Root rot destabilizes the Sanqi rhizosphere core fungal microbiome by reducing the negative connectivity of beneficial microbes.

The stability of microbial communities, especially among core taxa, is essential for supporting plant health. However, the impacts of disease infection on the stability of rhizosphere fungal core microbiome remain largely unexplored. In this study, we delved into the effects of root rot infestation on the community structure, function, network complexity, and stability of Sanqi fungal core microbiomes, employing amplicon sequencing combined with co-occurrence network and cohesion analyses. Our investigation revealed that root rot disease led to a decrease in the α-diversity but an increase in the ß-diversity of the Sanqi fungal core microbiomes in the rhizosphere. Notably, Ilyonectria, Plectosphaerella, and Fusarium emerged as indicator species in the rhizosphere core microbiome of root rot-infected Sanqi plants, while Mortierella predominated as the dominant biomarker taxa in healthy soils. Additionally, root rot diminished the complexity and modularity of the rhizosphere networks by reducing the metrics associated with nodes, edges, degrees, and modularity. Furthermore, root rot resulted in a reduction in the proportion of negative connections in the network and the negative/positive cohesion of the entire core fungal microbiome. Particularly noteworthy was the observation that root rot infection destabilized the rhizosphere core fungal microbiome by weakening the negative connectivity associated with beneficial agents. Collectively, these results highlight the significance of the negative connectivity of beneficial agents in ensuring the stability of core microbial community.IMPORTANCERoot rot disease has been reported as the most devastating disease in the production process of artificial cultivated Sanqi ginseng, which seriously threatens the Sanqi industry. This study provides valuable insights into how root rot influences microbial relationships within the community. These findings open up opportunities for disease prevention and the promotion of plant health by regulating microbial interactions. In summary, the research sheds light on the ecological consequences of root rot on rhizosphere fungal microbiomes and offers potential strategies for managing soil-borne diseases and enhancing plant health.

Soil recalcitrant but not labile organic nitrogen mineralization contributes to microbial nitrogen immobilization and plant nitrogen uptake.

Soil organic nitrogen (N) mineralization not only supports ecosystem productivity but also weakens carbon and N accumulation in soils. Recalcitrant (mainly mineral-associated organic matter) and labile (mainly particulate organic matter) organic materials differ dramatically in nature. Yet, the patterns and drivers of recalcitrant (MNrec) and labile (MNlab) organic N mineralization rates and their consequences on ecosystem N retention are still unclear. By collecting MNrec (299 observations) and MNlab (299 observations) from 57 15N tracing studies, we found that soil pH and total N were the master factors controlling MNrec and MNlab, respectively. This was consistent with the significantly higher rates of MNrec in alkaline soils and of MNlab in natural ecosystems. Interestingly, our analysis revealed that MNrec directly stimulated microbial N immobilization and plant N uptake, while MNlab stimulated the soil gross autotrophic nitrification which discouraged ammonium immobilization and accelerated nitrate production. We also noted that MNrec was more efficient at lower precipitation and higher temperatures due to increased soil pH. In contrast, MNlab was more efficient at higher precipitation and lower temperatures due to increased soil total N. Overall, we suggest that increasing MNrec may lead to a conservative N cycle, improving the ecosystem services and functions, while increasing MNlab may stimulate the potential risk of soil N loss.

Warming-Induced Stimulation of Soil N2O Emissions Counteracted by Elevated CO2 from Nine-Year Agroecosystem Temperature and Free Air Carbon Dioxide Enrichment.

Globally, agricultural soils account for approximately one-third of anthropogenic emissions of the potent greenhouse gas and stratospheric ozone-depleting substance nitrous oxide (N2O). Emissions of N2O from agricultural soils are affected by a number of global change factors, such as elevated air temperatures and elevated atmospheric carbon dioxide (CO2). Yet, a mechanistic understanding of how these climatic factors affect N2O emissions in agricultural soils remains largely unresolved. Here, we investigate the soil N2O emission pathway using a 15N tracing approach in a nine-year field experiment using a combined temperature and free air carbon dioxide enrichment (T-FACE). We show that the effect of CO2 enrichment completely counteracts warming-induced stimulation of both nitrification- and denitrification-derived N2O emissions. The elevated CO2 induced decrease in pH and labile organic nitrogen (N) masked the stimulation of organic carbon and N by warming. Unexpectedly, both elevated CO2 and warming had little effect on the abundances of the nitrifying and denitrifying genes. Overall, our study confirms the importance of multifactorial experiments to understand N2O emission pathways from agricultural soils under climate change. This better understanding is a prerequisite for more accurate models and the development of effective options to combat climate change.

High carbon resource diversity enhances the certainty of successful plant pathogen and disease control.

The host-associated microbiome highly determines plant health. Available organic resources, such as food for microbes, are important in shaping microbial community structure and multifunctionality. However, how using organic resources precisely manipulates the soil microbiome and makes it supportive of plant health remains unclear. Here, we experimentally tested the influence of carbon resource diversity on the microbial trophic network and pathogen invasion success in a microcosm study. We further explored how resource diversity affects microbial evenness, community functions, and plant disease outcomes in systems involving tomato plants and the in vivo soil microbiome. Increasing available resource diversity altered trophic network architecture, increased microbial evenness, and thus increased the certainty of successful pathogen control. By contrast, the invasion resistance effects of low resource diversity were less effective and highly varied. Accordingly, increases in the evenness and connection of dominant species induced by high resource diversity significantly contributed to plant disease suppression. Furthermore, high carbohydrate diversity upregulated plant immune system regulation-related microbial functions. Our results deepen the biodiversity-invasion resistance theory and provide practical guidance for the control of plant pathogens and diseases by using organic resource-mediated approaches, such as crop rotation, intercropping, and organic amendments.

Effects of Reductive Soil Disinfestation Combined with Liquid-Readily Decomposable Compounds and Solid Plant Residues on the Bacterial Community and Functional Composition.

Reductive soil disinfestation (RSD) incorporated with sole plant residues or liquid-readily decomposable compounds is an effective management strategy to improve soil health. However, the synthetic effects of RSD incorporated with liquid-readily decomposable compounds and solid plant residues on soil ecosystem services remain unclear. Field experiments were carried out to investigate the effects of untreated soil (CK), RSD incorporated with sawdust (SA), molasses (MO), and their combinations (SA + MO) on the bacterial community and functional composition. The results showed that RSD treatments significantly altered soil bacterial community structure compared to CK treatment. The bacterial community structure and composition in MO and SA + MO treatments were clustered compared to SA treatment. This was mainly attributed to the readily decomposable carbon sources in molasses having a stronger driving force to reshape the soil microbial community during the RSD process. Furthermore, the functional compositions, such as the disinfestation efficiency of F. oxysporum (96.4 - 99.1%), abundances of nitrogen functional genes, soil metabolic activity, and functional diversity, were significantly increased in all of the RSD treatments. The highest disinfestation efficiency and abundances of denitrification (nirS and nrfA) and nitrogen fixation (nifH) genes were observed in SA + MO treatment. Specifically, SA + MO treatment enriched more abundant beneficial genera, e.g., Oxobacter, Paenibacillus, Cohnella, Rummeliibacillus, and Streptomyces, which were significantly and positively linked to disinfestation efficiency, soil metabolic activity, and denitrification processes. Our results indicated that combining RSD practices with liquid-readily decomposable compounds and solid plant residues could effectively improve soil microbial community and functional composition.

Deciphering the Synergies of Reductive Soil Disinfestation Combined with Biochar and Antagonistic Microbial Inoculation in Cucumber Fusarium Wilt Suppression Through Rhizosphere Microbiota Structure.

Application of reductive soil disinfestation (RSD), biochar, and antagonistic microbes have become increasingly popular strategies in a microbiome-based approach to control soil-borne diseases. The combined effect of these remediation methods on the suppression of cucumber Fusarium wilt associated with microbiota reconstruction, however, is still unknown. In this study, we applied RSD treatment together with biochar and microbial application of Trichoderma and Bacillus spp. in Fusarium-diseased cucumbers to investigate their effects on wilt suppression, soil chemical changes, microbial abundances, and the rhizosphere communities. The results showed that initial RSD treatment followed by biochar amendment (RSD-BC) and combined applications of microbial inoculation and biochar (RSD-SQR-T37-BC) decreased nitrate concentration and raised soil pH, soil organic carbon (SOC), and ammonium in the treated soils. Under RSD, the applications of Bacillus (RSD-SQR), Trichoderma (RSD-T37), and biochar (RSD-BC) suppressed wilt incidence by 26.8%, 37.5%, and 32.5%, respectively, compared to non-RSD treatments. Moreover, RSD-SQR-T37-BC and RSD-T37 caused greater suppressiveness of Fusarium wilt and F. oxysporum by 57.0 and 33.5%, respectively. Rhizosphere beta diversity and alpha diversity revealed a difference between RSD-treated and non-RSD microbial groups. The significant increase in the abundance, richness, and diversity of bacteria, and the decrease in the abundance and diversity of fungi under RSD-induced treatments attributed to the general suppression. Identified bacterial (Bacillus, Pseudoxanthomonas, Flavobacterium, Flavisolibacter, and Arthrobacter) and fungal (Trichoderma, Chaetomium, Cladosporium, Psathyrella, and Westerdykella) genera were likely the potential antagonists of specific disease suppression for their significant increase of abundances under RSD-treated soils and high relative importance in linear models. This study infers that the RSD treatment induces potential synergies with biochar amendment and microbial applications, resulting in enhanced general-to-specific suppression mechanisms by changing the microbial community composition in the cucumber rhizosphere.

Global patterns of soil gross immobilization of ammonium and nitrate in terrestrial ecosystems.

Microbial nitrogen (N) immobilization, which typically results in soil N retention but based on the balance of gross N immobilization over gross N production, affects the fate of the anthropogenic reactive N. However, global patterns and drivers of soil gross immobilization of ammonium (INH4 ) and nitrate (INO3 ) are still only tentatively known. Here, we provide a comprehensive analysis considering gross N production rates, soil properties, and climate and their interactions for a deeper understanding of the patterns and drivers of INH4 and INO3 . By compiling and analyzing 1966 observations from 274 15 N-labelled studies, we found a global average of INH4 and INO3 of 7.41 ± 0.72 and 2.03 ± 0.30 mg N kg-1  day-1 with a ratio of INO3 to INH4 (INO3 :INH4 ) of 0.79 ± 0.11. Soil INH4 and INO3 increased with increasing soil gross N mineralization (GNM) and nitrification (GN), microbial biomass, organic carbon, and total N and decreasing soil bulk density. Our analysis revealed that GNM and GN were the main stimulators for INH4 and INO3 , respectively. The structural equation modeling showed that higher soil microbial biomass, total N, pH, and precipitation stimulate INH4 and INO3 through enhancing GNM and GN. However, higher temperature and soil bulk density suppress INH4 and INO3 by reducing microbial biomass and total N. Soil INH4 varied with terrestrial ecosystems, being greater in grasslands and forests, which have higher rates of GNM, than in croplands. The highest INO3 :INH4 was observed in croplands, which had higher rates of GN. The global average of GN to INH4 was 2.86 ± 0.31, manifesting a high potential risk of N loss. We highlight that anthropogenic activities that influence soil properties and gross N production rates likely interact with future climate changes and land uses to affect soil N immobilization and, eventually, the fate of the anthropogenic reactive N.

Global Patterns and Drivers of Soil Dissimilatory Nitrate Reduction to Ammonium.

Dissimilatory nitrate reduction to ammonium (DNRA), the nearly forgotten process in the terrestrial nitrogen (N) cycle, can conserve N by converting the mobile nitrate into non-mobile ammonium avoiding nitrate losses via denitrification, leaching, and runoff. However, global patterns and controlling factors of soil DNRA are still only rudimentarily known. By a meta-analysis of 231 observations from 85 published studies across terrestrial ecosystems, we find a global mean DNRA rate of 0.31 ± 0.05 mg N kg-1 day-1, being significantly greater in paddy soils (1.30 ± 0.59) than in forests (0.24 ± 0.03), grasslands (0.52 ± 0.15), and unfertilized croplands (0.18 ± 0.04). Soil DNRA was significantly enhanced at higher altitude and lower latitude. Soil DNRA was positively correlated with precipitation, temperature, pH, soil total carbon, and soil total N. Precipitation was the main stimulator for soil DNRA. Total carbon and pH were also important factors, but their effects were ecosystem-specific as total carbon stimulates DNRA in forest soils, whereas pH stimulates DNRA in unfertilized croplands and paddy soils. Higher temperatures inhibit soil DNRA via decreasing total carbon. Moreover, nitrous oxide (N2O) emissions were negatively related to soil DNRA. Thus, future changes in climate and land-use may interact with management practices that alter soil substrate availability and/or soil pH to enhance soil DNRA with positive effects on N conservation and lower N2O emissions.

Inhibition of Elevated Atmospheric Carbon Dioxide to Soil Gross Nitrogen Mineralization Aggravated by Warming in an Agroecosystem.

The response of soil gross nitrogen (N) cycling to elevated carbon dioxide (CO2) concentration and temperature has been extensively studied in natural and semi-natural ecosystems. However, how these factors and their interaction affect soil gross N dynamics in agroecosystems, strongly disturbed by human activity, remains largely unknown. Here, a 15N tracer study under aerobic incubation was conducted to quantify soil gross N transformation rates in a paddy field exposed to elevated CO2 and/or temperature for 9 years in a warming and free air CO2 enrichment experiment. Results show that long-term exposure to elevated CO2 significantly inhibited or tended to inhibit gross N mineralization at elevated and ambient temperatures, respectively. The inhibition of soil gross N mineralization by elevating CO2 was aggravated by warming in this paddy field. The inhibition of gross N mineralization under elevated CO2 could be due to decreased soil pH. Long-term exposure to elevated CO2 also significantly reduced gross autotrophic nitrification at ambient temperature, probably due to decreased soil pH and gross N mineralization. In contrast, none of the gross N transformation rates were affected by long-term exposure to warming alone. Our study provides strong evidence that long-term dual exposure to elevated CO2 and temperature has a greater negative effect on gross N mineralization rate than the single exposure, potentially resulting in progressive N limitation in this agroecosystem and ultimately increasing demand for N fertilizer.

Patterns and drivers of global gross nitrogen mineralization in soils.

Soil gross nitrogen (N) mineralization (GNM), a key microbial process in the global N cycle, is mainly controlled by climate and soil properties. This study provides for the first time a comprehensive analysis of the role of soil physicochemical properties and climate and their interactions with soil microbial biomass (MB) in controlling GNM globally. Through a meta-analysis of 970 observations from 337 published papers from various ecosystems, we found that GNM was positively correlated with MB, total carbon, total N and precipitation, and negatively correlated with bulk density (BD) and soil pH. Our multivariate analysis and structural equation modeling revealed that GNM is driven by MB and dominantly influenced by BD and precipitation. The higher total N accelerates GNM via increasing MB. The decrease in BD stimulates GNM via increasing total N and MB, whereas higher precipitation stimulates GNM via increasing total N. Moreover, the GNM varies with ecosystem type, being greater in forests and grasslands with high total carbon and MB contents and low BD and pH compared to croplands. The highest GNM was observed in tropical wet soils that receive high precipitation, which increases the supply of soil substrate (total N) to microbes. Our findings suggest that anthropogenic activities that affect soil microbial population size, BD, soil substrate availability, or soil pH may interact with changes in precipitation regime and land use to influence GNM, which may ultimately affect ecosystem productivity and N loss to the environment.

Global gross nitrification rates are dominantly driven by soil carbon-to-nitrogen stoichiometry and total nitrogen.

Soil gross nitrification (GN) is a critical process in the global nitrogen (N) cycle that results in the formation of nitrate through microbial oxidation of ammonium or organic N, and can both increase N availability to plants and nitrous oxide emissions. Soil GN is thought to be mainly controlled by soil characteristics and the climate, but a comprehensive analysis taking into account the climate, soil characteristics, including microbial characteristics, and their interactions to better understand the direct and indirect controlling factors of GN rates globally is lacking. Using a global meta-analysis based on 901 observations from 330 15 N-labeled studies, we show that GN differs significantly among ecosystem types, with the highest rates found in croplands, in association with higher pH which stimulates nitrifying bacteria activities. Autotrophic and heterotrophic nitrifications contribute 63% and 37%, respectively, to global GN. Soil GN increases significantly with soil total N, microbial biomass, and soil pH, but decreases significantly with soil carbon (C) to N ratio (C:N). Structural equation modeling suggested that GN is mainly controlled by C:N and soil total N. Microbial biomass and pH are also important factors controlling GN and their effects are similar. Precipitation and temperature affect GN by altering C:N and/or soil total N. Soil total N and temperature drive heterotrophic nitrification, whereas C:N and pH drive autotrophic nitrification. Moreover, GN is positively related to nitrous oxide and carbon dioxide emissions. This synthesis suggests that changes in soil C:N, soil total N, microbial population size, and/or soil pH due to anthropogenic activities may influence GN, which will affect nitrate accumulation and gaseous emissions of soils under global climate and land-use changes.

The fungal community outperforms the bacterial community in predicting plant health status.

Characterizing the relationship between soil biotic and abiotic properties and plant health status is crucial to understanding the pathogenesis of soil-borne diseases. Here, we compared these properties in the soils of lisianthus with different disease incidence plots and report the cause-effect relationship between soil properties and plant health status using heat treatment coupled with microbiota self/across re-inoculations. The relative importance of soil bacterial and fungal communities in predicting plant health was also analyzed. Results showed that the soils with low and high disease incidences (LDS and HDS) harbored differential microbial communities and physicochemical properties. The LDS soil had relatively low Fusarium oxysporum abundance, electrical conductivity (EC), and NO3--N content. Soil microbial community was the direct determinant of plant health. The disease-suppressive activity of the microbiome in the LDS soil could be transferred to the HDS soil. Also, the relative importance of the fungal community in predicting plant health status was greater than that of the bacterial community, as reflected by (1) the fungal community could drive more complex networks related to healthy plants and (2) the diversity and core taxa of the fungal community had higher mean predictor importance values for plant health. The relative abundances of core genera Acremonium, Mycothermus, and Chryseolinea were significantly and negatively correlated with the disease incidence and the abundances of pathogens, identifying these genera as potential disease-suppressive agents. Taken together, our results reveal a direct relationship between soil properties and plant health status, in which the fungal community composition is most important for predicting plant health status. KEY POINTS: • Soil with differing pathological groups harbors distinct microbial communities. • Soil microbial communities directly determine the plant's health status. • Fungal community is a better predictor of plant health than the bacterial community.

The food nitrogen footprint for African countries under fertilized and unfertilized farms.

Although nitrogen (N) is a limiting factor for food production (FP) in Africa, and African food security is seriously threatened by the phenomenon of soil N depletion, there is a dearth of information that shows the points to focus on throughout the chain of FP and food consumption (FC) in all African countries to minimize N loss while securing food N supply. Food N footprint (NF) is an indicator for tracing the losses of reactive N (Nr) with regard to the FP and FC chain. This is the first study to calculate the food NF for all African countries under fertilized and unfertilized farms, by calculating two sets of virtual N factors (VNFs; kg Nr released to the environment kg-1 N in consumed product): one for unfertilized farms (the unfertilized scenario) and one for fertilized farms (the fertilized scenario). The fertilized and unfertilized VNFs were utilized to calculate a weighted average set of VNFs (the combined scenario). From the percentage of farms that utilize N fertilizer, and the N percentage in production that comes from soil depletion, the proportion used for the combined scenario was determined. Soil N depletion factors (SNDFs; kg N taken from the unfertilized soil kg-1 N in food consumed) were also computed to identify the quantity of N extracted from the soil for food production. We have also provided the changes in N inputs, N outputs, and N use efficiency (NUE) for North Africa and Sub-Saharan Africa (SSA) during the last 57 years. The average total N input to croplands increased from 24 and 19 kg N ha-1 yr-1 in 1961-1965 to 100 and 42 kg N ha-1 yr-1 in 2010-2017 for North Africa and SSA, respectively. The NUE declined from 109% and 67% (1961-1965) to 47% and 63% (2010-2017) for North Africa and SSA, respectively. The total average per-capita food NF was 11 and 5.8 kg N cap-1 yr-1 in unfertilized farms; 21 and 14 kg N cap-1 yr-1 in fertilized farms; and 19 and 7.5 kg N cap-1 yr-1 under the combined scenario for North Africa and SSA, respectively. Vegetable-fruit and beef have the highest SDNFs in Africa. FP in Africa contributes approximately 70% of the total food NF. Therefore, if possible, the best way for Africans to reduce soil N depletion and N emissions is to encourage the production and consumption of livestock and crops products with less VNF and SNDF. However, African people do not have this luxury of choice because of poverty and ignorance. Therefore, African policy-makers must adopt integrated approaches that provide effective tools to control the production of animals and crops in conjunction with the improvement of NUE. Trying to completely change the African agricultural system is impossible, but strategies must be developed to reduce soil depletion in a gradual way, as well as a shift towards low-VNF foods.

Autotoxic Ginsenoside Disrupts Soil Fungal Microbiomes by Stimulating Potentially Pathogenic Microbes.

Autotoxic ginsenosides have been implicated as one of the major causes for replant failure of Sanqi ginseng (Panax notoginseng); however, the impact of autotoxic ginsenosides on the fungal microbiome, especially on soilborne fungal pathogens, remains poorly understood. In this study, we aimed to investigate the influence of the ginsenoside monomers Rg1, Rb1, and Rh1, and that of their mixture (Mix), on the composition and diversity of the soil fungal community, as well as on the abundance and growth of the soilborne pathogen Fusarium oxysporum in pure culture. The addition of autotoxic ginsenosides altered the composition of the total fungal microbiome, as well as the taxa within the shared and unique treatment-based components, but did not alter alpha diversity (α-diversity). In particular, autotoxic ginsenosides enriched potentially pathogenic taxa, such as Alternaria, Cylindrocarpon, Gibberella, Phoma, and Fusarium, and decreased the abundances of beneficial taxa such as Acremonium, Mucor, and Ochroconis Relative abundances of pathogenic taxa were significantly and negatively correlated with those of beneficial taxa. Among the pathogenic fungi, the genus Fusarium was most responsive to ginsenoside addition, with the abundance of Fusarium oxysporum consistently enhanced in the ginsenoside-treated soils. Validation tests confirmed that autotoxic ginsenosides promoted mycelial growth and conidial germination of the root rot pathogen F. oxysporum In addition, the autotoxic ginsenoside mixture exhibited synergistic effects on pathogen proliferation. Collectively, these results highlight that autotoxic ginsenosides are capable of disrupting the equilibrium of fungal microbiomes through the stimulation of potential soilborne pathogens, which presents a significant hurdle in remediating replant failure of Sanqi ginseng.IMPORTANCE Sanqi ginseng [Panax notoginseng (Burk.) F. H. Chen] is geoauthentically produced in a restricted area of southwest China, and successful replanting requires a rotation cycle of more than 15 to 30 years. The increasing demand for Sanqi ginseng and diminishing arable land resources drive farmers to employ consecutive monoculture systems. Replant failure has severely threatened the sustainable production of Sanqi ginseng and causes great economic losses annually. Worse still, the acreage and severity of replant failure are increased yearly, which may destroy the Sanqi ginseng industry in the near future. The significance of this work is to decipher the mechanism of how autotoxic ginsenosides promote the accumulation of soilborne pathogens and disrupt the equilibrium of soil fungal microbiomes. This result may help us to develop effective approaches to successfully conquer the replant failure of Sanqi ginseng.

Dynamics of nitrite in acidic soil during extraction with potassium chloride studied using 15 N tracing.

RATIONALE: Nitrite is well known to be unstable, including during soil extraction with KCl (especially in acidic soils), but the source and fate of NO2 - in the short duration of the extraction process remain unclear. METHODS: A series of 15 N-tracing studies explored NO2 - transformations during KCl extraction in acidic and alkaline soils. Tests considering multiple factors assessed the interactions of such factors as soil sterilization, extraction time, and pH adjustment. After addition of 15 NO2 - , 15 NH4 + , and 15 NO3 - tracers, the concentrations and isotopic compositions of N2 O, N2 , NH4 + , NO3 - , NO2 - , and dissolved organic nitrogen (DON) were measured to investigate the production and consumption of NO2 - . RESULTS: Nitrite was stable in alkaline soils during KCl extraction. In contrast, changes did occur in acidic soils during KCl extraction: NO2 - declined rapidly in the first 10 min of extraction although the subsequent rate of decrease lessened as the extraction time progressed. Significant dilution of 15 NO2 - suggested high rates of NO2 - production and even higher rates of consumption. The soil's organic N was the only source of NO2 - and also its main destination. Soil sterilization showed that NO2 - processes during extraction were chemical, not microbial. The pH adjustment of acidic soil stabilized its NO2 - . CONCLUSIONS: Overall, the pH adjustment of KCl solution appears favorable for investigating NO2 - dynamics. For example, this work recommends an extraction solution comprising a 4:1 mixture of 2.5 M KCl solution and pH 8.4 buffer, which was more convenient to operate than the method reported by Stevens and Laughlin.

Reductive soil disinfestation incorporated with organic residue combination significantly improves soil microbial activity and functional diversity than sole residue incorporation.

Reductive soil disinfestation (RSD) is an effective agricultural practice to eliminate soil-borne pathogens that heavily relies on the organic substrate used. However, the influences of combined application of organic residues on disinfestation efficiency, soil microbiomes, and their associated functional characteristics are still not well-characterized. In this work, four treatments, i.e., untreated soil (CK), RSD with 15 t ha-1 sugarcane bagasse (SB), bean dregs (BD), and their combinations (1:1, SB+BD), were conducted to investigate their influence on disinfestation efficiency, microbial functional diversity, community diversity, and composition using Biolog analysis, real-time PCR, and high-throughput sequencing. The SB+BD treatment had synergetic effects on soil microbial activity, metabolic activity, and functional diversity with similar efficacy in pathogen elimination and soil salinization alleviation, as compared to the SB and BD treatments. Moreover, the SB+BD treatment distinctly altered the structure and composition of bacterial and fungal communities, especially enriched the core microbiomes associated with soil general functions such as organic decomposition and nitrate removal. The SB+BD treatment also strengthened the soil specific functions including disease suppression through the regulation of unique microbiomes. In addition, the microbial richness, diversity, and evenness were significantly higher in the SB+BD-treated soil as compared to the SB- and BD-treated soils. Taken together, RSD incorporated with organic residue combination not only efficiently restore the degraded soils, but also considerably improve soil functions, which may benefit to the health for the future plant generations. KEY POINTS: • Organic residue combination effectively declines pathogen density. • Organic residue combination improves soil microbial activity and functional diversity. • The enriched core microbiome is responsible for soil general functions. • The induced unique microbiome is important for soil specific functions.

Garlic Substrate Induces Cucumber Growth Development and Decreases Fusarium Wilt through Regulation of Soil Microbial Community Structure and Diversity in Replanted Disturbed Soil.

Garlic substrate could influence plant growth through affecting soil microbiome structure. The relationship mechanism between changes in soil microbial communities, disease suppression and plant development, however, remains unclear, particularly in the degraded soil micro-ecological environment. In this study, garlic substrates as a soil amendment were incorporated with different ratios (1:100, 3:100 and 5:100 g/100 g of soil) in a replanted disturbed soil of long-term cucumber monoculture (annual double cropping system in a greenhouse). The results indicated that higher amount of C-amended garlic substrate significantly induced soil suppressiveness (35.9% greater than control (CK) against the foliar disease incidence rate. This inhibitory effect consequently improved the cucumber growth performance and fruit yield to 20% higher than the non-amended soil. Short-term garlic substrate addition modified the soil quality through an increase in soil organic matter (SOM), nutrient availability and enzymatic activities. Illumina MiSeq sequencing analysis revealed that soil bacterial and fungal communities in the garlic amendment were significantly different from the control. Species richness and diversity indices significantly increased under treated soil. The correlation-based heat map analysis suggested that soil OM, nutrient contents and biological activators were the primary drivers reshaping the microbial community structure. Furthermore, garlic substrate inhibited soil-borne pathogen taxa (Fusarium and Nematoda), and their reduced abundances, significantly affecting the crop yield. In addition, the host plant recruited certain plant-beneficial microbes due to substrate addition that could directly contribute to plant-pathogen inhibition and crop biomass production. For example, abundant Acidobacteria, Ascomycota and Glomeromycota taxa were significantly associated with cucumber yield promotion. Firmicutes, Actinobacteria, Bacteroidetes, Basidiomycota and Glomeromycota were the associated microbial taxa that possibly performed as antagonists of Fusarium wilt, with plant pathogen suppression potential in monocropped cucumber-planted soil.

Characterizing the Key Agents in a Disease-Suppressed Soil Managed by Reductive Soil Disinfestation.

Many agricultural soil management strategies have been shown to be effective in preventing soilborne diseases. However, their underlying mechanisms of action remain unknown. In this study, we used reductive soil disinfestation (RSD), also named anaerobic soil disinfestation (ASD) and biological soil disinfestation (BSD), as a representative method for disease management and cucumber damping-off diseased soil as a model system to identify the disease-suppressive agents in artificially managed soil. The results showed that RSD created a soil environment that was different from that of the diseased soil, where the pH level and the carbon content were greater. Heat treatment and pathogen or soil microbiota self- and cross-reinoculations resulted in the expansion of various soil microbial communities harbored by the two soil environments, as well as various disease incidences. Environmental factors were the primary determinant of the reassembled bacterial community, followed by initial microbiota, whereas initial microbiota was the key driver of the reassembled fungal community. The relative abundances of the bacterial order Sphingobacteriales and fungal order Sordariales, as well as their affiliated genera Sphingobacterium, unclassified genus within Sphingobacteriaceae, Zopfiella, and unclassified genera within Lasiosphaeriaceae and Chaetomiaceae, were negatively correlated with disease incidence and positively associated with RSD-conditioned soil environment. Furthermore, we validated that both the microbial disease-suppressive agent and its adapted abiotic environment contributed to disease suppression. Our results elucidate the abiotic and biotic foundations of soilborne disease suppression under artificial management and highlight that the abiotic environment is as important as the microbial agents in disease suppression.IMPORTANCE Most defined systems have identified microbial elements as the primary factors determining disease suppression, but the involvement of the soil abiotic environment is less defined. The significance of this work is that the soil abiotic environment plays a critical role in the establishment of the soil microbial community and key microbial agents that directly contribute to the prevention of soilborne diseases. We highlight the importance of the soil abiotic environment in disease suppression. Furthermore, we provide a framework for the characterization of disease-suppressing agents in artificially managed soil. These results will gradually close the gap in knowledge on soil environment-microbe interactions.

Toward a Generic Analytical Framework for Sustainable Nitrogen Management: Application for China.

Managing reactive nitrogen (Nr) to achieve a sustainable balance between production of food, feed and fiber, and environmental protection is a grand challenge in the context of an increasingly affluent society. Here, we propose a novel framework for national nitrogen (N) assessments enabling a more consistent comparison of the uses, losses and impacts of Nr between countries, and improvement of Nr management for sustainable development at national and regional scales. This framework includes four key components: national scale N budgets, validation of N fluxes, cost-benefit analysis and Nr management strategies. We identify four critical factors for Nr management to achieve the sustainable development goals: N use efficiency (NUE), Nr recycling ratio (e.g., ratio of livestock excretion applied to cropland), human dietary patterns and food waste ratio. This framework was partly adopted from the European Nitrogen Assessment and now is successfully applied to China, where it contributed to trigger policy interventions toward improvements for future sustainable use of Nr. We demonstrate how other countries can also benefit from the application our framework, in order to include sustainable Nr management under future challenges of growing population, hence contributing to the achievement of some key sustainable development goals (SDGs).

Reductive soil disinfestation effectively alleviates the replant failure of Sanqi ginseng through allelochemical degradation and pathogen suppression.

Replant failure has threatened the production of Sanqi ginseng (Panax notoginseng) mainly due to the accumulation of soil-borne pathogens and allelochemicals. Reductive soil disinfestation (RSD) is an effective practice used to eliminate soil-borne pathogens; however, the potential impact of RSD on the degradation of allelochemicals and the growth of replant Sanqi ginseng seedlings remain poorly understood. In this study, RSD was conducted on a Sanqi ginseng monoculture system (SGMS) and a maize-Sanqi ginseng system (MSGS), defined as SGMS_RSD and MSGS_RSD, respectively. The aim was to investigate the impact of RSD on allelochemicals, soil microbiomes, and survival rates of replant seedlings. Both short-term maize planting and RSD treatment significantly degraded the ginsenosides in Sanqi ginseng-cultivated soils, with the degradation rate being higher in the RSD treatment. The population of Fusarium oxysporum and the relative abundance of genus Fusarium were dramatically suppressed by RSD treatment. Furthermore, the RSD treatment, but not maize planting, markedly alleviated the replant failure of Sanqi ginseng, with the seedling survival rate being 52.7-70.7% 6 months after transplanting. Interestingly, RSD followed by short-term maize planting promoted microbial activity restoration, ginsenoside degradation, and ultimately alleviated the replant failure much better than RSD treatment alone (70.7% vs. 52.7%). Collectively, these results indicate that RSD treatment could considerably reduce the obstacles and might also act as a potential agriculture regime for overcoming the replant failure of Sanqi ginseng. Additional practices, such as crop rotation, beneficial microorganism inoculation, etc. may also still be needed to ensure the long-term efficacy of seedling survival.