Morphological identification and molecular validation of anchovies (Engraulidae) in the Persian Gulf and Oman Sea.

Validation of species using independent lines of evidence is sometimes desirable when their identification using only one approach is difficult or questionable. The identification of anchovies (Engraulidae) are often challenging based on morphology because closely related species exhibit only slight morphological differentiation. This study utilized morphological characteristics and DNA barcodes for identification and validation of anchovies in the Persian Gulf and Oman Sea. Based on morphology, we identified eight species: Thryssa hamiltonii, T. setirostris, T. vitrirostris, T. whiteheadi, T. dussumieri, Encrasicholina punctifer, E. pseudoheteroloba and Stolephorus indicus. A 658 bp region of mitochondrial cytochrome oxidase subunit I (COI) was generated for 53 specimens from these eight species. From these sequences, we built a Maximum Likelihood phylogenetic tree. In this tree, each species forms a monophyletic group confirming our initial morphological identification. In addition, we provided (and registered in GenBank) the first barcode sequences for T. whiteheadi, an endemic species of this region. Interspecies genetic distances were comprised between 0.168 to 0.275. The largest genetic distance was found between T. vitrirostris and S. indicus and the smallest between T. dussumieri and T. whiteheadi. This study successfully identified eight species of anchovies in the Persian Gulf and Oman Sea based on both morphological and molecular characters.

Nesterenkonia sp. strain F, a halophilic bacterium producing acetone, butanol, and ethanol under aerobic conditions.

The moderately halophilic bacterium Nesterenkonia sp. strain F, which was isolated from Aran-Bidgol Lake (Iran), has the ability to produce acetone, butanol, and ethanol (ABE) as well as acetic and butyric acids under aerobic and anaerobic conditions. This result is the first report of ABE production with a wild microorganism from a family other than Clostridia and also the first halophilic species shown to produce butanol under aerobic cultivation. The cultivation of Nesterenkonia sp. strain F under anaerobic conditions with 50 g/l of glucose for 72 h resulted in the production of 105 mg/l of butanol, 122 mg/l of acetone, 0.2 g/l of acetic acid, and 2.5 g/l of butyric acid. Furthermore, the strain was cultivated on media with different glucose concentrations (20, 50, and 80 g/l) under aerobic and anaerobic conditions. Through fermentation with a 50 g/l initial glucose concentration under aerobic conditions, 66 mg/l of butanol, 125 mg/l of acetone, 291 mg/l of ethanol, 5.9 g/l of acetic acid, and 1.2 g/l of butyric acid were produced. The enzymes pertaining to the fermentation pathway in the strain were compared with the enzymes of Clostridium spp., and the metabolic pathway of fermentation used by Nesterenkonia sp. strain F was investigated.

Genome-Wide Analysis of Oceanimonas sp. GK1 Isolated from Gavkhouni Wetland (Iran) Demonstrates Presence of Genes for Virulence and Pathogenicity.

OBJECTIVE: The bacterium Oceanimonas sp. (O. sp.) GK1 is a member of the Aeromonadaceae family and its genome represents several virulence genes involved in fish and human pathogenicity. In this original research study we aimed to identify and characterize the putative virulence factors and pathogenicity of this halotolerant marine bacterium using genome wide analysis. MATERIALS AND METHODS: The genome data of O. sp. GK1 was obtained from NCBI. Comparative genomic study was done using MetaCyc database. RESULTS: Whole genome data analysis of the O. sp. GK1 revealed that the bacterium possesses some important virulence genes (e.g. ZOT, RTX toxin, thermostable hemolysin, lateral flagella and type IV pili) which have been implicated in adhesion and biofilm formation and infection in some other pathogenic bacteria. CONCLUSION: This is the first report of the putative pathogenicity of O. sp.GK1. The genome wide analysis of the bacterium demonstrates the presence of virulence genes causing infectious diseases in many warmand cold-blooded animals.

Draft genome sequence of Ureibacillus thermosphaericus strain thermo-BF, isolated from Ramsar hot springs in Iran.

Ureibacillus thermosphaericus strain Thermo-BF is an aerobic, thermophilic bacillus which has been characterized to biosynthesize gold nanoparticles. Here we present the draft genome sequence of Ureibacillus thermosphaericus strain Thermo-BF which consists of a 2,864,162-bp chromosome. This is the first report of a shotgun sequenced draft genome of a species in the Ureibacillus genus.

Complete genome sequence of Oceanimonas sp. GK1, a halotolerant bacterium from Gavkhouni Wetland in Iran.

Oceanimonas sp. GK1 (IBRC-M 10197) is a marine halotolerant gammaproteobacterium which was characterized as producing large amounts of poly-ß-hydroxybutyrate. Here we present the whole-genome sequence of Oceanimonas sp. GK1, which consists of a single circular chromosome of 3,514,537 bp and two plasmids 8,462 and 4,245 bp in length.

Halopenitus persicus gen. nov., sp. nov., an archaeon from an inland salt lake.

A novel pale pink-pigmented halophilic archaeon, strain DC30(T), was isolated from Aran-Bidgol salt lake, a hypersaline playa in Iran. Cells of strain DC30(T) were non-motile and pleomorphic, from rods to triangular or disc-shaped. Strain DC30(T) required at least 1.7 M NaCl and 0.05 M MgCl(2) for growth (optimum, 3 M NaCl and 0.1 M MgCl(2)). The optimum pH and temperature for growth of strain DC30(T) were pH 7.5 and 40 °C, respectively, although it was capable of growth over pH and temperature ranges of 6.5-8.5 and 25-50 °C, respectively. Analysis of the 16S rRNA gene sequence showed that strain DC30(T) was a member of the family Halobacteriaceae. However, it had low 16S rRNA gene sequence similarities of 92.4%, 89.4% and 89.1% to the most closely related haloarchaeal taxa, the type species of the genera Halorubrum, Halogranum and Haloplanus, respectively. The DNA G+C content was 66.0 mol%. Phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, common phospholipids found in haloarchaea, were present. Three minor phospholipids and one unidentified glycolipid were also observed. The only quinone present was MK-8(II-H(2)). The physiological, biochemical and phylogenetic differences between strain DC30(T) and other previously described genera of extremely halophilic archaea suggest that strain DC30(T) represents a novel species in a new genus within the family Halobacteriaceae, for which the name Halopenitus persicus gen. nov., sp. nov. is proposed. The type strain of Halopenitus persicus is DC30(T) ( = IBRC 10041(T) = KCTC 4046(T)).

Draft genome sequence of Nesterenkonia sp. strain F, isolated from Aran-Bidgol Salt Lake in Iran.

The draft genome of the aerobic, Gram-positive, halophilic chemoorganotroph Nesterenkonia sp. strain F consists of a 2,812,133-bp chromosome. This study is the first to report the shotgun-sequenced draft genome of a member of the genus Nesterenkonia.

A robust universal method for extraction of genomic DNA from bacterial species.

The intactness of DNA is the keystone of genome-based clinical investigations, where rapid molecular detection of life-threatening bacteria is largely dependent on the isolation of high-quality DNA. Various protocols have been so far developed for genomic DNA isolation from bacteria, most of which have been claimed to be reproducible with relatively good yields of high-quality DNA. Nonetheless, they are not fully applicable to various types of bacteria, their processing cost is relatively high, and some toxic reagents are used. The routine protocols for DNA extraction appear to be sensitive to species diversity, and may fail to produce high-quality DNA from different species. Such protocols remain time-consuming and tedious, thus to resolve some of these impediments, we report development of a very simple, rapid, and high-throughput protocol for extracting of high-quality DNA from different bacterial species. Based upon our protocol, interfering phenolic compounds were removed from extraction using polyvinylpyrrolidone (PVP) and RNA contamination was precipitated using LiCI. The UV spectrophotometric and gel electrophoresis analysis resulted in high A260/A280 ratio (>1.8) with high intactness of DNA. Subsequent evaluations were performed using some quality-dependent techniques (e.g., RAPD marker and restriction digestions). The isolated DNA from 9 different bacterial species confirmed the accuracy of this protocol which requires no enzymatic processing and accordingly its low-cost making it an appropriate method f r large-scale DNA isolation fromvarious bacterial species.