Distinct impacts of reductive soil disinfestation and chemical soil disinfestation on soil fungal communities and memberships

Soil Solarization Efficiently Reduces Fungal Soilborne Pathogen Populations, Promotes Lettuce Plant Growth, and Affects the Soil Bacterial Community

Lettuce is the most cultivated leafy vegetable in Greece; however, due to the adopted intensive cropping system, its cultivation is susceptible to many soilborne pathogens that cause significant yield and quality losses. In the current study, the impact of various soil disinfestation methods such as solarization, chemical disinfestation, and application of a biofungicide were evaluated in a commercial field that has been repeatedly used for lettuce cultivation. The populations of soilborne pathogens Rhizoctonia solani, Pythium ultimum, Fusarium oxysporum, and Fusarium equiseti were measured via qPCR before and after the implementation of the specific disinfestation methods. Although all the tested methods significantly reduced the population of the four soilborne pathogens, soil solarization was the most effective one. In addition, solarization reduced the number of lettuce plants affected by the pathogens R. solani and F. equiseti, and at the same time, significantly influenced the growth of lettuce plants. Amplicon sequence analysis of 16S rRNA-encoding genes used to study the soil bacterial community structure showed that Firmicutes, Proteobacteria, and Actinobacteria were the predominant bacterial phyla in soil samples. In general, solarization had positive effects on Firmicutes and negative effects on Proteobacteria and Actinobacteria; soil fumigation with dazomet increased the relative abundance of Firmicutes and Proteobacteria and reduced the corresponding values of Actinobacteria; and biofungicide had no significant effects on the three predominant bacterial phyla. The bacterial community composition and structure varied after the application of the soil disinfestation treatments since they imposed changes in the α- and β-diversity levels. The results of this study are expected to contribute towards implementing the most effective control method against the most common soilborne pathogens in intensively cultivated fields, such as those cultivated with leafy vegetables.

Influences of tobacco straw return with lime on microbial community structure of tobacco-planting soil and tobacco leaf quality

Soil amendment is an important strategy for improving soil quality and crop yield. From 2014 to 2019, we conducted a study to investigate the effects of tobacco straw return with lime on soil nutrients, soil microbial community structure, tobacco leaf yield, and quality in southern Anhui, China. A field experiment was conducted with four treatments: straw removed (CK), straw return (St), straw return with dolomite (St + D), and straw return with lime (St + L). Results showed that after 5 years of application, the St + L significantly increased the soil pH by 16.9%, and the contents of soil alkaline nitrogen (N) and available potassium (K) by 17.2% and 23.0%, respectively, compared with the CK. Moreover, the St + L significantly increased tobacco leaf yield (24.0%) and the appearance (9.1%) and sensory (5.9%) quality of flue-cured tobacco leaves. The addition of soil conditioners (straw, dolomite, and lime) increased both the total reads and effective sequences of soil microorganisms. Bacterial diversity was more sensitive to changes in the external environment compared to soil fungi. The application of soil amendments (lime and straw) promoted the growth of beneficial microorganisms in the soil. Additionally, bacterial species had greater competition and limited availability of resources for survival compared to fungi. The results showed that soil microorganisms were significantly influenced by the presence of AK, AN, and pH contents. These findings can provide an effective method for improving the quality of flue-cured tobacco leaves and guiding the amelioration of acidic soil in regions where tobacco-rice rotation is practiced.

Evaluating the effects of mefenoxam on taxonomic and functional dynamics of nontarget fungal communities during carrot cultivation

Ridomil Gold SL (45.3% a.i. mefenoxam) is a widely used chemical fungicide for the control of oomycetes. However, its impact on fungal communities remains unexplored. Therefore, the goal of this study was to examine the effects of mefenoxam on the temporal dynamics of fungal taxonomic and functional diversities during carrot cultivation under four treatment groups: mefenoxam application with and without Pythium inoculation, and untreated control groups with and without Pythium inoculation. Our in vitro sensitivity assay showed that the maximum recommended concentration of mefenoxam, 0.24 ppm, did not suppress the mycelial growth of P. irregulare. At 100 ppm, mycelial growth was only reduced by 11.4%, indicating that the isolate was resistant to mefenoxam. MiSeq sequencing data revealed transient taxonomic variations among treatments 2 weeks post-treatment. Mortierella dominated the fungal community in the mefenoxam-Pythium combination treatment, as confirmed through PCR using our newly designed Mortierella-specific primers. Conversely, mefenoxam-Pythium combination had adverse effects on Penicillium, Trichoderma, and Fusarium, and decrease the overall alpha diversity. However, these compositional changes gradually reverted to those observed in the control by the 12th week. The predicted ecological functions of fungal communities in all Pythium and mefenoxam treatments shifted, leading to a decrease in symbiotrophs and plant pathogen functional groups. Moreover, the community-level physiological profiling approach, utilizing 96-well Biolog FF microplates, showed discernible variations in the utilization of 95 diverse carbon sources among the treatments. Notably, arbutin, L-arabinose, Tween 80, and succinamic acid demonstrated a strong positive association with Mortierella. Our findings demonstrate that a single application of mefenoxam at its recommended rate triggers substantial taxonomic and functional shifts in the soil fungal community. Considering this impact, the conventional agricultural practice of repeated mefenoxam application is likely to exert considerable shifts on the soil ecosystem that may affect agricultural sustainability.

Facilitating Effects of Reductive Soil Disinfestation on Soil Health and Physiological Properties of Panax ginseng

Chemical soil fumigation (CSF) and reductive soil disinfestation (RSD) have been proven to be effective agricultural strategies to improve soil quality, restructure microbial communities, and promote plant growth in soil degradation remediation. However, it is still unclear how RSD and CSF ensure soil and plant health by altering fungal communities. Field experiments were conducted to investigate the effects of CSF with chloropicrin, and RSD with animal feces on soil properties, fungal communities and functional composition, and plant physiological characteristics were evaluated. Results showed that RSD and CSF treatment improved soil properties, restructured fungal community composition and structure, enhanced fungal interactions and functions, and facilitated plant growth. There was a significant increase in OM, AN, and AP contents in the soil with both CSF and RSD treatments compared to CK. Meanwhile, compared with CK and CSF, RSD treatment significantly increased biocontrol Chaetomium relative abundance while reducing pathogenic Neonectria relative abundance, indicating that RSD has strong inhibition potential. Furthermore, the microbial network of RSD treatment was more complex and interconnected, and the functions of plant pathogens, and animal pathogen were decreased. Importantly, RSD treatment significantly increased plant SOD, CAT, POD activity, SP, Ca, Zn content, and decreased MDA, ABA, Mg, K, and Fe content. In summary, RSD treatment is more effective than CSF treatment, by stimulating the proliferation of probiotic communities to further enhance soil health and plant disease resistance.

Effects of reductive soil disinfestation combined with different types of organic materials on the microbial community and functions

Reductive soil disinfestation (RSD) is an effective method to inhibit soilborne pathogens. However, it remains unclear how RSD combined with different types of organic materials affects the soil ecosystems of perennial plants. Pot experiments were conducted to investigate the effects of RSD incorporated with perilla (PF), alfalfa (MS), ethanol, and acetic acid on soil properties, enzyme activities, microbial communities and functions, and seedling growth. Results showed that RSD-related treatments improved soil properties and enzyme activities, changed microbial community composition and structure, enhanced microbial interactions and functions, and facilitated seedling growth. Compared with CK, RSD-related treatments increased soil pH, available nitrogen, and available potassium contents, sucrase and catalase activities, and decreased soil electric conductivity values. Meanwhile, RSD-related treatment also significantly reduced the relative abundance of Fusarium while increasing the relative abundance of Arthrobacter, Terrabacter, and Gemmatimonas. The reduction was more evident in PF and MS treatment, suggesting the potential for RSD combined with solid agricultural wastes to suppress pathogens. Furthermore, the microbial network of RSD-related treatment was more complex and interconnected, and the functions related to carbon, nitrogen, sulfur, and hydrogen cycling were significantly increased, while the functions of bacterial and fungal plant pathogens were decreased. Importantly, RSD-related treatments also significantly promoted seed germination and seedling growth. In summary, RSD combined with solid agricultural wastes is better than liquid easily degradable compounds by regulating the composition and function of microbial communities to improve soil quality and promote plant growth.IMPORTANCEReductive soil disinfestation (RSD) is an effective agricultural practice. We found that RSD combined with solid agricultural wastes is better than that of liquid easily degradable compounds, may improve soil quality and microbial community structure, inhibit the proliferation of pathogenic bacteria, and contribute to the growth of replanted crops. Thus, RSD combined with solid agricultural wastes is more effective than liquid easily degradable compounds.

Reductive soil disinfestation and Fe amendment improve soil microbial composition and Fritillaria production

The continuous obstacles of cropping cause severe economic loss, which seriously threaten agricultural sustainable development. In addition, managing excess waste, such as potato peel and mineral waste residues, is a vital burden for industry and agriculture. Therefore, we explored the feasibility of reductive soil disinfestation (RSD) with potato peel and amendment with iron mineral waste residues for the production of Fritillaria thunbergii, which is vulnerable to continuous obstacles. In this study, the influences of iron mineral, RSD with different organic maters, as well as the combined effects of iron mineral and RSD on Fritillaria rhizosphere soil physicochemical properties, microbial communities, and Fritillaria production were investigated. The results revealed that the RSD treatments with potato peel significantly reduced the soil salinity and increased the soil pH, microbial activity, organic matter, and the contents of K and Ca. RSD with potato peel also significantly thrived of the beneficial microbes (Bacillus, Azotobacter, Microvirga, and Chaetomium), and down-regulated potential plant pathogens. RSD with potato peel significantly promoted F. thunbergii yield and quality. Moreover, the combined effects of RSD and iron mineral amendment further enhanced soil health, improved microbial community composition, and increased the yield and peimisine content of F. thunbergii by 24.2% and 49.3%, respectively. Overall, our results demonstrated that RSD with potato peel and amendment with iron mineral waste residues can efficiently improve soil fertility, modify the microbial community, and benefit for both the sustainable production of F. thunbergii and the management of waste. KEY POINTS: • RSD increases soil pH, organic matter, microbial activity, and mineral content • RSD with potato peel enriches beneficial microbes and decreases plant pathogens • PP + Fe treatment increases Fritillaria yield by 24.2% and peimisine content by 49.3.

Pathogen resistance in soils associated with bacteriome network reconstruction through reductive soil disinfestation

Reductive soil disinfestation (RSD) is an effective bioremediation technique to restructure the soil microbial community and eliminate soilborne phytopathogens. Yet we still lack a comprehensive understanding of the keystone taxa involved and their roles in ecosystem functioning in degraded soils treated by RSD. In this study, the bacteriome network structure in RSD-treated soil and the subsequent cultivation process were explored. As a result, bacterial communities in RSD-treated soil developed more complex topologies and stable co-occurrence patterns. The richness and diversity of keystone taxa were higher in the RSD group (module hub: 0.57%; connector: 23.98%) than in the Control group (module hub: 0.16%; connector: 19.34%). The restoration of keystone taxa in RSD-treated soil was significantly (P < 0.01) correlated with soil pH, total organic carbon, and total nitrogen. Moreover, a strong negative correlation (r =  -0.712; P < 0.01) was found between keystone taxa richness and Fusarium abundance. Our results suggest that keystone taxa involved in the RSD network structure are capable of maintaining a flexible generalist mode of metabolism, namely with respect to nitrogen fixation, methylotrophy, and methanotrophy. Furthermore, distinct network modules composed by numerous anti-pathogen agents were formed in RSD-treated soil; i.e., the genera Hydrogenispora, Azotobacter, Sphingomonas, and Clostridium_8 under the soil treatment stage, and the genera Anaerolinea and Pseudarthrobacter under the plant cultivation stage. The study provides novel insights into the association between fungistasis and keystone or sensitive taxa in RSD-treated soil, with significant implications for comprehending the mechanisms of RSD. KEY POINTS: • RSD enhanced bacteriome network stability and restored keystone taxa. • Keystone taxa richness was negatively correlated with Fusarium abundance. • Distinct sensitive OTUs and modules were formed in RSD soil.

Root exudates influence rhizosphere fungi and thereby synergistically regulate Panax ginseng yield and quality

Root exudates contain a complex array of primary and specialized metabolites that play important roles in plant growth due to their stimulatory and inhibitory activities that can select for specific microbes. In this study, we investigated the effects of different root exudate concentrations on the growth of ginseng (Panax ginseng C. A. Mey), ginsenoside levels, and soil fungal community composition and diversity. The results showed that low root exudate concentrations in the soil promoted ginseng rhizome biomass and ginsenoside levels (Rg1, Re, Rf, Rg2, Rb1, Ro, Rc, Rb2, Rb3, and Rd) in rhizomes. However, the rhizome biomass and ginsenoside levels gradually decreased with further increases in the root exudate concentration. ITS sequencing showed that low root exudate concentrations in the soil hardly altered the rhizosphere fungal community structure. High root exudate concentrations altered the structure, involving microecological imbalance, with reduced abundances of potentially beneficial fungi (such as Mortierella) and increased abundances of potentially pathogenic fungi (such as Fusarium). Correlation analysis showed that rhizome biomass and ginsenoside levels were significantly positively correlated with the abundances of potentially beneficial fungi, while the opposite was true for potentially pathogenic fungi. Overall, low root exudate concentrations promote the growth and development of ginseng; high root exudate concentrations lead to an imbalance in the rhizosphere fungal community of ginseng and reduce the plant's adaptability. This may be an important factor in the reduced ginseng yield and quality and soil sickness when ginseng is grown continuously.

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.

Contributions of carbon source, crop cultivation, and chemical property on microbial community assemblage in soil subjected to reductive disinfestation

In agricultural practice, reductive soil disinfestation (RSD) is an effective method for eliminating soil-borne pathogens that depends heavily on carbon source. However, knowledge regarding the assembly of soil microbial communities in RDS-treated soils amended with different carbon sources after continuous crop cultivation is still not well-characterized. RSD treatments were performed on greenhouse soil with six different carbon sources (ethanol, glucose, alfalfa, wheat bran, rice bran, and sugarcane residue), which have different C:N ratios (Org C/N) and easily oxidized carbon contents (Org EOC). After RSD, two consecutive seasons of pepper pot experiments were conducted. Then, the effects of carbon source property, crop cultivation, and soil chemical property on soil microbial community reestablishment, pathogen reproduction, and crop performance were investigated in the RSD-cropping system. Variation partition analysis indicated that carbon source property, crop cultivation, and soil chemical property explained 66.2 and 39.0% of bacterial and fungal community variation, respectively. Specifically, Mantel tests showed that Org C/N, crop cultivation, soil available phosphorus and potassium were the most important factors shaping bacterial community composition, while Org C/N, Org EOC, and crop cultivation were the most important factors shaping fungal community composition. After two planting seasons, the number of cultivable Fusarium was positively correlated with Org EOC, and negatively correlated with soil total organic carbon, Fungal Chao1, and Fungal PC1. Crop yield of complex-carbon soils (Al, Wh, Ri and Su) was negatively affected by Org C/N after the first season, and it was highest in Al, and lower in Et and Su after the second season. Overall, Org EOC and Org C/N of carbon source were vitally important for soil microbe reestablishment, Fusarium reproduction and crop performance. Our findings further broaden the important role of carbon source in the RSD-cropping system, and provide a theoretical basis for organic carbon selection in RSD practice.

Insights into Pyrroloquinoline Quinone (PQQ) Effects on Soil Nutrients and Pathogens from Pepper Monocropping Soil under Anaerobic and Aerobic Conditions

Imbalances of soil available nutrients and soilborne diseases have seriously restricted the productivity of crops and jeopardized food security worldwide. Pyrroloquinoline quinone (PQQ), a redox cofactor in some bacteria involved in glucose metabolism and phosphorus mineralization, could be anticipated to alter soil ecosystems to a certain extent. However, there is limited information on PQQ defending soilborne pathogens and regulating soil main nutrients. Here, a pot experiment based on mono-cropping soils of pepper was conducted to examine the effects of PQQ amendment on reconstructing soil microbial communities and soil nutrients under aerobic/anaerobic conditions comprising three treatments, namely, control, PQQ (aerobic), and FL-PQQ (anaerobic). The results revealed that soil microbial community composition and soil nutrients were distinctly altered by PQQ regimes. Compared to control, PQQ treatment significantly increased the content of soil available phosphorus (AP), while FL_PQQ treatment strongly improved the content of soil available nitrogen (AN). In terms of pathogens, relative to control, both PQQ treatments suppressed the abundances of pathogens, of which FL_PQQ treatment significantly decreased the abundance of the pathotrophic fungal by 64% and the abundance of Fusarium oxysporum by 57%, largely attributed to the increase of organic acid generators (Oxobacter, Hydrogenispora) and potential antagonists (Bacillus, Talaromyces). Structural equation modeling (SEM) showed that PQQ regimes suppressed pathogens by indirectly regulating soil physicochemical properties and microbial communities. Overall, we proposed that PQQ application both in aerobic/anaerobic conditions could improve soil available nutrients and suppress soil pathogens in pepper monocropping soils.

IMPORTANCE The attention to PQQ (pyrroloquinoline quinone) effect on soil nutrients and pathogens was less paid in monocropping soils. However, the underlying microbial interacting mechanism remains unclear. Adopting a novel external bio-additive, the effects of PQQ on soil main nutrients and the pathotrophic fungal under aerobic and anaerobic regimes will be investigated, which would help to improve soil quality health. Our main conclusion was that PQQ would help to remediate monocropping obstacle soils in terms of soil nutrients and soil pathogens by associating with the microbial community, and anaerobic PQQ application more favored amelioration of continuous obstacle soils. These results will benefit the health and sustainable development of pepper production as well as other greenhouse vegetable production.

Optimal NPK Fertilizer Combination Increases Panax ginseng Yield and Quality and Affects Diversity and Structure of Rhizosphere Fungal Communities

Soil microorganisms affect crop rhizospheres via the transformation and transport of nutrients, which has important influences on soil fertility, carbon sequestration, and plant yield and health in agroecosystems. There are few reports on the effects of fertilizer application on the growth of Panax ginseng (C. A. Mey.) or the structure of its rhizosphere microbial communities. In this study, an orthogonal experimental design was used to explore the effects of nine different combinations of nitrogen (N), phosphorus (P), and potassium (K) fertilizers with different amounts and proportions on ginseng growth and accumulation of ginsenosides and the structure of rhizosphere soil fungal communities. Soil without fertilization was the control. With the combined application of NPK, ginseng growth and development increased. The fertilization scheme N₃P₁K₃, with N fertilizer at 50 g·m⁻², P fertilizer at 15 g·m⁻², and K fertilizer at 60 g·m⁻², had the most comprehensive benefit and significantly increased ginseng rhizome biomass and ginsenoside contents (Rg1, Re, Rf, Rg2, Rb1, Ro, Rc, Rb2, Rb3, and Rd). Amplicon sequencing showed that NPK application increased the diversity of fungal communities in ginseng rhizospheres, whereas richness was bidirectionally regulated by proportions and amounts of NPK. Ascomycota was the dominant fungal phylum in ginseng rhizosphere soil, and relative abundances decreased with combined NPK application. Combined NPK application increased the relative abundance of potential beneficial fungi, such as Mortierella, but decreased that of potentially pathogenic fungi, such as Fusarium. Correlation analysis showed that potential beneficial fungi were significantly positively correlated with ginseng rhizome yield and ginsenoside contents, whereas the opposite relation was observed with potential pathogenic fungi. Thus, in addition to directly increasing crop growth, precise NPK application can also increase crop adaptability to the environment by shaping specific microbial communities. The results of this study suggest that the combined effects of biotic and abiotic processes on agricultural production determine crop yield and quality.

Reductive Soil Disinfestation Enhances Microbial Network Complexity and Function in Intensively Cropped Greenhouse Soil

Reductive soil disinfestation (RSD) is an effective practice to eliminate plant pathogens and improve the soil microbial community. However, little is known about how RSD treatment affects microbial interactions and functions. Previous study has shown that RSD-regulated microbiomes may degenerate after re-planting with former crops, while the effect of planting with different crops is still unclear. Here, the effects of both RSD treatment and succession planting with different crops on microbial community composition, interactions, and functions were investigated. Results showed that RSD treatment improves the soil microbial community, decreases the relative abundance of plant pathogens, and effectively enhances microbial interactions and functions. The microbial network associated with RSD treatment was more complex and connected. The functions of hydrocarbon (C, H), nitrogen (N), and sulfur (S) cycling were significantly increased in RSD-treated soil, while the functions of bacterial and fungal plant pathogens were decreased. Furthermore, the bacterial and fungal communities present in the RSD-treated soil, and soil succession planted with different crops, were found to be significantly different compared to untreated soil. In summary, we report that RSD treatment can improve soil quality by regulating the interactions of microbial communities and multifunctionality.

Impact of ozonated water disinfestation on soil fungal community composition in continuous ginger field

This study aimed to explore the impact of ozonated water (OW) disinfestation on soil fungal community composition in continuous ginger field. All soil samples were collected in continuous ginger field. There were two groups and 5 time points (0, 1, 3, 5, 9 day) in our study, including OW disinfestation treatment group (O3 group) and control group (CK group). Via internal transcribed spacer (ITS) sequencing and further analysis, the changes of fungal community composition were determined. As a result, at 0 and 9 days after aeration, the operational taxonomic units (OTUs) in O3 group were significantly higher than that in CK group. Compared with the CK group, in O3 group: the ACE and Chao1 index significantly increased on day 1, and the Shannon index significantly decreased while Simpson index significantly increased on day 0 after aeration. In O3 group, there were dynamic changes of top 10 abundance fungi from the genus-level and the growth of Trichoderma and Rhodotorula had been promoted while Hannaella was inhibited. In conclusion, OW disinfestation had complicated impacts on fungal communities in continuous ginger fields. The growth of Trichoderma and Rhodotorula has been promoted during disinfestation, which provided more reference information for soil OW disinfestation research.

Impact of fumigants on non-target soil microorganisms: a review

Fumigants have been used for decades to control soil-borne pathogens of high-value crops, and increasing evidence indicates they can affect non-target soil microbial communities. Understanding the impacts of these products on soil microorganisms is of critical importance not only for evaluating their environmental safety, but also because soil microbial communities have a central role in soil quality and nutrient cycling, plant growth, and crop production. Thus, we conducted a systematic review and metanalysis study of fumigant impacts on non-target soil microorganisms. In general, we found that fumigation decreases the bacterial diversity and abundance of total bacteria and nitrogen-cycling genes by approximately 10-50% during the first four weeks after application compared to non-treated soils. These decreases appear transient and tend to diminish or disappear after four weeks. Increases in bacterial diversity and abundance can occur after fumigation but are less common. Fumigant application can also alter bacterial community composition during the first six weeks after treatment by significantly increasing and/or decreasing the relative abundance of bacterial taxa involved in key soil functions such as N-cycling and plant-growth promotion. Knowledge gaps and areas where future research efforts should be prioritized to improve our understanding of the impact of organic fumigants on non-target soil microorganisms are discussed.

Soil Fungal Community Composition and Diversity of Culturable Endophytic Fungi from Plant Roots in the Reclaimed Area of the Eastern Coast of China

As an important resource for screening microbial strains capable of conferring stress tolerance in plants, the fungal community associated with the plants grown in stressful environments has received great attention. In this study, high-throughput sequencing was employed to study the rhizosphere fungal community in the reclaimed area (i.e., sites F, H, and T) of the eastern coast of China. Moreover, endophytic fungi from the root of six plant species colonizing the investigated sites were isolated and identified. The differences in soil physicochemical parameters, fungal diversity, and community structure were detected among the sampling sites and between the seasons. Ectomycorrhizal (ECM) fungi (e.g., genera Tuber and Geopora) were dominant at site F, which was characterized by high soil total carbon (SC) and total nitrogen (SN) contents and low soil electrical conductivity (EC) value. Arbuscular mycorrhizal (AM) fungi, including genera Glomus, Rhizophagus, and Entrophospora were dominant at sites H (winter), H (summer), and T (summer), respectively. The positive relationship between the EC value and the abundance of genus Glomus indicated the ability of this AM fungus to protect plants against the salt stress. Endophytic fungi at sites F (Aspergillus and Tetracladium), H (Nigrospora), and T (Nigrospora, Coniochaeta and Zopfiella) were recognized as the biomarkers or keystone taxa, among which only genus Aspergillus was isolated from the plant roots. The aforementioned AM fungi and endophytic fungi could contribute to the promotion of plant growth in the newly reclaimed land.

Comparative Microbial Nitrogen Functional Gene Abundances in the Topsoil vs. Subsoil of Three Grassland Habitats in Northern China

The microbial groups of nitrogen fixers, ammonia oxidizers, and denitrifiers play vital roles in driving the nitrogen cycle in grassland ecosystems. However, the understanding of the abundance and distribution of these functional microorganisms as well as their driving factors were limited mainly to topsoil. In this study, the abundances of nitrogen functional genes (NFGs) involved in nitrogen fixation (nifH), ammonia oxidation (amoA), and denitrification (nirK, nirS, and nosZ) were investigated in both topsoil (0-10 cm, soil layer with concentrated root) and subsoil (30-40 cm, soil layer with spare root) of three grassland habitats in northern China. The abundance of NFGs decreased with soil depth except for the archaeal amoA gene and the distribution of nifH, archaeal amoA, nirK, and nirS gene was significantly impacted by grassland habitats. Moreover, the distribution of NFGs was more responsive to the vertical difference than horizontal spatial heterogeneity. Redundancy analysis revealed that the distribution pattern of overall NFGs was regulated by grassland habitats, and these regulations were more obvious in the subsoil than in the topsoil. Variance partitioning analysis further indicated that soil resource supply (e.g., organic matter) may control the vertical distribution of NFGs. Taken together, the findings in this study could fundamentally improve our understanding of the distribution of N cycling-associated microorganisms across a vertical scale, which would be useful for predicting the soil N availability and guiding the soil N management in grassland ecosystems.

Different Responses of Soil Environmental Factors, Soil Bacterial Community, and Root Performance to Reductive Soil Disinfestation and Soil Fumigant Chloropicrin

Reductive soil disinfestation (RSD) and soil fumigant chloropicrin (SFC) are two common agricultural strategies for the elimination of soil-borne pathogens. However, the differences in soil environmental factors, soil bacterial microbiome, and root performance between SFC and RSD are poorly understood. In this study, three soil treatments, untreated control (CK), SFC with 0.5 t⋅ha–1 chloropicrin, and RSD with 15 t⋅ha–1 animal feces, were compared. We evaluated their effects on soil environmental factors, bacterial community structure, and root activity using chemical analysis and high-throughput sequencing. RSD treatment improved soil composition structure, bacterial diversity, and root performance to a greater extent. Carbon source utilization preference and bacterial community structure were strikingly altered by SFC and RSD practices. Bacterial richness, diversity, and evenness were notably lowered in the SFC- and RSD-treated soil compared with the CK-treated soil. However, RSD-treated soil harbored distinct unique and core microbiomes that were composed of more abundant and diverse potentially disease-suppressive and organic-decomposable agents. Also, soil bacterial diversity and composition were closely related to soil physicochemical properties and enzyme activity, of which pH, available Na (ANa), available Mg (AMg), available Mn (AMn), total Na (TNa), total Ca (TCa), total Cu (TCu), total Sr (TSr), urease (S-UE), acid phosphatase (S-ACP), and sucrase (S-SC) were the main drivers. Moreover, RSD treatment also significantly increased ginseng root activity. Collectively, these results suggest that RSD practices could considerably restore soil nutrient structure and bacterial diversity and improve root performance, which can be applied as a potential agricultural practice for the development of disease-suppressive soil.

Diversity of the Bacterial Microbiome Associated With the Endosphere and Rhizosphere of Different Cassava (Manihot esculenta Crantz) Genotypes

Root-associated microbial communities play important roles in plant growth and development. However, little attention has been paid to the microbial community structures associated with cassava, which is a staple food for approximately 800 million people worldwide. Here, we studied the diversity and structure of tuber endosphere and rhizosphere bacterial communities in fourteen cassava genotypes: SC5, SC8, SC9, SC205, KU50, R72, XL1, FX01, SC16, 4612, 587, 045, S0061, and 1110. The results of bacterial 16S rDNA sequencing showed that the richness and diversity of bacteria in the rhizosphere were higher than those in the tuber endosphere across the 14 cassava genotypes. After sequencing, 21 phyla and 310 genera were identified in the tuberous roots, and 36 phyla and 906 genera were identified in the rhizosphere soils. The dominant phylum across all tuber samples was Firmicutes, and the dominant phyla across all rhizosphere samples were Actinobacteria, Proteobacteria, and Acidobacteria. The numbers of core bacterial taxa within the tuber endospheres and the rhizospheres of all cassava genotypes were 11 and 236, respectively. Principal coordinate analysis and hierarchical cluster analysis demonstrated significant differences in the compositions of rhizosphere soil microbiota associated with the different cassava genotypes. Furthermore, we investigated the metabolic changes in tuber roots of three genotypes, KU50, SC205, and SC9. The result showed that the abundances of Firmicutes, Proteobacteria, and Actinobacteria in tuber samples were positively correlated with organic acids and lipids and negatively correlated with vitamins and cofactors. These results strongly indicate that there are clear differences in the structure and diversity of the bacterial communities associated with different cassava genotypes.

Reductive soil disinfestation attenuates antibiotic resistance genes in greenhouse vegetable soils

Reductive soil disinfestation (RSD) is an emerging technique that ameliorates soil degradation, but its effects against antibiotic resistance genes (ARGs) were unclear. Here, we examined soil properties, ARG types and numbers, and ARG profiles, and bacterial community compositions following 4 soil treatments: control; straw addition (SA); water flooding (WF); and RSD, both straw addition and water flooding. The results showed that the numbers of ARG types and subtypes decreased by 10.8% and 21.1%, respectively, after RSD, and the numbers of ARGs decreased by 18.6%. The attenuated multidrug, beta-lactam, macrolide, and phenicol resistance genes in the RSD soil corresponded to a decreased relative abundance of ARG subtypes (i.e., adeF, mdtM, TypeB_NfxB, mecA, nalC, OXA-60, and cmlA4). Taxa in phyla Proteobacteria, Actinobacteria, and Deinococcus-Thermus were the main hosts for dominant ARG subtypes and were inhibited by RSD. The selected bacterial genera and soil properties explained 83.4% of the variance in ARG composition, suggesting that the improved soil properties and the reduced potential ARG hosts produced by the interactions of straw addition and water flooding are likely responsible for ARG attenuation by RSD. Therefore, RSD has the potential to mitigate ARG pollution in soils.

Microbial community responses to multiple soil disinfestation change drivers

Soil continuous cropping obstacles lead to yield and economic losses in agriculture. Reductive soil disinfestation (RSD) is an effective technology for alleviating it. However, the key factors influencing microbial community composition and how do they promote functional transformation of core microbes under RSD practice remain poorly understood. Hence, a short-term field experiment was performed integrating real-time polymerase chain reaction, average well color development (AWCD), and MiSeq pyrosequencing to investigate relationships between environmental factors and microorganisms in five different disinfestation treatments, i.e., untreated monoculture soil (CK), soil with high temperature heating (HT), soil with dazomet (DZ), RSD with sugarcane bagasse (SB), or with bean dregs (BD). The results showed that compared to non-RSD treatments, both RSD treatments significantly increased soil microbial abundance and soil available K and organic matter (OM). Further analysis found that available K and OM were the key factors inducing microbial community change. Additionally, relative to non-RSD treatments, the relative abundances of phyla Proteobacteria, Acidobacteria, Rokubacteria, and Ascomycota were higher, whereas those of Actinobacteria, Gemmatimonadetes, and Basidiomycota were lower in RSD treatments. Changes in microbial diversity and abundance led to variation of soil microbial community functions. AWCD and community function prediction showed that, in contrast with non-RSD treatments, soil metabolism activity significantly increased, bacterial community functions including terpenoids and polyketides metabolism, signal transduction and cell motility increased, and the number of saprotroph fungi increased under RSD treatments. Overall, RSD incorporated with sugarcane bagasse or bean dregs efficiently improved soil fertility, and considerably increased soil microbial activity and function, which may benefit future sustainable agriculture production. Key points • Reductive soil disinfestation can alleviate continuous cropping obstacles by improving soil fertility. • Organic matter and available potassium as the key factors affected microbial community reconstruction and function. • Reductive soil disinfestation can improve soil metabolic activity and functional diversity by altering microorganism community.

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.

Synergy of Anaerobic Soil Disinfestation and Trichoderma spp. in Rhizoctonia Root Rot Suppression

Potential synergy between anaerobic soil disinfestation (ASD) and Trichoderma spp. in suppression of Rhizoctonia root rot in radish was evaluated. A split-plot design with three replications was used; main plots were Trichoderma harzianum T22, Trichoderma asperellum NT25 and a non-Trichoderma control. Subplots were ASD carbon sources wheat bran, molasses, chicken manure, and mustard greens and two non-amended controls: anaerobic (covered and flooded) and aerobic (not covered or flooded). Carbon sources and Rhizoctonia solani inoculant were mixed with soil, placed in pots, and flooded, followed by drenching Trichoderma spore suspensions and sealing the pots in zip-lock bags. After 3 weeks, bags were removed, soil was aired for 1 week and radish “SSR-RR-27” was seeded. Rhizoctonia root rot severity and incidence were lowest in radish plants grown in ASD-treated soil amended with wheat bran, molasses, or mustard greens across all Trichoderma treatments. Disease severity was lower in radish plants treated with NT25 than with T22 or the non-Trichoderma control across all ASD treatments, and in radish grown in ASD-treated soil amended with wheat bran plus NT25 compared to ASD-wheat bran or NT25 alone. Rhizoctonia solani populations were significantly reduced by ASD treatment regardless of carbon source, while Trichoderma populations were not affected by ASD treatment with the exception of ASD-mustard greens. The interactions of either Trichoderma isolate and ASD with most carbon sources were additive, while T22 with ASD-molasses and NT25 with ASD–wheat bran interactions were synergistic in reducing disease severity. One interaction, T22 with ASD-chicken manure was antagonistic. Enhancement of ASD efficacy in suppressing soilborne diseases such as Rhizoctonia root rot by additional soil amendment with Trichoderma spp. during the process appears to be dependent on both Trichoderma isolate and ASD carbon source.

Opportunities and Challenges in Studies of Host-Pathogen Interactions and Management of Verticillium dahliae in Tomatoes

Tomatoes (Solanum lycopersicum L.) are a valuable horticultural crop that are grown and consumed worldwide. Optimal production is hindered by several factors, among which Verticillium dahliae, the cause of Verticillium wilt, is considered a major biological constraint in temperate production regions. V. dahliae is difficult to mitigate because it is a vascular pathogen, has a broad host range and worldwide distribution, and can persist in soil for years. Understanding pathogen virulence and genetic diversity, host resistance, and plant-pathogen interactions could ultimately inform the development of integrated strategies to manage the disease. In recent years, considerable research has focused on providing new insights into these processes, as well as the development and integration of environment-friendly management approaches. Here, we discuss the current knowledge on the race and population structure of V. dahliae, including pathogenicity factors, host genes, proteins, enzymes involved in defense, and the emergent management strategies and future research directions for managing Verticillium wilt in tomatoes.

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.

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.

Effect of Different Substrates on Soil Microbial Community Structure and the Mechanisms of Reductive Soil Disinfestation

Reductive soil disinfestation (RSD) has recently attracted much attention owing to its effectiveness for controlling pathogens. In this study, we aimed to evaluate the effects of different C/N substrates on RSD and to explore the changes in microbial community structure during RSD treatment. The experimental set up included 10 groups, as follows: CK, without substrates; RSD treatments with alfalfa (Medicago sativa L.)[AL], maize (Zea mays Linn. Sp.) straw [MS], and rice (Oryza sativa L.) straw [RS], with three levels of addition (0.5% [L], 2% [M], and 5% [H]), yielding ALL, ALM, ALH, MSL, MSM, MSH, RSL, RSM, and RSH groups. Compared with CK, RSD treatments significantly increased the content of NH4+-N, and effectively eliminated the accumulated NO3--N in the soil. The relative abundances of organic acid producers, including Clostridium, Coprococcus, and Oxobacter, in all RSD groups were significantly higher than those in the CK by day 21. Moreover, on day 21, Aspergillus and Fusarium in all RSD groups were significantly lower than those in the CK. In summary, RSD treatments clearly increased the relative abundances of organic acid generators and effectively inhibited pathogens; however, when the C/N was too low and the amount of addition too high, ammonia poisoning and rapid growth of some microorganisms (e.g., Pseudallescheria and Arthrographis) may occur.

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.