Occurrence and distribution of PAHs and microbial communities in nearshore sediments of the Knysna Estuary, South Africa

Spatial distribution of PAHs and microbial communities in intertidal sediments of the Pearl River Estuary, South China

The exploration of sediment pollution caused by PAHs and its impact on microbial communities can provide valuable insights for the remediation of sediments. The spatial distribution of PAHs and their impact on the microbial community within the Pearl River Estuary were investigated in this study. The findings revealed that the total concentration ranges of 16 PAHs were between 24.26 and 3075.93 ng/g, with naphthalene, fluorene, and phenanthrene potentially exerting adverse biological effects. More PAHs were found to accumulate in subsurface sediments, and their average accumulation rates gradually decreased as the number of rings in PAHs increased, ranging from 180 % for 2-ring to 36 % for 6-ring. The phyla Proteobacteria, Bacteroidetes, Actinobacteria, and Chloroflexi were found to dominate both surface and subsurface sediments The correlation between microbial genera and PAHs contents was weak in sediments with low levels of PAHs contamination, while a more significant positive relationship was observed in sediments with high levels of PAHs contamination. The physicochemical properties of sediments, such as pH, soil structure and Cu significantly influence bacterial community composition in highly contaminated sediments. Additionally, the network analysis revealed that certain bacterial genera, including Novosphingobium, Robiginitalea and Synechococcus_CC9902, played a pivotal role in the degradation of PAHs. These findings are significant in comprehending the correlation between bacterial communities and environmental factors in intertidal ecosystems, and establish a scientific foundation for bioremediation of intertidal zones.

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

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

Microbial community assembly responses to polycyclic aromatic hydrocarbon contamination across water and sediment habitats in the Pearl River Estuary

Along with rapid urbanization and intensive human activities, polycyclic aromatic hydrocarbon (PAH) pollution in the Pearl River Estuary (PRE) and its effects on the microbial community have attracted extensive attention. However, the potential and mechanism of microbial degradation of PAHs across water and sediment habitats remain obscure. Herein, the estuarine microbial community structure, function, assembly process and co-occurrence patterns impacted by PAHs were comprehensively analyzed using environmental DNA-based approaches. The contamination and distribution of PAHs were jointly affected by anthropogenic and natural factors. Some of the keystone taxa were identified as PAH-degrading bacteria (i.e., genera Defluviimonas, Mycobacterium, families 67-14, Rhodobacteraceae, Microbacteriaceae and order Gaiellales in water) or biomarkers (i.e., Gaiellales in sediment) that were significantly correlated with PAH levels. The proportion of deterministic process in the high PAH-polluted water (76%) was much higher than that in the low pollution area (7%), confirming the significant effect of PAHs on the microbial community assembly. In sediment, the communities with high phylogenetic diversity demonstrated a great extent of niche differentiation, exhibited a stronger response to environmental variables and were strongly influenced by deterministic processes (40%). Overall, deterministic and stochastic processes are closely related to the distribution and mass transfer of pollutants, and substantially affect the biological aggregation and interspecies interaction within communities in the habitats.

Mangroves leaves phyllosphere bacteria community and its ability to survive under pyrene stress during the acclimation process

Plants in general and mangroves in particular can harbor hyper-diverse microorganisms in their different compartments including the phyllosphere area. This study used the leaves of three mangrove species; black mangrove (Avicenia germinans), red mangrove (Rhizophora mangle) and mangrove apple (Sonneratia alba) in order to evaluate the phyllosphere epiphytic bacterial community on their leaves surface and assess the ability of some epiphytic bacteria to tolerate and survive under pyrene stress. Through the 16S rRNA genes sequencing, 380203, 405203 and 344863 OTUs were identified respectively in the leaves of mangroves apple, black and red mangroves. The identified OTUs was positively correlated with leaves-wax (p < 0.05, r² = 0.904), nitrogen (r² = 0.72), phosphorus content (r² = 0.62) and the water factor (r² = 0.93). It was however highly and negatively correlated with the canopy cover (r² = 0.93). The pyrene degradation rate in the mineral salt medium (MSM) containing pyrene as external stress was different in each mangrove species and varied depending on various factors. Therefore, through the succession culture in MSM, several bacteria strain belonging to Rhizobiales and Enterobacteres were found to be abundant in red mangroves. Bacteria belonging to Bacilliales and Sphingobacteriales were more abundant in mangroves apples and bacteria from Xanthomonadales and Sphingomonadales were more presents in back mangroves. The important finding was to reveal that the black mangrove at the non-submerged substrate, recorded the highest number of OTU, coinciding with its highest leaf's nitrogen and phosphorus content and most importantly, its highest rate of pyrene degradation. The general result of this study join previous research results and get place in the mangrove agenda, as part of a better understanding insight into the role of plant identity in driving the phyllosphere epiphytic microbial community structures in mangrove ecosystems.

Novel synergistic metabolic processes for phenanthrene biodegradation by a nitrate-reducing phenanthrene-degrading culture and an anammox culture

The synergistic metabolism by anammox cultures and nitrate-reducers for anaerobic PAH biodegradation is largely unknown, including whether anammox culture and which kind of anammox bacterium can perform nitrogen metabolism in the anaerobic PAH biodegradation processes, the inhibitory effect of PAH on anammox activity and nitrite on PAH-degrading nitrate-reducers activity, and the synergistic metabolic processes. Herein, an anammox culture that can eliminate nitrite accumulation and decrease inorganic carbon emission during anaerobic phenanthrene (a model of PAH in this study) biodegradation, the synergistic mechanism for phenanthrene biodegradation by a nitrate-reducer and such anammox culture, and the inhibition effect of phenanthrene on such anammox culture and nitrite on a phenanthrene-degrading nitrate-reducer were newly discussed. The results showed that nitrite largely accumulated during anaerobic phenanthrene biodegradation (nitrate accumulation is a common phenomenon for the biodegradation of refractory matter, including PAHs, by nitrate-reducers) by a nitrate-reducer, PheN2, which mineralizes phenanthrene to inorganic carbon, and nitrite was verified as an inhibiting factor for further biodegradation. Anaerobic phenanthrene biodegradation rates and nitrite concentrations (0-7 mM) appeared to have a negative linear correlation. The anammox culture that mainly contained Candidatus Kuenenia was newly found to efficiently reduce nitrite accumulation and inorganic carbon emissions and significantly promote biodegradation efficiency by ∼1.94-fold. Our results showed that phenanthrene absorbed in and on anammox cells had a more direct relationship with the inhibitory effect on anammox activity than phenanthrene in the environment, and 15.2 mg/gVSS phenanthrene absorbed in and on the cells (4 mM concentration in the culture) showed nearly complete inhibition of anammox culture in this study. In addition, few (less than 2% abundance) anammox bacteria were found to be enough for the removal of nitrite produced from anaerobic phenanthrene biodegradation. In an ideal world, co-pollutants of ammonia, nitrate, phenanthrene, and nitrite could be converted to nitrogen gas and biomass by the synergistic metabolism of anammox cultures and nitrate reducers. Our study reveals a new synergistic process that may exist in our environments for PAH elimination by an anammox culture and a nitrate-reducer, which provides a new strategy for the bioremediation of PAH-polluted anoxic zones.

Assessment of biological community in riparian zone contaminated by PAHs: Linking source apportionment to biodiversity

Riparian zone, an important land-water interface, plays an essential role in maintaining the ecological health of rivers, whereas the effects of Polycyclic aromatic hydrocarbons (PAHs) on the health of biological communities in riparian groundwater remain undetermined. To understand the responses of multiple communities to environmental variables, the distribution and ecosystem risk of 16 PAHs have been investigated in the Beiluo River, China. The distribution of multiple communities in riparian groundwater was investigated by environmental DNA metabarcoding, including 16S rRNA, 18S rRNA, and COI gene sequencing for bacteria, microbial eukaryotes (including algae, fungi, and protozoa), and metazoan, respectively, followed by correlation analysis between multiple communities and PAH contamination levels. The concentration of PAHs in the Beiluo River ranged largely from 35.32 to 728.59 ng/L. Here, the Shannon's diversity index of bacteria (Firmicutes) decreased possibly due to the occurrence of Pyrene, which mainly derives from coal and biomass combustion. Furthermore, the reduced richness of fungi (Ascomycota, Basidiomycota) and algae (Chlorophyta, Chrysophyceae) can be attributed to the presence of medium molecular weight (MMW) PAHs (Pyrene, Benz(a)anthracene, Chrysene), and low molecular weight (LMW) PAHs (Naphthalene, Fluorene, Phenanthrene). The richness and Shannon's diversity index of metazoan (Arthropoda) were promoted owing to MMW PAHs (Chrysene, Fluoranthene) generated from coal and biomass combustion and traffic emission. The ecological risk of PAHs in the groundwater environment of the Beiluo River was characterized as low to medium, where LMW and MMW PAHs posed higher risk than the high molecular weight (HMW) compounds. Overall, this study provides insights into the structures of riparian multi-biological communities altered by PAHs.

Influence of bacterial community diversity, functionality, and soil factors on polycyclic aromatic hydrocarbons under various vegetation types in mangrove wetlands

Polycyclic aromatic hydrocarbons (PAHs) are prevalent organic pollutants in coastal ecosystems, particularly in mangrove wetlands. However, it is still largely unclear how PAHs affect the soil bacterial community under various vegetation types in the Greater Bay Area. Here, we selected soil samples from four sites with different vegetation types (native mangrove forest dominated by Kandelia candel, invasive mangrove forest dominated by Sonneratia apetala, unvegetated mudflat, and riverine runoff outlet) in the Qi'ao and Futian Nature Reserves. We investigated the effects of PAHs on soil bacterial community composition and diversity, function, and co-occurrence via 16S rRNA high-throughput sequencing. PAHs obviously reduced soil bacterial community diversity and richness. Based on PICRUSt 2, PAHs demonstrated positive influences on PAHs degradation metabolism related bacterial genes. Meanwhile, we predicted that riverine runoff outlets can potentially degrade PAHs, may donate to sustain healthy mangrove ecosystem. Also, PAHs and total nitrogen (TN) were crucial factors driving the soil bacterial community in Qi'ao sites, whereas in the Futian sites, PAHs and SOC were more important. PAHs, SOC and TN showed negative effects on specific bacteria abundance. Subsequently, environmental factors and PAHs levels influenced the soil bacterial ecological functions community. Co-occurrence network analysis revealed non-random assembly patterns of the bacterial communities. SBR1031 and A4b were the keystone genera and played a crucial role whgich played an irreplaceable role in PAHs degradation in Qi'ao and Futian sites. PAHs inhibited specific microbial activity and metabolism in native mangrove forest, while affects positively to bacterial community in riverine runoff outlet which might profoundly affect the whole soil quality under various vegetation types. Overall, this study might identify existing health problems and provide insights for enhancing protection and utilization management for mangrove ecosystem in the Greater Bay Area.

Distributions and potential sources of traditional and emerging polycyclic aromatic hydrocarbons in sediments from the lower reach of the Yangtze River, China

This study investigated the current contamination status and potential sources of traditional and emerging polycyclic aromatic hydrocarbons (t-PAHs and e-PAHs) in the sediments across a wide area of the Yangtze River, spanning nine cities. Fifty-seven sediment samples were collected in 2019, from which 15 t-PAHs and 11 e-PAHs were analyzed using GC-MSD. In addition, organic carbon (OC), total nitrogen (TN), and carbon and nitrogen stable isotope ratios (δ¹³C and δ¹⁵N) in sediments were measured to evaluate associations with PAHs contamination. OC, TN, and their stable isotope ratios showed a wide range of site-specific contents and values, indicating high variation in contamination and sources. Concentrations of t-PAHs and e-PAHs in sediments ranged from 0.6 to 200,000 ng g^-1 dry weight (dw) and 1.1 to 20,000 ng g^-1 dw, respectively. Hotspot sites located in Nanjing (PuKou), Taizhou (JingJiang), and Suzhou (ZhangJiaGang). PAHs contamination reflected land use type and human activity in the surrounding area. Positive matrix factorization (PMF) modeling showed that, on average (n = 57), vehicle emissions were the most dominant contribution (57%), followed by petroleum (28%) and fossil fuel combustion (15%). Sites with high PAHs contamination in sediments were of severe ecological risk. Contributions to the potential risks of PAHs were most significant in the order of dibenz[a,h]anthracene, benzo[b]fluoranthene, and benzo[a]pyrene. The primary origin of these compounds appeared to be fossil fuel combustion. The results of this study are expected to provide useful baseline data on the current contamination status and potential sources of traditional and emerging pollutants in the sediments of the Yangtze River, China.

Insights into the effects of Fenton oxidation on PAH removal and indigenous bacteria in aged subsurface soil

Combined chemical oxidation and bioremediation is a promising method of treating polycyclic aromatic hydrocarbon (PAH) contaminated soil, wherein indigenous soil bacteria play a critical role in the subsequent biodegradation of PAHs after the depletion of the oxidant. In this study, different Fenton conditions were applied by varying either the oxidation mode (conventional Fenton (CF), Fenton-like (LF), modified Fenton (MF), and graded modified Fenton (GMF)) or the H₂O₂ dosage (0%, 3%, 6%, and 10% (v/v)) to treat PAH contaminated soil. The results revealed that when equal dosages of H₂O₂ are applied, PAHs are significantly removed following oxidation treatment, and the removal percentages obeyed the following sequence: CF > GMF > MF > LF. In addition, higher dosages of H₂O₂ improved the PAH removal from soil treated with the same oxidation mode. The ranges of total PAHs removal efficiencies in the soil added 3%, 6%, and 10% of H₂O₂ (v/v) were 18.04%∼59.48%, 31.88%∼71.83%, and 47.56%∼78.16%, respectively. The PAH removal efficiency decreased with increasing ring numbers for the same oxidation treatment. However, the negative influences on soil bacterial abundance, community composition, and function were observed after Fenton treatment. After Fenton oxidation, the bacterial abundance in the soil received 3%, 6%, and 10% of H₂O₂ (v/v) decreased 1.96-2.69, 2.44-3.22, and 3.09-3.42 orders of magnitude compared to the untreated soil. The soil bacterial abundance tended to be impacted by the oxidation mode and H₂O₂ dosage simultaneously. While the main factor influencing the soil bacterial community composition was the H₂O₂ dosages. The results of this study showed that different oxidation mode and H₂O₂ dosage exhibited different effects on PAHs removal and soil bacteria (including abundance, community composition, and function), and there was a trade-off between the removal of PAHs and the adverse impact on soil bacteria.

Soil microbiomes divergently respond to heavy metals and polycyclic aromatic hydrocarbons in contaminated industrial sites

Contaminated sites from electronic waste (e-waste) dismantling and coking plants feature high concentrations of heavy metals (HMs) and/or polycyclic aromatic hydrocarbons (PAHs) in soil. Mixed contamination (HMs + PAHs) hinders land reclamation and affects the microbial diversity and function of soil microbiomes. In this study, we analyzed HM and PAH contamination from an e-waste dismantling plant and a coking plant and evaluated the influences of HM and PAH contamination on soil microbiomes. It was noticed that HMs and PAHs were found in all sites, although the major contaminants of the e-waste dismantling plant site were HMs (such as Cu at 5,947.58 ± 433.44 mg kg^-1, Zn at 4,961.38 ± 436.51 mg kg^-1, and Mn at 2,379.07 ± 227.46 mg kg^-1), and the major contaminants of the coking plant site were PAHs (such as fluorene at 11,740.06 ± 620.1 mg kg^-1, acenaphthylene at 211.69 ± 7.04 mg kg^-1, and pyrene at 183.14 ± 18.89 mg kg^-1). The microbiomes (diversity and abundance) of all sites were determined via high-throughput sequencing of 16S rRNA genes, and redundancy analysis was conducted to investigate the relations between soil microbiomes and contaminants. The results showed that the microbiomes of the contaminated sites divergently responded to HMs and PAHs. The abundances of the bacterial genera Sulfuritalea, Pseudomonas, and Sphingobium were positively related to PAHs, while the abundances of the bacterial genera Bryobacter, Nitrospira, and Steroidobacter were positively related to HMs. This study promotes an understanding of how soil microbiomes respond to single and mixed contamination with HMs and PAHs.

Variation of the mangrove sediment microbiomes and their phenanthrene biodegradation rates during the dry and wet seasons

Mangrove sediment is a major sink for phenanthrene in natural environments. Consequently, this study investigated the effects of seasonal variation on the biodegradation rates of low (150 mg kg^-1), moderate (600 mg kg^-1), and high (1200 mg kg^-1) phenanthrene-contaminated mangrove sediments using a microcosm study and identified potential key phenanthrene-degrading bacteria using high throughput sequencing of 16 S rRNA gene and quantitative-PCR of the PAH-ring hydroxylating dioxygenase (PAH-RHD_α) genes. The biodegradation rates of phenanthrene in all treatments were higher in the wet-season sediments (11.58, 14.51, and 8.94 mg kg^-1 sediment day^-1) than in the dry-season sediments (3.51, 12.56, and 5.91 mg kg^-1 sediment day^-1) possibly due to higher nutrient accumulation caused by rainfall and higher diversity of potential phenanthrene-degrading bacteria. The results suggested that the mangrove sediment microbiome significantly clustered according to season. Although Gram-negative phenanthrene-degrading bacteria (i.e., Anaerolineaceae, Marinobacter, and Rhodobacteraceae) played a key role in both dry and wet seasons, distinctly different phenanthrene-degrading bacterial taxa were observed in each season. Halomonas and Porticoccus were potentially responsible for the degradation of phenanthrene in the dry and wet seasons, respectively. The knowledge gained from this study contributes to the development of effective and rationally designed microbiome innovations for oil removal.

Application of constructed wetlands in the PAH remediation of surface water: A review

Polycyclic aromatic hydrocarbons (PAHs) pose adverse risks to ecosystems and public health because of their carcinogenicity and mutagenicity. As such, the extensive occurrence of PAHs represents a worldwide concern that requires urgent solutions. Wastewater treatment plants are not, however, designed for PAH removal and often become sources of the PAHs entering surface waters. Among the technologies applied in PAH remediation, constructed wetlands (CWs) exhibit several cost-effective and eco-friendly advantages, yet a systematic examination of the application and success of CWs for PAH remediation is missing. This review discusses PAH occurrence, distribution, and seasonal patterns in surface waters during the last decade to provide baseline information for risk control and further treatment. Furthermore, based on the application of CWs in PAH remediation, progress in understanding and optimising PAH-removal mechanisms is discussed focussing on sediments, plants, and microorganisms. Wetland plant traits are key factors affecting the mechanisms of PAH removal in CWs, including adsorption, uptake, phytovolatilization, and biodegradation. The physico-chemical characteristics of PAHs, environmental conditions, wetland configuration, and operation parameters are also reviewed as important factors affecting PAH removal efficiency. Whilst significant progress has been made, several key problems need to be addressed to ensure the success of large-scale CW projects. These include improving performance in cold climates and addressing the toxic threshold effects of PAHs on wetland plants. Overall, this review provides future direction for research on PAH removal using CWs and their large-scale operation for the treatment of PAH-contaminated surface waters.