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

The effect of natural products used as pesticides on the soil microbiota: OECD 216 nitrogen transformation test fails to identify effects that were detected via q-PCR microbial abundance measurement

BACKGROUND

Natural products present an environmentally attractive alternative to synthetic pesticides which have been implicated in the off-target effect. Currently, the assessment of pesticide toxicity on soil microorganisms relies on the OECD 216 N transformation assay (OECD stands for the Organisation Economic Co-operation and Development, which is a key international standard-setting organisation). We tested the hypotheses that (i) the OECD 216 assay fails to identify unacceptable effects of pesticides on soil microbiota compared to more advanced molecular and standardized tests, and (ii) the natural products tested (dihydrochalcone, isoflavone, aliphatic phenol, and spinosad) are less toxic to soil microbiota compared to a synthetic pesticide compound (3,5-dichloraniline). We determined the following in three different soils: (i) ammonium (NH4 +) and nitrate (NO3 -) soil concentrations, as dictated by the OECD 216 test, and (ii) the abundance of phylogenetically (bacteria and fungi) and functionally distinct microbial groups [ammonia-oxidizing archaea (AOA) and bacteria (AOB)] using quantitative polymerase chain reaction (q-PCR).

RESULTS

All pesticides tested exhibited limited persistence, with spinosad demonstrating the highest persistence. None of the pesticides tested showed clear dose-dependent effects on NH4 + and NO3 - levels and the observed effects were <25% of the control, suggesting no unacceptable impacts on soil microorganisms. In contrast, q-PCR measurements revealed (i) distinct negative effects on the abundance of total bacteria and fungi, which were though limited to one of the studied soils, and (ii) a significant reduction in the abundance of both AOA and AOB across soils. This reduction was attributed to both natural products and 3,5-dichloraniline.

CONCLUSION

Our findings strongly advocate for a revision of the current regulatory framework regarding the toxicity of pesticides to soil microbiota, which should integrate advanced and well-standardized tools. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Soil microeukaryotic communities and phosphorus-cycling microorganisms respond to chloropicrin fumigation and azoxystrobin application

Fumigants and fungicides are effective at controlling soil-borne pathogens but might also adversely affect soil beneficial microbes, such as soil phosphorus (P) solubilizing microbes, further altering nutrient cycling processes. Therefore, this study investigated the effects of the fumigant chloropicrin (CP) and the fungicide azoxystrobin (AZO) on soil microeukaryotes and P-cycling related soil bacteria through a greenhouse experiment. Soil microeukaryotic communities and bacterial communities containing two phosphomonoesterase encoding genes (phoC and phoD) were analysed using high-throughput sequencing methods. Results showed that, when applied at the field recommended application dosage, the fungicide AZO had no significant influence on the community structure of soil microeukaryotes and phoD-containing bacteria. However, in CP-fumigated soils, the soil microeukaryotic community composition changed from fungi-dominated to protist-dominated. CP fumigation significantly decreased the total phoC/phoD gene copy number but increased the relative abundance of some phoC/phoD-containing bacteria (such as Sinorhizobium and Streptomyces), which are significantly positively correlated to available P compositions in soil. The structural equation model (SEM) confirmed that CP fumigation could affect soil available P content directly by altering phoC-/phoD-containing bacteria, or indirectly by affecting phoC/phoD gene abundance and acid/alkaline phosphatases activity in soil. The inconsistent changes in phoC/phoD-containing bacteria, phoC/phoD gene number, and the phosphomonoesterase activities indicated that enzyme secretion may not be the only way for P solubilizing soil microorganisms to regulate P availability after soil fumigation. The outcome of this study can provide theoretical support for the design of soil beneficial microorganism recovery strategies and the regulation of phosphate fertilizer after soil fumigation.

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.

Improvement in the quality and productivity of Codonopsis pilosula seedlings by dazomet soil fumigation

Dazomet is a dry powder formulation that releases toxic gas containing methyl isothiocyanate, which controls soil-borne pests and weeds, improving crop yields when applied to moist soils. To explore the efficacy of dazomet fumigation in the cultivation of the perennial herb Codonopsis pilosula, four typical cultivars (G1, G2, W1 and TCK) in Gansu Province were selected for seedling cultivation after soil fumigation (F) by dazomet, and non-fumigated soil was used as a control (CK). The experiments took 2 years to complete. The functional diversity of the soil enzymes and microorganisms, seedling emergence and physiological characteristics, and the quality and yield of Codonopsis seedlings and Radix were assessed. The results showed that the seed emergence rate, seedling re-green rate and several antioxidant enzymatic activities improved in the treatments involving soil fumigation with dazomet, and membrane lipid peroxidation in the seedlings decreased. On average, compared with those of the respective controls, the root viability and yield of the seedlings of the tested cultivars also increased by 34.87% and 42.4%, respectively, and the incidence of root rot in the seedlings was reduced by 83.9%, compared with their respective controls. After harvest, the yield increased by 23.9%, the incidence of root rot decreased by 61.3%, increase in yield and a 61.3% reduction in incidence, and the medicinal materials were determined to be safe and residue-free. The effects of fumigation were cultivar-specific and were especially prominent in G2. Therefore, soil fumigation with dazomet could improve the quality and productivity of Codonopsis pilosula seedlings. Taken together, these findings suggest that when herbs are bred by seedling transplantation, especially cultivars of good quality but poor resistance or species with rare germplasm resources, soil fumigation provides a way to improve cultivation effectiveness and, more importantly, ensures the probability of successfully breeding the species.

Long-term effects of chloropicrin fumigation on soil microbe recovery and growth promotion of Panax notoginseng

Introduction

Panax notoginseng is a precious Chinese medicinal material. Soil fumigation can control soil-borne disease and overcome the continuous cropping obstacles of P. notoginseng. However, chloropicrin (CP) fumigation can kill non-target soil microorganisms and reduce microbial diversity, but the long-time impacts of CP fumigation on soil microbial are less reported.

Methods

We studied the long-term effects of CP fumigation on soil microbes with high-throughput gene sequencing, and correlated the changes in the composition of microbial communities with environmental factors like soil physicochemical properties and soil enzyme activities. This study mainly focuses on the recovery characteristics of soil microbe after soil fumigation by evaluating the ecological restoration of P. notoginseng soil, its sustained control effect on plant diseases, and its promotion effect on crop growth by focusing on the CP fumigation treatment.

Results

The results showed that CP fumigation significantly increased soil available phosphorus (P) to 34.6 ~ 101.6 mg/kg and electrical conductivity (EC) by 18.7% ~ 34.1%, respectively. High-throughput gene sequencing showed that soil fumigation with CP altered the relative abundance of Trichoderma, Chaetomium, Proteobacteria, and Chloroflexi in the soil while inhibiting a lot of Fusarium and Phytophthora. The inhibition rate of Phytophthora spp. was still 75.0% in the third year after fumigation. Fumigation with CP enhanced P. notoginseng's survival rate and stimulated plant growth, ensuring P. notoginseng's healthy in the growth period. The impact of fumigation on microbial community assembly and changes in microbial ecological niches were characterized using normalized stochasticity ratio (NST) and Levins' niche breadth index. Stochasticity dominated bacterial community assembly, while the fungal community was initially dominated by stochasticity and later by determinism. Fumigation with CP reduced the ecological niches of both fungi and bacteria.

Conclusion

In summary, the decrease in microbial diversity and niche caused by CP fumigation could be recovered over time, and the control of soil pathogens by CP fumigation remained sustainable. Moreover, CP fumigation could overcome continuous cropping obstacles of P. notoginseng and promote the healthy growth of P. notoginseng.

Mechanisms by which chloropicrin fumigation promotes soil potassium conversion and absorption

Fumigation of soil using chloropicrin has been proven to significantly affect soil nutrient cycling, but the mechanism by which soil potassium conversion and plant uptake is promoted remains unclear. In this study, we conducted a fumigation experiment to investigate the effects of chloropicrin soil fumigation on the conversion of soil potassium post-fumigation (days 7-70), and its mechanisms, tomatos were planted in fumigated and non-fumigated soils to enable further comparisons. Results showed that the content of rapidly available potassium and available potassium decreased by 16-24% and 17-23% at day 28 respectively, when tomato was planted in chloropicrin-fumigated soils compared to the non-fumigated soils. The potassium content of tomato planted in fumigated soil was significantly higher than that planted in non-fumigated soil (30.3 vs. 21.9 mg g^-1 dry weight). Chloropicrin fumigation resulted in a significant change in the soil bacterial and fungal community structures, and trigged a long-term (at least 70-day) decrease in microbial diversity. Network analysis showed that chloropicrin soil fumigation changed microbial co-occurrence patterns by decreasing bacterial total links, nodes, and average degree, and increasing fungal total links, nodes, and average degree. Chloropicrin fumigation caused significant changes in the relative abundance of Bacillus species, which are involved in potassium dissolution. Structural equation model (SEM) suggested that fumigation with chloropicrin enhanced the contribution of soil potassium to tomato growth and reduced the contribution of bacterial communities. Together, the results of our study help in understanding the crop yield enhancement mechanism of soil fumigation.

Silica modified copper-based alginate/chitosan hybrid hydrogel to control soil fumigant release, reduce emission and enhance bioactivity

Soil fumigant has been extensively used for excellent efficacy on soil-borne diseases. However, rapid emission and insufficient effective duration typically limit its application. In this study, hybrid silica/polysaccharide hydrogel was proposed (SIL/Cu/DMDS) by emulsion-gelation method to encapsulate dimethyl disulfide (DMDS). The orthogonal study was used to optimize the preparation parameters for LC and EE of SIL/Cu/DMDS, which was 10.39 % and 71.05 %, respectively. Compared with silica, the time for 90 % of the total emissions was extended by 4.36 times. The hydrogel possessed a longer persistent duration and the degradation half-life of DMDS was 3.47 times greater than that of silica alone. Moreover, the electrostatic interaction between abundant groups of polysaccharide hydrogel bestowed DMDS with pH-triggered release behavior. Additionally, SIL/Cu/DMDS had excellent water holding and water retention capacity. The bioactivity of the hydrogel was 58.1 % higher than that of DMDS TC due to the strong synergistic effect between DMDS and the carriers (chitosan and Cu²⁺), and showed obvious biosafety to cucumber seeds. This study seeks to provide a potential approach to develop hybrid polysaccharide hydrogel to control soil fumigants release, reduce emission and enhance bioactivity in plant protection.

Biopesticides as a promising alternative to synthetic pesticides: A case for microbial pesticides, phytopesticides, and nanobiopesticides

Over the years, synthetic pesticides like herbicides, algicides, miticides, bactericides, fumigants, termiticides, repellents, insecticides, molluscicides, nematicides, and pheromones have been used to improve crop yield. When pesticides are used, the over-application and excess discharge into water bodies during rainfall often lead to death of fish and other aquatic life. Even when the fishes still live, their consumption by humans may lead to the biomagnification of chemicals in the body system and can cause deadly diseases, such as cancer, kidney diseases, diabetes, liver dysfunction, eczema, neurological destruction, cardiovascular diseases, and so on. Equally, synthetic pesticides harm the soil texture, soil microbes, animals, and plants. The dangers associated with the use of synthetic pesticides have necessitated the need for alternative use of organic pesticides (biopesticides), which are cheaper, environment friendly, and sustainable. Biopesticides can be sourced from microbes (e.g., metabolites), plants (e.g., from their exudates, essential oil, and extracts from bark, root, and leaves), and nanoparticles of biological origin (e.g., silver and gold nanoparticles). Unlike synthetic pesticides, microbial pesticides are specific in action, can be easily sourced without the need for expensive chemicals, and are environmentally sustainable without residual effects. Phytopesticides have myriad of phytochemical compounds that make them exhibit various mechanisms of action, likewise, they are not associated with the release of greenhouse gases and are of lesser risks to human health compared to the available synthetic pesticides. Nanobiopesticides have higher pesticidal activity, targeted or controlled release with top-notch biocompatibility and biodegradability. In this review, we examined the different types of pesticides, the merits, and demerits of synthetic pesticides and biopesticides, but more importantly, we x-rayed appropriate and sustainable approaches to improve the acceptability and commercial usage of microbial pesticides, phytopesticides, and nanobiopesticides for plant nutrition, crop protection/yield, animal/human health promotion, and their possible incorporation into the integrated pest management system.

Soil bacterial communities are influenced by soil chemical characteristics and dispersal limitation in commercial strawberry production systems

Bacterial communities play multiple functional roles in soil that have positive and negative feedbacks on plant health. However, relatively few studies have focused on the ecology of soil bacterial communities in commercial strawberry production systems. The objective of this study was to determine if ecological processes influencing soil bacterial communities are consistent among commercial strawberry production locations and plots within the same geographic region. Soil samples were collected using a spatially explicit design from three plots in two commercial strawberry production locations in the Salinas Valley region of California. Soil carbon, nitrogen, and pH were measured for each of the 72 soil samples and bacterial communities were characterized using 16 S rRNA sequencing. Multivariate analyses showed bacterial community composition was differentiated between the two strawberry production locations. Analyses of communities within plots demonstrated soil pH and nitrogen were significant predictors of bacterial community composition in one of the three sampled plots. Bacterial communities displayed spatial structure in two plots at one location based on a significant increase in community dissimilarity with increasing spatial distance. Null model analyses identified a lack of phylogenetic turnover among bacterial communities in all plots, but a greater frequency of dispersal limitation in the two plots where spatial structure was also observed. Overall, this work suggests that ecological factors influencing soil bacterial communities are not consistent among different strawberry production locations or plots which may impact the ability to predict or manage the effect of soil microbiomes on strawberry health.

Application of microbial organic fertilizers promotes the utilization of nutrients and restoration of microbial community structure and function in rhizosphere soils after dazomet fumigation

Introduction

Soil fumigant dazomet is a broad-spectrum nematicide and fungicide that can kill non-target microbes. Fungicides or organic fertilizers are often added after fumigation to improve the recovery of soil microbes. However, the effect of adding microbial organic fertilizers (MOF) after fumigation on the structure and function of rhizosphere soil microbial communities of crops is unclear.

Methods

Therefore, we investigated the effects of adding Junweinong and Junlisu MOFs after dazomet fumigation on the structure and function of rhizosphere microbial communities and its relationship with soil properties and enzyme activities.

Results and discussion

The results showed that the addition of these two MOFs after dazomet fumigation significantly reduced the rhizosphere soil available phosphorus, available potassium, organic matter content, and urease, alkaline phosphatase, and catalase activities, but increased the soil pH compared with the fumigation treatment. The application of MOFs after fumigation resulted in significant enrichment of bacteria such as Gaiella, norank_f_Vicinamibacteraceae, and Flavisolibacter and fungi such as Peroneutypa, Olpidium, and Microascus in the rhizosphere soil of the crop and increased the relative abundance of functional genes of 13 kinds of amino acids metabolism, pyruvate metabolism, TCA cycle, and pentose phosphate pathway as well as endophytic and epiphytic functional groups in the rhizosphere soil. In particular, NH₄ ⁺-N, pH, and AK had the greatest effect on rhizosphere microorganisms. Overall, the addition of MOFs after fumigation promoted crop root nutrient uptake, enhanced rhizosphere soil microbial metabolism, allowed more beneficial communities to colonize the roots, and promoted soil microbiological health.

Pesticide soil microbial toxicity: setting the scene for a new pesticide risk assessment for soil microorganisms (IUPAC Technical Report)

Pesticides constitute an integral part of modern agriculture. However, there are still concerns about their effects on non-target organisms. To address this the European Commission has imposed a stringent regulatory scheme for new pesticide compounds. Assessment of the aquatic toxicity of pesticides is based on a range of advanced tests. This does not apply to terrestrial ecosystems, where the toxicity of pesticides on soil microorganisms, is based on an outdated and crude test (N mineralization). This regulatory gap is reinforced by the recent methodological and standardization advances in soil microbial ecology. The inclusion of such standardized tools in a revised risk assessment scheme will enable the accurate estimation of the toxicity of pesticides on soil microorganisms and on associated ecosystem services. In this review we (i) summarize recent work in the assessment of the soil microbial toxicity of pesticides and point to ammonia-oxidizing microorganisms (AOM) and arbuscular mycorrhizal fungi (AMF) as most relevant bioindicator groups (ii) identify limitations in the experimental approaches used and propose mitigation solutions, (iii) identify scientific gaps and (iv) propose a new risk assessment procedure to assess the effects of pesticides on soil microorganisms.

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.

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.

Multifaceted synergistic electron transfer mechanism for enhancing denitrification by clay minerals

The performance and mechanism of denitrification enhanced by three clay minerals, montmorillonite (Mmt), illite and kaolinite, were first studied. Batch experiments indicated that clay minerals significantly enhanced denitrification at certain concentrations (0.1-1 g/L). The denitrification rate with 1 g/L Mmt was increased by 5.0-fold. The mechanism of clay minerals promoting denitrification was analyzed from three aspects: electron transfer characteristics, interfacial interaction and metabolism activity. Electrochemical tests showed that the clay minerals promoted electron transfer rate by improving current efficiency and electronic accommodation capacity. The biofilm formation on the clay minerals interface indicated that micro-domain catalytic phases were formed, which was beneficial to improve the nitrate reduction rate. In addition, nicotinamide adenine dinucleotide, nitrate reductase and nitrite reductase activities in Mmt-supplemented system were increased by 283.3%, 128.1% and 126.2%, respectively; and extracellular polymeric substance secretion was enhanced, indicating that the addition of clay minerals promoted microbial metabolic activity. Higher microbial diversity and enrichment of electroactive bacteria were observed in the Mmt-supplemented system. Based on the above exploration, the multifaceted synergistic mechanism was proposed to account for the enhanced denitrification performance on clay minerals. Overall, this study expanded understanding of the roles of clay minerals on denitrification and provided strategies for accelerating the biological transformation process.

Impact of Biochar on Rhizosphere Bacterial Diversity Restoration Following Chloropicrin Fumigation of Planted Soil

Chloropicrin (CP) can effectively combat soil-borne diseases but has significant side effects on nontarget microorganisms. The rhizosphere microflora play a crucial role in promoting plant growth and protecting plants from infection by soil-borne pathogens. We conducted a laboratory pot experiment to evaluate the effect of CP on the rhizosphere soil bacterial flora and the effect of biochar amendments on the reconstruction of microbial communities. Our results show that CP fumigation and biochar additions promoted the growth of cucumber plants in the later stage of the pot experiment. CP significantly inhibited the rhizobacterial diversity and changed the community composition. Biochar amendments after CP fumigation shortened the time for the rhizobacterial diversity to recover to unfumigated levels. Biochar amendments promoted the transplantation of new populations to empty microbiome niches that were caused by CP and, in particular, stimulated many beneficial microorganisms to become the predominant flora. The relative abundances of many functional taxa related to plant-disease suppressiveness and pollutant bioremediation increased, including Pseudomonas, Stenotrophomonas, Bacillus, Massilia, Acinetobacter, Delftia, Micromonospora, Cytophagaceae, and Flavisolibacter. These changes stimulated by biochar amendments would promote multifunctionality in the soil rhizosphere and benefit plant growth and disease resistance.

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.

Fungicides alter the distribution and diversity of bacterial and fungal communities in ginseng fields

The present study was focused on comparison of four typical fungicides in ginseng field to evaluate the impact of the different fungicides on the soil bacterial and fungal communities’ composition and diversity by using high-throughput sequencing. Five treatments were designed comprising carbendazim (D), dimethyl disulfide (E), dazomet (M), calcium cyanamide (S), and control (C). The application of fungicide obviously altered the distribution of dominant fungal and bacterial communities and remarkably decreased the diversity (1099-763 and 6457-2245). The most abundant Proteobacteria obviously degenerate in fungicide-treated soil and minimum in E (0.09%) compared to control (25.72%). The relative abundance of Acidobacteria was reduced from 27.76 (C) to 7.14% after applying fungicide and minimum in E. The phylum Actinobacteria are both decomposers of organic matter and enemies of soil-borne pathogens, elevated from 11.62 to 51.54% and are high in E. The fungi community mainly distributed into Ascomycota that enriched from 66.09 to 88.21% and highin M and E (88.21 and 85.10%), and Basidiomycota reduced from 21.13 to 3.23% and low in M and E (5.27 and 3.23%). Overall, environmentally related fungicides decreased the diversity and altered the composition of bacterial and fungal communities, highest sensitivity present in dimethyl disulfide-treated soil.

Influence of cell lysis by Fenton oxidation on cryptic growth in sequencing batch reactor (SBR): Implication of reducing sludge source discharge

The cell lysis-cryptic growth was implemented by Fenton oxidation in sequencing batch reactor. Optimizing sludge lysis condition could maximize the release of nutrients and sludge disintegration degree. After Fenton oxidation, the extracellular polymeric substance was obviously destroyed with the sludge average particle decreased from 64 μm to 36 μm. After 5% of the settled sludge in sequencing batch reactor (SBR) was oxidized by Fenton and then returned to SBR, the mixed liquor suspended solids (MLSS) decreased by 19.3% at the end of 35 days operation, the average mixed liquor volatile suspended solids/mixed liquor suspended solids (MLVSS/MLSS) was promoted by 13.3% during the entire operation. Returning lysed sludge had no significant influence on the organics and nitrogen removal, but the total phosphorus removal was distinctly enhanced by generating FePO4 precipitate. Additionally, returning lysed sludge suppressed nitrifying bacteria and promoted denitrifying bacteria slightly. Consequently, the cell lysis-cryptic growth for reducing sludge source discharge from wastewater biological treatment could be achieved on the premise of ensuring effluent quality.

Impact of Soil Disinfestation on Fungal and Bacterial Communities in Soil With Cucumber Cultivation

Soil treatment with disinfectants has been used for controlling soilborne phytopathogens. Besides suppressing specific pathogens, how these disinfectants impact soil health, especially soil microbial communities, is yet to be systemically determined. The objectives of this study were to examine the effects of three representative disinfectants, including the dazomet fumigant, fenaminosulf fungicide, and kasugamycin antibiotic on chemical properties, enzymatic activities, and microbial communities in soil for cucumber cultivation. Results showed that 14 days after soil treatment with these chemicals, residual content of dazomet and kasugamycin quickly declined in soil and were undetectable, while fenaminosulf residues were found at 0.48 ± 0.01 mg/kg. Total nitrogen and total carbon increased in soil after dazomet treatment. Urease and sucrase activities were significantly restrained after disinfectant application. The disinfectants did not significantly change the taxon of predominant bacteria and fungi but altered the relative abundance and diversity of soil microbiome, as well as microbial interspecific relationships. Moreover, cucumber cultivation enhanced the overall soil microbial diversity and enzymatic activities, which diminished the difference of soil microbiome among four treatments. The difference in soil microbial diversity among the four treatments became smaller after planting cucumber. Thus, soil microbial communities were affected by soil disinfectants and gradually recovered by cucumber application.

Bio-activation of soil with beneficial microbes after soil fumigation reduces soil-borne pathogens and increases tomato yield

Soil-borne diseases have become increasingly problematic for farmers producing crops intensively under protected agriculture. Although soil fumigants are convenient and effective for minimizing the impact of soil-borne disease, they are most often detrimental to beneficial soil microorganisms. Previous research showed that bio-activation of soil using biological control agents present in biofertilizers or organic fertilizers offered promise as a strategy for controlling soil-borne pathogens when the soil was bio-activated after fumigation. Our research sought to determine how bio-activation can selectively inhibit pathogens while promoting the recovery of beneficial microbes. We monitored changes in the soil's physicochemical properties, its microbial community and reductions in soil-borne pathogens. We found that the population density of Fusarium and Phytophthora were significantly reduced and tomato yield was significantly increased when the soil was bio-activated. Soil pH and soil catalase activity were significantly increased, and the soil's microbial community structure was changed, which may have enhanced the soil's ability to reduce Fusarium and Phytophthora. Our results showed that soil microbial diversity and relative abundance of beneficial microorganisms (such as Sphingomonas, Bacillus, Mortierella and Trichoderma) increased shortly after bio-activation of the soil, and were significantly and positively correlated with pathogen suppression. The reduction in pathogens may have been due to a combination of fumigation-fertilizer that reduced pathogens directly, or the indirect effect of an optimized soil microbiome that improved the soil's non-biological factors (such as soil pH, fertility structure), enhanced the soil's functional properties and increased tomato yield.

Influence of Allyl Isothiocyanate on the Soil Microbial Community Structure and Composition during Pepper Cultivation

Allyl isothiocyanate (AITC), as a fumigant, plays an important role in soil control of nematodes, soilborne pathogens, and weeds, but its effects on soil microorganisms are unclear. In this study, the effects of AITC on microbial diversity and community composition of Capsicum annuum L. soil were investigated through Illumina high-throughput sequencing. The results showed that microbial diversity and community structure were significantly influenced by AITC. AITC reduced the diversity of soil bacteria, stimulated the diversity of the soil fungal community, and significantly changed the structure of fungal community. AITC decreased the relative abundance of dominant bacteria Planctomycetes, Acinetobacter, Pseudodeganella, and RB41, but increased that of Lysobacter, Sphingomonas, Pseudomonas, Luteimonas, Pseudoxanthomonas, and Bacillus at the genera level, while for fungi, Trichoderma, Neurospora, and Lasiodiplodia decreased significantly and Aspergillus, Cladosporium, Fusarium, Penicillium, and Saccharomyces were higher than the control. The correlation analysis suggested cellulase had a significant correlation with fungal operational taxonomic units and there was a significant correlation between cellulase and fungal diversity, while catalase, cellulose, sucrase, and urease were the major contributors in the shift of the community structure. Our results will provide useful information for the use of AITC in the assessment of environmental and ecological security.

2-Hydroxypropyl-β-cyclodextrin encapsulates dimethyl disulfide producing a controlled release formulation

Dimethyl disulfide (DMDS), a soil fumigant, is an effective, broad-spectrum compound that often replaces bromomethane (MB) in the prevention and treatment of soil-borne diseases. However, the disadvantages of DMDS include toxicity, volatility, pungent odor, risk of human exposure, and environmental pollution. Cyclodextrin (CD) has been widely used as a carrier of chemicals in many industries due to its functional advantages and safety. In this study, a DMDS-controlled release formulation was developed by encapsulating DMDS in the cavity of 2-hydroxypropyl-β-cyclodextrin (HP-β-CD). This formulation reduced DMDS usage and production costs. Orthogonal experimental design, Fourier transform infrared (FT-IR), Scanning electron microscopy (SEM), Thermal gravity analysis (TGA) characterization, efficacy comparison, safety, and other aspects of the evaluation showed that under the best preparation conditions, the encapsulation rate was 81.49%. The efficacy of DMDS@HP-β-CD was similar to unformulated DMDS. The efficacy duration of the formulation was about two times longer than DMDS, and it was safer to use. This study reveals a cyclodextrin-DMDS formulation with reduced toxicity, longer duration, environmental safety and sustainability.

Holobiont nitrogen control and its potential for eutrophication resistance in an obligate photosymbiotic jellyfish

BACKGROUND

Marine holobionts depend on microbial members for health and nutrient cycling. This is particularly evident in cnidarian-algae symbioses that facilitate energy and nutrient acquisition. However, this partnership is highly sensitive to environmental change-including eutrophication-that causes dysbiosis and contributes to global coral reef decline. Yet, some holobionts exhibit resistance to dysbiosis in eutrophic environments, including the obligate photosymbiotic scyphomedusa Cassiopea xamachana.

METHODS

Our aim was to assess the mechanisms in C. xamachana that stabilize symbiotic relationships. We combined labelled bicarbonate (13C) and nitrate (15N) with metabarcoding approaches to evaluate nutrient cycling and microbial community composition in symbiotic and aposymbiotic medusae.

RESULTS

C-fixation and cycling by algal Symbiodiniaceae was essential for C. xamachana as even at high heterotrophic feeding rates aposymbiotic medusae continuously lost weight. Heterotrophically acquired C and N were readily shared among host and algae. This was in sharp contrast to nitrate assimilation by Symbiodiniaceae, which appeared to be strongly restricted. Instead, the bacterial microbiome seemed to play a major role in the holobiont's DIN assimilation as uptake rates showed a significant positive relationship with phylogenetic diversity of medusa-associated bacteria. This is corroborated by inferred functional capacity that links the dominant bacterial taxa (~90 %) to nitrogen cycling. Observed bacterial community structure differed between apo- and symbiotic C. xamachana putatively highlighting enrichment of ammonium oxidizers and nitrite reducers and depletion of nitrogen-fixers in symbiotic medusae.

CONCLUSION

Host, algal symbionts, and bacterial associates contribute to regulated nutrient assimilation and cycling in C. xamachana. We found that the bacterial microbiome of symbiotic medusae was seemingly structured to increase DIN removal and enforce algal N-limitation-a mechanism that would help to stabilize the host-algae relationship even under eutrophic conditions. Video abstract.

Effects of sulfoxaflor on greenhouse vegetable soil N2O emissions and its microbial driving mechanism

The wide application of pesticides ensures the safety of food production, but it also has a serious impact on soil ecosystem. Although sulfoxaflor as a pesticide has great potential for application due to its excellent insecticidal activity and low crossresistance, little is known about its soil environmental safety risks. In this study, the effects of sulfoxaflor on N₂O emissions and microorganisms in greenhouse vegetable soils were studied by indoor simulation culture experiments. Dynamic changes of soil main inorganic N and N₂O emission rate were tested, and the abundance and community of total bacteria and microorganisms related to N cycle were analyzed. The results indicated that soil microorganisms rapidly degraded sulfoxaflor, and the N₂O emissions rate and ammonium nitrogen (NH₄⁺-N) content significantly increased, while nitrate nitrogen (NO₃^--N) content was significantly decreased. Sulfoxaflor significantly changed the abundance and community of total bacteria, nitrite reducing and nitrous oxide reducing bacteria, but had no significant effect on ammoxidation microorganisms. The N₂O emission rate was positively correlated with gene abundance of denitrifying microorganisms. Under 65% soil maximum water holding capacity, sulfoxaflor may broke the dynamic balance of N₂O production and consumption in the denitrification process, which caused a significant increase in N₂O emission. Therefore, the application of sulfoxaflor had a certain effect on N cycling and utilization in greenhouse vegetable soil.

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.

Sub-Lethal Effects of Pesticides on the DNA of Soil Organisms as Early Ecotoxicological Biomarkers

This review describes the researches performed in the last years to assess the impact of pesticide sub-lethal doses on soil microorganisms and non-target organisms in agricultural soil ecosystems. The overview was developed through the careful description and a critical analysis of three methodologies based on culture-independent approaches involving DNA extraction and sequencing (denaturing gradient gel electrophoresis, DGGE; next-generation sequencing, NGS) to characterize the microbial population and DNA damage assessment (comet assay) to determine the effect on soil invertebrates. The examination of the related published articles showed a continuous improvement of the possibility to detect the detrimental effect of the pesticides on soil microorganisms and non-target organisms at sub-lethal doses, i.e., doses which have no lethal effect on the organisms. Considering the overall critical discussion on microbial soil monitoring in the function of pesticide treatments, we can confirm the usefulness of PCR-DGGE as a screening technique to assess the genetic diversity of microbial communities. Nowadays, DGGE remains a preliminary technique to highlight rapidly the main differences in microbial community composition, which is able to give further information if coupled with culture-dependent microbiological approaches, while thorough assessments must be gained by high-throughput techniques such as NGS. The comet assay represents an elective technique for assessing genotoxicity in environmental biomonitoring, being mature after decades of implementation and widely used worldwide for its direct, simple, and affordable implementation. Nonetheless, in order to promote the consistency and reliability of results, regulatory bodies should provide guidelines on the optimal use of this tool, strongly indicating the most reliable indicators of DNA damage. This review may help the European Regulation Authority in deriving new ecotoxicological endpoints to be included in the Registration Procedure of new pesticides.