Effect of fumigation with 1,3-dichloropropene on soil bacterial communities

Impact of repeated fumigant applications on soil properties, crop yield, and microbial communities in a plastic-mulched tomato production system

Pre-plant soil fumigation is widely applied to control nematodes, soil-borne fungal pathogens, and weeds in vegetable crops. However, most of the research evaluating the effect of fumigants on crop yield and soil microbial communities has been done on single compounds despite growers mainly applying fumigant combinations. We studied the effect of different fumigant combinations (chloropicrin, 1,3-dichloropropene, and metam potassium) on soil properties, crop yield, and the soil bacterial and fungal microbiome for two consecutive years in a plastic-mulched tomato production system in Florida (United States). While combinations of fumigants did not improve plant productivity more than the individual application of these products, application of fumigants with >60 % chloropicrin did significantly increase yield. Fumigant combinations had no significant effect on bacterial diversity, but fumigants with >35 % chloropicrin reduced soil fungal diversity and induced temporary changes in the soil bacterial and fungal community composition. These changes included short-term increases in the relative abundance of Firmicutes and Ascomycota, as well as decreases in other bacterial and fungal taxa. Repeated fumigation reduced network complexity and the relative abundance of several predicted bacterial functions and fungal guilds, particularly after fumigation and at end of harvest (3-months post fumigation). A structural equation model (SEM) showed fumigants not only directly impact crop yield, but they can also indirectly determine variations in plant productivity through effects on the soil microbiome. Overall, this study increases our understanding of the environmental and agricultural impacts of fumigants in a plastic-mulched tomato production system.

Diversity and function of soybean rhizosphere microbiome under nature farming

Nature farming is a farming system that entails cultivating crops without using chemical fertilizers and pesticides. The present study investigated the bacterial and fungal communities in the rhizosphere of soybean grown in conventional and nature farming soils using wild-type and non-nodulating mutant soybean. The effect of soil fumigant was also analyzed to reveal its perturbation of microbial communities and subsequent effects on the growth of soybean. Overall, the wild-type soybean exhibited a better growth index compared to mutant soybean and especially in nature farming. Nodulation and arbuscular mycorrhiza (AM) fungi colonization were higher in plants under nature farming than in conventionally managed soil; however, fumigation drastically affected these symbioses with greater impacts on plants in nature farming soil. The rhizosphere microbiome diversity in nature farming was higher than that in conventional farming for both cultivars. However, the diversity was significantly decreased after fumigation treatment with a greater impact on nature farming. Principal coordinate analysis revealed that nature farming and conventional farming soil harbored distinct microbial communities and that soil fumigation significantly altered the communities in nature farming soils but not in conventional farming soils. Intriguingly, some beneficial microbial taxa related to plant growth and health, including Rhizobium, Streptomyces, and Burkholderia, were found as distinct microbes in the nature farming soil but were selectively bleached by fumigant treatment. Network analysis revealed a highly complex microbial network with high taxa connectivity observed under nature farming soil than in conventional soil; however, fumigation strongly broke it. Overall, the results highlighted that nature farming embraced higher microbial diversity and the abundance of beneficial soil microbes with a complex and interconnected network structure, and also demonstrated the underlying resilience of the microbial community to environmental perturbations, which is critical under nature farming where chemical fertilizers and pesticides are not applied.

Chitin amendments eliminate the negative impacts of continuous cropping obstacles on soil properties and microbial assemblage

Continuous cropping of soybean leads to soil environment deterioration and soil-borne disease exacerbation, which in turn limits the sustainability of agricultural production. Chitin amendments are considered promising methods for alleviating soybean continuous cropping obstacles; however, the underlying mechanisms of soil sickness reduction remain unclear. In this study, soil amendments with pure and crude chitin at different addition dosages were employed to treat diseased soil induced by continuous cropping of soybean for five years. Chitin amendments, especially crude chitin, remarkably increased soil pH, available phosphorus (AP), potassium (AK) and nitrate nitrogen ( NO 3 - -N) contents, and improved soybean plant growth and soil microbial activities (FDA). Additionally, chitin application significantly enriched the relative abundances of the potential biocontrol bacteria Sphingomonas, Streptomyces, and Bacillus and the fungi Mortierella, Purpureocillium, and Metarhizium while depleted those of the potential plant pathogens Fusarium, Cylindrocarpon and Paraphoma. Moreover, chitin amendments induced looser pathogenic subnetwork structures and less pathogenic cooperation with other connected microbial taxa in the rhizosphere soils. The structural equation model (SEM) revealed that pure and crude chitin amendments promoted soybean plant growth by indirectly regulating soil pH-mediated soil microbial activities and potentially beneficial microbes, respectively. Therefore, the reduction strategies for continuous cropping obstacles by adding pure and crude chitin were distinct; pure chitin amendments showed general disease suppression, while crude chitin exhibited specific disease suppression. Overall, chitin amendments could suppress potential plant pathogens and improve soil health, thereby promoting soybean growth, which provides new prospects for cultivation practices to control soybean continuous cropping obstacles.

Chemical fumigants control apple replant disease: Microbial community structure-mediated inhibition of Fusarium and degradation of phenolic acids

Fusarium and phenolic acids in apple replant soil have deleterious effects on soil, which affects the growth of young replanted apple trees. Here, we studied the effects of different chemical fumigants (metham sodium, dazomet, calcium cyanamide, 1,3-dichloropropene, and methyl bromide) on Fusarium and phenolic acids in soil. The chemical fumigants disturbed the apple replant soil microbial community to different degrees in the order from highest to the lowest as methyl bromide > 1,3-dichloropropene > dazomet > metham sodium > calcium cyanamide. Compared with the control, the total numbers of Operational Taxonomic Unit (OTU) were 104.63 % and 9.38 % lower in the methyl bromide and calcium cyanamide treatments, respectively while the average contents of Fusarium were 88.04 % and 59.18% lower in these treatments, respectively. Higher disturbance degrees resulted in a slower recovery rate of the soil microbial community, which facilitated the transformation of the soil into a disease-suppressing state. During the recovery process, the roots recruited Streptomyces OTU2796 and Bacillus OTU2243, which alleviated Fusarium-induced stress via the synthesis of polyketones and macrolides. The roots also recruited Sphingomonas OTU3488, OTU5572, and OTU8147, which alleviated phenolic acid-induced stress through the degradation of benzoate and polycyclic aromatic hydrocarbons.

Synergistic Effect of Cold Treatment Combined with Ethyl Formate Fumigation against Drosophila suzukii (Diptera: Drosophilidae)

Drosophila suzukii is a quarantine pest that is rapidly spreading in berries. This study evaluated the synergistic effect of combination treatment with ethyl formate (EF) and cold temperature for D. suzukii control on imported grapes. A higher insecticidal effect was observed at 1 °C than at 5 °C at all developmental stages, and the pupal stage showed the strongest tolerance to cold temperature. After EF fumigation alone, eggs showed the highest tolerance at 216.67 mg·h/L (LCT99 value), and adults showed the highest susceptibility at <27.24 mg·h/L. Among the combination treatment methods, cold temperature after fumigation resulted in the best synergistic effect. The effect of this combination was significant, with 23.3% higher mortality for eggs, 22.4% for larvae, and 23.4% for pupae than observed with EF fumigation alone. Furthermore, the period of complete D. suzukii control in the 12 L desiccator was shorter in the combination treatment group at the LCT80 value than at the LCT50 value of the egg stage. EF showed a very high sorption rate (24%) after 4 h of exposure at a grape loading ratio of 15% in a 0.65 m3 fumigation chamber. As the grape loading ratio for combination treatment decreased, D. suzukii mortality increased, but when EF was administered at the LCT80 value, there was little difference in the mortalities of the eggs and larvae but not the pupae. All D. suzukii developmental stages were completely controlled within 7 days after combination treatment, and phytotoxicity was not observed in grapes. These results suggest that the combination of cold-temperature treatment and EF fumigation could be used for D. suzukii control.

Spatial and Temporal Changes of Soil Microbial Communities in Field Tomato Production as Affected by Anaerobic Soil Disinfestation

Anaerobic soil disinfestation (ASD) has been demonstrated as an effective alternative to pre-plant chemical soil fumigation (CSF) commonly used to control soilborne pathogens. However, the ASD effects on spatial and temporal changes in soil microbial communities remain poorly understood in production systems with low soilborne disease pressure. The objective of this study was to assess the influence of ASD treatments on soil microbial community composition at different soil depths during the spring tomato production season in Florida. Soil treatments included ASD using 6.9 m3 ha−1 of molasses with 11 Mg ha−1 of composted poultry litter (CPL) (ASD0.5), ASD with 13.9 m3 ha−1 of molasses and 22 Mg ha−1 CPL (ASD1.0), and chemical soil fumigation (CSF) using a mixture of 1,3-dichloropropene and chloropicrin. Soil microbial community composition was measured at soil depths of 0–15 and 15–30 cm using phospholipid fatty acid (PLFA) analysis at 0, 36, 76, and 99 days after transplanting (DAT). Fatty acid methyl esters were categorized into biomarker groups including total microbial biomass (TMB), G+ bacteria (G+), G− bacteria (G−), actinomycetes (Actino), arbuscular mycorrhizal fungi (AMF), protozoa, and general fungi (F). Soil concentrations of G+, Actino, F, AMF, and the ratio of F:bacteria (B) were significantly impacted by a soil treatment × soil depth × sampling time three-way interaction. All the microbial biomarkers were significantly affected by soil treatment × sampling depth two-way interactions except for protozoa and F:B ratio. Concentrations of TMB, Actino, AMF, F, G+, and G− bacteria were significantly increased in ASD treated soils at both 0–15 and 15–30 cm soil depths across different sampling times compared with CSF. In addition, the concentrations of G+ and G− bacteria, AMF, F, and TMB were higher at 0–15 vs. 15–30 cm soil depth under ASD treatments, whereas no soil depth differences were observed in CSF. Discriminant analysis further confirmed that soil microbial community composition was distinctly different in CSF compared with ASD treatments. The soil microbial profile was well-differentiated between the two soil depths under ASD treatments but not in CSF, while the enhancement of PLFA biomarkers by ASD decreased with increasing soil depth.

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.

An emerging chemical fumigant: two-sided effects of dazomet on soil microbial environment and plant response

Methyl bromide has been banned worldwide because it causes damage to the ozone layer and the environment. To find a substitute for methyl bromide, the relationships among fumigation, plant growth, and the microbial community in replant soil require further study. We performed pot and field experiments to investigate the effects of dazomet fumigation on soil properties and plant performance. Changes in soil microbial community structure and diversity were assessed using high-throughput sequencing, and plant physiological performance and soil physicochemical properties were also measured. Dazomet fumigation enhanced photosynthesis and promoted plant growth in replant soil; it altered soil physical and chemical properties and reduced soil enzyme activities, although these parameters gradually recovered over time. After dazomet fumigation, the dominant soil phyla changed, microbial diversity decreased significantly, the relative abundance of biocontrol bacteria such as Mortierella increased, and the relative abundance of pathogenic bacteria such as Fusarium decreased. Over the course of the experiment, the soil microbial flora changed dynamically, and soil enzyme activities and other physical and chemical properties also recovered to a certain extent. This result suggested that the effect of dazomet on soil microorganisms was temporary. However, fumigation also led to an increase in some resistant pathogens, such as Trichosporon, that affect soil function and health. Therefore, it is necessary to consider potential negative impacts of dazomet on the soil environment and to perform active environmental risk management in China.

Effects of Tilletia foetida on Microbial Communities in the Rhizosphere Soil of Wheat Seeds Coated with Different Concentrations of Jianzhuang

Tilletia foetida (syn. T. laevis) leads to wheat common bunt, a worldwide disease that can lead to 80% yield loss and even total loss of production, together with degrading the quality of grains and flour by producing a rotten fish smell. To explore the potential microbial community that may contribute to the control of soil- and seed-borne pathogens, in this study, we analyzed the effects of the plant pathogenic fungus T. foetida on rhizosphere soil microorganisms in wheat seeds coated with different concentrations of a fungicide (Jianzhuang) used to control the disease. To analyze the bacterial and fungal abundance in T. foetida-infected and mock-infected plants, the microorganisms were sequenced using high-throughput HiSeq 2500 gene sequencing. The results showed that bacterial communities, including Verrucomicrobia, Patescibacteria, Armatimonadetes, Nitrospirae, Fibrobacteres, Chlamydiae, and Hydrogenedentes, and fungal communities, including Basidiomycota and Ciliophora, were more prevalent in the mock group than in the T. foetida-infected group, which may contribute to the control of wheat common bunt. Moreover, cluster and PCoA analysis revealed that replicates of the same samples were clustered together, and these results were also found in the distance index within-group analysis for bacterial and fungal communities in the T. foetida-infected and mock groups.

Effects of Chemical and Solar Soil-Disinfection Methods on Soil Bacterial Communities

The actctivated carbon + solar radiation membrane is an eco-friendly soil disinfestations method for managing soil-borne plant pathogens. However, little was known the impact of Activated carbon + solar radiation membrane on bacterial community structure in strawberry production systems under field conditions. A comprehensive evaluation of the impacts of different soil disinfection methods on the bacterial community structure is fundamental to understand the role of disinfection in maintaining soil health. The changes in the soil bacterial diversity and community composition were detected using realtime fluorescence quantitative PCR (RTFQ PCR) and next-generation sequencing techniques to better understand the effect of soil disinfection. The bacterial community composition was monitored after disinfection using dazomet (DZ), chloropicrin (CP), 100 kg/ha activated carbon + solar radiation membrane (AC1), 200 kg/ha activated carbon + solar radiation membrane (AC2), and 300 kg/ha activated carbon + solar radiation membrane (AC3) and compared with the control (CT). The results indicated that the different dosages of activated carbon (AC1, AC2, and AC3) did not affect the bacterial community structure. On the other hand, DZ and CP considerably reduced the soil biomass and abundance of bacterial species. Chemical fumigants influenced the bacterial community structure, with DZ treatment leading to the dominance of the phylum Firmicutes, accounting for approximately 54%. After fumigation with CP, Proteobacteria and Acidobacteria were the dominant phyla. Beta diversity analysis and principal coordinate analysis revealed that the bacterial communities in the soil treated with DZ and CP formed clusters. Redundancy analysis indicated that soil pH, available potassium, and available phosphorus were the key factors influencing microbial metabolic functional diversity. Thus, it was verified that the damage caused by activated carbon + solar radiation membrane—a potential alternative for chemical fumigant—to the soil bacterial community was less than that caused by chemicals DZ and CP.

Effects of Fumigation with Allyl Isothiocyanate on Soil Microbial Diversity and Community Structure of Tomato

As a substitute for methyl bromide, effects of allyl isothiocyanate (AITC) on nontarget microorganisms in soil are poorly understood. This study measured the half-life of AITC in the soil as well as its effects on the soil substrate-induced respiration (SIR) and on communities of soil bacteria and fungi. The results showed that AITC had a short half-life and a short-term inhibition of SIR; high-throughput sequencing analysis showed that AITC had less effect on bacterial than fungal communities. Fumigation reduced the diversity of soil bacteria temporarily, but stimulated the diversity of soil fungi in the long-term and significantly changed the structure of the fungal community. Following AITC fumigation there were significant increases in the relative abundance of probiotics such as Sphingomonas, Streptomyces, Hypocreales, Acremonium, Aspergillus, and Pseudallescheria that help to control plant diseases. Our study provided useful information for assessing the ecological safety of AITC.

Comparative analysis of the effects of five soil fumigants on the abundance of denitrifying microbes and changes in bacterial community composition

Soil fumigation is currently the most effective method for controlling soil-borne pests and diseases in high-value crops. To better understand the effect of chloropicrin (CP), dazomet (DZ), dimethyl disulfide (DMDS), allyl isothiocyanate (AITC) and 1,3-dichloropropene (1,3-D) fumigants on soil microorganisms, this study monitored changes in the diversity and community composition of soil bacteria involved in denitrification using real-time PCR and high-throughput gene sequencing techniques. These five fumigants significantly decreased the bacterial population size in some phyla including Proteobacteria, Chloroflexi and Acidobacteria, and increased the bacterial population size in other phyla such as Firmicutes, Gemmatimonadetes, Actinobacteria, Verrucomicrobia, Saccharibacteria and Parcubacteria. Although bacterial diversity declined after CP fumigation, it was briefly stimulated by the other four fumigants. Meanwhile, all five fumigants temporarily decreased populations of denitrifying bacteria containing the napA, narG, nirS or nirK enzyme-encoding genes. Denitrifiers bearing the cnorB, qnorB or nosZ genes were relatively stable following DZ and DMDS fumigation. However, cnorB and nosZ decreased initially following CP, AITC and 1,3-D fumigation. Simultaneously, the abundance of qnorB significantly increased in AITC and 1,3-D fumigated soils. These results showed that soil fumigation significantly shifted the abundance and community structure of denitrifying bacteria. This study will help to predict the response of different phyla of denitrifying bacteria to soil fumigation.

Effects of fumigation with 1,3-dichloropropene on soil enzyme activities and microbial communities in continuous-cropping soil

The compound 1,3-D (1,3-dichloropropene) is a potential candidate soil fumigant due to the restrictions on methyl bromide (MB). To date, little is known about the soil microbial community changes induced by 1,3-D fumigation. Therefore, soil properties, related soil enzymes, genes encoding the key enzymes of ammonia oxidation in both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) and bacterial diversity were investigated to assess the effects of 1,3-D fumigation on the soil microbial community. The results exhibited that fumigation with 1,3-D caused accumulation of NH₄⁺-N, but it led to decrease in the rate of NO₃^--N, and the concentration of NO₃^--N gradually recovered. At 12 weeks after transplant (WAT) of tomato seedlings, the concentration of NH₄⁺-N and NO₃^--N were not statistically significant between the 1,3-D treatment groups and the untreated control group. A similar tendency was found for organic matter, soil pH, urease and protease activities. Moreover, quantitative real-time PCR (qPCR) showed that 1,3-D decreased total bacterial abundance, AOA-amoA and AOB-amoA genes. In addition, Illumina MiSeq sequencing analysis revealed that soil bacterial community diversities were significantly reduced at earlier sampling time points, and at later sampling time points, soil bacterial diversity gradually recovered, there was no significant difference compared to the control group. The present study provides useful information to evaluate the environmental safety of 1,3-D.

Changes in the abundance and community composition of different nitrogen cycling groups in response to fumigation with 1,3-dichloropropene

The fumigant 1,3-dichloropropene (1,3-D) is widely-used to control pathogenic bacteria, fungi, nematodes and insects in soil before a crop is planted. Although fumigants in general have been reported to have a 'fertilizer effect' in the soil by increasing nitrogen availability, little is known of how a specific fumigant such as 1,3-D affects available nitrogen. This study used real-time quantitative PCR (qPCR) and 16S rRNA gene amplicon sequencing techniques to investigate the effects of 1,3-D on microorganisms involved in nitrogen cycling that were present in 2 soils: Jiangxi lateritic red soil and Beijing fluvo-aquic soil. The fumigant 1,3-D temporarily decreased the abundance of 11 functional genes involved in nitrogen-fixing, nitrification and denitrification in both soil types. Different nitrogen cycling groups recovered to the unfumigated level in various incubation phases. Microorganisms containing nifH, nxrB, napA and qnorB genes were most vulnerable to 1,3-D fumigation. However, a stronger and longer inhibition effect of 1,3-D on these 11 functional genes was observed in Jiangxi soil than in Beijing soil. At the same time, the abundance of nifH, AOBamoA, nirS, qnorB and cnorB genes was significantly increased 59 days after 1,3-D fumigation. Fumigation with 1,3-D significantly reduced the nitrogen-fixing bacteria Azospirillum and Paenibacillus; the nitrifiers Nitrosomonas and Nitrospira; and the denitrifiers Pseudomonas, Paracoccus and Sphingomonas. Conversely, fumigation with 1,3-D increased the nitrogen-fixing bacteria Bradyrhizobium and Rhizobium; the nitrification bacteria Nitrosospira and Nitrolancea; and the denitrification bacteria Sphingobium, Alcanivorax, Bacillus, Streptomyces and Aeromonas. Fumigation with 1,3-D therefore caused significant shifts in the species composition and number of microbes directly involved in nitrogen cycling in the short-term. These results contribute toward a better understanding of the impact of 1,3-D fumigation on various types of soil nitrogen-cycling groups.

Responses of Nitrogen-Cycling Microorganisms to Dazomet Fumigation

The influence of soil fumigation on microorganisms involved in transforming nitrogen remains little understood, despite the use of fumigants for many decades to control soil-borne pathogens and plant-parasitic nematodes. We used real-time PCR (quantitative polymerase chain reaction) and 16S rRNA gene amplicon sequencing techniques to monitor changes in the diversity and community structure of microorganisms associated with nitrogen transfer after the soil was fumigated with dazomet (DZ). We also examined nitrous oxide (N₂O) emissions from these microorganisms present in fumigated fluvo-aquic soil and lateritic red soil. Fumigation with DZ significantly reduced the abundance of 16S rRNA and nitrogen cycling functional genes (nifH, AOA amoA, AOB amoA, nxrB, narG, napA, nirK, nirS, cnorB, qnorB, and nosZ). At the same time, N₂O production rates increased between 9.9 and 30 times after fumigation. N₂O emissions were significantly correlated with NH 4 + , dissolved amino acids and microbial biomass nitrogen, but uncorrelated with functional gene abundance. Diversity indices showed that DZ temporarily stimulated bacterial diversity as well as caused a significant change in bacterial community composition. For example, DZ significantly decreased populations of N₂-fixing bacteria Mesorhizobium and Paenibacillus, nitrifiers Nitrosomonas, and the denitrifiers Bacillus, Pseudomonas, and Paracoccus. The soil microbial community had the ability to recover to similar population levels recorded in unfumigated soils when the inhibitory effects of DZ fumigation were no longer evident. The microbial recovery rate, however, depended on the physicochemical properties of the soil. These results provided useful information for environmental safety assessments of DZ in China, for improving our understanding of the N-cycling pathways in fumigated soils, and for determining the potential responses of different N-cycling groups after fumigation.

Rational dose of insecticide chlorantraniliprole displays a transient impact on the microbial metabolic functions and bacterial community in a silty-loam paddy soil

Chlorantraniliprole (CAP) is a newly developed insecticide widely used in rice fields in China. There have been few studies regarding its effects on soil microbial functional diversity and bacterial community composition. An 85-day microcosm experiment was performed to reveal the dissipation dynamics of CAP under different application doses in a silty-loam paddy soil in subtropical China. The half-life of CAP was 51.3 and 62.5d for low (1mgkg^-1) and high (10mgkg^-1) application dose, respectively. We used a combination of community level physiological profile (CLPP) and 16S rRNA gene sequencing analysis to get insights into the soil microbial features responded to CAP during the experiment. Non-metric multidimensional scaling (NMDS) performed on CLPP and the sequence results indicated that the soil microbial functional diversity and bacterial community composition were significantly changed by CAP application at day 14, and recovered to the similar level as no CAP treatment (CK) under low dose of CAP at day 36. However, high dose of CAP imposed longer effect on these soil microbial features, and was still significantly different from CK at day 36. Mcrobial taxa analysis at phylum level showed that high dose of CAP decreased the relative abundance of Nitrospirae at day 14, while increased Bacteroidetes and decreased Actinobacteria, Nitrospirae, and Firmicutes at day 36 in relative to CK. Low dose of CAP only increased Crenarchaeota and decreased Nitrospirae at day 14. The response ratio (RR) analysis was used to quantify significant responses of OTUs to different doses of CAP and found that CAP significantly affected the microbes involving the N transformation. This study provides a basic information to aid in the development of application regulations regarding the safe use of CAP in soil and inspire us to apply CAP at rational dose to minimize its ecotoxicity on soil microbes.

Replacing methyl bromide with a combination of 1,3-dichloropropene and metam sodium for cucumber production in China

The combination of 1,3-dichloropropene (1,3-D) and metam sodium (MNa) is a potential resource to replace methyl bromide (MB) as a soil fumigant. The efficacy of 1,3-D+MNa as a crucial factor to limit soil-borne pests was evaluated in one laboratory experiment and two cucumber greenhouse studies conducted in commercial operations. Laboratory results revealed that 1,3-D and MNa (10+20 mg a.i. kg-1 soil) provided the best complementary control of the root-knot nematode, Fusarium oxysporum and two species of weed seeds. Greenhouse trials revealed that the blend of 1,3-D and MNa (10+20 g a.i. m-2) greatly inhibited the ability of Meloidogyne incognita to form root galls. In addition, the number of colony-forming units of F. oxysporum declined substantially after growth on media, resulting in higher fruit yields and greater economic benefits. The combined use of 1,3-D and MNa exhibited a higher control efficacy than when 1,3-D or MNa was utilized alone. The ability of this chemical combination to control soil-borne organisms did not differ significantly from the MB treatment and maintained high cucumber yields, enhancing the income of the farmers. Compared to the untreated control group, all the chemical treatments prominently improved the control of the pests. These results show that applying a combination of 1,3-D and MNa provides a promising alternative to MB that enables the sustained growth of cucumber production in China.

Effects of fumigation with metam-sodium on soil microbial biomass, respiration, nitrogen transformation, bacterial community diversity and genes encoding key enzymes involved in nitrogen cycling

Metam-sodium (MS) is widely used as a soil pre-plant fumigant as methyl bromide is phased out of agriculture. However, the information about how fumigation with MS affects the soil microbial community is still limited. In this study, a 66-day-long experiment was conducted to ascertain the effects of MS on soil substrate-induced respiration (SIR), microbial biomass nitrogen (MBN), NH₄⁺-N and NO₃^--N concentrations, as well as the abundance of the total bacteria and fungi and the expression of genes involved in nitrogen cycling. In addition, 16S rRNA amplicon sequencing was used to investigate the effect of MS on the soil bacterial community. The half-lives of high and low doses of methyl isothiocyanate (MITC) are 10.51h and 9.93h, respectively. MS caused a short-term inhibition of SIR, MBN; had an accumulation effect on NH4⁺-N concentration in the short term; reduced the abundance of the total bacteria and fungi; and suppressed the expression of the nifH, AOA-amoA, anammox bacteria, nosZ, nirS, and narG. In addition, under the influence of MS, soil bacterial diversity decreased significantly in the long term, bacterial community structure was affected, and there was a shift in the predominant population; for example, some genera, such as Paenibacillus and Luteimonas, significantly increased in number. These changes in bacterial flora may be closely related to the growth of crops. Our study provides useful information for environmental safety assessments of MS in China.

Legacy effects of continuous chloropicrin-fumigation for 3-years on soil microbial community composition and metabolic activity

Chloropicrin is widely used to control ginger wilt in China, which have an enormous impact on soil microbial diversity. However, little is known on the possible legacy effects on soil microbial community composition with continuous fumigation over different years. In this report, we used high throughput Illumina sequencing and Biolog ECO microplates to determine the bacterial community and microbial metabolic activity in ginger harvest fields of non-fumigation (NF), chloropicrin-fumigation for 1 year (F_1) and continuous chloropicrin-fumigation for 3 years (F_3). The results showed that microbial richness and diversity in F_3 were the lowest, while the metabolic activity had no significant difference. With the increase of fumigation years, the incidence of bacterial wilt was decreased, the relative abundance of Actinobacteria and Saccharibacteria were gradually increased. Using LEfSe analyses, we found that Saccharibacteria was the most prominent biomarker in F_3. Eight genera associated with antibiotic production in F_3 were screened out, of which seven belonged to Actinobacteria, and one belonged to Bacteroidetes. The study indicated that with the increase of fumigation years, soil antibacterial capacity may be increased (possible reason for reduced the incidence of bacterial wilt), and Saccharibacteria played a potential role in evaluating the biological effects of continuous fumigation.

Effect of fumigation with chloropicrin on soil bacterial communities and genes encoding key enzymes involved in nitrogen cycling

Chloropicrin (CP) is a potential alternative for methyl bromide as a soil fumigant given that the use of methyl bromide has become limited. However, little is known about how fumigation with CP affects the condition of the soil microbial community. In this study, 16S rRNA amplicon sequencing and quantitative PCR were combined to investigate the effect of CP on soil bacterial community. In total, 938,922 effective reads were obtained from 18 samples and clustered into 58,662 operational taxonomic units at a similarity cut-off of 97%. Both approaches showed that the primary structure of bacterial community in soil did not significantly change at the phylum level after fumigation, but CP had a significant impact on the abundance of the bacterial microbiome that was recovered and identified. Additionally, bacterial community diversity decreased significantly, and there was a shift in the predominant populations. Staphylococcus, Actinomadura, Acinetobacter and Streptomyces significantly decreased in number or disappeared, and Bacteroides, Lachnoclostridium, Pseudoalteromonas, Colwellia, Idiomarina and Cobetia became the new predominant populations. In addition, some species associated with biodegradation, such as Sphingomonas spp. and Rhodococcus spp., significantly increased in number. The abundance of ammonia-oxidizing archaea (AOA) were significantly inhibited, yet the abundance of ammonia-oxidizing bacteria (AOB) significantly increased, and denitrification was significantly promoted. These changes in bacterial flora can considerably impact soil function and health and lead to negative effects on the environment surrounding fumigated soils, indicating the need for proactive risk management. Our study provides useful information for environmental safety assessments of CP in China.

Analysis of the inhibitory effects of chloropicrin fumigation on nitrification in various soil types

Chloropicrin retards the conversion of ammonia to nitrite during the nitrification process in soil. In our study, the dynamic effect of chloropicrin fumigation on soil nitrification was evaluated in five different soil types to identify relationships between soil properties and the effect of fumigation on nitrification. Chloropicrin significantly inhibited nitrification in all soils; however, the recovery of nitrification varied greatly between the soils. Following chloropicrin fumigation, nitrification recovered to the control level in all soils, except in the acidic Guangxi soil. Nitrification recovered faster in fumigated sandy loam Beijing soil than in the other four fumigated soils. Soil texture and pH were two important factors that influenced chloropicrin's inhibitory effect on nitrification. An S-shaped function was fitted to soil NO₃^--N content to assess the nitrification recovery tendency in different soils. The time taken to reach maximum nitrification (t_max) ranged from 2.4 to 3.0 weeks in all unfumigated soils. Results demonstrated that t_max was greater in all fumigated soils than in untreated soils. Correlation calculations showed that t_max was strongly correlated to soil texture. The correlation analysis results indicated that the recovery rate of nitrification after chloropicrin fumigation is much faster in sandy loam soil than silty loam soil.

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.