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

Abstract

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.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3

Abbreviations

AMD:

Acid mine drainage

FACS:

Fluorescence-activated cell sorting

GEBA:

Genomic encyclopedia of bacteria and archaea

MDA:

Multiple displacement amplification

MDM:

“Microbial dark matter”

SAG:

Single amplified genome

SSU rRNA:

Small subunit ribosomal RNA

References

  1. Baker BJ, Dick GJ (2013) Omic approaches in microbial ecology: charting the unknown. Microbe 8:353–360

    Google Scholar 

  2. Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, Banfield JF (2006) Lineages of acidophilic archaea revealed by community genomic analysis. Science 314:1933–1935

    CAS  PubMed  Article  Google Scholar 

  3. Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, Banfield JF (2010) Enigmatic, ultrasmall, uncultivated Archaea. Proc Natl Acad Sci 107:8806–8811

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  4. Barns SM, Fundyga RE, Jeffries MW, Pace NR (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci 91:1609–1613

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  5. Barns SM, Delwiche CF, Palmer JD, Pace NR (1996) Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci 93:9188–9193

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  6. Behrens S, Loesekann T, Pett-Ridge J, Weber PK, Ng JW-O, Stevenson BS, Hutcheon ID, Relman DA, Spormann AM (2008) Linking phylogeny with metabolic activity of single microbial cells using FISH-NanoSIMS. Appl Environ Microbiol 74:3143–3150

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  7. Biddle JF, Cardman Z, Mendlovitz H, Albert DB, Lloyd KG, Boetius A, Teske A (2012) Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments. ISME J 6:1018–1031

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  8. Blainey PC (2013) The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol Rev 37:407–427

    CAS  PubMed  Article  Google Scholar 

  9. Blainey PC, Quake SR (2014) Dissecting genomic diversity, one cell at a time. Nat Methods 11:19–21

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  10. Burggraf S, Heyder P, Eis N (1997) A pivotal Archaea group. Nature 385:780

    CAS  PubMed  Article  Google Scholar 

  11. Cole JK, Peacock JP, Dodsworth JA, Williams AJ, Thompson DB, Dong H, Wu G, Hedlund BP (2013) Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities. ISME J 7:718–729

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  12. Costa KC, Navarro JB, Shock EL, Zhang CL, Soukup D, Hedlund BP (2009) Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin. Extremophiles 13:447–459

    CAS  PubMed  Article  Google Scholar 

  13. de Bont JA, Staley JT, Pankratz HS (1970) Isolation and description of a non-motile, fusiform, stalked bacterium, a representative of a new genus. Antonie Van Leeuwenhoek 36:397–407

    PubMed  Article  Google Scholar 

  14. Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP, Banfield JF (2009) Community-wide analysis of microbial genome sequence signatures. Genome Biol 10:R85

    PubMed Central  PubMed  Article  Google Scholar 

  15. Dodsworth JA, Hedlund BP (2010) Microbiology and geochemistry of Smith Creek and Grass Valley hot springs: emerging evidence for wide distribution of novel thermophilic lineages in the US Great Basin. J. Earth Sci 21:315–318

    CAS  Article  Google Scholar 

  16. Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA, Tringe SG, Chain PSG, Raymond J, Quake SR, Hedlund BP (2013) Single-cell and metagenomic analyses indicate a fermentative, saccharolytic lifestyle for members of the OP9 lineage. Nature Commun 4:1854

    Article  Google Scholar 

  17. Dodsworth JA, Gevorkian J, Despujos F, Cole JK, Murugapiran SK, Ming H, Li WJ, Zhang G, Dohnalkova A, Hedlund BP (2014) Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.055855-0

    PubMed  Google Scholar 

  18. Dröge J, McHardy AC, 66 (2012) Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. Brief Bioinform 13(66):646–655

    PubMed  Article  Google Scholar 

  19. Druschel GK, Baker BJ, Gihring TM, Banfield JF (2004) Acid mine drainage biogeochemistry at Iron Mountain, California. Geochem Trans 5:13–32

    CAS  PubMed Central  Article  Google Scholar 

  20. Elkins JG, Kunin V, Anderson I, Barry K, Goltsman E, Lapidus A, Hedlund BP, Hugenholtz P, Kyrpides N, Graham D, Keller M, Wanner G, Richardson P, Stetter KO (2008) A korarchaeal genome reveals insights into the evolution of archaea. Proc Natl Acad Sci 105:8102–8107

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  21. Fraser CM, Eisen JA, Salzberg SL (2000) Microbial genome sequencing. Nature 406:799–803

    CAS  PubMed  Article  Google Scholar 

  22. Ghai R, Pašić L, Fernández AB, Martin-Cuadrado AB, Mizuno CM, McMahon KD, Papke RT, Stepanauskas R, Rodriguez-Brito B, Rohwer F, Sánchez-Porro C, Ventosa A, Rodríguez-Valera F (2011) New abundant microbial groups in aquatic hypersaline environments. Sci Rep 1:135

    PubMed Central  PubMed  Article  Google Scholar 

  23. Gittel A, Sørensen KB, Skovhus TL, Ingvorsen K, Schramm A (2009) Prokaryotic community structure and sulfate reducer activity in water from high-temperature oil reservoirs with and without nitrate treatment. Appl Environ Microbiol 75:7086–7096

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  24. Grasby SE, Richards BC, Sharp CE, Brady AL, Jones GM, Dunfield PF (2013) The Paint Pots, Kootenay National Park, Canada—a natural acid spring analogue for Mars. Can J Earth Sci 50:94–108

    CAS  Article  Google Scholar 

  25. Guy L, Ettema TJ (2011) The archaeal ‘TACK’ superphylum and the origin of eukaryotes. Trends Microbiol 19:580–587

    CAS  PubMed  Article  Google Scholar 

  26. Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  27. Harris JK, Caporaso JG, Walker JJ, Spear JR, Gold NJ, Robertson CE, Hugenholtz P, Goodrich J, McDonald D, Knights D, Marshall P, Tufo H, Knight R, Pace NR (2013) Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME J 7:50–60

    PubMed  Article  Google Scholar 

  28. Hedlund BP, Gosink JJ, Staley JT (1997) Verrucomicrobia div. nov., a new division of the bacteria containing three new species of Prosthecobacter. Antonie Van Leeuwenhoek 72:29–38

    CAS  PubMed  Article  Google Scholar 

  29. Henrici AT (1933) Studies of freshwater bacteria. I. A direct microscopic technique. J Bacteriol 25:277–286

    CAS  PubMed Central  PubMed  Google Scholar 

  30. Henrici AT, Johnson DE (1935) Studies of freshwater bacteria. II. Stalked bacteria, a new order of Schizomycetes. J Bacteriol 30:61–92

    CAS  PubMed Central  PubMed  Google Scholar 

  31. Hou W, Wang S, Dong H, Jiang H, Briggs BR, Peacock JP, Huang Q, Huang L, Wu G, Zhi X, Li W, Dodsworth JA, Hedlund BP, Zhang C, Hartnett HE, Dijkstra P, Hungate BA (2013) A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan Province China using 16S rRNA gene pyrosequencing. PLoS One 8:e53350

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  32. Hugenholtz P, Goebel BM, Pace NR (1998a) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774

    CAS  PubMed Central  PubMed  Google Scholar 

  33. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR (1998b) Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180:366–376

    CAS  PubMed Central  PubMed  Google Scholar 

  34. Kantor RS, Wrighton KC, Handley KM, Sharon I, Hug LA, Castelle CJ, Thomas BC, Banfield JF (2013) Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. MBio 4:e00708–e00713

    PubMed Central  PubMed  Article  Google Scholar 

  35. Konstantinidis KT, Ramette A, Tiedje JM (2006) The bacterial species definition in the genomic era. Phil Trans R Soc 361:1929–1940

    Article  Google Scholar 

  36. Landry ZC, Giovanonni SJ, Quake SR, Blainey PC (2013) Optofluidic cell selection from complex microbial communities for single-genome analysis. Methods Enzymol 531:61–90

    CAS  PubMed  Article  Google Scholar 

  37. Lasken RS (2012) Genomic sequencing of uncultured microorganisms from single cells. Nat Rev Microbiol 10:631–640

    CAS  PubMed  Article  Google Scholar 

  38. Lloyd KG, Schreiber L, Petersen DG, Kjeldsen KU, Lever MA, Steen AD, Stepanauskas R, Richter M, Kleindienst S, Lenk S, Schramm A, Jørgensen BB (2013) Predominant archaea in marine sediments degrade detrital proteins. Nature 496:215–218

    CAS  PubMed  Article  Google Scholar 

  39. Mande SS, Mohammed MH, Ghosh TS (2012) Classification of metagenomic sequences: methods and challenges. Brief Bioinform 13:669–681

    PubMed  Article  Google Scholar 

  40. Marcy Y, Ouverney C, Bik EM, Lösekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relman DA, Quake SR (2007) Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci 104:11889–11894

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  41. Marshall IPG, Blainey PC, Spormann AM, Quake SR (2012) A single-cell genome for Thiovulum sp. Appl Environ Microbiol 78:8555–8563

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  42. Mayali X, Weber PK, Brodie EL, Mabery S, Hoeprich PD, Pett-Ridge J (2012) High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use. ISME J 6:1210–1221

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  43. Mayali X, Weber PK, Pett-Ridge J (2013) Taxon-specific C/N relative use efficiency for amino acids in an estuarine community. FEMS Microbiol Ecol 83:402–412

    CAS  PubMed  Article  Google Scholar 

  44. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6:610–618

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  45. Mori K, Yamaguchi K, Sakiyama Y, Urabe T, Suzuki K (2009) Caldisericum exile gen. nov., sp. nov., an anaerobic, thermophilic, filamentous bacterium of a novel bacterial phylum, Caldiserica phyl. nov., originally called the candidate phylum OP5, and description of Caldisericaceae fam. nov., Caldisericales ord. nov. and Caldisericia classis nov. Int J Syst Evol Microbiol 59:2894–2898

    CAS  PubMed  Article  Google Scholar 

  46. Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson JB, Brocks JJ, Heidelberg KB, Banfield JF, Allen EE (2012) De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J 6:81–93

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  47. Neufeld JD, Murrell JC (2007) Witnessing the last supper of uncultivated microbial cells with Raman-FISH. ISME J 1:269–270

    PubMed  Google Scholar 

  48. Nichols D, Cahoon N, Trakhtenberg EM, Pham L, Mehta A, Belanger A, Kanigan T, Lewis K, Epstein SS (2010) Use of ichip for high-throughput in situ cultivation of “uncultivable” microbial species. Appl Environ Microbiol 76:2445–2450

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  49. Nunoura T, Hirayama H, Takami H, Oida H, Nishi S, Shimamura S, Suzuki Y, Inagaki F, Takai K, Nealson KH (2005) Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments. Environ Microbiol 7:1967–1984

    CAS  PubMed  Article  Google Scholar 

  50. Nunoura T, Takaki Y, Kakuta J, Nishi S, Sugahara J, Kazama H, Chee GJ, Hattori M, Kanai A, Atomi H, Takai K, Takami H (2011) Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res 39:3204–3223

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  51. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA (2013) Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 20:714–737

    CAS  PubMed  Article  Google Scholar 

  52. Oger PM, Jebbar M (2010) The many ways of coping with pressure. Res Microbiol 161:799–809

    PubMed  Article  Google Scholar 

  53. Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40:337–365

    CAS  PubMed  Article  Google Scholar 

  54. Peacock JP, Cole JK, Murugapiran SK, Dodsworth JA, Fisher JC, Moser DP, Hedlund BP (2013) Pyrosequencing reveals high-temperature cellulolytic microbial consortia in Great Boiling Spring after in situ lignocellulose enrichment. PLoS One 8:e59927

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  55. Podosokorskaya OA, Kadnikov VV, Gavrilov SN, Mardanov AV, Merkel AY, Karnachuk OV, Ravin NV, Bonch-Osmolovskaya EA, Kublanov IV (2013) Characterization of Melioribacter roseus gen. nov., sp. nov., a novel facultatively anaerobic thermophilic cellulolytic bacterium from the class Ignavibacteria, and a proposal of a novel bacterial phylum Ignavibacteriae. Environ Microbiol 15:1759–1771

    CAS  PubMed  Article  Google Scholar 

  56. Ram RJ, Verberkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC 2nd, Shah M, Hettich RL, Banfield JF (2005) Community proteomics of a natural microbial biofilm. Science 308:1915–1920

    CAS  PubMed  Article  Google Scholar 

  57. Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394

    PubMed  Article  Google Scholar 

  58. Reysenbach AL, Wickham GS, Pace NR (1994) Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park. Appl Environ Microbiol 60:2113–2119

    CAS  PubMed Central  PubMed  Google Scholar 

  59. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–437

    CAS  PubMed  Article  Google Scholar 

  60. Rinke C, Lee J, Nath N, Goudeau D, Thompson B, Poulton N, Dmitrieff E, Malmstrom R, Stepanauskas R, Woyke T (2014) Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics. Nat Protoc. doi:10.1038/nprot.2014.067

    PubMed  Google Scholar 

  61. Rivière D, Desvignes V, Pelletier E, Chaussonnerie S, Guermazi S, Weissenbach J, Li T, Camacho P, Sghir A (2009) Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. ISME J 3:700–714

    PubMed  Article  Google Scholar 

  62. Scholz MB, Lo CC, Chain PS (2012) Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr Opin Biotechnol 23:9–15

    CAS  PubMed  Article  Google Scholar 

  63. Sievert SM, Vetriani C (2012) Chemoautotrophy at deep-sea vents: past, present, and future. Oceanography 25:218–233

    Article  Google Scholar 

  64. Spang A, Martijn J, Saw JH, Lind AE, Guy L, Ettema TJ (2013) Close encounters of the third domain: the emerging genomic view of archaeal diversity and evolution. Archaea 2013:202358

  65. Stackebrandt E, Ludwig W, Schubert W, Klink F, Schlesner H, Roggentin T, Hirsch P (1984) Molecular genetic evidence for early evolutionary origin of budding peptidoglycan-less eubacteria. Nature 307:735–737

    CAS  PubMed  Article  Google Scholar 

  66. Stahl DA, Lane DJ, Olsen GJ, Pace NR (1984) Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science 224:409–411

    CAS  PubMed  Article  Google Scholar 

  67. Staley JT (1973) Budding bacteria of the Pasteuria-Blastobacter group. Can J Microbiol 19:609–614

    CAS  PubMed  Article  Google Scholar 

  68. Stepanauskas R (2012) Single cell genomics: an individual look at microbes. Curr Opin Microbiol 15:613–620

    CAS  PubMed  Article  Google Scholar 

  69. Stetter KO (2013) A brief history of the discovery of hyperthermophilic life. Biochem Soc Trans 41:416–420

    CAS  PubMed  Article  Google Scholar 

  70. Stetter KO, König H, Stackebrandt E (1983) Pyrodictium gen. nov., a new genus of submarine disc-shaped sulphur reducing Archaebacteria growing optimally at 105°C. Syst Appl Microbiol 4:535–551

    CAS  PubMed  Article  Google Scholar 

  71. Stetter KO, Lauerer G, Thomm M, Neuner A (1987) Isolation of extremely thermophilic sulfate reducers: evidence for a novel branch of archaebacteria. Science 236:822–824

    CAS  PubMed  Article  Google Scholar 

  72. Stott MB, Crowe MA, Mountain BW, Smirnova AV, Hou S, Alam M, Dunfield PF (2008) Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. Environ Microbiol 10:2030–2041

    CAS  PubMed  Article  Google Scholar 

  73. Strous M, Kraft B, Bisdorf R, Tegetmeyer HE (2012) The binning of metagenomic contigs for microbial physiology of mixed cultures. Front Microbiol 3:410

    PubMed Central  PubMed  Google Scholar 

  74. Takami H, Noguchi H, Takaki Y, Uchiyama I, Toyoda A, Nishi S, Chee GJ, Arai W, Nunoura T, Itoh T, Hattori M, Takai K (2012) A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem. PLoS One 7:e30559

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  75. Temme K, Zhao D, Voigt CA (2012) Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc Natl Acad Sci 109:7085–7090

    PubMed Central  PubMed  Article  Google Scholar 

  76. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43

    CAS  PubMed  Article  Google Scholar 

  77. Vick TJ, Dodsworth JA, Costa KC, Shock EL, Hedlund BP (2010) Microbiology and geochemistry of Little Hot Creek, a hot spring environment in the Long Valley Caldera. Geobiology 8:140–154

    CAS  PubMed  Article  Google Scholar 

  78. Wagner M, Nielsen PH, Loy A, Nielsen JL, Daims H (2006) Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays. Curr Opin Biotechnol 17:1–9

    CAS  Article  Google Scholar 

  79. Walker A (2014) Adding genomic ‘foliage’ to the tree of life. Nat Rev Microbiol 12:78

    CAS  PubMed  Article  Google Scholar 

  80. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci 74:5088–5090

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  81. Woyke T, Sczyrba A, Lee J, Rinke C, Tighe D, Clingenpeel S, Malmstrom R, Stepanauskas R, Cheng J-F (2011) Decontamination of MDA reagents for single cell whole genome amplification. PLoS One 6:e26161

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  82. Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, Wilkins MJ, Hettich RL, Lipton MS, Williams KH, Long PE, Banfield JF (2012) Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 337:1661–1665

    CAS  PubMed  Article  Google Scholar 

  83. Wrighton KC, Castelle CJ, Wilkins MJ, Hug LA, Sharon I, Thomas BC, Handley KM, Mullin SW, Nicora CD, Singh A, Lipton MS, Long PE, Williams KH, Banfield JF (2014) Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer. ISME J. doi:10.1038/ismej.2013.249

    Google Scholar 

  84. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D’haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462:1056–1060

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  85. Zillig W, Gierl A, Schreiber G, Wunderl S, Janekovic D, Stetter KO, Klenk HP (1983) The archaebacterium Thermofilum pendens represents, a novel genus of the thermophilic, anaerobic sulfur respiring Thermoproteales. Syst Appl Microbiol 4:79–87

    CAS  PubMed  Article  Google Scholar 

  86. Zioutas K, Hoffmann DH, Dennerl K, Papaevangelou T (2004) What is dark matter made of? Science 306:1485–1488

    CAS  PubMed  Article  Google Scholar 

  87. Zong C, Lu S, Chapman AR, Xie XS (2012) Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 338:1622–1626

    CAS  PubMed Central  PubMed  Article  Google Scholar 

Download references

Acknowledgments

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.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Brian P. Hedlund.

Additional information

This article is part of a special issue based on the 10th International Congress on Extremophiles held in Saint Petersburg, Russia, September 7-11, 2014.

Communicated by H. Santos.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Hedlund, B.P., Dodsworth, J.A., Murugapiran, S.K. et al. Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”. Extremophiles 18, 865–875 (2014). https://doi.org/10.1007/s00792-014-0664-7

Download citation

Keywords

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