Microbial nitrification in urban streams: from single cell activity to ecosystem
Notice bibliographique
Résumé
The main goal of this PhD thesis was the study of the ammonium oxidation process in high nutrient loaded urban streams. We aimed to unveil regulating factors and driving mechanisms from the organisms to the ecosystem scales using a combined biogeochemistry-microbial ecology approach. \n\n\t\t\t\t Ammonia oxidization is the first and rate-limiting step of nitrification. Nitrification is the key process linking nitrogen (N) inputs (fixation, mineralization) and losses (denitrification, anamox) in the aquatic ecosystem. Ammonia oxidizing archaea (AOA) and bacteria (AOB) drive this process through the enzyme ammonia monooxygenase. Although sharing a common function, AOB and AOA are phylogenetically distinct, suggesting different evolution and phenotypic characteristics. \n\n\t\t\t\t AOA and AOB were detected in the stream biofilms. The abundance, community composition and distribution of these microbial components were driven by environmental physical and chemical conditions, mainly ammonia (NH4) concentrations and sun irradiance.\n\t\t\t\t Ammonia oxidizing activity in biofilms under low NH4 availability was low and only 2 % of the inorganic NH4 was nitrified. Under these conditions AOA dominated ammonia oxidizing community and were key players of the observed ammonia oxidation (Nitrososophaera cluster). Conversely, under high NH4 load in the stream up to 100 % of the inorganic NH4 was oxidized to nitrate (NO3). Such high ammonia oxidizing activity was mostly driven by AOB (Nitrosospira and N. oligotropha clusters). Under these conditions AOB outnumbered AOA by orders of magnitude. AOA in contrast were poorly active under high NH4 concentrations and a consistent community composition shift was observed between high and low NH4 conditions. \n\n\t\t\t\t In laboratory cultures the growth of AOA and AOB was immediately inhibited by light. In particular, at lower light intensities, archaeal growth was much more photosensitive than bacterial growth and unlike AOB, AOA showed no evidence of recovery during dark phases. These findings provide evidence for niche differentiation in aquatic environments and suggested light as a main driving factor for the distribution and activity of ammonia oxidizers in the aquatic environment. Accordingly, in early stage biofilms developing on streams cobbles the percentage of ammonia oxidizers was higher in darkness (i.e., sediment facing side or dark-side biofilms) than in biofilms grown on the upper, light exposed side of the cobbles (light-side biofilm). However, this spatial segregation was missed in mature biofilms suggesting that the complex microbial structure present in light-side biofilms may protect both AOA and AOB against photoinhibition. This finding was further confirmed by a significant relationship found between light-side biofilm biomass and the abundance of ammonia oxidizers in situ. In contrast, for dark-side biofilms the relationship was missed. Therefore, irradiance was not an inhibitory factor for AOA and AOB in mature light-side biofilms probably due to an “umbrella effect”. The umbrella effect and the fact that AOA and AOB were highly abundant in the sediment (light avoiding strategy) are probably the reasons why nitrification at the ecosystem scale was independent from both light intensity and dial light cycling. Altogether these results highly contributed to improve the current knowledge on nitrification in urban streams and provided insights on niche differentiation between AOA and AOB.
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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) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,001 | 0,001 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,001 | 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) | 0,001 | 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 ».