Polycyclic aromatic hydrocarbons (PAHs) biodegradation potential and diversity of microbial consortia enriched from tsunami sediments in Miyagi, Japan

A novel immobilized bacteria consortium enhanced remediation efficiency of PAHs in soil: Insights into key removal mechanism and main driving factor

The remediation of sites co-contaminated with polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs) poses challenges for efficient and ecofriendly restoration methods. In this study, three strains (Pseudomonas sp. PDC-1, Rhodococcus sp. RDC-1, and Enterobacter sp. EDC-1) were isolated from sites contaminated with PAHs and HMs. The constructed bacteria consortium was then immobilized using biochar, bentonite, and peat. The immobilized bacteria consortium (IBC) demonstrated efficient removal ability of phenanthrene (58.1 %-73.4 %) and benzo[a]pyrene (69.6 %-83.5 %) during 60 days. Additionally, the IBC decreased soil bacterial richness and diversity, but increased the relative abundance of Proteobacteria phylum and Ochrobactrum genus, which were capable of degrading PAHs. Soil microbial co-occurrence network with IBC was classified into three main modules, and 14 genera were identified as keystone taxa linked to PAHs degradation and HMs resistance. The IBC enhanced the dioxygenase metabolic pathways for PAHs degradation, including phthalic acid and salicylic acid pathways, which became the main driving factor affecting PAHs removal efficiency based on the structural equation modeling analysis. This study confirmed the potential application of the constructed IBC in the bioremediation of soil co-contaminated with PAHs-HMs, and provides insights into key removal mechanism and main driving factor of the enhanced elimination of PAHs.

Impact of glyphosate on soil bacterial communities and degradation mechanisms in large-leaf tea plantations

This study investigated the impact of glyphosate on bacterial communities and their degradation mechanisms in large-leaf tea soil, through exposure microcosm and enrichment culture experiments. Soils from three tea gardens in Yunnan, China, were used: two glyphosate-free (JM and KL) for microcosm study and one long-term exposed (G2) for enrichment culture experiment. The results revealed a two-phase degradation process with half-lives of 12.7 to 268 days, while the metabolite AMPA was notably persistent. The acidic conditions and high organic content of tea soils may retard glyphosate microbial availability and degradation. Glyphosate initially stimulated bacterial growth but led to abundance declines with prolonged exposure. It tended to enhance bacterial diversity at lower doses. Network complexity increased in JM soil where strong adsorption moderated glyphosate exposure, yet decreased in KL soil where weak adsorption enabled greater microbial-glyphosate interactions. Community structure analysis revealed soil-specific responses, with decreased Proteobacteria in JM soil and Actinobacteria in KL soil, while several phyla including Proteobacteria, Acidobacteriota, Chloroflexi, Myxococcota, and Verrucomicrobiota showed increased abundance. PICRUSt2 analysis indicated enhanced biosynthesis and cell growth pathways, while carbohydrate metabolism, nitrogen metabolism, and xenobiotics biodegradation pathways were reduced. LEfSe analysis identified potential degrading biomarkers primarily from Proteobacteria, Acidobacteriota, Myxococcota, Chloroflexi, and Actinobacteriota, suggesting their putative role in degradation. The enriched consortium G2 efficiently degraded 400 mg/L glyphosate within 7 days, with notable increases in Afipia, Dokdonella, and Cohnella abundance. This study provides insights into bacterial interactions with glyphosate in tea soils, suggesting strategies for contamination mitigation and environmental restoration.

The accumulation, elimination characteristics, and toxic effects of intertidal sediment crude oil contamination in Sinonvacula constricta

Marine oil spills lead to intertidal sediment pollution, causing benthic bioaccumulation and toxicity. However, relatively few studies have been conducted on the effects of crude oil sediment pollution on benthos. In this study, Sinonovacula constricta was used as the research object in a sediment environment to study the accumulation and elimination effects of S. constricta on long-term exposure to crude oil pollution as well as the toxicity effects at the biochemical and tissue levels through laboratory exposure tests. The objective of this study was to provide theoretical support for monitoring the biological toxicity of intertidal crude oil pollution. The results showed that S. constricta accumulated petroleum hydrocarbons in the sediment, which were positively correlated with pollution concentration and time. The fitting results of the two-compartment kinetic model were good and could be applied to the accumulation and elimination of sediment crude oil pollution. The activity of antioxidant enzymes and the content of malondialdehyde in the gills were mainly induced, and there was a dose- and time-dependent relationship. Crude oil pollution can cause digestive tube ablation, lumen swelling, and blood cell infiltration in the viscera of S. constricta. S. constricta can be used as an indicator organism for oil pollution in the intertidal zone, and its gills and visceral mass can be used as target tissues.

Coal mining activities driving the changes in bacterial community

The mechanism of the difference in bacterial community composition caused by environmental factors in the underground coal mine is unclear. In order to reveal the influence of coal mining activities on the characteristics of bacterial community structure in coal seam, 16S rRNA gene amplicon sequencing technology was used to determine the species abundance, biodiversity, and gene abundance of bacterial community in a coal mine in Shanxi Province, and the environmental factors such as metal elements, non-metal elements, pH value, and gas concentration of coal samples were determined. The results showed that environmental factors and bacterial communities had obvious regional characteristics. Mining activities greatly affected the α diversity of bacterial communities, mining working face > main airway > roadway roof > unexposed coal seam > tunneling roadway. The bacterial community composition of each sample point is also very different. The main airway, roadway roof, and unexposed coal seam are dominated by Actinobacteria while the mining working face and tunneling roadway are dominated by Proteobacteria. Among the gene abundances of metabolic pathways in each site, Citrate cycle had the greatest difference, followed by glycine, serine and threonine metabolism, and oxidative phosphorylation and methane metabolism had little difference. RDA analysis showed that the environmental factors affecting the bacterial community were mainly cadmium, oxygen, hydrogen, and gas content. CCA analysis divided the bacterial community into three categories. Degradation functional bacteria are located in mining working face, bacteria that tolerate poor environments are located in main airway and tunneling roadway, and human pathogens are mostly located in roadway roof and unexposed coal seam. The research results would provide support for realizing green and safe mining in coal mines.

Effects of biodegradable microplastics coexistence with biochars produced at low and high temperatures on bacterial community structure and phenanthrene degradation in soil

The increasing use of biodegradable plastics may result in more serious pollution of microplastics which often coexist with biochar in soil, this will affect how organic pollutants move and transform in the soil. This work investigated the effect of biodegradable polybutylene adipate-co-terephthalate (PBAT) coexistence with biochars produced at temperatures of 400 and 700 °C (W4 and W7) on soil bacterial communities and phenanthrene degradation. The results showed that coexistence of PBAT and biochar paticles greatly boosted the relative abundance of Nocardioides while decreased the relative abundance of Sphingomonas as compared to soils with a single addition of PBAT or biochar. Changes in soil Eh values were the most influential factor in bacterial communities (more than 40% contribution). The degradation ratio of phenanthrene when PBAT coexisted with W7 (39.6 ± 3.6%) was not significantly different from the treatment with a single W7 addition (35.0 ± 2.3%, P＞0.05), and was related to phenanthrene degradation in the adsorbed state of W7 in soil. In contrast, the degradation ratio of phenanthrene in PBAT coexisting with W4 (35.1 ± 3.5%) was intermediate between that of single PBAT (49.8 ± 0.9%) and W4 (13.7 ± 5.8%) treatments. This was primarily due to changes in the experiment's initial bioavailable phenanthrene content. Furthermore, after the introduction of earthworms, phenanthrene degradation ratio in coexistence treatments were very similar to that described above in the absence of earthworms. Except for two treatments that contain W7, phenanthrene degradation ratio in the other treatments was increased by the presence of earthworms (up to 23%), which is related to the enhanced relative abundance of polycyclic aromatic hydrocarbon-degraders. Our findings indicated that PBAT coexistence with high-temperature or low-temperature biochar had a completely different impact on bacterial communities and phenanthrene degradation in soil.

Effects of Chinese "double carbon strategy" on soil polycyclic aromatic hydrocarbons pollution

Polycyclic aromatic hydrocarbons (PAHs) and carbon dioxide primarily originate from the combustion of fossil fuels and biomass. The implementation of the Chinese "double carbon strategy" is expected to impact the distribution of PAH emissions, consequently influencing the spatial distribution trend of PAHs in surface soil. Therefore, it is crucial to quantitatively evaluate the effectiveness of the Chinese "double carbon strategy" on soil PAH pollution for the purpose of "the reduction of pollution and carbon emissions". This study utilized 15,088 individual PAH concentration data from 943 soil samples collected between 2003 and 2020 in China, in conjunction with PAH emissions at a 10 km resolution, for meta-analysis. The calculated PAH emissions in this study are in line with the global PAH emission inventory (PKU-PAH-2007), with a relative standard deviation at the provincial level of less than 25 %. Subsequently, a novel method was developed using emission density and Kow of PAHs to predict PAH concentrations in surface soil based on a least-squares regression model. Compared to other environmental models, the method established in this study significantly reduced the percent sample deviation to less than 70 %. Furthermore, energy consumption data for China were simulated based on the implementation plan of the "double carbon strategy" to project PAH emissions and soil PAH levels for the years 2030 and 2060. The predicted PAH emissions in China were estimated to decrease to 41,300 t in 2030 and 10,406.5 t in 2060 from 78,815 t in 2020. Moreover, the heavily contaminated areas of soil PAHs (i.e., total PAH concentrations in soil exceeding 1000 μg kg-1) were projected to decrease by 45 % and 82 % in 2030 and 2060, respectively, compared to levels in 2020. These findings suggest that the implementation of the "double carbon strategy" can fundamentally reduce the pollution of PAHs in surface soil of China.

Risk assessment and biodegradation potential of PAHs originating from Map Ta Phut Industrial Estate, Rayong, Thailand

Petroleum hydrocarbon contamination is a serious concern across the globe. Here, the capability of native bacterial consortium enriched from sediment samples of Map Ta Phut Industrial Estate (MTPIE), Rayong, Thailand was described. The distribution of PAHs was assessed from the sediment samples collected from MTPIE by GC-FID and the toxic unit (TU) was calculated to assess the potential ecological risk to the surrounding biota. This study investigated the degradation potential and determined the PAH-degrading bacterial cultures by enriching collected sediments in PAHs mixtures (naphthalene, phenanthrene, and pyrene). The TPH degradation capacity of each bacterial consortium was validated in a soil microcosm using aged crude oil-contaminated soil. The MTPIE sediments were highly contaminated with PAHs (843.99-3904.39 ng g-1) and posed extremely high ecological risks to benthic biota (TU > 1). The consortium S5-P most significantly removed naphthalene (90.03%) and phenanthrene (88.14%) while the highest removal of pyrene was achieved by the S3-P consortium. Other consortia only partially degraded the PAHs. The dominant microbes in the consortia were determined using PCR-DGGE, it was found that the PAH degrading consortia were known PAH degraders such as Annwoodia, Bacillus, Brevibacillus, Lysinibacillus, Paracoccus, Rhodococcus, Sphingopyxis, Sulfurovum, and Sulfurimonas species and unknown PAH degraders such as Lithuaxuella species. The consortium S5-P showed the highest degradation capacity, removing 74.99% of TPHs in the soil microcosm. Furthermore, the inoculation of PAH-biodegrading bacterial consortia significantly promoted the catechol-2,3-dioxygenase (C23O) and dehydrogenase (DHA) activities which directly correlated with the degradation efficiency of petroleum hydrocarbons (p < 0.05).

Construction of an effective method combining in situ capping with electric field-enhanced biodegradation for treating PAH-contaminated soil at abandoned coking sites

The simultaneous application of in situ capping and electro-enhanced biodegradation may be a suitable method for ensuring the feasibility and safety of reusing abandoned coking sites. However, the capping layer type and applied electric field pattern may affect the efficiency of sequestering and removing pollutants. This study investigated changes in electric current, soil moisture content and pH, polycyclic aromatic hydrocarbon (PAH) concentration, bacterial number, and microbial community structure and metabolic function during soil remediation at abandoned coking plant sites under different applied electric field patterns and barrier types. The results indicated that polarity-reversal electric field was more conducive to maintaining electric current, soil properties, resulting in higher microbial number, community diversity, and functional gene abundance. At 21d, the mean PAH concentrations in contaminated soil, the capping layer's clean soil and barrier were 78.79, 7.56, and 1.57 mg kg-1 lower than those with a unidirectional electric field, respectively. The mean degradation rate of PAHs in the bio-barrier was 10.12 % higher than that in the C-Fe barrier. In the experiment combining a polarity-reversal electric field and a bio-barrier, the mean PAH concentrations in contaminated soil and the capping layer were 706.68 and 27.15 mg kg-1 lower than those in other experiments, respectively, and no PAHs were detected in the clean soil, demonstrating that the combination of the polarity-reversal electric field and the bio-barrier was effective in treating soil at abandoned coking plant sites. The established method of combining in situ capping with electro-enhanced biodegradation will provide technical support for the treatment and reuse of heavily PAH-contaminated soil at abandoned coking plant sites.

Engineering non-conservative substrate recognition sites of extradiol dioxygenase: Computation guided design to diversify and accelerate degradation of aromatic compounds

Extradiol dioxygenases (EDOs) catalyzing meta-cleavage of catecholic compounds promise an effective way to detoxify aromatic pollutants. This work reported a novel scenario to engineer our recently identified Type I EDO from Tcu3516 for a broader substrate scope and enhanced activity, which was based on 2,3-dihydroxybiphenyl (2,3-DHB)-liganded molecular docking of Tcu3516 and multiple sequence alignment with other 22 Type I EDOs. 11 non-conservative residues of Tcu3516 within 6 Å distance to the 2,3-DHB ligand center were selected as potential hotspots and subjected to semi-rational design using 6 catecholic analogues as substrates; the mutants V186L and V212N returned with progressive evolution in substrate scope and catalytic activity. Both mutants were combined with D285A for construction of double mutants and final triple mutant V186L/V212N/D285A. Except for 2,3-DHB (the mutant V186L/D285A gave the best catalytic performance), the triple mutant prevailed all other 5 catecholic compounds for their degradation; affording the catalytic efficiency kcat/Km value increase by 10-30 folds, protein Tm (structural rigidity) increase by 15 °C and the half-life time enhancement by 10 times compared to the wild type Tcu3516. The molecular dynamic simulation suggested that a stabler core and a more flexible entrance are likely accounting for enhanced catalytic activity and stability of enzymes.

The unique biodegradation pathway of benzo[a]pyrene in moderately halophilic Pontibacillus chungwhensis HN14

Benzo[a]pyrene (BaP), as the typical representative of polycyclic aromatic hydrocarbons (PAHs), is a serious hazard to human health and natural environments. Though the study of microbial degradation of PAHs has persisted for decades, the degradation pathway of BaP is still unclear. Previously, Pontibacillus chungwhensis HN14 was isolated from high salinity environment exhibiting a high BaP degradation ability. Here, based on the intermediates identified, BaP was found to be transformed to 4,5-epoxide-BaP, BaP-trans-4,5-dihydrodiol, 1,2-dihydroxy-phenanthrene, 2-carboxy-1-naphthol, and 4,5-dimethoxybenzo[a]pyrene by the strain HN14. Furthermore, functional genes involved in degradation of BaP were identified using genome and transcriptome data. Heterogeneous co-expression of monooxygenase CYP102(HN14) and epoxide hydrolase EH(HN14) suggested that CYP102(HN14) could transform BaP to 4,5-epoxide-BaP, which was further transformed to BaP-trans-4,5-dihydrodiol by EH(HN14). Moreover, gene cyp102(HN14) knockout was performed using CRISPR/Cas9 gene-editing system which confirmed that CYP102(HN14) play a key role in the initial conversion of BaP. Finally, a novel BaP degradation pathway was constructed in bacteria, which showed BaP could be converted into chrysene, phenanthrene, naphthalene pathways for the first time. These findings enhanced our understanding of microbial degradation process for BaP and suggested the potential of using P. chungwhensis HN14 for bioremediation in PAH-contaminated environments.

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

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

Comparative genomics reveals evidence of polycyclic aromatic hydrocarbon degradation in the moderately halophilic genus Pontibacillus

Polycyclic aromatic hydrocarbons (PAHs) are a common class of persistent organic pollutants (POPs) that are widely distributed in various environments and pose significant threats to both environmental and human health. The genus Pontibacillus, a type of moderately halophilic bacteria, has demonstrated potential for biodegrading aromatic compounds in high-salinity environments. However, no previous study has comprehensively investigated the PAH degradation mechanisms and environmental adaptability in the genus Pontibacillus. In this study, we sequenced the whole genome of the PAH-degrading strain Pontibacillus chungwhensis HN14 and conducted a comparative genomics analysis of genes associated with PAH degradation, as well as salt and arsenic tolerance using ten other Pontibacillus sp. strains. Here, we elucidated potential degradation pathways for benzo[a]pyrene and phenanthrene, which were initiated by cytochrome P450 monooxygenases, in most Pontibacillus strains. Moreover, four Pontibacillus strains were selected to investigate the biodegradation of benzo[a]pyrene and phenanthrene under high-salt (5% NaCl) stress, and all four strains exhibited exceptional degradation abilities. The results of comparative genomics and phenotypic analyses demonstrate that the genus Pontibacillus have the potential to degrade polycyclic aromatic hydrocarbons in high-salinity environments, thus providing valuable insights for biodegradation in extreme environments.

A novel mechanism of enhanced PCBs degradation associated with nitrogen in the rhizosphere of the wetland plant Myriophyllum aquaticum

Co-contamination of polychlorinated biphenyls (PCBs) and nitrogen (N) is widespread. Here, N removal and PCBs degradation were investigated in constructed wetlands populated with Myriophyllum aquaticum, and the role of N in PCBs degradation was explored as well. Nearly 97% of N was removed in the planted system, whereas less than 40% was removed in the plant-free system. Compared to the treatment with plants and no N amendment, N addition enhanced plant growth by 31.9% and PCBs removal by 9.90%. PCBs attenuation was mainly attributed to microbial degradation rather than plant uptake. Using DNA stable-isotope probing, 26 operational taxonomic units were identified across all treatments, of which 25 were linked to PCBs degradation for the first time. Some PCB-degraders were associated with nitrification/denitrification and were significantly enriched in the treatment that included both plants and N application, indicating that PCBs degradation was promoted by recruiting ammonia-oxidising and denitrifying microbes with PCBs metabolic ability. This was confirmed by the higher A13/A12 ratios for the bphC, amoA, and nirK genes and their significant positive correlations. Overall, the findings clarify the novel mechanism by which N promotes PCBs degradation in constructed wetlands and offers a theoretical basis for efficiently removing inorganic elements and persistent organic pollutants.

Tar pollution event (2021) at the Southeastern Levantine oligotrophic basin, short-term impacts and operational oceanography perspectives

The Levantine basin (LB) in the Southeastern Mediterranean Sea is a high-risk oil pollution hot spot owing to its dense maritime traffic and intense oil and gas exploration and exploitation activities. In February 2021 the Israeli LB shorelines were impacted by an exceptional tar pollution event (~550 tons; average distribution: ~3 kg tar m-1 front beach) of an unknown oil spill source. Here we report on the immediate numerical modelling assessment of the oil spill propagation and tar distribution; operational use of underwater gliders for tracking water column anomalies of dissolved polycyclic aromatic hydrocarbons (PAHs) and turbidity signals; the beached tar composition and amounts and the short-term response of the microbial population along the ~180 km shoreline. This pollution event emphasizes the need for improving the early warning systems for oil spills and implementing continuous operational monitoring at high-risk, ecologically sensitive and valuable resource areas like the Israeli LB waters.

Effects of the polyhalogenated carbazoles 3-bromocarbazole and 1,3,6,8-tetrabromocarbazole on soil microbial communities

Soil ecosystems are being more contaminated with polyhalogenated carbazoles (PHCZs), which raising much attention about their impact on soil microorganisms. 3-Bromocarbazole (3-BCZ) and 1,3,6,8-tetrabromocarbazole (1,3,6,8-TBCZ) are two typical PHCZs with high detection rates in the soil environment. However, ecological risk research on these two PHCZs in soil is still lacking. In the present study, after 80 days of exposure, the ecological influence of 3-BCZ and 1,3,6,8-TBCZ was investigated based on 16S rDNA sequencing, ITS sequencing, gene (16S rDNA, ITS, amoA, nifH, narG and cbbL) abundance and soil enzyme activity. The results showed that the bacterial 16S rDNA gene abundance significantly decreased under 3-BCZ and 1,3,6,8-TBCZ exposure after 80 days of incubation. The fungal ITS gene abundance significantly decreased under 1,3,6,8-TBCZ (10 mg/kg) exposure. PHCZs contributed to the alteration of bacteria and fungi community abundance. Bacteria Sphingomonas, RB41 and fungus Mortierella, Cercophora were identified as the most dominant genera. The two PHCZs consistently decreased the relative abundance of Sphingomonas, Lysobacter, Dokdonella, Mortierella and Cercophora etc at 80th day. These keystone taxa are related to the degradation of organic compounds, carbon metabolism, and nitrogen metabolism and may thus have influence on soil ecological functions. Bacterial and fungal functions were estimated using functional annotation of prokaryotic taxa (FAPROTAX) and fungi functional guild (FUNGuild), respectively. The nitrogen and carbon metabolism pathway were affected by 3-BCZ and 1,3,6,8-TBCZ. The soil nitrogen-related functions of aerobic ammonia oxidation were decreased but the soil carbon-related functions of methanol oxidation, fermentation, and hydrocarbon degradation were increased at 80th day. The effects of 3-BCZ and 1,3,6,8-TBCZ on the abundances of the amoA, nifH, narG, and cbbL genes showed a negative trend. These results elucidate the ecological effects of PHCZs and extend our knowledge on the structure and function of soil microorganisms in PHCZ-contaminated ecosystems.

Self-assembling a 1,4-dioxane-degrading consortium and identifying the key role of Shinella sp. through dilution-to-extinction and reculturing

IMPORTANCE

Assembling a functional microbial consortium and identifying key degraders involved in the degradation of 1,4-dioxane are crucial for the design of synergistic consortia used in enhancing the bioremediation of 1,4-dioxane-contaminated sites. However, due to the vast diversity of microbes, assembling a functional consortium and identifying novel degraders through a simple method remain a challenge. In this study, we reassembled 1,4-dioxane-degrading microbial consortia using a simple and easy-to-operate method by combining dilution-to-extinction and reculture techniques. We combined differential analysis of community structure and metabolic function and confirmed that Shinella species have a stronger 1,4-dioxane degradation ability than Xanthobacter species in the enriched consortium. In addition, a new dioxane-degrading bacterium was isolated, Shinella yambaruensis, which verified our findings. These results demonstrate that DTE and reculture techniques can be used beyond diversity reduction to assemble functional microbial communities, particularly to identify key degraders in contaminant-degrading consortia.

Metagenomics and metatranscriptomics suggest pathways of 3-chloroaniline degradation in wastewater reactors

Biological wastewater treatment systems are often affected by shifts in influent quality, including the input of toxic chemicals. Yet the mechanisms underlying the adaptation of activated sludge process performance are rarely studied in a controlled and replicated experimental setting, particularly when challenged with a sustained toxin input. Three replicate bench-scale bioreactors were subjected to a chemical disturbance in the form of 3-chloroaniline (3-CA) over 132 days, after an acclimation period of 58 days, while three control reactors received no 3-CA input. Ammonia oxidation was initially affected by 3-CA. Within three weeks of the experiment, microbial communities in all three treatment reactors adapted to biologically degrade 3-CA resulting in partial ammonia oxidation recovery. Combining process and microbial community data from amplicon sequencing with potential functions gleaned from assembled metagenomics and metatranscriptomics data, two putative degradation pathways for 3-CA were identified. The first pathway, determined from metagenomics data, involves a benzoate dioxygenase and subsequent meta-cleavage of the aromatic ring. The second, determined from intensive short-term sampling for gene expression data in tandem with 3-CA degradation, involves a phenol monooxygenase followed by ortho-cleavage of the aromatic ring. The relative abundances of amplicon sequence variants associated with the genera Gemmatimonas, OLB8, and Taibaiella correlated significantly with 3-CA degradation. Metagenome-assembled genome data also showed the genus OLB8 to be differentially enriched in treatment reactors, making it a strong candidate as 3-CA degrader. Using replicated reactors, this study has demonstrated the impact of a sustained stress on the activated sludge process. The unique and novel features of this study include the identification of putative pathways and potential degraders of 3-CA using long-term and short-term sampling in tandem with multiple methods in a controlled and replicated experiment.

Establishment of microbial model communities capable of removing trace organic chemicals for biotransformation mechanisms research

BACKGROUND

Removal of trace organic chemicals (TOrCs) in aquatic environments has been intensively studied. Some members of natural microbial communities play a vital role in transforming chemical contaminants, however, complex microbial interactions impede us from gaining adequate understanding of TOrC biotransformation mechanisms. To simplify, in this study, we propose a strategy of establishing reduced-richness model communities capable of removing diverse TOrCs via pre-adaptation and dilution-to-extinction.

RESULTS

Microbial communities were adapted from tap water, soil, sand, sediment deep and sediment surface to changing concentrations of 27 TOrCs mixture. After adaptation, the communities were further diluted to reduce diversity into 96 deep well plates for high-throughput cultivation. After characterizing microbial structure and TOrC removal performance, thirty taxonomically non-redundant model communities with different removal abilities were obtained. The pre-adaptation process was found to reduce the microbial richness but to increase the evenness and phylogenetic diversity of resulting model communities. Moreover, phylogenetic diversity showed a positive effect on the number of TOrCs that can be transformed simultaneously. Pre-adaptation also improved the overall TOrC removal rates, which was found to be positively correlated with the growth rates of model communities.

CONCLUSIONS

This is the first study that investigated a wide range of TOrC biotransformation based on different model communities derived from varying natural microbial systems. This study provides a standardized workflow of establishing model communities for different metabolic purposes with changeable inoculum and substrates. The obtained model communities can be further used to find the driving agents of TOrC biotransformation at the enzyme/gene level.

Vertical and seasonal dynamics of bacterial pathogenic communities at an aged organic contaminated site: Insights into microbial diversity, composition, interactions, and assembly processes

Under the background of the Coronavirus Disease 2019 (COVID-19) pandemic, research on pathogens deserves greater attention in the natural environment, especially in the widely distributed contaminated sites with complicated and severe organic pollution. In this study, the community composition and assembly of soil pathogens identified by the newly-developed 16S-based pipeline of multiple bacterial pathogen detection (MBPD) have been investigated on spatiotemporal scales in the selected organic polluted site. We demonstrated that the richness and diversity of the pathogenic communities were primarily controlled by soil depth, while the structure and composition of pathogenic communities varied pronouncedly with seasonal changes, which were driven by the alterations in both physiochemical parameters and organic contaminants over time. Network analysis revealed that the overwhelmingly positive interactions, identified multiple keystone species, and a well-organized modular structure maintained the stability and functionality of the pathogenic communities under environmental pressures. Additionally, the null-model analysis showed that deterministic processes dominated the pathogenic community assembly across soil profiles. In three seasons, stochasticity-dominated processes in spring and summer changed into determinism-dominated processes in winter. These findings extend our knowledge of the response of the bacterial pathogenic community to environmental disruptions brought on by organic contaminated sites.

Responses of rhizosphere microbial community structure and metabolic function to heavy metal coinhibition

Metal mineral mining results in releases of large amounts of heavy metals into the environment, and it is necessary to better understand the response of rhizosphere microbial communities to simultaneous stress from multiple heavy metals (HMs), which directly impacts plant growth and human health. In this study, by adding different concentrations of cadmium (Cd) to a soil with high background concentrations of vanadium (V) and chromium (Cr), the growth of maize during the jointing stage was explored under limiting conditions. High-throughput sequencing was used to explore the response and survival strategies of rhizosphere soil microbial communities to complex HM stress. The results showed that complex HMs inhibited the growth of maize at the jointing stage, and the diversity and abundance of maize rhizosphere soil microorganisms were significantly different at different metal enrichment levels. In addition, according to the different stress levels, the maize rhizosphere attracted many tolerant colonizing bacteria, and cooccurrence network analysis showed that these bacteria interacted very closely. The effects of residual heavy metals on beneficial microorganisms (such as Xanthomonas, Sphingomonas, and lysozyme) were significantly stronger than those of bioavailable metals and soil physical and chemical properties. PICRUSt analysis revealed that the different forms of V and Cd had significantly greater effects on microbial metabolic pathways than all forms of Cr. Cr mainly affected the two major metabolic pathways: microbial cell growth and division and environmental information transmission. In addition, significant differences in rhizosphere microbial metabolism under different concentrations were found, and this can serve as a reference for subsequent metagenomic analysis. This study is helpful for exploring the threshold for the growth of crops in toxic HM soils in mining areas and achieving further biological remediation.

Treatment of PAHs contaminated soil in abandoned industrial site using combined method of improved in situ capping and electrokinetic enhanced-bioremediation

In situ capping and bioremediation are common technologies for treating contaminated soil at industrial sites. However, these two technologies have some shortcomings for treating soil heavily contaminated with organic matter, such as the limited adsorption in capping layer and the low biodegradation efficiency. This study proposed the method of an improved in situ capping combined with electrokinetic enhanced-bioremediation, and investigated its feasibility for treating heavily polycyclic aromatic hydrocarbons (PAHs) contaminated soil at an abandoned industrial site. By analyzing the changes in soil properties, PAHs concentration, and microbial community in experiments with voltages of 0, 0.8, 1.2, and 1.6 V cm^-1, it was found that improved in situ capping could effectively sequester PAHs migration by adsorption and biodegradation, and electric field could enhance PAHs removal from contaminated soil and bio-barrier. In the experiments with electric field, soil environment under the voltage of 1.2 V cm^-1 was more favorable for the growth and metabolism of microorganisms, and the residual PAHs concentrations (19.47 ± 0.76 mg kg^-1 and 619.38 ± 20.05 mg kg^-1) in the bio-barrier and contaminated soil of experiment with 1.2 V cm^-1 were the lowest, which indicated that optimization of the electric field conditions could lead to better effects.

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) by microbial consortium from paddy rice soil

Polycyclic aromatic hydrocarbons (PAHs) are among the most widely spread pollutants in the environment including the agricultural soil. PAH degradation by indigenous bacteria is an effective and economical means to remove these pollutants from the environment. Here, we report a bacterial consortium (Pdy-1) isolated from paddy rice soil in northern Japan able to degrade polycyclic aromatic hydrocarbons (PAHs) at high rates. Pdy-1 was incubated with a mixture of PAH compounds (fluorene, phenanthrene, and pyrene) in Bushnell Haas Medium at a final concentration of 100 mg/L each. PDY-1 degraded 100% of fluorene, 95% of phenanthrene, and 52% of pyrene in 5 days. Phenanthrene and pyrene were completely degraded at 10 d and 15 d, respectively. Cloning of the 16S rRNA gene revealed that the consortium was composed of 40% Achromobacter and 7% each of Castelaniella, Rhodanobacter, and Hypomicrobium. Comamonas, Ferrovibrio, Terrimonas, Bordetella, Rhizobium, and Pseudonocardia were also detected. PCR-DGGE showed the dynamics of the consortium during the incubation period. Real-time PCR revealed that PAH degrading genes such as the gram-positive ring dihydroxylating genes (PAH-RDH) and pyrene dioxygenase (nidA) were most abundant at day 5 when the rapid biodegradation of the PAHs was observed. This study improves our understanding on dynamics and characteristics of an effective PAH-degrading bacterial consortium from paddy rice soil.

Characterization of the simultaneous degradation of pyrene and removal of Cr(VI) by a bacteria consortium YH

Microorganisms that can simultaneously remediate organic pollutants and heavy metal contamination are great significance in bioremediation. Nevertheless, reports of such microorganisms are still scarce. Here, Pseudomonas sp. YH-1 and Rhodococcus sp. YH-3 were isolated and identified, and they showed greater tolerance to hexavalent (VI) (750 and 800 mg·L^-1). The constructed bacteria consortium YH (YH-1:YH-3 = 1:1) could simultaneously degrade 41.69% of pyrene (50 mg·L^-1) and remove 76.67% of Cr(VI) (30 mg·L^-1) within 5 days. The potential mechanism of Cr(VI) tolerance of YH was further explored by genomic and microscopic analysis. The results showed that YH responded to Cr(VI) stress mainly through efflux of Cr(VI) by chrA and copZ, chromate reduction, DNA-repaired proteases reduces ROS damage, and biosorption by carboxyl, hydroxyl, amino functional groups. Strains YH-1 and YH-3 also contained a variety of genes associated with resistance to other heavy metals, such as cadmium (czcBD), mercury (merAPTR), manganese (mntABC) and copper (copAC, cusABRF and pcoBD). Based on GC-MS and genomic analysis, pyrene was degraded via salicylic acid and phthalic acid pathways. Moreover, a great number of genes related to aromatic hydrocarbon catabolism were identified in the genomes of YH-1 and YH-3. These results confirmed the potential application of the bacteria consortium YH in the bioremediation of water and soil co-contaminated with PAHs-heavy metals.

Construction of microbial consortia for microbial degradation of complex compounds

Increasingly complex synthetic environmental pollutants are prompting further research into bioremediation, which is one of the most economical and safest means of environmental restoration. From the current research, using microbial consortia to degrade complex compounds is more advantageous compared to using isolated bacteria, as the former is more adaptable and stable within the growth environment and can provide a suitable catalytic environment for each enzyme required by the biodegradation pathway. With the development of synthetic biology and gene-editing tools, artificial microbial consortia systems can be designed to be more efficient, stable, and robust, and they can be used to produce high-value-added products with their strong degradation ability. Furthermore, microbial consortia systems are shown to be promising in the degradation of complex compounds. In this review, the strategies for constructing stable and robust microbial consortia are discussed. The current advances in the degradation of complex compounds by microbial consortia are also classified and detailed, including plastics, petroleum, antibiotics, azo dyes, and some pollutants present in sewage. Thus, this paper aims to support some helps to those who focus on the degradation of complex compounds by microbial consortia.

Comparison of the efficiency and microbial mechanisms of chemical- and bio-surfactants in remediation of petroleum hydrocarbon

Surfactant-enhanced remediation (SER) is one of the most effective methods for petroleum hydrocarbon-contaminated sites compared to single physical and chemical methods. However, biosurfactants are not as commonly used as chemical surfactants, and the actual remediation effects and related mechanisms remain undefined. Therefore, to comprehensively compare the remediation effects and biological mechanisms of biosurfactants and chemical surfactants, soil column leaching experiments including two biosurfactants (rhamnolipids and lipopeptide) and three commercially used chemical surfactants (Tween 80, Triton X-100, and Berol 226SA) were conducted. After seven days of leaching, rhamnolipids exhibited the highest petroleum hydrocarbon removal rate of 61.01%, which was superior to that of chemical surfactants (11.73-18.75%) in n-alkanes C10-C30. Meanwhile, rhamnolipids exhibited a great degradation advantage of n-alkanes C13-C28, which was 1.22-30.55 times that of chemical surfactants. Compared to chemical surfactants, biosurfactants significantly upregulated the soil's biological functions, including soil conductivity (80.90-155.56%), and soil enzyme activities of lipase (90.31-497.10%), dehydrogenase (325.00-655.56%), core enzyme activities of petroleum hydrocarbon degradation, and quorum sensing between species. Biosurfactants significantly changed the composition of Pseudomonas, Citrobacter, Acidobacteriota, and Enterobacter at the genus level. Meanwhile, chemical surfactants had less influence on the bacterial community and interactions between species. Moreover, the biosurfactants enhanced the microbial interactions and centrality of petroleum hydrocarbon degraders in the community based on the network. Overall, this work provides a systematic comparison and understanding of the chemical- and bio-surfactants used in bioremediation. In the future, we intend to apply biosurfactants to practical petroleum hydrocarbon-contaminated fields to observe realistic remediation effects and compare their functional mechanisms.

Mn oxides enhanced pyrene removal with both rhizosphere and non-rhizosphere microorganisms in subsurface flow constructed wetlands

The polycyclic aromatic hydrocarbons (PAHs) are substantial wastewater pollutants emitted mostly by petroleum refineries and petrochemical industries, and their environmental fate has been of increasing concern among the public. Consequently, subsurface flow constructed wetlands (SFCWs) filled with Mn oxides (W-CW) or without Mn oxides (K-CW) were established to investigate the performance and mechanisms of pyrene (PYR) removal. The average removal rates of PYR in W-CW and K-CW were 96.00% and 92.33%, respectively. The PYR removal via other pathways (microbial degradation, photolysis, volatilisation, etc.) occupied a sizeable proportion, while the total PYR content in K-CW plant roots was significantly higher than that of W-CW. The microorganisms on the root surface and rhizosphere played an important role in PYR degradation in W-CW and K-CW and were higher in W-CW than that in K-CW in all matrix zones. The microorganisms between the 10-16 cm zone from the bottom of W-CW filled with Mn oxides (W-16) were positively correlated with PYR-degrading microorganisms, aerobic bacteria and facultative anaerobes, whereas K-16 without birnessite-coated sand was negatively correlated with these microorganisms.

Biodegradation performance and diversity of enriched bacterial consortia capable of degrading high-molecular-weight polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are key organic pollutants in the environment that pose threats to the ecosystem and human health. The degradation of high molecular weight (HMW) PAHs by enriched bacterial consortia has been previously studied, while the involved metabolisms and microbial communities are still unclear and warrant further investigations. In this study, five bacterial consortia capable of utilizing different PAHs (naphthalene, anthracene, and pyrene) as the sole carbon and energy sources were enriched from PAH-contaminated soil samples. Among the five consortia, consortium TC exhibited the highest pyrene degradation efficiency (91%) after 19 d of incubation. The degradation efficiency was further enhanced up to 99% by supplementing yeast extract. Besides, consortium TC showed tolerances to high concentrations of pyrene (up to 1000 mg/L) and different heavy metal stresses (including Zn²⁺, Cd²⁺, and Pb²⁺). The dominant genus in consortium TC, GS, and PL showing relatively higher degradation efficiency for anthracene and pyrene was Pseudomonas, whereas consortium PG and GD were predominated by genus Achromobacter and class Enterobacteriaceae, respectively. Consortium TC, as a highly efficient HMW PAH-degrading consortium, could be applied for synergistic biodegradation of HMW PAHs and in situ bioremediation of the sites contaminated with both PAHs and heavy metals.

Biogasification of methanol extract of lignite and its residue: A case study of Yima coalfield, China

To investigate the biogas generation characteristics of the organic matter in lignite, methanol extraction was conducted to obtain the soluble fraction and the residual of lignite, which were subsequently taken as the sole carbon source for biogas production by a methanogenic consortium. Afterward, the composition of compounds before and after the fermentation was characterized by UV-Vis, GC-MS, and HPLC-MS analysis. The results indicated that the methanogenic microorganisms could produce H2 and CO2 without accumulating CH4 by utilizing the extract, and the methane production of the residue was 18% larger than that of raw lignite, reaching 1.03 mmol/g. Moreover, the organic compounds in the methanol extract were degraded and their molecular weight was reduced. Compounds such as 1, 6-dimethyl-4-(2-methylethyl) naphthalene, 7-butyl-1-hexylnaphthalene, simonellite, and retene were completely degraded by microorganisms. In addition, both aromatic and non-aromatic metabolites produced in the biodegradation were detected, some of which may have a negative effect on the methanogenesis process. These results revealed the complexity of the interaction between coal and organism from another point of view.

Pollution pressure and soil depth drive prokaryotic microbial assemblage and co-occurrence patterns in an organic polluted site

Organic polluted sites have become a global concern of soil contamination, yet little is known about microbial vertical distribution and community assembly in organic polluted sites. Here, high-throughput sequencing technology was employed to investigate prokaryotic microbial diversity and community assembly along soil profile in an abandoned chemical organic contaminated site. Results showed that there was no significant difference (P > 0.05) observed in microbial alpha diversity among different soil layers, whereas the structure of microbial communities presented significantly different (P < 0.05) in the superficial layer (0-0.5 m) compared with intermediate (1-1.5 m) and bottom (2.5-3 m) layers. Soil prokaryotic microbial community evolved to possess the potential of degrading organic pollutants under long-term organic pollution stress. A relatively homogeneous environment created by the organic polluted site mainly induced the ecological process of homogeneous selection driving community assembly, while dispersal limitation gained importance with the increase of soil depth. Organic contaminants were identified as the key driver of destabilizing co-occurrence networks, while the frequent cooperative behaviors among species could combat organic pollution stress and sustain prokaryotic community stability. Collectively, pollution pressure and soil depth jointly affected prokaryotic microbial assemblage and co-occurrence that underpinned the spatial scaling patterns of organic contaminated sites microbiota.

Polyaromatic hydrocarbons biodegradation using mix culture of microorganisms from sewage waste sludge: application of artificial neural network modelling

PURPOSE

In this study, we aimed to examine the tolerance of mixed culture of microorganisms isolated from sewage waste sludge to degrade high concentrations of polyaromatic hydrocarbons, naphthalene, and phenanthrene. The performance of the artificial neural network (ANN) model to predict and simulate the experimental biodegradation results was investigated.

METHODS

The mixed culture of microorganisms was isolated from sewage waste sludge and adopted to biodegrade naphthalene and phenanthrene at different concentrations (100-1000mg/L). Sewage waste sludge obtained from wastewater treatment plants. A three-layer feed-forward network with a sigmoid transfer function (logsig) at the hidden layer, a linear transfer function (purelin) at the output layer, and a backpropagation training algorithm was used to set the ANN model.

RESULTS

The results of this study show that naphthalene at concentrations of 100, 300, 700, and 1000 mg/L was depleted after incubation with the mixed culture for 6, 8, 14, and 16 days, respectively. For phenanthrene, depletion of 100, 300, 600, and 1000 mg/L was achieved after 8, 11, 16, and 19 days of incubation, respectively. A high correlation coefficient of 99.5% between the predicted and the experimental results were obtained by using the AAN model.

CONCLUSION

The results indicated that the mixed culture of microorganisms from sewage waste sludge could effectively consume naphthalene and phenanthrene as carbon and energy sources. Also, the ANN model could efficiently predict the experimental results for biodegradation treatment.

Effect of arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) on microorganism of phenanthrene and pyrene contaminated soils

A pot experiment was performed to investigate the effect of phytoremediation (CK, using tall fescue), fungi remediation (GV, using Glomus versiforme), bacterial remediation (PS, using Pseudomonas fluorescens Ps2-6), and microbial-phytoremediation (GVPS, using three species) on removing polycyclic aromatic hydrocarbons (PAHs) and the microbial diversity in soils. Inoculation with G. versiforme and P. fluorescens could increase the biomass of tall fescue and the accumulation of phenanthrene (PHE) and pyrene (PYR) in plants. Among them, the highest PHE and PYR removal efficiencies and highest biomass of tall fescue were observed in the GVPS treatment and the microbial diversity in contaminated soil was changed, the result revealed that Proteobacteria and Ascomycota were the dominant bacterial phylum and fungal phylum in all treatments, while more Proteobacteria were detected in GVPS treatment. At the genus level, the abundance of Sphingomonas (3.17%), Pseudomonas (2.05%), and Fusarium (8.65%) treated with GVPS increased compared with other treatments. These pieces of evidence contribute to a better understanding of the mechanisms involved in the combined microbial-phytoremediation strategies for PAHs-contaminated soils, especially the effects of microbial-phytoremediation on rhizosphere microbial diversity.

Strategy to Promote the Biodegradation of Phenanthrene in Contaminated Soil by a Novel Bacterial Consortium in Slurry Bioreactors

Polycyclic aromatic hydrocarbons (PAHs) are typical high-risk, persistent organic pollutants. Biological slurry reactors are widely used for enhanced bioremediation. In this experiment, a highly efficient phenanthrene-degrading bacteria group was obtained through screening and domestication, and the community was named MZJ_21. After the addition of MZJ_21 to the aerobic slurry bioreactor, with the optimum conditions of the temperature, stirring speed, and aeration rate of 30 °C, 120 rpm, and 1 L/min, respectively, the phenanthrene degradation ratio reached 95.41% within 48 h. The exploration of the degradation of phenanthrene by MZJ_21 indicated that most MZJ_21 communities adsorbed on the soil particle, mainly because MZI_21 could secrete extracellular polymers, which could stably adhere MZJ_21 on the solid phase. At the same time, the distribution ratio of phenanthrene in the solid phase is increased, so that the efficient phenanthrene degradation reaction takes place in the solid phase.

Shifts in microbial community structure and function in polycyclic aromatic hydrocarbon contaminated soils at petrochemical landfill sites revealed by metagenomics

Investigations of the microbial community structures, potential functions and polycyclic aromatic hydrocarbon (PAH) degradation-related genes in PAH-polluted soils are useful for risk assessments, microbial monitoring, and the potential bioremediation of soils polluted by PAHs. In this study, five soil sampling sites were selected at a petrochemical landfill in Beijing, China, to analyze the contamination characteristics of PAHs and their impact on microorganisms. The concentrations of 16 PAHs were detected by gas chromatography-mass spectrometry. The total concentrations of the PAHs ranged from ND to 3166.52 μg/kg, while phenanthrene, pyrene, fluoranthene and benzo [ghi]perylene were the main components in the soil samples. According to the specific PAH ratios, the PAHs mostly originated from petrochemical wastes in the landfill. The levels of the total toxic benzo [a]pyrene equivalent (1.63-107.73 μg/kg) suggested that PAHs might result in adverse effects on soil ecosystems. The metagenomic analysis showed that the most abundant phyla in the soils were Proteobacteria and Actinobacteria, and Solirubrobacter was the most important genus. At the genus level, Bradyrhizobium, Mycobacterium and Anaeromyxobacter significantly increased under PAH stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, the most abundant category of functions that are involved in adapting to contaminant pressures was identified. Ten PAH degradation-related genes were significantly influenced by PAH pressure and showed correlations with PAH concentrations. All of the results suggested that the PAHs from the petrochemical landfill could be harmful to soil environments and impact the soil microbial community structures, while microorganisms would change their physiological functions to resist pollutant stress.

From Surface Water to the Deep Sea: A Review on Factors Affecting the Biodegradation of Spilled Oil in Marine Environment

Over the past century, the demand for petroleum products has increased rapidly, leading to higher oil extraction, processing and transportation, which result in numerous oil spills in coastal-marine environments. As the spilled oil can negatively affect the coastal-marine ecosystems, its transport and fates captured a significant interest of the scientific community and regulatory agencies. Typically, the environment has natural mechanisms (e.g., photooxidation, biodegradation, evaporation) to weather/degrade and remove the spilled oil from the environment. Among various oil weathering mechanisms, biodegradation by naturally occurring bacterial populations removes a majority of spilled oil, thus the focus on bioremediation has increased significantly. Helping in the marginal recognition of this promising technique for oil-spill degradation, this paper reviews recently published articles that will help broaden the understanding of the factors affecting biodegradation of spilled oil in coastal-marine environments. The goal of this review is to examine the effects of various environmental variables that contribute to oil degradation in the coastal-marine environments, as well as the factors that influence these processes. Physico-chemical parameters such as temperature, oxygen level, pressure, shoreline energy, salinity, and pH are taken into account. In general, increase in temperature, exposure to sunlight (photooxidation), dissolved oxygen (DO), nutrients (nitrogen, phosphorous and potassium), shoreline energy (physical advection—waves) and diverse hydrocarbon-degrading microorganisms consortium were found to increase spilled oil degradation in marine environments. In contrast, higher initial oil concentration and seawater pressure can lower oil degradation rates. There is limited information on the influences of seawater pH and salinity on oil degradation, thus warranting additional research. This comprehensive review can be used as a guide for bioremediation modeling and mitigating future oil spill pollution in the marine environment by utilizing the bacteria adapted to certain conditions.

Predicting the total PAHs concentrations in sediments from selected congeners using a multiple linear relationship

In this study, we observed that four congeners, including naphthalene (Nap), acenaphthylene (Acy), phenanthrene (Phe), and benz(a)anthracene (BaA), are the characteristic congeners for predicting the emission and the sediment concentrations of polycyclic aromatic hydrocarbons (PAHs). A novel multiple relationship of the total PAHs concentrations (C_∑PAHs) in sediments with the concentrations of four congeners was established (p < 0.01, R² = 0.95) using published data over the past 30 years. Moreover, the multiple linear relationship of the total PAHs emission factors with the emission factors of four congeners was also established (p < 0.01, R² = 0.99). Interestingly, the ratio of multicomponents coefficient from the multiple linear relationship in sediments to that from the multiple linear relationship in emission sources correlated positively with octanol–water partition coefficient (logK_ow) (p < 0.01, R² = 0.88) of the four PAHs congeners. Therefore, a novel model was established to predict C_ΣPAHs in sediments using the emissions and logK_ow of the four characteristic PAHs congeners. The percent sample deviation between calculated C_∑PAHs and their observed values was 54%, suggesting the established model can accurately predict C_ΣPAHs in sediments.

Bioremediation of PAHs and heavy metals co-contaminated soils: Challenges and enhancement strategies

Systemic studies on the bioremediation of co-contaminated PAHs and heavy metals are lacking, and this paper provides an in-depth review on the topic. The released sources and transport of co-contaminated PAHs and heavy metals, including their co-occurrence through formation of cation-π interactions and their adsorption in soil are examined. Moreover, it is investigated that co-contamination of PAHs and heavy metals can drive a synergistic positive influence on bioremediation through enhanced secretion of extracellular polymeric substances (EPSs), production of biosynthetic genes, organic acid and enzymatic proliferation. However, PAHs molecular structure, PAHs-heavy metals bioavailability and their interactive cytotoxic effects on microorganisms can exert a challenging influence on the bioremediation under co-contaminated conditions. The fluctuations in bioavailability for microorganisms are associated with soil properties, chemical coordinative interactions, and biological activities under the co-contaminated PAHs-heavy metals conditions. The interactive cytotoxicity caused by the emergence of co-contaminants includes microbial cell disruption, denaturation of DNA and protein structure, and deregulation of antioxidant biological molecules. Finally, this paper presents the emerging strategies to overcome the bioavailability problems and recommends the use of biostimulation and bioaugmentation along with the microbial immobilization for enhanced bioremediation of PAHs-heavy metals co-contaminated sites. Better knowledge of the bioremediation potential is imperative to improve the use of these approaches for the sustainable and cost-effective remediation of PAHs and heavy metals co-contamination in the near future.

Mechanism of bio-electrokinetic remediation of pyrene contaminated soil: Effects of an electric field on the degradation pathway and microbial metabolic processes

In this study, the mechanism of bio-electrokinetic (BIO-EK) remediation to improve the degradation of pyrene was evaluated based on an analysis of the intermediate products and the microbial community. The results show that BIO-EK remediation has a higher pyrene degradation efficiency on pyrene and its intermediate products than the bioremediation and electrokinetic (EK) remediation processes. A series of intermediate products were detected. According to the type of the intermediate products, two degradation pathways, biological metabolism and electrochemical oxidation, are proposed in the BIO-EK remediation of pyrene. Furthermore, the primary microbial taxa involved in the pollutant degradation changed, which led to variations in the functional gene components. The abundant and functional genes related to metabolism were specifically analyzed. The results indicate that the electric field promotes the expression of metabolisms associated with 14 carbohydrates, 13 lipids, 13 amino acids, five energies, and in particular, 11 xenobiotics. These results suggest that in addition to the promotion effect on the microbial metabolism caused by the electric field, BIO-EK remediation can promote the degradation of pollutants due to the coexistence of a microbial metabolic pathway and an electrochemical oxidation pathway.

Selective acceleration of 2-hydroxyl pyridine mono-oxygenation using specially acclimated biomass

Biodegradation of pyridine starts with two mono-oxygenation reactions, and 2-hydroxyl pyridine (2-HP) accumulates as pyridine is mono-oxygenated in the first reaction. The accumulation of 2-HP inhibits both initial reactions. Therefore, selective acceleration of the second mono-oxygenation reaction should significantly enhance pyridine transformation and mineralization. Activated-sludge biomass was separately acclimated with pyridine or 2-HP to produce pyridine- and 2-HP-acclimated biomasses. The pyridine-acclimated biomass was superior for pyridine biodegradation, but the 2-HP-acclimated biomass was superior for 2-HP biodegradation. As a consequence, the pyridine-acclimated biomass by itself achieved faster mono-oxygenation of pyridine to 2-HP, but 2-HP accumulated, which limited mineralization to 60%. In contrast, mineralization reached 90% when one-third of the pyridine-acclimated was replaced with 2-HP-acclimated biomass, because 2-HP did not accumulate during pyridine biodegradation. The lack of 2-HP accumulation relieved its inhibition: e.g., the pyridine removal rates, normalized to the mass of pyridine-acclimated biomass, increased from 0.52 to 0.57 mM^0.5⋅h^-1 when one-third of the pyridine-acclimated biomass was replaced by 2-HP-acclimated biomass. Phylogenetic analysis showed that microbiological communities of pyridine-acclimated biomass and 2-HP-acclimated biomass differed in important ways. On the one hand, the 2-HP-acclimated biomass was richer and dominated by a rare biosphere, or genera having <0.1% of total reads. On the other hand, the most-enriched genus in the pyridine-acclimated community (Methylibium) is associated with the first mono-oxygenation of pyridine, while enriched genera in the 2-HP-acclimated community (Sediminibacterium and Dokdonella) are associated with the second mono-oxygenation of pyridine.

Enhanced anaerobic degradation of quinoline and indole with the coupling of sodium citrate and polyurethane

A coupling system of sodium citrate and biofilm based on polyurethane was prepared to analyse the coupling enhancement degradation on quinoline and indole. Four reactors (R1: sludge, R2: sludge + sodium citrate, R3: biofilm on polyurethane, and R4: biofilm + sodium citrate) were operated 120 days to compare the degradation efficiency. During whole running phases, R4 showed high degradation efficiency on quinoline (≥98.55%) and indole (≥95.44%). Analysis of bacterial colony showed anaerobic sludge reactors benefited the enrichment of Aminicenantes, Levilinea, and Longilinea, while anaerobic biofilm reactors benefited the enrichment of Giesbergeria and Comamonas. Furthermore, analysis of archaea colony showed acetic acid metabolism to produce methane was the main mode in anaerobic sludge reactors, while acetic acid and hydrogen metabolism to produce methane were both the main modes in biofilm reactors. This study can provide some references for the treatment of nitrogen heterocyclic wastewater.

Bacterial and archaeal diversity in oil fields and reservoirs and their potential role in hydrocarbon recovery and bioprospecting

Hydrocarbon is a primary source of energy in the current urbanized society. Considering the increasing demand, worldwide oil productions are declining due to maturity of oil fields and because of difficulty in discovering new oil fields to substitute the exploited ones. To meet current and future energy demands, further exploitation of oil resources is highly required. Microorganisms inhabiting in these areas exhibit highly diverse catabolic activities to degrade, transform, or accumulate various hydrocarbons. Enrichment of hydrocarbon-utilizing bacteria in oil basin is caused by continuous long duration and low molecular weight hydrocarbon microseepage which plays a very important role as an indicator for petroleum prospecting. The important microbial metabolic processes in most of the oil reservoir are sulfate reduction, fermentation, acetogenesis, methanogenesis, NO3- reduction, and Fe (III) and Mn (IV) reduction. The microorganisms residing in these sites have critical control on petroleum composition, recovery, and production methods. Physical characteristics of heavy oil are altered by microbial biotransformation and biosurfactant production. Considering oil to be one of the most vital energy resources, it is important to have a comprehensive understanding of petroleum microbiology. This manuscript reviews the recent research work referring to the diversity of bacteria in oil field and reservoir sites and their applications for enhancing oil transformation in the target reservoir and geomicrobial prospecting scope for petroleum exploration.

Octanol-water partition coefficient (logKow) dependent movement and time lagging of polycyclic aromatic hydrocarbons (PAHs) from emission sources to lake sediments: A case study of Taihu Lake, China

Understanding the movement of polycyclic aromatic hydrocarbons (PAHs) from emission sources to sediments is important for achieving long-term pollution control of PAHs in sediments. In this study, by exploring the correlation of individual PAHs concentrations (C_PAHs) in Taihu Lake sediments reported in the past twenty years with their annual emissions (E_PAHs) in the lake region, it was observed that mean concentrations of PAHs with low logK_ow (i.e., logK_ow≤4.00) in Taihu Lake sediments were correlated best with their emissions without lagging between the sediment sampling time and the PAHs emitting time. However, for PAHs with middle logK_ow (i.e., 4.00<logK_ow≤4.57) or high logK_ow (i.e., logK_ow>4.57), their mean concentrations in sediments were correlated best with the emissions of PAHs emitted 1 or 2 years before the sediment sampling time. The longer lagging time of PAHs with middle or high logK_ow from emission sources to lake sediments could be attributed to their retardation in soils and river sediments around the lake. Moreover, the retardation in soils and river sediments is dependent on PAHs logK_ow and degradation half-life, indicating the dependence of PAHs concentration in sediments on their environmental behaviors, including sorption and degradation. K_ow dependent movement and the time lagging observed in Taihu Lake for PAHs from emission sources to sediments could be valuable for developing measures to control PAHs, especially for congeners with high logK_ow.

Biochar decreased enantioselective uptake of chiral pesticide metalaxyl by lettuce and shifted bacterial community in agricultural soil

A 35-day microcosmic experiment was conducted with lettuce (Lactuca sativa L.) and two metalaxyl (MET) enantiomers (R-MET and S-MET) to understand the roles of biochar in the enantioselective fate of chiral pesticides in soil-plant ecosystems. Wood waste-derived biochar (WBC) amendment effectively decreased the shoot concentrations of R-MET/S-MET and their metabolites R-MET/S-MET acid by 57.7-86.3% and 13.3-32.5%, respectively. The reduced uptake was mainly attributed to the decreased bioavailability of R-MET and S-MET. A lower fraction of R-MET was accumulated by the lettuce in the WBC-amended soils relative to the control, suggesting a decrease in the enantioselective uptake of the chiral pesticide MET in the presence of biochar. Regardless of the WBC amendment, no enantiomerization of MET or MET acid occurred. The application of WBC stimulated soil bacterial diversity, shifted the bacterial community, and enhanced the abundance of pesticide degrading bacteria (e.g., Luteimonas, Methylophilus, and Hydrogenophaga), which were responsible for the enantioselective degradation of MET in the soil. This work expands our understanding of the enantioselective fate of chiral pesticides in the biochar-amended soil ecosystems. These findings can be used to develop biochar-based technologies to remediate soils contaminated with these chiral pesticides to ensure food safety.

Biotreatment of Cr(VI) and pyrene combined water pollution by loofa-immobilized bacteria

Hexavalent chromium (Cr(VI)) and pyrene are toxic pollutants that are difficult to remediate from soils and wastewater. Serratia sp. strains have been previously demonstrated to remove either Cr(VI) or pyrene and here a new isolate, called the Z6 strain, was demonstrated to remove both simultaneously. The removal occurs primarily by Cr(VI) reduction and pyrene biodegradation, and genome analysis suggests the removal mechanisms are the putative chromate reductase and two assumable pathways of pyrene degradation. The Z6 strain effectively removed most Cr(VI) (up to approximately 86%) and pyrene (up to approximately 57%) in seven different types of wastewater after 7 days of biotreatment. Additionally, the carrier loofa used for bacteria immobilization did not change the kinetics of Cr(VI) reduction or pyrene degradation. The carrier loofa was also effective for multiple uses, with removal capacity not being significantly affected over the first seven cycles with the same carrier loofa. These results provide data for developing practical biotreatment applications of Cr(VI) and pyrene contaminated sites.

Enhancing biomethane production and pyrene biodegradation by addition of bio-nano FeS or magnetic carbon during sludge anaerobic digestion

Pyrene exerts toxic effects on methanogens during anaerobic digestion of sludge, thus affecting the efficiency of sludge treatment. This study evaluated the facilitated direct interspecific electron transfer (DIET) between bacteria and methanogens when bio-nano FeS or magnetic carbon is added into anaerobic reactors. Results showed that adding 200 mg/L bio-nano FeS or magnetic carbon clearly reduced the accumulation of short-chain fatty acids and avoided acidification during 25 days of anaerobic digestion. The methane productions were 98.38 L/kg total solid (TS) and 73.69 L/kg TS in the bio-nano FeS and magnetic carbon systems, respectively, which accelerated methane production by 58.1% and 33.4%, respectively, compared with the control system (40.26 L/kg TS). The pyrene removal rates reached 77.5% and 72.1% in the bio-nano FeS and magnetic carbon systems, whereas it was only 40.8% in the control system. Analysis of microbial community structure revealed that methanogens (e.g. Methanosarcina and Methanosaeta) and extracellular electron-transfer bacteria (e.g. Pseudomonas, Cloastridia, and Synergistetes) were enriched in the reactors added with bio-nano FeS or magnetic carbon. This result indicates that the addition of bio-nano FeS or magnetic carbon may promote the activity and growth of microorganisms to improve the efficiency of methane production and pyrene degradation by enhancing DIET.

Construction of biotreatment platforms for aromatic hydrocarbons and their future perspectives

Aromatic hydrocarbons (AHCs) are one of the major environmental pollutants introduced from both natural and anthropogenic sources. Many AHCs are well known for their toxic, carcinogenic, and mutagenic impact on human health and ecological systems. Biodegradation is an eco-friendly and cost-effective option as microorganisms (e.g., bacteria, fungi, and algae) can efficiently breakdown or transform such pollutants into less harmful and simple metabolites (e.g., carbon dioxide (aerobic), methane (anaerobic), water, and inorganic salts). This paper is organized to offer a state-of-the-art review on the biodegradation of AHCs (monocyclic aromatic hydrocarbons (MAHs) and polycyclic aromatic hydrocarbons (PAHs)) and associated mechanisms. The recent progress in biological treatment using suspended and attached growth bioreactors for the biodegradation of AHCs is also discussed. In addition, various substrate growth and inhibition models are introduced along with the key factors governing their biodegradation kinetics. The growth and inhibition models have helped gain a better understanding of substrate inhibition in biodegradation. Techno-economic analysis (TEA) and life cycle assessment (LCA) aspects are also described to assess the technical, economical, and environmental impacts of the biological treatment system.

Recovery of the nitrifying ability of acclimated biomass exposed to para-nitrophenol

Para-nitrophenol (PNP) is often detected in industrial wastewater that is discharged into municipal wastewater treatment plants. Intermittent discharge of PNP into municipal treatment facilities puts their biological process at risk of inhibition, and the risk is especially great for nitrification. In this work, nitrifying biomass was acclimated to PNP. The acclimated biomass retained most of its ammonium-removal activity when it was exposed to PNP at up to 100 mg/L, while the normal (unacclimated) biomass had nearly complete inhibition. PNP was effectively biodegraded by the acclimated biomass, but the normal biomass had minimal PNP biodegradation. After PNP disappeared, the acclimated biomass recovered its ability for NH₄⁺-N removals within one to two days, but the normal biomass did not fully recovery even after seven days. The acclimated biomass had superior ability to sustain nitrification due to its ability to biodegrade PNP and its selection of nitrifying bacteria more resistant to PNP. The PNP-acclimated community was enriched in genera that could have been active in the biodegradation of PNP, such as Chloroflexi. Although the abundance of well-known nitrifiers, Nitrosomonas and Nitrospira, decreased, Nitrosospira and other genera within the Proetobacteria phylum increased, presumably because they were more resistant to PNP.