Single-Cell Sequencing of Microorganisms

Abstract

Only a small fraction (estimated to be less than 1 %) of microbial species on Earth can be cultivated in the laboratory; thus, the standard microbial research methods based on pure culture isolation and observation can provide only very limited information about an environmental microbial community. The development and successful application of microbial small sub-unit ribosomal RNA (16S rRNA) gene PCR analysis has greatly expanded our knowledge of the diversity and phylogeny of microorganisms. Novel, yet-uncultivated microorganisms have been continually discovered by the 16S rRNA gene approach, revealing an “uncultured microbial majority”, which is estimated to comprise 40–50 as yet-uncultivated candidate phyla of bacteria and a similar number of as-yet uncultivated major lineages of archaea (Rappé and Giovannoni 2003). In an allusion to astrophysics that highlights its importance, the “uncultured microbial majority” has been called “biological dark matter” or “microbial dark matter” (Marcy et al. 2007). Recent achievements in metagenomics (genomic sequences from the entire environmental community) and single-cell genomics are now opening the window to observation and analysis of this “biological dark matter”.