The effects of nutrient amendment on biodegradation and cytochrome P450 activity of an n-alkane degrading strain of Burkholderia sp. GS3C

Multi-omics association study of hexadecane degradation in haloarchaeal strain Halogranum rubrum RO2-11

Haloarchaea with the capacity to degrade alkanes is promising to deal with petroleum pollution in hypersaline environments. However, only a limited number of haloarchaeal species are investigated, and their pathway and mechanism for alkane degradation remain unclear. In this study, Halogranum rubrum RO2-11, a haloarchaeal strain, verified the ability to degrade kerosene and hexadecane in 184 g/L NaCl, with 53% and 52% degradation rates after 9 and 4 days, respectively. Genome sequencing and gene annotation indicated that strain RO2-11 possesses a complete potential alkane-degrading pathway, of which alkane hydroxylases may include CYP450, AlmA, and LadA. Transcriptome and metabolome analyses revealed that the upregulation of related genes in TCA cycle, lysine biosynthesis, and acetylation may help improve hexadecane degradation. Additionally, an alternative degrading pathway of hexadecane based on dual-terminal β-oxidation may occur in strain RO2-11. It is likely to be the first report of alkane degradation by the genus Halogranum, which may be helpful for applications of oil-pollution bioremediation under high-salt conditions.

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.

A Novel, Highly Potent NADPH-Dependent Cytochrome P450 Reductase from Waste Liza klunzingeri Liver

The use of marine enzymes as catalysts for biotechnological applications is a topical subject. Marine enzymes usually display better operational properties than their animal, plant or bacterial counterparts, enlarging the range of possible biotechnological applications. Due to the fact that cytochrome P450 enzymes can degrade many different toxic environmental compounds, these enzymes have emerged as valuable tools in bioremediation processes. The present work describes the isolation, purification and biochemical characterization of a liver NADPH-dependent cytochrome P450 reductase (CPR) from the marine fish Liza klunzingeri (LkCPR). Experimental results revealed that LkCPR is a monomer of approximately 75 kDa that is active in a wide range of pH values (6-9) and temperatures (40-60 °C), showing the highest catalytic activity at pH 8 and 50 °C. The activation energy of the enzyme reaction was 16.3 kcal mol^-1 K^-1. The K_M values for cytochrome C and NADPH were 8.83 μM and 7.26 μM, and the k_cat values were 206.79 s^-1 and 202.93 s^-1, respectively. LkCPR displayed a specific activity versus cytochrome C of 402.07 µmol min^-1 mg¹, the highest activity value described for a CPR up to date (3.2-4.7 times higher than the most active reported CPRs) and showed the highest thermostability described for a CPR. Taking into account all these remarkable catalytic features, LkCPR offers great potential to be used as a suitable biocatalyst.

Assessment of bioremediation potential of petroleum-contaminated soils from the shanbei oilfield of China revealed by qPCR and high throughput sequencing

With the crude oil exploration activities in the Shanbei oilfield of China, the risk of soil contamination with crude oil spills has become a major concern. This study aimed at assessing the bioremediation potential of the petroleum polluted soils by investigating the expression of key functional genes decoding alkane and aromatic component degradation using an array of primers and real-time quantitative PCR (qPCR), and the functional microbiomes were determined using a combination of substrate-induced metabolic responses and high throughput sequencing. The results showed that the species that were more inclined to degrade aliphatic fraction of crude oil included Acinetobacter, Stenotrophomonas, Neorhizobium and Olivebacter. And Pseudomonas genus was a highly specific keystone species with the potential to degrade PAH fraction. Both aliphatic and PAH-degrading genes were upregulated when the soil petroleum contents were less than 10,000 mg/kg but downregulated when the oil contents were over 10,000 mg/kg. Bioremediation potential could be feasible for medium pollution with petroleum contents of less than 10,000 mg/kg. Optimization of the niche of Acinetobacter, Stenotrophomonas, Pseudomonas, Neorhizobium and Olivebacter species was beneficial to the biodegradation of refractory hydrocarbon components in the Shanbei plateau oilfield.

Strategies for Enhancing in vitro Degradation of Linuron by Variovorax sp. Strain SRS 16 Under the Guidance of Metabolic Modeling

Phenyl urea herbicides are being extensively used for weed control in both agricultural and non-agricultural applications. Linuron is one of the key herbicides in this family and is in wide use. Like other phenyl urea herbicides, it is known to have toxic effects as a result of its persistence in the environment. The natural removal of linuron from the environment is mainly carried through microbial biodegradation. Some microorganisms have been reported to mineralize linuron completely and utilize it as a carbon and nitrogen source. Variovorax sp. strain SRS 16 is one of the known efficient degraders with a recently sequenced genome. The genomic data provide an opportunity to use a genome-scale model for improving biodegradation. The aim of our study is the construction of a genome-scale metabolic model following automatic and manual protocols and its application for improving its metabolic potential through iterative simulations. Applying flux balance analysis (FBA), growth and degradation performances of SRS 16 in different media considering the influence of selected supplements (potential carbon and nitrogen sources) were simulated. Outcomes are predictions for the suitable media modification, allowing faster degradation of linuron by SRS 16. Seven metabolites were selected for in vitro validation of the predictions through laboratory experiments confirming the degradation-promoting effect of specific amino acids (glutamine and asparagine) on linuron degradation and SRS 16 growth. Overall, simulations are shown to be efficient in predicting the degradation potential of SRS 16 in the presence of specific supplements. The generated information contributes to the understanding of the biochemistry of linuron degradation and can be further utilized for the development of new cleanup solutions without any genetic manipulation.

Identity and hydrocarbon degradation activity of enriched microorganisms from natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI)

A previous cultivation-independent investigation of the microbial community structure of natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI) revealed the dominance of uncultured bacterial taxa belonging to the phyla Deferribacterota and Coprothermobacterota and the orders Thermodesulfobacteriales, Thermales, and Burkholderiales. Here we report on a cultivation-dependent approach to identify members of these groups involved in hydrocarbon degradation in the KRI oil and asphalt seeps. For this purpose, we set up anoxic crude oil-degrading enrichment cultures based on cultivation media known to support the growth of members of the above-mentioned taxonomic groups. During 100-200 days incubation periods, nitrate-reducing and fermentative enrichments showed up to 90% degradation of C₈-C₁₇ alkanes and up to 28% degradation of C₁₈-C₃₃ alkanes along with aromatic hydrocarbons. Community profiling of the enrichment cultures showed that they were dominated by diverse bacterial taxa, which were rare in situ community members in the investigated seeps. Groups initially targeted by our approach were not enriched, possibly because their members are slow-growing and involved in the degradation of recalcitrant hydrocarbons. Nevertheless, the enriched taxa were taxonomically related to phylotypes recovered from hydrocarbon-impacted environments as well as to characterized bacterial isolates not previously known to be involved in hydrocarbon degradation. Marker genes (assA and bssA), diagnostic for fumarate addition-based anaerobic hydrocarbon degradation, were not detectable in the enrichment cultures by PCR. We conclude that hydrocarbon biodegradation in our enrichments occurred via unknown pathways and synergistic interactions among the enriched taxa. We suggest, that although not representing abundant populations in situ, studies of the cultured close relatives of these taxa will reveal an unrecognized potential for anaerobic hydrocarbon degradation, possibly involving poorly characterized mechanisms.

Biodegradation of hydrolyzed polyacrylamide by a Bacillus megaterium strain SZK-5: Functional enzymes and antioxidant defense mechanism

Hydrolyzed polyacrylamide (HPAM) is the most widely used water-soluble linear polymer with high molecular weight in polymer flooding. Microbiological degradation is an environment-friendly and effective method of treating HPAM-containing oilfield produced water. In this study, a strain SZK-5 that could degrade HPAM was isolated from soil contaminated by oilfield produced water. Based on morphological, biochemical characteristics and 16S rDNA sequence homology analysis, the strain was identified as Bacillus megaterium. The biodegradation capability of strain SZK-5 was determined by incubation in a mineral salt medium (MSM) containing HPAM under different environmental conditions, showing 55.93% of the HPAM removed after 7 d of incubation under the optimum conditions ((NH₄)₂SO₄ = 1667.9 mg L^-1, temperature = 24.05 °C and pH = 8.19). Cytochrome P450 (CYP) and urease (URE) played significant roles in biological carbon and nitrogen removal, respectively. The strain SZK-5 could resist the damages caused by oxidative stress given by crude oil and HPAM. To our knowledge, this is the first report about the biodegradation of HPAM by B. megaterium. These results suggest that strain SZK-5 might be a new auxiliary microbiological resource for the biodegradation of HPAM residue in wastewater and soil.

Enhanced bio-decolorization of 1-amino-4-bromoanthraquinone-2-sulfonic acid by Sphingomonas xenophaga with nutrient amendment

Bacterial decolorization of anthraquinone dye intermediates is a slow process under aerobic conditions. To speed up the process, in the present study, effects of various nutrients on 1-amino-4-bromoanthraquinone-2-sulfonic acid (ABAS) decolorization by Sphingomonas xenophaga QYY were investigated. The results showed that peptone, yeast extract and casamino acid amendments promoted ABAS bio-decolorization. In particular, the addition of peptone and casamino acids could improve the decolorization activity of strain QYY. Further experiments showed that l-proline had a more significant accelerating effect on ABAS decolorization compared with other amino acids. l-Proline not only supported cell growth, but also significantly increased the decolorization activity of strain QYY. Membrane proteins of strain QYY exhibited ABAS decolorization activities in the presence of l-proline or reduced nicotinamide adenine dinucleotide, while this behavior was not observed in the presence of other amino acids. Moreover, the positive correlation between l-proline concentration and the decolorization activity of membrane proteins was observed, indicating that l-proline plays an important role in ABAS decolorization. The above findings provide us not only a novel insight into bacterial ABAS decolorization, but also an l-proline-supplemented bioaugmentation strategy for enhancing ABAS bio-decolorization.

Characterization of a novel Rieske-type alkane monooxygenase system in Pusillimonas sp. strain T7-7

The cold-tolerant bacterium Pusillimonas sp. strain T7-7 is able to utilize diesel oils (C5 to C30 alkanes) as a sole carbon and energy source. In the present study, bioinformatics, proteomics, and real-time reverse transcriptase PCR approaches were used to identify the alkane hydroxylation system present in this bacterium. This system is composed of a Rieske-type monooxygenase, a ferredoxin, and an NADH-dependent reductase. The function of the monooxygenase, which consists of one large (46.711 kDa) and one small (15.355 kDa) subunit, was further studied using in vitro biochemical analysis and in vivo heterologous functional complementation tests. The purified large subunit of the monooxygenase was able to oxidize alkanes ranging from pentane (C5) to tetracosane (C24) using NADH as a cofactor, with greatest activity on the C15 substrate. The large subunit also showed activity on several alkane derivatives, including nitromethane and methane sulfonic acid, but it did not act on any aromatic hydrocarbons. The optimal reaction condition of the large subunit is pH 7.5 at 30°C. Fe(2+) can enhance the activity of the enzyme evidently. This is the first time that an alkane monooxygenase system belonging to the Rieske non-heme iron oxygenase family has been identified in a bacterium.

Metagenomic analysis reveals the prevalence of biodegradation genes for organic pollutants in activated sludge

The abundance, diversity, and distribution of biodegradation genes (BDGs) and phenol degradation genes (PDGs) in activated sludge (AS) from two wastewater treatment plants (WWTPs) at different sampling times were assessed by metagenomic analysis using a total of 15 datasets derived from Illumina high-throughput sequencing and BLAST comparisons to BDGs and PDGs databases. The results showed that the abundance (0.015-0.030%) and diversity of BDGs in AS varied with the WWTP and the sampling times. The p450 and pmo genes were the most abundant genes in the BDGs and PDGs subgroups, respectively. MG-RAST analysis revealed that 87 detected bacterial genera potentially capable of degrading pollutants were mostly affiliated with Proteobacteria (59.8%), Bacteroidetes (17.2%), and Actinobacteria (9.2%). Mycobacterium, belonging to Actinobacteria, was found to be the most abundant genus (23.4%). This method could be used to monitor an AS's biodegradation ability for organic pollutants and to evaluate its wastewater treatment efficiency.

Integrated perspective for effective bioremediation

Identification of factors which can influence the natural attenuation process with available microbial genetic capacities can support the bioremediation which has been viewed as the safest procedure to combat with anthropogenic compounds in ecosystems. With the advent of molecular techniques, assimilatory capacity of an ecosystem can be defined with changing community dynamics, and if required, the essential genetic potential can be met through bioaugmentation. At the same time, intensification of microbial processes with nutrient balancing, expressing and enhancing the degradative capacities, could reduce the time frame of restoration of the ecosystem. The new concept of ecosystems biology has added greatly to conceptualize the networking of the evolving microbiota of the niche that helps in effective application of bioremediation tools to manage pollutants as additional carbon source.