16S RRNA Gene

Two bacteria were isolated from anoxic denitrifying
reactor for treatment of domestic wastewater. The analysis of the
16S rDNA gene sequences showed that the isolated strains were
affiliated with Bacillus cereus and Bacillus tequilensis.
Denitrification was compared between Bacillus cereus and
Bacillus tequilensis in this study. Two bacilli were able to
denitrify and Bacillus cereus was more efficient than Bacillus
tequilensis. Bacillus cereus reduced 80% of high amount of
nitrate; however, Bacillus tequilensis could reduce 37.4% of
nitrate. These heterotrophic bacteria are able to eliminate organic
matter with the same trend reducing 74.5% for Bacillus
tequilensis and 70.2% for Bacillus cereus.

The present study has been carried out with focus on Muticaria macrostoma group from the Maltese Islands to characterize and define, from a molecular standpoint, their identity and relationships with topotypical Sicilian Muticaria (i.e. M. syracusana, M. neuteboomi, M. cyclopica and M. brancatoi). Molecular study included amplification of 16S rDNA (ca. 300 bp) and COI (ca. 700 bp) gene partial sequences which were used for single and combined gene analysis by Bayesian Inference to achieve the phylogenetic reconstructions with the highest posterior probabilities. Obtained results showed that, within M. macrostoma group, the taxa mamotica and os-citans can be elevated to the specific rank, thus bringing to three the Maltese Muticaria species, i.e. M. macrostoma, M. mamotica, and M. oscitans; whereas scalaris may be considered a sub-species, or even a synonim. Present findings confirmed the validity of the Sicilian species M. syracusana, M. neuteboomi, M. cyclopica and M. brancatoi. Furthermore, the populations of the Sicilian and Maltese Muticaria seem to belong to two different levels of differentiation. Finally , we have also examined some Lampedusa populations but the position of this genus still remains to be clarified. In particular, it is confirmed that Lampedusa and Muticaria are different genera, but at present, the relations within the Lampedusa group need further studies to be analysed in details.

Fourteen species of the Malaysian fruit bats (Pteropodidae) were used in this DNA taxonomy using 1,334bp of the 12S ribosomal RNA (rRNA), transfer RNA (tRNA) valine and 16S rRNA gene segments. Previous studies using DNA found contradictions between morphology and molecular data in inferring the phylogeny of the fruit bats proposed by Andersen (1912). Our phylogenetic analysis using the neighbor-joining and the maximum parsimony methods did not support the monophyly of the subfamily Macroglossinae and the cynopterine group of the subfamily Pteropodinae as proposed by classical taxonomists. This is congruent with previous molecular studies. Here, we provide the first registered 12S rRNA, tRNA valine and 16S rRNA sequence records for Dyacopterus spadiceus in the GenBank database. This study represents the first attempt to infer the phylogenetic relationship of fruit bats from Malaysia using molecular methods.

This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright a b s t r a c t Patterns in soil bacterial communities, and the factors that determine them, have been little explored in arid and semi-arid environments. It is unclear to what extent the diversity and community composition of arid-land soil bacterial communities follow vegetation habitats, or conversely other relatively independent soil variables. It is also unclear whether the factors (e.g. pH) that contribute to variation in bacterial communities in some moister environments also operate on a local scale in semi-arid environments. To identify the main factors in shaping bacterial community structure in semi-arid environments , we sampled a mosaic of habitats under different vegetation, landscape and edaphic conditions in central Mongolia, including steppe, forest-steppe, and abandoned wheat field. Soil DNA was extracted and pyrosequenced for 16S rRNA gene identification. NMDS results showed that bacterial community structures are slightly different from one habitat to another. However, the similarity between communities both within and between habitats is determined more strongly by soil texture than by vegetation type and drainage conditions. Moreover, the relative abundances of certain phyla are correlated with specific soil properties such as salinity and soil texture, in ways that have not previously been found in semi-arid environments. Actinobacteria, for example, show a negative correlation with salinity and Bacteroidetes display a positive relationship with percentage silt and clay. It also appears that the most important environmental variables (soil texture and salinity) affecting the bacterial community within this semi-arid environment are different from those found in moister environments, with no detectable effect of pH.

Background
Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The objectives of this study were to characterize and curate archaeal 16S rRNA gene introns from high-temperature habitats, evaluate the conservation and distribution of archaeal 16S rRNA introns in geothermal systems, and determine which “universal” archaeal 16S rRNA gene primers are impacted by the presence of intron sequences.

Results
Several new introns were identified and their insertion loci were constrained to thirteen locations across the 16S rRNA gene. Many of these introns encode homing endonucleases, although some introns were short or partial sequences. Pyrobaculum, Thermoproteus, and Caldivirga 16S rRNA genes contained the most abundant and diverse intron sequences. Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically. The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes.

Conclusions
The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different “universal” 16S rRNA primers employed in environmental microbial community analysis.

The aim of this research work was to explore psychrotrophic microbes from soil sample of NyAlesund, Svalbard, arctic region and to investigate their potential use as an effective tool for industrial application. A novel psychrotrophic bacterial strain showed good growth on minimal medium containing lipid as the only carbon source. Microbiological characterisation of the isolate showed that it was a gram negative rod. The strain was tested for the production of extracellular lipase enzyme. The enzymes were partially purified by 90% saturated ammonium sulfate and dialysis for desalting. The bacterium was identified as Pseudomonas sp ADT3 by 16S rRNA amplification and sequencing which had been deposited in the NCBI GenBank with accession number JX914667. Phylogenetic tree was also constructed with MEGA5 software and showed the highest level of sequence similarity with Pseudomonas sp. HC3-13 strain. The microorganism had a growth optimum at pH 8.0 and temperature 22°C. Optimization of different parameters e.g. temperature, pH, incubation time, cofactors etc. was performed for the extracellular lipase activity. The hydrolytic activity of the enzyme was enhanced 5 times by Pb2+ but strongly inhibited by heavy metals Hg2+ as well as EDTA and β-mercaptoethanol. For the molecular weight estimation of enzyme SDS-PAGE was done which showed an inducible band of approximately 13.9 KDa. Activity staining and mass spectrometry techniques were also performed.

Aim: This research aimed to identify Staphylococcus species isolated from preputial swabs of healthy Aceh cattle, based on 16S ribosomal RNA gene analysis. Materials and Methods: The bacterium was isolated from preputial swabs of healthy Aceh cattle. The total DNA from the isolated bacteria was extracted using the Genomic DNA Mini Kit followed by polymerase chain reaction (PCR) amplification of the 16S rRNA gene. The product of PCR amplification was then sequenced and aligned to the known sequences in the GenBank database by multiple alignments and was also analyzed by bioinformatics software to construct a phylogenetic tree. Results: The results revealed that the bacterial isolate 3A had genetically closed relation to Staphylococcus pasteuri with <97% maximum identity. Data derived from the phylogenetic tree revealed that the bacterial isolate 3A was also related to Staphylococcus warneri, yet, it shows a different evolutionary distance with the ancestors (S. pasteuri). Conclusion: The results of this research suggested that the bacterium 3A, isolated from preputial swabs of healthy Aceh cattle, is a Staphylococcus species.