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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Journal ArticleDOI
Efficacy of Hollow‐Fiber Ultrafiltration for Microbial Sampling in Groundwater
Peter S.K. Knappett,Alice C. Layton,Larry D. McKay,Daniel E. Williams,Brian J. Mailloux,M. R. Huq,Md. Jahangir Alam,Kazi Matin Ahmed,Yasuyuki Akita,Marc L. Serre,Gary S. Sayler,Alexander van Geen +11 more
TL;DR: Hollow-fiber ultrafiltration appears to be effective for concentrating microorganisms in environmental water samples, but additional research is needed to quantify losses during filtration.
Journal ArticleDOI
Marine aerosol as a possible source for endotoxins in coastal areas.
TL;DR: It is concluded that marine cyanobacteria may be a dominant contributor to elevated endotoxin levels in coastal areas and may influence human health by inflammation and allergic reactions when inhaled.
Journal ArticleDOI
The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms
Timothy M. LaPara,Katheryn Hope Wilkinson,Jacqueline M. Strait,Raymond M. Hozalski,Michael J. Sadowksy,Matthew J. Hamilton +5 more
TL;DR: The bacterial community composition of the full-scale biologically active, granular activated carbon filters operated at the St. Paul Regional Water Services was investigated using Illumina MiSeq analysis of PCR-amplified 16S rRNA gene fragments to conclude that the BAC filters potentially contained significant numbers of unidentified and novel ammonia-oxidizing microorganisms that possess amoA genes similar to those of previously described AOB.
Journal ArticleDOI
Quantification of Nitrosomonas oligotropha and Nitrospira spp. using competitive polymerase chain reaction in bench-scale wastewater treatment reactors operating at different solids retention times.
Hebe M. Dionisi,Alice C. Layton,Kevin G. Robinson,J. R. Brown,I. R. Gregory,J. J. Parker,Gary S. Sayler +6 more
TL;DR: The effect of solids retention time (SRT) on ammonia and nitrite‐oxidizing bacteria was measured by Nitrosomonas oligotropha‐like ammonia monooxygenase A and Nitrospira 16S rDNA competitive polymerase chain reaction assays in a complete‐mix, bench‐scale, activated‐sludge system.
Journal ArticleDOI
Microbial communities of the carapace, gut, and hemolymph of the Atlantic blue crab, Callinectes sapidus
TL;DR: It is found that the carapace, gut and hemolymph microflora have a core Proteobacteria community with contributions from other phyla including Bacteroidetes, Firmicutes, Spirochetes, and Tenericutes.
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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Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA.
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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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