Researchers Decipher the Inner Workings of a Bacterium

A Robot Punches Out Pinhead Sized Pieces From a Gel Layer

A robot punches out pinhead-sized pieces from a gel layer. The narrow blue bands contain proteins from a bacterial culture. Subsequently, the proteins contained in the tiny gel pieces will be sorted in greater detail. Credit: University of Oldenburg/Mohssen Assanimoghaddam

A comprehensive understanding of metabolism enables the prediction of the growth of a crucial environmental microbe.

A group led by Professor Ralf Rabus, a microbiologist at the University of Oldenburg, and his Ph.D. student Patrick Becker has made significant advancements in comprehending the cellular processes of a widespread environmental bacterium. The team conducted an extensive analysis of the entire metabolic network of the bacterial strain Aromatoleum aromaticum EbN1T and utilized the findings to construct a metabolic model that allows them to forecast the growth of these microbes in various environmental conditions.

According to their report in the journal mSystems, the researchers uncovered surprising mechanisms that enable the bacteria to adjust to fluctuating environmental conditions. These results are crucial for the study of ecosystems, where the Aromatoleum strain, as a representative of a significant group of environmental bacteria, can act as a model organism. The findings could also have implications for the cleanup of contaminated sites and biotechnological applications.

The studied bacterial strain specializes in the utilization of organic substances that are difficult to break down and is generally found in soil and in aquatic sediments. The microbes thrive in a variety of conditions including oxygen, low-oxygen, and oxygen-free layers, and are also extremely versatile in terms of nutrient intake. They metabolize more than 40 different organic compounds including highly stable, naturally occurring substances such as components of lignin, the main structural material found in wood, and long-lived pollutants and components of petroleum.

Patrick Becker

Ph.D. student Patrick Becker gained a holistic understanding of the metabolism of the bacterium Aromatoleum aromaticum through careful laboratory studies. Credit: University of Oldenburg

A microbe with special abilities

In particular, substances with a benzene ring composed of six carbon atoms, known as aromatic compounds, can be biodegraded by these microbes – with or without the aid of oxygen. Due to these abilities, Aromatoleum plays an important environmental role in the complete degradation of organic compounds in soil and sediments to carbon dioxide – a process which is also useful in biological soil remediation.

The aim of the current study was to gain a holistic understanding of the functioning of this unicellular organism. To this end, the researchers cultivated the microbes under both oxic and anoxic conditions – i.e. with and without oxygen – using five different nutrient substrates. For each of these ten different growth conditions, they grew 25 cultures and then examined the various samples using molecular biology methods (technical term: multi-omics) which enable simultaneous analysis of all the transcribed genes in a cell, all the proteins produced, and all its metabolic products.

Interactions of Aromatoleum

The bacterium Aromatoleum aromaticum EbN1T (outlined in black, at the bottom) interacts with the biotic and abiotic environment in many ways: anthropogenic input, the activity of other microorganisms and processes in nature generate different organic substances (different colored dots), which the bacterium uses as food. At the same time, these substances are also utilized by other microorganisms (food competition). The metabolic network within the bacterial cell converts and degrades the substances via different pathways (left). The cell in turn produces building materials such as DNA, proteins, sugar compounds, or lipids (right), which it needs for growth. Depending on environmental conditions, the cell obtains energy with the help of oxygen or nitrate (NO3-) – shown on the far left of the image. Credit: Ralf Rabus and Patrick Becker/University of Oldenburg

Systems biology approach

“With this systems biology approach, you gain a deep understanding of all the inner workings of an organism,” explains Rabus, who heads the General and Molecular Microbiology research group at the University of Oldenburg’s Institute for Chemistry and Biology of the Marine Environment (ICBM). “You break down the bacterium into its individual components and then you can put them back together – in a model that predicts how fast a culture will grow and how much biomass it will produce.”

Through their meticulous work, the researchers obtained a comprehensive understanding of the metabolic reactions of this bacterial strain. They found that around 200 genes are involved in the degradation processes and determined which enzymes break down the substances added as nutrients and via which intermediates the various nutrients are decomposed. The scientists incorporated their findings about the metabolic network into a growth model, and demonstrated that the model predictions largely corresponded to the measured data.

“We can now describe the organism with a level of precision that has so far only been possible with very few other bacteria,” says Rabus. This holistic view of the bacteria’s cellular inner workings forms the basis for a better understanding of the interactions between the analyzed strain (and related bacteria) and their biotic and abiotic environment, he adds, and can also help scientists to better predict the activity of these unicellular organisms in polluted soils and thus, for example, determine the optimal conditions for the remediation of a contaminated site.

A surprising waste of energy

By combining different methods, the team was able to uncover unexpected mechanisms in the metabolism of these bacteria. Much to the researchers’ surprise, it emerged that the microbe produces several enzymes which they cannot use under the given growth conditions – which at first glance would seem to be a superfluous expenditure of energy. “Usually the bacterial cells detect whether oxygen is present in their environment and then, via specific mechanisms, activate only the nutrient-specific metabolic pathway with the corresponding enzymes,” Rabus explains.

But with some substrates, the microbe produced all the enzymes for aerobic and anaerobic degradation pathways regardless of oxygen levels – even though some of these enzymes were entirely superfluous. Rabus suspects that this apparent waste is in fact a strategy for surviving in an unstable environment: “Even if oxygen levels suddenly fluctuate – which is often the case in natural environments – Aromatoleum remains flexible and can utilize this nutrient and produce energy as required,” the microbiologist explains, adding that so far, no other bacteria are known to use such a mechanism.

Reference: “Systems Biology of Aromatic Compound Catabolism in Facultative Anaerobic Aromatoleum aromaticum EbN1T” by Patrick Becker, Sarah Kirstein, Daniel Wünsch, Julia Koblitz, Ramona Buschen, Lars Wöhlbrand, Boyke Bunk and Ralf Rabus, 29 November 2022, mSystems.
DOI: 10.1128/msystems.00685-22

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