Response of the soil microbial community to petroleum hydrocarbon stress shows a threshold effect: research on aged realistic contaminated fields

Biodegradation of Phenanthrene by Mycobacterium sp. TJFP1: Genetic Basis and Environmental Validation

The development of efficient bioremediation technologies for polycyclic aromatic hydrocarbons contamination is a hot research topic in the environmental field. In this study, we found that the Mycobacterium sp., TJFP1, has the function of degrading low molecular weight PAHs, and further investigated its degradation characteristics using the PAH model compound phenanthrene as a target pollutant. The optimal growth and degradation conditions were determined by single-factor experiments to be 37 °C, pH 9.0, and an initial concentration of 100 mg/L phenanthrene. Under this condition, the degradation efficiency of phenanthrene reached 100% after 106 h of incubation, and the average degradation rate could reach 24.48 mg/L/day. Combined with whole genome sequencing analysis, it was revealed that its genome carries a more complete phenanthrene degradation pathway, including functional gene clusters related to the metabolism of PAHs, such as phd and nid. Meanwhile, intermediates such as phthalic acid were detected; it was determined that TJFP1 metabolizes phenanthrene via the phthalic acid pathway. Simulated contaminated soil experiments were also conducted, and the results showed that the removal rate of phenanthrene from the soil after 20 days of inoculation with the bacterial strain was about 3.7 times higher than that of the control group (natural remediation). At the same time from the soil physical and chemical properties and soil microbial community structure of two levels to explore the changes in different means of remediation, indicating that it can be successfully colonized in the soil, and as a dominant group of bacteria to play the function of remediation, verifying the environmental remediation function of the strains, for the actual inter-soil remediation to provide theoretical evidence. This study provides efficient strain resources for the bioremediation of PAH contamination.

Natural Revegetation Alters Habitat Conditions, Bacterial Components, and Polycyclic Aromatic Hydrocarbon (PAH)-Degrading Communities in Aged PAH-Polluted Soils

The vegetation restoration of contaminated sites plays a critical role in ensuring the sustained stability and functional integrity of natural ecosystems. However, during the natural revegetation process, the variations in habitat conditions, bacterial community structure, and metabolic functions in aged, polluted soil are still unclear. In the present study, we investigated aged, polycyclic aromatic hydrocarbon (PAH)-polluted soils at closed, abandoned oil well sites from the Yellow River Delta. Using gene amplification and real-time qPCR methods, the abundance, taxonomy, and diversity characteristics of indigenous bacterial communities and functional bacteria carrying C12O genes in both vegetated soils and bare soils were investigated. The results show that natural revegetation significantly changes the physicochemical parameters, PAH content, and bacterial community structure of aged, PAH-polluted soils. When comparing the abundance and components of PAH-degrading bacterial communities in vegetated and bare soils, the PAH-degrading potential was revealed to be stimulated by vegetation communities. Through correlation analysis, dual stress from soil salinity and PAH contamination in bacterial communities was revealed to be mediated through alterations in the soil's physicochemical properties by local vegetation. The network analysis revealed that bacterial communities in vegetated soils have higher network connectivity. These results elucidate the alterations in habitat conditions, bacterial components, and PAH-degrading communities following vegetation restoration, providing critical insights for optimizing ecological rehabilitation strategies in salinized and contaminated ecosystems.

Long-term response mechanism of bacterial communities to chemical oxidation remediation in petroleum hydrocarbon contaminated groundwater

The limited understanding of microbial response mechanism remains as a bottleneck to evaluate the long-term remediation effectiveness of in situ chemical oxidation in contaminated groundwater. In this study, we investigated long-term response of bacterial communities throughout five remediation stages of pre-oxidation, early-oxidation, late-oxidation, early-recovery and late-recovery. By analyzing bacterial biomass, taxa, diversity and metabolic functions, this work identified the consistently suppressed glyceraldehyde-3-phosphate dehydrogenase pathway and the enrichment of naphthalene degradation pathways for secondary products, suggesting persistent oxidation stress and enhanced microbial utilization of lower-molecular weight carbon sources at the oxidation and early-recovery stages. The dominant microbial clusters shifted from r-strategists to K-strategists and then back to r-strategists, indicating their higher degradation efficiency of petroleum hydrocarbons throughout the oxidation process. The changes in stability and stochastic assembly of bacterial communities during in situ chemical oxidation suggested that oxidative stress, carbon source addition and carbon source limitation as the main influential factors of bacterial community succession at the oxidation, early-recovery and late-recovery stage, respectively. Our findings highlighted the complex recovery and underlying mechanisms of groundwater bacterial communities during in situ chemical oxidation process, and provided valuable insights for effective and long-term site management after in situ chemical oxidation practices.

Rhizodegradation of diesel and PAH contaminated soils with Miscanthus × giganteus: Soil, plants, microbes and pollutants interactions after two seasons

Miscanthus × giganteus, a high-yielding perennial grass, has recently shown promise for phytomanagement of petroleum hydrocarbons (PHC) contaminated sites, however the mechanisms of plant-soil interactions are not clear. This study followed the second growing season of miscanthus cultivation on soil spiked with representatives of the most common PHC pollutants: diesel (dominantly aliphatic hydrocarbons), pyrene + phenanthrene (polycyclic aromatic hydrocarbons; PAH) and their mixture. Miscanthus demonstrated tolerance to PHC-contaminated soils, although high diesel concentrations significantly reduced biomass, limiting the overall benefits of cultivation. This was evident in reduced carbon sequestration, plant-induced soil respiration and root exudate content in diesel-treated soils. Despite comparable PHC levels in planted and unplanted soils after two seasons, several indicators of ongoing rhizodegradation were observed. These included increased root exudates production, a higher fungal-to-bacterial ratio and, at lower diesel levels, increased abundance of actinobacteria, i.e. shifts towards biodegraders capable of biodegradation of more recalcitrant components of petroleum. A comprehensive analysis revealed significant PHC impacts on soil microbial communities. While biomass and respiration increased, bacterial diversity decreased with increasing diesel concentrations. The microbial community shifted towards potentially PHC-degrading microorganisms, such as fungi and specific bacterial genera (e.g., AlkB gene abundance increased 100-fold). PAH contamination primarily affected the abundance of the pahGP marker, but its overall impact was limited due to low residual PAH levels in the second season. These findings show changing role of M. × giganteus in PHC bioremediation from the support of biodegradation in the first year to stabilization and enrichment of soil in the second.

Abiotic and biotic dissipation in natural attenuation of phenanthrene and benzo[a]pyrene: A systematic quantification study in contrasting soils

Natural attenuation represents a significant ecosystem function for mitigating the quantity and toxicity of polycyclic aromatic hydrocarbons (PAHs) through both abiotic and biotic dissipation processes. This study systematically investigated abiotic and biotic dissipation of phenanthrene (Phe) and benzo[a]pyrene (BaP) in four soils over 360 days, using CSIA to quantitatively analyze δ1³C changes and demonstrate biodegradation. The results indicated that extractable Phe was primarily attenuated via biodegradation (65%-81%), as revealed by CSIA, with the δ1³C changes ranging from 2.06‰ to 4.20‰ across the four soil types. Only 17%-27% of Phe dissipated by forming Type II non-extractable residues (NERs), while its Type I NERs remained available for microbial utilization. Notably, the microbial genera Gemmatimonas and Sphingomonas emerged as key contributors to the biotic dissipation of Phe. Conversely, extractable BaP was predominantly attenuated through abiotic process (35%-52%), particularly via the formation of Type I and Type II NERs, with a smaller fraction (6%-17%) undergoing biotic dissipation. Although the changes in δ1³C values for BaP were only 0.76‰-1.06‰, the significant changes (p < 0.05) supported the microbial degradation of BaP. Additionally, soil organic matter and pH influenced the extractable and residual Phe, whereas soil electrical conductivity and texture primarily affected BaP rather than Phe. These findings underscore the multiple dissipation mechanisms involved in the natural attenuation of PAHs in soils and offer valuable quantitative data for remediation strategies of PAHs-contaminated soils.

Metagenomic and isotopic insights into carbon fixation by autotrophic microorganisms in a petroleum hydrocarbon impacted red clay aquifer

Autotrophic microorganisms, the pivotal carbon fixers, exhibit a broad distribution across diverse environments, playing critical roles in the process of carbon sequestration. However, insights into their distribution characteristics in aquifers, particularly in those petroleum-hydrocarbon-contaminated (PHC) aquifers that were known for rich in heterotrophs, have been limited. In the study, groundwater samples were collected from red clay aquifers in the storage tank leakage area of a PHC site, a prevalent aquifer type in southern China and other regions. Metagenomics combined with hydrochemical and inorganic carbon isotope analyses were employed to elucidate the presence of microbial carbon fixation and its driving forces. Results showed that there were hundreds of autotrophic microorganisms participating in distinct carbon fixation processes in the red clay PHC aquifers. Reductive tricarboxylic acid (rTCA) and dicarboxylate/4-hydroxybutyrate (DC/4HB), as well as 3-hydroxypropionate (3HP or/and 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB)) were the predominant carbon fixation pathways. The abundances of carbon fixation genes and autotrophic microorganisms were significantly and positively correlated with hydrocarbon concentrations and δ13C of dissolved inorganic carbon (δ13C-DIC) values. This finding indicated that the petroleum hydrocarbon significantly promoted the proliferation of carbon fixation microorganisms, leading to a substantial uptake of inorganic carbon. Therefore, we deduce that this process holds considerable potential for carbon sequestration in PHC-contaminated aquifers.

An animal charcoal contaminated cottage industry soil highlighted by halophilic archaea dominance and decimation of bacteria

An animal charcoal contaminated cottage industry soil in Lagos, Nigeria (ACGT) was compared in an ex post facto study with a nearby unimpacted soil (ACGC). Hydrocarbon content was higher than regulatory limits in ACGT (180.2 mg/kg) but lower in ACGC (19.28 mg/kg). Heavy metals like nickel, cadmium, chromium and lead were below detection limit in ACGC. However, all these metals, except cadmium, were detected in ACGT, but at concentrations below regulatory limits. Furthermore, copper (253.205 mg/kg) and zinc (422.630 mg/kg) were above regulatory limits in ACGT. Next generation sequencing revealed that the procaryotic community was dominated by bacteria in ACGC (62%) while in ACGT archaea dominated (76%). Dominant phyla in ACGC were Euryarchaeota (37%), Pseudomonadota (16%) and Actinomycetota (12%). In ACGT it was Euryarchaeota (76%), Bacillota (9%), Pseudomonadota (7%) and Candidatus Nanohaloarchaeota (5%). Dominant Halobacteria genera in ACGT were Halobacterium (16%), Halorientalis (16%), unranked halophilic archaeon (13%) Salarchaeum (6%) and Candidatus Nanohalobium (5%), whereas ACGC showed greater diversity dominated by bacterial genera Salimicrobium (7%) and Halomonas (3%). Heavy metals homeostasis genes, especially for copper, were fairly represented in both soils but with bacterial taxonomic affiliations. Sites like ACGT, hitherto poorly studied and understood, could be sources of novel bioresources.

Metagenomic analysis reveals the microbial response to petroleum contamination in oilfield soils

The response of the microbes to total petroleum hydrocarbons (TPHs) in three types of oilfield soils was researched using metagenomic analysis. The ranges of TPH concentrations in the grassland, abandoned well, working well soils were 1.16 × 102-3.50 × 102 mg/kg, 1.14 × 103-1.62 × 104 mg/kg, and 5.57 × 103-3.33 × 104 mg/kg, respectively. The highest concentration of n-alkanes and 16 PAHs were found in the working well soil of Shengli (SL) oilfield compared with those in Nanyang (NY) and Yanchang (YC) oilfields. The abandoned well soils showed a greater extent of petroleum biodegradation than the grassland and working well soils. Α-diversity indexes based on metagenomic taxonomy showed higher microbial diversity in grassland soils, whereas petroleum-degrading microbes Actinobacteria and Proteobacteria were more abundant in working and abandoned well soils. RDA demonstrated that low moisture content (MOI) in YC oilfield inhibited the accumulation of the petroleum-degrading microbes. Synergistic networks of functional genes and Spearman's correlation analysis showed that heavy petroleum contamination (over 2.10 × 104 mg/kg) negatively correlated with the abundance of the nitrogen fixation genes nifHK, however, in grassland soils, low petroleum content facilitated the accumulation of nitrogen fixation genes. A positive correlation was observed between the abundance of petroleum-degrading genes and denitrification genes (bphAa vs. nirD, todC vs. nirS, and nahB vs. nosZ), whereas a negative correlation was observed between alkB (alkane- degrading genes) and amo (ammonia oxidation), hao (nitrification). The ecotoxicity of petroleum contamination, coupled with petroleum hydrocarbons (PH) degradation competing with nitrifiers for ammonia inhibited ammonia oxidation and nitrification, whereas PH metabolism promoted the denitrification process. Moreover, positive correlations were observed between the abundance of amo gene and MOI, as well as between the abundance of the dissimilatory nitrate reduction gene nirA and clay content. Thus, improving the soil physicochemical properties is a promising approach for decreasing nitrogen loss and alleviating petroleum contamination in oilfield soils.

Unraveling the functional instability of bacterial consortia in crude oil degradation via integrated co-occurrence networks

Introduction

Soil ecosystems are threatened by crude oil contamination, requiring effective microbial remediation. However, our understanding of the key microbial taxa within the community, their interactions impacting crude oil degradation, and the stability of microbial functionality in oil degradation remain limited.

Methods

To better understand these key points, we enriched a crude oil-degrading bacterial consortium generation 1 (G1) from contaminated soil and conducted three successive transfer passages (G2, G3, and G4). Integrated Co-occurrence Networks method was used to analyze microbial species correlation with crude oil components across G1-G4.

Results and discussion

In this study, G1 achieved a total petroleum hydrocarbon (TPH) degradation rate of 32.29% within 10 days. Through three successive transfer passages, G2-G4 consortia were established, resulting in a gradual decrease in TPH degradation to 23.14% at the same time. Specifically, saturated hydrocarbon degradation rates ranged from 18.32% to 14.17% among G1-G4, and only G1 exhibited significant aromatic hydrocarbon degradation (15.59%). Functional annotation based on PICRUSt2 and FAPROTAX showed that functional potential of hydrocarbons degradation diminished across generations. These results demonstrated the functional instability of the bacterial consortium in crude oil degradation. The relative abundance of the Dietzia genus showed the highest positive correlation with the degradation efficiency of TPH and saturated hydrocarbons (19.48, 18.38, p < 0.05, respectively), Bacillus genus demonstrated the highest positive correlation (21.94, p < 0.05) with the efficiency of aromatic hydrocarbon degradation. The key scores of Dietzia genus decreased in successive generations. A significant positive correlation (16.56, p < 0.05) was observed between the Bacillus and Mycetocola genera exclusively in the G1 generation. The decline in crude oil degradation function during transfers was closely related to changes in the relative abundance of key genera such as Dietzia and Bacillus as well as their interactions with other genera including Mycetocola genus. Our study identified key bacterial genera involved in crude oil remediation microbiome construction, providing a theoretical basis for the next step in the construction of the oil pollution remediation microbiome.