Linuron effects on microbiological characteristics of sandy soils as determined in a pot study

Effects of agrochemicals on the beneficial plant rhizobacteria in agricultural systems

Conventional agriculture relies heavily on chemical pesticides and fertilizers to control plant pests and diseases and improve production. Nevertheless, the intensive and prolonged use of agrochemicals may have undesirable consequences on the structure, diversity, and activities of soil microbiomes, including the beneficial plant rhizobacteria in agricultural systems. Although literature continues to mount regarding the effects of these chemicals on the beneficial plant rhizobacteria in agricultural systems, our understanding of them is still limited, and a proper account is required. With the renewed efforts and focus on agricultural and environmental sustainability, understanding the effects of different agrochemicals on the beneficial plant rhizobacteria in agricultural systems is both urgent and important to deduce practical solutions towards agricultural sustainability. This review critically evaluates the effects of various agrochemicals on the structure, diversity, and functions of the beneficial plant rhizobacteria in agricultural systems and propounds on the prospects and general solutions that can be considered to realize sustainable agricultural systems. This can be useful in understanding the anthropogenic effects of common and constantly applied agrochemicals on symbiotic systems in agricultural soils and shed light on the need for more environmentally friendly and sustainable agricultural practices.

Comprehensive characterization of stress tolerant bacteria with plant growth-promoting potential isolated from glyphosate-treated environment

The application of plant growth-promoting bacteria in agricultural systems is an efficient and environment-friendly strategy to improve crop yields and maintain soil quality. However, as different soils have diverse and specific ecological characteristics and may represent adverse abiotic conditions, in vivo application requires the careful selection of the desired beneficial microorganisms. In this study we report Ensifer adhaerens SZMC 25856 and Pseudomonas resinovorans SZMC 25875 isolates recovered from glyphosate-treated soil to possess yet undiscovered plant growth-enhancing potential. The strains were found to promote the growth of tomato seedlings significantly, to have the ability of synthesizing indole-3-acetic acid and siderophores, to tolerate pH in the range of 6.59-7.96, salinity up to 12.5 g L-1 NaCl and drought up to 125 g L-1 polyethylene glycol 6000, as well as to survive in the presence of various pesticides including glyphosate, diuron, chlorotoluron, carbendazim and thiabendazole, and heavy metals such as Al, Fe, Mn, Zn, Pb and Cu. The plant growth-promoting traits of the examined E. adhaerens and P. resinovorans isolates and their tolerance to numerous abiotic stress factors make them promising candidates for application in different agricultural environments, including soils polluted with glyphosate.

Functional Diversity of Soil Microbial Communities in Response to the Application of Cefuroxime and/or Antibiotic-Resistant Pseudomonas putida Strain MC1

Cefuroxime (XM), the most commonly prescribed antibiotic from the cephalosporin group, may cause changes in the structure of the soil microbial community, and these changes may also be reflected in the alteration of its functionality. Therefore, due to the lack of studies on this topic, the scope of this study was to assess the functional diversity and catabolic activity of the microbial community in soil treated with XM (1 mg/kg and 10 mg/kg soil) using the community-level physiological profile (CLPP) approach during a 90-day experiment. In addition, the effect of antibiotic-resistant Pseudomonas putida strain MC1 (Ps) was also evaluated. The resistance/resilience concept and multifactorial analysis were used to interpret the data. The results showed that the introduction of XM and/or Ps into the soil caused changes in the catabolic activity and functional diversity of the microbial community. A decrease in the values of the CLPP indices (i.e., microbial activity expressed as the average well-color development (AWCD), substrate richness (R), the Shannon-Wiener (H) and evenness (E) indices and the AWCD values for the six carbon substrate groups) for the XM-treated soil was generally detected up to 30 days. In turn, at the same time, the activity measured in the Ps-inoculated soil was higher compared to the control soil. A stimulatory effect of XM at 10 mg/kg (XM10) and XM10+Ps on the utilization pattern of each substrate group was found at the following sampling times (days 60 and 90). The AWCD values for the utilization of amines, amino acids, carbohydrates, carboxylic acids, miscellaneous compounds and polymers for these treatments were found to be up to 2.3-, 3.1-, 2.3-, 13-, 3.4- and 3.3-fold higher compared to the values for the nontreated control, respectively. The resistance of the CLPP indices and the AWCD values for the carbon substrate groups were categorized as follows: E > H > R > AWCD and amino acids = carbohydrates > polymers > amines > miscellaneous > carboxylic acids, respectively. The results suggest a low initial resistance of the soil microbial community to XM and/or Ps, and despite the short-term negative effect, the balance of the soil ecosystem may be disturbed.

Use of the PCR-DGGE Method for the Analysis of the Bacterial Community Structure in Soil Treated With the Cephalosporin Antibiotic Cefuroxime and/or Inoculated With a Multidrug-Resistant Pseudomonas putida Strain MC1

The widespread use of cefuroxime (XM) has resulted in the increase in its concentration in hospital and domestic wastewaters. Due to the limited removal of antibiotics and antibiotic-resistant genes in conventional systems, the drugs enter the surface water and soils. Moreover, the introduction of XM and/or XM-resistant bacteria into soil may cause a significant modification of the biodiversity of soil bacterial communities. Therefore, the goal of this research was to assess the genetic diversity of a bacterial community in the cefuroxime (XM1 – 1 mg/kg and XM10 – 10 mg/kg) and/or antibiotic-resistant Pseudomonas putida strain MC1 (Ps – 1.6 × 10⁷ cells/g)-treated soils as determined by the DGGE (denaturing gradient gel electrophoresis) method. The obtained data were also evaluated using a multivariate analysis and the resistance (RS)/resilience (RL) concept. Strain MC1 was isolated from raw sewage in the presence of XM and was resistant not only to this antibiotic but also to vancomycin, clindamycin and erythromycin. The DGGE patterns revealed that the XM10 and XM10+Ps treatments modified the composition of the bacterial community by the alteration of the DGGE profiles as well as a decline in the DGGE indices, in particular on days 30, 60, and 90. In turn, the XM1 and XM1+Ps or Ps treatments did not affect the values of richness and diversity of the soil bacteria members. A principal component analysis (PCA) also indicated that XM markedly changed the diversity of bacterial assemblages in the second part of the experiment. Moreover, there were differences in the RS/RL of the DGGE indices to the disturbances caused by XM and/or Ps. Considering the mean values of the RS index, the resistance was categorized in the following order: diversity (0.997) > evenness (0.993) > richness (0.970). The soil RL index was found to be negative, thus reflecting the progressing detrimental impact of XM on the genetic biodiversity of bacteria within the experiment. These results indicate that the introduction of XM at higher dosages into the soil environment may exert a potential risk for functioning of microorganism.

Vancomycin and/or Multidrug-Resistant Citrobacter Freundii Altered the Metabolic Pattern of Soil Microbial Community

Despite many studies, our knowledge on the impact of antibiotics and antibiotic-resistant bacteria on the metabolic activity of soil microbial communities is still limited. To ascertain this impact, the community level physiological profiles (CLPPs) and the activity of selected enzymes (dehydrogenase, urease, and phosphatases) in soils treated with vancomycin (VA) and/or multidrug resistant Citrobacter freundii were determined during a 90-day experiment. A multivariate analysis and the resistance (RS)/resilience (RL) concept were used to assess the potential of native microorganisms to maintain their catabolic activity under exposure of VA and/or a high level of C. freundii. In addition, the dissipation rate of VA was evaluated in non-sterile (nsS) and sterile (sS) soils. The results revealed a negative impact of VA on the metabolic activity of soil microorganisms on days 1, 15, and 30 as was showed by a decrease in the values of the CLPP indices (10-69%) and the enzyme activities (6-32%) for treated soils as compared to the control. These observations suggested a low initial resistance of soil microorganisms to VA and/or C. freundii but they were resilient in the long term. Considering the mean values of the RS index, the resistance of measured parameters was categorized in the following order: alkaline phosphatase (0.919) > acid phosphatase (0.899) > dehydrogenase (0.853) > the evenness index (0.840) > urease (0.833) > the Shannon-Wiener index (0.735) > substrate richness (0.485) > the AWCD (0.301). The dissipation process of VA was relatively fast and independent of the concentration used. The DT50 values for VA applied at both concentrations were about 16 days. In addition, the dissipation of VA in nsS was three times faster compared to the dissipation of antibiotic in sS. In conclusion, both CLPP and enzyme activities assays appeared to be useful tool for the determination of disturbances within soil microbial communities and used together may be helpful to understand the changes in their catabolic features. The entry of large quantities of VA and/or C. freundii into soil may temporarily change microbial activity thus pose a potential risk for soil functioning.

Non-target effect of continuous application of chlorpyrifos on soil microbes, nematodes and its persistence under sub-humid tropical rice-rice cropping system

Application of pesticide in agricultural fields is "unnecessary evil" for non-target microflora and fauna. Hence, to identify the safer pesticide molecules against non-target microbes, a long-term pesticide experiment was initiated at National Rice Research Institute, Cuttack, India. In the present study, the effect of continuous application of chlorpyrifos (0.5kgha^-1) in rice fields on non-target groups of soil microbes and nematodes was studied for seven seasons (four wet and three dry seasons) during 2009-2013. Treatments were arranged in a randomized complete block design with four replications of chlorpyrifos-treated (0.5kg a.i. ha^-1) (CT) and untreated control (UT) plots. During seven seasons of experimentation, regular application of chlorpyrifos had no significant effect on population of heterotrophic aerobic, anaerobic, oligotrophic and copiotrophic bacteria in CT compared to UT, whereas, population of asymbiotic aerobic nitrogen fixer, nitrifiers, denitrifiers, gram positive and spore-forming bacteria were significantly reduced by nearly 0.25-2 fold in CT than UT. However, comparatively less deviation in population of actinomycetes, fungi, phosphate solubilizing and sulfur oxidizing bacteria were observed in CT than UT. Significant interactions were found between effects of chlorpyrifos with time in population dynamics of microbes. In plant parasitic nematode species, Meloidogyne graminicola (RRKN) and Hirschmanniella spp. (RRN), were significantly lower (p<0.01) in CT compared to UT after first year onwards. The overall observation of five years data indicated that the RRKN population showed a decreasing trend (R²=0.644) whereas RRN showed increasing trend (R²=0.932) in CT. The drastic chlorpyrifos dissipation was noticed after 15 days of application from the initial residue of 0.25mgkg^-1 soil, which indicated that chlorpyrifos residue in rice field soil was not persistent and its half-life was found to be 4.02 days. Overall, the present findings revealed that non-target effect of repetitive application of chloropyrifos (0.5kgha^-1) on soil microbes and nematodes was found less under rice-rice cropping system.

Variable Effects of Non-steroidal Anti-inflammatory Drugs (NSAIDs) on Selected Biochemical Processes Mediated by Soil Microorganisms

Non-steroidal anti-inflammatory drugs (NSAIDs) are the most frequently used group of pharmaceuticals. The high consumption and the uncontrolled disposal of unused drugs into municipal waste or their deposit in landfills can result in an increased concentration of these compounds in soils. Moreover, these drugs can affect the microbial activity. However, there is a lack of knowledge about these effects or it is very limited. Therefore, the objective of this study was to compare the impact of selected commercially available NSAIDs, i.e., diclofenac (DCF), naproxen (NPX), ibuprofen (IBF) and ketoprofen (KTP), applied at concentrations of 1 and 10 mg/kg soil, on the activity of soil microorganisms during the 90-day experiment. To ascertain this impact, substrate-induced respiration (SIR), soil enzyme activities, i.e., dehydrogenase (DHA), acid and alkaline phosphatases (PHOS-H and PHOS-OH) and urease (URE) as well as changes in the rates of nitrification and ammonification processes were determined. In addition, the number of culturable bacteria and fungi were enumerated. In general, the obtained data showed a significant stimulatory effect of NSAIDs on the microbial activity. Higher concentrations of NSAIDs caused a greater effect, which was observed for SIR, PHOS-H, PHOS-OH, URE, N-NO3- and N-NH4+, even during the whole incubation period. Moreover, the number of heterotrophic bacteria and fungi increased significantly during the experiment, which was probably a consequence of the evolution of specific microorganisms that were capable of degrading NSAIDs and used them as an additional source of carbon and energy. However, an inhibitory effect of NPX, IBF or KTP for SIR, DHA, on both phosphatases and culturable bacteria and fungi was observed at the beginning of the experiment. At lower concentrations of NSAIDs, in turn, the effects were negligible or transient. In conclusion, the application of NSAIDs altered the biochemical and microbial activity of soil what may cause the disturbance in soil functioning. It is reasonable to assume that some components of the NSAID formulations could stimulate soil microorganisms, thus resulting in an increase in biochemical activities of the soil.

Perspectives of using fungi as bioresource for bioremediation of pesticides in the environment: a critical review

Pesticides are used for controlling the development of various pests in agricultural crops worldwide. Despite their agricultural benefits, pesticides are often considered a serious threat to the environment because of their persistent nature and the anomalies they create. Hence removal of such pesticides from the environment is a topic of interest for the researchers nowadays. During the recent years, use of biological resources to degrade or remove pesticides has emerged as a powerful tool for their in situ degradation and remediation. Fungi are among such bioresources that have been widely characterized and applied for biodegradation and bioremediation of pesticides. This review article presents the perspectives of using fungi for biodegradation and bioremediation of pesticides in liquid and soil media. This review clearly indicates that fungal isolates are an effective bioresource to degrade different pesticides including lindane, methamidophos, endosulfan, chlorpyrifos, atrazine, cypermethrin, dieldrin, methyl parathion, heptachlor, etc. However, rate of fungal degradation of pesticides depends on soil moisture content, nutrient availability, pH, temperature, oxygen level, etc. Fungal strains were found to harbor different processes including hydroxylation, demethylation, dechlorination, dioxygenation, esterification, dehydrochlorination, oxidation, etc during the biodegradation of different pesticides having varying functional groups. Moreover, the biodegradation of different pesticides was found to be mediated by involvement of different enzymes including laccase, hydrolase, peroxidase, esterase, dehydrogenase, manganese peroxidase, lignin peroxidase, etc. The recent advances in understanding the fungal biodegradation of pesticides focusing on the processes, pathways, genes/enzymes and factors affecting the biodegradation have also been presented in this review article.

Microbial and enzymatic activity of soil contaminated with a mixture of diflufenican + mesosulfuron-methyl + iodosulfuron-methyl-sodium

The aim of this study was to determine the effect of three active substances, diflufenican, mesosulfuron-methyl and iodosulfuron-methyl-sodium, applied in combination, on soil microbial counts, the structure of soil microbial communities, activity of soil enzymes and their resistance to the tested product, the biochemical indicator of soil fertility, and spring wheat yield. Soil samples with the granulometric composition of sandy loam with pHKCl 7.0 were used in a pot experiment. The herbicide was applied to soil at seven doses: 0.057 (dose recommended by the manufacturer), 1.140, 2.280, 4.560, 9.120, 18.240 and 36.480 mg kg(-1) soil DM. Uncontaminated soil served as the control treatment. It was found that a mixture of the tested active substances increased the counts of total oligotrophic bacteria and spore-forming oligotrophic bacteria, organotrophic bacteria and actinomycetes, decreased the counts of Azotobacter and fungi, and modified the structure of soil microbial communities. The highest values of the colony development (CD) index and the ecophysiological (EP) index were observed in fungi and organotrophic bacteria, respectively. The herbicide applied in the recommended dose stimulated the activity of catalase, urease and acid phosphatase, but it had no effect on the activity of dehydrogenases, alkaline phosphatase, arylsulfatase and β-glucosidase. The highest dose of the analyzed substances (36.480 mg kg(-1)) significantly inhibited the activity of dehydrogenases, acid phosphatase, alkaline phosphatase and arylsulfatase. The values of the biochemical soil fertility indicator (BA21) decreased in response to high doses of the herbicide. Urease was most resistant and dehydrogenases were least resistant to soil contamination with a mixture of diflufenican + mesosulfuron-methyl + iodosulfuron-methyl-sodium. The analyzed herbicide had an adverse influence on spring wheat yield, and doses of 18.240 and 36.480 mg kg(-1) led to eventual death of plants.

Soil microbial community toxic response to atrazine and its residues under atrazine and lead contamination

Intensive use of atrazine and extensive dispersal of lead (Pb) have occurred in farmland with chemical agriculture development. However, the toxicological effect of their presence on soil microorganism remains unknown. The objective of this study was to investigate the impacts of atrazine or Pb on the soil microbiota, soil net nitrogen mineralization, and atrazine residues over a 28-day microcosm incubation. The Shannon-Wiener diversity index, typical microbe species, and a Neighbor-joining tree of typical species from sequencing denaturing gradient gel electrophoresis (DGGE) bands were determined across periodical sampling times. The results showed that the existence of atrazine or Pb (especially high concentration) in soils reduced microbial diversity (the lowest H value is 2.23) compared to the control (H = 2.59) after a 28-day incubation. The species richness reduced little (from 17~19 species to 16~17 species) over the research time. But soil microbial community was significantly affected by the incubation time after the exposure to atrazine or Pb. The combination of atrazine and Pb had a significant inhibition effect on soil net nitrogen nitrification. Atrazine and Pb significantly stimulated soil cumulative net nitrogen mineralization and nitrification. Pb (300 and 600 mg kg(-1)) accelerated the level of atrazine dissipation. The exposure might stimulate the significant growth of the autochthonous soil degraders which may use atrazine as C source and accelerate the dissipation of atrazine in soils.

The combined effects of atrazine and lead (Pb): relative microbial activities and herbicide dissipation

The experiment was conducted to investigate the effects of single and combined pollution from different concentrations of atrazine (field rate, FR, 2.0 mg kg(-1) and 5 times FR, 10 mg kg(-1)) and lead (Pb) (300 mg kg(-1) and 600 mg kg(-1)) on enzyme activity, basal soil respiration (BSR), and net nitrogen (N) mineralization (NNM) in soil after exposure for 0, 7, 14, 21, and 28 days. In addition, residual atrazine was measured in the samples of combined contamination. Results showed that the notable effects of either or both contaminants on the microbial activity and biological processes. Enzyme activity data demonstrated that the order of sensitivity to contamination was urease>invertase>catalase. BSR was strongly stimulated by atrazine/Pb at the early exposure (0-7 days for single contaminant and 7-14 days for combined contaminants). The stimulation effects on BSR were higher at low concentrations of the contamination (FR and Pb300). The combined treatments of 5FR+Pb600 inhibit BSR and NNM. Overall, the parameters associated with N cycling (urease and NNM) were more sensitive than others. Both Pb concentrations (300 and 600 mg/kg) had little influence on the dissipation of high concentrations of atrazine (5FR) during the 28-day-incubation. This study has provided useful information on potential ecotoxicology effects of combined contamination of atrazine and Pb on relative microbial biological process.