A new version of the RDP (Ribosomal Database Project)

Maidak, B.; Cole, James R.; Larsen, Niels; Li, Bing; Lilburn, Timothy; McCaughey, Michael J.; Olsen, Gary J.; Overbeek, Ross; Pramanik, Sakti; Schmidt, Thomas M.; Tiedje, James M.; Woese, Carl R.

doi:10.1093/nar/27.1.171

Cited by 882 publications

(607 citation statements)

References 6 publications

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“…Prominent bands were excised and subjected to sequencing. Sequence identification was performed by use of the BLASTN facility of the National Center for Biotechnology Information and ''Sequence Match'' facility of the Ribosomal Database Project [19], respectively, accession numbers AY245556 to AY245577. Sequences were assembled using ''SeqPup Version 0.6'' [8].…”

Section: Dna Extraction and Pcr Amplificationmentioning

confidence: 99%

Utilization of Microbial Biofilms as Monitors of Bioremediation

et al. 2004

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A down-well aquifer microbial sampling system was developed using glass wool or Bio-Sep beads as a solidphase support matrix. Here we describe the use of these devices to monitor the groundwater microbial community dynamics during field bioremediation experiments at the U.S. Department of Energy Natural and Accelerated Bioremediation Research Program's Field Research Center at the Oak Ridge National Laboratory. During the 6-week deployment, microbial biofilms colonized glass wool and bead internal surfaces. Changes in viable biomass, community composition, metabolic status, and respiratory state were reflected in sampler composition, type of donor, and groundwater pH. Biofilms that formed on Bio-Sep beads had 2-13 times greater viable biomass; however, the bead communities were less metabolically active [higher cyclopropane/monoenoic phospholipid fatty acid (PLFA) ratios] and had a lower aerobic respiratory state (lower total respiratory quinone/ PLFA ratio and ubiquinone/menaquinone ratio) than the biofilms formed on glass wool. Anaerobic growth in these systems was characterized by plasmalogen phospholipids and was greater in the wells that received electron donor additions. Partial 16S rDNA sequences indicated that Geobacter and nitrate-reducing organisms were induced by the acetate, ethanol, or glucose additions. DNA and lipid biomarkers were extracted and recovered without the complications that commonly plague sediment samples due to the presence of clay or dissolved organic matter. Although microbial community composition in the groundwater or adjacent sediments may differ from those formed on down-well biofilm samplers, the metabolic activity responses of the biofilms to modifications in groundwater geochemistry record the responses of the microbial community to biostimulation while providing integrative sampling and ease of recovery for biomarker analysis.

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Section: Dna Extraction and Pcr Amplificationmentioning

confidence: 99%

Utilization of Microbial Biofilms as Monitors of Bioremediation

et al. 2004

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“…Positive recombinants were then submitted for sequencing with an M13 primer on an ABI3730 DNA Sequencer (USA) at the Shanghai Invitrogen Biotech Co., Ltd. The obtained sequences were analyzed against sequences in the Ribosomal Database Project (RDP) using the Classier tool, and against GenBank sequences using the Basic Local Alignment Search Tool (BLAST) program [21,22]. Phylogenetic trees of 16S rDNA partial sequences were generated using the neighbor-joining algorithms in Mega IV software [23].…”

Section: Dna Extraction Pcr Amplification and Dggementioning

confidence: 99%

Spatial variability of cyanobacterial community composition in Sanya Bay as determined by DGGE fingerprinting and multivariate analysis

et al. 2012

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The cyanobacterial communities in the surface and bottom waters of Sanya Bay were investigated on April 24 and 25, 2010. Flow cytometry showed that the total cyanobacterial abundance in the surface and bottom layers ranged from 0.7×10 4 to 2.38×10 4 cells mL −1 and from 1×10 4 to 1.8×10 4 cells mL −1 , respectively. Cyanobacterial diversity was analyzed using a molecular fingerprinting technique called denaturing gradient gel electrophoresis (DGGE), followed by DNA sequencing. The results were then interpreted through multivariate statistical analysis. Differences in the compositions of cyanobacterial communities were observed in the surface and bottom waters at the same station, with some bands obtained from both the surface and bottom layers, whereas some bands were present only in one layer. The predominant cyanobacterial species of the excised DGGE bands were related to Synechococcus or Synechococcus-like species (56.2%). Other phylogenetic groups identified included Chroococcidiopsis (6.3%), Cyanobium (6.3%) and some unclassified cyanobacteria (31.2%). A redundancy analysis (RDA) was conducted to reveal the relationships between the cyanobacterial community composition and environmental factors. Analysis results showed that the spatial variations in the cyanobacterial community composition in surface waters was significantly related to chlorophyll a (Chla), the biochemical oxygen demand (BOD), nitrate and phosphate (P<0.05). Meanwhile, the spatial variations in the bottom waters was significantly affected by nitrate, nitrite, and phosphate (P<0.05). Environmental parameters could explain 99.3% and 58.3% of the variations in the surface and bottom layers, respectively. cyanobacterial community composition, PCR-DGGE, Synechococcus, redundancy analysis Citation:Ling J, Zhang Y Y, Dong J D, et al. Spatial variability of cyanobacterial community composition in Sanya Bay as determined by DGGE fingerprinting and multivariate analysis.

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“…Purified reactions were electrophoresed using a model 310 Genetic Analyzer (Applied Biosystems). The 16S rRNA gene sequences were aligned against representative reference sequences of members of the low G + C Gram-positive phylum using the ae2 editor (Maidak et al 1999). The method of Jukes and Cantor (1969) was used to calculate evolutionary distances.…”

Section: Phenotypic Characterizationmentioning

confidence: 99%

Salinicoccus salsiraiae sp. nov.: a new moderately halophilic gram-positive bacterium isolated from salted skate

et al. 2006

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Two moderately halophilic low G + C Grampositive bacteria were isolated from a sample of salted skate (Class Chondrychthyes, Genus Raja). Phylogenetic analysis of the 16S rRNA gene sequence of strains RH1 T and RH4 showed that these organisms represented a novel species of the genus Salinicoccus. The new isolates formed pink-red colonies and flocculated in liquid media, with optimum growth in media containing 4% NaCl and pH of about 8.0. These organisms are aerobic but reduce nitrate to nitrite under anaerobic conditions. Acid is produced from several carbohydrates. Oxidase and catalase were detected. Menaquinone 6 was the major respiratory quinone. The major fatty acids of strains RH1 T and RH4 were 15:0 anteiso and 15:0 iso. The G + C contents of DNA were 46.2 and 46.0 mol%, respectively. The peptidoglycan was of A3alpha L-LysGly 5-6 type. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we suggest that strain RH1 T (=LMG 22840 = CIP 108576) represents a new species of the genus Salinicoccus, for which we propose the name Salinicoccus salsiraiae.

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A new version of the RDP (Ribosomal Database Project)

Cited by 882 publications

References 6 publications

Utilization of Microbial Biofilms as Monitors of Bioremediation

Utilization of Microbial Biofilms as Monitors of Bioremediation

Spatial variability of cyanobacterial community composition in Sanya Bay as determined by DGGE fingerprinting and multivariate analysis

Salinicoccus salsiraiae sp. nov.: a new moderately halophilic gram-positive bacterium isolated from salted skate

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