Assessment of polycyclic aromatic hydrocarbon biodegradation potential in mangrove sediment from Don Hoi Lot, Samut Songkram Province, Thailand

Pseudomonas and Pseudarthrobacter are the key players in synergistic phenanthrene biodegradation at low temperatures

Hydrocarbon contamination, including contamination with polycyclic aromatic hydrocarbons (PAHs), is a major concern in Antarctica due to the toxicity, recalcitrance and persistence of these compounds. Under the Antarctic Treaty, nonindigenous species are not permitted for use in bioremediation at polluted sites in the Antarctic region. In this study, three bacterial consortia (C13, C15, and C23) were isolated from Antarctic soils for phenanthrene degradation. All isolated bacterial consortia demonstrated phenanthrene degradation percentages ranging from 45 to 85% for 50 mg/L phenanthrene at 15 ℃ within 5 days. Furthermore, consortium C13 exhibited efficient phenanthrene degradation potential across a wide range of environmental conditions, including different temperature (4-30 ℃) and water availability (without polyethylene glycol (PEG) 6000 or 30% PEG 6000 (w/v)) conditions. Sequencing analysis of 16S rRNA genes revealed that Pseudomonas and Pseudarthrobacter were the dominant genera in the phenanthrene-degrading consortia. Moreover, six cultivable strains were isolated from these consortia, comprising four strains of Pseudomonas, one strain of Pseudarthrobacter, and one strain of Paeniglutamicibacter. These isolated strains exhibited the ability to degrade 50 mg/L phenanthrene, with degradation percentages ranging from 4 to 22% at 15 ℃ within 15 days. Additionally, the constructed consortia containing Pseudomonas spp. and Pseudarthrobacter sp. exhibited more effective phenanthrene degradation (43-52%) than did the individual strains. These results provide evidence that Pseudomonas and Pseudarthrobacter can be potential candidates for synergistic phenanthrene degradation at low temperatures. Overall, our study offers valuable information for the bioremediation of PAH contamination in Antarctic environments.

Novel insights into the synergetic degradation of pyrene by microbial communities from mangroves in China

Pyrene is a high molecular weight polycyclic aromatic hydrocarbon (HMW-PAHs). It is a ubiquitous, persistent, and carcinogenic environmental contaminant that has raised concern worldwide. This research explored synergistic bacterial communities for efficient pyrene degradation in seven typical Southern China mangroves. The bacterial communities of seven typical mangroves were enriched by pyrene, and enriched bacterial communities showed an excellent pyrene degradation capacity of > 95% (except for HK mangrove and ZJ mangrove). Devosia, Hyphomicrobium, Flavobacterium, Marinobacter, Algoriphahus, and Youhaiella all have significant positive correlations with pyrene (R>0, p < 0.05) by 16SrRNA gene sequencing and metagenomics analysis, indicated that these genera play a vital role in pyrene metabolism. Meanwhile, the functional genes were involved in pyrene degradation that was enriched in the bacterial communities, including the genes of nagAa, ndoR, pcaG, etc. Furthermore, the analyses of functional genes and binning genomes demonstrated that some bacterial communities as a unique teamwork to cooperatively participate in pyrene degradation. Interestingly, the genes related to biogeochemical cycles were enriched, such as narG , soxA, and cyxJ, suggested that bacterial communities were also helpful in maintaining the stability of the ecological environment. In addition, some novel species with pyrene-degradation potential were identified in the pyrene-degrading bacterial communities, which can enrich the resource pool of pyrene-degrading strains. Overall, this study will help develop further research strategies for pollutant removal.

Effects of electron acceptors and donors on anaerobic biodegradation of PAHs in marine sediments

Polycyclic aromatic hydrocarbons (PAHs) are typical organic pollutants accumulated in the environment. PAHs' bioremediation in sediments can be promoted by adding electron acceptor (EA) and electron donor (ED). Bicarbonate and sulfate were chosen as two EAs, and acetate and lactate were selected as two EDs. Six groups of amendments were added into the sediments to access their role in the anaerobic biodegradation of five PAHs, containing phenanthrene, anthracene, fluoranthene, pyrene, and benzo[a]pyrene. The concentrations of PAHs, EAs and EDs, electron transport system activity, and microbial diversity were analyzed during 126-day biodegradation in serum bottles. The HA group (bicarbonate and acetate) achieved the maximum PAH degradation efficiency of 89.67 %, followed by the SL group (sulfate and lactate) with 87.10 %. As the main PAHs degrading bacteria, the abundance of Marinobacter in H group was 8.62 %, and the addition of acetate significantly increased the abundance of Marinobacter in the HA group by 75.65 %.

Paddy cultivation in degraded karst wetland soil can significantly improve the physiological and ecological functions of carbon-fixing resident microorganisms

Microorganisms play an important role in carbon fixation in karst wetland soils. However, the carbon fixation capacity of karst wetland soils and active microorganisms involved in the carbon fixation process are poorly understood. In this study, carbon fixation capacity and active microorganisms involved in the fixation of inorganic carbon into organic carbon were studied in native, naturally degraded, and reclaimed karst wetland soils by the combination of stable isotope probing (SIP) and high-throughput sequencing. Under light conditions, the soil carbon fixation capacity ranked: the reclaimed wetland soil (1.58 mg C kg-1 day-1) > native wetland soil (1.43 mg C kg-1 day-1) > degraded wetland soil (0.62 mg C kg-1 day-1). In the dark, the soils ranked: the native wetland soil (0.24 mg C kg-1 day-1) > reclaimed wetland soil (0.18 mg C kg-1 day-1) > degraded wetland soil (0.06 mg C kg-1 day-1). Active microorganisms fixing inorganic carbon in the karst wetland soils were mainly Sulfurovum, Thermovirga, Dethiosulfatibacter, Allochromatium, Methylorubrum, and Bradyrhizobium. Thus, paddy cultivation can restore the carbon fixation capacity of microorganisms in the degraded karst wetland soil. This study provides an experimental basis for improving soil carbon fixation capacity and repairing degraded soil in karst wetlands.

Microbial remediation of oil-contaminated shorelines: a review

Frequent marine oil spills have led to increasingly serious oil pollution along shorelines. Microbial remediation has become a research hotspot of intertidal oil pollution remediation because of its high efficiency, low cost, environmental friendliness, and simple operation. Many microorganisms are able to convert oil pollutants into non-toxic substances through their growth and metabolism. Microorganisms use enzymes' catalytic activities to degrade oil pollutants. However, microbial remediation efficiency is affected by the properties of the oil pollutants, microbial community, and environmental conditions. Feasible field microbial remediation technologies for oil spill pollution in the shorelines mainly include the addition of high-efficiency oil degrading bacteria (immobilized bacteria), nutrients, biosurfactants, and enzymes. Limitations to the field application of microbial remediation technology mainly include slow start-up, rapid failure, long remediation time, and uncontrolled environmental impact. Improving the environmental adaptability of microbial remediation technology and developing sustainable microbial remediation technology will be the focus of future research. The feasibility of microbial remediation techniques should also be evaluated comprehensively.

Phenanthrene Degradation by Photosynthetic Bacterial Consortium Dominated by Fischerella sp

Microbial degradation of aromatic hydrocarbons is an emerging technology, and it is well recognized for its economic methods, efficiency, and safety; however, its exploration is still scarce and greater emphasis on cyanobacteria-bacterial mutualistic interactions is needed. We evaluated and characterized the phenanthrene biodegradation capacity of consortium dominated by Fischerella sp. under holoxenic conditions with aerobic heterotrophic bacteria and their molecular identification through 16S rRNA Illumina sequencing. Results indicated that our microbial consortium can degrade up to 92% of phenanthrene in five days. Bioinformatic analyses revealed that consortium was dominated by Fischerella sp., however different members of Nostocaceae and Weeksellaceae, as well as several other bacteria, such as Chryseobacterium, and Porphyrobacter, were found to be putatively involved in the biological degradation of phenanthrene. This work contributes to a better understanding of biodegradation of phenanthrene by cyanobacteria and identify the microbial diversity related.

Use of Shotgun Metagenomics to Assess the Microbial Diversity and Hydrocarbons Degrading Functions of Auto-Mechanic Workshops Soils Polluted with Gasoline and Diesel Fuel

Bioaugmentation is a valuable technique for oil recovery. This study investigates the composition and functions of microbial communities in gasoline- and diesel-contaminated soils of garages Matoko (SGM) and Guy et Paul (SGP) originating from auto mechanic workshops as well as the concentration of soil enzymes β-glucosidase, β-glucosaminidase, and acid phosphatase. The work aimed to evaluate the presence of petroleum-hydrocarbon-degrading bacteria for the development of foreseen bioremediation of oil-contaminated soils. Microbial diversity, as given by shotgun metagenomics, indicated the presence of 16 classes, among which Actinobacteria and Gammaproteobacteria dominated, as well as more than 50 families, including the dominant Gordoniaceae (26.63%) in SGM and Pseudomonadaceae (57.89%) in SGP. The dominant bacterial genera in the two soils were, respectively, Gordonia (26.7%) and Pseudomonas (57.9%). The exploration of the bacterial metabolic abilities using HUMANn2 allowed to detect genes and pathways involved in alkanes and aromatic hydrocarbons in the two contaminated soils. Furthermore, enzymes β-glucosidase, β-glucosaminidase, and acid phosphatase were found in high concentrations ranging between 90.27 ± 5.3 and 804.17 ± 20.5 µg pN/g soil/h, which indicated active microbial metabolism. The high diversity of microorganisms with a hydrocarbon degradation genetic package revealed that the bacteria inhabiting the two soils are likely good candidates for the bioaugmentation of oil-contaminated soils.

Mechanism of visible light enhances microbial degradation of Bisphenol A

Bisphenol A (BPA) is a toxic endocrine disruptor detected in various environments. Microbial metabolic/enzymatic degradation has been thought to be the main pathway for BPA attenuation in natural environments. In this study, we found that under visible light conditions, superoxide produced by bacteria was the main reason for the rapid removal of BPA, accounting for 57 % of the total removal rate. With visible light, the bacteria degraded BPA at a rate of 0.22 mg/L/d, and the total removal within 8 days reached 85 %, which is 4.7 times compared with that of dark culture. The intermediate product 4-iso-propenylphenol, which was considered as an end-product of microbial degradation of BPA in previous reports, was detected in large quantities at 24 h in culture but gradually decreased in our experiment. Community analysis suggested bacteria with aromatic hydrocarbon degradation ability were more enriched under light incubation. Moreover, the bacteria showed well degradation ability to various pharmaceutically active but nonbiodegradable compounds including diclofenac and fluoxetine, with a removal rate of 88 % and 20 %, respectively. Our study revealed the organic pollutant transformation pathway under the combined action of light and microorganisms, providing new insights into the microbial treatment of aromatic hydrocarbon pollutants.

Enhanced performance and mechanism of the combined process of ozonation and a semiaerobic aged refuse biofilter for mature landfill leachate treatment

A semiaerobic aged refuse biofilter (SAARB) can effectively treat mature landfill leachate (ML), but prolonged operation can lead to the enrichment of pollutants in the biofilter, resulting in severely degraded treatment performance. In this study, we constructed a combination process of ozonation and a SAARB to treat ML based on the principles of selective oxidation of aromatic organics by ozone and the preference of microorganisms for ozonation products. The results showed that the removal of organic and nitrogen pollutants became extremely poor after long-term treatment of ML using the SAARB alone. The decrease of chemical oxygen demand (COD), light absorbance at 254 nm (UV₂₅₄), NH₄⁺, and total nitrogen (TN) improved significantly after recirculating the ozonated ML effluent (OLE) into the SAARB, and the removal extents increased significantly to 63.59% (COD), 26.14% (UV₂₅₄), 92.85% (NH₄⁺), and 52.04% (TN), respectively. In addition, the recirculation of OLE enhanced the complete denitrification and tolerance to high NH₄⁺ loading by the SAARB. An analysis of the community composition of 16S_bacteria and ammonia oxidation bacteria (AOB) showed that long-term treatment of ML using the SAARB alone had difficulty enriching the dominant functional bacteria. In the OLE recirculation stage, environmental factors-such as influent organic matter species and concentration, nitrogen pollutant concentration, and pH-were changed to influence the community composition of 16S_bacteria and AOB and enrich functional bacteria (e.g., Truepera, Luteibacter, and Nitrosospira). Therefore, ozonation combined with a SAARB can remove organic and nitrogen pollutants more effectively. In particular, this can be used to solve the problem of inefficient total nitrogen removal using the SAARB alone. This study provides a theoretical reference for the efficient and stable operation of biological processes when treating ML.

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

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

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.

Bioballs carrying a syntrophic Rhodococcus and Mycolicibacterium consortium for simultaneous sorption and biodegradation of fuel oil in contaminated freshwater

Nonpathogenic effective bacterial hydrocarbon degraders, Rhodococcus ruber S103, Mycolicibacterium parafortuitum J101 and Mycolicibacterium austroafricanum Y502, were isolated from mixed polycyclic aromatic hydrocarbon (PAH)-enriched river sediments. They possessed broad substrate specificities toward various PAHs and aliphatic compounds as sole carbon sources. These strains exhibited promising characteristics, including biosurfactant production, high cell hydrophobicity, biofilm formation and no antagonistic interactions, and contained genes encoding hydrocarbon-degrading enzymes. The mixed bacterial consortium combining S103, J101 and Y502, showed more effective syntrophic degradation of two types of refined petroleum products, diesel and fuel oils, than monocultures. The defined consortium immobilized on plastic balls achieved over 50% removal efficiency of high fuel oil concentration (3000 mg L^-1) in a synthetic medium and contaminated freshwater. Furthermore, the immobilized cells simultaneously degraded more than 46% of total fuel oil adsorbed on plastic balls in both culture systems. SEM imaging confirmed that the immobilized consortium exhibited biofilm formation with the bacterial community covering most of the bioball surface, resulting in high bacterial survival against toxic contaminants. The results of this study showed the potential use of the cooperative interaction between Rhodococcus and Mycolicibacterium as immobilized bioballs for the bioremediation of fuel oil-contaminated environments. Additionally, this research has motivated further investigations into the development of bioremediation products for fuel oil degradation.

Influence of polycyclic aromatic hydrocarbon pollution on the diversity and function of bacterial communities in urban wetlands

Human disturbance has become the primary driving factor behind declining urban wetland ecological health due to rapid urbanization. Sediment microbial communities are critical for wetland ecosystem functioning but experience a range of natural and anthropogenic stressors due to rapid urbanization and land use changes, especially in developing countries. Polycyclic aromatic hydrocarbons (PAHs) released into the environment primarily come from anthropogenic sources like industrial activities and traffic emissions. Environmental PAH contamination is accelerating due to rapid urbanization, which also increases potential PAH-related dangers to human health. However, PAHs are widely distributed and not easy to centrally control. Microorganisms are the primary mediators of wetland purification, with most PAH-degrading microorganisms being bacteria. To better understand the influence of PAH contamination on urban wetland microbial communities, bacterial community compositions within sediments of urban wetlands in three land use types were investigated using high-throughput DNA sequencing and bioinformatics analyses. Statistical analyses revealed significant differences in overall microbial compositions among the three land use types, although γ-proteobacteria was the dominant phyla across all samples. Among the potential PAH-degrading bacterial taxa in sediments, Sphingomonas was the most prevalent. The distributions of PAH-degrading taxa were primarily affected by variance in organic compound abundances in addition to various physico-chemical variables, among which high-ring PAH content was a key parameter associated with bacterial distributions, except in the riverine wetlands. Functional inference via phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) indicated that 30 of the 43 genes related to PAH metabolism were predicted to be present within the genomes of bacteria among the three land use type. In particular, dioxygenase and dehydrogenase genes involved in PAH degradation were inferred to be prevalent, indicating that the host urban wetlands exhibited strong potential for organic pollutant degradation.

Efficient anaerobic bioremediation of high-concentration benzo[a]pyrene in marine environments

Benzo[a]pyrene (BaP), a persistent organic pollutant that may accumulate in sea sediments after oil spill or BaP chemical leakage accidents, considerably harms marine ecosystems and human health. Previous studies have been predominantly focused on its degradation at low concentrations, while the remediation of BaP pollution with high concentrations was neglected. Additionally, the metabolic pathways associated with its anaerobic degradation remain unclear. As a first attempt, super-efficient systems for BaP anaerobic degradation were established, and the corresponding metabolic pathways were elucidated in this study. The results showed that the BaP removal rate in BaP-only system with initial concentrations of 200 mg/L reached 3.09 mg/(L·d) within 45 days. Co-solvent, acetone promoted anaerobic BaP degradation (4.252 mg/(L·d)), while dichloromethane showed a newly-discovered co-metabolic effect. In the system with 500 mg/L of BaP and dichloromethane addition, the removal rate increased drastically (14.64 mg/(L·d)) at 400 mg/L turn point of BaP. Additionally, the corresponding microbial community-level metabolic network was firstly proposed.

Biodegradation potential of polycyclic aromatic hydrocarbons in Taihu Lake sediments

ABSTRACTTo assess the biodegradation potential of polycyclic aromatic hydrocarbons (PAHs) in sediments, sediment microcosms were constructed with sediments collected from six lake zones with different trophic statuses in Taihu Lake. The presence and concentration of PAH-degrading bacteria (PDB) were estimated by the most probable number (MPN) method. After 85 d of aerobic and anaerobic incubation, spiked PAHs (phenanthrene, pyrene, and benzo[a]pyrene) were partially degraded by indigenous sediment microorganisms. Large differences in PAH degradation were observed depending on the molecular size of the PAHs. The PAH removal efficiency in sediments under aerobic conditions was higher than that under anaerobic conditions. MPN analyses showed a higher abundance of degrading microflora in the high PAH-contaminated sites than in the low PAH-contaminated sites. Moreover, the anaerobic PDB populations in the sediments from the six different sites were much higher than those of aerobic PDB. The PAH biodegradation capability in sediments was associated with the geochemical conditions and bacterial populations. PDB showed a broad spatial distribution, thereby implying that they played an important role in the natural attenuation and cycling of PAHs in Taihu Lake. This work indicates that PAHs remain a concern in Taihu Lake sediments and can provide useful information for further bioremediation of PAH-contaminated sediments.

Molecular-level variation of dissolved organic matter and microbial structure of produced water during its early storage in Fuling shale gas field, China

Shale gas-produced water (PW), the waste fluid generated during gas production, contains a large number of organic contaminants and high salinity matrix. Previous studies generally focused on the end-of-pipe treatment of the PW and ignored the early collection process. In this study, the transformation of the molecular composition and microbial community structure of the PW in the transportation and storage process (i.e., from the gas-liquid separator to the storage tank) were investigated. As the PW was transported from the gas-liquid separator to the portable storage tank, the dissolved organic matter (DOM) showed greater saturation, less oxidation, and lower polarity. DOMs with high O/C and low H/C ratios (numbers of oxygen and hydrogen divided by numbers of carbon) were eliminated, which may be due to precipitation or adsorption by the solids suspended in the PW. The values of double-bond equivalent (DBE), DBE/C (DBE divided by the number of carbon), and aromatic index (AI) decreased, likely because of the microbial degradation of aromatic compounds. The PW in the gas-liquid separator presented a lower biodiversity than that in the storage tank. The microbial community in the storage tank showed the coexistence of anaerobes and aerobes. Genera related to biocorrosion and souring were detected in the two facilities, thus indicating the necessity of more efficient anticorrosion strategies. This study helps to enhance the understanding of the environmental behavior of PW during shale gas collection and provides a scientific reference for the design and formulation of efficient transportation and storage strategies to prevent and control the environmental risk of shale gas-derived PW.

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.

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

This study investigated the polycyclic aromatic hydrocarbons (PAHs) occurrence, and their impact on the microbial community and PAH-degrading genera and genes in the Knysna Estuary of South Africa. The results reveal that the estuary exhibits low PAH levels (114.1-356.0 ng g^-1). Ignavibacteriae and Deferribacteres, as well as Proteobacteria and Bacteroidetes, are keystone phyla. Among measured environmental factors, total organic carbon (TOC), nutrients such as nitrite and nitrate, metals as Al, Cr, Cu, Ni, Pb and Zn, and environmental properties (pH and salinity) are primary contributors to structuring the bacterial community assemblage. The abundance of alpha subunit genes of the PAH-ring hydroxylating dioxygenases (PAH-RHDα) of Gram-negative bacteria lies in the range of (2.0-4.2) × 10⁵ copies g^-1, while that of Gram-positive bacteria ranges from 3.0 × 10⁵ to 1.3 × 10⁷ copies g^-1. The PAH-degrading bacteria account for up to 0.1% of the bacterial community and respond mainly to nitrate, TOC and salinity, while PAHs at low concentration are not significant influencing factors. PAH degraders such as Xanthomonadales, Pseudomonas, and Mycobacterium, which play a central role in PAH-metabolization coupled with other biogeochemical processes (e.g. iron cycling), may contribute to maintaining a healthy estuarine ecosystem. These results are important for developing appropriate utilization and protection strategies for pristine estuaries worldwide.

Inhibitory effect of phenol on wastewater ammonification

This study aimed to elucidate inhibitory effect of phenol on ammonification of dissolved organic nitrogen (DON) in wastewater. Laboratory incubation experiments were conducted using primary and secondary effluent samples spiked with phenol (100-1000 mg/L) and inoculated with mixed cultures, pure strains of phenol-degrading bacteria (Acinetobacter sp. and Pseudomonas putida F1), and/or an ammonia oxidizing bacterium (Nitrosomonas europaea). DON concentration was monitored with incubation time. Phenol suppressed the ammonification rate of DON up to 62.9%. No or minimal ammonification inhibition was observed at 100 mg/L of phenol while the inhibition increased with increasing phenol concentration from 250 to 1000 mg/L. The inhibition was curtailed by the presence of the phenol-degrading bacteria. DON was ammonified in the samples inoculated with only N. europaea and the ammonification was also inhibited by phenol. The findings suggest that high phenol in wastewater could result in low ammonification and high DON in the effluent.

Treatment of High-Concentration Wastewater from an Oil and Gas Field via a Paired Sequencing Batch and Ceramic Membrane Reactor

A sequencing batch reactor (SBR) and a ceramic membrane bioreactor (CMBR) were used in conjunction (SBR+CMBR) to treat high-concentration oil and gas field wastewater (HCOGW) from the China National Offshore Oil Corporation Zhanjiang Branch (Zhanjiang, Guangdong, China). The chemical oxygen demand (COD) and the oil concentrations in the wastewater were 20,000–76,000 and 600–2200 mg/L, respectively. After the SBR+CMBR process, the effluent COD and oil content values were less than 250 mg/L and 2 mg/L, respectively, which met the third level of the Integrated Wastewater Discharge Standards of China (GB8978-1996). Through microbiological analysis, it was found that the CMBR domesticated a previously unreported functional microorganism (JF922467.1) that successfully formed a new microbial ecosystem suitable for HCOGW treatment. In conjunction with the SBR process, the CMBR process effectively reduced pollutant concentrations in HCOGW. Moreover, economic analyses indicated that the total investment required to implement the proposed infrastructure would be approximately 671,776.61 USD, and the per-unit water treatment cost would be 1.04 USD/m³.

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.

First Characterization of PAH-degrading bacteria from Río de la Plata and high-resolution melting: an encouraging step toward bioremediation

The Río de la Plata, one of the most important estuarine environments in South America that sustains valuable fisheries, is affected by PAH contamination associated with oil industry and port activities. A total of 95 bacteria with potential to degrade phenanthrene were obtained from water samples using traditional culture methods. PCR-RFLP analysis of 16S rDNA partial fragments was used as a screening tool for reducing the number of isolates during diversity studies, obtaining 42 strains with different fingerprint patterns. Phylogenetic analysis indicated that they were affiliated to 19 different genera of Gamma- and Alpha-Proteobacteria, and Actinobacteria. Some of them showed an efficient phenanthrene degradation by HPLC (between 83% and 97%) and surfactant production (between 40% and 55%). They could be an alternative for microbial selection in the degradation of PAHs in this estuarine system. In order to detect and monitor PAH-degrading bacteria in this highly productive area, rDNA amplicons of the 33 isolates, produced by PCR real time, were tested by the high-resolution melting (HRM) technique. After analyzing the generated melting curves, it was possible to accurately distinguish nine patterns corresponding to eight different genera. HRM analysis allowed a differentiation at the species level for genera Pseudomonas, Halomonas and Vibrio. The implementation of this method as a fast and sensitive scanning approach to identify PAH-degrading bacteria, avoiding the sequencing step, would mean an advance in bioremediation technologies.

Biodegradation of Phenanthrene and Heavy Metal Removal by Acid-Tolerant Burkholderia fungorum FM-2

Phenanthrene (PHE) is a common pollutant of acidic and non-acidic environments that is recalcitrant to biodegradation. Herein, Burkholderia fungorum FM-2 (GenBank accession no. KM263605) was isolated from oil-contaminated soil in Xinjiang and characterized morphologically, physiologically, and phylogenetically. Environmental parameters including PHE concentration, pH, temperature, and salinity were optimized, and heavy metal tolerance was investigated. The MIC of strain FM-2 tolerant to Pb(II) and Cd(II) was 50 and 400 mg L⁻¹, respectively, while the MIC of Zn(II) was >1,200 mg L⁻¹. Atypically for a B. fungorum strain, FM-2 utilized PHE (300 mg L⁻¹) as a sole carbon source over a wide pH range (between pH 3 and 9). PHE and heavy metal metabolism were assessed using gas chromatography (GC), inductively coupled plasma optical emission spectroscopy (ICP-OES), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), Fourier-transform infrared (FTIR) spectroscopy and ultraviolet (UV) absorption spectrometry. The effects of heavy metals on the bioremediation of PHE in soil were investigated, and the findings suggest that FM-2 has potential for combined bioremediation of soils co-contaminated with PHE and heavy metals.

Mangrove Facies Drives Resistance and Resilience of Sediment Microbes Exposed to Anthropic Disturbance

Mangrove forests are coastal ecosystems continuously affected by various environmental stresses and organized along constraint gradients perpendicular to the coastline. The aim of this study was to evaluate the resistance and resilience of sediment microbial communities in contrasted vegetation facies, during and after exposure to an anthropic disturbance. Our hypothesis was that microbial communities should be the most stable in the facies where the consequences of the anthropic disturbance are the most similar to those of natural disturbances. To test this, we focused on communities involved in N-cycle. We used an in situ experimental system set up in Mayotte Island where 2 zones dominated by different mangrove trees are daily exposed since 2008 to pretreated domestic wastewater (PW) discharges. These freshwater and nutrients inputs should increase microbial activities and hence the anoxia of sediments. We monitored during 1 year the long-term impact of this disturbance, its short-term impact and the resilience of microbial communities on plots where PW discharges were interrupted. Microorganism densities were estimated by qPCR, the nitrification (NEA) and denitrification (DEA) enzyme activities were evaluated by potential activity measurements and pigment analyses were performed to assess the composition of microbial photosynthetic communities. At long-term PW discharges significantly modified the structure of phototrophic communities and increased the total density of bacteria, the density of denitrifying bacteria and DEA. Similar effects were observed at short-term, notably in the facies dominated by Ceriops tagal. The results showed a partial resilience of microbial communities. This resilience was faster in the facies dominated by Rhizophora mucronata, which is more subjected to tides and sediment anoxia. The higher stability of microbial communities in this facies confirms our hypothesis. Such information should be taken into account in mangrove utilization and conservation policies.

Bacterial Diversity and the Geochemical Landscape in the Southwestern Gulf of Mexico

Marine sediments are an example of one of the most complex microbial habitats. These bacterial communities play an important role in several biogeochemical cycles in the marine ecosystem. In particular, the Gulf of Mexico has a ubiquitous concentration of hydrocarbons in its sediments, representing a very interesting niche to explore. Additionally, the Mexican government has opened its oil industry, offering several exploration and production blocks in shallow and deep water in the southwestern Gulf of Mexico (swGoM), from which there are no public results of conducted studies. Given the higher risk of large-scale oil spills, the design of contingency plans and mitigation activities before oil exploitation is of growing concern. Therefore, a bacterial taxonomic baseline profile is crucial to understanding the impact of any eventual oil spill. Here, we show a genus level taxonomic profile to elucidate the bacterial baseline, pointing out richness and relative abundance, as well as relationships with 79 abiotic parameters, in an area encompassing ∼150,000 km2, including a region where the exploitation of new oil wells has already been authorized. Our results describe for the first time the bacterial landscape of the swGoM, establishing a bacterial baseline "core" of 450 genera for marine sediments in this region. We can also differentiate bacterial populations from shallow and deep zones of the swGoM based on their community structure. Shallow sediments have been chronically exposed to aromatic hydrocarbons, unlike deep zones. Our results reveal that the bacterial community structure is particularly enriched with hydrocarbon-degrading bacteria in the shallow zone, where a greater aromatic hydrocarbon concentration was determined. Differences in the bacterial communities in the swGoM were also observed through a comprehensive comparative analysis relative to various marine sediment sequencing projects, including sampled sites from the Deep Water Horizon oil spill. This study in the swGoM provides clues to the bacterial population adaptation to the ubiquitous presence of hydrocarbons and reveals organisms such as Thioprofundum bacteria with potential applications in ecological surveillance. This resource will allow us to differentiate between natural conditions and alterations generated by oil extraction activities, which, in turn, enables us to assess the environmental impact of such activities.

16S metagenomic analysis reveals adaptability of a mixed-PAH-degrading consortium isolated from crude oil-contaminated seawater to changing environmental conditions

A bacterial consortium, named SWO, was enriched from crude oil-contaminated seawater from Phrao Bay in Rayong Province, Thailand, after a large oil spill in 2013. The bacterial consortium degraded a polycyclic aromatic hydrocarbon (PAH) mixture consisting of phenanthrene, anthracene, fluoranthene, and pyrene (50 mg L^-1 each) by approximately 73%, 69%, 52%, and 48%, respectively, within 21 days. This consortium exhibited excellent adaptation to a wide range of environmental conditions. It could degrade a mixture of four PAHs under a range of pH values (4.0-9.0), temperatures (25 °C-37 °C), and salinities (0-10 g L^-1 with NaCl). In addition, this consortium degraded 20-30% of benzo[a]pyrene and perylene (10 mg L^-1 each), high molecular weight PAHs, in the presence of other PAHs within 35 days, and degraded 40% of 2% (v/v) crude oil within 20 days. The 16S rRNA gene amplicon sequencing analysis demonstrated that Pseudomonas and Methylophaga were the dominant genera of consortium SWO in almost all treatments, while Pseudidiomarina, Thalassospira and Alcanivorax were predominant under higher salt concentrations. Moreover, Pseudomonas and Alcanivorax were dominant in the crude oil-degradation treatment. Our results suggest that the consortium SWO maintained its biodegradation ability by altering the bacterial community profile upon encountering changes in the environmental conditions.

Potential microbial consortium involved in the biodegradation of diesel, hexadecane and phenanthrene in mangrove sediment explored by metagenomics analysis

Hydrocarbon contamination is a serious problem that degrades the quality of mangrove ecosystems, and bioremediation using autochthonous bacteria is a promising technology to recover an impacted environment. This research investigates the biodegradation rates of diesel, hexadecane and phenanthrene, by conducting a microcosm study and survey of the autochthonous microbial community in contaminated mangrove sediment, using an Illumina MiSeq platform. The biodegradation rates of diesel, hexadecane and phenanthrene were 82, 86 and 8 mg kg^-1 sediment day^-1, respectively. The removal efficiencies of hexadecane and phenanthrene were >99%, whereas the removal efficiency of diesel was 88%. A 16S rRNA gene amplicon sequence analysis revealed that the major bacterial assemblages detected were Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria. The bacterial compositions were relatively constant, while reductions of the supplemented hydrocarbons were observed. The results imply that the autochthonous microorganisms in the mangrove sediment were responsible for the degradation of the respective hydrocarbons. Diesel-, hexadecane- and phenanthrene-degrading bacteria, namely Bacillus sp., Pseudomonas sp., Acinetobacter sp. and Staphylococcus sp., were also isolated from the mangrove sediment. The mangrove sediment provides a potential resource of effective hydrocarbon-degrading bacteria that can be used as an inoculum or further developed as a ready-to-use microbial consortium for the purpose of bioremediation.

Continuous treatment of Acid Red B with activated sludge bioaugmented by a yeast Candida tropicalis TL-F1 and microbial community dynamics

Continuous treatment of Acid Red B (ARB) with activated sludge (AS) bioaugmented by an azo-degrading yeast Candida tropicalis TL-F1 under aerobic conditions was investigated in the form of sequencing batch tests. Dynamics of both bacterial and fungal communities were analyzed using polymerase chain reaction followed by denaturing gradient gel electrophoresis (PCR-DGGE) method. The results showed that bioaugmentation with the yeast TL-F1 improved the performance of AS for continuously decolorizing, degrading and detoxifying ARB. Meanwhile, the AS systems bioaugmented by the yeast TL-F1 showed higher sludge concentration and better AS settleability. The result of PCR-DGGE suggested that microbial communities of both bacteria and fungi shifted due to treatment of ARB and bioaugmentation. Some dominant bacteria and fungi were identified as probably efficient degraders of ARB or its decolorization byproducts. Furthermore, the yeast TL-F1 was found as one of the dominant fungi in all the three bioaugmented systems, suggesting that bioaugmentation was successful due to the colonization of the yeast TL-F1 in AS systems.

Biodegradation of high concentrations of mixed polycyclic aromatic hydrocarbons by indigenous bacteria from a river sediment: a microcosm study and bacterial community analysis

This study assessed the biodegradation of mixtures of polycyclic aromatic hydrocarbons (PAHs) by indigenous bacteria in river sediment. Microcosms were constructed from sediment from the Chao Phraya River (the main river in Thailand) by supplementation with high concentrations of fluorene, phenanthrene, pyrene (300 mg kg^-1 of each PAH), and acenaphthene (600 mg kg^-1). Fluorene and phenanthrene were completely degraded, whereas 50% of the pyrene and acenaphthene were removed at the end of the incubation period (70 days). Community analyses revealed the dynamics of the bacterial profiles in the PAH-degrading microcosms after PAH exposure. Actinobacteria predominated and became significantly more abundant in the microcosms after 14 days of incubation at room temperature under aerobic conditions. Furthermore, the remaining PAHs and alpha diversity were positively correlated. The sequencing of clone libraries of the PAH-RHDα genes also revealed that the dioxygenase genes of Mycobacterium sp. comprised 100% of the PAH-RHDα library at the end of the microcosm setup. Moreover, two PAH-degrading Actinobacteria (Arthrobacter sp. and Rhodococcus ruber) were isolated from the original sediment sample and showed high activity in the degradation of phenanthrene and fluorene in liquid cultivation. This study reveals that indigenous bacteria had the ability to degrade high concentrations of mixed PAHs and provide clear evidence that Actinobacteria may be potential candidates to play a major role in PAH degradation in the river sediment.

The microbial degradation of 2,4,6-tribromophenol (TBP) in water/sediments interface: Investigating bioaugmentation using Bacillus sp. GZT

The substance 2,4,6-Tribromophenol (TBP) is used as a flame retardant in electronic and electric devices, and is a replacement for pentachlorophenol in wood preservation. TBP is a contaminant in different environmental matrices, at levels where treatment is required. This study examined the relationship between the bioaugmention of TBP degradation and the evolution of the microbial community in river water/sediment microcosms. When compared with unamended controls, bioaugmentation with Bacillus sp. GZT effectively enhanced TBP biodegradation, with approximately 40.7% of the TBP removal after a 7-week incubation period, without a lag phase (p<0.01). Amendments with 2-bromophenol, 2,6-dibromophenol, and 2,4-dibromophenol did not promote TBP biodegradation in river water/sediments (p>0.05). However, TBP biodegradation was enhanced by adding other additives, including NaCl, humic acid, sodium lactate, and sodium propionate alone, especially glucose and yeast extract. A metagenomics analysis of the total 16S rRNA genes from the treatment system with bioaugmentation showed that four microbial phyla were dominant: Proteobacteria (52.08-66.22%), Actinobacteria (20.03-5.47%), Bacteroidetes (6.68-13.68%), and Firmicutes (4.53-20.83%). This study highlights the possible benefits using bioaugmentation with GZT to remediate TBP-polluted water and sediments.

A new approach for pyrene bioremediation using bacteria immobilized in layer-by-layer assembled microcapsules: dynamics of soil bacterial community

Pyrene-degrading bacteria immobilized in layer-by-layer assembled microcapsules were prepared and inoculated into pyrene-contaminated soil. The microcapsules enhanced the pyrene removal ability and improved the bacterial community construction.

Bioaugmentation and biostimulation as strategies for the bioremediation of a burned woodland soil contaminated by toxic hydrocarbons: a comparative study

In this work, the natural attenuation strategy (no soil amendments done) was compared with two different bioremediation approaches, namely bioaugmentation through soil inoculation with a suspension of Trichoderma sp. mycelium and biostimulation by soil addition with a microbial growth promoting formulation, in order to verify the effectiveness of these methods in terms of degradation efficiency towards toxic hydrocarbons, with particular attention to the high molecular weight (HMW) fraction, in a forest area impacted by recent wildfire in Northern Italy. The area under investigation, divided into three parcels, was monitored to figure out the dynamics of decay in soil concentration of C₁₂₋₄₀ hydrocarbons (including isoalkanes, cycloalkanes, alkyl-benzenes and alkyl-naphthalenes besides PAHs) and low molecular weight (LMW) PAHs, following the adoption of the foregoing different remediation strategies. Soil hydrocarbonoclastic potential was even checked by characterizing the autochthonous microbial cenoses. Field experiments proved that the best performance in the abatement of HMW hydrocarbons was reached 60 days after soil treatment through the biostimulation protocol, when about 70% of the initial concentration of HMW hydrocarbons was depleted. Within the same time, about 55% degradation was obtained with the bioaugmentation protocol, whilst natural attenuation allowed only a 45% removal of the starting C12-40 hydrocarbon fraction. Therefore, biostimulation seems to significantly reduce the time required for the remediation, most likely because of the enhancement of microbial degradation through the improvement of nutrient balance in the burned soil.

Abundance and diversity of functional genes involved in the degradation of aromatic hydrocarbons in Antarctic soils and sediments around Syowa Station

Hydrocarbon catabolic genes were investigated in soils and sediments in nine different locations around Syowa Station, Antarctica, using conventional PCR, real-time PCR, cloning, and sequencing analysis. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD)-coding genes from both Gram-positive and Gram-negative bacteria were observed. Clone libraries of Gram-positive RHD genes were related to (i) nidA3 of Mycobacterium sp. py146, (ii) pdoA of Terrabacter sp. HH4, (iii) nidA of Diaphorobacter sp. KOTLB, and (iv) pdoA2 of Mycobacterium sp. CH-2, with 95-99% similarity. Clone libraries of Gram-negative RHD genes were related to the following: (i) naphthalene dioxygenase of Burkholderia glathei, (ii) phnAc of Burkholderia sartisoli, and (iii) RHD alpha subunit of uncultured bacterium, with 41-46% similarity. Interestingly, the diversity of the Gram-positive RHD genes found around this area was higher than those of the Gram-negative RHD genes. Real-time PCR showed different abundance of dioxygenase genes between locations. Moreover, the PCR-denaturing gradient gel electrophoresis (DGGE) profile demonstrated diverse bacterial populations, according to their location. Forty dominant fragments in the DGGE profiles were excised and sequenced. All of the sequences belonged to ten bacterial phyla: Proteobacteria, Actinobacteria, Verrucomicrobia, Bacteroidetes, Firmicutes, Chloroflexi, Gemmatimonadetes, Cyanobacteria, Chlorobium, and Acidobacteria. In addition, the bacterial genus Sphingomonas, which has been suggested to be one of the major PAH degraders in the environment, was observed in some locations. The results demonstrated that indigenous bacteria have the potential ability to degrade PAHs and provided information to support the conclusion that bioremediation processes can occur in the Antarctic soils and sediments studied here.