Functional Classification of Uncultured "Candidatus Caldiarchaeum subterraneum" Using the Maple System
Hideto Takami1, Wataru Arai1, Kazuhiro Takemoto2
1Microbial Genome Research Group, Yokohama Institute, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Kanagawa, Japan.
Plos One
|July 22, 2015
Summary
This study reveals the unique metabolic functions of "Candidatus Caldiarchaeum subterraneum," a thermophilic archaeon. Despite similarities to thaumarchaeota, it lacks nitrification genes but possesses robust carbohydrate metabolism, indicating a heterotrophic lifestyle.
Area of Science:
- Microbiology
- Metagenomics
- Bioinformatics
Background:
- Understanding the functionome of uncultivated microorganisms is crucial for microbial ecology.
- Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules provide a framework for metabolic potential analysis.
- Archaea play significant roles in various ecosystems, yet many remain uncharacterized.
Purpose of the Study:
- To functionally classify archaeal species using KEGG modules.
- To determine the comprehensive metabolic and physiological potential (functionome) of "Candidatus Caldiarchaeum subterraneum" (Ca. C. subterraneum).
- To elucidate the lifestyle and ecological role of Ca. C. subterraneum in its native environment.
Main Methods:
- Phylogenetic analysis using concatenated protein sequences from archaea, bacteria, and eukaryotes.
- Clustering and principal component analyses based on KEGG module completion ratios across 79 archaeal species.
- Comparative genomics to identify specific metabolic pathways present or absent in Ca. C. subterraneum.
Main Results:
- Phylogenetic analysis suggests Ca. C. subterraneum is closely related to thaumarchaeotic species.
- Metabolic potential analysis indicates overall similarity to thaumarchaeota, but with key differences.
- Ca. C. subterraneum lacks genes for nitrification and the hydroxypropionate-hydroxybutyrate cycle but possesses complete central carbohydrate metabolism (glycolysis, TCA cycle, etc.) and multiple ABC transporters.
Conclusions:
- Ca. C. subterraneum exhibits a distinct metabolic profile compared to typical thaumarchaeota.
- The presence of extensive carbohydrate metabolism supports a heterotrophic lifestyle.
- Its metabolic capabilities are adapted to a predominantly aerobic, thermophilic, subsurface environment.
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