Unveiling the novel role of ryegrass rhizospheric metabolites in benzo[a]pyrene biodegradation

Synergistic effects of surfactant biostimulation and indigenous fungal bioaugmentation for enhanced bioremediation of PAH-contaminated soils

Surfactant biostimulation and autochthonous fungal bioaugmentation have emerged as promising strategies for the bioremediation of soils contaminated with polycyclic aromatic hydrocarbons (PAHs). However, the mechanisms driving their combined effects remain poorly understood. This study investigates the degradation mechanisms associated with bioaugmentation using the indigenous fungus Aspergillus fumigatus LJD-29 and surfactant Tween 80. By employing stable-isotope probing and high-throughput sequencing, we comprehensively assessed these processes. In our study, the results demonstrate that both Aspergillus fumigatus LJD-29 and Tween 80 significantly enhanced the degradation efficiency of phenanthrene and modified the microbial community composition, particularly among active degraders. Extracellular enzymes were identified as key players in the phenanthrene transformation process. Tween 80 improved the bioavailability of phenanthrene, stimulating the growth of native PAH degraders, with Pseudonocardia emerging as a prominent genus. Although the combined surfactant-fungal treatment did not substantially increase terminal degradation efficiency due to limitations in phenanthrene bioavailability, it accelerated the degradation rate. Additionally, Tween 80 helped restore the microbial community structure disrupted by fungal bioaugmentation. These findings provide valuable insights into the mechanisms of surfactant biostimulation and indigenous fungal bioaugmentation, highlighting the potential of this integrated bioremediation strategy for managing PAH-contaminated soils.

Single-Cell Analysis of Microbial Degradation Mechanisms and Remediation Potential for Emerging Pollutants: A Case Study on Methylnaphthalene

Polycyclic aromatic hydrocarbon (PAH) derivatives, including alkyl-PAHs, are significant emerging environmental contaminants. Traditional culture techniques often fail to isolate functional microorganisms responsible for their in situ degradation, leaving their metabolic interactions and pathways largely uncharacterized. This study employs 2-methylnaphthalene (MP) as a model compound and utilizes Raman-activated cell sorting with stable isotope probing (RACS-SIP) and single-cell genome sequencing to investigate alkyl-PAH degradation in petroleum-contaminated wastewater. RACS-SIP identified two key in situ MP-degrading microbes, Sphingomonas sp. and Pseudomonas sp., showing Raman shifts from 1001 to 968 cm-1 and 782 to 768 cm-1. Genome analysis linked these microorganisms to their specific genes and metabolic pathways, revealing distinct degradation mechanisms: Sphingomonas sp. hydroxylates nonmethyl-substituted aromatic rings, while Pseudomonas sp. utilizes both hydroxylation and methyl end oxidation. These findings were substantiated by functional gene quantification, emphasizing the potential of microbial consortia with diverse metabolic pathways to enhance degradation efficiency through cooperative interactions and reduced metabolic load. Moreover, the successful cultivation of RACS-sorted bacteria demonstrated superior pollutant removal compared to traditional methods. This study advances our understanding of microbial biotransformation of emerging contaminants and demonstrates the necessity of precisely identifying and cultivating in situ functional microorganisms to develop robust consortia for sustainable pollutant degradation.

Mechanism of microplastics promoting sulfamethoxazole biodegradation in activated sludge as revealed by DNA-stable isotope probing

Microplastics (MPs) often coexist with sulfonamide antibiotics (SAs) in the activated sludge of wastewater treatment plants (WWTPs). Microbial degradation is a crucial pathway for SAs removal in the activated sludge, though its response to MPs still yet to be disclosed. Here, we combined DNA-stable isotope probing (DNA-SIP), PICRUSt and MENA techniques to explore the impact of MPs on the microbial biodegradation of sulfamethoxazole (SMX) in the activated sludge. DNA-SIP revealed 20 genera were responsible for the SMX degradation in the activated sludge, with 13 of these genera being firstly linked with sulfonamide biodegradation. The potential SMX-degrading bacteria showed complex synergistic interaction with the other microbes. Eight degradation pathways were constructed based on the nine identified SMX-related degradation genes. MPs addition enhanced the SMX biodegradation by altering the structure of degrading microbes, increasing their relative abundance and promoting the synergistic interactions between potential SMX-degrading bacteria and other microbes in activated sludge. Besides, genes related to abundant energy production and biofilm formation were involved in SMX degradation in the activated sludge with MPs. Our study reveals the MPs influence on SMX biodegradation in activated sludge, and disclose the potential underlying mechanisms, which will benefit the regulation on antibiotic removal in WWTPs.

Silicate-based mineral materials promote submerged plant growth: Insights from plant physiology and microbiomes

Restoring submerged plants naturally has been a significant challenge in water ecology restoration programs. Some silicate-based mineral materials have shown promise in improving the substrate properties for plant growth. While it is well-established that silicate mineral materials enhance submerged plant growth by improving salt release and reducing salt stress, the influence of rhizosphere microorganisms on phytohormone synthesis and key enzyme activities has been underestimated. This study focused on two typical silicate mineral materials, bentonite and maifanite, to investigate their effects on Myriophyllum oguraense from both plant physiology and microbiome perspectives. The results demonstrated that both bentonite and maifanite regulated the synthesis of phytohormones such as gibberellin (GA) and methyl salicylate (MESA), leading to inhibition of cellular senescence and promotion of cell division. Moreover, these silicate mineral materials enhanced the activity of antioxidant enzymes, thereby reducing intracellular reactive oxygen species levels. They also optimized the structure of rhizosphere microbial communities, increasing the proportion of functional microorganisms like Nitrospirota and Sva0485, which indirectly influenced plant metabolism. Analysis of sediment physicochemical properties revealed increased rare earth elements, macronutrients, and oxygen content in pore water in the presence of silicate materials, creating favorable conditions for root growth. Overall, these findings shed light on the multifaceted mechanisms by which natural silicate mineral materials promote the growth of aquatic plants, offering a promising solution for restoring aquatic vegetation in eutrophic lake sediments.

SIP-metagenomics reveals key drivers of rhizospheric Benzo[a]pyrene bioremediation via bioaugmentation with indigenous soil microbes

Rhizoremediation and bioaugmentation have proven effective in promoting benzo[a]pyrene (BaP) degradation in contaminated soils. However, the mechanism underlying bioaugmented rhizospheric BaP degradation with native microbes is poorly understood. In this study, an indigenous BaP degrader (Stenotrophomonas BaP-1) isolated from petroleum-contaminated soil was introduced into ryegrass rhizosphere to investigate the relationship between indigenous degraders and rhizospheric BaP degradation. Stable isotope probing and 16S rRNA gene amplicon sequencing subsequently revealed 15 BaP degraders, 8 of which were directly associated with BaP degradation including Bradyrhizobium and Streptomyces. Bioaugmentation with strain BaP-1 significantly enhanced rhizospheric BaP degradation and shaped the microbial community structure. A correlation of BaP degraders, BaP degradation efficiency, and functional genes identified active degraders and genes encoding polycyclic aromatic hydrocarbon-ring hydroxylating dioxygenase (PAH-RHD) genes as the primary drivers of rhizospheric BaP degradation. Furthermore, strain BaP-1 was shown to not only engage in BaP metabolism but also to increase the abundance of other BaP degraders and PAH-RHD genes, resulting in enhanced rhizospheric BaP degradation. Metagenomic and correlation analyses indicated a significant positive relationship between glyoxylate and dicarboxylate metabolism and BaP degradation, suggesting a role for these pathways in rhizospheric BaP biodegradation. By identifying BaP degraders and characterizing their metabolic characteristics within intricate microbial communities, our study offers valuable insights into the mechanisms of bioaugmented rhizoremediation with indigenous bacteria for high-molecular-weight PAHs in petroleum-contaminated soils.

Synergism of endophytic microbiota and plants promotes the removal of polycyclic aromatic hydrocarbons from the Alfalfa rhizosphere

Endophytic bacteria can promote plant growth and accelerate pollutant degradation. However, it is unclear whether endophytic consortia (Consortium_E) can stabilize colonisation and degradation. We inoculated Consortium_E into the rhizosphere to enhance endophytic bacteria survival and promote pollutant degradation. Rhizosphere-inoculated Consortium_E enhanced polycyclic aromatic hydrocarbon (PAH) degradation rates by 11.5-13.1 % compared with sole bioaugmentation and plant treatments. Stable-isotope-probing (SIP) showed that the rhizosphere-inoculated Consortium_E had the largest number of degraders (8 amplicon sequence variants). Furthermore, only microbes from Consortium_E were identified among the degraders in bioaugmentation treatments, indicating that directly participated in phenanthrene metabolism. Interestingly, Consortium_E reshaped the community structure of degraders without significantly altering the rhizosphere community structure, and strengthened the core position of degraders in the network, facilitating close interactions between degraders and non-degraders in the rhizosphere, which were crucial for ensuring stable functionality. The synergistic effect between plants and Consortium_E significantly enhanced the upregulation of aromatic hydrocarbon degradation and auxiliary degradation pathways in the rhizosphere. These pathways showed a non-significant increasing trend in the uninoculated rhizosphere compared with the control, indicating that Consortium_E primarily promotes rhizosphere effects. Our results explore the Consortium_E bioaugmentation mechanism, providing a theoretical basis for the ecological restoration of contaminated soils.

Driving mechanisms for the adaptation and degradation of petroleum hydrocarbons by native microbiota from seas prone to oil spills

Offshore waters have a high incidence of oil pollution, which poses an elevated risk of ecological damage. The microbial community composition and metabolic mechanisms influenced by petroleum hydrocarbons vary across different marine regions. However, research on metabolic strategies for in-situ petroleum degradation and pollution adaptation remains in its nascent stages. This study combines metagenomic techniques with gas chromatography-mass spectrometry (GC-MS) analysis. The data show that the genera Pseudoalteromonas, Hellea, Lentisphaera, and Polaribacter exhibit significant oil-degradation capacity, and that the exertion of their degradation capacity is correlated with nutrient and oil pollution stimuli. Furthermore, tmoA, badA, phdF, nahAc, and fadA were found to be the key genes involved in the degradation of benzene, polycyclic aromatic hydrocarbons, and their intermediates. Key genes (INSR, SLC2A1, and ORC1) regulate microbial adaptation to oil-contaminated seawater, activating oil degradation processes. This process enhances the biological activity of microbial communities and accounts for the geographical variation in their compositional structure. Our results enrich the gene pool for oil pollution adaptation and degradation and provide an application basis for optimizing bioremediation intervention strategies.

Determination of soil phenanthrene degradation through a fungal-bacterial consortium

Fungal-bacterial consortia enhance organic pollutant removal, but the underlying mechanisms are unclear. We used stable isotope probing (SIP) to explore the mechanism of bioaugmentation involved in polycyclic aromatic hydrocarbon (PAH) biodegradation in petroleum-contaminated soil by introducing the indigenous fungal strain Aspergillus sp. LJD-29 and the bacterial strain Pseudomonas XH-1. While each strain alone increased phenanthrene (PHE) degradation, the simultaneous addition of both strains showed no significant enhancement compared to treatment with XH-1 alone. Nonetheless, the assimilation effect of microorganisms on PHE was significantly enhanced. SIP revealed a role of XH-1 in PHE degradation, while the absence of LJD-29 in 13C-DNA indicated a supporting role. The correlations between fungal abundance, degradation efficiency, and soil extracellular enzyme activity indicated that LJD-29, while not directly involved in PHE assimilation, played a crucial role in the breakdown of PHE through extracellular enzymes, facilitating the assimilation of metabolites by bacteria. This observation was substantiated by the results of metabolite analysis. Furthermore, the combination of fungus and bacterium significantly influenced the diversity of PHE degraders. Taken together, this study highlighted the synergistic effects of fungi and bacteria in PAH degradation, revealed a new fungal-bacterial bioaugmentation mechanism and diversity of PAH-degrading microorganisms, and provided insights for in situ bioremediation of PAH-contaminated soil.IMPORTANCEThis study was performed to explore the mechanism of bioaugmentation by a fungal-bacterial consortium for phenanthrene (PHE) degradation in petroleum-contaminated soil. Using the indigenous fungal strain Aspergillus sp. LJD-29 and bacterial strain Pseudomonas XH-1, we performed stable isotope probing (SIP) to trace active PHE-degrading microorganisms. While inoculation of either organism alone significantly enhanced PHE degradation, the simultaneous addition of both strains revealed complex interactions. The efficiency plateaued, highlighting the nuanced microbial interactions. SIP identified XH-1 as the primary contributor to in situ PHE degradation, in contrast to the limited role of LJD-29. Correlations between fungal abundance, degradation efficiency, and extracellular enzyme activity underscored the pivotal role of LJD-29 in enzymatically facilitating PHE breakdown and enriching bacterial assimilation. Metabolite analysis validated this synergy, unveiling distinct biodegradation mechanisms. Furthermore, this fungal-bacterial alliance significantly impacted PHE-degrading microorganism diversity. These findings advance our understanding of fungal-bacterial bioaugmentation and microorganism diversity in polycyclic aromatic hydrocarbon (PAH) degradation as well as providing insights for theoretical guidance in the in situ bioremediation of PAH-contaminated soil.

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

Autochthonous bioaugmentation and nutrient biostimulation are promising bioremediation methods for polycyclic aromatic hydrocarbons (PAHs) in contaminated agricultural soils, but little is known about their combined working mechanism. In this study, a microcosm trial was conducted to explore the combined mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation, using DNA stable-isotope-probing (DNA-SIP) and microbial network analysis. Both treatments significantly improved phenanthrene (PHE) removal, with their combined application producing the best results. The microbial community composition was notably altered by all bioremediation treatments, particularly the PHE-degrading bacterial and fungal taxa. Fungal bioaugmentation removed PAHs through extracellular enzyme secretion but reduced soil microbial diversity and ecological stability, while nitrogen biostimulation promoted PAH dissipation by stimulating indigenous soil degrading microbes, including fungi and key bacteria in the soil co-occurrence networks, ensuring the ecological diversity of soil microorganisms. The combination of both approaches proved to be the most effective strategy, maintaining a high degradation efficiency and relatively stable soil biodiversity through the secretion of lignin hydrolytic enzymes by fungi, and stimulating the reproduction of soil native degrading microbes, especially the key degraders in the co-occurrence networks. Our findings provide a fresh perspective of the synergy between fungal bioaugmentation and nitrogen biostimulation, highlighting the potential of this combined bioremediation approach for in situ PAH-contaminated soils.

Response and adaptation of rhizosphere microbiome to organic pollutants with enriching pollutant-degraders and genes for bioremediation: A critical review

Phytoremediation largely involves microbial degradation of organic pollutants in rhizosphere for removing organic pollutants like polycyclic aromatic hydrocarbons, phthalates and polychlorinated biphenyls. Microbial community in rhizosphere experiences complex processes of response-adaptation-feedback up on exposure to organic pollutants. This review summarizes recent research on the response and adaptation of rhizosphere microbial community to the stress of organic pollutants, and discusses the enrichment of the pollutant-degrading microbial community and genes in the rhizosphere for promoting bioremediation. Soil pollution by organic contaminants often reduces the diversity of rhizosphere microbial community, and changes its functions. Responses vary among rhizosphere microbiomes up on different classes of organic pollutants (including co-contamination with heavy metals), plant species, root-associated niches (e.g., rhizosphere, rhizoplane and endosphere), geographical location and soil properties. Soil pollution can deplete some sensitive microbial taxa and enrich some tolerant microbial taxa in rhizosphere. Furthermore, rhizosphere enriches pollutant-degrading microbial community and functional genes including different gene clusters responsible for biodegradation of organic pollutants and their intermediates, which improve the adaptation of microbiome and enhance the remediation efficiency of the polluted soil. The knowledge gaps and future research challenges are highlighted on rhizosphere microbiome in response-adaptation-feedback processes to organic pollution and rhizoremediation. This review will hopefully update understanding on response-adaptation-feedback processes of rhizosphere microbiomes and rhizoremediation for the soil with organic pollutants.

Transfer and Degradation of PAHs in the Soil-Plant System: A Review

Polycyclic aromatic hydrocarbons (PAHs) are highly toxic, persistent organic pollutants that threaten ecosystems and human health. Consistent monitoring is essential to minimize the entry of PAHs into plants and reduce food chain contamination. PAHs infiltrate plants through multiple pathways, causing detrimental effects and triggering diverse plant responses, ultimately increasing either toxicity or tolerance. Primary plant detoxification processes include enzymatic transformation, conjugation, and accumulation of contaminants in cell walls/vacuoles. Plants also play a crucial role in stimulating microbial PAHs degradation by producing root exudates, enhancing bioavailability, supplying nutrients, and promoting soil microbial diversity and activity. Thus, synergistic plant-microbe interactions efficiently decrease PAHs uptake by plants and, thereby, their accumulation along the food chain. This review highlights PAHs uptake pathways and their overall fate as contaminants of emerging concern (CEC). Understanding plant uptake mechanisms, responses to contaminants, and interactions with rhizosphere microbiota is vital for addressing PAH pollution in soil and ensuring food safety and quality.

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

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 utilizing 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 Raman-activated cell sorting-stable-isotope probing, 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.