Exploring Microbial Dark Matter and the Status of Bacterial and Archaeal Taxonomy: Challenges and Opportunities in the Future

There are very few places on Earth that are free of diverse microbial cellular life forms that can colonize in a variety of environmental niches and with both living and nonliving things. In contrast, the limitations of current and existing culture methods only allowed us to culture 0.1–1% of actual bacterial and archaeal taxa in this mysterious microbial world. The remaining vast majority of microorganisms that haven’t been recognized are referred to as “Microbial Dark Matter” (MDM) by taxonomists. If we wish to cultivate the enormous diversity of yet-to-be-cultivated microbes, perhaps next-generation sequencing will help us access them. In recent years, several multinational projects, such as the Global Catalogue of Microorganisms (GCM) and the Genetic Encyclopedia of Bacteria and Archaea (GEBA), have been initiated to methodically fill in genomic gaps among farmed microorganisms. In addition, the Earth Microbiome Project, the Genomic Encyclopedia of Bacteria and Archaea-Microbial Dark Matter Project (GEBA-MDM), and the primate microbiome studies have disclosed information on MDM at scale, ranging from the gene to the genome level. These research findings have significantly improved our understanding of the magnitude and distribution of microbial diversity; nevertheless, much remains unknown about the functional diversity of MDM. This chapter explores the scientific importance of MDM and the challenges and opportunities that lay ahead for the research of these mysteries.