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Pesticides and insecticides are the chemicals widely used in the agricultural industry, but their ecotoxicological effects on the environment are not still well understood. In this study, the remediation of chlorpyrifos (CP) and deltamethrin (DM) and their impacts on soil microbial diversity was investigated. Four different soils with various salinity (0%, 1%, 2% and 4%) were artificially contaminated by CP and DM. Then, natural attenuation of the pesticides in soil microcosms and their effects on soil microbial composition were studied by metagenomics. The pesticide natural attenuation analysis showed higher CP remediation in slightly saline soils with 1% and 2% salinity and faster removal of DM in 1% saline soil in comparison to non-saline control microcosm. The complete natural attenuation of the contaminants took around 60 days. The metagenomics analysis indicated that pesticide contamination had significant impacts on the soil flora and some dominant species in the control microcosm were completely eliminated by CP and DM. In addition, Paenibacillus (2% salinity and DM), Bacillus (4% salinity and CP), Paeniclostridium (1% salinity and DM) and Lachnospiraceae (1% salinity and CP) were the dominant genus by 77%, 50%, 41% and 39% relative abundances, respectively. At phylum level, the sequences belonged to Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were considerably enriched during natural attenuation of both DM and CP pesticides. Furthermore, Shannon and Simpson Indexes were identified more sensitive to the microbial community evenness, while, Chao1 and ACE indexes were changed by the community abundance. It was revealed that the highest negative impacts of deltamethrin and chlorpyrifos on the culturable and unculturable communities were related to the non-saline soil.

Bioremediation is a proven technology for treatment of contaminated soils. Soil physico-chemical properties and microbial composition are key factors for the successful implementation of this technology. In this study, we evaluated the bacterial diversity during bioremediation of gasoil-contaminated soils with different salinities. The results of TPH analysis indicated an inverse relationship between soil salinity and TPH degradation extent, so that TPH removal decreased from 61% in the non-saline soil to 33% in hypersaline soil (8% NaCl) from the Hoze Soltan salt lake. Culture-independent analysis of soil bacterial diversity during bioremediation process showed that Xanthomonas was dominant in the microcosm of Hoze Soltan (8% salinity), Marinobacter and KSA1 were dominant in microcosm of the Rudeshur (5% salinity) and Achromobacter, Iamia and Xanthomonas had the highest frequency in microcosm of the Khorshid-Abad farmland (0% salinity) during bioremediation. The results of culture-dependent analysis showed that Bacillus genus was dominant in the microcosms of Hoze Soltan and Rudeshur. However, Proteobacteria including the genera Microvirga, Brevundimonas, and Hyphomonas were dominant in microcosm of the Khorshid-Abad. The obtained results suggest that the soil salinity has a considerable effect on the microbial flora and bioremediation success of gasoil-contaminated soil and accordingly the simultaneous application of both culture-dependent and independent methods can provide a better comprehension about petroleum hydrocarbon biodegradation.

The Persian Gulf, hosting ca. 48% of the world’s oil reserves, has been chronically exposed to natural oil seepage. Oil spill studies show a shift in microbial community composition in response to oil pollution; however, the influence of chronic oil exposure on the microbial community remains unknown. We performed genome-resolved comparative analyses of the water and sediment samples along Persian Gulf’s pollution continuum (Strait of Hormuz, Asalouyeh, and Khark Island). Continuous exposure to trace amounts of pollution primed the intrinsic and rare marine oil-degrading microbes such as Oceanospirillales, Flavobacteriales, Alteromonadales, and Rhodobacterales to bloom in response to oil pollution in Asalouyeh and Khark samples. Comparative analysis of the Persian Gulf samples with 106 oil-polluted marine samples reveals that the hydrocarbon type, exposure time, and sediment depth are the main determinants of microbial response to pollution. High aliphatic content of the pollution enriched for Oceanospirillales, Alteromonadales, and Pseudomonadales whereas, Alteromonadales, Cellvibrionales, Flavobacteriales, and Rhodobacterales dominate polyaromatic polluted samples. In chronic exposure and oil spill events, the community composition converges towards higher dominance of oil-degrading constituents while promoting the division of labor for successful bioremediation.

This study investigated the applicability of synthesized calcium peroxide (CaO2) nanoparticles for naphthalene bioremediation by permeable reactive barrier (PRB) from groundwater. According to the batch experiments the application of 400 mg/L of CaO2 nanoparticles was the optimum concentration for naphthalene (20 mg/L) bioremediation. Furthermore, the effect of environmental conditions on the stability of nanoparticles showed the tremendous impacts of the initial pH and temperature on the stability and oxygen releasing potential of CaO2. Therefore, raising the initial pH from 3 to 12 elevated the dissolved oxygen from 4 to 13.6 mg/L and the stability of nanoparticles was significantly improved around 70 d. Moreover, by increasing the temperature from 4 to 30 °C, the stability of CaO2 declined from 120 to 30 d. The continuous-flow experiments revealed that the naphthalene-contaminated groundwater was completely bio-remediated in the presence of CaO2 nanoparticles and microorganisms from the effluent of the column within 50 d. While, the natural remediation of the contaminant resulted in 19.7% removal at the end of the experiments (350 d). Additionally, the attached biofilm on the surface of the PRB zone was studied by scanning electron microscopy (SEM) which showed the higher biofilm formation on the pumice surfaces in the bioremediation column in comparison to the natural remediation column. The physic-chemical characteristics of the effluents from each column was also analyzed and indicated no negative impact of the bioremediation process on the groundwater. Consequently, the present paper provides a comprehensive study on the application of the CaO2 nanoparticles in PAH-contaminated groundwater treatment.

Background: Petroleum drilling and exploration operations generate a significant amount of oily wastes. Comparing with physical and chemical remediation methods, bioremediation is cost-effective, highly efficient, and environment-friendly technology.Objectives: The aim of this study was to evaluate biological treatment efficiency for an oil-contaminated soil prepared from an abandoned drilling mud pit located in the Khangiran region , Khorasan Razavi Provinvce, Iran.Materials and Methods: Following chemical analysis of the contamination, isolation and phylogenetic analysis of the predominant hydrocarbon-utilizing bacteria were performed in order to elucidate microbial diversity. Afterwards, the full factorial design was used to optimize the concentration of nitrogen (0, 100, 250, and 500 ppm) and phosphate (0, 10, 25, and 50 ppm) in the soil. The prepared microcosms were incubated at 30 °C for a 60-day period. The total heterotrophic bacterial content was enumerated during bioremediation process. The total petroleum hydrocarbon concentration was analyzed after 60 days to evaluate biodegradation extent.Results: The mud pit was mainly contaminated with the weathered diesel compounds ranging from C12 to C30. Investigation of the indigenous microflora showed that a variety of hydrocarbon-utilizing bacteria were present in the untreated soil dominated by Actinobacteria including the genera Gordonia, Nocardia, Nocardioides, and Rhodococcus. The full-factorial soil microcosms’ nutrient optimization indicated that nitrogen amendment could be the most effective at 250 ppm, while excess nitrogen would lead to a diminished microbial activity. The main effect statistical analysis demonstrated that addition of phosphate did not cause a significant improvement in the remediation process. In the optimal nutrient conditions, the total microbial count increased from 1.76 × 107 CFU.g-1 to 1.24 × 109 CFU.g-1 and led into 75.4 % w/w biodegradation in two months, while in the control microcosm without nutrient amendment only 36.6 % of the depletion was observed.Conclusions: These results indicate that biostimulation could be a promising candidate for a successful field-scale bioremediation process in the studied drilling mud pit.

A crude-oil-degrading, Gram-stain-positive actinobacterial strain, RIPIT, was isolated from a soil sample collected from an oil-contaminated mud pit in Khangiran oil and gas field, in the north-east of Iran. RIPIT was strictly aerobic, catalase- and oxidase-positive. The strain grew with 0–12.5 % (w/v) NaCl (optimum 3–5 %), at 25–55 °C (optimum 45 °C) and at pH 6.0–9.5 (optimum pH 7.0). The results of 16S rRNA gene sequence comparative analysis indicated that RIPIT represents a member of the genus Prauserella , with high phylogenetic similarity to Prauserella coralliicola SCSIO 11529T (97.5 %), Prauserella endophytica SP28S-3T (97.5 %) and Prauserella marina MS498T (97.2 %). DNA–DNA relatedness values between the novel strain and P. coralliicola DSM 45821T, P. endophytica DSM 46655T and P. marina DSM 45268T were 28 , 19 and 23 %, respectively. The cell wall peptidoglycan of RIPIT contained meso-diaminopimelic acid as the diamino acid and the whole-cell sugars are galactose and arabinose. The polar lipids pattern contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and two unknown phospholipids. Its cellular fatty acids pattern consisted of C17 : 1ω6c, iso-C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), and the major respiratory quinone was MK-9(H4). The G+C content of the genomic DNA was 69 mol%. On the basis of polyphasic taxonomic data we propose that RIPIT represents a novel species of the genus Prauserella , for which the name Prauserella oleivorans sp. nov. is proposed. The type strain of Prauserella oleivorans is RIPIT (=IBRC-M 10906T=LMG 28389T).

Background Dental caries is considered as one of the most significant global health problem over the world. Dental caries initiates from bacterial shifts within the supragingival biofilm, then a polymicrobial biofilm is formed on the surface of tooth, and finally various bacterial species aggregate in a complex-organized manner. The exploiting variability in 16S rRNA gene sequence has been considered as a cost-efficient high-throughput characterization approach in human oral microbiome investigations. The aim of this study is to characterize bacterial species associated with superficial dental biofilm, underlying carious dentine and root caries lesion by16S rRNA gene-based metagenomic analysis. Material and Methods Herein, the bacterial communities in carious dentin lesion, biofilm and root canal samples of 30 subjects (aged 4–76 years) admitted to a clinic in Tehran during 2017 were investigated using a culture independent approach. Total genomic DNA of each tissue was subjected to metagenomic identification of bacteria using a nested PCR assay and 16S rRNA library construction method. Results 31 samples collected from 30 consenting patients (29 samples from 29 patients ant two biofilm samples from one patient). Bioinformatics analyses of a-800bp sequences of the second step of Nested-PCR revealed presence of 156 bacterial isolates in carious (n=45), biofilm (n=81) and root canal (n=30) specimens. Prevotella spp., Lactobacillus vaginalis, and streptococcus spp. showed higher prevalence in carious dentin, root and biofilm samples, respectively. Conclusions Exploring the dental microbiota and comparing them in health or diseased conditions is critical step in the determination of human general health. The method applied in this study could identify bacteria related to the three dental lesions. However, due to lack of data for comparison in Genbank or because of the sequence similarity lower than 98% for most identified bacteria, the use of more powerful approaches like NGS platforms or typing of multiple loci (MLST) in future studies is recommended. Key words:Bacterial composition, dental caries, dental biofilm, oral microbiome.

In this study, through a multistep enrichment and isolation procedure, a halophilic bacterial strain was isolated from unpolluted saline soil, which was able to effectively and preferentially degrade long chain alkanes (especially tetracosane and octacosane). The strain was identified by 16S rRNA gene sequence as an Alcanivorax sp. The growth of strain Est-02 was optimized at the presence of tetracosane in different NaCl concentrations, temperatures, and pH. The consumption of different heavy alkanes was also investigated. Optimal culture conditions of the strain were determined to be as follows: 10% NaCl, temperature 25–35 °C and pH 7. Alcanivorax sp. strain Est-02 was able to use a wide range of aliphatic substrates ranging from C14 to C28 with clear tendency to utilize heavy chain hydrocarbons of C24 and C28. During growth on a mixture of alkanes (C14–C28), the strain consumed 60% and 65% of tetracosane and octacosane, respectively, while only about 40% of the lower chain alkanes were degraded. This unique ability of the strain Est-02 in efficient and selective biodegradation of long chain hydrocarbons could be further exploited for remediation of wax and heavy oil contaminated soils or upgrading of heavy crude oils. Comparison of the sequence of alkane hydroxylase gene (alkB) of strain Est-02 with previously reported sequences for Alcanivorax spp. and other hydrocarbon degraders, showed a remarkable phylogenetic distance between the sequence alkB of Est-02 and other alkane-degrading bacteria.

In this study, through a multistep enrichment and isolation procedure, a halophilic bacterial strain was isolated from unpolluted saline soil, which was able to effectively and preferentially degrade long chain alkanes (especially tetracosane and octacosane). The strain was identified by 16S rRNA gene sequence as an Alcanivorax sp. The growth of strain Est-02 was optimized at the presence of tetracosane in different NaCl concentrations, temperatures, and pH. The consumption of different heavy alkanes was also investigated. Optimal culture conditions of the strain were determined to be as follows: 10% NaCl, temperature 25–35 °C and pH 7. Alcanivorax sp. strain Est-02 was able to use a wide range of aliphatic substrates ranging from C(14) to C(28) with clear tendency to utilize heavy chain hydrocarbons of C(24) and C(28). During growth on a mixture of alkanes (C(14)–C(28)), the strain consumed 60% and 65% of tetracosane and octacosane, respectively, while only about 40% of the lower chain alkanes were degraded. This unique ability of the strain Est-02 in efficient and selective biodegradation of long chain hydrocarbons could be further exploited for remediation of wax and heavy oil contaminated soils or upgrading of heavy crude oils. Comparison of the sequence of alkane hydroxylase gene (alkB) of strain Est-02 with previously reported sequences for Alcanivorax spp. and other hydrocarbon degraders, showed a remarkable phylogenetic distance between the sequence alkB of Est-02 and other alkane-degrading bacteria. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-019-1670-3) contains supplementary material, which is available to authorized users.

Oil-based drill cuttings are hazardous wastes containing complex hydrocarbons, heavy metals, and brine. Their remediation is a crucial step before release to the environment. In this work, we enriched a halophilic consortium, from oil-polluted saline soil, which is capable of degrading diesel as the main pollutant of oil-based drill cuttings. The degradation ability of the consortium was evaluated in microcosms using two different diluting agents (fine sand and biologically active soil). During the bioremediation process, the bacterial community dynamics of the microcosms was surveyed using PCR amplification of a fragment of 16S rRNA gene followed by denaturing gradient gel electrophoresis (DGGE). The diesel degradation rates were monitored by total petroleum hydrocarbon (TPH) measurement and the total count of heterotrophic and diesel-degrading bacteria. After 3 months, the microcosm containing fine sand and drill cuttings with the ratio of 1:1 (initial TPH of 36,000 mg/kg) showed the highest TPH removal (40%) and its dominant bacterial isolates belonged to the genera Dietzia, Arthrobacter, and Halomonas. DGGE results also confirmed the role of these genera in drill cuttings remediation. DGGE analysis of the bacterial diversity showed that Propionibacterium, Salinimicrobium, Marinobacter, and Dietzia are dominant in active soil microcosm; whereas Bacillus, Salinibacillus, and Marinobacter are abundant in sand microcosm. Our results suggest that the bioaugmentation strategy would be more successful if the diluting agent does not contain a complex microbial community.

Nano-size calcium peroxide (nCaO2) is an appropriate oxygen source which can meet the needs of in situ chemical oxidation (ISCO) for contaminant remediation from groundwater. In the present study, an easy to handle procedure for synthesis of CaO2 nanoparticles has been investigated. Modeling and optimization of synthesis process was performed by application of response surface methodology (RSM) and central composite rotatable design (CCRD) method. Synthesized nanoparticles were characterized by XRD and FESEM techniques. The optimal synthesis conditions were found to be 5:1, 570 rpm and 10 °C for H2O2:CaSO2 ratio, mixing rate and reaction temperature, respectively. Predicted values showed to be in good agreement with experimental results (R 2 values were 0.915 and 0.965 for CaO2 weight and nanoparticle size, respectively). To study the efficiency of synthesized nanoparticles for benzene removal from groundwater, batch experiments were applied in biotic and abiotic (chemical removal) conditions by 100, 200, 400, and 800 mg/L of nanoparticles within 70 days. Results indicated that application of 400 mg/L of CaO2 in biotic condition was able to remediate benzene completely from groundwater after 60 days. Furthermore, comparison of biotic and abiotic experiments showed a great potential of microbial stimulation using CaO2 nanoparticles in benzene remediation from groundwater.

Phenolic compounds are hazardous pollutants known to be toxic at low concentration. Removal of phenols from industrial wastewater streams before their discharge into receiving water bodies is thus obligatory. Numerous phenol-degrading non-halophilic bacterial isolates have been described, but detailed information regarding phenol degradation by halophiles is rather sparse. Here we report a new phenol-degrading halophilic bacterium isolated from a hypersaline soil. The bacterium was identified as Halomonas sp. strain PH2-2 using 16S rDNA sequence analysis (GenBank accession number HM543189 ). Strain PH2-2 was isolated by a multistep enrichment and screening techniques on mineral medium containing 100 mg l −1 of phenol as sole source of carbon. The strain was able to utilize phenol and p -cresol as sole source of carbon and energy but not nitrophenols and chlorophenols. The bacterium was able to degrade up to 1100 mg l −1 of phenol but cell growth was inhibited at higher phenol concentrations. The strain was able to remove phenol in media containing 18% NaCl but the removal efficiency decreased from 95% to 64% in comparison to media containing 7% NaCl. The results indicated the potential application of the strain PH2-2 for treatment of hypersaline phenol-containing industrial wastewaters.

In this study we investigated the phenanthrene degradation by a halophilic consortium obtained from a saline soil sample. This consortium, named Qphe, could efficiently utilize phenanthrene in a wide range of NaCl concentrations, from 1% to 17% (w/v). Since none of the purified isolates could degrade phenanthrene, serial dilutions were performed and resulted in a simple polycyclic aromatic hydrocarbon (PAH)-degrading culture named Qphe-SubIV which was shown to contain one culturable Halomonas strain and one unculturable strain belonging to the genus Marinobacter. Qphe-SubIV was shown to grow on phenanthrene at salinities as high as 15% NaCl (w/v) and similarly to Qphe, at the optimal NaCl concentration of 5% (w/v), could degrade more than 90% of the amended phenanthrene in 6 days. The comparison of the substrate range of the two consortiums showed that the simplified culture had lost the ability to degrade chrysene but still could grow on other polyaromatic substrates utilized by Qphe. Metabolite analysis by HPLC and GC-MS showed that 2-hydroxy 1-naphthoic acid and 2-naphthol were among the major metabolites accumulated in the Qphe-SubIV culture media, indicating that an initial dioxygenation step might proceed at C1 and C2 positions. By investigating the growth ability on various substrates along with the detection of catechol dioxygenase gene, it was postulated that the uncultured Marinobacter strain had the central role in phenanthrene degradation and the Halomonas strain played an auxiliary role in the culture by utilizing phenanthrene metabolites whose accumulation in the media could be toxic.

Strain RIPI 110T was isolated from a soil sample collected from an oil-contaminated site on Siri Island, Persian Gulf, Iran. Cells of the novel isolate were Gram-stain-negative, facultatively anaerobic, non-motile and rod-shaped. Cells divided asymmetrically by budding and formed rosette-like clusters. The optimum pH and temperature for growth were pH 7 and 30 °C, while the strain was able to grow at pH 5.5–8 and 15–35 °C. Strain RIPI 110T utilized only complex carbon sources and pyruvate as the sole carbon source and could not grow under photoautotrophic conditions. The highest 16S rRNA gene sequence similarities, 93.9, 93.9 and 93.5 %, were obtained with Variibacter gotjawalensis GJW-30T, Rhodoplanes roseus 941T and Rhodoplanes elegans AS130T, respectively. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c/ω6c), C16 : 0 and C19 : 0 cyclo ω8c. Polar lipid analyses revealed that strain RIPI 110T contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid and four unknown phospholipids. Ubiquinone-10 was the predominant quinone component. The DNA G+C content was 59.4 mol%. On the basis of the 16S rRNA gene sequence analysis, in combination with chemotaxonomic and physiological data, the novel isolate could not be classified in any recognized genera. Strain RIPI 110T is thus considered to represent a novel species of a new genus within the order Rhizobiales, for which the name Pseudorhodoplanes sinuspersici gen. nov., sp. nov. is proposed. The type strain of the type species is RIPI 110T ( = IBRC-M 10770T = CECT 8374T).

The bacterium Gordonia alkanivorans RIPI90A has been previously reported as dibenzothiophene-desulfurizing strain. The present study provides a complete investigation of the dsz operon including dsz promoter analysis from desulfurization competent strain belonging to the genus Gordonia. PCR was used to amplify the dszABC genes and adaptor ligation-based PCR-walking strategy used to isolate the dsz promoter. Unlike the dsz operon of Rhodococcus erythropolis, the operon of RIPI90A was located on chromosome. Despite the remarkably high homology between dsz genes of G. alkanivorans RIPI90A and R. erythropolis IGST8, promoter sequences of the strains were not very similar. The dsz promoter of G. alkanivorans RIPI90A shows only 52.5% homology to that of R. erythropolis IGTS8 and Gordonia nitida. Deletion analysis of the dsz promoter from RIPI90A using luciferase as a reporter gene revealed that the dsz promoter was located in regions from −156 to −50.