Biodiversity of arbuscular mycorrhizal fungi and ecosystem function

Co-inoculation of Trichoderma and tea root-associated bacteria enhance flavonoid production and abundance of mycorrhizal colonization in tea (Camellia sinensis)

Tea is one of the most popular nonalcoholic beverages, that contains several medicinally important flavonoids. Due to seasonal variation and various environmental stresses, the overall consistency of tea flavonoids affects the tea quality. To combat stress, plants stimulate symbiotic relationships with root-associated beneficial microbiomes that sustain nutrient allocation. Therefore, a study has been designed to understand the role of the tea root microbiome in sustaining tea leaf flavonoid production. To enumerate the microbiome, tea root and rhizoplane soil were collected from 3 years of healthy plants from Jalpaiguri district, West Bengal, India. A culture-independent approach was adopted to identify root and rhizosphere microbial diversity (BioSample: SAMN31404869; SRA: SRS15503027 [rhizosphere soil metagenome] BioSample: SAMN31404868;SRA:SRS15503030 [root metagenome]. In addition to diverse microbes, four mycorrhiza fungi, i.e., Glomus intraradices, Glomus irregulare, Paraglomus occultum and Scutellospora heterogama were predominant in collected root samples. A culture-dependent approach was also adopted to isolate several plant growth-promoting bacteria [Bacillus sp. D56, Bacillus sp. D42, Bacillus sp. DR15, Rhizobium sp. DR23 (NCBI Accession: OR821747-OR821750)] and one fungal [Trichoderma sp. AM6 (NCBI Accession:OM915414)] strain. A pot experiment was designed to assess the impact of that isolated microbiome on tea seedlings. After six months of microbiome inoculation, tea plants' physicochemical and transcriptional parameters were evaluated. The results confer that the microbiome-treated treatments [(T1-without any microbial inoculation; NCBI Accession: SAMN33591153), Trichoderma sp. AM6 (T2; NCBI Accession: SAMN33591155) and Trichoderma sp. AM6 +VAM containing tea root+synthetic microbial consortia (T5; NCBI Accession: SAMN33591154)] could enhance the total flavonoid content in tea seedlings by upregulating certain transcripts associated with the flavonoid biosynthesis pathway of tea.

Opposite effects of N on warming-induced changes in bacterial and fungal diversity

The diversity of bacteria and fungi is linked to distinct ecosystem functions, and divergent responses to global changes in these two kingdoms affect the relative contributions of the kingdoms to the soil carbon and nutrient cycles. Climate warming and nitrogen (N) enrichment, which are projected to increase concurrently through modelling efforts, are considered the main drivers of biodiversity loss. However, it is unclear how bacterial and fungal diversity respond differently to the simultaneous occurrence of climate warming and nitrogen enrichment, and the underlying mechanisms involved remain unknown. Using a 9-yr warming and N enrichment experiment in an alpine permafrost area of the Tibetan Plateau, we demonstrated the contrasting response of bacterial and fungal diversity to combined warming and N enrichment, showing a reduction in bacterial richness (8.8%) and an increase in fungal diversity (33.6%). Furthermore, the negative effects of warming on fungal richness were reversed by N enrichment, and the negative effects of nitrogen enrichment on bacteria were amplified by warming. Our results also demonstrated that both biotic interactions, such as bacterial-fungal antagonism, and abiotic factors, primarily the soil C/N ratio and pH, play crucial roles in shaping microbial biodiversity. Our findings suggest that fungal diversity is expected to greatly increase in a warmer and more nitrogen-enriched world, potentially leading to the enhancement of ecosystem functions driven by fungi.

Impact of long-term loquat cultivation on rhizosphere soil characteristics and AMF community structure: implications for fertilizer management

The role of arbuscular mycorrhizal fungi (AMF) in assisting the growth of different fruit tree species is well-established, yet the impact of loquat cultivation under long-term human management on the rhizosphere soil characteristics and AMF community structure remains unresolved. To address this knowledge gap, we collected roots and soil samples from 20-year-old loquat in a loquat germplasm resources nursery with consistent water and nutrient conditions including one wild species (YS), three pure species (GXQH, MHH, DWX), and four hybrid species (ZJ90, JT, JTH, ZU7). Our analysis revealed that AMF colonization rates ranged from 40.57% to 65.54%, with Glomus (30.72%) and Paraglomus (29.46%) being the dominant genera across all varieties. Paraglomus dominated in pure species, while Glomus prevailed in wild species. YS exhibited the highest AMF richness than cultivars. Significant variations in soil nutrients and enzyme activities in the rhizosphere among different varieties. Total nitrogen (TN) and total potassium (TK) were significantly negatively correlated with relative abundance of AMF genera, suggesting that nitrogen and potassium may reduce AMF abundance. Mantel test showed that total carbon (TC) and soil organic matter (SOM) were the key factors influencing AMF community composition (P<0.01). These nutrients were positively correlated with dominant AMF genus (0.06, R2 = 0.05) but negatively with rare genus such as Ambispora (-0.08, R2 = 0.24). Overall, these findings confirmed that plant varieties or genotypes drive changes in AMF communities and further demonstrated that long-term nutrient enrichment reduces the diversity of loquat rhizosphere AMF communities. These results support the use of AMF biofertilizers and reducing fertilizer application.

Capacity to form common mycorrhizal networks reduces the positive impact of clonal integration between plants

Both clonal plant capabilities for physiological integration and common mycorrhizal networks (CMNs) formed by arbuscular mycorrhizal fungi (AMF) can influence the distribution of nutrients and growth among interconnected individuals. Using a microcosm model system, we aimed to disentangle how CMNs interact with clonal integration to influence plant growth and development. We grew Sphagneticola trilobata clones with isolated root systems in individual, adjacent containers while preventing, disrupting, or allowing clonal integration aboveground via spacers and belowground CMNs to form. We assessed multiple metrics of plant development (e.g., growth, specific leaf area, soluble sugar content), 15N transfer from donor (mother) to receiver (daughter) plants, and variation in AMF communities. We show that spacer formation between ramets and the capacity to form CMNs promoted and inhibited the growth of smaller daughter plants, respectively. In contrast to the independent effects of CMNs and spacers, CMNs, in combination with spacers, significantly weakened the promotion of daughter plants by clonal integration. AMF species richness was also negatively correlated with overall plant growth. Our results demonstrate that two common modes of plant interconnection interact in non-additive ways to affect clonal plant integration and growth. These findings, based on Sphagneticola trilobata, question the underlying assumptions of the positive effects of both AMF CMNs and species richness in comparison to direct plant interconnections.

The AMSlide for noninvasive time-lapse imaging of arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal (AM) symbiosis, the nutritional partnership between AM fungi and most plant species, is globally ubiquitous and of great ecological and agricultural importance. Studying the processes of AM symbiosis is confounded by its highly spatiotemporally dynamic nature. While microscopy methods exist to probe the spatial side of this plant-fungal interaction, the temporal side remains more challenging, as reliable deep-tissue time-lapse imaging requires both symbiotic partners to remain undisturbed over prolonged time periods. Here, we introduce the AMSlide: a noninvasive, high-resolution, live-imaging system optimised for AM symbiosis research. We demonstrate the AMSlide's applications in confocal microscopy of mycorrhizal roots, from whole colonisation zones to subcellular structures, over timeframes from minutes to weeks. The AMSlide's versatility for different microscope set-ups, imaging techniques, and plant and fungal species is also outlined. It is hoped that the AMSlide will be applied in future research to fill in the temporal blanks in our understanding of AM symbiosis, as well as broader root and rhizosphere processes.

Pulling nutrients from Mo-polluted soil by arbuscular mycorrhizal fungi extraradical mycelia is quenching thirsty with poison

As an extension of plant root system, arbuscular mycorrhizal fungi (AMF) extraradical mycelium (ERM) can break the limitation of rhizosphere and play an important role in plant nutrient acquisition. However, it remains unclear whether ERM is smart enough to pick out nutrients while avoiding poison, or is unable to pick out nutrients and have to absorb poisons together. Therefore, the present study employed a compartment device to separate the mycelia from roots, aiming to explore the nutrient absorption pathways of mycelia in molybdenum (Mo) pollution soil after inoculation with AMF in maize and vetch plants. The results showed that mycelia increased the absorption of nutrients in maize and vetch plants, while reducing the biomass of the plants. In addition, mycelia increased the Mo concentration of plants. The highest contribution of mycelia to Mo concentration in plants reached 114.06%. For different plants, maize tends to immobilize Mo in roots, while vetch tend to transport Mo to shoots under Mo stress. Additionally, variance partitioning analysis proved that the contribution of nutrients to biomass was the largest, with the interpretation rates reaching 65.09% and 47.26% in maize and vetch plants, respectively. The decrease in plant biomass was due to the toxic effects of Mo. Furthermore, the negative effect of the interaction of Mo, mycelia and nutrients on biomass further proved that the nutrients absorption of mycelia under Mo-polluted soil may be carried out in the way of quenching thirsty with poison.

Terroir and farming practices drive arbuscular mycorrhizal fungal communities in French vineyards

Background

Nature-based management of vineyards is at the heart of a sustainable development for the next decades. Although much is known about grapevine benefits from Arbuscular Mycorrhizal Fungi (AMF), little is known about the influence of vineyard terroir and farming practices on AMF communities.

Methods

We examined the relative effect of wine terroir and agricultural practices (organic, conversion, and conventional) on AMF abundance and diversity across 75 vineyards distributed over 14 wine terroirs in 6 winegrowing regions in France. We estimate AMF abundance by measuring spore density and root mycorrhization rates, and characterize AMF communities composition using metabarcoding by sampling both root and spore compartments for each vineyard.

Results

Organic farming slightly increases AMF abundance (spore density and mycorrhization rate). Vineyards under conversion and using organic practices display a higher AMF diversity than conventional ones. Terroirs vary widely in terms of AMF abundance and diversity, with the median of OTUs count per sample ranging from 9 (Côte des Blancs) to 35 (Gigondas). The composition of AMF communities is structured mainly by terroir and in a lesser extent by practice. The effect of terroir on AMF communities is partially explained by distance decay and soil properties, but the majority of variation is still explained only by the terroir identity. Organic practices improve both abundance and diversity of AMF in vineyards, possibly leading to more productivity and resilience of grapevines.

Conclusion

This large-scale study highlights the importance of terroir in our understanding of vineyard microbiome and paves the way to incorporation of AMF in microbial terroir studies and applications.

Long-term diverse straw management influences arbuscular mycorrhizal fungal community structure and plant growth in a rice-rotated wheat cropping system

Communities of arbuscular mycorrhizal fungi (AMF) in soil are influenced by various agricultural managements, which in turn affects crop productivity. However, the impacts of straw returning on AMF communities are sparsely understood. Here, a 7-year field experiment including three sets of straw managements - returning methods (CK: no-tillage without straw; RT-SR: rotary tillage with straw; DB-SR: ditch-buried tillage with straw), burial amount, burial depth - were applied to evaluate the influences of straw managements on AMF composition. With full amounts of straw return, AMF diversity was similar between DB-SR and CK at a depth of 20 cm, whilst it was 13% higher than that under RT-SR. This could be explained by the increased rhizodeposition under DB-SR may counterbalance the negative effect of tillage under RT-SR on AMF hyphal growth. DB-SR changed AMF composition and enhanced the abundance of Glomeraceae, as well as the amount of glomalin-related protein, as a consequence increased plant P uptake by 68% than RT-SR. DB-SR remained stable plant P uptake and wheat biomass at a burial depth of 40 cm, but it decreased AMF diversity and the abundance of Glomeraceae as compared to DB-SR at a burial of 20 cm. This indicated DB-SR at a burial depth of 40 cm may be not beneficial to crop growth. Our results suggest that ditch-buried straw return with a depth of 20 cm and full amounts of straws is promising to improve soil health (via regulating AMF community diversity and composition) and promote crop production (via increasing plant P uptake).

Toward harnessing biodiversity-ecosystem function relationships in fungi

Fungi are crucial for terrestrial ecosystems, yet the role of fungal diversity in ecosystem functions remains unclear. We synthesize fungal biodiversity and ecosystem function (BEF) relationships, focusing on plant biomass production, carbon storage, decomposition, and pathogen or parasite resistance. The observed BEF relationships for these ecosystem functions vary in strength and direction, complicating generalizations. Strong positive relationships are generally observed when multiple ecosystem functions are addressed simultaneously. Often, fungal community composition outperforms species richness in predicting ecosystem functions. For more comprehensive fungal BEF research, we recommend studying natural communities, considering the simultaneous functions of a broader array of fungal guilds across spatiotemporal scales, and integrating community assembly concepts into BEF research. For this, we propose a conceptual framework and testable hypotheses.

Interactive effects of leaf pathogens and plant mycorrhizal type on plant diversity-productivity relationships

Diversity-productivity relationships can differ between forests dominated by different mycorrhizal types and be modulated by specialist and generalist pathogens. However, little is known about how these factors interact to modulate biodiversity effects. We addressed this knowledge gap with a 2-year experiment combining the manipulation of plant richness (one, two, four, eight species) and mycorrhizal tree type (arbuscular mycorrhizal [AM] tree-dominated; ecto-mycorrhizal [ECM] tree-dominated) with fungicide application for leaf pathogens (added or control). Biodiversity effects were quantified for community productivity and its two components (shoots and roots). We observed nonlinear diversity-productivity relationships, with the productivity of ECM tree-dominated communities increasing at low to intermediate diversity and declining at the highest species richness. Foliar fungicide application reduced positive complementarity effects and increased productivity in both ECM tree monocultures as well as eight-species mixtures. This finding suggests that the dilution effects of specialized pathogens may dominate at low diversity, while the spillover effects of generalist pathogens may become dominant at high diversity, resulting in unimodal diversity-productivity relationships. In AM tree-dominated communities, aboveground productivity strongly increased in response to leaf pathogen suppression in eight-species mixtures, and the release from leaf pathogens benefited most of the species that were most productive in fungicide-treated monocultures. This agrees with the prediction that spillover effects of generalist pathogens in diverse plant communities could differentially suppress highly productive species due to the trade-off between growth and defense. In addition, positive biodiversity effects on root production were significantly stronger in AM tree- than ECM tree-dominated communities. Our results demonstrate that relationships between plant diversity and productivity can be nonlinear due to the combined effects of specialized and generalized plant-fungal interactions, depend on plant mycorrhizal type, and differ between aboveground and belowground compartments.

Fungal communities in boreal soils are influenced by land use, agricultural soil management, and depth

Land use and agricultural soil management affect soil fungal communities that ultimately influence soil health. Subsoils harbor nutrient reservoir for plants and can play a significant role in plant growth and soil carbon sequestration. Typically, microbial analyses are restricted to topsoil (0-30 cm) leaving subsoil fungal communities underexplored. To address this knowledge gap, we analyzed fungal communities in the vertical profile of four boreal soil treatments: long-term (24 years) organic and conventional crop rotation, meadow, and forest. Internal transcribed spacer (ITS2) amplicon sequencing revealed soil-layer-specific land use or agricultural soil management effects on fungal communities down to the deepest measured soil layer (40-80 cm). Compared to other treatments, higher proportion of symbiotrophs, saprotrophs, and pathotrophs + plant pathogens were found in forest, meadow and crop rotations, respectively. The proportion of arbuscular mycorrhizal fungi was higher in deeper (>20 cm) soil than in topsoil. Forest soil below 20 cm was dominated by fungal functional groups with proposed interactions with plants or other soil biota, whether symbiotrophic or pathotrophic. Ferrous oxide was an important factor shaping fungal communities throughout the vertical profile of meadow and cropping systems. Our results emphasize the importance of including subsoil in microbial community analyses in differently managed soils.

Characteristics of Soil Microbial Community Structure in Different Land Use Types of the Huanghe Alluvial Plain

The Huanghe alluvial plain plays a crucial role in biodiversity conservation. However, its ecosystem has become sensitive and fragile due to long-term human disturbances. Enhancing the resilience of this ecosystem and promoting the sustainable use of land resources are key to addressing its ecological challenges. Soil microbial communities are vital to ecosystem functioning, and land use is a major human factor influencing their structure and diversity. Existing research on the Huanghe alluvial plain primarily focuses on soil physicochemical properties and moisture content, with relatively limited attention given to soil microorganisms. Therefore, this study, using the Wudi Tanyang Forest Farm in the Huanghe alluvial plain as a case study, employs high-throughput metagenomic sequencing to analyze the composition and diversity of soil bacteria, eukaryota, archaea, and virus communities in five different land use types (Tamarix chinensis forest, Fraxinus chinensis forest, farmland, wetland, and grassland). The results indicate that: (1) At the phylum level, the top three bacteria communities were Pseudomonadota, Acidobacteriota, and Actinomycetota; the top three in the eukaryota communities were Ascomycota, Mucoromycota, and Basidiomycotina; the top three in the archaea communities were Nitrososphaerota, Euryarchaeota, and Candidatus Thermoplasmatota; and the virus communities were dominated by Uroviricota; (2) The microbial community structure of the Tamarix chinensis forest and the Fraxinus chinensis forest was similar, and was significantly different from the other three land use types; (3) The land use type had a significant effect on the diversity of the soil microbial communities, with a higher diversity in the wetland and grassland soils; (4) The dominant species of the soil microbial communities under different land use types showed significant differences. This study provides theoretical support for land use optimization and sustainable soil management in the Huanghe alluvial plain region.

Root carbon inputs outweigh litter in shaping grassland soil microbiomes and ecosystem multifunctionality

Global change has the potential to alter soil carbon (C) inputs from above- and below-ground sources, with subsequent influences on soil microbial communities and ecological functions. Using data from a 13-year field experiment in a semi-arid grassland, we investigated the effects of litter manipulations and plant removal on soil microbiomes and ecosystem multifunctionality (EMF). Litter addition did not affect soil microbial α-diversity whereas litter removal reduced bacterial and fungal α-diversity due to decreased C substrate supply and soil moisture. By contrast, plant removal led to larger declines in bacterial and fungal α-diversity, lower microbial network stability and complexity. EMF was enhanced by litter addition but largely reduced by plant removal, primarily attributed to the loss of fungal diversity. Our findings underscore the importance of C inputs in shaping soil microbiomes and highlight the dominant role of plant root-derived C inputs in maintaining ecological functions under global change scenarios.

Protecting plants from pathogens through arbuscular mycorrhiza: Role of fungal diversity

Arbuscular mycorrhizal (AM) fungi play a crucial role in protecting host plants from pathogens. AM fungal taxa show varying abilities to hinder the development of plant pathogens with various underlying mechanisms of action, and plant defense through mycorrhization should be viewed to have a continuum of several possible mechanisms. However, an additive or synergistic effect is not always achieved. This review examines the potential mechanisms by which AM fungi enhance plant tolerance and defense against pathogens, as well as the possible interactive mechanisms among AM fungal traits that may lead to facilitative and antagonistic effect on plant defense outcomes. It also provides evidence demonstrating the benefits of AM fungal consortia used so far to protect crop plants from various pathogens. It concludes by proposing some biotechnological applications aimed at unraveling the connections between AM fungal diversity and their function to enhance efficacy of plant pathogen protection.

Recycling steel slag as fertiliser proxy in agriculture is good circular economy but disrupts plant microbial symbioses in the soil

Modern agriculture depends on synthetic fertilisers to ensure food security but their manufacture and use accounts for ~5 % of the global greenhouse gas emissions. Achieving climate change targets therefore requires alternatives, that while maintaining crop productivity, reduce emissions across the lifecycle of fertiliser utilisation. Steel slag, a nutrient-rich by-product of steel manufacture, offers a viable alternative. Being substantially cheaper than fertilisers, it is economically attractive for farmers, particularly in low-middle income countries of the Global South. However, slag application in agriculture poses risk of pollutant transfer to the human food chain and disruption of key plant-microbe symbioses like the arbuscular mycorrhizal fungi (AMF). Here, using barley as a model crop, we tested the suitability of slag as a fertiliser proxy. Mycorrhizal and non-mycorrhizal barley were grown in soils ameliorated with slag in concentrations of 0, 2, 5 and 10 t ha-1. We analysed slag-mycorrhiza interaction and their combined effects on crop yield and risks to human nourishment. Slag increased grain yield by respective 32 and 21 % in mycorrhizal and non-mycorrhizal barley. Grain concentration of metal pollutants in mycorrhizal and non-mycorrhizal barley fertilised with slag were within the WHO recommended limits. But slag reduced mycorrhizal colonisation in barley roots and extraradical hyphal spread in the soil. The consequent decline in symbiont function lowered AMF-mediated plant nutrient uptake and increased mineral losses in leachates. AMF are keystone species of the soil microbiome. Loss of AMF function presents long-term ecological consequences for agriculture and necessitates a careful evaluation of slag application to soil.

Increasing Phylogenetic Clustering of Arbuscular Mycorrhizal Fungal Communities in Roots Explains Enhanced Plant Growth and Phosphorus Uptake

Temporal variation during the assembly of arbuscular mycorrhizal (AM) fungal communities within plant roots have been posited as critical drivers of the plant-fungal symbiotic outcomes. However, functional implications of these dynamics for the host plant remain poorly understood. We conducted a controlled pot experiment with Sorghum bicolor to investigate how temporal shifts in AM fungal community composition and phylogenetic diversity influence plant growth and phosphorus responses to the symbiosis. We characterised the root-colonising AM fungal communities across three time points and explored their community assembly processes by analysing their phylogenetic diversity and employing joint species distribution modelling with the Hierarchical Modelling of Species Communities (HMSC) framework. We found strong AM fungal turnover through time with a high phylogenetic signal, indicating recruitment of phylogenetically clustered AM fungal species in the host. This temporal phylogenetic clustering of communities coincided with marked increases in plant biomass and phosphorus responses to the AM fungal symbiosis, suggesting that host selection for specific fungi may be a key determinant of these benefits.

Deciphering differences in microbial community characteristics and main factors between healthy and root rot-infected Carya cathayensis rhizosphere soils

Introduction

Fusarium-induced root rot of Carya cathayensis (C. cathayensis) is a typical soil-borne disease that has severely damaged the Carya cathayensis industry in China. Understanding the interaction among soil microbial communities, soil characteristics, and pathogenic bacteria is very important for the ecological prevention and control of Carya cathayensis root rot.

Methods

We used Miseq Illumina high-throughput sequencing technology to study the microbial community in the rhizosphere soil of healthy and diseased C. cathayensis, quantified the abundance of bacteria, fungi, and pathogenic fungi, and combined these with soil chemistry and enzyme activity indicators to analyze the characteristics of healthy and diseased rhizosphere soils.

Results

We found that the pH, soil organic carbon(SOC), available nitrogen (AN), available phosphorus (AP), available potassium (AK),N-acetyl-β-D-glucosaminidase (NAG) β-glucosidase (BG), fungal gene copy number, bacterial community diversity and network complexity of the diseased soil were significantly lower (p < 0.05), while Fusarium graminearum copies number levels increased (p < 0.05). Additionally, the study found that healthy soils were enriched with beneficial bacteria such as Subgroup_7 (0.08%), MND1 (0.29%), SWB02 (0.08%), and Bradyrhizobium (0.09%), as well as potential pathogen-suppressing fungi such as Mortierella (0.13%), Preussia (0.03%), and Humicol (0.37%), were found to be associated with the growth and development of C. cathayensis.

Discussion

In summary, this research comprehensively reveals the differences in environmental and biological factors between healthy and diseased soils, as well as their correlations. It provides a theoretical basis for optimal soil environmental regulation and the construction of healthy microbial communities. This foundation facilitates the development of multifaceted strategies for the prevention and control of C. cathayensis root rot.

Bacillus quorum quenching shapes the citrus mycobiome through interkingdom signaling

Microbiomes are sustained through infinite yet mutually interacting microbial communities, with bacteria and fungi serving as the major constituents. In recent times, microbial interventions have become popular for microbiome manipulation to achieve sustainable goals. Whether and how the introduced biocontrol agent drives fungal microbial assemblages (mycobiome) and the role of interkingdom signaling in shaping the microbiome structure and function remain poorly understood. Here, we implemented wild-type (WT) Bacillus subtilis L1-21 and its quorum quenching (QQ) mutants (L1-21Δytnp, and L1-21Δyxel) individually and as consortia to explore the enrichment patterns of key mycobiome members in Huanglongbing (HLB) infected citrus compartments including leaf endosphere, root endosphere, and rhizosphere soil. The application of WT and its QQ mutants produced differential mycobiome enrichment across citrus compartments. Our findings reveal that application of WT B. subtilis enriched beneficial fungi such as Trichoderma (15.82 %) in leaf endosphere. In contrast, pathogenic fungi Fusarium (47.5 %) and Gibberella (0.47 %) involved in citrus root decline were adundant in the L1-21Δytnp treated root endosphere while Nigrospora (11 %) was predominant in L1-21Δyxel treated leaf endosphere, affirming the role of bacterial quorum sensing (QS) molecules in shaping the fungal community composition. In general, based on the fungal functional prediction, fungal pathogens were highly abundant in mutant-treated plants, particularly in leaf endosphere (L1-21Δytnp: 25 %; L1-21Δyxel: 36.35 %) compared to WT (20.93%). Additionally, some fungal members exhibited strong compartment specificity and both mutants induced distinct mycobiome shifts in rhizosphere soil, leaf, and root endopshere. In conclusion, B. subtilis QQ modifies bacterial QS networks facilitating beneficial fungi to establish, while loss of QQ leads to enrichment of pathogenic fungal groups. Our study provides a direct link of perception and regulation of mycobiome through bacterial-based QS and QQ system, and its association with disease outcomes.

Exploring agro-ecological significance, knowledge gaps, and research priorities in arbuscular mycorrhizal fungi

This systematic review examines the global agricultural relevance and practical environmental implications of arbuscular mycorrhizal fungi (AMF) within the phylum Glomeromycota. Following PRISMA guidelines, ensuring a comprehensive and unbiased literature review, a literature search was conducted, focusing on the functional roles of AMF in enhancing crop productivity, nutrient uptake, and soil health. Key findings reveal that AMF contribute significantly to sustainable agriculture by reducing the need for chemical fertilizers and increasing plant resilience to environmental stressors like drought, salinity, or pest resistance. The review highlights the importance of AMF in forming symbiotic relationships with plants, which enhance nutrient absorption and improve soil structure, showcasing long-term benefits such as reduced erosion or improved water retention. However, the current literature lacks in-depth exploration of the taxonomy and evolutionary aspects of AMF, as well as the specific functional roles they play in different agricultural contexts, e.g., understanding evolution could enhance strain selection for specific crops. This review identifies several urgent research gaps, including a need for a more refined understanding of AMF community dynamics under varying land management practices. For example, there are gaps in and a critical evaluation of advanced molecular techniques. Such techniques are essential for studying these interactions. Addressing these gaps will enhance the integration of AMF into sustainable agricultural systems and improve ecosystem management practices across different geographical regions. Future research should prioritize developing precise molecular imaging techniques and optimizing AMF applications for different crops and soil types to maximize their ecological and agricultural benefits. This could be practical through interdisciplinary collaboration (e.g., involving molecular biologists, agronomists, etc.). In conclusion, this review advances the practical application of AMF in agriculture and its contribution to biodiversity conservation in agroecosystems. Integrating these findings into policy frameworks could encourage sustainable farming practices, promote the adoption of AMF inoculants, and foster incentives for environmentally friendly land management strategies.

Systematic review registration

https://www.bmj.com/content/372/bmj.n71.

Multiple taxa inoculants of arbuscular mycorrhizal fungi enhanced colonization frequency, biomass production, and water use efficiency of cassava (Manihot esculenta)

Increasing water use efficiency (WUE) in crops is critical to maintaining agricultural production under climate change-exacerbated drought. One of these approaches may consist of leveraging on the beneficial interactions between crops and arbuscular mycorrhizal fungi (AMF). In this study, we investigated how inoculation with AMF from three different taxa (Claroideoglomus etunicatum (T1), Gigaspora margarita (T2), and Rhizophagus irregularis (T3)) and their combination (T123) and a non-inoculated "control" treatment in a greenhouse could achieve increased biomass production and water use efficiency in cassava under three levels of water availability (100% PC, 60%-moderate stress, and 30%-severe stress). Whereas T1 and T2 resulted in a lower growth rate for the plants than the control, T123 enhanced cassava height and the number of petioles and leaves. T123 and T3 increased the total plant dry biomass in comparison with uninoculated plants by 30% and 26%, respectively. The T123 and plants inoculated with T3 significantly increased cassava above-ground biomass by 19% as compared to T1 (8.68 ± 2.44 g) and T2 (8.68 ± 2.44 g) inoculated plants. T123 resulted in higher WUE, which was validated by the leaf carbon (δ13C) isotopic signature, significantly outperforming cassava with T1 and T2, yet there was no difference between the control and T3. Overall, this study demonstrated that the use of multiple AMF from different taxa can increase cassava growth and WUE under greenhouse conditions.

Mycorrhization enhances plant growth and stabilizes biomass allocation under drought

Plants and their symbionts, such as arbuscular mycorrhizal (AM) fungi, are increasingly subjected to various environmental stressors due to climate change, including drought. As a response to drought, plants generally allocate more biomass to roots over shoots, thereby facilitating water uptake. However, whether this biomass allocation shift is modulated by AM fungi remains unknown. Based on 5691 paired observations from 154 plant species, we conducted a meta-analysis to evaluate how AM fungi modulate the responses of plant growth and biomass allocation (e.g., root-to-shoot ratio, R/S) to drought. We found that AM fungi attenuate the negative impact of drought on plant growth, including biomass production, photosynthetic performance and resource (e.g. nutrient and water) uptake. Accordingly, drought significantly increased R/S in non-inoculated plants, but not in plants symbiotic with established AM fungal symbioses. These results suggest that AM fungi promote plant growth and stabilize their R/S through facilitating nutrient and water uptake in plants under drought. Our findings highlight the crucial role of AM fungi in enhancing plant resilience to drought by optimizing resource allocation. This knowledge opens avenues for sustainable agricultural practices that leverage symbiotic relationships for climate adaptation.

Unveiling the resistance of native weed communities: insights for managing invasive weed species in disturbed environments

Weed communities influence the dynamics of ecosystems, particularly in disturbed environments where anthropogenic activities often result in higher pollution. Understanding the dynamics existing between native weed communities and invasive species in disturbed environments is crucial for effective management and normal ecosystem functioning. Recognising the potential resistance of native weed communities to invasion in disturbed environments can help identify suitable native plants for restoration operations. This review aims to investigate the adaptations exhibited by native and non-native weeds that may affect invasions within disturbed environments. Factors such as ecological characteristics, altered soil conditions, and adaptations of native weed communities that potentially confer a competitive advantage relative to non-native or invasive weeds in disturbed environments are analysed. Moreover, the roles of biotic interactions such as competition, mutualistic relationships, and allelopathy in shaping the invasion resistance of native weed communities are described. Emphasis is given to the consideration of the resistance of native weeds as a key factor in invasion dynamics that provides insights for conservation and restoration efforts in disturbed environments. Additionally, this review underscores the need for further research to unravel the underlying mechanisms and to devise targeted management strategies. These strategies aim to promote the resistance of native weed communities and mitigate the negative effects of invasive weed species in disturbed environments. By delving deeper into these insights, we can gain an understanding of the ecological dynamics within disturbed ecosystems and develop valuable insights for the management of invasive species, and to restore long-term ecosystem sustainability.

Mycorrhizal type and tree diversity affect foliar elemental pools and stoichiometry

Species-specific differences in nutrient acquisition strategies allow for complementary use of resources among plants in mixtures, which may be further shaped by mycorrhizal associations. However, empirical evidence of this potential role of mycorrhizae is scarce, particularly for tree communities. We investigated the impact of tree species richness and mycorrhizal types, arbuscular mycorrhizal fungi (AM) and ectomycorrhizal fungi (EM), on above- and belowground carbon (C), nitrogen (N), and phosphorus (P) dynamics. Soil and soil microbial biomass elemental dynamics showed weak responses to tree species richness and none to mycorrhizal type. However, foliar elemental concentrations, stoichiometry, and pools were significantly affected by both treatments. Tree species richness increased foliar C and P pools but not N pools. Additive partitioning analyses showed that net biodiversity effects of foliar C, N, P pools in EM tree communities were driven by selection effects, but in mixtures of both mycorrhizal types by complementarity effects. Furthermore, increased tree species richness reduced soil nitrate availability, over 2 yr. Our results indicate that positive effects of tree diversity on aboveground nutrient storage are mediated by complementary mycorrhizal strategies and highlight the importance of using mixtures composed of tree species with different types of mycorrhizae to achieve more multifunctional afforestation.

Arbuscular mycorrhizal symbiosis modulates nitrogen uptake and assimilation to enhance drought tolerance of Populus cathayana

This study aims to investigate effects of arbuscular mycorrhizal fungi (AMF) inoculation on nitrogen (N) uptake and assimilation in Populus cathayana under drought stress (DS). Herein, we measured photosynthetic performance, antioxidant enzyme system, N level and N assimilation enzymes, proteins content and distribution, transcripts of genes associated with N uptake or transport in P. cathayana with AMF (AM) or without AMF (NM) under soil water limitation and adequate irrigation. Compared with NM-DS P. cathayana, the growth, gas exchange properties, antioxidant enzyme activities, total N content and the proportion of water-soluble and membrane-bound proteins in AM-DS P. cathayana were increased. Meanwhile, nitrate reductase (NR) activity, NO3- and NO2- concentrations in AM-DS P. cathayana were reduced, while NH4+ concentration, glutamine synthetase (GS) and glutamate synthetase (GOGAT) activities were elevated, indicating that AM symbiosis reduces NO3- assimilation while promoting NH4+ assimilation. Furthermore, the transcriptional levels of NH4+ transporter genes (PcAMT1-4 and PcAMT2-1) and NO3- transporter genes (PcNRT2-1 and PcNRT3-1) in AM-DS P. cathayana roots were significantly down-regulated, as well as NH4+ transporter genes (PcAMT1-6 and PcAMT4-3) in leaves. In AM P. cathayana roots, DS significantly up-regulated the transcriptional levels of RiCPSI and RiURE, the key N transport regulatory genes in AMF compared with adequate irrigation. These results indicated that AM N transport pathway play an essential role on N uptake and utilization in AM P. cathayana to cope with DS. Therefore, this research offers a novel perspective on how AM symbiosis enhances plant resilience to drought at aspect of N acquisition and assimilation.

Tracking arbuscular mycorrhizal fungi to their source: active inoculation and passive dispersal differentially affect community assembly in urban soils

Communities of arbuscular mycorrhizal (AM) fungi assemble passively over time via biotic and abiotic mechanisms. In degraded soils, AM fungal communities can assemble actively when humans manage mycorrhizas for ecosystem restoration. We investigated mechanisms of urban AM fungal community assembly in a 2-yr green roof experiment. We compared AM fungal communities in inoculated and uninoculated trays to samples from two potential sources: the inoculum and air. Active inoculation stimulated more distinct and diverse AM fungal communities, an effect that intensified over time. In the treatment trays, 45% of AM fungal taxa were detected in the inoculum, 2% were detected in aerial samples, 23% were detected in both inoculum and air, and 30% were not detected in either source. Passive dispersal of AM fungi likely resulted in the successful establishment of a small number of species, but active inoculation with native AM fungal species resulted in an immediate shift to a diverse and unique fungal community. When urban soils are constructed or modified by human activity, this is an opportunity for intervention with AM fungi that will persist and add diversity to that system.

Spores of arbuscular mycorrhizal fungi host surprisingly diverse communities of endobacteria

Arbuscular mycorrhizal fungi (AMF) are ubiquitous plant root symbionts, which can house two endobacteria: Ca. Moeniiplasma glomeromycotorum (CaMg) and Ca. Glomeribacter gigasporarum (CaGg). However, little is known about their distribution and population structure in natural AMF populations and whether AMF can harbour other endobacteria. We isolated AMF from two environments and conducted detailed analyses of endobacterial communities associated with surface-sterilised AMF spores. Consistent with the previous reports, we found that CaMg were extremely abundant (80%) and CaGg were extremely rare (2%) in both environments. Unexpectedly, we discovered an additional and previously unknown level of bacterial diversity within AMF spores, which extended beyond the known endosymbionts, with bacteria belonging to 10 other phyla detected across our spore data set. Detailed analysis revealed that: CaGg were not limited in distribution to the Gigasporaceae family of AMF, as previously thought; CaMg population structure was driven by AMF host genotype; and a significant inverse correlation existed between the diversity of CaMg and diversity of all other endobacteria. Based on these data, we generate novel testable hypotheses regarding the function of CaMg in AMF biology by proposing that they might act as conditional mutualists of AMF.

Mycorrhizal effects on crop yield and soil ecosystem functions in a long-term tillage and fertilization experiment

It is well understood that agricultural management influences arbuscular mycorrhizal (AM) fungi, but there is controversy about whether farmers should manage for AM symbiosis. We assessed AM fungal communities colonizing wheat roots for three consecutive years in a long-term (> 14 yr) tillage and fertilization experiment. Relationships among mycorrhizas, crop performance, and soil ecosystem functions were quantified. Tillage, fertilizers and continuous monoculture all reduced AM fungal richness and shifted community composition toward dominance of a few ruderal taxa. Rhizophagus and Dominikia were depressed by tillage and/or fertilization, and their abundances as well as AM fungal richness correlated positively with soil aggregate stability and nutrient cycling functions across all or no-tilled samples. In the field, wheat yield was unrelated to AM fungal abundance and correlated negatively with AM fungal richness. In a complementary glasshouse study, wheat biomass was enhanced by soil inoculum from unfertilized, no-till plots while neutral to depressed growth was observed in wheat inoculated with soils from fertilized and conventionally tilled plots. This study demonstrates contrasting impacts of low-input and conventional agricultural practices on AM symbiosis and highlights the importance of considering both crop yield and soil ecosystem functions when managing mycorrhizas for more sustainable agroecosystems.

Sustainable Development versus Extractivist Deforestation in Tropical, Subtropical, and Boreal Forest Ecosystems: Repercussions and Controversies about the Mother Tree and the Mycorrhizal Network Hypothesis

This research reviews the phenomenon of extractive deforestation as a possible trigger for cascade reactions that could affect part of the forest ecosystem and its biodiversity (surface, aerial, and underground) in tropical, subtropical, and boreal forests. The controversy and disparities in criteria generated in the international scientific community around the hypothesis of a possible link between "mother trees" and mycorrhizal networks in coopetition for nutrients, nitrogen, and carbon are analyzed. The objective is to promote awareness to generate more scientific knowledge about the eventual impacts of forest extraction. Public policies are emphasized as crucial mediators for balanced sustainable development. Currently, the effects of extractive deforestation on forest ecosystems are poorly understood, which requires caution and forest protection. Continued research to increase our knowledge in molecular biology is advocated to understand the adaptation of biological organisms to the new conditions of the ecosystem both in the face of extractive deforestation and reforestation. The environmental impacts of extractive deforestation, such as the loss of biodiversity, soil degradation, altered water cycles, and the contribution of climate change, remain largely unknown. Long-term and high-quality research is essential to ensure forest sustainability and the preservation of biodiversity for future generations.

Impacts of Managed Vegetation Restoration on Arbuscular Mycorrhizal Fungi and Diazotrophs in Karst Ecosystems

The crucial functional arbuscular mycorrhizal fungi (AMF) and diazotrophs play pivotal roles in nutrient cycling during vegetation restoration. However, the impact of managed vegetation restoration strategies on AMF and diazotroph communities remains unclear. In this study, we investigated the community structure and diversity of AMF and diazotrophs in a karst region undergoing managed vegetation restoration from cropland. Soil samples were collected from soils under three vegetation restoration strategies, plantation forest (PF), forage grass (FG), and a mixture of plantation forest and forage grass (FF), along with a control for cropland rotation (CR). The diversity of both AMF and diazotrophs was impacted by managed vegetation restoration. Specifically, the AMF Shannon index was higher in CR and PF compared to FF. Conversely, diazotroph richness was lower in CR, PF, and FG than in FF. Furthermore, both AMF and diazotroph community compositions differed between CR and FF. The relative abundance of AMF taxa, such as Glomus, was lower in FF compared to the other three land-use types, while Racocetra showed the opposite trend. Among diazotroph taxa, the relative abundance of Anabaena, Nostoc, and Rhizobium was higher in FF than in CR. Soil properties such as total potassium, available potassium, pH, and total nitrogen were identified as the main factors influencing AMF and diazotroph diversity. These findings suggest that AMF and diazotroph communities were more sensitive to FF rather than PF and FG after managed vegetation restoration from cropland, despite similar levels of soil nutrients among PF, FG, and FF. Consequently, the integration of diverse economic tree species and forage grasses in mixed plantations notably altered the diversity and species composition of AMF and diazotrophs, primarily through the promotion of biocrust formation and root establishment.

Grassland degradation amplifies the negative effect of nitrogen enrichment on soil microbial community stability

Although nitrogen (N) enrichment is known to threaten the temporal stability of aboveground net primary productivity, it remains unclear how it alters that of belowground microbial abundance and whether its impact can be regulated by grassland degradation. Using data from N enrichment experiments at temperate grasslands with no, moderate, severe, and extreme degradation degrees, we quantified the temporal stability of soil microbial abundance (hereafter 'microbial community stability') using the ratio of the mean quantitative PCR to its standard deviation over 4 years. Both bacterial and fungal community stability sharply decreased when N input exceeded 30 g N m-2  year-1 in non-degraded grasslands, whereas a reduction in this threshold occurred in degraded grasslands. Microbial species diversity, species asynchrony, and species associations jointly altered microbial community stability. Interestingly, the linkages between plant and microbial community stability were strengthened in degraded grasslands, suggesting that plants and soil microbes might depend on each other to keep stable communities in harsh environments. Our findings highlighted the importance of grassland degradation in regulating the responses of microbial community stability to N enrichment and provided experimental evidence for understanding the relationships between plant and microbial community stability.

Distinct biogeographic patterns in Glomeromycotinian and Mucoromycotinian arbuscular mycorrhizal fungi across China: A meta-analysis

Fine root endophytes, recently reclassified as Mucoromycotinian arbuscular mycorrhizal fungi (M-AMF), are now recognized as functionally important as Glomeromycotinian AMF (G-AMF). However, little is known about the biogeography and ecology of M-AMF and G-AMF communities, particularly on a large scale, preventing a systematic assessment of ecosystem diversity and functioning. Here, we investigated the biogeographic assemblies and ecological diversity patterns of both G-AMF and M-AMF, using published 18S rDNA amplicon datasets and associated metadata from 575 soil samples in six ecosystems across China. Contrasting with G-AMF, putative M-AMF were rare in natural/semi-natural sites, where their communities were a subset of those in agricultural sites characterized by intensive disturbances, suggesting different ecological niches that they could occupy. Spatial and environmental factors (e.g., vegetation type) significantly influenced both fungal communities, with soil total‑nitrogen and mean-annual-precipitation being the strongest predictors for G-AMF and M-AMF richness, respectively. Both groups exhibited a strong spatial distance-decay relationship, shaped more by environmental filtering than spatial effects for M-AMF, and the opposite for G-AMF, presumably because stochasticity (e.g., drift) dominantly structured G-AMF communities; while the narrower niche breadth (at community-level) of M-AMF compared to G-AMF suggested its more susceptibility to environmental differences. Furthermore, co-occurrence network links between G-AMF and M-AMF were prevalent across ecosystems, and were predicted to play a key role in stabilizing overall communities harboring both fungi. Based on the macroecological spatial scale datasets, this study provides solid evidence that the two AMF groups have distinct ecological preferences at the continental scale in China, and also highlights the potential impacts of anthropogenic activities on distributions of AMF. These results advance our knowledge of the ecological differences between the two fungal groups in terrestrial ecosystems, suggesting the need for further field-based investigation that may lead to a more sophisticated understanding of ecosystem function and sustainable management.

Co-inoculations of bacteria and mycorrhizal fungi often drive additive plant growth responses

Controlled greenhouse studies have shown the numerous ways that soil microbes can impact plant growth and development. However, natural soil communities are highly complex, and plants interact with many bacterial and fungal taxa simultaneously. Due to logistical challenges associated with manipulating more complex microbiome communities, how microbial communities impact emergent patterns of plant growth therefore remains poorly understood. For instance, do the interactions between bacteria and fungi generally yield additive (i.e. sum of their parts) or nonadditive, higher order plant growth responses? Without this information, our ability to accurately predict plant responses to microbial inoculants is weakened. To address these issues, we conducted a meta-analysis to determine the type (additive or higher-order, nonadditive interactions), frequency, direction (positive or negative), and strength that bacteria and mycorrhizal fungi (arbuscular and ectomycorrhizal) have on six phenotypic plant growth responses. Our results demonstrate that co-inoculations of bacteria and mycorrhizal fungi tend to have positive additive effects on many commonly reported plant responses. However, ectomycorrhizal plant shoot height responds positively and nonadditively to co-inoculations of bacteria and ectomycorrhizal fungi, and the strength of additive effects also differs between mycorrhizae type. These findings suggest that inferences from greenhouse studies likely scale to more complex field settings and that inoculating plants with diverse, beneficial microbes is a sound strategy to support plant growth.

The Effects of Local Weed Species on Arbuscular Mycorrhizal Fungal Communities in an Organic Winter Wheat (Triticum durum L.) Field in Lebanon

We examined the potential effects of weed species on the arbuscular mycorrhizal fungi (AMF) in an organic winter wheat (Triticum durum) field in Lebanon. In this agroecosystem, the field and its surroundings were covered with spontaneous vegetation corresponding to local weeds. The coexistence between wheat and weeds did not modify AM fungal community diversity and colonization in T. durum but changed their composition. We evidenced 22 operational taxonomic units (OTUs) specifically shared between wheat associated with weeds (Tdw) and weeds, regardless of their localization and 12 OTUs with an abundance of variation between wheat without neighboring weeds (Td) and Tdw. The number of AM propagules and total C and N contents were higher in soil covered with wheat associated with weeds (TdWsoil) vs. wheat without neighboring weeds (Tdsoil). In greenhouse experiments, the shoot biomass and root mycorrhizal intensity of Medicago sativa, used as a trap plant, were higher using TdWsoil vs. Tdsoil as the inoculum. Positive correlations were observed between soil AM propagule numbers and M. sativa shoot biomass, on the one hand and M. sativa mycorrhizal intensity, on the other hand. Weeds seemed to exert significant effects on root AM fungal composition in T. durum and these effects may contribute to enhanced AMF development in the field.

Afforestation changed the fungal functional community of paddy fields and dry farmlands differently

Afforestation currently makes a great contribution to carbon uptake in terrestrial ecosystems, while dramatically affects soil ecosystem functions too. Little is known, however, about the changes in soil fungal functional groups and their interactions following afforestation. Here, based on high-throughput sequencing and FUNGuild annotation, we investigated the functional characteristics of soil fungi as well as environmental factors in a watershed where paddy field and dry farmland were changed to eucalyptus plantation. The results showed that afforestation on paddy field resulted in greater changes in diversity, community structure and taxon interactions of fungal functional groups than afforestation on dry farmland. The most complex and distinctive community structure was found in eucalyptus plantation, as well as the greatest taxon interactions, and the lowest alpha-diversity of functional guilds of symbiotrophic fungi because of the dominant ectomycorrhizal fungi. Paddy field exhibited the highest proportion of saprotrophic fungi, but the lowest taxonomic diversity of saprotrophic and pathotrophic fungi. The taxonomic diversity of undefined saprotrophic fungi shaped the differences in community structure and network complexity between eucalyptus plantation and cropland. Limited cooperation within dominant fungi was the main reason for the establishment of a loose co-occurrence network in paddy field. From croplands to artificial forests, reduced soil pH boosted the taxonomic diversity of fungal functional groups. All of these findings suggested that afforestation may lead to an increase in the taxonomic diversity of soil fungal functional groups, which would further intensify the taxon interactions.

Arbuscular mycorrhizal fungi benefit plants in response to major global change factors

Land plants play a key role in global carbon cycling, but the potential role of arbuscular mycorrhizal fungi (AMF) in the responses of a wide range of plant species to global change factors (GCFs) remains limited. Based on 1100 paired observations from 181 plant species, we conducted a meta-analysis to test the role of AMF in plant responses to four GCFs: drought, warming, nitrogen (N) addition and elevated CO2 . We show that AMF significantly ameliorate the negative effects of drought on plant performance. The GCFs N addition and elevated CO2 significantly enhance the performance of AM plants but not of non-inoculated plants. AM plants show better performance than their non-inoculated counterparts under warming, although neither of them showed a significant response to this GCF. These results suggest that AMF benefit plants in response to GCFs. Our study highlights the importance of AMF in enhancing plant performance under ongoing global change.

The threat of micro/nanoplastic to aquatic plants: current knowledge, gaps, and future perspectives

Plastics have been recognized as an emerging pollutant and have raised global concerns due to their widespread distribution in the environment and potential harm to living systems. However, research on the threat of micro/nanoplastics (MPs/NPs) to the unique group of aquatic plants is far behind, necessitating a comprehensive review to summarize current research progress and identify future research needs. This review explores the sources and distribution patterns of MPs/NPs in aquatic environments, highlighting their uptake by aquatic plants through roots and leaves, and subsequent translocation via the vascular system facilitated by the transpiration stream. Exposure to MPs/NPs elicits diverse effects on the growth, physiology, and ecological interactions of aquatic plants, with variations influenced by plastic properties, plant species, and experimental conditions. Furthermore, the presence of MPs/NPs can impact the toxicity and bioavailability of other associated toxicants to aquatic plants. This review shows critical knowledge gaps and emphasizes the need for future research to bridge the current understanding of the limitations and challenges posed by MPs/NPs in aquatic ecosystems.

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

BACKGROUND

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

RESULTS

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

CONCLUSION

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

Unveiling the effect of microplastics on agricultural crops - a review

Microplastics (MPs), ever since they were identified as a potential and widely distributed persistent contaminant, the number of studies highlighting their impacts on various terrestrial ecosystems have been increasing. Recently, the effect of MPs on the agricultural ecosystem has gained momentum. Hence, the present review examines the impact of microplastics on agricultural crop systems and the mechanism underlying its toxicity. The current review revealed that most of the studies were conducted at a laboratory scale and under controlled conditions. Additionally, it was observed that polystyrene (PS) followed by polyethylene (PE) are the most studied polymer type, while the most studied plants are wheat and maize. Hitherto, literature studies suggest that the microplastics' influence on plant growth can be negative or sometimes neutral; while in some cases it exerts a hormetic effect which depends on other factors determining plant growth. Notably, the main mechanisms through which microplastics influence plant growth are mechanical damage, alteration of soil properties, or by leaching of additives. Overall, with burgeoning research interest in this aspect, the current review has significant implications for the toxicity of MPs on plants and throws light on the need to develop novel guidelines toward the sustainable use of plastics in agricultural sector. However, realistic field-level studies and estimating the MPs concentration at various region are essential to develop remediation approaches. Future studies should also focus on translocation and accumulation of micron sized MPs in edible portion of crops and their effect on food safety.

Agricultural tillage practice and rhizosphere selection interactively drive the improvement of soybean plant biomass

Rhizosphere microbes play key roles in plant growth and productivity in agricultural systems. One of the critical issues is revealing the interaction of agricultural management (M) and rhizosphere selection effects (R) on soil microbial communities, root exudates and plant productivity. Through a field management experiment, we found that bacteria were more sensitive to the M × R interaction effect than fungi, and the positive effect of rhizosphere bacterial diversity on plant biomass existed in the bacterial three two-tillage system. In addition, inoculation experiments demonstrated that the nitrogen cycle-related isolate Stenotrophomonas could promote plant growth and alter the activities of extracellular enzymes N-acetyl- d-glucosaminidase and leucine aminopeptidase in rhizosphere soil. Microbe-metabolites network analysis revealed that hubnodes Burkholderia-Caballeronia-Paraburkholderia and Pseudomonas were recruited by specific root metabolites under the M × R interaction effect, and the inoculation of 10 rhizosphere-matched isolates further proved that these microbes could promote the growth of soybean seedlings. Kyoto Encyclopaedia of Genes and Genomes pathway analysis indicated that the growth-promoting mechanisms of these beneficial genera were closely related to metabolic pathways such as amino acid metabolism, melatonin biosynthesis, aerobactin biosynthesis and so on. This study provides field observation and experimental evidence to reveal the close relationship between beneficial rhizosphere microbes and plant productivity under the M × R interaction effect.

Towards a farmer-feasible soil health assessment that is globally applicable

Globally, agriculture has had a significant and often detrimental impact on soil. The continued capacity of soil to function as a living ecosystem that sustains microbes, plants, and animals (including humans), its metaphorical health, is of vital importance across geographic scales. Healthy soil underpins food production and ecosystem resilience against a changing climate. This paper focuses on assessing soil health, an area of increasing interest for farming communities, researchers, industry and policy-makers. Without accessible and reliable soil assessment, any management and interventions to improve soil health are likely to be sub-optimal. Here we explore available soil health assessments (SHAs) that may be feasible for farmers of varying income levels and suitable for broad geographic application. Whilst there is a range of existing approaches to SHA, we find that no one framework currently meets these broad aims. Firstly, reliance on expensive and logistically complex laboratory methods reduces viability and accessibility for many farmers. Secondly, lack of defined indicator baselines and associated thresholds or gradients for soil health prevents the assessment of soil measurements against achieving optima for a given set of local soil-climate conditions. Since soils vary greatly, these baselines and thresholds must be defined considering the local biogeographic context; it is inappropriate to simply transfer calibrated information between contexts. These shortcomings demand progress towards a feasible, globally applicable and context-relevant SHA framework. The most feasible SHAs we identified were developed locally in conjunction with farmers, who have been repeatedly found to assess the health of their soils accurately, often using relatively simple, observable indications. To progress, we propose assessment of which indicators add information to a SHA in local contexts, with a focus on sufficiency, to reduce data burden. Provision of a standardised protocol for measurement and sampling that considers the reliability and accuracy of different methods would also be extremely valuable. For greatest impact, future work should be taken forward through a cross-industry collaborative approach involving researchers, businesses, policy makers, and, above all, farmers, who are both experts and users.

Can cardiolipins be used as a biomarker for arbuscular mycorrhizal fungi?

Specific biomarker molecules are increasingly being used for detection and quantification in plant and soil samples of arbuscular mycorrhizal (AM) fungi, an important and widespread microbial guild heavily implicated in transfers of nutrients and carbon between plants and soils and in the maintenance of soil physico-chemical properties. Yet, concerns have previously been raised as to the validity of a range of previously used approaches (e.g., microscopy, AM-specific fatty acids, sterols, glomalin-like molecules, ribosomal DNA sequences), justifying further research into novel biomarkers for AM fungal abundance and/or functioning. Here, we focused on complex polar lipids contained in pure biomass of Rhizophagus irregularis and in nonmycorrhizal and mycorrhizal roots of chicory (Cichorium intybus), leek (Allium porrum), and big bluestem (Andropogon gerardii). The lipids were analyzed by shotgun lipidomics using a high-resolution hybrid mass spectrometer. Size range between 1350 and 1550 Da was chosen for the detection of potential biomarkers among cardiolipins (1,3-bis(sn-3'-phosphatidyl)-sn-glycerols), a specific class of phospholipids. The analysis revealed a variety of molecular species, including cardiolipins containing one or two polyunsaturated fatty acids with 20 carbon atoms each, i.e., arachidonic and/or eicosapentaenoic acids, some of them apparently specific for the mycorrhizal samples. Although further verification using a greater variety of AM fungal species and samples from various soils/ecosystems/environmental conditions is needed, current results suggest the possibility to identify novel biochemical signatures specific for AM fungi within mycorrhizal roots. Whether they could be used for quantification of both root and soil colonization by the AM fungi merits further scrutiny.

Extreme summers impact cropland and grassland soil microbiomes

The increasing frequency of extreme weather events highlights the need to understand how soil microbiomes respond to such disturbances. Here, metagenomics was used to investigate the effects of future climate scenarios (+0.6 °C warming and altered precipitation) on soil microbiomes during the summers of 2014-2019. Unexpectedly, Central Europe experienced extreme heatwaves and droughts during 2018-2019, causing significant impacts on the structure, assembly, and function of soil microbiomes. Specifically, the relative abundance of Actinobacteria (bacteria), Eurotiales (fungi), and Vilmaviridae (viruses) was significantly increased in both cropland and grassland. The contribution of homogeneous selection to bacterial community assembly increased significantly from 40.0% in normal summers to 51.9% in extreme summers. Moreover, genes associated with microbial antioxidant (Ni-SOD), cell wall biosynthesis (glmSMU, murABCDEF), heat shock proteins (GroES/GroEL, Hsp40), and sporulation (spoIID, spoVK) were identified as potential contributors to drought-enriched taxa, and their expressions were confirmed by metatranscriptomics in 2022. The impact of extreme summers was further evident in the taxonomic profiles of 721 recovered metagenome-assembled genomes (MAGs). Annotation of contigs and MAGs suggested that Actinobacteria may have a competitive advantage in extreme summers due to the biosynthesis of geosmin and 2-methylisoborneol. Future climate scenarios caused a similar pattern of changes in microbial communities as extreme summers, but to a much lesser extent. Soil microbiomes in grassland showed greater resilience to climate change than those in cropland. Overall, this study provides a comprehensive framework for understanding the response of soil microbiomes to extreme summers.

Contrasting effects of bioenergy crops on biodiversity

Agriculture is driving biodiversity loss, and future bioenergy cropping systems have the potential to ameliorate or exacerbate these effects. Using a long-term experimental array of 10 bioenergy cropping systems, we quantified diversity of plants, invertebrates, vertebrates, and microbes in each crop. For many taxonomic groups, alternative annual cropping systems provided no biodiversity benefits when compared to corn (the business-as-usual bioenergy crop in the United States), and simple perennial grass-based systems provided only modest gains. In contrast, for most animal groups, richness in plant-diverse perennial systems was much higher than in annual crops or simple perennial systems. Microbial richness patterns were more eclectic, although some groups responded positively to plant diversity. Future agricultural landscapes incorporating plant-diverse perennial bioenergy cropping systems could be of high conservation value. However, increased use of annual crops will continue to have negative effects, and simple perennial grass systems may provide little improvement over annual crops.

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

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

AM fungal-bacterial relationships: what can they tell us about ecosystem sustainability and soil functioning?

Considering our growing population and our continuous degradation of soil environments, understanding the fundamental ecology of soil biota and plant microbiomes will be imperative to sustaining soil systems. Arbuscular mycorrhizal (AM) fungi extend their hyphae beyond plant root zones, creating microhabitats with bacterial symbionts for nutrient acquisition through a tripartite symbiotic relationship along with plants. Nonetheless, it is unclear what drives these AM fungal-bacterial relationships and how AM fungal functional traits contribute to these relationships. By delving into the literature, we look at the drivers and complexity behind AM fungal-bacterial relationships, describe the shift needed in AM fungal research towards the inclusion of interdisciplinary tools, and discuss the utilization of bacterial datasets to provide contextual evidence behind these complex relationships, bringing insights and new hypotheses to AM fungal functional traits. From this synthesis, we gather that interdependent microbial relationships are at the foundation of understanding microbiome functionality and deciphering microbial functional traits. We suggest using pattern-based inference tools along with machine learning to elucidate AM fungal-bacterial relationship trends, along with the utilization of synthetic communities, functional gene analyses, and metabolomics to understand how AM fungal and bacterial communities facilitate communication for the survival of host plant communities. These suggestions could result in improving microbial inocula and products, as well as a better understanding of complex relationships in terrestrial ecosystems that contribute to plant-soil feedbacks.

Abundance and distribution of arbuscular mycorrhizal fungi associated with oil-yielding plants

Due to their role in nutrient transmission, arbuscular mycorrhizal fungi (AMF) are widespread plant root symbionts. They may improve plant production by altering plant community structure and function. Therefore, a study was conducted in the state of Haryana to analyze the distribution pattern, diversity, and association of different AMF species with oil-yielding plants. The results of the study revealed the percentage of root colonization, sporulation, and diversity of fungal species associated with the selected 30 oil-yielding plants. The percentage root colonization ranged from 0% to 100%, the highest in Helianthus annuus (100.00 ± 0.00) and Zea mays (100.00 ± 0.00) and the least in Citrus aurantium (11.87 ± 1.43). At the same time, there was no root colonization in the Brassicaceae family. The number of AMF spores present in 50 g of soil samples varied from 17.41 ± 5.28 to 497.2 ± 8.38, with maximum spore population in Glycine max (497.2 ± 8.38) and minimum in Brassica napus (17.41 ± 5.28). Besides, the presence of several species of different genera of AMF was reported in all the studied oil-yielding plants, that is, 60 AMF belonging to six genera viz. Acaulospora, Entrophospora, Glomus, Gigaspora, Sclerocystis, and Scutellospora were observed. Overall, this study will promote AMF usage in oil-yielding plants.

Arbuscular mycorrhizal fungi-induced tolerance to chromium stress in plants

Chromium (Cr) is one of the toxic elements that harms all forms of life, including plants. Industrial discharges and mining largely contribute to Cr release into the soil environment. Excessive Cr pollution in arable land significantly reduces the yield and quality of important agricultural crops. Therefore, remediation of polluted soil is imperative not only for agricultural sustainability but also for food safety. Arbuscular mycorrhizal fungi (AMF) are widespread soil-borne endophytic fungi that form mutualistic relationships with the vast majority of land plants. In mycorrhizal symbiosis, AMF are largely dependent on the host plant-supplied carbohydrates and lipids, in return, AMF aid the host plants in acquiring water and mineral nutrients, especially phosphorus, nitrogen and sulfur from distant soils, and this distinguishing feature of the two-way exchange of resources is a functional requirement for such mutualism and ecosystem services. In addition to supplying nutrients and water to plants, the AMF symbiosis enhances plant resilience to biotic and abiotic stresses including Cr stress. Studies have revealed vital physiological and molecular mechanisms by which AMF alleviate Cr phytotoxicity and aid plants in nutrient acquisition under Cr stress. Notably, plant Cr tolerance is enhanced by both the direct effects of AMF on Cr stabilization and transformation, and the indirect effects of AMF symbiosis on plant nutrient uptake and physiological regulation. In this article, we summarized the research progress on AMF and associated mechanisms of Cr tolerance in plants. In addition, we reviewed the present understanding of AMF-assisted Cr remediation. Since AMF symbiosis can enhance plant resilience to Cr pollution, AMF may have promising prospects in agricultural production, bioremediation, and ecological restoration in Cr-polluted soils.

Isolation and identification of arbuscular mycorrhizal fungi from an abandoned uranium mine and their role in soil-to-plant transfer of radionuclides and metals

Arbuscular mycorrhizal fungi were recovered from soil samples from the naturally radioactive soil at the long-abandoned South Terras uranium mine in Cornwall, UK. Species of Rhizophagus, Claroideoglomus, Paraglomus, Septoglomus, and Ambispora were recovered, and pot cultures from all except Ambispora were established. Cultures were identified to species level using morphological observation and rRNA gene sequencing combined with phylogenetic analysis. These cultures were used in pot experiments designed with a compartmentalised system to assess the contribution of fungal hyphae to the accumulation of essential elements, such as copper and zinc, and non-essential elements, such as lead, arsenic, thorium, and uranium into root and shoot tissues of Plantago lanceolata. The results indicated that none of the treatments had any positive or negative impact on shoot and root biomass. However, Rhizophagus irregularis treatments showed higher accumulation of copper and zinc in shoots, while R. irregularis and Septoglomus constrictum enhanced arsenic accumulation in roots. Moreover, R. irregularis increased uranium concentration in roots and shoots of the P. lanceolata plant. This study provides useful insight into fungal-plant interactions that determine metal and radionuclide transfer from soil into the biosphere at contaminated sites such as mine workings.

Disturbance induces similar shifts in arbuscular mycorrhizal fungal communities from grassland and arable field soils

Anthropogenic disturbances play an increasingly important role in structuring the diversity and functioning of soil organisms such as arbuscular mycorrhizal (AM) fungi. Frequently, multiple land-use practices, which may represent disturbances for AM fungal communities, operate simultaneously in different habitats. It is not known, however, how previous land-use history and specific habitat type influence AM fungal community response to disturbances. We applied mechanical (cutting to stimulate tillage) and chemical (herbicide addition) disturbances to AM fungal communities from meadow and arable field soils. Our results indicated that AM fungal communities from meadows, which previously had experienced mowing, were more species rich than communities from fields that had experienced intensive land-use practices. There were no significant differences, however, in the responses to disturbance of the AM fungal communities from field and meadow soils. We expected mechanical disturbance to promote taxa from the family Glomeraceae which are expected to exhibit a ruderal life-history strategy; instead, the abundance of this family increased in response to chemical disturbance. Simultaneous application of mechanical disturbance and herbicide decreased only the abundance of Diversisporaceae. No AM fungal families increased in abundance when both mechanical and chemical disturbances were applied simultaneously, but all disturbances increased the abundance of culturable AM fungi. Our study demonstrates that although chemical and mechanical forms of disturbance favor different AM fungal families, existing information about family-level characteristics may not adequately characterize the life history strategies of AM fungus species.