Towards an Integrated Mycorrhizal Technology: Harnessing Mycorrhiza for Sustainable Intensification in Agriculture

Native arbuscular mycorrhizal fungi drive ecophysiology through phenotypic integration and functional plasticity under the Sonoran desert conditions

Knowledge is scarce to what extent environmental drivers and native symbiotic fungi in soil induce abrupt (short-term), systemic (multiple traits), or specific (a subset of traits) shifts in C3 plants' ecophysiological/mycorrhizal responses. We cultivated an emblematic native C3 species (Capsicum annuum var. glabriusculum, "Chiltepín") to look at how the extreme heat of the Sonoran desert, sunlight regimes (low = 2, intermediate = 15, high = 46 mol m2 d-1) and density of native arbuscular mycorrhizal fungi in soil (low AMF = 1% v/v, high AMF = 100% v/v), drive shifts on mycorrhizal responses through multiple functional traits (106 traits). The warming thresholds were relentlessly harsh even under intensive shade (e.g. superheat maximum thresholds reached ranged between 47-63°C), and several pivotal traits were synergistically driven by AMF (e.g. photosynthetic capacity, biomass gain/allometry, and mycorrhizal colonization traits); whereas concurrently, sunlight regimes promoted most (76%) alterations in functional acclimation traits in the short-term and opposite directions (e.g. survival, phenology, photosynthetic, carbon/nitrogen economy). Multidimensional reduction analysis suggests that the AMF promotes a synergistic impact on plants' phenotypic integration and functional plasticity in response to sunlight regimes; however, complex relationships among traits suggest that phenotypic variation determines the robustness degree of ecophysiological/mycorrhizal phenotypes between/within environments. Photosynthetic canopy surface expansion, Rubisco activity, photosynthetic nitrogen allocation, carbon gain, and differential colonization traits could be central to plants' overall ecophysiological/mycorrhizal fitness strengthening. In conclusion, we found evidence that a strong combined effect among environmental factors in which AMF are key effectors could drive important trade-offs on plants' ecophysiological/mycorrhizal fitness in the short term.

Cross-kingdom nutrient exchange in the plant-arbuscular mycorrhizal fungus-bacterium continuum

The association between plants and arbuscular mycorrhizal fungi (AMF) affects plant performance and ecosystem functioning. Recent studies have identified AMF-associated bacteria as cooperative partners that participate in AMF-plant symbiosis: specific endobacteria live inside AMF, and hyphospheric bacteria colonize the soil that surrounds the extraradical hyphae. In this Review, we describe the concept of a plant-AMF-bacterium continuum, summarize current advances and provide perspectives on soil microbiology. First, we review the top-down carbon flow and the bottom-up mineral flow (especially phosphorus and nitrogen) in this continuum, as well as how AMF-bacteria interactions influence the biogeochemical cycling of nutrients (for example, carbon, phosphorus and nitrogen). Second, we discuss how AMF interact with hyphospheric bacteria or endobacteria to regulate nutrient exchange between plants and AMF, and the possible molecular mechanisms that underpin this continuum. Finally, we explore future prospects for studies on the hyphosphere to facilitate the utilization of AMF and hyphospheric bacteria in sustainable agriculture.

Do commercial arbuscular mycorrhizal inoculants contain the species that they claim?

The use of arbuscular mycorrhizal (AM) fungal inoculants as a means to promote plant growth is gaining momentum worldwide. Although there is an increasing number of commercial products available for various applications, the quality of these remains uncertain. We determined the AM fungal species composition in eleven inoculants from four producers by using DNA metabarcoding and compared them to the AM fungal species declared on the product labels. Our DNA metabarcoding of the inoculants revealed a concerning discrepancy between the declared and detected AM fungal species compositions of the products. While nine products contained at least one declared species, two did not contain any matching species and all inoculants but one contained additional species not declared on the product label. These findings highlight the need for better guidelines and industry standards to ensure consumer protection in the AM fungal inoculum market. Additionally, we call for caution when using commercial AM fungal inoculants in scientific experiments without confirmatory information about their species composition.

The biological and biochemical composition of wheat (Triticum aestivum) as affected by the bio and organic fertilizers

Microorganisms and organic compounds (humic and fulvic acid) offer viable alternatives to insecticides and mineral fertilizers. Even though many studies have shown the effects of biofertilizers and organic substances separately, little information is available on plant responses to the combined application of these bio-stimulants, even though these biological inputs have a high potential for simultaneous action. A two-year (2020/21-2021/22) field experiment was conducted to investigate the impact of organic and biofertilizers application on the growth, yield, and biochemical attributes of wheat (cv. Misr-1). Pre-planting, wheat seeds were inoculated with two biofertilizers including Mycorrhizae, and Azotobacter, and their combination (MIX), and control (un-inoculation) were considered the main plot factor. The subplot factor contained the foliar sprays of humic acid, fulvic acid, and control (no spray). The results revealed that the seed inoculation with mycorrhizae and azotobacter in combination with foliar-applied humic acid markedly (p ≤ 0.05) affected the growth, yield, and seed biochemical composition of wheat. Combination of mycorrhiza and azotobacter significantly (p ≤ 0.05) increased) plant height (100 cm), crop growth rate (18.69 g), number of spikelets per spike (22), biological yield (13.4 ton ha-1), grain yield (5.56 ton ha-1), straw yield (8.21 ton ha-1),), nitrogen (2.07%), phosphorous (0.91%), potassium (1.64%), protein content (12.76%), starch (51.81%), and gluten content (30.90%) compared to control. Among organic fertilizers, humic acid caused the maximum increase in plant height (93 cm), crop growth rate ( 15 g day-1 m-2),1000 grain weight (51 g), biological yield ( 11ton ha-1), grain yield (4.5 ton ha-1), protein content (11%), chlorophyll content (46 SPAD), and gluten (29.45%) as compared to all other treatments. The foliar application of humic acid combined with the mycorrhizae or azotobacter seed inoculation was efficient to induce wheat vegetative growth development, as well as yield and its components.

High-throughput shoot phenotyping reveals temporal growth responses to nitrogen and inorganic and organic phosphorus sources in tomato

The application of nitrogen (N) and phosphorus (P) fertilizers to soils is required to maintain crop yields, so the sufficient and timely delivery of nutrients to match crop demand is important in fertilizer management. We quantified temporal growth responses of tomato plants with different rates of N and P application using high-throughput shoot phenotyping. The tomato plants were grown in soil that had organic, inorganic or a combination of sources of P incorporated. Additional N was added to each pot at low and high rates, 13 days after planting. At the same rate of total P application, the inorganic P source resulted in greater shoot growth at the early time points. Later on, the plants supplied with organic or mixed P sources grew faster than those that received the inorganic P source, resulting in comparable shoot biomass in all treatments at the time of destructive harvest. The shoot phenotyping data demonstrated that readily available soil P was important for early tomato growth while available N was more important in later stages of vegetative growth. These results suggest that a fertilizer formulation of combined inorganic and organic P sources may be able to sustain rapid and great shoot growth in tomato plants, while also reducing additional N input.

Diverse mycorrhizal maize inbred lines differentially modulate mycelial traits and the expression of plant and fungal phosphate transporters

Food production is heavily dependent on soil phosphorus (P), a non-renewable mineral resource essential for plant growth and development. Alas, about 80% is unavailable for plant uptake. Arbuscular mycorrhizal fungi may promote soil P efficient use, although the mechanistic aspects are yet to be completely understood. In this study, plant and fungal variables involved in P acquisition were investigated in maize inbred lines, differing for mycorrhizal responsiveness and low-P tolerance, when inoculated with the symbiont Rhizoglomus irregulare (synonym Rhizophagus irregularis). The expression patterns of phosphate transporter (PT) genes in extraradical and intraradical mycelium (ERM/IRM) and in mycorrhizal and control maize roots were assessed, together with plant growth responses and ERM extent and structure. The diverse maize lines differed in plant and fungal accumulation patterns of PT transcripts, ERM phenotypic traits and plant performance. Mycorrhizal plants of the low-P tolerant maize line Mo17 displayed increased expression of roots and ERM PT genes, compared with the low-P susceptible line B73, which revealed larger ERM hyphal densities and interconnectedness. ERM structural traits showed significant correlations with plant/fungal expression levels of PT genes and mycorrhizal host benefit, suggesting that both structural and functional traits are differentially involved in the regulation of P foraging capacity in mycorrhizal networks.

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

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

Plant Foraging Strategies Driven by Distinct Genetic Modules: Cross-Ecosystem Transcriptomics Approach

Plants have evolved diverse strategies for foraging, e.g., mycorrhizae, modification of root system architecture, and secretion of phosphatase. Despite extensive molecular/physiological studies on individual strategies under laboratory/greenhouse conditions, there is little information about how plants orchestrate these strategies in the field. We hypothesized that individual strategies are independently driven by corresponding genetic modules in response to deficiency/unbalance in nutrients. Roots colonized by mycorrhizal fungi, leaves, and root-zone soils were collected from 251 maize plants grown across the United States Corn Belt and Japan, which provided a large gradient of soil characteristics/agricultural practice and thus gene expression for foraging. RNA was extracted from the roots, sequenced, and subjected to gene coexpression network analysis. Nineteen genetic modules were defined and functionally characterized, from which three genetic modules, mycorrhiza formation, phosphate starvation response (PSR), and root development, were selected as those directly involved in foraging. The mycorrhizal module consists of genes responsible for mycorrhiza formation and was upregulated by both phosphorus and nitrogen deficiencies. The PSR module that consists of genes encoding phosphate transporter, secreted acid phosphatase, and enzymes involved in internal-phosphate recycling was regulated independent of the mycorrhizal module and strongly upregulated by phosphorus deficiency relative to nitrogen. The root development module that consists of regulatory genes for root development and cellulose biogenesis was upregulated by phosphorus and nitrogen enrichment. The expression of this module was negatively correlated with that of the mycorrhizal module, suggesting that root development is intrinsically an opposite strategy of mycorrhizae. Our approach provides new insights into understanding plant foraging strategies in complex environments at the molecular level.

Development of an organomineral fertiliser formulation that improves tomato growth and sustains arbuscular mycorrhizal colonisation

Achieving sustainable agricultural development requires the efficient use of nutrient resources for crop production. Recovering nutrients from animal manures may play a key role in achieving this. Animal manures typically have low nutrient concentrations, and in ratios that are often not ideal for balanced crop nutrition. Here, combinations of organic and inorganic phosphorus (P) were formulated as granular products (organomineral fertilisers) with granule size suitable for transport and spreading. The fertilisers were produced by granulating powdered chicken litter with MAP and urea powders making the following formulations: 0:4, 1:3, 2:2, 3:1, 4:0. The kinetics of NH₄⁺-N and P release from the fertilisers, and the effects on tomato growth and nutrition, as well as arbuscular mycorrhizal formation in roots following fertiliser application, were determined. Cumulative NH₄⁺-N release ceased within 12 h, and was lower in the formulations with higher proportions of chicken litter. The cumulative P released reached approximately 80% of total P in all formulations, and the time to obtain maximum P dissolution was 19 days in the formulation that contained only chicken litter. The organomineral fertilisers increased tomato shoot growth by 15-28% compared to the chicken litter only, MAP only and MAP/urea formulations. Reasonable levels of mycorrhizal colonisation of tomato roots was achieved with the organomineral fertilisers. The results demonstrated that optimum plant growth does not depend solely on immediately available P, and that timing of nutrient supply to match plant demand is important. The combination of chicken litter with MAP sustained nutrient supply and improved plant growth. Taken together, organomineral fertiliser formulations are potential alternatives to inorganic P fertilisers that can improve crop growth and nutrition, while provide a sustainable use for animal production wastes.

Microbe-assisted crop improvement: a sustainable weapon to restore holobiont functionality and resilience

In the past years, breeding programs have been mainly addressed on pushing the commercial features, forgetting important traits, such as those related to environmental stress resilience, that are instead present in wild relatives. Among the traits neglected by breeding processes, the ability to recruit beneficial microorganisms that recently is receiving a growing attention due to its potentiality. In this context, this review will provide a spotlight on critical issues of the anthropocentric point of view that, until now, has characterized the selection of elite plant genotypes. Its effects on the plant-microbiome interactions, and the possibility to develop novel strategies mediated by the exploitation of beneficial root-microbe interactions, will be discussed. More sustainable microbial-assisted strategies might in fact foster the green revolution and the achievement of a more sustainable agriculture in a climatic change scenario.

Arbuscular mycorrhizal fungi increase crop yields by improving biomass under rainfed condition: a meta-analysis

BACKGROUND

Rainfed agriculture plays key role in ensuring food security and maintain ecological balance. Especially in developing areas, most grain food are produced rainfed agricultural ecosystem. Therefore, the increase of crop yields in rainfed agricultural ecosystem becomes vital as well as ensuring global food security.

METHODS

The potential roles of arbuscular mycorrhizal fungi (AMF) in improving crop yields under rainfed condition were explored based on 546 pairs of observations published from 1950 to 2021.

RESULTS

AMF inoculation increased 23.0% crop yields based on 13 popular crops under rainfed condition. Not only was crop biomass of shoot and root increased 24.2% and 29.6% by AMF inocula, respectively but also seed number and pod/fruit number per plant were enhanced markedly. Further, the effect of AMF on crop yields depended on different crop groups. AMF improved more yield of N-fixing crops than non-N-fixing crops. The effect of AMF changed between grain and non-grain crops with the effect size of 0.216 and 0.352, respectively. AMF inoculation enhances stress resistance and photosynthesis of host crop in rainfed agriculture.

CONCLUSION

AMF increased crop yields by enhancing shoot biomass due to the improvement of plant nutrition, photosynthesis, and stress resistance in rainfed field. Our findings provide a new view for understanding the sustainable productivity in rainfed agroecosystem, which enriched the theory of AMF functional diversity. This study provided a theoretical and technical way for sustainable production under rainfed agriculture.

New approaches to improve crop tolerance to biotic and abiotic stresses

During the last years, a great effort has been dedicated at the development and employment of diverse approaches for achieving more stress-tolerant and climate-flexible crops and sustainable yield increases to meet the food and energy demands of the future. The ongoing climate change is in fact leading to more frequent extreme events with a negative impact on food production, such as increased temperatures, drought, and soil salinization as well as invasive arthropod pests and diseases. In this review, diverse "green strategies" (e.g., chemical priming, root-associated microorganisms), and advanced technologies (e.g., genome editing, high-throughput phenotyping) are described on the basis of the most recent research evidence. Particularly, attention has been focused on the potential use in a context of sustainable and climate-smart agriculture (the so called "next agriculture generation") to improve plant tolerance and resilience to abiotic and biotic stresses. In addition, the gap between the results obtained in controlled experiments and those from application of these technologies in real field conditions (lab to field step) is also discussed.

A commercial arbuscular mycorrhizal inoculum increases root colonization across wheat cultivars but does not increase assimilation of mycorrhiza-acquired nutrients

Production and heavy application of chemical-based fertilizers to maintain crop yields is unsustainable due to pollution from run-off, high CO2 emissions, and diminishing yield returns. Access to fertilizers will be limited in the future due to rising energy costs and dwindling rock phosphate resources. A growing number of companies produce and sell arbuscular mycorrhizal fungal (AMF) inoculants, intended to help reduce fertilizer usage by facilitating crop nutrient uptake through arbuscular mycorrhizas. However, their success has been variable. Here, we present information about the efficacy of a commercially available AMF inoculant in increasing AMF root colonization and fungal contribution to plant nutrient uptake, which are critical considerations within the growing AMF inoculant industry. Summary Arable agriculture needs sustainable solutions to reduce reliance on large inputs of nutrient fertilizers while continuing to improve crop yields. By harnessing arbuscular mycorrhizal symbiosis, there is potential to improve crop nutrient assimilation and growth without additional inputs, although the efficacy of commercially available mycorrhizal inocula in agricultural systems remains controversial.Using stable and radioisotope tracing, carbon-for-nutrient exchange between arbuscular mycorrhizal fungi and three modern cultivars of wheat was quantified in a non-sterile, agricultural soil, with or without the addition of a commercial mycorrhizal inoculant.While there was no effect of inoculum addition on above-ground plant biomass, there was increased root colonization by arbuscular mycorrhizal fungi and changes in community structure. Inoculation increased phosphorus uptake across all wheat cultivars by up to 30%, although this increase was not directly attributable to mycorrhizal fungi. Carbon-for-nutrient exchange between symbionts varied substantially between the wheat cultivars.Plant tissue phosphorus increased in inoculated plants potentially because of changes induced by inoculation in microbial community composition and/or nutrient cycling within the rhizosphere. Our data contribute to the growing consensus that mycorrhizal inoculants could play a role in sustainable food production systems of the future.

Crop diversity enriches arbuscular mycorrhizal fungal communities in an intensive agricultural landscape

Arbuscular mycorrhizal fungi (AMF) are keystone symbionts of agricultural soils but agricultural intensification has negatively impacted AMF communities. Increasing crop diversity could ameliorate some of these impacts by positively affecting AMF. However, the underlying relationship between plant diversity and AMF community composition has not been fully resolved. We examined how greater crop diversity affected AMF across farms in an intensive agricultural landscape, defined by high nutrient input, low crop diversity and high tillage frequency. We assessed AMF communities across 31 field sites that were either monocultures or polycultures (growing > 20 different crop types) in three ways: richness, diversity and composition. We also determined root colonization across these sites. We found that polycultures drive the available AMF community into richer and more diverse communities while soil properties structure AMF community composition. AMF root colonization did not vary by farm management (monocultures vs polycultures), but did vary by crop host. We demonstrate that crop diversity enriches AMF communities, counteracting the negative effects of agricultural intensification on AMF, providing the potential to increase agroecosystem functioning and sustainability.

Biofertilizers and Biocontrol Agents for Agriculture: How to Identify and Develop New Potent Microbial Strains and Traits

Microbiological tools, biofertilizers, and biocontrol agents, which are bacteria and fungi capable of providing beneficial outcomes in crop plant growth and health, have been developed for several decades. Currently we have a selection of strains available as products for agriculture, predominantly based on plant-growth-promoting rhizobacteria (PGPR), soil, epiphytic, and mycorrhizal fungi, each having specific challenges in their production and use, with the main one being inconsistency of field performance. With the growing global concern about pollution, greenhouse gas accumulation, and increased need for plant-based foods, the demand for biofertilizers and biocontrol agents is expected to grow. What are the prospects of finding solutions to the challenges on existing tools? The inconsistent field performance could be overcome by using combinations of several different types of microbial strains, consisting various members of the full plant microbiome. However, a thorough understanding of each microbiological tool, microbial communities, and their mechanisms of action must precede the product development. In this review, we offer a brief overview of the available tools and consider various techniques and approaches that can produce information on new beneficial traits in biofertilizer and biocontrol strains. We also discuss innovative ideas on how and where to identify efficient new members for the biofertilizer and biocontrol strain family.

Potential Effects of Microplastic on Arbuscular Mycorrhizal Fungi

Microplastics (MPs) are ubiquitously found in terrestrial ecosystems and are increasingly recognized as a factor of global change (GCF). Current research shows that MP can alter plant growth, soil inherent properties, and the composition and activity of microbial communities. However, knowledge about how microplastic affects arbuscular mycorrhizal fungi (AMF) is scarce. For plants it has been shown that microplastic can both increase and decrease the aboveground biomass and reduce the root diameter, which could indirectly cause a change in AMF abundance and activity. One of the main direct effects of microplastic is the reduction of the soil bulk density, which translates to an altered soil pore structure and water transport. Moreover, especially fibers can have considerable impacts on soil structure, namely the size distribution and stability of soil aggregates. Therefore, microplastic alters a number of soil parameters that determine habitat space and conditions for AMF. We expect that this will influence functions mediated by AMF, such as soil aggregation, water and nutrient transport. We discuss how the impacts of microplastic on AMF could alter how plants deal with other GCFs in the context of sustainable food production. The co-occurrence of several GCFs, e.g., elevated temperature, drought, pesticides, and microplastic could modify the impact of microplastic on AMF. Furthermore, the ubiquitous presence of microplastic also relates to earth system processes, e.g., net primary production (NPP), carbon and nitrogen cycling, which involve AMF as key soil organisms. For future research, we outline which experiments should be prioritized.

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

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

Epichloë Fungal Endophytes-From a Biological Curiosity in Wild Grasses to an Essential Component of Resilient High Performing Ryegrass and Fescue Pastures

The relationship between Epichloë endophytes found in a wide range of temperate grasses spans the continuum from antagonistic to mutualistic. The diversity of asexual mutualistic types can be characterised by the types of alkaloids they produce in planta. Some of these are responsible for detrimental health and welfare issues of ruminants when consumed, while others protect the host plant from insect pests and pathogens. In many temperate regions they are an essential component of high producing resilient tall fescue and ryegrass swards. This obligate mutualism between fungus and host is a seed-borne technology that has resulted in several commercial products being used with high uptake rates by end-user farmers, particularly in New Zealand and to a lesser extent Australia and USA. However, this has not happened by chance. It has been reliant on multi-disciplinary research teams undertaking excellent science to understand the taxonomic relationships of these endophytes, their life cycle, symbiosis regulation at both the cellular and molecular level, and the impact of secondary metabolites, including an understanding of their mammalian toxicity and bioactivity against insects and pathogens. Additionally, agronomic trials and seed biology studies of these microbes have all contributed to the delivery of robust and efficacious products. The supply chain from science, through seed companies and retailers to the end-user farmer needs to be well resourced providing convincing information on the efficacy and ensuring effective quality control to result in a strong uptake of these Epichloë endophyte technologies in pastoral agriculture.

Serendipita bescii promotes winter wheat growth and modulates the host root transcriptome under phosphorus and nitrogen starvation

Serendipita vermifera ssp. bescii, hereafter referred to as S. bescii, is a root‐associated fungus that promotes plant growth in both its native switchgrass host and a variety of monocots and dicots. Winter wheat (Triticum aestivum L.), a dual‐purpose crop, used for both forage and grain production, significantly contributes to the agricultural economies of the Southern Great Plains, USA. In this study, we investigated the influence of S. bescii on growth and transcriptome regulation of nitrogen (N) and phosphorus (P) metabolism in winter wheat. Serendipita bescii significantly improved lateral root growth and forage biomass under a limited N or P regime. Further, S. bescii activated sets of host genes regulating N and P starvation responses. These genes include, root‐specific auxin transport, strigolactone and gibberellin biosynthesis, degradation of phospholipids and biosynthesis of glycerolipid, downregulation of ammonium transport and nitrate assimilation, restriction of protein degradation by autophagy and subsequent N remobilization. All these genes are hypothesized to regulate acquisition, assimilation and remobilization of N and P. Based on transcriptional level gene regulation and physiological responses to N or P limitation, we suggest S. bescii plays a critical role in modulating stress imposed by limitation of these two critical nutrients in winter wheat.

Community Structure of Arbuscular Mycorrhizal Fungi in Soils of Switchgrass Harvested for Bioenergy

Learning more about the biodiversity and composition of arbuscular mycorrhizal fungi (AMF) under alternative agricultural management scenarios may be important to the sustainable intensification of switchgrass grown as a bioenergy crop. Using PacBio single-molecule sequencing and taxonomic resolution to the level of amplicon sequence variant (ASV), we assessed the effects of nitrogen amendment on AMF associating with switchgrass and explored relationships between AMF and switchgrass yield across three sites of various productivities in Wisconsin. Nitrogen amendment had little effect on AMF diversity metrics or community composition. While AMF ASV diversity was not correlated with switchgrass yield, AMF family richness and switchgrass yield had a strong, positive relationship at one of our three sites. Each of our sites was dominated by unique ASVs of the species Paraglomus brasilianum, indicating regional segregation of AMF at the intraspecific level. Our molecular biodiversity survey identified putative core members of the switchgrass microbiome, as well as novel clades of AMF, especially in the order Paraglomerales and the genus Nanoglomus Furthermore, our phylogenies unite the cosmopolitan, soil-inhabiting clade deemed GS24 with Pervetustaceae, an enigmatic family prevalent in stressful environments. Future studies should isolate and characterize the novel genetic diversity found in switchgrass agroecosystems and explore the potential yield benefits of AMF richness.IMPORTANCE We assessed the different species of beneficial fungi living in agricultural fields of switchgrass, a large grass grown for biofuels, using high-resolution DNA sequencing. Contrary to our expectations, the fungi were not greatly affected by fertilization. However, we found a positive relationship between plant productivity and the number of families of beneficial fungi at one site. Furthermore, we sequenced many species that could not be identified with existing reference databases. One group of fungi was highlighted in an earlier study for being widely distributed but of unknown taxonomy. We discovered that this group belonged to a family called Pervetustaceae, which may benefit switchgrass in stressful environments. To produce higher-yielding switchgrass in a more sustainable manner, it could help to study these undescribed fungi and the ways in which they may contribute to greater switchgrass yield in the absence of fertilization.

Myristate and the ecology of AM fungi: significance, opportunities, applications and challenges

A recent study by Sugiura and coworkers reported the non-symbiotic growth and spore production of an arbuscular mycorrhizal (AM) fungus, Rhizophagus irregularis, when the fungus received an external supply of certain fatty acids, myristates (C:14). This discovery follows the insight that AM fungi receive fatty acids from their hosts when in symbiosis. If this result holds up and can be repeated under nonsterile conditions and with a broader range of fungi, it has numerous consequences for our understanding of AM fungal ecology, from the level of the fungus, at the plant community level, and to functional consequences in ecosystems. In addition, myristate may open up several avenues from a more applied perspective, including improved fungal culture and supplementation of AM fungi or inoculum in the field. We here map these potential opportunities, and additionally offer thoughts on potential risks of this potentially new technology. Lastly, we discuss the specific research challenges that need to be overcome to come to an understanding of the potential role of myristate in AM ecology.

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.

Nitrogen Type and Availability Drive Mycorrhizal Effects on Wheat Performance, Nitrogen Uptake and Recovery, and Production Sustainability

Plant performance is strongly dependent on nitrogen (N), and thus increasing N nutrition is of great relevance for the productivity of agroecosystems. The effects of arbuscular mycorrhizal (AM) fungi on plant N acquisition are debated because contradictory results have been reported. Using 15N-labeled fertilizers as a tracer, we evaluated the effects of AM fungi on N uptake and recovery from mineral or organic sources in durum wheat. Under sufficient N availability, AM fungi had no effects on plant biomass but increased N concentrations in plant tissue, plant N uptake, and total N recovered from the fertilizer. In N-deficient soil, AM fungi led to decreased aboveground biomass, which suggests that plants and AM fungi may have competed for N. When the organic source had a low C:N ratio, AM fungi favored both plant N uptake and N recovery. In contrast, when the organic source had a high C:N ratio, a clear reduction in N recovery from the fertilizer was observed. Overall, the results indicate an active role of arbuscular mycorrhizae in favoring plant N-related traits when N is not a limiting factor and show that these fungi help in N recovery from the fertilizer. These results hold great potential for increasing the sustainability of durum wheat production.

Different wheat cultivars exhibit variable responses to inoculation with arbuscular mycorrhizal fungi from organic and conventional farms

The present study aimed to investigate the effects of arbuscular mycorrhizal (AM) fungal communities originating from organic and conventional agriculture on wheat growth and yield. Six different spring wheat cultivars released in different years in north and central European countries were considered. We hypothesised that AM fungal inoculum collected from organic agricultural fields would elicit a greater positive growth response than inoculum collected from conventional agricultural fields; and that older cultivars, which were developed under conditions of low fertilizer input, would exhibit overall greater growth responses to the presence of AM fungi, compared with more recent cultivars, and that AM fungal inoculum from conventional fields might have the most beneficial effect on the growth and yield of recent cultivars. The results showed that the overall effects on the growth and yield of spring wheat grown with organic and conventional AM fungal inocula did not differ greatly. However, the inoculation growth response, showing the difference of the effects of organic and conventional inocula, varied between particular wheat cultivars. Inoculation growth response of the cultivar Pikker (released in 1959) was the most positive, while that of the cultivar Arabella (released in 2012) was the most negative. The use of AM fungal inoculum from organic fields resulted in slightly taller plant individuals. Pikker showed relatively higher yield and stronger growth when the organic AM fungal inoculum was used. Arabella exhibited relatively lower yield and weaker growth when the organic inoculum was used. Whether the positive response of Pikker to Estonian organic inoculation reflects adaptation to the locally occurring AM fungal community needs to be established by further studies of the communities of AM fungi colonizing wheat roots.

Towards a Sustainable Agriculture: Strategies Involving Phytoprotectants against Salt Stress

Salinity is one of the main constraints for agriculture productivity worldwide. This important abiotic stress has worsened in the last 20 years due to the increase in water demands in arid and semi-arid areas. In this context, increasing tolerance of crop plants to salt stress is needed to guarantee future food supply to a growing population. This review compiles knowledge on the use of phytoprotectants of microbial origin (arbuscular mycorrhizal fungi and plant growth-promoting rhizobacteria), osmoprotectants, melatonin, phytohormones and antioxidant metabolism-related compounds as alleviators of salt stress in numerous plant species. Phytoprotectants are discussed in detail, including their nature, applicability, and role in the plant in terms of physiological and phenotype effects. As a result, increased crop yield and crop quality can be achieved, which in turn positively impact food security. Herein, efforts from academic and industrial sectors should focus on defining the treatment conditions and plant-phytoprotectant associations providing higher benefits.

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.

Contrasting Nitrogen Fertilisation Rates Alter Mycorrhizal Contribution to Barley Nutrition in a Field Trial

Controlled environment studies show that arbuscular mycorrhizal fungi (AMF) may contribute to plant nitrogen (N) uptake, but the role of these near-ubiquitous symbionts in crop plant N nutrition under natural field conditions remains largely unknown. In a field trial, we tested the effects of N fertilisation and barley (Hordeum vulgare L.) cultivar identity on the contribution of AMF to barley N uptake using 15N tracers added to rhizosphere soil compartments. AMF were shown capable of significantly increasing plant 15N acquisition from root exclusion zones, and this was influenced by nitrogen addition type, N fertiliser application rate and barley cultivar identity. Our data demonstrate a previously overlooked potential route of crop plant N uptake which may be influenced substantially and rapidly in response to shifting agricultural management practices.

The relative importance of ecological drivers of arbuscular mycorrhizal fungal distribution varies with taxon phylogenetic resolution

The phylogenetic depth at which arbuscular mycorrhizal (AM) fungi harbor a coherent ecological niche is unknown, which has consequences for operational taxonomic unit (OTU) delineation from sequence data and the study of their biogeography. We tested how changes in AM fungi community composition across habitats (beta diversity) vary with OTU phylogenetic resolution. We inferred exact sequence variants (ESVs) to resolve phylotypes at resolutions finer than provided by traditional sequence clustering and analyzed beta diversity profiles up to order-level sequence clusters. At the ESV level, we detected the environmental predictors revealed with traditional OTUs or at higher genetic distances. However, the correlation between environmental predictors and community turnover steeply increased at a genetic distance of c. 0.03 substitutions per site. Furthermore, we observed a turnover of either closely or distantly related taxa (respectively at or above 0.03 substitutions per site) along different environmental gradients. This study suggests that different axes of AM fungal ecological niche are conserved at different phylogenetic depths. Delineating AM fungal phylotypes using DNA sequences should screen different phylogenetic resolutions to better elucidate the factors that shape communities and predict the fate of AM symbioses in a changing environment.

Discussion paper: Sustainable increase of crop production through improved technical strategies, breeding and adapted management - A European perspective

During the next decade it will be necessary to develop novel combinations of management strategies to sustainably increase crop production and soil resilience. Improving agricultural productivity, while conserving and enhancing biotic and abiotic resources, is an essential requirement to increase global food production on a sustainable basis. The role of farmers in increasing agricultural productivity growth sustainably will be crucial. Farmers are at the center of any process of change involving natural resources and for this reason they need to be encouraged and guided, through appropriate incentives and governance practices, to conserve natural ecosystems and their biodiversity, and minimize the negative impact agriculture can have on the environment. Farmers and stakeholders need to revise traditional approaches not as productive as the modern approaches but more friendly with natural and environmental ecosystems values as well as emerging novel tools and approaches addressing precise farming, organic amendments, lowered water consumption, integrated pest control and beneficial plant-microbe interactions. While practical solutions are developing, science based recommendations for crop rotations, breeding and harvest/postharvest strategies leading to environmentally sound and pollinator friendly production and better life in rural areas have to be provided.

Arbuscular Mycorrhizal Fungi Alter the Community Structure of Ammonia Oxidizers at High Fertility via Competition for Soil NH4. MICROBIAL ECOLOGY 2019;78:147-158. [PMID: 30402724 DOI: 10.1007/s00248-018-1281-2]

Nitrification represents a central process in the cycling of nitrogen (N) which in high-fertility habitats can occasionally be undesirable. Here, we explore how arbuscular mycorrhiza (AM) impacts nitrification when N availability is not limiting to plant growth. We wanted to test which of the mechanisms that have been proposed in the literature best describes how AM influences nitrification. We manipulated the growth settings of Plantago lanceolata so that we could control the mycorrhizal state of our plants. AM induced no changes in the potential nitrification rates or the estimates of ammonium oxidizing (AO) bacteria. However, we could observe a moderate shift in the community of ammonia-oxidizers, which matched the shift we saw when comparing hyphosphere to rhizosphere soil samples and mirrored well changes in the availability of ammonium in soil. We interpret our results as support that it is competition for N that drives the interaction between AM and AO. Our experiment sheds light on an understudied interaction which is pertinent to typical management practices in agricultural systems.

Subsoil Arbuscular Mycorrhizal Fungi for Sustainability and Climate-Smart Agriculture: A Solution Right Under Our Feet?

With growing populations and climate change, assuring food and nutrition security is an increasingly challenging task. Climate-smart and sustainable agriculture, that is, conceiving agriculture to be resistant and resilient to a changing climate while keeping it viable in the long term, is probably the best solution. The role of soil biota and particularly arbuscular mycorrhizal (AM) fungi in this new agriculture is believed to be of paramount importance. However, the large nutrient pools and the microbiota of subsoils are rarely considered in the equation. Here we explore the potential contributions of subsoil AM fungi to a reduced and more efficient fertilization, carbon sequestration, and reduction of greenhouse gas emissions in agriculture. We discuss the use of crop rotations and cover cropping with deep rooting mycorrhizal plants, and low-disturbance management, as means of fostering subsoil AM communities. Finally, we suggest future research goals that would allow us to maximize these benefits.

Arbuscular mycorrhizal fungi increase grain yields: a meta-analysis

Increasing grain yields of food cereal crops is a major goal in future sustainable agriculture. We quantitatively analyzed the potential role of arbuscular mycorrhizal (AM) fungi in enhancing grain yields of seven cereal crops with exceptional importance for human nutrition across the globe: corn, wheat, rice, barley, sorghum, millet and oat. We conducted a meta-analysis for three datasets including both English and Chinese language publications: the 'whole' dataset including both laboratory and field studies (168 articles); the 'field' dataset comprising only field studies (97 studies); and the 'field-inoculation' dataset including only AM fungal inoculation studies conducted in field conditions (70 articles). We found that the AM fungal effect on grain yield was less pronounced in field and noninoculation studies. AM fungal inoculation in field led to a 16% increase (overall effect) based on the 'field-inoculation' dataset; this effect was variable (77% trials had positive values), crop-specific, lower for new cultivars released after 1950 and further modulated by soil pH. Although there are neutral and negative effects of AM fungi on grain yields, we emphasize the importance of integrating AM fungi in sustainable agriculture to increase grain yields of cereal crops.

Biodiversity of arbuscular mycorrhizal fungi and ecosystem function

Contents Summary 1059 I. Introduction: pathways of influence and pervasiveness of effects 1060 II. AM fungal richness effects on ecosystem functions 1062 III. Other dimensions of biodiversity 1062 IV. Back to basics - primary axes of niche differentiation by AM fungi 1066 V. Functional diversity of AM fungi - a role for biological stoichiometry? 1067 VI. Past, novel and future ecosystems 1068 VII. Opportunities and the way forward 1071 Acknowledgements 1072 References 1072 SUMMARY: Arbuscular mycorrhizal (AM) fungi play important functional roles in ecosystems, including the uptake and transfer of nutrients, modification of the physical soil environment and alteration of plant interactions with other biota. Several studies have demonstrated the potential for variation in AM fungal diversity to also affect ecosystem functioning, mainly via effects on primary productivity. Diversity in these studies is usually characterized in terms of the number of species, unique evolutionary lineages or complementary mycorrhizal traits, as well as the ability of plants to discriminate among AM fungi in space and time. However, the emergent outcomes of these relationships are usually indirect, and thus context dependent, and difficult to predict with certainty. Here, we advocate a fungal-centric view of AM fungal biodiversity-ecosystem function relationships that focuses on the direct and specific links between AM fungal fitness and consequences for their roles in ecosystems, especially highlighting functional diversity in hyphal resource economics. We conclude by arguing that an understanding of AM fungal functional diversity is fundamental to determine whether AM fungi have a role in the exploitation of marginal/novel environments (whether past, present or future) and highlight avenues for future research.

Impacts of domestication on the arbuscular mycorrhizal symbiosis of 27 crop species

The arbuscular mycorrhizal (AM) symbiosis is key to plant nutrition, and hence is potentially key in sustainable agriculture. Fertilization and other agricultural practices reduce soil AM fungi and root colonization. Such conditions might promote the evolution of low mycorrhizal responsive crops. Therefore, we ask if and how evolution under domestication has altered AM symbioses of crops. We measured the effect of domestication on mycorrhizal responsiveness across 27 crop species and their wild progenitors. Additionally, in a subset of 14 crops, we tested if domestication effects differed under contrasting phosphorus (P) availabilities. The response of AM symbiosis to domestication varied with P availability. On average, wild progenitors benefited from the AM symbiosis irrespective of P availability, while domesticated crops only profited under P-limited conditions. Magnitudes and directions of response were diverse among the 27 crops, and were unrelated to phylogenetic affinities or to the coordinated evolution with fine root traits. Our results indicate disruptions in the efficiency of the AM symbiosis linked to domestication. Under high fertilization, domestication could have altered the regulation of resource trafficking between AM fungi and associated plant hosts. Provided that crops are commonly raised under high fertilization, this result has important implications for sustainable agriculture.

Arbuscular mycorrhizal fungal and soil microbial communities in African Dark Earths

The socio-economic values of fertile and carbon-rich Dark Earth soils are well described from the Amazon region. Very recently, Dark Earth soils were also identified in tropical West Africa, with comparable beneficial soil properties and plant growth-promoting effects. The impact of this management technique on soil microbial communities, however, is less well understood, especially with respect to the ecologically relevant group of arbuscular mycorrhizal (AM) fungi. Thus, we tested the hypotheses that (1) improved soil quality in African Dark Earth (AfDE) will increase soil microbial biomass and shift community composition and (2) concurrently increased nutrient availability will negatively affect AM fungal communities. Microbial communities were distinct in AfDE in comparison to adjacent sites, with an increased fungal:bacterial ratio of 71%, a pattern mainly related to shifts in pH. AM fungal abundance and diversity, however, did not differ despite clearly increased soil fertility in AfDE, with 3.7 and 1.7 times greater extractable P and total N content, respectively. The absence of detrimental effects on AM fungi, often seen following applications of inorganic fertilizers, and the enhanced role of saprobic fungi relevant for mineralization and C sequestration support previous assertions of this management type as a sustainable alternative agricultural practice.

Agricultural practices to improve nitrogen use efficiency through the use of arbuscular mycorrhizae: Basic and agronomic aspects

Nitrogen cycling in agroecosystems is heavily dependent upon arbuscular mycorrhizal fungi (AMF) present in the soil microbiome. These fungi develop obligate symbioses with various host plant species, thus increasing their ability to acquire nutrients. However, AMF are particularly sensitive to physical, chemical and biological disturbances caused by human actions that limit their establishment. For a more sustainable agriculture, it will be necessary to further investigate which agricultural practices could be favorable to maximize the benefits of AMF to improve crop nitrogen use efficiency (NUE), thus reducing nitrogen (N) fertilizer usage. Direct seeding, mulch-based cropping systems prevent soil mycelium disruption and increase AMF propagule abundance. Such cropping systems lead to more efficient root colonization by AMF and thus a better establishment of the plant/fungal symbiosis. In addition, the use of continuous cover cropping systems can also enhance the formation of more efficient interconnected hyphal networks between mycorrhizae colonized plants. Taking into account both fundamental and agronomic aspects of mineral nutrition by plant/AMF symbioses, we have critically described, how improving fungal colonization through the reduction of soil perturbation and maintenance of an ecological balance could be helpful for increasing crop NUE.

Technological Microbiology: Development and Applications

Over thousands of years, modernization could be predicted for the use of microorganisms in the production of foods and beverages. However, the current accelerated pace of new food production is due to the rapid incorporation of biotechnological techniques that allow the rapid identification of new molecules and microorganisms or even the genetic improvement of known species. At no other time in history have microorganisms been so present in areas such as agriculture and medicine, except as recognized villains. Currently, however, beneficial microorganisms such as plant growth promoters and phytopathogen controllers are required by various agricultural crops, and many species are being used as biofactories of important pharmacological molecules. The use of biofactories does not end there: microorganisms have been explored for the synthesis of diverse chemicals, fuel molecules, and industrial polymers, and strains environmentally important due to their biodecomposing or biosorption capacity have gained interest in research laboratories and in industrial activities. We call this new microbiology Technological Microbiology, and we believe that complex techniques, such as heterologous expression and metabolic engineering, can be increasingly incorporated into this applied science, allowing the generation of new and improved products and services.