جستجوی مقالات مرتبط با کلیدواژه « 16s rrna » در نشریات گروه « زیست شناسی »

Anthropogenic pollutants are known to have adverse effect on ecosystem, and human health. Biodegradation is an option that has been widely used to remediate organic contaminants and reduce the risk of these hazardous materials. Microorganisms are readily available to screen and can be rapidly characterized to be applied in many extreme environmental conditions. Actinomycetes have a great potential for the production of bioactive secondary metabolites which have biodegradation activity. This study aimed to screen and characterize Nocardia species with biodegradation potential from diverse Iranian ecosystems. The isolates were screened from 90 collected environmental samples, identified and characterized using conventional and molecular microbiological methods including the PCR amplification and sequencing analysis of 16S rRNA and rpoB genetic markers. Growth rate in presence of pollutants, chromatography, Gibbs and turbidometric methods were used to determine bioremediation ability. A total of 19 Nocardia isolates were recovered from the cultured samples (21.1%) that belonged to 10 various species. The most prevalent species was N. farcinica; 4 isolate (21%), followed by N. cyriacigeorgica and N. cashijiensis; 3 isolates each (15.7%) and N. asteroides 2 isolates (10.5%). In this study isolates showed biodegradation activity against PAHs, phenol and oil derivations. Discussion and Our results showed that various Nocardia species isolated from Iranian ecosystems have great potential for biodegradation of environmental contaminant, therefore we can used this bacteria in bioremediation process, although they have not received much attention for such significant usage.

The aim of this study was to isolate and identify a-amylase-producing bacteria present in mangrove ecosystems on Qeshm Island, Hormozgan, Iran. Samples of mangrove leaves and roots were screened for a-amylase activity using Lugol’s solution. Crude extracts were prepared of positive samples, and their a-amylase activity was determined by the Bernfeld method. The two strains with the highest activity were identified by molecular analysis of their 16S rRNA genes. a-Amylase production and activity were optimized by varying temperature and pH. 46 bacterial strains were isolated from mangrove tree leaf and root samples. Of these, 28 strains were capable of producing a-amylase. 16S rRNA gene sequence analysis of two strains with the highest enzyme production identified them as Bacillus sp. strain HR10 and Bacillus sp. strain HR11. The optimum temperature for enzyme production was 35 and 30 °C for strains HR10 and HR11, respectively, and the optimum pH was pH 8 for both strains. The highest enzyme activity was observed at 70 °C and 60 °C for the HR10 and HR11 strains, respectively, and the optimum pH was pH 8 for both strains. In conclusion, we have shown that bacteria isolated from mangrove leaf and root samples are potential source of a-amylases, tolerating a wide range of temperature and pH. Such a-amylases may be of interest for use in environmentally friendly industries.

Phytoplasmas are specialized prokaryotes and obligate parasites of plant and insect vectors. Because these organisms are not culturable in vitro, many of the conventional phenotypic tests used for the taxonomy of cultured maillots are not applicable to phytoplasmas. This indicates the importance of molecular and phylogenetic properties in relation to phenotypic properties in determining the taxonomic position of phytoplasmas. In the last decade, methods based on biology and molecular genetics, such as comparing the nucleotide sequence of a portion of ribosomal RNA, have made it possible to establish evolutionary and phylogenetic relationships between different isolates of phytoplasmas with each other and with other prokaryotes. Comparison of the nucleotide sequence of a part of the 16S rRNA gene or the 16S-23S and tRNA-Ile gene regions can still be used to analyze a large number of unknown (large-scale) phytoplasmas. Subgroup clustering is done using less conserved regions, such as the ribosomal protein-coding gene and the 16S and 23S intergenic, the general cpn60 target gene, the SecA coding gene, the secY gene, the ribosomal protein (rp) gene, and the tuf gene.

In this study, we developed a single specific primer PCR (SSP-PCR) method for specific identification of Shigella genus with the use of ribosomal RNA gene. Regarding high copy number and stability in cells, rRNA is one of the efficient targets to detect cells exclusively. 16S rRNA gene is considered as a standard biomarker for classifying and identifying prokaryotic cells. With respect to high sequence homology among 16S rRNA gene and shortness of specific heterogenic region in this gene, SSP-PCR is used to facilitate the specific identification of 16S rRNA gene in this study. In this method, only one specific primer is designed for amplification of target genes. 16S rRNA gene of different species of Shigella genus was aligned with 57 other related bacteria and then a single specific primer was designed in the V6 variable region. The amplicon was analyzed on a two-dimension agarose gel electrophoresis. The 263 bp band was considered as positive result in the tested samples and was observed for all species of Shigella (Sh. flexneri, Sh. boydii, Sh. dysenteriae, Sh. sonnei), whereas other species remained unidentified. The specificity of the assay was evaluated to be complete. Combination of targeting 16S rRNA and using SSP-PCR method, is an efficacious method for specific detection of bacteria in a minimum required time with a great ease. Among the applications are namely the early-phase diagnosis of bacterial infections in acute emergency conditions such as natural disasters and countries’ defense industry in the form of diagnostic kits for clinical laboratories.

Hamedan province is one of the most important regions for cultivation of stone fruit trees, such as apricots (Prunus armeniaca) due to its suitable climatic conditions. Bacterial canker disease of stone fruit trees caused by Pseudomonas syringae pv. syringae, is one of the most serious diseases in this province, Iran and all over the world. The study was performed to identify the causative agent of the disease.

Samples of diseased apricots were collected in early spring and fall autumn of 2018. From the collected samples a total of 130 bacterial strains were isolated of which 65 representative’s strains were selected based on the color and type of colonies on the culture medium for further study. SDS-PAGE technique was used to group the representative’s strains. Pathogenicity of the representative’s strains were performed on apricot seedlings under greenhouse condition. The studied strains were identified based on their phenotypic features, using standard bacteriological method and followed by sequencing of the 16S rRNA encoding gene.

30 strains showed hypersensitivity reaction on geranium leaves.  According to the pattern of cellular soluble proteins on polyacrylamide gel (SDS-PAGE), the strains were divided into seven groups. BLAST of partial sequence of 16S rRNA encoding gene from this strain showed 98/7% similarity to P. syringae NCPPB 281. Another strain (FB46 strain) was identified as P. agglomerans due to 95.33% similarity with Pantoea agglomerans RSG19 by BLAST of 16S rRNA encoding gene sequence.

The results obtained are in agreement with of Vasebi et al. isolated P. syringae as a causative agent of apricot canker in East Azerbaijan province. P. agglomerans has also been reported as one of the factors associated with stone fruits, pome fruits and walnut trees in Alborz province. This is the first report for the presence of Pseudomonas syringae as a causative agent of apricot canker disease in Hamedan province. The bacterium Pantoea agglomerans is reported from the first time in the world as the causative agent which induce apricot canker symptoms.

Enzymes are selective proteins that catalyze all metabolic reactions found in living organisms. Millions of enzymes are produced by prokaryotes and eukaryotes. Marine sponges have developed a enormous quantity of diverse microorganisms such as bacteria, fungi, viruses, protozoa, and single-celled algae and the nature of the sponge-microbe interaction is diverse. Marine sponge's symbiotic bacteria can comprise as much as 40% of sponge tissue volume. At least 32 bacterial phyla and candidate phyla were described from marine sponges by both cultivation-dependent and cultivation-independent techniques. Symbiotic microorganisms in sponges can be sources of various natural products, because metabolites previously ascribed to sponges have recently been demonstrated to be biosynthesized by symbionts. If symbiotic microorganisms from which some natural products are derived can be cultured, the microorganism could be used in a mass production of the bioactive comopounds. The goal of this research is isolation of Amylolytic bacteria from marine sponges and optimization of bacterial growth and amylase production in most amylolytic isolate. Symbiot bacteria were isolated using serial dilution method and differential analyses done for isolated bacteria. Most effective isolate was selected by using qualitative starch hydrolysis method.

Morphological and biochemical characteristics were studied using Bergey’s manual of systematic bacteriology. Differential analyses were performed by catalase and Gram test TSI, H2S, VP, MR tests. Preliminary screening and quantification of amylase activities were analysed in selected isolates by starch agar plate and dinitrosalicylic acid (DNS) method respectively. In order to optimize the enzyme production, the fermentation process was carried out under M9 medium using various sodium chloride concentrations (2–14%). To evaluate the effect of pH on the production of Amylase, the best amylase producer isolate was cultured at M9 medium with different pH rang 4-8. After incubation time it was subjected to amylase activity assay. Isolate SS1 was grown in M1 medium at 28°C for 7 days. DNA extraction was done using Cinnapure DNA Kit for isolation of DNA from gram positive bacteria. PCR amplification of 16S rRNA gene was performed, the specific actinomycete primers, F27 and R1492 were used to amplify 16S rDNA. The resultant 16S rRNA gene sequences were aligned manually with corresponding almost complete sequences. The 16S rRNA gene sequence search was performed using the BLAST program available from the National Centre for Biotechnology Information (NCBI) and the isolate was identified to generic level Using the CLUSTAL-X Multiple Sequence Alignment Program (Strasburg, France), The Phylogenetic tree was constructed by Neighbor-Joining method using MEGA 6.06. The reliability of the phylogenetic tree was tested by bootstrap analysis using 1,000 replicates.

Biochemical analyses showed that all tests were catalase and Gram positive none of them produced H2S and TSI, MR, VP tests were negative. According to 16S rRNA sequences result the most effective isolate was belong to Bacillus genus and Optimum growth condition was found at 12% NaCl concentration, 35˚C temperature and pH 12. Maximum amylase activity in optimum condition was 109 Unit (one Unit is amount of enzyme that release one microgram of glucose in a minute).

The results showed that enzyme production is related to growth of bacteria conditions and the amylase gene should amplify from selected isolate and clone in suitable host for more studies.

Polyhydroxybutyrate is a biopolymer Produced by bacteria. Also, with having chemical and physical characteristics similar with artificial plastics are completely biodegradable and compatible with life-environment. This study has been done with the purpose of separating and knowing one local strain with the ability of high-production for industrial purposes.

In the present analytical research, the sampling from petrochemical wastewater has been done. The existence of polyhydroxybutyrate in separations has been studied with Sudan black staining. One separation of bacillus was chosen to increase the production of polyhydroxybutyrate. This separation was distinguished with biochemical methods and determining 16S rRNA gene sequencing. The final confirmation of Polyhydroxybutyrate synthesis was done through Fourier transform infrared spectroscopy and Proton nuclear magnetic resonance. To increase more production of polyhydroxybutyrate, the effect of different factors including carbone, nitrogen, pH and temperature were assessed.

As a whole, eight bacterial isolation producing polyhydroxybutyrate were separated that among them the one novel strain of bacillus cereus was chosen as better separation. The best conditions to increase more production of polyhydroxybutyrate, was the application and use of glucose as carbon source, ammonium sulphate as nitrogen source, 7 pH and 30°C temperature.

Valuable data on optimized conditions for PHB production has been obtained through the present research that can be used at industrial level for PHB production, so it can be called a quick appearing alternation for petroleum based on synthetic plastic.

Actinomycetes, Gram positive bacteria, are rich sources of bioactive compounds. Secondary metabolites of these bacteria are used as pharmaceutical compounds Enzymes are one of the most important secondary metabolites which act as bio-catalysts to perform reactions in bio-processes in an economical and environmentally-friendly manner. Enzyme production from actinomycetes makes significant facility in industrial and world economic. So, that it is becoming one of the economic indexes of developed countries. The goal of this research is isolation of actinomycetes from Shadegan estuary, optimization of bacterial growth and amylase production. Molecular identification was done by amplification of 16S rRNA gene using R1492 and F27 primers. Optimum growth condition was found at 6% NaCl concentration, 35˚C temperature and pH 8 . Maximum amylase activity in optimum condition was 80150 Unit (one Unit is amount of enzyme that release one microgram of glucose in a minute). The results showed that enzyme production is related to growth of bacteria conditions.

In this study, sea stars Aquilonastra watersi and Patiriella paradoxa were collected from the rocky intertidal area in Tis Port on the western coast.and the rocky shallows depths of 7-8m at Konarak on the Iranian eastern coast of Chabahar Bay, respectively in November 2014. Specimens were collected in plastic sampling boxes containing seawater and transferred to the laboratory of Chabahar Maritime University. The specimens were morphologically assessed. Then in order to examine gene sequences, DNA was extracted by CTAB method and after performing PCR, mitochondrial 16S rRNA gene was sequenced. The phylogenetic-trees for these species were drawn by Maximum Likelihood methods. The evaluations of results showed that despite differences in morphology, A. watersi is sister group of Aquilonastra. Batheri. Based on the results P. paradoxa from present study andP. regularis are in a monophyletic clade, supported by high bootstrap.