Different acetonitrile degraders and degrading genes between anaerobic ammonium oxidation and sequencing batch reactor as revealed by stable isotope probing and magnetic-nanoparticle mediated isolation

Sun, Yujiao; Yin, Meng; Zheng, Danyang; Wang, Tiandai; Zhao, Xiaohui; Luo, Chunling; Li, Jibing; Liu, Yueqiao; Xu, Shangwei; Deng, Songqiang; Wang, Xinzi; Zhang, Dayi

doi:10.1016/j.scitotenv.2020.143588

Cited by 16 publications

(7 citation statements)

References 79 publications

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“…To identify active petroleum degraders in six Shengli Oilfield areas, the relative enrichment factor (REF) was calculated using Equation from previous studies (Y. Sun et al., 2021). Operational taxonomic units with REF >1.0 among the top 100 were selected as active degraders, followed by phylogenetic analysis as described previously (J. Li, Luo, Zhang, & Zhang, 2018).…”

Section: Methodsmentioning

confidence: 99%

Metabolic Characterization and Geochemical Drivers of Active Hydrocarbon‐Degrading Microorganisms

Li,

Huang,

Cai

et al. 2024

JGR Biogeosciences

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Understanding the metabolic characteristics and controlled geochemical factors of functional microorganisms in petroleum‐contaminated areas at different locations is pivotal for enhancing pollutant removal strategies. To address the existing research gap in this domain, we employed stable‐isotope‐probing (SIP) with multi‐isotope labeling substrates, combined with 16S amplicon sequencing, metagenomic sequencing, and geochemical factor analysis. Utilizing n‐hexadecane and phenanthrene as model compounds, our study revealed location‐specific differences in the composition of functional microorganisms. Despite these variances, key players such as Pseudomonas, Marinobacter, Alcanivorax, Ochrobactrum, and Sphingomonas consistently emerged as active degraders of n‐hexadecane and/or phenanthrene. Several genera, including Pseudomonas, Ochrobactrum, Alcanivorax, Nitriliruptoraceae, and Sphingobacterium, demonstrated versatility by effectively degrading both contaminants. SIP‐metagenomic binning facilitated the acquisition of genomes from key active degraders, such as Pseudomonas sp., Ochrobactrum sp., Sphingomonas sp., and Shinella sp. This enabled a comprehensive analysis of petroleum hydrocarbon degradation pathways and genes, encompassing PAH dioxygenase genes, alkB genes, phthalate, and salicylate‐related pathways. Environmental factor and variation partitioning analysis revealed that oil pollution significantly influences the functional microbial community (12%), followed by available potassium and available nitrogen. Geochemical parameters and geographic location independently explained 14% and 21% of total variations, respectively. Intriguingly, more than half (51%) of the variation in functional microbial community structure remains unexplained, possibly due to unmeasured environmental variables. Our study contributes valuable insights into the in situ bioremediation mechanism for petroleum‐contaminated soil, elucidating factors influencing functional microbial structures across locations. These findings provide a vital theoretical reference for in situ regulation and bioremediation of petroleum hydrocarbon pollution in diverse environmental contexts.

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Section: Methodsmentioning

confidence: 99%

Metabolic Characterization and Geochemical Drivers of Active Hydrocarbon‐Degrading Microorganisms

Li,

Huang,

Cai

et al. 2024

JGR Biogeosciences

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“…30,31 The active PHE degraders in SIP, MMI, and MMI−SIP treatments were determined by comparing the relative enrichment factor (REF) using eqs 1 and 2, as described in previous studies. 32…”

Section: Methodsmentioning

confidence: 99%

Identifying the Active Phenanthrene Degraders and Characterizing Their Metabolic Activities at the Single-Cell Level by the Combination of Magnetic-Nanoparticle-Mediated Isolation, Stable-Isotope Probing, and Raman-Activated Cell Sorting (MMI–SIP–RACS)

Zhang

et al. 2022

Environ. Sci. Technol.

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Magnetic-nanoparticle-mediated isolation coupled with stable-isotope probing (MMI−SIP) is a cultivation-independent higher-resolution approach for isolating active degraders in their natural habitats. However, it addresses the community level and cannot directly link the microbial identities, phenotypes, and in situ functions of the active degraders at the single-cell level within complex microbial communities. Here, we used 13 C-labeled phenanthrene as the target and developed a new method coupling MMI−SIP and Ramanactivated cell sorting (RACS), namely, MMI−SIP−RACS, to identify the active phenanthrene-degrading bacterial cells from polycyclic aromatic hydrocarbon (PAH)-contaminated wastewater. MMI−SIP− RACS significantly enriched the active phenanthrene degraders and successfully isolated the representative single cells. Amplicon sequencing analysis by SIP, 13 C shift of the single cell in Raman spectra, and the 16S rRNA gene from single cell sequencing via RACS confirmed that Novosphingobium was the active phenanthrene degrader. Additionally, MMI−SIP−RACS reconstructed the phenanthrene metabolic pathway and genes of Novosphingobium, including two novel genes encoding phenanthrene dioxygenase and naphthalene dioxygenase. Our findings suggested that MMI−SIP−RACS is a powerful method to efficiently and precisely isolate active PAH degraders from complex microbial communities and directly link their identities to functions at the single-cell level.

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“…This challenge was partially addressed by a study using magnetic nanoparticles (MNP) to assist isolation of active phenol degraders and compared to those identified through DNA-SIP application of 13 C-labeleld phenol ( Zhang et al., 2015 ). Subsequent applications of MNP with SIP and cell-sorting techniques have been reported to identify active acetonitrile degraders ( Sun et al., 2021 ) and phenanthrene degraders ( Li et al., 2018 , 2022 ). Yet, as magnetic Fe 3 O 4 nanoparticles have been shown toxicity to microbes ( Manke et al., 2013 ), this aspect needs to be thoroughly investigated to determine whether MNP can truly capture the targeted metabolically active microbes under various environmental conditions.…”

Section: Future Research Priorities and Trendmentioning

confidence: 99%

Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation

et al. 2023

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Different acetonitrile degraders and degrading genes between anaerobic ammonium oxidation and sequencing batch reactor as revealed by stable isotope probing and magnetic-nanoparticle mediated isolation

Cited by 16 publications

References 79 publications

Metabolic Characterization and Geochemical Drivers of Active Hydrocarbon‐Degrading Microorganisms

Metabolic Characterization and Geochemical Drivers of Active Hydrocarbon‐Degrading Microorganisms

Identifying the Active Phenanthrene Degraders and Characterizing Their Metabolic Activities at the Single-Cell Level by the Combination of Magnetic-Nanoparticle-Mediated Isolation, Stable-Isotope Probing, and Raman-Activated Cell Sorting (MMI–SIP–RACS)

Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation

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