Production of extracellular DNA (eDNA) of the γ-Proteobacterium Rheinheimera sp. F8 in biofilms
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Bibliographic record
Abstract
Abstract F8 is a gram-negative γ-Proteobacterium, which belongs to the genus Rheinheimera. The strain has been isolated from the South Saskatchewan River in Canada (Böckelmann, 2002). It has been discovered in previous studies that F8 releases DNA into the extracellular space (Böckelmann et al., 2006; Böckelmann et al., 2007). The aim of this study was a more detailed analysis of the F8 extracellular DNA (eDNA), whereby a main focus was placed on the analysis of F8 biofilms from continuous flow reactors and their visualization with different microscopical methods. For this purpose, two different systems were adapted and employed: a continuous flow reactor and a flow cell, which were operated with oligotrophic freshwater basal medium. Biofilm architecture was visualized by fluorescence microscopy, confocal laser scanning microscopy, scanning electron microscopy and transmission electron microscopy. Cell numbers in the continuous flow reactor were monitored by flow cytometry and by the drop plate method. eDNA under continuous flow conditions could be detected over the whole time course analyzed (1-21 days) and it was found to be integrated in different ways into the biofilm. It was shown that eDNA develops different morphological structures: it occured as an amorphous mass, but it also formed typical filaments and net-like structures. The results suggested different roles for eDNA in F8-biofilms. Due to its adhesive properties it may facilitate the formation of a characteristic biofilm architecture (e.g. by facilitating microcolony formation). It was observed, that the formation of filaments and nets is especially pronounced under highly nutrient-limited conditions. This indicates that eDNA may confer advantages to the bacteria by improving nutrient access: either by capturing nutrients or by serving as a nutrient source itself. Furthermore, it has been shown by LIVE/DEAD Baclight staining that the vast majority of cells in the biofilms displayed green fluorescent signals and almost all of them were closely associated with small clouds of eDNA. This indicates that F8 cells excrete eDNA (also) by a lysis-independent mechanism. A draft sequence of the F8 genome was determined de novo by shot gun-sequencing and the genome was annotated with the RAST server. These data build an important base for the further elucidation of eDNA-production, -excretion and -utilization in F8 biofilms. In the final assembly of the draft genome, a 4,464,511-bp sequence was generated. 3,970 protein coding sequences, 9 genes for rRNAs (including 3 versions for 16S rRNA) and 83 genes for tRNAs were found. The G+C content is 51.8 %.
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| 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 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 it