Salt Adaptation and Evolutionary Implication of a Nah-related PAHs Dioxygenase cloned from a Halophilic Phenanthrene Degrading Consortium

Mechanism of phenanthrene degradation by the halophilic Pelagerythrobacter sp. N7

PAHs has shown worldwide accumulation and causes a significant environmental problem especially in saline and hypersaline environments. Moderately halophilic bacteria could be useful for the bioremediation of PAH pollution in hypersaline environments. Pelagerythrobacter sp. N7 was isolated from the PAH-degrading consortium 5H, which was enriched from mixed saline soil samples collected in Shanxi Province, China. 16S rRNA in the genomic DNA revealed that strain N7 belonged to Pelagerythrobacter. Strain N7 exhibited a high tolerance to a wide range of salinities (1-10%) and was highly efficient under neutral to weak alkaline conditions (pH 6-9). The whole genome of strain N7 was sequenced and analyzed, revealing an abundance of catabolic genes. Using the whole genome information, we conducted preliminary research on key enzymes and gene clusters involved in the upstream and downstream PAH degradation pathways of strain N7, thereby inferring its degradation pathway for phenanthrene and naphthalene. This study adds to our understanding of PAH degradation in hypersaline environments and, for the first time, identifies a Pelagerythrobacter with PAH-degrading capability. Strain N7, with its high efficiency in phenanthrene degradation, represents a promising resource for the bioremediation of PAHs in hypersaline environments.

Adaptive characteristics of indigenous microflora in an organically contaminated high salinity groundwater

Salinity, a critical factor, could directly or indirectly affect the microbial community structure and diversity. Changes in salinity levels act as environmental filters that influence the transformation of key microbial species. This study investigates the adaptive characteristics of indigenous microflora in groundwater in relation to external organic pollutants under high salinity stress. A highly mineralized shallow groundwater in Northwest China was conducted as the study area, and six representative sampling points were chosen to explore the response of groundwater hydrochemical parameters and microflora, as well as to identify the tolerance mechanisms of indigenous microflora to combined pollution. The results revealed that the dominant genera found in high salinity groundwater contaminated with organic pollutants possess the remarkable ability to degrade such pollutants even under challenging high salinity conditions, including Halomonas, Pseudomonas, Halothiobacillus, Sphingomonas, Lutibacter, Aquabacterium, Thiomicrospira, Aequorivita, etc. The hydrochemical factors, including total dissolved solids (TDS), sulfide, nitrite, nitrate, oxidation reduction potential (ORP), NH3-N, Na, Fe, benzene series, phenols, and halogenated hydrocarbons, demonstrated a significant influence on microflora. High levels of sulphate and sulfide in groundwater can exhibit dual effects on microflora. On one hand, these compounds can inhibit the growth and metabolism of microorganisms. On the other hand, they can also serve as effective electron donors/receptors during the microbial degradation of organic pollutants. Microorganisms exhibit resilience to the inhibitory effects of high salinity and organic pollutants via a series of tolerance mechanisms, such as strengthening the extracellular membrane barrier, enhancing the synthesis of relevant enzymes, initiating novel biochemical reactions, improving cellular self-healing capabilities, responding to unfavorable environmental conditions by migration, and enhancing the S cycle for the microbial metabolism of organic pollutants.

Effect of terminal electron acceptors on the anaerobic biodegradation of PAHs in marine sediments

The existing polycyclic aromatic hydrocarbons (PAHs) in marine sediment has become a critical threat to biological security. Terminal electron acceptor (TEA) amendment has been applied as a potential strategy to accelerate bioremediation in sediment. HCO₃^-, NO₃^-, and SO₄^2- were separately added to anaerobic sediment system containing five kinds of PAH, namely, phenanthrene, anthracene, fluoranthene, pyrene and benzo(a)pyrene. PAH concentration, PAH metabolites, TEA concentration, and electron transport system (ETS) activity were investigated. The HCO₃^- amendment group achieved the max PAH degradation efficiency of 84.98 %. SO₄^2- group led to the highest benzo(a)pyrene removal rate of 69.26 %. NO₃^- had the lowest PAH degradation rate of 76.16 %. ETS activity test showed that NO₃^- significantly inhibited electron transport activity in the sediment. The identified PAH metabolites were the same in each group, including 4,5-dimethylphenanthrene, 3-acetylphenanthrene, 9,10-anthracenedione, pyrene-7-hydroxy-8-carboxylic acid, anthrone, and dibenzothiophene. After 126 d's anaerobic degradation at 25 °C, the utilization of HCO₃^- and SO₄^2- as selected TEAs promoted the PAH biodegradation performance better than the utilization of NO₃^-.

Prospects in the bioremediation of petroleum hydrocarbon contaminants from hypersaline environments: A review

Hypersaline environments are underappreciated and are frequently exposed to pollution from petroleum hydrocarbons. Unlike other environs, the high salinity conditions present are a deterrent to various remediation techniques. There is also production of hypersaline waters from oil-polluted ecosystems which contain toxic hydrophobic pollutants that are threat to public health, environmental protection, and sustainability. Currently, innovative advances are being proposed for the remediation of oil-contaminated hypersaline regions. Such advancements include the exploration and stimulation of native microbial communities capable of utilizing and degrading petroleum hydrocarbons. However, prevailing salinity in these environments is unfavourable for the growth of non-halophylic microorganisms, thus limiting effective bioremediation options. An in-depth understanding of the potentials of various remediation technologies of hydrocarbon-polluted hypersaline environments is lacking. Thus, we present an overview of petroleum hydrocarbon pollution in hypersaline ecosystems and discuss the challenges and prospects associated with several technologies that may be employed in remediation of hydrocarbon pollution in the presence of delimiting high salinities. The application of biological remediation technologies including the utilization of halophilic and halotolerant microorganisms is also discussed.

Soil bioremediation by Pseudomonas brassicacearum MPDS and its enzyme involved in degrading PAHs

Polycyclic aromatic hydrocarbons (PAHs) commonly coexist in contaminated sites, posing a significant threat to ecosystem. Strains that degrade a wide range of substrates play important roles in bioremediation of contaminated environment. In this study, we reveal that Pseudomonas brassicacearum MPDS was able to remove 31.1% naphthalene of 500 mg/kg from soil within 2 d, while its relative abundance decreased significantly on Day 20, indicating its applicable potential in soil remediation. In addition to naphthalene, dibenzofuran, dibenzothiophene, and fluorene as reported previously, strain MPDS is able to degrade carbazole, phenanthrene, pyrene, and 2-bromonaphthalene. Moreover, NahA from strain MPDS has multi-substrate catalytic capacities on naphthalene, dibenzofuran, dibenzothiophene, phenanthrene, and 2-bromonaphthalene into dihydrodiols, while converts fluorene and carbazole into monohydroxy compounds according to GC-MS analysis. This study provides further insights into the exploration of soil remediation by strain MPDS and the mining of enzymes involved in the degradation of PAHs.

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

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

Insights Into Mechanism of the Naphthalene-Enhanced Biodegradation of Phenanthrene by Pseudomonas sp. SL-6 Based on Omics Analysis

The existence of polycyclic aromatic hydrocarbons (PAHs) in contaminated environment is multifarious. At present, studies of metabolic regulation focus on the degradation process of single PAH. The global metabolic regulatory mechanisms of microorganisms facing coexisting PAHs are poorly understood, which is the major bottleneck for efficient bioremediation of PAHs pollution. Naphthalene (NAP) significantly enhanced the biodegradation of phenanthrene (PHE) by Pseudomonas sp. SL-6. To explore the underlying mechanism, isobaric tags for relative and absolute quantification (iTRAQ) labeled quantitative proteomics was used to characterize the differentially expressed proteins of SL-6 cultured with PHE or NAP + PHE as carbon source. Through joint analysis of proteome and genome, unique proteins were identified and quantified. The up-regulated proteins mainly concentrated in PAH catabolism, Transporters and Electron transfer carriers. In the process, the regulator NahR, activated by salicylate (intermediate of NAP-biodegradation), up-regulates degradation enzymes (NahABCDE and SalABCDEFGH), which enhances the biodegradation of PHE and accumulation of toxic intermediate–1-hydroxy-2-naphthoic acid (1H2Na); 1H2Na stimulates the expression of ABC transporter, which maintains intracellular physiological activity by excreting 1H2Na; the up-regulation of cytochrome C promotes the above process running smoothly. Salicylate works as a trigger that stimulates cell to respond globally. The conjecture was verified at transcriptional and metabolic levels. These new insights contribute to improving the overall understanding of PAHs-biodegradation processes under complex natural conditions, and promoting the application of microbial remediation technology for PAHs pollution.

The catabolic pathways of in situ rhizosphere PAH degraders and the main factors driving PAH rhizoremediation in oil-contaminated soil

Rhizoremediation is a potential technique for polycyclic aromatic hydrocarbon (PAH) remediation; however, the catabolic pathways of in situ rhizosphere PAH degraders and the main factors driving PAH rhizoremediation remain unclear. To address these issues, stable-isotope-probing coupled with metagenomics and molecular ecological network analyses were first used to investigate the phenanthrene rhizoremediation by three different prairie grasses in this study. All rhizospheres exhibited a significant increase in phenanthrene removal and markedly modified the diversity of phenanthrene degraders by increasing their populations and interactions with other microbes. Of all the active phenanthrene degraders, Marinobacter and Enterobacteriaceae dominated in the bare and switchgrass rhizosphere respectively; Achromobacter was markedly enriched in ryegrass and tall fescue rhizospheres. Metagenomes of ¹³ C-DNA illustrated several complete pathways of phenanthrene degradation for each rhizosphere, which clearly explained their unique rhizoremediation mechanisms. Additionally, propanoate and inositol phosphate of carbohydrates were identified as the dominant factors that drove PAH rhizoremediation by strengthening the ecological networks of soil microbial communities. This was verified by the results of rhizospheric and non-rhizospheric treatments supplemented with these two substances, further confirming their key roles in PAH removal and in situ PAH rhizoremediation. Our study offers novel insights into the mechanisms of in situ rhizoremediation at PAH-contaminated sites.

Application of integrated extremophilic (halo-alkalo-thermophilic) bacterial consortium in the degradation of petroleum hydrocarbons and treatment of petroleum refinery wastewater under extreme condition

Degradation of petroleum hydrocarbon under extreme conditions such as high salinity, temperature and pH was difficult due to unavailability of potential bacterial strains. The present study details the efficiency of extremophilic bacterial consortium in biodegradation of different petroleum hydrocarbons and treatment of petroleum refinery wastewater under extreme condition. Extreme condition for the degradation of petroleum hydrocarbons was optimized at 8% salinity, pH-10 and temperature-60 °C. The consortium recorded complete degradation of low molecular weight (LMW) petroleum hydrocarbons (200 ppm) such as anthracene, phenanthrene, fluorene and naphthalene in 8 days under optimized extreme condition. High molecular weight (HMW) hydrocarbons such as pyrene (100 ppm), benzo(e)pyrene (20 ppm), benzo(k)fluoranthene (20 ppm) and benzo(a)pyrene (20 ppm), revealed 93%, 60%, 55% and 51% degradation by the extremophilic consortium under optimized extreme condition. The extremophilic consortium mineralized fluorene (61%) at high saline condition up to 24%. Addition of yeast extract potently accelerated the biodegradation under extreme condition. Treatment of petroleum refinery wastewater in continuous stirred tank reactor recorded 92% COD removal with complete removal of LMW hydrocarbons in 16 days and 91% of HMW hydrocarbons in 32 days under extreme condition. The hydrocarbons degrading extremophilic consortium possessed Ochrobactrum, Bacillus, Marinobacter, Pseudomonas, Martelella, Stenotrophomonas and Rhodococcus.

Separation, biochemical characterization and salt-tolerant mechanisms of alkaline protease from Aspergillus oryzae

BACKGROUND

The salt tolerance of proteases secreted by Aspergillus oryzae 3.042 closely relates to the utilization of raw materials and the quality of soy sauce. However, little is known about the salt-tolerant proteases and their salt-tolerant mechanisms.

RESULTS

In this study, we isolated and identified a salt-tolerant alkaline protease (AP, approximately 29 kDa) produced by A. oryzae 3.042. It was considered as a metal-ion-independent serine protease. The optimum and stable pH values were both pH 9.0 and the optimum temperature was 40 °C. Over 20% relative activity of AP remained in the presence of 3.0 mol L^-1 NaCl after 7 days, but its K_m and V_max were only mildly influenced by the presence of 3.0 mol L^-1 NaCl, indicating its outstanding salt tolerance. Furthermore, AP was more stable than non-salt-tolerant protease at high salinity. The salt-tolerant mechanisms of AP could be due to more salt bridges, higher proportion of ordered secondary structures and stronger hydrophobic amino acid residues in the interior.

CONCLUSIONS

The above results are vital for maintaining, activating and/or modulating the activity of AP in high-salt environments. They would also provide theoretical guidance for the modification of AP and the engineering of A. oryzae 3.042 so as to secrete more AP. © 2018 Society of Chemical Industry.

Salinity effect on the metabolic pathway and microbial function in phenanthrene degradation by a halophilic consortium

With the close relationship between saline environments and industry, polycyclic aromatic hydrocarbons (PAHs) accumulate in saline/hypersaline environments. Therefore, PAHs degradation by halotolerant/halophilic bacteria has received increasing attention. In this study, the metabolic pathway of phenanthrene degradation by halophilic consortium CY-1 was first studied which showed a single upstream pathway initiated by dioxygenation at the C1 and C2 positions, and at several downstream pathways, including the catechol pathway, gentisic acid pathway and protocatechuic acid pathway. The effects of salinity on the community structure and expression of catabolic genes were further studied by a combination of high-throughput sequencing, catabolic gene clone library and real-time PCR. Pure cultures were also isolated from consortium CY-1 to investigate the contribution made by different microbes in the PAH-degrading process. Marinobacter is the dominant genus that contributed to the upstream degradation of phenanthrene especially in high salt content. Genus Halomonas made a great contribution in transforming intermediates in the subsequent degradation of catechol by using catechol 1,2-dioxygenase (C12O). Other microbes were predicted to be mediating bacteria that were able to utilize intermediates via different downstream pathways. Salinity was investigated to have negative effects on both microbial diversity and activity of consortium CY-1 and consortium CY-1 was found with a high degree of functional redundancy in saline environments.