PCR primers and functional probes for amplification and detection of bacterial genes for extracellular peptidases in single strains and in soil

Bach, H.-J.; Hartmann, Anton; Schloter, Michael; Munch, J. C.

doi:10.1016/s0167-7012(00)00239-6

Cited by 102 publications

(50 citation statements)

References 17 publications

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“…Bacterial protease genes ( apr , npr , and sub genes) were amplified using specific primer pairs (3) (Table 1). Takara Ex Taq (Takara Bio) polymerase was used to amplify the protease genes.…”

Section: Methodsmentioning

confidence: 99%

Linking Temporal Changes in Bacterial Community Structures with the Detection and Phylogenetic Analysis of Neutral Metalloprotease Genes in the Sediments of a Hypereutrophic Lake

et al. 2014

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We investigated spatial and temporal variations in bacterial community structures as well as the presence of three functional proteolytic enzyme genes in the sediments of a hypereutrophic freshwater lake in order to acquire an insight into dynamic links between bacterial community structures and proteolytic functions. Bacterial communities determined from 16S rRNA gene clone libraries markedly changed bimonthly, rather than vertically in the sediment cores. The phylum Firmicutes dominated in the 4–6 cm deep sediment layer sample after August in 2007, and this correlated with increases in interstitial ammonium concentrations (p < 0.01). The Firmicutes clones were mostly composed of the genus Bacillus. npr genes encoding neutral metalloprotease, an extracellular protease gene, were detected after the phylum Firmicutes became dominant. The deduced Npr protein sequences from the retrieved npr genes also showed that most of the Npr sequences used in this study were closely related to those of the genus Bacillus, with similarities ranging from 61% to 100%. Synchronous temporal occurrences of the 16S rRNA gene and Npr sequences, both from the genus Bacillus, were positively associated with increases in interstitial ammonium concentrations, which may imply that proteolysis by Npr from the genus Bacillus may contribute to the marked increases observed in ammonium concentrations in the sediments. Our results suggest that sedimentary bacteria may play an important role in the biogeochemical nitrogen cycle of freshwater lakes.

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Section: Methodsmentioning

confidence: 99%

Linking Temporal Changes in Bacterial Community Structures with the Detection and Phylogenetic Analysis of Neutral Metalloprotease Genes in the Sediments of a Hypereutrophic Lake

et al. 2014

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“…In the total bacterial qPCR, 16S rRNA gene fragments were amplified using primers EUBf and EUBr with dual-labeled probe EUBp (15). The 25-l PCR mix contained 12.5 l of IQ supermix (Bio-Rad), 1 M liter Ϫ1 of each primer, 0.5 M liter Ϫ1 of probe, and 2 l of DNA extract or serial dilutions of TOPO-TA cloning vector (Invitrogen, Carlsbad, CA, USA) carrying an Escherichia coli ATCC 25922 16S rRNA gene fragment (1,320 bp) as the standard (from 10 2 to 10 7 copies per reaction).…”

Section: Methodsmentioning

confidence: 99%

Microbial Contents of Vacuum Cleaner Bag Dust and Emitted Bioaerosols and Their Implications for Human Exposure Indoors

Veillette

Knibbs

Pelletier

et al. 2013

Appl Environ Microbiol

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Vacuum cleaners can release large concentrations of particles, both in their exhaust air and from resuspension of settled dust. However, the size, variability, and microbial diversity of these emissions are unknown, despite evidence to suggest they may contribute to allergic responses and infection transmission indoors. This study aimed to evaluate bioaerosol emission from various vacuum cleaners. We sampled the air in an experimental flow tunnel where vacuum cleaners were run, and their airborne emissions were sampled with closed-face cassettes. Dust samples were also collected from the dust bag. Total bacteria, total archaea, Penicillium/Aspergillus, and total Clostridium cluster 1 were quantified with specific quantitative PCR protocols, and emission rates were calculated. Clostridium botulinum and antibiotic resistance genes were detected in each sample using endpoint PCR. Bacterial diversity was also analyzed using denaturing gradient gel electrophoresis (DGGE), image analysis, and band sequencing. We demonstrated that emission of bacteria and molds (Penicillium/Aspergillus) can reach values as high as 1E5 cell equivalents/min and that those emissions are not related to each other. The bag dust bacterial and mold content was also consistent across the vacuums we assessed, reaching up to 1E7 bacterial or mold cell equivalents/g. Antibiotic resistance genes were detected in several samples. No archaea or C. botulinum was detected in any air samples. Diversity analyses showed that most bacteria are from human sources, in keeping with other recent results. These results highlight the potential capability of vacuum cleaners to disseminate appreciable quantities of molds and human-associated bacteria indoors and their role as a source of exposure to bioaerosols.

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“…PCR was carried out using the primers FP aprI/RP aprII (Bach, Hartmann, Schloter, & Munch, 2001;Martins et al, 2005), SM2F/SM3R (Marchand et al, 2009b) and 16SPSEfluF/16SPSER (Scarpellini et al, 2004) Table 1 Polymerase chain reaction (PCR) primer sets used in this study. Table 1).…”

Section: Pcr Sensitivity For the Detection Of P Fluorescens In Milkmentioning

confidence: 99%

Development of a PCR method for detecting proteolytic psychrotrophic bacteria in raw milk

Machado

Bazzolli

Vanetti

2013

International Dairy Journal

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PCR primers and functional probes for amplification and detection of bacterial genes for extracellular peptidases in single strains and in soil

Cited by 102 publications

References 17 publications

Linking Temporal Changes in Bacterial Community Structures with the Detection and Phylogenetic Analysis of Neutral Metalloprotease Genes in the Sediments of a Hypereutrophic Lake

Linking Temporal Changes in Bacterial Community Structures with the Detection and Phylogenetic Analysis of Neutral Metalloprotease Genes in the Sediments of a Hypereutrophic Lake

Microbial Contents of Vacuum Cleaner Bag Dust and Emitted Bioaerosols and Their Implications for Human Exposure Indoors

Development of a PCR method for detecting proteolytic psychrotrophic bacteria in raw milk

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