Production of extracellular DNA (eDNA) of the γ-Proteobacterium Rheinheimera sp. F8 in biofilms
Notice bibliographique
Résumé
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 %.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,001 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».