Structured model for denitrifier diauxic growth

Hamilton, Ryan; Casasús, Anna I.; Rasche, Madeline E.; Narang, Atul; Svoronos, Spyros A.; Koopman, Ben

doi:10.1002/bit.20462

Cited by 14 publications

(10 citation statements)

References 18 publications

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“…This is possibly a more plausible explanation than suggested by the authors and further elaborated by Hamilton et al [35], claiming that there is a true lag caused by extremely slow production of denitrification enzymes due to energy limitation. Our explanation of the apparent diauxic lag is corroborated by a chemostat culturing experiment conducted by Bauman et al [36]: A steady state carbon (acetate) limited continuous culture with Pa. denitrificans was made anoxic and monitored for denitrification gene transcription, N-gas production, and acetate concentrations.…”

Section: Resultsmentioning

confidence: 79%

Low Probability of Initiating nirS Transcription Explains Observed Gas Kinetics and Growth of Bacteria Switching from Aerobic Respiration to Denitrification

et al. 2014

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In response to impending anoxic conditions, denitrifying bacteria sustain respiratory metabolism by producing enzymes for reducing nitrogen oxyanions/-oxides (NOx) to N2 (denitrification). Since denitrifying bacteria are non-fermentative, the initial production of denitrification proteome depends on energy from aerobic respiration. Thus, if a cell fails to synthesise a minimum of denitrification proteome before O2 is completely exhausted, it will be unable to produce it later due to energy-limitation. Such entrapment in anoxia is recently claimed to be a major phenomenon in batch cultures of the model organism Paracoccus denitrificans on the basis of measured e−-flow rates to O2 and NOx. Here we constructed a dynamic model and explicitly simulated actual kinetics of recruitment of the cells to denitrification to directly and more accurately estimate the recruited fraction (). Transcription of nirS is pivotal for denitrification, for it triggers a cascade of events leading to the synthesis of a full-fledged denitrification proteome. The model is based on the hypothesis that nirS has a low probability (, h−1) of initial transcription, but once initiated, the transcription is greatly enhanced through positive feedback by NO, resulting in the recruitment of the transcribing cell to denitrification. We assume that the recruitment is initiated as [O2] falls below a critical threshold and terminates (assuming energy-limitation) as [O2] exhausts. With = 0.005 h−1, the model robustly simulates observed denitrification kinetics for a range of culture conditions. The resulting (fraction of the cells recruited to denitrification) falls within 0.038–0.161. In contrast, if the recruitment of the entire population is assumed, the simulated denitrification kinetics deviate grossly from those observed. The phenomenon can be understood as a ‘bet-hedging strategy’: switching to denitrification is a gain if anoxic spell lasts long but is a waste of energy if anoxia turns out to be a ‘false alarm’.

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Section: Resultsmentioning

confidence: 79%

Low Probability of Initiating nirS Transcription Explains Observed Gas Kinetics and Growth of Bacteria Switching from Aerobic Respiration to Denitrification

et al. 2014

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“…We hypothesize that increasing the extract dose resulted in faster transport of nitrate into the cell, thus hastening the onset of Nar biosynthesis [9]. Furthermore, the higher specific growth observed with higher dosage of extract suggests that more energy is available for growth, and the origin of energy resource is due to enhanced electron transport rate that is linked to the intrecellular Nar concentration [10,11].…”

Section: Nar-extract Elevated the Growth Of Kd After Switching From Amentioning

confidence: 99%

Effect of Protein Crude Extract on Oxic/Anoxic Diauxic Growth of a Napdeficient Mutant of Paracoccus pantotrophus

Yin¹,

Stevenson²,

Koopman³

et al. 2016

J Bioremediat Biodegrad

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In this study it is shown that addition of crude protein extract containing either membrane bound nitrate reductase (Nar) or periplasmic nitrate reductase (Nap) shortens the diauxic lag of denitrifying bacteria switched from aerobic to anoxic conditions. The specific growth rate under anoxic conditions, following resumption of exponential growth, was found to be linearly related to the extract dose.

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“…The proposed explanation for the diauxic lag is that after switching from aerobic to anaerobic growth, substantial time is required to build up the activity of denitrifying enzymes. The length of the lag before denitrification commenced was dependent upon the length of the preceding aerobic period, which influences the nitrate flux needed to induce and stimulate denitrifying enzyme activity (Hamilton et al 2005). …”

Section: Denitrification Ratesmentioning

confidence: 99%

Organic carbon, and not copper, controls denitrification in oxygen minimum zones of the ocean

Ward

Tuit

Jayakumar

et al. 2008

Deep Sea Research Part I: Oceanographic Research Papers

123

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Structured model for denitrifier diauxic growth

Cited by 14 publications

References 18 publications

Low Probability of Initiating nirS Transcription Explains Observed Gas Kinetics and Growth of Bacteria Switching from Aerobic Respiration to Denitrification

Low Probability of Initiating nirS Transcription Explains Observed Gas Kinetics and Growth of Bacteria Switching from Aerobic Respiration to Denitrification

Effect of Protein Crude Extract on Oxic/Anoxic Diauxic Growth of a Napdeficient Mutant of Paracoccus pantotrophus

Organic carbon, and not copper, controls denitrification in oxygen minimum zones of the ocean

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