The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy

Cole, James R.

doi:10.1093/nar/gkg039

Cited by 1,279 publications

(945 citation statements)

References 5 publications

Supporting

Mentioning

928

Contrasting

Unclassified

Order By: Relevance

“…DNA was extracted from soil samples (0.500 g), and DNA was isolated (0.5 ml overnight culture) using the MoBio PowerSoil DNA extraction kit, following the manufacturer's instructions with slight modifications, whereby the 15 min of shaking on a flat bed vortex was replaced by a 30-s bead beading step (5.5 m s Ϫ1 ; Fastprep). Primers that would amplify 16S rRNA gene sequences of R. leguminosarum from soil samples were designed using sequences (285 bp in length) from the Ribosomal Database Project II (RDPII, release 10; http://rdp.cme.msu.edu/ [12]) and the NCBI website (http: //www.ncbi.nlm.nih.gov/). Multiple sequence alignment was performed using MUSCLE alignment software (http://www.ebi.ac.uk/Tools/muscle/index.html [20]), and regions potentially specific for the detection of R. leguminosarum were identified using BioEdit (23).…”

Section: Methodsmentioning

confidence: 99%

Development of a Real-Time PCR Assay for Detection and Quantification of Rhizobium leguminosarum Bacteria and Discrimination between Different Biovars in Zinc-Contaminated Soil

Macdonald

Clark

Hirsch

et al. 2011

Appl Environ Microbiol

View full text Add to dashboard Cite

Primers were designed to target 16S rRNA and nodD genes of Rhizobium leguminosarum from DNA extracted from two different soil types contaminated with Zn applied in sewage sludge. Numbers of rhizobia estimated using 16S rRNA gene copy number showed higher abundance than those estimated by both nodD and the most-probable-number (MPN) enumeration method using a plant trap host. Both 16S rRNA gene copies and the MPN rhizobia declined with increased levels of Zn contamination, as did the abundance of the functional gene nodD, providing compelling evidence of a toxic effect of Zn on R. leguminosarum populations in the soil. Regression analysis suggested the total Zn concentration in soil as a better predictor of rhizobial numbers than both NH 4 NO 3 -extractable and soil solution Zn. R. leguminosarum bv. viciae nodD gene copies were generally less sensitive to Zn than R. leguminosarum bv. trifolii nodD. The latter were generally below detection limits at Zn levels of >250 mg kg ؊1 . Although there were differences in the actual numbers estimated by each approach, the response to Zn was broadly similar across all methods. These differences were likely to result from the fact that the molecular approaches assess the potential for nodulation while the MPN approach assesses actual nodulation. The results demonstrate that the use of targeted gene probes for assessing environmental perturbations of indigenous soil rhizobial populations may be more sensitive than the conventional plant bioassay and MPN methods.Rhizobia are agronomically important as the nitrogen-fixing symbionts of legumes. Rhizobium leguminosarum bv. trifolii is an important species because of its symbiosis with white clover (Trifolium repens), the most common in-field legume contributing to N 2 fixation in the 11 million hectares of farmland currently under pasture in the United Kingdom (18). Numerous studies have demonstrated the negative effects of metals associated with sewage sludge application to land on the population size of Rhizobium in agricultural soils (e.g., see references 3, 15, 22, 24, and 30) and on rates of N 2 fixation (31). Zinc derived from sewage sludge has been shown to have an adverse effect on R. leguminosarum bv. trifolii (e.g., see references 4, 7, 8, and 9), as well as other Rhizobium species, including the closely related R. leguminosarum bv. viciae (6, 27), which is the symbiont of several legume species, including pea (Pisum sativum), field bean (Vicia faba), and hairy vetch (Vicia hirsuta), both at Zn levels in soil near the upper EU limit of 300 mg kg Ϫ1 (5). This is of concern if sewage sludge is to be used on land as a sustainable management practice.Most studies to date have investigated the number of symbiotically competent rhizobia using the conventional trap plant nodulation bioassay, which estimates the most probable number of nodule-forming bacteria in soil (MPN). Although laborious and time-consuming, the trap plant MPN approach is still the most commonly used method for assessing the effects of perturbation on rhizo...

show abstract

Section: Methodsmentioning

confidence: 99%

Development of a Real-Time PCR Assay for Detection and Quantification of Rhizobium leguminosarum Bacteria and Discrimination between Different Biovars in Zinc-Contaminated Soil

Macdonald

Clark

Hirsch

et al. 2011

Appl Environ Microbiol

View full text Add to dashboard Cite

show abstract

“…Recent work by Uzilnov et al [143] proposed a method that does not require an initial alignment by using Dynalign, a tool for conserved secondary structure prediction. 24 Dynalign simultaneously aligns and folds two sequences considering only thermodynamic information. Since the program outputs the free-energy of the alignment, this can be used to calculate the alignment's 22 We can say that "other" means "I have no idea".…”

Section: Comparative Methodsmentioning

confidence: 99%

“…The O(n 4 ) time complexity means a long time waiting for the analysis of longer sequences. To speed up this process, parsing constrains were implemented in the SCFG-based RNACAD [14] package, a software used in the Ribosomal Database Project (RDP-II) [24]. Each constrain limits the subsequences that may be recognized by a given non-terminal.…”

Section: Comparative Methodsmentioning

confidence: 99%

Computational methods in noncoding RNA research

2007

View full text Add to dashboard Cite

Non protein-coding RNAs (ncRNAs) are a research hotspot in bioinformatics. Recent discoveries have revealed new ncRNA families performing a variety of roles, from gene expression regulation to catalytic activities. It is also believed that other families are still to be unveiled. Computational methods developed for protein coding genes often fail when searching for ncRNAs. Noncoding RNAs functionality is often heavily dependent on their secondary structure, which makes gene discovery very different from protein coding RNA genes. This motivated the development of specific methods for ncRNA research. This article reviews the main approaches used to identify ncRNAs and predict secondary structure.

show abstract

“…The data obtained for both directions were aligned and manually corrected using AutoAssembler 2.1 software (Applied Biosystems). The nucleotide sequences were checked by the Chimera Check program (Ribosomal Database Project II, http://rdp.cme.msu.edu) (Cole et al, 2003) to eliminate chimeras which could result from the amplification of an accidental mixture of bacterial genes; however, no chimeric sequences were detected. Nucleotide sequences were analysed by a BLASTN search (European Bioinformatics Institute, in DDBJ homepage, http:// www.ddbj.nig.ac.jp) (Altschul et al, 1997) for the nearest matches.…”

Section: Collection Of Samplesmentioning

confidence: 99%

Detection of potentially novel bacterial components of the human skin microbiota using culture-independent molecular profiling

Dekio

Hayashi

Sakamoto

et al. 2005

Journal of Medical Microbiology

130

109

View full text Add to dashboard Cite

Although the micro-organisms forming the cutaneous microbiota are considered to play important roles in the modification and prevention of skin diseases, a comprehensive analysis of their composition has not yet been carried out because of difficulties in determining yet-to-be-cultured micro-organisms in the samples. Swab-scrubbed forehead skin samples of five healthy volunteers were analysed by profiling 16S rRNA genes, as well as by conventional culture methods, to provide a profile of the cutaneous microbiota that included yet-to-be-cultured bacteria from normal human skin. Cluster analyses of the 16S rRNA gene sequences indicated a marked increase in diversity compared with that derived from the culture methods. Nineteen previously recognized species and 13 novel phylotypes were obtained from the analysis of 416 clones. In addition to well-known bacteria such as Staphylococcus epidermidis and Propionibacterium acnes, phylotype A, the 16S rRNA gene of which is 97 % similar to that of Methylophilus methylotrophus, was detected in three of the five samples, in one of which it was the predominant clone. Culture-independent genetic profiling of 16S rRNA genes for detecting human cutaneous microbiota has allowed us to detect potentially novel components of the cutaneous microbiota in humans.

show abstract

The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy

Cited by 1,279 publications

References 5 publications

Development of a Real-Time PCR Assay for Detection and Quantification of Rhizobium leguminosarum Bacteria and Discrimination between Different Biovars in Zinc-Contaminated Soil

Development of a Real-Time PCR Assay for Detection and Quantification of Rhizobium leguminosarum Bacteria and Discrimination between Different Biovars in Zinc-Contaminated Soil

Computational methods in noncoding RNA research

Detection of potentially novel bacterial components of the human skin microbiota using culture-independent molecular profiling

Contact Info

Product

Resources

About