, Volume 18, Issue 5, pp 865–875 | Cite as

Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”

  • Brian P. HedlundEmail author
  • Jeremy A. Dodsworth
  • Senthil K. Murugapiran
  • Christian Rinke
  • Tanja Woyke
Special Issue: Review 10th International Congress on Extremophiles
Part of the following topical collections:
  1. 10th International Congress on Extremophiles


Despite >130 years of microbial cultivation studies, many microorganisms remain resistant to traditional cultivation approaches, including numerous candidate phyla of bacteria and archaea. Unraveling the mysteries of these candidate phyla is a grand challenge in microbiology and is especially important in habitats where they are abundant, including some extreme environments and low-energy ecosystems. Over the past decade, parallel advances in DNA amplification, DNA sequencing and computing have enabled rapid progress on this problem, particularly through metagenomics and single-cell genomics. Although each approach suffers limitations, metagenomics and single-cell genomics are particularly powerful when combined synergistically. Studies focused on extreme environments have revealed the first substantial genomic information for several candidate phyla, encompassing putative acidophiles (Parvarchaeota), halophiles (Nanohaloarchaeota), thermophiles (Acetothermia, Aigarchaeota, Atribacteria, Calescamantes, Korarchaeota, and Fervidibacteria), and piezophiles (Gracilibacteria). These data have enabled insights into the biology of these organisms, including catabolic and anabolic potential, molecular adaptations to life in extreme environments, unique genomic features such as stop codon reassignments, and predictions about cell ultrastructure. In addition, the rapid expansion of genomic coverage enabled by these studies continues to yield insights into the early diversification of microbial lineages and the relationships within and between the phyla of Bacteria and Archaea. In the next 5 years, the genomic foliage within the tree of life will continue to grow and the study of yet-uncultivated candidate phyla will firmly transition into the post-genomic era.


Single-cell genomics Metagenomics Candidate phyla Genomic encyclopedia of bacteria and archaea (GEBA) “Microbial dark matter” 



Acid mine drainage


Fluorescence-activated cell sorting


Genomic encyclopedia of bacteria and archaea


Multiple displacement amplification


“Microbial dark matter”


Single amplified genome


Small subunit ribosomal RNA



This work was supported by NASA Exobiology grant EXO-NNX11AR78G; U.S. National Science Foundation grant OISE 0968421; U.S. Department of Energy (DOE) grant DE-EE-0000716; and the Joint Genome Institute (CSP-182), supported by the Office of Science of the U.S. DOE under Contract No. DE-AC02-05CH11231. B. P. H. acknowledges generous support from Greg Fullmer through the UNLV Foundation.


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Copyright information

© Springer Japan 2014

Authors and Affiliations

  • Brian P. Hedlund
    • 1
    Email author
  • Jeremy A. Dodsworth
    • 1
  • Senthil K. Murugapiran
    • 1
  • Christian Rinke
    • 2
  • Tanja Woyke
    • 2
  1. 1.School of Life SciencesUniversity of Nevada Las VegasLas VegasUSA
  2. 2.DOE Joint Genome InstituteWalnut CreekUSA

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