فصلنامه زیست شناسی میکروارگانیسم ها
پیاپی 23 (پاییز 1396)

Azo dyes are the biggest group of colors. One of the special characteristic of this group of dye is the presence of double bonds of Nitrogen (N=N). Several studies reported biodecolorization using microorganisms, so far. However, it is for the first time to our knowledge that decolorization by halophilic archaea have been reported.
Among the 15 strains of archaea isolated from Qeshm saline cave and 7 type strains from Iranian biological resource center, 2 strains showed high ability in decolorization of azo dye. Effects of different factors including pH (5-9), temperature (30-50 °C), various salt concentrations (12.5-30%), different concentrations of dye (400-5000 mg/L), different carbon sources and several nitrogen sources and agitation have been measured after 4 days of incubation in static condition. Moreover, the toxicity tolerance of halo archaeal strains to dye, growth and decolorization rates were studied. Statistical significance was assessed by ANOVA Tukey’s multiple comparison test.
Strain A with 99.1 % similarity to Halogeometricum borinquense and strain B with 99.4 % similarity to Haloferax mediterranei were the best decolorizing strains. Both strains had their highest decolorization rate in the presence of NaCl (15-17.5 %), pH 7, microaerophilic condition and yeast extract as nitrogen source. Halogeometricum borinquense showed higher decolorization rate in the presence of saccharose and glucose as carbon sources at 45 oC temperature and for Haloferax mediterranei temperature of 40 oC and propionic acid as carbon source were best decolorizing conditions. These strains were able to decolorize dyes at 1000 mg/L concentration and tolerate dye concentrations to the highest level of 5000 mg/L.
Discussion and In conclusion, our results indicate that halophilic archaea have very high potential to decolorize azo dyes. Regarding high amounts of salts in textile wastewaters, using such microorganisms which can tolerate the harsh environment in order to decolorize azo dyes, could be a new approach in this field.

Biosurfactants are biological surface active agents which are used in many applications such as oil bioremediation of contaminated soils.
In this study, first soil samples were collected from crude oil contaminated regions of Iran. Fungal isolates were enriched in MSM medium supplemented with crude oil and purified and then all isolates were screened for biosurfactant activity. Then, the capacity of crude oil degradation in the selected isolate was measured using Total Petroleum Hydrocarbon (TPH) assay by spectrophotometry and FT-IR analysis. Finally, morphological and molecular identification was carried out by sequencing amplification of beta-tubuline beta-tubulin and ITS gene.
Among 40 purified fungal isolated, the isolate SH-02 was selected as the best strain according to the oil spreading and parafilm M test., This isolate was purified from petroleum contaminated soil of Arak refinery. Morphological and molecular identification revealed that this isolate has 99% similarity to Fusarium redolens in ITS geneand was deposited in the University of Tehran Microorganisms Collection under the accession number, UTMC 5039. Measurement of surface tension reduction by Du Nouy Ring method showed that Fusarium sp. UTMC 5039 can reduce surface tension to 26.6 mN/m and this reduction amount is significant compared with the previous reports. According to the obtained results from TPH and FTIR assays, 60 % of crude oil was degraded biodegradation was measured for by Fusarium sp. UTMC 5039.
Discussion and The current study results indicate that Fusarium sp. UTMC 5039 has a high capacity in biosurfactant production and introduced as a potent fungal strain for crude oil bioremediation.

Growing evidence exists that agriculture affects antibiotic resistance in human pathogens. Beta-lactam antibiotics are the most commonly used antimicrobial agents in many countries. The abundance of beta-lactamase encoding genes can be used as an indicator of antibiotic resistance in the environment. So, to determine the beta-lactamase resistance genes, the abundance of culturable bacteria having bla-TEM genesin the soils under different land uses wasexamined.
44 Gram-positive and 34 Gram-negative bacteria plated on nutrient agar were isolated from agricultural, pasture and mining soils and selected to study the presence of TEM-class gene using PCR amplification. Antibiotic sensitivity test of bla-TEM諊╪힬솫 done adopting the Kirby-Bauer disk diffusion method and antibiotic discs used were: ampicillin, amoxicillin, vancomicin, streptomycin, tetracycline and gentamicin. Finally, five multi-drug resistant and bla-TEM isolates were identified using universal primers.
The highest level of beta-lactamase genes was observed in the Gram-positive and Gram-negative isolates from the pasture soils. In the agricultural and mining soils, a high abundance of bla-TEM isolateswasfound which also showed resistance to beta-lactam antibiotics. The identified multi-drug resistant and bla-TEM isolates were from these genera: Achromobacter, Bacillus, Brevibacillus, Aminobacter and Brevundimonas.
Discussion and The high number of bla-TEM bacteria in all the soils may be attributed to the other important feature of bla genes which is their capability to extrude toxic compounds like heavy metals in contaminated environments. Sensitivity of some bla-TEM bacteria to beta-lactam antibiotics was interesting. This result shows that bla-TEM genes confer resistance to beta-lactamase inhibitors in a different degree. Some of the identified isolates were pathogen. These pathogens in soils can transfer to plants and human which induce health problems. A high abundance of bla-TEM bacteria in the agricultural soil indicates the inefficiency of beta-lactam antibiotics.

Laccases (EC 1.10.3.2; benzenediol: oxygen oxidoreductase) are copper-containing oxidases that use molecular oxygen to oxidize various aromatic and non-aromatic compounds. Laccase is applied in delignification of lignocellulosic compounds for production of bioethanol, bioremediation of industrial wastewaters especially textile, food industries, and making biosensors.
The Taguchi experimental design method was used for optimization of laccase production in recombinant strain Yarrowia lipolytica YL4. A L-16 Taguchi orthogonal array was used to optimize the carbon and nitrogen sources along with vitamin in four levels.
The results showed that glucose, ammonium chloride, yeast extract and thiamine have significant effects on the production of laccase, respectively. The laccase activity reached to 1.52 U/mL after optimization of medium which is 7.6-fold higher than un-optimized medium.
Discussion and According to the analysis of results, the Taguchi experimental design method is a successful approach to increase laccase and recombinant proteins production in Y. lipolytica.

Foot and Mouth Disease (FMD) is the most contagious disease in cloven-hoofed animals which causes a lot of economical losses. FMD virus belongs to Picornaviridae family and Aphthovirus genus. The aim of the study is evaluation of humoral and cellular immune responses triggered by a Gamma-irradiated FMD vaccine in the guinea-pig model.
FMD virus type Asia-1 was multiplied on BHK21 cell line and irradiated by gamma ray in different doses. According to dose/survival curve, D10 value and optimum dose of virus inactivation were calculated 7.69 and 50 kGy, respectively. Antigenic characteristic of irradiated and un-irradiated virus samples were evaluated by complement fixation test (CF test) and safety test was done by four blind passages cell culture on IBRS2 cell line. The inactivated virus sample was formulated as Radio- vaccine and immune responses were evaluated in three groups of ginea-pigs; the first group Radio-vaccine, the second group conventional vaccine and the last one was negative control.
The results of neutralizing antibody titration for two vaccinated groups were significant (PDiscussion and The Gamma irradiated inactivated FMD type Asia-1 vaccine is a good candidate for immunization of guinea-pig without the problems such as residue, virus escape and etc. And it can use for vaccination of cattle in the future.

Poly-β-hydroxybutyrate (PHB) is a natural polymer that can be depolymerized by bacterial extracellular enzymes into β-hydroxybutyric acid monomers.
In this study, the effects of PHB and it’s degrading bacteria on the metabolic diversity of anaerobic bacteria in Siberian sturgeon hindgut were investigated in four treatments (Control, 2% PHB, combination of two degrading bacteria, 2% PHB two bateria) for 60 days. The Shanon diversity index, Evenness and Pareto-Lorenz curve was calculated with BiologTM Ecoplates data.
The results indicated that using supplemented diets significantly increased Shanon index and evenness then control (PDiscussion and Our results suggest that the diet supplemented with PHB and it’s degrading bacteria increase anaerobic bacterial diversity, however, degrading bacteria cannot accelerate PHB degradation in fish hindgut.

Escherichia coli is a common bacterium in the intestinal microflora of warm-blooded animals. They are routinely shed into the environment through feces and can contaminate water and soil, and, consequently fruits and vegetables .Enterohemorrhagic E. coli strains are recently emerged group of food-borne pathogens that are a significant public health threat. This group causes bloody diarrhea and hemolytic uremic syndrome (HUS), and the disease is prevalent in developed countries. The purpose of this study was to isolate and identify the E.coli O157: H7 and other verotoxigenic ones and major virulence genes (rfbE, eaeA, stx1, stx2) in fecal swab samples by PCR in Shahrekord area.
In Spring and Summer 2015, 400 cow fecal swab samples were collected from farms in Shahrekord area. Bacteriological and biochemical examinations were done for detection of E.coli. PCR assay was done for identification of O157:H7 serotype and other verotoxigenic E. coli using rfbE, eae, stx1 and stx2 genes.
E. coli O157:H7 was not detected in any strains tested. But PCR showed that out of 384 E.coli strain, 104(27/08%) isolates carried stx1 gene, 36(9/37%) carried stx2 gene and 16 (4.16%) carried both stx1 and stx2 genes. Intimin (eaeA) gene was detected in 280(72/91%) of the isolates. Among verotoxigenic strain antibiotic resistance to Tetracycline 87/1%, Ampiciline 51/62%, Cefotaxime 48/38%, Gentamycin 25/81%,, Ciprofeloxacin 3/22% and Sulfamethoxazol 3/22% were observed.
Discussion and According to the results, although the serotype O157: H7 did not isolate from the feces of cattle but other verotoxigenic strains that showed high resistance to antibiotic were isolated so it is a risk for human health.

Salmonella serovar typhimurium is one of the most important foodborne pathogens and common causes of salmonellosis that in some conditions lead to septicemia or even death in humans. Therefore, the present study sought to detect this pathogenic serovar using loop-mediated isothermal amplification (LAMP) assay.
In the present study, six special primers were used to amplify STM4497 gene and accordingly to detect Salmonella typhimurium strains. The detection of the amplified products was performed by both turbidity and gel electrophoresis methods. Furthermore, the efficiency of LAMP assay for the detection of Salmonella typhimurium strains was examined in several artificially contaminated chicken meat samples.
The specificity of the assay was evaluated by various isolates of Salmonella and non-Salmonella, and positive results were only obtained from Salmonella typhimurium isolates. The detection limit of the assay was determined to be 10 CFU/reaction, which was lower than the previously developed competing assays. The results of the assay on artificially contaminated chicken meats showed that this assay enables detecting Salmonella typhimurium strains with a detection limit 103 CFU/mL without pre-enrichment and 10 CFU/mL after a four-hour pre-enrichment.
Discussion and As a result of a high sensitivity and specificity of the method as well as its low cost per assay, it could be concluded that the present LAMP assay is a powerful, accurate, and efficient method for detecting pathogenic serovar Salmonella typhimurium in food-processing industries and diagnostic laboratories.

Plant growth-promoting rhizobacteria (PGPR) are a group of plant rhizosphere inhabitants bacteria which stimulate plant growth and increase host tolerance to environmental stresses using several mechanisms. Fluorescent pseudomonads are considered as the most important plant growth promoting rhizobacteria. The aim of this study is screening Pseudomonas fluorescens strains isolated from barley rhizosphere in Bushehr province for growth stimulating properties and tolerace to salt stre.
25 P. fluorscens strains were evaluated for growth stimulating properties including siderophore, indole-3-acetic acid (IAA) and hydrogen cyanide (HCN) production, inorganic phosphate solubilization and the ability to tolerate salinity levels (0, 200, 400 and 600 mM of sodium chloride) under in vitro conditions.
The results revealed that among the 25 strains studied, all were siderophore-producers (1.34-8.48 µM/ml) and 88% were able to produce HCN. The ability to solubilize mineral phosphate was observed in 88% of strains. Superior strains with PGP traits (B2-10, B4-6, B10, P68 and CHA0) were able to produce IAA (1.78-2.29 mg/ml). All strains were able to tolerate NaCl concentrations of 200-600 mM, however, their colony diameter decreased with increase in salinity levels.
Discussion and The current study showed that some P. fluorescens strains isolated from barley rhizosphere like B2-10, B4-6, B2-11 and B10, had plant growth-promoting characteristics and salt tolerance ability, so it can be concluded that these strains have the potential to be applied as useful microorganisms in bifertilizers to enhance plant growth under salt stress conditions.

Phytase can be used as a feed additive to catalyze the hydrolytic degradation of phytate as the major storage form of natural phosphorus. Phytase is produced by a wide range of bacteria, fungi and yeasts. Isolation and identification of phytase-producing strains from soil, is of great interest for commercial application in different industries. The aim of the current study was the isolation and identification of phytase-producing strains from soil samples and optimizing the enzyme production.
For isolation and identification of phytase-producing strains, soil samples were collected from farms near Qazvin. Diluted samples were spread onto PSM solid media and production of the clear zones about the colonies gave a visual indication of phytase production. The selection of the best phytase-producing strain was performed by measuring the enzyme activity in the liquid medium. The selected strain was identified by slide-culture technique and the effect of carbon source (phytate and wheat bran), pH and time of incubation were also investigated for optimal enzyme production.
In this study, a Penicillium sp. was isolated from a soil sample near Qazvin and was selected as the best phytase-producing strain. The maximum phytase activity (171 U/ml) was obtained in the medium containing % 2 (w/v) phytate, at pH 5, after 72 h of incubation. By using wheat bran as the source of carbon and phytate, the maximum phytase activity, which was 61.7 U/mL, was produced at pH 7 and after the same time of incubation.
Discussion and Penicillium sp. isolated from a soil sample near Qazvin, was able to produce highly active phytase in optimized environmental conditions, which could be a suitable candidate for commercial production of phytase to be used as complement in poultry feeding industries.