The impacts of cypermethrin pesticide application on the non-target microbial community of the pepper plant phyllosphere

Comparative analysis of grape berry microbiota uncovers sour rot associates from a Maryland vineyard

Grape sour rot (GSR) is a disease complex involving fungi and bacteria that can cause significant yield losses of susceptible varieties. It is widely spread in the eastern U.S. and other grape-growing regions globally. Previous studies suggest that damaged fruit skin and feeding insects like Drosophila spp. are required for the disease to occur. Current control strategies for the management of sour rot are not sustainable, and research on the implications of chemical management of the disease on microbiome diversity is scarce. Our aim was to: i) investigate the effect of insecticide application and netting treatment on the microbiota of GSR-susceptible and tolerant grape varieties; and ii) identify the core microbial assemblages potentially associated with grape sour rot development in Maryland. Using a combined analysis of culture-dependent and independent data, we found that microbiota diversity of healthy grape berries did not change with netting, insecticide application, and between varieties. There was a significant difference in bacterial diversity between healthy and sour rot-affected berries. Komagataeibacter was consistently associated with infected berries followed by Acetobacter and Gluconobacter. This is the first study to report the association of Komagataeibacter with GSR-infected berries. It is thus imperative to investigate its role alongside that of other identified core microbiomes in sour rot development. Candida and Pichia were also consistent genera in infected berries. Several unidentified Candida, Pichia, and other fungal species from infected berries formed the core mycobiomes and it would be worth investigating their involvement in GSR development in Mid-Atlantic vineyards.

Beta-cypermethrin-induced stress response and ABC transporter-mediated detoxification in Tetrahymena thermophila

β-Cypermethrin (β-CYP), a synthetic pyrethroid pesticide, is widely used for insect management. However, it also affects non-target organisms and pollutes aquatic ecosystems. Tetrahymena thermophila, a unicellular ciliated protist found in fresh water, is in direct contact with aquatic environments and sensitive to environmental changes. The proliferation of T. thermophila was inhibited and the cellular morphology changed under β-CYP stress. The intracellular ROS level significantly increased, and SOD activity gradually rose with increasing β-CYP concentrations. Under 25 mg/L β-CYP stress, 687 genes were up-regulated, primarily enriched in the organic cyclic compound binding and heterocyclic compound binding pathways. These include 8 ATP-binding cassette transporters (ABC) family genes, 2 cytochrome P450 monooxygenase genes, and 2 glutathione peroxidase related genes. Among of them, ABCG14 knockdown affected cellular proliferation under β-CYP stress. In contrast, overexpression of ABCG14 enhanced cellular tolerance to β-CYP. The results demonstrated that Tetrahymena tolerates high β-CYP concentration stress through various detoxification mechanisms, with ABCG14 playing a crucial role in detoxification of β-CYP.

Agricultural practices and pollinators modulate the anthosphere microbiome

The flower microbiome is pivotal in plant health, influencing reproductive success, fruit quality, and pathogen vulnerability. However, the impact of intensified agricultural practices on these microbial communities remains to be understood. This study examines how specific agricultural practices influence the bacterial composition of the strawberry anthosphere, focusing on cultivation intensification. Intensified systems were defined by practices such as indoor glasshouse substrate-based cultivation, increased use of plant protection products, larger cultivation areas, and reliance on managed pollinators. Using citizen science and V4 16S rRNA gene sequencing, we found that flowers in these more intensively managed systems had lower bacterial diversity, more variable microbiomes, and loss of core taxa such as Sphingomonas and Pseudomonas. To determine if pollinators could help mitigate these effects, we conducted exclusion experiments. In a tunnel system, we observed that foraging pollinators facilitated the dispersal of specific bacteria, such as Staphylococcus and Pseudomonas, and increased flower bacterial richness. However, in an open field, foraging pollinators had no significant impact. Our findings highlight the significant impact of cultivation intensification on the anthosphere microbiome and suggest that pollinators may play a role in restoring microbiome diversity. This research fills a critical gap in understanding how agricultural practices shape plant microbiomes and underscores the potential for microbe-based strategies to improve plant health in intensively managed systems.

Characterization of Boxwood Shoot Bacterial Communities and Potential Impact from Fungicide Treatments

Phyllosphere bacterial communities play important roles in plant fitness and growth. The objective of this study was to characterize the epiphytic and endophytic bacterial communities of boxwood shoots and determine how they may respond to commonly used fungicides. In early summer and early fall, shoot samples were collected immediately before and 1, 7, and 14 days after three fungicides containing chlorothalonil and/or propiconazole were applied to the canopy. Total genomic DNA from shoot surface washings and surface-sterilized shoot tissues was used as the template for 16S rRNA metabarcoding, and the amplicons were sequenced on a Nanopore MinION sequencer to characterize the epiphytic and endophytic communities. The bacterial communities were phylogenetically more diverse on the boxwood shoot surface than in the internal tissue, although the two communities shared 12.7% of the total 1,649 identified genera. The most abundant epiphytes were Methylobacterium and Pantoea, while Stenotrophomonas and Brevundimonas were the dominant endophytes. Fungicide treatments had strong impacts on epiphytic bacterial community structure and composition. Analysis of compositions of microbiomes with bias correction (ANCOM-BC) and analysis of variance (ANOVA)-like differential expression (ALDEx2) together identified 312 and 1,362 epiphytes changed in abundance due to fungicide treatments in early summer and early fall, respectively, and over 50% of these epiphytes were negatively impacted by fungicide. The two chlorothalonil-based contact fungicides demonstrated more marked effects than the propiconazole-based systemic fungicide. These results are foundational for exploring and utilizing the full potential of the microbiome and fungicide applications and developing a systems approach to boxwood health and production. IMPORTANCE Agrochemicals are important tools for safeguarding plants from invasive pathogens, insects, mites, and weeds. How they may affect the plant microbiome, a critical component of crop health and production, was poorly understood. Here, we used boxwood, an iconic low-maintenance landscape plant, to characterize shoot epiphytic and endophytic bacterial communities and their responses to contact and systemic fungicides. This study expanded our understanding of the above-ground microbiome in ornamental plants and is foundational for utilizing the full benefits of the microbiome in concert with different fungicide chemistries to improve boxwood health. This study also sets an example for a more thorough evaluation of these and other agrochemicals for their effects on boxwood microbiomes during production and offers an expanded systems approach that could be used with other crops for enhanced integrated pest management.

The Impact of Permethrin and Cypermethrin on Plants, Soil Enzyme Activity, and Microbial Communities

Pyrethroids are insecticides most commonly used for insect control to boost agricultural production. The aim of the present research was to determine the effect of permethrin and cypermethrin on cultured and non-cultivated bacteria and fungi and on the activity of soil enzymes, as well as to determine the usefulness of Zea mays in mitigating the adverse effects of the tested pyrethroids on the soil microbiome. The analyses were carried out in the samples of both soil not sown with any plant and soil sown with Zea mays. Permethrin and cypermethrin were found to stimulate the multiplication of cultured organotrophic bacteria (on average by 38.3%) and actinomycetes (on average by 80.2%), and to inhibit fungi growth (on average by 31.7%) and the enzymatic activity of the soil, reducing the soil biochemical fertility index (BA) by 27.7%. They also modified the number of operational taxonomic units (OTUs) of the Actinobacteria and Proteobacteria phyla and the Ascomycota and Basidiomycota phyla. The pressure of permethrin and cypermethrin was tolerated well by the bacteria Sphingomonas (clone 3214512, 1052559, 237613, 1048605) and Bacillus (clone New.ReferenceOTU111, 593219, 578257), and by the fungi Penicillium (SH1533734.08FU, SH1692798.08FU) and Trichocladium (SH1615601.08FU). Both insecticides disturbed the growth and yielding of Zea mays, as a result of which its yield and leaf greenness index decreased. The cultivation of Zea mays had a positive effect on both soil enzymes and soil microorganisms and mitigated the anomalies caused by the tested insecticides in the microbiome and activity of soil enzymes. Permethrin decreased the yield of its aerial parts by 37.9% and its roots by 33.9%, whereas respective decreases caused by cypermethrin reached 16.8% and 4.3%.

Ecotoxicological implications of residual pesticides to beneficial soil bacteria: A review

Optimization of crop production in recent times has become essential to fulfil food demands of constantly increasing human populations worldwide. To address this formidable challenge, application of agro-chemicals including synthetic pesticides in intensive farm practices has increased alarmingly. The excessive and indiscriminate application of pesticides to foster food production however, leads to its exorbitant deposition in soils. After accumulation in soils beyond threshold limits, pesticides harmfully affect the abundance, diversity and composition and functions of rhizosphere microbiome. Also, the cost of pesticides and emergence of resistance among insect-pests against pesticides are other reasons that require attention. Due to this, loss in soil nutrient pool cause a substantive reduction in agricultural production which warrant the search for newer environmentally friendly technology for sustainable crop production. Rhizosphere microbes, in this context, play vital roles in detoxifying the polluted environment making soil amenable for cultivation through detoxification of pollutants, rhizoremediation, bioremediation, pesticide degradation, and stress alleviation, leading to yield optimization. The response of soil microorganisms to range of chemical pesticides is variable ranging from unfavourable to the death of beneficial microbes. At cellular and biochemical levels, pesticides destruct the morphology, ultrastructure, viability/cellular permeability, and many biochemical reactions including protein profiles of soil bacteria. Several classes of pesticides also disturb the molecular interaction between crops and their symbionts impeding the overall useful biological processes. The harmful impact of pesticides on soil microbes, however, is poorly researched. In this review, the recent findings related with potential effects of synthetic pesticides on a range of soil microbiota is highlighted. Emphasis is given to find and suggest strategies to minimize the chemical pesticides usage in the real field conditions to preserve the viability of soil beneficial bacteria and soil quality for safe and sustainable crop production even in pesticide contaminated soils.

Impact of twenty pesticides on soil carbon microbial functions and community composition

Pesticides are known to affect non-targeted soil microorganisms. Still, studies comparing the effect of multiple pesticides on a wide range of microbial endpoints associated with carbon cycling are scarce. Here, we employed fluorescence enzymatic assay and real-time PCR to evaluate the effect of 20 commercial pesticides, applied at their recommended dose and five times their recommended dose, on soil carbon cycling related enzymatic activities (α-1,4-glucosidase, β-1,4-glucosidase, β-d-cellobiohydrolase and β-xylosidase), and on the absolute abundance of functional genes (cbhl and chiA), in three different South Australian agricultural soils. The effects on cellulolytic and chitinolytic microorganisms, and the total microbial community composition were determined using shotgun metagenomic sequencing in selected pesticide-treated and untreated samples. The application of insecticides significantly increased the cbhl and chiA genes absolute abundance in the acidic soil. At the community level, insecticide fipronil had the greatest stimulating effect on cellulolytic and chitinolytic microorganisms, followed by fungicide metalaxyl-M and insecticide imidacloprid. A shift towards a fungal dominated microbial community was observed in metalaxyl-M treated soil. Overall, our results suggest that the application of pesticides might affect the soil carbon cycle and may disrupt the formation of soil organic matter and structure stabilisation.

Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review

Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.

Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review

Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.

Endophytic colonization of entomopathogenic fungi increases plant disease resistance by changing the endophytic bacterial community

Various mechanisms are involved in plant disease resistance mediated by entomopathogenic fungi; however, the role of plant endophytic microbes in disease resistance is unknown. In the present study, we showed that the disease incidence of northern corn leaf blight caused by Exserohilum turcicum (Et) on maize was reduced significantly by soil inoculation with Beauveria bassiana (Bb). Meanwhile, B. bassiana colonization and E. turcicum infection increased the diversity and abundance and diversity of endophytic bacteria and fungi, respectively, while the abundance of endophytic bacterial of the Bb + Et treatment decreased significantly compared with that of Et treatment alone. However, Bb + Et treatment increased the relative abundance of plant beneficial bacteria significantly, for example, Burkholderia and Pseudomonas. Network analyses showed that the microbiome complexity increased after soil inoculation with B. bassiana. Taken together, these results revealed the potential mechanism by which entomopathogenic fungi exert biological control of maize leaf spot disease.

Transcriptome analysis of Plantago major as a phytoremediator to identify some genes related to cypermethrin detoxification

Cypermethrin (CYP) is a toxic manmade chemical compound belonging to pyrethroid insecticides contaminating the environment. Plantago major (PM) has numerous excellent advantages like high biomass yield and great stress tolerance, which make it able to increase the efficacy of phytoremediation. So far, no study has directly or indirectly made a transcriptome analysis (RNA-seq) of PM under CYP stress. The aim of this study is to identify the genes in PM related to CYP detoxification (10 μg mL^-1) and compared with control. In this study, BGISEQ-500 high-throughput sequencing technology independently developed by BGI was used to sequence the transcriptome of P. major. Six libraries were constructed including (CK_1, CK_2, and CK_3) and (CYP_1, CYP_2, and CYP_3) were sequenced for transcripts involved in CYP detoxification. Our data showed that de novo assembly generated 138,806 unigenes with an average length of 1129 bp. Analyzing the annotation results of the KEGG database between the samples revealed 37,177 differentially expressed genes (DEGs), 18,062 down- and 19,115 upregulated under CYP treatment compared with control. A set of 107 genes of cytochrome P450 (Cyt P450), 43 genes of glutathione S-transferases (GST), 25 genes of glycosyltransferases (GTs), 113 genes from ABC transporters, 21 genes from multidrug and toxin efflux (MATE), 11 genes from oligopeptide transporter (OPT), and 3 genes of metallothioneins (MT) were upregulated notably. By using quantitative real-time PCR (qRT-PCR), the results of gene expression for 12 randomly selected DEGs were confirmed, showing the different patterns of response to CYP in PM tissues. Furthermore, the enzyme activity of Cyt P450 and GST in PM under CYP stress was significantly increased in roots and leaves than in control. This study introduces a clue to understand the metabolic pathways of plants used in phytoremediation by identifying the highly expressed genes related to phytoremediation which would be utilized to enhance pesticide detoxification and reduce pollution problem.

Neonicotinoid Seed Treatments Have Significant Non-target Effects on Phyllosphere and Soil Bacterial Communities

The phyllosphere and soil are dynamic habitats for microbial communities. Non-pathogenic microbiota, including leaf and soil beneficial bacteria, plays a crucial role in plant growth and health, as well as in soil fertility and organic matter production. In sustainable agriculture, it is important to understand the composition of these bacterial communities, their changes in response to disturbances, and their resilience to agricultural practices. Widespread pesticide application may have had non-target impacts on these beneficial microorganisms. Neonicotinoids are a family of systemic insecticides being vastly used to control soil and foliar pests in recent decades. A few studies have demonstrated the long-term and non-target effects of neonicotinoids on agroecosystem microbiota, but the generality of these findings remains unclear. In this study, we used 16S rRNA gene amplicon sequencing to characterize the effects of neonicotinoid seed treatment on soil and phyllosphere bacterial community diversity, composition and temporal dynamics in a 3-year soybean/corn rotation in Quebec, Canada. We found that habitat, host species and time are stronger drivers of variation in bacterial composition than neonicotinoid application. They, respectively, explained 37.3, 3.2, and 2.9% of the community variation. However, neonicotinoids did have an impact on bacterial community structure, especially on the taxonomic composition of soil communities (2.6%) and over time (2.4%). They also caused a decrease in soil alpha diversity in the middle of the growing season. While the neonicotinoid treatment favored some bacterial genera known as neonicotinoid biodegraders, there was a decline in the relative abundance of some potentially beneficial soil bacteria in response to the pesticide application. Some of these bacteria, such as the plant growth-promoting rhizobacteria and the bacteria involved in the nitrogen cycle, are vital for plant growth and improve soil fertility. Overall, our results indicate that neonicotinoids have non-target effects on phyllosphere and soil bacterial communities in a soybean-corn agroecosystem. Exploring the interactions among bacteria and other organisms, as well as the bacterial functional responses to the pesticide treatment, may enhance our understanding of these non-target effects and help us adapt agricultural practices to control these impacts.

The response of soil and phyllosphere microbial communities to repeated application of the fungicide iprodione: accelerated biodegradation or toxicity?

Pesticides interact with microorganisms in various ways with the outcome being negative or positive for the soil microbiota. Pesticides' effects on soil microorganisms have been studied extensively in soil but not in other pesticides-exposed microbial habitats like the phyllosphere. We tested the hypothesis that soil and phyllosphere support distinct microbial communities, but exhibit a similar response (accelerated biodegradation or toxicity) to repeated exposure to the fungicide iprodione. Pepper plants received four repeated foliage or soil applications of iprodione, which accelerated its degradation in soil (DT50_1st = 1.23 and DT50_4th = 0.48 days) and on plant leaves (DT50_1st > 365 and DT50_4th = 5.95 days). The composition of the epiphytic and soil bacterial and fungal communities, determined by amplicon sequencing, was significantly altered by iprodione. The archaeal epiphytic and soil communities responded differently; the former showed no response to iprodione. Three iprodione-degrading Paenarthrobacter strains were isolated from soil and phyllosphere. They hydrolyzed iprodione to 3,5-dichloraniline via the formation of 3,5-dichlorophenyl-carboxiamide and 3,5-dichlorophenylurea-acetate, a pathway shared by other soil-derived arthrobacters implying a phylogenetic specialization in iprodione biotransformation. Our results suggest that iprodione-repeated application could affect soil and epiphytic microbial communities with implications for the homeostasis of the plant-soil system and agricultural production.

Suppression of Rice Planthopper Populations by the Entomopathogenic Fungus Metarhizium anisopliae without Affecting the Rice Microbiota

Entomopathogenic fungi can regulate insect populations and function as crucial biological control agents against insect pests, but their impacts on nontarget microorganisms are poorly understood. In this study, we investigated the potential of the fungal strain Metarhizium anisopliae CQMa421 to control rice planthoppers under field conditions and its effects on rice microbiota. This fungus suppressed rice planthoppers during this period, and its control efficiency was more than 60% 7 days after application and did not significantly differ from that of the chemical treatment except in 2019. Both treatments showed a smaller population of rice planthoppers than the controls. After application, M. anisopliae was maintained on rice plants for approximately 14 days, showing a decreasing trend over time. Furthermore, the results showed that the bacterial and fungal richness (operational taxonomic units) and diversity (Shannon index) did not significantly differ between the fungal treatment and the controls after application. The major bacterial taxa of Proteobacteria (including Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria), Actinobacteria, Bacteroidetes, and Cyanobacteria accounted for more than 80% of the bacterial community after fungal application, and the major fungal taxa Ascomycota (including Eurotiomycetes, Dothideomycetes, and Sordariomycetes) and Basidiomycota (including Ustilaginomycetes) represented more than 90% of the fungal community. However, the microbial communities of the rice phyllosphere did not significantly change after entomopathogenic-agent application, indicating that the indigenous microbial communities may adapt to fungal insecticide application. Taken together, the results suggest that this fungal agent has good potential for rice planthopper control with no substantial effects on rice microbial communities.IMPORTANCE Entomopathogenic fungi may be used as crucial biocontrol agents for the control of insect pests, but few effective fungal strains have been reported for the control of the rice planthopper, a major pest of rice. More importantly, the impacts of fungal insecticide application on nontarget microorganisms have not been well evaluated, especially under field conditions. Therefore, in this study, we investigated the effects of the fungal strain M. anisopliae CQMa421 on rice planthopper populations from 2017 to 2019 and evaluated its potential impacts on the microbiota of rice plants after application. The results suggested that this fungal agent has good potential for use in the control of rice planthoppers with no significant effects on rice microbial communities, representing an alternative strategy for the control of rice pests.

It takes three to tango: the importance of microbes, host plant, and soil management to elucidate manipulation strategies for the plant microbiome

The world’s population is expected to grow to almost 10 billion by 2050, placing unprecedented demands on agriculture and natural resources. The risk in food security is also aggravated by climate change and land degradation, which compromise agricultural productivity. In recent years, our understanding of the role of microbial communities on ecosystem functioning, including plant-associated microbes, has advanced considerably. Yet, translating this knowledge into practical agricultural technologies is challenged by the intrinsic complexity of agroecosystems. Here, we review current strategies for plant microbiome manipulation, classifying them into three main pillars: (i) introducing and engineering microbiomes, (ii) breeding and engineering the host plant, and (iii) selecting agricultural practices that enhance resident soil and plant-associated microbial communities. In each of these areas, we analyze current trends in research, as well as research priorities and future perspectives.

Variety features differentiate microbiota in the grape leaves

The dependence of plant health and crop quality on the epiphytic microbial community has been extensively addressed, but little is known about plant-associated microbial communities under natural conditions. In this study, the bacterial and fungal communities on grape leaves were analyzed by 16S rRNA gene and internal transcribed spacer high-throughput sequencing, respectively. The results showed differences in the composition of the microbial communities on leaf samples of nine wine grape varieties. The most abundant bacterial genus was Pseudomonas, and the top three varieties with Pseudomonas were Zinfandel (22.6%), Syrah (21.6%), and Merlot (13.5%). The most abundant fungal genus was Alternaria, and the cultivar with the lowest abundance of Alternaria was Zinfandel (33.6%), indicating that these communities had different habitat preferences. The linear discriminant analysis effect size of all species showed that the bacteria Enterococcus, Massilia, and Kocuria were significantly enriched on the leaves of Merlot, Syrah, Cabernet Sauvignon, respectively; Pseudomonadales and Pantoea on Zinfandel; and Bacillus, Turicibacter, and Romboutsia on Pinot Noir. Similarly, the fungi Cladosporium, Phoma, and Sporormiella were significantly enriched on Zinfandel, Lon, and Gem, respectively. Both Bray-Curtis and unweighted UniFrac revealed that bacteria and fungi have a significant impact (P < 0.01), and the results further proved that variety is the most important factor affecting the microbial community. The findings indicate that some beneficial or harmful microorganisms existing on the wine grape leaves might affect the health of the grape plants and the wine-making process.

Pesticide application inhibit the microbial carbonic anhydrase-mediated carbon sequestration in a soil microcosm

Heterotrophic system for carbon sequestration is gaining importance in the recent decades. Carbonic anhydrase (CA) is a major enzyme involved in carbon sequestration and biomineralization process. In this paper, we evaluate the effect of pesticide on CA activity using inhibitory assay. 2,4-D, being one of the most extensively used pesticide, being deleterious to soil health, its usage should be minimized to regain the soil health. Maximum inhibitory constant (K_i) was observed for 5% 2,4-D (49.53 mM) followed by 5% glyphosate (43.92 mM). The maximum Km increase with increase in pesticide concentration by 3.05-fold was in case of glyphosate which was higher than that of 2,4-D (2.08-fold) and dichlorvos (2.38-fold). Moreover, we evaluated the carbon sequestration using CA enzyme in the soil microcosm. In the present study, we identified the negative impact of 2,4-D on carbonic anhydrase produced by Bacillus halodurans PO15. The inhibition was a mixed type and had significantly lowered the carbon reduction to about 2.38 ± 0.17% in a soil microcosm study. Based on the molecular docking, the inhibition was contributed due to weak H-bonding interaction with amino acid residues (Gly65, Gly95, Val147, Ser150 and Gly65, Ser146, and Ser150).

Tolerance of dark septate endophytic fungi (DSE) to agrochemicals in vitro

Dark septate endophytes (DSE) are a heterogeneous group of fungi, mostly belonging to the Phylum Ascomycota, that are involved in a mutualistic symbiosis with plant roots. The aim of this study is to evaluate the behavior of two strains of DSE isolated from wheat roots of two cropping areas in the province of Buenos Aires, Argentina, against some agrochemicals. Of all the isolates obtained, two strains were identified as Alternaria alternata and Cochliobolus sp. These DSE were found to be tolerant to glyphosate, carbendazim and cypermethrin when evaluated at the recommended agronomic dose (AD), 2 AD and, in some cases, 10 AD. This work contributes to the study of the biology of this group of fungi and their tolerance in the presence of xenobiotics widely used in agriculture.

Monitoring Opportunistic Pathogens in Domestic Wastewater from a Pilot-Scale Anaerobic Biofilm Reactor to Reuse in Agricultural Irrigation

Wastewater reuse for agricultural irrigation in many developing countries is an increasingly common practice. Regular monitoring of indicators can help to identify potential health risks; therefore, there is an urgent need to understand the presence and abundance of opportunistic pathogens in wastewater, as well as plant phyllosphere and rhizosphere. In this study, an anaerobic biofilm reactor (ABR) was developed to treat rural domestic wastewater; the performance of pollutants removal and pathogenic bacteria elimination were investigated. Additionally, we also assessed the physicochemical and microbiological profiles of soil and lettuces after wastewater irrigation. Aeromonas hydrophila, Arcobacter sp., Bacillus cereus, Bacteroides sp., Escherichia coli, Legionella sp., and Mycobacterium sp. were monitored in the irrigation water, as well as in the phyllosphere and rhizosphere of lettuces. Pathogens like B. cereus, Legionella sp. and Mycobacterium sp. were present in treated effluent with relatively high concentrations, and the levels of A. hydrophila, Arcobacter sp., and E. coli were higher in the phyllosphere. The physicochemical properties of soil and lettuce did not vary significantly. These data indicated that treated wastewater irrigation across a short time period may not alter the soil and crop properties, while the pathogens present in the wastewater may transfer to soil and plant, posing risks to human health.

Investigating the bacterial community and amoebae population in rural domestic wastewater reclamation for irrigation

Reclamation of domestic wastewater for agricultural irrigation is viewed as a sustainable option to create an alternative water source and address water scarcity. Free-living amoebae (FLA), which are amphizoic protozoa, are widely distributed in various environmental sources. The FLA could cause considerable environmental and health risks. However, little information is available on the risk of these protozoa. In this study, we evaluated the feasibility using rural domestic wastewater for agricultural irrigation, and analyzed dynamic changes of the microbial community structure and FLA populations in raw and treated wastewater, as well as the phyllosphere and rhizosphere of lettuce production sites that were irrigated with different water sources. The bacterial community dynamics were analyzed by terminal restriction fragment length polymorphism (T-RFLP). The bacterial community structures in the influent were similar to that in the effluent, while in some cases relative abundances varied significantly. The populations of Acanthamoeba spp. and Hartmannella vermiformis in the anaerobically treated wastewater were significantly higher than in the raw wastewater. The vegetables could harbor diverse amoebae, and the abundances of Acanthamoeba spp. and H. vermiformis in the rhizosphere were significantly higher than in the phyllosphere. Accordingly, our studies show insight into the distribution and dissemination of amoebae in wastewater treatment and irrigation practices.

Interaction of Chemical Pesticides and Their Formulation Ingredients with Microbes Associated with Plants and Plant Pests

Chemical pesticides and their formulation ingredients can have unintended effects on microbes associated with plants and plant pests. These effects can be due to direct effects on the microbes or to effects on crops or weeds that subsequently affect the microbes. In addition to fungicides, some insecticides, herbicides, and formulation compounds are toxic to plant pathogenic microbes, as well as to potentially beneficial microbes, such as those that infect insect pests. These chemicals, especially herbicides, can also indirectly affect microbes through their effects on crops and weeds. For example, glyphosate strongly impairs shikimic acid pathway-based plant defenses to microbial diseases in glyphosate-susceptible plants, significantly increasing its efficacy as an herbicide. Some herbicides induce plant defenses against plant pathogens. For a complete understanding of integrated pest management and overall cost/benefit of pesticide use, much more information is needed on microbial/pesticide interactions.

Plant-Pesticide Interactions and the Global Chloromethane Budget

Ecological, signaling, metabolic, and chemical processes in plant-microorganism systems and in plant-derived material may link the use of chlorinated pesticides in the environment with plant chloromethane emission. This neglected factor should be taken into account to assess global planetary budgets of chloromethane and impacts on atmospheric ozone depletion.

Impact of fomesafen on the soil microbial communities in soybean fields in Northeastern China

Fomesafen, a widely adopted residual herbicide, is used throughout the soybean region of northern China for the spring planting. However, the ecological risks of using fomesafen in soil remain unknown. The aim of this work was to evaluate the impact of fomesafen on the microbial community structure of soil using laboratory and field experiments. Under laboratory conditions, the application of fomesafen at concentrations of 3.75 and 37.5mg/kg decreased the basal respiration (RB) and microbial biomass carbon (MBC). In contrast, treatment with 375mg/kg of fomesafen resulted in a significant decrease in the RB, MBC, abundance of both Gram+ and Gram- bacteria, and fungal biomass. Analysis of variance showed that the treatment accounted for most of the variance (38.3%) observed in the soil microbial communities. Furthermore, the field experiment showed that long-term fomesafen application in continuously cropped soybean fields affected the soil bacterial community composition by increasing the relative average abundance of Proteobacteria and Actinobacteria species and decreasing the abundance of Verrucomicrobia species. In addition, Acidobacteria and Chloroflexi species showed a pattern of activation-inhibition. Taken together, our results suggest that the application of fomesafen can affect the community structure of soil bacteria in the spring planting soybean region of northern China.

Application of the entomogenous fungus, Metarhizium anisopliae, for leafroller (Cnaphalocrocis medinalis) control and its effect on rice phyllosphere microbial diversity

Microbial pesticides form critical components of integrated pest management (IPM) practices. Little, however, is known regarding the impacts of these organisms on the indigenous microbial community. We show that Metarhizium anisopliae strain CQMa421 was highly effective in controlling the rice leafroller, Cnaphalocrocis medinalis Guenee. In addition, M. anisopliae distribution and its effects on phyllosphere microbial diversity after application in field trials were investigated. Phylloplane specific distribution of the fungus was observed over time, with more rapid declines of M. anisopliae CFUs (colony-forming units) seen in the top leaf layer as compared to lower layers. Application of the fungus resulted in transient changes in the endogenous microbial diversity with variations seen in the bacterial observed species and Shannon index. Notable increases in both parameters were seen at 6-day post-application of M. anisopliae, although significant variation within sample replicates for bacteria and fungi were noted. Application of M. anisopliae increased the relative distribution of bacterial species implicated in plant growth promotion and organic pollutant degradation, e.g., Methylobacterium, Sphingobium, and Deinococcus. These data show minimal impact of M. anisopliae on endogenous microbial diversity with transient changes in bacterial abundance/diversity that may result in added benefits to crops.

Ecotoxicological assessment of pesticides and their combination on rhizospheric microbial community structure and function of Vigna radiata

India is one of the leading countries in production and indiscriminate consumption of pesticides. Owing to their xenobiotic nature, pesticides affect soil microorganisms that serve as mediators in plant growth promotion. Our study aimed to deliver a comprehensive picture, by comparing the effects of synthetic pesticides (chlorpyriphos, cypermethrin, and a combination of both) with a biopesticide (azadirachtin) at their recommended field application level (L), and three times the recommended dosage (H) on structure and function of microbial community in rhizosphere of Vigna radiata. Effect on culturable fraction was assessed by enumeration on selective media, while PCR-denaturing gradient gel electrophoresis (DGGE) was employed to capture total bacterial community diversity. This was followed by a metabolic sketch using community-level physiological profiling (CLPP), to obtain a broader picture of the non-target effects on rhizospheric microbial community. Although plant parameters were not significantly affected by pesticide application, the microbial community structure experienced an undesirable impact as compared to control devoid of pesticide treatment. Examination of DGGE banding patterns through cluster analysis revealed that microbial community structure of pesticide-treated soils had only 70% resemblance to control rhizospheric soil even at 45 days post application. Drastic changes in the metabolic profiles of pesticide-treated soils were also detected in terms of substrate utilization, rhizospheric diversity, and evenness. It is noteworthy that the effects exacerbated by biopesticide were comparable to that of synthetic pesticides, thus emphasizing the significance of ecotoxicological assessments before tagging biopesticides as "safe alternatives."

Diazinon dissipation in pesticide-contaminated paddy soil: kinetic modeling and isolation of a degrading mixed bacterial culture

Dissipation kinetics of diazinon was investigated in soils culled from a paddy field with a long history of the pesticide application. Goodness of fit statistical indices derived from several fitted mono- and bi-exponential kinetic models revealed a bi-phasic pattern of the diazinon dissipation curve at 15 and 150 mg kg^-1 spiking levels, which could be described best by the first-order double exponential decay (FODED) model. Parameters obtained from this model were able to describe the enhanced dissipation of diazinon as the result of repeated soil applications, where a larger fraction of the pesticide readily available in the solution phase was dissipated with a fast rate. Cluster and principal component analysis (PCA) of denaturing gradient gel electrophoresis (DGGE) obtained from soil bacterial populations revealed that they were only affected at the 150 mg kg^-1 diazinon concentration. This was also supported by the phylogenetic tree obtained from sequences of the main gel bands. Accordingly, bacterial populations belonging to Proteobacteria were enriched in the soil following three treatments with diazinon at 150 mg kg^-1. The Shannon's index revealed a nonsignificant increase (P ≤ 0.05) in overall diversity of soil bacteria following diazinon application. Diazinon-degrading bacteria were isolated from the paddy soils in a mineral salt medium. Results showed that the isolated mixed culture was able to remove 90% of the pesticide at two concentrations of 50 and 100 mg L^-1 by 16.81 and 19.60 days, respectively. Sequencing the DGGE bands confirmed the role of Betaproteobacteria as the main components of the isolated mixed culture in the degradation of diazinon.

Pyrethroid-Degrading Microorganisms and Their Potential for the Bioremediation of Contaminated Soils: A Review

Pyrethroid insecticides have been used to control pests in agriculture, forestry, horticulture, public health and for indoor home use for more than 20 years. Because pyrethroids were considered to be a safer alternative to organophosphate pesticides (OPs), their applications significantly increased when the use of OPs was banned or limited. Although, pyrethroids have agricultural benefits, their widespread and continuous use is a major problem as they pollute the terrestrial and aquatic environments and affect non-target organisms. Since pyrethroids are not degraded immediately after application and because their residues are detected in soils, there is an urgent need to remediate pyrethroid-polluted environments. Various remediation technologies have been developed for this purpose; however, bioremediation, which involves bioaugmentation and/or biostimulation and is a cost-effective and eco-friendly approach, has emerged as the most advantageous method for cleaning-up pesticide-contaminated soils. This review presents an overview of the microorganisms that have been isolated from pyrethroid-polluted sites, characterized and applied for the degradation of pyrethroids in liquid and soil media. The paper is focused on the microbial degradation of the pyrethroids that have been most commonly used for many years such as allethrin, bifenthrin, cyfluthrin, cyhalothrin, cypermethrin, deltamethrin, fenpropathrin, fenvalerate, and permethrin. Special attention is given to the bacterial strains from the genera Achromobacter, Acidomonas, Bacillus, Brevibacterium, Catellibacterium, Clostridium, Lysinibacillus, Micrococcus, Ochrobactrum, Pseudomonas, Serratia, Sphingobium, Streptomyces, and the fungal strains from the genera Aspergillus, Candida, Cladosporium, and Trichoderma, which are characterized by their ability to degrade various pyrethroids. Moreover, the current knowledge on the degradation pathways of pyrethroids, the enzymes that are involved in the cleavage of pesticide molecules, the factors/conditions that influence the survival of strains that are introduced into soil and the rate of the removal of pyrethroids are also discussed. This knowledge may be useful to optimize the environmental conditions of bioremediation and may be crucial for the effective removal of pyrethroids from polluted soils.

A low dose of an organophosphate insecticide causes dysbiosis and sex-dependent responses in the intestinal microbiota of the Japanese quail (Coturnix japonica)

Organophosphate insecticides have been directly or indirectly implicated in avian populations declining worldwide. Birds in agricultural environments are commonly exposed to these insecticides, mainly through ingestion of invertebrates after insecticide application. Despite insecticide exposure in birds occurring mostly by ingestion, the impact of organophosphates on the avian digestive system has been poorly researched. In this work we used the Japanese quail (Coturnix japonica) as an avian model to study short-term microbial community responses to a single dose of trichlorfon at low concentration in three sample origins of the gastrointestinal tract (GIT): caecum, large intestine and faeces. Using next-generation sequencing of 16S rRNA gene amplicons as bacterial markers, the study showed that ingestion of insecticide caused significant changes in the GIT microbiome. Specifically, microbiota composition and diversity differed between treated and untreated quail. Insecticide-associated responses in the caecum showed differences between sexes which did not occur with the other sample types. In caecal microbiota, only treated females showed significant shifts in a number of genera within the Lachnospiraceae and the Enterobacteriaceae families. The major responses in the large intestine were a significant reduction in the genus Lactobacillus and increases in abundance of a number of Proteobacteria genera. All microbial shifts in faeces occurred in phylotypes that were represented at low relative abundances. In general, changes in microbiota possibly resulted from contrasting responses towards the insecticide, either positive (e.g., biodegrading bacteria) or negative (e.g., insecticide-susceptible bacteria). This study demonstrates the significant impact that organophosphate insecticides have on the avian gut microbiota; showing that a single small dose of trichlorfon caused dysbiosis in the GIT of the Japanese quail. Further research is necessary to understand the implications on birds’ health, especially in females.

Effect of Dursban 480 EC (chlorpyrifos) and Talstar 10 EC (bifenthrin) on the physiological and genetic diversity of microorganisms in soil

This investigation was undertaken to determine the impact of the insecticides Dursban 480 EC (with organophosphate compound chlorpyrifos as the active ingredient) and Talstar 10 EC (with pyrethroid bifenthrin as the active ingredient) on the respiration activity and microbial diversity in a sandy loam luvisol soil. The insecticides were applied in two doses: the maximum recommended dose for field application (15 mg kg(-1) for Dursban 480 EC and 6 mg kg(-1) for Talstar 10 EC) and a 100-fold higher dose for extrapolation of their effect. Bacterial and fungal genetic diversity was analysed in soil samples using PCR DGGE and the functional diversity (catabolic potential) was studied using BIOLOG EcoPlates at 1, 3, 7, 14, 28, 56 and 112 days after insecticide application. Five bacterial groups (α, β, γ proteobacteria, firmibacteria and actinomycetes) and five groups of fungi or fungus-like microorganisms (Ascomycota, Basidiomycota, Chytridiomycota, Oomycota and Zygomycota) were analysed using specific primer sets. This approach provides high resolution of the analysis covering majority of microorganisms in the soil. Only the high-dose Dursban 480 EC significantly changed the community of microorganisms. We observed its negative effect on α- and γ-proteobacteria, as the number of OTUs (operational taxonomic units) decreased until the end of incubation. In the β-proteobacteria group, initial increase of OTUs was followed by strong decrease. Diversity in the firmibacteria, actinomycetes and Zygomycota groups was minimally disturbed by the insecticide application. Dursban 480 EC, however, both positively and negatively affected certain species. Among negatively affected species Sphingomonas, Flavobacterium or Penicillium were detected, but Achromobacter, Luteibacter or Aspergillus were supported by applied insecticide. The analysis of BIOLOG plates using AWCD values indicated a significant increase in metabolic potential of microorganisms in the soil after the high-dose Dursban application. Analysis of respiration demonstrated high microbial activity after insecticide treatments; thus, microbial degradation was relatively fast. The half-life of the active insecticide compounds were estimated within the range of 25 to 27 days for Talstar and 6 to 11 days for Dursban and higher doses stimulated degradation. The recommended dose levels of both insecticides can be considered as safe for microbial community in the soil.

Nontarget effects of chemical pesticides and biological pesticide on rhizospheric microbial community structure and function in Vigna radiata

Intensive agriculture has resulted in an indiscriminate use of pesticides, which demands in-depth analysis of their impact on indigenous rhizospheric microbial community structure and function. Hence, the objective of the present work was to study the impact of two chemical pesticides (chlorpyrifos and cypermethrin) and one biological pesticide (azadirachtin) at two dosages on the microbial community structure using cultivation-dependent approach and on rhizospheric bacterial communities involved in nitrogen cycle in Vigna radiata rhizosphere through cultivation-independent technique of real-time PCR. Cultivation-dependent study highlighted the adverse effects of both chemical pesticide and biopesticide on rhizospheric bacterial and fungal communities at different plant growth stages. Also, an adverse effect on number of genes and transcripts of nifH (nitrogen fixation); amoA (nitrification); and narG, nirK, and nirS (denitrification) was observed. The results from the present study highlighted two points, firstly that nontarget effects of pesticides are significantly detrimental to soil microflora, and despite being of biological origin, azadirachtin exerted negative impact on rhizospheric microbial community of V. radiata behaving similar to chemical pesticides. Hence, such nontarget effects of chemical pesticide and biopesticide in plants' rhizosphere, which bring out the larger picture in terms of their ecotoxicological effect, demand a proper risk assessment before application of pesticides as agricultural amendments.

Response of soil microbial activity and biodiversity in soils polluted with different concentrations of cypermethrin insecticide

We performed a laboratory study into the effect of cypermethrin insecticide applied to different concentrations on biological properties in two soils [Typic Xerofluvent (soil A) and Xerollic Calciorthid (soil B)]. Two kg of each soil were polluted with cypermethrin at a rate of 60, 300, 600, and 1,200 g ha(-1) (C1, C2, C3, and C4 treatments). A nonpolluted soil was used as a control (C0 treatment). For all treatments and each experimental soil, soil dehydrogenase, urease, β-glucosidase, phosphatase, and arylsulphatase activities and soil microbial community were analysed by phospholipid fatty acids, which were measured at six incubation times (3, 7, 15, 30, 60, and 90 days). The behavior of the enzymatic activities and microbial population were dependent on the dose of insecticide applied to the soil. Compared with the C0 treatment, in soil A, the maximum inhibition of the enzymatic activities was at 15, 30, 45, and 90 days for the C1, C2, C3, and C4 treatments, respectively. However, in soil B, the maximum inhibition occurred at 7, 15, 30, and 45 days for the C1, C2, C3, and C4 treatments, respectively. These results suggest that the cypermethrin insecticide caused a negative effect on soil enzymatic activities and microbial diversity. This negative impact was greater when a greater dose of insecticide was used; this impact was also greater in soil with lower organic matter content. For both soils, and from these respective days onward, the enzymatic activities and microbial populations progressively increased by the end of the experimental period. This is possibly due to the fact that the insecticide or its breakdown products and killed microbial cells, subsequently killed by the insecticide, are being used as a source of energy or as a carbon source for the surviving microorganisms for cell proliferation.

Does nature make provision for backups in the modification of bacterial community structures?

Self-balancing is an inherent character in nature in response to community structure modification pressure and modern biotechnology has revolutionized the way such detections are made. Presented here is an overview of the forces and process interactions between released bacteria and indigenous microflora which encompass soil bacterial diversity, community structure, indigenous endorhizosphere micro-organisms, molecular detection methodologies, and transgenic plants and microbes. Issues of soil bacterial diversity and community structure as well as the interpretation of results from various findings are highlighted and discussed as inferred from research articles. An understanding of the factors influencing bio-inoculant modification of bacterial community structure in the colonization of the rhizosphere is essential for improved establishment of biocontrol agents, and is critically reviewed.

Resilience of the natural phyllosphere microbiota of the grapevine to chemical and biological pesticides

The phyllosphere is colonized by complex microbial communities, which are adapted to the harsh habitat. Although the role and ecology of nonpathogenic microorganisms of the phyllosphere are only partially understood, leaf microbiota could have a beneficial role in plant growth and health. Pesticides and biocontrol agents are frequently applied to grapevines, but the impact on nontarget microorganisms of the phyllosphere has been marginally considered. In this study, we investigated the effect of a chemical fungicide (penconazole) and a biological control agent (Lysobacter capsici AZ78) on the leaf microbiota of the grapevine at three locations. Amplicons of the 16S rRNA gene and of the internal transcribed spacer were sequenced for bacterial and fungal identification, respectively. Pyrosequencing analysis revealed that the richness and diversity of bacterial and fungal populations were only minimally affected by the chemical and biological treatments tested, and they mainly differed according to grapevine locations. Indigenous microbial communities of the phyllosphere are adapted to environmental and biotic factors in the areas where the grapevines are grown, and they are resilient to the treatments tested. The biocontrol properties of phyllosphere communities against downy mildew differed among grapevine locations and were not affected by treatments, suggesting that biocontrol communities could be improved with agronomic practices to enrich beneficial populations in vineyards.

Response of microbial community to a new fungicide fluopyram in the silty-loam agricultural soil

The impacts of fluopyram on a soil microbial community were studied at three application rates: at the recommended field rate (T1, 0.5mg/kg soil), three-fold recommended field rate (T3, 1.5mg/kg soil) and ten-fold recommended field rate (T10, 5mg/kg soil). Soil samples were taken after 7, 15, 30, 45, 60 and 90 days of application to determine the fluopyram residue and microbial properties (i.e., basal respiration, substrate-induced respiration, microbial biomass carbon, microbial community function and structure). The half-lives of the fluopyram at levels of 0.5, 1.5 and 5mg/kg in soil were calculated to be 64.2, 81.5 and 93.6 days, respectively. The results demonstrated that fluopyram treatment (T1, T3 and T10) decreased microbial biomass C but increased the basal respiration, substrate-induced respiration, and ecophysiological indices (qCO2). Average well color development (AWCD) represents the oxidative capacity of soil microorganisms cultivated in the BIOLOG micro-plates and usually indicates the overall microbial metabolic capacity. The BIOLOG results revealed that the AWCD in the soil treated with 1.5 and 5mg/kg fluopyram (T3 and T10) was significantly lower than that of the control during the incubation period. A similar variation in the diversity indices (Simpson index and McIntosh index) was observed. Phospholipid fatty acid (PLFA) analysis revealed that the addition of fluopyram decreased the total amount of PLFAs, bacterial biomass (both Gram-positive (GP) bacteria and Gram-negative (GN)), fungal biomass, the ratios of the GN/GP and fungi/bacteria at all incubation times. Principal component analyses (PCA) suggested that the addition of fluopyram shifted the soil microbial community structure and function. Hence, fluopyram has a harmful effect on overall soil microbial activity, and changed soil microbial community structure and function.

Resistance and resilience responses of a range of soil eukaryote and bacterial taxa to fungicide application

The application of plant protection products has the potential to significantly affect soil microbial community structure and function. However, the extent to which soil microbial communities from different trophic levels exhibit resistance and resilience to such compounds remains poorly understood. The resistance and resilience responses of a range of microbial communities (bacteria, fungi, archaea, pseudomonads, and nematodes) to different concentrations of the strobilurin fungicide, azoxystrobin were studied. A significant concentration-dependent decrease, and subsequent recovery in soil dehydrogenase activity was recorded, but no significant impact on total microbial biomass was observed. Impacts on specific microbial communities were studied using small subunit (SSU) rRNA terminal restriction fragment length polymorphism (T-RFLP) profiling using soil DNA and RNA. The application of azoxystrobin significantly affected fungal and nematode community structure and diversity but had no impact on other communities. Community impacts were more pronounced in the RNA-derived T-RFLP profiles than in the DNA-derived profiles. qPCR confirmed that azoxystrobin application significantly reduced fungal, but not bacterial, SSU rRNA gene copy number. Azoxystrobin application reduced the prevalence of ascomycete fungi, but increased the relative abundance of zygomycetes. Azoxystrobin amendment also reduced the relative abundance of nematodes in the order Enoplia, but stimulated a large increase in the relative abundance of nematodes from the order Araeolaimida.

The ecological roles of Bacillus thuringiensis within phyllosphere environments

Bacillus thuringiensis (Bt) is one of the most used bio-control agents to control plant insects, but little is known about its effect on the microbial population and communities on plant leaves. With the culture dependent method, it has been observed that the dynamics of Bt within the phyllosphere varied dependent on both the doses of Bt sprayed on the leaves and the plant species, however, Bt's population size kept stable at about 1000 cfu g(-1) after 15 d since inoculation. By comparing the bacterial abundances and community structures within the phyllosphere of three plant species, we confirmed that Bt at the doses of 1.5×10(7) and 1.5×10(9) cfu mL(-1) respectively did not significantly influence the natural bacterial population size on the leaf surfaces based on culture dependent assay. However, based on culture independent denaturing gradient gel electrophoresis (DGGE), Shannon-Wiener index (H') and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) analysis, Bt has a significant influence on the bacterial communities within the phyllosphere of amaranth and cotton, but not rice. These results indicate that Bt exhibits different behaviors and ecological roles on the microbial diversity within the phyllosphere, and its environmental safety has to be concerned and evaluated in the future.

Resilience of the natural phyllosphere microbiota of the grapevine to chemical and biological pesticides

The phyllosphere is colonized by complex microbial communities, which are adapted to the harsh habitat. Although the role and ecology of nonpathogenic microorganisms of the phyllosphere are only partially understood, leaf microbiota could have a beneficial role in plant growth and health. Pesticides and biocontrol agents are frequently applied to grapevines, but the impact on nontarget microorganisms of the phyllosphere has been marginally considered. In this study, we investigated the effect of a chemical fungicide (penconazole) and a biological control agent (Lysobacter capsici AZ78) on the leaf microbiota of the grapevine at three locations. Amplicons of the 16S rRNA gene and of the internal transcribed spacer were sequenced for bacterial and fungal identification, respectively. Pyrosequencing analysis revealed that the richness and diversity of bacterial and fungal populations were only minimally affected by the chemical and biological treatments tested, and they mainly differed according to grapevine locations. Indigenous microbial communities of the phyllosphere are adapted to environmental and biotic factors in the areas where the grapevines are grown, and they are resilient to the treatments tested. The biocontrol properties of phyllosphere communities against downy mildew differed among grapevine locations and were not affected by treatments, suggesting that biocontrol communities could be improved with agronomic practices to enrich beneficial populations in vineyards.

Responses of soil microbial community to different concentration of fomesafen

Fomesafen degrades slowly in soils and has been linked to crop damage. However, the effect of its residues on soil microbial communities is unknown. The goal of this work was to assess the effect of applying three different doses of fomesafen on microbial community structure and functional diversity as measured by phospholipid fatty acid (PLFA) levels, community-level physiological profiles (CLPPs) and real-time PCR. Our results indicate that applying 100 times the recommended dose of fomesafen (T100) adversely affects soil microbial activity and stresses soil microbial communities as reflected by the reduced respiratory quotient (qCO2, QR). The PLFA analysis showed that high levels of fomesafen treatment (T100) decreased the total amount of PLFAs and both bacterial (both Gram-positive (GP) bacteria and Gram-negative (GN) bacteria) and fungal biomass but increased the microbial stress level. However, the BIOLOG results are not consistent with our other results. The addition of fomesafen significantly increased the average well color development, substrate utilization, and the functional diversity index (H'). Additionally, the abundance of the nifH (N2-fixing bacteria) gene was reduced in the presence of high concentrations of fomesafen (T100). Taken together, these results suggest that the addition of fomesafen can alter the microbial community structure and functional diversity of the soil, and these parameters do not recover even after a 90-day incubation period.

Species composition of a soil invertebrate multi-species test system determines the level of ecotoxicity

A soil multi-species, SMS, experimental test system consisting of the natural microbial community, five collembolan species and a predatory mite along with either Enchytraeus crypticus or the earthworm Eisenia fetida were exposed to α-cypermethrin. A comparison of the performance of these two types of SMSs is given to aid the development of a standard test system. E. fetida had a positive effect on the majority of the species, reducing the negative insecticide effect. E. fetida affected the species sensitivity and decreased the degradation of the insecticide due to the organic matter incorporation of earthworm food. After 8 weeks, the EC50 was 0.76 mg kg(-1) for enchytraeids and ranged between 2.7 and 18.9 mg kg(-1) for collembolans, more sensitive than previously observed with single species. Changes observed in the community structure and function illustrates the strength of a multi-species test system as an ecotoxicological tool compared to single species tests.

Leaf microbiota of strawberries as affected by biological control agents

The increasing use of biological control agents (BCAs) against Botrytis cinerea in strawberry raises the question of whether there are any undesirable impacts of foliar applications of BCAs on nontarget microorganisms in the phyllosphere. Therefore, our objective was to investigate this issue within a field study. Strawberry plants were repeatedly sprayed with three BCAs-namely, RhizoVital 42 fl. (Bacillus amyloliquefaciens FZB42), Trianum-P (Trichoderma harzianum T22), and Naturalis (Beauveria bassiana ATCC 74040)-to suppress Botrytis cinerea infections. Microbial communities of differentially treated leaves were analyzed using plate counts and pyrosequencing and compared with the microbial community of nontreated leaves. Plate count results indicate that the applied Bacillus and Trichoderma spp. survived in the strawberry phyllosphere throughout the strawberry season. However, no significant impacts on the leaf microbiota could be detected by this culture-dependent technique. Pyrosequencing of internal transcribed spacer ribosomal RNA and 16S RNA sequences revealed a change in fungal composition and diversity at class level after the introduction of T. harzianum T22 to the phyllosphere, whereas the bacterial composition and diversity was not affected by either this Trichoderma preparation or the other two BCAs. Our results suggest that pyrosequencing represents a useful method for studying microbial interactions in the phyllosphere.

Effects of systemic pesticides imidacloprid and metalaxyl on the phyllosphere of pepper plants

Microbes inhabiting the phyllosphere of crops are exposed to pesticides applied either directly onto plant foliage or indirectly through soil. Although, phyllosphere microbiology has been rapidly evolving, little is still known regarding the impact of pesticides on the epiphytic microbial community and especially on fungi. We determined the impact of two systemic pesticides (metalaxyl and imidacloprid), applied either on foliage or through soil, on the epiphytic fungal and bacterial communities via DGGE and cloning. Both pesticides induced mild effects on the fungal and the bacterial communities. The only exception was the foliage application of imidacloprid which showed a more prominent effect on the fungal community. Cloning showed that the fungal community was dominated by putative plant pathogenic ascomycetes (Erysiphaceae and Cladosporium), while a few basidiomycetes were also present. The former ribotypes were not affected by pesticides application, while selected yeasts (Cryptococcus) were stimulated by the application of imidacloprid suggesting a potential role in its degradation. A less diverse bacterial community was identified in pepper plants. Metalaxyl stimulated an Enterobacteriaceae clone which is an indication of the involvement of members of this family in fungicide degradation. Further studies will focus on the isolation of epiphytic microbes which appear to be stimulated by pesticides application.

Effects of the fungicide metiram in outdoor freshwater microcosms: responses of invertebrates, primary producers and microbes

The ecological impact of the dithiocarbamate fungicide metiram was studied in outdoor freshwater microcosms, consisting of 14 enclosures placed in an experimental ditch. The microcosms were treated three times (interval 7 days) with the formulated product BAS 222 28F (Polyram®). Intended metiram concentrations in the overlying water were 0, 4, 12, 36, 108 and 324 μg a.i./L. Responses of zooplankton, macroinvertebrates, phytoplankton, macrophytes, microbes and community metabolism endpoints were investigated. Dissipation half-life (DT₅₀) of metiram was approximately 1-6 h in the water column of the microcosm test system and the metabolites formed were not persistent. Multivariate analysis indicated treatment-related effects on the zooplankton (NOEC(community) = 36 μg a.i./L). Consistent treatment-related effects on the phytoplankton and macroinvertebrate communities and on the sediment microbial community could not be demonstrated or were minor. There was no evidence that metiram affected the biomass, abundance or functioning of aquatic hyphomycetes on decomposing alder leaves. The most sensitive populations in the microcosms comprised representatives of Rotifera with a NOEC of 12 μg a.i./L on isolated sampling days and a NOEC of 36 μg a.i./L on consecutive samplings. At the highest treatment-level populations of Copepoda (zooplankton) and the blue-green alga Anabaena (phytoplankton) also showed a short-term decline on consecutive sampling days (NOEC = 108 μg a.i./L). Indirect effects in the form of short-term increases in the abundance of a few macroinvertebrate and several phytoplankton taxa were also observed. The overall community and population level no-observed-effect concentration (NOEC(microcosm)) was 12-36 μg a.i./L. At higher treatment levels, including the test systems that received the highest dose, ecological recovery of affected measurement endpoints was fast (effect period < 8 weeks).

Response of leaf-associated bacterial communities to primary acyl-homoserine lactone in the tobacco phyllosphere

The phyllosphere is inhabited by large populations of epiphytic bacteria that are able to modulate their phenotypes and behavior by quorum sensing (QS). However, the impact of acyl-homoserine lactones (AHLs) involved in QS on the ecology of bacteria in their natural habitat remains unclear. Therefore, we used a bioassay and liquid chromatography-mass spectrometry to detect AHLs in the tobacco phyllosphere. Our results identified several AHLs in the tobacco phyllosphere, the majority of which were short-chain AHLs. Furthermore, the addition of an exogenous N-(3-oxohexanoyl) homoserine lactone (3OC6HSL), which is seen in the naturally occurring tobacco phyllosphere, generated variability in the composition of the bacterial community as determined by denaturing gradient gel electrophoresis (DGGE) analysis and phospholipid fatty acid (PLFA) analysis. Notably, the ratio of Gram-positive (GP) bacteria increased in response to treatment with 1 μM AHL, but decreased incipiently when treated with 10 μM AHL. These observations provide insight into the composition of the leaf-colonizing epiphyte community responsible for AHLs, particularly GP bacteria as they do not use AHLs as signaling molecules for QS.