University of Isfahan Journal of Microbial Biology 3060-7647 1 1 2012 05 21 Priliminary Pages ( 1 st.Year No.1) Priliminary Pages ( 1 st.Year No.1) 1 19458 FA Journal Article 2016 06 14 https://bjm.ui.ac.ir/article_19458_70fb6b70c05a01ec21cdd7f4c93b50c8.pdf

University of Isfahan Journal of Microbial Biology 3060-7647 1 1 2012 05 21 Isolation and characterization of a Facultative chemolithotrophic sulphur and iron oxidizing bacterium from Ardabil acidic springs Isolation and characterization of a Facultative chemolithotrophic sulphur and iron oxidizing bacterium from Ardabil acidic springs 1 10 19452 FA Nima Salamian MSc of Microbiology, Shahid Beheshti University, Tehran, Iran GolamHossein Ebrahimipour Associate Professor of Microbiology, Shahid Beheshti University, Tehran, Iran Mahdi Ghasemi PhD student of Microbiology, University of Isfahan, Isfahan, Iran Javad Fakhari Lecturer of Microbiology, Shahid Beheshti University, Tehran, Iran Journal Article 2016 06 14 Introduction: Since metal extraction from sulfide ores by physicochemical methods is expensive and also detrimental to the environment, microorganisms, mainly bacteria are being increasingly used for desulfurization of sulfide minerals. Microbial leaching or bioleaching is an inexpensive and environmentally friendly technology for metal recovery.Materials and Methods: In the present study, to isolate iron and sulfur-oxidizing bacteria which are active in bioleaching process, spring water samples were collected and enriched by iron and sulfur-containing media. In order to identify the isolated bacteria, several morphological, physiological, biochemical and 16S rDNA phylogenetical methods were implemented. Results: After several sub-cultures, a gram-positive spore-forming rod (NS strain) was isolated and then characterized. Sequence analysis of 16S rDNA revealed that the isolated strain was closely related to Bacillus firmus strain IAM 12464 (99%), that was capable to oxidize several sulphur and iron component such as: thiosulfate 5%, elemental sulphur 3%, sodium sulphate 3%, pyrite 3%, pyrrhotite 3%, ferrous sulphate 4.5% and Iron powder 2%. Also, this isolate could dissolve copper of SARCHESHME ore to copper sulphate and change the colour of medium to blue-green. The optimal growth of the isolate was observed at 25Â°C and pH 4. Discussion and Conclusion: Due to the optimum pH and temperature, and the iron and sulphur oxidizing activity of this isolate, this bacterium together with a consortium of lithotrophic bacteria could be used in bioleaching processes. Introduction: Since metal extraction from sulfide ores by physicochemical methods is expensive and also detrimental to the environment, microorganisms, mainly bacteria are being increasingly used for desulfurization of sulfide minerals. Microbial leaching or bioleaching is an inexpensive and environmentally friendly technology for metal recovery.Materials and Methods: In the present study, to isolate iron and sulfur-oxidizing bacteria which are active in bioleaching process, spring water samples were collected and enriched by iron and sulfur-containing media. In order to identify the isolated bacteria, several morphological, physiological, biochemical and 16S rDNA phylogenetical methods were implemented. Results: After several sub-cultures, a gram-positive spore-forming rod (NS strain) was isolated and then characterized. Sequence analysis of 16S rDNA revealed that the isolated strain was closely related to Bacillus firmus strain IAM 12464 (99%), that was capable to oxidize several sulphur and iron component such as: thiosulfate 5%, elemental sulphur 3%, sodium sulphate 3%, pyrite 3%, pyrrhotite 3%, ferrous sulphate 4.5% and Iron powder 2%. Also, this isolate could dissolve copper of SARCHESHME ore to copper sulphate and change the colour of medium to blue-green. The optimal growth of the isolate was observed at 25Â°C and pH 4. Discussion and Conclusion: Due to the optimum pH and temperature, and the iron and sulphur oxidizing activity of this isolate, this bacterium together with a consortium of lithotrophic bacteria could be used in bioleaching processes.

https://bjm.ui.ac.ir/article_19452_0f7f3cfa76e31d214e209ce1986361d5.pdf

University of Isfahan Journal of Microbial Biology 3060-7647 1 1 2012 05 21 Application of ordination technique in investigating Diatom populations and their relation with environmental factors (Case study: Masooleh Roudkhan) Application of ordination technique in investigating Diatom populations and their relation with environmental factors (Case study: Masooleh Roudkhan) 11 22 19453 FA Moslem Sharifinia MSc of Aquatic Ecology, University of Guilan, Guilan, Iran Javid Imanpour Namin Associate Professor of Ecology of running water, University of Guilan, Guilan, Iran Zohreh Ramezanpoor Associate Professor of Ecology of running water, International Sturgeon Research Institute, Guilan, Iran Journal Article 2016 06 14 Abstract Introduction: Benthic diatom populations are highly diverse and ubiquitous, and consistently correlate with environmental variables. The present study was conducted to evaluate effects of some physical and chemical parameters on abundance of diatoms in a tributary of the Masooleh River in summer, autumn and winter in the year 2011. Materials and Methods: The samples were collected from surface layers of Epilithon, Epidendron, Epipssamon and Epipelon as natural substrates. The collected samples were processed and slides were prepared for LM examination. Masooleh River is located at 37o 22’ to 37o 23’ northern latitude and 49o17’- 49o19’ eastern longitude in Guilan Province, north of Iran. Five sampling sites were chosen along 15 km of the river Results: In this study 23 genera of diatoms were identified. The analyses showed that pH and Fe were negatively correlated with Diploneis, Gomphonema, Cymbella and Surirella and positively with Amphora, Achnanthes, Diatoma, Melosira, Nitzschia, Cymatopleura and Rhoicosphenia (P<0.05). The pH, Nitrate and EC were negatively correlated with Synedra, Navicula, Rhopalodia, Gyrosigma and positively with Nitzschia, Reimeria and Cocconeis (P<0.05). Discussion and Conclusion: Effects of salinity and water temperature on the diatom populations (Group 1: Cymbella, Surirella, Gomphonema, Diploneis, Cocconeis) were higher than other agents and factors such as pH, iron (Fe2+) and silicate (SiO2) were second rate in terms of importance. Abstract Introduction: Benthic diatom populations are highly diverse and ubiquitous, and consistently correlate with environmental variables. The present study was conducted to evaluate effects of some physical and chemical parameters on abundance of diatoms in a tributary of the Masooleh River in summer, autumn and winter in the year 2011. Materials and Methods: The samples were collected from surface layers of Epilithon, Epidendron, Epipssamon and Epipelon as natural substrates. The collected samples were processed and slides were prepared for LM examination. Masooleh River is located at 37o 22’ to 37o 23’ northern latitude and 49o17’- 49o19’ eastern longitude in Guilan Province, north of Iran. Five sampling sites were chosen along 15 km of the river Results: In this study 23 genera of diatoms were identified. The analyses showed that pH and Fe were negatively correlated with Diploneis, Gomphonema, Cymbella and Surirella and positively with Amphora, Achnanthes, Diatoma, Melosira, Nitzschia, Cymatopleura and Rhoicosphenia (P<0.05). The pH, Nitrate and EC were negatively correlated with Synedra, Navicula, Rhopalodia, Gyrosigma and positively with Nitzschia, Reimeria and Cocconeis (P<0.05). Discussion and Conclusion: Effects of salinity and water temperature on the diatom populations (Group 1: Cymbella, Surirella, Gomphonema, Diploneis, Cocconeis) were higher than other agents and factors such as pH, iron (Fe2+) and silicate (SiO2) were second rate in terms of importance.

https://bjm.ui.ac.ir/article_19453_0b1cde6fb72baaa86cdce2f5dc029fca.pdf

University of Isfahan Journal of Microbial Biology 3060-7647 1 1 2012 05 21 Optimization of exopectinase activity of the fungus Monilia isolated from tangerine in submerged fermentation Optimization of exopectinase activity of the fungus Monilia isolated from tangerine in submerged fermentation 23 30 19454 FA Nafiseh Sadat Naghavi Assistant Professor of Microbiology, Islamic Azad University, Falavarjan branch, Isfahan, Iran Saeide Naderi MSc of Microbiology, Islamic Azad University, Falavarjan branch, Isfahan, Iran Kahin Shahanipoor Assistant Professor of biochemistry, Islamic Azad University, Falavarjan branch, Isfahan, Iran, Mohammad Ali Zia Assistant Professor of medical and veterinary mycology, Islamic Azad University, Khorasgan branch, Isfahan, Ali Asghar Rastegari Esfahani Assistant Professor of molecular biophysics, Islamic Azad University, Falavarjan branch, Isfahan, Iran Journal Article 2016 06 14 Introduction: Diverse groups of microscopic fungi are able to degrade polymeric plant tissues such as pectin. Biodegradation of these materials are mostly applicable in food industries. Materials and Methods: In the present study, the exopectinase producing fungus was isolated from decaying tangerine and its exopectinase activity was studied in submerged fermenting condition. Also, the enzyme production of the isolated fungus was compared to the industrial fungus, Aspergillus niger PTCC 5013. The exopectinase production and activity of the extracted enzyme solution with respect to pH, temperature, activity timing and substrate concentration were scrutinized. Results: According to the morphological macroscopic and microscopic features, the isolated fungus was identified as the genus Monilia in the Moniliaceae family. The best exopectinase production was in pH 7 and the best enzyme activity achieved at 50Â°C, in 30 to 40 minute, 1.5% substrate and the 1:1 of the enzyme solution to the substrate solution ratio. The isolated fungus, Monilia, was fast growing and produced highly active exopectinase enzyme. In optimum condition, its exopectinase activity was 20 units higher than the fungus Aspergillus niger PTCC 5013. Discussion and Conclusion: The exopectinase enzyme was active in a wide ranges of pH and temperatures. As Monilia does not produce toxic compounds, it is proposed for pectinase production, especially in the food industries. Introduction: Diverse groups of microscopic fungi are able to degrade polymeric plant tissues such as pectin. Biodegradation of these materials are mostly applicable in food industries. Materials and Methods: In the present study, the exopectinase producing fungus was isolated from decaying tangerine and its exopectinase activity was studied in submerged fermenting condition. Also, the enzyme production of the isolated fungus was compared to the industrial fungus, Aspergillus niger PTCC 5013. The exopectinase production and activity of the extracted enzyme solution with respect to pH, temperature, activity timing and substrate concentration were scrutinized. Results: According to the morphological macroscopic and microscopic features, the isolated fungus was identified as the genus Monilia in the Moniliaceae family. The best exopectinase production was in pH 7 and the best enzyme activity achieved at 50Â°C, in 30 to 40 minute, 1.5% substrate and the 1:1 of the enzyme solution to the substrate solution ratio. The isolated fungus, Monilia, was fast growing and produced highly active exopectinase enzyme. In optimum condition, its exopectinase activity was 20 units higher than the fungus Aspergillus niger PTCC 5013. Discussion and Conclusion: The exopectinase enzyme was active in a wide ranges of pH and temperatures. As Monilia does not produce toxic compounds, it is proposed for pectinase production, especially in the food industries.

https://bjm.ui.ac.ir/article_19454_6f13f2e4c491fb4bae390911ed843091.pdf

University of Isfahan Journal of Microbial Biology 3060-7647 1 1 2012 05 21 Isolation, and molecular detection of Alcanivorax dieselolei in the Persian Gulf and the study of biodegradation ability for remediation of oil pollution Isolation, and molecular detection of Alcanivorax dieselolei in the Persian Gulf and the study of biodegradation ability for remediation of oil pollution 31 40 19455 FA Mehdi Hassanshahian Assistant Professor of Microbiology, Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran, Giti Emtiazi Professor of Microbiology, University of Isfahan, Isfahan, Iran Journal Article 2016 06 14 Introduction: Oil pollution in marine environments is a global problem. The Persian Gulf is a specific region because over than 60 % of world crude oil transports through the strait of Hormoz. Obligate marine hydrocarbon-degrading microbes have been recently reported. Alcanivorax, a member of this family is predominant in oil polluted sea.Materials and Methods: In this survey, seawater samples were collected from oil contaminated regions in the Persian Gulf. Bacteria were enriched in ONR7a medium and colonies were purified in marine agar and ONR7a media. All colonies were screened for ability to degrade crude oil. Molecular identification was carried out by amplification of 16S rDNA gene and sequencing analysis. Also, biodegradation of some hydrocarbon and crude oil were analyzed. Results: Totally, eleven different colonies were isolated that were able to degrade crude oil. Two strains (PG-24 and PG-12) showed higher growth rates on crude oil than other strains. Molecular identification showed 99% homology of these two strains with Alcanivorax dieselolei. These two strains could grow on aliphatic hydrocarbon and the highest growth rates were observed on C16 and C18 substrates, also 80 % of crude oil was degraded. Discussion and Conclusion: This article is the first report on isolation of Alcanivorax genus from the Persian Gulf, thereby further studies and optimization of biodegradation of oil pollution by these bacteria are important for modulate oil pollution in the Persian Gulf. Introduction: Oil pollution in marine environments is a global problem. The Persian Gulf is a specific region because over than 60 % of world crude oil transports through the strait of Hormoz. Obligate marine hydrocarbon-degrading microbes have been recently reported. Alcanivorax, a member of this family is predominant in oil polluted sea.Materials and Methods: In this survey, seawater samples were collected from oil contaminated regions in the Persian Gulf. Bacteria were enriched in ONR7a medium and colonies were purified in marine agar and ONR7a media. All colonies were screened for ability to degrade crude oil. Molecular identification was carried out by amplification of 16S rDNA gene and sequencing analysis. Also, biodegradation of some hydrocarbon and crude oil were analyzed. Results: Totally, eleven different colonies were isolated that were able to degrade crude oil. Two strains (PG-24 and PG-12) showed higher growth rates on crude oil than other strains. Molecular identification showed 99% homology of these two strains with Alcanivorax dieselolei. These two strains could grow on aliphatic hydrocarbon and the highest growth rates were observed on C16 and C18 substrates, also 80 % of crude oil was degraded. Discussion and Conclusion: This article is the first report on isolation of Alcanivorax genus from the Persian Gulf, thereby further studies and optimization of biodegradation of oil pollution by these bacteria are important for modulate oil pollution in the Persian Gulf.

https://bjm.ui.ac.ir/article_19455_5d016cd58836d58dbef516b11c2fa9a8.pdf

University of Isfahan Journal of Microbial Biology 3060-7647 1 1 2012 05 21 Molecular detection of Listeria monocytogenes and Listeria ivanovii in pigeons in the city of Yazd, Iran Molecular detection of Listeria monocytogenes and Listeria ivanovii in pigeons in the city of Yazd, Iran 41 46 19456 FA Abdolkarim Zamani Zamani Moghadam Associate Professor of Poultry Diseases and Hygiene, University of Shahrekord, Shahrekord, Iran Hossein Tahmasby DVM Student, University of Shahrekord, Shahrekord, Iran Hassan Momtaz Associate Professor of Microbiology, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran Naser Salehi DVM Student, University of Shahrekord, Shahrekord, Iran Samaneh Mehrabiyan DVM Student, University of Shahrekord, Shahrekord, Iran Journal Article 2016 06 14 Introduction: Birds can harbor human pathogens, including L. monocytogenes and L. ivanovii and transmit then to the humans. Due to many people's interests to keep pigeons, present study was conducted to determine the occurrence of L. monocytogenes and L. ivanovii from pigeon faeces in Yazd. Materials and Methods: In the present study, 150 samples of bird faeces were collected with sterile cotton swabs from different areas of the city of Yazd, Iran. Swabs were placed directly into Listeria enrichment broth. One ml of primary enrichments was transferred to 9 ml of Frazer broth. Secondly enrichments were streaked on Palcam agar. Then, they were evaluated for detection of L. monocytogenes and L. ivanovii by PCR method. Results: Although overall prevalence of Listeria species was 2% (3 out of 150), no L. monocytogenes and no L. ivanovii were found in our study. Discussion and Conclusion: The sources of Listeria spp. in birds are the foods they eat and the environments they live. Since nutritions, living environments, and hygiene level of pigeons are better than those of the wild birds, L. monocytogenes and L. ivanovii were not found in any samples. The present result is suggesting that pigeons are not the source or the carrier of L. monocytogenes and L. ivanovii in the region. Introduction: Birds can harbor human pathogens, including L. monocytogenes and L. ivanovii and transmit then to the humans. Due to many people's interests to keep pigeons, present study was conducted to determine the occurrence of L. monocytogenes and L. ivanovii from pigeon faeces in Yazd. Materials and Methods: In the present study, 150 samples of bird faeces were collected with sterile cotton swabs from different areas of the city of Yazd, Iran. Swabs were placed directly into Listeria enrichment broth. One ml of primary enrichments was transferred to 9 ml of Frazer broth. Secondly enrichments were streaked on Palcam agar. Then, they were evaluated for detection of L. monocytogenes and L. ivanovii by PCR method. Results: Although overall prevalence of Listeria species was 2% (3 out of 150), no L. monocytogenes and no L. ivanovii were found in our study. Discussion and Conclusion: The sources of Listeria spp. in birds are the foods they eat and the environments they live. Since nutritions, living environments, and hygiene level of pigeons are better than those of the wild birds, L. monocytogenes and L. ivanovii were not found in any samples. The present result is suggesting that pigeons are not the source or the carrier of L. monocytogenes and L. ivanovii in the region.

https://bjm.ui.ac.ir/article_19456_5bbc2a8eae9507491f41c0fe41f75a42.pdf

University of Isfahan Journal of Microbial Biology 3060-7647 1 1 2012 05 21 Evaluation of parameters effective in nickel uptake by Pseudomonas and Bacillus Evaluation of parameters effective in nickel uptake by Pseudomonas and Bacillus 47 56 19457 FA Salman Ahmady-Asbchin Assistant Professor of Industrial Microbiology, Ilam University, Ilam, Iran Naser Jafari Assistant Professor of Biology, Mazandaran University, Mazandaran, Iran, Journal Article 2016 06 14 Introduction: The heavy metal pollution has turned out to be one of the most important environmental problems. Due to their high stability in the presence of large amounts of wastewater factory, water treatment is necessary. Materials and Methods: In this study, Pseudomonas bacteria were isolated Ilam Town industrial waste water used as an example of Gram-negative bacteria. And Bacillus was isolated from desert dust Maranjab Kashan, as representative of Gram-positive bacteria Then, they were investigated in the biological uptake of nickel from aqueous solution in batch reactors. Results: In this research, factors such as the rate of absorption of nickel, the effect of pH solution, metal reproducibility, metal uptake by Pseudomonas and Bacillus, were studied. Adsorption equilibrium time was approximately 10 minutes by Bacillus and the maximum metal uptake by the bacteria was 0.71 mmol/g dry weight of cells. Discussion and Conclusion: Nickel uptake by Pseudomonas was about 0.12 mmol/g dry weight cell mass and the equilibrium time was about 5 minutes. Best nickel release factors were Bacillus and Pseudomonas, respectively, of EDTA and nitric acid. The results showed that gram-positive bacterium Bacillus was a better choice for the removal of nickel from contaminated solutions. Introduction: The heavy metal pollution has turned out to be one of the most important environmental problems. Due to their high stability in the presence of large amounts of wastewater factory, water treatment is necessary. Materials and Methods: In this study, Pseudomonas bacteria were isolated Ilam Town industrial waste water used as an example of Gram-negative bacteria. And Bacillus was isolated from desert dust Maranjab Kashan, as representative of Gram-positive bacteria Then, they were investigated in the biological uptake of nickel from aqueous solution in batch reactors. Results: In this research, factors such as the rate of absorption of nickel, the effect of pH solution, metal reproducibility, metal uptake by Pseudomonas and Bacillus, were studied. Adsorption equilibrium time was approximately 10 minutes by Bacillus and the maximum metal uptake by the bacteria was 0.71 mmol/g dry weight of cells. Discussion and Conclusion: Nickel uptake by Pseudomonas was about 0.12 mmol/g dry weight cell mass and the equilibrium time was about 5 minutes. Best nickel release factors were Bacillus and Pseudomonas, respectively, of EDTA and nitric acid. The results showed that gram-positive bacterium Bacillus was a better choice for the removal of nickel from contaminated solutions.

https://bjm.ui.ac.ir/article_19457_b3a7e496ed9b574bfb69a851e31f3138.pdf