The impact of biofumigation and chemical fumigation methods on the structure and function of the soil microbial community

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.

Application of plant specialized metabolites to modulate soil microbiota

Plant specialized metabolites (PSMs) are considerably diverse compounds with multifaceted roles in the adaptation of plants to various abiotic and biotic stresses. PSMs are frequently secreted into the rhizosphere, a small region around the roots, where they facilitate interactions between plants and soil microorganisms. PSMs shape the host-specific rhizosphere microbial communities that potentially influence plant growth and tolerance to adverse conditions. Plant mutants defective in PSM biosynthesis contribute to reveal the roles of each PSM in plant-microbiota interactions in the rhizosphere. Recently, various approaches have been used to directly supply PSMs to soil by in vitro methods or through addition in pots with plants. This review focuses on the feasibility of the direct PSM application methods to reveal rhizospheric plant-microbiota interactions and discusses the possibility of applying the knowledge gained to future engineering of rhizospheric traits.

N-Source Determines Barley Productivity, Nutrient Accumulation, and Grain Quality in Cyprus Rainfed Agricultural Systems

The Eastern Mediterranean and Middle East (EMME) region is already experiencing the negative effects of increased temperatures and the increase in prolonged drought periods. The use of organic fertilization could be a valuable tool to meet the main challenges of climate change and maintain the productivity, quality, and sustainability of rainfed agricultural ecosystems. In the current study, we compare the effect of manure, compost, and chemical fertilization (NH₄NO₃) on barley grain and straw yield in a field study for three consecutive growing seasons. The hypothesis that the barley productivity, nutrient accumulation, and grain quality remain similar among the different nutrient management strategies was tested. The results showed that both growing season and type of nutrient source significantly affected barley grain and straw yield (F_6,96 = 13.57, p < 0.01). The lowest productivity was noticed in the non-fertilized plots while chemical and organic fertilization exhibited similar grain yield, ranging from 2 to 3.4 t/ha throughout the growing seasons. For straw, the use of compost had no effect on the yield in any of the growing seasons examined. The use of manure and compost had a significant effect on grain macro- and micronutrient content but this was highly related to growing season. Principal component analysis (PCA) clearly demonstrated the discrimination of the different type of fertilization on barley performance during the course of the study, while the application of compost was highly associated with an increase in micronutrients in grain samples. Furthermore, structural equational modeling (SEM) showed that both chemical and organic fertilization had a direct positive effect on macro- (r = 0.44, p < 0.01) and micronutrient (r = 0.88, p < 0.01) content of barley grain and a positive indirect effect on barley productivity through N accumulation in grain (β = 0.15, p = 0.007). The current study showed that barley grain and straw yield was similar between manure and NH₄NO₃ treatments, while compost exhibited a residual positive effect causing an increase in grain yield during the growing season. The results highlight that N fertilization under rainfed conditions is beneficial to barley productivity through its indirect effects on N accumulation in grain and straw, while it improves grain quality through the increased accumulation of micronutrients.

Resporulation of Calcium Alginate Encapsulated Metarhizium anisopliae on Metham®-Fumigated Soil and Infectivity on Larvae of Tenebrio molitor

Metarhizium anisopliae infects and kills a large range of insects and is a promising biocontrol agent to manage soil insects, such as wireworm in sweetpotato. The presence of other soil microbes, which exhibit competitive fungistasis, may inhibit the establishment of M. anisopliae in soil. Microbially depleted soil, for example, sterilized soil, has been shown to improve the resporulation of the fungus from nutrient-fortified M. anisopliae. Prior to planting, sweetpotato plant beds can be disinfected with fumigants, such as Metham®, to control soil-borne pests and weeds. Metham® is a broad-spectrum soil microbial suppressant; however, its effect on Metarhizium spp. is unclear. In the research presented here, fungal resporulation was examined in Metham®-fumigated soil and the infectivity of the resulting granule sporulation was evaluated on mealworm, as a proxy for wireworm. The fungal granules grown on different soil treatments (fumigated, field and pasteurized soil) resporulated profusely (for example, 4.14 × 107 (±2.17 × 106) conidia per granule on fumigated soil), but the resporulation was not significantly different among the three soil treatments. However, the conidial germination of the resporulated granules on fumigated soil was >80%, which was significantly higher than those on pasteurized soil or field soil. The resporulated fungal granules were highly infective, causing 100% insect mortality 9 days after the inoculation, regardless of soil treatments. The results from this research show that the fungal granules applied to soils could be an infective inoculant in sweetpotato fields in conjunction with soil fumigation. Additional field studies are required to validate these results and to demonstrate integration with current farming practices.

Bacterial Volatile-Mediated Suppression of Root-Knot Nematode (Meloidogyne incognita)

Root-knot nematodes (Meloidogyne spp.) are obligate plant parasites that cause severe economic losses to agricultural crops worldwide. Because of serious health and environmental concerns related to the use of chemical nematicides, the development of efficient alternatives is of great importance. Biological control through exploiting the potential of rhizosphere microorganisms is currently accepted as an important approach for pest management in sustainable agriculture. In our research, during screening of rhizosphere bacteria against the root-knot nematodes Meloidogyne incognita, Ochrobactrum pseudogrignonense strain NC1 from the rhizosphere of healthy tomatoes showed strong nematode inhibition. A volatile nematicidal assay showed that the cell-free fermentation filtrate in the first-row wells of 12-well tissue culture plates caused M. incognita juvenile mortality in the second-row wells. Gas chromatography-mass spectrometry analysis revealed that dimethyl disulfide (DMDS) and benzaldehyde were the main volatile compounds produced by strain NC1. The nematicidal activity of these compounds indicated that the lethal concentration 50 against the M. incognita juveniles in the second-row wells and the fourth-row wells were 23.4 μmol/ml and 30.7 μmol/ml for DMDS and 4.7 μmol/ml and 15.2 μmol/ml for benzaldehyde, respectively. A greenhouse trial using O. pseudogrignonense strain NC1 provided management efficiencies of root-knot nematodes of 88 to 100% compared with the untreated control. This study demonstrated that nematode-induced root-gall suppression mediated by the bacterial volatiles DMDS and benzaldehyde presents a new opportunity for root-knot nematode management.

Interactions between Brassica Biofumigants and Soil Microbiota: Causes and Impacts

Biofumigation is used to control soil-borne plant diseases, and it has paramount importance to reduce the cost of chemical fumigants. Information about the field control efficacies and impacts of Brassica-based biofumigation (BBF) on soil bacterial and fungal microbiota is scattered in the literature. Therefore, this review summarizes and discusses the nature and the underlying causes of soil bacterial and fungal community dynamics in response to BBF. In addition, the major factors influencing the interaction between a biofumigant and soil microbiota are discussed. The pros and cons of BBF to soil microbiota and the subsequent impacts on sustainable farming practices are also highlighted.

Effects of Glucosinolate-Derived Isothiocyanates on Fungi: A Comprehensive Review on Direct Effects, Mechanisms, Structure-Activity Relationship Data and Possible Agricultural Applications

Plants heavily rely on chemical defense systems against a variety of stressors. The glucosinolates in the Brassicaceae and some allies are the core molecules of one of the most researched such pathways. These natural products are enzymatically converted into isothiocyanates (ITCs) and occasionally other defensive volatile organic constituents (VOCs) upon fungal challenge or tissue disruption to protect the host against the stressor. The current review provides a comprehensive insight on the effects of the isothiocyanates on fungi, including, but not limited to mycorrhizal fungi and pathogens of Brassicaceae. In the review, our current knowledge on the following topics are summarized: direct antifungal activity and the proposed mechanisms of antifungal action, QSAR (quantitative structure-activity relationships), synergistic activity of ITCs with other agents, effects of ITCs on soil microbial composition and allelopathic activity. A detailed insight into the possible applications is also provided: the literature of biofumigation studies, inhibition of post-harvest pathogenesis and protection of various products including grains and fruits is also reviewed herein.

Manipulating the soil microbiomes during a community recovery process with plant beneficial species for the suppression of Fusarium wilt of watermelon

Fusarium wilt is a devastating disease which impacts watermelon production. Soil fumigation using dazomet followed by biological organic fertilizer was applied to suppress the Fusarium wilt disease. We propose that fumigation suppresses the soil indigenous community, especially the soil-borne pathogens, while the utilization of bio-organic fertilizer facilitates the recovery of the soil microbiome to a beneficial, suppressive state through the introduction of plant growth-promoting microorganisms. Greenhouse experiment showed that applied biological organic fertilizer after dazomet fumigation effective restrain the disease incidence with a 93.6% disease control. Fumigation strongly decreased soil microbial diversity and altered relative taxa abundances, suggesting the possibility of niche release by the resident soil microbial community. Fumigation followed by bio-fertilizer transformed the soil microbial community composition and resulted in higher relative abundances of beneficial microbial groups such as Bacillus (8.5%) and Trichoderma (13.5%), coupled with lower Fusarium abundance compared to other treatments. Network analysis illustrated that soil fumigation decreased interactions within the soil microbial community with less nodes and links while bio-fertilizer addition promoted node interactions. In addition, bio-fertilizer addition after fumigation resulted in the beneficial species becoming the key network connectors. Collectively, fumigation appears to release the resident soil niche resulting in lower diversity while the beneficial microbes introduced by bio-fertilizer addition colonize these niches, leading to a more complex community with fewer pathogens that suppresses Fusarium wilt disease incidence.

Epidemiology, Biotic Interactions and Biological Control of Armillarioids in the Northern Hemisphere

Armillarioids, including the genera Armillaria, Desarmillaria and Guyanagaster, represent white-rot specific fungal saprotrophs with soilborne pathogenic potentials on woody hosts. They propagate in the soil by root-like rhizomorphs, connecting between susceptible root sections of their hosts, and often forming extended colonies in native forests. Pathogenic abilities of Armillaria and Desarmillaria genets can readily manifest in compromised hosts, or hosts with full vigour can be invaded by virulent mycelia when exposed to a larger number of newly formed genets. Armillaria root rot-related symptoms are indicators of ecological imbalances in native forests and plantations at the rhizosphere levels, often related to abiotic environmental threats, and most likely unfavourable changes in the microbiome compositions in the interactive zone of the roots. The less-studied biotic impacts that contribute to armillarioid host infection include fungi and insects, as well as forest conditions. On the other hand, negative biotic impactors, like bacterial communities, antagonistic fungi, nematodes and plant-derived substances may find applications in the environment-friendly, biological control of armillarioid root diseases, which can be used instead of, or in combination with the classical, but frequently problematic silvicultural and chemical control measures.

Nematicidal Amendments and Soil Remediation

The intensification of agriculture has created concerns about soil degradation and toxicity of agricultural chemicals to non-target organisms. As a result, there is great urgency for discovering new ecofriendly tools for pest management and plant nutrition. Botanical matrices and their extracts and purified secondary metabolites have received much research interest, but time-consuming registration issues have slowed their adoption. In contrast, cultural practices such as use of plant matrices as soil amendments could be immediately used as plant protectants or organic fertilizers. Herein, we focus on some types of soil amendments of botanical origin and their utilization for nematicidal activity and enhancement of plant nutrition. The mode of action is discussed in terms of parasite control as well as plant growth stimulation.

Biofumigation for Fighting Replant Disease- A Review

Replant disease is a soil (micro-) biome-based, harmfully-disturbed physiological and morphological reaction of plants to replanting similar cultures on the same sites by demonstrating growth retardation and leading to economic losses especially in Rosaceae plant production. Commonly, replant disease is overcome by soil fumigation with toxic chemicals. With chemical soil fumigation being restricted in many countries, other strategies are needed. Biofumigation, which is characterized by the incorporation of Brassicaceae plant materials into soil, is a promising method. We review the potential of biofumigation in the fight against replant disease. Biofumigation using optimized Brassicaceae seed meal compositions in combination with replant disease tolerant plant genotypes shows promising results, but the efficacy is still soil and site-dependent. Therefore, future studies should address the optimal timing as well as amount and type of incorporated plant material and environmental conditions during incubation in dependence of the soil physical and chemical characteristics.

Effect of Organic Inputs and Solarization for the Suppression of Rhizoctonia solani in Woody Ornamental Plant Production

Soilborne diseases are the most economically significant problem faced by Southern region nursery producers. The goal of this research was to improve Rhizoctonia root rot disease management through the use of soil solarization alone and in combination with biofumigant cover crops-arugula 'Astro' (Eruca vesicaria ssp. sativa), mustard green 'Amara' (Brassica carinata), and turnip 'Purple top forage' (B. rapa); good quality compost and mustard meal amendment. The experiments were established as on-farm trials in 2016 and 2017 with prevalent Rhizoctonia solani population in propagation beds. All three biofumigant cover crops, arugula 'Astro', mustard green 'Amara', and turnip 'Purple top forage' in combination with solarization were able to reduce the Rhizoctonia root rot in flowering cherry 'Kwanzan' plants in nursery propagation beds. Compost amendment increased the flowering cherry rooted cuttings growth (plant weight, root weight, and plant height) compared to other treatments. Soil solarization in combination with cover crops and organic inputs could be used as part of an integrated approach to manage Rhizoctonia root rot in nursery crop propagation beds.

Fungal Community Structural and Microbial Functional Pattern Changes After Soil Amendments by Oilseed Meals of Jatropha curcas and Camelina sativa: A Microcosm Study

The meals after oil extraction from many oilseed crops have nutrition and biofumigation potential for land application. Oilseed meal (SM) from the dedicated bioenergy crop Jatropha curcas were implicated to contain compounds that have antibacterial properties on some soil pathogens. However, little is known about its effect on non-targeted soil microbial community, especially on fungi. SM from Camelina sativa contains moderate level of glucosinolates (GLS) and was under studied. To investigate soil fungal community responses to jatropha and camelina SMs, we conducted a lab based microcosm study, amending soil with 1% SMs of jatropha, camelina, flax, and biomass of wheat straw. Fungal community abundance and structure were analyzed based on the ITS region using qPCR and tag-pyrosequencing. Microbial functional changes were examined by community level physiological profile (CLPP) using Biolog assay. Both SMs from jatropha and camelina showed biofumigant properties and inhibited fungal proliferation. Jatropha SM significantly altered soil fungal community structures with lower fungal biodiversity and higher Chaetomium composition. Camelina SM amended soil promoted Fusarium proliferation. CLPP indicated sequential hierarchy for C metabolism in the oilseed-amended microcosms was generally complex C > phosphate-associated C > carboxylic acids > carbohydrates > amines > amino acids. No significant difference in CLPP was detected due to the type of SM treatment. Our data indicate that both SMs of jatropha and camelina have biofumigant properties and can differentially impact soil microbial communities, and the changes were relatively persistent over time. Microbial functional patterns on the other side were not impacted by SM type. Our study revealed biofumigant and nutritional influence of SMs from dedicated biofuel plants on soil microbial community. This information will help properly using jatropha and camelina SMs for pathogen control while minimizing their negative impacts on non-target microorganisms. However, further studies in the field are demanded to investigate their influences in real practice.

Disruption of microbial community composition and identification of plant growth promoting microorganisms after exposure of soil to rapeseed-derived glucosinolates

Land plants are engaged in intricate communities with soil bacteria and fungi indispensable for plant survival and growth. The plant-microbial interactions are largely governed by specific metabolites. We employed a combination of lipid-fingerprinting, enzyme activity assays, high-throughput DNA sequencing and isolation of cultivable microorganisms to uncover the dynamics of the bacterial and fungal community structures in the soil after exposure to isothiocyanates (ITC) obtained from rapeseed glucosinolates. Rapeseed-derived ITCs, including the cyclic, stable goitrin, are secondary metabolites with strong allelopathic affects against other plants, fungi and nematodes, and in addition can represent a health risk for human and animals. However, the effects of ITC application on the different bacterial and fungal organisms in soil are not known in detail. ITCs diminished the diversity of bacteria and fungi. After exposure, only few bacterial taxa of the Gammaproteobacteria, Bacteriodetes and Acidobacteria proliferated while Trichosporon (Zygomycota) dominated the fungal soil community. Many surviving microorganisms in ITC-treated soil where previously shown to harbor plant growth promoting properties. Cultivable fungi and bacteria were isolated from treated soils. A large number of cultivable microbial strains was capable of mobilizing soluble phosphate from insoluble calcium phosphate, and their application to Arabidopsis plants resulted in increased biomass production, thus revealing growth promoting activities. Therefore, inclusion of rapeseed-derived glucosinolates during biofumigation causes losses of microbiota, but also results in enrichment with ITC-tolerant plant microorganisms, a number of which show growth promoting activities, suggesting that Brassicaceae plants can shape soil microbiota community structure favoring bacteria and fungi beneficial for Brassica plants.

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

Soil disinfestation is an important agricultural practice to conquer soil-borne diseases and thereby ensure crop productivity. Reductive soil disinfestation (RSD) had been developed as an environmentally friendly alternative to chemical soil disinfestation (CSD). However, the differences between CSD and RSD on soil-borne pathogen suppression and fungal community structure remain poorly understood. In this work, five treatments, i.e., untreated soil (CK), CSD with 0.5 t ha^-1 dazomet (DZ), RSD with 10 t ha^-1 ethanol (ET), 15 t ha^-1 sugarcane bagasse (SB), and 15 t ha^-1 bean dregs (BD), were performed to investigate their influences on disinfestation efficiency, fungal abundance, diversity, and community structure via quantitative PCR and high-throughput sequencing. RSD-related treatments, especially the BD treatment, effectively alleviated soil acidification and salinization. The fungal abundance and microbial activity considerably increased in the BD treatment and significantly declined in the DZ treatment as compared to the CK treatment. Moreover, both CSD and RSD-related treatments significantly inhibited the population of Fusarium oxysporum and the relative abundance of genus Fusarium. Fungal community structure was notably altered by CSD and RSD practices. Furthermore, both CSD and RSD harbored a distinct unique microbiome, with the DZ treatment dominated by the genus Mortierella and BD treatment predominated by the genera Zopfiella, Chaetomium, and Penicillium. Taken together, these results indicate that the BD treatment could considerably alleviate the soil deterioration, improve soil microbial activity, and reassemble a non-pathogen unique microbiome that have more disease-suppressive agents and thus might be a promising disinfestation practice to control soil-borne disease in monoculture system.

Soil Bacterial Community Was Changed after Brassicaceous Seed Meal Application for Suppression of Fusarium Wilt on Pepper

Application of Brassicaceous seed meal (BSM) is a promising biologically based disease-control practice but BSM could directly and indirectly also affect the non-target bacterial communities, including the beneficial populations. Understanding the bacterial response to BSM at the community level is of great significance for directing plant disease management through the manipulation of resident bacterial communities. Fusarium wilt is a devastating disease on pepper. However, little is known about the response of bacterial communities, especially the rhizosphere bacterial community, to BSM application to soil heavily infested with Fusarium wilt pathogen and cropped with peppers. In this study, a 25-day microcosm incubation of a natural Fusarium wilt pathogen-infested soil supplemented with three BSMs, i.e., Camelina sativa 'Crantz' (CAME), Brassica juncea 'Pacific Gold' (PG), and a mixture of PG and Sinapis alba cv. 'IdaGold' (IG) (PG+IG, 1:1 ratio), was performed. Then, a further 35-day pot experiment was established with pepper plants growing in the BSM treated soils. The changes in the bacterial community in the soil after 25 days of incubation and changes in the rhizosphere after an additional 35 days of pepper growth were investigated by 454 pyrosequencing technique. The results show that the application of PG and PG+IG reduced the disease index by 100% and 72.8%, respectively, after 35 days of pepper growth, while the application of CAME did not have an evident suppressive effect. All BSM treatments altered the bacterial community structure and decreased the bacterial richness and diversity after 25 days of incubation, although this effect was weakened after an additional 35 days of pepper growth. At the phylum/class and the genus levels, the changes in specific bacterial populations resulting from the PG and PG+IG treatments, especially the significant increase in Actinobacteria-affiliated Streptomyces and an unclassified genus and the significant decrease in Chloroflexi, were suspected to be one of the microbial mechanisms involved in PG-containing BSM-induced disease suppression. This study is helpful for our understanding of the mechanisms that lead to contrasting plant disease severity after the addition of different BSMs.

Free-Living Nematodes Together With Associated Microbes Play an Essential Role in Apple Replant Disease

Apple replant disease (ARD) is a severe problem in apple production worldwide. It is caused by a complex of soil biota, leading to small discolorated roots, as well as increased biosynthesis of phytoalexins, total phenolic compounds and antioxidants. We sampled soil from randomized field plots with either apple trees affected by ARD, which were five times replanted every second year, or with healthy trees growing in plots, which had a grass cover during this period. We investigated the contribution of nematodes to ARD by dissecting the soil biota from plots infested with ARD and non-infested control plots into a nematode and a microbe fraction. Nematode communities significantly differed between ARD and control soil as revealed by high-throughput sequencing of 18S rRNA genes. Plant-parasitic nematodes were too low in abundance to explain root damage, and did not significantly differ between ARD and control soil. Their separate and synergistic effect on ARD symptoms of susceptible M26 apple rootstocks was analyzed 4 and 8 weeks after inoculation in three greenhouse experiments. Inoculants were either nematodes from ARD plots (N_ARD), N_ARD plus microbes from ARD plots (M_ARD), N_ARD plus microbes from control plots (M_Con), nematodes from control plots N_Con plus M_ARD, N_Con plus M_Con, M_ARD, or M_Con, or non-inoculated control. In all three experiments, the combination N_ARD plus M_ARD had the strongest adverse effect on the plants, with respect to growth parameters of shoots and roots, total phenolic compounds and phytoalexins in roots, and antioxidants in leaves. N_ARD also induced ARD but less than N_ARD plus M_ARD. N_ARD plus M_Con had delayed effects on the plants compared to N_ARD plus M_ARD, suggesting that detrimental nematode-microbe interactions built up with time. Effects of M_ARD or N_Con plus M_ARD were minor or not distinguishable from those of M_Con or non-inoculated control. Overall, the source of the inoculated nematodes -ARD or control soil- and the interaction between ARD nematodes and microbes were highly significant factors determining ARD. In conclusion, exploring the associations of nematodes and microbes in ARD soils will give the chance to unravel the etiology of ARD.

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses

Greenhouse eggplant monocropping in China has contributed to the aggravation of soil-borne diseases, reductions in crop quality and yield, and the degradation of physical and chemical soil properties. Crop rotation is one effective way of alleviating the problems of continuous cropping worldwide; however, few studies have reported changes in soil bacterial community structures and physical and chemical soil properties after Brassica vegetables had been rotated with eggplant in greenhouses. In this experiment, mustard-eggplant (BFN) and oilseed rape-eggplant (BFC) rotations were studied to identify changes in the physicochemical properties and bacterial community structure in soil that was previously subject to monocropping. Samples were taken after two types of Brassica plants incorporated into soil for 15 days to compare with continually planted eggplant (control, CN) and chemical disinfection of soil (CF) in greenhouses. MiSeq pyrosequencing was used to analyze soil bacterial diversity and structure in the four different treatments. A total of 55,129 reads were identified, and rarefaction analysis showed that the soil treatments were equally sampled. The bacterial richness of the BFC treatment and the diversity of the BFN treatment were significantly higher than those of the other treatments. Further comparison showed that the bacterial community structures of BFC and BFN treatments were also different from CN and CF treatments. The relative abundance of several dominant bacterial genera in the BFC and BFN treatments (such as Flavobacteria, Stenotrophomonas, Massilia and Cellvibrio, which played different roles in improving soil fertility and advancing plant growth) was distinctly higher than the CN or CF treatments. Additionally, the total organic matter and Olsen-P content of the BFC and BFN treatments were significantly greater than the CN treatment. We conclude that Brassica vegetables-eggplant crop rotations could provide a more effective means of solving the problems of greenhouse eggplant monocultures.

Degradation of Biofumigant Isothiocyanates and Allyl Glucosinolate in Soil and Their Effects on the Microbial Community Composition

Brassicales species rich in glucosinolates are used for biofumigation, a process based on releasing enzymatically toxic isothiocyanates into the soil. These hydrolysis products are volatile and often reactive compounds. Moreover, glucosinolates can be degraded also without the presence of the hydrolytic enzyme myrosinase which might contribute to bioactive effects. Thus, in the present study the stability of Brassicaceae plant-derived and pure glucosinolates hydrolysis products was studied using three different soils (model biofumigation). In addition, the degradation of pure 2-propenyl glucosinolate was investigated with special regard to the formation of volatile breakdown products. Finally, the influence of pure glucosinolate degradation on the bacterial community composition was evaluated using denaturing gradient gel electrophoresis of 16S rRNA gene amplified from total community DNA. The model biofumigation study revealed that the structure of the hydrolysis products had a significant impact on their stability in the soil but not the soil type. Following the degradation of pure 2-propenyl glucosinolate in the soils, the nitrile as well as the isothiocyanate can be the main degradation products, depending on the soil type. Furthermore, the degradation was shown to be both chemically as well as biologically mediated as autoclaving reduced degradation. The nitrile was the major product of the chemical degradation and its formation increased with iron content of the soil. Additionally, the bacterial community composition was significantly affected by adding pure 2-propenyl glucosinolate, the effect being more pronounced than in treatments with myrosinase added to the glucosinolate. Therefore, glucosinolates can have a greater effect on soil bacterial community composition than their hydrolysis products.

Evaluation of methyl bromide alternatives efficacy against soil-borne pathogens, nematodes and soil microbial community

Methyl bromide (MB) and other alternatives were evaluated for suppression of Fusarium spp., Phytophthora spp., and Meloidogyne spp. and their influence on soil microbial communities. Both Fusarium spp. and Phytophthora spp. were significantly reduced by the MB (30.74 mg kg-1), methyl iodide (MI: 45.58 mg kg-1), metham sodium (MS: 53.92 mg kg-1) treatments. MS exhibited comparable effectiveness to MB in controlling Meloidogyne spp. and total nematodes, followed by MI at the tested rate. By contrast, sulfuryl fluoride (SF: 33.04 mg kg-1) and chloroform (CF: 23.68 mg kg-1) showed low efficacy in controlling Fusarium spp., Phytophthora spp., and Meloidogyne spp. MB, MI and MS significantly lowered the abundance of different microbial populations and microbial biomass in soil, whereas SF and CF had limited influence on them compared with the control. Diversity indices in Biolog studies decreased in response to fumigation, but no significant difference was found among treatments in PLFA studies. Principal component and cluster analyses of Biolog and PLFA data sets revealed that MB and MI treatments greatly influenced the soil microbial community functional and structural diversity compared with SF treatment. These results suggest that fumigants with high effectiveness in suppressing soil-borne disease could significantly influence soil microbial community.

Soil bacterial and fungal communities respond differently to various isothiocyanates added for biofumigation

The meals from many oilseed crops have potential for biofumigation due to their release of biocidal compounds such as isothiocyanates (ITCs). Various ITCs are known to inhibit numerous pathogens; however, much less is known about how the soil microbial community responds to the different types of ITCs released from oilseed meals (SMs). To simulate applying ITC-releasing SMs to soil, we amended soil with 1% flax SM (contains no biocidal chemicals) along with four types of ITCs (allyl, butyl, phenyl, and benzyl ITC) in order to determine their effects on soil fungal and bacterial communities in a replicated microcosm study. Microbial communities were analyzed based on the ITS region for fungi and 16S rRNA gene for bacteria using qPCR and tag-pyrosequencing with 454 GS FLX titanium technology. A dramatic decrease in fungal populations (~85% reduction) was observed after allyl ITC addition. Fungal community compositions also shifted following ITC amendments (e.g., Humicola increased in allyl and Mortierella in butyl ITC amendments). Bacterial populations were less impacted by ITCs, although there was a transient increase in the proportion of Firmicutes, related to bacteria know to be antagonistic to plant pathogens, following amendment with allyl ITC. Our results indicate that the type of ITC released from SMs can result in differential impacts on soil microorganisms. This information will aid selection and breeding of plants for biofumigation-based control of soil-borne pathogens while minimizing the impacts on non-target microorganisms.

Synergistic Effect of Dazomet Soil Fumigation and Clonostachys rosea Against Cucumber Fusarium Wilt

Soil fumigation and biological control are two control measures frequently used against soilborne diseases. In this study, the chemical fumigant dazomet was applied in combination with the biocontrol agent (BCA) Clonostachys rosea 67-1 to combat cucumber wilt caused by Fusarium oxysporum f. sp. cucumerinum KW2-1. When the mycoparasite C. rosea 67-1 was applied after dazomet fumigation, disease control reached 100%, compared with 88.1 and 69.8% for dazomet and 67-1 agent, respectively, applied alone, indicating a synergistic effect of dazomet and C. rosea in combating cucumber Fusarium wilt based on analysis of Bliss Independence. To understand the synergistic mechanism, the effects of chemical fumigation on the colonization potential and activity of F. oxysporum f. sp. cucumerinum, and the interaction between the BCA and the pathogen were investigated. The results showed that growth of the pathogen decreased with increasing dazomet concentration subsequent to fumigation. When exposed to dazomet at 100 ppm, the fungal sporulation rate decreased by 94.4%. Severe damage was observed in fumigated isolates using scanning electron microscopy. In the greenhouse, disease incidence of cucumber caused by fumigated F. oxysporum f. sp. cucumerinum significantly decreased. Whereas germination of C. rosea 67-1 spores increased by >sixfold in fumigated soil, and its ability to parasitize fumigated F. oxysporum f. sp. cucumerinum significantly increased (P = 0.014).

Impact of fungicides on the diversity and function of non-target ammonia-oxidizing microorganisms residing in a litter soil cover

Litter soil cover constitutes an important micro-ecosystem in sustainable viticulture having a key role in nutrient cycling and serving as a habitat of complex microbial communities. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are known to regulate nitrification in soil while little is known regarding their function and diversity in litter. We investigated the effects of two fungicides, penconazole and cyprodinil, commonly used in vineyards, on the function and diversity of total and active AOB and AOA in a microcosm study. Functional changes measured via potential nitrification and structural changes assessed via denaturating gradient gel electrophoresis (DGGE) at the DNA and RNA levels were contrasted with pesticide dissipation in the litter layer. The latter was inversely correlated with potential nitrification, which was temporarily inhibited at the initial sampling dates (0 to 21 days) when nearly 100 % of the applied pesticide amounts was still present in the litter. Fungicides induced changes in AOB and AOA communities with RNA-DGGE analysis showing a higher sensitivity. AOA were more responsive to pesticide application compared to AOB. Potential nitrification was less sensitive to the fungicides and was restored faster than structural changes, which persisted. These results support the theory of microbial redundancy for nitrification in a stressed litter environment.

Microbial diversity determines the invasion of soil by a bacterial pathogen

Natural ecosystems show variable resistance to invasion by alien species, and this resistance can relate to the species diversity in the system. In soil, microorganisms are key components that determine life support functions, but the functional redundancy in the microbiota of most soils has long been thought to overwhelm microbial diversity-function relationships. We here show an inverse relationship between soil microbial diversity and survival of the invading species Escherichia coli O157:H7, assessed by using the marked derivative strain T. The invader's fate in soil was determined in the presence of (i) differentially constructed culturable bacterial communities, and (ii) microbial communities established using a dilution-to-extinction approach. Both approaches revealed a negative correlation between the diversity of the soil microbiota and survival of the invader. The relationship could be explained by a decrease in the competitive ability of the invader in species-rich vs. species-poor bacterial communities, reflected in the amount of resources used and the rate of their consumption. Soil microbial diversity is a key factor that controls the extent to which bacterial invaders can establish.