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Biodegradation has been applied to remediate explosives contaminants, and bacteria have a high potential for the degradation of explosives, such as hexahydro‐1,3,5‐trinitro‐1,3,5‐triazine (RDX) and 2,4,6‐trinitrotoluene (TNT). The present study aims to screen and characterize explosive biodegradable Actinomycetes from water, wastewater, and sludge. Actinomycetes isolates were recovered from 80 environmental samples from diverse environmental resources in explosive contaminated areas of Iran and identified to the genus and species levels using conventional and molecular methods. The growth rate in the presence of pollutants and chromatography was used to determine their biodegradation capability. Twenty‐nine isolates (36.25%) of Actinomycetes were characterized from the cultured samples that belonged to 6 genus and 24 validated species. The most prevalent Actinomycetes isolated were genus Mycobacterium with 11 isolates (37.94%), genus Rhodococcus with seven isolates (24.13%), genus Nocardia with four isolates (13.8%), and genus Streptomyces with three isolates (10.33%). Moreover, our results showed that these isolates could degrade and consume 50–80% of RDX and TNT as their sole carbon and energy source. In conclusion, we showed that Actinomycetes from explosive‐contaminated areas of Iran could degrade TNT and RDX. Hence, seeking and screening untapped ecosystems that possess unexplored Actinomycetes will increase the chances of discovering the resident microorganism that has been capable of degrading TNT and RDX for application in the bioremediation process. The results of this study can be useful in using intact bacteria in nature to eliminate environmental pollution, which is one of the major environmental problems in the world. [ABSTRACT FROM AUTHOR]

Given the potential for urban green spaces to provide fresh and healthy environments for humans, exploring the issues that threaten plants in these places is crucial. Phytoplasma‐related symptoms were encountered on some plants in urban green spaces in the province of Kerman, southeastern Iran, between 2017 and 2019. Affected periwinkles and petunias exhibited phytoplasma disease symptoms, including virescence, phyllody, and witches'‐broom. However, ball or disc‐like shoot proliferation symptoms were noticed on the trunks and branches of pine trees. PCR was performed with phytoplasma‐detecting universal primers, targetting and amplifying the 16S rRNA gene, and determining whether phytoplasmas are implicated in the symptomatic plants. The infection of the symptomatic plants was confirmed using nested‐PCR amplification of expected DNA sizes for phytoplasmas. No product, however, was amplified from sampled symptomless plants. The sequencing of nested‐PCR products was performed to obtain sequences encasing the standard F2nR2 fragments. The resulted sequences were submitted to iPhyClassifier, the universal phytoplasma classification platform, for the taxonomic assignment of the found phytoplasmas compared with previously identified 'Candidatus Phytoplasma' species, groups, and subgroups. The results revealed that phytoplasma strains related to the species 'Ca. P. trifolii' (16SrVI‐A subgroup) infect periwinkles and pines. However, strains from the species 'Ca. P. aurantifolia' (16SrII‐D subgroup) and 'Ca. P. phoenicium' (16SrIX‐C subgroup) were found in petunias and periwinkles, respectively. To the best of our knowledge, phytoplasmas from the 16SrVI‐A and 16SrII‐D subgroups are the first reported to infect these plants in Kerman province, while a related strain from the subgroup 16SrIX‐C is the first recorded to infect periwinkles in Iran and the second in the world. [ABSTRACT FROM AUTHOR]

In order to appraise the bacterial endophyte communities that help resist disease in potato tuber, the separation, the population density, biodiversity and the antagonistic activity of endophytic bacteria, from the tuber peel of potato cultivars (Fontan90, Agria, Sante'a and Jeli89), were examined in the Fars province in Iran. In this study, the bacterial endophyte Colony Forming Units (CFU) were counted based on the most suitable dilution in petri dishes and expressed per g of wet weight of tuber tissue. The presence of bacteria was found mostly in the outer layer. A wide variety of endophyte species biodiversity was in Agria cultivar. To estimate the antagonistic effect of potato associated endophytic bacteria, 115 bacterial isolates were evaluated by dual culture method against main soil-borne potato pathogens Fusarium oxysporum, Rhizoctonia solani, Verticillium dahliae, Streptomyces scabies and Ralstonia solanacearum. Endophyte strains were identified based on physiological, morphological and chemical characteristics and the 16S rRNA gene sequence analysis. The highest degree of the inhibitory activity in all layers of potato cultivars was related to Bacillus subtilis, Bacillus mojavensis and Klebsiella variicola. Antagonistic activity of endophytic bacteria against the pathogens was significantly higher (p<0.01) in the examined strains from the outermost layer of tuber peel and decreased progressively toward the center of the tuber. In this research, Klebsiella variicola was reported as endophyte bacteria in the four commercial potato cultivars mentioned above, for the first time. [ABSTRACT FROM AUTHOR]

The common rhizobial population in the soil is neither high enough nor effective enough to maximize nodulation and nitrogen fixation. In order to find novel rhizobia with specific characteristics, root nodule bacteria in a symbiotic relation with wildly grown legume species in rangeland areas of Iran were studied, and their biodiversity and phylogenetics were also determined. Bacterial strains were isolated from root nodules of 13 legume species in rangelands of Alborz and Qazvin provinces. Serial dilutions were prepared from root nodules and cultured on the YMA medium. Single colonies were subjected to morphological and biochemical evaluations. Genetic identification and phylogenetic study of 14 isolated strains were done based on the sequences of 16S rRNA, atpD, nodA, and nifH genes. Fourteen identified strains belonged to three families, six genera and nine species. For the first time, Paenibacillus sp. (Tal6), Rhizobium laguerreae (Tal71), Neorhizobium alkalisoli (Krj1 and Ghg71), Rhizobium arenae (Ghg21) and Paenibacillus endophyticus (Ghg31-2) were isolated from root nodules of Onobrychis sativa, Trifolium pratense, Colutea buhsei, Astragalus sp., Glycyrrhiza glabra, and Melilotus sp., respectively. Phylogenetic trees were constructed by the maximum-likelihood method. The findings indicated that the complete host range of root nodule bacterial strains remained to be determined. Thus, the host range of specific nodule-forming bacterial species could be much wider than that proposed previously. Finally, different strains of the same bacterial species isolated from various host plants, demonstrated very diverse characteristics based on the biochemical tests and phylogenetic studies, indicating the possible effects that host plants themselves have on the genome of the bacterial strain. [ABSTRACT FROM AUTHOR]

Among predatory bacteria, Bdellovibrio and Like Organisms (BALOs) have a high potential for application as biocontrol agents. The objective of this study was to isolate and characterize native BALO strains from different water and soil samples in Iran. Nineteen BALO strains were obtained from the samples using Escherichia coli as prey. Analysis of 16S rRNA gene sequences showed that Na2, Tal2, Mm1, and Ja2 strains belong to a different species than B. bacteriovorus HD100 as a type strain. Also, Z2, B2, Ch2, Kan1, and Pj strains could be separate from the Bdellovibrio genera. The strains showed different host range and predation efficiency when they were tested with 17 different Gram-negative bacteria subsequently. The prey range of six strains including Sar, Pj, Kan1, C1, Z2, and Ch2 was limited to only E. coli. The most versatile predators were strains Zar3 and Kash2 that exhibited almost the same prey range as type strain HD100. They are also placed close to each other in the phylogenetic tree. The host range of strain Na2 was narrow and attacked only Ralstonia solanacearum, which is less susceptible to predation by the other strains. Native BALOs from water and soils in Iran were isolated, forming a group of potential biocontrol agents adapted to local conditions. [ABSTRACT FROM AUTHOR]

Instability of the morphological and some physiological characteristics under the different environmental conditions may cause misidentification of many cyanobacteria. It is recently revealed that molecular markers (e.g., 16S rRNA and 16S-23S ITS), biochemical parameters (e.g., fatty acid composition), as well as 16S-23S ITS secondary structure could be considered as more validated markers for reliable identification of cyanobacteria. Here, we used morphological, molecular, and biochemical data to identify three cyanobacteria species from the Kani Barazan international wetland which is located in northwest Iran. Our morphological results showed that Dolichospermum (Anabaena), Chroococcus, and Microcystis genera are common and existing in the wetland. Further, we identified the cyanobacteria as Dolichospermum planctonica strain KANI, Chroococcus turgidus strain KANI, and Microcystis aeruginosa strain KANI based on 16S rRNA and 16S-23S ITS markers. The phylogenetic position of the identified cyanobacteria represented a high level of homology to the previous reports. Importantly, we confirmed that the 16S-23S ITS secondary structure could be used as a simple and reliable tool for the precise phylogenetic analysis of different cyanobacteria. In addition, the results of gas chromatography-mass spectrometry (GC-MS) revealed that the isolated cyanobacteria contain considerable amounts of several fatty acids (FAs) including linolenic, linoleic, oleic, and palmitic acid in different ratios, which can be considered as a promising biochemical marker for further phylogenetic approaches. [ABSTRACT FROM AUTHOR]

Introduction: 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. Materials and Methods: 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. Results: 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. Discussion and Conclusion: 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. [ABSTRACT FROM AUTHOR]

Background: Plant growth-promoting bacteria (PGPB) can be used as a safe and sustainable agricultural measure to increase plant yield. In this study, cultivable rhizospheric, endophytic, and epiphytic bacteria associated with canola were isolated on nutrient agar medium. The SDS-PAGE method was used for grouping the bacterial strains. Bacterial strains with more than 80% similarity in their protein patterns were placed in the same species and selected as a representative for partial 16S rRNA encoding gene sequence analysis. Results: It was found that the bacteria used in this study belonged to Pseudomonas, Frigoribacterium, Sphingomonas, Sphingobacterium, Microbacterium, Bacillus, and Rhodococcus genera. Three PGP bioactivities including siderophore production, nitrogen fixation ability, and phosphate solubilization were evaluated for 18 Pseudomonas representative strains. All tested strains were able to produce siderophore, although only 5 strains could fix nitrogen and none was able to solubilize phosphate. Greenhouse experiments showed that 4 bacterial strains (i.e., 8312, 642, 1313W, and 9421) significantly affected canola seed germination and seedling growth. Bacterial strain 8312, which was identified as Pseudomonas sp., showed the highest effect on the growth of the canola plant. These results indicated the potential of strain 8312 to be used as a biofertilizer in canola cultivation. Conclusions: The results of this research indicated that canola-related bacteria were diverse during the flowering stage. One isolate had a significant effect on all canola plant growth factors in the greenhouse. Hence, it is recommended to investigate this strain further in field infestation experiments. [ABSTRACT FROM AUTHOR]

The microbial population of soil is diverse and is regulated by different soil properties. This study aimed to determine the impact of climate and grazing on soil community composition in two semiarid areas, Kerman province, Iran. Soil samples were taken from four zones which were either cold or warm and either grazed by cattle or not grazed. Soil chemical analyses were determined by standard methods and the bacterial community by DNA extraction from soil followed by next generation sequencing of the 16S rRNA gene. Soil at cold areas had higher moisture, organic carbon, total nitrogen, available phosphorous and exchangeable potassium concentrations than warm sites. The abundance of Proteobacteria (28.3% ± 1.0) and Actinobacteria (44.6% ± 1.1) was highest at the cold-grazed and warm-grazed zones, respectively, which account for ~70% of all OTUs. Greater richness and evenness of bacteria at the cold areas, compared to the warm areas, was also observed and is attributed to more vegetation cover and soil organic matter, nutrient availability and moisture. There was no significant difference of chemical soil properties between the grazed and not grazed sites. However, significant differences were observed in bacterial diversity between the grazed and not grazed sites, suggesting that bacteria respond much more rapidly to grazing than to soil chemical properties. According to the Chao1 and J values, the least richness and the highest evenness belonged to the warm-grazed zone, indicating grazing had a greater effect at the warm areas, compared to the cold areas. In conclusion, change in community composition at managed (i.e. grazed versus not grazed) semiarid sites, estimated by next generation sequencing, precede detectable changes in soil chemical properties, thereby providing an early sign of change in soil quality. [ABSTRACT FROM AUTHOR]

Background and objectives: One of the most important causes of urinary tract infections (UTI) is Escherichia coli. The infection is mainly due to the uropathogenic strain (UPEC), which has key virulence factors, including hemolysis. In this study, we evaluated the frequency of hlyA, hlyB, hlyC and hlyD genes in UPEC strains isolated from clinical samples from Shiraz city, Iran. Materials and methods: 130 urine samples with suspected UTI were collected from Shiraz medical centers and cultured on blood agar and EMB media. Colonies were then characterized by biochemical methods. The genomes were extracted and the presence of hemolysis genes was detected by polymerase chain reaction (PCR) using hly gene specific primers and 16S rRNA. Drug resistance was assessed by using 10 antibiotic disks in the disk diffusion method, according to CLSI criteria. Results: Out of the 130 collected UTI samples, 100 were identified as UPECs. Within isolates, the hlyD gene had the highest frequency – 95% – and hlyC had the lowest, with 23%. The frequencies of hlyA and hlyB genes were calculated as 50% and 43%, respectively. The rates of antibiotic resistance to Azithromycin, Ampicillin, Cefotaxime, Nalidixic Acid, Tetracycline, Trimethoprim-Sulfamethoxazole, Cefepime, Aztreonam, Gentamicin, and Nitrofurantoin were 95%, 86%, 68%, 66%, 65%, 64%, 51%, 46%, 44%, 14%, respectively. 98% of these isolates belonged to the MDR group. Conclusion: This study shows diversity of hemolysis virulence factor in UPECs and unique UPEC drug resistance that would indicate a high antibiotic use in the general population. [ABSTRACT FROM AUTHOR]

Bacterial wilt disease caused by Ralstonia solanacearum is one of the most destructive diseases in the world, including Kurdistan province of Iran. Using the endophytic bacteria is one of the most effective and applicable methods to control of the disease. In this study, Bacillus sp. Bp91 which was isolated from potato fields in Kurdistan province was used as a superior antagonist against R. solanacearum. The results of the supplementary tests showed that the production of protease in the mentioned strain is positive. This was negative and relatively weak for hydrogen cyanide and siderophore production, respectively. The phylogenetic tree derived from 16S rRNA gene sequence showed the stain belongs to the genus Bacillus sharing the highest level of sequence homology with to B. pumilus. Metabolic studies by GC-mass were also indicated that the two metabolites Eicosane and Dibutyl phthalate are the most prominent antimicrobial metabolites produced by the bacterium. [ABSTRACT FROM AUTHOR]

Objective: The potential use of symbiotic bacteria for the control of mosquito-borne diseases has attracted the attention of scientists over the past few years. Culiseta longiareolata is among the medically important mosquitoes that transmit a wide range of vector-borne diseases worldwide. However, no extensive studies have been done on the identification of its symbiotic bacteria. Given the role of this species in the transmission of some important diseases and its widespread presence in different parts of the world, including northwestern parts and the West Azerbaijan Province in Iran, a knowledge about the symbiotic bacteria of this species may provide a valuable tool for the biological control of this mosquito. Accordingly, the present study was conducted to isolate and identify the cultivable isolates bacterial symbionts of Culiseta longiareolata using 16S rRNA fragment analysis. Results: The midguts of 42 specimens of Cs. longiareolata were dissected, and the bacteria were cultured on agar plates. After the purification of the bacterial colonies, 16srRNA region amplification and gene sequence analysis were performed, and the sequences were confirmed by biochemical methods. In the present study, 21 isolates belonging to the genera Acinetobacter, Aerococcus, Aeromonas, Bacillus, Carnobacterium, Klebsiella, Morganella, Pseudomonas, Shewanella and Staphylococcus were identified. [ABSTRACT FROM AUTHOR]

Introduction: Although bacteria and archaea are able to grow and adapted to the petrol reservoirs during several years, there are no results from microbial diversity of oilfields with high temperature in Iran. Hence, the present study tried to identify microbial community in non-water flooding Zeilaei (ZZ) oil reservoir. Materials and methods: In this study, for the first time, non-water flooded high temperature Zeilaei oilfield was analyzed for its microbial community based on next generation sequencing of 16S rRNA genes. Results: The results obtained from this study indicated that the most abundant bacterial community belonged to phylum of Firmicutes (Bacilli) and Thermotoga, while other phyla (Proteobacteria, Actinobacteria and Synergistetes) were much less abundant. Bacillus subtilis, B. licheniformis, Petrotoga mobilis, P. miotherma, Fervidobacterium pennivorans, and Thermotoga subterranea were observed with high frequency. In addition, the most abundant archaea were Methanothermobacter thermautotrophicus. Discussion and conclusion: Although there are many reports on the microbial community of oil filed reservoirs, this is the first report of large quantities of Bacillus spp. from a high temperature oil reservoir. [ABSTRACT FROM AUTHOR]

Children with malignancies are vulnerable to various infections, including sinus infections. Sinusitis is primarily caused by bacterial infections, followed by fungal infections. Due to this, evaluating the occurrence, diversity, and antibiotic susceptibility patterns of bacterial species that cause paranasal sinus infections in children with malignancy and unexplained fever is important. To investigate the bacterial species accountable for sinusitis in children with malignancy and unexplained fever, and determine their susceptibility to antibiotics. The study involved collecting 90 sinus samples from children aged 5 to 15 years with malignancy in Arak City, Iran. The isolates were identified using a combination of phenotypic, biochemical, and molecular techniques, including specific polymerase chain reaction and 16S ribosomal RNA gene sequencing. Drug susceptibility testing was performed following the Clinical & Laboratory Standards Institute 2021 guidelines. A total of 36 isolates (40%) were obtained, including 4 isolates of Nocardia (11.12%), 4 isolates of Escherichia coli (11.12%), 3 isolates of Klebsiella pneumoniae (8.33%), 5 isolates of Pseudomonas aeruginosa (13.88%), 3 isolates of Acinetobacter baumannii (8.33%), 4 isolates of Staphylococcus aureus (11.12%), 3 isolates of Staphylococcus epidermidis (8.33%), 5 isolates of Streptococcus agalactiae (13.88%), 2 isolates of Streptococcus pneumoniae (5.55%), and 3 isolates of Enterococcus faecium (8.33%). The isolates showed the most sensitivity to imipenem and trimethoprim-sulfamethoxazole and the least sensitivity to erythromycin and tetracycline. The findings of the study indicate that sinusitis can contribute to fever of unknown origin in patients with cancer. Therefore, it is recommended to use a combination of molecular and phenotypic methods for accurate identification of isolates. This approach can provide more reliable and precise results, leading to better diagnosis and treatment of sinusitis infections in children with malignancy. [ABSTRACT FROM AUTHOR]

Recent studies have shown that oilfield harbours diverse microbial communities. Water-flooding is believed to be the main contaminating factor of oil reservoirs, however, less attempts have been made to study the effect of natural gas injection on microbial community of oilfields. Molecular methods were used to evaluate the microbial diversity of Haftkel (HK) and Lali (LA) petroleum reservoirs in the south of Iran. The HK oilfield has been injected with natural gas for long duration, but LA oilfield had no enhanced oil recovery (EOR) process. Next generation sequencing (NGS) of 16S rRNA archaeal genes indicated that the genus Methanofollis was observed with high presence in 89.7% and 92.6% frequency in the HK and LA oilfields, respectively. Most abundant phyla in HK oilfield were Synergistes (58.1%), Firmicutes (17%), Proteobacteria (Betaproteobacteria) 12.8% and unclassified bacteria (5.2%), while Thermotogae (78%), Firmicutes (10.8%), Synergistes (4%) and unclassified bacteria (3.8%) were observed in LA oilfield. The comparison of the results indicated that the injection of natural gas could increase bacterial diversity and most probable cause to increase frequency of bacterial genus Anaerobaculum belonging to the Synergistes. [ABSTRACT FROM AUTHOR]

Two strains of true branched heterocytous cyanobacteria, SA33 and SA16, isolated from dried paddy fields of Mazandaran, Iran, were studied using morphological, ecological, and molecular tools. Morphological characterization of the strains indicated them to be commonly showing profuse T-type branching, large irregularly shaped cells of main filament and tapering branches. Strain SA33 showed development of interesting biseriate filaments with unilateral branching, while strain SA16 showed uniseriate filaments with bilateral branching. Ecological examination of the localities consisted of the assessment of the habitat and correlations with the overall environment of the habitats. 16S rRNA gene-based molecular and phylogenetic assessment gave unique positioning to both the strains separated with good bootstrap support from rest of the members of the true branched clade. Full length sequencing of the 16S-23S ITS region and folding of the secondary structures gave interesting secondary structures and comparison with the closely related sequences clearly indicated the secondary structures of both the strains to be unique. All the results indicated the strains to be members of a morphologically cryptic but phylogenetically distinct unknown genus of cyanobacteria. Comprehensive evaluation of all the findings and comparative assessment of previous studies indicate that SA33 and SA16 are indeed two new species of a new genus of true branched cyanobacteria. In accordance with the International Code of Nomenclature for algae, fungi and plants, we propose the name of the new genus as Neowestiellopsis with the names of the species being Neowestiellopsis persica and Neowestiellopsis bilateralis. [ABSTRACT FROM AUTHOR]

Introduction: The Rhizobium-legume interaction leads to biological nitrogen-fixation and increases nitrogen of soil. The aim of this study was to characterize the properties of Sinorhizobium isolates from the roots of alfalfa plants in Iran. Materials and methods: Bacteria were isolated in yeast extract mannitol Agar and confirmed by plant infection test. After evaluation from the point of morphological and biochemical properties, a fragment of 16S rDNA gene with a size of approximately 1500 base pair was amplified using fD1 and rD1 primers. PCR (polymerase chain reaction) products were analyzed for digestion pattern by Taq1 endonuclease. Results: 63 bacteria were isolated from homogenized nodules. 42 isolates generated nodules in three replicates in infection test. Of the 42 isolates 8, were resistant to salinity. Seven isolates had better growth than others at pH 4. All isolates were resistant to CuCl2 (0.5 mmol), CdCl2 (0.65 mmol), MnSO4 (0.75 and 1.5 mmol) and ZnSO4 (0.125 mmol). Isolates S3Q and S22K were more resistant to salinity, acidity, temperature and heavy metals stresses. PCR products of all bacteria had the same restricted profile after digestion by Taq1 nuclease. Discussion and conclusion: The results showed that among isolated bacteria, there were some differences in the resistance to salinity, acidity, temperature and heavy metals stresses. Identification of native strains of rhizobia, especially strains resistant to salinity, temperature, heavy metals and acidity could be valuable due to their potentiality for using biological fertilizers in harsh conditions. [ABSTRACT FROM AUTHOR]

Nontuberculous mycobacteria (NTM) have emerged as an important cause of opportunistic nosocomial infections. NTM has frequently been isolated from hospital water distribution systems. The aim of this study was to survey the risk of NTM infections and determine the prevalence of NTM species in the hospital water distribution systems in Tabriz, Iran. One hundred and twenty samples of water from different sources of Tabriz hospitals were collected. The samples were filtered through 0.45-µm pore size membranes and decontaminated with 0.01% cetylpyridinium chloride. The sediment was inoculated onto Lowenstein--Jensen medium and incubated for 8 weeks. For identification to the species level, partial sequence analysis of the hsp65 and 16S rRNA genes were used. NTM were detected in 76 (63.3%) of 120 samples. Potentially pathogenic mycobacteria and saprophytic mycobacteria were isolated. Mycobacterium gordonae was the only single species that was present in all types of water. The prevalence of NTM in Tabriz hospitals' water compared with many investigations on hospital waters was high. This indicates that the immunocompromised patients and transplant recipients are at risk of contamination which necessitates considering decontamination of water sources to prevent such potential hazards. [ABSTRACT FROM AUTHOR]

During 2010-2013 surveys for the presence of phytoplasma diseases in Yazd province (Iran), a parsley witches' broom (PrWB) disease was observed. Characteristic symptoms were excessive development of short spindly shoots from crown buds, little leaf, yellowing, witches' broom, stunting, flower virescence and phyllody. The disease causative agent was dodder transmitted from symptomatic parsley to periwinkle and from periwinkle to periwinkle by grafting inducing phytoplasma-type symptoms. Expected length DNA fragments of nearly 1800 and 1250 bp were, respectively, amplified from naturally infected parsley and experimentally inoculated periwinkle plants in direct polymerase chain reaction ( PCR) using phytoplasma primer pair P1/P7 or nested PCR using the same primer pair followed by R16F2n/R16R2 primers. Restriction fragment length polymorphism and phylogenetic analyses of 16S rRNA gene sequences showed that the phytoplasma associated with Pr WB disease in Yazd province belong to 16Sr II-D phytoplasma subgroup. This is the first report of association of a 16Sr II-related phytoplasma with PrWB disease in Iran. [ABSTRACT FROM AUTHOR]

This study was done to determine the molecular and biochemical identification of some causative agents of lactococcosis in farmed rainbow trout in Mazandaran provenience (northern Iran). A total of 200 moribund rainbow trout, suspected of lactococcosis from 10 rainbow trout farms in Mazandaran province, were collected during spring 2012 to winter 2012. Sampling was done from the kidney, spleen, liver and brain and cultured aseptically onto brain heart infusion (BHI) agar plates and incubated at 25 °C for 24 - 48 h. Results of bacteriological cultures of these organs showed 19 % Lactococcus garvieae (38 fish), 9 % Streptococcus spp., (18 fish), 17 % Yersinia spp. (36 fish), and 55 % of fish were culture negative. The PCR assay was developed based on the 16s rRNA gene of L. garvieae for the rapid and specific detection and identification of this pathogen from different sources. Two pairs of primers were designed based on the nucleotide sequences of the 16s rRNA gene of L. garvieae. After PCR assay on isolated bacterial colonies, DNAs extracted from 38 L. garvieae gave the expected 1107 bp PCR fragment of 16S rDNA sequences, which is specific for L. garvieae. The results of this study suggest the use of molecular methods along with current biochemical methods are effective diagnostic tools in the identification of L. garvieae. The combination of these methods for diagnosis of other bacterial disease is recommended. [ABSTRACT FROM AUTHOR]

The present work was performed to investigate the presence of Legionella spp. and its common species in hospital water supplies. Considering the drawback of culture method, polymerase chain reaction (PCR) assays were developed to detect the gene 16S rRNA regardless of the bacterial serotype. Four well-established DNA extraction protocols (freeze & thaw and phenol-chloroform as two manual protocols and two commercial kits) were examined and critiqued to release DNA from bacterial cells. A total of 45 samples were collected from seven distinct hospitals' sites during a period of 10 months. The PCR assay was exploited to amplify a 654-bp fragment of the 16S rRNA gene. Legionella were detected in 13 samples (28.9%) by all of the methods applied for DNA extraction. Considerable differences were noted in the yield of extracted nucleic acids. Legionella were not detected in any of the samples when DNA extraction by freeze & thaw was used. Omitting this method and comparing manual protocol with commercial kits, Kappa coefficient was calculated as 0.619 with p < 0.05. Although no meaningful differences were found between the kits, DNA extraction with Bioneer kit displayed a higher sensitivity than classical Qiagen. Showerheads and cold-water taps were the most and least contaminated sources with 55.5 and 9 percent positive samples, respectively. Moreover two positive samples were identified for species by DNA sequencing and submitted to the Gene Bank database with accession Nos. FJ480932 and FJ480933. [ABSTRACT FROM AUTHOR]

In 2009–2010, crown tumours were collected from walnut (Juglans regiaL.) trees in northern Iran. Gram-negative, rod shaped and aerobic bacteria with circular, convex and white-coloured colonies on potato dextrose agar plus CaCO3 medium were isolated from galls. In pathogenicity tests, tomato seedlings were inoculated with all strains and tumours started to appear three weeks after inoculation. Strains yielded a 224?bp amplicon from thevirD2gene in PCR. When the 16S rRNA gene sequence of strains was compared by BLASTn with nucleotide sequences from GenBank, it showed 99.6% identity with the 16S rRNA sequence ofAgrobacterium tumefaciensATCC 33970. Based on phenotypic and genotypic properties, the bacterium that causes crown gall of walnut trees was identified asA. tumefaciens. [ABSTRACT FROM PUBLISHER]

Background: The presence of microbiome in the blood samples of healthy individuals has been addressed. However, no information can be found on the healthy human blood microbiome of Iranian subjects. The current study is thus aimed to investigate the existence of bacteria or bacterial DNA in healthy individuals., Methods: Blood samples of healthy subjects were incubated in BHI broth at 37 °C for 72 h. The 16S rRNA PCR and sequencing were performed to analyze bacterial isolates. The 16S rRNA PCR was directly carried out on DNA samples extracted from the blood of healthy individuals. Next generation sequencing (NGS) was conducted on blood samples with culture-positive results., Results: Fifty blood samples were tested, and six samples were positive by culture as confirmed by Gram staining and microscopy. The obtained 16S rRNA sequences of cultured bacterial isolates revealed the presence of Bacilli and Staphylococcus species by clustering in the GeneBank database (≥97% identity). The 16S rRNA gene sequencing results of one non-cultured blood specimen showed the presence of Burkholderia. NGS results illustrated the presence of Romboutsia, Lactobacillus, Streptococcus, Bacteroides, and Staphylococcus in the blood samples of positive cultures., Conclusion: The dormant blood microbiome of healthy individuals may give the idea that the steady transfer of bacteria into the blood does not necessarily lead to sepsis. However, the origins and identities of blood-associated bacterial rDNA sequences need more evaluation in the healthy population.

Ralstonia solanacearum , as a causative agent of potato wilt disease, is one of the deadliest diseases worldwide, and also in the Kurdistan province, Iran. Given the importance of the disease, the aim of the present study was to isolate endophytic bacteria from potato plant tissues such as the tuber, root, stem, and leaf, to investigate their antagonistic effects on R. solanacearum. In this regard, 236 endophytic bacteria were isolated and screened in vitro. As a result, 31 isolates were found as potential antagonists against potato wilt pathogen. For phenotypic and genotypic characterization, biochemical and pathogenicity tests as well as 16S rRNA gene sequence analyses were performed. 11 isolates as representatives of different taxa were selected for further investigations. These were identified as: Bacillus pumilus Bp91, B. pumilus Bp1, B. pumilus Bp49, B. licheniformis Bl17, Paenibacillus peoriae Pa86, Pseudomonas brassicacearum Psb101, P. brassicacearum Ps169, P. putida Ps52, Chryseobacterium indologenes Ch54, C. lathyri Chl98, and Microbacterium phyllosphaerae Mi41. Notably, the maximum inhibitory effects were observed by Pseudomonas brassicacearum Psb101, P. brassicacearum Ps169, Paenibacillus peoriae Pa86, Pseudomonas putida Ps52, and Bacillus licheniformis Bl17, by forming 17.6, 17.4, 17.3, 15.5, 15.2 mm diameter inhibition zones against R. solanacearum on nutrient agar medium, respectively. Based on the results of the greenhouse test, all 11 selected isolates simultaneously reduced the disease by 27–55% and also significantly increased plant growth. Among these, the five strains Pseudomonas brassicacearum Psb101, P. brassicacearum Ps169, P. putida Ps52, Paenibacillus peoriae Pa86, and Bacillus licheniformis Bl17 were introduced hereby as the most effective antagonists and growth enhancers under both laboratory and greenhouse conditions. • Pseudomonas brassicacearum , Microbacterium and Chryseobacterium are reported as endophytic bacteria from potato plants. • Bacillus licheniformis is a novel antagonist on R. solanacearum. • These biocontrol and PGPR agents are new endophytes for Kurdistan-Iran. [ABSTRACT FROM AUTHOR]

In order to confirm Koch's postulates, artificial inoculations were carried out with the representative strains (YMAP1, YMAP7, and YMAP9) on immature pear fruits, detached pear shoots, and detached pear blossoms as described by Roselló et al. ([3]), but necrosis symptoms were reproduced only on pear blossoms in pear. 3 Roselló M, Peñalver J, Llop P, Gorris M, Cambra M, López M, Chartier R, García F, Montón C. Identification of an Erwinia sp. different from Erwinia amylovora and responsible for necrosis on pear blossoms. [Extracted from the article]

In Iran, polyphasic studies of unicellular cyanobacteria are still scarce, with more emphasis being placed on filamentous cyanobacteria in paddy fields and fresh water regions. In an effort to increase the knowledge of the diversity of unicellular cyanobacteria from paddy fields in Iran, we have isolated and characterized a new unicellular cyanobacterium strain. The strain was studied using a polyphasic approach based on morphological, ecological and phylogenetic analyses of the 16S-23S ITS rRNA gene region. Complementarily, we have searched for the presence of cyanotoxin genes and analysed the pigment content of the strain. Results showed that the strain was morphologically indistinguishable from the genus Chroococcus , but phylogenetic analyses based on the Bayesian inference and maximum-likelihood methods placed the strain in a separated monophyletic and highly supported (0.99/98, posterior probability/maximum-likelihood) genus-level cluster, distant from Chroococcus sensu stricto and with Chalicogloea cavernicola as sister taxa. The calculated p -distance for the 16S rRNA gene also reinforced the presence of a new genus, by showing 92 % similarity to C. cavernicola . The D1-D1', Box-B and V3 ITS secondary structures showed the uniqueness of this strain, as it shared no similar pattern with closest genera within the Chroococcales. For all these reasons, and in accordance with the International Code of Nomenclature for Algae, Fungi and Plants, we here proposed the description of a new genus with the name Alborzia gen. nov. along with the description of a new species, Alborzia kermanshahica sp. nov. (holotype: CCC1399-a; reference strains CCC1399-b; MCC 4116).

Objective: Nocardiosis is an opportunistic infection in individuals who had organ transplants and in patients with immunosuppressive diseases such as pemphigus Vulgaris (PV), diabetes mellitus, and HIV. Nocardiosis rate has not been assessed in Iranian PV patients, and this was the first study to estimate nocardiosis rate in these patients., Methods: In this study, 103 patients with PV were examined. BAL samples were obtained and direct smear was prepared and visualized by microscopy after PAS staining. Samples were cultured on antibiotic-containing blood and chocolate agar media. DNA extraction and PCR were performed on positive cultures, and final identification was done by 16S rRNA gene sequencing. Drug susceptibility testing was done by microbroth dilution method., Results: Four positive cultures (3.88%) were found in the samples (n = 103). According to sequence analysis, 2 isolates were identified as Nocardia cyriacigeorgica and 2 as Nocardia otitidiscaviarum and Nocardia cerradoensis. Nocardia cerradoensis was isolated from an invasive brain infection. Isolated bacteria were susceptible to majority of the tested antibiotics, except for 2 strains of Nocardia cyriacigeorgica and Nocardia cerradoensis. This was the first isolation of Nocardia cerradoensis of human infection in Asia. Patients with PV are susceptible to nocardiosis, similar to other immunocompromised patients., Conclusion: Pemphigus Vulgaris is a severe autoimmune disease which is treated by a high dosage of corticosteroids. Opportunistic infections are one of the greatest challenges of these patients. One of the neglected agents of opportunistic infection in this disorder is Nocardiosis which can cause a high mortality rate in PV patients., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Applying a desirable disinfestation process is necessary to control the pathogenic microorganisms in the swimming pools and prevent both dermal and intestinal effects. Therefore, the present study was conducted to compare the bacterial community and diversity in the two swimming pools disinfected by the chlorine and ozone (O 3 )-chlorine processes. A total of 24 samples were taken from the two swimming pools in three distinct seasons to analyze the bacterial and physico-chemical indicators. Culture and molecular methods were used to evaluate the microbial quality. Two sets of sample taken from the pools with the maximum swimmer load in the summer were investigated by the next-generation sequencing (NGS) technique. In total, 410 and 406 bacterial species were identified in the chlorine- and ozone-chlorine-disinfected pools, respectively. Among the eight dominant bacterial species in each swimming pool, Pseudomonas alcaliphila, Pseudomonas stutzeri, and Pseudomonas acnes were common species between the two studied pools. Oleomonas sagaranensis (350 reads/18593), Staphylococcus caprae (302 reads /18593), and Anaerococcus octavius (110 reads/18593) were among the dominant bacteria in the chlorine-disinfected pool. Bacterial diversity was lower in the ozone-chlorine-disinfected pool than the other one, and the highest bacterial sequencing belonged to the genus Pseudomonas (85.79%). Results showed that water quality of in O 3 -chlorine-disinfected pool was more desirable than the chlorine-disinfected pool. Molecular methods along with conventional culture methods would be advantageous for microbial assessment in the swimming pools.

Strains of Pseudomonas syringae pv. syringae (Pss) were isolated from P. armeniaca in different geographic areas in East Azerbaijan province, Iran, and studied for genetic diversity and host preference. Results of morphological, physiological and biochemical tests showed no differences among strains and syrB gene was determined to be present in all strains by PCR using gene-specific primers. Results of antibiotic assays showed that all strains were resistant to ceftriaxone and erythromycin, while tetracycline induced the strongest growth inhibition. In pathogenicity tests, all strains incited progressive necrotic lesions on apricot twigs at inoculated sites. Severity of symptoms was variable on mango leaves, lemon fruits, bean pods and tomato seedlings. To assess genetic diversity among strains, clustering of strains was performed based on partial sequences of the 16S rRNA and the rpo D housekeeping genes and DNA fingerprinting using IS50-PCR analysis. Cluster analysis was performed using the Unweighted Pair Group Method with Arithmetic (UPGMA) method and Jaccard's similarity coefficients. High genetic diversity was detected among strains. All Pss strains were divided into two distinct clusters at the 37% similarity level. In summary, this study indicates that Pss strains isolated from apricot in East Azerbaijan province in Iran, are genetically diverse, do not display host specificity, but are heterogeneous in regard to aggressiveness. • All Iranian Pss strains were resistant to ceftriaxone and erythromycin antibiotics. • Pss strains didn't display host specificity, but were heterogeneous in regard to aggressiveness. • Pss strains were genetically diverse based on housekeeping gene sequencing and DNA fingerprinting. [ABSTRACT FROM AUTHOR]

Introduction: Aeromonas have recently emerged as opportunistic pathogens and only a few studies are available regarding the isolation of these bacteria from burn wound infections. This study aimed at isolating Aeromonas as an infrequent cause of infection in this group of immunocompromised patients., Methods: A total of 300 samples were collected from the wounds of burn patients hospitalized in Gotbodin Shirazi Burn Center in 2013. The samples were cultured on Aeromonas specific media and then confirmed using standard biochemical tests and 16S rRNA gene amplification and sequencing. The antibiotic susceptibility of the isolates was determined using the disk diffusion and broth microdilution methods., Results: Biochemical tests demonstrated five presumptive samples of Aeromonas, while, molecular testing confirmed only three. All isolates were resistant to ampicillin-sulbactam, erythromycin, oxacillin, and vancomycin. However, they were susceptible to gentamicin, meropenem, nitrofurantoin, chloramphenicol, cephalexin, and cefotaxime. Two Aeromonas veronii isolates were resistant to sulfamethoxazole-trimethoprim and sensitive to nalidixic acid, while Aeromonas bestiarum was sensitive to the former and resistant to the latter antibiotics. Lastly, only one of the A. veronii isolates was found to be resistant to tetracycline., Conclusion: This study is the first to report on the isolation of Aeromonas spp. from burn patients in Iran. Moreover, this is the first report of isolating A. bestiarum from burn wounds. The results of this study confirm earlier findings that the use of molecular methods is essential to accurately identify these bacteria., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Thiobacillus, as useful soil bacteria, plays an important role in sulfur cycling. The purpose of this study was to identify the species Thiobacillus thioparus, Thiobacillus novellas and Thiobacillus denitrificans in rainfed and irrigated lands soil in Ajabshir, Ilam, Qorveh, Rojintaak, Sonqor, Kermanshah and Research Farm of Razi University in Iran. Sampling was performed as randomized completely with three replications at depth of 0-30 cm. The Thiobacillus species were determined via 16S rRNA characteristics. The results of agarose gel electrophoresis indicated that T. thioparus was the highest amount in the irrigated land in Research Farm and its lowest amount was in the Rojintaak rainfed land. These species not found in four locations and conditions including the Ajabshir irrigated, Qorveh rainfed, Research Farm rainfed and Rojintaak irrigated lands. The results of the T. novellas indicated that this was found in Ilam irrigated, Qorveh rainfed, Research Farm irrigated, Rojintaak irrigated and Rojintaak rainfed lands. The highest and lowest amount of T. novellas was indicated in the Rojintaak and Ilam irrigated lands respectively. The T. denitrificans gene showed that this bacterium was observed only in both samples of Ajabshir. Our study showed that Thiobacillus was not detected in all of the soils. If sulfur fertilizer is given to the soil without this bacterium, it is necessary to use sulfur fertilizer with Thiobacillus bacteria inoculation for better sulfur oxidation.

The taxonomic status of species included in the genus Heremites in Iran and Iraq is uncertain. Three of these species have been assigned to the genus based on morphology: Heremites auratus transcaucasica, H. vittatus, and H. septemtaeniatus. We examined the phylogenetic relationships and taxonomic status of the Iranian and Iraqi species of Heremites by performing phylogenetic analyses using mitochondrial DNA sequences (cytochrome b and 16S rRNA). Phylogenetic relationships and estimated genetic distances indicated that the Heremites populations of the area (Iran and Iraq) form five distinct clades. Three of these clades are found only in Iran, specifically in: (1) Fars and Hormozgan provinces; (2) Northeastern Khuzestan; and (3) Khorasan and Isfahan provinces. The fourth clade (H. septemtaeniatus) is found in west and Mahshahr in Iran as well as in eastern and northern parts of Iraq. The fifth clade, Heremites vittatus, is found in Iran and Iraq. We also confirm the absence of H. auratus in Iran and Iraq. It also indicated that H. vittatus is sister taxon to the other groups that our analyses estimate the divergence of this clade in the Middle Miocene (15.9 Mya). The clade containing the Fars-Hormozgan and Khuzestan populations diverged at the end of the Miocene (8.5 Mya). The Isfahan and Khorasan populations separated at the Pliocene (4.2 Mya) from the western Iranian group, the group in Mahshahr, Iran and the groups in northern and eastern Iraq.

Mycobacterium canariasense was first isolated as a novel species in 2004 from clinical specimens in Spain. Since then there have only been a few additional reports from Spain, the USA, and Lebanon on the isolation of this rare species from clinical specimens. We herein present the first report on isolation of this organism from hospital water, which provides evidence for determining the natural habitat of this rare species. The water samples were collected from hospital departments and cultured on Löwenstein-Jensen and Sauton's media. The isolates, i.e. WP5, WP20, and AW2-3, were subjected to identification by conventional and molecular tests including sequencing analysis of 16S rRNA. The water isolates revealed phenotypic and molecular features consistent with M. canariasense including a genus-specific amplicon of the hsp65 gene and 100% similarities with those of M. canariasense CIP: 107998(T) 16S rRNA gene sequences. The current report might be of value in tracing the probable source of infection in patients.

Background and Purpose: The clinical and epidemiologic features of Kawasaki disease (KD) suggest an infectious etiology; however, the agent(s) remain unknown. Our purpose was to isolate the causative bacterial gene from peripheral blood leukocytes of patients with acute KD, by Universal polymerase chain reaction (UPCR), in Tehran Children's Medical Center. Materials and Methods: Universal polymerase chain reaction (UPCR) assay was used to amplify the bacterial l6S ribosomal RNA gene (rDNA). Results: Forty three (28 boys and 15 girls) were diagnosed with acute Kawasaki disease included in this study. The median age at diagnosis was 3.5 years (range: 0.5 -9 years). Twenty Nine (29) cases had typical KD criteria and 14 patients had atypical KD at diagnosis. Two of the 43 KD patients were positive for the Universal PCR assay for 16S rRNA, prior to intravenous γ-globulin therapy (IVGT), while all specimens were negative by conventional blood culture. In our study, there was fever in 100%, conjunctivitis in 62.7%, rash in 83 .72%, oral mucosal changes in 76.74%, peripheral changes in 37.20%, and cervical lymphadenopathy in 39.53% cases. Conclusion: The 16S rDNA sequence was positive in 4.65% of acute KID patients; this data shows that an infectious KD agent is traced in peripheral leukocytes. The question remains as to what true frequency of the 16S rDNA sequence in KD is. [ABSTRACT FROM AUTHOR]