Abundance dynamics and sequence variation of neomycin phosphotransferase gene (nptII) homologs in river water
Bibliographic record
Abstract
AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 48:131-140 (2007) - doi:10.3354/ame048131 Abundance dynamics and sequence variation of neomycin phosphotransferase gene (nptII) homologs in river water Bin Zhu* National Water Research Institute, Environment Canada, 11 Innovation Blvd, Saskatoon, Saskatchewan S7N 3H5, Canada *Email: bin.zhu@ec.gc.ca ABSTRACT: Monitoring the abundance and dynamics of antibiotic resistance genes is essential for assessing their potential effects on environmental and human health. The objectives of the present study were to investigate: (1) the abundance of neomycin phosphotransferase (nptII) gene homologs in water samples collected monthly from the South Saskatchewan River (Canada) for 24 mo, and (2) sequence variation of the cloned nptII gene homologs retrieved from the river. DNA from river microbial communities was used to transform a natural competent Pseudomonas stutzeri strain containing a truncated nptII gene on a plasmid (P. stutzeri pMR7). Of the 24 water samples, the recovery of kanamycin resistant (KmR) transformants from DNA of 4 samples indicated the presence of nptII gene homologous sequences. However, the natural transformation process required ~3.2 × 104 copies of the nptII gene to recover a single KmR transformant. To overcome the limitation of detection, a real-time PCR assay using SYBR Green I was developed to quantify the abundance of nptII gene homologous sequences in river microbial communities. The results showed that nptII gene homologous sequences were present in the river, and their abundance varied over the course of this study, ranging from undetectable levels to 4.36 × 106 copies l–1 water. Furthermore, nptII gene homologous sequences amplified from river microbial community DNA were cloned, and unique clones were sequenced. Comparison of the nucleotide and deduced amino acid sequences of the cloned fragments to those of the nptII gene on transposon Tn5 showed that they had over 96% homology. KEY WORDS: Neomycin phosphotransferase gene · nptII · Abundance dynamics · Water samples · Homologous sequence · Real-time PCR Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 48, No. 2. Online publication date: July 10, 2007 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2007 Inter-Research.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".