Effects of a sulfonylurea herbicide on the soil bacterial community

Comparative analysis of bacterial populations in sulfonylurea-sensitive and -resistant weeds: insights into community composition and catabolic gene dynamics

This study aimed to compare the impact of iodosulfuron-methyl-sodium and an iodosulfuron-based herbicidal ionic liquid (HIL) on the microbiomes constituting the epiphytes and endophytes of cornflower (Centaurea cyanus L.). The experiment involved biotypes of cornflower susceptible and resistant to acetolactate synthase inhibition, examining potential bacterial involvement in sulfonylurea herbicide detoxification. We focused on microbial communities present on the surface and in the plant tissues of roots and shoots. The research included the synthesis and physicochemical analysis of a novel HIL, evaluation of shifts in bacterial community composition, analysis of the presence of catabolic genes associated with sulfonylurea herbicide degradation and determination of their abundance in all experimental variants. Overall, for the susceptible biotype, the biodiversity of the root microbiome was higher compared to shoot microbiome; however, both decreased notably after herbicide or HIL applications. The herbicide-resistant biotype showed lower degree of biodiversity changes, but shifts in community composition occurred, particularly in case of HIL treatment.

Versatility of Stenotrophomonas maltophilia: Ecological roles of RND efflux pumps

S. maltophilia is a widely distributed bacterium found in natural, anthropized and clinical environments. The genome of this opportunistic pathogen of environmental origin includes a large number of genes encoding RND efflux pumps independently of the clinical or environmental origin of the strains. These pumps have been historically associated with the uptake of antibiotics and clinically relevant molecules because they confer resistance to many antibiotics. However, considering the environmental origin of S. maltophilia, the ecological role of these pumps needs to be clarified. RND efflux systems are highly conserved within bacteria and encountered both in pathogenic and non-pathogenic species. Moreover, their evolutionary origin, conservation and multiple copies in bacterial genomes suggest a primordial role in cellular functions and environmental adaptation. This review is aimed at elucidating the ecological role of S. maltophilia RND efflux pumps in the environmental context and providing an exhaustive description of the environmental niches of S. maltophilia. By looking at the substrates and functions of the pumps, we propose different involvements and roles according to the adaptation of the bacterium to various niches. We highlight that i°) regulatory mechanisms and inducer molecules help to understand the conditions leading to their expression, and ii°) association and functional redundancy of RND pumps and other efflux systems demonstrate their complex role within S. maltophilia cells. These observations emphasize that RND efflux pumps play a role in the versatility of S. maltophilia.

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.

Biodegradation and Subsequent Toxicity Reduction of Co-contaminants Tribenuron Methyl and Metsulfuron Methyl by a Bacterial Consortium B2R

AllyMax is a widely used herbicide formulation in wheat-rice cropping areas of the world. The residues of its active ingredients, tribenuron methyl (TBM) and metsulfuron methyl (MET), persist in soil and water as co-contaminants, and cause serious threats to nontarget organisms. This study was performed to assess the potential of a bacterial consortium for the degradation and detoxification of TBM and MET individually and as co-contaminants. A bacterial consortium (B2R), comprising Bacillus cereus SU-1, Bacillus velezensis OS-2, and Rhodococcus rhodochrous AQ1, capable of degrading TBM and MET in liquid cultures was developed. Biodegradation of TBM and MET was optimized using the Taguchi design of experiment. Optimum degradation of both TBM and MET was obtained at pH 7 and 37 °C. Regarding media composition, optimum degradation of TBM and MET was obtained in minimal salt medium (MSM) supplemented with glucose, and MSM without glucose, respectively. The consortium simultaneously degraded TBM and MET (94.8 and 80.4%, respectively) in cultures containing the formulation AllyMax, where TBM and MET existed as co-contaminants at 2.5 mg/L each. Mass spectrometry analysis confirmed that during biodegradation, TBM and MET were metabolized into simpler compounds. Onion (Allium cepa) root inhibition and Comet assays revealed that the bacterial consortium B2R detoxified TBM and MET separately and as co-contaminants. The consortium B2R can potentially be used for the remediation of soil and water co-contaminated with TBM and MET.

Evaluation on persistence and mobility of metsulfuron-methyl at oil palm plantation: residue field trial experiment versus VARLEACH model

The present paper discussed the comparison of the persistence and mobility of metsulfuron-methyl from a residue field trial experiment and simulation using a VARLEACH model. The residue field trial experiment was performed at Sungai Buloh Oil Palm Estate, Selangor. The plots were treated with metsulfuron-methyl at two treatment rates of 15 g a.i ha^-1 (T1) and 30 g a.i ha^-1 (T2). Soil samples were collected at 0, 1, 3, 7, 14, 21, 30, 60 and 90 days after treatment (DAT) and analysed subsequently by HPLC-UV. The results show that metsulfuron-methyl degraded rapidly in the soil with the half-life (t½) of 6.3 days in T1 and 7.9 days in T2. The simulation of VARLEACH model gave similar pattern of persistence and mobility of metsulfuron-methyl in the soil profile. However, total residues and the mobility of the metsulfuron-methyl were poorly simulated by the VARLEACH model due to consistent overestimation of the quantified residues. Results indicated that the metsulfuron-methyl lost more rapidly than the prediction values from VARLEACH model. In this case, simulation models which use transformation routines similar and which include additional degraded processes such as leaching, volatilisation, plant uptake or runoff could be considered. Albeit, overestimated values on the concentrations of metsulfuron-methyl are reported using VARLEACH model, the model still can be used as rapid and fast approach to predict the behaviour of pesticide at minimum cost.

Sorption-desorption and biodegradation of sulfometuron-methyl and its effects on the bacterial communities in Amazonian soils amended with aged biochar

Sulfometuron-methyl is a broad-spectrum herbicide, used throughout Brazil; however, its environmental impacts in biochar (BC) amended soils is not fully understood. Biochar is known to enhance soil quality but can also have undesired effects such as altering the bioavailability and behavior of herbicides. Microbial communities can degrade herbicides such as sulfometuron-methyl in soils; however, they are known to be affected by BC. Therefore, it is important to understand the tripartite interaction between these factors. This research aimed to evaluate the sorption-desorption and biodegradation of sulfometuron-methyl in Amazonian soils amended with BC, and to assess the effects of the interactions between BC and sulfometuron-methyl on soil bacterial communities. Soil samples were collected from field plots amended with BC at three doses (0, 40 and 80 t ha^-1) applied ten years ago. The herbicide sorption and desorption were evaluated using a batch equilibrium method. Mineralization and biodegradation studies were conducted in microcosms incubated with ¹⁴C-sulfometuron-methyl for 80 days. Systematic soil sampling, followed by DNA extraction, quantification (qPCR) and 16S rRNA amplicon sequencing were performed. The presence of BC increased the sorption of the herbicide to the soil by 11% (BC40) and 16% (BC80) compared to unamended soil. The presence of BC also affected the degradation of ¹⁴C-sulfometuron-methyl, reducing the mineralization rate and increasing the degradation half-life times (DT50) from 36.67 days in unamended soil to 52.11 and 55.45 days in BC40 and BC80 soils, respectively. The herbicide application altered the bacterial communities, affecting abundance and richness, and changing the taxonomic diversity (i.e., some taxa were promoted and other inhibited). A tripartite interaction was found between BC, the herbicide and soil bacterial communities, suggesting that it is important to consider the environmental impact of soil applied herbicides in biochar amended soils.

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.

The Shewanella genus: ubiquitous organisms sustaining and preserving aquatic ecosystems

The Gram-negative Shewanella bacterial genus currently includes about 70 species of mostly aquatic γ­-proteobacteria, which were isolated around the globe in a multitude of environments such as surface freshwater and the deepest marine trenches. Their survival in such a wide range of ecological niches is due to their impressive physiological and respiratory versatility. Some strains are among the organisms with the highest number of respiratory systems, depending on a complex and rich metabolic network. Implicated in the recycling of organic and inorganic matter, they are important components of organism-rich oxic/anoxic interfaces, but they also belong to the microflora of a broad group of eukaryotes from metazoans to green algae. Examples of long-term biological interactions like mutualism or pathogeny have been described, although molecular determinants of such symbioses are still poorly understood. Some of these bacteria are key organisms for various biotechnological applications, especially the bioremediation of hydrocarbons and metallic pollutants. The natural ability of these prokaryotes to thrive and detoxify deleterious compounds explains their use in wastewater treatment, their use in energy generation by microbial fuel cells and their importance for resilience of aquatic ecosystems.

Effects of herbicide on non-target microorganisms: Towards a new class of biomarkers?

Conventional agriculture still relies on the general use of agrochemicals (herbicides, fungicides and insecticides) to control various pests (weeds, fungal pathogens and insects), to ensure the yield of crop and to feed a constantly growing population. The generalized use of pesticides in agriculture leads to the contamination of soil and other connected environmental resources. The persistence of pesticide residues in soil is identified as a major threat for in-soil living organisms that are supporting an important number of ecosystem services. Although authorities released pesticides on the market only after their careful and thorough evaluation, the risk assessment for in-soil living organisms is unsatisfactory, particularly for microorganisms for which pesticide toxicity is solely considered by one global test measuring N mineralization. Recently, European Food Safety Authority (EFSA) underlined the lack of standardized methods to assess pesticide ecotoxicological effects on soil microorganisms. Within this context, there is an obvious need to develop innovative microbial markers sensitive to pesticide exposure. Biomarkers that reveal direct effects of pesticides on microorganisms are often viewed as the panacea. Such biomarkers can only be developed for pesticides having a mode of action inhibiting a specific enzyme not only found in the targeted organisms but also in microorganisms which are considered as "non-target organisms" by current regulations. This review explores possible ways of innovation to develop such biomarkers for herbicides. We scanned the herbicide classification by considering the mode of action, the targeted enzyme and the ecotoxicological effects of each class of active substance in order to identify those that can be tracked using sensitive microbial markers.

First Characterization of PAH-degrading bacteria from Río de la Plata and high-resolution melting: an encouraging step toward bioremediation

The Río de la Plata, one of the most important estuarine environments in South America that sustains valuable fisheries, is affected by PAH contamination associated with oil industry and port activities. A total of 95 bacteria with potential to degrade phenanthrene were obtained from water samples using traditional culture methods. PCR-RFLP analysis of 16S rDNA partial fragments was used as a screening tool for reducing the number of isolates during diversity studies, obtaining 42 strains with different fingerprint patterns. Phylogenetic analysis indicated that they were affiliated to 19 different genera of Gamma- and Alpha-Proteobacteria, and Actinobacteria. Some of them showed an efficient phenanthrene degradation by HPLC (between 83% and 97%) and surfactant production (between 40% and 55%). They could be an alternative for microbial selection in the degradation of PAHs in this estuarine system. In order to detect and monitor PAH-degrading bacteria in this highly productive area, rDNA amplicons of the 33 isolates, produced by PCR real time, were tested by the high-resolution melting (HRM) technique. After analyzing the generated melting curves, it was possible to accurately distinguish nine patterns corresponding to eight different genera. HRM analysis allowed a differentiation at the species level for genera Pseudomonas, Halomonas and Vibrio. The implementation of this method as a fast and sensitive scanning approach to identify PAH-degrading bacteria, avoiding the sequencing step, would mean an advance in bioremediation technologies.

Influence of agro-environmental pollutants on a biocontrol strain of Bacillus velezensis

Metal- and pesticide-tolerant biocontrol agents are preferred in integrated pest management, as such strains can be applied in combination with different pesticides. The Bacillus velezensis strain SZMC 6161J proved to be sensitive to copper, nickel, zinc, and cadmium, while manganese elevated its growth. At concentrations higher than 1 mmol L^-1 , zinc and iron inhibited the chymotrypsin-like activity of this strain. In addition, trypsin-like protease and palmitoyl esterase activities were insensitive to all tested heavy metals in the applied concentration range. We studied the effects of some widely used herbicides and fungicides on the growth of this strain. The presence of sulfonylurea herbicides, like bensulfuron-methyl, cinosulfuron, chlorsulfuron, ethoxysulfuron, triasulfuron, and primisulfuron-methyl strongly inhibited the biomass production of the strain even at the concentration of 6.25 mg L^-1 . Glyphosate also inhibited the growth above 30 mg L^-1 . Similarly, contact fungicides like captan, maneb, mancozeb, and thiram resulted in total inhibition at the concentration as low as 6.25 mg L^-1 . Interestingly, the sterol-biosynthesis-inhibiting fungicides imazalil, fenarimol, penconazole, and tebuconazole also proved to be potent inhibitors. Heavy metal- and fungicide-tolerant strains were isolated from the parental strain and their antagonistic abilities were evaluated. There was no substantial difference between the antagonism capability of wild-type strain and the resistant mutants.

Rhizoremediation of residual sulfonylurea herbicides in agricultural soils using Lens culinaris and a commercial supplement

Sulfonylureas (SU) are a popular herbicide used today for controlling weeds. While beneficial for this purpose they present a persistent problem in agricultural treated areas, with this treatment proving detrimental for successive crops. This study assessed the phytoremediative properties of lentils (Lens culinaris) grown in uncontaminated and chlorsulfuron-contaminated soil, with and without the addition of a growth supplement, PulseAider™. The results show that in the presence of lentils the degradation of chlorsulfuron is enhanced and this degradation rate is significantly increased when the PulseAider™ supplement was included during seed sowing. The supplement PulseAider™ also significantly increased shoot and root biomass, root branching, and nodule number under control conditions. While this was not so for plants grown in contaminated soils, the PulseAider™ supplement seemed to alter root branching and morphology. Most Probable Number (MPN) assays showed increased numbers of potential chlorsulfuron-degrading bacteria in soil treated with PulseAider™, although this was found to be significant only in the control soil. Sequencing of the 16S ribosomal gene showed the presence of Pseudomonas fluorescens bacterial species which is a known chlorsulfuron-degrading bacterium. This study is one of the first to address the remediation of residual SU herbicides and offers an economically feasible solution that may have an impact on global food security.

Effect of sulfonylurea tribenuron methyl herbicide on soil Actinobacteria growth and characterization of resistant strains

Repeated application of pesticides disturbs microbial communities and cause dysfunctions on soil biological processes. Granstar® 75 DF is one of the most used sulfonylurea herbicides on cereal crops; it contains 75% of tribenuron-methyl. Assessing the changes on soil microbiota, particularly on the most abundant bacterial groups, will be a useful approach to determine the impact of Granstar® herbicide. For this purpose, we analyzed Actinobacteria, which are known for their diversity, abundance, and aptitude to resist to xenobiotic substances. Using a selective medium for Actinobacteria, 42 strains were isolated from both untreated and Granstar® treated soils. The number of isolates recovered from the treated agricultural soil was fewer than that isolated from the corresponding untreated soil, suggesting a negative effect of Granstar® herbicide on Actinobacteria community. Even so, the number of strains isolated from untreated and treated forest soil was quite similar. Among the isolates, resistant strains, tolerating high doses of Granstar® ranging from 0.3 to 0.6% (v/v), were obtained. The two most resistant strains (SRK12 and SRK17) were isolated from treated soils showing the importance of prior exposure to herbicides for bacterial adaptation. SRK12 and SRK17 strains showed different morphological features. The phylogenetic analysis, based on 16S rRNA gene sequencing, clustered the SRK12 strain with four Streptomyces type strains (S. vinaceusdrappus, S. mutabilis, S. ghanaensis and S. enissocaesilis), while SRK17 strain was closely related to Streptomyces africanus. Both strains were unable to grow on tribenuron methyl as unique source of carbon, despite its advanced dissipation. On the other hand, when glucose was added to tribenuron methyl, the bacterial development was evident with even an improvement of the tribenuron methyl degradation. In all cases, as tribenuron methyl disappeared, two compounds were detected with increased concentrations. These by-products appeared to be persistent and were not degraded either chemically or by the studied strains. Based on these observations, we suggested that bacterial activity on carbon substrates could be directly involved in the partial breakdown of tribenuron methyl, by generating the required acidity for the first step of the hydrolysis. Such a process would be interesting to consider in bioremediation of neutral and alkaline tribenuron methyl-polluted soils.