Unveiling the Secrets of Microbial Dark Matter
In the vast and mysterious world of microorganisms, there exists a realm known as "microbial dark matter" - a term that hints at the immense potential and untapped knowledge waiting to be discovered. Researchers at the RIKEN BioResource Research Center (BRC) in Japan have embarked on a fascinating journey, delving into the genomes of thousands of microorganisms to uncover their hidden abilities, particularly their potential to capture carbon dioxide (CO2).
The BRC, a hub of scientific excellence, houses a unique collection of biological resources, including microorganisms, that are carefully managed and shared with researchers worldwide. This collection, with its focus on reproducibility and credibility, is a treasure trove for scientific exploration.
A Massive Microbial Collection
The Microbe Division, or the Japan Collection of Microorganisms (JCM), within BRC, boasts an impressive collection of over 32,000 microbial strains. These strains, discovered and cultured by microbiologists globally, are accompanied by valuable data on their environments, growth conditions, and genomic information. Approximately 21,000 of these strains are publicly available, with over 4,000 being provided annually to researchers, both domestically and internationally.
Exploring CO2 Fixation
The current research project, led by Arisa Nishihara, a postdoctoral researcher, focused on exploring the CO2 fixation capabilities of these microorganisms. Nishihara humorously admits that this was a research topic she had hoped someone else would take on, highlighting the complexity and time-consuming nature of the task. The project involved a meticulous two-year analysis process, diving into the vast realm of microbial life, where millions of species of bacteria and archaea exist, yet only a fraction have been formally described and named.
The Calvin-Benson Cycle: A Key to Carbon Fixation
Plants, through photosynthesis, capture CO2 from the atmosphere and convert it into organic compounds. This process is driven by a series of chemical reactions known as the Calvin-Benson cycle, a major pathway for CO2 fixation on Earth. However, plants are not the only organisms capable of carbon fixation. Many microorganisms can also utilize this cycle or other pathways to capture CO2, even in complete darkness.
The researchers decided to analyze the genomes of 6,749 JCM strains, specifically searching for genes associated with the Calvin-Benson cycle. Simultaneously, they cross-referenced this data with existing literature to determine if these microorganisms were indeed capable of CO2 fixation. This systematic approach aimed to bridge the gap between genomic data and concrete research, particularly in the field of microbial CO2 fixation.
Uncovering 306 Candidates
After approximately two years of research, the team identified 306 strains carrying genes associated with the Calvin-Benson cycle. These strains belonged to 147 genera, with 74 of those genera already reported to have CO2 fixation capabilities. The remaining 73 genera represent a promising avenue for further research, as they possess the potential for CO2 fixation but have not been extensively studied in this context.
Senior Research Scientist Shingo Kato explains the significance of this finding: "While photosynthesis in plants requires light for CO2 fixation, there are many microorganisms that can fix CO2 in the dark. If we can harness this ability in places where light doesn't reach, it could contribute to the realization of a low-carbon society."
Focusing on the Enzyme Rubisco
The research team decided to further investigate the enzyme Rubisco, which catalyzes a key step in the Calvin-Benson cycle. By classifying the 306 strains based on their type, habitat, and metabolic properties, they discovered significant differences in the energy sources utilized and habitats of these microorganisms.
Using genetic data, the team identified 173 strains with potential CO2 fixation abilities, despite belonging to genera not previously reported for CO2 fixation. These findings suggest that many prokaryotes may possess the potential to fix CO2 using hydrogen or sulfur compounds.
Nishihara elaborates: "There are diverse types of microorganisms. Some prefer hydrogen, some sulfur, and some thrive in oxygen-free environments. By altering culture conditions, we might discover microorganisms that exhibit CO2 fixation ability."
Enhancing the Value of the Microbial Collection
This meticulous research enhances the value of the JCM's microbial collection by specifically noting "CO2 fixation" as a characteristic in the catalog. This will enable researchers worldwide to select microorganisms best suited for their CO2 fixation goals.
Looking ahead, Nishihara aims to discover new microorganisms capable of CO2 fixation, potentially utilizing AI for this purpose. However, she recognizes that applied research is outside her expertise and wishes to focus on gathering high-quality primary data on microbial habitats and culture conditions.
The Future: Predictive Science and AI
RIKEN's TRIP initiative aims to connect cutting-edge research infrastructure and data across disciplines. The initiative has three pillars: organizing high-quality data, achieving breakthroughs in quantum chemical calculations through AI and mathematical sciences integration, and creating predictive science. The research conducted by Kato and his team aligns with the first pillar, but they aspire to go further, utilizing AI to add value and make predictions about the use of these microorganisms in specific research areas and industries.
Kato concludes: "We strongly believe that we, too, will be able to make a significant contribution to the TRIP initiative."
This research not only sheds light on the fascinating world of microbial dark matter but also showcases the potential for these microorganisms to contribute to a low-carbon future.
