Degradation of 3,5,6-trichloro-2-pyridinol by a microbial consortium in dryland soil with anaerobic incubation

Exploring the biodegradation activity of Priestia aryabhattai 1-3I, a promising chlorpyrifos-degrading strain isolated from a local phosphogypsum landfill

The current study emphasizes the potential of the microbial community within phosphogypsum landfills to identify promising microorganisms involved in Chlorpyrifos (CP) biodegradation, an organophosphorus pesticide extensively employed in the agricultural sector. We isolated 26 bacterial strains from CP-enriched phosphogypsum sample contaminated with 100 mg Kg-1 CP and subsequently identified them through 16S rRNA sequencing. Among these isolates, Priestia aryabhattai 1-3I displayed remarkable proficiency in utilizing CP as a sole carbon source. Furthermore, P. aryabhattai 1-3I was found to harbor an oph-encoding gene, a crucial component in the CP degradation pathway, with a highly conserved 694 bp region shared by at least 24 homologous oph bacterial genes. The CP-degrading ability of P. aryabhattai 1-3I was assessed both in liquid medium and soil samples, achieving degradation rates of 95 % and 60 %, respectively, starting from an initial concentration of 100 mg L-1 CP after 4 weeks. This pronounced CP-degrading activity correlated with a rapid and significant increase in oph transcripts and was accompanied by a notable rise in the accumulation of a major protein band with a molecular weight of 39 kDa, consistent with the molecular weight of previously characterized oph proteins. Of particular interest, the toxicity of CP degradation products resulting from both CP-bacterial biodegradation experiments exhibited minimal effects on neural cells, as indicated by acetylcholinesterase (AChE) activity and cell viability, underscoring the safety of CP-metabilties. Our study underscores the exceptional biodegradation capability of P. aryabhattai 1-3I in breaking down CP in soil, highlighting its potential for effective remediation of CP-contaminated environments.

Photo-aging promotes the inhibitory effect of polystyrene microplastics on microbial reductive dechlorination of a polychlorinated biphenyl mixture (Aroclor 1260)

Polychlorinated biphenyls (PCBs) and microplastics (MPs) commonly co-exist in various environments. MPs inevitably start aging once they enter environment. In this study, the effect of photo-aged polystyrene MPs on microbial PCB dechlorination was investigated. After a UV aging treatment, the proportion of oxygen-containing groups in MPs increased. Photo-aging promoted the inhibitory effect of MPs on microbial reductive dechlorination of PCBs, mainly attributed to the inhibition of meta-chlorine removal. The inhibitory effects on hydrogenase and adenosine triphosphatase activity by MPs increased with increasing aging degree, which may be attributed to electron transfer chain inhibition. PERMANOVA showed significant differences in microbial community structure between culturing systems with and without MPs (p < 0.05). Co-occurrence network showed a simpler structure and higher proportion of negative correlation in the presence of MPs, especially for biofilms, resulting in increased potential for competition among bacteria. MP addition altered microbial community diversity, structure, interactions, and assembly processes, which was more deterministic in biofilms than in suspension cultures, especially regarding the bins of Dehalococcoides. This study sheds light on the microbial reductive dechlorination metabolisms and mechanisms where PCBs and MPs co-exist and provides theoretical guidance for in situ application of PCB bioremediation technology.

Dissipation kinetics of chlorpyrifos and 3,5,6 trichloro-2-pyridinol under vegetation of different aromatic grasses: Linkage with enzyme kinetics and microbial community of soil

The dissipation of chlorpyrifos (CP) and its hydrolytic metabolite 3,5,6-trichloro-2-pyridinol (TCP) in the soil is crucial for safe agriculture. However, there is still lacking relevant information about its dissipation under different vegetation for remediation purposes. In the present study, evaluation of dissipation of CP and TCP in non-planted and planted soil with different cultivars of three types of aromatic grass viz Cymbopogon martinii (Roxb. Wats), Cymbopogon flexuosus, and Chrysopogon zizaniodes (L.) Nash was examined in light of soil enzyme kinetics, microbial communities, and root exudation. Results revealed that the dissipation of CP was well-fitted into a single first-order exponential model (SFO). A significant reduction in the half-life (DT₅₀) of CP was observed in planted soil (30-63 days) than in non-planted soil (95 days). The presence of TCP in all soil samples was observed. The three types of the inhibitory effect of CP i.e. linear mixed inhibition (increase in enzyme-substrate affinity (Km) and decrease in enzyme pool (Vmax), un-competitive inhibition (decrease in Km and Vmax), and simple competitive inhibition were observed on soil enzymes involved in mineralization of carbon, nitrogen, phosphorus, and sulfur. The improvement in the enzyme pool (Vmax) was observed in planted soil. Streptomyces, Clostridium, Kaistobacter, Planctomyces, and Bacillus were the dominant genera in CP stress soil. CP contamination in soil demonstrated a reduction of richness in microbial diversity and enhancement of functional gene family related to cellular process, metabolism, genetic, and environmental information processing. Among all the cultivars, C. flexuosus cultivars demonstrated a higher dissipation rate of CP along with more root exudation.

Identification of two possible metabolic pathways responsible for the biodegradation of 3, 5, 6-trichloro-2-pyridinol in Micrococcus luteus ML

3, 5, 6-Trichloro-2-pyridinol (TCP) is a metabolite of the insecticide chlorpyrifos and the herbicide triclopyr, and it is higher toxic than the parent compounds. Microbially-mediated mineralization appears to be the primary degradative pathway and the important biological process of detoxification. However, little information is available on TCP complete metabolic pathways and mechanisms. In this study, the degradation of TCP was studied with a novel strain Micrococcus luteus ML isolated from a stable TCP degrading microbiota. Strain ML was capable of degrading 61.6% of TCP (50 mg/L) and 35.4% of chlorpyrifos (50 mg/L) at 24 h and 48 h under the optimal conditions (temperature: 35 °C; pH: 7.0), respectively. It could also degrade 3, 5-dichloro-2-pyridone, 6-chloropyridin-2-ol, 2-hydroxypyridine and phoxim when provided as sole carbon and energy sources. Seven TCP intermediate metabolites were detected in strain ML and two possible degradation pathways of TCP were proposed on the basis of LC-MS analysis. Both the hydrolytic-oxidative dechlorination pathway and the denitrification pathway might be involved in TCP biodegradation by strain ML. To the best of our knowledge, this is the first report on two different pathways responsible for TCP degradation in one strain, and this finding also provides novel information for studying the metabolic mechanism of TCP in pure culture.

Assessing the fate of antibiotics and agrochemicals during anaerobic digestion of animal manure

Antibiotics and pesticides are used extensively by the livestock industry. Agricultural chemicals can pose potential human and environmental health risks due to their toxicity and through their contributions to antimicrobial resistance, and strategies to reduce their emission into the environment are urgently needed. Anaerobic digestion (AD) is a sustainable technology for manure management that produces biogas while also providing an opportunity to degrade agricultural chemicals that are present in manure. While the effects of selected chemicals on biogas production have been investigated previously, little is known about chemical transformations during AD. Using lab-scale AD batch reactors containing dairy manure, degradation kinetics and transformation products (TPs) were investigated for twenty compounds that are likely to be present in manure management systems and that we hypothesized would transform during AD. Digestate samples were extracted using a modified quick, easy, cheap, effective, rugged, and safe (QuEChERS) method and analyzed using liquid chromatography - high-resolution mass spectrometry. Eleven of the tested chemicals degraded, leading to the formation of 47 TPs. Three compounds degraded abiotically only, two degraded biotically only, and six degraded both abiotically and biotically. These results suggest that in addition to renewable energy generation, AD contributes to the degradation of chemical contaminants present in agricultural waste streams. However, the potential toxic effects of TPs require further investigation.

Diversity-triggered bottom-up trophic interactions impair key soil functions under lindane pollution stress

A growing amount of evidence suggests that microbial diversity loss may have negative effects on soil ecosystem function. However, less attention has been paid to the determinants of the relationship between community diversity and soil functioning under pollution stress. Here we manipulated microbial diversity to observe how biotic and abiotic factors influenced soil multi-functions (e.g. lindane degradation, soil respiration and nutrient cycling). Results showed that protist community was more sensitive to dilution, pollution stress, and sodium acetate addition than bacterial and fungal community. Acetate addition accelerated the lindane removal. Any declines in microbial diversity reduced the specialized soil processes (NO₃-N production, and N₂O flux), but increased soil respiration rate. Dilution led to a significant increase in consumers-bacterial and fungi-bacterial interaction as evidenced by co-occurrence network, which possibly played roles in maintaining microbiome stability and resilience. Interestingly, pollution stress and resource availability weaken the relationship between microbial diversity and soil functions through the bottom-up trophic interaction and environmental preference of soil microbiome. Overall, this work provides experimental evidence that loss in microbial diversity, accompanied with changes in trophic interactions mediated biotic and abiotic factors, could have important consequences for specialized soil functioning in farmland ecosystems.

Towards the Development of Microbial Ecotoxicology Testing Using Chlorpyrifos Contaminated Sediments and Marine Yeast Isolates as a Model

Chlorpyrifos (CP), a widely used pesticide, and its metabolite 3,5,6-trichloro-2-pyridinol (3,5,6-TCP), are xenobiotic compounds detected in many biomes, notably in marine sediments, all over the world. These compounds are posing a serious environmental and health problem given their toxicity to wildlife and possible exposure effects to human neurodevelopment. Microorganisms at CP-impacted environments could harbor metabolic capabilities that can be used as indicators of the biological effects of the contaminant and could encode selected functions reactive against contaminants. Those features could be used for microbial ecotoxicology applications by collectively using analytical, enzymatic, microbiological and toxicological techniques in order to assess the biological effects of pollutants and other environmental/climatic stressors in ecosystems. The objective of this study was to assess the variability in the metabolic responses of yeast isolates from CP-contaminated marine sediments as potential biological indicators for microbial ecotoxicology testing. Sediment samples from a South Caribbean tropical shore (Cartagena Bay, Colombia) were collected, and deoxyribonucleic acid (DNA) was recovered from lyophilized aliquots. The DGGE (Denaturing Gradient Gel Electrophoresis) technique targeting fungal Internal Transcribed Spacer (ITS) showed the great diversity of fungal types. Simultaneously, yeast strains were isolated from the freshly collected sediment samples. Physiological characterization including API 20C and antibiosis tests, growth patterns at salt concentrations (2/4/10/25%), temperatures (4/25/37/45 °C), esterase activity assay and resistance tests to CP/TCP toxicity resulted in 10 isolated yeast strains, identified as Candida spp. (6), Cryptococcus spp. (3). and Rhodotorula spp. (1), showing promising characteristics to be used as a test for yeast-based ecotoxicity indicators. The patterns of carbohydrate assimilation, low antibiosis, presence of esterases/lipases, growth in a wide range of temperatures and salt concentrations, and tolerance to minimal inhibitory concentrations of CP and TCP are factors useful for testing environmental samples.

Toxicity evaluation of chlorpyrifos and its main metabolite 3,5,6-trichloro-2-pyridinol (TCP) to Eisenia fetida in different soils

The present study utilized a biomarker response method to evaluate the effect of 3,5,6-trichloro-2-pyridinol (TCP) in artificial and natural soils on Eisenia fetida after 7, 14, 28, 42 and 56 days exposure. Results indicated that TCP induced excessive reactive oxygen species, caused oxidative stress and DNA damage to Eisenia fetida. Biomarker responses were standardized to calculate the Integrated Biomarker Response (IBR) index. The IBR index of three enzymes (superoxide dismutase, catalase and glutathione S-transferase) activities showed that TCP induced the oxidative stress to E. fetida in red clay was stronger than in the other three soils. Specifically, chlorpyrifos exposure group showed a lower toxicity than TCP exposure group after 28 days exposure but a higher toxicity than TCP exposure group after 56 days exposure. Despite the deficiencies of this study, the above information is of great significance for assessing the risk of chlorpyrifos and its metabolite TCP pollution in soil ecosystems.

Fate of chlorpyrifos bound residues in paddy soils: Release, transformation, and phytoavailability

Chlorpyrifos (CPF) is a widely used organophosphorus insecticide that tends to form bound residues (BRs) in soils. However, the stability and biological activity of CPF-BRs remain to be explored. Facilitated by carbon-14 tracing, this study obtained CPF-BRs initially formed in two typical paddy soils (14C-CPF-BRin), and further investigated their release, transformation and phytoavailability using duckweed (Lemna minor) as a model aquatic organism. Most 14C-CPF-BRin in soils were composed of the parent CPF and its metabolite 3,5,6-trichloro-2-pyridinol (2-OH-TCP), which was mainly formed through reversible entrapment by soil fulvic acids and humin (>80%). At 36 d, 66.67-80.90% of the 14C-CPF-BRin was released, of which only 2-OH-TCP could be released into the water and absorbed by the duckweed, with bioconcentration factors ranging from 247.99 to 324.68 L kg-1. The subsequent metabolism of released 14C-CPF-BRin in duckweed included phase I metabolism from 2-OH-TCP to 4-OH-TCP and phase II metabolism of conjugation of TCP with plant endogenous amino acids. The study suggested that CPF bound residues have high bioavailability in paddy field environments. Given that many pesticides and non-pesticide chemicals share structures analogous to CPF, the findings have important implications for better understanding the environmental and human health risks of man-made chemicals.

Reducing the Environmental Risk of Chlorpyrifos Application through Appropriate Agricultural Management: Evidence from Carbon-14 Tracking

Chlorpyrifos (CPF) is one of the most critical insecticides in the world. However, many countries are gradually banning its use due to its reported hazardous impacts on humans. This study explored the possibility of reducing the environmental risk of CPF through appropriate agricultural management practices. Results showed that the environmental risk of CPF is lower under drainage conditions because there is more mineralization and less bound residues (BRs) than under submerged conditions. Bioaugmentation significantly enhanced the CPF mineralization and inhibited the formation of CPF-BRs. Biochar adsorbed CPF and thus reduced its bioavailability, but it could not completely eliminate the toxicity of CPF. In addition, bioaugmentation did not significantly affect the native microbial community of CPF-contaminated soil, suggesting its safety in reducing the environmental risk of CPF. The study indicated that the environmental risk of CPF could be reduced by appropriate agricultural management such as water management, bioaugmentation, soil biochar amendment, and selecting suitable soil types.

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.

Community diversity metrics, interactions, and metabolic functions of bacteria associated with municipal solid waste landfills at different maturation stages

Municipal landfills are hot spots of dynamic bioprocesses facilitated by complex interactions of a multifaceted microbiome, whose functioning in municipal landfills at different maturing stages is poorly understood. This study determined bacterial community composition, interaction conetworks, metabolic functions, and controlling physicochemical properties in two landfills aged 14 and 36 years. High throughput sequencing revealed a similar distribution of bacterial diversity, evenness, and richness in the 14‐ and 36‐year‐old landfills in the 0–90 cm depth. At deeper layers (120–150 cm), the 14‐year‐old landfill had significantly greater bacterial diversity and richness indicating that it is a more active microcosm than the 36‐year‐old landfill, where phylum Epsilonbacteraeota was overwhelmingly dominant. The taxonomic and functional diversity in the 14‐year‐old landfill was further reflected by the abundant presence of indicator genera Pseudomonas,Lutispora,Hydrogenspora, and Sulfurimonas coupled with the presence of biomarker enzymes associated with carbon (C), nitrogen (N), and sulfur (S) metabolism. Furthermore, canonical correspondence analysis revealed that bacteria in the 14‐year‐old landfill were positively correlated with high C, N, S, and phosphorus resulting in positive cooccurrence interactions. In the 36‐year‐old landfill, negative coexclusion interactions populated by members of N fixing Rhizobiales were dominant, with metabolic functions and biomarker enzymes predicting significant N fixation that, as indicated by interaction network, potentially inhibited ammonia‐intolerant bacteria. Overall, our findings show that diverse bacterial community in the 14‐year‐old landfill was dominated by copiotrophs associated with positive conetworks, whereas the 36‐year‐old landfill was dominated by lithotrophs linked to coexclusion interactions that greatly reduced bacterial diversity and richness.