Peer Review #2 of "Dynamics of a methanol-fed marine denitrifying biofilm: 2—impact of environmental changes on the microbial community (v0.1)"
Bibliographic record
Abstract
Background.The biofilm of a methanol-fed, marine denitrification system is composed of a multi-species microbial community, among which Hyphomicrobium nitrativorans and Methylophaga nitratireducenticrescens are the principal bacteria involved in the denitrifying activities.To assess its resilience to environmental changes, the biofilm was cultivated in artificial seawater (ASW) under anoxic conditions and exposed to a range of specific environmental conditions.We previously reported the impact of these changes on the denitrifying activities and the co-occurrence of H. nitrativorans strain NL23 and M. nitratireducenticrescens in the biofilm cultures.Here, we report the impact of these changes on the dynamics of the overall microbial community of the denitrifying biofilm.Methods.The original biofilm (OB) taken from the denitrification system was cultivated in ASW under anoxic conditions with a range of NaCl concentrations, and with four combinations of nitrate/methanol concentrations and temperatures.The OB was also cultivated in the commercial Instant Ocean seawater (IO).The bacterial diversity of the biofilm cultures and the OB was determined by 16S ribosomal RNA gene sequences.Culture approach was used to isolate other denitrifying bacteria from the biofilm cultures.The metatranscriptomes of selected biofilm cultures were derived, along with the transcriptomes of planktonic pure cultures of H. nitrativorans strain NL23 and M. nitratireducenticrescens strain GP59.Results.High proportions of M. nitratireducenticrescens occurred in the biofilm cultures.H. nitrativorans strain NL23 was found in high proportion in the OB, but was absent in the biofilm cultures cultivated in the ASW medium at 2.75% NaCl.It was found however in low proportions in the biofilm cultures cultivated in the ASW medium at 0 to 1% NaCl and in the IO biofilm cultures.Denitrifying bacterial isolates affiliated to Marinobacter spp.and Paracoccus spp.were isolated.Up regulation of the denitrification genes of strains GP59 and NL23 occurred in the biofilm cultures compared to the planktonic pure cultures.Denitrifying bacteria affiliated to the Stappia spp.were metabolically active in the biofilm cultures.Conclusions.These results illustrate the dynamics of the microbial community in the denitrifying biofilm cultures in adapting to different environmental conditions.The NaCl concentration is an important factor affecting the microbial community in the biofilm cultures.Up regulation of the denitrification genes of M. nitratireducenticrescens strain GP59 and H. nitrativorans strain NL23 in the biofilm cultures suggests different mechanisms of regulation of the denitrification pathway in the biofilm.Other denitrifying heterotrophic bacteria are present in low proportions, suggesting that the biofilm has the potential to PeerJ reviewing
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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 | 0.009 | 0.052 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.006 | 0.003 |
| Science and technology studies | 0.004 | 0.001 |
| Scholarly communication | 0.006 | 0.003 |
| Open science | 0.003 | 0.004 |
| Research integrity | 0.003 | 0.001 |
| Insufficient payload (model declined to judge) | 0.155 | 0.089 |
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".