Diversity, Relative Abundance, and Functional Potential of Viral and Bacterial Communities
Bibliographic record
Abstract
Viral and bacterial communities in Hamilton Harbour were explored to discern seasonal and spatial changes in diversity, relative abundance, and functional potentials. The following chapters describe findings derived from metagenomic sequencing and analysis of environmental DNA using a variety of techniques. In the study outlined in Chapter 2, virus diversity and relative abundances were found to be highly variable over small spatial scales. Virophages were often the most abundant group, and discrete virophage taxa were stable despite fluctuations in Mimiviridae community composition. Diverse and distinct Mimiviridae populations were detected, suggesting that Mimiviridae are important algal viruses. The results from Chapter 3 demonstrated that several insights into virus diversity, relative abundances, and host inferences are lost by the common practice of filtering water samples to separate viruses from cells prior to DNA extraction and sequencing. Many viruses of eukaryotes, such as Mimiviridae, Phycodnaviridae, Iridoviridae and Poxviridae, were detected exclusively in the often-disregarded larger size fractions, while higher Caudovirales diversity was captured by the smaller size fractions. Cyanophages were more abundant in the larger size fractions, which may indicate replication within cells during ongoing infections. Analysis of either size fraction alone provides only a partial perspective of dsDNA viruses in the environment, highlighting the need for more comprehensive approaches for metagenomic analyses of aquatic viruses. Unlike the virus communities, the results from Chapter 4 revealed that bacterial communities were similar at different sites within the harbour and demonstrated strong seasonality regarding taxonomy and functional potentials. Some functional categories were highly variable while others were stable, suggesting the presence of generalist gene categories that are always essential versus specialist gene categories that fluctuate based on selective pressures. The results presented in this thesis expand the documented diversity of freshwater viruses and abundant Cyanobacteria in Hamilton Harbour, providing the first observations of highly abundant and potentially ecological important virophage, Mimiviridae, and Limnoraphis robusta populations. Ultimately, this work revealed seasonal and spatial dynamics in microbial community diversity, relative abundances, and functional potentials that can be used to inform ongoing monitoring and remediation efforts in Hamilton Harbour and likely apply broadly to other temperate freshwater lakes.
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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 | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 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".