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World Journal of Microbiology and Biotechnology (09593993) 41(5)
Antibiotic residues, as emerging micropollutants in surface water, threaten human health and ecosystems. The degradation of antibiotics is an essential process for safeguarding public health. This study identifies and optimizes a novel yeast strain for co-amoxiclav (AMC) degradation. Meyerozyma guilliermondii DF3 (Accession No. MZ477354) was isolated from soil using a basal mineral medium (BMM) supplemented with AMC. The strain degraded 75% of AMC within 72 h. Key culture conditions (temperature (20–35 °C), carbon sources (glucose/glycerol), inoculum size (1–5% v/v), and pH (5–9) were optimized via single-factor experiments and Box-Behnken design (BBD). Residual antibiotic levels were quantified by UV spectroscopy and HPLC. Optimal biodegradation occurred with glycerol/glucose, pH 6, and 1% inoculum (1 × 10⁸ cells/mL) at 30 °C. Response surface methodology (RSM) predicted complete degradation (100%) at pH 6.25, 1.02% inoculum, and 95.76 h, with pH being the most influential factor. These findings highlight M. guilliermondii DF3 as a promising candidate for AMC bioremediation in aquatic environments, advancing yeast-based strategies for water treatment. © The Author(s), under exclusive licence to Springer Nature B.V. 2025.
Food Bioscience (22124306) 69
The edible filamentous fungus, Neurospora intermedia, has attracted significant attention over the past decade as a novel candidate for sustainable food and feed sources. This study aimed to evaluate the factors that enhance the content of B vitamins and carotenoid pigments in fungal biomass. We investigated the influence of physiological growth conditions, as well as other factors affecting the biosynthesis of these bioactive compounds, including precursors, metal cofactors, and stress conditions. Optimal conditions for biomass and carotenoid production were identified as 15 g/L glucose, 0.5 % (w/v) yeast extract, pH 6, and a 1 % (v/v) inoculum level in basic mineral medium. Among the metal cofactors tested, 5 mmol Mo2+ exhibited a highly significant effect on pigment production. The synthesis of B-group vitamins was influenced by disodium succinate after 72 h and 96 h, and by ribose after 72 h incubation. The maximum production levels recorded for biomass, carotenoids, and vitamins B1, B2, B3, and B6 were 4.90 g DM/L, 168.23 μg/g, 3.85, 12.49, 0.35, and 3.81 mg/g, respectively. This study highlights the biotechnological potential for producing biomass and bioactive compounds as viable resources for food and feed applications. © 2025 The Authors
Naeij, H.B. ,
Etemadifar, Z. ,
Kilbane, J. ,
Karimi-jafari, M.H. ,
Mofidifar, S. PLoS ONE (19326203) 20(1 January)
Exophiala spinifera strain FM, a black yeast and melanized ascomycete, shows potential for oil biodesulfurization by utilizing dibenzothiophene (DBT) as its sole sulfur source. However, the specific pathway and enzymes involved in this process remain unclear due to limited genome sequencing and metabolic understanding of E. spinifera. In this study, we sequenced the complete genome of E. spinifera FM to construct the first genome-scale metabolic model (GSMM) for this organism. Through bioinformatics analysis, we identified genes potentially involved in DBT desulfurization and degradation pathways for hazardous pollutants. We focused on understanding the cost associated with metabolites in sulfur assimilation pathway to assess economic feasibility, optimize resource allocation, and guide metabolic engineering and process design. To overcome knowledge gaps, we developed a genome-scale model for E. spinifera, iEsp1694, enabling a comprehensive investigation into its metabolism. The model was rigorously validated against growth phenotypes and gene essentiality data. Through shadow price analysis, we identified costly metabolites such as 3’-phospho-5’-adenylyl sulfate, 5’-adenylyl sulfate, and choline sulfate when DBT was used as the sulfur source. iEsp1694 encompasses the degradation of aromatic compounds, which serves as a crucial first step in comprehending the pan metabolic capabilities of this strain. © 2025 Naeij et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Etemadifar, Z. ,
Rafieyan S. ,
Moridshahi R. ,
Dianatdar f., F. ,
Harirchi, S. ,
Rafieyan S. ,
Rafieyan S. ,
Rafieyan S. ,
Rafieyan S. ,
Etemadifar, Z. ,
Etemadifar, Z. ,
Etemadifar, Z. ,
Etemadifar, Z. ,
Moridshahi R. ,
Moridshahi R. ,
Moridshahi R. ,
Moridshahi R. ,
Dianatdar f., F. ,
Dianatdar f., F. ,
Dianatdar f., F. ,
Dianatdar f., F. ,
Harirchi, S. ,
Harirchi, S. ,
Harirchi, S. ,
Harirchi, S. 2025 29th International Computer Conference, Computer Society of Iran, CSICC 2025 pp. 174-199
The world population is growing rapidly, and consequently, the increased need for healthy food and appropriate hygiene requires more effort to produce and employ medicinal and antimicrobial substances. Antibiotics are the most commonly used pharmaceuticals, but there is a significant concern with their incomplete metabolism in both human and animal bodies, as well as with the effectiveness of conventional methods for completely removing them from wastewater treatment plants. The excessive use of antibiotics causes a continuous and uncontrollable release of them into the soil and aquatic environments through household waste, animal manures, sewage treatment facilities, and hospital wastewater. These bioactive materials extensively persist in different environments due to the complexity of the removal processes. Antibiotics cause a discriminating pressure on various microbial groups and communities and lead to the establishment of antibiotic-resistant bacteria (ARB) harboring antibiotic resistance genes (ARGs). Hence, understanding the fate of antibiotics in the environment and identification of ARGs is crucial to mitigate or prevent the distribution of antibiotic-resistant microorganisms. Numerous studies have been done to scrutinize the efficiency of several physiochemical and biological techniques for managing and eliminating different antibiotics and ARGs. Among different physicochemical treatment methods, filtration, Fenton reaction, ozonation, and chlorination are broadly employed for antibiotic removal. Moreover, biological methods are alternatives to these conventional approaches, in which plants, microorganisms, and biocatalysts play a key role in the bioremediation or biodegradation of antibiotics. This chapter discusses antibiotic and ARGs pollution and techniques for removing these pollutants. We discussed bioremediation as an effective strategy to access a conceptual understanding of the microbial communities' structure and their abilities to remove antibiotics, as well as related genomes, in order to provide comprehensive maps for the identification of ARB and ARGs in the environments by metagenomics technique as a culture- and amplification-independent method.
International Biodeterioration and Biodegradation (09648305) 195
Environmental contamination by nitrogen compounds such as ammonium and nitrate has increased extensively in the recent past, which necessitates the development of eco-friendly remediation technologies. In this study, three matrix types including pumice, aquarium ceramic filter, and calcium alginate beads were used to facilitate nitrogen removal with an immobilized heterotrophic nitrifying-aerobic denitrifying (HNAD) bacterial consortium. The HNAD bacterial consortium was made of Pseudomonas monteilii Nht, Pseudomonas mendocina AquaN, Rhodococcus erythropolis R1, and Acinetobacter calcoaceticus SCC2. The quality parameters for immobilization, such as the number of immobilized cells and their viability, were assessed. The highest number of bacterial cells (3.4 × 10 9) was immobilized on the aquarium ceramic filter, with 53% cell viability at 30°Ⅽ for two months. Pumice, aquarium ceramic filter, and calcium alginate achieved NH4+-N removal efficiencies of 85.3 ± 1.7%, 87.3 ± 2.2%, and 77.5 ± 3.99% within 24 h, respectively, and removed NO3−-N by 88.23 ± 0.36%, 93.95 ± 0.00%, and 71.29 ± 6.49% over 60 h. Additionally, immobilized cells on pumice and ceramic filter retained up to 84% of NH4+-N removal efficiency after 14 reuse cycles. These findings indicate that the immobilized HNAD bacterial consortium on the aquarium ceramic filter can be used as a suitable biofilter for treatment of high nitrogen wastewater. © 2024 Elsevier Ltd
International Journal of Environmental Science and Technology (17351472) 21(15)pp. 9377-9390
Antibiotics as micro-pollutants enter the environment through pharmaceutical effluents, human urine and faeces, and sweat and increase antibiotic resistance genes. The purpose of this study was to isolate amoxicillin (AMX) and co-amoxiclav (AMC) biodegrading bacteria from agricultural soil. From 15 isolates, Stenotrofomonas maltophilia strain DF1 (accession no. MW898434) was identified by phenotypic and molecular methods as the best degrading strain in the base mineral medium contained AMX or AMC. S. maltophilia strain DF1 was capable of removing 88.7% (w/v) of 43 ppm AMX and nearly 100% (w/v) of 15.2 ppm clavulanic acid after 72 h, which was measured by UV spectrophotometry and HPLC analysis. The maximum antibiotic biodegradation for S. maltophilia DF1 strain by one factor at a time was obtained after 72 h, without any additional carbon source, at 150 rpm shaking, the inoculum size of 5% (v/v), pH 7, and temperature 30 °C. According to the one-way ANOVA, the pH was affected on the AMX and AMC biodegradation. Optimal condition AMX and AMC biodegradation were determined by response surface method (RSM) with Design Expert12 software for three factors included inoculum level (1, 3, 5% (v/v)), pH (6.5, 7.25, and 8), and incubation time (40, 55, 70 h). Optimum degradation of AMC predicted by RSM at pH 7.12, inoculum level 4.78% (v/v), and 60.19 h. According to the results of this study, microbial degradation of AMX and AMC by S. maltophilia DF1 is a suitable strategy for the elimination of these micropollutants from aquatic media in aerobic conditions. Graphical abstract: (Figure presented.) © The Author(s) under exclusive licence to Iranian Society of Environmentalists (IRSEN) and Science and Research Branch, Islamic Azad University 2024.
Microbial Ecology (00953628) 85(2)pp. 698-707
Urease-producing bacteria are abundant in soils, which can precipitate calcium carbonate nanocrystals by enzymatic hydrolysis of urea in the presence of calcium ions. This process is known as microbially induced calcium carbonate precipitation (MICP), and it has received much attention in recent years as an eco-friendly technology. Therefore, the purpose of the present study was to isolate local extremophile bacterial strains capable of producing calcium carbonate. Among a total of 44 isolated urease-producing strains from sandy soils, one strain with a high level of urease activity (8.16 U/ml) and production of a large amount of calcium carbonate (410 mg/100 ml) was selected for further investigation. 16S rRNA gene sequencing showed that this strain had 99.66% sequence identity to Bhargavaea cecembensis. The SEM-EDX and XRD analyses indicated that irregular vaterite and aggregated nanocalcite were the dominant polymorphs produced by this strain. The size of these nanocalcite crystals ranged between 25 and 42 nm. The selected strain showed high levels of tolerance to different conditions of temperature, pH, and salinity. This strain grows at high temperatures up to 50 °C, alkaline pH (9–11), and high concentrations of NaCl (20–25% w/v). Flow cytometry analysis demonstrated 96% cell viability of the isolated strain after desiccation stress. Bhargavaea was first reported in 2009 as a new genus, and it belongs to the Firmicutes. So far, there has been no report on its MICP potential. The present study is the first one to report nanocrystal calcium carbonate precipitation in polyextremophile Bhargavaea cecembensis, which makes it a suitable candidate for bio-cementation under extreme circumstances. Graphical abstract: [Figure not available: see fulltext.] © 2022, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Avicenna Journal Of Medical Biotechnology (20084625) 15(1)pp. 28-37
Background: The screen of Polyketide Synthase (PKS) and Nonribosomal Peptide Synthetase (NRPS) gene groups is a quick way to discover new therapeutic agents. However, errors in laboratory techniques cause a loss of touch with reality. This study aimed to evaluate the presence of PKS and NRPS gene groups in previously isolated strains by optimizing their specialized amplification by degenerate primers and indicating the evolutionary relationships with reference strains. Methods: PKS-I, II, and NRPS genes PCR amplification was performed using three degenerate primer sets for 22 actinomycete strains with antibacterial activity. Annealing temperature and the amount of template DNA and primers were optimized. PCR products of PKS-I, II, and NRPS from three strains were sequenced after TA cloning. Besides, strains with high antibacterial activity were identified by biochemical features and partial 16S rDNA sequencing and hypothetically classified by a phylogenetic tree. Results: High frequencies of PKS-I (86.4%), PKS-II (81.8%), and NRPS (95.4%) genes were found among the strains after optimization. Fourteen strains (64%) contained all of the genes, and 100% of strains had at least two genes. These numbers are pretty distinct in comparison with the previous researches. All of the sequenced strains were members of Streptomyces genus. Conclusion: Our research showed that degenerate PCR strongly depends on the variation of annealing temperature and primer concentration, resulting in an unexpected shift in PCR outputs. The sequencing results confirmed the optimized conditions for specialized PCR of PKS-I, PKS-II, and NRPS gene groups. © 2023, Avicenna Journal of Medical Biotechnology. All rights reserved.
Harirchi, S. ,
Sar, T. ,
Ramezani, M. ,
Aliyu, H. ,
Etemadifar, Z. ,
Nojoumi, S.A. ,
Yazdian, F. ,
Awasthi, M.K. ,
Taherzadeh, M.J. Microorganisms (20762607) 10(12)
For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature. © 2022 by the authors.
Iranian Journal of Science and Technology, Transaction A: Science (10286276) 46(6)pp. 1523-1530
Microbially induced calcium carbonate precipitation (MICP) is an abundant process in nature and involves the microorganism's activities. Therefore, our aim was to characterize the crystals precipitated by locally isolated urease-producing bacteria (Sporosarcina pasteurii N4, Lysinibacillus boronitolerance N6, Bacillus sp. N2, and Bacillus sp. N5) and to evaluate their resistance under extreme conditions. The Fourier transform infrared spectroscopy analysis confirmed the presence of calcium carbonate in the precipitates. The X-ray diffraction analysis demonstrated that calcite is the dominant polymorph produced using strains. The scanning electron microscope micrograph showed that precipitated calcium carbonate was in the shape of nanocrystal aggregates. The size of particles ranged between 20 and 50 nm. All survived strains were halotolerant and were able to grow in acidic and alkaline medium, but at an optimal pH level of 7. Bacterial growth obtained in the temperature range of 20–47 °C. Also, they showed 44–70% viability after 28-day desiccation stress using flow cytometry. These local bacteria can tolerate extreme conditions as well as production of calcium carbonate, and this suggests that four local strains are suitable candidates for the MICP applications. They can be a good alternative to conventional methods in the soil stabilization and other MICP-related applications. © 2022, The Author(s), under exclusive licence to Shiraz University.
Etemadifar, Z. ,
Harirchi, S. ,
Rafieyan S. ,
Nojoumi, S.A. ,
Harirchi, S. ,
Harirchi, S. ,
Harirchi, S. ,
Harirchi, S. ,
Rafieyan S. ,
Rafieyan S. ,
Rafieyan S. ,
Rafieyan S. ,
Nojoumi, S.A. ,
Nojoumi, S.A. ,
Nojoumi, S.A. ,
Nojoumi, S.A. ,
Etemadifar, Z. ,
Etemadifar, Z. ,
Etemadifar, Z. ,
Etemadifar, Z. 2025 29th International Computer Conference, Computer Society of Iran, CSICC 2025 pp. 487-514
Nowadays, pollution and the number of contaminated sites are increasing due to widespread industrialization around the world, which threatens the lives of humans and every living organism on Earth. Biological methods such as biodegradation, bioremediation, phytoremediation, and vermiremediation are effective ways to reduce pollution in contaminated sites. Microorganisms play an imperative role in the biodegradation and bioremediation of pollutants by catalyzing chemical and biochemical reactions via their enzymes. At present, exceptional novel enzymes with exceptional functions is in progress around the world. To date, many researchers have taken considerable efforts to improve the properties of the available enzymes by various methods such as protein engineering. However, there is still a great demand for enzymes with extraordinary properties that make them resistant yet still active under harsh conditions and extreme environments. The most important source of current enzymes is culturable microorganisms (nearly 0.1% of these microorganisms), whereas unculturable microorganisms have a great potential to be the source of novel enzymes. In this context, metagenomics, a culture-independent approach, enables us to excavate this diverse source. In this chapter, the metagenomic principle, along with recent advances, has been reviewed. Thereafter, contaminated sites and microbial biodegradation pathways are introduced. The main focus of this chapter is on exploring degrading enzymes by metagenomics and their applications in microbial biodegradation. © Springer Nature Singapore Pte Ltd. 2022.
Annals of Microbiology (18692044) 71(1)
Purpose: To characterize and optimize the productivity of melanin using an extremotolerant actinobacterium, Dietzia schimae NM3, for the first time. Methods: An extracellular brown pigment produced by D. schimae NM3 in the nutrient broth and cheese whey medium by adding L-tyrosine. The extracted melanin was analyzed by UV-visible, HPLC, and FTIR assays. The radical scavenging activity (by DPPH) and sun protection factor (SPF) of the extracted melanin were measured. The melanin cytotoxicity was assayed by MTT and chromate biosorption was measured by atomic absorption spectroscopy. Finally, melanin production by D. schimae NM3 was optimized by response surface methodology (RSM) using Box-Behnken design in the whey medium. Result: The purified melanin showed similar peak to the standard melanin (SIGMA) at 3.5 min in HPLC, and C=O bands, NH2, CH, C-N, and aromatic groups by FTIR. The radical scavenging activity (by DPPH) and SPF of the extracted melanin were obtained 188.9% and 20.22, respectively. Using MTT assay, the melanin revealed non-toxic effect on the normal human fibroblast (HFB) cell culture. The melanin yield 790 mg l−1, and tyrosinase activity 3400 U ml−1 were obtained in the medium contained whey powder [5% (w v−1)], L-tyrosine 2.5 g l−1, CuSO4 0.013 g l−1, and pH 10.5, incubated at 32 °C for 3 days. The ANOVA results indicated significant P-value, model F-value, and probability, with insignificant lack of fit. After optimization with mono-factors, the nutrient broth came up with melanin yield as 1.2 g l−1 and tyrosinase activity as 4040 U ml−1. Conclusion: This is the first report of melanin production by D. schimae NM3 and this natural melanin showed valuable biological properties such as high antioxidant activity and radioprotection (SPF) and the biocompatibility to human cell line. © 2021, The Author(s).
Biotechnologia (08607796) 102(2)pp. 197-207
In the present study, the effect of various fermentation media on the production of carotenoid pigment in a radia-tion-resistant strain of Dietzia maris was reported. The biomass and pigment production of this strain was evaluated using various sources of carbon and nitrogen as well as different concentrations of whey medium. The anti-oxidant and cytotoxic activities of the extracted pigment were also determined using ferric reducing antioxidant power (FRAP), 2,2-diphenyl-1-picrylhydrazyl radicals (DPPH), and MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) assays. The antibacterial activity of the carotenoid pigment was also evaluated. All carbon sources increased the pigment production of D. maris in the following order: glucose > raffinose = starch = xylose > sorbitol > sucrose. However, only glucose, xylose, and sorbitol significantly increased the microbial biomass as compared to the control. Moreover, all organic nitrogen sources and ammonium sulfate enhanced the pigment production of the studied strain by approximately 6–9 folds. The free radical scavenging capacity and FRAP of the D. maris carotenoid extract were reported as half-maximal effective concentration or EC50 = 3.30 mg/ml and EC50 =28.46 μg/ml, respectively. The maximum amount of biomass and carotenoid pigment produced by D. maris was obtained in the fermentation medium containing 1 g/l glucose and 1 g/l yeast extract (18 mg/l). This strain can be considered as a promising biocatalyst for the commercial production of natural carotenoids due to its antioxidant capacity and noncytotoxic activity. © 2021, Termedia Publishing House Ltd. All rights reserved.
Journal of Applied Microbiology (13652672) 131(3)pp. 1331-1343
Aims: Bacterial melanins are UV-absorber biopolymers with potential applications in cosmetics and pharmaceutical industries. However, the cost concern of these pigments remains a limiting factor for their commercial production. Hence, the present study was aimed to isolate a bacterium with high yield of melanin by optimization of an inexpensive waste sources. Methods and Results: Pseudomonas koreensis UIS 19 (accession number: MG548583), which displayed significant bioproduction of melanin along with high tyrosinase enzyme activity was isolated from soil and introduced as a melanin-producing bacterium. Scanning and transmission electron microscope studies revealed that melanin pigments accumulated inside as well as the extracellular space of the cells. Melanin was extracted from the isolated strain and its detection was investigated using NMR and HPLC analyses. Here, we showed that the DPPH radical scavenging activity of 20 mg ml−1 melanin extracted from the isolated strain was >92·42% and its sun protection factor (SPF) value was 61·55. Melanin production by the UIS 19 in molasses medium showed sugar consumption (32 g l−1) for biomass production (5·4 g dry wt) and melanin yield of 0·44 g dry wt g−1 biomass from l-tyrosine. Some critical intermediated such tyramine, l-dopa, dopamine and dopaquinone related to the melanin Raper Mason pathway were detected by H-NMR. Furthermore, to achieve high bioproduction of melanin in inexpensive media include 5% molasses 5 Brix as an industrial waste, nutritional and environmental parameters were screened using response surface methodology by Box-Behnken design in which, maximum melanin yield of 5·5 g dry wt l−1 was obtained. Conclusions: The bioproduction of melanin as valuable compound from P. koreensis was performed using an optimized waste medium. The purified melanin showed high radical scavenging activity and high SPF value. Significance and Impact of the Study: Pseudomonas koreensis UIS 19 is a promising candidate for industrial production of melanin as cosmetic skin-care product. © 2021 The Society for Applied Microbiology
Iranian Journal Of Fisheries Sciences (15622916) 19(4)pp. 1994-2009
Capability of cyanobacterium, Microcystis aeruginosa, in the removal of cadmium and lead ions was investigated which was obtained after isolation from wastewater stabilization pond effluents. Influence of operational parameters including metal concentrations, pH, temperature and biomass dosage on removal efficiency was investigated. Also, applicability of closed reflux techniques for the digestion of cyanobacterial pellet was studied. A multi-phase washing method was developed in order to attain more elevated desorption efficiency. 1-5 washing cycles were repeated consecutively by the addition of new EDTA solution (4mM), stirring on mixer and centrifugation for each cycle. Maximum removal efficiency occurred at pH 7, temperature 28℃ and biomass dosage of 0.2g for Cd2+ and corresponding values of 6, 25℃ and 0.1g for Pb2+. In all tested concentrations of Cd2+ and Pb2+, extracellular absorption overweighed intracellular uptake with highest ratio of the former to the latter of 172 for Cd2+and 143 for Pb2+. EC50 values attained for Cd2+and Pb2+were 20 mg L-1 and 15 mg L-1, respectively. The closed-reflux digestion method was found as a suitable choice for cyanobacterial pellet digestion. Three-stage consecutive washing procedure devised in our study gave desorption efficiencies of 92 and 86 percent for Cd2+ and Pb2+ respectively as compared with values of 52 and 44 percent for Cd2+ and Pb2+, respectively obtained by the conventional washing procedure. This investigation verifies the possibility of employing M. aeruginosa for removal of Cd2+ and Pb2+ from aqueous and wastewater solutions. © 2020 Iranian Fisheries Research Organization. All rights reserved.
Bioresource Technology (09608524) 313
This work aimed to evaluate the applicability of Aeribacillus pallidus for the aerobic treatment of the concentrated beet vinasse with high chemical oxygen demand (COD 685 g.L−1) that is defined as an environmental pollutant. This bacterium is a polyextremophilic strain and grow aerobically up to 7.5% vinasse at high temperature (50 °C). In the bioreactor and under controlled conditions, A. pallidus reduced the soluble COD content of 5% vinasse up to 27% during 48 h and utilized glucose and glycerol, completely. Furthermore, a reduction of manganese, copper, aluminum, and nickel concentrations was observed in the treated vinasse with A. pallidus. The obtained results make this strain as an appropriate alternative to be used for the aerobic bioprocessing of the vinasse. © 2020 The Author(s)
Iranian Journal Of Medical Microbiology (23454342) 14(1)pp. 70-83
Background: Melanin is a negative charge hydrophobic complex pigment. Melanin is produced naturally in bacteria to protect them against UV, free radicals and environmental stresses. Pigment production in bacteria has more advantages than other biosources due to its rapid growth, higher efficiency and easier extraction. The aim of this study was the isolation, biochemical and molecular identification the melanin pigment producing bacterium in the presence of l-tyrosine and the evaluation of the pigment biological properties. Materials & Methods: The soil sample was collected from the University of Isfahan Park, and cultured in nutrient agar medium containing l-tyrosine. The colony with brown halo was isolated and identified using phenotypic and molecular methods. The bacterial growth and melanin production were evaluated by spectrophotometry at 600 and 400 nm, respectively. The melanin pigment was extracted by increasing the acidity of the broth culture supernatant. The melanin production yield, antioxidant activity and sun protection factor (SPF) of melanin were determined. Results: Pseudomonas stutzeri strain UIS2 capable to grow in nutrient agar and melanin production, was isolated and registered in NCBI GenBank with accession no. MG519615. The maximum melanin production was obtained 600 mg l-1 by isolated strain. The antioxidant property of melanin in DPPH test was determined as 74.9% and its SPF was 49.05 U/mL. Conclusion: The melanin pigment from the isolated Pseudomonas showed high SPF and high antioxidant activity against ROS stresses. So, it can be suggested as a suitable candidate for application in cosmetic, pharmaceutical, and environmental decontaminant. © 2020. This is an original open-access article distributed under the terms of the Creative Commons Attribution-noncommercial 4.0 International License which permits copy and redistribution of the material just in noncommercial usages with proper citation. All rights reserved.
Boroumand, Y. ,
Razmjou, A. ,
Moazzam, P. ,
Mohagheghian, F. ,
Eshaghi, G. ,
Etemadifar, Z. ,
Asadnia, M. ,
Shafiei, R. Journal of Water Process Engineering (22147144) 33
Nitrate is currently one of the most significant causes of water pollution in many parts of the world due to its detrimental effects on humans and the environment. The purpose of this study was to find a novel immobilization method based on bacterial adsorption to adhesive coating material, for use in water denitrification. The fractal formation capability of polydopamine (PDA) allowed coating of the surface of in-house asymmetric polyethersulfone (PES) beads (1.65–2.35 mm in diameter), and immobilizing the denitrifying bacteria Pseudomonas stutzeri with noticeable denitrification potential, on the surface of hyper-branched PDA coated beads. For surface characterization, SEM, wettability measurement, and ATR-FTIR spectroscopy were performed. Nitrate and nitrite concentrations were measured by APHA standard method 4500-NO3 −-B and a colourimetric method using two reagents respectively. The effects of temperature, pH and different carbon sources (Acetic acid, methanol, and ethanol) on the denitrification process were also investigated. The results revealed that the bacterial immobilization on PES surface with fractal patterns of PDA (with fractal dimension (Df) value of 1.57) was successful, and the optimum parameters for nitrate removal were established as 25 °C, pH = 8, and 420 mg/L ethanol as the carbon source. Finally, this research showed that under the optimum conditions the immobilized bacteria exhibited 100 % removal efficiency for 28 mg of NO3–N in 22 h (removal rate: 8.06 mg NO3-N/h/mg biomass of bacteria). We found that the immobilization of bacteria on the PDA coated beads is practicable and that the denitrification rate is adequate. © 2019 Elsevier Ltd
Harirchi, S. ,
Etemadifar, Z. ,
Mahboubi, A. ,
Yazdian, F. ,
Taherzadeh, M.J. Current Microbiology (03438651) 77(10)pp. 2565-2574
Hot springs are fascinating extreme environments for the isolation of polyextremophilic microorganisms with extraordinary characteristics. Since polyextremophilic bacterial growth are not as high as routine bacteria, the objective of this study was to investigate the effect of some environmental factors on biomass and metabolites productions in the newly isolated strain, from Larijan hot spring in Iran. The strain was identified as Aeribacillus pallidus Lhs-10 and deposited as CCUG 72355 and IBRC-M 11202 in Sweden and Iran, respectively. This thermoalkaliphilic strain can grow best at 50 °C, pH 8 and in the presence of 25 g/l NaCl. The physiological characterization of this strain show that [Ca/Mg] ratio affect its growth and biomass production with the best results obtained at the ratio of 2.5. Moreover, lactic and acetic acids production by this strain was affected by pH, aeration, and temperature, where a metabolic shift was detected from lactate to acetate production when the culture was aerated. Besides, its spores could tolerate heating at 80, 85, 90, 95 and 98 °C for 30 min without any reduction in the initial spore population, whereas D-value was defined 50 min at 98 °C. This newly lactic acid-producing strain of A. pallidus can be a promising strain that can be used in the harsh conditions in industrial processes. © 2020, Springer Science+Business Media, LLC, part of Springer Nature.
SN Applied Sciences (25233971) 2(12)
In the present study, the response surface methodology based on a rotatable central composite design was applied to optimize the production of the carotenoid pigment using a strain of Cellulosimicrobium that has not been reported so far for this genus. The microbial biomass and pigment production of strain AZ were investigated in the presence of tricarboxylic acid cycle intermediates (citrate, malate, succinate), and glutamate. Besides, the influence of the pH of the fermentation medium was also evaluated. The design consisted of a total of 32 experiments at five levels for each factor. Optimum carotenoid production (28.86 mg/L) was observed in the fermentation medium (pH 8.04) containing citrate (11.18 mM), glutamate (12.48 mM), malate (14.19 mM), and succinate (13.38 mM). It was 1.65-fold more than that of the OFAT method (17.5 mg/L) and 12-fold more than the unoptimized conditions (2.4 mg/L). The results were fitted with a quadratic model that could predict the responses to new observations significantly (pred-R2 = 0.9686). Optimum microbial biomass (10.61 g/L) was observed in the presence of citrate (10.27 mM), glutamate (14.03 mM), malate (13.1 mM), and succinate (10.39 mM) as well as pH 8.36. In contrast to the results of one-factor-at-a-time, the carotenoid production had not a direct relationship with bacterial biomass. The established model could describe the variability of above 99.85% in the response based on the determination coefficient (R2). © 2020, Springer Nature Switzerland AG.
Geomicrobiology Journal (01490451) 36(2)pp. 123-129
Coal is one of the most important sources of fossil energy on earth. However, direct combustion of coal with a high sulfur content can cause various environmental problems. Other constituents of coal that can cause environmental problems include iron oxide (hematite), iron hydroxide, and silica. In this study, growing and resting cells of Rhodococcus erythropolis strains PD1, R1, and FMF, and R. qingshengii were used in heterotrophic removal of sulfur and bioleaching of iron and silica from coal. All of the mentioned strains have an ability of dibenzothiophene (DBT) desulfurization via 4-S pathway. 2-hydroxybiphenyl, sulfate, and ferric ions (Fe 3+ ) were assayed by Gibb’s test, barium chloride (BaCl 2 ), and thiocyanate ions (SCN − ), respectively. FTIR and XRF analyzer were used for detection of the coal bioleaching process by the selected strain of R. erythropolis (PD1). Results indicated that all strains have the ability to grow on coal as the sulfur source. Among them, strain PD1 produced the highest optical density and continued to grow even after 150-h incubation. In both growing- and resting-cells experiments, strain PD1 desulfurized coal most readily compared to other strains. Results of XRF showed that growing cells of strain PD1 had high desulfurizing ability of coal (46%) compared to resting cells in the absence of any carbon sources (24%). Growing cells of strain PD1 also leached 46% of the iron and 14% of the silicate after 7 days of incubation. Resting cells of PD1 leached 32% of the iron as determined by XRF analysis. Also, growing cells of PD1 removed most SiO 2 from coal as detected and confirmed by FTIR and XRF. To the best of our knowledge, this is the first report on bioleaching of iron and silica from coal by R. erythropolis strain PD1, making it a suitable candidate for coal bioremediation. © 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group.
Materials Science and Engineering C (09284931) 98pp. 826-833
An innovative, facile, low- cost and one-pot hydrothermal synthesis was developed for preparing a high fluorescence carbon dots (CDs). In this report for the first time, Lawsonia inermis (Henna) plant as a carbon source was used to produce CDs without adding any chemical reagent and it was characterized by different techniques. The as-synthesized CDs exhibit high stability under various conditions and exceptionally solubility in hydrophilic solvents such as water and ethanol. In addition, the CDs were employed as a biocompatible probe for determination of methotrexate (MTX) in the range of 0.02 μmol L −1 to 18 μmol L −1 with a detection limit as 7 nmol L −1 . Highly selective and sensitive determination of MTX was carried out through the fluorescence resonance energy transfer (FRET) mechanism. It is noteworthy that, the antibacterial studies of this CDs lead to interesting results which suggested Henna CDs kill Gram-positive and Gram-negative bacteria like an antibiotic drug. Also, compared with the henna plant, CDs show antibacterial properties in much lower concentrations. © 2019 Elsevier B.V.
Iranian Journal of Science and Technology, Transaction A: Science (10286276) 42(4)pp. 1771-1778
Neutral proteases have a large variety of industrial applications. Therefore, the optimization of their production for the large-scale commercial purpose is critical. The present study was aimed to the optimization of nutritional and physical conditions affecting neutral protease production of Aeromonas hydrophila MSB16, not previously reported for this genus. Four key determinants (pH, temperature, glucose and peptone concentration), were selected based on the results of the one-factor-at-a-time (OFAT) method and then optimized by the response surface methodology (RSM). Maximum enzyme production (229.72 U/ml) which was 2.3 folds higher than that of the OFAT method (99.25 U/ml) and 3.15 times higher than unoptimized conditions (72.86 U/ml) was observed at 30 °C, pH 7, 4.5% w/v glucose and 4.5%w/v peptone by using a rotatable central composite design (RCCD). The results showed that the OFAT and RSM strategies were a useful screening and optimization methods for enhancing the protease production of the strain MSB16, respectively. © 2017, Shiraz University.
Journal of Veterinary Research (20082525) 73(1)pp. 83-92
BACKGROUND: Colostrum is the first milk produced after birth and is particularly rich in immunoglobulins, growth factors and antimicrobial peptides. Therefore, maintenance and storage of bovine colostrum has always been considered due to benefits of colostrum for the calf. Microbial contamination of colostrum is a concern because it is thought that bacteria in colostrum may interfere with passive absorption of colostral antibodies. OBJECTIVES: The aim of this study was to evaluate the effects of chemical preservatives and natural fermentation on quality and storage of colostrum. METHODS: Colostrum from the first milking of five Holstein cows was stored separately. Then colostrum samples were studied at days 1, 10, 20, and 30 of storage after treatment. All samples underwent microbiological culture for total plate count and detection of Escherichia coli, Coliforms, mold and yeast. Then whey was provided from untreated and treated samples at the end of 30th day and SRID (single radial immune diffusion) test was performed for assaying IgG antibody. Then the effect of treatments on colostrum antibody level was studied. RESULTS: The results showed that potassium sorbate did not have a role in reducing E.coli and coli-forms count. However, it has prevented an increase in E.coli and coliform count during 30 days. Formic acid and propionic acid reduced the number of E. coli and coliform (p<0.05). In addition, the two organic acids promoted the growth of mold and yeasts compared with potassium sorbate. Nonetheless, the mentioned three treatments did not have an important role in reducing total count (p>0.05). The natural fermentation contributed to the decline of E. coli and coliform count while total count increased one day after treatment compared with other treatments, however among the treatments, formic acid and potassium sorbate were more effective than propionic acid and natural fermentation treatment for maintaining hygienic quality of colostrum. The result of measuring IgG antibody indicated that potassium sorbate has had more protective effect than other treatments. CONCLUSIONS: The results exposed that potassium sorbate and formic acid are better than other treatments to maintain colostrum quality with regard to increasing shelf life of colostrum. © 2018 University of Tehran. All rights reserved.
Journal Of Food Quality And Hazards Control (2345685X) 5(2)pp. 54-60
Background: Nowadays, colostrum has been known as a considerable and valuable by-product of large-scale dairy production in the world. The main objective of this study was to evaluate the effects of pasteurization, spray-drying and freeze-drying methods on bacterial loads and Immunoglobulin G (IgG) level of bovine colostrums. Methods: Colostrum samples were collected from the first milking postpartum of Iranian Holstein dairy cattle farms. The samples were treated by pasteurization (60 °C for 30 min and 55 °C for 60 min), spray-drying and freeze-drying methods. Standard Plate Counts (SPC), Escherichia coli count, and Total Coliform Count (TCC) were analyzed at days 1, 10, 20, and 30 of storage. Also, IgG level were assessed at the end of 30-day storage. Statistical analysis was performed using SPSS 17.0 (Chicago, IL, USA) software. Results: Although all four treatments showed direct impact on reduction of SPC, TCC, and E. coli count in colostrum stored at 1, 10, 20, and 30 days, but the spray-drying and freeze-drying methods were significantly (p < 0.05) more effective to reduce microbial loads. The mean IgG levels of the samples were 60.35 mg/ml for untreated samples (control); 30.65±6.95 mg/ml for spray-dried treatment; 36.97±6.79 mg/ml for freeze-dried treatment; 28.12±6.53 mg/ml for heated treatment at 60 °C/30 min; and 34.97±9.80 mg/ml for heated treatment at 55 °C/60 min. All four treatments resulted in significant (p < 0.05) reduction of the IgG levels. Conclusion: Considering the obtained results, it seems that freeze-drying and spraydrying methods could be more effective than pasteurization ones to enhance quality and shelf life of bovine colostrum for a long time. © 2018, Shahid Sadoughi University of Medical Sciences.
Annals of Microbiology (18692044) 68(12)pp. 931-942
The purpose of this study was to investigate the potential of immobilized lead- and cadmium-resistant Pseudomonas putida strain PT to remove heavy metals from aqueous medium under extreme conditions. The tolerance and accumulation of cadmium and lead ions by strain PT were investigated by minimal inhibitory concentration (MIC) determination and polymerase chain reaction (PCR) of cadA gene, respectively. The surface chemical functional groups of P. putida PT involved in the metal biosorption were identified by Fourier transform infrared (FTIR). Pseudomonas putida PT was immobilized in three matrices include carboxy-methyl cellulose (CMC), rice bran, and a new composite made of alginate, polyvinyl alcohol (PVA), and CaCO3 to prepare heavy metal adsorbent. The biosorbents were analyzed by SEM, and their metal removal capability was assayed in two consecutive cycles by atomic absorption spectroscopy. The viability of immobilized bacterial cells was determined by flow cytometry during storage at 4 °C and exposure to the environmental stresses (pH and temperature). The results showed that PT strain was resistant up to 10 mM Pb2+ and 8 mM Cd2+. FTIR analysis revealed that alcohol, sulfur, phosphate, esters, and amide groups played important roles in metal biosorption process and, also change in metabolic reactions like hydration and polyesters accumulation was observed after metal biosorption. The presence of cadA gene, a heavy metal translocating pump-coding gene, indicated the ability of metals bioaccumulation by the PT strain. Immobilized cells in alginate–PVA–CaCO3 and rice bran showed the highest metal removal efficiency for Pb2+ as 75% and Cd2+ as 96.7%, respectively. Metal adsorbents were reusable, and the highest removal efficiency in the second cycle was observed in inoculated alginate–PVA–CaCO3 (79.5% Pb2+ and 45% Cd2+). Flow cytometric analysis represented that the immobilized cell viability was retained (< 97%) after 4 weeks storage at 4 °C. Viability under two environmental stresses in all matrices was as follows: < 96% at 25 °C, < 87% at 45 °C, < 85% at pH 4, < 96% at pH 7, and < 89% at pH 11. The results signify that these metal adsorbents are efficient technological tools for bioremediation even in harsh environmental conditions. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature and the University of Milan.
Iranian Journal of Science and Technology, Transaction A: Science (10286276) 42(3)pp. 1139-1147
The main purpose of this research was to search various collections of soil samples for isolating antibacterial agent-producing actinomycetes against drug-resistant pathogens and find the relationship between growth and antibacterial agent production in broth culture. Primary screening for antibacterial agent production was done by overlay agar technique. Production kinetics was assessed by minimum inhibitory concentration (MIC) determination using dilution method for 10 days and compared to growth in broth culture. The Hypothetical growth cycle in solid medium was studied using slide culture technique. Among 110 isolated strains, 17% were active against Staphylococcus aureus (ATCC 6538), 17% against Bacillus subtilis (ATCC 12711), 8% against methicillin-resistant Staphylococcus aureus (MRSA), 4.5% against vancomycin-resistant enterococci (VRE), and 0.9% against Escherichia coli (ATCC 1399). Two of the best strains, F9 and Is5, were selected for assessing production kinetics. They showed an irregular growth in liquid medium. Fluctuations are the continuous growth/death processes. Antibacterial agent production reached the highest expression level in the end and middle of the first descending phase in growth curve for strains F9 and Is5, respectively. The best MIC values of strain F9 extract were 0.97, 0.97, 1.37, and 1.1 mg/L against S. aureus, B. subtilis, MRSA, and VRE, while the best MIC value of Is5 extract was 1.92 and 1.67 mg/L against S. aureus and B. subtilis, respectively. No change was seen in growth of E. coli in the presence of nearly 1500 mg/L strain Is5 extract during 10 days. Comparing the 16S rDNA gene sequences of isolates and type strains retrieved from GenBank/EzTaxon showed that strains F9 and Is5 have 99.88 and 95.68% similarity with Streptomyces chryseus and S. anulatus, respectively. 16S rDNA gene sequence of the isolates was deposited in the NCBI GenBank database, under the accession numbers KX417085 and KX417086. Based on the results obtained in the present study, it can be concluded that the separation possibility of the antibacterial agent-producing actinomycetes against Gram-negative and drug resistance bacteria is very low. However, new places can be a promising source for isolation of strains with the ability to produce new, diverse and effective antibacterial agents. © 2017, Shiraz University.
Soleymani, S. ,
Alizadeh, H. ,
Mohammadian, H. ,
Rabbani, E. ,
Moazen, F. ,
Sadeghi, H.M.M. ,
Shariat, Z.S. ,
Etemadifar, Z. ,
Rabbani, M. Avicenna Journal Of Medical Biotechnology (20084625) 9(2)pp. 82-86
Background: Lipase enzymes have applications in a wide range of industries. A crucial determining factor of industrial prices of these enzymes is the culture media composition that is constantly under review by researchers. In this work, for maximum lipase production by Bacillus sp. ZR-5, culture media compositions were optimized using "one variable at a time" strategy. Methods: For this purpose, the culture medium parameters such as low and high cost carbon and nitrogen sources, substrates and incubation times were evaluated. Results: Maximum lipase activity was achieved after 24 hr of incubation with 1.5% of glucose syrup (1600±69.1 u/mg), 1% of fish powder (1238±36.7 u/mg) and olive oil (1407±2.1 u/mg) as low cost carbon and nitrogen sources and substrate, respectively. Conclusion: Our results show a significant increase in lipase activity with usage of low cost sources; this could help in reducing the media prices for industrial application of lipase enzyme. © 2017, Avicenna Journal of Medical Biotechnology. All rights reserved.
Journal of Biology and Today's World (discontinued) (23223308) 6(11)pp. 230-239
Worldwide industrial activities produce large amount of metal wastes. Metals remediation by microbial activities associated with phosphorus metabolism is a promising method. The goals of this study were the removal of some heavy metals by isolated phosphate solubilizing rhizobacterium (PSR) and survey the effect of total secreted materials including extracellular phosphatase on this phenomenon. PSR strain was isolated by Pikovskaya (PVK) medium and identified by 16S rDNA sequencing. Its phosphatase enzyme was assayed by colorimetric method. Metal resistance of the isolate was measured by the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). The metal removal was detected by atomic absorption spectroscopy. The culture supernatant was analyzed for metal removal by secreted phosphatase enzyme with or without tri-calcium phosphate (TCP), as its substrate. The isolated rhizobacterium was identified as Acinetobacter calcoaceticus that produced acid phosphatase enzyme. The MICs50 were obtained 2.5 mM Pb(II), 2 mM Ni(II), 0.2 mM Cr(II) and <1 mM Cd(II); and the MBCs were >100 mM Ni(II), 40 mM Cd(II), 20 mM Pb(II), and 1 mM (Cr(II). The removal of metals by the cells were obtained 29.45% Cr(II), 25.74% Pb(II), 18.85% Cd(II) and 11.43% Ni(II). It was not seen any nickel removal by microbial secreted products in PVK medium without TCP, whereas removal was obtained in PVK complimented by TCP 28.3%; lead removal was almost the same in both media (99%) and was not related to TCP. © 2017 Fatemeh Ghoreishi et al.
Naghoni, A. ,
Emtiazi, G. ,
Amoozegar, M.A. ,
Cretoiu, M.S. ,
Stal, L.J. ,
Etemadifar, Z. ,
Shahzadeh fazeli, S.A. ,
Bolhuis, H. Scientific Reports (20452322) 7(1)
Lake Meyghan is one of the largest and commercially most important salt lakes in Iran. Despite its inland location and high altitude, Lake Meyghan has a thalassohaline salt composition suggesting a marine origin. Inputs of fresh water by rivers and rainfall formed various basins characterized by different salinities. We analyzed the microbial community composition of three basins by isolation and culturing of microorganisms and by analysis of the metagenome. The basins that were investigated comprised a green ~50 g kg-1 salinity brine, a red ~180 g kg-1 salinity brine and a white ~300 g kg-1 salinity brine. Using different growth media, 57 strains of Bacteria and 48 strains of Archaea were isolated. Two bacterial isolates represent potential novel species with less than 96% 16S rRNA gene sequence identity to known species. Abundant isolates were also well represented in the metagenome. Bacteria dominated the low salinity brine, with Alteromonadales (Gammaproteobacteria) as a particularly important taxon, whereas the high salinity brines were dominated by haloarchaea. Although the brines of Lake Meyghan differ in geochemical composition, their ecosystem function appears largely conserved amongst each other while being driven by different microbial communities. © 2017 The Author(s).
Naghoni, A. ,
Emtiazi, G. ,
Amoozegar, M.A. ,
Rasooli, M. ,
Etemadifar, Z. ,
Shahzadeh fazeli, S.A. ,
Minegishi, H. ,
Ventosa, A. International Journal of Systematic and Evolutionary Microbiology (14665026) 67(9)pp. 3339-3344
A novel halophilic archaeon, designated strain WIIAL99T, was isolated from Lake Meyghan, a hypersaline lake in Iran. Cells of strain WIIAL99T were non-motile, catalase-positive and oxidase-negative. Strain WIIAL99T required at least 2.5 M NaCl and 0.05 M MgCl2 for growth. Optimal growth was achieved at 3.5 M NaCl and 0.1 M MgCl2. The optimum pH and temperature for growth were pH 7.0 and 37–40 °C; it was able to grow at pH 6.0–8.5 and 20–55 °C. Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8% (w/v). The major polar lipids of strain WIIAL99T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, disulfated diglycosyl diether and one unidentified glycolipid. The DNA G+C content of strain WIIAL99T was 66.7 mol%. The closest relative was Natronoarchaeum rubrum JCM 17119T with 98.2% similarity in the orthologous 16S rRNA gene sequence. Analysis of 16S rRNA and rpoB′ gene sequences indicated that strain WIIAL99T is a member of the genus Natronoarchaeum in the family Halobacteriaceae and forms a distinct cluster. It was concluded that strain WIIAL99T (=IBRC-M 11062T=LMG 29814T) represents a novel species of the genus Natronoarchaeum, for which the name Natronoarchaeum persicum sp. nov. is proposed. © 2017 IUMS.
Comparative Clinical Pathology (1618565X) 25(1)pp. 59-65
The postburn infections especially antibiotic-resistant bacterial infections have been recognized as a significant and major public health problem. Staphylococcus aureus, Escherichia coli, Acinetobacter, Klebsiella pneumoniae, and Pseudomonas aeruginosa are among very important bacterial pathogens isolated from postburn infections. The present study has evaluated the antimicrobial activity of some plant extracts (Melissa officinalis and Lawsonia inermis) against some bacterial pathogens causing burn wound infection. The minimal inhibitory concentration (MIC) and the minimal bactericidal concentration (MBC) of the extracts were determined using the microdilution method. Aqueous and alcoholic extracts of L. inermis leaves or powder and hydro-alcoholic extract of M. officinalis were studied. All extracts had the highest antibacterial activity against S. aureus. Although there was no significant difference between antibacterial activity of L. inermis leaves and powder extracts, significant difference was observed between alcoholic and aqueous extracts of this plant. In addition, the results showed that alcoholic extract of L. inermis powder and M. officinalis extracts showed synergistic effect. Overall, these findings support the potential benefits of M. officinalis and L. inermis extracts in the treatment of burn infections. © 2015, Springer-Verlag London.
Biotechnology Letters (15736776) 38(9)pp. 1565-1570
Objectives: To improve the production and activity of an alkaline zinc metalloprotease from Salinivibrio proteolyticus in response to ZnSO4 (ionic and nanoparticle forms) and low intensity direct electric current (LIDC). Results: A DC of 50 µA for 10 min increased enzyme production from 35 to 53 U ml−1 when applied to the stationary phase bacterial cells. Zn2+ improved enzyme production better than zinc nanoparticles (52 vs. 43.5 U ml−1). Zinc nanoparticles (0.5 mM) added to an enzyme reaction mixture containing casein (0.65 %) and 20 mM Tris/HCl buffer (pH 8) improved enzyme activity more than Zn2+ (42 vs. 36 U ml−1). Conclusion: LIDC exposure (50 µA, 10 min) to the stationary phase bacterial cells increases metalloprotease production in Salinivibrio. A low concentration of zinc nanoparticles (0.5 mM) increases maximum enzyme activity. © 2016, Springer Science+Business Media Dordrecht.
Current Microbiology (03438651) 72(6)pp. 707-715
Coal is the most abundant fossil fuel containing sulfur and other elements which promote environmental pollution after burning. Also the silicon impurities make the transportation of coal expensive. In this research, two isolated fungi from oil contaminated soil with accessory number KF554100 (Fusarium oxysporum FE) and KC925672 (Exophiala spinifera FM) were used for heterotrophic biological leaching of coal. The leaching were detected by FTIR, CHNS, XRF analyzer and compared with iron and sulfate released in the supernatant. The results showed that E. spinifera FM produced more acidic metabolites in growing cells, promoting the iron and sulfate ions removal while resting cells of F. oxysporum FE enhanced the removal of aromatic sulfur. XRF analysis showed that the resting cells of E. spinifera FM proceeded maximum leaching for iron and silicon (48.8, 43.2 %, respectively). CHNS analysis demonstrated that 34.21 % of sulfur leaching was due to the activities of resting cells of F. oxysporum FE. Also F. oxysporum FE removed organic sulfur more than E. spinifera FM in both growing and resting cells. FTIR data showed that both fungi had the ability to remove pyrite and quartz from coal. These data indicated that inoculations of these fungi to the coal are cheap and impurity removals were faster than autotrophic bacteria. Also due to the removal of dibenzothiophene, pyrite, and quartz, we speculated that they are excellent candidates for bioleaching of coal, oil, and gas. © 2016, Springer Science+Business Media New York.
Geomicrobiology Journal (01490451) 33(7)pp. 1-7
The high UV radiation and scarcity of liquid water in desert areas make these regions among the most challenging environments for life. Here we studied the multitolerant microbial communities of deserts in Iran. Three bacterial strains were isolated and identified as Microbacterium phyllosphaerae MG3, Kocuria flava MG5 and Exiguobacterium acetylicum MG7. UV resistance and desiccation tolerance in MG7 and MG5 strains were comparable to multiresistant Deinococcus radiodurans. Also, resistance to mitomycin C and hydrogen peroxide in all isolated strains were significant. The strain MG3 showed moderate to poor salt tolerance but strains MG5 and MG7 showed high NaCl tolerance. © 2016 Taylor & Francis Group, LLC.
World Journal of Microbiology and Biotechnology (09593993) 31(5)pp. 813-821
Sulfur dioxide which is released from petroleum oil combustion causes pollution over the atmosphere and the soil. Biodesulfurization can be used as a complementary method of hydrodesulfurization, the common method of petroleum desulfurization in refineries. Many studies have been carried out to develop biological desulfurization of dibenzothiophene (DBT) with bacterial biocatalysts. However, fungi are capable to metabolize a wide range of aromatic hydrocarbons through cytochrome P450 and their extracellular enzymes. The aim of the present work was isolation and identification of fungi biocatalysts capable for DBT utilization as sulfur source and production of novel metabolites. DBT consumption and the related produced metabolites were analyzed by HPLC and GC–MS respectively. One of the isolated fungi that could utilize DBT as sole sulfur source was identified by both traditional and molecular experiments and registered in NCBI as Exophiala spinifera FM strain (accession no. KC952672). This strain could desulfurize 99 % of DBT (0.3 mM) as sulfur source by co-metabolism reaction with other carbon sources through the same pathway as 4S and produced 2-hydroxy biphenyl (2-HBP) during 7 days of incubation at 30 °C and 180 rpm shaking. However, the isolate was able to transform 2-HBP to 1,3-benzenediol, 5-hexyl. While biphenyl compounds are toxic to leaving cells, biotransformation of them can reduce their toxicity and the fungi will be more tolerant to the final product. These data are the first report about the desulfurization of DBT comparable to 4S-pathway and production of innovative metabolite by E. spinifera FM strain. © 2015, Springer Science+Business Media Dordrecht.
Waste Management and Research (0734242X) 33(1)pp. 89-89
Journal of Environmental Radioactivity (18791700) 144pp. 113-119
A new actinobacterial strain was isolated from Ab-e-Siah spring (dark water) taken from the Ramsar city in Iran, and subjected to several stress conditions investigation. The isolate, named MG2 strain, was Gram-positive, aerobic, diplococci or tetrad shaped, non-spore forming and non-motile. Phylogenetic analysis of the isolate using 16S rDNA sequence indicated that the organism matched best with the genus Kocuria and the highest sequence similarities (98.55%) being found with Kocuria rosea. The 16S rDNA sequence determined in this study has been deposited in the NCBI database with the accession no. JX534199, K. rosea strain MG2. The isolated strain was an alkaliphilic-mesophilic bacterium because the optimal growth was observed at pH 9.2 and temperature of 28°C under aerobic condition. MG2 was a halotolerant strain and tolerated maximally to 15% NaCl concentraion. Viability analysis by flow cytometry indicated that this strain had highly resistance to UV-C radiation and moderately resistance to desiccation after 28 days. The viability of K. rosea strains MG2 and Deinococcus radiodurans R1 were determined D87 and D98 according to D index, respectively, by a dose radiation 25J/cm (Appukuttan etal., 2006). Thus the UV resistance of strain MG2 was comparable with representative radiation resistant Deinococcus. Also MG2 was grown at 1-4% of H2O2 as an oxidant agent. This research is the first study on multiple extreme resistance of Kocuria rosea new strain (MG2) isolated in Iran. © 2015 Elsevier Ltd.
Rabbani, M. ,
Shafiee, F. ,
Shayegh, Z. ,
Sadeghi, H.M.M. ,
Shariat, Z.S. ,
Etemadifar, Z. ,
Moazena, F. Iranian Journal Of Pharmaceutical Research (17350328) 14(3)pp. 901-906
Lipases are diversified enzymes in their properties and substrate specificity, which make them attractive tools for various industrial applications. In this study, an alkalinethermostable lipase producing bacteria were isolated from soil of different regions of Isfahan province (Iran) and its lipase was purified by ammonium sulfate precipitation and ion exchange chromatography. To select a thermoalkalophil lipase producing bacterium, Rhodamine B and Horikoshi media were used and the strain that can grow at 45 °C was selected. The isolated strain was identified using microbial and biochemical tests. One strain showed an orange colored zone on plate and grew on Horikoshi plate. Microbial and biochemical tests showed that the isolated strain was Bacillus subtilis, a Gram positive rod. In PCR, an expected band was obtained with about 371 bp. The activity of the purified lipase was 10.2 folds that of the standard enzyme using ammonium sulfate precipitation and ion exchange chromatography. The molecular weight of lipase determined by SDS-PAGE electrophoresis, was 21 and 35 KDa. Existence of two bands in SDS-PAGE electrophoresis and low amount of obtained purified enzyme highlights the necessity of optimization of purification and concentrating process. © 2015 by School of Pharmacy Shaheed Beheshti University of Medical Sciences and Health Service.
Microbiology (Russian Federation) (16083237) 84(3)pp. 389-397
An ultraviolet (UV) radiation resistant gram-positive bacterium, Dietzia sp. MG4 strain, was isolated from the Sirch Hot Spring (Kerman, Iran), then it was identified on the basis of morphological and biochemical characteristics, and 16S rRNA gene sequencing. The effects of temperature, pH, desiccation, different percentage of NaCl, hydrogen peroxide (H2O2), mitomycin C (MMC) and high levels of radiation on viability or growth rate of MG4 strain were investigated. Also heavy metal tolerance of MG4 strain was assayed. 16S rDNA sequence of the isolate exhibited 99.69% similarity with Dietzia sp. and this result was confirmed by phylogenetic analysis. Viability of this strain was obtained D91 according to D index after exposure to 25 J/cm2 UV radiation dose, and D30 after desiccation stress (for 28 days) using flow cytometery. The D10 value for a microorganism is defined as the stress dose necessary to provide 10% survivors. Therefore, this strain showed high resistance to UV-C radiation and moderate resistance to desiccation. Optimal growth of MG4 strain was observed at pH 9, temperature of 30°C and 5% (w/v) NaCl. Isolated Dietzia was resisted up to 3 mM of nickel and 0.2 mM of mercury ions. Also this strain could tolerate 1–4% (v/v) H2O2 and 8 µg/mL of MMC as oxidant agents. To the best of our knowledge, this is the first study on multiple extreme resistant Dietzia sp. MG4 strain. © 2015, Pleiades Publishing, Ltd.
Brazilian Journal Of Microbiology (15178382) 46(3)pp. 791-797
One of the most economically important bacterial pathogens of plants and plant products is Dickeya dadantii. This bacterium causes soft rot disease in tubers and other parts of the potato and other plants of the Solanaceae family. The application of restricted host range bacteriophages as biocontrol agents has recently gained widespread interest. This study purposed to isolate the infectious agent of the potato and evaluate its biocontrol by bacteriophages. Two phytopathogenic strains were isolated from infected potatoes, identified based on biochemical and 16S rRNA gene sequencing, and submitted to GenBank as D. dadantii strain pis3 (accession no. HQ423668) and D. dadantii strain sip4 (accession no. HQ423669). Their bacteriophages were isolated from Caspian Sea water by enriching the water filtrate with D. dadantii strains as hosts using spot or overlay methods. On the basis of morphotypes, the isolated bacteriophages were identified as members of the Myoviridae and Siphoviridae families and could inhibit the growth of antibiotic resistant D. dadantii strains in culture medium. Moreover, in Dickeya infected plants treated with bacteriophage, no disease progression was detected. No significant difference was seen between phage-treated and control plants. Thus, isolated bacteriophages can be suggested for the biocontrol of plant disease caused by Dickeya strains. © 2015, Sociedade Brasileira de Microbiologia.
Journal of Environmental Radioactivity (18791700) 147pp. 155-156
Polish Journal of Microbiology (17331331) 64(1)pp. 47-54
Dibenzothiophene (DBT) is an organic sulfur compound which remains in oil after hydrodesulfurization (HDS) process and can be removed by biodesulfurization (BDS). A new strain of Paenibacillus validus (strain PD2) was isolated from oil contaminated soils that is able to desulfurize DBT. HPLC analysis and Gibb's assay showed that this strain was capable to convert DBT to 2-Hydroxybiphenyl (2-HBP) as final product. The presence of dszC gene confirmed that DBT desulfurization occurred through the 4S pathway. Maximum growth and the highest induction in dsz operon obtained in the presence of dimethyl sulfoxide (DMSO) as sole sulfur source. DBT concentration, temperature and pH were optimized statistically for growing and resting cells by using Response Surface Methodology (RSM). All parameters in growing cells had a significant effect on 2-HBP production during BDS of DBT by P. validus PD2, although in resting cells temperature in range of 20-40°C was not a significant factor. Maximum BDS for growing cells was obtained at 0.41 mM DBT concentration, pH 6.92 and temperature 31.23°C. For resting cells, optimum pH, temperature and DBT concentration were 6.62, 27.73°C and 7.86 mM respectively. The results of this study showed that high concentrations of DBT could be desulfurized by P. validus strain PD2 in model-oil. Thus, the isolated strain could be introduced as a proper candidate for biodesulfurization of organic sulfur in the oil industry.
Synthesis and Reactivity in Inorganic, Metal-Organic and Nano-Metal Chemistry (15533174) 45(12)pp. 1759-1763
To remove sulfur compounds in petroleum, the authors prepared intracellular enzymes that could degrade dibenzothiophene (DBT) in the presence of titania nanolayer coated on glass as photocatalyst. The titania nanolayer was synthesized by the sol-gel method coated on glass by doctor blade method using titanium tetra isopropoxide (TTIP) as precursor and characterized by Fourier transmission infrared (FT-IR), X-ray diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM) techniques, atomic force microscopy (AFM), and UV-Vis spectroscopy (DRS). The enzymatic action of the intracellular enzymes in aqueous media containing a titania was evaluated as a feasible system for the degradation of dibenzothiophene as a model sulfur compound. Dibenzothiophene was degraded to a large extent after a very short period of 20 min. Intracellular enzymes in the presence of titania nanolayer possess synergic effect in photocatalytic and enzymatic degradation of dibenzothiophene by titania nanolayer coated on glass using doctor blade method and intracellular enzymes. © 2015 Copyright © Taylor & Francis Group, LLC.
Jundishapur Journal Of Microbiology (20084161) 7(3)
Background: Sulfur oxides released from the burning of oil causes severe environmental pollution. The sulfur can be removed via the 4S pathway in biodesulfurization (BDS). Immobilization approaches have been developed to prevent cell contamination of oil during the BDS process. Objectives: The encapsulation of Rhodococcus erythropolis R1 in calcium alginate beads was studied in order to enhance conversion of dibenzothiophene (DBT) to 2-hydroxy biphenyl (2-HBP) as the final product. Also the effect of different factors on the BDS process was investigated. Materials and Methods: Calcium alginate capsules were prepared using peristaltic pumps with different needle sizes to control the beads sizes. Scanning electron microscopy and flow cytometry methods were used to study the distribution and viability of encapsulated cells, respectively. Two non-ionic surfactants and also nano Y{hooktop}-Al2O3were used with the ratio of 0.5% (v/v) and 1:5 (v/v) respectively to investigate their BDS efficiency. In addition, the effect of different bead sizes and different concentrations of sodium alginate in BDS activity was studied. Results: The 2% (w/v) sodium alginate beads with 1.5mm size were found to be the optimum for beads stability and efficient 2-HBP production. The viability of encapsulated cells decreased by 12% after 20 h of desulfurization, compared to free cells. Adding the non-ionic surfactants markedly enhanced the rate of BDS, because of increasing mass transfer of DBT to the gel matrix. In addition, Span 80 was more effective than Tween 80. The nanoY{hooktop}-Al2O3 particles could increase BDS rate by up to two-folds greater than that of the control beads. Conclusions: The nano Y{hooktop}-Al2O3 can improve the immobilized biocatalyst for excellent efficiency of DBT desulfurization. Also the BDS activity can be enhanced by setting the other explained factors at optimum levels. © 2014, Ahvaz Jundishapur University of Medical Sciences; Published by Kowsar Corp.
Rabbani, M. ,
Bagherinejad, M.R. ,
Sadeghi, H.M.M. ,
Shariat, Z.S. ,
Etemadifar, Z. ,
Moazen, F. ,
Rahbari, M. ,
Mafakher, L. ,
Zaghian, S. Brazilian Journal Of Microbiology (15178382) 44(4)pp. 1113-1119
The purpose of the present study was to screen and identify the lipase-producing microorganisms from various regions of Iran. Samples collected from hot spring, Persian Gulf, desert area and oil-contaminated soil, were analyzed for thermophilic extracellular-lipase producing organisms. Six strains with high activity on rhodamine B plates were selected for chemical identification and further study. Among these isolated bacteria, four strains show higher activity in pH-Stat method at 55 °C. These strains were identified by PCR amplification of 16s rRNA genes using universal primers. Fermentation increased the activity up to 50%. The growth medium, designed for lipase production, increased the activity up to 4.55 folds. The crude supernatant of ZR-5 after fermentation and separation the cells, was lyophilized and the activity was measured. Total activity of this strain was 12 kU/g that shows its potential for industrial uses. Further study is required for purification of enzyme and calculation its specific activity. Immobilization is another approach should be considered. © 2013, Sociedade Brasileira de Microbiologia.
Jundishapur Journal Of Microbiology (20084161) 5(4)pp. 550-554
Background: In recent decades bacteriophages have been used as treating agents against some pathogens. Also, bacteriophages could be considered as alternatives of antimicrobial agents in plant protection. Objectives: This study aimed to isolate a pathogen from potato (Solanum tubersom) tubers (Pseudomonas putida), and of its specific bacteriophage from soil and wastewater. Materials and Methods: Infected samples of soft rot potato tubers were collected from Flavarjan farms (Isfahan province, Iran) to isolate and identify P. putida by biochemical and molecular methods. Soil and wastewater samples were obtained locally to isolate the bacteriophage attributed to P. putida. Soil suspension was centrifuged and then filtrated by 0.2 micrometer Millipore filter. The wastewater was directly filtrated by 0.2 micrometer filter after centrifugation. After incubation of isolated bacteria together with phage contained solution, plaques were detected in nutrient agar. Subsequently, clearance of P. putida liquid culture incubated by added filtrated bacteriophage was observed. The structure and morphological characteristics of P. putida related bacteriophage was remarked by transmission electron microscopy (TEM). Results: Isolated strain sda2 was identified as Pseudomonas putida with related accession number HQ423667. The result showed that isolated bacteriophage belonged to Cystoviridae family. Conclusions: We isolated a new strain of P. putida as well as a novel bacteriophage through which potato disease caused by the bacterium could be treated. © 2012 Ahvaz Jundishapur University of Medical Sciences; Published by Kowsar Corp.
Rabbani, M. ,
Sadeghi, H.M.M. ,
Ani, M. ,
Chegini, K.G. ,
Etemadifar, Z. ,
Moazen, F. Research In Pharmaceutical Sciences (17355362) 4(1)pp. 25-32
The present study was aimed to isolate and characterize the lipolytic enzyme producing bacteria from soil samples of regions around Zayande-rood river of Isfahan, Iran. Soil samples were collected from 15 cm depth of soil surface. Based on morphology, distinct colonies were isolated and purified through streak culture onto standard agar plates. Isolated colonies were examined for lipase activity using egg-yolk agar medium. Total of 15 isolates developed clear zones around their growth area which were considered as lipase positive. Preliminary identification of lipolytic active isolates revealed them to be gram-positive, rod-shaped, endospore-forming and catalase positive bacteria, characteristics indicative of the genus bacillus. The gene coding for an extracellular lipase was cloned using PCR techniques. The gene was identified to be 639 bp in length and encoded a peptide of 212 amino acids with calculated molecular mass of 19353.96. Da, and pI 9.28. The DNA sequence and deduced amino acid sequence of the hypothetical lipase showed striking similarities to lipases from B. subtilis strains.
Rabbani, M. ,
Sadeghi, H.M.M. ,
Ani, M. ,
Chegini, K.G. ,
Etemadifar, Z. ,
Moazen, F. Annals of Microbiology (18692044) 59(4)pp. 763-769
The aim of the present study was to express and evaluate a previously cloned lipase gene. In this study, the cloned gene was subcloned in the pET15b Escherichia coli BL21(DE3) expression system. The expression of the recombinant lipase was induced using 1 mM IPTG for 3 hours. The enzyme activity was measured using p-nitrophenyl-decanoate as substrate. The recombinant lipase showed a molecular weight of 26 kDa by SDS-PAGE. Maximum activity was found at pH 9-10 and 40-50 °C. ZnCl2 at 1, 0.3, 0.1, 0.03, and 0.01 mM concentrations were found to be inhibitory to the enzyme activity and did not improve enzyme thermostability. The recombinant lipase showed an optimum temperature higher than lipase of Bacillus subtilis (its closest relative in primary structure) while similar activity in the alkaline pH.
Zeitschrift fur Naturforschung - Section C Journal of Biosciences (09395075) 63(7-8)pp. 599-604
Gasoline-contaminated soil from Isfahan, Iran was selected to isolate a bacterium capable of desulfurizing dibenzothiophene (DBT). The isolated strain was named R1 and identified as Rhodococcus erythropolis through biochemical tests as well as sequencing of 16S rRNA gene. This strain could efficiently produce 2-hydroxybiphenyl (HBP) from DBT via the 4S metabolic pathway. The highest HBP amount was produced at 2 mM DBT with addition of glucose (10 g l-1), ethanol (3 g l-1), glycerol (2 g l-1) or succinate (10 g l-1) as carbon sources at pH 7. Highest respiration and growth rates were observed by microplate titration on 0.1 mM HBP, and addition of 0.2 mM HBP to glucose (1 g l-1) and DBT (0.3 mM) could inhibite the respiration of the isolate. The isolated strain could grow up to 0.4 mM of HBP when it is used with mineral sulfur as sole sulfur source. To the best of our knowledge this is the first report on a microtiter assay for the production and utilization of HBP by Rhodococcus. © 2008 Verlag der Zeitschrift für Naturforschung.
African Journal of Biotechnology (16845315) 3(6)pp. 330-333
Two Azotobacter strains were isolated from alkaline and acid soils. The production of alginate and exopolymer from these two strains showed that, strain AC2 produced high polymer in 2% beet molasses or 1% sucrose broth and addition of nitrogen sources (yeast extract) reduced production of this polymer. The optimum condition for production of maximum polymer production (7.5 mg/ml) was at 200 rpm shaking, pH 7 without addition of nitrogen sources. The production of polymer was reduced at pH 4. The polymer adsorbed Cu, Zn, and Fe, at 15.5, 20 and 25 mg, respectively. © 2004 Academic Journals.
Biomass and Bioenergy (09619534) 25(4)pp. 423-426
A Gram-negative bacterium was isolated from corn root. This isolate is ellipsoidal to rod-shaped and slightly curved. The size of bacterium is 0.6 × (1 - 4) nm and occurring singly, in pairs or in chains. The isolated strain reduces nitrate, oxidizes ethanol to acetic acid, and hydrolyses starch and cellulose. The maximum amylase and Cellulase activities are 20 and 5.5 u ml-1, respectively. In addition, the isolate fixes nitrogen and has a good growth on the media without any nitrogen sources. A nitrogen fixation negative strain (Nif-) was obtained from the isolate by UV mutation. This mutant strain Nif- dose not grow on the media without nitrogen sources, but it has cellulase activities. © 2003 Elsevier Ltd. All rights reserved.
