Viral infection of bacteria and phytoplankton in the Arctic Ocean as viewed through the lens of fingerprint analysis
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 72:47-61 (2014) - DOI: https://doi.org/10.3354/ame01684 Viral infection of bacteria and phytoplankton in the Arctic Ocean as viewed through the lens of fingerprint analysis Jérôme P. Payet1,5, Curtis A. Suttle1,2,3,4,* 1Department of Earth, Ocean and Atmospheric Sciences, 2Department of Microbiology and Immunology, 3Department of Botany, and 4Canadian Institute for Advanced Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada 5Present address: Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA *Corresponding author: suttle@science.ubc.ca ABSTRACT: Viruses are the most abundant biological entities in the oceans and play crucial roles as mortality agents and as catalysts in biogeochemical cycles. During a year-long study in the southeastern Beaufort Sea and Amundsen Gulf in the Canadian Arctic, we used denaturing gradient gel electrophoresis (DGGE) to investigate temporal and spatial changes in gene sequences encoding DNA polymerase B ( polB) and the major capsid protein (g23) that are specific for the virus families Phycodnaviridae and Myoviridae, which infect phytoplankton and bacteria, respectively. Multivariate analysis indicated that the genetic composition of viruses infecting phytoplankton was related to changes in productivity and hydrological conditions, as well as with changes in the potential host community, as indicated by DGGE fingerprints of 18S rDNA. In contrast, changes in the composition of viruses infecting bacteria could not be related to changes in environmental variables or DGGE fingerprints of bacterial (16S) or eukaryotic (18S) rDNA. Overall, these results document persistent and highly dynamic T4-like viruses and phycodnaviruses on the Canadian Arctic Shelf, implying that they are important in shaping microbial communities in the Arctic Ocean. KEY WORDS: Virus diversity · T4-like viruses · Phycodnaviruses · DNA polymerase B · g23 major capsid protein · DGGE fingerprint · Arctic Ocean · Marine viruses Full text in pdf format Supplementary material PreviousNextCite this article as: Payet JP, Suttle CA (2014) Viral infection of bacteria and phytoplankton in the Arctic Ocean as viewed through the lens of fingerprint analysis. Aquat Microb Ecol 72:47-61. https://doi.org/10.3354/ame01684 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 72, No. 1. Online publication date: March 07, 2014 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2014 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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| 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".