Scientists at the University of Oldenburg in Germany have gained insights into the cellular mechanisms of a common environmental bacterium, Aromatoleum aromaticum EbN1T, that could have implications for the remediation of contaminated sites and biotechnological applications. The researchers examined the entire metabolic network of the bacterial strain, using the results to develop a metabolic model with which they can predict the growth of these microbes under diverse environmental conditions.
The studied bacterial strain specializes in utilizing organic substances that are difficult to break down and is generally found in soil and aquatic sediments. The microbes thrive in oxygen, low-oxygen and oxygen-free layers and are also highly versatile in nutrient intake. They metabolize more than 40 different organic compounds, including highly stable, naturally occurring substances such as lignin components, the primary structural material found in wood, and long-lived pollutants and components of petroleum.
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 useful in biological soil remediation.
The objective of the current study, published in the journal mSystems, was to get a comprehensive understanding of how this unicellular organism functions. To do this, the researchers used five various nutritional substrates to cultivate the microorganisms in both oxic and anoxic settings, or with and without oxygen. They grew and examined 25 cultures for each of these ten different growth conditions, enabling simultaneous analysis of all the transcribed genes in a cell, all the proteins produced, and all its metabolic products.
The approach allowed the team to understand this bacterial strain's metabolic processes thoroughly. They discovered that over 200 genes are involved in the processes of degradation. They also identified the enzymes that degrade the compounds provided as nutrients and the intermediates by which the various nutrients are broken down. The researchers developed a growth model using their discoveries on the metabolic network and showed that the model's predictions mainly agreed with the obtained data.
The scientists uncovered unexpected mechanisms in the metabolism of these bacteria. To their surprise, it turned out that the microbe produces several enzymes they cannot use under the given growth conditions – which would seem to be an excessive 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," the study's senior author Rabus explains. But with some substrates, microbes produce 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 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," Rabus explains, adding that so far, no other bacteria are known to use such a mechanism.