Proteome Dynamics During Transition From Exponential to Stationary Phase Under Aerobic and Anaerobic Conditions in Yeast

Ridder, Maxime den; Brandeler, Wiebeke van den; Altiner, Meryem; Daran‐Lapujade, Pascale; Pabst, Martin

doi:10.1016/j.mcpro.2023.100552

Cited by 7 publications

(5 citation statements)

References 88 publications

(118 reference statements)

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“…Shotgun metaproteomics experiments were performed as recently described [ 62 , 63 ]. Briefly, aliquots corresponding to ~0.5-μg protein digest were analysed using a nano-liquid-chromatography system consisting of an EASY nano-LC 1200, equipped with an Acclaim PepMap RSLC RP C18 separation column (50 μm × 150 mm, 2 μm, Cat.…”

Section: Methodsmentioning

confidence: 99%

Aerobic denitrification as an N2O source from microbial communities

Roothans,

Gabriëls,

Abeel

et al. 2024

The ISME Journal

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Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Oxic and anoxic emissions are commonly ascribed to autotrophic nitrification and heterotrophic denitrification, respectively. Beyond this established dichotomy, we quantitatively show that heterotrophic denitrification can significantly contribute to aerobic nitrogen turnover and N2O emissions in complex microbiomes exposed to frequent oxic/anoxic transitions. Two planktonic, nitrification-inhibited enrichment cultures were established under continuous organic carbon and nitrate feeding, and cyclic oxygen availability. Over a third of the influent organic substrate was respired with nitrate as electron acceptor at high oxygen concentrations (> 6.5 mg/L). N2O accounted for up to one quarter of the nitrate reduced under oxic conditions. The enriched microorganisms maintained a constitutive abundance of denitrifying enzymes due to the oxic/anoxic frequencies exceeding their protein turnover - a common scenario in natural and engineered ecosystems. The aerobic denitrification rates are ascribed primarily to the residual activity of anaerobically synthesized enzymes. From an ecological perspective, the selection of organisms capable of sustaining significant denitrifying activity during aeration shows their competitive advantage over other heterotrophs under varying oxygen availabilities. Ultimately, we propose that the contribution of heterotrophic denitrification to aerobic nitrogen turnover and N2O emissions is currently underestimated in dynamic environments.

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Section: Methodsmentioning

confidence: 99%

Aerobic denitrification as an N2O source from microbial communities

Roothans,

Gabriëls,

Abeel

et al. 2024

The ISME Journal

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“…If needed, samples were diluted to a concentration of 0.5 mg/mL. Shotgun metaproteomics experiments were performed as recently described 76,77 . Briefly, aliquots corresponding to approximately 0.5 µg protein digest were analysed using a nanoliquid-chromatography system consisting of an EASY nano-LC 1200, equipped with an Acclaim PepMap RSLC RP C18 separation column (50 μm x 150 mm, 2 μm, Cat.…”

Section: Shotgun Metaproteomicsmentioning

confidence: 99%

Aerobic denitrification as N₂O source in microbial communities

Roothans,

Gabriëls,

Pabst

et al. 2023

Preprint

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Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Aerobic and anoxic emissions are commonly ascribed to nitrification and denitrification, respectively. Beyond this established dichotomy, we quantitatively prove that heterotrophic denitrification can significantly contribute to aerobic nitrogen turnover and N2O emissions in complex microbiomes exposed to frequent oxic/anoxic transitions. Planktonic, nitrification-inhibited denitrifying enrichments respired over a third of the influent organic substrate with nitrate at high oxygen concentrations. N2O accounted for up to one quarter of the aerobically respired nitrate. The constitutive detection of all denitrification enzymes in both anoxic and oxic periods highlight the selective advantage offered by metabolic preparedness in dynamic environments. We posit that aerobic denitrification and associated N2O formation is currently underestimated in dynamic microbial ecosystems.

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“…Saccharomyces cerevisiae ( S. cerevisiae ) serves as a probiotic feed additive for nutrition of animals that are not true ruminants or those with pseudo‐ruminant feeding processes. It is notable feature lies in its metabolic flexibility, enabling it to switch between complete respiratory sugar dissimilation and the process of alcoholic fermentation (den Ridder et al., 2023 ). Both metabolic pathways result in the generation of ATP, with the first pathway producing a significant amount of ATP (den Ridder et al., 2023 ).…”

Section: Introductionmentioning

confidence: 99%

“…It is notable feature lies in its metabolic flexibility, enabling it to switch between complete respiratory sugar dissimilation and the process of alcoholic fermentation (den Ridder et al., 2023 ). Both metabolic pathways result in the generation of ATP, with the first pathway producing a significant amount of ATP (den Ridder et al., 2023 ). However, only a portion of the chemical energy released during the hydrolysis of ATP by the Ca 2+ ‐ATPase is converted into osmotic energy.…”

Section: Introductionmentioning

confidence: 99%

Investigating the efficacy of an exopolysaccharide (EPS)‐producing strain Lactiplantibacillus plantarum L75 on oat silage fermentation at different temperatures

Su,

Liang,

Chen

et al. 2024

Microbial Biotechnology

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This study investigates the effectiveness of an exopolysaccharide (EPS)‐producing strain (Lactiplantibacillus plantarum L75) alone or in combination with Saccharomyces cerevisiae on the fermentation characteristics, antioxidant capacities and microbial community successions of oat silage stored at various temperatures. A rapid decrease in pH and lactic acid accumulation was observed in silages treated with L. plantarum and S. cerevisiae (LS) as early as 3 days of ensiling (p < 0.05). Over the ensiling period of 7–60 days, L. plantarum (L)‐inoculated groups showed the lowest pH, lowest ammonia nitrogen and the highest amount of lactic acid regardless of the storage temperatures. When the oat silage was stored at 15°C, LS‐inoculated group exhibited a higher superoxide dismutase (SOD) activity than control and L‐inoculated group. Furthermore, the proportion of Lactiplantibacillus in the combined inoculation group increased by 65.42% compared to the L‐inoculated group (33.26%). Fungal community data revealed abundant Penicillium carneum in the control and L‐inoculated groups stored at 15°C. Conclusively, these results showed that combined inoculation of L. plantarum L75 and S. cerevisiae improved the fermentation quality of oat silage at 15°C, thus proposing a technique for enhancing the fermentation quality of silage in regions with low temperatures during harvest season.

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Proteome Dynamics During Transition From Exponential to Stationary Phase Under Aerobic and Anaerobic Conditions in Yeast

Cited by 7 publications

References 88 publications

Aerobic denitrification as an N2O source from microbial communities

Aerobic denitrification as an N2O source from microbial communities

Aerobic denitrification as N₂O source in microbial communities

Investigating the efficacy of an exopolysaccharide (EPS)‐producing strain Lactiplantibacillus plantarum L75 on oat silage fermentation at different temperatures

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Proteome Dynamics During Transition From Exponential to Stationary Phase Under Aerobic and Anaerobic Conditions in Yeast

Cited by 7 publications

References 88 publications

Aerobic denitrification as an N2O source from microbial communities

Aerobic denitrification as an N2O source from microbial communities

Aerobic denitrification as N2O source in microbial communities

Investigating the efficacy of an exopolysaccharide (EPS)‐producing strain Lactiplantibacillus plantarum L75 on oat silage fermentation at different temperatures

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Product

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Aerobic denitrification as N₂O source in microbial communities