How do we adapt crops to better fit agricultural environments? ( b) What is the nature of the diversity upon which breeding can act? ( c) How do we deal with deleterious variants? Answering these questions and then translating them to actual gains for farmers will be a significant part of achieving global food security in the twenty-first century.

Transcriptional Changes in Mycorrhizal and Nonmycorrhizal Soybean Plants upon Infection with the Fungal Pathogen Macrophomina phaseolina

Macrophomina phaseolina is a soil-borne fungal pathogen with a wide host range that causes charcoal rot in soybean [Glycine max (L.) Merr.]. Control of the disease is a challenge, due to the absence of genetic resistance and effective chemical control. Alternative or complementary measures are needed, such as the use of biological control agents, in an integrated approach. Several studies have demonstrated the role of arbuscular mycorrhizal fungi (AMF) in enhancing plant resistance or tolerance to biotic stresses, decreasing the symptoms and pressure caused by various pests and diseases, including M. phaseolina in soybean. However, the specific contribution of AMF in the regulation of the plant response to M. phaseolina remains unclear. Therefore, the objective of the present study was to investigate, under strict in-vitro culture conditions, the global transcriptional changes in roots of premycorrhized soybean plantlets challenged by M. phaseolina (+AMF+Mp) as compared with nonmycorrhizal soybean plantlets (-AMF+Mp). MapMan software was used to distinguish transcriptional changes, with special emphasis on those related to plant defense responses. Soybean genes identified as strongly upregulated during infection by the pathogen included pathogenesis-related proteins, disease-resistance proteins, transcription factors, and secondary metabolism-related genes, as well as those encoding for signaling hormones. Remarkably, the +AMF+Mp treatment displayed a lower number of upregulated genes as compared with the -AMF+Mp treatment. AMF seemed to counteract or balance costs upon M. phaseolina infection, which could be associated to a negative impact on biomass and seed production. These detailed insights in soybean-AMF interaction help us to understand the complex underlying mechanisms involved in AMF-mediated biocontrol and support the importance of preserving and stimulating the existing plant-AMF associates, via adequate agricultural practices, to optimize their agro-ecological potential.

Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses

Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION (NIN) and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN, RPG, and NOD FACTOR PERCEPTION Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.

Genetic conflict with a parasitic nematode disrupts the legume-rhizobia mutualism

Genetic variation for partner quality in mutualisms is an evolutionary paradox. One possible resolution to this puzzle is that there is a tradeoff between partner quality and other fitness‐related traits. Here, we tested whether susceptibility to parasitism is one such tradeoff in the mutualism between legumes and nitrogen‐fixing bacteria (rhizobia). We performed two greenhouse experiments with the legume Medicago truncatula. In the first, we inoculated each plant with the rhizobia Ensifer meliloti and with one of 40 genotypes of the parasitic root‐knot nematode Meloidogyne hapla. In the second experiment, we inoculated all plants with rhizobia and half of the plants with a genetically variable population of nematodes. Using the number of nematode galls as a proxy for infection severity, we found that plant genotypes differed in susceptibility to nematode infection, and nematode genotypes differed in infectivity. Second, we showed that there was a genetic correlation between the number of mutualistic structures formed by rhizobia (nodules) and the number of parasitic structures formed by nematodes (galls). Finally, we found that nematodes disrupt the rhizobia mutualism: nematode‐infected plants formed fewer nodules and had less nodule biomass than uninfected plants. Our results demonstrate that there is genetic conflict between attracting rhizobia and repelling nematodes in Medicago. If genetic conflict with parasitism is a general feature of mutualism, it could account for the maintenance of genetic variation in partner quality and influence the evolutionary dynamics of positive species interactions.

Chemical signaling involved in plant-microbe interactions

Microorganisms are found everywhere, and they are closely associated with plants. Because the establishment of any plant-microbe association involves chemical communication, understanding crosstalk processes is fundamental to defining the type of relationship. Although several metabolites from plants and microbes have been fully characterized, their roles in the chemical interplay between these partners are not well understood in most cases, and they require further investigation. In this review, we describe different plant-microbe associations from colonization to microbial establishment processes in plants along with future prospects, including agricultural benefits.