Identifying the core bacterial and fungal communities within four agricultural biobeds used for the treatment of pesticide rinsates

A review on the management of rinse wastewater in the agricultural sector

Pesticides have become indispensable compounds to sustain global food production. However, a series of sustainable agricultural practices must be ensured to minimize health and environmental risks, such as eco-friendly cultivation techniques, the transition to biopesticides, appropriate hygiene measures, etc. Hygiene measures should include the management of rinse wastewater (RWW) produced when cleaning agricultural equipment and machinery contaminated with pesticides (among other pollutants), such as sprayers or containers. Although some technical guidelines encourage the reuse of RWW in agricultural fields, in many cases the application of specialized treatments is a more environmentally friendly option. Solar photocatalysis was found to be the most widely studied physical-chemical method, especially in regions with intense solar radiation, generally using catalysts such as TiO2, Na2S2O8, and H2O2, operating for relatively short treatment periods (usually from 10 min to 9 h) and requiring accumulated radiation levels typically ranging from 3000 to 10000 kJ m-2. Biological treatments seem to be particularly suitable for this application. Among them, biobed is a well-established and robust technology for the treatment of pesticide-concentrated water in some countries, with operating periods that typically range from 1 to 24 months, and with temperatures preferably close to 20 °C; but further research is required for its implementation in other regions and/or conditions. Solar photocatalysis and biobeds are the only two systems that have been tested in full-scale treatments. Alternatively, fungal bioremediation using white rot fungi has shown excellent efficiencies in the degradation of pesticides from agricultural wastewater. However, greater efforts should be invested in gathering more information to consolidate these technologies and expand their use in the agricultural sector.

Metabolic Profiling and Comparative Proteomic Insight in Respect of Amidases during Iprodione Biodegradation

The fungicide iprodione (IPR) (3-(3,5-dichlorophenyl) N-isopropyl-2,4-dioxoimidazolidine-1-carboxamide) is a highly toxic compound. Although IPR has been restricted, it is still being applied in many places around the world, constituting an environmental risk. The biodegradation of IPR is an attractive option for reducing its residues. In this study, we isolated thirteen IPR-tolerant bacteria from a biopurification system designed to treat pesticides. A study of biodegradation using different strains was comparatively evaluated, and the best degradation rate of IPR was presented by Achromobacter sp. C1 with a half-life (T1/2) of 9 days. Based on a nano-LC-MS/MS analysis for the strains, proteins solely expressed in the IPR treatment were identified by highlighting the strain Achromobacter sp. C1, with 445 proteins primarily involved in the biosynthesis of secondary metabolites and microbial metabolism in diverse environments. Differentially expressed protein amidases were involved in six metabolic pathways. Interestingly, formamidase was inhibited while other cyclases, i.e., amidase and mandelamide hydrolase, were overexpressed, thereby minimizing the effect of IPR on the metabolism of strain C1. The dynamic changes in the protein profiles of bacteria that degrade IPR have been poorly studied; therefore, our results offer new insight into the metabolism of IPR-degrading microorganisms, with special attention paid to amidases.

Using the Pesticide Toxicity Index to show the potential ecosystem benefits of on-farm biobeds

The influent and effluent of two single-cell biobeds (Province of Alberta, Canada) and two dual cell-biobeds (Province of Saskatchewan, Canada) were monitored during a number of growing seasons. A total of 59 unique pesticide active ingredients were detected, with all biobed influent samples (n = 54) and 93% of effluent samples (n = 54) containing pesticide mixtures. About one-half of the effluent samples in both single-cell (56%) and dual-cell (45%) biobeds contained active ingredients that have Groundwater Ubiquity Score (GUS) values >2.8 and so were more likely to move through the biomatrix materials into effluent. The Pesticide Toxicity Index (PTI) calculated for aquatic indicator species (i.e., vascular and nonvascular plants, invertebrates, and fish) was always larger for influent samples (e.g., median PTI >500 for invertebrates in dual-cell biobed) than effluent samples (i.e., median PTI <1). As such, this study demonstrates the potential ecosystem benefits of the broad adoption of on-farm biobeds in the Canadian Prairies for recycling tank rinsate as a strategy to accelerate a green economy. Although biobeds were highly effective in reducing the concentrations for pesticides with a wide range of soil organic carbon coefficient and half-life values, the biobed effectiveness was relatively poor for the herbicides clopyralid, diclofop, fluroxypyr, and imazethapyr. Clopyralid (3.02), fluroxypyr (3.70), and imazethapyr (3.90) all have relatively high GUS values (>2.8) and are thus more likely to be detected in effluent than active ingredients with smaller GUS values. This suggests that further improvements in biosystem design need to be made for optimizing the recycling of these pesticides.

Using biobeds for the treatment of fungicide-contaminated effluents from various agro-food processing industries: Microbiome responses and mobile genetic element dynamics

Agro-food processing industries generate large amounts of pesticide-contaminated effluents that pose a significant environmental threat if managed improperly. Biopurification systems like biobeds could be utilized for the depuration of these effluents although direct evidence for their efficiency are still lacking. We employed a column leaching experiment with pilot biobeds to (i) assess the depuration potential of biobeds against fungicide-contaminated effluents from seed-producing (carboxin, metalaxyl-M, fluxapyroxad), bulb-handling (thiabendazole, fludioxonil and chlorothalonil) and fruit-packaging (fludioxonil, imazalil) industries, (ii) to monitor microbial succession via amplicon sequencing and (iii) to determine the presence and dynamics of mobile genetic elements like intl1, IS1071, IncP-1 and IncP-1ε often associated with the transposition of pesticide-degrading genes. Biobeds could effectively retain (adsorbed but extractable with organic solvents) and dissipate (degraded and/or not extractable with organic solvents) the fungicides that were contained in the agro-industrial effluents with 93.1-99.98% removal efficiency in all cases. Lipophilic substances like fluxapyroxad were mostly retained in the biobed while more polar substances like metalaxyl-M and carboxin were mostly dissipated or showed higher leaching potential like metalaxyl-M. Biobeds supported a bacterial and fungal community that was not affected by fungicide application but showed clear temporal patterns in the different biobed horizons. This was most probably driven by the establishment of microaerophilic conditions upon water saturation of biobeds, as supported by the significant increase in the abundance of facultative or strict anaerobes like Chloroflexi/Anaerolinae, Acidibacter and Myxococcota. Wastewater application did not affect the dynamics of mobile genetic elements in biobeds whose abundance (intl1, IS1071, IncP-1ε) showed significant increases with time. Our findings suggest that biobeds could effectively decontaminate fungicide-contaminated effluents produced by agro-food industries and support a rather resilient microbial community.

Metagenomic and metatranscriptomic analysis reveals enrichment for xenobiotic-degrading bacterial specialists and xenobiotic-degrading genes in a Canadian Prairie two-cell biobed system

Biobeds are agriculture-based bioremediation tools used to safely contain and microbially degrade on-farm pesticide waste and rinsate, thereby reducing the negative environmental impacts associated with pesticide use. While these engineered ecosystems demonstrate efficient pesticide removal, the microbiomes in these environments remain largely understudied both taxonomically and functionally. This study used metagenomic and metatranscriptomic techniques to characterize the microbial community in a two-cell Canadian biobed system before and after a field season of pesticide application. These culture-independent approaches identified an enrichment of xenobiotic-degrading bacteria, such as Afipia, Sphingopyxis and Pseudomonas, and enrichment and transcription of xenobiotic-degrading genes, such as peroxidases, oxygenases, and hydroxylases, among others; we were able to directly link the transcription of these genes to Pseudomonas, Oligotropha, Mesorhizobium, Rhodopseudomonas, and Stenotrophomonas taxa.

Pesticide bioremediation in liquid media using a microbial consortium and bacteria-pure strains isolated from a biomixture used in agricultural areas

Microorganisms' role in pesticide degradation has been studied widely. Insitu treatments of effluents containing pesticides such as biological beds (biobeds) are efficient biological systems where biomixture (mixture of substrates) and microorganisms are the keys in pesticide treatment; however, microbial activity has been studied poorly, and its potential beyond biobeds has not been widely explored. In this study, the capacity of microbial consortium and bacteria-pure strains isolated from a biomixture (soil-straw; 1:1, v/v) used to treat agricultural effluents under real conditions were evaluated during a bioremediation process of five pesticides commonly used Yucatan Mexico. Atrazine, carbofuran, and glyphosate had the highest degradations (>90%) using the microbial consortium; 2,4-D and diazinon were the most persistent (DT50 = 8.64 and 6.63 days). From the 21 identified bacteria species in the microbial consortium, Pseudomonas nitroreducens was the most abundant (52%) according to identified sequences. For the pure strains evaluation 2,4-D (DT50 = 9.87 days), carbofuran (DT50 = 8.27 days), diazinon (DT50 = 8.80 days) and glyphosate (DT50 = 8.59 days) were less persistent in the presence of the mixed consortium (Ochrobactrum sp. DGG-1-3, Ochrobactrum sp. Ge-14, Ochrobactrum sp. B18 and Pseudomonas citronellolis strain ADA-23B). Time, pesticide, and strain type were significant (P < 0.05) in pesticide degradation, so this process is multifactorial. Microbial consortium and pure strains can be used to increase the biobed efficiency by inoculation, even in the remediation of soil contaminated by pesticides in agricultural areas.

Insights into the Function and Horizontal Transfer of Isoproturon Degradation Genes (pdmAB) in a Biobed System

Biobeds, designed to minimize pesticide point source contamination, rely mainly on biodegradation processes. We studied the interactions of a biobed microbial community with the herbicide isoproturon (IPU) to explore the role of the pdmA gene, encoding the large subunit of an N-demethylase responsible for the initial demethylation of IPU, via quantitative PCR (qPCR) and reverse transcription-PCR (RT-qPCR) and the effect of IPU on the diversity of the total bacterial community and its active fraction through amplicon sequencing of DNA and RNA, respectively. We further investigated the localization and dispersal mechanisms of pdmAB in the biobed packing material by measuring the abundance of the plasmid pSH (harboring pdmAB) of the IPU-degrading Sphingomonas sp. strain SH (previously isolated from the soil used in the biobed) compared with the abundance of the pdmA gene and metagenomic fosmid library screening. pdmA abundance and expression increased concomitantly with IPU mineralization, verifying its major role in IPU transformation in the biobed system. DNA- and RNA-based 16S rRNA gene sequencing analysis showed no effects on bacterial diversity. The pdmAB-harboring plasmid pSH showed a consistently lower abundance than pdmA, suggesting the localization of pdmAB in replicons other than pSH. Metagenomic analysis identified four pdmAB-carrying fosmids. In three of these fosmids, the pdmAB genes were organized in a well-conserved operon carried by sphingomonad plasmids with low synteny with pSH, while the fourth fosmid contained an incomplete pdmAB cassette localized in a genomic fragment of a Rhodanobacter strain. Further analysis suggested a potentially crucial role of IS6 and IS256 in the transposition and activation of the pdmAB operon.IMPORTANCE Our study provides novel insights into the interactions of IPU with the bacterial community of biobed systems, reinforces the assumption of a transposable nature of IPU-degrading genes, and verifies that on-farm biobed systems are hot spots for the evolution of pesticide catabolic traits.

Earthworms to improve glyphosate degradation in biobeds

In this work, earthworm effect on the efficiency of biobeds for glyphosate degradation was studied. Three biomixtures with and without the addition of earthworms (Eisenia fetida species) were evaluated. The initial concentration of glyphosate was 1000 mg/kg biomixture. Glyphosate and biological parameters were measured as a function of time. Earthworm survival, biomass, and reproduction were evaluated as well. All biomixtures that contain earthworms reached 90% of glyphosate degradation at 90 days in comparison with the biomixtures without earthworms that reached 80% approximately at the same time. Also, within the biomixtures that contained earthworms, glyphosate degradation rate was significantly higher in the one made up with soil and wheat stubble (Ws-E) showing excellent capacity for aminomethylphosphonic acid (AMPA) degradation, the main metabolite of glyphosate degradation. In addition, a study performed after the vermiremediation process showed that E. fetida can tolerate high glyphosate concentration without modifications in its life traits. It can be concluded that the use of E. fetida within the biobeds is an excellent combination to improve glyphosate and AMPA removal.

Pesticide-tolerant bacteria isolated from a biopurification system to remove commonly used pesticides to protect water resources

In this study, we selected and characterized different pesticide-tolerant bacteria isolated from a biomixture of a biopurification system that had received continuous applications of a pesticides mixture. The amplicon analysis of biomixture reported that the phyla Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were predominant. Six strains grew in the presence of chlorpyrifos and iprodione. Biochemical characterization showed that all isolates were positive for esterase, acid phosphatase, among others, and they were identified as Pseudomonas, Rhodococcus and Achromobacter based on molecular and proteomic analysis. Bacterial growth decreased as both pesticide concentrations increased from 10 to 100 mg L^-1 in liquid culture. The Achromobacter sp. strain C1 showed the best chlorpyrifos removal rate of 0.072–0.147 d^-1 a half-life of 4.7–9.7 d and a maximum metabolite concentration of 2.10 mg L^-1 at 120 h. On the other hand, Pseudomonas sp. strain C9 showed the highest iprodione removal rate of 0.100–0.193 d^-1 a half-life of 4–7 d and maximum metabolite concentration of 0.95 mg L^-1 at 48 h. The Achromobacter and Pseudomonas strains showed a good potential as chlorpyrifos and iprodione-degrading bacteria.

Expanding the use of biobeds: Degradation and adsorption of pesticides contained in effluents from seed-coating, bulb disinfestation and fruit-packaging activities

Agro-food industries that use pesticides constitute significant point sources for the contamination of natural water resources. Despite that, little is known about the treatment of their pesticide-contaminated effluents. Biobeds could be a possible solution for the depuration of these effluents. In this context, we explored the degradation and adsorption of pesticides used in seed-coating (carboxin (CBX), metalaxyl-M (MET-M), fluxapyroxad (FLX), fludioxonil (FLD)), bulb-dipping (chlorothalonil (CHT), thiabendazole (TBZ), FLD) and fruit-packaging activities (FLD) in a biomixture, used as biobed packing material, and in soil. The degradation of pesticides was tested individually and in mixtures relevant to their industrial use, while FLD was also tested at different concentrations (10, 20, and 150 mg kg^-1) representing its use in the different industries. CBX, FLD, and CHT, when applied individually, and all other pesticides when applied in mixtures, degraded more rapidly in biomixture than in soil. In most cases pesticides application in mixtures retarded their degradation. This was more pronounced in soil than in biomixture, especially for MET-M and FLD. CHT had the most prominent inhibitory effect on the degradation of TBZ and FLD. FLD degradation showed a dose-dependent pattern (DT₅₀ 42.4 days at 10 mg kg^-1 and 107.6 days at 150 mg kg^-1). All pesticides showed higher adsorption affinity in the biomixture (K_f = 3.23-123.3 g mL^-1) compared to soil (K_f = 1.15-31.2 g mL^-1). We provide initial evidence for the potential of the tested biomixture to remove pesticides contained in effluents produced by different agro-industrial activities. Tests in full-scale biobeds packed with this biomixture will unravel their full depuration potential for the treatment of these agro-industrial effluents.