Impacts on soil microbial characteristics and their restorability with different soil disinfestation approaches in intensively cropped greenhouse soils

Impacts of the Ban on the Soil-Applied Fumigant Methyl Bromide

The loss of the soil fumigant methyl bromide (MeBr) and adoption of soil fumigant alternatives has been challenging for farmers, particularly for those crops in which pathogens previously controlled by MeBr have emerged as significant problems, but it has resulted in some unanticipated benefits for the scientific community and the environment. Applauded as one of the most effective environmental agreements to date, the universally accepted Montreal Protocol on Ozone Depleting Substances has had a significant impact on the environment, reducing the release of halogenated compounds from anthropogenic sources enough to mitigate global warming by an estimated 1.1°C by 2021. The funding associated with various MeBr transition programs has increased collaboration across scientific disciplines, commodity groups, industry, and regulatory agencies. Chemical alternatives and improved application strategies, including the development of gas-retentive agricultural films, coupled with sound efficacy data and grower ingenuity have resulted in the sustained production of many of the impacted crops; although there has been some loss of acreage and value, particularly for Florida fumigated crops, for some, value has continued to increase, allowing production to continue. The loss of a single, broad-spectrum tool for pest control has led to a deeper understanding of the specific pest complexes impacting these at-risk crops, as well as the development of new, biologically based management tools for their control while increasing our understanding of the role of the soil microbiome in pest control and crop production.

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.

A double-edged sword: Reductive soil disinfestation changes the fates of trace metal elements in soil

Although the effects of reductive soil disinfestation (RSD) in soil sterilization have been proven in several countries, the potential risks of trace metal elements (TMEs) caused by RSD require further assessment. Here, freshly Cd-spiked soil and historically contaminated greenhouse soil were exposed to RSD and the fates of TMEs, Cd, Co, Cu, Ni, Pb, and Zn, were investigated. All RSD treatments lasted for 21 days and subsamples were collected at different time intervals. Samples were open-air incubated for another 7 days until day 28 to simulate the situation after drainage. The bioavailability and geochemical fractionation of TMEs were investigated based on single and sequential extraction procedures and the environmental risks were assessed. The results showed that RSD increased the relative abundance of Firmicutes and Bacteroidetes, and the content of functional groups, including Fe, Mn, and S compounds respirations increased after RSD, highlighting the possible reductive dissolution of FeMn oxides and precipitation of TMEs. The dissolution decreased the reducible fractions of TMEs and increased the acid-soluble fractions of Co, Ni, Pb, and Zn, in the European Community Bureau of Reference results, reflecting the activation of TMEs in soils. However, the precipitation of sulfate resulted in the stabilization of Cd and Cu in two types of soils, increased their residual fractions, and decreased their acid-soluble fractions and bioavailabilities. After drainage, because the influence caused by precipitation rapidly disappeared and the impact of FeMn oxides dissolution remained, the acid-solubility of TMEs was greater than their initial status in the two soils. Furthermore, as a highly toxic metal, the activation of Cd at 28 days caused the rapid increase of ecological risks, which is particularly concerning. The results suggest that RSD temporarily increases the potential risks of TMEs and that certain measures must be taken.

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.

Degradation of chlorinated solvents with reactive iron minerals in subsurface sediments from redox transition zones

Reactive iron (Fe) mineral coatings found in subsurface reduction-oxidation transition zones (RTZs) contribute to the attenuation of contaminants. An 18.3-m anoxic core was collected from the site, where constituents of concern (COCs) in groundwater included chlorinated solvents. Reactive Fe mineral coatings were found to be abundant in the RTZs. This research focused on evaluating reaction kinetics with anoxic sediments bearing ferrous mineral nano-coatings spiked with either tetrachloroethylene (PCE), trichloroethylene (TCE), or 1,4-dichlorobenzene (1,4-DCB). Reaction kinetics with RTZ sediments followed pseudo-first-order reactions for the three contaminants with 90% degradation achieved in less than 39 days. The second-order rate constants for the three COCs ranged from 6.20 × 10^-4 to 1.73 × 10^-3 Lg^-1h^-1 with pyrite (FeS₂), 4.97 × 10^-5 to 1.24 × 10^-3 Lg^-1h^-1with mackinawite (FeS), 1.25 × 10^-4 to 1.89 × 10^-4 Lg^-1h^-1 with siderite (FeCO₃), and 1.79 × 10^-4 to 1.10 × 10^-3 Lg^-1h^-1 with magnetite (Fe₃O₄). For these three chlorinated solvents, the trend for the rate constants followed: Fe(II) sulfide minerals > magnetite > siderite. The high reactivity of Fe mineral coatings is hypothesized to be due to the large surface areas of the nano-mineral coatings. As a result, these surfaces are expected to play an important role in the attenuation of chlorinated solvents in contaminated subsurface environments.

Facilitating effects of the reductive soil disinfestation process combined with Paenibacillus sp. amendment on soil health and physiological properties of Momordica charantia

Reductive soil disinfestation (RSD) is an anaerobic and facultative anaerobic microbial-mediated soil management process. The extent of improvement of diseased soil properties by RSD relative to comparable healthy soil is, however, not well characterized. Importantly, how to promote the colonization efficiency of these facultative anaerobic functional species to ensure soil and plant health remain unknown. Here, Fusarium wilt-diseased soil of Momordica charantia grown under a plastic-shed field (PS-CK) was used to conduct molasses-RSD (MO-RSD) along with Paenibacillus sp. (a model of facultative anaerobic species) (MO_PA-RSD) treatment, and the soil from a nearby open-air paddy field was considered comparable healthy soil (OA-CK). Both RSD treatments significantly improved the properties of PS-CK soil, and the extent of improvement of soil pH, Fusarium oxysporum reduction efficiency (98.36%~99.56%), and microbial community and functional composition were higher than that achieved for OA-CK soil, which indicated that RSD-regulated most soil properties outperformed those of the comparable healthy soil. The disease incidence and ascorbic acid content of M. charantia in MO-RSD- and MO_PA-RSD-treated soils were considerably decreased, while the weight and soluble protein contents were correspondingly increased, as compared to those of M. charantia in PS-CK soil. Specifically, the changes in these physiological properties of M. charantia in MO_PA-RSD soil performed well than that in MO-RSD soil. The relative abundances of Cohnella, Effusibacillus, Rummeliibacillus, Oxobacter, Thermicanus, and Penicillium enriched in both RSD-treated soils were positively correlated with Paenibacillus and negatively correlated with F. oxysporum population and disease incidence (P < 0.05). Notably, the relative abundances of these potential probiotics were considerably higher in MO_PA-RSD-treated soil than in MO-RSD alone-treated soil. These results show that the RSD process with inoculation of Paenibacillus sp. could promote the colonization of this species and simultaneously stimulate the proliferation of other probiotic consortia to further enhance soil health and plant disease resistance.

Microbial Fertilization Improves Soil Health When Compared to Chemical Fumigation in Sweet Lily

Lanzhou Lily(Lilium davidii) var. unicolor, which is also known as sweet lily in China, is used as a type of food. This lily is distributed in narrow regions, propagates asexually, cultivates perennially, and cultivates commonly in serious consecutive replant problems (CRPs). Soil fumigation is commonly used to control soil-borne disease to alleviate crops’ consecutive replant problems (CRPs). However, due to the improper fumigation application, it is common to cause chemical hazard to crops. In this study, we designed a two-factor experiment to explore the bacterial and fungal community structure and some specific microbial groups in the lily rhizosphere soil after chemical versus bacterial fertilizer treatments, by using a metagenomic analysis of the treated soils. The results showed that metham-sodium soil fumigation (SMF treatment) significantly decreased plant growth, as well as it significantly decreased both soil fungal diversity and abundance at the OTUs levels, while Special 8™ microbial fertilizer supplement (MF treatment) significantly improved plant growth and increased fungal diversity and abundance. Under FM treatment, Chao1 richness and Shannon’s diversity increased by 6.70% and 35.09% compared to CK (no treatment). However, the bacterial diversity and abundance were not significantly changed among these treatments. The fungal and bacterial community structure were different in all treatments. In SMF treatment, the pathogenic fungal species Fusarium oxysporum increased compared to CK, but it significantly decreased in MF treatment; in MF and MMF treatments, some beneficial bacteria groups such as the bacterial phylum Proteobacteria and its member genus Sphingomonas, as well as the fungal genus Mortierella, increased compared to CK and SFM treatments, but the harmful bacterial genera Gemmatimona was decreased, as well as the harmful fungal genus Cryptococcus. Thus, we concluded that under chemical fumigation conditions, both fungal diversity loss and overall microorganism reduction, which impair multiple ecosystem function, in conjunction with the increase of harmful fungal species such as Fusarium oxysporum, are causes for soil degradation. On the other hand, under microbial fertilizer supplement, it was the fungal diversity increase, as well as these beneficial microorganisms groups’ accumulation, together with those harmful groups’ depletion, played important roles in restoring and improving soil health that suffered from the chemical fumigant hazard. In addition, the bacterial phylum Proteobacteria and its member genus Sphingomonas are involved in soil health recovery and promotion. The results also emphasized that whether soil is chemically fumigated or not, beneficial microorganism supplementary is effective in ensuring soil productivity.

Soil Disinfestation: From Soil Treatment to Soil and Plant Health

This feature article tracks 100 years of soil disinfestation, from the goal of eradicating soilborne pathogens and pests to much milder approaches, aimed at establishing a healthier soil, by favoring or enhancing the beneficial soil microflora and introducing biological control agents. Restrictions on the use of many chemical fumigants is favoring the adoption of nonchemical strategies, from soilless cultivation to the use of physical or biological control measures, with more focus on maintaining soil microbial diversity, thus enhancing soil and plant health. Such approaches are described and discussed, with special focus on their integrated use.

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.

Effects of Plastic Shed Cultivation System on the Properties of Red Paddy Soil and Its Management by Reductive Soil Disinfestation

Red paddy soil is widely distributed in the south of China and has become an important production system for food and cash crops. However, the key factors limiting the quality of this soil type under the plastic shed cultivation system and the effective management strategies are still unclear. In the present study, the physicochemical and microbial properties of red paddy soil in a plastic shed (PS-Soil) and open-air (OA-Soil) cultivation systems were compared. Subsequently, reductive soil disinfestation (RSD) and organic fertilizer treatment (OF) were used to improve the soil properties in a representative PS-Soil. Results showed that the physicochemical and microbial properties in PS-Soil were significantly altered compared with those in the nearby OA-Soil, and those differences were primarily dominated by the cultivation system rather than the sampling site. Specifically, the electrical conductivity (EC) and available nutrients (NO3−-N, NH4+-N, available K, and available P) contents, as well as the abundances of fungi, potential fungal soil-borne pathogens (F. oxysporum and F. solani), and fungi/bacteria were significantly increased in PS-Soil. In addition, the OF treatment could not effectively improve the above-mentioned soil properties, which was mainly reflected by that soil EC and the abundances of potential fungal soil-borne pathogens were considerably increased in the OF-treated soil. In contrast, soil EC and NO3−-N content, the abundances of fungi, F. oxysporum, F. solani, and fungi/bacteria were remarkably decreased by 76%, 99%, 98%, 92%, 73%, and 85%, respectively. Moreover, soil pH, the abundance of bacteria, total microbial activity, metabolic activity, and carbon source utilization were significantly increased in the RSD-treated soil. Collectively, red paddy soil is significantly degraded under the plastic shed cultivation system, and RSD rather than OF can effectively improve the quality of this soil type.

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.

Application of vermicompost and biochar suppresses Fusarium root rot of replanted American ginseng

Soil sterilization integrated with agronomic measures is an effective method to reduce soilborne replant diseases. However, the effect of vermicompost or biochar application after soil sterilization on soilborne diseases is poorly understood. A pot experiment was conducted in American ginseng to investigate the effects of vermicompost (VF), biochar (BF), and a combination of vermicompost and biochar (VBF) applied after soil sterilization on the incidence of Fusarium root rot using natural recovery (F) as control. After one growing season, the disease index of root rot, the phenolic acids, and the microbial communities of American ginseng rhizosphere soil were analyzed. The disease index of VF, BF, and VBF decreased by 33.32%, 19.03%, and 80.96%, respectively, compared with F. The highest bacterial richness and diversity were observed in the rhizosphere soil of VBF. Besides, VF and VBF significantly increased the relative abundance of beneficial bacteria (Pseudomonas, Lysobacter, and Chryseolinea) in the rhizosphere soil. Higher concentrations of vanillin, one of the phenolic acids in the roots exudates, were recorded in the rhizosphere soils of BF and VBF. The vanillin concentration showed a significant negative correlation with the disease index. To conclude, vermicompost improved the beneficial bacteria of the rhizosphere soil, while biochar regulated the allelopathic effect of the phenolic acids. The study proposes a combined application of biochar and vermicompost to the rhizosphere soil to control Fusarium root rot of replanted American ginseng effectively. KEY POINTS: Vermicompost improves the relative abundance of rhizosphere beneficial bacteria. Biochar inhibits the degradation of phenolic acids by adsorption. The combination of vermicompost and biochar enhances the disease control effect.

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.

Anaerobic Soil Disinfestation Efficacy Against Fusarium oxysporum Is Affected by Soil Temperature, Amendment Type, Rate, and C:N Ratio

A meta-analysis of anaerobic soil disinfestation (ASD) efficacy against Fusarium oxysporum and F. oxysporum f. sp. lycopersici was conducted emphasizing effects of environment and organic amendment characteristics and pot and field studies conducted on ASD amendment C:N ratio and soil temperature effects on F. oxysporum f. sp. lycopersici inoculum survival. In a pot study, two organic amendments, dry molasses-based or wheat bran-based, applied at 4 mg of C/g of soil, with 40:1, 30:1, 20:1, and 10:1 C:N ratios, were evaluated against F. oxysporum f. sp. lycopersici at 15 to 25°C. This study was followed by a pot study with temperature regimes of 15 to 25°C and 25 to 35°C and two C:N ratios (20:1 and 40:1), and a field study at 40:1, 30:1, 20:1, and 10:1 C:N ratios, a 30:1 C:N ratio at a lower C rate (2 mg of C/g of soil), and an anaerobic control. Soil temperature >25°C and more labile amendments increased ASD suppression of F. oxysporum/F. oxysporum f. sp. lycopersici in the meta-analysis. In pot studies, F. oxysporum f. sp. lycopersici survival was reduced for molasses-based mixtures at 20:1 and 30:1 C:N ratios compared with wheat bran-based mixtures but not compared with the anaerobic control. At 25 to 35°C, all ASD treatments suppressed F. oxysporum f. sp. lycopersici relative to controls. In the field, all ASD treatments reduced F. oxysporum f. sp. lycopersici survival compared with the anaerobic control, and 4 mg of C/g of soil amendment rates induced higher anaerobic conditions and higher F. oxysporum f. sp. lycopersici mortality compared with the 2 mg of C/g of soil rate. Although amendment C:N ratios from 10 to 40:1 were similarly suppressive of F. oxysporum, lower temperatures reduced ASD effectiveness against F. oxysporum/F. oxysporum f. sp. lycopersici and further work is warranted to enhance suppression at soil temperatures <25°C.

Improved immobilization of soil cadmium by regulating soil characteristics and microbial community through reductive soil disinfestation

Cadmium (Cd) contamination arising from industrialization has attracted increasing attention in recent years. Reductive soil disinfestation (RSD) as an effective agricultural practice has been widely applied for soil sterilization. However, there is little research regarding RSD affecting Cd immobilization. Here, five treatments, namely untreated soil (CK), flooding-treated soil (FL), RSD with 2% ethyl alcohol (EA), 2% sugarcane bagasse (SB), and 2% bean dregs (BD) were designed to detect their performance for Cd immobilization in contaminated soils, and the change of soil properties and microbial communities were monitored. The results revealed that pH significantly increased in FL and RSD-treated soils, but was negatively correlated with the exchangeable fraction of Cd (EX-Cd), while Oxidation-Reduction Potential (Eh) significantly decreased in FL and RSD-treated soils, and was positively correlated with EX-Cd. BD treatment might contribute to the increase of CaCO₃ as shown by X-Ray Diffractomer analysis and strongly decreased the EX-Cd in the soil, but increased the relative abundances of Firmicutes, Planctomycetes, Acidobacteria, and Gemmatimonadetes, which may promote Fe (III) reduction or induce resistance to Cd. Bacterial communities at the phylum and genus levels were closely related to Cd fraction. The FL and RSD treatments moderately altered bacterial specific functions, including iron respiration, which may contribute to remediation of Cd-polluted soil by Fe (III) reduction. Field experiments were conducted to confirm that BD treatment resulted in a significant increase in pH whereas the content of total available Cd was reduced in soils. Compared to the control, concentration of total available Cd of red amaranth, sweet potato, towel gourd, and cowpeas were reduced by approximately 46%, 74%, 72%, and 76% in a BD-treated field, respectively. Our study highlights the potential of RSD as an effective method for Cd immobilization in contaminated soils by improving soil characteristics and altering the composition of the microbial community.

Organic Amendments for Pathogen and Nematode Control

The loss of methyl bromide as a soil fumigant and minimal advances in the development and registration of new chemical fumigants has resulted in a resurgence of interest in the application of organic amendments (OAs) for soilborne plant pathogen and plant-parasitic nematode management. Significant progress has been made in the characterization of OAs, application of strategies for their use, and elucidation of mechanisms by which they suppress soilborne pests. Nonetheless, their utility is limited by the variability of disease control, expense, and the logistics of introducing them into crop production systems. Recent advances in molecular techniques have led to significant progress in the elucidation of the role of bacteria and fungi and their metabolic products on disease suppression with the addition of OAs. Biosolarization and anaerobic soil disinfestation, developed to manipulate systems and favor beneficial microorganisms to maximize their impact on plant pathogens, are built on a strong historical research foundation in OAs and the physical, chemical, and biological characteristics of disease-suppressive soils. This review focuses on recent applications of OAs and their potential for the management of soilborne plant pathogens and plant-parasitic nematodes, with emphasis primarily on annual fruit and vegetable production systems.

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.