فصلنامه دنیای میکروب ها
سال یازدهم شماره 1 (پیاپی 34، بهار 1397)

Microbial oils are of great interest to researchers as they provide essential fatty acids and are among renewable energy sources. Oleaginous microorganisms have the ability to produce oils up to 60% of their weight, most of which are accumulated in the form of triglycerides. Fouroleaginous genera including bacteria, microalgae, fungi, and yeasts are among the largestproducers of microbial oils. A variety of physical and chemical factors are effective in microbial oils production, among which carbon source, nutrient deficiency, temperature, light intensity and pH of the environment can be noticed. Considering theconstraints faced by various physical and chemical treatments in microbial oils production, most researches are currently focusing ongenetic modifications to enhance lipid production in oleaginous microorganisms. This article reviewed 210 peer-reviewed articles entitled engineering of lipid production in oleaginous microorganisms in scientific databases during 1990-2017, among which 89 to particles wereselected for further assessments. In order to have the best achievement in replacement of new oil sources on a large scale, these resources should be optimized in terms of unique properties such as unsaturated fatty acids production, lipid yield, as well as lipid profile. The present study is ana ttempt to recommend some basic approaches to increase microbial oils production by oleaginous microorganisms. These strategies should be in line with genetic and environment-protection priorities. Concurrently, they could be useful for knowledge-based enterprises from the economical point of view

Pseudomonas aeruginosa is an opportunistic pathogen especially in immunocompromised patients. Drug resistance in P. aeruginosa is caused by different mechanisms such as mutations in topoisomerases subunits and negative regulators of efflux pump systems. This study was aimed to investigate mutations in gyrB, parC, and nfxB genes in ciprofloxacin-resistant P.aeruginosa isolates in Guilan province.
In this cross-sectional study, 200 isolates were obtained from different clinical samples of Rasht and Lahijan hospitals and laboratories and subsequently identified by biochemical tests. Antibiotic susceptibility pattern was determined by Kirby Bauer disk diffusion susceptibility test and Minimum Inhibitory Concentration (MIC) test. PCR-sequencing was used to assess mutations in gyrB, parC, and nfxB genes in ciprofloxacin-resistant P. aeruginosa isolates.
Out of 69 P. aeruginosa isolates, 26 isolates were ciprofloxacin-resistant. MIC of ciprofloxacin in resistant isolates was determined between 32-1024 µg/ml. PCR-sequencing analysis revealed that some resistant isolates have missense mutations in gyrB, parC, and nfxB genes. It seems that N368S, I424L, L464I, E468D, M520L, and I524V mutations in gyrB were reported for the first time in Iran.
It seems that reported mutations in gyrB and parC genes affect topoisomerases affinity to ciprofloxacin in resistant isolates. Furthermore, mutations in the nfxB gene may lead to overexpression of MexCD-OprJ efflux pump and ciprofloxacin resistance.

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most important causes of opportunistic infections in the community as well as hospitals. Nowadays, an increase in the antibiotic resistance has caused concern to the medical community. Meanwhile, resistance to methicillin is important because of limiting treatment. This study was conducted to track methicillin resistance gene and to type staphylococcal cassette chromosome (SCCmec) in S. aureus strains isolated from nasal swabs of healthy hospital workers and to determine the antibiotic sensitivity pattern of the strains.
In this descriptive cross-sectional study, 230 specimens were collected from healthy workers nasal swabs of Larestan hospital during 2015. S. aureus strains were identified using laboratory standard methods. The antibiotic susceptibility pattern was characterized using disk diffusion test, minimum inhibitory concentration (MIC) was determined by E-test and sensitivity to methicillin was assessed by agar screening test. Furthermore, the presence of antibiotic-resistant mecA gene and SCCmec genotyping were investigated using the multiplex-PCR method.
Among all nasal swab samples, 37 (14.8%) S. aureus isolates were recovered. 28 (75.7%) out of 37 S. aureus isolates were confirmed as MRSA. 21 (75%) of 28 MRSA isolates were community-associated MRSA (CA-MRSA), and the remaining 7 (25%) were hospital-acquired MRSA (HA-MRSA). SCCmec genotyping showed the most frequent isolates as follows: 9 (32.1%) isolates as SCCmec type I, 8 (28.6%) isolates as SCCmec type IV, 5 (17.9%) isolates as SCCmec type II, 4 (14.3%) isolates as SCCmec type V and 2 (7.1%) isolates as SCCmec type III. Evaluation of antibiotic resistance pattern showed the highest resistance to penicillin (100%) and oxacillin (60%) respectively, and the lowest resistance to vancomycin (0%). E-test results confirmed 28.5% of the isolates as intermediate vancomycin-resistant. Using agar screening test, oxacillin resistance was shown as 92.8%.
Our result showed that 70% methicillin resistance in the S. aureus which is mostly CA-MRSA strains. This could be a serious warning about the need to treat infections caused by this bacterium and control the carriers in the hospital environment

Microbially induced carbonate precipitation (MICP) is one of the proposed methods for soil stabilization and strengthening. The aim of this study was to isolate and characterize biocement-producing ureolytic bacteria from arid soils.
In this cross-sectional descriptive study, 280 soil samples were collected from different areas of Iran. Samples were cultured using urea broth medium. Urease-positive bacteria were assessed for the level of urease activity. Identification of active strains was performed based on conventional biochemical tests and 16S rRNA gene sequencing. Optimum temperature and pH conditions for biocement production were evaluated in urease-positive
bacteria and was compared with sporosaicina pasteurii (ATCC 11589) strain. Finally, calcium carbonate crystals were assessed byX-ray diffraction (XRD) crystallography test at the temperature of 25 °C and pH of 8.5 as optimal conditions.
304 strains were isolated from 5 different bacterial genera. Bacillus and Sporosarcina were the major ureolytic isolates of arid regions. The most amount of calcium carbonate was produced at the temperature of 25 °C and a pH of 8.5. Ten most effective isolates in the production of urease enzymes and biocement were identified by molecular analysis and subsequently registered in NCBI Genbank. In addition, biocement production by selected isolates was confirmed by XRD test.
Our results showed that the amount of urea and calcium chloride plays an important role in calcium carbonate crystals production. S. pasteurii was one of the most important biocement-producing bacteria. Therefore, optimization of growth conditions in higher scale is recommended for further applications in stabilizing the sand, ground strength and bridging

Given the high diversity, biotechnological applications and the effective role of bacteria in making and maintaining the ecosystem balance; biodiversity research are very important. Meanwhile, the halophilic bacteria and archaea have been considered because of their biotechnological importance and specific ecological condition. In this study, we investigated the diversity of heterotrophic bacteria and archaea of Namakdan cave in Qeshm Island.
This cross-sectional study was carried out by sampling from Qeshm Namakdan cave in November 2013. The diversity of the cave heterotrophic aerobic bacteria was analyzed using the culture method. Halophilic and halotolerant bacteria and Archaea under aerobic conditions were isolated by MGM and Marine agar media, respectively. Isolates were separated according to morphological differences, and primary biochemical features. Finally, 16s rRNA sequencing was performed for 32 isolates.
Among 172 isolates 16S rRNA sequencing was carried out for 27 strains. Phylogenetic analysis placed archaea in the euryarchaeota division and Halococcus, Haloferax, Haloarcula, Halogeometricum genus branches and bacteria in Firmicutes and Bacteroides divisions and in Aliifodinibius, Paenibacillus, Aquibacillus, Paraliobacillus, and Bacillus genus branches. Among the sequenced isolates, 11 isolates showed less than 89.7% similarity to the standard species, which is considered as a borderline point to present new microbial species.
Placing the identified isolates in different phylogenetic divisions and genus branches demonstrates the wide microbial diversity of Qeshm Namakdan cave ecosystem. Presenting native microorganisms in new species and genera from unique ecosystems by introducing new genetic content provides access to new native genes and pathways.

Heavy metals are environmentally sustainable and durable pollutants that have become a world problem. As microorganisms show high resistance to heavy metals and can purify the environment and produce nanoparticles, the present study was designed to produce copper nanoparticles from copper-resistant bacteria isolated from wastewater of two copper workshops in Isfahan.
In this cross-sectional study, wastewater samples were collected from two copper workshops in Isfahan. The physicochemical factors of the wastewater, the minimum inhibitory concentration of bacteria (MIC) to copper and their resistance to several antibiotics were investigated. Morphological, biochemical and molecular identification tests were carried out on samples. Then the biomass of copper-resistant bacteria was added to the copper sulfate pentahydrate stock (CuSO4.5H2O) and the results were evaluated by Ultraviolet-Visible
spectrophotometer (UV-VIS), X-ray diffraction (XRD) and Transient Electron Microscopy (TEM).
Among the studied bacteria, the Bacillus toyonensis strain NE2 with the MIC of 3.5 mM and Arthrobacteragilis NE1 with MIC of 4 mM from copper workshop 2 and Stenotrophomonas maltophilia strain 5633 with the MIC of 6 mM from copper workshop 1 were isolated. Among these isolates, only S. maltophilia strain 5633 was able to synthesize copper nanoparticles. Peaks created in the range of 250-430 nm confirmed the presence of Copper (Cu) and Copper Oxide (CuO) particles.
The findings of this study showed that the isolated bacteria could be a good candidate to remove copper from wastewater and to biosynthesize copper nanoparticle.

Rosemary is a very important medicinal herb which its effect on toxin-causing and pathogenic fungi is not studied very well. This study was aimed to investigate the antifungal effect of the extract of Rosemary extract on various fungal groups including Aspergillus flavus, Candida albicans, Epidermophyton floccussom, Trichophyton verrucosum and its effect on AFL1 gene expression in A. flavus using real-time PCR method. Achieving an
effective herbal medicine can be significant due to the limited amount of antifungal drugs and the prevalence of antifungal drug resistance.
First of all A. flavus and C. albicans were cultured on sabouraud dextrose agar (SDA) media and T. verrucosum and E. floccosum were cultured on Mycocell agar media with 0.5 McFarland turbidity standard. Antifungal property of the rosemary extract was investigated using disk diffusion test. Then, the effective Rosemary extract concentration was evaluated using 10 standard tubes and sabouraud dextrose broth. Finally, the effect of Rosemary extract on AFL1 gene expression was examined.
Our results indicated that Rosemary extract has an inhibitory effect on various types of fungi so that the mean diameter of the inhibition zone was measured as about 16 to 18 mm. The effective MCI for C. albicans was observed as approximately 4 to 6 mg / L, for A. flavus as 3 to 5 mg /L and for E. floccosum and T. verrucosum as 4 to 6 mg /L. RT-PCR analysis confirmed the inhibitory effect of Rosemary extracts on aflatoxin- producing AFL1 gene expression at the molecular level, very well.
The extract of Rosemary can have a considerable inhibitory effect on fungal growth, AFL1 gene expression and aflatoxin production in A. flavus.

Protease is one of the most important industrial enzymes occupying nearly 60% of global enzyme sales. Extracellular protease finds numerous applications in industrial processes like in leather tanning, detergents, dairy, brewery as well as meat tenderization industries. In spite of that, the low level of enzyme production is the main challenge of industrial production of enzyme. Therefore, optimization of industrial protease production and its application in blood de-staining were the aims of this study. The sewage samples were cultivated on the skim milk agar. BYK27 isolates with the highest clear halo around the colonies were selected for further studies. Optimization of parameters affecting protease production by Chryseobacterium indologenes BYK27 was studied by Taguchi approach. De-staining ability of protease was also investigated by de-colorization of bloody cotton cloth. The optimal factors for protease production by Ch. indologenes BYK27 were found to be the temperature of 40 ˚C, pH of 9.0, 0.06% yeast extract and 1% glucose supplements. Protease production under optimal condition was found to be 590 (U/ml) which was improved by 63%, as compared to the basal medium. The protease activity and stability were increased 50% by beta-mercaptoethanol but inhibited about 88% by DMF. In addition, BYK27 protease was able to completely de-stain blood after 20 min of incubation. The results of this study indicate that BYK27 protease has biotechnological potential, specifically in the detergent industry and provision of valuable compounds