New insight into the mechanisms of autochthonous fungal bioaugmentation of phenanthrene in petroleum contaminated soil by stable isotope probing

Dai, Yeliang; Li, Jibing; Yang, Xiu‐Wei; Wang, Shuang; Zhao, Xuan; Wang, Yujie; Zhang, Dayi; Luo, Chunling; Zhang, Gan

doi:10.1016/j.jhazmat.2023.131271

Cited by 14 publications

(6 citation statements)

References 73 publications

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“…Despite the satisfactory performance of several bioaugmentation applications to treat SA-containing wastewaters by the addition of exogenous degraders [ 17 , 18 , 47 ], no study has confirmed the activities or degrading capacities of the reintroduced strains in SA degradation. DNA-SIP has found successful applications in exploring active PAHs-degraders in bioaugmented soils [ 13 , 45 , 58 , 59 ], and this method can also help to unveil the mechanisms of promoting SMX removal by exogenous degraders. The present study for the first time revealed the mechanism of exogenous degrading bacteria in the bioaugmentation treatment of SMX.…”

Section: Discussionmentioning

confidence: 99%

“…M2 could promote SMX removal by stimulating the SMX-degrading activity of indigenous microorganisms ( Paenarthrobacter ) in the bacterial community. Previous reports on PAHs removal using bioaugmentation treatment also suggested that exogenous degrading bacteria enhanced the biodegradation of pollutants mainly by changing the composition and diversity of in situ degrading bacteria as well as co-metabolism with them, rather than directly participating in the metabolism of pollutants [ 13 , 45 , 58 ].The production of surfactants by exogenous bacteria, like Pseudomonas , was a possible reason for the activation of indigenous degrading bacteria [ 45 , 68 – 70 ]. Besides, Pseudomonas has been proven to catalyze the ipso -hydroxylation of sulfonamide based on pure culture experiments in our previous study [ 22 ]; thus, it could also achieve SMX assimilation by catalyzing the initial biotransformation of SMX and with the cooperation of other microorganisms.…”

Section: Discussionmentioning

confidence: 99%

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New insights into bioaugmented removal of sulfamethoxazole in sediment microcosms: degradation efficiency, ecological risk and microbial mechanisms

Chen,

Zhu

et al. 2024

Microbiome

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Background Bioaugmentation has the potential to enhance the ability of ecological technology to treat sulfonamide-containing wastewater, but the low viability of the exogenous degraders limits their practical application. Understanding the mechanism is important to enhance and optimize performance of the bioaugmentation, which requires a multifaceted analysis of the microbial communities. Here, DNA-stable isotope probing (DNA-SIP) and metagenomic analysis were conducted to decipher the bioaugmentation mechanisms in stabilization pond sediment microcosms inoculated with sulfamethoxazole (SMX)-degrading bacteria (Pseudomonas sp. M2 or Paenarthrobacter sp. R1). Results The bioaugmentation with both strains M2 and R1, especially strain R1, significantly improved the biodegradation rate of SMX, and its biodegradation capacity was sustainable within a certain cycle (subjected to three repeated SMX additions). The removal strategy using exogenous degrading bacteria also significantly abated the accumulation and transmission risk of antibiotic resistance genes (ARGs). Strain M2 inoculation significantly lowered bacterial diversity and altered the sediment bacterial community, while strain R1 inoculation had a slight effect on the bacterial community and was closely associated with indigenous microorganisms. Paenarthrobacter was identified as the primary SMX-assimilating bacteria in both bioaugmentation systems based on DNA-SIP analysis. Combining genomic information with pure culture evidence, strain R1 enhanced SMX removal by directly participating in SMX degradation, while strain M2 did it by both participating in SMX degradation and stimulating SMX-degrading activity of indigenous microorganisms (Paenarthrobacter) in the community. Conclusions Our findings demonstrate that bioaugmentation using SMX-degrading bacteria was a feasible strategy for SMX clean-up in terms of the degradation efficiency of SMX, the risk of ARG transmission, as well as the impact on the bacterial community, and the advantage of bioaugmentation with Paenarthrobacter sp. R1 was also highlighted.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

New insights into bioaugmented removal of sulfamethoxazole in sediment microcosms: degradation efficiency, ecological risk and microbial mechanisms

Chen,

Zhu

et al. 2024

Microbiome

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“…Accurately and comprehensively detecting functional microorganisms and their metabolic genes in petroleum hydrocarbon‐contaminated soil poses significant challenges for traditional methods (J. 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%

“…Ultracentrifugation at 47,500 rpm for 48 hr yielded 14 fractions, and DNA underwent ethanol precipitation for purification, quantification and amplicon sequencing (J. Li et al., 2019a; J. 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: Methodsmentioning

confidence: 99%

“…DNA was extracted using the PowerSoil DNA Isolation Kit. CsCl gradient ultracentrifugation was employed to separate DNA from the 12 C and 13 C microcosms based on the methods described previously (Dai et al, 2023;Zhao et al, 2022). Ultracentrifugation at 47,500 rpm for 48 hr yielded 14 fractions, and DNA underwent ethanol precipitation for purification, quantification and amplicon sequencing (J.…”

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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Bioremediation of petroleum-contaminated soil based on both toxicity risk control and hydrocarbon removal—progress and prospect

Wu,

Feng,

Liu

et al. 2024

Environ Sci Pollut Res

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New insight into the mechanisms of autochthonous fungal bioaugmentation of phenanthrene in petroleum contaminated soil by stable isotope probing

Cited by 14 publications

References 73 publications

New insights into bioaugmented removal of sulfamethoxazole in sediment microcosms: degradation efficiency, ecological risk and microbial mechanisms

New insights into bioaugmented removal of sulfamethoxazole in sediment microcosms: degradation efficiency, ecological risk and microbial mechanisms

Metabolic Characterization and Geochemical Drivers of Active Hydrocarbon‐Degrading Microorganisms

Bioremediation of petroleum-contaminated soil based on both toxicity risk control and hydrocarbon removal—progress and prospect

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