Nocardioides: “Specialists” for Hard-to-Degrade Pollutants in the Environment

Ma, Yecheng; Wang, Jinxiu; Liu, Yang; Wang, Xinyue; Zhang, Binglin; Zhang, Wei; Chen, Tuo; Liu, Guangxiu; Xue, Lingui; Cui, Xiaowen

doi:10.3390/molecules28217433

Cited by 11 publications

(3 citation statements)

References 111 publications

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“…Analyses using FAPROTAX and KEGG suggested that the increased abundances of Nocardioides and Rhodococcus were responsible for the biodegradation and metabolism of xenobiotics, particularly aromatic compounds, by Cyps and other enzymes (Figure c,d). The results obtained align with prior research indicating that Nocardioides and Rhodococcus , both categorized within the bacterial taxon Actinobacteria, possess unique advantages in the effective degradation of recalcitrant pollutants. − These findings reveal the participation of intestinal microbiota in 6PPDQ detoxification.…”

Section: Discussionsupporting

confidence: 86%

Tissue Accumulation and Biotransformation of 6PPD-Quinone in Adult Zebrafish and Its Effects on the Intestinal Microbial Community

Liao,

Chen,

Liu

et al. 2024

Environ. Sci. Technol.

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The pronounced lethality of N-(1,3-dimethylbutyl)-N′-phenyl-p-phenylenediamine quinone (6PPD-quinone or 6PPDQ) toward specific salmonids, while sparing other fish species, has received considerable attention. However, the underlying cause of this species-specific toxicity remains unresolved. This study explored 6PPDQ toxicokinetics and intestinal microbiota composition in adult zebrafish during a 14-day exposure to environmentally realistic concentrations, followed by a 7-day recovery phase. Predominant accumulation occurred in the brain, intestine, and eyes, with the lowest levels in the liver. Six metabolites were found to undergo hydroxylation, with two additionally undergoing O-sulfonation. Semiquantitative analyses revealed that the predominant metabolite featured a hydroxy group situated on the phenyl ring adjacent to the quinone. This was further validated by assessing enzyme activity and determining in silico binding interactions. Notably, the binding affinity between 6PPDQ and zebrafish phase I and II enzymes exceeded that with the corresponding coho salmon enzymes by 1.04−1.53 times, suggesting a higher potential for 6PPDQ detoxification in tolerant species. Whole-genome sequencing revealed significant increases in the genera Nocardioides and Rhodococcus after exposure to 6PPDQ. Functional annotation and pathway enrichment analyses predicted that these two genera would be responsible for the biodegradation and metabolism of xenobiotics. These findings offer crucial data for comprehending 6PPDQ-induced species-specific toxicity.

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Section: Discussionsupporting

confidence: 86%

Tissue Accumulation and Biotransformation of 6PPD-Quinone in Adult Zebrafish and Its Effects on the Intestinal Microbial Community

Liao,

Chen,

Liu

et al. 2024

Environ. Sci. Technol.

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“…Actinobacteria are oleophilic organisms frequently found in petroleum-contaminated soils (Nocardia genu) [ 77 ]. Nocardioides has a significantly higher degradation rate than other PAH-degrading bacteria and needs less time to break down these compounds [ 78 ]. Anaeromyxobacteraceae (Mixococcia) is an unusual myxobacterial genus that has been described in a wide variety of habitats due to its bioactive spectrum and secondary metabolites [ 79 ].…”

Section: Discussionmentioning

confidence: 99%

Bacterial Diversity in Old Hydrocarbon Polluted Sediments of Ecuadorian Amazon River Basins

Corral-García,

Molina,

Bautista

et al. 2024

Toxics

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The Ecuadorian Amazon rainforest stands out as one of the world’s most biodiverse regions, yet faces significant threats due to oil extraction activities dating back to the 1970s in the northeastern provinces. This research investigates the environmental and societal consequences of prolonged petroleum exploitation and oil spills in Ecuador’s Amazon. Conducted in June 2015, the study involved a comprehensive analysis of freshwater sediment samples from 24 locations in the Rio Aguarico and Napo basins. Parameters such as water and air temperature, conductivity, soil pH, and hydrocarbon concentrations were examined. Total petroleum hydrocarbon (TPH) concentrations ranged from 9.4 to 847.4 mg kg−1, with polycyclic aromatic hydrocarbon (PAH) levels varying from 10.15 to 711.1 mg kg−1. The pristane/phytane ratio indicated historic hydrocarbon pollution in 8 of the 15 chemically analyzed sediments. Using non-culturable techniques (Illumina), bacterial analyses identified over 350 ASV, with prominent families including Comamonadaceae, Chitinophagaceae, Anaeromyxobacteraceae, Sphingomonadaceae, and Xanthobacteraceae. Bacterial diversity, assessed in eight samples, exhibited a positive correlation with PAH concentrations. The study provides insights into how microbial communities respond to varying levels of hydrocarbon pollution, shedding light on the enduring impact of oil exploitation in the Amazonian region. Its objective is to deepen our understanding of the environmental and human well-being in the affected area, underscoring the pressing need for remedial actions in the face of ongoing ecological challenges.

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“…The use of a large number of chemical pesticides, insecticides, fungicides, bactericides, and soil fumigants has a negative impact on soil, water resources, air, and human health ( Deng et al, 2019 ). It is reported that Blastococcus , Solirubrobacter , Gemmatimonas , among others, have the ability to degrade pesticides ( Du et al, 2022 ), while Nocardioides can withstand various low-nutrient conditions and concurrently degrade pollutants ( Ma et al, 2023 ). We observed that the relative abundances of Blastococcus, Nocardioides, Solirubrobacter , and Gemmatimonas in the rhizosphere soil samples of Akihime were significantly higher than those of F. nilgerrensis ( p < 0.05).…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of the microbiomes of strawberry wild species Fragaria nilgerrensis and cultivated variety Akihime using amplicon-based next-generation sequencing

Wang,

Dai,

et al. 2024

Front. Microbiol.

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Fragaria nilgerrensis is a wild strawberry species widely distributed in southwest China and has strong ecological adaptability. Akihime (F. × ananassa Duch. cv. Akihime) is one of the main cultivated strawberry varieties in China and is prone to infection with a variety of diseases. In this study, high-throughput sequencing was used to analyze and compare the soil and root microbiomes of F. nilgerrensis and Akihime. Results indicate that the wild species F. nilgerrensis showed higher microbial diversity in nonrhizosphere soil and rhizosphere soil and possessed a more complex microbial network structure compared with the cultivated variety Akihime. Genera such as Bradyrhizobium and Anaeromyxobacter, which are associated with nitrogen fixation and ammonification, and Conexibacter, which is associated with ecological toxicity resistance, exhibited higher relative abundances in the rhizosphere and nonrhizosphere soil samples of F. nilgerrensis compared with those of Akihime. Meanwhile, the ammonia-oxidizing archaea Candidatus Nitrososphaera and Candidatus Nitrocosmicus showed the opposite tendencies. We also found that the relative abundances of potential pathogenic genera and biocontrol bacteria in the Akihime samples were higher than those in the F. nilgerrensis samples. The relative abundances of Blastococcus, Nocardioides, Solirubrobacter, and Gemmatimonas, which are related to pesticide degradation, and genus Variovorax, which is associated with root growth regulation, were also significantly higher in the Akihime samples than in the F. nilgerrensis samples. Moreover, the root endophytic microbiomes of both strawberry species, especially the wild F. nilgerrensis, were mainly composed of potential biocontrol and beneficial bacteria, making them important sources for the isolation of these bacteria. This study is the first to compare the differences in nonrhizosphere and rhizosphere soils and root endogenous microorganisms between wild and cultivated strawberries. The findings have great value for the research of microbiomes, disease control, and germplasm innovation of strawberry.

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Nocardioides: “Specialists” for Hard-to-Degrade Pollutants in the Environment

Cited by 11 publications

References 111 publications

Tissue Accumulation and Biotransformation of 6PPD-Quinone in Adult Zebrafish and Its Effects on the Intestinal Microbial Community

Tissue Accumulation and Biotransformation of 6PPD-Quinone in Adult Zebrafish and Its Effects on the Intestinal Microbial Community

Bacterial Diversity in Old Hydrocarbon Polluted Sediments of Ecuadorian Amazon River Basins

Comparative analysis of the microbiomes of strawberry wild species Fragaria nilgerrensis and cultivated variety Akihime using amplicon-based next-generation sequencing

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