A robot punches out pinhead-sized pieces from a gel layer. The narrow blue bands contain proteins from a bacterial culture. Subsequently, the proteins consisted of in the small gel pieces will be sorted in greater information. Credit: University of Oldenburg/Mohssen Assanimoghaddam
An extensive understanding of metabolism allows the forecast of the growth of an important environmental microorganism.
A group led by Professor Ralf Rabus, a microbiologist at the University of Oldenburg, and his Ph.D. student Patrick Becker has made significant developments in understanding the cellular processes of a widespread environmental bacterium. The group conducted a substantial analysis of the whole metabolic network of the bacterial pressure Aromatoleum aromaticum EbN1T and used the findings to construct a metabolic model that allows them to anticipate the growth of these microorganisms in various ecological conditions.
According to their report in the journal mSystems, the researchers uncovered unexpected systems that enable the germs to adapt to varying ecological conditions. These results are important for the study of environments, where the Aromatoleum strain, as a representative of a considerable group of environmental bacteria, can act as a design organism. The findings might also have implications for the cleanup of polluted websites and biotechnological applications.
The studied bacterial strain focuses on the usage of organic compounds that are hard to break down and is normally discovered in soil and in water sediments. The microorganisms prosper in a variety of conditions including oxygen, low-oxygen, and oxygen-free layers, and are also extremely versatile in regards to nutrient intake. They metabolize more than 40 different organic compounds including highly steady, naturally happening compounds such as elements of lignin, the main structural product discovered in wood, and long-lived toxins and elements of petroleum.
According to their report in the journal mSystems, the researchers uncovered surprising mechanisms that make it possible for the bacteria to change to fluctuating ecological conditions. These results are essential for the study of communities, where the Aromatoleum pressure, as a representative of a substantial group of environmental bacteria, can act as a design organism. For each of these ten different development conditions, they grew 25 cultures and then analyzed the numerous samples using molecular biology approaches (technical term: multi-omics) which enable synchronised analysis of all the transcribed genes in a cell, all the proteins produced, and all its metabolic items.
The germs Aromatoleum aromaticum EbN1T (outlined in black, at the bottom) interacts with the abiotic and biotic environment in many methods: anthropogenic input, the activity of other microorganisms and processes in nature produce different organic compounds (various colored dots), which the bacterium uses as food. By combining various techniques, the group was able to uncover unforeseen mechanisms in the metabolic process of these bacteria.
Ph.D. trainee Patrick Becker gained a holistic understanding of the metabolic process of the germs Aromatoleum aromaticum through careful laboratory research studies. Credit: University of Oldenburg
A microbe with unique capabilities
In particular, compounds with a benzene ring made up of 6 carbon atoms, called fragrant substances, can be biodegraded by these microbes– with or without the help of oxygen. Due to these capabilities, Aromatoleum plays an important environmental role in the total degradation of organic substances in soil and sediments to carbon dioxide– a procedure which is also useful in biological soil removal.
The aim of the current research study was to gain a holistic understanding of the performance of this unicellular organism. To this end, the scientists cultivated the microbes under both anoxic and oxic conditions– i.e. with and without oxygen– utilizing five various nutrient substrates. For each of these 10 various growth conditions, they grew 25 cultures and then analyzed the different samples using molecular biology techniques (technical term: multi-omics) which allow synchronised analysis of all the transcribed genes in a cell, all the proteins produced, and all its metabolic products.
The bacterium Aromatoleum aromaticum EbN1T (outlined in black, at the bottom) interacts with the biotic and abiotic environment in lots of ways: anthropogenic input, the activity of other microorganisms and processes in nature generate different organic substances (different colored dots), which the germs utilizes as food. At the exact same time, these compounds are also used by other bacteria (food competitors). The metabolic network within the bacterial cell converts and degrades the compounds through various pathways (left). The cell in turn produces structure products such as DNA, proteins, sugar compounds, or lipids (right), which it needs for growth. Depending upon ecological conditions, the cell obtains energy with the assistance of oxygen or nitrate (NO3-)– shown on the far left of the image. Credit: Ralf Rabus and Patrick Becker/University of Oldenburg
Systems biology technique
” With this systems biology approach, you get a deep understanding of all the inner operations of an organism,” describes Rabus, who heads the General and Molecular Microbiology research study group at the University of Oldenburgs Institute for Chemistry and Biology of the Marine Environment (ICBM). “You break down the bacterium into its specific components and after that you can put them back together– in a model that predicts how fast a culture will grow and just how much biomass it will produce.”
Through their precise work, the scientists got an extensive understanding of the metabolic reactions of this bacterial strain. They discovered that around 200 genes are associated with the deterioration processes and determined which enzymes break down the compounds added as nutrients and via which intermediates the various nutrients are decayed. The researchers included their findings about the metabolic network into a growth model, and demonstrated that the design forecasts mainly corresponded to the determined information.
” We can now explain the organism with a level of accuracy that has up until now just been possible with extremely few other bacteria,” states Rabus. This holistic view of the bacterias cellular inner workings forms the basis for a much better understanding of the interactions between the evaluated pressure (and related germs) and their abiotic and biotic environment, he includes, and can also help researchers to better predict the activity of these unicellular organisms in contaminated soils and hence, for example, figure out the optimum conditions for the removal of a polluted website.
An unexpected waste of energy
By integrating different techniques, the team had the ability to reveal unforeseen systems in the metabolic process of these bacteria. Much to the scientists surprise, it emerged that the microbe produces numerous enzymes which they can not utilize under the given development conditions– which at first glance would appear to be a superfluous expense of energy. “Usually the bacterial cells find whether oxygen exists in their environment and then, by means of specific systems, activate only the nutrient-specific metabolic path with the corresponding enzymes,” Rabus discusses.
With some substrates, the microorganism produced all the enzymes for anaerobic and aerobic destruction paths regardless of oxygen levels– even though some of these enzymes were entirely unneeded. Rabus suspects that this apparent waste remains in truth a technique for surviving in an unsteady environment: “Even if oxygen levels suddenly fluctuate– which is typically the case in natural environments– Aromatoleum remains flexible and can use this nutrient and produce energy as needed,” the microbiologist discusses, including that up until now, no other germs are known to utilize such a mechanism.
Recommendation: “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.