Niche-specification of aerobic 2,4-dichlorophenoxyacetic acid biodegradation by tfd-carrying bacteria in the rice paddy ecosystem

This study aimed for a better understanding of the niche specification of bacteria carrying the tfd-genes for aerobic 2,4-dichlorphenoxyacetic acid (2,4-D) degradation in the rice paddy ecosystem. To achieve this, a dedicated microcosm experiment was set up to mimic the rice paddy system, with and without 2,4-D addition, allowing spatial sampling of the different rice paddy compartments and niches, i.e., the main anaerobic bulk soil and the aerobic surface water, surface soil, root surface and rhizosphere compartments. No effect of 2,4-D on the growth and morphology of the rice plant was noted. 2,4-D removal was faster in the upper soil layers compared to the deeper layers and was more rapid after the second 2,4-D addition compared to the first. Moreover, higher relative abundances of the 2,4-D catabolic gene tfdA and of the mobile genetic elements IncP-1 and IS1071 reported to carry the tfd-genes, were observed in surface water and surface soil when 2,4-D was added. tfdA was also detected in the root surface and rhizosphere compartment but without response to 2,4-D addition. While analysis of the bacterial community composition using high-throughput 16S rRNA gene amplicon sequencing did not reveal expected tfd-carrying taxa, subtle community changes linked with 2,4-D treatment and the presence of the plant were observed. These findings suggest (i) that the surface soil and surface water are the primary and most favorable compartements/niches for tfd-mediated aerobic 2,4-D biodegradation and (ii) that the community structure in the 2,4-D treated rice paddy ecosystem is determined by a niche-dependent complex interplay between the effects of the plant and of 2,4-D.

Short-term responses of plant growth-promoting bacterial community to the herbicides imazethapyr and flumioxazin

Imazethapyr and flumioxazin are widely recommended herbicides for soybean fields due to their broad-spectrum effects. However, although both herbicides present low persistence, their potential impact on the community of plant growth-promoting bacteria (PGPB) is unclear. To address this gap, this study assessed the short-term effect of imazethapyr, flumioxazin, and their mixture on the PGPB community. Soil samples from soybean fields were treated with these herbicides and incubated for 60 days. We extracted soil DNA at 0, 15, 30, and 60 days and sequenced the 16S rRNA gene. In general, the herbicides presented temporary and short-term effects on PGPB. The relative abundance of Bradyrhizobium increased, while Sphingomonas decreased on the 30th day with the application of all herbicides. Both herbicides increased the potential function of nitrogen fixation at 15th days and decreased at 30th and 60th days of incubation. The proportions of generalists were similar (∼42%) comparing each herbicide and the control, while the proportion of specialists increased (varying from 24.9% to 27.6%) with the application of herbicides. Imazethapyr, flumioxazin and their mixture did not change the complexity and interactions of the PGPB network. In conclusion, this study showed that, in the short term, the application of imazethapyr, flumioxazin, and their mixture, at the recommended field rates, does not negatively affect the community of plant growth-promoting bacteria.

Effects of long-term exposure to the herbicide nicosulfuron on the bacterial community structure in a factory field

This study aims to investigate the effects of long-term nicosulfuron residue on an herbicide factory ecosystem. High-throughput sequencing was used to investigate the environmental microbial community structure and interactions. The results showed that the main contributor to the differences in the microbial community structure was the sample type, followed by oxygen content, pH and nicosulfuron residue concentration. Regardless of the presence or absence of nicosulfuron, soil, sludge, and sewage were dominated by groups of Bacteroidetes, Actinobacteria, and Proteobacteria. Long-term exposure to nicosulfuron increased alpha diversity of bacteria and archaea but significantly decreased the abundance of Bacteroidetes and Acidobateria compared to soils without nicosulfuron residue. A total of 81 possible nicosulfuron-degrading bacterial genera, e.g., Rhodococcus, Chryseobacterium, Thermomonas, Stenotrophomonas, and Bacillus, were isolated from the nicosulfuron factory environmental samples through culturomics. The co-occurrence network analysis indicated that the keystone taxa were Rhodococcus, Stenotrophomonas, Nitrospira, Terrimonas, and Nitrosomonadaceae_MND1. The strong ecological relationship between microorganisms with the same network module was related to anaerobic respiration, the carbon and nitrogen cycle, and the degradation of environmental contaminants. Synthetic community (SynCom), which provides an effective top-down approach for the critical degradation strains obtained, enhanced the degradation efficiency of nicosulfuron. The results indicated that Rhodococcus sp. was the key genus in the environment of long-term nicosulfuron exposure.

Composition of bacterial community and isolation of bacteria responsible for diuron degradation in sediment and soil under anaerobic condition

The herbicide diuron is extensively used in the agriculture sector and is detected widely in the environment. Although several studies on the degradation of diuron by aerobic microorganisms have been reported, the degradation of diuron by anaerobic microorganisms has not been received much attention. Also, no pure culture that can degrade diuron under anaerobic conditions has yet been reported. The evaluation of diuron degradation in the soil and sediment slurries showed that diuron led to a decrease in the biodiversity of the bacterial communities. Two mixed bacterial cultures, one from the soil and the other from sediment slurries, were isolated from the enrichment media under anaerobic conditions. After 30 days of incubation at 30 °C, the mixed bacterial culture from the soil degraded 84.5 ± 5.5%, and that from the sediment slurry degraded 94.5 ± 3.0% of diuron in liquid mineral medium at an initial concentration of 20 mg/L. 1-(3,4-dichlorophenylurea (DCPU), 3-(3-chlorophenyl)-1,1-dimethylurea (CPDMU), and 3,4-dichloroaniline (3,4-DCA) were the major diuron metabolites produced by both the indigenous microorganisms and the isolated bacteria.

Degradation of Diuron by a Bacterial Mixture and Shifts in the Bacterial Community During Bioremediation of Contaminated Soil

Diuron, a phenylurea herbicide, has been extensively applied in controlling a wide range of weeds in several crops. In the current study, a mixed culture of three bacterial strains, i.e., Bacillus subtilis DU1, Acinetobacter baumannii DU, and Pseudomonas sp. DUK, isolated from sugarcane soil, completely degraded diuron and 3,4-DCA in liquid media at 20 mg L^-1 within 48 h. During diuron degradation, a few metabolites (DCPMU, DCPU, and 3,4-DCA) were produced. Further determination of ring-cleavage pathways demonstrated that Acinetobacter baumannii DU and Pseudomonas fluorescens DUK degraded diuron and 3,4-DCA via ortho-cleavage. In contrast, Bacillus subtilis DU transformed these compounds via meta-cleavage pathways. Moreover, diuron caused a significant shift in the bacterial community in soil without diuron history. The augmentation of mountain soil with the isolated bacteria resulted in nearly three times higher degradation rate of diuron than the degradation by indigenous microorganisms. This study provides important information on in situ diuron bioremediation from contaminated sites by bioaugmentation with a mixed bacterial culture.

Specific quorum sensing molecules are possibly associated with responses to herbicide toxicity in a Pseudomonas strain

Pesticides contribute to pest control and increase agricultural production; however, they are toxic to non-target organisms, and they contaminate the environment. The exposure of bacteria to these substances can lead to the need for physiological and structural changes for survival, which can be determined by genes whose expression is regulated by quorum sensing (QS). However, it is not yet clear whether these processes can be induced by herbicides. Thus, the aim of this work was to determine whether there is a QS response system in the Pseudomonas fluorescens CMA55 strain that is modulated by herbicides. This strain was isolated from water storage tanks used for washing pesticide packaging and was tested against herbicides containing saflufenacil, glyphosate, sulfentrazone, 2,4-D, and dicamba as active molecules. Our results showed that in the presence of herbicides containing saflufenacil and glyphosate (the latter was not present at the bacterial isolation site) the strain had a profile of QS signaling molecules that may be involved in controlling the production of reactive oxygen species. Alternatively, the same strain, in the presence of sulfentrazone (it was not present at the bacterial isolation site), 2,4-D and dicamba-containing herbicides, presented another profile of molecules that may be involved in different stages of biofilm formation. These findings, as a first screening, suggest that this strain used strategies to activate antioxidant enzymes and biofilm production under the signaling of QS molecules to respond to herbicides, regardless of previous contact, representing a model of phenotypic plasticity for adaptation to agricultural environments that can be used in studies of herbicide bioremediation.

Herbicides Tolerance in a Pseudomonas Strain Is Associated With Metabolic Plasticity of Antioxidative Enzymes Regardless of Selection

Agriculture uses many food production chains, and herbicides participate in this process by eliminating weeds through different biochemical strategies. However, herbicides can affect non-target organisms such as bacteria, which can suffer damage if there is no efficient control of reactive oxygen species. It is not clear, according to the literature, whether the efficiency of this control needs to be selected by the presence of xenobiotics. Thus, the Pseudomonas sp. CMA 6.9 strain, collected from biofilms in an herbicide packaging washing tank, was selected for its tolerance to pesticides and analyzed for activities of different antioxidative enzymes against the herbicides Boral^®, absent at the isolation site, and Heat^®, present at the site; both herbicides have the same mode of action, the inhibition of the enzyme protoporphyrinogen oxidase. The strain showed tolerance to both herbicides in doses up to 45 times than those applied in agriculture. The toxicity of these herbicides, which is greater for Boral^®, was assessed by means of oxidative stress indicators, growth kinetics, viability, and amounts of peroxide and malondialdehyde. However, the studied strain showed two characteristic antioxidant response systems for each herbicide: glutathione-s-transferase acting to control malondialdehyde in treatments with Boral^®; and catalase, ascorbate peroxidase, and guaiacol peroxidase in the control of peroxide induced by Heat^®. It is possible that this modulation of the activity of different enzymes independent of previous selection characterizes a system of metabolic plasticity that may be more general in the adaptation of microorganisms in soil and water environments subjected to chemical contaminants. This is relevant to the impact of pesticides on the diversity and abundance of microbial species as well as a promising line of metabolic studies in microbial consortia for use in bioremediation.

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.

Effects of sulfonylurea herbicides chlorsulfuron and sulfosulfuron on enzymatic activities and microbial communities in two agricultural soils

Sulfonylurea herbicides are widely used for weed control in agriculture, and they are suspected to alter microbial communities and activities in the soil. This study investigates the impact of two sulfonylurea herbicides chlorsulfuron and sulfosulfuron on microbial community and activity in two different soils taken from two sites in west part of the Slovak Republic. The soil from the Malanta site was silt-loam luvisol with pH_(H2O) 5.78 while the soil from the Stefanov site was sandy-loam regosol with pH_(H2O) 8.25. These soils were not treated by sulfonylurea herbicides at least for 2 years prior to the study. In laboratory assay, the herbicides were applied to soil in their maximal recommended doses 26 and 25 g per hectare of chlorsulfuron and sulfosulfuron, respectively. Their effect was evaluated on the 3rd, 7th, 14th, 28th, 56th, and 112th day after application to soil. Illumina high-throughput amplicon sequencing of the 16S rRNA gene and ITS region was used to monitor changes on prokaryotic and fungal community composition. Enzymatic activity was evaluated using 11 substrates. Physiological profile of microbial community was analyzed using Biolog© ecoplates. Significant changes in enzymatic activity caused by the application of herbicides were found during the first 28 days. The application of herbicides altered the activity of cellobiohydrolase, arylsulphatase, dehydrogenase, phosphatase, and FDA hydrolase. Chlorsulfuron caused a more varying response of enzymatic activity than sulfosulfuron, and observed changes were not the same for both soils. In Malanta soil, chlorsulfuron decreased dehydrogenase activity while it was increased in the Stefanov soil. Phosphatase activity was decreased in both soils on 7th and 14th day. There were only minor changes in prokaryotic or fungal community or physiological profiles regarding pesticide application. Differences between soils and incubation time explained most of the variability in these parameters. Diversity indices, physiological parameters, and enzymatic activity decreased over time. The results have shown that chlorsulfuron and sulfosulfuron can affect the function and activity of the soil microbial community without significant change in its composition.

Hypervirulence and cross-resistance to a clinical antifungal are induced by an environmental fungicide in Cryptococcus gattii

The increasing human population requires ongoing efforts in food production. This is frequently associated with an increased use of agrochemicals, leading to environmental contamination and altering microbial communities, including human fungal pathogens that reside in the environment. Cryptococcus gattii is an environmental yeast and is one of the etiological agents of cryptococcosis. Benomyl (BEN) is a broad-spectrum fungicide used on several crops. To study the effects of agrochemicals on fungal pathogens, we first evaluated the susceptibility of C. gattii to BEN and the interactions with clinical antifungals. Antagonistic interaction between BEN and fluconazole was seen and was strain- and concentration-dependent. We then induced BEN-resistance by culturing strains in increasing drug concentrations. One strain demonstrated to be more resistant and showed increased multidrug efflux pump gene (MDR1) expression and increased rhodamine 6G efflux, leading to cross-resistance between BEN and fluconazole. Morphologically, BEN-adapted cells had a reduced polysaccharide capsule; an increased surface/volume ratio; increased growth rate in vitro and inside macrophages and also higher ability in crossing an in vitro model of blood-brain-barrier. BEN-adapted strain demonstrated to be hypervirulent in mice, leading to severe symptoms of cryptococcosis, early mortality and higher fungal burden in the organs, particularly the brain. The parental strain was avirulent in murine model. In vivo cross-resistance between BEN and fluconazole was observed, with mice infected with the adapted strain unable to present any improvement in survival and behavior when treated with this antifungal. Furthermore, BEN-adapted cells cultured in drug-free media maintained the hypervirulent and cross-resistant phenotype, suggesting a persistent effect of BEN on C. gattii. In conclusion, exposure to BEN induces cross-resistance with fluconazole and increases the virulence of C. gattii. Altogether, our results indicate that agrochemicals may lead to unintended consequences on non-target species and this could result in severe healthy problems worldwide.

Change in the antimicrobial resistance profile of Pseudomonas aeruginosa from soil after exposure to herbicides

The extensive use of pesticides represents a risk to human health and to the environment. This study aimed to investigate if the exposure to atrazine and diuron, two herbicides widely used in Brazil, could induce changes in the susceptibility profile to aztreonam, colistin and polymyxin B antimicrobials in isolates of P. aeruginosa obtained from soil samples by using the determination of minimum inhibitory concentration (MIC) test. Three isolates had an increase of MIC to aztreonam after exposure to both herbicides and one isolate did not show any MIC change. The MexAB-OprM efflux pump has already been upregulated in these isolates and the herbicides atrazine and diuron did not increase MexAB-OprM overexpression. Therefore, the decrease in aztreonam susceptibility was not directly related to this pump, suggesting that probably other mechanisms should be involved.