Biodegradation of polycyclic aromatic hydrocarbons by a halotolerant bacterial strain Ochrobactrum sp. VA1

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.

Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments

Anthropogenic activities and industrial effluents are the major sources of petroleum hydrocarbon contamination in different environments. Microbe-based remediation techniques are known to be effective, inexpensive, and environmentally safe. In this review, the metabolic-target-specific pathway engineering processes used for improving the bioremediation of hydrocarbon-contaminated environments have been described. The microbiomes are characterised using environmental genomics approaches that can provide a means to determine the unique structural, functional, and metabolic pathways used by the microbial community for the degradation of contaminants. The bacterial metabolism of aromatic hydrocarbons has been explained via peripheral pathways by the catabolic actions of enzymes, such as dehydrogenases, hydrolases, oxygenases, and isomerases. We proposed that by using microbiome engineering techniques, specific pathways in an environment can be detected and manipulated as targets. Using the combination of metabolic engineering with synthetic biology, systemic biology, and evolutionary engineering approaches, highly efficient microbial strains may be utilised to facilitate the target-dependent bioprocessing and degradation of petroleum hydrocarbons. Moreover, the use of CRISPR-cas and genetic engineering methods for editing metabolic genes and modifying degradation pathways leads to the selection of recombinants that have improved degradation abilities. The idea of growing metabolically engineered microbial communities, which play a crucial role in breaking down a range of pollutants, has also been explained. However, the limitations of the in-situ implementation of genetically modified organisms pose a challenge that needs to be addressed in future research.

Benzo[A]Pyrene Biodegradation by Multiple and Individual Mesophilic Bacteria under Axenic Conditions and in Soil Samples

To date, only a handful of bacterial strains that can independently degrade and utilize benzo[a]pyrene (BaP) as the sole carbon source has been isolated and characterized. Here, three new bacterial strains-JBZ1A, JBZ2B, and JBZ5E-were isolated from contaminated soil and, using 16S rRNA sequencing, were identified as Brad rhizobium japonicum, Micrococcus luteus, and Bacillus cereus, respectively. The growth ability of each individual strain and a consortium of all strains in the presence of BaP (4-400 µmol·L^-1, pH 7, 37 °C) was identified by the doubling time (dt). The results illustrate that dt decreased with increasing BaP concentrations for individual strains and the consortium. The optimum growth conditions of the consortium were 37 °C, 0.5% NaCl (w/v), and pH 7. Under these conditions, the degradation rate was 1.06 µmol·L^-1·day^-1, whereas that of individual strains ranged from 0.9 to 0.38 µmol·L^-1·day^-1. B. cereus had the strongest contribution to the consortium's activity, with a degradation rate of 0.9 µmol·L^-1·day^-1. The consortium could also remove BaP spiked with soil but at a lower rate (0.01 µmol L^-1.day^-1). High-performance liquid chromatography-high-resolution tandem mass spectrometry permitted the detection of the metabolites of these strains, and a biodegradation pathway is proposed.

Degradation of phenanthrene by consortium 5H under hypersaline conditions

PAHs have been widely detected to accumulate in saline and hypersaline environments. Moderately halophilic microbes are considered the most suitable player for the elimination of PAHs in such environments. In this study, consortium 5H was enriched under 5% salinity and completely degraded phenanthrene in 5 days. By high-throughput sequencing, consortium 5H was identified as being mainly composed of Methylophaga, Marinobacter and Thalassospira. Combined with the investigation of intermediates and enzymatic activities, the degradation pathway of consortium 5H on phenanthrene was proposed. Consortium 5H was identified as having the ability to tolerate a wide range of salinities (1%-10%) and initial PAH concentrations (50 mg/L to 400 mg/L). It was also able to function under neutral to weak alkaline conditions (pH from 6 to 9) and the phytotoxicity of the produced intermediates showed no significant difference with distilled water. Furthermore, the metagenome of consortium 5H was measured and analyzed, which showed a great abundance of catabolic genes contained in consortium 5H. This study expanded the knowledge of PAH-degradation under hypersaline environments and consortium 5H was proposed to have good potential for the elimination of PAH pollution in saline/hypersaline environments.

Investigating the effect of nanoparticle on phenanthrene biodegradation by Labedella gwakjiensis strain KDI

Polycyclic aromatic hydrocarbons (PAHs), as persistent organic contaminants, are a major source of concern due to their toxic effect on ecosystems and human health. This study attempted to isolate halotolerant PAHs degrading bacteria from saline oil-contaminated soils. Among the isolates, strain KDI with the highest 16S rRNA gene sequence similarity to Labedella gwakjiensis was able to reduce surface tension (ST) from 65.42 to 26.60 mN m^-1 and increase the emulsification index to 81.04%, as a result of significant biosurfactant production. Response Surface Methodology (RSM) analysis was applied to optimize the factors, i.e. PAHs concentration and NaCl concentration as well as to determine the effect of these important variables on PAHs biodegradation. The Carbon Quantum Dots. Iron Oxide (CQDs.Fe₃O₄) nanoparticles were characterized by several popular analytical techniques, after which the effect of CQD.Fe₃O₄ nanoparticles on biodegradation was examined. PAHs biodegradation rate and efficiency of strain KDI to degrade PHE in the presence of CQD.Fe₃O₄ nanoparticles was analyzed by GC. According to the results during biodegradation both the concentration of PAHs and the amount of NaCl were effective. The biodegradation rate significantly increased in the presence of CQD.Fe₃O₄. The highest biodegradation of PHE occurred in the presence of 0.5 g/L of CQD.Fe₃O₄ which was 63.63% and 81.77% after 48 and 72 h of incubation. To the best of our knowledge, this is the first report on optimization of PAHs concentration and salinity by RSM and nanobioremediation of PHE using a bacterial strain in the presence of CQD.Fe₃O₄ nanoparticles.

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.

Heavy metals and antibiotics resistance of bacteria isolated from Marchica lagoon: biodegradation of anthracene on submerged aerated fixed bed reactor

Heavy metals resistant and polyaromatic hydrocarbon (PAH)-degrading bacteria isolated from Marchica lagoon. Six isolates, Pseudomonas putida, Orchobactrum antropi, Staphylococus epidermidis, Brevundimonas diminuta, Serratia ficaria and Bacillus anthracis were characterized on the basis of biochemical and 16S rDNA. The strains that showed high resistance to heavy metals were also studied for their antibiotics resistance and growth kinetics. The minimal inhibitory concentrations (MIC) of metals at variant concentrations (10-38 mM) were determined in liquid and solid medium. Strains were showed an extreme resistance against metals with the MIC values of Cu (9 mM), Cd (6.25 mM), Cr (2.5 mM), Ag (0,625), and Hg (0,156). Furthermore, growth rates were decreased in the presence of metals (compared to the control). The anthracene elimination from synthetic wastewater was determined in a submerged aerobic fixed-film reactor. Optimal conditions for bacterium growth and biodegradation of anthracene are determined as: temperature of 37 °C, pH 7, and initial anthracene concentration of 20 mg/l. It emerged that at anthracene concentrations 5-40 mg/l, COD removal efficiency were 84.62%; 90.62%; 91.36% and 71.4% respectively.

Current perspective of innovative strategies for bioremediation of organic pollutants from wastewater

Organic contaminants in water are a growing environmental threat to sustainable development, with detrimental effects on the biosphere. In recent years, researchers have increasingly focused their attention on the area of bioremediation as an important tool to eliminate harmful pollutants from the environment. This review examines the application of bioremediation technologies to the removal of organic pollutants, with an emphasis on hydrocarbons and textile dyes. It applies a descriptive bibliometric analysis to study statistical practicality-vs-applicability of bioremediation of emerging organic pollutants. The paper identifies efficient pathways for bioremediation of different types of organic pollutants and outlines the potential for an eco-friendly and economical approach for the biological remediation of micropollutants by microalgae. Facts and figures on various hazardous pollutants, constraints in their current removal from water at an industrial level, and promising future solutions are carefully presented here.

Characterization of lipopeptide biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis: The role of biosurfactant in carbazole solubilisation

AIM

Characterization of biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis and proteomic analysis of intracellular proteins of bacterium while growing on glucose and carbazole medium.

METHODS AND RESULTS

The bacterium R. cervicalis was isolated from a soil sample contaminated with crude petroleum oil. PCR amplification ascertained the existence of some hydrocarbon-degrading catabolic genes (alkB and PAH-RHDα, C12O, and C23O) in the bacterial genome. GC-MS and RP-HPLC analyses demonstrated 62% and 60% carbazole degradation, respectively, by R. cervicalis 144 h post-incubation at 37℃ and pH 6.5. Due to the paucity of protein databases, expressions of only 29 and 14 intracellular proteins were explicitly recognized and quantitated by mass spectrometry analysis when R. cervicalis was grown in carbazole and glucose medium, respectively. FTIR, NMR and HR-MS/MS analyses demonstrated the lipopeptide nature of the purified biosurfactant produced by R. cervicalis. The biosurfactant is also presumed to assist in the solubilization of carbazole.

CONCLUSION

The isolated R. cervicalis strain is a potential candidate for the bioremediation of carbazole in petroleum-oil-contaminated sites.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report of the promising R. cervicalis strain proficient in carbazole biodegradation.

Corksorb Enhances Alkane Degradation by Hydrocarbonoclastic Bacteria

Biosorbent materials are effective in the removal of spilled oil from water, but their effect on hydrocarbonoclastic bacteria is not known. Here, we show that corksorb, a cork-based biosorbent, enhances growth and alkane degradation by Rhodococcus opacus B4 (Ro) and Alcanivorax borkumensis SK2 (Ab). Ro and Ab degraded 96 ± 1% and 72 ± 2%, respectively, of a mixture of n-alkanes (2 g L-1) in the presence of corksorb. These values represent an increase of 6 and 24%, respectively, relative to the assays without corksorb. The biosorbent also increased the growth of Ab by 51%. However, no significant changes were detected in the expression of genes involved in alkane uptake and degradation in the presence of corksorb relative to the control without the biosorbent. Nevertheless, transcriptomics analysis revealed an increased expression of rRNA and tRNA coding genes, which confirms the higher metabolic activity of Ab in the presence of corksorb. The effect of corksorb is not related to the release of soluble stimulating compounds, but rather to the presence of the biosorbent, which was shown to be essential. Indeed, scanning electron microscopy images and downregulation of pili formation coding genes, which are involved in cell mobility, suggest that cell attachment on corksorb is a determinant for the improved activity. Furthermore, the existence of native alkane-degrading bacteria in corksorb was revealed, which may assist in situ bioremediation. Hence, the use of corksorb in marine oil spills may induce a combined effect of sorption and stimulated biodegradation, with high potential for enhancing in situ bioremediation processes.

Bacterial Enrichment Cultures Biotransform the Mycotoxin Deoxynivalenol into a Novel Metabolite Toxic to Plant and Porcine Cells

The mycotoxin deoxynivalenol (DON), produced in wheat, barley and maize by Fusarium graminearum and Fusarium culmorum, is threatening the health of humans and animals. With its worldwide high incidence in food and feed, mitigation strategies are needed to detoxify DON, maintaining the nutritional value and palatability of decontaminated commodities. A promising technique is biological degradation, where microorganisms are used to biotransform mycotoxins into less toxic metabolites. In this study, bacterial enrichment cultures were screened for their DON detoxification potential, where DON and its potential derivatives were monitored. The residual phytotoxicity was determined through a bioassay using the aquatic plant Lemna minor L. Two bacterial enrichment cultures were found to biotransform DON into a still highly toxic metabolite for plants. Furthermore, a cytotoxic effect was observed on the cellular viability of intestinal porcine epithelial cells. Through liquid chromatography high-resolution mass spectrometry analysis, an unknown compound was detected, and tentatively characterized with a molecular weight of 30.0 Da (i.e., CH₂O) higher than DON. Metabarcoding of the subsequently enriched bacterial communities revealed a shift towards the genera Sphingopyxis, Pseudoxanthomonas, Ochrobactrum and Pseudarthrobacter. This work describes the discovery of a novel bacterial DON-derived metabolite, toxic to plant and porcine cells.

Haloarchaea, excellent candidates for removing pollutants from hypersaline wastewater

Hypersaline wastewater is difficult to treat due to the inhibition of salt stress on microbes' viability and metabolic capabilities. Haloarchaea, native microorganisms that thrive in hypersaline habitats, overcome this key obstacle naturally. This review provides a comprehensive overview of the metabolic versatility of Haloarchaea in hypersaline wastewater treatment, including carbon, nitrogen, phosphorus, sulfur, and heavy metal metabolism. It also analyzes factors affecting pollutant removal and addresses metabolic mechanisms. Additionally, haloarchaea microbial characteristics and strategies to cope with salt stress are highlighted. Finally, the biotechnological potential of biomolecules produced from haloarchaea is investigated. To get better insight into the potential of haloarchaea, a deeper investigation of basic metabolism and more in-depth studies of their genomics and applications in actual wastewater are also necessary.

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.

Di-n-octyl phthalate degradation by a halotolerant bacterial consortium LF and its application in soil

Di-n-octyl phthalate (DOP), a plasticizer used in many different industrial products, is a frequently observed pollutant in the environment. Biodegradation by microorganisms is considered to be a realistic choice for the remediation of DOP contamination. In the present research, the halotolerant bacterial consortium (LF) enriched in our previous research was used to degrade DOP. It was found that the optimal conditions for LF to degrade DOP was temperature 30^oC, pH 6.0, inoculum size >5%, and salt content <3%. LF could degrade a high concentration of DOP (2000 mg/L) with the removal efficiency of 96.33%. Substrate inhibition analyses indicated that the inhibition constant, maximum specific degradation rate and half-saturation constant were 2544.6 mg/L, 0.7 d^-1 and 59.1 mg/L, respectively. Based on the analysis of the gas chromatography-mass spectrometry (GC-MS), the biodegradation pathway for DOP by LF was proposed. Furthermore, LF could degrade DOP in soil (100 mg/kg) with the highest removal efficiency of 89.3%. This study is the first report on DOP biodegradation by bacterial consortium. These results suggest that LF can be used to remediate DOP-contaminated environment.

Chemo-metric engineering designs for deciphering the biodegradation of polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are non-polar organic compounds that are omnipresent in the environment and released due to anthropogenic activities through emissions and discharges. PAHs, being xenobiotic and exerts health impacts, thus they attract serious concern by the environmentalists. The stringent regulations and the need of sustainable development urges the hunt for a technically feasible and cost-effective wastewater treatment. Although the conventional physico-chemical treatment are widely preferred, they cause secondary pollution problems and demand subsequent treatment options. This comprehensive review intends to address the (a) different PAHs and their associated toxicity, (b) the remedial strategies, particularly biodegradation. The biological wastewater treatment techniques that involve microbial systems are highly influenced by the different physio-chemical and environmental parameters. Therefore, suitable optimization techniques are prerequisite for effective functioning of the biological treatment that sustains judiciously and interpreted in a lesser time. Here we have aimed to discuss (a) different chemo-metric tools involved in the design of experiments (DoE), (b) design equations and models, (c) tools for evaluating the model's adequacy and (d) plots for graphically interpreting the chemo-metric designs. However, to best of our knowledge, this is a first review to discuss the PAHs biodegradation that are tailored by chemo-metric designs. The associated challenges, available opportunities and techno-economic aspects of PAHs degradation using chemo-metric engineering designs are explained. Additionally, the review highlights how well these DoE tools can be suited for the sustainable socio-industrial sectors. Concomitantly, the futuristic scope and prospects to undertake new areas of research exploration were emphasized to unravel the least explored chemo-metric designs.

Effects of environmental factors and coexisting substrates on PAH degradation and transcriptomic responses of the defined bacterial consortium OPK

The present study showed that syntrophic associations in a defined bacterial consortium, named OPK, containing Mycolicibacterium strains PO1 and PO2, Novosphingobium pentaromativorans PY1 and Bacillus subtilis FW1, led to effective pyrene degradation over a wide range of pH values, temperatures and salinities, as well as in the presence of a second polycyclic aromatic hydrocarbon (PAH). Anthracene, phenanthrene or fluorene facilitated complete pyrene degradation within 9 days, while fluoranthene delayed pyrene degradation. Interestingly, fluoranthene degradation was enhanced in the presence of pyrene. Transcriptome analysis confirmed that Mycolicibacterium strains were the key PAH-degraders during the cometabolism of pyrene and fluoranthene. Notably, the transcription of genes encoding pyrene-degrading enzymes were shown to be important for enhanced fluoranthene degradation. NidAB was the major initial oxygenase involved in the degradation of pyrene and fluoranthene mixture. Other functional genes encoding ribosomal proteins, an iron transporter, ABC transporters and stress response proteins were induced in strains PO1 and PO2. Furthermore, an intermediate pyrene-degrading Novosphingobium strain contributed to protocatechuate degradation. The results demonstrated that synergistic interactions among the bacterial members (PO1, PO2 and PY1) of the consortium OPK promoted the simultaneous degradation of two high molecular weight (HMW) PAHs.

Occurrence and biodegradation of hydrocarbons at high salinities

Hypersaline environments are found around the world, above and below ground, and many are exposed to hydrocarbons on a continuous or a frequent basis. Some surface hypersaline environments are exposed to hydrocarbons because they have active petroleum seeps while others are exposed because of oil exploration and production, or nearby human activities. Many oil reservoirs overlie highly saline connate water, and some national oil reserves are stored in salt caverns. Surface hypersaline ecosystems contain consortia of halophilic and halotolerant microorganisms that decompose organic compounds including hydrocarbons, and subterranean ones are likely to contain the same. However, the rates and extents of hydrocarbon biodegradation are poorly understood in such ecosystems. Here we describe hypersaline environments potentially or likely to become contaminated with hydrocarbons, including perennial and transient environments above and below ground, and discuss what is known about the microbes degrading hydrocarbons and the extent of their activities. We also discuss what limits the microbial hydrocarbon degradation in hypersaline environments and whether there are opportunities for inhibiting (oil storage) or stimulating (oil spills) such biodegradation as the situation requires.

Degradation of benzo[a]pyrene by halophilic bacterial strain Staphylococcus haemoliticus strain 10SBZ1A

The exploitation of petroleum oil generates a considerable amount of “produced water or petroleum waste effluent (PWE)” that is contaminated with polycyclic aromatic hydrocarbons (PAHs), including Benzo[a]pyrene (BaP). PWE is characterised by its high salinity, which can be as high as 30% NaCl, thus the exploitation of biodegradation to remove PAHs necessitates the use of active halophilic microbes. The strain 10SBZ1A was isolated from oil contaminated soils, by enrichment experiment in medium containing 10% NaCl (w/v). Homology analyses of 16S rRNA sequences identified 10SBZ1A as a Staphylococcus haemoliticus species, based on 99.99% homology (NCBI, accession number GI: MN388897). The strain could grow in the presence of 4–200 μmol l^-1 of BaP as the sole source of carbon, with a doubling time of 17–42 h. This strain optimum conditions for growth were 37 ^oC, 10% NaCl (w/v) and pH 7, and under these conditions, it degraded BaP at a rate of 0.8 μmol l^-1 per day. The strain 10SBZ1A actively degraded PAHs of lower molecular weights than that of BaP, including pyrene, phenanthrene, anthracene. This strain was also capable of removing 80% of BaP in the context of soil spiked with BaP (10 μmol l^-1 in 100 g of soil) within 30 days. Finally, a metabolic pathway of BaP was proposed, based on the identified metabolites using liquid chromatography-high resolution tandem mass spectrometry. To the best of our knowledge, this is the first report of a halophilic BaP degrading bacterial strain at salinity > 5% NaCl.

Isolation and Identification of Organics-Degrading Bacteria From Gas-to-Liquid Process Water

The gas-to-liquid (GTL) process generates considerable amounts of wastewater that are highly acidic and characterized by its high chemical oxygen demand (COD) content, due to the presence of several organic pollutants, such as alcohols, ketones, aldehydes, and fatty acids. The presence of these organics in the process water may lead to adverse effect on the environment and aquatic life. Thus, it is necessary to reduce the COD content of GTL process water to an acceptable limit before discharging or reusing the treated water. Due to several advantages, biological treatment is often utilized as the main step in GTL process water treatment plants. In order to have a successful biotreatment process, it is required to choose effective and suitable bacterial strains that have the ability to degrade the organic pollutants in GTL process water. In this work, bacterial strains were isolated from the GTL process water, identified by 16S rRNA gene sequencing and then used in the biodegradation process. The detailed identification of the strains confirmed the presence of three organics-degrading bacteria identified as Alcaligenes faecalis, Stenotrophomonas sp., and Ochrobactrum sp. Furthermore, biodegradation experiments were carried out and confirmed that the pure culture as well as the mixed culture consortium of the bacterial strains has the ability to reduce the organic pollutants in GTL process water. However, the growth rate and biodegradation efficiency depend on the type of strains and the initial COD content. Indeed, the removal percentage and growth rate were enhanced after 7 days for all cultures and resulted in COD reduction up to 60%. Moreover, the mixed culture of bacterial strains can tolerate and treat GTL process water with a variety of ranges of COD contents.

Bacterial community characterization of Batura Glacier in the Karakoram Range of Pakistan

High-altitude cold habitats of the Karakoram are rarely explored for their bacterial community characterization and metabolite productions. In the present study, bacterial communities in ice, water, and sediments of Batura Glacier were investigated using culture-dependent and culture-independent methods. Twenty-seven cold-adapted bacterial strains (mostly psychrotrophic) were isolated using R2A, Tryptic Soy Agar (TSA), and Luria-Bertani (LB) media, at 4 °C and 15 °C. Most of the isolates exhibited growth at a wide range of temperature (4-35 °C), pH (5-12), and salinity (1-6%). Among the bacterial isolates, 52% were identified as Gram-positive and the remaining 48% represented as Gram-negative. The results of phylogenetic analysis indicated that all the culturable bacteria belonged to 3 major phylogenetic groups, i.e., Actinobacteria (48%), Bacteroidetes (26%), and Proteobacteria (22%), while Flavobacterium (26%), Arthrobacter (22%), and Pseudomonas (19%) were represented as the dominant genera. Similarly, Illumina amplicon sequencing of 16S rRNA genes after PCR amplification of DNA from the whole community revealed dominance of the same phylogenetic groups, Proteobacteria, Actinobacteria, and Bacteroidetes, while Arthrobacter, Mycoplana, Ochrobactrum, Kaistobacter, Janthinobacterium, and Flavobacterium were found as the dominant genera. Among the culturable isolates, 70% demonstrated activity for cellulases, 48% lipases, 41% proteases, 41% DNases, and only 7% for amylases. Most of the glacial isolates demonstrated antimicrobial activity against other microorganisms including the multiple-drug-resistant strains of Candida albicans, Klebsiella pneumoniae, Acinetobacter sp., and Bacillus sp. 67% of Gram-negative while 46% of Gram-positive glacial bacteria were resistant to trimethoprim/sulfamethoxazole. Resistance against methicillin and vancomycin among the Gram-positive isolates was 23% and 15%, respectively, while 11% of the Gram-negative isolates exhibited resistance against both colistin sulfate and nalidixic acid.

Current Status of and Future Perspectives in Bacterial Degradation of Benzo[a]pyrene

Benzo[a]pyrene (BaP) is one the main pollutants belonging to the high-molecular-weight PAHs (HMW-PAHs) class and its degradation by microorganisms remains an important strategy for its removal from the environment. Extensive studies have been carried out on the isolation and characterisation of microorganisms that can actively degrade low-molecular-weight PAHs (LMW-PAHs), and to a certain extent, the HMW-PAH pyrene. However, so far, limited work has been carried out on BaP biodegradation. BaP consists of five fused aromatic rings, which confers this compound a high chemical stability, rendering it less amenable to biodegradation. The current review summarizes the emerging reports on BaP biodegradation. More specifically, work carried out on BaP bacterial degradation and current knowledge gaps that limit our understanding of BaP degradation are highlighted. Moreover, new avenues of research on BaP degradation are proposed, specifically in the context of the development of "omics" approaches.

Multispecies Diesel Fuel Biodegradation and Niche Formation Are Ignited by Pioneer Hydrocarbon-Utilizing Proteobacteria in a Soil Bacterial Consortium

A soil bacterial consortium that was grown on diesel fuel and consisted of more than 10 members from different genera was maintained through repetitive subculturing and was utilized as a practical model to investigate a bacterial community that was continuously exposed to petroleum hydrocarbons. Through metagenomics analyses, consortium member isolation, growth assays, and metabolite identification which supported the linkage of genomic data and functionality, two pioneering genera, Sphingobium and Pseudomonas, whose catabolic capabilities were differentiated, were found to be responsible for the creation of specialized ecological niches that were apparently occupied by other bacterial members for survival within the consortium. Coexisting genera Achromobacter and Cupriavidus maintained their existence in the consortium through metabolic dependencies by utilizing hydrocarbon biotransformation products of pioneer metabolism, which was confirmed through growth tests and identification of biotransformation products of the isolated strains. Pioneering Sphingobium and Pseudomonas spp. utilized relatively water-insoluble hydrocarbon parent compounds and facilitated the development of a consortium community structure that resulted in the creation of niches in response to diesel fuel exposure which were created through the production of more-water-soluble biotransformation products available to cocolonizers. That these and other organisms were still present in the consortium after multiple transfers spanning 15 years provided evidence for these ecological niches. Member survival through occupation of these niches led to robustness of each group within the multispecies bacterial community. Overall, these results contribute to our understanding of the complex ecological relationships that may evolve during prokaryotic hydrocarbon pollutant biodegradation.IMPORTANCE There are few metagenome studies that have explored soil consortia maintained on a complex hydrocarbon substrate after the community interrelationships were formed. A soil bacterial consortium maintained on diesel fuel was utilized as a practical model to investigate bacterial community relationships through metagenomics analyses, consortium member isolation, growth assays, and metabolite identification, which supported the linkage of genomic data and functionality. Two pioneering genera were responsible for the biodegradation of aromatics and alkanes by initiating biotransformation and thereby created specialized niches that were populated by other members. A model that represents these relationships was constructed, which contributes to our understanding of the complex ecological relationships that evolve during prokaryotic hydrocarbon pollutant biodegradation.

Whole genome characterization and phenanthrene catabolic pathway of a biofilm forming marine bacterium Pseudomonas aeruginosa PFL-P1

Pseudomonas aeruginosa is a small rod shaped Gram-negative bacterium of Gammaproteobacteria class known for its metabolic versatility. P. aeruginosa PFL-P1 was isolated from Polycyclic Aromatic Hydrocarbons (PAHs) contaminated site of Paradip Port, Odisha Coast, India. The strain showed excellent biofilm formation and could retain its ability to form biofilm grown with different PAHs in monoculture as well as co-cultures. To explore mechanistic insights of PAHs metabolism, the whole genome of the strain was sequenced. Next generation sequencing unfolded a genome size of 6,333,060 bp encoding 5857 CDSs. Gene ontology distribution assigned to a total of 2862 genes, wherein 2235 genes were allocated to biological process, 1549 genes to cellular component and 2339 genes to molecular function. A total of 318 horizontally transferred genes were identified when the genome was compared with the reference genomes of P. aeruginosa PAO1 and P. aeruginosa DSM 50071. Further comparison of P. aeruginosa PFL-P1 genome with P. putida containing TOL plasmids revealed similarities in the meta cleavage pathway employed for degradation of aromatic compounds like xylene and toluene. Gene annotation and pathway analysis unveiled 145 genes involved in xenobiotic biodegradation and metabolism. The biofilm cultures of P. aeruginosa PFL-P1 could degrade ~74% phenanthrene within 120 h while degradation increased up to ~76% in co-culture condition. GC-MS analysis indicated presence of diverse metabolites indicating the involvement of multiple pathways for one of the PAHs (phenanthrene) degradation. The strain also possesses the genetic machinery to utilize diverse toxic aromatic compounds such as naphthalene, benzoate, aminobenzoate, fluorobenzoate, toluene, xylene, styrene, atrazine, caprolactam etc. Common catabolic gene clusters such as benABCD, xylXYZ and catAB were observed within the genome of P. aeruginosa PFL-P1 which play key roles in the degradation of various toxic aromatic compounds.

Formulation of Bio-Based Washing Agent and Its Application for Removal of Petroleum Hydrocarbons From Drill Cuttings Before Bioremediation

Drill cuttings from petroleum exploration and production sites can cause diverse environmental problems. Total petroleum hydrocarbons (TPHs) are a major pollutant from the use of polyolefin-based mud. As an alternative to incineration, this study investigated the application of surfactant-enhanced washing technology prior to bioremediation. The washing step was necessary because the initial TPH concentrations were quite high at approximately 15% (w/w). Washing agents were formulated by varying the concentration of lipopeptide biosurfactant (in foamate or cell-free broth), Dehydol LS7TH (fatty alcohol ethoxylate 7EO, oleochemical surfactant) and butanol (as a lipophilic linker) at different salinities. The most efficient formula produced a Winsor Type I microemulsion (oil-in-water microemulsion) with polyolefin and contained only 20% (v/v) foamate and 2% (v/v) Dehydol LS7TH in water. Due to the synergistic behavior between the anionic lipopeptides and non-ionic Dehydol LS7TH, the formula efficiently removed 92% of the TPHs from the drill cuttings when applied in a jar test. To reduce the cost, the concentrations of each surfactant should be reduced; thus, the formula was optimized by the simplex lattice mixture design. In addition, cell-free broth, at a pH of 10, containing 3.0 g/L lipopeptides was applied instead of foamate because it was easy to prepare. The optimized formula removed 81.2% of the TPHs and contained 72.0% cell-free broth and 1.4% Dehydol LS7TH in water. A 20-kg soil washing system was later tested where the petroleum removal efficiency decreased to 70.7% due to polyolefin redeposition during separation of the washing solution. The remaining TPHs (4.5%) in the washed drilled cuttings were further degraded by a mixture of Marinobacter salsuginis RK5, Microbacterium saccharophilum RK15 and Gordonia amicalis JC11. To promote TPH biodegradation, biochar and fertilizer were applied along with bacterial consortia in a microcosm experiment. After 49-day incubation, the TPHs were reduced to 0.9% by both physical and biological mechanisms, while the TPHs in the unamended samples remained unaffected. With the use of the formulated bio-based washing agent and bioremediation approach, the on-site treatment of drill cuttings could be conducted with an acceptable cost and low environmental impacts.

Lack of evidence for the role of gut microbiota in PAH biodegradation by the polychaete Capitella teleta

Capitella teleta is a marine sediment-feeding polychaete known to degrade various polycyclic aromatic hydrocarbons (PAHs) and reported to possess genes involved in PAH transformation, such as those in the P450 cytochrome superfamily. Previous research focusing on biodegradation of PAHs by C. teleta demonstrated that these worms are effective biodegraders, but overlooked the possible role of its gut microbiota in facilitating PAH metabolism. Recently, C. teleta's microbiome was characterized and found to contain several bacterial genera known to contain PAH-degrading members, including Acinetobacter, Thalassotalea, and Achromobacter. Despite this, however, no data have thus far been presented demonstrating the role of C. teleta's gut microbiota in PAH degradation. The present study was designed to more conclusively determine the presence of PAH-degrading bacteria in worm digestive tracts and to more clearly distinguish the relative roles of worm versus gut-microbial metabolism in the removal of PAH from sediment. To do this, we manipulated marine sediment microorganisms and worm gut microbiota by autoclaving and antibiotic treatment, respectively. Our results showed that no fluoranthene degradation occurred in microcosms in the absence of worms. More importantly, there was no significant difference in fluoranthene degradation between antibiotic-treated and non-treated worms. We also found no evidence of fluoranthene degradation using resting cells of gut microbes of C. teleta, and we were unable to isolate fluoranthene-degrading bacterial strains from enrichments of polychaete gut contents, despite multiple attempts. Gut microbiota in worms treated with antibiotics recovered, through bidirectional transfer, between worms and sediment after 2 weeks of microcosm incubation, and gut microbes appear to be required for the survival and growth of C. teleta. Our results build on previous studies suggesting that C. teleta itself is primarily responsible for the metabolism of fluoranthene in ingested sediment. We hypothesize that C. teleta's core microbiota, which includes members of Propionibacterium as the most abundant genus, likely aid worms in obtaining key nutrients (e.g., vitamins) from its sediment diet.

Quantification of Naphthalene Dioxygenase (NahAC) and Catechol Dioxygenase (C23O) Catabolic Genes Produced by Phenanthrene-Degrading Pseudomonas fluorescens AH-40

Background

Petroleum polycyclic aromatic hydrocarbons (PAHs) are known to be toxic and carcinogenic for humans and their contamination of soils and water is of great environmental concern. Identification of the key microorganisms that play a role in pollutant degradation processes is relevant to the development of optimal in situ bioremediation strategies.

Objective

Detection of the ability of Pseudomonas fluorescens AH-40 to consume phenanthrene as a sole carbon source and determining the variation in the concentration of both nahAC and C23O catabolic genes during 15 days of the incubation period.

Methods

In the current study, a bacterial strain AH-40 was isolated from crude oil polluted soil by enrichment technique in mineral basal salts (MBS) medium supplemented with phenanthrene (PAH) as a sole carbon and energy source. The isolated strain was genetically identified based on 16S rDNA sequence analysis. The degradation of PAHs by this strain was confirmed by HPLC analysis. The detection and quantification of naphthalene dioxygenase (nahAc) and catechol 2,3-dioxygenase (C23O) genes, which play a critical role during the mineralization of PAHs in the liquid bacterial culture were achieved by quantitative PCR.

Results

Strain AH-40 was identified as pseudomonas fluorescens. It degraded 97% of 150 mg phenanthrene L^-1 within 15 days, which is faster than previously reported pure cultures. The copy numbers of chromosomal encoding catabolic genes nahAc and C23O increased during the process of phenanthrene degradation.

Conclusion

nahAc and C23O genes are the main marker genes for phenanthrene degradation by strain AH-40. P. fluorescence AH-40 could be recommended for bioremediation of phenanthrene contaminated site.

Identification and Characterization of the First Virulent Phages, Including a Novel Jumbo Virus, Infecting Ochrobactrum spp

The Ochrobactrum genus consists of an extensive repertoire of biotechnologically valuable bacterial strains but also opportunistic pathogens. In our previous study, a novel strain, Ochrobactrum sp. POC9, which enhances biogas production in wastewater treatment plants (WWTPs) was identified and thoroughly characterized. Despite an insightful analysis of that bacterium, its susceptibility to bacteriophages present in WWTPs has not been evaluated. Using raw sewage sample from WWTP and applying the enrichment method, two virulent phages, vB_OspM_OC and vB_OspP_OH, which infect the POC9 strain, were isolated. These are the first virulent phages infecting Ochrobactrum spp. identified so far. Both phages were subjected to thorough functional and genomic analyses, which allowed classification of the vB_OspM_OC virus as a novel jumbo phage, with a genome size of over 227 kb. This phage encodes DNA methyltransferase, which mimics the specificity of cell cycle regulated CcrM methylase, a component of the epigenetic regulatory circuits in Alphaproteobacteria. In this study, an analysis of the overall diversity of Ochrobactrum-specific (pro)phages retrieved from databases and extracted in silico from bacterial genomes was also performed. Complex genome mining allowed us to build similarity networks to compare 281 Ochrobactrum-specific viruses. Analyses of the obtained networks revealed a high diversity of Ochrobactrum phages and their dissimilarity to the viruses infecting other bacteria.

Isolation and characterization of a newly naphthalene-degrading Halomonas pacifica, strain Cnaph3: biodegradation and biosurfactant production studies

A newly marine Halomonas pacifica strain Cnaph3 was isolated, as a naphthalene degrader and biosurfactant producer, from contaminated seawater collected in Ataya's fishing harbor, located in Kerkennah Islands, Tunisia. Chromatography flame ionization detector analysis revealed that 98.8% of naphthalene (200 mg/L) was degraded after 7 days of incubation, at 30 g/L NaCl and 37 °C. Strain Cnaph3 showed also a noticeable capacity to grow on a wide range of aliphatic, aromatic, and complex hydrocarbons. Interestingly, strain Cnaph3 showed a significant potential to produce biosurfactants in the presence of all tested substrates, particularly on glycerol (1%, v/v). Electrospray ionization analysis of the biosurfactant, designated Bios-Cnaph3, suggested a lipopeptide composition. The critical micelle concentration of Bios-Cnaph3 was about 500 mg/L. At this concentration, the surface tension of the water was reduced to 27.6 mN/m. Furthermore, Bios-Cnaph3 displayed interesting stabilities over a wide range of temperatures (4-105 °C), salinities (0-100 g/L NaCl), and pH (2.2-12.5). In addition, it showed promising capacities to remove used motor oil from contaminated soils. The biodegradation and biosurfactant-production potential of the Halomonas sp. strain Cnaph3 would present this strain as a favorite agent for bioremediation of hydrocarbon-contaminated sites under saline conditions.

Ochrobactrum teleogrylli sp. nov., a pesticide-degrading bacterium isolated from the insect Teleogryllus occipitalis living in deserted cropland

A Gram-stain-negative, non-spore-forming, motile, aerobic, rod-shaped bacteria strain, designated LCB8^T, was isolated from the insect Teleogryllus occipitalis captured from a deserted cropland in Shuangliu district, Chengdu, PR China. Phylogenetic analysis on the basis of 16S rRNA gene sequence indicated that the strain represented a member of the genus Ochrobactrum, family Brucellaceae, class Alphaproteobacteria. Ochrobactrum pecoris CCUG 60088^T (97.9 %) and Ochrobactrum haematophilum CCUG 38531^T (98.8 %) were identified as the most closely related phylogenetic neighbours of strain LCB8^T. The novel strain was able to grow at salt concentrations of 0-4.5 % (w/v), pH 5-9 and temperatures of 20-42 °C. The major quinone system was ubiquinone Q-10, the major fatty acids were C_18 : 1ω7c, C_16 : 0 and C_18 : 0. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and four undefined aminolipids. The major polyamines were putrescine and spermidine. Genome sequencing revealed a genome size of 4.76 Mbp and a DNA G+C content of 57.1 mol%. These phenotypic, genotypic and chemotaxonomic traits excellently supported the affiliation of LCB8^T to the genus Ochrobactrum. Pairwise determined whole-genome average nucleotide identity (ANI) values indicated that strain LCB8^T represents a novel species, for which we propose the name Ochrobactrum teleogrylli sp. nov. with the type strain LCB8^T (=KCTC 72031^T=CGMCC 1.13984^T).

Coupling of electricity generation and denitrification in three-phase single-chamber MFCs in high-salt conditions

High-salt conditions reduce the efficiency of electricity generation and nitrogen removal in microbial fuel cells (MFCs). In this work, we propose a three-phase single-chamber MFC (TP-MFC) by setting up a phase with immobilized cells in a conventional bipolar single-chamber MFC (common MFC). Cells from Halomonas were used as the immobilized phase, because these cells secrete the compatible solute ectoine and exhibit simultaneous nitrification and denitrification (SND). This enhanced the efficiency of SND and subsequent electricity generation under high-salt conditions. The average voltage of TP-MFC generated during the stable period in the presence of 30 g/L NaCl was 439.3 mV, which was 55.2% higher than that generated in common MFC. In addition, the N-removal rate of TP-MFC at 72 h was 63.4%, which was 38.4% higher than that of common MFC. The 16S rRNA diversity analysis showed an improved abundance of Pseudomonas, Acinetobacter, Alcaligenes, and Halomonas in TP-MFC, indicating that the ectoine secreted by immobilized Halomonas conferred substantial salt-tolerance on the electrogenic bacteria growing in a high-salt environment. This paper establishes an efficient and convenient method for improving the salt tolerance of microbial flora in MFCs, which is of great significance for the application of MFCs in high-strength wastewater treatment.

Biodegradation of phenanthrene as a model hydrocarbon: Power display of a super-hydrophobic halotolerant enriched culture derived from a saline-sodic soil

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Bacterial isolates are found to be both hydrophobe and halotolerant.

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This bacterial enriched culture degraded 87.66% of the phenanthrene after 10 days.

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The high hydrophobicity of cells is the main rationale behind phenanthrene degradation.

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Both alfalfa and barley seeds can germinate after biodegradation of phenanthrene in the contaminated soil.

In this study, after evaluating the degradation activity of enriched cultures from four crude oil-contaminated soils in mineral salt medium, the most efficient ones were selected for further studies. The chemical analysis of cell-free extract containing phenanthrene by HPLC suggested the superior enriched culture was able to degrade 87.66% of phenanthrene at the concentration of 40 mg L-1 within 10 days. This experiment was done under optimal conditions (37 °C, 10% salinity, and pH around 7 to 7.5). The 16S rRNA sequencing of isolates from this superior enriched culture indicated the highest similarity to Acidovorax delafieldii (Q-SH3), Bacillus hwajinpoensis (Q-SH12), and Bacillus rhizosphaerae (Q-SH14). After biodegradation of phenanthrene in liquid medium, the extracts were analyzed to measure barley and alfalfa germination. Results showed a lower level of toxicity to the seeds, hence this enriched culture could be used for bioremediation of saline environments contaminated by phenanthrene and other similar compounds.

Evaluation and entomopathogenicity of gut bacteria associated with dauer juveniles of Oscheius chongmingensis (Nematoda: Rhabditidae)

The nematodes of genus Oscheius are insect parasites with a potential role as biological control agents. The composition of gut microbiota and its potential assistant role in the complex pathogenic mechanism of nematodes have been poorly illustrated. In this study, the intestinal bacteria associated with dauer juveniles of the nematode Oscheius chongmingensis Tumian were classified by 16S rDNA high-throughput sequencing. The raw reads were assigned to 845 operational taxonomic units (OTUs) after quality filtering. The results showed that the genus Ochrobactrum, with a proportion of 59.82%, was the most abundant genus, followed by 7.13% Bacillus, 4.7% Albidiferax, 4.26% Acinetobacter, and 3.09% Rhodococcus. The two dominant bacteria, Ochrobactrum and Bacillus, were further isolated by culturing on NBTA and LB medium respectively, and then identified as Ochrobactrum tritici and Bacillus cereus by morphological and 16S rDNA sequence analysis. Furthermore, the entomopathogenicity of these two bacterial species was studied. The results showed that O. tritici caused 93.33% mortality within 144 hr in the 4th -instar larvae of Galleria mellonella treated with 2 × 109  CFU/ml, whereas B. cereus showed 100% mortality at a concentration of 3.3 × 107  CFU/ml within 48 hr. These findings, especially the presence of O. tritici, which had not been found in other nematode species in the genus Oscheius, indicate that the associated nematode O. chongmingensis may have particular utility as a biocontrol agent.

Influence of two polarization potentials on a bioanode microbial community isolated from a hypersaline coastal lagoon of the Yucatan peninsula, in México

In recent years, halotolerant biofilms have become a subject of interest for its application in Bioelectrochemical systems for wastewater treatment. To determine if the polarization potential affects the microbial community of a halotolerant bioanode, four bioanodes were poised at potentials of +0.34 V/SHE and - 0.16 V/SHE and the 16S rRNA gene was analyzed through a MiSeq (Ilumina) system. Oceanospirillum, Halomonas and Marinobacterium were the most predominant genus; no previous studies have reported the presence of Oceanospirillum in anodic biofilms. The fitness with the dataset for +0.34 V/SHE with a modified Butler Volmer Monod model, gives a value of K₁ was 0.0002 (2.64 A m^-2 and 38% coulombic efficiency), indicating the fastest electrochemical reaction. Whereas that -0.16 V/SHE case, the high value of K₁ (12.2 with 1.82 A m^-2 and 10% coulombic efficiency) indicated that the electron transfer was far from being reversible (Nernstian).

Co-metabolic degradation of naphthalene and pyrene by acclimated strain and competitive inhibition kinetics

A dominant strain named Ochrobactrum sp. was isolated from soils contaminated with coal tar. The batch experiments were carried out to study the co-metabolic degradation of pyrene by Ochrobactrum MB-2 with naphthalene as the main substrate and the effects of several significant parameters such as naphthalene concentration, pH and temperature on removal efficiency were explored. The results showed that Ochrobactrum MB-2 effectively degraded naphthalene and that the addition of naphthalene favored the degradation of pyrene. The maximum elimination efficiency of naphthalene (10 mg L^-1) and pyrene (1 mg L^-1) was achieved at pH 7 and 25 °C, and the corresponding values were 99 and 41%, respectively. A competitive inhibition model based on the Michaelis-Menten equation was used to characterize the inhibitory effect of pyrene on naphthalene degradation. The values of the half-saturation coefficient for naphthalene (K_S) and dissociation constant of enzyme-inhibitor complex (K_C) were determined to be 4.93 and 1.38 mg L^-1, respectively.

Ochrobactrum cytisi IPA7.2 promotes growth of potato microplants and is resistant to abiotic stress

Bacteria in natural associations with agricultural crops are promising for use in the improvement of clonal micropropagation of plants. We clarified the taxonomic position of Ochrobactrum cytisi strain IPA7.2 and investigated its tolerance for salinity, high temperature, and glyphosate pollution. We also tested the strain's potential to promote the growth of potato (Solanum tuberosum L.) microplants. Using the IPA7.2 draft genome (no. NZ_MOEC00000000), we searched for housekeeping genes and also for the target genes encoding glyphosate tolerance and plant-growth-promoting ability. A multilocus sequence analysis of the gap, rpoB, dnaK, trpE, aroC, and recA housekeeping genes led us to identify isolate IPA7.2 as O. cytisi. The strain tolerated temperatures up to 50 °C and NaCl concentrations up to 3-4%, and it produced 8 µg ml-1 of indole-3-acetic acid. It also tolerated 6 mM glyphosate owing to the presence of type II 5-enolpyruvylshikimate-3-phosphate synthase. Finally, it was able to colonize the roots and tissues of potato microplants, an ability preserved by several generations after subculturing. We identified the development phase of potato microplants that was optimal for inoculation with O. cytisi IPA7.2. Inoculation of in vitro-grown 15-day-old microplants increased the mitotic index of root meristem cells (by 50%), the length of shoots (by 34%), the number of leaves (by 7%), and the number of roots (by 16%). Under ex vitro conditions, the inoculated plants had a greater leaf area (by 77%) and greater shoot and root dry weight (by 84 and 61%, respectively) than did the control plants. We recommend O. cytisi IPA 7.2 for use in the growing of potato microplants to improve the production of elite seed material.

Cave Drip Water-Related Samples as a Natural Environment for Aromatic Hydrocarbon-Degrading Bacteria

Restricted contact with the external environment has allowed the development of microbial communities adapted to the oligotrophy of caves. However, nutrients can be transported to caves by drip water and affect the microbial communities inside the cave. To evaluate the influence of aromatic compounds carried by drip water on the microbial community, two limestone caves were selected in Brazil. Drip-water-saturated and unsaturated sediment, and dripping water itself, were collected from each cave and bacterial 16S rDNA amplicon sequencing and denaturing gradient gel electrophoresis (DGGE) of naphthalene dioxygenase (ndo) genes were performed. Energy-dispersive X-ray spectroscopy (EDX) and atomic absorption spectroscopy (AAS) were performed to evaluate inorganic nutrients, and GC was performed to estimate aromatic compounds in the samples. The high frequency of Sphingomonadaceae in drip water samples indicates the presence of aromatic hydrocarbon-degrading bacteria. This finding was consistent with the detection of naphthalene and acenaphthene and the presence of ndo genes in drip-water-related samples. The aromatic compounds, aromatic hydrocarbon-degrading bacteria and 16S rDNA sequencing indicate that aromatic compounds may be one of the sources of energy and carbon to the system and the drip-water-associated bacterial community contains several potentially aromatic hydrocarbon-degrading bacteria. To the best of our knowledge, this is the first work to present compelling evidence for the presence of aromatic hydrocarbon-degrading bacteria in cave drip water.

Degradation of Polycyclic Aromatic Hydrocarbons by Moderately Halophilic Bacteria from Luzon Salt Beds

BACKGROUND

Polycyclic aromatic hydrocarbons (PAHs) are common environmental contaminants which are highly toxic due to their carcinogenic and mutagenic effects. They are released into the environment by incomplete combustion of solid and liquid fuels, accidental spillage of oils and seepage from industrial activities. One of the promising processes mitigating PAHs is through biodegradation. However, conventional microbiological treatment processes do not function well at high salt concentrations. Hence, utilization of halophilic bacteria should be considered.

OBJECTIVES

This study aimed to assess the ability of halophilic bacteria isolated from local salt beds in Pangasinan and Cavite, the Philippines, to degrade PAHs pyrene, fluorene and fluoranthene.

METHODS

Polycyclic aromatic hydrocarbon-tolerant halophilic bacteria collected from two sampling sites were phenotypically characterized, molecularly identified and tested to determine their potential to degrade the PAHs pyrene, fluorene and fluoranthene at a hypersaline condition. Best PAH degraders were then assayed to identify the optimal degradation using such parameters as pH, temperature and PAH concentration. Testing for enzyme degradation was also done to determine their baseline information. Extraction and analysis of degraded PAHs were performed using centrifugation and UV-vis spectrophotometry.

RESULTS

Twelve isolates from both collection sites tolerated and grew in culture with selected PAHs. These were identified into four genera (Halobacillus, Halomonas, Chromohalobacter, and Pontibacillus). Selected best isolates in a series of biodegradation assays with the above-mentioned parameters were Halobacillus B (Collection of Microbial Strains (CMS) 1802) (=trueperi) (Gram-positive) for pyrene and fluoranthene, and Halomonas A (CMS 1901) (Gram-negative) for fluorene. Degrader biomass and PAH degradation were invariably negatively correlated. Qualitative tests with and without peptone as a nitrogen source implied enzymatic degradation.

DISCUSSION

Polycyclic aromatic hydrocarbons utilized by these halophilic bacteria served as a sole source of carbon and energy. Implications of biodegradation of the two best isolates show that high molecular weight (HMW) (4-ring) pyrene tends to be degraded better by Gram-positive bacteria and low molecular weight (3-ring) fluorene by Gram-negative degraders.

CONCLUSIONS

Halophilic bacteria constitute an untapped natural resource for biotechnology in the Philippines. The present study demonstrated their potential use in bioremediation of recalcitrant hydrocarbons in the environment.

COMPETING INTERESTS

The authors declare no competing financial interests.

Anthracene biodegradation capacity of newly isolated rhizospheric bacteria Bacillus cereus S13

Biodegradation of hazardous pollutants is of immense importance for maintaining a clean environment. However, the concentration of such contaminants/pollutants can be minimized with the help of microorganisms that has the ability to degrade the toxic pollutants into non-toxic metabolites. In the current study, 23 bacterial isolates were purified from the rhizospheric soil of Sysimbrium irio, growing as a wild plant in the vicinity of gas filling stations in Peshawar city. The isolated strains were initially screened on solid nutrient agar and further purified by culturing it on anthracene amended mineral media (PNR). The bacterial growth and anthracene disappearance were observed by calculating optical density (OD). The isolates showed a concentration-dependent growth on anthracene amended PNR media at 30°C and pH7. Also, an increase in bacterial OD from 0.351 to 1.80 with increased shaking speed was noticed. On the contrary, alternate carbon sources (glucose, fructose, sucrose) or nitrogen sources (KNO₃, NaNO₃, NH₄NO₃ and CaNO₃) posed inhibitory effect on bacterial growth during anthracene degradation. The recorded efficiency of anthracene degradation by the selected bacterial isolate (1.4×10²³ CFUmL^-1 and 1.80 OD) was 82.29%, after 120 h of incubation. The anthracene was degraded to 9, 10, dihydroxy-anthracene and anthraquinone, detected through GC-MS. The efficient bacterial isolate was identified as S₁₃, a new strain of Bacillus cereus, using 16S rRNA analysis, showing 98% homology. The isolated bacterial strain S₁₃ may be used as a potential tool for bioremediation of toxic hydrocarbons and to keep the environment free from PAH pollutants.

Genome-Guided Characterization of Ochrobactrum sp. POC9 Enhancing Sewage Sludge Utilization-Biotechnological Potential and Biosafety Considerations

Sewage sludge is an abundant source of microorganisms that are metabolically active against numerous contaminants, and thus possibly useful in environmental biotechnologies. However, amongst the sewage sludge isolates, pathogenic bacteria can potentially be found, and such isolates should therefore be carefully tested before their application. A novel bacterial strain, Ochrobactrum sp. POC9, was isolated from a sewage sludge sample collected from a wastewater treatment plant. The strain exhibited lipolytic, proteolytic, cellulolytic, and amylolytic activities, which supports its application in biodegradation of complex organic compounds. We demonstrated that bioaugmentation with this strain substantially improved the overall biogas production and methane content during anaerobic digestion of sewage sludge. The POC9 genome content analysis provided a deeper insight into the biotechnological potential of this bacterium and revealed that it is a metalotolerant and a biofilm-producing strain capable of utilizing various toxic compounds. The strain is resistant to rifampicin, chloramphenicol and β-lactams. The corresponding antibiotic resistance genes (including bla_OCH and cmlA/floR) were identified in the POC9 genome. Nevertheless, as only few genes in the POC9 genome might be linked to pathogenicity, and none of those genes is a critical virulence factor found in severe pathogens, the strain appears safe for application in environmental biotechnologies.

Degradation of petroleum hydrocarbons and treatment of refinery wastewater under saline condition by a halophilic bacterial consortium enriched from marine environment (Red Sea), Jeddah, Saudi Arabia

A halophilic bacterial consortium was enriched from Red Sea saline water and sediment samples collected from Abhor, Jeddah, Saudi Arabia. The consortium potentially degraded different low (above 90% for phenanthrene and fluorene) and high (69 ± 1.4 and 56 ± 1.8% at 50 and 100 mg/L of pyrene) molecular weight polycyclic aromatic hydrocarbons (PAHs) at different concentrations under saline condition (40 g/L NaCl concentration). The cell hydrophobicity (91° ± 1°) and biosurfactant production (30 mN/m) confirmed potential bacterial cell interaction with PAHs to facilitate biodegradation process. Co-metabolic study with phenanthrene as co-substrate during pyrene degradation recorded 90% degradation in 12 days. The consortium in continuous stirred tank reactor with petroleum refinery wastewater showed complete and 90% degradation of low and high molecular weight PAHs, respectively. The reactor study also revealed 94 ± 1.8% chemical oxygen demand removal by the halophilic consortium under saline condition (40 g/L NaCl concentration). The halophilic bacterial strains present in the consortium were identified as Ochrobactrum halosaudis strain CEES1 (KX377976), Stenotrophomonas maltophilia strain CEES2 (KX377977), Achromobacter xylosoxidans strain CEES3 (KX377978) and Mesorhizobium halosaudis strain CEES4 (KX377979). Thus, the promising halophilic consortium was highly recommended to be employed in petroleum saline wastewater treatment process.

Development of a Stable Lung Microbiome in Healthy Neonatal Mice

The lower respiratory tract has been previously considered sterile in a healthy state, but advances in culture-independent techniques for microbial identification and characterization have revealed that the lung harbors a diverse microbiome. Although research on the lung microbiome is increasing and important questions were already addressed, longitudinal studies aiming to describe developmental stages of the microbial communities from the early neonatal period to adulthood are lacking. Thus, little is known about the early-life development of the lung microbiome and the impact of external factors during these stages. In this study, we applied a barcoding approach based on high-throughput sequencing of 16S ribosomal RNA gene amplicon libraries to determine age-dependent differences in the bacterial fraction of the murine lung microbiome and to assess potential influences of differing "environmental microbiomes" (simulated by the application of used litter material to the cages). We could clearly show that the diversity of the bacterial community harbored in the murine lung increases with age. Interestingly, bacteria belonging to the genera Delftia and Rhodococcus formed an age-independent core microbiome. The addition of the used litter material influenced the lung microbiota of young mice but did not significantly alter the community composition of adult animals. Our findings elucidate the dynamic nature of the early-life lung microbiota and its stabilization with age. Further, this study indicates that even slight environmental changes modulate the bacterial community composition of the lung microbiome in early life, whereas the lung microbes of adults demonstrate higher resilience towards environmental variations.

Diuron degradation by bacteria from soil of sugarcane crops

The isolation of microorganisms from soil impacted by xenobiotic chemicals and exposing them in the laboratory to the contaminant can provide important information about their response to the contaminants. The purpose of this study was to isolate bacteria from soil with historical application of herbicides and to evaluate their potential to degrade diuron. The isolation media contained either glucose or diuron as carbon source. A total of 400 bacteria were isolated, with 68% being Gram-positive and 32% Gram-negative. Most isolates showed potential to degrade between 10 and 30% diuron after five days of cultivation; however Stenotrophomonas acidophila TD4.7 and Bacillus cereus TD4.31 were able to degrade 87% and 68%, respectively. The degradation of diuron resulted in the formation of the metabolites DCPMU, DCPU, DCA, 3,4-CAC, 4-CA, 4-CAC and aniline. Based on these results it was proposed that Pseudomonas aeruginosa TD2.3, Stenotrophomonas acidaminiphila TD4.7, B. cereus TD4.31 and Alcaligenes faecalis TG 4.48, act on 3,4-DCA and 4-CA by alkylation and dealkylation while Micrococcus luteus and Achromobacter sp follow dehalogenation directly to aniline. Growth on aniline as sole carbon source demonstrates the capacity of strains to open the aromatic ring. In conclusion, the results show that the role of microorganisms in the degradation of xenobiotics in the environment depends on their own metabolism and also on their synergistic interactions.

Microbial fuel cells in saline and hypersaline environments: Advancements, challenges and future perspectives

This review is aimed to report the possibility to utilize microbial fuel cells for the treatment of saline and hypersaline solutions. An introduction to the issues related with the biological treatment of saline and hypersaline wastewater is reported, discussing the limitation that characterizes classical aerobic and anaerobic digestions. The microbial fuel cell (MFC) technology, and the possibility to be applied in the presence of high salinity, is discussed before reviewing the most recent advancements in the development of MFCs operating in saline and hypersaline conditions, with their different and interesting applications. Specifically, the research performed in the last 5years will be the main focus of this review. Finally, the future perspectives for this technology, together with the most urgent research needs, are presented.

Anaerobic treatment of pharmaceutical wastewater: A critical review

Pharmaceutical wastewaters are usually produced by chemical-synthetic process, and thus contain high levels of organic pollutants, biotoxicity and salinity. Anaerobic technology is a viable option for treating pharmaceutical wastewater owing to its advantages of withstanding high organic-loading, less sludge production and lower operating cost as compared with conventional activated sludge process. In this paper, several types of modern anaerobic or hybrid systems were reviewed on their pollutant reduction performance and operating conditions for treating pharmaceutical wastewater. Meanwhile, the typical predominant microbial populations found in anaerobic process treating pharmaceutical wastewater were summarized. Moreover, the environmental impact of antibiotic residues and health risk of spreading of antibiotic resistant genes (ARGs) were also assessed to offer an in-depth understanding of the growing concern on the discharge of treated pharmaceutical effluent.

Characterization and application of a newly isolated pyrene-degrading bacterium, Pseudomonas monteilii

Pseudomonas monteilii PL5 (PL5) was newly isolated from soil sample and was identified by 16S rDNA sequence analysis. The strain PL5 had a high potential to degrade pyrene (PYR) in both liquid solution and soil and was able to degrade 51.8% of PYR at 25 °C and pH 7.0 condition within 10 days. At 25 °C, the ability of strain PL5 to degrade PYR at different pH values followed the following order pH 6.0 > pH 7.0 > pH 8.0 > pH 9.0. Degradation of total PYR was 56.5 and 51.8% after 10 days at pH 6.0 and 7.0 with PYR half-lives of 8.8 and 9.2 days, respectively. The ability of strain PL5 degraded PYR under different temperatures was 35 > 25 > 15 °C at pH 6.0. Among the tested soils contaminated by PYR, the best degradation of PYR by strain PL5 occurred in paddy soil where the degradation was 57.5% after 10 days, and the half-life of PYR was reduced 19-fold in the presence of strain PL5. This study suggested that P. monteilii PL5 could be used for the bioremediation of the contaminated soil and water through the degradation of PYR.