Microbiome Analysis of the Eastern Oyster As a Function of Ploidy and Seasons
Bibliographic record
Abstract
Abstract Shellfish, such as the eastern oysters ( Crassostrea virginica ) are not only valued as seafood but also for the ecosystem services they provide, including improving water quality and reducing eutrophication. Excess N causes eutrophication, harmful algal blooms, fish kills and overall decline of estuarine ecosystems resulting in economic losses. Oyster reefs sequester N and enhance denitrification processes, however, information on the N cycling oyster microbiome is scarce with most studies focusing on random grab samples or on pathogens, such as Vibri o spp. Further, triploid oysters are often used for aquaculture, as they grow faster than diploids, but there is little information on potential microbiome differences with ploidy. To address these knowledge gaps, diploid and triploid farmed oysters were collected at monthly intervals over one year and analyzed using a coupled approach encompassing shotgun metagenomics and quantitative microbial elemental cycling (QMEC) qPCR assays. Overall, the genus Psychrobacter dominated the core microbiome across all samples, regardless of season or ploidy, followed by Synechococcus , Pseudomonas , Pseudoalteromonas and Clostridium . Psychrobacter abundances increased significantly in the colder months; the same trend was also observed in the alpha and beta diversity. However, warmer months had increased bacterial diversity relative to colder months. Gene functional profiles were similar among seasons and ploidy, with respiration and metabolism of carbohydrates, RNA, and proteins as dominant functions. There were strong positive correlations between abundance of the “core” microbiome taxa and gene functions associated with central metabolism, DNA and carbohydrate metabolism, strongly suggesting the functional role of Psychrobacter in the microbiome. Metagenome assembly was performed to characterize dominant species, followed by phylogenetic analysis of select MAGs (metagenome-assembled genomes), further supporting the presence of multiple Psychrobacter spp. Sequence-based identification of denitrification genes in the Pyschrobacter MAGs indicated the presence of norB , narH , narI , nirK , and norB . QMEC analysis indicated C and N cycling genes were most abundant, with no discernable patterns due to seasons or ploidy. Among N cycling genes, the nosZII clade was dominant, which is likely responsible for the eastern oysters potential for bioextraction and enhancing water quality via denitrification.
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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 | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.001 |
| 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".