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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Aeolian dispersal of bacteria in southwest Greenland: their sources, abundance, diversity and physiological states
Tina Šantl-Temkiv,Ulrich Gosewinkel,Piotr Starnawski,Mark A. Lever,Mark A. Lever,Kai Finster +5 more
TL;DR: Bacteria in the atmosphere over southwest Greenland was studied and it was found that the diversity of bacterial communities correlated positively with air temperature and negatively with relative humidity, and that bacterial clades differed in their activity potential.
Journal ArticleDOI
Occurrence and distribution of Vibrio vulnificus and Vibrio parahaemolyticus--potential roles for fish, oyster, sediment and water.
TL;DR: Fish intestines are a significant source of pathogenic vibrios in the environment, and both V. vulnificus and V. parahaemolyticus were consistently detected in fish intestines, but infrequently detected and at lower levels in oysters and during the less favourable period.
Journal ArticleDOI
Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties.
Irene Stefanini,Duccio Cavalieri +1 more
TL;DR: This review is aimed at highlighting the major technical and experimental challenges in dissecting the contribution of the vineyard and native environments microbiota to the wine fermentation process, and how metagenomic approaches can help in understanding microbial fluxes and selections across the environments and specimens related to wine fermentation.
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Distribution of High Bacterial Taxa Across the Chronosequence of Two Alpine Glacier Forelands
TL;DR: The overall composition of the bacterial community was more affected than the abundance of the targeted taxa by changes in environmental conditions along the chronosequences, indicating that the overall composition.
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Methanogenic population dynamics during semi‐continuous biogas fermentation and acidification by overloading
F. Blume,Ingo Bergmann,Ingo Bergmann,Edith Nettmann,Edith Nettmann,H. Schelle,G. Rehde,Kerstin Mundt,Michael Klocke +8 more
TL;DR: The methanogenic community in a biogas reactor from start‐up to acidification conditions was investigated and reliability and accuracy of the applied quantitative real‐time PCR method (Q‐PCR) was briefly evaluated.
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.
Journal ArticleDOI
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.
Journal ArticleDOI
Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA.
TL;DR: Computer-simulated analysis of terminal restriction fragment length polymorphisms (T-RFLP) for 1,002 eubacterial sequences showed that with proper selection of PCR primers and restriction enzymes, 686 sequences could be PCR amplified and classified into 233 unique terminal restriction fragments lengths or "ribotypes."
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Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology
Gerard Muyzer,Kornelia Smalla +1 more
TL;DR: The potentials and limitations of these techniques will be discussed, and it will be indicated why their use in ecological studies has become so important.
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