Arbuscular mycorrhizal fungi increase organic carbon decomposition under elevated CO2

Soil resource acquisition strategy modulates global plant nutrient and water economics

Natural selection favors growth by selecting a combination of plant traits that maximize photosynthetic CO2 assimilation at the lowest combined carbon costs of resource acquisition and use. We quantified how soil nutrient availability, plant nutrient acquisition strategies, and aridity modulate the variability in plant costs of nutrient acquisition relative to water acquisition (β). We used an eco-evolutionary optimality framework and a global carbon isotope dataset to quantify β. Under low soil nitrogen-to-carbon (N : C) ratios, a mining strategy (symbioses with ectomycorrhizal and ericoid mycorrhizal fungi) reduced β by mining organic nitrogen, compared with a scavenging strategy (symbioses with arbuscular mycorrhizal fungi). Conversely, under high N : C ratios, scavenging strategies reduced β by effectively scavenging soluble nitrogen, compared with mining strategies. N2-fixing plants did not exhibit reduced β under low N : C ratios compared with non-N2-fixing plants. Moisture increased β only in plants using a scavenging strategy, reflecting direct impacts of aridity on the carbon costs of maintaining transpiration in these plants. Nitrogen and phosphorus colimitation further modulated β. Our findings provide a framework for simulating the variability of plant economics due to plant nutrient acquisition strategies in earth system models.

Bacterial community in the hyphosphere of an arbuscular mycorrhizal fungus differs from that in the surrounding environment and is influenced by hyphal disruption

Bacterial composition and functions in the hyphosphere of arbuscular mycorrhizal (AM) fungi are complex because AM fungal hyphae transport carbon compounds from plant photosynthesis which feed bacteria and act as signaling molecules. This function is lost when hyphae separate from roots, a common occurrence in soil. However, the impact of such disturbances on hyphal surface bacteria remains unclear. We used in vitro bi-compartmented Petri plates with carrot roots and the AM fungus Rhizophagus irregularis MUCL 43194, separating root and hyphal compartments. Treatments included hyphae connected to roots (+ AM), no hyphae (-AM), and hyphae cut at different times (C3D and C0D, where C3D indicates hyphae cut 3 days before inoculation and C0D indicates hyphae cut on the day of inoculation) subjected to a bacterial suspension extracted from a field soil. Thirteen bacterial phyla were identified, with Streptomyces, Pseudomonas, Rhodococcus, and Cellulomonas dominating. Hyphae increased bacterial ASV relative abundance, notably enriching Actinobacteria ASVs. After 14 days, α-diversity decreased from -AM to C3D, C0D, and + AM, with fewer Bacteroidetes species in + AM compared to -AM. Root-connected hyphae led to deterministic bacterial assembly, while cut hyphae resulted in stochastic assembly. Our findings show that physical disruption of hyphae significantly affects bacterial diversity and may influence ecological functions.

Soil microbiome interventions for carbon sequestration and climate mitigation

Mitigating climate change in soil ecosystems involves complex plant and microbial processes regulating carbon pools and flows. Here, we advocate for the use of soil microbiome interventions to help increase soil carbon stocks and curb greenhouse gas emissions from managed soils. Direct interventions include the introduction of microbial strains, consortia, phage, and soil transplants, whereas indirect interventions include managing soil conditions or additives to modulate community composition or its activities. Approaches to increase soil carbon stocks using microbially catalyzed processes include increasing carbon inputs from plants, promoting soil organic matter (SOM) formation, and reducing SOM turnover and production of diverse greenhouse gases. Marginal or degraded soils may provide the greatest opportunities for enhancing global soil carbon stocks. Among the many knowledge gaps in this field, crucial gaps include the processes influencing the transformation of plant-derived soil carbon inputs into SOM and the identity of the microbes and microbial activities impacting this transformation. As a critical step forward, we encourage broadening the current widespread screening of potentially beneficial soil microorganisms to encompass functions relevant to stimulating soil carbon stocks. Moreover, in developing these interventions, we must consider the potential ecological ramifications and uncertainties, such as incurred by the widespread introduction of homogenous inoculants and consortia, and the need for site-specificity given the extreme variation among soil habitats. Incentivization and implementation at large spatial scales could effectively harness increases in soil carbon stocks, helping to mitigate the impacts of climate change.

Influence of Arbuscular Mycorrhizal Fungi on Nitrogen Dynamics During Cinnamomum camphora Litter Decomposition

Arbuscular mycorrhizal fungi (AMF) can preferentially absorb the released ammonium (NH4+) over nitrate (NO3-) during litter decomposition. However, the impact of AMF's absorption of NH4+ on litter nitrogen (N) decomposition is still unclear. In this study, we investigated the effects of AMF uptake for NH4+ on litter N metabolic characteristics by enriching NH4+ via AMF suppression and nitrification inhibition in a subtropical Cinnamomum camphora forest. The results showed that AMF suppression and nitrification inhibition significantly decelerated litter decomposition in the early stage due to the repression of NH4+ in extracellular enzyme activity. In the late stage, when soil NH4+ content was low, in contrast, they promoted litter decomposition by increasing the extracellular enzyme activities. Nitrification inhibition mainly promoted the utilization of plant-derived N by promoting the degradation of the amide I, amide II, and III bands by increasing protease activity, and it promoted ammonification by increasing urease activities, whereas it reduced the utilization of microbial-derived N by decreasing chitinase activity. On the contrary, AMF suppression, which significantly reduced the ammonification rate and increased the nitrification rate, only facilitated the degradation of the amide II band. Moreover, it intensified the microbial-derived N decomposition by increasing chitinase activity. The degradation of the amide I and II bands still relied on the priming effects of AMF on soil saprotrophs. This was likely driven by AMF-mediated phosphorus (P) mineralization. Nutrient acquiring, especially P by phosphatase, were the main factors in predicting litter decomposition and protein degradation. Thus, AMF could relieve the end-product repression of locally enriched NH4+ in extracellular enzyme activity and promote early-stage litter decomposition. However, the promotive effects of AMF on litter protein degradation and NH4+ release rely on P mineralization. Our results demonstrated that AMF could alleviate the N limitation for net primary production via accelerating litter N decomposition and reducing N loss. Moreover, they could restrict the decomposition of recalcitrant components by competing with saprotrophs for nutrients. Both pathways will contribute to C sequestration in forest ecosystems, which advances our understanding of AMF's contribution to nutrient cycling and ecosystem processes in subtropical forests.

Soil microbial carbon use efficiency differs between mycorrhizal trees: insights from substrate stoichiometry and microbial networks

The role of mycorrhizal associations in controlling forest soil carbon storage remains under debate. This uncertainty is potentially due to an incomplete understanding of their influence on the free-living soil microbiome and its functions. In this study, rhizosphere and non-rhizosphere soils were collected from eight arbuscular mycorrhizal (AM) and seven ectomycorrhizal (ECM) tree species in a temperate forest. We employed high-throughput sequencing and 18O-H2O labeling to analyze the soil microbial community and carbon use efficiency (CUE), respectively. We find microbial respiration rates are higher in rhizosphere than that in non-rhizosphere soils for ECM trees, whereas microbial growth rates show no significant differences. Consequently, microbial CUE is lower in rhizosphere compared to non-rhizosphere soils for ECM trees. In addition, we find that non-rhizosphere soils from ECM trees exhibited higher CUE compared to those from AM trees. Furthermore, we observe that bacterial-fungal co-occurrence networks in ECM soils exhibit greater complexity relative to AM ones. Using random forest and structural equation modeling analyses, we find that microbial stoichiometric carbon/nitrogen imbalance and network complexity are key predictors of soil microbial CUE for AM and ECM trees, respectively. Our findings shed new light on the pivotal role of mycorrhizal associations in shaping free-living microbial communities and their metabolic characteristics in the studied soils. These insights are critical for predicting soil carbon sequestration in response to shifts in ECM and AM species within temperate forest under climate change.

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.

Metagenomic Insights into the Enhancement of Bioavailable Nitrogen in Continuous Cropping Soil Through the Application of Traditional Chinese Medicine Residue Following Fumigation

Background/Objectives: Chemical fumigation can effectively inhibit the occurrence of soil-borne diseases; however, this approach can negatively affect the structure of the soil microbial community. The combination of soil fumigant and organic fertilizer application thus represents a widely adopted strategy in agricultural practice. Traditional Chinese medicine residue (TCMR) is a high-quality organic fertilizer; however, the impact of post-fumigation TCMR application on keystone taxa and their functional traits remains uncertain. Methods: This study examined the effects of five fertilization treatments on the diversity, key species, and related functional genes of microbial communities in rhizosphere soil of continuous cropping pepper. Results: Chemical fumigation followed by TCMR application markedly enhanced soil nutrient content in the rhizosphere and significantly influenced microbial community composition as well as functional gene patterns associated with microbial nitrogen cycling. It was also strongly correlated with soil bioavailable nitrogen content. The abundance of keystone bacterial species (Pseudomonadota, Actinomycetota, and Bacillota) substantially increased following TCMR application, alongside a notable rise in Ascomycota abundance within the fungal community. This shift contributed to an increase in beneficial bacterial abundance while reducing that of harmful bacteria. Additionally, TCMR addition affected the abundance of denitrification and DNRA genes involved in nitrogen cycling; specifically, nirB and nirK were strongly associated with soil organic nitrogen content. Conclusions: The combined application of chemical fumigants and TCMR modified the composition of keystone microbial community species by influencing rhizosphere soil TN and other nutrients, and these alterations were linked to multiple nitrogen-cycling functional genes.

Inoculation with arbuscular mycorrhizal fungi improves plant biomass and nitrogen and phosphorus nutrients: a meta-analysis

Arbuscular mycorrhizal fungi (AMF) have profound effects on plant growth and nitrogen (N) and phosphorus (P) nutrition. However, a comprehensive evaluation of how plant N and P respond to AMF inoculation is still unavailable. Here, we complied data from 187 original researches and carried out a meta-analysis to assess the effects of AMF inoculation on plant growth and N and P nutrition. We observe overall positive effects of AMF inoculation on plant performance. The mean increases of plant biomass, N concentration, P concentration, N and P uptake of whole plant are 47%, 16%, 27%, 67%, and 105%, respectively. AMF inoculation induces more increases in plant concentrations and storage of P than N. Plant responses to AMF inoculation are substantially higher with single AMF species than with mixed AMF species, in laboratory experiments than in field experiments, and in legumes than in non-legumes. The response ratios of plant N and P nutrition are positively correlated with AMF colonization rate, N addition, P addition, and water condition, while unvaried with experiment duration. The biggest and smallest effect sizes of AMF inoculation on plant performance are observed in the application of nitrate and ammonium, respectively. Accordingly, this meta-analysis study clearly suggests that AMF inoculation improves both plant N and P nutrients and systematically clarifies the variation patterns in AMF effects with various biotic and abiotic factors. These findings highlight the important role of AMF inoculation in enhancing plant N and P resource acquisitions and provide useful references for evaluating the AMF functions under the future global changes.

Ecology and diversity of arbuscular mycorrhizal fungi (AMF) in rice (Oryza sativa L.) in South India: an ecological analysis of factors influencing AMF in rice fields

AIMS

This study examined the diversity of arbuscular mycorrhizal fungi (AMF), mean spore density (MSD), and root colonization in relation to factors such as agroclimatic zones, rice varieties and soil types in paddy fields of South India. The aim was to understand how these factors influence AMF association in rice, facilitating their effective use as a biological tool in paddy cultivation.

METHODS AND RESULTS

AMF were identified through light microscopy of spores, while MSD and percentage-root-length colonization (PRLC) were measured using standard methods. Correlation and principal component analyses were performed to explore the interrelationships between AMF characteristics and various environmental, soil, and plant variables. Sixteen AMF species were identified across 29 rice varieties from three agroclimatic zones, 6 soil orders, and 18 soil series over 2 seasons. Notably, 70% of chemicalized rice fields lacked AMF spores, and only 50% exhibited root colonization. This study offers new insights into the role of AMF in rice cultivation.

CONCLUSION

The AMF diversity and root colonization in relation to environmental variables underscore their significant impact on AMF in particular crop fields.

Resolving the Intricate Effects of Multiple Global Change Drivers on Root Litter Decomposition

Plant roots represent about a quarter of global plant biomass and constitute a primary source of soil organic carbon (C). Yet, considerable uncertainty persists regarding root litter decomposition and their responses to global change factors (GCFs). Much of this uncertainty stems from a limited understanding of the multifactorial effects of GCFs and it remains unclear how these effects are mediated by litter quality, soil conditions and microbial functionality. Using complementary field decomposition and laboratory incubation approaches, we assessed the relative controls of GCF-mediated changes in root litter traits and soil and microbial properties on fine-root decomposition under warming, nitrogen (N) enrichment, and precipitation alteration. We found that warming and N enrichment accelerated fine-root decomposition by over 10%, and their combination showed an additive effect, while precipitation reduction suppressed decomposition overall by 12%, with the suppressive effect being most significant under warming-alone and N enrichment-alone conditions. Significantly, changes in litter quality played a dominant role and accelerated fine-root decomposition by 15% ~ 18% under warming and N enrichment, while changes in soil and microbial properties were predominant and reduced decomposition by 7% ~ 10% under precipitation reduction and the combined warming and N enrichment. Examining only the decomposition environment or litter properties in isolation can distort global change effects on root decomposition, underestimating precipitation reduction impacts by 38% and overstating warming and N effects by up to 73%. These findings highlight that the net impact of GCFs on root litter decomposition hinges on the interplay between GCF-modulated root decomposability and decomposition environment, as well as on the synergistic or antagonistic relationships among GCFs themselves. Our study emphasizes that integrating the legacy effects of multiple GCFs on root traits, soil conditions and microbial functionality would improve our prediction of C and nutrient cycling under interactive global change scenarios.

Arbuscular mycorrhizal fungi attenuate negative impact of drought on soil functions

Although positive effects of arbuscular mycorrhizal (AM) fungi on plant performance under drought have been well documented, how AM fungi regulate soil functions and multifunctionality requires further investigation. In this study, we first performed a meta-analysis to test the potential role of AM fungi in maintaining soil functions under drought. Then, we conducted a greenhouse experiment, using a pair of hyphal ingrowth cores to spatially separate the growth of AM fungal hyphae and plant roots, to further investigate the effects of AM fungi on soil multifunctionality and its resistance against drought. Our meta-analysis showed that AM fungi promote multiple soil functions, including soil aggregation, microbial biomass and activities of soil enzymes related to nutrient cycling. The greenhouse experiment further demonstrated that AM fungi attenuate the negative impact of drought on these soil functions and thus multifunctionality, therefore, increasing their resistance against drought. Moreover, this buffering effect of AM fungi persists across different frequencies of water supply and plant species. These findings highlight the unique role of AM fungi in maintaining multiple soil functions by mitigating the negative impact of drought. Our study highlights the importance of AM fungi as a nature-based solution to sustaining multiple soil functions in a world where drought events are intensifying.

Arbuscular Mycorrhizal Fungi as Biostimulant and Biocontrol Agents: A Review

Arbuscular mycorrhizal fungi (AMF) are soil microorganisms living in symbiosis with most terrestrial plants. They are known to improve plant tolerance to numerous abiotic and biotic stresses through the systemic induction of resistance mechanisms. With the aim of developing more sustainable agriculture, reducing the use of chemical inputs is becoming a major concern. After providing an overview on AMF history, phylogeny, development cycle and symbiosis benefits, the current review aims to explore the potential of AMF as biostimulants and/or biocontrol agents. Nowadays, AMF inoculums are already increasingly used as biostimulants, improving mineral nutrient plant acquisition. However, their role as a promising tool in the biocontrol market, as an alternative to chemical phytosanitary products, is underexplored and underdiscussed. Thus, in the current review, we will address the mechanisms of mycorrhized plant resistance to biotic stresses induced by AMF, and highlight the various factors in favor of inoculum application, but also the challenges that remain to be overcome.

Mycorrhizal fungi modify decomposition: a meta-analysis

It has been proposed that ectomycorrhizal fungi can reduce decomposition while arbuscular mycorrhizal fungi may enhance it. These phenomena are known as the 'Gadgil effect' and 'priming effect', respectively. However, it is unclear which one predominates globally. We evaluated whether mycorrhizal fungi decrease or increase decomposition, and identified conditions that mediate this effect. We obtained decomposition data from 43 studies (97 trials) conducted in field or laboratory settings that controlled the access of mycorrhizal fungi to substrates colonized by saprotrophs. Across studies, mycorrhizal fungi promoted decomposition of different substrates by 6.7% overall by favoring the priming effect over the Gadgil effect. However, we observed significant variation among studies. The substrate C : N ratio and absolute latitude influenced the effect of mycorrhizal fungi on decomposition and contributed to the variation. Specifically, mycorrhizal fungi increased decomposition at low substrate C : N and absolute latitude, but there was no discernable effect at high values. Unexpectedly, the effect of mycorrhizal fungi was not influenced by the mycorrhizal type. Our findings challenge previous assumptions about the universality of the Gadgil effect but highlight the potential of mycorrhizal fungi to negatively influence soil carbon storage by promoting the priming effect.

Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral-associated organic matter

Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, a precursor of soil organic matter (SOM), and a driver of soil microbial dynamics. Using two-chamber microcosms where an air gap isolated AMF from roots, we 13CO2-labeled Avena barbata for 6 wk and measured the C Rhizophagus intraradices transferred to SOM and hyphosphere microorganisms. NanoSIMS imaging revealed hyphae and roots had similar 13C enrichment. SOM density fractionation, 13C NMR, and IRMS showed AMF transferred 0.77 mg C g-1 of soil (increasing total C by 2% relative to non-mycorrhizal controls); 33% was found in occluded or mineral-associated pools. In the AMF hyphosphere, there was no overall change in community diversity but 36 bacterial ASVs significantly changed in relative abundance. With stable isotope probing (SIP)-enabled shotgun sequencing, we found taxa from the Solibacterales, Sphingobacteriales, Myxococcales, and Nitrososphaerales (ammonium oxidizing archaea) were highly enriched in AMF-imported 13C (> 20 atom%). Mapping sequences from 13C-SIP metagenomes to total ASVs showed at least 92 bacteria and archaea were significantly 13C-enriched. Our results illustrate the quantitative and ecological impact of hyphal C transport on the formation of potentially protective SOM pools and microbial roles in the AMF hyphosphere soil food web.

Improving soil fertility through dual inoculation with arbuscular mycorrhizal fungi and Rhizobium on a eutric cambisol cultivated with forage legumes in a semi-arid region

The Sub-Saharan region of southern Africa is characterized by high temperatures, low rainfall, and poor land-use management practices such as continuous cropping without replenishment of soil nutrients. The combination of these factors has resulted in nutrient depletion and land degradation. The current study aimed at investigating the effect of arbuscular mycorrhizal fungi (AMF) and Rhizobium bacteria inoculation on soil chemical properties in field-grown forage legumes, namely, Mucuna pruriens (mucuna), Lablab purpureus (lablab) and Vigna unguiculata (cowpea), in the semi-arid region of the Eastern Cape Province (South Africa). Forage legumes were inoculated with the AMF species Paraglomus occulum and the Rhizobia bacteria species Bradyrhizobium strain and grown for 120 days. Soil samples were collected in the following sequence: prior to planting, before flowering and after harvesting the forage legumes in each of the two seasons (2017/2018 and 2018/2019) and soil chemical properties were determined using standard procedures. The results showed that the addition of dual inoculation over time greatly improved soil chemical properties when compared to the control treatment. This was advocated by the significant (P ≤ 0.05) increase in soil pH, soil organic carbon, soil organic matter, total nitrogen, phosphorus, calcium, potassium, magnesium, sodium, sulfur and iron in soils. The concentration of cation exchange capacity was significantly (P ≤ 0.05) higher in cowpea treated with Rhizobium as compared to other treatment combinations. The control treatment of mucuna forage greatly improved the concentrations of manganese, boron, copper, molybdenum, and zinc over other treatment combinations only before the flowering stage. However, the concentrations of micronutrients were significantly higher on the treatment combination of lablab and single inoculation of AMF after harvesting. Generally, dual inoculation with AMF and Rhizobia enhanced soil properties when compared to a single inoculation or untreated control.

Unveiling the crucial role of soil microorganisms in carbon cycling: A review

Soil microorganisms, by actively participating in the decomposition and transformation of organic matter through diverse metabolic pathways, play a pivotal role in carbon cycling within soil systems and contribute to the stabilization of organic carbon, thereby influencing soil carbon storage and turnover. Investigating the processes, mechanisms, and driving factors of soil microbial carbon cycling is crucial for understanding the functionality of terrestrial carbon sinks and effectively addressing climate change. This review comprehensively discusses the role of soil microorganisms in soil carbon cycling from three perspectives: metabolic pathways, microbial communities, and environmental influences. It elucidates the roles of different microbial species in carbon cycling and highlights the impact of microbial interactions and environmental factors on carbon cycling. Through the synthesis of 2171 relevant papers in the Web of Science Core database, we elucidated the ecological community structure, activity, and assembly mechanisms of soil microorganisms crucial to the soil carbon cycle that have been widely analyzed. The integration of soil microbial carbon cycle and its driving factors are vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change. Such integration is vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change.

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

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

Various green manure-fertilizer combinations affect the soil microbial community and function in immature red soil

Green manure application is a common practice to improve soil fertility in China. However, the impact of different green manure-fertilizer combinations on the soil microbial communities in the low-fertility immature red soil in southern China remains unclear. In this study, we conducted a pot experiment using two common green manure crops, ryegrass (Lolium perenne L.) and Chinese milk vetch (Astragalus sinicus L.), along with a fallow treatment. We also considered three combined fertilizer management strategies, including mineral, humic acid, and organic manure fertilizers. We evaluated the soil microbial biomass, activity, communities, functional prediction and their correlation with soil properties during green manure growth and incorporation periods, to assess the potential alterations caused by different green manure and fertilizer combinations. Our findings indicate that green manure application, particularly in combination with organic fertilizers, increased the alpha diversity of the soil bacterial community, while the opposite trend was observed in the fungal community. The application of green manure altered the soil microbial communities during both growth and incorporation periods, especially the taxa that participate in carbon, nitrogen and sulfur cycles. Notably, ryegrass significantly increased the relative abundance of bacterial phylum Firmicutes and fungal phylum Ascomycota, whereas Chinese milk vetch significantly stimulated the bacterial phylum Acidobacteria and fungal phylum Glomeromycota. Compared with fallow treatments, green manure application significantly increased the soil pH by 4.1%-12.4%, and microbial biomass carbon by 29.8%-72.9%, regardless of the types of combined fertilizer. Additionally, the application of green manure resulted in a 35.6%-142.6% increase in urease activity and a 65.9%-172.9% increase in β-glucosidase activity compared to fallow treatments, while led to a 22.5%-55.6% decrease in catalase activity. Further analysis revealed that the changes in both bacterial and fungal communities positively correlated with soil pH, soil organic matter, total nitrogen and alkali hydrolyzed nitrogen contents. Moreover, the relationship between the soil microbial community and soil enzyme activities was regulated by the specific green manure species. In conclusion, our results provide insight into the effects of different green manure-fertilizer combinations on soil microorganisms and their underlying mechanisms in improving soil fertility in the low-fertility immature red soil.

Change in glomalin-related soil protein along latitudinal gradient encompassing subtropical and temperate blue carbon zones

Glomalin-related soil protein (GRSP), an abundant and eco-friendly bioproduct associated with arbuscular mycorrhizal fungi (AMF), contributes significantly to the soil particle aggregation and carbon sequestration. Although much research has been conducted on the storage of GRSP at different spatio-temporal scales in terrestrial ecosystems. However, the deposition of GRSP in large-scale coastal environments has not been revealed, which hinders an in-depth understanding of GRSP storage patterns and environmental controls, and this knowledge gap has become one of the key uncertainties in understanding the ecological functions of GRSP as blue carbon components in coastal environments. Therefore, we conducted large-scale experiments (spanning subtropical and warm temperate climate zones, coastlines over 2500 km) to test the relative contributions of environmental drivers that shape unique GRSP storage. In salt marshes of China, we found that the abundance of GRSP ranges from 0.29 mg g-1 to 1.10 mg g-1, and its concentration decreases with increasing latitude (R2 = 0.30, p < 0.01). The GRSP-C/SOC of salt marshes ranged from 4 % to 43 % and increased with the increase in latitude (R2 = 0.13, p < 0.05). The carbon contribution of GRSP does not follow the trend of increasing abundance, but is limited by the total amount of background organic carbon. In salt marsh wetlands, precipitation, clay content and pH are the main factors influencing GRSP storage. GRSP is positively correlated with precipitation (R2 = 0.42, p < 0.01) and clay content (R2 = 0.59, p < 0.01), but negatively correlated with pH (R2 = 0.48, p < 0.01). The relative contributions of the main factors to the GRSP differed across climatic zones. Soil properties, such as clay content and pH, explained 19.8 % of the GRSP in subtropical salt marshes (20°N < 34°N), however, in warm temperate salt marshes (34°N < 40°N), precipitation explained 18.9 % of the GRSP variation. Our study provides insight into the distribution and function of GRSP in coastal environments.

Mycorrhizae enhance reactive minerals but reduce mineral-associated carbon

Soil organic carbon (C) is the largest active C pool of Earth's surface and is thus vital in sustaining terrestrial productivity and climate stability. Arbuscular mycorrhizal fungi (AMF) form symbioses with most terrestrial plants and critically modulate soil C dynamics. Yet, it remains unclear whether and how AMF-root associations (i.e., mycorrhizae) interact with soil minerals to affect soil C cycling. Here we showed that the presence of both roots and AMF increased soil dissolved organic C and reactive Fe minerals, as well as litter decomposition and soil CO2 emissions. However, it reduced mineral-associated C. Also, high-resolution nanoscale secondary ion mass spectrometry images showed the existence of a thin coating (0.5-1.0 μm thick) of 56 Fe16 O- (Fe minerals) on the surface of 12 C14 N- (fungal biomass), illustrating the close physical association between fungal hyphae and soil Fe minerals. In addition, AMF genera were divergently related to reactive Fe minerals, with Glomus being positively but Paraglomus and Acaulospora negatively correlated with reactive Fe minerals. Moreover, the presence of roots and AMF, particularly when combined with litter addition, enhanced the abundances of several critical soil bacterial genera that are associated with the formation of reactive minerals in soils. A conceptual framework was further proposed to illustrate how AMF-root associations impact soil C cycling in the rhizosphere. Briefly, root exudates and the inoculated AMF not only stimulated the decomposition of litter and SOC and promoted the production of CO2 emission, but also drove soil C persistence by unlocking mineral elements and promoting the formation of reactive minerals. Together, these findings provide new insights into the mechanisms that underlie the formation of reactive minerals and have significant implications for understanding and managing soil C persistence.

Synergistic mechanisms of bioorganic fertilizer and AMF driving rhizosphere bacterial community to improve phytoremediation efficiency of multiple HMs-contaminated saline soil

The addition of Arbuscular mycorrhizal fungi (AMF) or bioorganic fertilizer (BOF) alone has been reported to enhance plant tolerance to heavy metals and salt stress and promote plant growth, while their synergistic effects on plant growth and rhizosphere microorganism are largely unknown. This study explored the effects of AMF (Rhizophagus intraradices), BOF and BOF + RI assisted phytoremediation on heavy metals contaminated saline soil improvement and revealed the microbial mechanism. For this purpose, a pot trial consisting of four treatments (CK, RI, BOF and BOF + RI) was carried out. The results showed that the biomass, nutrient element contents, the accumulation of heavy metals and Na of Astragalus adsurgens and soil properties were most significantly improved by BOF + RI. BOF + RI significantly impacted rhizosphere microbial diversity, abundance and community composition. Chloroflexi and Patescibacteria at the phylum level and Actinomadura, Iamia, and Desulfosporosinus at the genus level were significantly enriched in BOF + RI. Network analysis revealed that BOF + RI significantly changed the keystone and enhanced complexity and interaction. Most of the keystones had roles in promoting plant growth and stress resistance. This study suggested that phytoremediation assisted by BOF and AMF is an attractive approach to ameliorate heavy metals contaminated saline soil.

Plant -microbe assisted emerging contaminants (ECs) removal and carbon cycling

Continuous increase in the level of atmospheric CO₂ and environmental contaminates has aggravated various threats resulting from environmental pollution and climate change. Research into plant -microbe interaction has been a central concern of ecology for over the year. However, despite the clear contribution of plant -microbe to the global carbon cycle, the role of plant -microbe interaction in carbon pools, fluxes and emerging contaminants (ECs) removal are still a poorly understood. The use of plant and microbes in ECs removal and carbon cycling is an attractive strategy because microbes operate as biocatalysts to remove contaminants and plant roots offer a rich niche for their growth and carbon cycling. However, bio-mitigation of CO₂ and removal of ECs is still under research phase because of the CO₂ capture and fixation efficiency is too low for industrial purposes and cutting-edge removal methods have not been created for such emerging contaminants.

Drought Eliminates the Difference in Root Trait Plasticity and Mycorrhizal Responsiveness of Two Semiarid Grassland Species with Contrasting Root System

Root traits and arbuscular mycorrhizal (AM) fungi are important in determining the access of plants to soil resources. However, whether plants with different root systems (i.e., taproot vs. fibrous-root) exhibit different root trait plasticity and mycorrhizal responsiveness under drought remains largely unexplored. Tap-rooted Lespedeza davurica and fibrous-rooted Stipa bungeana were grown in monocultures in sterilized and live soils, followed by a drought treatment. Biomass, root traits, root colonization by AM fungi, and nutrient availability were evaluated. Drought decreased biomass and root diameter but increased the root:shoot ratio (RSR), specific root length (SRL), soil NO₃^--N, and available P for the two species. Under control and drought conditions, soil sterilization significantly increased the RSR, SRL, and soil NO₃^--N for L. davurica, but this only occurs under drought condition for S. bungeana. Soil sterilization significantly reduced AM fungal root colonization of both species, but drought significantly increased it in live soil. In water-abundant conditions, tap-rooted L. davurica may depend more on AM fungi than fibrous-rooted S. bungeana; however, under drought conditions, AM fungi are of equal importance in favoring both plant species to forage soil resources. These findings provide new insights for understanding the resource utilization strategies under climate change.

Arbuscular mycorrhizas accelerate the degradation of colour containing organic pollutants present in distillery spent wash leachates

Distillery spent wash (DSW) from molasses-based distilleries is being used as a low-cost alternative to chemical fertilizers in countries like India and Brazil. However, using DSW as a fertilizer substitute causes organic pollutant leaching, including melanoidins and caramel colourants that turn bodies of water dark brown. This study investigated the arbuscular mycorrhiza (AM) mediated degradation of organic pollutants in DSW. Mycorrhizal and non-mycorrhizal Sorghum bicolor were grown in microcosms for 16 weeks. The plants were fertilized with either raw DSW or Hoagland solution. Leachates draining from the microcosms after fertilization were collected three times in 30-day intervals. Each 30-day collection was preceded by two fertilizations. A gas chromatography-mass spectrometry comparative analyses of raw DSW with leachates of the third collection from mycorrhizal and non-mycorrhizal microcosms was made. Sixty-five and 42 complex organic compounds were detected in raw DSW and leachate collected from the non-mycorrhizal pots respectively. Only 26 compounds were detected in leachate collected from mycorrhizal pots. Absent from leachate of the mycorrhizal pots were: colour-containing organic compounds diacetone alcohol; 3-amino-2-cyano-6-methyl-6,7-dihydrothieno[2,3-b]pyrazine S-oxide; cyclohexane; 1,2-benzenedicarboxylic acid, butyl 8-methylnonyl ester; 2-pyrrolidinone; and acetic acid, dodecyl ester present in raw DSW. The results indicate that AM fungi can degrade organic pollutants in DSW.

Does elevated CO2 enhance the arsenic uptake by rice? Yes or maybe: Evidences from FACE experiments

Elevated CO₂ (eCO₂) strongly affects rice yield and quality in arsenic (As) paddy soils. However, understanding of the As accumulation in rice under coupled stress of eCO₂ and soil As is still limited while data are scarce. It greatly limits the prediction for future rice safety. This study investigated the As uptake by rice grown in different As paddy soils under two CO₂ conditions (ambient and ambient +200 μmol mol^-1) in the free-air CO₂ enrichment (FACE) system. Results showed that eCO₂ lowered soil Eh at the tillering stage and caused higher concentrations of dissolved As and Fe²⁺ in soil pore water. Compared with the control, the increased As transfer abilities in rice straws under eCO₂ contributed to the higher As accumulation in rice grains, and their total As concentrations were increased by 10.3-31.2%. Besides, the increased amounts of iron plaque (IP) under eCO₂ failed to effectively inhibit the As uptake by rice due to the difference in critical stage between As immobilized by IP (mainly in maturing stage) and uptake by rice roots (about 50% contribution before filling stage). Risk assessments suggest that eCO₂ enhanced the human health risks of As intake from rice grains produced in low-As paddy soils (<30 mg kg^-1). In order to alleviate the As threats to rice under eCO₂, we consider that proper soil drainage before filling stage to improve soil Eh can serve as an effective way to reduce As uptake by rice. Pursuing appropriate rice varieties to reduce the As transfer ability may be the other positive strategy.

Nitrogen availability mediates soil carbon cycling response to climate warming: A meta-analysis

Global climate warming may induce a positive feedback through increasing soil carbon (C) release to the atmosphere. Although warming can affect both C input to and output from soil, direct and convincing evidence illustrating that warming induces a net change in soil C is still lacking. We synthesized the results from field warming experiments at 165 sites across the globe and found that climate warming had no significant effect on soil C stock. On average, warming significantly increased root biomass and soil respiration, but warming effects on root biomass and soil respiration strongly depended on soil nitrogen (N) availability. Under high N availability (soil C:N ratio < 15), warming had no significant effect on root biomass, but promoted the coupling between effect sizes of root biomass and soil C stock. Under relative N limitation (soil C:N ratio > 15), warming significantly enhanced root biomass. However, the enhancement of root biomass did not induce a corresponding C accumulation in soil, possibly because warming promoted microbial CO₂ release that offset the increased root C input. Also, reactive N input alleviated warming-induced C loss from soil, but elevated atmospheric CO₂ or precipitation increase/reduction did not. Together, our findings indicate that the relative availability of soil C to N (i.e., soil C:N ratio) critically mediates warming effects on soil C dynamics, suggesting that its incorporation into C-climate models may improve the prediction of soil C cycling under future global warming scenarios.

A core microbiome in the hyphosphere of arbuscular mycorrhizal fungi has functional significance in organic phosphorus mineralization

The mycorrhizal pathway is an important phosphorus (P) uptake pathway for more than two-thirds of land plants. The arbuscular mycorrhizal (AM) fungi-associated hyphosphere microbiome has been considered as the second genome of mycorrhizal P uptake pathway and functionality in mobilizing soil organic P (Po). However, whether there is a core microbiome in the hyphosphere and how this is implicated in mining soil Po are less understood. We established on-site field trials located in humid, semiarid, and arid zones and a microcosm experiment in a glasshouse with specific AM fungi and varying soil types to answer the above questions. The hyphosphere microbiome of AM fungi enhanced soil phosphatase activity and promoted Po mineralization in all sites. Although the assemblage of hyphosphere microbiomes identified in three climate zones was mediated by environmental factors, we detected a core set in three sites and the subsequent microcosm experiment. The core members were co-enriched in the hyphosphere and dominated by Alphaproteobacteria, Actinobacteria, and Gammaproteobacteria. Moreover, these core bacterial members aggregate into stable guilds that contributed to phosphatase activity. The core hyphosphere microbiome is taxonomically conserved and provides functions, with respect to the mineralization of Po, that AM fungi lack.

Mycorrhiza-mediated recruitment of complete denitrifying Pseudomonas reduces N2O emissions from soil

BACKGROUND

Arbuscular mycorrhizal fungi (AMF) are key soil organisms and their extensive hyphae create a unique hyphosphere associated with microbes actively involved in N cycling. However, the underlying mechanisms how AMF and hyphae-associated microbes may cooperate to influence N₂O emissions from "hot spot" residue patches remain unclear. Here we explored the key microbes in the hyphosphere involved in N₂O production and consumption using amplicon and shotgun metagenomic sequencing. Chemotaxis, growth and N₂O emissions of isolated N₂O-reducing bacteria in response to hyphal exudates were tested using in vitro cultures and inoculation experiments.

RESULTS

AMF hyphae reduced denitrification-derived N₂O emission (max. 63%) in C- and N-rich residue patches. AMF consistently enhanced the abundance and expression of clade I nosZ gene, and inconsistently increased that of nirS and nirK genes. The reduction of N₂O emissions in the hyphosphere was linked to N₂O-reducing Pseudomonas specifically enriched by AMF, concurring with the increase in the relative abundance of the key genes involved in bacterial citrate cycle. Phenotypic characterization of the isolated complete denitrifying P. fluorescens strain JL1 (possessing clade I nosZ) indicated that the decline of net N₂O emission was a result of upregulated nosZ expression in P. fluorescens following hyphal exudation (e.g. carboxylates). These findings were further validated by re-inoculating sterilized residue patches with P. fluorescens and by an 11-year-long field experiment showing significant positive correlation between hyphal length density with the abundance of clade I nosZ gene.

CONCLUSIONS

The cooperation between AMF and the N₂O-reducing Pseudomonas residing on hyphae significantly reduce N₂O emissions in the microsites. Carboxylates exuded by hyphae act as attractants in recruiting P. fluorescens and also as stimulants triggering nosZ gene expression. Our discovery indicates that reinforcing synergies between AMF and hyphosphere microbiome may provide unexplored opportunities to stimulate N₂O consumption in nutrient-enriched microsites, and consequently reduce N₂O emissions from soils. This knowledge opens novel avenues to exploit cross-kingdom microbial interactions for sustainable agriculture and for climate change mitigation. Video Abstract.

Tree mycorrhizal association types control biodiversity-productivity relationship in a subtropical forest

Mycorrhizae are symbiotic associations between terrestrial plants and fungi in which fungi obtain nutrients in exchange for plant photosynthates. However, it remains unclear how different types of mycorrhizae affect their host interactions and productivity. Using a long-term experiment with a diversity gradient of arbuscular (AM) and ectomycorrhizal (EcM) tree species, we show that the type of mycorrhizae critically controls the effect of diversity on productivity. With increasing diversity, the net primary production of AM trees increased, but EcM trees decreased, largely because AM trees are more effective in acquiring nitrogen and phosphorus. Specifically, with diversity increase, AM trees enhance both nutrient resorption and litter decomposition, while there was a trade-off between litter decomposability and nutrient resorption in EcM trees. These results provide a mechanistic understanding of why AM trees using a different nutrient acquisition strategy from EcM trees can dominate in subtropical forests and at the same time their diversity enhances productivity.

Effects of elevated CO2 on the Cd uptake by rice in Cd-contaminated paddy soils

The rising atmospheric CO₂ is a major driver for climate change, directly affects rice production. Cadmium (Cd) in paddy soils also serves as a persistent concern. Currently, few studies consider the rice response to coupled stresses of elevated CO₂ (eCO₂) and soil Cd. Experimental evidence understanding the effects and mechanisms of eCO₂ on Cd uptake by rice is lacking yet. In a free-air CO₂ enrichment (FACE) system, a 3-year pot experiment was conducted to explore the Cd uptake by rice under two CO₂ conditions (ambient and ambient + 200 µmol·mol^-1) using combinations of in-situ Cd-contaminated soils and associated rice varieties. Results showed that more low-crystalline Fe oxides (Feh) in iron plaque (IP) were deposited on root surface with the increased dissolved Fe²⁺ due to lower soil redox status under eCO₂. The Cd accumulation in rice was hindered due to more Cd associated with Feh (Feh-Cd) rather than uptake by roots. Taken together, the relative effects of eCO₂ on Cd uptake by rice were consistent across years under different Cd-contaminated soils. Our findings will help to better understand the Cd uptake by rice under future climate conditions, and thus push the development of climate-crop-soil models and accurate prediction for food security.

The effects of ectomycorrhizal and saprotropic fungi on soil nitrogen mineralization differ from those of arbuscular and ericoid mycorrhizal fungi on the eastern Qinghai-Tibetan Plateau

Interactions between soil fungi and soil environmental factors regulate soil nitrogen (N) mineralization rates on the eastern Qinghai-Tibetan Plateau. Some studies have also illuminated differences in soil N mineralization rate based on different mycorrhizal forests, but the associated effect of soil fungal functional guilds and soil environmental factors underlying this process are not well-understood. Three primary forests respectively dominated by Abies fargesii var. faxoniana (ectomycorrhizal, EcM), Cupressus chengiana (arbuscular mycorrhizal, AM) and Rhododendron phaeochrysum (ericoid mycorrhizal, ErM) trees were selected in this area. Meanwhile, soil net N mineralization rate, soil fungal composition and soil enzyme activity among these three mycorrhizal forests were studied. Our results showed that there were significant differences in the seasonal variation of soil net N mineralization rates among three mycorrhizal forests. Soil net N mineralization rate in the AM forest was faster. EcM fungi and saprotroph are the main functional guilds in these three mycorrhizal forests. Meanwhile, the relative abundances of soil fungal functional guilds, soil temperature and soil peroxidase activity could explain 85.0% in the difference of soil net ammonification rate among three mycorrhizal forests. In addition, soil temperature, soil water-filled pore space and soil ammonium content play a central role in controlling the differing soil net nitrification rate among three mycorrhizal forests. Our results suggest differences in soil net mineralization among different mycorrhizal forest types are driven mainly by soil net ammonification. Soil fungal functional guilds and temperature regulate the rate of soil net ammonification by modulating soil peroxidase activity.

Diversity characteristics of arbuscular mycorrhizal fungi communities in the soil along successional altitudes of Helan Mountain, arid, and semi-arid regions of China

Introduction

Arbuscular mycorrhizal fungi (AMF) perform a vital role in terrestrial ecosystems.

Methods

To investigate the diversity of AMF communities on the western slope of Helan Mountain at different altitudes and their influence factors, high-throughput sequencing was used to study the structure and diversity of soil AMF communities under different environments and their interrelationships between AMF and environmental factors.

Results

The results revealed that there were significant differences (p < 0.05) in the physical and chemical properties of the soil along the different altitudes. A total of 1,145 OTUs were obtained by high-throughput sequencing, belonging to 1 phylum, 4 class, 6 orders, 13 families, 18 genera and 135 species, with the dominant genus being Glomus, which accounted for 75.27% of the relative abundance of the community. Soil AMF community structure was shown to be variable at the generic level according to NMDS analysis. Correlation analysis showed that soil pH, water content (WC), organic matter (OM), available K, available P and N were significantly correlated with AMF community diversity and species abundance (p < 0.05, p < 0.01). Based on redundancy analysis (RDA) and Monte Carlo test results, soil pH, WC and OM had highly significant effects (p < 0.01) on AMF community diversity and species abundance.

Discussion

This study investigates the relationship between AMF community structure and diversity and soil physicochemical properties at different elevations on the western slope of Helan Mountain, which is of great significance to the study of the Helan Mountain ecosystem.

Arbuscular mycorrhizal hyphal respiration makes a large contribution to soil respiration in a subtropical forest under various N input rates

Arbuscular mycorrhizal fungi (AMF) are widespread in subtropical forests and play a crucial role in belowground carbon (C) dynamics. Nitrogen (N) deposition or fertilization may affect AMF and thus the flux of plant-derived C back to the atmosphere via AMF hyphae. However, the contribution of AMF hyphal respiration to soil respiration and the response AMF hyphal respiration to increased soil N availability remain unknown. We studied the effect of N fertilization (0, 50, 100 and 200 kg N ha^-1 yr^-1) on AMF hyphal respiration, root respiration and heterotrophic (microbial) respiration in a subtropical Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) plantation. We found that short-term N addition did not affect root, AMF hyphal and soil microbial respiration, because soil N availability and extraradical hyphae were not affected by N addition. The AMF hyphal respiration contributed 12 % of total soil respiration and 25 % of the autotrophic respiration. Root, AMF hyphal and soil microbial respiration were positively correlated with soil moisture content but not with soil temperature. Our results indicate that AMF hyphal respiration is a large source of soil respiration, and should be considered in partitioning soil respiration into different components in future studies to better understand the response of soil respiration to N addition.

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

BACKGROUND

Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing-SIP-remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance-the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling.

RESULTS

Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to 13C-AMF hyphosphere DNA from a 13CO2 plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10-33 atom% 13C), even though the soils' overall enrichment was low (1.8 atom% 13C). We assembled 212 13C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived 13C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera.

CONCLUSIONS

Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP-fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat-generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs' phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling. Video Abstract.

The future of fungi: threats and opportunities

The fungal kingdom represents an extraordinary diversity of organisms with profound impacts across animal, plant, and ecosystem health. Fungi simultaneously support life, by forming beneficial symbioses with plants and producing life-saving medicines, and bring death, by causing devastating diseases in humans, plants, and animals. With climate change, increased antimicrobial resistance, global trade, environmental degradation, and novel viruses altering the impact of fungi on health and disease, developing new approaches is now more crucial than ever to combat the threats posed by fungi and to harness their extraordinary potential for applications in human health, food supply, and environmental remediation. To address this aim, the Canadian Institute for Advanced Research (CIFAR) and the Burroughs Wellcome Fund convened a workshop to unite leading experts on fungal biology from academia and industry to strategize innovative solutions to global challenges and fungal threats. This report provides recommendations to accelerate fungal research and highlights the major research advances and ideas discussed at the meeting pertaining to 5 major topics: (1) Connections between fungi and climate change and ways to avert climate catastrophe; (2) Fungal threats to humans and ways to mitigate them; (3) Fungal threats to agriculture and food security and approaches to ensure a robust global food supply; (4) Fungal threats to animals and approaches to avoid species collapse and extinction; and (5) Opportunities presented by the fungal kingdom, including novel medicines and enzymes.

Arbuscular Mycorrhizae Shift Community Composition of N-Cycling Microbes and Suppress Soil N2O Emission

Mycorrhizae are ubiquitous symbiotic associations between arbuscular mycorrhizal fungi (AMF) and terrestrial plants, in which AMF receive photosynthates from and acquire soil nutrients for their host plants. Plant uptake of soil nitrogen (N) reduces N substrate for microbial processes that generate nitrous oxide (N₂O), a potent greenhouse gas. However, the underlying microbial mechanisms remain poorly understood, particularly in agroecosystems with high reactive N inputs. We examined how plant roots and AMF affect N₂O emissions, N₂O-producing (nirK and nirS) and N₂O-consuming (nosZ) microbes under normal and high N inputs in conventional (CONV) and organically managed (OM) soils. Here, we show that high N input increased soil N₂O emissions and the ratio of nirK to nirS microbes. Roots and AMF did not affect the (nirK + nirS)/nosZ ratio but significantly reduced N₂O emissions and the nirK/nirS ratio. They reduced the nirK/nirS ratio by reducing nirK-Rhodobacterales but increasing nirS-Rhodocyclales in the CONV soil while decreasing nirK-Burkholderiales but increasing nirS-Rhizobiales in the OM soil. Our results indicate that plant roots and AMF reduced N₂O emission directly by reducing soil N and indirectly through shifting the community composition of N₂O-producing microbes in N-enriched agroecosystems, suggesting that harnessing the rhizosphere microbiome through agricultural management might offer additional potential for N₂O emission mitigation.

Nutrient loading decreases blue carbon by mediating fungi activities within seagrass meadows

Coastal pollution, including nutrient loading, can negatively impact seagrass health and cover and may consequently alter soil organic carbon (SOC) accumulation and preservation. Key to understanding how eutrophication impacts SOC cycling in seagrass ecosystems is how nutrient loading changes the sources of carbon being deposited and how these changes in resources, both nutrients and carbon availability, influence soil microbiota community and activity. Currently, the direction and magnitude of nutrient loading impacts on seagrass SOC dynamics are poorly understood at a meadow scale, limiting our ability to reveal the driving mechanisms of SOC remineralisation. The purpose of this study was to assess the response of surface SOC and soil microbiomes to nutrient loading within tropical seagrass meadows. To achieve this, we quantified both total SOC and recalcitrant soil organic carbon (RSOC) concentrations and sources, in addition to the composition of bacterial and fungal communities and soil extracellular enzyme activities. We found that nutrient loading elevated SOC and RSOC content, mainly facilitated by enhanced algal growth. There was no nutrient effect on the soil prokaryotic communities, however, saprotrophic fungi groups (i.e. Trapeliales, Sordaridales, Saccharomycetales and Polyporales) and fungal activities were elevated under high nutrient conditions, including extracellular enzyme activities linked to seagrass-based cellulose and lignin decomposition. This relative increase in RSOC transformation may decrease the relative contribution of seagrass carbon to RSOC pools. Additionally, significantly different fungal communities were observed between adjacent T. hemprichii and E. acoroides areas, which coincided with elevated RSOC-decomposing enzyme activity in T. hemprichii meadows, even though the mixed seagrass meadow received allochthonous SOC and RSOC from the same sources. These results suggest that nutrient loading stimulated fungal activity and community shifts specific to the local seagrass species, thereby causing fine-scale (within-meadow) variability in SOC cycling in response to nutrient loading. This study provides evidence that fungal composition and activity, mediated by human activities (e.g. nutrient loading), can be an important influence on seagrass blue carbon accumulation and remineralisation.

The Grain-for-Green project offsets warming-induced soil organic carbon loss and increases soil carbon stock in Chinese Loess Plateau

The dynamics of soil organic carbon (SOC) stock is a vital element affecting the climate, and ecological restoration is potentially an effective measure to mitigate climate change by enhancing vegetation and soil carbon stocks and thereby offsetting greenhouse gas emissions. The Grain-for-Green project (GFGP) implemented in Chinese Loess Plateau (LP) since 1999 is one of the largest ecological restoration projects in the world. However, the contributions of ecological restoration and climate change to ecosystem soil carbon sequestration are still unclear. In this study, we improved a soil carbon decomposition framework by optimizing the initial SOC stock based on full spatial simulation of SOC and incorporating the priming effect to investigate the SOC dynamics across the LP GFGP region from 1982 through 2017. Our results indicated that SOC stock in the GFGP region increased by 20.18 Tg C from 1982 through 2017. Most portion (15.83 Tg C) of the SOC increase was accumulated when the GFGP was initiated, with a SOC sink of 16.12 Tg C owing to revegetation restoration and a carbon loss of 0.29 Tg C due to warming during this period. The relationships between SOC and forest canopy height and investigations on the SOC dynamics after afforestation revealed that the accumulation rate of SOC could be as high as 24.68 g C m^-2 yr^-1 during the 70 years following afforestation, and that SOC could decline thereafter (-8.89 g C m^-2 yr^-1), which was mainly caused by warming. This study provides a new method for quantifying the contribution of ecological restoration to SOC changes, and also cautions the potential risk of LP SOC loss in the mature forest soil under future warming.

Calling for comprehensive explorations between soil invertebrates and arbuscular mycorrhizas

Arbuscular mycorrhizal (AM) fungi and soil invertebrates represent a large proportion of total soil biomass and biodiversity and are vital for plant performance, soil structure, and biogeochemical cycling. However, the role of soil invertebrates in AM fungi development remains elusive. In this opinion article, we summarize the ecological importance of AM fungi and soil invertebrates in the plant-soil continuum and highlight the effects of soil invertebrates on AM fungal hyphae development and functioning. In a context of global change, we envision that better mechanistic understanding of the complex feedback via chemical signaling pathways across the interactions between soil invertebrates and AM fungi is critical to predict their ecological consequences and will open new avenues for promoting ecosystem resilience and sustainability.

Decipher soil organic carbon dynamics and driving forces across China using machine learning

The dynamics of soil organic carbon (SOC) play a critical role in modulating global warming. However, the long-term spatiotemporal changes of SOC at large scale, and the impacts of driving forces remain unclear. In this study, we investigated the dynamics of SOC in different soil layers across China through the1980s to 2010s using a machine learning approach and quantified the impacts of the key factors based on factorial simulation experiments.Our results showed that the latest (2000-2014) SOC stock in the first meter soil (SOC₁₀₀ ) was 80.68 ± 3.49 Pg C, of which 42.6% was stored in the top 20 cm, sequestrating carbon with a rate of 30.80 ± 12.37 g C m^-2  yr^-1 since the 1980s. Our experiments focusing on the recent two periods (2000s and 2010s) revealed that climate change exerted the largest relative contributions to SOC dynamics in both layers and warming or drying can result in SOC loss. However, the influence of climate change weakened with soil depth, while the opposite for vegetation growth. Relationships between SOC and forest canopy height further confirmed this strengthened impact of vegetation with soil depth and highlighted the carbon sink function of deep soil in mature forest. Moreover, our estimates suggested that SOC dynamics in 71% of topsoil were controlled by climate change and its coupled influence with environmental variation (CE). Meanwhile, CE and the combined influence of climate change and vegetation growth dominated the SOC dynamics in 82.05% of the first meter soil. Additionally, the national cropland topsoil organic carbon increased with a rate of 23.6 ± 7.6 g C m^-2  yr^-1 since the 1980s, and the widely applied nitrogenous fertilizer was a key stimulus. Overall, our study extended the knowledge about the dynamics of SOC and deepened our understanding about the impacts of the primary factors.

Nutrients Regulate the Effects of Arbuscular Mycorrhizal Fungi on the Growth and Reproduction of Cherry Tomato

Arbuscular mycorrhizal fungi (AMF) colonize the rhizosphere of plants and form a symbiotic association with plants. Mycorrhizal symbionts have diversified ecological roles and functions which are affected by soil conditions. Understanding the effects of different AMF inoculation on plants under varied nutritional conditions is of great significance for further understanding the effects of the external environment regulating mycorrhizal symbiosis on plant phenotypic traits. In this study, the effects of four AMF inoculation treatments on the growth and reproductive performance of cherry tomato (Solanum lycopersicum var. cerasiforme) were investigated under three nutrient levels by pot experiment. It was found that the growth-promoting effect of AMF on cherry tomato decreased with nutrient reduction, and the effects of the same AMF inoculation treatment on cherry tomato were different at different nutrient levels. Nutrient levels and AMF had interactive effects on flower characteristics, fruit yield, resource allocation, and seed germination of the cherry tomato. In addition, AMF could promote sexual reproductive investment. Nutrient levels and AMF also affected the accumulation of nitrogen and phosphorus in cherry tomato, and there were significant differences among different AMF inoculation treatments. The results indicated that nutrient differences could affect the symbiosis between AMF and plants, and confirmed that there were differences in the effects of the four AMF inoculation treatments on the growth and reproductive traits of plants. The differences in growth and reproduction characteristics of cherry tomato between different AMF inoculation treatments at different nutrient levels indicated that the effects of AMF mycorrhizal on the traits of cherry tomato were regulated by nutrients.

Arbuscular mycorrhizal fungi conducting the hyphosphere bacterial orchestra

More than two-thirds of terrestrial plants acquire nutrients by forming a symbiosis with arbuscular mycorrhizal (AM) fungi. AM fungal hyphae recruit distinct microbes into their hyphosphere, the narrow region of soil influenced by hyphal exudates. They thereby shape this so-called second genome of AM fungi, which significantly contributes to nutrient mobilization and turnover. We summarize current insights into characteristics of the hyphosphere microbiome and the role of hyphal exudates on orchestrating its composition. The hyphal exudates not only contain carbon-rich compounds but also promote bacterial growth and activity and influence the microbial community structure. These effects lead to shifts in function and cause changes in organic nutrient cycling, making the hyphosphere a unique and largely overlooked functional zone in ecosystems.

Alternative stable states of the forest mycobiome are maintained through positive feedbacks

Most trees on Earth forms a symbiosis with either arbuscular mycorrhizal or ectomycorrhizal fungi. By forming common mycorrhizal networks, actively modifying the soil environment, and other ecological mechanisms - these contrasting symbioses may generate positive feedbacks that favor their own mycorrhizal strategy (i.e. the con-mycorrhizal strategy) at the expense of the alternative strategy. Positive con-mycorrhizal feedbacks set the stage for alternative stable states of forests and their fungi, where the presence of different forest mycorrhizal strategies is determined not only by external environmental conditions but also mycorrhiza-mediated feedbacks embedded within the forest ecosystem. Here we test this hypothesis using thousands of U.S. forest inventory sites to show arbuscular and ectomycorrhizal tree recruitment and survival exhibit positive con-mycorrhizal density dependence. Data-driven simulations show these positive feedbacks are sufficient in magnitude to generate and maintain alternative stable states of the forest mycobiome. Given the links between forest mycorrhizal strategy and carbon sequestration potential, the presence of mycorrhizal-mediated alternative stable states affects how we forecast forest composition, carbon sequestration and terrestrial climate feedbacks.

Using aquatic animals as partners to increase yield and maintain soil nitrogen in the paddy ecosystems

Whether species coculture can overcome the shortcomings of crop monoculture requires additional study. Here, we show how aquatic animals (i.e. carp, crabs, and softshell turtles) benefit paddy ecosystems when cocultured with rice. Three separate field experiments and three separate mesocosm experiments were conducted. Each experiment included a rice monoculture (RM) treatment and a rice-aquatic animal (RA) coculture treatment; RA included feed addition for aquatic animals. In the field experiments, rice yield was higher with RA than with RM, and RA also produced aquatic animal yields that averaged 0.52–2.57 t ha^-1. Compared to their corresponding RMs, the three RAs had significantly higher apparent nitrogen (N)-use efficiency and lower weed infestation, while soil N contents were stable over time. Dietary reconstruction analysis based on ¹³C and ¹⁵N showed that 16.0–50.2% of aquatic animal foods were from naturally occurring organisms in the rice fields. Stable-isotope-labeling (¹³C) in the field experiments indicated that the organic matter decomposition rate was greater with RA than with RM. Isotope ¹⁵N labeling in the mesocosm experiments indicated that rice used 13.0–35.1% of the aquatic animal feed-N. All these results suggest that rice-aquatic animal coculture increases food production, increases N-use efficiency, and maintains soil N content by reducing weeds and promoting decomposition and complementary N use. Our study supports the view that adding species to monocultures may enhance agroecosystem functions.

Monoculture, where only one type of crop is grown to the exclusion of any other organism, is a pillar of modern agriculture. Yet this narrow focus disregards how complex inter-species interactions can increase crop yield and biodiversity while decreasing the need for fertilizers or pesticides. For example, many farmers across Asia introduce carps, crabs, turtles or other freshwater grazers into their rice paddies. This coculture approach yields promising results but remains poorly understood. In particular, it is unclear how these animals’ behaviours and biological processes benefit the ecosystem.

To examine these questions, Guo, Zhao et al. conducted three separate four-year field experiments; they compared rice plots inhabited by either carp, mitten crabs or Chinese softshell turtles with fields where these organisms were not present.

With animals, the rice paddies had less weeds, better crop yields and steady levels of nitrogen (a natural fertiliser) in their soil. These ecosystems could breakdown organic matter faster, use it better and had a reduced need for added fertilizer. While animal feed was provided in the areas that were studied, carp, crabs and turtles obtained up to half their food from the field itself, eating weeds, algae and pests and therefore reducing competition for the crops.

This work helps to understand the importance of species interactions, showing that diversifying monocultures may boost yields and make agriculture more sustainable.

Plant nitrogen nutrition: The roles of arbuscular mycorrhizal fungi

Nitrogen (N) is the most abundant mineral nutrient required by plants, and crop productivity depends heavily on N fertilization in many soils. Production and application of N fertilizers consume huge amounts of energy and substantially increase the costs of agricultural production. Excess N compounds released from agricultural systems are also detrimental to the environment. Thus, increasing plant N uptake efficiency is essential for the development of sustainable agriculture. Arbuscular mycorrhizal (AM) fungi are beneficial symbionts of most terrestrial plants that facilitate plant nutrient uptake and increase host resistance to diverse environmental stresses. AM association is an endosymbiotic process that relies on the differentiation of both host plant roots and AM fungi to create novel contact interfaces within the cells of plant roots. AM plants have two pathways for nutrient uptake: either direct uptake via the root hairs and root epidermis, or indirectly through AM fungal hyphae into root cortical cells. Over the last few years, great progress has been made in deciphering the molecular mechanisms underlying the AM-mediated modulation of nutrient uptake processes, and a growing number of fungal and plant genes responsible for the uptake of nutrients from soil or transfer across the fungi-root interface have been identified. Here, we mainly summarize the recent advances in N uptake, assimilation, and translocation in AM symbiosis, and also discuss how N interplays with C and P in modulating AM development, as well as the synergies between AM fungi and soil microbial communities in N uptake.

Effect of AM Fungi Inoculation on Litter Bacterial Community Characteristics under Heavy Metal Stress

Because microorganisms are the primary driving force behind litter decomposition, they play an important role in maintaining ecosystem material and chemical cycling. Arbuscular mycorrhizal (AM) fungi can improve host plant tolerance to various environmental stressors, making their application in mining area remediation important. In this study, litter from the dominant plant species (Imperata cylindrica) in a copper tailings mining area was selected as the experimental material. We conducted a greenhouse-based heavy metal stress experiment to investigate how AM fungi affect litter microbial community characteristics and key ecological factors. Results showed that AM fungi species, heavy metal treatments, and their combined interaction had significant impacts on litter pH. Additionally, enzyme activities in litter were significantly affected by interactions between AM fungi species and heavy metal contaminates. Ralstonia was significantly positively correlated to lead (Pb) content, indicating that Ralstonia had a certain tolerance to Pb pollution. Sucrase and urease activity were increased when plants were inoculated with Rhizophagus irregularis under Pb stress. Furthermore, Microbacterium, Brevundimonas, and Pseudonocardia all may play important roles in litter decomposition, while a certain tolerance was observed in Kushneria and Roseivivax to heavy metal pollution when plants were inoculated with Glomus mosseae. Results showed that AM fungi affected litter bacterial community structure and function by influencing plant litter properties. By exploring interactions between AM fungi and bacterial communities in plant litter under heavy metal stress, we will better understand associative processes that promote the cycling of soil organic matter and nutrients contaminated by non-ferrous metal tailings.

N enrichment affects the arbuscular mycorrhizal fungi-mediated relationship between a C4 grass and a legume

Arbuscular mycorrhizal fungi (AMF) regulate soil nutrient cycling, directly supplying a host plant with nitrogen (N). AMF can also affect the outcome of interspecific interactions, but a mechanistic understanding of how soil N availability affects AMF-mediated interspecific relationships is currently lacking. We selected one dominant (Bothriochloa ischaemum; C4 grass) and one subordinate (Lespedeza davurica; legume) species in a natural grassland climax community to investigate the mechanism by which AMF influence interspecific interaction (mixed and monoculture) under three levels of N addition (0, low, and high N addition). Under the non-N addition treatment, AMF preferentially supplied N to the roots of B. ischaemum at the expense of N uptake by L. davurica, resulting in inhibited AMF benefits for L. davurica shoot growth. Under the low N addition treatment, interspecific interaction via AMF promoted L. davurica growth. Compared to the non-N addition treatment, N addition largely mitigated the effects, both positive (for B. ischaemum) and negative (for L. davurica), of AMF-mediated interspecific interaction on plant N uptake via AMF. When soil N availability severely limited plant growth, preferential N supply to the C4 grass by AMF was important for maintaining the abundance of the dominant species. When the N limitation for plant growth was alleviated by N addition, the interaction between AMF and soil microorganisms improved nutrient availability for the legume by stimulating activity of the enzyme responsible for soil organic matter mineralization, which is important for maintaining the abundance of the subordinate species. These data could influence strategies for maintaining biodiversity.

Potential metabolic mechanisms for inhibited chloroplast nitrogen assimilation under high CO2

Improving photosynthesis is considered a major and feasible option to dramatically increase crop yield potential. Increased atmospheric CO2 concentration often stimulates both photosynthesis and crop yield, but decreases protein content in the main C3 cereal crops. This decreased protein content in crops constrains the benefits of elevated CO2 on crop yield and affects their nutritional value for humans. To support studies of photosynthetic nitrogen assimilation and its complex interaction with photosynthetic carbon metabolism for crop improvement, we developed a dynamic systems model of plant primary metabolism, which includes the Calvin-Benson cycle, the photorespiration pathway, starch synthesis, glycolysis-gluconeogenesis, the tricarboxylic acid cycle, and chloroplastic nitrogen assimilation. This model successfully captures responses of net photosynthetic CO2 uptake rate (A), respiration rate, and nitrogen assimilation rate to different irradiance and CO2 levels. We then used this model to predict inhibition of nitrogen assimilation under elevated CO2. The potential mechanisms underlying inhibited nitrogen assimilation under elevated CO2 were further explored with this model. Simulations suggest that enhancing the supply of α-ketoglutarate is a potential strategy to maintain high rates of nitrogen assimilation under elevated CO2. This model can be used as a heuristic tool to support research on interactions between photosynthesis, respiration, and nitrogen assimilation. It also provides a basic framework to support the design and engineering of C3 plant primary metabolism for enhanced photosynthetic efficiency and nitrogen assimilation in the coming high-CO2 world.