Mycoplasma Gallisepticum strain S6 genome contains three regions hybridizing with 16 S rRNA and two regions hybridizing with 23 S and 5 S rRNA

AbstractSouthern hybridization and cloning experiments revealed existence of 3 regions hybridizing with 16 S rRNA and 2 regions hybridizing with 23 S and 5 S rRNA in Mycoplasma Gallisepticum strain S6 genome thus forming 4 separate contiguous regions. One set of a putative rRNA genes is organized classically for eubacteria order 16 S-23 S-5 S. The other two 16 S rRNA and the other one 23 S-5 S rRNA hybridizing regions are separated from each other and from the complete rRNA operon for a distance of more than 6 kb

Taxonomy and antimicrobial activities of a new Streptomyces sp. TN17 isolated in the soil from an oasis in Tunis

An actinomycete strain referred to as TN17 was screened for its antimicrobial activities. The taxonomic status of this strain was established. The organism was found to have morphological and chemotaxonomic characteristics typical of Streptomycetes. Based on the 16S rRNA nucleotide sequences, Streptomyces sp. TN17 was found to have a relationship with Streptomyces lilaceus, Streptomyces gobitricini and Streptomyces lavendofoliae. Combined analysis of the 16 S rRNA gene sequence (FN687757), phylogenetic analysis, fatty acids profile and physiological tests indicated that there are genotypic and phenotypic differences between TN17 and neighboring Streptomyces species’ neighbors. Therefore, TN17 is a novel species: Streptomyces sp. TN17 (=DSM 42020T=CTM50229T). A cultured extract of this strain inhibits the growth of several Gram positive and Gram negative bacteria and fungi

Molecular Identification of Rickettsial Endosymbionts in the Non-Phagotrophic Volvocalean Green Algae

Background: The order Rickettsiales comprises Gram-negative obligate intracellular bacteria (also called rickettsias) that are mainly associated with arthropod hosts. This group is medically important because it contains human-pathogenic species that cause dangerous diseases. Until now, there has been no report of non-phagotrophic photosynthetic eukaryotes, such as green plants, harboring rickettsias. Methodology/Principal Findings: We examined the bacterial endosymbionts of two freshwater volvocalean green algae: unicellular Carteria cerasiformis and colonial Pleodorina japonica. Epifluorescence microscopy using 49-6-deamidino-2phenylindole staining revealed the presence of endosymbionts in all C. cerasiformis NIES-425 cells, and demonstrated a positive correlation between host cell size and the number of endosymbionts. Strains both containing and lacking endosymbionts of C. cerasiformis (NIES-425 and NIES-424) showed a.10-fold increase in cell number and typical sigmoid growth curves over 192 h. A phylogenetic analysis of 16 S ribosomal (r)RNA gene sequences from the endosymbionts of C. cerasiformis and P. japonica demonstrated that they formed a robust clade (hydra group) with endosymbionts of various non-arthropod hosts within the family Rickettsiaceae. There were significantly fewer differences in the 16 S rRNA sequences of the rickettsiacean endosymbionts between C. cerasiformis and P. japonica than in the chloroplast 16 S rRNA or 18 S rRNA of the host volvocalean cells. Fluorescence in situ hybridization demonstrated the existence of the rickettsiacea

Mutation at the position 2058 of the 23S rRNA as a cause of macrolide resistance in Streptococcus pyogenes

BACKGROUND: In streptococci, three macrolide resistance determinants (erm(B), erm(TR) and mef(A)) have been found. In addition, certain mutations at the ribosomal 23S RNA can cause resistance to macrolides. Mutation at the position 2058 of the 23S rRNA of the Streptococcus pyogenes as a cause of macrolide resistance has not been described before. METHODS: Antibiotic resistance determinations for the clinical S. pyogenes strain ni4277 were done using the agar dilution technique. Macrolide resistance mechanisms were studied by PCR and sequencing. All six rRNA operons were amplified using operon-specific PCR. The PCR products were partially sequenced in order to resolve the sequences of different 23S rRNA genes. RESULTS: One clinical isolate of S. pyogenes carrying an adenine to guanine mutation at the position 2058 of the 23S rRNA in five of the six possible rRNA genes but having no other known macrolide resistance determinants is described. The strain was highly resistant to macrolides and azalides, having erythromycin and azithromycin MICs > 256 microgram/ml. It was resistant to lincosamides (clindamycin MIC 16 microgram/ml) and also MIC values for ketolides were clearly elevated. The MIC for telithromycin was 16 microgram/ml. CONCLUSION: In this clinical S. pyogenes strain, a mutation at the position 2058 was detected. No other macrolide resistance-causing determinants were detected. This mutation is known to cause macrolide resistance in other bacteria. We can conclude that this mutation was the most probable cause of macrolide, lincosamide and ketolide resistance in this strain

Assessment of Microbial Diversity in Biofilms Recovered from Endotracheal Tubes Using Culture Dependent and Independent Approaches

Ventilator-associated pneumonia (VAP) is a common nosocomial infection in mechanically ventilated patients. Biofilm formation is one of the mechanisms through which the endotracheal tube (ET) facilitates bacterial contamination of the lower airways. In the present study, we analyzed the composition of the ET biofilm flora by means of culture dependent and culture independent (16 S rRNA gene clone libraries and pyrosequencing) approaches. Overall, the microbial diversity was high and members of different phylogenetic lineages were detected (Actinobacteria, beta-Proteobacteria, Candida spp., Clostridia, epsilon-Proteobacteria, Firmicutes, Fusobacteria and gamma-Proteobacteria). Culture dependent analysis, based on the use of selective growth media and conventional microbiological tests, resulted in the identification of typical aerobic nosocomial pathogens which are known to play a role in the development of VAP, e.g. Staphylococcus aureus and Pseudomonas aeruginosa. Other opportunistic pathogens were also identified, including Staphylococcus epidermidis and Kocuria varians. In general, there was little correlation between the results obtained by sequencing 16 S rRNA gene clone libraries and by cultivation. Pyrosequencing of PCR amplified 16 S rRNA genes of four selected samples resulted in the identification of a much wider variety of bacteria. The results from the pyrosequencing analysis suggest that these four samples were dominated by members of the normal oral flora such as Prevotella spp., Peptostreptococcus spp. and lactic acid bacteria. A combination of methods is recommended to obtain a complete picture of the microbial diversity of the ET biofilm

Isolation, Characterisation and Antagonistic Activity of Bacteria Symbionts Hardcoral Pavona sp. Isolated from Panjang Island, Jepara Against Infectious Multi-drug Resistant (MDR) Bacteria

Pavona sp. is highly spread over Indonesian waters including Panjang Island. Several studies showed that bacteria symbionts hardcoral were the big source of antibiotic product, but there was limited research of the bacteria symbionts with hardcoral Pavona sp. In this research bacteria symbionts from hardcoral Pavona sp. had been collected from Panjang Island, Jepara. Marine bacteria symbionts were isolated by serial dillution method, while antibacterial activity was performed by using overlay and agar block method. The total of 2 from 5 isolates were active to MDR bacteria such as Enterobacter aerogenes and Acinetobacter baumanii, the code were PHC 44/04 and PHC 44/05. Then both of them were identified by morphological and molecular DNA characterization using 16 S rRNA gene sequence. The result of 16 S rRNA identification shows PHC 44/04 has 99% similarities with Virgibacillus salarius strain sa-Vb 1, while PHC 44/05 shows 99% similarities with Pseudoalteromonas flavipulchra strain NCIMB 2033

Ammonia‐oxidizing archaea and nitrite‐oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system

This study analysed the nitrifier community in the biofilter of a zero discharge, recirculating aquaculture system ( RAS ) for the production of marine shrimp in a low density (low ammonium production) system. The ammonia‐oxidizing populations were examined by targeting 16 S rRNA and amoA genes of ammonia‐oxidizing bacteria ( AOB ) and archaea ( AOA ). The nitrite‐oxidizing bacteria ( NOB ) were investigated by targeting the 16 S rRNA gene. Archaeal amoA genes were more abundant in all compartments of the RAS than bacterial amoA genes. Analysis of bacterial and archaeal amoA gene sequences revealed that most ammonia oxidizers were related to N itrosomonas marina and N itrosopumilus maritimus . The NOB detected were related to N itrospira marina and N itrospira moscoviensis, and Nitrospira  marina ‐type NOB were more abundant than N . moscoviensis ‐type NOB . Water quality and biofilm attachment media played a role in the competitiveness of AOA over AOB and Nitrospira  marina‐ over N . moscoviensis‐ type NOB .Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95109/1/fem1448.pd

Ribosomal Rna-protein Interactions In Escherichia Coli: Binding Of Ribosomal Protein S20 To 16 Srrna And Processing Of 5 Srrna By Ribonuclease E

Specific ribonucleotides within the 5{dollar}\sp\prime{dollar} domain of 16 S rRNA were altered by deletion and/or substitution by site-directed mutagenesis of cloned DNA to assess the importance of these particular residues in defining the binding site for ribosomal protein S20. Gel filtration and sucrose gradient centrifugation were employed to measure the binding of S20 to synthetic transcripts containing various alterations. RNA transcripts containing residues 1-402 were sufficient for optimal S20 binding. The removal or the substitution of bulges at 250-251, 278-280 or 321/332 reduced S20-16 S rRNA association significantly. A variety of mutations was introduced into the stem and loop residues of a hairpin structure spanning residues 316-337. These changes demonstrated a strong requirement for both the specific A321*G332 bulge and for residues in the loop itself for proper S20 binding. The nucleotides identified as crucial for S20 binding probably constitute direct contacts between 16 S rRNA and S20.;Processing of 9 S precursor RNA requires the endoribonuclease RNase E which makes two cleavages to liberate p5, the immature form of 5 S rRNA. The contributions of primary and secondary structure to RNase E-mediated cleavage of 9 S RNA were investigated. Site-directed mutagenesis of a cloned 9 S RNA sequence was performed and synthetic transcripts derived from a variety of such mutant templates were assayed as substrates for RNase E-dependent endonuclease activity in fractionated extracts. Our results suggest that RNase E specifically recognizes and cleaves single-stranded RNA sequences only when presented in a proper conformational context. Adjacent secondary structures appear to play a direct and critical role in the enzyme\u27s recognition of its substrate. Additionally, it may serve to anchor single-stranded regions to ensure the availability of the RNase E cleavage sites.;The role of the polypeptide encoded by ams/rne/hmp1, a gene required for RNase E activity, was investigated. Northwestern blotting and UV crosslinking of substrate RNA to crude fractions containing RNase E unambiguously showed that overexpressed Ams/Rne/Hmp1 polypeptide has a high affinity for RNA. Our results demonstrate that the ams/rne/hmp1 gene product intimately associates with RNase E substrate RNA and supports the notion that Ams/Rne/Hmp1 is the nuclease responsible for RNase E activity. In addition, the RNA-binding domain of Ams/Rne/Hmp1 was localized and a putative RNase E-associated protein was identified

Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences

<p>Abstract</p> <p>Background</p> <p>For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly.</p> <p>Results</p> <p>We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform.</p> <p>Conclusions</p> <p>By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions.</p

Pyrosequencing of Bacterial Symbionts within Axinella corrugata Sponges: Diversity and Seasonal Variability

Background: Marine sponge species are of significant interest to many scientific fields including marine ecology, conservation biology, genetics, host-microbe symbiosis and pharmacology. One of the most intriguing aspects of the sponge ‘‘holobiont’’ system is the unique physiology, interaction with microbes from the marine environment and the development of a complex commensal microbial community. However, intraspecific variability and temporal stability of sponge-associated bacterial symbionts remain relatively unknown. Methodology/Principal Findings: We have characterized the bacterial symbiont community biodiversity of seven different individuals of the Caribbean reef sponge Axinella corrugata, from two different Florida reef locations during variable seasons using multiplex 454 pyrosequencing of 16 S rRNA amplicons. Over 265,512 high-quality 16 S rRNA sequences were generated and analyzed. Utilizing versatile bioinformatics methods and analytical software such as the QIIME and CloVR packages, we have identified 9,444 distinct bacterial operational taxonomic units (OTUs). Approximately 65,550 rRNA sequences (24%) could not be matched to bacteria at the class level, and may therefore represent novel taxa. Differentially abundant classes between seasonal Axinella communities included Gammaproteobacteria, Flavobacteria, Alphaproteobacteria, Cyanobacteria, Acidobacter and Nitrospira. Comparisons with a proximal outgroup sponge species (Amphimedon compressa), and the growing sponge symbiont literature, indicate that this study has identified approximately 330 A. corrugata-specific symbiotic OTUs, many of which are related to the sulfur-oxidizing Ectothiorhodospiraceae. This family appeared exclusively within A. corrugata, comprising \u3e34.5% of all sequenced amplicons. Other A. corrugata symbionts such as Deltaproteobacteria, Bdellovibrio, and Thiocystis among many others are described. Conclusions/Significance: Slight shifts in several bacterial taxa were observed between communities sampled during spring and fall seasons. New 16 S rDNA sequences and concomitant identifications greatly expand the microbial community profile for this model reef sponge, and will likely be useful as a baseline for any future comparisons regarding sponge microbial community dynamics