Unveiling the synergistic mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation for enhanced phenanthrene degradation in oil-contaminated soils

Dai, Yeliang; Li, Jibing; Wang, Shuang; Cai, Xixi; Zhao, Xuan; Cheng, Xianghui; Huang, Qihui; Yang, Xiumin; Luo, Chunling; Zhang, Gan

doi:10.1016/j.jhazmat.2023.133293

Cited by 13 publications

(3 citation statements)

References 75 publications

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“…Li et al, 2021;Thomas et al, 2019). SIP emerges as a potent tool for monitoring diverse functional microorganisms and their functional genes (Cramm, 2023;Dai et al, 2024;Zhao et al, 2022). Unlike previous studies using single-substrate approaches, our research pioneers the use of multi-isotope substrate labeling SIP to detect microbial communities degrading saturated and aromatic hydrocarbons (modeled with n-hexadecane and phenanthrene respectively) in various locations within an oil-contaminated area.…”

Section: Discussionmentioning

confidence: 99%

“…Li et al, 2020). 16S rRNA genes in DNA fractions from 12 C and 13 C microcosms were amplified using the 515F/806R primer set, cloned into pGEM-T plasmids, and sequenced following gel purification (Dai et al, 2024). A standard curve was established with 10-fold serial dilutions of recombinant E. coli sequences.…”

Section: Sip Microcosms Dna Ultracentrifugation and Real-time Quantit...mentioning

confidence: 99%

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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: Discussionmentioning

confidence: 99%

Section: Sip Microcosms Dna Ultracentrifugation and Real-time Quantit...mentioning

confidence: 99%

Metabolic Characterization and Geochemical Drivers of Active Hydrocarbon‐Degrading Microorganisms

Li,

Huang,

Cai

et al. 2024

JGR Biogeosciences

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“…In this study, we investigated active PAH-degrading bacteria in petroleum-contaminated soil using 13 C-labelled phenanthrene (PHE) as a metabolic tracer, based on its widespread occurrence in nature and unique fused-ring angular structure [ 21 , 22 ]. Through the innovative combination of RACS-SIP and genome-directed culture, we achieved the identification and cultivation of bacteria actively involved in PHE degradation within a real environment at the single-cell level.…”

Section: Introductionmentioning

confidence: 99%

Microbial consortium assembly and functional analysis via isotope labelling and single-cell manipulation of polycyclic aromatic hydrocarbon degraders

Li,

Luo,

Cai

et al. 2024

The ISME Journal

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Soil microbial flora constitutes a highly diverse and complex microbiome on Earth, often challenging to cultivation, with unclear metabolic mechanisms in situ. Here, we present a pioneering concept for the in situ construction of functional microbial consortia (FMCs) and introduce an innovative method for creating FMCs by utilising phenanthrene as a model compound to elucidate their in situ biodegradation mechanisms. Our methodology involves single-cell identification, sorting, and culture of functional microorganisms, resulting in the formation of a precise in situ FMC. Through RACS-SIP, we identified and isolated phenanthrene-degrading bacterial cells from Achromobacter sp. and Pseudomonas sp., achieving precise and controllable in situ consortia based on genome-guided cultivation. Our in situ FMC outperformed conventionally designed functional flora when tested in real soil, indicating its superior phenanthrene degradation capacity. We revealed that microorganisms with high degradation efficiency isolated through conventional methods may exhibit pollutant tolerance but lack actual degradation ability in natural environments. This finding highlights the potential to construct FMCs based on thorough elucidation of in situ functional degraders, thereby achieving sustained and efficient pollutant degradation. Single-cell sequencing linked degraders with their genes and metabolic pathways, providing insights regarding the construction of in situ FMCs. The consortium in situ comprising microorganisms with diverse phenanthrene metabolic pathways might offer distinct advantages for enhancing phenanthrene degradation efficiency, such as the division of labour and cooperation or communication among microbial species. Our approach underscores the importance of in situ, single-cell precision identification, isolation, and cultivation for comprehensive bacterial functional analysis and resource exploration, which can extend to investigate MFCs in archaea and fungi, clarifying FMC construction methods for element recycling and pollutant transformation in complex real-world ecosystems.

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Endophytic Bacillus species as multifaceted toolbox for agriculture, environment, and medicine

Singh,

Shukla,

Singh

2024

Environ Dev Sustain

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Unveiling the synergistic mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation for enhanced phenanthrene degradation in oil-contaminated soils

Cited by 13 publications

References 75 publications

Metabolic Characterization and Geochemical Drivers of Active Hydrocarbon‐Degrading Microorganisms

Metabolic Characterization and Geochemical Drivers of Active Hydrocarbon‐Degrading Microorganisms

Microbial consortium assembly and functional analysis via isotope labelling and single-cell manipulation of polycyclic aromatic hydrocarbon degraders

Endophytic Bacillus species as multifaceted toolbox for agriculture, environment, and medicine

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