Phenotypic diversification in denitrification: mechanisms, prevalence and implications

Informations

Funding country

Norway

Acronym

-

URL

-

Start date

1/1/2018

End date

12/31/2022

Budget

1,021,884 EUR

Fundings

Abstract

Microbes rule our planet, and they colonize every habitat imaginable. Their ubiquity is due to their impressive range of lifestyles and their sheer numbers make them important drivers of Earth's biogeochemical cycles, such as the carbon- and nitrogen cycle. If a substance can be eaten or breathed (respired), there will be microbes (i.e., bacteria, archaea, fungi) specialized to do just that. Like all other living organisms, bacteria require elements such as carbon and nitrogen to build their macromolecules (e.g., DNA and proteins) and they need energy to drive their metabolism. Respiration is a very efficient strategy to harvest energy. Whereas animals are limited to breathing oxygen (aerobic respiration), many bacteria can use other substances instead (anaerobic respiration). Denitrification, the stepwise reduction of nitrate (NO3-), via nitrite (NO2-), nitric oxide (NO) and nitrous oxide (N2O) to nitrogen gas (N2), is one type of anaerobic respiration which is found in a wide range of bacteria. These organisms usually prefer aerobic respiration but will switch to denitrification when necessary. In order to do this, they need to sense that oxygen is scarce, express the relevant genes and build myriad new proteins, including four core enzymes for each of the reduction steps. It is in the organisms' interest to keep this transition under stringent control because 1) aerobic respiration is energetically more profitable than denitrification and 2) building new proteins is costly. If the organism responds too quickly, while aerobic respiration is still possible, it will waste resources building an unnecessary machinery; if it is too slow, it risks becoming trapped in anoxia with no means of harvesting energy for life and growth. Bacteria have developed many ways of regulating denitrification, but a common trait is that low oxygen and the presence of nitrate/nitrite/NO induce gene expression. Until recently, the underlying consensus has been that in a population of cells belonging to the same denitrifying species, all would express their entire denitrification apparatus when facing anoxia. We have found that this is not true. Within the project, we have shown that some bacteria, such as the model organism Paracoccus denitrificans, hedge their bets. Instead of going all in and expressing the entire set of denitrification proteins in all cells, cells within the same population will differentiate. All cells will produce the N2O reductase, thus reducing N2O to N2, but only a fraction will carry out the entire four-step process. Hence, P. denitrificans becomes a net N2O sink when facing anoxia. Moreover, we have shown that P. denitrificans also hedges its bets when oxygen returns. It conserves the ability to denitrify in a sub-population of non-growing persister cells. Within the project, we have studied the regulatory mechanisms behind these phenomena as well as enquiring about the prevalence of bet-hedging among denitrifying bacteria. This has implications for our understanding of N2O emissions from natural systems. Another important result of this project is that our progress in understanding the physiology of denitrifying bacteria has put us un a position to invent new biotechnological processes. This will be further explored within the recently initiated project "AnaPro" (https://www.nmbu.no/prosjekter/node/43227), funded by the Novo Nordic Foundation.