Polycyclic aromatic hydrocarbons in deep sea sediments: Microbe-pollutant interactions in a remote environment

Effective and mechanistic insights into shale gas wastewater reverse osmosis concentrate treatment using ozonation-biological activated carbon process

Reverse osmosis (RO) plays a pivotal role in shale gas wastewater resource utilization. However, managing the reverse osmosis concentrate (ROC) characterized by high salinity and increased concentrations of organic matter is challenging. In this study, we aimed to elucidate the enhancement effects and mechanisms of pre-ozonation on organic matter removal efficacy in ROC using a biological activated carbon (BAC) system. Our findings revealed that during the stable operation phase, the ozonation (O3 and O3/granular activated carbon)-BAC system removes 43.6-72.2 % of dissolved organic carbon, achieving a 4-7 fold increase in efficiency compared with that in the BAC system alone. Through dynamic analysis of influent and effluent water quality, biofilm performance, and microbial community structure, succession, and function prediction, we elucidated the following primary enhancement mechanisms: 1) pre-ozonation significantly enhances the biodegradability of ROC by 4.5-6 times and diminishes the organic load on the BAC system; 2) pre-ozonation facilitates the selective enrichment of microbes capable of degrading organic compounds in the BAC system, thereby enhancing the biodegradation capacity and stability of the microbial community; and 3) pre-ozonation accelerates the regeneration rate of the granular activated carbon adsorption sites. Collectively, our findings provide valuable insights into treating ROC through pre-oxidation combined with biotreatment.

Benthic foraminifera in Gulf of Mexico show temporal and spatial dynamics of microplastics

Microplastics have accumulated in the environment since plastic production began, with present-day observations that range from marine trenches to mountains. However, research on microplastics has only recently begun so it is unclear how they have changed over time in many oceanic regions. Our study addressed this gap by quantifying the temporal and spatial dynamics of microplastics in two deep-water regions of the Gulf of Mexico (GOM). We isolated agglutinated foraminifera from sediment cores and assessed microplastics that were incorporated into their tests. Our results indicated that microplastics were incorporated by agglutinated foraminifera after plastic production began. Microplastics were higher at deep-water sites and closer to the Mississippi River. This study confirms the presence of microplastic incorporation into agglutinated foraminifera tests and investigates microplastics in deep-water sediments in the GOM. Additional work is needed to fully identify the distribution of microplastics across the GOM and other oceanic basins.

Marine Microbiota Responses to Shipping Scrubber Effluent Assessed at Community Structure and Function Endpoints

The use of novel high-throughput sequencing (HTS) technologies to examine the responses of natural multidomain microbial communities to scrubber effluent discharges to the marine environment is still limited. Thus, we applied metabarcoding sequencing targeting the planktonic unicellular eukaryotic and prokaryotic fraction (phytoplankton, bacterioplankton, and protozooplankton) in mesocosm experiments with natural microbial communities from a polluted and an unpolluted site. Furthermore, metagenomic analysis revealed changes in the taxonomic and functional dominance of multidomain marine microbial communities after scrubber effluent additions. The results indicated a clear shift in the microbial communities after such additions, which favored bacterial taxa with known oil and polycyclic aromatic hydrocarbons (PAHs) biodegradation capacities. These bacteria exhibited high connectedness with planktonic unicellular eukaryotes employing variable trophic strategies, suggesting that environmentally relevant bacteria can influence eukaryotic community structure. Furthermore, Clusters of Orthologous Genes associated with pathways of PAHs and monocyclic hydrocarbon degradation increased in numbers at treatments with high scrubber effluent additions acutely. These genes are known to express enzymes acting at various substrates including PAHs. These indications, in combination with the abrupt decrease in the most abundant PAHs in the scrubber effluent below the limit of detection-much faster than their known half-lives-could point toward a bacterioplankton-initiated rapid ultimate biodegradation of the most abundant toxic contaminants of the scrubber effluent. The implementation of HTS could be a valuable tool to develop multilevel biodiversity indicators of the scrubber effluent impacts on the marine environment, which could lead to improved impact assessment. Environ Toxicol Chem 2024;00:1-18. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Bacterial cell sensing and signaling pathway for external polycyclic aromatic hydrocarbons (PAHs)

The mechanism by which a bacterial cell senses external nutrients remains largely unknown. In this study, we identified a bacterial cell sensing system for polycyclic aromatic hydrocarbons (PAHs) in a common marine PAH-using bacterium, Cycloclasticus. It consists of an outer membrane receptor (PahS) and a periplasmic protein (PahP) in combination with a two-component sensing system (TCS) that ensures a rapid response to PAH occurrence by directly controlling serial reactions including chemotactic sensing and movement, PAH uptake and intracellular PAH metabolism. PahS protrudes from the cell and acts as a PAH sensor, transducing the PAH signal across the outer membrane to its periplasmic partner PahP, which in turn transduces the PAH signal across the periplasm to a specialized TCS. This sensing system plays a critical role in sensing and promoting the metabolism of PAHs, which can be scavenged by various hydrocarbon-degrading bacteria.

Patterns of Carbon-Bound Exogenous Compounds Impact Disease Pathophysiology in Lung Cancer Subtypes in Different Ways

Carbon-bound exogenous compounds, such as polycyclic aromatic hydrocarbons (PAHs), tobacco-specific nitrosamines, aromatic amines, and organohalogens, are known to affect both tumor characteristics and patient outcomes in lung squamous cell carcinoma (LUSC); however, the roles of these compounds in lung adenocarcinoma (LUAD) remain unclear. We analyzed 11 carbon-bound exogenous compounds in LUAD and LUSC samples using in situ high mass-resolution matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometry imaging and performed a cluster analysis to compare the patterns of carbon-bound exogenous compounds between these two lung cancer subtypes. Correlation analyses were conducted to investigate associations among exogenous compounds, endogenous metabolites, and clinical data, including patient survival outcomes and smoking behaviors. Additionally, we examined differences in exogenous compound patterns between normal and tumor tissues. Our analyses revealed that PAHs, aromatic amines, and organohalogens were more abundant in LUAD than in LUSC, whereas the tobacco-specific nitrosamine nicotine-derived nitrosamine ketone was more abundant in LUSC. Patients with LUAD and LUSC could be separated according to carbon-bound exogenous compound patterns detected in the tumor compartment. The same compounds had differential impacts on patient outcomes, depending on the cancer subtype. Correlation and network analyses indicated substantial differences between LUAD and LUSC metabolomes, associated with substantial differences in the patterns of the carbon-bound exogenous compounds. These data suggest that the contributions of these carcinogenic compounds to cancer biology may differ according to the cancer subtypes.

Microbial machinery dealing diverse aromatic compounds: Decoded from pelagic sediment ecogenomics in the gulfs of Kathiawar Peninsula and Arabian Sea

Aromatic hydrocarbons are persistent pollutants in aquatic systems as endocrine disruptors, significantly impacting natural ecosystems and human health. Microbes perform as natural bioremediators to remove and regulate aromatic hydrocarbons in the marine ecosystem. The present study focuses upon the comparative diversity and abundance of various hydrocarbon-degrading enzymes and their pathways from deep sediments along the Gulf of Kathiawar Peninsula and Arabian Sea, India. The elucidation of large number of degradation pathways in the study area under the presence of a wide range of pollutants whose fate needs to be addressed. Sediment core samples were collected, and the whole microbiome was sequenced. Analysis of the predicted ORFs (open reading frames) against the AromaDeg database revealed 2946 aromatic hydrocarbon-degrading enzyme sequences. Statistical analysis portrayed that the Gulfs were more diverse in degradation pathways compared to the open sea, with the Gulf of Kutch being more prosperous and more diverse than the Gulf of Cambay. The vast majority of the annotated ORFs belonged to groups of dioxygenases that included catechol, gentisate, and benzene dioxygenases, along with Rieske (2Fe-2S) and vicinal oxygen chelate (VOC) family proteins. From the sampling sites, only 960 of the total predicted genes were given taxonomic annotations, which mention the presence of many under-explored marine microorganism-derived hydrocarbon degrading genes and pathways. Through the present study, we tried to unveil the array of catabolic pathways of aromatic hydrocarbon degradation and genes from a marine ecosystem that upholds economic and ecological significance in India. Thus, this study provides vast opportunities and strategies for microbial resource recovery in marine ecosystems, which can be investigated to explore aromatic hydrocarbon degradation and their potential mechanisms under various oxic or anoxic environments. Future studies should focus on aromatic hydrocarbon degradation by considering degradation pathways, biochemical analysis, enzymatic, metabolic, and genetic systems, and regulations.

BTEX and PAH contributions to Lake Kinneret water: a seasonal-based study of volatile and semi-volatile anthropogenic pollutants in freshwater sources

Benzene , toluene, ethylbenzene, and xylenes (BTEX) BTEX molecules are toxic components, ubiquitous in the environment, often found in concentrations- a few orders of magnitude higher than the well-studied PAHs levels. This fact is demonstrated in either crude oil, fuels, water, and air samples. BTEX studies focus mainly on the airborne levels of these molecules, while their waterborne presence is understudied. In this study, BTEX levels were assessed at Lake Kinneret, Israel. As a result, 0-1.5 ppb of BTEX was recorded in five stations (2021-2022). Elevated BTEX levels (3-10 ppb) were recorded at the northern rivers nourishing this lake, implying the existence of remote polluting sources. Transect air samplings of BTEX conducted at the lake next to the bathing season of 2021 revealed airborne BTEX levels between 0.8 and 10 µg/m³, peaking up close to the bathing season, yet inconsistent with the BTEX water level trend. Lake water samples collected next to Tiberias city outfalls following the "Carmel" rainstorm showed elevated concentrations of BTEX up to 35 ppb and PAHs up to 0.47 ppb with an urban isotopic signal. The remote station's PAHs levels were less than one order of magnitude, with a distinct rural isotopic signal. Additionally, a human-specific microbial marker revealed increased sewer contributions at some of the urbansites. The results of this study show that a wide area dispersion of low atmospheric BTEX levels exists in the lake's perimeter. The dispersion rate is most likely influenced by season-based factors, e.g., motors and biomass fires. The unstudied waterborne BTEX levels in this lake are influenced by rivers, city runoff, and other yet unknown factors that may contribute to the sedimentation of these components. This process may result in a chronic pollution state. Despite the BTEX's medium-low solubility and high volatility, its under-evaluated waterborne transportation may lead to high toxic levels following bioaccumulation.

Phthalates contamination in the coastal and marine sediments of Rio de Janeiro, Brazil

Coastal and marine environments have been strongly influenced by anthropogenic activities, which may lead to high concentrations of different pollutants in sediments. Our study aimed to assess sediment contamination by polycyclic aromatic hydrocarbons (PAHs), phthalates (PAEs) and bisphenol A (BPA) in nine coastal and marine environments at Rio de Janeiro-Brazil. Physical and chemical water variables, grain-size parameters, moisture, and organic-matter content in sediments were assessed by sampling station. Multivariate analysis evidenced environmental differences between coastal lagoon and oceanic beaches, mostly influenced by marine waters. Differences among bay's beaches were mostly evidenced by sediment characteristics. PAHs and BPA were not detected in samples. For the first time, PAEs were found in sediments at Rio de Janeiro coast (South Atlantic). DEHP was detected in all coastal and marine environments, DBP was found in coastal lagoon and three marine environments. DnOP and DINP were solely found in the coastal lagoon.

Effects of combined remediation of pre-ozonation and bioaugmentation on degradation of benzo[a]pyrene and microbial community structure in soils

The combination technique of pre-ozonation and bioaugmentation is promising for remediating benzo[a]pyrene (BaP)-contaminated soil. However, little is known about the effect of coupling remediation on the soil biotoxicity, soil respiration, enzyme activity, microbial community structure, and microbial in the process of remediation. This study developed two coupling remediation strategies (pre-ozonation coupled with bioaugmentation by addition of polycyclic aromatic hydrocarbons (PAHs) specific degrading bacteria or activated sludge), compared with sole ozonation and sole bioaugmentation, to improve degradation of BaP and recovery of soil microbial activity and community structure. Results showed that the higher removal efficiency of BaP (92.69-93.19%) was found in coupling remediation, compared with sole bioaugmentation (17.71-23.28%). Meanwhile, coupling remediation significantly reduced the soil biological toxicity, promoted the rebound of microbial counts and activity, and recovered the species numbers and microbial community diversity, compared with sole ozonation and sole bioaugmentation. Besides, it was feasible to replace microbial screening with activated sludge, and coupling remediation by addition of activated sludge was more conducive to the recovery of soil microbial communities and diversity. This work provides a strategy of pre-ozonation coupled with bioaugmentation to further degrade BaP in soil by promoting the rebound of microbial counts and activity, as well as the recovery of species numbers and microbial community diversity.

Source identification and ecological risks of parent and substituted polycyclic aromatic hydrocarbons in river surface sediment-pore water systems: Effects of multiple factors

Substituted polycyclic aromatic hydrocarbons (SPAHs) have shown higher health and ecological risks than the corresponding parent PAHs (PPAHs) from laboratory studies, their variations in freshwater system, especially in surface sediment and pore water, remain inadequate understanding. In this study, we revealed the coexistence, ecological risk, and multiple factors affecting variations and sources of PPAHs and SPAHs (nitrated PAHs (NPAHs), oxygenated PAHs (OPAHs)) in the surface sediment-pore water system from a typical urban river in Northern China. The concentration ranges of Σ₂₆PPAHs, Σ₁₀NPAHs, and Σ₄OPAHs in the surface sediments were 153.0-5367.4, not detected (N.D.)-105.4, and 42.2-1177.0 ng·g^-1 dry weight, and fell within 0.6-38.8, N.D.-297.9, and N.D.-212.6 ng·mL^-1 in the pore waters. The t-distributed stochastic neighbor embedding (SNE) coupled with the partitioning around medoids (PAM) elucidated spatiotemporal the variations in PAHs, emphasizing the impacts of industrial activities and sewage discharges. Besides the geochemical and hydrochemical conditions, SPAHs were affected by the potential secondary formation, especially during the wet season. The method comparisons indicated the advantages of principal component analysis-multivariate linear regression (PCA-MLR) and n-alkanes model on source identification. PAHs mainly originated from fossil fuel combustion and vehicular exhaust. The top risk quotient (RQ) values for PAHs occurred in the urban and industrial sections. A majority of the surface sediment samples emerged with low to moderate exposure risks, while all the pore water samples showed high exposure risks. The RQs of OPAHs were significantly higher (p < 0.01) than those of PPAHs. The results suggested the secondary formation of SPAHs as an important role in ecological risks of PAHs in the urban river system.

Fine particles and pyrogenic carbon fractions regulate PAH partitioning and burial in a eutrophic shallow lake

Aquatic particles and organic carbon (OC) regulate the occurrence and transport of hydrophobic organic contaminants such as polycyclic aromatic hydrocarbons (PAHs) in water-suspended particle-sediment interfaces. Conventional studies on the mechanisms regulating the relationships between PAHs and total particles/OC have ignored micro-scale regulatory factors such as particle size and OC composition. Field research in the eutrophic shallow Lake Taihu, China, revealed that the fine particle fractions 2.7-10 μm in diameter had stronger PAH adsorption capacity and significantly regulated PAH particle size distribution and water-particle partitioning. Selective PAH biodegradation by planktonic microorganisms probably significantly weakened the capacity of the coarse fractions to regulate PAHs. OC fragments at different temperature gradients had markedly different influences on the particle size distribution of PAHs. High-temperature pyrogenic OC fractions (part of black carbon) were the principal OC regulatory factors for medium-to high-molecular-weight PAHs. However, the OC fragments did not directly affect the particle distribution of low-molecular-weight PAHs. During particle deposition and burial, microbial PAH utilization and efficiency probably regulated the burial potential of various hydrophobic PAH species. Biodegradation of relatively less hydrophobic PAHs with octanol-water partition coefficients (log K_ow) < 5.8 showed an increasing trend with decreasing PAH hydrophobicity. Biological pump action of the relatively higher hydrophobic PAH species (log K_ow > 5.8) showed a decreasing trend with increasing PAH hydrophobicity. The discoveries of the present work further clarified the mechanisms of PAH partitioning and burial in a eutrophic shallow lake and collectively provides a valuable reference for modeling the transport and dispersal mechanisms of hydrophobic, particle-bound organic contaminants in other aquatic ecosystems.

Polycyclic aromatic hydrocarbon removal from subsurface soil mediated by bacteria and archaea under methanogenic conditions: Performance and mechanisms

In situ anoxic bioremediation is an easy-to-use technology to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated soil. Degradation of PAHs mediated by soil bacteria and archaea using CO₂ as the electron acceptor is an important process for eliminating PAHs under methanogenic conditions; however, knowledge of the performance and mechanisms involved is poorly unveiled. In this study, the effectiveness and efficiency of NaHCO₃ (CO₂) as an electron acceptor to stimulate the degradation of PAHs by bacteria and archaea in highly contaminated soil were investigated. The results showed that CO₂ addition (EC2000) promoted PAH degradation compared to soil without added CO₂ (EC0), with 4.18%, 9.01%-8.05%, and 6.19%-12.45% increases for 2-, 3- and 4-ring PAHs after 250 days of incubation, respectively. Soil bacterial abundances increased with increasing incubation time, especially for EC2000 (2.90 × 10⁸ g^-1 soil higher than EC0, p < 0.05). Different succession patterns of the soil bacterial and archaeal communities during PAH degradation were observed. According to the PCoA and ANOSIM results, the soil bacterial communities were greatly (ANOSIM: R = 0.7232, P = 0.001) impacted by electron acceptors, whereas significant differences in the archaeal communities were not observed (ANOSIM: R = 0.553, P = 0.001). Soil bacterial and archaeal co-occurrence network analyses showed that positive correlations outnumbered the negative correlations throughout the incubation period for both treatments (e.g., EC0 and EC2000), suggesting the prevalence of coexistence/cooperation within and between these two domains rather than competition. The higher complexity, connectance, edge, and node numbers in EC2000 revealed stronger linkage and a more stable co-occurrence network compared to EC0. The results of this study could improve the knowledge on the removal of PAHs and the responses of soil bacteria and archaea to CO₂ application, as well as a scientific basis for the in situ anoxic bioremediation of PAH-contaminated industrial sites.

Comprehensive Genomic Characterization of Marine Bacteria Thalassospira spp. Provides Insights into Their Ecological Roles in Aromatic Hydrocarbon-Exposed Environments

The marine bacterial genus Thalassospira has often been identified as an abundant member of polycyclic aromatic hydrocarbon (PAH)-exposed microbial communities. However, despite their potential usability for biotechnological applications, functional genes that are conserved in their genomes have barely been investigated. Thus, the goal of this study was to comprehensively examine the functional genes that were potentially responsible for aromatic hydrocarbon biodegradation in the Thalassospira genomes available from databases, including a new isolate of Thalassospira, strain GO-4, isolated from a phenanthrene-enriched marine bacterial consortium. Strain GO-4 was used in this study as a model organism to link the genomic data and their metabolic functions. Strain GO-4 growth assays confirmed that it utilized a common phenanthrene biodegradation intermediate 2-carboxybenzaldehyde (CBA) as the sole source of carbon and energy, but did not utilize phenanthrene. Consistently, strain GO-4 was found to possess homologous genes of phdK, pht, and pca that encode enzymes for biodegradation of CBA, phthalic acid, and protocatechuic acid, respectively. Further comprehensive genomic analyses for 33 Thalassospira genomes from databases showed that a gene cluster that consisted of phdK and pht homologs was conserved in 13 of the 33 strains. pca gene homologs were found in all examined genomes; however, homologs of the known PAH-degrading genes, such as the pah, phn, or nah genes, were not found. Possibly Thalassospira spp. co-occupy niches with other PAH-degrading bacteria that provide them with PAH degradation intermediates and facilitated their inhabitation in PAH-exposed microbial ecosystems. IMPORTANCE Comprehensive investigation of multiple genomic data sets from targeted microbial taxa deposited in databases may provide substantial information to predict metabolic capabilities and ecological roles in different environments. This study is the first report that details the functional profiling of Thalassospira spp. that have repeatedly been found in polycyclic aromatic hydrocarbon (PAH)-exposed marine bacterial communities by using genomic data from a new isolate, Thalassospira strain GO-4, and other strains in databases. Through screening of functional genes potentially involved in aromatic hydrocarbon biodegradation across 33 Thalassospira genomes and growth assays for strain GO-4, it was suggested that Thalassospira spp. unexceptionally conserved the ability to metabolize single-ring, PAH biodegradation intermediates, while being incapable of utilizing PAHs. This expanded our understanding of this potentially important contributing member to PAH-degrading microbial ecosystems; such species are considered to be specialized in driving downstream reactions of PAH biodegradation.

Endocrine disrupting chemicals in the environment: Environmental sources, biological effects, remediation techniques, and perspective

Endocrine disrupting chemicals (EDCs) have been identified as emerging contaminants, which poses a great threat to human health and ecosystem. Pesticides, polycyclic aromatic hydrocarbons, dioxins, brominated flame retardants, steroid hormones and alkylphenols are representative of this type of contaminant, which are closely related to daily life. Unfortunately, many wastewater treatment plants (WWTPs) do not treat EDCs as targets in the normal treatment process, resulting in EDCs entering the environment. Few studies have systematically reviewed the related content of EDCs in terms of occurrence, harm and remediation. For this reason, in this article, the sources and exposure routes of common EDCs are systematically described. The existence of EDCs in the environment is mainly related to human activities (Wastewater discharges and industrial activities). The common hazards of these EDCs are clarified based on available toxicological data. At the same time, the mechanism and effect of some mainstream EDCs remediation technologies (such as adsorption, advanced oxidation, membrane bioreactor, constructed wetland, etc.) are separately mentioned. Moreover, our perspectives are provided for further research of EDCs.

Fe3O4@SiO2@VAN Nanoadsorbent Followed by GC-MS for the Determination of Polycyclic Aromatic Hydrocarbons at Ultra-Trace Levels in Environmental Water Samples

In the present study, silica-coated magnetic nanoparticles functionalized with vancomycin (Fe₃O₄@SiO₂@VAN) were synthesized. The Fe₃O₄@SiO₂@VAN nanocomposite was used as a sorbent for the magnetic solid-phase extraction (MSPE) of polycyclic aromatic hydrocarbons (PAHs) from environmental water, followed by GC-MS. The nanocomposite was characterized by Fourier-transform infrared spectroscopy, X-ray diffraction, scanning electron microscopy, transmission electron microscopy, vibrating sample magnetometry, and nitrogen sorption. Various experimental parameters were optimized, including extraction condition and desorption condition. Results show that Fe₃O₄@SiO₂@VAN combined the advantages of nanomaterials and magnetic separation technology, showing excellent dispersibility and high selectivity for PAHs in environmental water sample. Under the optimal extraction conditions, an analytical method was established with the sensitive limit of detection (LOD) of 0.03-0.16 μg L^-1. The method was successfully applied for the analysis of environmental water samples. The relative standard deviations (%) were in the range of 0.50-12.82%, and the extraction recovery (%) was in the range of 82.48% and 116.32%. MSPE-coupled gas chromatography-mass spectrometry quantification of PAHs is an accurate and repeatable method for the monitoring of PAH accumulation in environmental water samples. It also provides an effective strategy for the tracing and quantification of other environmental pollutants in complex samples.

Anaerobic phenanthrene biodegradation by a new salt-tolerant/halophilic and nitrate-reducing Virgibacillus halodenitrificans strain PheN4 and metabolic processes exploration

The biodegradation of polycyclic aromatic hydrocarbons (PAHs) under hypersaline environments has received increasing attention, whereas the study of anaerobic PAH biodegradation under hypersaline environments is still lacking. Here, we found a pure culture designated PheN4, which was affiliated with Virgibacillus halodenitrificans and could degrade phenanthrene with nitrate as the terminal electron acceptor and a wide range of salinities (from 0.3% to 20%) under anaerobic environments. The optimal salinity for biodegradation of phenanthrene by PheN4 was 5%, which could degrade 93.5% of 0.62 ± 0.04 mM phenanthrene within 10 days with the initial inoculum of 0.01 gVSS/L. Meanwhile, an increased microbial amount could efficiently promote the phenanthrene biodegradation rate. The metabolic processes of anaerobic phenanthrene biodegradation under hypersaline conditions by PheN4 were proposed based on intermediates and genome analyses. Phenanthrene was initially activated via methylation to form 2-methylphenanthrene. Next, fumarate addition and β-oxidation or direct oxidation of the methyl group, ring reduction and ring cleavage were identified as the midstream and downstream steps. In addition, PheN4 could utilize benzene, naphthalene, and anthracene as carbon sources, but Benz[a]anthracene, pyrene, and Benzo[a]pyrene could not be biodegraded by PheN4. This study could provide some guidance for the bioremediation of PAH pollutants in anaerobic and hypersaline zones.

Bacterial communities of the Black Sea exhibit activity against persistent organic pollutants in the water column and sediments

The ability of bacteria to degrade organic pollutants influences their fate in the environment, impact on the other biota and accumulation in the food web. The aim of this study was to evaluate abundance and expression activity of the catabolic genes targeting widespread pollutants, such as polyaromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and hexachloro-cyclohexane (HCH) in the Black Sea water column and sediments. Concentrations of PAHs, PCBs and HCH were determined by gas chromatography (GC) coupled to mass spectrometry (MS) and electron capture (ECD) detectors. bphA1, PAH-RHDα, nahAc, linA and linB that encode biphenyl 2,3 dioxygenase, α-subunits of ring hydroxylating dioxygenases, naphthalene dioxygenase, dehydrochlorinase and halidohydrolase correspondently were quantified by quantitative PCR. More recalcitrant PAHs, PCBs and HCH tended to accumulate in the Black Sea environments. In water samples, 3- and 4-ringed PAHs outnumbered naphthalene, while PAHs with > 4 rings prevailed in the sediments. Congeners with 4-8 chlorines with ortho-position of the substituents were the most abundant among the PCBs. β-HCH was determined at highest concentration in water samples, and total amount of HCH exceeded its legacy Environmental Quality Standard value. bphA1, was the most numerous gene in water layers (105 copies/mL) and sediments (105 copies/mg), followed by linB and PAH-RHDα genes (103 copies/mL; 105 copies/mg). The least abundant genes were linA (103 copies/mL; 104 copies/mg) and nahAc (102 copies/mL; 104 copies/mg). The most widely distributed gene bphА1 was one of the least expressed (10-3-10-2 copies/mL; 10-1 copies/mg). The most actively expressed genes were linB (101-102 copies/mL; 103 copies/mg), PAH-RHDα (101 copies/mL; 102 copies/mg) and linA (10-1-100 copies/mL; 100 copies/mg). Interaction of bacteria with PAHs, PCBs and HCH is evidenced by high copy numbers of the catabolic genes that initiate their degradation. More persistent compounds, such as high-molecular weight PAHs or β-HCH are accumulating in the Black Sea water and sediments, albeit microbial activity is directed against them.

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.

Antibiotic tolerance and degradation capacity of the organic pollutant-degrading bacterium Rhodococcus biphenylivorans TG9T

Antibiotics are ubiquitous in soil due to natural ecological competition, as well as emerging contaminants due to anthropogenic inputs. Under environmental factors like antibiotic stress, some bacteria, including those that degrade environmental pollutants, can enter a dormant state as a survival strategy, thereby limiting their metabolic activity and function. Dormancy has a critical influence on the degradative activity of bacteria, dramatically decreasing the rate at which they transform organic pollutants. To better understand this phenomenon in environmental pollutant-degrading bacteria, we investigated dormancy transitions induced with norfloxacin in Rhodococcus biphenylivorans TG9^T using next-generation proteomics, proteogenomics, and additional experiments. Our results suggest that exposure to norfloxacin inhibited DNA replication, which led to damage to the cell. Dormant cells then likely triggered DNA repair, particularly homologous recombination, for continued survival. The results also indicated that substrate transport (ATP-binding cassette transporter), ATP production, and the tricarboxylic acid (TCA) cycle were repressed during dormancy, and degradation of organic pollutants was down-regulated. Given the widespread phenomenon of dormancy among bacteria involved in pollutant removal systems, this study improves our understanding of possible implications of antibiotic survival strategies on biotransformation of mixtures containing antibiotics as well as other organics.

Diversity and Hydrocarbon-Degrading Potential of Deep-Sea Microbial Community from the Mid-Atlantic Ridge, South of the Azores (North Atlantic Ocean)

Deep-sea sediments (DSS) are one of the largest biotopes on Earth and host a surprisingly diverse microbial community. The harsh conditions of this cold environment lower the rate of natural attenuation, allowing the petroleum pollutants to persist for a long time in deep marine sediments raising problematic environmental concerns. The present work aims to contribute to the study of DSS microbial resources as biotechnological tools for bioremediation of petroleum hydrocarbon polluted environments. Four deep-sea sediment samples were collected in the Mid-Atlantic Ridge, south of the Azores (North Atlantic Ocean). Their autochthonous microbial diversity was investigated by 16S rRNA metabarcoding analysis. In addition, a total of 26 deep-sea bacteria strains with the ability to utilize crude oil as their sole carbon and energy source were isolated from the DSS samples. Eight of them were selected for a novel hydrocarbonoclastic-bacterial consortium and their potential to degrade petroleum hydrocarbons was tested in a bioremediation experiment. Bioaugmentation treatments (with inoculum pre-grown either in sodium acetate or petroleum) showed an increase in degradation of the hydrocarbons comparatively to natural attenuation. Our results provide new insights into deep-ocean oil spill bioremediation by applying DSS hydrocarbon-degrading consortium in lab-scale microcosm to simulate an oil spill in natural seawater.

Organic pollutants in deep sea: Occurrence, fate, and ecological implications

The deep sea - an oceanic layer below 200 m depths - has important global biogeochemical and nutrient cycling functions. It also receives organic pollutants from anthropogenic sources, which threatens the ecological function of the deep sea. In this Review, critically examined data on the distribution of organic pollutants in the deep sea to outline the role of biogeochemical and geophysical factors on the global distribution and regional chemodynamics of organic pollutants in the deep sea. We found that the contribution of deep water formation to the influx of perfluorinated compounds reached a maximum, following peak emission, faster in young deep waters (< 10 years) compared to older deep waters (> 100 years). For example, perfluorinated compounds had low concentrations (< 10 pg L^-1) and vertical variations in the South Pacific Ocean where the ocean currents are old (< 1000 years). Steep geomorphologies of submarine canyons, ridges, and valleys facilitated the transport of sediments and associated organic pollutants by oceanic currents from the continental shelf to remote deep seas. In addition, we found that, even though an estimated 1.2-4.2 million metric tons of plastic debris enter the ocean through riverine discharge annually, the role of microplastics as vectors of organic pollutants (e.g., plastic monomers, additives, and attached organic pollutants) in the deep sea is often overlooked. Finally, we recommend assessing the biological effects of organic pollutants in deep sea biota, large-scale monitoring of organic pollutants, reconstructing historical emissions using sediment cores, and assessing the impact of deep-sea mining on the ecosystem.

Port Sediments: Problem or Resource? A Review Concerning the Treatment and Decontamination of Port Sediments by Fungi and Bacteria

Contamination of marine sediments by organic and/or inorganic compounds represents one of the most critical problems in marine environments. This issue affects not only biodiversity but also ecosystems, with negative impacts on sea water quality. The scientific community and the European Commission have recently discussed marine environment and ecosystem protection and restoration by sustainable green technologies among the main objectives of their scientific programmes. One of the primary goals of sustainable restoration and remediation of contaminated marine sediments is research regarding new biotechnologies employable in the decontamination of marine sediments, to consider sediments as a resource in many fields such as industry. In this context, microorganisms—in particular, fungi and bacteria—play a central and crucial role as the best tools of sustainable and green remediation processes. This review, carried out in the framework of the Interreg IT-FR Maritime GEREMIA Project, collects and shows the bioremediation and mycoremediation studies carried out on marine sediments contaminated with ecotoxic metals and organic pollutants. This work evidences the potentialities and limiting factors of these biotechnologies and outlines the possible future scenarios of the bioremediation of marine sediments, and also highlights the opportunities of an integrated approach that involves fungi and bacteria together.

Anaerobic degradation of high-concentration polycyclic aromatic hydrocarbons (PAHs) in seawater sediments

Recurring oil spill accidents have been a global challenge and contribute to PAHs' heavy accumulation in marine sediments. The rapid bioremediation of PAHs with high concentrations in marine sediments has rarely been studied. In this study, four representative PAHs in crude oil were tested for fast anaerobic biodegradation. An efficient system for the anaerobic degradation of high-concentration PAHs was obtained using petroleum-acclimated marine sediments as inoculants in the treatment system. The degradation efficiencies of benzo[b]fluoranthene, benzo[a]pyrene, pyrene, and phenanthrene reached 0.21, 1.71, 3.89, and 4.10 mg/(L·d), respectively, which are 16, 2.8, 1.8, and 1.0 times higher than the reported values. Nitrate was preferred to sulfate as an electron acceptor. The acclimated sediment contains a high abundance of hydrocarbon-degrading bacteria. The number and diversity of species in the treatment system supplemented with PAHs decreased, but the abundance of some hydrocarbon-degrading bacteria and hydrocarbon-intermediate utilising bacteria increased, and ecological succession was observed.

High-throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments

Aquatic environments are the recipients of many sources of environmental stress that trigger both local and global changes. To evaluate the associated risks to organisms and ecosystems more sensitive and accurate strategies are required. The analysis of the microbiome is one of the most promising candidates for environmental diagnosis of aquatic systems. Culture-independent interconnected meta-omic approaches are being increasing used to fill the gaps that classical microbial approaches cannot resolve. Here, we provide a prospective view of the increasing application of these high-throughput molecular technologies to evaluate the structure and functional activity of microbial communities in response to changes and disturbances in the environment, mostly of anthropogenic origin. Some relevant topics are reviewed, such as: (i) the use of microorganisms for water quality assessment, highlighting the incidence of antimicrobial resistance as an increasingly serious threat to global public health; (ii) the crucial role of microorganisms and their complex relationships with the ongoing climate change, and other stress threats; (iii) the responses of the environmental microbiome to extreme pollution conditions, such as acid mine drainage or oil spills. Moreover, protists and viruses, due to their huge impacts on the structure of microbial communities, are emerging candidates for the assessment of aquatic environmental health.

Anthropogenic influence on the environmental health along Montenegro coast based on the bacterial and chemical characterization

Coastal marine sediments are particularly exposed to human activities. The function of a coastal ecosystem is largely affected by eutrophication, wastewater discharges, chemical pollution, port activities, industry and tourism. Bacterial classification can be used as a measure in assessing the harmful effects on the ecosystem. This study provided insight into the environmental health of the coastal region of Montenegro analyzing the possible impact of PAHs and PCBs upon the bacterial community diversity and function as well as nutrients. Two stations at the shipyards were defined as very high PAH polluted together with PCB concentration exceeding threshold values. The bacterial community at the OTU level clustered together all stations except the most polluted site (SBL), the main tourist destination in Montenegro (BDV) and the estuary site (ADB) forming the independent clusters. Bacterial community based on the OTU level was driven by PAHs, TOC and silt content. The lowest richness and diversity were indicated at the site with the highest concentration of PAHs and PCBs with the highest abundance of Alphaproteobacteria followed by Gammaproteobacteria. OTUs affiliated to phyla BRC1, Dadabacteria and Spirochaetes were present with a total abundance higher than 1% only at the most polluted site indicating their persistence and possible potential for degradation of aromatic compounds. To compare functional capabilities potentially related to biodegradation of aromatic compounds and active transport systems, PICRUSt was used to predict metagenomes of the sediments. From our data, we identified specific bacterial community and predicted metabolic pathways that give us a picture of the environmental health along the coast of Montenegro, which provides us a new insight into human-induced pollution impacts on the coastal ecosystem.

Investigation of halotolerant marine Staphylococcus sp. CO100, as a promising hydrocarbon-degrading and biosurfactant-producing bacterium, under saline conditions

A halotolerant strain CO100 of Staphylococcus sp. was isolated from contaminated sediments taken from the fishing harbour of Sfax, Tunisia, as an efficient hydrocarbonoclastic candidate. Strain CO100 exhibited a high capacity to break down almost 72% of the aliphatic hydrocarbons contained in crude oil (1%, v/v), used as the sole carbon and energy source, after 20 days of culture, at 100 g/l NaCl, 37 °C and 180 rpm. The isolate CO100 displayed also its ability to grow on phenanthrene, fluoranthene and pyrene (100 mg/l), at 100 g/l NaCl. Moreover, the isolate CO100 showed a notable aptitude to synthesize an efficient tensioactive agent namely BS-CO100, on low-value substrates including residual frying oil and expired milk powder, thus reducing the high cost of biosurfactant production. The ESI/MS analysis designated that BS-CO100 belonged to lipopeptide class, in particular lichenysin and iturine members. Critical micelle concentrations of BS-CO100 were varying between 65 and 750 mg/l, depending on of the purity of the biosurfactant and the used carbon sources. BS-CO100 showed a high steadiness against a wide spectrum of pH (4.3-12), temperature (4-121 °C) and salinity (0-300 g/l NaCl), supporting its powerful tensioactive properties under various environmental conditions. Likewise, BS-CO100 exhibited no cytotoxic effect toward human HEK293 cells, at concentrations within 125 and 1000 μg/ml. Furthermore, the biosurfactant BS-CO100 exhibited remarkable anti-adhesive and anti-biofilm activities, being able to avoid and disrupt the biofilm formation by certain pathogenic microorganisms. In addition, BS-CO100 was found to have more potential to remove hydrocarbons from contaminated soils, compared to some chemical surfactants. In light of these promising findings, strain CO100, as well as its biosurfactant, could be successfully used in different biotechnological applications including the bioremediation of oil-polluted areas, even under saline conditions.

Nonionic and anionic surfactant-washing of polycyclic aromatic hydrocarbons in estuarine sediments around an industrial harbor in southern Taiwan

Various surfactants, such as nonionic Triton X-100 and Simple Green™ (SG), and anionic sodium dodecylsulfate (SDS) and sodium dodecylbenzene sulfonate (SDBS) were utilized to remove polycyclic aromatic hydrocarbons (PAHs) from heavily contaminated harbor sediments dredged from Kaohsiung Harbor in Taiwan. Desorption/re-sorption equilibrium, kinetics, and washability of PAHs using the selected surfactant were evaluated under different critical micelle concentrations (CMC). Experimental results revealed that the desorption rate of high molecular weight PAHs was greater than those of low molecular weight PAHs, and the anionic SDS was relatively effective in the removal of total PAHs (>50%) compared to the other surfactants. The correlation between the effectiveness of the surfactant washing processes and the physicochemical properties of individual PAH was statistically analyzed. The resulting data suggested that hydrophobic factors (K_ow, K_oc and S_w) affected PAH treatability more than the reactivity of PAH (electron affinity and ionization potential). Since the adsorption of anionic surfactant altered the hydrophobicity of organic matter in the sediment, PAHs preferred transferring from the sediment to the hydrophobic core of micelles in aqueous solution. Nevertheless, the nonionic surfactant enhanced the PAH partition in the aqueous phase, thus increasing the micellar solubilization of PAH.

Overall comparison and source identification of PAHs in the sediments of European Baltic and North Seas, Chinese Bohai and Yellow Seas

An international sampling campaign was carried out to comprehensively investigate the occurrence of polycyclic aromatic hydrocarbons (PAHs) in the marine sediments from the European Baltic and North Seas, Chinese Bohai and Yellow Seas. The concentrations of ∑₁₈PAHs in the samples from these four seas were in the range of 0.91-5361 ng/g dry weight (dw), 0.46-227 ng/g dw, 25.0-308 ng/g dw and 4.3-659 ng/g dw, respectively. 4-rings PAHs, e.g., fluoranthene, pyrene and benzo(b)fluoranthene, were commonly the dominant compounds in all the samples. The PAH sources were identified via composition patterns, diagnostic ratios, principal component analysis (PCA) and positive matrix factorization (PMF). Coal combustion, vehicular emission, coke plant and petroleum residue were apportioned as the main sources in these marine sediments. However, through PMF modeling, different contributions of these sources were quantified to the deposited PAHs in the seas, suggesting distinct anthropogenic impacts on the adjacent marine system. It is note-worthy that biomass combustion may not be the main source of PAHs in the majority of sediments from these seas. This was evidenced by the ratios of naphthalene against its methylated derivatives (i.e. 1-,2-methylnaphthalenes) other than the composition pattern in the samples, of which the approach is in prospect of developing in future studies.

Monitoring of polycyclic aromatic hydrocarbons in transplanted mussels (Mytilus galloprovincialis) and sediments in the coastal region of Nemrut Bay (Eastern Aegean Sea)

Polycyclic aromatic hydrocarbons (PAHs) were determined in the coastal region of Nemrut Bay, Eastern Aegean. Sediment and caged mussels were evaluated for sixteen PAHs. High contamination was observed in the sediment sampling sites next to the petrochemical refinery. Low molecular weight PAH levels were dominant in the sediments and the ratio LMW/HMW were higher than one, indicating petrogenic origin pollution. The m-ERM-q values of the sediments were classified as high-priority sites near the refinery while other sites were categorized as medium-low sites. 4-ring PAHs were found to be dominant in the mussels. PAHs were originated from petroleum and mixed sources (petrogenic, pyrogenic) both two transplantation experiments. The assessment of human health risk based on the Carcinogenic `Toxic Equivalents suggested that the mussels have high capability to give rise to carcinogenic risks. PAH levels in the mussels were above the Recommended Total Carcinogenic PAH limits set by the European Union.

Spatiotemporal toxicity assessment of suspended particulate matter (SPM)-bound polycyclic aromatic hydrocarbons (PAHs) in Lake Chaohu, China: Application of a source-based quantitative method

The spatiotemporal associations between the emissions and environmental toxicities of polycyclic aromatic hydrocarbons (PAHs) in lake still remain an issue. Here, we focused on the suspended particulate matter (SPM)-bound PAHs in Lake Chaohu, China to quantitatively estimate their spatiotemporal toxicities from different sources. A source-based quantitative method, positive matrix factorization (PMF)-benzo[a]pyrene-based toxic equivalency (TEQ_BaP) model, was applied. Firstly, we investigated the spatiotemporal characteristics of SPM-bound PAHs. The concentrations of Σ₂₁ PAHs ranged from 1646 to 19267 ng·g^-1. Low-ring PAHs were found to have the highest fractions. T-distributed stochastic neighbor embedding (t-SNE)-partitioning around medoid (PAM) technic revealed significantly spatiotemporal variation characteristics of SPM-bound PAHs in Lake Chaohu. Season, location (west or east lake zone), and sample classification (estuary or lake) together governed the patterns. Then, their potential sources were apportioned. Our results found that diagnostic ratios did not work perfectly. However, 3 factors were separated by PMF model. Unburned petroleum (F1), biomass, coal and gasoline combustion (F2), and diesel, straw combustion (F3) were the main sources of PAHs, accounting for 36.16%, 48.96% and 14.88%, respectively. The patterns of the source profiles were season-dependent. Finally, the toxicity of SPM-bound PAHs from different sources were predicted by PMF-TEQ_BaP model, and the model predictions were satisfactorily acceptable. Overall, predicted Σ₁₉ TEQ_BaP of SPM-bound PAHs in Lake Chaohu ranged from 20.8 to 947.9 ng·g^-1. Benzo[e]pyrene (BeP), benzo[a]pyrene (BaP) and benzo[b]fluoranthene (BbF) were the main toxic species. Temporally, PAH toxicity posed significantly seasonal differences. F3 had primary contributions to Σ₁₉ TEQ_BaP. Cutting the diesel consumption and using cleaner energy substitutes were suggested to reduce the PAH toxicity in Lake Chaohu. Overall, we expected this study could give new insights into the spatiotemporal associations between the sources and toxicities of SPM-bound PAHs in lake ecosystem.

A novel concept for the biodegradation mechanism of dianionic catechol with homoprotocatechuate 2,3-dioxygenase: A non-proton-assisted process

The theory of "proton-assisted process" can well explain the catalytic mechanism of homoprotocatechuate 2,3-dioxygenase (2,3-HPCD) with a monoanionic substrate (homoprotocatechuate, HPCA). Here a "non-proton-assisted process" is presented to interpret catalytic mechanism of 2,3-HPCD with a dianionic substrate (4-nitrocatechol, 4NC). The ONIOM calculation is performed to investigate the reaction pathway of a wild-type 2,3-HPCD with 4NC (H200H-4NC system). The catalytic reaction is comprised of four steps: (1) A dioxygen attacks the aromatic ring to produce an alkylperoxo species. (2) O-O bond cleavage and the formation of an epoxide species occur. (3) A seven-membered O-heterocyclic compound is generated by the extinction of the epoxy structure. (4) The seven-membered ring undergoes ring opening to form the final product (C2-C3 cleavage product). The effective free energy barrier of the catalytic reaction of the H200H-4NC system is 26.2 kcal mol^-1, which is much higher than that of the H200H-HPCA system. Furthermore, two calculated electronic configurations (Fe(III)-O₂^•- and Fe(III)-SQ^•) have a high similarity to previously detected ones, which demonstrates that the Asn200 variant (H200N-4NC variant system) employs a C4 (para-carbon) pathway to produce a C4-C5 cleavage product. Our findings provide an in-depth understanding of the catalytic mechanisms of dianionic catechol and its derivatives.

Influences of nutritional conditions on degradation of dibutyl phthalate in coastal sediments with Cylindrotheca closterium

In this work, microphytobenthos Cylindrotheca closterium was planted on the surface of coastal sediments to investigate its influence on dibutyl phthalate (DBP) degradation in sediments under different nutritional conditions. The results indicated that C. closterium largely utilized nutrients from the overlying water. Addition of nitrogen, phosphorus or silicon increased algal biomass (as chlorophyll a) by 0.97-3.16, 1.75-2.36 and 1.61-3.09 times, respectively, meanwhile it changed bacterial community structure in sediments with C. closterium. Growth of C. closterium was more sensitive to nitrogen content in the overlying water. Inoculation of C. closterium increased the relative abundances of dominant aerobic bacteria by 10-67%. Compared with treatments without C. closterium, inoculation of C. closterium increased DBP degradation percentage in sediments (8.5-18.9% increment), which was positively correlated with chlorophyll a content. Thus, microphytobenthos showed the potential for improving the cleansing of polluted coastal sediments, which was obviously related to nutritional conditions in the overlying water.

Biosurfactant Production in Sub-Oxic Conditions Detected in Hydrocarbon-Degrading Isolates from Marine and Estuarine Sediments

Hydrocarbon bioremediation in anoxic sediment layers is still challenging not only because it involves metabolic pathways with lower energy yields but also because the production of biosurfactants that contribute to the dispersion of the pollutant is limited by oxygen availability. This work aims at screening populations of culturable hydrocarbonoclastic and biosurfactant (BSF) producing bacteria from deep sub-seafloor sediments (mud volcanos from Gulf of Cadiz) and estuarine sub-surface sediments (Ria de Aveiro) for strains with potential to operate in sub-oxic conditions. Isolates were retrieved from anaerobic selective cultures in which crude oil was provided as sole carbon source and different supplements were provided as electron acceptors. Twelve representative isolates were obtained from selective cultures with deep-sea and estuary sediments, six from each. These were identified by sequencing of 16S rRNA gene fragments belonging to Pseudomonas, Bacillus, Ochrobactrum, Brevundimonas, Psychrobacter, Staphylococcus, Marinobacter and Curtobacterium genera. BSF production by the isolates was tested by atomized oil assay, surface tension measurement and determination of the emulsification index. All isolates were able to produce BSFs under aerobic and anaerobic conditions, except for isolate DS27 which only produced BSF under aerobic conditions. These isolates presented potential to be applied in bioremediation or microbial enhanced oil recovery strategies under conditions of oxygen limitation. For the first time, members of Ochrobactrum, Brevundimonas, Psychrobacter, Staphylococcus, Marinobacter and Curtobacterium genera are described as anaerobic producers of BSFs.

Removal of polycyclic aromatic hydrocarbons (PAHs) and the response of indigenous bacteria in highly contaminated aged soil after persulfate oxidation

Integrated chemical-biological treatment is a promising alternative to remove PAHs from contaminated soil, wherein indigenous bacteria is the key factor for the biodegradation of residual PAHs after the application of chemical oxidation. However, systematical study on the impact of persulfate (PS) oxidation on indigenous bacteria as well as PAHs removal is still scarce. In this study, the influences of different PS dosages (1%, 3%, 6%, and 10% [w/w]), as well as various activation methods (native iron, H₂O₂, alkaline, ferrous iron, and heat) on PAHs removal and indigenous bacteria in highly contaminated aged soil were investigated. Apparent degradation of PAHs in the soil treated with PS oxidation was observed, and the removal efficiency of total PAHs in the soil ranged from 38.28% to 79.97%. The removal efficiency of total PAHs in the soil increased with increasing consumption of PS. However, the bacterial abundance in soil was negatively affected following oxidation for all of the treatments added with PS, with bacterial abundance in the soil decreased by 0.89-2.93 orders of magnitude compared to the untreated soil. Moreover, the number of total bacteria in the soil decreased as PS consumption increased. Different PS activation methods and PS dosages exhibited different influences on the bacterial community composition. Bacteria capable of degrading PAHs under anoxic conditions were composed predominantly by Proteobacteria and Firmicutes. The total amount of Proteobacteria and Firmicutes also decreased with increasing consumption of PS. The results of this study provide important insight for the design of PAHs contaminated soil remediation projects.

Effects of biological factors and seasonality on the level of polycyclic aromatic hydrocarbons in red mullet (Mullus barbatus)

This study evaluates the effects of biological factors of fish and seasonality on Polycyclic Aromatic Hydrocarbon (PAH) accumulation in red mullet (Mullus barbatus) tissue. Specimens were collected monthly with a bottom trawl net in an offshore fishing ground in the Northern and Central Adriatic Sea (Geographical Sub Area 17) throughout 2016. The edible fillets of 380 individuals were analyzed for the concentrations of individual PAH, total PAH, and low, medium and high molecular weight (MW) PAHs. PAH bioaccumulation was related to their physicochemical characteristics (MW, and logarithm of the octanol-water partition coefficient, log K_ow), some biological parameters of fish (body size, age, sex, reproductive stage and total lipid content), and catch season. The PAH bioaccumulation pattern and the effects of the different factors varied according to PAH MW. The heavier (medium and high MW) PAHs showed higher levels in winter-autumn and in pre-spawners compared with spawners and post-spawners. Our findings suggest that an important detoxification mechanism, albeit limited to the heavier PAHs, acts in the spawning and post-spawning stage. Low MW PAHs appeared to be unaffected by reproductive stage, lipid content and seasonality. Reproductive stage and seasonality seem to play an important role in the accumulation of heavier PAH, whereas total lipid content and age seem to exert a limited influence, and body size no effect at all.

Absence of the nahG-like gene caused the syntrophic interaction between Marinobacter and other microbes in PAH-degrading process

In this study, Marinobacter sp. N4 isolated from the halophilic consortium CY-1 was found to degrade phenanthrene as a sole carbon source with the accumulation of 1-Hydroxy-2-naphthoic acid (1H2N). With the assistance of Halomonas sp. G29, phenanthrene could be completely mineralized. The hpah1 and hpah2 gene cluster was amplified from the genome of strain N4, that were responsible for upstream and downstream of PAH degradation. Strain N4 was predicted for the transformation from phenanthrene to 1H2N, and strain G29 could transform the produced 1H2N into 1,2-dihydroxynaphthalene (1,2-DHN). The produced 1,2-DHN could be further transformed into salicylic acid (SALA) by strain N4. SALA could be catalyzed into catechol by strain G29 and further utilized by strains N4 and G29 via the catechol 2,3-dioxygenase pathway and catechol 1,2-dioxygenase pathway, respectively. NahG, encoding salicylate hydroxylase, was absent from the hpah2 gene cluster and predicted to be the reason for 1H2N accumulation in the PAH-degrading process by pure culture of strain N4. The syntrophic interaction mode among Marinobacter and other microbes was also predicted. According to our knowledge, this is the first report of the PAH-degrading gene cluster in Marinobacter and the syntrophic interaction between Marinobacter and other microbes in the PAH-degrading process.

PAES and PAHs in the surface sediments of the East China Sea: Occurrence, distribution and influence factors

A total of 29 sediment samples were collected from the East China Sea (ECS), with the Yangtze River estuary and the Zhejiang costal area. These sediment samples were analyzed for 6 phthalate esters (PAEs) and 16 polycyclic aromatic hydrocarbons (PAHs): the ΣPAEs and ΣPAHs concentrations ranged between 1649.5 and 8451.5 ng g^-1 (mean = 3446.3 ng g^-1) and 57.5-364.5 ng g^-1 (mean = 166.2 ng g^-1), respectively. Overall, the PAEs and PAHs concentrations gradually decreasing in the offshore and southward directions: their compositions and distributions suggest they could have mainly derived from the Yangtze River. In particular, their distribution was influenced by the sources' proximity, hydrodynamics, and sediment geochemistry (i.e., TOC content and grain size). A classical two-end member model was utilized to estimate the fraction of terrestrial organic carbon in the sediments of the ECS. When the sediment was dominated by terrestrial-derived organic matter (OM), the concentrations of PAEs and PAHs were significantly correlated to the TOC content and gran size of the sediments. In contrast, the poor correlation of TOC content and grain size with PAEs in those sediments dominated by marine-derived OM, implied that the distribution of PAEs in the ECS was mainly related to land-based inputs, (especially to that of the Yangtze River). Regardless of the origin of most of the OM contained in the sediments, we observed positive correlations between the TOC content, and grain size of those containing PAHs. These results suggest that the distribution of PAHs in the ECS was not only related to the Yangtze River input, but also to the geochemical characteristics of the sediments.

Characterization of the Genome Feature and Toxic Capacity of a Bacillus wiedmannii Isolate From the Hydrothermal Field in Okinawa Trough

The Bacillus cereus group is frequently isolated from soil, plants, food, and other environments. In this study, we report the first isolation and characterization of a B. cereus group member, Bacillus wiedmannii SR52, from the hydrothermal field in the Iheya Ridge of Okinawa Trough. SR52 was isolated from the gills of shrimp Alvinocaris longirostris, an invertebrate species found abundantly in the ecosystems of the hydrothermal vents, and is most closely related to B. wiedmannii FSL W8-0169. SR52 is aerobic, motile, and able to form endospores. SR52 can grow in NaCl concentrations up to 9%. SR52 has a circular chromosome of 5,448,361 bp and a plasmid of 137,592 bp, encoding 5,709 and 189 genes, respectively. The chromosome contains 297 putative virulence genes, including those encoding enterotoxins and hemolysins. Fourteen rRNA operons, 107 tRNAs, and 5 sRNAs are present in the chromosome, and 7 tRNAs are present in the plasmid. SR52 possesses 13 genomic islands (GIs), all on the chromosome. Comparing to FSL W8-0169, SR52 exhibits several streaking features in its genome, notably an exceedingly large number of non-coding RNAs and GIs. In vivo studies showed that following intramuscular injection into fish, SR52 was able to disseminate in tissues and cause mortality; when inoculated into mice, SR52 induced acute mortality and disseminated transiently in tissues. In vitro studies showed that SR52 possessed hemolytic activity, and the extracellular product of SR52 exhibited a strong cytotoxic effect. These results provided the first insight into the cytotoxicity and genomic feature of B. wiedmannii from the deep-sea hydrothermal environment.

Microcosm evaluation of the impact of oil contamination and chemical dispersant addition on bacterial communities and sediment remediation of an estuarine port environment

AIM

To evaluate the interactive effects of oil contamination and chemical dispersant application on bacterial composition and sediment remediation of an estuarine port environment.

METHODS AND RESULTS

A multifactorial controlled microcosm experiment was set up using sediment cores retrieved from an estuarine port area located at Ria de Aveiro lagoon (Aveiro, Portugal). An oil spill with and without chemical dispersant addition was simulated. Sediment oil hydrocarbon concentrations and benthic bacterial community structure were evaluated by GC-MS and 16S rRNA high-throughput sequencing respectively. Although initially (first 10 days) chemical dispersion of oil enhanced the concentrations of the heavier polycyclic aromatic hydrocarbons and of the C₂₂ -C₃₀ alkane group, with time (21 days), no significant differences in hydrocarbon concentrations were detected among treatments. Moreover, no significant changes were detected in the structure of sediment bacterial communities, which mainly consisted of operational taxonomic units related to hydrocarbon-contaminated marine environments. We hypothesize that the environmental background of the sampling site preconditioned the communities' response to additional contamination.

CONCLUSION

This experimental microcosm study showed that the chemical dispersion of oil did not influence sediment remediation or bacterial community composition.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study showed that chemical dispersion of oil may not improve the remediation of port sediments. Further studies are needed to investigate the impact of chemical dispersants in combination with bioremediation strategies on the process of sediment remediation in port areas.

Potential use of endophytic root bacteria and host plants to degrade hydrocarbons

Microbe-assisted phytoremediation depends on competent root-associated microorganisms that enhance remediation efficiency of organic compounds. Endophytic bacteria are a key element of the root microbiome and may assist plant degradation of contaminants. The aim of this study was to investigate the application of four hydrocarbon-degrading endophytic strains previously isolated from an oil sands reclamation area. Strains EA1-17 (Stenotrophomonas sp.), EA2-30 (Flavobacterium sp.), EA4-40 (Pantoea sp.), and EA6-5 (Pseudomonas sp.) were inoculated in white sweet clover growing on soils amended with diesel at 5,000, 10,000, and 20,000 mg·kg^-1. Our results indicate that plant growth inhibition caused by diesel fuel toxicity was overcome in inoculated plants, which showed significantly higher plant biomass. Analysis of soil F2 and F3 hydrocarbon fractions also revealed that these soils were remediated by inoculated plants when diesel was applied at 10,000 mg·kg^-1 and 20,000 mg·kg^-1. In addition, quantification of hydrocarbon-degrading genes suggests that all bacterial strains successfully colonized sweet clover plants. Overall, the endophytic strain EA6-5 (Pseudomonas sp.), which harbored hydrocarbon-degrading genes, was the most effective candidate in phytoremediation experiments and could be a strategy to increase plant tolerance and hydrocarbon degradation in contaminated (e.g., diesel fuel) soils.

State of the art and future challenges for polycyclic aromatic hydrocarbons is sediments: sources, fate, bioavailability and remediation techniques

Polycyclic aromatic hydrocarbons (PAHs) are amongst the most abundant contaminants found in the aquatic environment. Due to their toxicity and carcinogenicity, their sources, fate, behaviour, and cleanup techniques have been widely investigated in the last several decades. When entering the sediment-water system, PAH fate is determined by particular PAH and sediment physico-chemical properties. Most of the PAHs will be associated with fine-grained, organic-rich, sediment material. This makes sediment an ultimate sink for these pollutants. This association results in sediment contamination, and in this manner, sediments represent a permanent source of water pollution from which benthic organisms may accumulate toxic compounds, predominantly in lipid-rich tissues. A tendency for biomagnification can result in critical body burdens in higher trophic species. In recent years, researchers have developed numerous methods for measuring bioavailable fractions (chemical methods, non-exhaustive extraction, and biomimetic methods), as valuable tools in a risk-based approach for remediation or management of contaminated sites. Contaminated sediments pose challenging cleanup and management problems, as conventional environmental dredging techniques are invasive, expensive, and sometimes ineffective or hard to apply to large and diverse sediment sites. Recent studies have shown that a combination of strategies including in situ approaches is likely to provide the most effective long-term solution for dealing with contaminated sediments. Such in situ approaches include, but are not limited to: bioaugmentation, biostimulation, phytoremediation, electrokinetic remediation, surfactant addition and application of different sorbent amendments (carbon-rich such as activated carbon and biochar) that can reduce exposure and limit the redistribution of contaminants in the environment.

Pathways of inorganic and organic contaminants from land to deep sea: The case study of the Gulf of Cagliari (W Tyrrhenian Sea)

In continental margins, canyons appear to act as natural conduits of sediments and organic matter from the shelf to deep basins, providing an efficient physical pathway for transport and accumulation of particles with their associated land-produced contaminants. However, these mechanisms have not been yet sufficiently explored by geochemical markers. The continental slope of the south Sardinia has been used as a natural laboratory for investigating mechanisms and times of transfer dynamics of contaminants from land to sea and from shelf to deep sea through an articulated system of submarine canyons. Here, dynamics of contaminants have been investigated in a pilot area of the central Mediterranean basin (Gulf of Cagliari, S Sardinia) where important industrial plants are sited since beginning of the last century. Five sediment cores dated by ²¹⁰Pb and ¹³⁷Cs reveal: i) a complex dynamics of organic and inorganic contaminants from point source areas on land to the deep sea and ii) a crucial role played by canyons and bottom morphology as primary pathway conveying sediments and associated contaminants from sources to very far deep sea environments. In particular, this study provides new integrated tools to properly understand mechanisms of connection between coastal sectors and deep sea. This is challenging mostly in regions where coastal pollution could represent critical threats for larger areas of the Mediterranean Sea.

Sensitive detection of polycyclic aromatic hydrocarbons with gold colloid coupled chloride ion SERS sensor

Highly sensitive detection of PAH by non-functionally modified gold colloid was realized by chloride ion coupling.

Anthropogenic PAHs in lake sediments: a literature review (2002-2018)

Lake sediments are an important reservoir for toxic and hydrophobic polycyclic aromatic hydrocarbons (PAHs). Monitoring of PAHs in sediment is helpful to understand pollution mechanisms and anthropogenic activities. This study reviews studies of PAHs in lake sediments published during 2002-2018. The studies' findings are analyzed, distributions of PAHs in lake sediments are summarized, and the applicability of lake sediments for tracking changes in PAH emission sources is emphasized. Lake sediments heavily polluted with PAHs are distributed in China, Egypt, the USA, and some urban lakes in Africa. The high levels of PAHs are predominantly associated with human activities such as anthropogenic combustion, petroleum industries, road traffic, and socioeconomic factors. However, the concentrations of sedimentary PAHs in most lakes were below the international guideline values.

RNA-seq analysis reveals the significant effects of different light conditions on oil degradation by marine Chlorella vulgaris

Marine Chlorella vulgaris, an efficient hydrocarbon-degrading organism, is easily affected by light. In this study, we investigated the direct effects of different light conditions on crude oil degradation by C. vulgaris and its crude enzyme. Under 12 h illumination, the crude enzyme improved hydrocarbon removal by 39.36%, whereas the addition of the enzyme and C. vulgaris increased the degradation rate by 121.73%. Conversely, the addition of enzyme under heterotrophic condition was negatively related to oil degradation by C. vulgaris, and the degradation rate decreased from 74.32% to 48.65% and further reduced by 34.54%. The results of RNA sequencing analysis suggested that hydrocarbons removal was attributed to C. vulgaris metabolism in heterotrophic physiological state. While enhanced removal efficiency of hydrocarbons was achieved in mixotrophic physiological state due to the coupling of C. vulgaris metabolism with photocatalytic oxidation. Functional enzymes played key roles in photocatalysis and biodegradation processes.

Polycyclic Aromatic Hydrocarbon (PAH) Degradation Pathways of the Obligate Marine PAH Degrader Cycloclasticus sp. Strain P1

Bacteria play an important role in the removal of polycyclic aromatic hydrocarbons (PAHs) from polluted environments. In marine environments, Cycloclasticus is one of the most prevalent PAH-degrading bacterial genera. However, little is known regarding the degradation mechanisms for multiple PAHs by CycloclasticusCycloclasticus sp. strain P1 was isolated from deep-sea sediments and is known to degrade naphthalene, phenanthrene, pyrene, and other aromatic hydrocarbons. Here, six ring-hydroxylating dioxygenases (RHDs) were identified in the complete genome of Cycloclasticus sp. P1 and were confirmed to be involved in PAH degradation by enzymatic assays. Further, five gene clusters in its genome were identified to be responsible for PAH degradation. Degradation pathways for naphthalene, phenanthrene, and pyrene were elucidated in Cycloclasticus sp. P1 based on genomic and transcriptomic analysis and characterization of an interconnected metabolic network. The metabolic pathway overlaps in many steps in the degradation of pyrene, phenanthrene, and naphthalene, which were validated by the detection of metabolic intermediates in cultures. This study describes a pyrene degradation pathway for Cycloclasticus. Moreover, the study represents the integration of a PAH metabolic network that comprises pyrene, phenanthrene, and naphthalene degradation pathways. Taken together, these results provide a comprehensive investigation of PAH metabolism in CycloclasticusIMPORTANCE PAHs are ubiquitous in the environment and are carcinogenic compounds and tend to accumulate in food chains due to their low bioavailability and poor biodegradability. Cycloclasticus is an obligate marine PAH degrader and is widespread in marine environments, while the PAH degradation pathways remain unclear. In this report, the degradation pathways for naphthalene, phenanthrene, and pyrene were revealed, and an integrated PAH metabolic network covering pyrene, phenanthrene, and naphthalene was constructed in Cycloclasticus This overlapping network provides streamlined processing of PAHs to intermediates and ultimately to complete mineralization. Furthermore, these results provide an additional context for the prevalence of Cycloclasticus in oil-polluted marine environments and pelagic settings. In conclusion, these analyses provide a useful framework for understanding the cellular processes involved in PAH metabolism in an ecologically important marine bacterium.

Independent and interactive effects of reduced seawater pH and oil contamination on subsurface sediment bacterial communities

Ocean acidification may exacerbate the environmental impact of oil hydrocarbon pollution by disrupting the core composition of the superficial (0-1 cm) benthic bacterial communities. However, at the subsurface sediments (approximately 5 cm below sea floor), the local biochemical characteristics and the superjacent sediment barrier may buffer these environmental changes. In this study, we used a microcosm experimental approach to access the independent and interactive effects of reduced seawater pH and oil contamination on the composition of subsurface benthic bacterial communities, at two time points, by 16S rRNA gene-based high-throughput sequencing. An in-depth taxa-specific variance analysis revealed that the independent effects of reduced seawater pH and oil contamination were significant predictors of changes in the relative abundance of some specific bacterial groups (e.g., Firmicutes, Rhizobiales, and Desulfobulbaceae). However, our results indicated that the overall microbial community structure was not affected by independent and interactive effects of reduced pH and oil contamination. This study provides evidence that bacterial communities inhabiting subsurface sediment may be less susceptible to the effects of oil contamination in a scenario of reduced seawater pH.

Polycyclic aromatic hydrocarbons in sediments and marine organisms: Implications of anthropogenic effects on the coastal environment

Intensive human activities aggravate environmental pollution, particularly in the coastal environment. Sixteen priority polycyclic aromatic hydrocarbons (PAHs) were determined in the sediments and marine species from Zhanjiang Harbor, a large harbor in China. The total PAH concentrations ranged from 151 to 453 ng/g dry weight (dw) in sediments and from 86.7 to 256 ng/g wet weight (ww) in organism tissues. High levels of PAHs occurred in the sample sites next to the estuary. A decrease in PAH levels was observed in comparison to the previous survey prior to 2012. Fish exhibited lower lipid weight normalized PAH concentrations than the other species, which may be related to their efficient metabolic transformation. Three ring PAHs dominated both in marine sediments and species, but low molecular weight PAHs exhibited higher proportions in biota than in sediments (p < 0.05). Petrogenic and pyrolytic sources both contributed to the occurrence of PAHs, and the latter became increasingly important in the study area. The ecological risk from PAHs in the sediments was relatively low (9% incidence of adverse biological effect) according to the effects-based sediment quality guideline values. Exposure to PAHs via consuming seafoods might pose a health risk to local residents. Overall, these results revealed anthropogenic activities in the coastal area have an impact on the local ecosystem.