The role of community and population ecology in applying mycorrhizal fungi for improved food security

Bacteria Associated with Spores of Arbuscular Mycorrhizal Fungi Improve the Effectiveness of Fungal Inocula for Red Raspberry Biotization

Intensive crop production leads to the disruption of the symbiosis between plants and their associated microorganisms, resulting in suboptimal plant productivity and lower yield quality. Therefore, it is necessary to improve existing methods and explore modern, environmentally friendly approaches to crop production. One of these methods is biotization, which involves the inoculation of plants with appropriately selected symbiotic microorganisms which play a beneficial role in plant adaptation to the environment. In this study, we tested the possibility of using a multi-microorganismal inoculum composed of arbuscular mycorrhizal fungi (AMF) and AMF spore-associated bacteria for biotization of the red raspberry. Bacteria were isolated from the spores of AMF, and their plant growth-promoting properties were tested. AMF inocula were supplemented with selected bacterial strains to investigate their effect on the growth and vitality of the raspberry. The investigations were carried out in the laboratory and on a semi-industrial scale in a polytunnel where commercial production of seedlings is carried out. In the semi-industrial experiment, we tested the growth parameters of plants and physiological response of the plant to temporary water shortage. We isolated over fifty strains of bacteria associated with spores of AMF. Only part of them showed plant growth-promoting properties, and six of these (belonging to the Paenibacillus genus) were used for the inoculum. AMF inoculation and co-inoculation of AMF and bacteria isolated from AMF spores improved plant growth and vitality in both experimental setups. Plant dry weight was improved by 70%, and selected chlorophyll fluorescence parameters (the contribution of light to primary photochemistry and fraction of reaction centre chlorophyll per chlorophyll of the antennae) were increased. The inoculum improved carbon assimilation, photosynthetic rate, stomatal conductance and transpiration after temporary water shortage. Raspberry biotization with AMF and bacteria associated with spores has potential applications in horticulture where ecological methods based on plant microorganism interaction are in demand.

Effect the accumulation of bioactive constituents of a medicinal plant (Salvia Miltiorrhiza Bge.) by arbuscular mycorrhizal fungi community

BACKGROUND

Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with various terrestrial plants and have attracted considerable interest as biofertilizers for improving the quality and yield of medicinal plants. Despite the widespread distribution of AMFs in Salvia miltiorrhiza Bunge's roots, research on the impact of multiple AMFs on biomass and active ingredient accumulations has not been conducted. In this study, the effects of five native AMFs (Glomus formosanum, Septoglomus constrictum, Rhizophagus manihotis, Acaulospora laevis, and Ambispora gerdemannii) and twenty-six communities on the root biomass and active ingredient concentrations of S. miltiorrhiza were assessed using the total factor design method.

RESULTS

Thirty-one treatment groups formed symbiotic relationships with S. miltiorrhiza based on the pot culture results, and the colonization rate ranged from 54.83% to 89.97%. AMF communities had higher colonization rates and total phenolic acid concentration than single AMF, and communities also appeared to have higher root fresh weight, dry weight, and total phenolic acid concentration than single inoculations. As AMF richness increased, there was a rising trend in root biomass and total tanshinone accumulations (ATTS), while total phenolic acid accumulations (ATP) showed a decreasing trend. This suggests that plant productivity was influenced by the AMF richness, with higher inoculation benefits observed when the communities contained three or four AMFs. Additionally, the affinities of AMF members were also connected to plant productivity. The inoculation effect of closely related AMFs within the same family, such as G. formosanum, S. constrictum, and R. manihotis, consistently yielded lower than that of mono-inoculation when any combinations were applied. The co-inoculation of S. miltiorrhiza with nearby or distant AMFs from two families, such as G. formosanum, R. manihotis, and Ac. laevis or Am. gerdemannii resulted in an increase of ATP and ATTS by more than 50%. AMF communities appear to be more beneficial to the yield of bioactive constituents than the single AMF, but overall community inoculation effects are related to the composition of AMFs and the relationship between members.

CONCLUSION

This study reveals that the AMF community has great potential to improve the productivity and the accumulation of bioactive constituents in S. miltiorrhiza, indicating that it is an effective way to achieve sustainable agricultural development through using the AMF community.

Comparative RNA sequencing-based transcriptome profiling of ten grapevine rootstocks: shared and specific sets of genes respond to mycorrhizal symbiosis

Arbuscular mycorrhizal symbiosis improves water and nutrient uptake by plants and provides them other ecosystem services. Grapevine is one of the major crops in the world. Vitis vinifera scions generally are grafted onto a variety of rootstocks that confer different levels of resistance against different pests, tolerance to environmental stress, and influence the physiology of the scions. Arbuscular mycorrhizal fungi are involved in the root architecture and in the immune response to soil-borne pathogens. However, the fine-tuned regulation and the transcriptomic plasticity of rootstocks in response to mycorrhization are still unknown. We compared the responses of 10 different grapevine rootstocks to arbuscular mycorrhizal symbiosis (AMS) formed with Rhizophagus irregularis DAOM197198 using RNA sequencing-based transcriptome profiling. We have highlighted a few shared regulation mechanisms, but also specific rootstock responses to R. irregularis colonization. A set of 353 genes was regulated by AMS in all ten rootstocks. We also compared the expression level of this set of genes to more than 2000 transcriptome profiles from various grapevine varieties and tissues to identify a class of transcripts related to mycorrhizal associations in these 10 rootstocks. Then, we compared the response of the 351 genes upregulated by mycorrhiza in grapevine to their Medicago truncatula homologs in response to mycorrhizal colonization based on available transcriptomic studies. More than 97% of the 351 M. truncatula-homologous grapevine genes were expressed in at least one mycorrhizal transcriptomic study, and 64% in every single RNAseq dataset. At the intra-specific level, we described, for the first time, shared and specific grapevine rootstock genes in response to R. irregularis symbiosis. At the inter-specific level, we defined a shared subset of mycorrhiza-responsive genes.

MoNap1, a Nucleosome Assemble Protein 1, Regulates Growth, Development, and Pathogenicity in Magnaporthe oryzae

Nap1 is an evolutionarily conserved protein from yeast to human and is involved in diverse physiological processes, such as nucleosome assembly, histone shuttling between the nucleus and cytoplasm, transcriptional regulation, and the cell cycle regulation. In this paper, we identified nucleosome assemble protein MoNap1 in Magnaporthe oryzae and investigated its function in pathogenicity. Deletion of MoNAP1 resulted in reduced growth and conidiation, decreased appressorium formation rate, and impaired virulence. MoNap1 affects appressorium turgor and utilization of glycogen and lipid droplets. In addition, MoNap1 is involved in the regulation of cell wall, oxidation, and hyperosmotic stress. The subcellular localization experiments showed that MoNap1 is located in the cytoplasm. MoNap1 interacts with MoNbp2, MoClb3, and MoClb1 in M. oryzae. Moreover, deletion of MoNBP2 and MoCLB3 has no effects on vegetative growth, conidiation, and pathogenicity. Transcriptome analysis reveals that MoNAP1 is involved in regulating pathogenicity, the melanin biosynthetic process. Taken together, our results showed that MoNap1 plays a crucial role in growth, conidiation, and pathogenicity of M. oryzae.

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

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

Experimental duration determines the effect of arbuscular mycorrhizal fungi on plant biomass in pot experiments: A meta-analysis

Arbuscular mycorrhizal fungi (AMF) play various important roles in promoting plant growth. Numerous environmental and evolutionary factors influence the response of plants to AMF. However, the importance of the individual factors on the effects of AMF on plant biomass is not clearly understood. In this study, a meta-analysis using 1,640 observations from 639 published articles related to the influence of AMF on the plant shoot, root, and total biomass was performed; 13 different experimental setting factors that had an impact on the influence of AMF and their importance were quantitatively synthesized. The meta-analysis showed that AMF had positive effects on the plant shoot, root, and total biomass; moreover, the experimental duration, plant root-to-shoot ratio (R/S), AMF root length colonization, plant family, pot size, soil texture, and the soil pH all influenced the effects of AMF on the shoot, root, and total biomass. In addition, the plant root system and plant functional type had impacts on the effect of AMF on shoot biomass; AMF guild also impacted the effect of AMF on root biomass. Of these factors, the experimental duration, plant R/S, and pot size were the three most important predicting the effects of AMF on the plant shoot, root, and total biomass. This study comprehensively assessed the importance of the different factors that influenced the response of plants to AMF, highlighting that the experimental duration, plant R/S, and pot size should be taken into consideration in pot experiments in studies of the functions of AMF. Multiple unfavorable factors that may obscure or confound the observed functions of AMF should be excluded.

The Potential Applications of Commercial Arbuscular Mycorrhizal Fungal Inoculants and Their Ecological Consequences

Arbuscular mycorrhizal fungal (AMF) inoculants are sustainable biological materials that can provide several benefits to plants, especially in disturbed agroecosystems and in the context of phytomanagement interventions. However, it is difficult to predict the effectiveness of AMF inoculants and their impacts on indigenous AMF communities under field conditions. In this review, we examined the literature on the possible outcomes following the introduction of AMF-based inoculants in the field, including their establishment in soil and plant roots, persistence, and effects on the indigenous AMF community. Most studies indicate that introduced AMF can persist in the target field from a few months to several years but with declining abundance (60%) or complete exclusion (30%). Further analysis shows that AMF inoculation exerts both positive and negative impacts on native AMF species, including suppression (33%), stimulation (38%), exclusion (19%), and neutral impacts (10% of examined cases). The factors influencing the ecological fates of AMF inoculants, such as the inherent properties of the inoculum, dosage and frequency of inoculation, and soil physical and biological factors, are further discussed. While it is important to monitor the success and downstream impacts of commercial inoculants in the field, the sampling method and the molecular tools employed to resolve and quantify AMF taxa need to be improved and standardized to eliminate bias towards certain AMF strains and reduce discrepancies among studies. Lastly, inoculant producers must focus on selecting strains with a higher chance of success in the field, and having little or negligible downstream impacts.

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

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

Microbial inoculation and fertilizer application on growth of cowpea and spore-based assemblages of arbuscular mycorrhizal fungi in its rhizophere

In this study, the effect of microbial inoculants and fertilizer application on cowpea (BRS Pujante) growth and on the structure and composition of arbuscular mycorrhizal fungi (AMF) assemblages were evaluated. A completely randomized experiment was set up involving 17 treatments: four with AMF, three with nodulating bacteria, six with AMF + nodulating bacteria, two with phosphorus, one with nitrogen and one control (reference) in five replicates. Plant growth and nutritional content, mycorrhizal colonization, glomerospores number, spore-based AMF assemblages and ecological indices were evaluated. Mycorrhizal inoculants associated with Bradyrhizobium BR3267 strain were more effective than the Microvirga BR3296 strain. Multidimensional scaling analysis showed that Acaulospora longula treatments were more similar among themselves, and distinct from the other treatments. A difference was observed in the structure of AMF community assemblage between treatments with G. albida + Bradyrhizobium BR 3267 and A. longula, with greater Shannon diversity and Pielou equitability indices in the first treatment and greater dominance in the treatment with A. longula only. Long-term studies are required to determine if the successful establishment of A. longula among indigenous species persists over time and if its dominant behavior is not deleterious to the AMF native community.

Application of Arbuscular Mycorrhizal Fungi in Vineyards: Water and Biotic Stress Under a Climate Change Scenario: New Challenge for Chilean Grapevine Crop

The crop Vitis vinifera (L.) is of great economic importance as Chile is one of the main wine-producing countries, reaching a vineyard area of 145,000 ha. This vine crop is usually very sensitive to local condition changes and agronomic practices; therefore, strategies to counteract the expected future decrease in water level for agricultural irrigation, temperature increase, extreme water stress (abiotic stress), as well as increase in pathogenic diseases (biotic stress) related to climate change will be of vital importance for this crop. Studies carried out in recent years have suggested that arbuscular mycorrhizal fungi (AMF) can provide key ecosystem services to host plants, such as water uptake implementation and enhanced absorption of nutrients such as P and N, which are key factors for improving the nutritional status of the vine. AMF use in viticulture will contribute also to sustainable agronomic management and bioprotection against pathogens. Here we will present (1) the current status of grapevines in Chile, (2) the main problems in grapevines related to water stress and associated with climate change, (3) the importance of AMF to face water stress and pathogens, and (4) the application of AMF as a biotechnological and sustainable tool in vineyards.

Potential Application of Urease and Nitrification Inhibitors to Mitigate Emissions from the Livestock Sector: A Review

Human activities have caused an increase in greenhouse gas emissions, resulting in climate change that affects many factors of human life including its effect on water and food quality in certain areas with implications for human health. CH₄ and N₂O are known as potent non-CO₂ GHGs. The livestock industry contributes to direct emissions of CH₄ (38.24%) and N₂O (6.70%) through enteric fermentation and manure treatment, as well as indirect N₂O emissions via NH₃ volatilization. NH₃ is also a secondary precursor of particulate matter. Several approaches have been proposed to address this issue, including dietary management, manure treatment, and the possibility of inhibitor usage. Inhibitors, including urease and nitrification inhibitors, are widely used in agricultural fields. The use of urease and nitrification inhibitors is known to be effective in reducing nitrogen loss from agricultural soil in the form of NH₃ and N₂O and can further reduce CH₄ as a side effect. However, the effectiveness of inhibitors in livestock manure systems has not yet been explored. This review discusses the potential of inhibitor usage, specifically of N-(n-butyl) thiophosphoric triamide, dicyandiamide, and 3,4-dimethylpyrazole phosphate, to reduce emissions from livestock manure. This review focuses on the application of inhibitors to manure, as well as the association of these inhibitors with health, toxicity, and economic benefits.

Spatial variability and environmental drivers of cassava-arbuscular mycorrhiza fungi (AMF) associations across Southern Nigeria

Cassava, forming starch-rich, tuberous roots, is an important staple crop in smallholder farming systems in sub-Saharan Africa. Its relatively good tolerance to drought and nutrient-poor soils may be partly attributed to the crop's association with arbuscular mycorrhiza fungi (AMF). Yet insights into AMF-community composition and richness of cassava, and knowledge of its environmental drivers are still limited. Here, we sampled 60 cassava fields across three major cassava-growing agro-ecological zones in Nigeria and used a DNA meta-barcoding approach to quantify large-scale spatial variation and evaluate the effects of soil characteristics and common agricultural practices on AMF community composition, richness and Shannon diversity. We identified 515 AMF operational taxonomic units (OTUs), dominated by Glomus, with large variation across agro-ecological zones, and with soil pH explaining most of the variation in AMF community composition. High levels of soil available phosphorus reduced OTU richness without affecting Shannon diversity. Long fallow periods (> 5 years) reduced AMF richness compared with short fallows, whereas both zero tillage and tractor tillage reduced AMF diversity compared with hoe tillage. This study reveals that the symbiotic relationship between cassava and AMF is strongly influenced by soil characteristics and agricultural management and that it is possible to adjust cassava cultivation practices to modify AMF diversity and community structure.

A historical perspective on mycorrhizal mutualism emphasizing arbuscular mycorrhizas and their emerging challenges

Arbuscular mycorrhiza, one of the oldest interactions on earth (~ 450 million years old) and a first-class partner for plants to colonize emerged land, is considered one of the most pervasive ecological relationships on the globe. Despite how important and old this interaction is, its discovery was very recent compared to the long story of land plant evolution. The story of the arbuscular mycorrhiza cannot be addressed apart from the history, controversies, and speculations about mycorrhiza in its broad sense. The chronicle of mycorrhizal research is marked by multiple key milestones such as the initial description of a "persistent epiderm and pellicular wall structure" by Hartig; the introduction of the "Symbiotismus" and "Mycorrhiza" concepts by Frank; the description of diverse root-fungal morphologies; the first description of arbuscules by Gallaud; Mosse's pivotal statement of the beneficial nature of the arbuscular mycorrhizal symbiosis; the impact of molecular tools on the taxonomy of mycorrhizal fungi as well as the development of in vitro root organ cultures for producing axenic arbuscular mycorrhizal fungi (AMF). An appreciation of the story - full of twists and turns - of the arbuscular mycorrhiza, going from the roots of mycorrhiza history, along with the discovery of different mycorrhiza types such as ectomycorrhiza, can improve research to help face our days' challenge of developing sustainable agriculture that integrates the arbuscular mycorrhiza and its ecosystem services.

Pathogenic Microbes Increase Plant Dependence on Arbuscular Mycorrhizal Fungi: A Meta-Analysis

Numerous studies have confirmed that arbuscular mycorrhizal fungi (AMF) can promote plant nitrogen and phosphorus absorption, and prime systemic plant defense to plant pathogenic microbes. Despite that, the information on the interaction between AMF and plant pathogenic microbes is limited, especially the influence of plant pathogenic microbes on the effect of AMF promoting plant growth. In this study, 650 independent paired-wise observations from 136 published papers were collected and used to calculate the different effect of AMF with plant pathogenic microbes (DAPP) in promoting plant growth through meta-analysis. The results showed that AMF had a higher effect size on plant growth with pathogenic microbes comparing to without pathogenic microbes, including the significant effects in shoot and total fresh biomass, and shoot, root, and total dry biomass. The results of the selection models revealed that the most important factor determining the DAPP on plant dry biomass was the harm level of plant pathogenic microbes on the plant dry biomass, which was negatively correlated. Furthermore, the change of AMF root length colonization (RLC) was the sub-important factor, which was positively correlated with the DAPP. Taken together, these results have implications for understanding the potential and application of AMF in agroecosystems.

Improved genotypes and fertilizers, not fallow duration, increase cassava yields without compromising arbuscular mycorrhizal fungus richness or diversity

Arbuscular mycorrhizal fungi (AMF) are ubiquitous in agroecosystems, but their role in mediating agricultural yield remains contested. Field experiments testing effects of realistic agronomic practices of intensification on AM fungus composition and yields are scarce, especially in the low-input systems of sub-Saharan Africa. A large, full-factorial field experiment was conducted in South-Kivu (DR Congo), testing effects of fallow duration (6 vs. 12 months), genotype (landrace vs. improved), and fertilizer management (control vs. five combinations omitting N, P, K, and/or secondary macro- and micronutrients) on yields of cassava, an important staple crop strongly colonized by AMF. Furthermore, we used DNA-metabarcoding to evaluate effects of these agronomic practices on the AM fungal communities on the roots. The shorter fallow duration strongly increased diversity and richness of AMF, but this did not correspond with increased yields. Cassava yield was mainly determined by genotype, being largest for the improved genotype, which coincided with a significantly higher sum of AM fungal sequences. Effects of fertilizer or genotype on community composition were minor to absent. We found no evidence that increased AMF richness and diversity enhanced cassava yields. In contrast, the use of the improved genotype and mineral fertilizers strongly benefitted yields, without compromising richness or diversity of AMF. Cassava-AMF associations in this work appear robust to fertilizer amendments and modern genotype improvement.

AMF Inoculation Can Enhance Yield of Transgenic Bt Maize and Its Control Efficiency Against Mythimna separata Especially Under Elevated CO2

The promotion and application of transgenic Bt crops provides an approach for the prevention and control of target lepidopteran pests and effectively relieves the environmental pressure caused by the massive usage of chemical pesticides in fields. However, studies have shown that Bt crops will face a new risk due to a decrease in exogenous toxin content under elevated carbon dioxide (CO2) concentration, thus negatively affecting the ecological sustainability of Bt crops. Arbuscular mycorrhizal fungi (AMF) are important beneficial microorganisms that can effectively improve the nutrient status of host plants and are expected to relieve the ecological risk of Bt crops under increasing CO2 due to global climate change. In this study, the Bt maize and its parental line of non-transgenic Bt maize were selected and inoculated with a species of AMF (Funneliformis caledonium, synonyms: Glomus caledonium), in order to study the secondary defensive chemicals and yield of maize, and to explore the effects of F. caledonium inoculation on the growth, development, and reproduction of the pest Mythimna separata fed on Bt maize and non-Bt maize under ambient carbon dioxide concentration (aCO2) and elevated carbon dioxide concentration (eCO2). The results showed that eCO2 increased the AM fungal colonization, maize yield, and foliar contents of jasmonic acid (JA) and salicylic acid (SA), but decreased foliar Bt toxin content and Bt gene expression in Bt maize leaves. F. caledonium inoculation increased maize yield, foliar JA, SA contents, Bt toxin contents, and Bt gene expression in Bt maize leaves, and positively improved the growth, development, reproduction, and food utilization of the M. separata fed on non-Bt maize. However, F. caledonium inoculation was unfavorable for the fitness of M. separata fed on Bt maize, and the effect was intensified when combined with eCO2. It is indicated that F. caledonium inoculation had adverse effects on the production of non-Bt maize due to the high potential risk of population occurrence of M. separata, while it was just the opposite for Bt maize. Therefore, this study confirms that the AMF can increase the yield and promote the expression levels of its endogenous (JA, SA) and exogenous (Bt toxin) secondary defense substances of Bt maize under eCO2, and finally can enhance the insect resistance capacity of Bt crops, which will help ensure the sustainable utilization and safety of Bt crops under climate change.

Effects of plant growth-promoting rhizobacteria strains producing ACC deaminase on photosynthesis, isoprene emission, ethylene formation and growth of Mucuna pruriens (L.) DC. in response to water deficit

Agricultural sustainability is an increasing need considering the challenges posed by climate change and rapid human population growth. The use of plant growth-promoting rhizobacteria (PGPR) may represent an excellent, new agriculture practice to improve soil quality while promoting growth and yield of important crop species subjected to water stress conditions. In this study, two PGPR strains with 1-Aminocyclopropane-1-Carboxylate (ACC) deaminase activity were co-inoculated in velvet bean plants to verify the physiological, biochemical and molecular responses to progressive water stress. The results of our study show that the total biomass and the water use efficiency of inoculated plants were higher than uninoculated plants at the end of the water stress period. These positive effects may be derived from a lower root ACC content (-45 %) in water-stressed inoculated plants than in uninoculated ones resulting in lower root ethylene emission. Furthermore, the ability of inoculated plants to maintain higher levels of both isoprene emission, a priming compound that may help to protect leaves from oxidative damage, and carbon assimilation during water stress progression may indicate the underlining metabolic processes conferring water stress tolerance. Overall, the experimental results show that co-inoculation with ACC deaminase PGPR positively affects tolerance to water deficit, confirming the potential for biotechnological applications in water-stressed agricultural areas.

Trichoderma harzianum Strain T22 Modulates Direct Defense of Tomato Plants in Response to Nezara viridula Feeding Activity

Plant growth-promoting fungi belonging to genus Trichoderma are known to help plants when dealing with biotic stressors by enhancing plant defenses. While beneficial effects of Trichoderma spp. against plant pathogens have long been documented, fewer studies have investigated their effect on insect pests. Here, we studied the impact of Trichoderma root colonization on the plant defense responses against stink bug feeding attack. For this purpose, a model system consisting of tomato plant, Solanum lycopersicum cv Dwarf San Marzano, Trichoderma harzianum strain T22 and the southern green stink bug, Nezara viridula, was used. We firstly determined stink bug performance in terms of relative growth rate and survival on tomato plants inoculated by T. harzianum T22. Then, we evaluated relative expression of plant defense-related genes on inoculated plants induced by stink bug feeding. We found evidence that T. harzianum T22 affects tomato defense responses against N. viridula nymphs leading to reduction of growth rate. Our results also showed that T. harzianum T22 enhances plant direct defenses by an early increase of transcript levels of jasmonic acid marker genes. Yet this effect was time-dependent and only detected 8 h after herbivore induction. Taken together, our findings provide better understanding on the mechanisms underlying tomato induced resistance against herbivorous stink bugs.

Nitrogen Losses and Potential Mitigation Strategies for a Sustainable Agroecosystem

Nitrogen (N) in the agricultural production system influences many aspects of agroecosystems and several critical ecosystem services widely depend on the N availability in the soil. Cumulative changes in regional ecosystem services may lead to global environmental changes. Thus, the soil N status in agriculture is of critical importance to strategize its most efficient use. Nitrogen is also one of the most susceptible macronutrients to environmental loss, such as ammonia volatilization (NH3), nitrous oxide (N2O) emissions, nitrate leaching (NO3), etc. Any form of N losses from agricultural systems can be major limitations for crop production, soil sustainability, and environmental safeguard. There is a need to focus on mitigation strategies to minimize global N pollution and implement agricultural management practices that encourage regenerative and sustainable agriculture. In this review, we identified the avenues of N loss into the environment caused by current agronomic practices and discussed the potential practices that can be adapted to prevent this N loss in production agriculture. This review also explored the N status in agriculture during the COVID-19 pandemic and the existing knowledge gaps and questions that need to be addressed.

Diversity of a phosphate transporter gene among species and isolates of arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi (AMF) are a key group of beneficial obligate biotrophs, establishing a mutualistic symbiosis with the roots of most land plants. The molecular markers generally used for their characterization are mainly based on informative regions of nuclear rDNA (SSU-ITS-LSU), although protein-encoding genes have also been proposed. Within functional genes, those encoding for phosphate transporters (PT) are particularly important in AMF, given their primary ability to take up Pi from soil, and to differentially affect plant phosphate nutrition. In this work, we investigated the genetic diversity of PT1 gene sequences and sequences of the taxonomically relevant SSU-ITS-LSU region in two isolates of the species Funneliformis coronatus, three isolates of the species Funneliformis mosseae and two species of the genus Rhizoglomus, originated from geographically distant areas and cultured in vivo. Our results showed that partial PT1 sequences not only successfully differentiated AMF genera and species like ribosomal gene sequences but also highlighted intraspecific diversity among F. mosseae and F. coronatus isolates. The study of functional genes related to the uptake of key mineral nutrients for the assessment of AMF diversity represents a key step in the selection of efficient isolates to be used as inocula in sustainable agriculture.

Microbial consortium increases maize productivity and reduces grain phosphorus concentration under field conditions

BACKGROUND

The use of microbes that improve plant phosphorus (P) use efficiency is an avenue to boost crop yields while alleviating environmental impacts. We tested three microbial inoculants (Rhizoglomus irregulare alone - designated AMF; Pseudomonas putida alone - designated PSB; and R. irregulare and P. putida in consortium - designated AMF+PSB), combined with chemical fertilizers, in an intensive maize agricultural system.

RESULTS

As hypothesized: (i) despite the native soil microbial community and the application of P fertilizer, the microbial inoculants enhanced plant P uptake from the soil by 14-60%, and consequently improved P acquisition efficiency; (ii) PSB and AMF+PSB plants produced ±50% more biomass per unit of P taken up, and consequently enhanced plant internal P use efficiency (i.e. the biomass produced per unit of P); and (iii) the combined inoculation of AMF and PSB provided the best results in terms of productivity and P use efficiency. Further, the microbial inoculants altered P allocation within the plant, reducing grain P concentration.

CONCLUSION

By testing the microbial inoculants under field conditions, our study clearly shows that the microbial consortium (AMF+PSB) increased maize productivity, and at the same time improved P use efficiency. Further, the use of these microbial inoculants was shown to be compatible with conventional agricultural management practices.

Genetically Different Isolates of the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis Induce Differential Responses to Stress in Cassava

Water scarcity negatively impacts global crop yields and climate change is expected to greatly increase the severity of future droughts. The use of arbuscular mycorrhizal fungi (AMF) can potentially mitigate the effects of water stress in plants. Cassava is a crop that feeds approximately 800 million people daily. Genetically different isolates of the AMF R. irregularis as well as their clonal progeny have both been shown to greatly alter cassava growth in field conditions. Given that cassava experiences seasonal drought in many of the regions in which it is cultivated, we evaluated whether intraspecific variation in R. irregularis differentially alters physiological responses of cassava to water stress. In a first experiment, conducted in field conditions in Western Kenya, cassava was inoculated with two genetically different R. irregularis isolates and their clonal progeny. All cassava plants exhibited physiological signs of stress during the dry period, but the largest differences occurred among plants inoculated with clonal progeny of each of the two parental fungal isolates. Because drought had not been experimentally manipulated in the field, we conducted a second experiment in the greenhouse where cassava was inoculated with two genetically different R. irregularis isolates and subjected to drought, followed by re-watering, to allow recovery. Physiological stress responses of cassava to drought differed significantly between plants inoculated with the two different fungi. However, plants that experienced higher drought stress also recovered at a faster rate following re-watering. We conclude that intraspecific genetic variability in AMF significantly influences cassava physiological responses during water stress. This highlights the potential of using naturally existing variation in AMF to improve cassava tolerance undergoing water stress. However, the fact that clonal progeny of an AMF isolate can differentially affect how cassava copes with natural drought stress in field conditions, highlights the necessity to understand additional factors, beyond genetic variation, which can account for such large differences in cassava responses to drought.

Effects of Arbuscular Mycorrhization on Fruit Quality in Industrialized Tomato Production

Industrialized tomato production faces a decrease in flavors and nutritional value due to conventional breeding. Moreover, tomato production heavily relies on nitrogen and phosphate fertilization. Phosphate uptake and improvement of fruit quality by arbuscular mycorrhizal (AM) fungi are well-studied. We addressed the question of whether commercially used tomato cultivars grown in a hydroponic system can be mycorrhizal, leading to improved fruit quality. Tomato plants inoculated with Rhizophagus irregularis were grown under different phosphate concentrations and in substrates used in industrial tomato production. Changes in fruit gene expression and metabolite levels were checked by RNAseq and metabolite determination, respectively. The tests revealed that reduction of phosphate to 80% and use of mixed substrate allow AM establishment without affecting yield. By comparing green fruits from non-mycorrhizal and mycorrhizal plants, differentially expressed genes (DEGs) were found to possibly be involved in processes regulating fruit maturation and nutrition. Red fruits from mycorrhizal plants showed a trend of higher BRIX values and increased levels of carotenoids in comparison to those from non-mycorrhizal plants. Free amino acids exhibited up to four times higher levels in red fruits due to AM, showing the potential of mycorrhization to increase the nutritional value of tomatoes in industrialized production.

Alta presencia de cadmio resulta en baja diversidad de hongos formadores de micorrizas arbusculares asociados a cacao (Theobroma cacao L.)

Los hongos formadores de micorrizas arbusculares (HFMA) son simbiontes obligados presentes en la rizósfera de plantas de cacao y la diversidad de sus comunidades se modifica, dependiendo de diversos factores como la presencia de cadmio (Cd) en el suelo. La persistencia de HFMA en suelos enriquecidos naturalmente con Cd podría ser un indicador de su capacidad para tolerar esta condición. Esta investigación caracterizó la estructura de la comunidad de HFMA locales presentes en la rizósfera de plantas de cacao en dos suelos con baja (B-Cd: 0,1 mg kg-1) y alta (A-Cd: 20,9 mg kg-1) concentración de Cd. Esporas de HFMA se identificaron mediante claves taxonómicas y su abundancia, riqueza y diversidad se determinó en muestras de suelo originales y después de su multiplicación mediante cultivos trampa. Las comunidades de HFMA se compararon usando análisis de componentes principales (ACP) e índices de diversidad alfa y beta. Los resultados indican que A-Cd presentó valores significativamente menores de abundancia (21 %), riqueza (20 %) y diversidad (11 %) de morfoespecies de HFMA con respecto a B-Cd. Las dos comunidades de HFMA presentaron cinco de siete géneros en común, pero solo cuatro de las 23 morfoespecies descritas se encontraron en ambas comunidades.El análisis de diversidad beta y el ACP determinaron baja similaridad y tasa de recambio entre las comunidades de HFMA. La dominancia de Diversispora spurca, Rhizoglomus sp. yClaroideoglomus etunicatumen A-Cd sugiere que estas morfoespecies son estrés-tolerantes y candidatos potenciales para el desarrollo de estrategias de mitigación en suelos con Cd.

Unique and common traits in mycorrhizal symbioses

Mycorrhizas are among the most important biological interkingdom interactions, as they involve ~340,000 land plants and ~50,000 taxa of soil fungi. In these mutually beneficial interactions, fungi receive photosynthesis-derived carbon and provide the host plant with mineral nutrients such as phosphorus and nitrogen in exchange. More than 150 years of research on mycorrhizas has raised awareness of their biology, biodiversity and ecological impact. In this Review, we focus on recent phylogenomic, molecular and cell biology studies to present the current state of knowledge of the origin of mycorrhizal fungi and the evolutionary history of their relationship with land plants. As mycorrhizas feature a variety of phenotypes, depending on partner taxonomy, physiology and cellular interactions, we explore similarities and differences between mycorrhizal types. During evolution, mycorrhizal fungi have refined their biotrophic capabilities to take advantage of their hosts as food sources and protective niches, while plants have developed multiple strategies to accommodate diverse fungal symbionts. Intimate associations with pervasive ecological success have originated at the crossroads between these two evolutionary pathways. Our understanding of the biological processes underlying these symbioses, where fungi act as biofertilizers and bioprotectors, provides the tools to design biotechnological applications addressing environmental and agricultural challenges.

Genetic variation and evolutionary history of a mycorrhizal fungus regulate the currency of exchange in symbiosis with the food security crop cassava

Most land plants form symbioses with arbuscular mycorrhizal fungi (AMF). Diversity of AMF increases plant community productivity and plant diversity. For decades, it was known that plants trade carbohydrates for phosphate with their fungal symbionts. However, recent studies show that plant-derived lipids probably represent the most essential currency of exchange. Understanding the regulation of plant genes involved in the currency of exchange is crucial to understanding stability of this mutualism. Plants encounter many different AMF genotypes that vary greatly in the benefit they confer to plants. Yet the role that fungal genetic variation plays in the regulation of this currency has not received much attention. We used a high-resolution phylogeny of one AMF species (Rhizophagus irregularis) to show that fungal genetic variation drives the regulation of the plant fatty acid pathway in cassava (Manihot esculenta); a pathway regulating one of the essential currencies of trade in the symbiosis. The regulation of this pathway was explained by clearly defined patterns of fungal genome-wide variation representing the precise fungal evolutionary history. This represents the first demonstrated link between the genetics of AMF and reprogramming of an essential plant pathway regulating the currency of exchange in the symbiosis. The transcription factor RAM1 was also revealed as the dominant gene in the fatty acid plant gene co-expression network. Our study highlights the crucial role of variation in fungal genomes in the trade of resources in this important symbiosis and also opens the door to discovering characteristics of AMF genomes responsible for interactions between AMF and cassava that will lead to optimal cassava growth.

Investigation of Indigenous Arbuscular Mycorrhizal Performance Using a Lotus japonicus Mycorrhizal Mutant

Most plants are usually colonized with arbuscular mycorrhiza fungi (AMF) in the fields. AMF absorb mineral nutrients, especially phosphate, from the soil and transfer them to the host plants. Inoculation with exotic AMF is thought to be effective when indigenous AMF performance is low; however, there is no method for evaluating the performance of indigenous AMF. In this study, we developed a method to investigate the performance of indigenous AMF in promoting plant growth. As Lotus japonicus mutant (str) that are unable to form functional mycorrhizal roots were considered to be symbiosis negative for indigenous mycorrhizal performance, we examined the growth ratios of wild-type and str mycorrhizal mutant using 24 soils. Each soil had its own unique indigenous mycorrhizal performance, which was not directly related to the colonization level of indigenous AMF or soil phosphate level. The low indigenous mycorrhizal performance could not be compensated by the inoculation of exotic AMF. Importantly, indigenous mycorrhizal performance was never negative; however, the inoculation of exotic AMF into the same soil led to both positive and negative performances. These results suggest that indigenous mycorrhizal performance is affected by soil management history and is basically harmless to the plant.

Predatory Earwigs are Attracted by Herbivore-Induced Plant Volatiles Linked with Plant Growth-Promoting Rhizobacteria

Plant-associated microbes may induce plant defenses against herbivores. Plants, in turn, can attract natural enemies, such as predators, using herbivore-induced plant volatiles. Intricate communication occurs between microorganisms, plants, and insects. Given that many aspects related to mechanisms involved in this symbiotic system remain unknown, we evaluated how beneficial soil-borne microorganisms can affect the interactions between plants, herbivores, and natural enemies. For this study, we established a multitrophic system composed of the predatory earwig Doru luteipes (Dermaptera: Forficulidae), arugula (Eruca sativa, Brassicaceae) as the host plant, Plutella xylostella (Lepidoptera: Plutellidae) larvae as a specialist herbivore, Spodoptera frugiperda (Lepidoptera: Noctuidae) larvae as a generalist herbivore, and Bacillus amyloliquefaciens as the plant growth-promoting rhizobacteria (PGPR), in a series of nocturnal olfactometry experiments. By assessing earwig preference towards herbivore-induced and PGPR-inoculated plants in different combinations, we showed that the interaction between rhizobacteria, plants, and herbivores can affect the predatory earwig's behavior. Furthermore, we observed a synergistic effect in which earwigs were attracted by plants that presented as PGPR inoculated and herbivore damaged, for both specialist and generalist herbivores. Our findings help fill the important knowledge gap regarding multitrophic interactions and should provide useful guidelines for their application to agricultural fields.

Arbuscular mycorrhizal fungi (AMF) enhanced the growth, yield, fiber quality and phosphorus regulation in upland cotton (Gossypium hirsutum L.)

We previously reported on the strong symbiosis of AMF species (Rhizophagus irregularis CD1) with the cotton (Gossypium hirsutum L.) which is grown worldwide. In current study, it was thus investigated in farmland to determine the biological control effect of AMF on phosphorus acquisition and related gene expression regulation, plant growth and development, and a series of agronomic traits associated with yield and fiber quality in cotton. When AMF and cotton were symbiotic, the expression of the specific phosphate transporter family genes and P concentration in the cotton biomass were significantly enhanced. The photosynthesis, growth, boll number per plant and the maturity of the fiber were increased through the symbiosis between cotton and AMF. Statistical analysis showed a highly significant increase in yield for inoculated plots compared with that from the non inoculated controls, with an increase percentage of 28.54%. These findings clearly demonstrate here the benefits of AMF-based inoculation on phosphorus acquisition, growth, seed cotton yield and fiber quality in cotton. Further improvement of these beneficial inoculants on crops will help increase farmers' income all over the world both now and in the future.

Insights from invasion ecology: Can consideration of eco-evolutionary experience promote benefits from root mutualisms in plant production?

Mutualistic plant-microbial functioning relies on co-adapted symbiotic partners as well as conducive environmental conditions. Choosing particular plant genotypes for domestication and subsequent cultivar selection can narrow the gene pools of crop plants to a degree that they are no longer able to benefit from microbial mutualists. Elevated mineral nutrient levels in cultivated soils also reduce the dependence of crops on nutritional support by mutualists such as mycorrhizal fungi and rhizobia. Thus, current ways of crop production are predestined to compromise the propagation and function of microbial symbionts, limiting their long-term benefits for plant yield stability. The influence of mutualists on non-native plant establishment and spread, i.e. biological invasions, provides an unexplored analogue to contemporary crop production that accounts for mutualistic services from symbionts like rhizobia and mycorrhizae. The historical exposure of organisms to biotic interactions over evolutionary timescales, or so-called eco-evolutionary experience (EEE), has been used to explain the success of such invasions. In this paper, we stress that consideration of the EEE concept can shed light on how to overcome the loss of microbial mutualist functions following crop domestication and breeding. We propose specific experimental approaches to utilize the wild ancestors of crops to determine whether crop domestication compromised the benefits derived from root microbial symbioses or not. This can predict the potential for success of mutualistic symbiosis manipulation in modern crops and the maintenance of effective microbial mutualisms over the long term.

Arbuscular mycorrhizal fungi alter the food utilization, growth, development and reproduction of armyworm (Mythimna separata) fed on Bacillus thuringiensis maize

BACKGROUND

The cultivation of Bt maize (maize genetically modified with Bacillus thuringiensis) continues to expand globally. Arbuscular mycorrhizal fungi (AMF), an important kind of microorganism closely related to soil fertility and plant nutrition, may influence the ecological risk of target lepidopteran pests in Bt crops.

METHODS

In this study, transgenic Bt maize (Line IE09S034 with Cry1Ie vs. its parental line of non-Bt maize cv. Xianyu335) was inoculated with a species of AMF, Glomus caledonium (GC). Its effects on the food utilization, reproduction and development of armyworm, Mythimna separata, were studied in a potted experiment from 2017 to 2018.

RESULTS

GC inoculation increased the AMF colonization of both modified and non-modified maize, and also increased the grain weight per plant and 1,000-grain weight of modified and non-modified maize. However, the cultivation of Bt maize did not significantly affect the AMF colonization. The feeding of M. separata with Bt maize resulted in a notable decrease in RCR (relative consumption rate), RGR (relative growth rate), AD (approximate digestibility), ECD (efficiency of conversion of digested food) and ECI (efficiency of conversion of ingested food) parameters in comparison to those observed in larvae fed with non-Bt maize in 2017 and 2018, regardless of GC inoculation. Furthermore, remarkable prolongation of larval life span and decreases in the rate of pupation, weight of pupa, rate of eclosion, fecundity and adult longevity of M. separata were observed in the Bt treatment regardless of GC inoculation during the two-year experiment. Also, when M. separata was fed with Bt maize, a significant prolongation of larval life and significant decreases in the pupal weight, fecundity and adult longevity of M. separata were observed when inoculated with GC. However, it was just the opposite for larvae fed with non-Bt maize that was inoculated with GC. The increased percentage of larval life-span, the decreased percentages of the food utilization, and the other indexes of reproduction, growth, and development of M. separata fed on Bt maize relative to non-Bt maize were all visibly lower when under GC inoculation in contrast to the CK.

DISCUSSION

It is presumed that Bt maize has a marked adverse impact on M. separata development, reproduction and feeding, especially when in combination with the GC inoculation. Additionally, GC inoculation favors the effectiveness of Bt maize against M. separata larvae by reducing their food utilization ability, which negatively affects the development and reproduction of the armyworm. Thus, Bt maize inoculated with AMF (here, GC) can reduce the severe threats arising of armyworms, and hence the AMF inoculation may play an important ecological functions in the field of Bt maize ecosystem, with potentially high control efficiency for the target lepidopteran pests.

Mycorrhizal response in crop versus wild plants

We proposed a theoretical framework predicting mutualistic outcomes for the arbuscular mycorrhizal (AM) symbiosis based on host provenance (crop versus wild). To test the framework, we grew two isolates of Rhizoglomus irregulare (commercial versus an isolate locally isolated), with five crop plants and five wild plants endemic to the region that co-occur with the locally sourced fungus. While inoculation with either isolate had no effect on plant biomass, it decreased leaf P content, particularly for wild plants. All plants associating with the commercial fungus had lower leaf P. Overall, our data shows that wild plants may be more sensitive to differences in mutualistic quality among fungal isolates.

Effect of co-application of phosphorus fertilizer and in vitro-produced mycorrhizal fungal inoculants on yield and leaf nutrient concentration of cassava

The adaptability of cassava to low fertile and marginal soils facilitates its production in subsistent agriculture. As a result, smallholder farmers rarely apply fertilizers. The current yield gap is therefore very large, calling for application of fertilizers and soil amendments to improve its productivity. Field experiments were carried out to assess the potential of partially substituting Phosphorus (P) fertilizers by in vitro-produced arbuscular mycorrhizal fungal (AMF) inoculants in cassava production in two agro-ecologies of Nigeria: Northern Guinea Savanna (Samaru) and Sudan Savanna (Minjibir). The experiments were laid out in a split plot design with P levels (0, 17.5, 35 and 52.5 kg P2O5 ha-1) as main plot and AMF inoculants (Control, Glomygel, Glomygel carrier, Mycodrip, Mycodrip carrier) as subplots. The results in Samaru showed that there was significant interaction between AMF and P in root fresh weight, total biomass and root to shoot ratio. The root fresh weights of the inoculated cassava increased proportionally with application of P. However, highest root fresh weight of cassava inoculated with Glomygel was observed at 35 kg P2O5 ha-1 recording 25% yield increase compared to 52.5 kg P2O5 ha-1 application. Interestingly, Cassava inoculated with Glomygel at 17.5 kg P2O5 ha-1 gave root fresh yield statistically similar to where 35 kg P2O5 ha-1 was applied. This represented a 50% reduction in P fertilizer use. Also, cassava inoculated with Glomygel increased leaf nutrient concentrations, which strongly correlated with the root fresh yield. However, no effects of inoculant carriers were observed in yield and nutrient concentrations. Contrarily, there was no significant treatment effect in Minjibir for nearly all the measured parameters. Cassava yield was however, higher in Minjibir than Samaru probably due to soil fertility and structural differences, which resulted in few observable effects of AMF and P treatments at Minjibir. We conclude that under low P conditions inoculation with in vitro produced AMF inoculants could be employed to reduce P fertilizer requirements for cassava and improve yields, but the variability of the responses as a result of soil heterogeneity and the identity of the fungal strain in the inoculant require further investigations before recommending the practice.

Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields

Arbuscular mycorrhizal (AM) fungi are important members of the root microbiome and may be used as biofertilizers for sustainable agriculture. To elucidate the impact of AM fungal inoculation on indigenous root microbial communities, we used high-throughput sequencing and an analytical pipeline providing fixed operational taxonomic units (OTUs) as an output to investigate the bacterial and fungal communities of roots treated with a commercial AM fungal inoculum in six agricultural fields. AM fungal inoculation significantly influenced the root microbial community structure in all fields. Inoculation changed the abundance of indigenous AM fungi and other fungal members in a field-dependent manner. Inoculation consistently enriched several bacterial OTUs by changing the abundance of indigenous bacteria and introducing new bacteria. Some inoculum-associated bacteria closely interacted with the introduced AM fungi, some of which belonged to the genera Burkholderia, Cellulomonas, Microbacterium, Sphingomonas, and Streptomyces and may be candidate mycorrhizospheric bacteria that contribute to the establishment and/or function of the introduced AM fungi. Inoculated AM fungi also co-occurred with several indigenous bacteria with putative beneficial traits, suggesting that inoculated AM fungi may recruit specific taxa to confer better plant performance. The bacterial families Methylobacteriaceae, Acetobacteraceae, Armatimonadaceae, and Alicyclobacillaceae were consistently reduced by the inoculation, possibly due to changes in the host plant status caused by the inoculum. To the best of our knowledge, this is the first large-scale study to investigate interactions between AM fungal inoculation and indigenous root microbial communities in agricultural fields.

The future has roots in the past: the ideas and scientists that shaped mycorrhizal research

Contents Summary 982 I. Introduction 982 II. The portraits of our ancestors: a gallery of ideas from more than 100 years of mycorrhizal research 983 III. Mycorrhizal fungi in the 'omics' era: first puzzle, how to name mycorrhizal fungi 985 IV. Signalling: a central question of our time? 987 V. The colonization process: how cellular studies predicted future 'omics' data 989 VI. The genetics underlying colonization events 991 VII. Concluding thoughts: chance and needs in mycorrhizal symbioses 992 Acknowledgements 992 References 992 SUMMARY: Our knowledge of mycorrhizas dates back to at least 150 years ago, when the plant pathologists A. B. Frank and G. Gibelli described the surprisingly morphology of forest tree roots surrounded by a fungal mantle. Compared with this history, our molecular study of mycorrhizas remains a young science. To trace the history of mycorrhizal research, from its roots in the distant past, to the present and the future, this review outlines a few topics that were already central in the 19^th century and were seminal in revealing the biological meaning of mycorrhizal associations. These include investigations of nutrient exchange between partners, plant responses to mycorrhizal fungi, and the identity and evolution of mycorrhizal symbionts as just a few examples of how the most recent molecular studies of mycorrhizal biology sprouted from the roots of past research. In addition to clarifying the ecological role of mycorrhizas, some of the recent results have changed the perception of the relevance of mycorrhizas in the scientific community, and in the whole of society. Looking to past knowledge while foreseeing strategies for the next steps can help us catch a glimpse of the future of mycorrhizal research.

Reducing Water Availability Impacts the Development of the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis MUCL 41833 and Its Ability to Take Up and Transport Phosphorus Under in Vitro Conditions

Climate change scenarios predict a higher variability in rainfall and an increased risk of water deficits during summers for the coming decades. For this reason, arbuscular mycorrhizal fungi (AMF) and their mitigating effects on drought stress in plants are increasingly considered in crop management. However, the impact of a decrease in water availability on the development of AMF and their ability to take up and transport inorganic phosphorus (Pi) to their hosts remain poorly explored. Here, Medicago truncatula plantlets were grown in association with Rhizophagus irregularis MUCL 41833 in bi-compartmented Petri plates. The system consisted in associating the plant and AMF in a root compartment (RC), allowing only the hyphae to extend in a root-free hyphal compartment (HC). Water availability in the HC was then lowered by increasing the concentration of polyethylene glycol-8000 (PEG-8000) from 0 to 10, 25, and 50 g L-1 (corresponding to a slight decrease in water potential of -0.024, -0.025, -0.030, and -0.056 Mpa, respectively). Hyphal growth, spore production and germination were severely impaired at the lowest water availability. The dynamics of Pi uptake by the AMF was also impacted, although total Pi uptake evaluated after 24 h stayed unchanged. The percentage of metabolically active extraradical hyphae remained above 70%. Finally, at the lowest water availability, a higher P concentration was observed in the shoots of M. truncatula. At reduced water availability, the extraradical mycelium (ERM) development was impacted, potentially limiting its capacity to explore a higher volume of soil. Pi uptake was slowed down but not prevented. The sensitivity of R. irregularis MUCL 41833 to a, even small, decrease in water availability contrasted with several studies reporting tolerance of AMF to drought. This suggests a species or strain-dependent effect and support the necessity to compare the impact of water availability on morpho-anatomy, nutrient uptake and transport capacities of other, potentially more drought-tolerant (e.g., isolated from dry environments) AMF.

Suppression of the activity of arbuscular mycorrhizal fungi by the soil microbiota

Arbuscular mycorrhizal fungi (AMF) colonise roots of most plants; their extra-radical mycelium (ERM) extends into the soil and acquires nutrients for the plant. The ERM coexists with soil microbial communities and it is unresolved whether these communities stimulate or suppress the ERM activity. This work studied the prevalence of suppressed ERM activity and identified main components behind the suppression. ERM activity was determined by quantifying ERM-mediated P uptake from radioisotope-labelled unsterile soil into plants, and compared to soil physicochemical characteristics and soil microbiome composition. ERM activity varied considerably and was greatly suppressed in 4 of 21 soils. Suppression was mitigated by soil pasteurisation and had a dominating biotic component. AMF-suppressive soils had high abundances of Acidobacteria, and other bacterial taxa being putative fungal antagonists. Suppression was also associated with low soil pH, but this effect was likely indirect, as the relative abundance of, e.g., Acidobacteria decreased after liming. Suppression could not be transferred by adding small amounts of suppressive soil to conducive soil, and thus appeared to involve the common action of several taxa. The presence of AMF antagonists resembles the phenomenon of disease-suppressive soils and implies that ecosystem services of AMF will depend strongly on the specific soil microbiome.

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations of diversity. For instance, the completeness of reference databases cannot be generally estimated since it depends on the extant diversity sampled to date, which, with the exception of a few habitats such as the human gut, remains severely undersampled. Further, estimation of the degree of coverage of a microbial community by a metagenomic data set is prohibitively time-consuming for large data sets, and coverage values may not be directly comparable between data sets obtained with different sequencing technologies. Here, we extend Nonpareil, a database-independent tool for the estimation of coverage in metagenomic data sets, to a high-performance computing implementation that scales up to hundreds of cores and includes, in addition, a k-mer-based estimation as sensitive as the original alignment-based version but about three hundred times as fast. Further, we propose a metric of sequence diversity (N_d ) derived directly from Nonpareil curves that correlates well with alpha diversity assessed by traditional metrics. We use this metric in different experiments demonstrating the correlation with the Shannon index estimated on 16S rRNA gene profiles and show that N_d additionally reveals seasonal patterns in marine samples that are not captured by the Shannon index and more precise rankings of the magnitude of diversity of microbial communities in different habitats. Therefore, the new version of Nonpareil, called Nonpareil 3, advances the toolbox for metagenomic analyses of microbiomes. IMPORTANCE Estimation of the coverage provided by a metagenomic data set, i.e., what fraction of the microbial community was sampled by DNA sequencing, represents an essential first step of every culture-independent genomic study that aims to robustly assess the sequence diversity present in a sample. However, estimation of coverage remains elusive because of several technical limitations associated with high computational requirements and limiting statistical approaches to quantify diversity. Here we described Nonpareil 3, a new bioinformatics algorithm that circumvents several of these limitations and thus can facilitate culture-independent studies in clinical or environmental settings, independent of the sequencing platform employed. In addition, we present a new metric of sequence diversity based on rarefied coverage and demonstrate its use in communities from diverse ecosystems.