Isolation of a bacterial consortium able to degrade the fungicide thiabendazole: the key role of a Sphingomonas phylotype

Soil microbial community fragmentation reveals indirect effects of fungicide exposure mediated by biotic interactions between microorganisms

Fungicides are used worldwide to improve crop yields, but they can affect non-target soil microorganisms which are essential for ecosystem functioning. Microorganisms form complex communities characterized by a myriad of interspecies interactions, yet it remains unclear to what extent non-target microorganisms are indirectly affected by fungicides through biotic interactions with sensitive taxa. To quantify such indirect effects, we fragmented a soil microbial community by filtration to alter biotic interactions and compared the effect of the fungicide hymexazol between fractions in soil microcosms. We postulated that OTUs which are indirectly affected would exhibit a different response to the fungicide across the fragmented communities. We found that hymexazol primarily affected bacterial and fungal communities through indirect effects, which were responsible for more than 75% of the shifts in relative abundance of the dominant microbial OTUs after exposure to an agronomic dose of hymexazol. However, these indirect effects decreased for the bacterial community when hymexazol doses increased. Our results also suggest that N-cycling processes such as ammonia oxidation can be impacted indirectly by fungicide application. This work sheds light on the indirect impact of fungicide exposure on soil microorganisms through biotic interactions, which underscores the need for higher-tier risk assessment. ENVIRONMENTAL IMPLICATION: In this study, we used a novel approach based on the fragmentation of the soil microbial community to determine to which extent fungicide application could indirectly affect fungi and bacteria through biotic interactions. To assess off-target effects of fungicide on soil microorganisms, we selected hymexazol, which is used worldwide to control a variety of fungal plant pathogens, and exposed arable soil to the recommended field rate, as well as to higher rates. Our findings show that at least 75% of hymexazol-impacted microbial OTUs were indirectly affected, therefore emphasizing the importance of tiered risk assessment.

Antifungal drugs in the aquatic environment: A review on sources, occurrence, toxicity, health effects, removal strategies and future challenges

Fungal infections pose a significant global health burden, resulting in millions of severe cases and deaths annually. The escalating demand for effective antifungal treatments has led to a rise in the wholesale distribution of antifungal drugs, which consequently has led to their release into the environment, posing a threat to ecosystems and human health. This article aims to provide a comprehensive review of the presence and distribution of antifungal drugs in the environment, evaluate their potential ecological and health risks, and assess current methods for their removal. Reviewed studies from 2010 to 2023 period have revealed the widespread occurrence of 19 various antifungals in natural waters and other matrices at alarmingly high concentrations. Due to the inefficiency of conventional water treatment in removing these compounds, advanced oxidation processes, membrane filtration, and adsorption techniques have been developed as promising decontamination methods.In conclusion, this review emphasizes the urgent need for a comprehensive understanding of the presence, fate, and removal of antifungal drugs in the environment. By addressing the current knowledge gaps and exploring future prospects, this study contributes to the development of strategies for mitigating the environmental impact of antifungal drugs and protecting ecosystems and human health.

Identification of sulfamethazine degraders in swine farm-impacted river and farmland: A comparative study of aerobic and anaerobic environments

Sulfonamides (SAs) are extensively used antibiotics in the prevention and treatment of animal diseases, leading to significant SAs pollution in surrounding environments. Microbial degradation has been proposed as a crucial mechanism for removing SAs, but the taxonomic identification of microbial functional guilds responsible for SAs degradation in nature remain largely unexplored. Here, we employed 13C-sulfamethazine (SMZ)-based DNA-stable isotope probing (SIP) and metagenomic sequencing to investigate SMZ degraders in three distinct swine farm wastewater-receiving environments within an agricultural ecosystem. These environments include the aerobic riparian wetland soil, agricultural soil, and anaerobic river sediment. SMZ mineralization activities exhibited significant variation, with the highest rate observed in aerobic riparian wetland soil. SMZ had a substantial impact on the microbial community compositions across all samples. DNA-SIP analysis demonstrated that Thiobacillus, Auicella, Sphingomonas, and Rhodobacter were dominant active SMZ degraders in the wetland soil, whereas Ellin6067, Ilumatobacter, Dongia, and Steroidobacter predominated in the agricultural soil. The genus MND1 and family Vicinamibacteraceae were identified as SMZ degrader in both soils. In contrast, anaerobic SMZ degradation in the river sediment was mainly performed by genera Microvirga, Flavobacterium, Dechlorobacter, Atopostipes, and families Nocardioidaceae, Micrococcaceae, Anaerolineaceae. Metagenomic analysis of 13C-DNA identified key SAs degradation genes (sadA and sadC), and various of dioxygenases, and aromatic hydrocarbon degradation-related functional genes, indicating their involvement in degradation of SMZ and its intermediate products. These findings highlight the variations of indigenous SAs oxidizers in complex natural habitats and emphasize the consideration of applying these naturally active degraders in future antibiotic bioremediation.

Anthelmintics in the environment: Their occurrence, fate, and toxicity to non-target organisms

Anthelmintics are drugs used for the treatment and prevention of diseases caused by parasitic worms (helminths). While the importance of anthelmintics in human as well as in veterinary medicine is evident, they represent emerging contaminants of the environment. Human anthelmintics are mainly used in tropical and sub-tropical regions, while veterinary anthelmintics have become frequently-occurring environmental pollutants worldwide due to intensive agri- and aquaculture production. In the environment, anthelmintics are distributed in water and soil in relation to their structure and physicochemical properties. Consequently, they enter various organisms directly (e.g. plants, soil invertebrates, water animals) or indirectly through food-chain. Several anthelmintics elicit toxic effects in non-target species. Although new information has been made available, anthelmintics in ecosystems should be more thoroughly investigated to obtain complex knowledge on their impact in various environments. This review summarizes available information about the occurrence, behavior, and toxic effect of anthelmintics in environment. Several reasons why anthelmintics are dangerous contaminants are highlighted along with options to reduce contamination. Negative effects are also outlined.

A core epiphytic bacterial consortia synergistically protect citrus from postharvest disease

Biological antagonists are a series of microbes that can control pathogens to reduce the incidence of disease or reduce symptoms. Herein, four varieties of citrus fruit were selected to perform an amplicon sequencing on their epiphytic microbiota to get a systematic understanding of them. Co-occurrence network, Venn, and LefSe analysis were performed to filter to 24 genera which represent the universality, specificity, and correlation among samples. Functional analysis hinted that the genes related to chitinase, which most of these 24 bacteria carry, might lead to a disease-suppressive phenotype. 115 strains of epiphytic bacteria were isolated, and the bacterial synthetic community was constructed by 8 strains. The in vivo test results indicated they were able to reduce pathogen development for a longer time than separate inoculation. Collectively, this study showed the disease control potential provided by native epiphytic bacteria of fruit and give a new strategy to sustainable agriculture.

Significance of microbial genome in environmental remediation

Environmental pollutants seriously threaten the ecosystem and health of various life forms, particularly with the rapid industrialization and emerging population. Conventionally physical and chemical strategies are being opted for the removal of these pollutants. Bioremediation, through several advancements, has been a boon to combat the existing threat faced today. Microbes with enzymes degrade various pollutants and utilize them as a carbon and energy source. With the existing demand and through several research explorations, Genetically Engineered Microorganisms (GEMs) have paved to be a successful approach to abate pollution through bioremediation. The genome of the microbe determines its biodegradative nature. Thus, methods including pure culture techniques and metagenomics are used for analyzing the genome of microbes, which provides information about catabolic genes. The information obtained along with the aid of biotechnology helps to construct GEMs that are cost-effective and safer thereby exhibiting higher degradation of pollutants. The present review focuses on the role of microbes in the degradation of environmental pollutants, role of evolution in habitat and adaptation of microbes, microbial degenerative genes, their pathways, and the efficacy of recombinant DNA (rDNA) technology for creating GEMs for bioremediation. The present review also provides a gist of existing GEMs for bioremediation and their limitations, thereby providing a future scope of implementation of these GEMs for a sustainable environment.

Biodegradation of anthelmintics in soils: does prior exposure of soils to anthelmintics accelerate their dissipation?

Anthelmintics (AHs) control animal infections with gastrointestinal nematodes. They reach soil through animal faeces deposited on soils or through manuring. Although soil constitutes a major AH sink, we know little about the mechanisms controlling their soil dissipation. We employed studies with fumigated and non-fumigated soils collected from 12 sheep farms with a variable record of albendazole (ABZ), ivermectin (IVM) and eprinomectin (EPM) use. From each farm, we collected soils from inside small ruminant barn facilities (series A, high exposure) and the associated grazing pastures (series B, low exposure). We asked the following questions: (a) What is the role of soil microorganisms in AH dissipation? (b) Does repeated exposure of soils to AHs lead to their accelerated biodegradation? (c) Which soil physicochemical properties control AH dissipation? Soil fumigation significantly retarded ABZ (DT₅₀ 1.9 and 4.33 days), IVM (34.5 and 108.7 days) and EPM dissipation (30 and 121 days) suggesting a key role of soil microorganisms in AH dissipation. No significant acceleration in AH dissipation was evident in soils from units with a record of the administration of AHs or in soil series A vs series B, suggesting that the level of prior exposure was not adequate to induce their enhanced biodegradation. Significant positive and negative correlations of soil total organic carbon (TOC) and ABZ and IVM dissipation, respectively, were observed. Soil adsorption of AHs increased in the order IVM > ABZ > EPM. TOC controlled soil adsorption of IVM and EPM, but not of ABZ, in support of the contrasting effect of TOC on IVM and ABZ dissipation.

Nutritional inter-dependencies and a carbazole-dioxygenase are key elements of a bacterial consortium relying on a Sphingomonas for the degradation of the fungicide thiabendazole

Thiabendazole (TBZ), is a persistent fungicide/anthelminthic and a serious environmental threat. We previously enriched a TBZ-degrading bacterial consortium and provided first evidence for a Sphingomonas involvement in TBZ transformation. Here, using a multi-omic approach combined with DNA-stable isotope probing (SIP) we verified the key degrading role of Sphingomonas and identify potential microbial interactions governing consortium functioning. SIP and amplicon sequencing analysis of the heavy and light DNA fraction of cultures grown on ¹³ C-labelled versus ¹² C-TBZ showed that 66% of the ¹³ C-labelled TBZ was assimilated by Sphingomonas. Metagenomic analysis retrieved 18 metagenome-assembled genomes with the dominant belonging to Sphingomonas, Sinobacteriaceae, Bradyrhizobium, Filimonas and Hydrogenophaga. Meta-transcriptomics/-proteomics and non-target mass spectrometry suggested TBZ transformation by Sphingomonas via initial cleavage by a carbazole dioxygenase (car) to thiazole-4-carboxamidine (terminal compound) and catechol or a cleaved benzyl ring derivative, further transformed through an ortho-cleavage (cat) pathway. Microbial co-occurrence and gene expression networks suggested strong interactions between Sphingomonas and a Hydrogenophaga. The latter activated its cobalamin biosynthetic pathway and Sphingomonas its cobalamin salvage pathway to satisfy its B12 auxotrophy. Our findings indicate microbial interactions aligning with the 'black queen hypothesis' where Sphingomonas (detoxifier, B12 recipient) and Hydrogenophaga (B12 producer, enjoying detoxification) act as both helpers and beneficiaries.

Isolation, characterization and industrial application of a Cladosporium herbarum fungal strain able to degrade the fungicide imazalil

Imazalil (IMZ) is an imidazole fungicide commonly used by fruit-packaging plants (FPPs) to control fungal infections during storage. Its application leads to the production of pesticide-contaminated wastewaters, which, according to the European Commission, need to be treated on site. Considering the lack of efficient treatment methods, biodepuration systems inoculated with tailored-made inocula specialized on the removal of such persistent fungicides appear as an appropriate solution. However, nothing is known about the biodegradation of IMZ. We aimed to isolate and characterize microorganisms able to degrade the recalcitrant fungicide IMZ and eventually to test their removal efficiency under near practical bioengineering conditions. Enrichment cultures from a soil receiving regular discharges of effluents from a FPP, led to the isolation of a Cladosporium herbarum strain, which showed no pathogenicity on fruits, a trait essential for its biotechnological exploitation in FPPs. The fungus was able to degrade up to 100 mg L^-1 of IMZ. However, its degrading capacity and growth was reduced at increasing IMZ concentrations in a dose-dependent manner, suggesting the involvement of a detoxification rather than an energy-gain mechanism in the dissipation of IMZ. The isolate could tolerate and gradually degrade the fungicides fludioxonil (FLD) and thiabendazole (TBZ), also used in FPPs and expected to coincide alongside IMZ in FPP effluents. The capacity of the isolate to remove IMZ in a practical context was evaluated in a benchtop immobilized-cell bioreactor fed with artificial IMZ-contaminated wastewater (200 mg L^-1). The fungal strain established in the reactor, completely dominated the fungal community and effectively removed >96% of IMZ. The bioreactor also supported a diverse bacterial community composed of Sphingomonadales, Burkholderiales and Pseudomonadales. Our study reports the isolation of the first IMZ-degrading microorganism with high efficiency to remove IMZ from agro-industrial effluents under bioengineering conditions.

Bioaugmentation of animal feces as a mean to mitigate environmental contamination with anthelmintic benzimidazoles

Anthelmintics are used to control infestations of ruminants by gastrointestinal nematodes. The limited metabolism of anthelmintics in animals result in their excretion in feces. These could be piled up in the floor of livestock farms, constituting a point source of environmental contamination, or used as manures in agricultural soils where they persist or move to water bodies. Hence the removal of anthelmintics from feces could mitigate environmental contamination. We hypothesized that a thiabendazole-degrading bacterial consortium would also degrade other benzimidazole anthelmintics like albendazole, fenbendazole, ricobendazole, mebendazole and flubendazole. In liquid culture tests the consortium was more effective in degrading compounds with smaller benzimidazole substituents (thiabendazole, albendazole, ricobendazole), rather than benzimidazoles with bulky substituents (fenbendazole, flubendazole, mebendazole). We then explored the bioaugmentation capacity of the consortium in sheep feces fortified with 5 and 50 mg kg^-1 of thiabendazole, albendazole and fenbendazole. Bioaugmentation enhanced the degradation of all compounds and its efficiency was accelerated upon fumigation of feces, in the absence of the indigenous fecal microbial community. The latter contributes to anthelmintics degradation as suggested by the significantly lower DT₅₀ values in fumigated vs non-fumigated, non-bioaugmented feces. Overall, bioaugmentation could be an efficient means to reduce environmental exposure to recalcitrant anthelmintic benzimidazoles.

Microbial approaches for remediation of pollutants: Innovations, future outlook, and challenges

Environmental contamination with persistent organic pollutants has emerged as a serious threat of pollution. Bioremediation is a key to eliminate these harmful pollutants from the environment and has gained the interest of researchers during the past few decades. Scientific knowledge upon microbial interactions with individual pollutants over the past decades has helped to abate environmental pollution. Traditional bioremediation approaches have limitations for their applications; hence, it is essential to discover new bioremediation approaches with biotechnological interventions for best results. The developments in various methodologies are expected to increase the efficiency of bioremediation techniques and provide environmentally sound strategies. This paper deals with the profiling of microorganisms present in polluted sites using various techniques such as culture-based approaches and omics-based approaches. Besides this, it also provides up-to-date scientific literature on the microbial electrochemical technologies which are nowadays considered as the best approach for remediation of pollutants. Detailed information about future outlook and challenges to evaluate the effect of various treatment technologies for remediation of pollutants has been discussed.

Biotechnological basis of microbial consortia for the removal of pesticides from the environment

The application of microbial strains as axenic cultures has frequently been employed in a diverse range of sectors. In the natural environment, microbes exist as multispecies and perform better than monocultures. Cell signaling and communication pathways play a key role in engineering microbial consortia, because in a consortium, the microorganisms communicate via diffusible signal molecules. Mixed microbial cultures have gained little attention due to the lack of proper knowledge about their interactions with each other. Some ideas have been proposed to deal with and study various microbes when they live together as a community, for biotechnological application purposes. In natural environments, microbes can possess unique metabolic features. Therefore, microbial consortia divide the metabolic burden among strains in the group and robustly perform pesticide degradation. Synthetic microbial consortia can perform the desired functions at naturally contaminated sites. Therefore, in this article, special attention is paid to the microbial consortia and their function in the natural environment. This review comprehensively discusses the recent applications of microbial consortia in pesticide degradation and environmental bioremediation. Moreover, the future directions of synthetic consortia have been explored. The review also explores the future perspectives and new platforms for these approaches, besides highlighting the practical understanding of the scientific information behind consortia.

Efficient biodegradation of DEHP by CM9 consortium and shifts in the bacterial community structure during bioremediation of contaminated soil

Di(2-ethylhexyl) phthalate (DEHP), the most extensively used plasticizer in plastic formulations, is categorized as a priority environmental contaminant with carcinogenic, teratogenic, and mutagenic toxicities. Many isolated microorganisms exhibit outstanding performance as pure cultures in the laboratory but are unable to cope with harsh environmental conditions in the field. In the present study, a microbial consortium (CM9) with efficient functionality was isolated from contaminated farmland soil. CM9 could consistently degrade 94.85% and 100.00% of DEHP (1000 mg/L) within 24 h and 72 h, respectively, a higher efficiency than those of other reported pure and mixed microorganism cultures. The degradation efficiencies of DEHP and di-n-butyl phthalate were significantly higher than those of dimethyl phthalate and diethyl phthalate (p < 0.05). The primary members of the CM9 consortium were identified as Rhodococcus, Niabella, Sphingopyxis, Achromobacter, Tahibacter, and Xenophilus. The degradation pathway was hypothesized to include both de-esterification and β-oxidation. In contaminated soil, bioaugmentation with CM9 and biochar markedly enhanced the DEHP removal rate to 87.53% within 42 d, compared to that observed by the indigenous microbes (49.31%) (p < 0.05). During simulated bioaugmentation, the dominant genera in the CM9 consortium changed significantly over time, indicating their high adaptability to soil conditions and contribution to DEHP degradation. Rhodococcus, Pigmentiphaga and Sphingopyxis sharply decreased, whereas Tahibacter, Terrimonas, Niabella, Unclassified_f_Caulobacteraceae, and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium showed considerable increases. These results provide a theoretical framework for the development of in situ bioremediation of phthalate (PAE)-contaminated soil by composite microbial inocula.

Characterization of Acetamiprid Biodegradation by the Microbial Consortium ACE-3 Enriched From Contaminated Soil

Microbial consortia are ubiquitous in nature and exhibit several attractive features such as sophisticated metabolic capabilities and strong environmental robustness. This study aimed to decipher the metabolic and ecological characteristics of synergistic interactions in acetamiprid-degrading consortia, suggesting an optimal scheme for bioremediation of organic pollutants. The microbial consortium ACE-3 with excellent acetamiprid-degrading ability was enriched from the soil of an acetamiprid-contaminated site and characterized using high-throughput sequencing (HTS). Consortium ACE-3 was able to completely degrade 50 mg⋅L^–1 acetamiprid in 144 h, and was metabolically active at a wide range of pH values (6.0–8.0) and temperatures (20–42°C). Furthermore, plausible metabolic routes of acetamiprid biodegradation by the consortium were proposed based on the identification of intermediate metabolites (Compounds I, II, III and IV). The findings indicated that the consortium ACE-3 has promising potential for the removal and detoxification of pesticides because it produces downstream metabolites (Compounds I and II) that are less toxic to mammals and insects than acetamiprid. Finally, Illumina HTS revealed that β Proteobacteria were the dominant group, accounting for 85.61% of all sequences at the class level. Among the more than 50 genera identified in consortium ACE-3, Sphingobium, Acinetobacter, Afipia, Stenotrophomonas, and Microbacterium were dominant, respectively accounting for 3.07, 10.01, 24.45, and 49.12% of the total population.

Bioaugmentation of thiabendazole-contaminated soils from a wastewater disposal site: Factors driving the efficacy of this strategy and the diversity of the indigenous soil bacterial community

The application of the fungicide thiabendazole (TBZ) in fruit packaging plants (FPP) results in the production of effluents which are often disposed in adjacent field sites. These require remediation to prevent further environmental dispersal of TBZ. We assessed the bioaugmentation potential of a newly isolated TBZ-degrading bacterial consortium in a naturally contaminated soil (NCS) exhibiting a natural gradient of TBZ levels (12000, 400, 250 and 12 mg kg^-1). The effect of aging on bioaugmentation efficacy was comparatively tested in a soil with similar physicochemical properties and soil microbiota, which was artificially, contaminated with the same TBZ levels (ACS). The impact of bioaugmentation and TBZ on the bacterial diversity in the NCS was explored via amplicon sequencing. Bioaugmentation effectively removed TBZ from both soils at levels up to 400 mg kg^-1 but failed at the highest contamination level (12000 mg kg^-1). Dissipation of TBZ in bioaugmented samples showed a concentration-dependent pattern, while aging of TBZ had a slight effect on bioaugmentation efficiency. Bioaugmentation had no impact on the soil bacterial diversity, in contrast to TBZ contamination. Soils from the hotspots of TBZ contamination (12000 mg kg^-1) showed a drastically lower α-diversity driven by the dominance of β- and γ-proteobacteria at the expense of all other bacterial phyla, especially Actinobacteria. Overall, bioaugmentation with specialized microbial inocula could be an effective solution for the recovery of disposal sites contaminated with persistent chemicals like TBZ.