Bioaugmentation of acetamiprid-contaminated soil with Pigmentiphaga sp. strain D-2 and its effect on the soil microbial community

Experimental and computational approaches to characterize a novel amidase that initiates the biodegradation of the herbicide propanil in Bosea sp. P5

The herbicide propanil and its major metabolite 3,4-dichloroaniline (3,4-DCA) are difficult to biodegrade and pose great health and environmental risks. However, studies on the sole or synergistic mineralization of propanil by pure cultured strains are limited. A two-strain consortium (Comamonas sp. SWP-3 and Alicycliphilus sp. PH-34), obtained from a swep-mineralizing enrichment culture that can synergistically mineralize propanil, has been previously reported. Here, another propanil degradation strain, Bosea sp. P5, was successfully isolated from the same enrichment culture. A novel amidase, PsaA, responsible for initial propanil degradation, was identified from strain P5. PsaA shared low sequence identity (24.0-39.7 %) with other biochemically characterized amidases. PsaA exhibited optimal activity at 30 °C and pH 7.5 and had k_cat and K_m values of 5.7 s^-1 and 125 μM, respectively. PsaA could convert the herbicide propanil to 3,4-DCA but exhibited no activity toward other herbicide structural analogs. This catalytic specificity was explained by using propanil and swep as substrates and then analyzed by molecular docking, molecular dynamics simulation and thermodynamic calculations, which revealed that Tyr138 is the key residue that affects the substrate spectrum of PsaA. This is the first propanil amidase with a narrow substrate spectrum identified, providing new insights into the catalytic mechanism of amidase in propanil hydrolysis.

Enhanced remediation of oil-contaminated intertidal sediment by bacterial consortium of petroleum degraders and biosurfactant producers

Oil pollution in intertidal zones is an important environmental issue that has serious adverse effects on coastal ecosystems. This study investigated the efficacy of a bacterial consortium constructed from petroleum degraders and biosurfactant producers in the bioremediation of oil-polluted sediment. Inoculation of the constructed consortium significantly enhanced the removal of C₈-C₄₀n-alkanes (80.2 ± 2.8% removal efficiency) and aromatic compounds (34.4 ± 10.8% removal efficiency) within 10 weeks. The consortium played dual functions of petroleum degradation and biosurfactant production, greatly improving microbial growth and metabolic activities. Real-time quantitative polymerase chain reaction (PCR) showed that the consortium markedly increased the proportions of indigenous alkane-degrading populations (up to 3.88-times higher than that of the control treatment). Microbial community analysis demonstrated that the exogenous consortium activated the degradation functions of indigenous microflora and promoted synergistic cooperation among microorganisms. Our findings indicated that supplementation of a bacterial consortium of petroleum degraders and biosurfactant producers is a promising bioremediation strategy for oil-polluted sediments.

Biodegradation of neonicotinoid insecticide acetamiprid by earthworm gut bacteria Brucella intermedium PDB13 and its ecotoxicity

Extensive use of neonicotinoid insecticides in recent decade had contaminated water and soil systems and poses serious environmental and health risk. Microbial degradation of toxic contaminants in the environment has been established as a sustainable tool towards its remediation. Under this context, the present study focused on the biodegradation of neonicotinoid insecticide acetamiprid, by bacterial strain Brucella intermedia PDB13 isolated from the gut of the acetamiprid exposed earthworms. To enhance acetamiprid biodegradation, suitable parameters such as pH, temperature, inoculum size and acetamiprid concentration range were optimised using Response Surface Methodology (RSM). The experimental results showed that the Brucella intermedium PDB13 can tolerate and degrade relatively high concentrations of acetamiprid (50 - 350 mg L^-1). The results confirmed that maximum degradation of about 89.72% was achieved under optimized conditions. Further, confirmation of acetamiprid biodegradation was assessed through the occurrence of its degraded metabolites through HPLC, FTIR, and LCMS analysis. Based on this analysis, possible acetamiprid biodegradation pathway by Brucella intermedia PDB13 was proposed. Additionally, cytotoxicity, earthworm acute toxicity, and zebrafish embryo toxicity studies were also performed to assess the toxicity variations between the parent compound and its metabolites. The acetamiprid treated group resulted in cytotoxic effects apparently, with the increase in aberrant cells frequency (22.5 ± 3.3), when compared with its metabolites (2.3 ± 4.3) and control (1.9 ± 5.6) respectively. All these results evidently reported the degradation potential of Brucella intermedia PDB13, thereby establishing the scope for further advanced biodegradation studies towards mitigating the pesticide pollution.

Combination of Aspergillus niger MJ1 with Pseudomonas stutzeri DSM4166 or mutant Pseudomonas fluorescens CHA0-nif improved crop quality, soil properties, and microbial communities in barrier soil

Soil salinization and acidification seriously damage soil health and restricts the sustainable development of planting. Excessive application of chemical fertilizer and other reasons will lead to soil acidification and salinization. This study focus on acid and salinized soil, investigated the effect of phosphate-solubilizing bacteria, Aspergillus niger MJ1 combined with nitrogen-fixing bacteria Pseudomonas stutzeri DSM4166 or mutant Pseudomonas fluorescens CHA0-nif on crop quality, soil physicochemical properties, and microbial communities. A total of 5 treatments were set: regular fertilization (T1), regular fertilization with MJ1 and DSM4166 (T2), regular fertilization with MJ1 and CHA0-nif (T3), 30%-reducing fertilization with MJ1 and DSM4166 (T4), and 30%-reducing fertilization with MJ1 and CHA0-nif (T5). It was found that the soil properties (OM, HN, TN, AP, AK, and SS) and crop quality of cucumber (yield production, protein, and vitamin C) and lettuce (yield production, vitamin C, nitrate, soluble protein, and crude fiber) showed a significant response to the inoculated strains. The combination of MJ1 with DSM4166 or CHA0-nif influenced the diversity and richness of bacterial community in the lettuce-grown soil. The organismal system-, cellular process-, and metabolism-correlated bacteria and saprophytic fungi were enriched, which were speculated to mediate the response to inoculated strains. pH, OM, HN, and TN were identified to be the major factors correlated with the soil microbial community. The inoculation of MJ1 with DSM4166 and CHA0-nif could meet the requirement of lettuce and cucumber growth after reducing fertilization in acid and salinized soil, which provides a novel candidate for the eco-friendly technique to meet the carbon-neutral topic.

Rapid biodegradation of atrazine by a novel Paenarthrobacter ureafaciens ZY and its effects on soil native microbial community dynamic

An atrazine-utilizing bacterium, designated as ZY, was isolated from agricultural soil and identified as Paenarthrobacter ureafaciens. The P. ureafaciens ZY demonstrated a significant degradation capacity of atrazine, with the degradation efficiency of 12.5 mg L^-1 h^-1 in liquid media (at pH 7, 30°C, and the atrazine level of 100 mg L^-1). The P. ureafaciens ZY contained three atrazine-degrading genes (i.e., trzN, atzB, and atzC) could metabolize atrazine to form cyanuric acid, which showed lower biotoxicity than the parent atrazine as predicted by Ecological Structure Activity Relationships model. A laboratory-scale pot experiment was performed to examine the degradation of atrazine by P. ureafaciens ZY inoculation and investigate its effects on the native microbial communities. The results exhibited that the P. ureafaciens ZY was conductive to the degradation of atrazine, increased the total soil phospholipid fatty acids at the atrazine level of 50, 70, and 100 mg kg^-1. By using high-throughput sequencing analysis, Frateuria, Dyella, Burkholderia-Caballeronia-Paraburkholderia were considered as the most important indigenous atrazine-degrading microorganisms due to their relative abundances were positively correlated with the atrazine degradation rate. In addition, P. ureafaciens ZY also increased the abundance of atrazine-degrading genus Streptomyces and Bacillus, indicating that there may be a synergic relationship between them in the process of atrazine degradation. Our work provides a new insight between inoculums and native microorganisms on the degradation of atrazine.

The fate of erythromycin in soils and its effect on soil microbial community structure

Erythromycin is one of the most commonly used macrolide antibiotics. However, little is known currently about the environmental behavior and fate of erythromycin in soils. Here erythromycin was ¹⁴C-labeled to investigate its degradation, mineralization and bound residues (BRs) in three typical agricultural soils. Results indicated the fate of ¹⁴C-erythromycin in soils varied greatly with soils types. Erythromycin was rapidly mineralized in black soil (BS) and fluvo-aquic soil (FS), whereas it rapidly formed large amounts of BRs in red soil (RS) with slow mineralization. At 120 d, about 90% of the introduced ¹⁴C-erythromycin was mineralized as ¹⁴CO₂ in BS and FS, but only 30% in RS. There was still a certain proportion of BRs in all soils, especially in RS, up to 50%. Erythromycin residues (ERs) may be underestimated if its residues are only assessed by extractable residues. We recommend to include a practical silylation procedure to quantify Type I BRs in regular erythromycin residue monitoring, which can be used as signal of the need to initiate further laboratory BRs experiments. The degradation of erythromycin was mainly attributed to soil microorganisms, which promote erythromycin mineralization and lead to the re-release of BRs. Microbial analysis showed that erythromycin persisted longer in soils with lower microbial diversity and richness. Erythromycin at 2.5 mg kg^-1 showed no significant impact on soil microbial diversity in all treatments, but caused changes in soil community composition. This study provides a reference for scientific evaluation and pollution remediation of erythromycin in soils.

Bioaugmentation of Atrazine-Contaminated Soil With Paenarthrobacter sp. Strain AT-5 and Its Effect on the Soil Microbiome

Atrazine, a triazine herbicide, is widely used around the world. The residue of atrazine due to its application in the fore-rotating crop maize has caused phytotoxicity to the following crop sweet potato in China. Bioaugmentation of atrazine-contaminated soil with atrazine-degrading strains is considered as the most potential method to remove atrazine from soil. Nevertheless, the feasibility of bioaugmentation and its effect on soil microbiome still need investigation. In this study, Paenarthrobacter sp. AT-5, an atrazine-degrading strain, was inoculated into agricultural soils contaminated with atrazine to investigate the bioaugmentation process and the reassembly of the soil microbiome. It was found that 95.9% of 5 mg kg⁻¹ atrazine was removed from the soils when inoculated with strain AT-5 with 7 days, and the phytotoxicity of sweet potato caused by atrazine was significantly alleviated. qRT-PCR analysis revealed that the inoculated strain AT-5 survived well in the soils and maintained a relatively high abundance. The inoculation of strain AT-5 significantly affected the community structure of the soil microbiome, and the abundances of bacteria associated with atrazine degradation were improved.