Unique and common traits in mycorrhizal symbioses

Integrated transcriptomics and metabolomics elucidate how arbuscular mycorrhizal fungi alleviate drought stress in Juglans sigillata

Walnut (Juglans sigillata), an economically significant ecotype of the Juglans genus in the Juglandaceae family, is cultivated mainly in southwest China, a region prone to seasonal drought. Drought significantly reduced both the yield and quality of walnuts in this area. Arbuscular mycorrhizal fungi (AMF) are symbiotic fungi that colonize plant roots and play crucial roles in enhancing plant drought resistance. This study investigated the effects of AMF on the alleviation of drought stress. Compared to non-inoculated drought-stressed plants, AMF inoculation improved plant growth, increased photosynthetic capacity, enhanced reactive oxygen species (ROS) scavenging ability, and significantly activities of superoxide Dismutase, peroxidase, and catalase were significantly increased by 19.90 %, 18.43 %, and 8.39 %, respectively. malondialdehyde, Superoxide anion, and Hydrogen peroxide levels decreased by 18.39 %, 20.75 %, and 21.44 %, respectively, and soluble sugar and proline concentrations also significantly increased (P < 0.05), helping to maintain the osmotic balance. In addition, transcriptome results showed that ATP-binding cassette transporter related to drought resistance were significantly enriched in plants inoculated with AMF, and genes related to growth, such as IAA and CKT synthesis, transcription factors (BZIP, WRKY, and GTE), and related antioxidant enzymes. The mitogen-activated protein kinases pathway-related genes were upregulated in the inoculated drought treatment group, whereas pinobanksin and homoeriodictyol were upregulated in the inoculated drought treatment group, both of which provide support for drought resistance. In summary, AMF alleviated drought stress and promoted Juglans sigillata growth by modulating key physiological, biochemical, and molecular mechanisms involved in drought resistance. This study offers important theoretical insights that support the application of AMF in sustainable agricultural practices.

A fungal sRNA silences a host plant transcription factor to promote arbuscular mycorrhizal symbiosis

Cross-kingdom RNA interference (ckRNAi) is a mechanism of interspecies communication where small RNAs (sRNAs) are transported from one organism to another; these sRNAs silence target genes in trans by loading into host AGO proteins. In this work, we investigated the occurrence of ckRNAi in Arbuscular Mycorrhizal Symbiosis (AMS). We used an in silico prediction analysis to identify a sRNA (Rir2216) from the AM fungus Rhizophagus irregularis and its putative plant gene target, the Medicago truncatula MtWRKY69 transcription factor. Heterologous co-expression assays in Nicotiana benthamiana, 5' RACE reactions and AGO1-immunoprecipitation assays from mycorrhizal roots were used to characterize the Rir2216-MtWRKY69 interaction. We further analyzed MtWRKY69 expression profile and the contribution of constitutive and conditional MtWRKY69 expression to AMS. We show that Rir2216 is loaded into an AGO1 silencing complex from the host plant M. truncatula, leading to cleavage of a host target transcript encoding for the MtWRKY69 transcription factor. MtWRKY69 is specifically downregulated in arbusculated cells in mycorrhizal roots and increased levels of MtWRKY69 expression led to a reduced AM colonization level. Our results indicate that MtWRKY69 silencing, mediated by a fungal sRNA, is relevant for AMS; we thus present the first experimental evidence of fungus to plant ckRNAi in AMS.

Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health

Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.

How do arbuscular mycorrhizal fungi enhance drought resistance of Leymus chinensis?

BACKGROUND

Leymus chinensis is a vital, dominant grass species in Eurasian temperate grasslands, including the Inner Mongolian steppe. L. chinensis exhibits enhanced drought tolerance through symbiosis with arbuscular mycorrhizal fungi (AMF). The physiological mechanisms behind this drought resistance need to be unraveled. A pot experiment was conducted with four inoculation treatments (inoculation with Funneliformis mosseae, with Claroideoglomus etunicatum, or with both, and no inoculation) and three drought treatments (no drought (75.00% field capacity), mild drought (56.25% field capacity), severe drought (37.50% field capacity)) to analyze how AMF enhance drought resistance of L. chinensis.

RESULTS

The results showed that drought stress inhibited the growth of L. chinensis, depending on its intensity, whereas AMF inoculation significantly improved growth and alleviated the effects of drought stress. Regardless of drought conditions, AMF inoculation significantly enhanced key biochemistry parameters, including soluble sugar concentration and antioxidant enzyme activities, ultimately promoting plant productivity. Structural equation models (SEMs) further showed that the increase in biomass of L. chinensis inoculated with AMF during mild drought was primarily due to reduced catalase activity and increased cytokinin concentration by increased soluble sugar concentration. However, under severe drought, the increase in biomass of L. chinensis inoculated with AMF was associated with increased soluble sugar concentration caused by increased peroxidase activity and reduced cytokinin concentration.

CONCLUSIONS

The mechanisms by which AMF enhance the drought resistance of L. chinensis vary depending on the severity of drought. AMF increase the soluble sugar concentration by enhancing photosynthetic activity to improve drought resistance under mild drought. Under severe drought conditions, AMF enhance the concentration of soluble sugars in L. chinensis by further activating the expression of antioxidant enzyme genes, thereby improving its drought resistance. Additionally, C. etunicatum maintains high ectomycelium by requiring less carbon sources to efficiently absorb the residual soil moisture under severe drought, thus superiorly enhancing the drought resistance of L. chinensis. This study provides a theoretical foundation for the application of AMF fertilizer to improve the productivity of L. chinensis in arid grasslands.

Arbuscular Mycorrhizal Fungi Improve Rice Production in Zinc-Amended Soils by Altering Zinc Transport and Translocation Routes

Human activities including industry and overcultivation resulted in marginal soils, unbalanced in nutrients or polluted with heavy metals. Zinc (Zn) is an essential micronutrient and its nonoptimal soil bio-availability, negatively affects plant growth and production. Arbuscular mycorrhizal fungi (AMF) could improve Zn acquisition in limited conditions and prevent accumulation in plant tissue in contaminated soils. However, it is not clear how AMF impact host plant Zn uptake and transport routes. In this study we assessed the potential of commercial AMF inoculum to support rice growth and production in non-Zn-fertilised, Zn-fertilised and Zn-polluted soils alongside their impact on host plant nutrient balances and Zn uptake and translocation routes. The results demonstrated that AMF inoculation restores rice growth and grain production in Zn-amended soils and that Zn amendment improves root colonisation. Shoot ionomes were particularly sensitive to differences in Zn supply and differentially affected in AMF and mock-inoculated plants. When present in excess, AMF inoculation decreased accumulation of Zn in shoots and disturbed Zn-P (phosphorus) relationship. We could not detect a mycorrhiza-specific Zn transporter in rice but rather a modification of expression for Zn transporters in the direct uptake routes. AMF inoculation interacts with the Zn-dependent response of heavy metal ATPase (OsHMA) transporters involved in root-to-shoot translocation. All together, these data indicate a change in relative importance of different direct Zn transport routes upon AMF colonisation. These findings provide valuable insights into how AMF symbiosis influences Zn uptake and distribution in rice under varying Zn conditions, allowing for the development of plant-fungus bioremediation and biofortification technologies.

Fungal endophytes influence soil organic carbon and nitrogen fractions promoting carbon sequestration and improving grain yield in soybean

Fungal endophyte inoculants present a promising avenue for enhancing carbon sequestration in agricultural systems. These endophytes can significantly influence soil organic carbon (SOC) and nitrogen (N) fractions by modulating root exudation, soil aggregation, and organic matter decomposition. We investigated the effectiveness of commercial-stage fungal endophyte seed inoculants in an Australian soybean field trial to increase yield, total SOC, stable SOC fractions, and soil N. After one growing season, specific inoculants (Thozetella sp. and Leptodontidium sp.) and dosages increased soybean grain yield and stocks of soil organic matter (SOM) as aggregate occluded particulate organic matter (oPOM) C and N, and mineral-associated organic matter (MAOM) C and N in the topsoil layer (0-15 cm). Furthermore, positive correlations were established between grain yield and the stocks of oPOM (C and N) and MAOM (C and N) in the topsoil layer (0-15 cm). Importantly, increasing grain yield was significantly and positively associated with the proportion of oPOM-C and N stocks to total SOM stock, providing evidence of significant carbon sequestration in oPOM. However, the proportion of MAOM-C and N stock to total SOM stock decreased significantly with increasing grain yield, indicating higher proportion of MAOM is being turned over relative to other SOM fractions although the absolute amounts of MAOM-C and N remained stable. These findings suggest that fungal endophytes and dosages may have variable but potentially beneficial impacts on crop growth, yield and play a crucial role in altering SOM fractions. This alteration potentially leads to changed carbon sequestration strategies, emphasising the need for further research into fungal endophyte-mediated carbon sequestration mechanisms.

Divergent altitudinal patterns of arbuscular and ectomycorrhizal fungal communities in a mid-subtropical mountain ecosystem

Arbuscular mycorrhizal fungi (AMF) and ectomycorrhizal fungi (EMF) form ubiquitous symbiotic relationships with plants through co-evolutionary processes, providing multiple benefits for plant growth, productivity, health, and stress mitigation. Mountain ecosystem multifunctionality is significantly influenced by mycorrhizal responses to climate change, highlighting the importance of understanding the complex interactions between these fungi and environmental variables. In this study, we investigated five vegetation zones across an altitudinal gradient (675-2157 m a.s.l.) in Wuyi Mountain, one of the most well-preserved mid-subtropical mountain ecosystems in eastern China. Using high-throughput sequencing, we examined the altitudinal distribution patterns, community assembly mechanisms, and network interactions of soil AMF and EMF. Our analyses demonstrated significant altitudinal variations in the composition and diversity of mycorrhizal fungal communities. AMF richness peaked in the subalpine dwarf forest at intermediate elevations, whereas EMF richness was highest in the low-altitude evergreen broad-leaved forest, showing a marked decrease in the alpine meadow ecosystem. β-diversity decomposition revealed that species turnover constituted the primary mechanism of community differentiation for both fungal types, explaining >56% of the observed variation. Stochastic processes dominated community assembly, with the relative importance of dispersal limitation and drift showing distinct altitudinal patterns. Network analysis indicated that AMF networks reached maximum complexity in evergreen broad-leaved forests, while EMF networks showed similar complexity levels in coniferous forests. Among the examined factors, soil properties emerged as the predominant driver of altitudinal variations in ecosystem multifunctionality, followed by AMF communities and climatic variables. These findings provide critical insights into the ecological functions and environmental adaptations of mycorrhizal fungi, advancing our understanding of their responses to environmental changes in mountain ecosystems and informing evidence-based conservation strategies.

Omics approaches to investigate pre-symbiotic responses of the mycorrhizal fungus Tulasnella sp. SV6 to the orchid host Serapias vomeracea

Like other plant-microbe symbioses, the establishment of orchid mycorrhiza (ORM) is likely to require specific communication and metabolic adjustments between the two partners. However, while modulation of plant and fungal metabolism has been investigated in fully established mycorrhizal tissues, the molecular changes occurring during the pre-symbiotic stages of the interaction remain largely unexplored in ORM. In this study, we investigated the pre-symbiotic responses of the ORM fungus Tulasnella sp. SV6 to plantlets of the orchid host Serapias vomeracea in a dual in vitro cultivation system. The fungal mycelium was harvested prior to physical contact with the orchid roots and the fungal transcriptome and metabolome were analyzed using RNA-seq and untargeted metabolomics approaches. The results revealed distinct transcriptomic and metabolomic remodelling of the ORM fungus in the presence of orchid plantlets, as compared to the free-living condition. The ORM fungus responds to the presence of the host plant with a significant up-regulation of genes associated with protein synthesis, amino acid and lipid biosynthesis, indicating increased metabolic activity. Metabolomic analysis supported the RNA-seq data, showing increased levels of amino acids and phospholipids, suggesting a remodelling of cell structure and signalling during the pre-symbiotic interaction. In addition, we identified an increase of transcripts of a small secreted protein that may play a role in early symbiotic signalling. Taken together, our results suggest that Tulasnella sp. SV6 may perceive information from orchid roots, leading to a readjustment of its transcriptomic and metabolomic profiles.

Improving Lunar Soil Simulant for Plant Cultivation: Earthworm-Mediated Organic Waste Integration and Plant-Microbe Interactions

Long-term human residence on the Moon is an inevitable trend in lunar exploration, necessitating the development of Bioregenerative Life Support Systems (BLSSs). In BLSSs, plant cultivation serves as the core functional unit, requiring substantial amounts of cultivation substrates. Lunar soil has potential as a cultivation substrate, but its suitability for plant growth must be improved to meet life-support requirements. As a fine-grained, organics-free, in situ resource, lunar soil's high compaction significantly restricts crops' root access to oxygen, water, and nutrients. While the addition of organic solid waste-a byproduct of BLSSs-could alleviate compaction, issues such as salinization, incomplete decomposition, and the presence of pathogens pose risks to crop health. In this study, we introduced earthworms into wheat cultivation systems to gradually digest, transfer (as vermicompost), and mix solid waste with a lunar soil simulant substrate. We set five experimental groups: a positive control group using vermiculite (named as V) as the optimal growth substrate, a negative control group using pure lunar soil simulant (LS), and three treatment groups using lunar soil simulant with solid waste and 15 (LS+15ew), 30 (LS+30ew), and 45 (LS+45ew) earthworms added. Our results demonstrated significant improvements in both compaction (e.g., bulk density, hydraulic conductivity) and salinization (e.g., salinity, electrical conductivity), likely due to the improved soil aggregate structures, which increased the porosity and ion adsorption capacity of the soil. Additionally, the microbial community within the substrate shifted toward a cooperative pattern dominated by significantly enriched plant probiotics. Consequently, the cultivated wheat achieved approximately 80% of the growth parameters (including production) compared to the control group grown in vermiculite with nutrient solution (representing ideal cultivation conditions), indicating sufficient nutrient supply from the mineralized waste. We can conclude that the earthworms "complementarily" improved the lunar soil simulant and organic waste by addressing compaction and salinization, respectively, leading to comprehensive improvements in key parameters, including the microbial environment. This study proposes a conceptual framework for improving lunar soil for crop cultivation, and it innovatively introduces earthworms as a preliminary yet effective solution. These findings provide a feasible and inspiring foundation for future lunar agriculture.

Arsenic Uptake and Metabolism in Mycorrhizal As-Hyperaccumulator Pteris vittata: Symbiotic P Transporters and As Reductases

Arbuscular mycorrhiza (AM) often protect host plants from As accumulation under arsenic stress; however, the opposite is true for the As-hyperaccumulator Pteris vittata. With non-hyperaccumulator Pteris ensiformis as a comparison, the AM colonization, P and As uptake, and genes associated with As metabolism were investigated in P. vittata after growing 60-day with Rhizophagus irregularis inoculation under 0 (As0), 10 (As10), or 100 μM As (As100) treatments. Based on the As-induced increase in AM colonization (up to 21%), AM symbiosis promoted P. vittata growth by 24% and frond P content by 22% in the AM+As100 treatment than As100 treatment. These increases corresponded to 4.2- to 5.4-fold upregulation in symbiotic P transporter RiPT1/7 in AM fungi and PvPht1;6 in P. vittata roots, which probably supported 37% greater As accumulation at 4980 mg kg-1 in the fronds. Besides total As, enhanced arsenate reduction was evidenced by 19% greater arsenite and 15-fold upregulation of fungal arsenate reductase RiArsC in mycorrhizal roots. Further, the 2.1-fold upregulation of arsenite antiporters PvACR3/3;3 contributed to greater arsenite translocation to and sequestration in the fronds. Unlike P. ensiformis symbiont, which suffers from As stress, the mycorrhiza-specific P transporters (RiPT1/7 and PvPht1;6), arsenate reductases (RiArsC and PvHAC2), and arsenite antiporters (PvACR3/3;3) all benefited AM symbiosis and As accumulation in P. vittata.

A fusarioid fungus forms mutualistic interactions with poplar trees that resemble ectomycorrhizal symbiosis

Fusarium species, recognised as global priority pathogens, frequently induce severe diseases in crops; however, certain species exhibit alternative symbiotic lifestyles and are either non-pathogenic or endophytic. In this study, we characterised the mutualistic relationship between the eFp isolate of F.pseudograminearum and five poplar species, resulting in formation root structures reminiscent of ectomycorrhizal (ECM) symbiosis. This functional symbiosis is evidenced by enhanced plant growth, reciprocal nutrient exchange, improved nitrogen and phosphorus uptake and upregulation of root sugar transporter gene expression (PtSweet1). Comparative and population genomics confirmed that eFp maintains a structurally similar genome, but exhibits significant divergence from ten conspecific pathogenic isolates. Notably, eFp enhanced the growth of diverse plant lineages (Oryza, Arabidopsis, Pinus and non-vascular liverworts), indicating a near-complete loss of virulence. Although this specialised symbiosis has only been established in vitro, it holds significant value in elucidating the evolutionary track from endophytic to mycorrhizal associations.

A pair of LysM receptors mediates symbiosis and immunity discrimination in Marchantia

Most land plants form symbioses with microbes to acquire nutrients but also must restrict infection by pathogens. Here, we show that a single pair of lysin-motif-containing receptor-like kinases, MpaLYR and MpaCERK1, mediates both immunity and symbiosis in the liverwort Marchantia paleacea. MpaLYR has a higher affinity for long-chain (CO7) versus short-chain chitin oligomers (CO4). Although both CO7 and CO4 can activate symbiosis-related genes, CO7 triggers stronger immune responses than CO4 in a dosage-dependent manner. CO4 can inhibit CO7-induced strong immune responses, recapitulating the early response to inoculation with the symbiont arbuscular mycorrhizal fungi. We show that phosphate starvation of plants increases their production of strigolactone, which stimulates CO4/CO5 secretion from mycorrhizal fungi, thereby prioritizing symbiosis over immunity. Thus, a single pair of LysM receptors mediates dosage-dependent perception of different chitin oligomers to discern symbiotic and pathogenic microbes in M. paleacea, which may facilitate terrestrialization.

Genetic and molecular mechanisms underlying nitrogen use efficiency in maize

Nitrogen (N) is vital for crop growth and yield, impacting food quality. However, excessive use of N fertilizers leads to high agricultural costs and environmental challenges. This review offers a thorough synthesis of the genetic and molecular regulation of N uptake, assimilation, and remobilization in maize, emphasizing the role of key genes and metabolic pathways in enhancing N use efficiency (NUE). We summarize the genetic regulators of N transports for nitrate (NO3-) and ammonium (NH4+) that contribute to efficient N uptake and transportation. We further discuss the molecular mechanisms by which root system development adapts to N distribution and how N influences root system development and growth. Given the advancements in high-throughput microbiome studies, we delve into the impact of rhizosphere microorganisms on NUE and the complex plant-microbe interactions that regulate maize NUE. Additionally, we conclude with intricate regulatory mechanisms of N assimilation and remobilization in maize, involving key enzymes, transcription factors, and amino acid transporters. We also scrutinize the known N signaling perception and transduction mechanisms in maize. This review underscores the challenges in improving maize NUE and advocates for an integrative research approach that leverages genetic diversity and synthetic biology, paving the way for sustainable agriculture.

A travelling-wave strategy for plant-fungal trade

For nearly 450 million years, mycorrhizal fungi have constructed networks to collect and trade nutrient resources with plant roots1,2. Owing to their dependence on host-derived carbon, these fungi face conflicting trade-offs in building networks that balance construction costs against geographical coverage and long-distance resource transport to and from roots3. How they navigate these design challenges is unclear4. Here, to monitor the construction of living trade networks, we built a custom-designed robot for high-throughput time-lapse imaging that could track over 500,000 fungal nodes simultaneously. We then measured around 100,000 cytoplasmic flow trajectories inside the networks. We found that mycorrhizal fungi build networks as self-regulating travelling waves-pulses of growing tips pull an expanding wave of nutrient-absorbing mycelium, the density of which is self-regulated by fusion. This design offers a solution to conflicting trade demands because relatively small carbon investments fuel fungal range expansions beyond nutrient-depletion zones, fostering exploration for plant partners and nutrients. Over time, networks maintained highly constant transport efficiencies back to roots, while simultaneously adding loops that shorten paths to potential new trade partners. Fungi further enhance transport flux by both widening hyphal tubes and driving faster flows along 'trunk routes' of the network5. Our findings provide evidence that symbiotic fungi control network-level structure and flows to meet trade demands, and illuminate the design principles of a symbiotic supply-chain network shaped by millions of years of natural selection.

Intricate phytohormonal orchestration mediates mycorrhizal symbiosis and stress tolerance

Arbuscular mycorrhizal fungi (AMF) are an essential symbiotic partner colonizing more than 70% of land plants. In exchange for carbon sources, mycorrhizal association ameliorates plants' growth and yield and enhances stress tolerance and/or resistance. To achieve this symbiosis, plants mediate a series of biomolecular changes, including the regulation of phytohormones. This review focuses on the role of each phytohormone in establishing symbiosis. It encases phytohormone modulation, exogenous application of the hormones, and mutant studies. The review also comments on the plausible phytohormone cross-talk essential for maintaining balanced mycorrhization and preventing fungal parasitism. Finally, we briefly discuss AMF-mediated stress regulation and contribution of phytohormone modulation in plants. We must examine their interplay to understand how phytohormones act species-specific or concentration-dependent manner. The review summarizes the gaps in these studies to improve our understanding of processes underlying plant-AMF symbiosis.

The Rhizophagus irregularis permease RiFTR1 functions without a ferroxidase partner for reductive iron transport

The contribution of arbuscular mycorrhizal fungi (AM fungi) to plant iron (Fe) acquisition has been demonstrated in several studies. A previous investigation revealed that the AM fungus Rhizophagus irregularis utilizes a high-affinity reductive pathway for Fe uptake, mediated by the Fe transporter RiFTR1. In this study, we used a genome-wide approach in R. irregularis to find genes encoding ferroxidases of the multicopper oxidase (MCO) gene family in an attempt to identify the ferroxidase partner of RiFTR1. Nine genes putatively encoding MCOs (RiMCO1-9) were identified. Yeast complementation assays demonstrated that RiMCO1 and RiMCO3 can function as ferroxidases, suggesting their involvement in the reductive Fe uptake pathway. Surprisingly, RiFTR1 was capable of transporting Fe in yeast without a ferroxidase partner, resembling the Fe transport mechanism of plant IRT1-like systems. RiFTR1 exhibited increase expression in arbuscules. Overexpression of RiFTR1 in Medicago truncatula roots led to enhanced mycorrhizal colonization and arbuscule abundance, highlighting the significance of Fe for AM symbiosis.

Autoactive CNGC15 enhances root endosymbiosis in legume and wheat

Nutrient acquisition is crucial for sustaining life. Plants develop beneficial intracellular partnerships with arbuscular mycorrhiza (AM) and nitrogen-fixing bacteria to surmount the scarcity of soil nutrients and tap into atmospheric dinitrogen, respectively1,2. Initiation of these root endosymbioses requires symbiont-induced oscillations in nuclear calcium (Ca2+) concentrations in root cells3. How the nuclear-localized ion channels, cyclic nucleotide-gated channel (CNGC) 15 and DOESN'T MAKE INFECTIONS1 (DMI1)4 are coordinated to specify symbiotic-induced nuclear Ca2+ oscillations remains unknown. Here we discovered an autoactive CNGC15 mutant that generates spontaneous low-frequency Ca2+ oscillations. While CNGC15 produces nuclear Ca2+ oscillations via a gating mechanism involving its helix 1, DMI1 acts as a pacemaker to specify the frequency of the oscillations. We demonstrate that the specificity of symbiotic-induced nuclear Ca2+ oscillations is encoded in its frequency. A high frequency activates endosymbiosis programmes, whereas a low frequency modulates phenylpropanoid pathways. Consequently, the autoactive cngc15 mutant, which is capable of generating both frequencies, has increased flavonoids that enhance AM, root nodule symbiosis and nutrient acquisition. We transferred this trait to wheat, resulting in field-grown wheat with increased AM colonization and nutrient acquisition. Our findings reveal a new strategy to boost endosymbiosis in the field and reduce inorganic fertilizer use while sustaining plant growth.

Effect of AM fungi on the growth and powdery mildew development of Astragalus sinicus L. under water stress

Arbuscular mycorrhizal (AM) fungi are widely existing soil microorganisms that form symbiotic relationships with most terrestrial plants. They are important for enhancing adversity resistance, including resistance to disease and water stresses. Nevertheless, it is not clear whether the benefits can be maintained in regulating the occurrence of plant diseases under drought, flooding stress and during water restoration. In this study, we investigated the effect of AM fungus (Glomus versiforme) on the development of powdery mildew in Chinese milk vetch (Astragalus sinicus) under drought, flooding, and water recovery. The results showed that AM fungal symbiosis promoted the growth of Chinese milk vetch under water stress conditions. It increased the accumulation of ethylene (ET) and jasmonic acid (JA), enhanced the activities of antioxidant enzymes, and decreased the accumulation of salicylic acid (SA) and abscisic acid (ABA). The differentially expressed genes (DEGs) obtained from transcriptome sequencing under each stress were subjected to weighted gene co-expression network analysis (WGCNA), and a total of 12 gene co-expression modules were obtained. The analysis of the relationship between the co-expressed genes in the 12 modules and plant physiological traits showed that the magent, grey60 and darkturquoise modules were significantly associated with ET, SA, JA, ABA, plant defence enzyme activities, malondialdehyde (MDA) and H2O2 content. Water stress and disease were related with the up-regulated expression of genes in the flavonoid biosynthesis and oxidative phosphorylation, plant hormone signal transduction and plant-pathogen interaction pathways. Importantly, inoculation with AM fungus reduced the incidence of powdery mildew under drought stress by 16.54%. In summary, the results of this study showed that inoculation with AM had a positive effect on powdery mildew development tolerance in Chinese milk vetch under drought and flooding stresses and stress recovery. This provides a good basis for field management and sustainable growth of green manure crop Chinese milk vetch.

Mechanisms of cooperation in the plants-arbuscular mycorrhizal fungi-bacteria continuum

In nature, cooperation is an essential way for species, whether they belong to the same kingdom or to different kingdoms, to overcome the scarcity of resources and improve their fitness. Arbuscular mycorrhizal fungi are symbiotic microorganisms whose origin date back 400 million years. They form symbiotic associations with the vast majority of terrestrial plants, helping them to obtain nutrients from the soil in exchange for carbon. At the more complex level, soil bacteria participate in the symbiosis between arbuscular mycorrhizal fungi and plants: they obtain carbon from the exudation of hyphae connected to the roots and compensate for the limited saprophytic capacity of arbuscular mycorrhizal fungi by mineralizing organic compounds. Therefore, plants, arbuscular mycorrhizal fungi and soil bacteria constitute a continuum that may be accompanied by multiple forms of cooperation. In this review, we first analyzed the functional complementarities and differences between plants and arbuscular mycorrhizal fungi in arbuscular mycorrhizal symbiosis. Secondly, we discussed the resource exchange relationship between plants and arbuscular mycorrhizal fungi from the perspective of biological market theory and "surplus carbon" hypothesis. Finally, on the basis of mechanisms for maintaining cooperation, direct and indirect reciprocity in the hyphosphere, induced by the availability of external resource and species fitness, were examined. Exploring these reciprocal cooperations will provide a better understanding of the intricate ecological relationships between plants, arbuscular mycorrhizal fungi and soil bacteria as well as their evolutionary implications.

Nearly 30a shrub introduction in desert steppes has led to an increase in saprotrophic fungi, accelerating the degradation of carbon compounds and nitrate reduction

Clarifying how soil microbial communities respond to shrub introduction after overgrazing in desert steppe and their potential functions is crucial for understanding the biogeochemical processes involved in vegetation transformation and sustainability of desert grasslands. However, the dynamics of microbial communities remain poorly understood. We selected enclosed grasslands (20a), overgrazed grasslands, and shrublands (6a, 15a, and 25a) to explore how shrubs introduced influence soil microbial structure and functional groups over the long term after desert grassland degradation. The results showed that overgrazing and shrub introduction (Caragana korshinskii) had more significant impacts on microbial β diversity than on α diversity. Fungal communities were more sensitive to grassland degradation. In contrast, introducing shrubs affected both fungal and bacterial communities, and an increase in shrub age drove the synergistic effects of fungal species. Soil nitrate and microbial biomass nitrogen were the key factors affecting bacterial and fungal communities. Compared with enclosed grasslands, overgrazing and introducing shrubs significantly increased soil nitrate reduction, ectomycorrhizals, and endophytes. The introduction of shrubs after overgrazing in desert steppe further enhanced the decomposition of carbon compounds and reduced processes such as denitrification. During shrub introduction, total phosphorus, nitrate-nitrogen, and N-acetylglucosaminidase were key factors affecting carbon, nitrogen, and fungal functional groups. Variations in microbial diversity and functional groups, through their influence on extracellular enzymes activity and the availability of microbial biomass nutrients, ultimately explained 85%, 42%, and 34% the observed variations in soil carbon, nitrogen, and phosphorus content, respectively. This study aimed to investigate the long-term effects of anthropogenic shrub expansion on the structure and function of soil microbial communities in degraded desert steppes, provide a scientific basis for steppe restoration and management, and further understand their significance for ecosystem sustainability.

Preparation of agriculture film from cow manure for silage maize planting: Experimental study and life cycle assessment

With the development of modern breeding technology, the scale of dairy farming is becoming increasingly large, which leading to decoupling of planting and breeding. Hence, massive amounts of manure could not handled by traditional method in time, which caused serious environmental problems. Therefor, there is a urgent needs for industrialized treatment methods to treat cow manure for dairy farm industry. In order to expand the types of industrial treatment methods of cow manure, two types of industrialized cow manure based agriculture films were introduced in this research, manure slurry film (MSF) and manure paper film (MPF). Taking silage corn cultivation as an example, their feasibility were testified: the usage performances of the films were expanded by crop yield and soil physicochemical properties, and environmental impacts of the films was conducted by life cycle assessment (LCA). The results showed: (1) both MSF and MPF would decomposed in one growth period of silage maize, with MPF having better performance in temperature retention; (2) both MSF and MPF improved soil nutrients and agglomerate structures; (3) the yield of maize with MSF and MPF was increased from 62.6 t to 88.4 t and 84.6 t per hectare compared to control group; and (4) according to LCA, MPF had 39 % and 50 % lower average environment impact than PE film and MSF. In conclusion, manure based films could effectively promotes crop growth with lower environment impact compared with traditional methods, which thus might provide effective linkage strategies for coupling of planting and breeding.

A Meta-Analysis of the Human Gut Mycobiome Using Internal Transcribed Spacer Data

The intestinal mycobiome is closely related to human health. There have been several reports investigating the association between the gut fungi and disease, but there is still a lack of overall assessment of the human gut mycobiome. Here, we performed a meta-analysis based on 2372 ITS (Internal Transcribed Spacer) data collected publicly online. We found that the mycobiome diversity of human gut fungi varies significantly across diseases by using EasyAmplicon, and these fungi are mainly composed of three genera, Saccharomyces, Candida, and Aspergillus. In addition, we performed the construction of disease prediction models based on ITS data by using the random forest model and verified the generalization ability of the models. We hope that our results will provide strong support for subsequent studies of the intestinal mycobiome.

TML1 and TML2 synergistically regulate nodulation and affect arbuscular mycorrhiza in Medicago truncatula

Two symbiotic processes, nodulation and arbuscular mycorrhiza, are primarily controlled by the plant's need for nitrogen (N) and phosphorus (P), respectively. Autoregulation of nodulation (AON) and autoregulation of mycorrhizal symbiosis (AOM) both negatively regulate their respective processes and share multiple components-plants that make too many nodules usually have higher arbuscular mycorrhiza (AM) fungal root colonization. The protein TML (TOO MUCH LOVE) was shown to function in roots to maintain susceptibly to rhizobial infection under low N conditions and control nodule number through AON in Lotus japonicus. Medicago truncatula has two sequence homologs: MtTML1 and MtTML2. We report the generation of stable single and double mutants harboring multiple allelic variations in MtTML1 and MtTML2 using CRISPR-Cas9 targeted mutagenesis and screening of a transposon mutagenesis library. Plants containing single mutations in MtTML1 or MtTML2 produced two to three times the nodules of wild-type plants, whereas plants containing mutations in both genes displayed a synergistic effect, forming 20× more nodules compared to wild-type plants. Examination of expression and heterozygote effects suggests that genetic compensation may play a role in the observed synergy. Plants with mutations in both TMLs only showed mild increases in AM fungal root colonization at later timepoints in our experiments, suggesting that these genes may also play a minor role in AM symbiosis regulation. The mutants created will be useful tools to dissect the mechanism of synergistic action of MtTML1 and MtTML2 in M. truncatula symbiosis with beneficial microbes.

Fungal-bacterial endosymbiosis: Recreating an ancient symbiotic relationship

Fungal-bacterial endosymbioses, the most intimate typology of symbioses, have been described in different taxa of Mucoromycota, an early diverging group of Fungi. In a recent issue of Nature, Giger and colleagues describe how they implanted a Burkolderia-related microbe inside a Mucoromycota fungus, giving rise to a functional and stable endosymbiosis.

Symbiotic conserved arbuscular mycorrhiza fungi supports plant health

Arbuscular mycorrhiza fungi (AMF) forms a multi-beneficial symbiotic relationship with the host plant, therefore it is considered to be an effective helper to promote plant health. However, failure to consider the source or universality of AMF is often unstable during application. Therefore, it is necessary to screen potential AMF inoculants based on the source and the relationship with host. In search of more effective and broad-spectrum AMF inoculants, we studied AMF community structure properties of healthy and diseased plants in 24 fields from four sampling sites. The results indicated that the environmental filtering effect of roots was obvious, which was manifested as a decrease of α-diversity from rhizosphere to root. Differences in α-diversity between healthy and diseased roots further indicate the importance of AMF communities within roots for maintaining plant health. Glomus is significantly enriched and dominant in healthy roots, independent of environment and phylogenically conserved. Spores were further isolated and evaluated for their disease-preventing and pro-growth properties. Based on whether they were symbiotic with plant and root-enrichment characteristics, isolated AMF spores were classified as symbiotic conserved, symbiotic non-conserved, and non-symbiotic AMF. After spores were propagated and inoculated to plant roots, only symbiotic conserved AMF significantly promoted plant growth and maintained health, highlighting the potential of symbiotic conserved AMF in sustainable plant production.

Temperature governs the community assembly of root-associated ectomycorrhizal fungi in alpine forests on the Qinghai-Tibetan Plateau

Unraveling the assembly processes of ectomycorrhizal (ECM) fungal communities in changing environments is crucial for forecasting the impacts of climate change on forests. However, the assembly processes and key drivers of root-associated ECM fungal communities in alpine coniferous forests remain poorly understood. To address this knowledge gap, we conducted sampling in 65 monodominant alpine coniferous forests, which encompass 11 plant species belonging to three genera (Abies, Pinus, and Picea) within the Pinaceae family, all located on the Qinghai-Tibetan Plateau. We employed a combination of null model and multivariate analyses to elucidate the drivers and assembly processes of ECM fungal communities. Our results revealed significant variation in the composition and diversity of root-associated ECM fungal communities among Abies, Pinus, and Picea, indicating specific preferences for ECM fungi among Pinaceae genera. Importantly, mean annual temperature (MAT) emerged as the primary driver of these variations and regulated the assembly processes within the community of root-associated ECM fungi. As MAT temperature, the α-diversity of these fungi significantly decreased, suggesting that increased temperature may reduce the species diversity of root-associated ECM fungi in alpine forests. Furthermore, stochastic processes, such as dispersal limitation and drift, became more influential as MAT increased. Conversely, the role of deterministic processes, particularly heterogeneous selection, in shaping the ECM fungal community assembly weakened with increasing MAT. This study provides novel theoretical insights into the processes of ECM fungal community assembly in alpine forests, emphasizing the pivotal role of temperature in regulating the assembly processes and compositional dynamics of root-associated ECM fungal communities in these unique environments.

Establishment of an efficient Agrobacterium tumefaciens-mediated transformation system for an Armillaria species, a host of the fully mycoheterotrophic plant Gastrodia elata

The genus Armillaria (Basidiomycota, Agaricales, Physalacriaceae) comprises pathogenic fungi that cause root-rot disease in plants, as well as species with low pathogenicity, some of which are hosts of the fully mycoheterotrophic orchid plant Gastrodia elata (Orchidaceae). To investigate the mechanisms underlying such special interactions between Armillaria fungi and G. elata, it is crucial to establish genetic transformation platforms for the Armillaria fungi and G. elata. In this study, an Armillaria strain Arm37 was isolated from G. elata, which can form symbiosis with G. elata in axenic culture under laboratory conditions. A vector pYT-EV containing a cassette for hygromycin-resistance selection and a cassette for expressing or silencing target genes was constructed. An Agrobacterium tumefaciens-mediated transformation (ATMT) system for Arm37 was successfully developed and optimized to achieve a transformation efficiency of 32%. The ATMT system was successfully used to express the reporter genes eGFP encoding enhanced green fluorescent protein and GUS encoding β-glucuronidase and to effectively silence the endogenous gene URA3 encoding orotidine-5'-phosphate decarboxylase in Arm37. This ATMT system established for Arm37 provides an efficient genetic tool for exploring the Arm37 genes that are involved in the unique interaction between the Armillaria fungi and fully mycoheterotrophic plant G. elata.

Influence of rhizospheric symbiotic microorganisms on the behavioural effects of antimony in soil-plant system: Insights from a proteomic perspective

Antimony (Sb) pollution in soil-rice systems can affect human health by enriching of food chains. Currently, the mechanism of the negative role underlying microorganisms in plant responses to Sb stress remains clear. The results of this study showed that the presence of arbuscular mycorrhizal (AM) fungi, a common symbiotic microorganism in rhizosphere soil, significantly enhanced Sb uptake by upland rice and inhibited its growth. Furthermore, we explained the reasons for the adverse effects of AM fungi mediation on upland rice growth under Sb stress from a molecular perspective. The results also showed that AM fungi affect the biological processes of the response of upland rice to oxidative stress and the functions of its antioxidant active molecules throughout the vegetative growth phase of upland rice, and that the phenylpropanoid biosynthesis pathway is significantly downregulated. At the same time, phenylalanine/tyrosine ammonia-lyase (PTAL) in the pathway was significantly expressed in the middle and late stages of vegetative growth of upland rice. Therefore, PTAL can act as a potential reference protein to investigate the response of upland rice to Sb stress mediated by AM fungi. These findings enrich our understanding of the impact of Sb pollution on soil-plant systems in real soil environments.

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.

Different roles of the phytohormone gibberellin in the wide-spread arbuscular mycorrhiza and in orchid mycorrhiza

Gibberellin (GA) is a classical plant hormone that regulates many physiological processes, such as plant growth, development, and environmental responses. GA inhibits arbuscular mycorrhizal (AM) symbiosis, the most ancient and widespread type of mycorrhizal symbiosis. Knowledge about mycorrhizal symbioses at the molecular level has been obtained mainly in model plants such as legumes and rice. In contrast, molecular mechanisms in non-model plants are still unclear. Recent studies have revealed the novel roles of GA in mycorrhizal symbioses: its positive effect in Paris-type AM symbiosis in Eustoma grandiflorum and its negative effect on both seed germination and mycorrhizal symbiosis in orchids. This review focuses on the recent data on GA function in AM and orchid mycorrhizal symbioses.

Mycorrhizal status regulates plant phenological mismatch caused by warming

Mycorrhiza is an important functional feature of plants, which plays a vital role in regulating plant phenology in response to environmental changes. However, the effect of mycorrhiza on plant phenological asymmetry in response to climate changes is still rarely reported. Based on a global database of mycorrhizal statuses (obligately mycorrhizal, OM and facultatively mycorrhizal, FM) and phenology, we demonstrated that mycorrhizas reduce the phenological mismatches between above- and below-ground plant responses to climate warming under OM status. The mismatch of above- and below-ground growing season length of FM plants to warming was as high as 10.65 days, 9.1925 days and 12.36 days in total, herbaceous and woody plants, respectively. The mismatch of growing season length of OM plants was only 2.12 days, -0.61 days and 7.64 days among plant groups, which was much lower than that of FM plants. Correlation analysis indicated that OM plants stabilized plant phenology by regulating the relationship between the start of the growing season and the length of the growing season. Path analysis found that herbaceous plants and woody plants reduced phenological mismatches by stabilizing below-ground and above-ground phenology, respectively. In exploring the effects of mycorrhizal status on early- or late-season phenophases, we found that different mycorrhizal statuses affected the response of early- or late-season phenophase to warming. OM promoted the advance of early-season phenophase, and FM promoted the delay of late-season phenophase among different plant groups. In different regions, OM and FM promoted the advance of early-season phenophase in temperate and boreal regions, respectively. Our results indicate that mycorrhizal status mediates plant phenological response to warming, so the potential effects of mycorrhizal status should be considered when studying plant phenology changes.

Genetic and functional traits limit the success of colonisation by arbuscular mycorrhizal fungi in a tomato wild relative

To understand whether domestication had an impact on susceptibility and responsiveness to arbuscular mycorrhizal fungi (AMF) in tomato (Solanum lycopersicum), we investigated two tomato cultivars ("M82" and "Moneymaker") and a panel of wild relatives including S. neorickii, S. habrochaites and S. pennellii encompassing the whole Lycopersicon clade. Most genotypes revealed good AM colonisation levels when inoculated with the AMF Funneliformis mosseae. By contrast, both S. pennellii accessions analysed showed a very low colonisation, but with normal arbuscule morphology, and a negative response in terms of root and shoot biomass. This behaviour was independent of fungal identity and environmental conditions. Genomic and transcriptomic analyses revealed in S. pennellii the lack of genes identified within QTLs for AM colonisation, a limited transcriptional reprogramming upon mycorrhization and a differential regulation of strigolactones and AM-related genes compared to tomato. Donor plants experiments indicated that the AMF could represent a cost for S. pennellii: F. mosseae could extensively colonise the root only when it was part of a mycorrhizal network, but a higher mycorrhization led to a higher inhibition of plant growth. These results suggest that genetics and functional traits of S. pennellii are responsible for the limited extent of AMF colonisation.

Soil Physical Properties Affect Herbivory of Lampronadata cristata in a Cork Oak Forest

Studies have reported the important role of soil properties in regulating insect herbivory under controlled conditions or at relatively large scales. However, whether fine-scale variation of soil properties affects insect herbivory under natural conditions in forests is still unclear. We selected a ca. 300 ha Quercus variabilis forest area where the leaf damage was mainly caused by Lampronadata cristata (Lepidoptera: Notodontidae) and set 200 10 × 10 m plots within the area. We examined insect herbivory (percent leaf area damaged) on Q. variabilis and correlated it to soil properties and tree characteristics. Insect herbivory decreased with soil sand percentage and bulk density and increased with DBH and tree height. Effects of soil sand percentage and bulk density on insect herbivory were partly mediated by DBH and tree height. Our results indicated that soil physical properties may have significant effects on insect herbivory by directly influencing insect herbivores that need to complete their life cycle in the soil, or by indirectly affecting insect herbivores through influencing DBH and tree height which reflects the total leaf biomass available to the insect herbivore. This study may help to understand the complex relationship between soil and plant-insect interactions in forest ecosystems.

Integration of fungal transcriptomics and metabolomics provides insights into the early interaction between the ORM fungus Tulasnella sp. and the orchid Serapias vomeracea seeds

In nature, germination of orchid seeds and early plant development rely on a symbiotic association with orchid mycorrhizal (ORM) fungi. These fungi provide the host with the necessary nutrients and facilitate the transition from embryos to protocorms. Despite recent advances in omics technologies, our understanding of this symbiosis remains limited, particularly during the initial stages of the interaction. To address this gap, we employed transcriptomics and metabolomics to investigate the early responses occurring in the mycorrhizal fungus Tulasnella sp. isolate SV6 when co-cultivated with orchid seeds of Serapias vomeracea. The integration of data from gene expression and metabolite profiling revealed the activation of some fungal signalling pathways before the establishment of the symbiosis. Prior to seed contact, an indole-related metabolite was produced by the fungus, and significant changes in the fungal lipid profile occurred throughout the symbiotic process. Additionally, the expression of plant cell wall-degrading enzymes (PCWDEs) was observed during the pre-symbiotic stage, as the fungus approached the seeds, along with changes in amino acid metabolism. Thus, the dual-omics approach employed in this study yielded novel insights into the symbiotic relationship between orchids and ORM fungi and suggest that the ORM fungus responds to the presence of the orchid seeds prior to contact.

The physiology of plants in the context of space exploration

The stress that the space environment can induce on plant physiology is of both abiotic and biotic nature. The abiotic space environment is characterized by ionizing radiation and altered gravity, geomagnetic field (GMF), pressure, and light conditions. Biotic interactions include both pathogenic and beneficial interactions. Here, we provide an overall picture of the effects of abiotic and biotic space-related factors on plant physiology. The knowledge required for the success of future space missions will lead to a better understanding of fundamental aspects of plant physiological responses, thus providing useful tools for plant breeding and agricultural practices on Earth.

Cenococcum geophilum impedes cadmium toxicity in Pinus massoniana by modulating nitrogen metabolism

Nitrogen (N) is of great significance to the absorption, distribution and detoxification of cadmium (Cd). Ectomycorrhizal fungi (EMF) are able to affect the key processes of plant N uptake to resist Cd stress, while the mechanism is still unclear. Therefore, we explored potential strategies of Cenococcum geophilum (C. geophilum) symbiosis to alleviate Cd stress in Pinus massoniana (P. massoniana) from the perspective of plant N metabolism and soil N transformation. The results showed that inoculation of C. geophilum significantly increased the activities of NR, NiR and GS in the shoots and roots of P. massoniana, thereby promoting the assimilation of NO3- and NH4+ into amino acids. Moreover, C. geophilum promoted soil urease and protease activities, but decreased soil NH4+ content, indicating that C. geophilum might increase plant uptake of soil inorganic N. qRT-PCR results showed that C3 symbiosis significantly up-regulated the expression of genes encoding functions involved in NH4+ uptake (AMT3;1), NO3- uptake (NRT2.1, NRT2.4, NRT2.9), as well as Cd resistance (ABCC1 and ABCC2), meanwhile down-regulated the expression of NRT7.3, Cd transporter genes (HMA2 and NRAMP3) in the roots of P. massoniana seedlings. These results demonstrated that C. geophilum was able to alleviate Cd stress by increasing the absorption and assimilation of inorganic N in plants and inhibiting the transport of Cd from roots to shoots, which provided new insights into how EMF improved host resistance to abiotic stress.

Arbuscular mycorrhizal fungal inoculum and N2-fixing plants in ecological reclamation of arid mining areas: nutrient limitation of the moss biocrust microbiome

Ecoenzymatic stoichiometry can reflect the ability of soil microorganisms to acquire energy and nutrients and to determine their response to environmental stresses. However, the drivers of metabolic limitation of the moss biocrust microbiome during the ecological restoration of coal mining areas are poorly understood. Therefore, in this study, enzymatic stoichiometry modeling and high-throughput sequencing were used to simultaneously determine moss biocrust microbial metabolic limitation and its relationship with moss biocrust nutrients and arbuscular mycorrhizal fungal (AMF) diversity in five arid and semi-arid revegetation types (Hippophae rhamnoides, Amorpha fruticosa, Cerasus humilis, Cerasus szechuanica, and Xanthoceras sorbifolium) and two microbial treatments (AMF-inoculated and uninoculated). The activities of moss biocrust carbon (C)-, nitrogen (N)-, and phosphorus (P)-acquiring enzymes and organic carbon fractions in the AMF-inoculated treatment were significantly higher than those in the uninoculated control. Moss biocrust microbial community C and P limitations were observed in the five revegetation types, with lower limitation in general in the AMF-inoculated treatment. Dinitrogen-fixing plants (Amorpha fruticosa and Hippophae rhamnoides) significantly mitigated moss biocrust microbiome C and P limitation, especially in the AMF-inoculated treatment. Furthermore, partial least squares path modeling (PLS-PM) shows that moss biocrust organic carbon fractions (- 0.73 and - 0.81 of the total effects, respectively) and AMF diversity (- 0.73 and - 0.81 of the total effects) had negative effect on microbial C and P limitation, suggesting that more efficient active nutrients and AMF diversity are important factors alleviating limitation of moss biocrust microbial metabolism. This indicates that moss biocrust microbial communities under N2-fixing species with AMF inoculation were more stable under environmental stress; thus, AMF inoculation and/or N2-fixing plants may be recommended as preferred options for the ecological restoration of arid mining areas.

Strigolactones: A promising tool for nutrient acquisition through arbuscular mycorrhizal fungi symbiosis and abiotic stress tolerance

Strigolactones (SLs) constitute essential phytohormones that control pathogen defense, resilience to phosphate deficiency and abiotic stresses. Furthermore, SLs are released into the soil by roots, especially in conditions in which there is inadequate phosphate or nitrogen available. SLs have the aptitude to stimulate the root parasite plants and symbiotic cooperation with arbuscular mycorrhizal (AM) fungi in rhizosphere. The use of mineral resources, especially phosphorus (P), by host plants is accelerated by AMF, which also improves plant growth and resilience to a series of biotic and abiotic stresses. Thus, these SL treatments that promote rhizobial symbiosis are substitutes for artificial fertilizers and other chemicals, supporting ecologically friendly farming practices. Moreover, SLs have become a fascinating target for abiotic stress adaptation in plants, with an array of uses in sustainable agriculture. In this review, the biological activity has been summarized that SLs as a signaling hormone for AMF symbiosis, nutrient acquisition, and abiotic stress tolerance through interaction with other hormones. Furthermore, the processes behind the alterations in the microbial population caused by SL are clarified, emphasizing the interplay with other signaling mechanisms. This review covers the latest developments in SL studies as well as the properties of SLs on microbial populations, plant hormone transductions, interactions and abiotic stress tolerance.

Root Endophytic Microorganisms Contribute to the Attribute of Full-Year Shooting in Woody Bamboo Cephalostachyum pingbianense

Cephalostachyum pingbianense (Hsueh & Y.M. Yang ex Yi et al.) D.Z. Li & H.Q. Yang is unique among bamboo species for its ability to produce bamboo shoots in all seasons under natural conditions. Apart from the physiological mechanism, information regarding the effects of endophytic microorganisms on this full-year shooting characteristic is limited. We hypothesize that root endophytic microorganisms will have a positive impact on the full-year bamboo shooting characteristic of C. pingbianense by increasing the availability or supply of nutrients. To identify the seasonal variations in the root endophytic bacterial and fungal communities of C. pingbianense, and to assess their correlation with bamboo shoot productivity, the roots of C. pingbianense were selected as research materials, and the 16S rRNA and ITS rDNA genes of root endophytic microorganisms were sequenced using the Illumina platform. Following this sequencing, raw sequencing reads were processed, and OTUs were annotated. Alpha and beta diversity, microbial composition, and functional predictions were analyzed, with correlations to bamboo shoot numbers assessed. The results showed that seasonal changes significantly affected the community diversity and structure of root endophytic microbes of C. pingbianense. Bacterial communities in root samples from all seasons contained more nitrogen-fixing microorganisms, with members of the Burkholderiales and Rhizobiales predominating. The relative abundances of ectomycorrhizal and arbuscular mycorrhizal fungi in the autumn sample were significantly higher than in other seasons. Correlation analysis revealed that the bamboo shoot productivity was significantly and positively correlated with bacterial functions of nitrogen fixation, arsenate detoxification, and ureolysis, as well as with symbiotrophic fungi, ectomycorrhizal fungi, and arbuscular mycorrhizal fungi. At the genus level, the bacterial genus Herbaspirillum and the fungal genera Russula, unclassified_f_Acaulosporaceae, and unclassified_f_Glomeraceae were found to have a significant positive correlation with bamboo shoot number. Our study provides an ecological perspective for understanding the highly productive attribute of C. pingbianense and offers new insights into the forest management of woody bamboos.

A gap in the recognition of two mycorrhizal factors: new insights into two LysM-type mycorrhizal receptors

Arbuscular mycorrhizal (AM) fungi are crucial components of the plant microbiota and can form symbioses with 72% of land plants. Researchers have long known that AM symbioses have dramatic effects on plant performance and also provide multiple ecological services in terrestrial environments. The successful establishment of AM symbioses relies on the host plant recognition of the diffusible mycorrhizal (Myc) factors, lipo-chitooligosaccharides (LCOs) and chitooligosaccharides (COs). Among them, the short-chain COs such as CO4/5 secreted by AM fungi are the major Myc factors in COs. In this review, we summarize current advances, develop the concept of mycorrhizal biceptor complex (double receptor complexes for Myc-LCOs and CO4/5 in the same plant), and provide a perspective on the future development of mycorrhizal receptors. First, we focus on the distinct perception of two Myc factors by different host plant species, highlighting the essential role of Lysin-Motif (LysM)-type mycorrhizal receptors in perceiving them. Second, we propose the underlying molecular mechanisms by which LysM-type mycorrhizal receptors in various plants recognize both the Myc-LCOs and -COs. Finally, we explore future prospects for studies on the biceptor complex (Myc-LCO and -CO receptors) in dicots to facilitate the utilization of them in cereal crops (particularly in modern cultivated rice). In conclusion, our understanding of the precise perception processes during host plant interacting with AM fungi, where LysM-type mycorrhizal receptors act as recruiters, provides the tools to design biotechnological applications addressing agricultural challenges.

Applicability of metabolomics to improve sustainable grapevine production

Metabolites represent the end product of gene expression, protein interaction and other regulatory mechanisms. The metabolome reflects a biological system's response to genetic and environmental changes, providing a more accurate description of plants' phenotype than the transcriptome or the proteome. Grapevine (Vitis vinifera L.), established for the production of wine grapes, table grapes, and raisins, holds immense agronomical and economic significance not only in the Mediterranean region but worldwide. As all plants, grapevines face the adverse impact of biotic and abiotic stresses that negatively affect multiple stages of grape and wine industry, including plant and berry development pre- and post-harvest, fresh grapes processing and consequently wine quality. In the present review we highlight the applicability of metabolome analysis in the understanding of the mechanisms involved in grapevine response and acclimatization upon the main biotic and abiotic constrains. The metabolome of induced morphogenic processes such as adventitious rooting and somatic embryogenesis is also explored, as it adds knowledge on the physiological and molecular phenomena occurring in the explants used, and on the successfully propagation of grapevines with desired traits. Finally, the microbiome-induced metabolites in grapevine are discussed in view of beneficial applications derived from the plant symbioses.

SlDELLA interacts with SlPIF4 to regulate arbuscular mycorrhizal symbiosis and phosphate uptake in tomato

Arbuscular mycorrhizal symbiosis (AMS), a complex and delicate process, is precisely regulated by a multitude of transcription factors. PHYTOCHROME-INTERACTING FACTORS (PIFs) are critical in plant growth and stress responses. However, the involvement of PIFs in AMS and the molecular mechanisms underlying their regulator functions have not been well elucidated. Here, we show that SlPIF4 negatively regulates the arbuscular mycorrhizal fungi (AMF) colonization and AMS-induced phosphate uptake in tomato. Protein-protein interaction studies suggest that SlDELLA interacts with SlPIF4, reducing its protein stability and inhibiting its transcriptional activity towards downstream target genes. This interaction promotes the accumulation of strigolactones (SLs), facilitating AMS development and phosphate uptake. As a transcription factor, SlPIF4 directly transcriptionally regulates genes involved in SLs biosynthesis, including SlCCD7, SlCDD8, and SlMAX1, as well as the AMS-specific phosphate transporter genes PT4 and PT5. Collectively, our findings uncover a molecular mechanism by which the SlDELLA-SlPIF4 module regulates AMS and phosphate uptake in tomato. We clarify a molecular basis for how SlPIF4 interacts with SLs to regulate the AMS and propose a potential strategy to improve phosphate utilization efficiency by targeting the AMS-specific phosphate transporter genes PTs.

Identification and full-length genome characterization of a novel mitovirus hosted by the truffle species Tuber rufum

Studying the diversity of viruses found in uncultivated fungi, including those forming mycorrhizal relationships, is essential. It's equally important to explore viral communities in fungi that cause plant diseases or are economically significant. This dual approach helps us grasp the full scope of mycovirus diversity and evolution. Mycorrhizal fungi, in particular, host a wide range of viruses, shedding light on viral diversity and evolution. In this study, we present the discovery and complete genome characterization of a novel mitovirus infecting the hypogeous mycorrhizal fungus Tuber rufum. This virus, denominated "Tuber rufum mitovirus 1" (TrMV1) has a genome size of 2864 nucleotides with a G + C content of 37.53%. It contains a single open reading frame (ORF) responsible for encoding RNA dependent RNA polymerase (RdRp). Comparative analysis using BLASTp reveals that the protein encoded by TrMV1 shares significant sequence similarities with those found in the Triamitovirus genus. Specifically, TrMV1 shows the closest resemblance (43.35% identity) to Sopawar virus, a mitovirus previously detected in soil environments through metatranscriptomic analyses. Phylogenetic examination categorizes TrMV1 as a member of the Triamitovirus genus within the Mitoviridae family. This finding marks the first identification of a mitovirus within the hypogeous mycorrhizal fungus Tuber rufum. The discovery of TrMV1 expands our knowledge of Mitoviridae family diversity and evolution, contributing to the growing repository of mycovirus sequences.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-024-00887-6.

Plant Immunity Modulation in Arbuscular Mycorrhizal Symbiosis and Its Impact on Pathogens and Pests

Arbuscular mycorrhizal (AM) symbiosis is the oldest and most widespread mutualistic association on Earth and involves plants and soil fungi belonging to Glomeromycotina. A complex molecular, cellular, and genetic developmental program enables partner recognition, fungal accommodation in plant tissues, and activation of symbiotic functions such as transfer of phosphorus in exchange for carbohydrates and lipids. AM fungi, as ancient obligate biotrophs, have evolved strategies to circumvent plant defense responses to guarantee an intimate and long-lasting mutualism. They are among those root-associated microorganisms able to boost plants' ability to cope with biotic stresses leading to mycorrhiza-induced resistance (MIR), which can be effective across diverse hosts and against different attackers. Here, we examine the molecular mechanisms underlying the modulation of plant immunity during colonization by AM fungi and at the onset and display of MIR against belowground and aboveground pests and pathogens. Understanding the MIR efficiency spectrum and its regulation is of great importance to optimizing the biotechnological application of these beneficial microbes for sustainable crop protection.

Mycorrhizal inoculation and fertilizer microdosing interactions in pearl millet (Pennisetum glaucum) under greenhouse conditions

Introduction

Soil fertility is a major constraint to agricultural development in the Sahel region of Africa. One alternative to reducing the use of mineral fertilizers is to partially replace them with microbes that promote nutrition and growth, such as arbuscular mycorrhizal fungi (AMF). Mineral fertilizer microdosing is a technique developed to enhance fertilizer efficiency and encourage smallholder farmers to adopt higher mineral fertilizer applications.

Methods

A pot experiment was set up to study the effects of AMF inoculation on the mineral nutrition of pearl millet under mineral fertilizer microdosing conditions. The experimental setup followed a randomized complete block design with five replicates. The treatments tested on millet were an absolute control and eight microdoses derived from the combination of three doses of 15- 10-10 [nitrogen, phosphorus, and potassium (NPK)] mineral fertilizer (2 g, 3 g, and 5 g per pot), three doses of urea (1 g, 2 g, and 3 g per pot), and three doses of organic manure (OM) (200 g, 400 g, and 600 g), combined with and without AMF (Rhizophagus irregularis and Rhizophagus aggregatum). The parameters studied were growth, root colonization by AMF, and mineral nutrition. Plant height, stem diameter, root dry biomass, and percentage of root mycorrhization were measured.

Results and discussion

The results revealed a significant effect of the fertilizers on the growth of pearl millet compared to the control. AMF and OM treatments resulted in the highest biomass production. AMF combined with microdoses of NPK improved N and calcium (Ca) concentrations, while their combination with organic matter mainly improved the K concentration. Combining AMF with microdosed NPK and compost enhanced zinc (Zn) and nickel (Ni) concentrations. Root colonization varied from 0.55 to 56.4%. This investigation highlights the positive effects of AMF inoculation on nutrient uptake efficiency when combined with microdosing fertilization.

Arbuscular mycorrhizal fungi enhance drought resistance in Bombax ceiba by regulating SOD family genes

The physiological activity facilitated by arbuscular mycorrhizal fungi (AMF) contributes to plants' ability to tolerate drought. Nevertheless, it is unclear if AMF colonization affects the expression of genes in the host plant that encode antioxidant enzymes in the superoxide dismutase (SOD) family, which help alleviate drought stress in plants. Here, we conducted a pot trial to determine whether colonization by the AMF Rhizophagus irregularis improves drought resistance in Bombax ceiba. We comprehensively analyzed the SOD gene family and evaluated genome-wide expression patterns of SODs and SOD activity in AMF-colonized and non-mycorrhizal plants under simulated drought. We identified a total of 13 SODs in the genome of B. ceiba, including three FeSODs (BcFSDs), three MnSODs (BcMSDs), and seven Cu/ZnSODs (BcCSDs). Phylogenetic analysis based on binding domain revealed that SOD genes from B. ceiba and various other plant species can be divided into three separate groups, showing significant bootstrap values. Our examination of gene composition and patterns suggests that most BcSOD genes in these three subgroups are significantly conserved. Additionally, it was noted that hormones and stress-responsive cis-regulatory elements were found in all BcSOD promoters. Expression profiling by qRT-PCR demonstrated that AMF increased relative expression levels of Cu/Zn-SODs in both roots and shoots under drought stress, except for BcCSD3 in roots. Furthermore, AMF colonization increased the relative expression of BcMSD1a and BcMSD1b in roots, augmenting SOD activities and increasing ROS scavenging during drought. In general, this work offers molecular evidence in support of the beneficial effect of AMF colonization on drought tolerance in B. ceiba. It also elucidates the expression patterns of SOD genes, which will support efforts to optimize mycorrhizal seedling cultivation under stressful conditions.

Plant species diversity and functional diversity relations in the degradation process of desert steppe in an arid area of northwest China

Species and functional diversity play a major role in the stability and sustainability of grassland ecosystems. However, changes in species and functional diversity during grassland degradation in arid areas as well as the underlying mechanisms remain unclear. In this study, we surveyed the vegetation and soil properties of arid regions across a degradation gradient to explore the shifts in species and functional diversity in plant communities, their relationships and key determinants during desert steppe degradation. Our results found significant variability in species diversity and functional diversity across degradation stages. Species diversity (Shannon-Wiener index (H), and Pielou index) and functional diversity (functional evenness (FEve) index, and Rao's quadratic entropy (RaoQ) index) tended to increase initially and then decrease with increasing grassland degradation. The Patrick index, Simpson index, functional richness (FRic) index, functional divergence (FDiv) index, and functional dispersion (FDis) index declined as grassland degradation increased. The relationships between species diversity and functional diversity indices at different stages of degradation in the desert steppe were inconsistent. From no to heavy degradation grasslands, the correlation between species diversity and functional diversity gradually weakened. Specifically, there was a significant correlation between Patrick (R) and FRic indices (R2 > 0.7) on both non-degraded and light degraded grasslands, but there was no significant correlation between R and FRic indices in moderately and heavily degraded grasslands (R2 < 0.7), and R2 gradually decreased. Redundancy analysis and partial least squares path modeling showed that grassland degradation has a significant direct effect on the species diversity and functional diversity. In addition grassland degradation has direct and indirect effects on the species diversity through soil available nitrogen, organic matter and total nitrogen. Functional diversity is directly or indirectly affected by species diversity, soil available nitrogen, organic matter and total nitrogen, soil moisture content, soil bulk density, and pH value. In summary, the relationship between species and functional diversity indices gradually weakened from areas with no degradation to heavy degradation in arid desert grasslands. Our study reveals the patterns and relationships between species diversity and functional diversity throughout the process of grassland degradation, demonstrating a gradual decrease in ecosystem stability and sustainability as degradation advances. Our results have significant implications for the restoration of grassland degradation and the management of ecosystem services in arid steppe regions.

Desert plants, arbuscular mycorrhizal fungi and associated bacteria: Exploring the diversity and role of symbiosis under drought

Desert plants, such as Agave tequilana, A. salmiana and Myrtillocactus geometrizans, can survive harsh environmental conditions partly due to their symbiotic relationships with microorganisms, including arbuscular mycorrhizal fungi (AMF). Interestingly, some of these fungi also harbour endosymbiotic bacteria. Our research focused on investigating the diversity of these AMFs and their associated bacteria in these plants growing in arid soil. We found that agaves have a threefold higher AMF colonization than M. geometrizans. Metabarcoding techniques revealed that the composition of AMF communities was primarily influenced by the plant host, while the bacterial communities were more affected by the specific plant compartment or niche they inhabited. We identified both known and novel endofungal bacterial taxa, including Burkholderiales, and confirmed their presence within AMF spores using multiphoton microscopy. Our study also explored the effects of drought on the symbiosis between A. tequilana and AMF. We discovered that the severity of drought conditions could modulate the strength of this symbiosis and its outcomes for the plant holobiont. Severe drought conditions prevented the formation of this symbiosis, while moderate drought conditions promoted it, thereby conferring drought tolerance in A. tequilana. This research sheds light on the diversity of AMF and associated bacteria in Crassulacean Acid Metabolism (CAM) plants and underscores the crucial role of drought as a factor modulating the symbiosis between A. tequilana and AMF. Further research is needed to understand the role of endofungal bacteria in this response.