Effects of polycyclic aromatic hydrocarbons on microbial community structure and PAH ring hydroxylating dioxygenase gene abundance in soil

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.

Comparison of airborne bacterial communities in PM2.5 between a dry-season haze period and a wet-season non-haze period in thailand

Thailand experiencing severe air pollution for over a decade. Although the physical and chemical properties of particulate matter have been extensively studied, the biological aspects, particularly microorganisms present in fine particles during haze and non-haze periods, are still unclear. To address this gap, we aim to profile the bacterial communities in PM2.5 in Bangkok and Chiang Mai, Thailand. The samples were collected during the haze and non-haze periods in 2021-2022. Using 16 S rRNA gene sequencing, we identified a markedly higher number of bacterial genera in Chiang Mai (247) compared to Bangkok (31). In Bangkok, Actinobacteriota (80.4%) and Proteobacteria (18.3%) dominated, whereas Chiang Mai's samples were enriched with Firmicutes (52.2%) and Bacteroidota (13.0%). Interestingly, Bangkok's samples were dominated by Cutibacterium (68.4%) and Enhydrobacter (14.6%), while Chiang Mai had Bacillus (11.0%) and Blautia (7.6%). Despite substantially higher PM2.5 levels during haze, alpha diversity analyses showed that bacterial community structure was more strongly influenced by geographic location than by haze conditions. Chiang Mai consistently exhibited greater microbial richness and evenness than Bangkok. These findings highlight the importance of biological factors in urban air pollution studies and underscore the need to incorporate the biological aspects into health risk assessments and air quality management strategies.

Effects of Environmental Chemical Pollutants on Microbiome Diversity: Insights from Shotgun Metagenomics

Chemical exposure in the environment can adversely affect the biodiversity of living organisms, particularly when persistent chemicals accumulate over time and disrupt the balance of microbial populations. In this study, we examined how chemical contaminants influence microorganisms in sediment and overlaying water samples collected from the Kinnickinnic, Milwaukee, and Menomonee Rivers near Milwaukee, Wisconsin, USA. We characterized these samples using shotgun metagenomic sequencing to assess microbiome diversity and employed chemical analyses to quantify more than 200 compounds spanning 16 broad classes, including pesticides, industrial products, personal care products, and pharmaceuticals. Integrative and differential comparative analyses of the combined datasets revealed that microbial density, approximated by adjusted total sequence reads, declined with increasing total chemical concentrations. Protozoan, metazoan, and fungal populations were negatively correlated with higher chemical concentrations, whereas certain bacterial (particularly Proteobacteria) and archaeal populations showed positive correlations. As expected, sediment samples exhibited higher concentrations and a wider dynamic range of chemicals compared to water samples. Varying levels of chemical contamination appeared to shape the distribution of microbial taxa, with some bacterial, metazoan, and protozoan populations present only at certain sites or in specific sample types (sediment versus water). These findings suggest that microbial diversity may be linked to both the type and concentration of chemicals present. Additionally, this study demonstrates the potential roles of multiple microbial kingdoms in degrading environmental pollutants, emphasizing the metabolic versatility of bacteria and archaea in processing complex contaminants such as polyaromatic hydrocarbons and bisphenols. Through functional and resistance gene profiling, we observed that multi-kingdom microbial consortia-including bacteria, fungi, and protozoa-can contribute to bioremediation strategies and help restore ecological balance in contaminated ecosystems. This approach may also serve as a valuable proxy for assessing the types and levels of chemical pollutants, as well as their effects on biodiversity.

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.

Review on biochar as a sustainable green resource for the rehabilitation of petroleum hydrocarbon-contaminated soil

Petroleum pollution is one of the primary threats to the environment and public health. Therefore, it is essential to create new strategies and enhance current ones. The process of biological reclamation, which utilizes a biological agent to eliminate harmful substances from polluted soil, has drawn much interest. Biochars are inexpensive, environmentally beneficial carbon compounds extensively employed to remove petroleum hydrocarbons from the environment. Biochar has demonstrated an excellent capability to remediate soil pollutants because of its abundant supply of the required raw materials, sustainability, affordability, high efficacy, substantial specific surface area, and desired physical-chemical surface characteristics. This paper reviews biochar's methods, effectiveness, and possible toxic effects on the natural environment, amended biochar, and their integration with other remediating materials towards sustainable remediation of petroleum-polluted soil environments. Efforts are being undertaken to enhance the effectiveness of biochar in the hydrocarbon-based rehabilitation approach by altering its characteristics. Additionally, the adsorption, biodegradability, chemical breakdown, and regenerative facets of biochar amendment and combined usage culminated in augmenting the remedial effectiveness. Lastly, several shortcomings of the prevailing methods and prospective directions were provided to overcome the constraints in tailored biochar studies for long-term performance stability and ecological sustainability towards restoring petroleum hydrocarbon adultered soil environments.

Adaptation strategies and functional transitions of microbial community in pyrene-contaminated soils promoted by lead with Pseudomonas veronii and its extracellular polymeric substances

Pyrene was designated as a remediation target in this study, and low contamination of lead (Pb) was set to induce heavy metal stress. Pseudomonas veronii and its extracellular polymeric substances (EPSs) were chosen for biofortification, with the aim of elucidating the structural, metabolic, and functional responses of soil microbial communities. Community analysis of soil microorganisms using high-throughput sequencing showed that the co-addition of P. veronii and EPSs resulted in an increase in relative abundance of phyla associated with pyrene degradation, and formed a symbiotic system dominated by Firmicutes and Proteobacteria, which involved in pyrene metabolism. Co-occurrence network analysis revealed that the module containing P. veronii was the only one exhibiting a positive correlation between bacterial abundance and pyrene removal, indicating the potential of bioaugmentation in enriching functional taxa. Biofortification also enhanced the abundance of functional gene linked to EPS production (biofilm formation-Pseudomonas aeruginosa) and pyrene degradation. Furthermore, 17 potential functional bacteria were screened out using random forest algorithm. Lead contamination further promoted the growth of Proteobacteria, intensified cooperative associations among bacteria, and increased the abundance of bacteria with positive correlation with pyrene degradation. The results offer novel perspectives on alterations in microbial communities resulting from the synergistic impact of heavy metal stress and biofortification.

The role of microplastics in the process of laccase-assisted phytoremediation of phenanthrene-contaminated soil

Polycyclic aromatic hydrocarbons (PAHs) are highly toxic organic pollutants widely distributed in terrestrial environments and laccase was considered as an effective enzyme in PAHs bioremediation. However, laccase-assisted phytoremediation of PAHs-contaminated soil has not been reported. Moreover, the overuse of plastic films in agriculture greatly increased the risk of co-existence of PAHs and microplastics in soil. Microplastics can adsorb hydrophobic organics, thus altering the bioavailability of PAHs and ultimately affecting the removal of PAHs from soil. Therefore, this study aimed to evaluate the efficiency of laccase-assisted maize (Zea mays L.) in the remediation of phenanthrene (PHE)-contaminated soil and investigate the effect of microplastics on this remediation process. The results showed that the combined application of laccase and maize achieved a removal efficiency of 83.47 % for soil PHE, and laccase significantly reduced the accumulation of PHE in maize. However, microplastics significantly inhibited the removal of soil PHE (10.88 %) and reduced the translocation factor of PHE in maize (87.72 %), in comparison with PHE + L treatment. Moreover, microplastics reduced the laccase activity and the relative abundance of some PAHs-degrading bacteria in soil. This study provided an idea for evaluating the feasibility of the laccase-assisted plants in the remediation of PAHs-contaminated soil, paving the way for reducing the risk of secondary pollution in the process of phytoremediation.

Soil fauna-microbial interactions shifts fungal and bacterial communities under a contamination disturbance

The aim of this study was to determine whether the soil faunal-microbial interaction complexity (SFMIC) is a significant factor influencing the soil microbial communities and the willow growth in the context of PAH contamination. The SFMIC treatment had eight levels: just the microbial community, or the microbial community with nematodes, springtails, earthworms and all the possible combinations. SFMIC affected the height and biomass of willows after eight weeks or growth. SFMIC affected the structure and the composition of the bacterial, archaeal and fungal communities, with significant effects of SFMIC on the relative abundance of fungal genera such as Sphaerosporella, a known willow symbiont during phytoremediation, and bacterial phyla such as Actinobacteriota, containing many polycyclic aromatic hydrocarbons (PAH) degraders. These SFMIC effects on microbial communities were not clearly reflected in the community structure and abundance of PAH degraders, even though some degraders related to Actinobacteriota and the diversity of Gram-negative degraders were affected by the SFMIC treatments. Over 95% of PAH was degraded in all pots at the end of the experiment. Overall, our results suggest that, under our experimental conditions, SFMIC changes willow phytoremediation outcomes.

Bacterial enzymatic degradation of recalcitrant organic pollutants: catabolic pathways and genetic regulations

Contamination of soil and natural water bodies driven by increased organic pollutants remains a universal concern. Naturally, organic pollutants contain carcinogenic and toxic properties threatening all known life forms. The conventional physical and chemical methods employed to remove these organic pollutants ironically produce toxic and non-ecofriendly end-products. Whereas microbial-based degradation of organic pollutants provides an edge, they are usually cost-effective and take an eco-friendly approach towards remediation. Bacterial species, including Pseudomonas, Comamonas, Burkholderia, and Xanthomonas, have the unique genetic makeup to metabolically degrade toxic pollutants, conferring their survival in toxic environments. Several catabolic genes, such as alkB, xylE, catA, and nahAc, that encode enzymes and allow bacteria to degrade organic pollutants have been identified, characterized, and even engineered for better efficacy. Aerobic and anaerobic processes are followed by bacteria to metabolize aliphatic saturated and unsaturated hydrocarbons such as alkanes, cycloalkanes, aldehydes, and ethers. Bacteria use a variety of degrading pathways, including catechol, protocatechuate, gentisate, benzoate, and biphenyl, to remove aromatic organic contaminants such as polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pesticides from the environment. A better understanding of the principle, mechanisms, and genetics would be beneficial for improving the metabolic efficacy of bacteria to such ends. With a focus on comprehending the mechanisms involved in various catabolic pathways and the genetics of the biotransformation of these xenobiotic compounds, the present review offers insight into the various sources and types of known organic pollutants and their toxic effects on health and the environment.

Response characteristics of indigenous microbial community in polycyclic aromatic hydrocarbons (PAHs) contaminated aquifers under polyethylene microplastics stress: A microcosmic experimental study

To understand the response characteristics of indigenous microbial community in PAH-contaminated aquifers to the coexistence of microplastics. In this paper, we constructed a groundwater microecosystem using lithologic media collected from the field and subjected it to the stress of a polyethylene microplastics (PE-MPs) concentration gradient. By conducting adsorption experiments and 16S rRNA sequencing, we revealed the growth, structure, metabolism, and resistance mechanisms of the indigenous microbial community in the aquifer lithologic media exposed to varying levels of co-stress from PE-MPs and phenanthrene. Our findings suggest that the adsorption capacity of aquifer lithologic media for phenanthrene is significantly weaker than that of PE-MPs. Additionally, our observations indicated that small particle lithologic media had a greater adsorption capacity for phenanthrene than large particle lithologic media. The presence of PE-MPs was found to increase both the abundance and diversity of microbial communities, although the relationship was not linear with the content of PE-MPs. When exposed to the combined stress of PE-MPs and phenanthrene, the relative abundance of Proteobacteria decreased while that of Bacteroidetes increased. Several genera belonging to Proteobacteria (Aeromonas, Desulfovibrio, Klebsiella, Pantoea, and Microvirgula) and Bacteroidetes (Macellibacteroides and Bacteroides) occupied a central position in the microbial community interaction network and showed significant correlations with other genera. Furthermore, an increase in the proportion of genera capable of degrading various refractory organics was observed. The presence of PE-MPs increased the phenanthrene content in the aquifer lithologic media, thereby intensifying the inhibitory effect on indigenous microbial community in this environment. Despite an increase in the phenanthrene content of aquifer lithologic media due to the presence of PE-MPs, indigenous microbial community in this environment exhibited resistance to the combined inhibition of PE-MPs and phenanthrene through a series of resistance mechanisms. These mechanisms included strengthening the N-cycle process, enhancing metabolic capacity for phenanthrene, improving perception, response, and adaptation to changes in the external environment or intracellular state, modifying the transmembrane transport of the cell membrane to the substrate, and regulating life processes.

Soil physiochemical properties and bacterial community changes under long-term polycyclic aromatic hydrocarbon stress in situ steel plant soils

In situ soils were collected at two depths in Jinan and Hangzhou steel plants, which both have a long history of operation and polycyclic aromatic hydrocarbons (PAHs) contamination. The richness of 16 S rRNA gene and bacterial community of the soil were determined by real-time PCR and high-throughput sequencing. Soil physicochemical properties, PAHs contamination characteristics, and their interrelationships were also analyzed. In general, the PAHs contamination decreased with increasing soil depths. The physicochemical properties and PAH concentration of soil had synergistic impacts on the composition of the bacterial community. The long-term higher PAHs stress in Hangzhou contaminated soil (982 mg kg^-1) increased the bacterial abundance and diversity, while that of Jinan contaminated soil (63 mg kg^-1) decreased bacterial abundance and diversity. The pH value, sand content of the soil were positively correlated (P < 0.05) with the bacterial diversity including Simpson, Shannon, Observed_species and Chao1 indexes., and the other soil properties exhibited negative correlations with different strengths. The abundances of Curvibacter, Pseudomonas, Thiobacillus, Lysobacter, and Limnobacter were positively correlated with the PAHs concentration (P < 0.01). Additionally, the network structure of the PAHs-contaminated soils was more complex compared to that of uncontaminated soils, with stronger linkages and correlations between the different bacteria. These findings provide a theoretical basis for microbial remediation of PAHs-polluted soil.

Metal-free catalysis for organic micropollutant degradation in waste activated sludge via poly(3-hydroxybutyrate) biopolymers using Cupriavidus sp. L7L coupled with peroxymonosulfate

This study employed a novel and environment-friendly biopolymer/oxidant catalytic system, viz., poly(3-hydroxybutyrate)/peroxymonosulfate (PHB/PMS), for pretreating wastewater sludge for the first time. Under optimal conditions, i.e., 3.1 × 10^-4 M of PMS and 3.3 g/L of PHB at pH = 6.0, the PAHs in the sludge matrix was decreased by 79 % in 12 h. Increase in salinity (75 % synthetic seawater) achieved 83 % of PAHs degradation. Functional groups (CO) of the biopolymer matrix were active centers for biopolymer-mediated electron transfer that produced reactive oxygen species (SO₄^-, HO, and ¹O₂) for adsorption and catalytic oxidation of PAHs in the sludge. Functional metagenomic analysis revealed the main genus, Conexibacter (phylum, Actinobacteria) exhibited PAH-degrading function with high efficiency in the biodegradation of PAHs from sludge pretreated with PHB/PMS. Coupling chemical oxidation and biostimulation using bacterial polymer-based biomaterials is effective and beneficial for pretreating wastewater sludge toward circular bioeconomy.

Shifts of the new functional marker gene (pahE) of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial population and its relationship with PAHs biodegradation

Identification of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial populations and understanding their responses to PAHs are crucial for the designing of appropriate bioremediation strategies. In this study, the responses of PAHs-degrading bacterial populations to different PAHs were studied in terms of the compositions and abundance variations of their new functional marker gene (pahE) by gene-targeted metagenomic and qPCR analysis. Overall, PAHs species significantly affected the composition and abundance of pahE gene within the PAHs-degrading bacteria in each treatment and different pahE of PAHs-degrading bacteria involved in the different stages of PAHs degradation. Noted that new pahE genotypes were also discovered in all PAHs treatment groups, indicating that some potential new PAHs-degrading bacterial genera were also involved in PAHs degradation. Besides, all three PAH removal rates were significantly positively related with pahE gene abundances (R² = 0.908 ~ 0.922, p < 0.01), demonstrating that pahE could be a good indicator of PAHs degradation activity or potential. This is the first study focusing on the dynamic changes of the pahE gene within PAHs-degrading bacterial community during the degradation of PAHs in mangrove sediment, providing novel insights into the use of pahE gene as the functional marker to indicate PAH degradation.

Long-term metal pollution shifts microbial functional profiles of nitrification and denitrification in agricultural soils

The increasing contamination of heavy metals in agricultural soils and its impact on the nitrogen (N) cycle and N use efficiency have attracted considerable attention in recent years. In this study, agricultural soils neighboring the Dabaoshan copper mining area (DBS) and Qingyuan electronic-waste recycling area (QY), in Guangdong, China, were sampled to study the interaction between heavy metals and nitrification/denitrification processes, especially the related microbial functional profiles. Results showed that the contamination of heavy metals affected nitrifiers and denitrifiers differently. The potential nitrification activity was about four times lower in metal-polluted soils compared with the unpolluted ones, with a significant decrease in the abundance of amoA and nxrB (p < 0.05) in the polluted samples. On the other hand, the potential denitrification activity was more metal-resistant, which attributed to its complex species composition as shown by a slightly higher α-diversity index, and was slightly higher (p > 0.05) in the polluted samples. Among the five denitrifying genes tested, nosZ gene had the highest increase and the nirK gene the most decrease in numbers and in the polluted soils. The metal-polluted soils had fewer correlations among N functional genes based on the co-occurrence network analysis. In addition, the core taxa of the whole bacterial community changed from copiotrophic to oligotrophic bacteria in the presence of heavy metals. Mantel test indicated that heavy metals were the dominant factors determining N-related genes while the bacterial community composition was due to a combination of heavy metal presence and soil properties such as TOC, NO₂^-, and pH. It is concluded that long-term heavy metals pollution potentially affected nitrifiers and denitrifiers differently as indicated by the shift in N functional genes and the change in nitrification/denitrification processes.

Structural, metabolic, and functional characteristics of soil microbial communities in response to benzo[a]pyrene stress

Understanding the characteristics of soil microbes responding to benzo[a]pyrene (BaP) helps to deepen the knowledge of the risks of BaP to soil ecosystem. In this study, the structural, metabolic, and functional responses of soil microbial communities to BaP (8.11 mg kg^-1) were investigated. Analysis of microbial community structure based on 16 S rRNA and ITS gene sequencing indicated that BaP addition enriched microbes associated with aromatic compound degradation (Sphingomonas, Bacilli, Fusarium) and oligotrophs (Blastocatellaceae, Rokubacteriales), but inhibited Cyanobacteria involved in nitrogen-fixing process. Network analysis showed that the bacterial community enhanced intraspecific cooperation, while fungal community mainly altered the keystone taxa under BaP stress. Biolog EcoPlate assay demonstrated that microbial metabolism of carbon sources, especially nitrogen-containing sources, was stimulated by BaP addition. Functional analysis based on enzyme activity tests, functional gene quantification, and function annotation showed that nitrogen-cycling processes, especially nitrogen fixation, were significantly inhibited. These results suggest that BaP-tolerant microbes may establish cooperative relationships and compete for resources and ecological niches with sensitive microbes, especially those associated with nitrogen cycling, ultimately leading to enhanced carbon source utilization and restricted nitrogen cycling. This study clearly elucidates the adaptation strategies and functional shifts of soil microbial communities to BaP contamination.

Mechanism of salicylic acid in promoting the rhizosphere benzo[a]pyrene biodegradation as revealed by DNA-stable isotope probing

Benzo[a]pyrene (BaP) is a typical high-molecular-weight PAH with carcinogenicity. Rhizoremediation is commonly applied to remove soil BaP, but its mechanism remains unclear. The role of inducers in root exudates in BaP rhizoremediation is rarely studied. Here, to address this problem, we firstly investigated the effect of the inducer salicylic acid on BaP rhizoremediation, rhizosphere BaP degraders, and PAH degradation-related genes by combining DNA-stable-isotope-probing, high-throughput sequencing, and gene function prediction. BaP removal in the rhizosphere was significantly increased by stimulation with salicylic acid, and the rhizosphere BaP-degrading microbial community structure was significantly changed. Fourteen microbes were responsible for the BaP metabolism, and most degraders, e.g. Aeromicrobium and Myceligenerans, were firstly linked with BaP biodegradation. The enrichment of the PAH-ring hydroxylating dioxygenase (PAH-RHD) gene in the heavy fractions of all ¹³C-treatments further indicated their involvement in the BaP biodegradation, which was also confirmed by the enrichment of dominant PAH degradation-related genes (e.g. PAH dioxygenase and protocatechuate 3,4-dioxygenase genes) based on gene function prediction. Overall, our study demonstrates that salicylic acid can enhance the rhizosphere BaP biodegradation by altering the community structure of rhizosphere BaP-degrading bacteria and the abundance of PAH degradation-related genes, which provides new insights into BaP rhizoremediation mechanisms in petroleum-contaminated sites.

Microbial communities in petroleum-contaminated sites: Structure and metabolisms

Over recent decades, hydrocarbon concentrations have been augmented in soil and water, mainly derived from accidents or operations that input crude oil and petroleum into the environment. Different techniques for remediation have been proposed and used to mitigate oil contamination. Among the available environmental recovery approaches, bioremediation stands out since these hydrocarbon compounds can be used as growth substrates for microorganisms. In turn, microorganisms can play an important role with significant contributions to the stabilization of impacted areas. In this review, we present the current knowledge about responses from natural microbial communities (using DNA barcoding, multiomics, and functional gene markers) and bioremediation experiments (microcosm and mesocosm) conducted in the presence of petroleum and chemical dispersants in different samples, including soil, sediment, and water. Additionally, we present metabolic mechanisms for aerobic/anaerobic hydrocarbon degradation and alternative pathways, as well as a summary of studies showing functional genes and other mechanisms involved in petroleum biodegradation processes.

Can biochar be an effective and reliable biostimulating agent for the remediation of hydrocarbon-contaminated soils?

Petroleum hydrocarbons represent one of the most common soil contaminants, whose presence poses a significant risk to soil biota and human health; for example, in Europe, hydrocarbon contamination accounts for more than 30% of contaminated sites. The use of biochar as a proposed alternative to the conventional remediation of soil contaminated with petroleum hydrocarbons has gained credence in recent times because of its cost-effectiveness and environmentally friendly nature. Biochar is a carbonaceous material produced by heating biomass in an oxygen-limited environment at high temperature. This review provides an overview of the application of biochar to remediate petroleum hydrocarbon-contaminated soils, with emphasis on the possibility of biochar functioning as a biostimulation agent. The properties of biochar were also examined. Furthermore, the mechanism, ecotoxicological impact and possible factors affecting biochar-based remediation are discussed. The review concludes by examining the drawbacks of biochar use in the remediation of hydrocarbon-contaminated soils and how to mitigate them. Biochar impacts soil microbes, which may result in the promotion of the degradation of petroleum hydrocarbons in the soil. Linear regression between bacterial population and degradation efficiency showed that R² was higher (0.50) and significant in treatment amended with biochar or both biochar and nutrient/fertiliser (p < 0.01), compared to treatment with nutrient/fertiliser only or no amendment (R² = 0.11). This suggest that one of the key impacts of biochar is enhancing microbial biomass and thus the biodegradation of petroleum hydrocarbons. Biochar represents a promising biostimulation agent for the remediation of hydrocarbon-contaminated soil. However, there remains key questions to be answered.

Phenanthrene degradation in soil using biochar hybrid modified bio-microcapsules: Determining the mechanism of action via comparative metagenomic analysis

A strategy involving biochar (BC) hybrid modification was developed to promote the bioremediation effect of degrading bacteria immobilized in layer-by-layer assembly (LBL) microcapsules for the treatment of phenanthrene (PHE) polluted soil. A taxonomic and functional metagenomic approach was used to investigate changes in the microbial community structures and functional gene compositions in the PHE-polluted soil during the bioremediation process. Biofortification with an initial PHE concentration of 100 mg kg^-1 dry soil in soils using the BC (3%) hybrid LBL bio-microcapsule (BC-LBL, 2.0 g kg^-1 dry soil, 10⁷ colony forming unite cell g^-1 dry soil) was faster; further, a higher PHE degradation efficiency (80.5% after 25 d) was achieved when compared with that by the LBL agent (66.2% after 25 d) used. Sphingomonas, Streptomyces, Gemmatirosa, Ramlibacter, Flavisolibacter, Phycicoccus, Micromonospora, Acidobacter, Mycobacterium and Gemmatimonas were more abundant in BC-LBL treatment than those in LBL one. Functional gene annotation results showed that more gene number with BC-LBL treatment than those with LBL one. More abundant functions in the former were primarily related to the growth, reproduction, metabolism, and transportation of bacteria. BC hybridization promoting PHE degradation by microencapsulated bacteria may be due to the strong adsorption property of BC, which results in the enrichment of the nutrients that needed for bacterial growth and reproduction, as well as enhancing the mass transfer performance of PHE to BC-LBL; Meanwhile, BC could also stimulate and improve the metabolism and membrane transportation of the degrading bacteria, and finally improving the degradation function.

Root exudates enhance the PAH degradation and degrading gene abundance in soils

Root exudates could influence the bioavailability of polycyclic aromatic hydrocarbons (PAHs), provide nutrients for soil microorganisms, and affect PAH biodegradation. However, it remains unclear how a bacterial community and its PAH-degrading genes play crucial roles in PAH biodegradation and respond to root exudates. In this study, a 32-day soil microcosm study was conducted to explore the impacts of artificial and actual root exudates on PAH degradation, degrading genes, and bacterial community structure. The results showed that 10-100 mg DOC/kg artificial and actual root exudates promoted the degradation of naphthalene, phenanthrene, and pyrene in soils, and their percent removal increased initially and then decreased with the increasing root exudates. Quantitative polymerase chain reaction analysis and 16S rRNA gene high-throughput sequencing suggested that the artificial root exudates significantly promoted the Nocardioides and Arthrobacter genera, which may harbor the nidA gene (the representative PAH-degrading gene from Gram-positive bacteria). In contrast, actual root exudates significantly stimulated the Pseudomonas genus that may harbor the nahAc gene (the representative PAH-degrading gene from Gram-negative bacteria). The correlation analysis further indicated that the absolute abundance of PAH degraders and degrading genes had strong correlations with PAH degradation efficiency. Therefore, these findings suggest that root exudates enhanced PAH biodegradation probably due to increases in abundance of both PAH-degraders and their degrading genes.

Bacterial communities and functional genes stimulated during phenanthrene degradation in soil by bio-microcapsules

In this study, a taxonomic and functional metagenomic method was used to investigate the difference produced between degrading bacteria immobilized in layer-by-layer assembly (LBL) microcapsules or not during the bioremediation of a soil polluted with phenanthrene (PHE). Bioaugmentation with LBL microcapsule immobilized degrading bacteria could result in different changes of native microbial communities, shifting the functional gene constructions of polluted soils. The LBL treatment enhanced PHE degradation (initial concentration of 100 mg kg^-1 dry soil) by 60% after 25 d compared to the free bacteria (FB). The enhancing effect of PHE degradation produced by the LBL treatment was found to be significantly associated with some crucial phyla (e.g., Bacteroides, Gemmatimonadetes and Acidobacteria) and genera including Streptomyces, Ramlibacter, Mycobacterium, Phycicoccus, Gemmatirosa, Flavisolibacter, Micromonospora, Acid_Candidatus_Koribacter and Gemmatimonas. The main differences of functional metagenomics between LBL and FB treatments were observed in higher levels in metabolism of aromatic hydrocarbons and its related functions or enzymes in the former, e.g., membrane transport systems, binding, substrate transporter, cleavage enzymes, dehydrogenation, oxidase, esterase and glycosidase, greatly favoring PHE mineralization. Therefore, our results provide useful findings on understanding of how immobilization strategies can influence the taxonomic and functional gene composition in soils, as well as polycyclic aromatic hydrocarbons (PAH) degradation.

Response of soil bacterial communities to polycyclic aromatic hydrocarbons during the phyto-microbial remediation of a contaminated soil

Rhizo-box experiments were conducted to analyze the phyto-microbial remediation potential of a grass (Lolium multiflorum L.) and a crop (Glycine max L.) combined with exogenous strain (Pseudomonas sp.) for polycyclic aromatic hydrocarbons (PAHs) contaminated soils. The dynamics of bacterial community composition, abundances of 16 S rDNA and ring hydroxylating dioxygenases (RHDα) genes, and removal of PAHs were evaluated and compared on four culture stages (days 0, 10, 20, and 30). The results showed that 8.65%-47.42% of Σ12 PAHs were removed after 30 days of cultivation. Quantitative polymerase chain reaction (qPCR) analysis indicated that treatments with soybean and ryegrass rhizosphere markedly increased the abundances of total bacteria and PAH-degraders, especially facilitated the growth of gram-negative degrading bacteria. Flavobacterium sp. and Pseudomonas sp. were the main and active strains in the control soil. However, the presence of plants and/or exogenous Pseudomonas sp. changed the soil bacterial community structure and modified the bacterial diversity of PAH-degraders. On the whole, this study showed that the high molecular weight PAHs removal efficiency of phyto-microbial remediation with ryegrass was better than those of remediation with soybean. Furthermore, the removals of PAHs strongly coincided with the abundance of PAH-degraders and bacterial community structure.

Acute effects of PAH contamination on microbial community of different forest soils

Polycyclic aromatic hydrocarbons (PAHs) are hazardous organic compounds with mutagenic, genotoxic and carcinogenic properties. Although PAHs in soil can cause toxicity to microorganisms, the microbial community is able to degrade these compounds. For this reason, it is important to study acute and short-term effects of PAH contamination on soil microbial community, also to shed light on its possible exploitation in soil restoration. The effects of acute PAH contamination on the structure and metabolic activity of microbial communities in three forest (beech, holm oak, black pine) soils were studied. The soils were spiked with phenanthrene, pyrene or benzo[a]pyrene and incubated in experimental mesocosms, under controlled conditions. Enzymatic activities (laccase, total peroxidase and hydrolase), as well as microbial biomass and community structure (through phospholipid fatty acid and ergosterol analyses), were evaluated in the three soil systems 4 days after contamination and compared to no-spiked soils. In soil under holm oak, there was a stimulation of Gram+ bacteria after contamination with all the 3 PAHs, whereas in soil under pine, pyrene and phenanthrene additions mainly stimulated fungi and actinomycetes.

Toxicity of UV filters on marine bacteria: Combined effects with damaging solar radiation

Organic UV filters are of emerging concern due to their occurrence and persistence in coastal ecosystems. Because marine bacteria are crucial in the major biogeochemical cycles, there is an urgent need to understand to what extent these microorganisms are affected by those chemicals. This study deciphers the impact of five common sunscreen UV filters on twenty-seven marine bacteria, combining both photobiology and toxicity analysis on environmentally relevant species. Seven bacteria were sensitive to different organic UV filters at 1000 μg L^-1, including octinoxate and oxybenzone. This is the first report demonstrating inhibition of bacterial growth from 100 μg L^-1. None of the UV filters showed any toxicity at 1000 μg L^-1 on stationary phase cells, demonstrating that physiological state was found to be a key parameter in the bacterial response to UV-filters. Indeed, non-growing bacteria were resistant to UV filters whereas growing cells exhibited UV filter dependent sensitivity. Octinoxate was the most toxic chemical at 1000 μg L^-1 on growing cells. Interestingly, photobiology experiments revealed that the toxicity of octinoxate and homosalate decreased after light exposure while the other compounds were not affected. In terms of environmental risk characterization, our results revealed that the increasing use of sun blockers could have detrimental impacts on bacterioplanktonic communities in coastal areas. Our findings contribute to a better understanding of the impact of the most common UV filters on bacterial species and corroborate the importance to consider environmental parameters such as solar radiation in ecotoxicology studies.

The legacy of industrial pollution in estuarine sediments: spatial and temporal variability implications for ecosystem stress

The direct impacts of anthropogenic pollution are widely known public and environmental health concerns, and details on the indirect impact of these are starting to emerge, for example affecting the environmental microbiome. Anthropogenic activities throughout history with associated pollution burdens are notable contributors. Focusing on the historically heavily industrialised River Clyde, Scotland, we investigate spatial and temporal contributions to stressful/hostile environments using a geochemical framework, e.g. pH, EC, total organic carbon and potentially toxic elements: As, Co, Cr, Cu, Ni, Pb and Zn and enrichment indicators. With regular breaches of the sediment quality standards in the estuarine system we focused on PTE correlations instead. Multivariate statistical analysis (principle component analysis) identifies two dominant components, PC1: As, Cr, Cu, Pb and Zn, as well as PC2: Ni, Co and total organic carbon. Our assessment confirms hot spots in the Clyde Estuary indicative of localised inputs. In addition, there are sites with high variability indicative of excessive mixing. We demonstrate that industrialised areas are dynamic environmental sites dependant on historical anthropogenic activity with short-scale variation. This work supports the development of 'contamination' mapping to enable an assessment of the impact of historical anthropogenic pollution, identifying specific 'stressors' that can impact the microbiome, neglecting in estuarine recovery dynamics and potentially supporting the emergence of antimicrobial resistance in the environment.

Biodegradation of naphthenic acids: identification of Rhodococcus opacus R7 genes as molecular markers for environmental monitoring and their application in slurry microcosms

Nowadays, the increase of the unconventional oil deposit exploitation and the amount of oil sands process-affected waters (OSPW) in tailing ponds emerges the importance of developing bio-monitoring strategies for the restoration of these habitats. The major constituents of such deposits are naphthenic acids (NAs), emerging contaminant mixtures with toxic and recalcitrant properties. With the aim of developing bio-monitoring strategies based on culture-independent approach, we identified genes coding for enzymes involved in NA degradation from Rhodococcus opacus R7 genome, after the evaluation of its ability to mineralize model NAs. R. opacus R7 whole-genome analysis unveiled the presence of pobA and chcpca gene clusters putatively involved in NAs degradation. Gene expression analysis demonstrated the specific induction of R7 aliA1 gene, encoding for a long-chain-fatty-acid-CoA ligase, in the presence of cyclohexanecarboxylic acid (CHCA) and hexanoic acid (HA), selected as representative compounds for alicyclic and linear NAs, respectively. Therefore, aliA1 gene was selected as a molecular marker to monitor the biodegradative potential of slurry-phase sand microcosms in different conditions: spiked with CHCA, in the presence of R. opacus R7, the autochthonous microbial community, and combining these factors. Results revealed that the aliA1-targeting culture-independent approach could be a useful method for bio-monitoring of NA degradation in a model laboratory system.

The distinct response of phenanthrene enriched bacterial consortia to different PAHs and their degradation potential: a mangrove sediment microcosm study

Understanding the microbial community succession to polycyclic aromatic hydrocarbons (PAHs) and identification of important degrading microbial groups are crucial for the designing of appropriate bioremediation strategies. In the present study, two distinct phenanthrene enriched bacterial consortia were treated against high molecular weight (Pyrene, Benzo (a) pyrene and Benzo (a) fluoranthene) and the response was studied in term of taxonomic variations by using High Throughput Illumina sequencing and qPCR analysis. Overall, the type of PAHs significantly affected the composition and the relative abundance of bacterial communities while no obvious difference was detected between bacterial communities of benzo (a) pyrene and benzo (a) fluoranthene treatments. Genera, Novosphingobium, Pseudomonas, Flavobacterium, Mycobacterium, Hoeflae, and Algoriphagus dominated all PAHs treatment groups indicating that they could be the key PAHs degrading phylotypes. Due to the higher abundance of gram-negative PAH-ring hydroxylating dioxygenase gene than that of gram-positive bacteria in all treated groups, we speculated that gram-negative bacteria may contribute more in the PAH degradation. The studied sediments harbored rich PAHs degrading bacterial assemblages involved in both low and high molecular weight PAHs and these findings provided new insight into the perspective of microbial PAHs bioremediation in the mangrove ecosystem.

DNA stable isotope probing reveals contrasted activity and phenanthrene-degrading bacteria identity in a gradient of anthropized soils

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil organic pollutants. Although PAH-degrading bacteria are present in almost all soils, their selection and enrichment have been shown in historically high PAH contaminated soils. We can wonder if the effectiveness of PAH biodegradation and the PAH-degrading bacterial diversity differ among soils. The stable isotope probing (SIP) technique with 13C-phenanthrene (PHE) as a model PAH was used to: (i) compare for the first time a range of 10 soils with various PAH contamination levels, (ii) determine their PHE-degradation efficiency and (iii) identify the active PHE-degraders using 16S rRNA gene amplicon sequencing from 13C-labeled DNA. Surprisingly, the PHE degradation rate was not directly correlated to the initial level of total PAHs and phenanthrene in the soils, but was mostly explained by the initial abundance and richness of soil bacterial communities. A large diversity of PAH-degrading bacteria was identified for seven of the soils, with differences among soils. In the soils where the PHE degradation activities were the higher, Mycobacterium species were always the dominant active PHE degraders. A positive correlation between PHE-degradation level and the diversity of active PHE-degraders (Shannon index) supported the hypothesis that cooperation between strains led to a more efficient PAH degradation.

Microbial metatranscriptomic investigations across contaminant gradients of the Detroit River

Microbial community function in freshwater sediments is influenced by the presence and persistence of anthropogenic pollutants, yet simultaneously imposes significant control on their transformation. Thus, microbes provide valuable ecosystem services in terms of biodegradation and bioindicators of compromised habitats. From a remediation perspective it is valuable to leverage the suite of microbial genes at the transcriptional level that are active in either natural versus stressed environments to provide insight into the cycling and fate of contaminants. Metatranscriptomic analysis of total bacterial and archaeal messenger RNA (mRNA) is a useful tool in this facet and was applied to sediments sampled from the Detroit River; a binational Area of Concern (AOC) in the Great Lakes. Previously established sediment surveys and modelling delineated the river into contaminant gradients based on concentrations of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and metals. Differential expression analysis through DESeq2 revealed that microbial transcripts associated with nitrate reduction, methanogenesis, and beta-oxidation were significant in legacy polluted sediments and linked with energetic pathways key in the generation of cellular currencies (acetyl-CoA, succinyl-CoA). Gluconeogenesis and polyester synthesis also showed high abundance in contaminated regions, along with increased expression of stress response genes and transposons, despite decreases in community α-diversity. Aromatic cleavage genes were detected, but in low abundance across the contaminant gradient. These results suggest that microbial communities within the Detroit River exploit unique anabolic and catabolic pathways to derive and store energy from legacy organic contaminants while simultaneously recruiting stress-response and gene transfer mechanisms to cope with xenobiotic pressures. By coupling well-resolved chemical datasets with metatranscriptomics, this study adds to the spatial understanding of in-situ microbial activities in pristine and perturbed freshwater sediments.

A PAH-degrading bacterial community enriched with contaminated agricultural soil and its utility for microbial bioremediation

A bacterial community was enriched with polycyclic aromatic hydrocarbons (PAHs) polluted soil to better study PAH degradation by indigenous soil bacteria. The consortium degraded more than 52% of low molecular weight and 35% of high molecular weight (HMW) PAHs during 16 days in a soil leachate medium. 16S rRNA gene high-throughput sequencing and quantitative polymerase chain reaction analyses for alpha subunit genes of ring-hydroxylating-dioxygenase (RHDα) suggested that Proteobacteria and Actinobacteria at the phylum level, Pseudomonas, Methylobacillus, Nocardioides, Methylophilaceae, Achromobacter, Pseudoxanthomonas, and Caulobacter at the generic level were involved in PAH degradation and might have the ability to carry RHDα genes (nidA and nahAc). The community was selected and collected according to biomass and RHDα gene contents, and added back to the PAH-polluted soil. The 16 EPA priority PAHs decreased from 95.23 to 23.41 mg kg^-1 over 35 days. Compared with soil without the introduction of this bacterial community, adding the community with RHDα genes significantly decreased soil PAH contents, particularly HMW PAHs. The metabolic rate of PAHs in soil was positively correlated with nidA and nahAc gene contents. These results indicate that adding an indigenous bacterial consortium containing RHDα genes to contaminated soil may be a feasible and environmentally friendly method to clean up PAHs in agricultural soil.

Soil Properties and Multi-Pollution Affect Taxonomic and Functional Bacterial Diversity in a Range of French Soils Displaying an Anthropisation Gradient

The intensive industrial activities of the twentieth century have left behind highly contaminated wasteland soils. It is well known that soil parameters and the presence of pollutants shape microbial communities. But in such industrial waste sites, the soil multi-contamination with organic (polycyclic aromatic hydrocarbons, PAH) and metallic (Zn, Pb, Cd) pollutants and long-term exposure may induce a selection pressure on microbial communities that may modify soil functioning. The aim of our study was to evaluate the impact of long-term multi-contamination and soil characteristics on bacterial taxonomic and functional diversity as related to the carbon cycle. We worked on 10 soils from northeast of France distributed into three groups (low anthropised controls, slag heaps, and settling ponds) based on their physico-chemical properties (texture, C, N) and pollution level. We assessed bacterial taxonomic diversity by 16S rDNA Illumina sequencing, and functional diversity using Biolog® and MicroResp™ microtiter plate tools. Although taxonomic diversity at the phylum level was not different among the soil groups, many operational taxonomic units were influenced by metal or PAH pollution, and by soil texture and total nitrogen content. Functional diversity was not influenced by PAH contamination while metal pollution selected microbial communities with reduced metabolic functional diversity but more tolerant to zinc. Limited microbial utilisation of carbon substrates in metal-polluted soils was mainly due to the nitrogen content. Based on these two observations, we hypothesised that reduced microbial activity and lower carbon cycle-related functional diversity may have contributed to the accumulation of organic matter in the soils that exhibited the highest levels of metal pollution.

pahE, a Functional Marker Gene for Polycyclic Aromatic Hydrocarbon-Degrading Bacteria

The characterization of native polycyclic aromatic hydrocarbon (PAH)-degrading bacteria is significant for understanding the PAH degradation process in the natural environment and developing effective remediation technologies. Most previous investigations of PAH-degrading bacteria in environmental samples employ pahAc, which encodes the α-subunit of PAH ring-hydroxylating dioxygenase, as a functional marker gene. However, the poor phylogenetic resolution and nonspecificity of pahAc result in a misestimation of PAH-degrading bacteria. Here, we propose a PAH hydratase-aldolase-encoding gene, pahE, as a superior biomarker for PAH-degrading bacteria. Comparative phylogenetic analysis of the key enzymes involved in the upper pathway of PAH degradation indicated that pahE evolved dependently from a common ancestor. A phylogenetic tree constructed based on PahE is largely congruent with PahAc-based phylogenies, except for the dispersion of several clades of other non-PAH-degrading aromatic hydrocarbon dioxygenases present in the PahAc tree. Analysis of pure strains by PCR confirmed that pahE can specifically distinguish PAH-degrading bacteria, while pahAc cannot. Illumina sequencing of pahE and pahAc amplicons showed more genotypes and higher specificity and resolution for pahE Novel reads were also discovered among the pahE amplicons, suggesting the presence of novel PAH-degrading populations. These results suggest that pahE is a more powerful biomarker for exploring the ecological role and degradation potential of PAH-degrading bacteria in ecosystems, which is significant to the bioremediation of PAH pollution and environmental microbial ecology.IMPORTANCE PAH contamination has become a worldwide environmental issue because of the potential toxic effects on natural ecosystems and human health. Biotransformation and biodegradation are considered the main natural elimination forms of PAHs from contaminated sites. Therefore, the knowledge of the degradation potential of the microbial community in contaminated sites is crucial for PAH pollution bioremediation. However, the nonspecificity of pahAc as a functional marker of PAH-degrading bacteria has resulted neither in a reliable prediction of PAH degradation potential nor an accurate assessment of degradation. Here, we introduced pahE encoding the PAH hydratase-aldolase as a new and better functional marker gene of PAH-degrading bacteria. This study provides a powerful molecular tool to more effectively explore the ecological role and degradation potential of PAH-degrading bacteria in ecosystems, which is significant to the bioremediation of PAH pollution.

Enhanced polycyclic aromatic hydrocarbons degradation in rhizosphere soil planted with tall fescue: Bacterial community and functional gene expression mechanisms

To investigate the bacterial mechanisms of polycyclic aromatic hydrocarbons (PAHs) degradation in an aged-contaminated agricultural soil planted with tall fescue (Festuca arundinacea), a rhizo-box experiment was carried out for 60 d. Shifts in bacterial community structure in the soils during the experiment were performed using denaturing gradient gel electrophoresis. The abundance and activity of total bacteria and PAH-degraders were measured by quantification of 16S rDNA, PAH-ring hydroxylating dioxygenase (PAH-RHDα) genes and their transcripts, respectively. The residual PAH concentrations were monitored using high-performance liquid chromatography analysis. Results showed that the removal percentage of total PAHs in rhizosphere soil was 11% higher than that in unplanted soil. Soil bacteria were dominated by Alphaproteobacteria (48.4%) and Gammaproteobacteria (25.8%). Tall fescue positively affected the abundance and activity of total bacteria in the soil, and stimulated RHDα gram-negative (GN) gene expression while inhibiting RHDα gram-positive gene expression. PAH dissipation in rhizosphere soil could be ascribed to modifications in the bacterial community structure, increase in the abundance of PAH-degraders, and enhancement of the RHDα GN gene expression during the incubation.

Opportunistic Bacteria Dominate the Soil Microbiome Response to Phenanthrene in a Microcosm-Based Study

Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDα) encoding a ring hydroxylating dioxygenase involved in PAH degradation were examined during degradation of phenanthrene in a podzolic soil from the site of a former timber treatment facility. The 10,000-fold greater abundance of this gene associated with Gram-positive bacteria found in phenanthrene-amended soil compared to unamended soil indicated the likely role of Gram-positive bacteria in PAH degradation. In contrast, the abundance of the Gram-negative PAHs-RHDα gene was very low throughout the experiment. While phenanthrene induced increases in the abundance of a small number of OTUs from the Actinomycetales and Sphingomonadale, most of the remainder of the community remained stable. A single unclassified OTU from the Micrococcaceae family increased ~20-fold in relative abundance, reaching 32% of the total sequences in amended microcosms on day 7 of the experiment. The relative abundance of this same OTU increased 4.5-fold in unamended soils, and a similar pattern was observed for the second most abundant PAH-responsive OTU, classified into the Sphingomonas genus. Furthermore, the relative abundance of both of these OTUs decreased substantially between days 7 and 17 in the phenanthrene-amended and control microcosms. This suggests that their opportunistic phenotype, in addition to likely PAH-degrading ability, was determinant in the vigorous growth of dominant PAH-responsive OTUs following phenanthrene amendment. This study provides new information on the temporal response of soil microbial communities to the presence and degradation of a significant environmental pollutant, and as such has the potential to inform the design of PAH bioremediation protocols.

Response of soil phosphatase activities to contamination with two types of tar oil

Tar oil is a complex mixture of hydrocarbon compounds obtained from high-temperature distillation of coal tar. It has been used for over 100 years from now to protect wood and has been applied to wood products, primary utility poles, and railroad ties by pressure methods. Composition of the tar oil depends on the source and typically consists of 85% polycyclic aromatic hydrocarbons (PAHs), 10% phenolic compounds, and 5% heterocyclic compounds. In this research, we performed the laboratory experiment to compare two types of tar oil: C and GX-Plus, and their effects on P-cycling enzymes (phosphatases) in sandy loam and loamy sand. Tar oil was applied to soil samples at the following doses: 2, 10, and 50 g kg^-1. Soil without tar oil was used as a control sample. The experiment showed that the contamination of soil with tar oil affects the enzyme activities measured and with this most probably the P-cycle in soil. Phosphomonoesterases were the most sensitive to the contamination of soil with both type of tar oil: typeC and type GX-Plus. Greater changes in the enzymatic activity were observed in the loamy sand. Moreover, the type C tar oil demonstrated higher toxicity for phosphatases than type GX-Plus.

High PAH degradation and activity of degrading bacteria during alfalfa growth where a contrasted active community developed in comparison to unplanted soil

PAH biodegradation in plant rhizosphere has been investigated in many studies, but the timescale of degradation and degrading bacteria activity was rarely considered. We explored the impact of plants on the temporal variability of PAH degradation, microbial abundance, activity, and bacterial community structure in a rhizotron experiment. A historically contaminated soil was spiked with PAHs, planted or not with alfalfa, over 22 days with sampling once a week. In both conditions, most of the spiked PAHs were dissipated during the first week, conducting to polar polycyclic aromatic compound production and to decreased richness and diversity of bacterial communities. We showed a rapid impact of the rhizosphere on PAH degradation via the increased activity of PAH-degrading bacteria. After 12 days, PAH degradation was significantly higher in the planted (100% degradation) than in unplanted (70%) soil. Gram-negative (Proteobacteria) PAH-dioxygenase genes and transcripts were higher in planted than unplanted soil and were correlated to the spiked PAH degradation. Conversely, Gram-positive (Actinobacteria) PAH-dioxygenase gene transcription was constant over time in both conditions. At 12 days, plant growth favored the activity of many Gammaproteobacteria (Pseudomonadaceae, Stenotrophomonas, and Acinetobacter) while in unplanted soil Alphaproteobacteria (Sphingomonadaceae, Sphingobium, and Magnetospirillum) and Actinobacteria (Iamia, Geodermatophilaceae, and Solirubrobacterales) were more active.

The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil

Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, the interactions between microbiome and plant roots in the process of rhizosphere mediated remediation of PAH still needs attention. Most of the current researches target PAH degradation by plant or single microorganism, separately, whereas the interactions between plants and whole microbiome are overlooked and its role has been ignored. This review summarizes recent knowledge of PAH degradation in the rhizosphere in the process of plant-microbiome interactions based on emerging omics approaches such as metagenomics, metatranscriptomics, metabolomics and metaproteomics. These omics approaches with combinations to bioinformatics tools provide us a better understanding in integrated activity patterns between plants and rhizosphere microbes, and insight into the biochemical and molecular modification of the meta-organisms (plant-microbiome) to maximize rhizoremediation activity. Moreover, a better understanding of the interactions could lead to the development of techniques to engineer rhizosphere microbiome for better hydrocarbon degradation.

Characterization of a Microbial Consortium for the Bioremoval of Polycyclic Aromatic Hydrocarbons (PAHs) in Water

Pollution of freshwater ecosystems from polycyclic aromatic hydrocarbons (PAHs) is a global concern. The US Environmental Protection Agency (EPA) has included the PAHs pyrene, phenanthrene, and naphthalene among the 16 priority compounds of special concern for their toxicological effects. The aim of this study was to adapt and characterize a microbial consortium from ore waste with the potential to remove these three PAHs from water. This microbial consortium was exposed to the target PAHs at levels of 5, 10, 20, 50, and 100 mg L−1 for 14 days. PAH bioremoval was measured using the analytical technique of solid phase microextraction, followed by gas chromatography mass spectrometry (SPME-GC/MS). The results revealed that up to 90% of the target PAHs can be removed from water after 14 days at a concentration level of 100 mg L−1. The predominant group of microorganisms identified at the phylum taxonomic level were the Proteobacteria, while the Actinobacteria were the predominant subgroup. The removal of phenanthrene, naphthalene, and pyrene predominantly occurred in specimens of genera Stenotrophomonas, Williamsia, and Chitinophagaceae, respectively. This study demonstrates that the use of specific microorganisms is an alternative method of reducing PAH levels in water.

Half-lives of PAHs and temporal microbiota changes in commonly used urban landscaping materials

Background

Polycyclic aromatic hydrocarbons (PAHs) accumulate in urban soils, and PAH contamination can change soil microbial community composition. Environmental microbiota is associated with human commensal microbiota, immune system and health. Therefore, studies investigating the degradation of PAHs, and the consequences of soil pollution on microbial communities in urban landscaping materials, are crucial.

Methods

Four landscaping materials (organic matter 1, 2, 13 and 56%) were contaminated with PAHs commonly found at urban sites (phenanthrene, fluoranthene, pyrene, chrysene and benzo(b)fluoranthene) in PAH concentrations that reflect urban soils in Finland (2.4 µg g ^-1 soil dry weight). PAHs were analyzed initially and after 2, 4, 8 and 12 weeks by gas chromatography-mass spectrometry. Half-lives of PAHs were determined based on 12-weeks degradation. Bacterial communities were analyzed at 1 and 12 weeks after contamination using Illumina MiSeq 16S rRNA gene metabarcoding.

Results

Half-lives ranged from 1.5 to 4.4 weeks for PAHs with relatively low molecular weights (phenanthrene, fluoranthene and pyrene) in landscaping materials containing 1–2% organic matter. In contrast, in materials containing 13% and 56% organic matter, the half-lives ranged from 2.5 to 52 weeks. Shorter half-lives of phenanthrene and fluoranthene were thus associated with low organic matter content. The half-life of pyrene was inversely related to the relative abundance of Beta-, Delta- and Gammaproteobacteria, and diversity of Bacteroidetes and Betaprotebacteria. Compounds with higher molecular weights followed compound-specific patterns. Benzo(b)fluoranthene was resistant to degradation and half-life of chrysene was shorter when the relative abundance of Betaproteobacteria was high. Temporal microbiota changes involved increase in the relative abundance of Deltaproteobacteria and decrease in genera Flavobacterium and Rhodanobacter. Exposure to PAHs seems to adjust microbial community composition, particularly within class Beta- and Deltaproteobacteria.

Conclusions

In this study, PAH degradation depended on the organic matter content and bacterial community composition of landscaping materials. Contamination seems to alter bacterial community composition in landscaping materials depending on material type. This alteration includes changes in bacterial phyla associated with human health and immune system. This may open new possibilities for managing urban environments by careful selection of landscaping materials, to benefit health and wellbeing.

The influence of e-waste recycling on the molecular ecological network of soil microbial communities in Pakistan and China

Primitive electronic waste (e-waste) recycling releases large amounts of organic pollutants and heavy metals into the environment. As crucial moderators of geochemical cycling processes and pollutant remediation, soil microbes may be affected by these contaminants. We collected soil samples heavily contaminated by e-waste recycling in China and Pakistan, and analyzed the indigenous microbial communities. The results of this work revealed that the microbial community composition and diversity, at both whole and core community levels, were affected significantly by polycyclic aromatic hydrocarbons (PAHs), polybrominated diphenyl ethers (PBDEs) and heavy metals (e.g., Cu, Zn, and Pb). The geographical distance showed limited impacts on microbial communities compared with geochemical factors. The constructed ecological network of soil microbial communities illustrated microbial co-occurrence, competition and antagonism across soils, revealing the response of microbes to soil properties and pollutants. Two of the three main modules constructed with core operational taxonomic units (OTUs) were sensitive to nutrition (total organic carbon and total nitrogen) and pollutants. Five key OTUs assigned to Acidobacteria, Proteobacteria, and Nitrospirae in ecological network were identified. This is the first study to report the effects of e-waste pollutants on soil microbial network, providing a deeper understanding of the ecological influence of crude e-waste recycling activities on soil ecological functions.

The abundance of health-associated bacteria is altered in PAH polluted soils-Implications for health in urban areas?

Long-term exposure to polyaromatic hydrocarbons (PAHs) has been connected to chronic human health disorders. It is also well-known that i) PAH contamination alters soil bacterial communities, ii) human microbiome is associated with environmental microbiome, and iii) alteration in the abundance of members in several bacterial phyla is associated with adverse or beneficial human health effects. We hypothesized that soil pollution by PAHs altered soil bacterial communities that had known associations with human health. The rationale behind our study was to increase understanding and potentially facilitate reconsidering factors that lead to health disorders in areas characterized by PAH contamination. Large containers filled with either spruce forest soil, pine forest soil, peat, or glacial sand were left to incubate or contaminated with creosote. Biological degradation of PAHs was monitored using GC-MS, and the bacterial community composition was analyzed using 454 pyrosequencing. Proteobacteria had higher and Actinobacteria and Bacteroidetes had lower relative abundance in creosote contaminated soils than in non-contaminated soils. Earlier studies have demonstrated that an increase in the abundance of Proteobacteria and decreased abundance of the phyla Actinobacteria and Bacteroidetes are particularly associated with adverse health outcomes and immunological disorders. Therefore, we propose that pollution-induced shifts in natural soil bacterial community, like in PAH-polluted areas, can contribute to the prevalence of chronic diseases. We encourage studies that simultaneously address the classic “adverse toxin effect” paradigm and our novel “altered environmental microbiome” hypothesis.

Environmental Pollutant Benzo[a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota

Benzo[a]pyrene (B[a]P) is a ubiquitous, persistent, and carcinogenic pollutant that belongs to the large family of polycyclic aromatic hydrocarbons. Population exposure primarily occurs via contaminated food products, which introduces the pollutant to the digestive tract. Although the metabolism of B[a]P by host cells is well known, its impacts on the human gut microbiota, which plays a key role in health and disease, remain unexplored. We performed an in vitro assay using 16S barcoding, metatranscriptomics and volatile metabolomics to study the impact of B[a]P on two distinct human fecal microbiota. B[a]P exposure did not induce a significant change in the microbial structure; however, it altered the microbial volatolome in a dose-dependent manner. The transcript levels related to several metabolic pathways, such as vitamin and cofactor metabolism, cell wall compound metabolism, DNA repair and replication systems, and aromatic compound metabolism, were upregulated, whereas the transcript levels related to the glycolysis-gluconeogenesis pathway and bacterial chemotaxis toward simple carbohydrates were downregulated. These primary findings show that food pollutants, such as B[a]P, alter human gut microbiota activity. The observed shift in the volatolome demonstrates that B[a]P induces a specific deviation in the microbial metabolism.

Soil properties and microbial ecology of a paddy field after repeated applications of domestic and industrial sewage sludges

The effects of repeated application of two types of sewage sludge, domestic and industrial (petrochemical, PSS) sludges, into paddy fields over a 5-year period on the soil properties and microbial ecology were studied and compared with conventional NPK fertilizer application. Soil organic matter and total nitrogen contents were significantly higher in the two sludge treatments than that in fertilized plots after 5 years. Soil concentrations of potentially toxic metals were low after 5 years of both sludge treatments, but the polycyclic aromatic hydrocarbons (PAHs) showed differences between the two sludge types. Concentrations of high-molecular-weight PAHs were significantly higher (p < 0.05) in the petrochemical sludge treatment than the domestic sludge treatment or the fertilizer control, although the total concentrations of 16 types of PAH in the petrochemical sludge treatment were only slightly higher than in the domestic sludge treatment and the control. The biological toxicity of soil dimethyl sulfoxide extracts from the petrochemical sludge treatment was also significantly higher (p < 0.05) than those from the fertilizer control and the domestic sludge treatment when evaluated using Photobacterium phosphoreum T3. Both types of sewage sludge increased soil microbial activity, but only the petrochemical sludge led to enrichment with specific PAH degraders such as Mycobacterium, Nocardioides, and Sphingomonas.

Benzo(a)pyrene degradation and microbial community responses in composted soil

Benzo(a)pyrene degradation was compared in soil that was either composted, incubated at a constant temperature of 22 °C, or incubated under a temperature regime typical of a composting process. After 84 days, significantly more (61%) benzo(a)pyrene was removed from composted soil compared to soils incubated at a constant temperature (29%) or at composting temperatures (46%). Molecular fingerprinting approaches indicated that in composted soils, bacterial community changes were driven by both temperature and organic amendment, while fungal community changes were primarily driven by temperature. Next-generation sequencing data revealed that the bacterial community in composted soil was dominated by Actinobacteria (order Actinomycetales), Firmicutes (class Bacilli), and Proteobacteria (classes Gammaproteobacteria and Alphaproteobacteria), regardless of whether benzo(a)pyrene was present or not. The relative abundance of unclassified Actinomycetales (Actinobacteria) was significantly higher in composted soil when degradation was occurring, indicating a potential role for these organisms in benzo(a)pyrene metabolism. This study provides baseline data for employing straw-based composting strategies for the removal of high molecular weight PAHs from soil and contributes to the knowledge of how microbial communities respond to incubation conditions and pollutant degradation.

pH is the primary determinant of the bacterial community structure in agricultural soils impacted by polycyclic aromatic hydrocarbon pollution

Acidification and pollution are two major threats to agricultural ecosystems; however, microbial community responses to co-existed soil acidification and pollution remain less explored. In this study, arable soils of broad pH (4.26-8.43) and polycyclic aromatic hydrocarbon (PAH) gradients (0.18-20.68 mg kg-1) were collected from vegetable farmlands. Bacterial community characteristics including abundance, diversity and composition were revealed by quantitative PCR and high-throughput sequencing. The bacterial 16S rRNA gene copies significantly correlated with soil carbon and nitrogen contents, suggesting the control of nutrients accessibility on bacterial abundance. The bacterial diversity was strongly related to soil pH, with higher diversity in neutral samples and lower in acidic samples. Soil pH was also identified by an ordination analysis as important factor shaping bacterial community composition. The relative abundances of some dominant phyla varied along the pH gradient, and the enrichment of a few phylotypes suggested their adaptation to low pH condition. In contrast, at the current pollution level, PAH showed marginal effects on soil bacterial community. Overall, these findings suggest pH was the primary determinant of bacterial community in these arable soils, indicative of a more substantial influence of acidification than PAH pollution on bacteria driven ecological processes.

Comparative Investigation of Bacterial, Fungal, and Archaeal Community Structures in Soils in a Typical Oilfield in Jianghan, China

Agricultural soils in oilfields have high risk for polycyclic aromatic hydrocarbon (PAH) pollution. In this study, from the Jianghan Oilfield (Hubei Province, China) with a history of >50 years, 7 soil samples (OS-1 to OS-7) were collected. Subsequently, the bacterial, archaeal, and fungal community structures were investigated by Illumina MiSeq sequencing, and the relationship between microbial community structure and soil PAH content was analyzed. The results indicated that bacterial and archaeal Chao 1 indices showed a significantly negative relationship with soil PAH content, and only the bacterial Shannon index had a significantly negative relationship with soil PAH content. Moreover, the community structure of bacteria (r ² = 0.9001, p = 0.013) showed a stronger correlation with PAH content than that of fungi (r ² = 0.7357, p = 0.045), and no significant relationship was found between archaeal community structure (r ² = 0.4553, p = 0.262) and soil PAH content. In addition, the relative greater abundances of some bacterial genus belonging to Actinobacteria (Mycobacterium and Micromonospora) and Proteobacteria (Pseudomonas, Lysobacter, Idiomarina, Oxalobacteraceae, and Massilia), fungal genus belonging to Ascomycota (Sordariales and Pleosporales), and archaeal phylum (Euryarchaeota) were detected in the soil samples (OS-3 and OS-5) with greater PAH content. In summary, soil PAHs showed an obvious influence and selectivity on the soil microbiota. Furthermore, compared with fungi and archaea, bacteria was more sensitive to soil PAH pollution, and the diversity indices and community structure of bacteria both might be suitable indicators for assessment of soil PAH stress on the soil ecosystem.

Polycyclic Aromatic Hydrocarbon-Induced Changes in Bacterial Community Structure under Anoxic Nitrate Reducing Conditions

Although bacterial anaerobic degradation of mono-aromatic compounds has been characterized in depth, the degradation of polycyclic aromatic hydrocarbons (PAHs) such as naphthalene has only started to be understood in sulfate reducing bacteria, and little is known about the anaerobic degradation of PAHs in nitrate reducing bacteria. Starting from a series of environments which had suffered different degrees of hydrocarbon pollution, we used most probable number (MPN) enumeration to detect and quantify the presence of bacterial communities able to degrade several PAHs using nitrate as electron acceptor. We detected the presence of a substantial nitrate reducing community able to degrade naphthalene, 2-methylnaphthalene (2MN), and anthracene in some of the sites. With the aim of isolating strains able to degrade PAHs under denitrifying conditions, we set up a series of enrichment cultures with nitrate as terminal electron acceptor and PAHs as the only carbon source and followed the changes in the bacterial communities throughout the process. Results evidenced changes attributable to the imposed nitrate respiration regime, which in several samples were exacerbated in the presence of the PAHs. The presence of naphthalene or 2MN enriched the community in groups of uncultured and poorly characterized organisms, and notably in the Acidobacteria uncultured group iii1-8, which in some cases was only a minor component of the initial samples. Other phylotypes selected by PAHs in these conditions included Bacilli, which were enriched in naphthalene enrichments. Several nitrate reducing strains showing the capacity to grow on PAHs could be isolated on solid media, although the phenotype could not be reproduced in liquid cultures. Analysis of known PAH anaerobic degradation genes in the original samples and enrichment cultures did not reveal the presence of PAH-related nmsA-like sequences but confirmed the presence of bssA-like genes related to anaerobic toluene degradation. Altogether, our results suggest that PAH degradation by nitrate reducing bacteria may require the contribution of different strains, under culture conditions that still need to be defined.