rrndb: the Ribosomal RNA Operon Copy Number Database
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TLDR
This work has created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms in an attempt to understand the evolutionary implications of rRNA operon redundancy.Abstract:
The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon in prokaryotic genomes, yet the rRNA genes can vary from one to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. In an attempt to understand the evolutionary implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using 16S rRNA gene sequences. The rrndb web site is directly accessible on the WWW at http://rrndb.cme.msu.edu.read more
Citations
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Effects of aerosol pollution on PM2.5-associated bacteria in typical inland and coastal cities of northern China during the winter heating season.
TL;DR: The airborne bacterial community structure and concentration, during typical pollution episodes that occurred during the winter heating season of 2017-2018 in Jinan and Weihai, indicated that Cyanobacterial genera were dominant in clean or slight pollution.
Journal ArticleDOI
Fate of Antibiotic Resistant Pseudomonas putida and Broad Host Range Plasmid in Natural Soil Microcosms.
TL;DR: The results emphasize the prolonged persistence of P. putida and RP4 in natural soil microcosms, and highlight the potential risks of increased spread potential of plasmid and broader range of host bacteria in disseminating ARGs in soil.
Journal ArticleDOI
Response of nitrifying bacterial communities to the increased thiocyanate concentration in pre-denitrification process.
TL;DR: Changes in process performance and the nitrifying bacterial community associated with an increase of thiocyanate (SCN-) loading were investigated in a pre-denitrification process treating industrial wastewater, resulting in the high dominance of Nitrospira over Nitrobacter.
Journal ArticleDOI
Effect of inhibition of acetoclastic methanogenesis on growth of archaeal populations in an anoxic model environment.
Holger Penning,Ralf Conrad +1 more
TL;DR: Inhibition experiments with CH3F seem to be a suitable method for quantifying acetoclastic CH4 production and the growth and final population size of methanogens were consistent with energetic conditions that at least covered the maintenance requirements of the population.
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Broad-range real time PCR and DNA sequencing for the diagnosis of bacterial meningitis
Susanna Deutch,Lisbeth Nørum Pedersen,Lone Pødenphant,Rikke Olesen,Michael B. Schmidt,Jens Kjølseth Møller,Lars Østergaard +6 more
TL;DR: Broad-range real time PCR was generally comparable to culture of CSF and may be a useful supplement, particularly when antimicrobial therapy has been administered, and was more sensitive than broad-range conventional PCR and microscopy.
References
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Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
TL;DR: Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment.
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Prokaryotes: The unseen majority
TL;DR: The number of prokaryotes and the total amount of their cellular carbon on earth are estimated to be 4-6 x 10(30) cells and 350-550 Pg of C (1 Pg = 10(15) g), respectively, which is 60-100% of the estimated total carbon in plants.
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