Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Microbial diversity in extreme environments

Abstract

A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth’s extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: Global distribution of representative extreme environments.
Fig. 2: Microbial community composition of different extreme environments.
Fig. 3: Genomic tree of the domain Archaea showing currently proposed major lineages (phyla).
Fig. 4: Compositional and functional shifts of the microbial community along specific environmental gradients.

References

  1. 1.

    Rothschild, L. J. & Mancinelli, R. L. Life in extreme environments. Nature 409, 1092–1101 (2001).

    CAS  PubMed  Google Scholar 

  2. 2.

    Schmid, A. K., Allers, T. & DiRuggiero, J. Snapshot: microbial extremophiles. Cell 180, 818–818.e1 (2020).

    CAS  PubMed  Google Scholar 

  3. 3.

    Denef, V. J., Mueller, R. S. & Banfield, J. F. AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J. 4, 599–610 (2010).

    PubMed  Google Scholar 

  4. 4.

    Inskeep, W. P. et al. The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem. Front. Microbiol. 4, 67 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. 5.

    Oren, A. Halophilic microbial communities and their environments. Curr. Opin. Microbiol. 33, 119–124 (2015).

    CAS  Google Scholar 

  6. 6.

    Reysenbach, A. L., Wickham, G. S. & Pace, N. R. Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park. Appl. Environ. Microbiol. 60, 2113–2119 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7.

    Bond, P. L., Smriga, S. P. & Banfield, J. F. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl. Environ. Microbiol. 66, 3842–3849 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Huber, J. A. et al. Microbial population structures in the deep marine biosphere. Science 318, 97–100 (2007).

    CAS  PubMed  Google Scholar 

  9. 9.

    Kuang, J. L. et al. Contemporary environmental variation determines microbial diversity patterns in acid mine drainage. ISME J. 7, 1038–1050 (2013).

    CAS  PubMed  Google Scholar 

  10. 10.

    Power, J. F. et al. Microbial biogeography of 925 geothermal springs in New Zealand. Nat. Commun. 9, 2876 (2018). Extensive sampling and high-throughput 16S rRNA gene sequencing have provided deeper insights into the patterns and ecological drivers of microbial communities inhabiting geothermal springs.

    PubMed  PubMed Central  Google Scholar 

  11. 11.

    Podell, S. et al. Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME J. 8, 979–990 (2014).

    CAS  PubMed  Google Scholar 

  12. 12.

    Chen, L. X. et al. Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage. ISME J. 9, 1579–1592 (2015).

    PubMed  Google Scholar 

  13. 13.

    Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013).

    CAS  PubMed  Google Scholar 

  14. 14.

    Brown, C. T. et al. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523, 208–211 (2015).

    CAS  PubMed  Google Scholar 

  15. 15.

    Castelle, C. J. et al. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr. Biol. 25, 690–701 (2015). The cultivation-independent reconstruction of the first complete genomes for members of the DPANN archaea allowed confident prediction of incomplete or absent pathways for these enigmatic organisms.

    CAS  PubMed  Google Scholar 

  16. 16.

    Sharp, C. E. et al. Humboldt’s spa: microbial diversity is controlled by temperature in geothermal environments. ISME J. 8, 1166–1174 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Hedlund, B. P. et al. Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’. Curr. Opin. Microbiol. 25, 136–145 (2015).

    CAS  PubMed  Google Scholar 

  18. 18.

    Hua, Z. S. et al. Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. ISME J. 9, 1280–1294 (2015).

    CAS  PubMed  Google Scholar 

  19. 19.

    Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37–43 (2004). This is the first shotgun metagenomic sequencing study that enabled reconstruction of near-complete microbial genomes directly (without cultivation) from a natural community.

    CAS  PubMed  Google Scholar 

  20. 20.

    Castelle, C. J. & Banfield, J. F. Major new microbial groups expand diversity and alter our understanding of the tree of life. Cell 172, 1181–1197 (2018).

    CAS  PubMed  Google Scholar 

  21. 21.

    Chen, L. X. et al. Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota. ISME J. 12, 756–775 (2018).

    CAS  PubMed  Google Scholar 

  22. 22.

    Baker, B. J. et al. Enigmatic, ultrasmall, uncultivated Archaea. Proc. Natl Acad. Sci. USA 107, 8806–8811 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. 23.

    Narasingarao, P. et al. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J. 6, 81–93 (2012).

    CAS  PubMed  Google Scholar 

  24. 24.

    Brock, T. D. Life at high temperatures. Science 158, 1012–1019 (1967).

    CAS  PubMed  Google Scholar 

  25. 25.

    Cole, J. K. et al. Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities. ISME J. 7, 718–729 (2013).

    CAS  PubMed  Google Scholar 

  26. 26.

    Colman, D. R. et al. Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs. FEMS Microbiol. Ecol. 92, fiw137 (2016).

    PubMed  Google Scholar 

  27. 27.

    Ward, D. M. et al. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345, 63–65 (1990).

    CAS  PubMed  Google Scholar 

  28. 28.

    Miller, S. R. et al. Bar-coded pyrosequencing reveals shared bacterial community properties along the temperature gradients of two alkaline hot springs in Yellowstone National Park. Appl. Environ. Microbiol. 75, 4565–4572 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. 29.

    Ward, L. et al. Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring. ISME J. 11, 1158–1167 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. 30.

    Barns, S. M., Fundyga, R. E., Jeffries, M. W. & Pace, N. R. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl Acad. Sci. USA 91, 1609–1613 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Takai, K. & Yoshihiko, S. A molecular view of archaeal diversity in marine and terrestrial hot water environments. FEMS Microbiol. Ecol. 28, 177–188 (1999).

    CAS  Google Scholar 

  32. 32.

    Elkins, J. G. et al. A korarchaeal genome reveals insights into the evolution of the Archaea. Proc. Natl Acad. Sci. USA 105, 8102–8107 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. 33.

    Dombrowski, N., Teske, A. P. & Baker, B. J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun. 9, 4999 (2018).

    PubMed  PubMed Central  Google Scholar 

  34. 34.

    Nunoura, T. et al. 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 (2005).

    CAS  PubMed  Google Scholar 

  35. 35.

    Nunoura, T. et al. 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 (2011).

    CAS  PubMed  Google Scholar 

  36. 36.

    Beam, J. P. et al. Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous ‘streamer’ community. ISME J. 10, 210–224 (2016).

    CAS  PubMed  Google Scholar 

  37. 37.

    Hua, Z. S. et al. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat. Commun. 9, 2832 (2018).

    PubMed  PubMed Central  Google Scholar 

  38. 38.

    Takami, H. et al. A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem. PLoS ONE 7, e30559 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Colman, D. R. et al. Novel, deep-branching heterotrophic bacterial populations recovered from thermal spring metagenomes. Front. Microbiol. 7, 304 (2016).

    PubMed  PubMed Central  Google Scholar 

  40. 40.

    Nobu, M. et al. Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics. ISME J. 10, 273–286 (2016).

    CAS  PubMed  Google Scholar 

  41. 41.

    Hugenholtz, P., Pitulle, C., Hershberger, K. L. & Pace, N. R. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180, 366–376 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. 42.

    Orcutt, B. N., Sylvan, J. B., Knab, N. J. & Edwards, K. J. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol. Mol. Biol. Rev. 75, 361–422 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. 43.

    Eloe-Fadrosh, E. A. et al. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nat. Commun. 7, 10476 (2016). This is a good example of how analysis of the increasing wealth of metagenomic data collected from diverse environments may lead to the discovery of novel major lineages.

    CAS  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Kelley, D. S., Baross, J. A. & Delaney, J. R. Volcanoes, fluids, and life at Mid-Ocean Ridge spreading centers. Annu. Rev. Earth Planet. Sci. 30, 385–491 (2002).

    CAS  Google Scholar 

  45. 45.

    Perner, M. et al. In situ chemistry and microbial community compositions in five deep-sea hydrothermal fluid samples from Irina II in the Logatchev field. Environ. Microbiol. 15, 1551–1560 (2013).

    CAS  PubMed  Google Scholar 

  46. 46.

    Flores, G. E. et al. Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge. Environ. Microbiol. 13, 2158–2171 (2011).

    CAS  PubMed  Google Scholar 

  47. 47.

    Dick, G. J. et al. The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally. Nat. Rev. Microbiol. 17, 271–283 (2019).

    CAS  PubMed  Google Scholar 

  48. 48.

    Campbell, B. J., Summers Engel, A., Porter, M. L. & Takai, K. The versatile ε-proteobacteria: key players in sulphidic habitats. Nat. Rev. Microbiol. 4, 458–468 (2006).

    CAS  PubMed  Google Scholar 

  49. 49.

    Reysenbach, A. L., Longnecker, K. & Kirshtein, J. Novel bacterial and archaeal lineages from an in situ growth chamber deployed at a Mid-Atlantic Ridge hydrothermal vent. Appl. Environ. Microbiol. 66, 3798–3806 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Takai, K., Komatsu, T., Inagaki, F. & Horikoshi, K. Distribution of archaea in a black smoker chimney structure. Appl. Environ. Microbiol. 67, 3618–3629 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. 51.

    Schrenk, M. O., Kelley, D. S., Bolton, S. A. & Baross, J. A. Low archaeal diversity linked to subseafloor geochemical processes at the Lost City Hydrothermal Field, Mid-Atlantic Ridge. Environ. Microbiol. 6, 1086–1095 (2004).

    CAS  PubMed  Google Scholar 

  52. 52.

    Brazelton, W. J., Schrenk, M. O., Kelley, D. S. & Baross, J. A. Methane- and sulfur-metabolizing microbial communities dominate the Lost City Hydrothermal Field ecosystem. Appl. Environ. Microbiol. 72, 6257–6270 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. 53.

    Reveillaud, J. et al. Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise. Environ. Microbiol. 18, 1970–1987 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. 54.

    Brazelton, W. J. et al. Archaea and bacteria with surprising micro-diversity show shifts in dominance over 1000-year time scales in hydrothermal chimneys. Proc. Natl Acad. Sci. USA 107, 1612–1617 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. 55.

    Huber, H. et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417, 63–67 (2002).

    CAS  PubMed  Google Scholar 

  56. 56.

    Waters, E. et al. The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc. Natl Acad. Sci. USA 100, 12984–12988 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. 57.

    Casanueva, A. et al. Nanoarchaeal 16S rRNA gene sequences are widely dispersed in hyperthermophilic and mesophilic halophilic environments. Extremophiles 12, 651–656 (2008).

    CAS  PubMed  Google Scholar 

  58. 58.

    Wurch, L. et al. Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment. Nat. Commun. 7, 12115 (2016). This is an interesting study demonstrating that insights from genomic studies may help develop effective cultivation strategies for the isolation of novel microbial species.

    CAS  PubMed  PubMed Central  Google Scholar 

  59. 59.

    Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015). The discovery and genomic characterization of Lokiarchaeota have unveiled insights into eukaryogenesis.

    CAS  PubMed  PubMed Central  Google Scholar 

  60. 60.

    Seitz, K. W., Lazar, C. S., Hinrichs, K. U., Teske, A. P. & Baker, B. J. Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction. ISME J. 10, 1696–1705 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. 61.

    Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017).

    CAS  PubMed  Google Scholar 

  62. 62.

    Imachi, H. et al. Isolation of an archaeon at the prokaryote-eukaryote interface. Nature 577, 519–525 (2020). This study reports the isolation of the first member of the superphylum Asgard, confirming the existence of these archaea and their close phylogenetic relatedness to eukaryotes.

    CAS  PubMed  PubMed Central  Google Scholar 

  63. 63.

    Margesin, R. & Collins, T. Microbial ecology of the cryosphere (glacial and permafrost habitats): current knowledge. Appl. Microbiol. Biotechnol. 103, 2537–2549 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. 64.

    Boetius, A., Anesio, A. M., Deming, J. W., Mikucki, J. A. & Rapp, J. Z. Microbial ecology of the cryosphere: sea ice and glacial habitats. Nat. Rev. Microbiol. 13, 677–690 (2015).

    CAS  PubMed  Google Scholar 

  65. 65.

    Hoham, R. W. & Duval, B. in Snow Ecology (eds Jones, H. et al.) 168–228 (Cambridge Univ. Press, 2001).

  66. 66.

    Edwards, A. et al. Coupled cryoconite ecosystem structure-function relationships are revealed by comparing bacterial communities in alpine and Arctic glaciers. FEMS Microbiol. Ecol. 89, 222–237 (2014).

    CAS  PubMed  Google Scholar 

  67. 67.

    Jungblut, A. D., Lovejoy, C. & Vincent, W. F. Global distribution of cyanobacterial ecotypes in the cold biosphere. ISME J. 4, 191–202 (2010).

    CAS  PubMed  Google Scholar 

  68. 68.

    Franzetti, A. et al. Temporal variability of bacterial communities in cryoconite on an alpine glacier. Environ. Microbiol. Rep. 9, 71–78 (2017).

    CAS  PubMed  Google Scholar 

  69. 69.

    Anesio, A. M., Hodson, A. J., Fritz, A., Psenner, R. & Sattler, B. High microbial activity on glaciers: importance to the global carbon cycle. Glob. Chang. Biol. 15, 955–960 (2009).

    Google Scholar 

  70. 70.

    Christner, B. C. et al. A microbial ecosystem beneath the West Antarctic ice sheet. Nature 512, 310–313 (2014).

    CAS  PubMed  Google Scholar 

  71. 71.

    Hultman, J. et al. Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521, 208–212 (2015).

    CAS  PubMed  Google Scholar 

  72. 72.

    Mackelprang, R. et al. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480, 368–371 (2011).

    CAS  PubMed  Google Scholar 

  73. 73.

    Frey, B. et al. Microbial diversity in European alpine permafrost and active layers. FEMS Microbiol. Ecol. 92, fiw018 (2016).

    PubMed  Google Scholar 

  74. 74.

    Fernández, A. B. et al. Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics. FEMS Microbiol. Ecol. 88, 623–635 (2014).

    PubMed  Google Scholar 

  75. 75.

    Ventosa, A. et al. Microbial diversity of hypersaline environments: a metagenomic approach. Curr. Opin. Microbiol. 25, 80–87 (2015).

    CAS  PubMed  Google Scholar 

  76. 76.

    Emerson, J. B. et al. Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia. Archaea 2013, 370871 (2013).

    PubMed  PubMed Central  Google Scholar 

  77. 77.

    Ley, R. E. et al. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl. Environ. Microbiol. 72, 3685–3695 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. 78.

    Harris, J. K. et al. Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME J. 7, 50–60 (2013). This study retrieves an unprecedented number of nearly full length 16S rRNA gene sequences from the microbial mats of the Guerrero Negro hypersaline environment, Mexico, demonstrating them to be among the most diverse, complex and novel microbial ecosystems known.

    PubMed  Google Scholar 

  79. 79.

    Vavourakis, C. D. et al. Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines. Front. Microbiol. 7, 211 (2016).

    PubMed  PubMed Central  Google Scholar 

  80. 80.

    Hamm, J. N. et al. Unexpected host dependency of Antarctic Nanohaloarchaeota. Proc. Natl Acad. Sci. USA. 116, 14661–14670 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. 81.

    Nigro, L. M., Hyde, A. S., MacGregor, B. J. & Teske, A. Phylogeography, salinity adaptations and metabolic potential of the candidate division KB1 bacteria based on a partial single cell genome. Front. Microbiol. 7, 1266 (2016).

    PubMed  PubMed Central  Google Scholar 

  82. 82.

    Vavourakis, C. D. et al. A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. Microbiome 6, 168 (2018).

    PubMed  PubMed Central  Google Scholar 

  83. 83.

    Edwards, K. J., Becker, K. & Colwell, F. The deep, dark energy biosphere: intraterrestrial life on Earth. Annu. Rev. Earth Planet. Sci. 40, 551–568 (2012).

    CAS  Google Scholar 

  84. 84.

    Parkes, R. J. et al. A review of prokaryotic populations and processes in sub-seafloor sediments, including biosphere: geosphere interactions. Mar. Geol. 352, 409–425 (2014).

    CAS  Google Scholar 

  85. 85.

    Starnawski, P. et al. Microbial community assembly and evolution in subseafloor sediment. Proc. Natl Acad. Sci. USA 114, 2940–2945 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. 86.

    Ciobanu, M. C. et al. Microorganisms persist at record depths in the subseafloor of the Canterbury Basin. ISME J. 8, 1370–1380 (2014).

    PubMed  PubMed Central  Google Scholar 

  87. 87.

    Inagaki, F. et al. Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor. Science 349, 420–424 (2015).

    CAS  PubMed  Google Scholar 

  88. 88.

    D’Hondt, S., Pockalny, R., Fulfer, V. M. & Spivack, A. J. Subseafloor life and its biogeochemical impacts. Nat. Commun. 10, 3519 (2019).

    PubMed  PubMed Central  Google Scholar 

  89. 89.

    Petro, C., Starnawski, P., Schramm, A. & Kjeldsen, K. U. Microbial community assembly in marine sediments. Aquat. Microb. Ecol. 79, 177–195 (2017).

    Google Scholar 

  90. 90.

    Teske, A. & Sørensen, K. B. Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J. 2, 3–18 (2008).

    CAS  PubMed  Google Scholar 

  91. 91.

    Orsi, W. D. Ecology and evolution of seafloor and subseafloor microbial communities. Nat. Rev. Microbiol. 16, 671–683 (2018).

    CAS  PubMed  Google Scholar 

  92. 92.

    Sørensen, K. B. & Teske, A. Stratified communities of active Archaea in deep marine subsurface sediments. Appl. Environ. Microbiol. 72, 4596–4603 (2006).

    PubMed  PubMed Central  Google Scholar 

  93. 93.

    Walsh, E. A. et al. Relationship of bacterial richness to organic degradation rate and sediment age in subseafloor sediment. Appl. Environ. Microbiol. 82, 4994–4999 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  94. 94.

    Petro, C. et al. Marine deep biosphere microbial communities assemble in near-surface sediments in Aarhus Bay. Front. Microbiol. 10, 758 (2019).

    PubMed  PubMed Central  Google Scholar 

  95. 95.

    Jorgensen, S. L. et al. Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge. Proc. Natl Acad. Sci. USA 109, E2846–E2855 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  96. 96.

    Edwards, K. J., Wheat, C. G. & Sylvan, J. B. Under the sea: microbial life in volcanic oceanic crust. Nat. Rev. Microbiol. 9, 703–712 (2011).

    CAS  PubMed  Google Scholar 

  97. 97.

    Li, J. et al. Recycling and metabolic flexibility dictate life in the lower oceanic crust. Nature 579, 250–255 (2020). This is a multiple-approach exploration to provide the first insights into the ultralow-biomass microbial assemblages inhabiting the lithified lower oceanic crust.

    CAS  PubMed  Google Scholar 

  98. 98.

    Bar-On, Y. M., Phillips, R. & Milo, R. The biomass distribution on Earth. Proc. Natl Acad. Sci. USA 115, 6506–6511 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. 99.

    Nyyssönen, M. et al. Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield. ISME J. 8, 126–138 (2014).

    PubMed  Google Scholar 

  100. 100.

    Lin, X., Kennedy, D., Fredrickson, J., Bjornstad, B. & Konopka, A. Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site. Environ. Microbiol. 14, 414–425 (2012).

    CAS  PubMed  Google Scholar 

  101. 101.

    Osburn, M. R. et al. Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA. Front. Microbiol. 5, 610 (2014).

    PubMed  PubMed Central  Google Scholar 

  102. 102.

    Magnabosco, C. et al. The biomass and biodiversity of the continental subsurface. Nat. Geosci. 11, 707–717 (2018).

    CAS  Google Scholar 

  103. 103.

    Navarro-Noya, Y. E. et al. Pyrosequencing analysis of the bacterial community in drinking water wells. Microb. Ecol. 66, 19–29 (2013).

    PubMed  Google Scholar 

  104. 104.

    Wrighton, K. C. et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 337, 1661–1665 (2012).

    CAS  PubMed  Google Scholar 

  105. 105.

    Bagnoud, A. et al. Reconstructing a hydrogen driven microbial metabolic network in Opalinus Clay rock. Nat. Commun. 7, 12770 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  106. 106.

    Magnabosco, C. et al. A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust. ISME J. 10, 730–741 (2016).

    CAS  PubMed  Google Scholar 

  107. 107.

    Hernsdorf, A. W. et al. Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. ISME J. 11, 1915–1929 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  108. 108.

    Anantharaman, K. et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat. Commun. 7, 13219 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  109. 109.

    Kantor, R. S. et al. Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. mBio 4, e00708–e00713 (2013).

    PubMed  PubMed Central  Google Scholar 

  110. 110.

    Wrighton, K. C. et al. Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer. ISME J. 8, 1452–1463 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  111. 111.

    Hallberg, K. B., Coupland, K., Kimura, S. & Johnson, D. B. Macroscopic streamer growths in acidic, metal-rich mine waters in north Wales consist of novel and remarkably simple bacterial communities. Appl. Environ. Microbiol. 72, 2022–2030 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. 112.

    Belnap, C. P. et al. Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions. ISME J. 5, 1152–1161 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  113. 113.

    Edwards, K. J. et al. Seasonal variations in microbial populations and environmental conditions in an extreme acid mine drainage environment. Appl. Environ. Microbiol. 65, 3627–3632 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  114. 114.

    Liu, J. et al. Correlating microbial diversity patterns with geochemistry in an extreme and heterogeneous environment of mine tailings. Appl. Environ. Microbiol. 80, 3677–3686 (2014).

    PubMed  PubMed Central  Google Scholar 

  115. 115.

    Golyshina, O. V. et al. ‘ARMAN’ archaea depend on association with euryarchaeal host in culture and in situ. Nat. Commun. 8, 60 (2017).

    PubMed  PubMed Central  Google Scholar 

  116. 116.

    Antony, C. P. et al. Microbiology of Lonar Lake and other soda lakes. ISME J. 7, 468–476 (2013).

    PubMed  Google Scholar 

  117. 117.

    Sorokin, D. Y. et al. Microbial diversity and biogeochemical cycling in soda lakes. Extremophiles 18, 791–809 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  118. 118.

    Reynolds, J. F. et al. Global desertification: building a science for dryland development. Science 316, 847–851 (2007).

    CAS  PubMed  Google Scholar 

  119. 119.

    Maestre, F. T. et al. Increasing aridity reduces soil microbial diversity and abundance in global drylands. Proc. Natl Acad. Sci. USA. 112, 15684–15689 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  120. 120.

    Makhalanyane, T. P. et al. Microbial ecology of hot desert edaphic systems. FEMS Microbiol. Rev. 39, 203–221 (2015).

    CAS  PubMed  Google Scholar 

  121. 121.

    Reinthaler, T. et al. Prokaryotic respiration and production in the meso- and bathypelagic realm of the eastern and western North Atlantic basin. Limnol. Oceanogr. 51, 1262–1273 (2006).

    CAS  Google Scholar 

  122. 122.

    Hewson, I., Steele, J. A., Capone, D. G. & Fuhrman, J. A. Remarkable heterogeneity in meso- and bathypelagic bacterioplankton assemblage composition. Limnol. Oceanogr. 51, 1274–1283 (2006).

    Google Scholar 

  123. 123.

    DeLong, E. F. et al. Community genomics among stratified microbial assemblages in the ocean’s interior. Science 311, 496–503 (2006).

    CAS  PubMed  Google Scholar 

  124. 124.

    Pham, V. D., Konstantinidis, K. T., Palden, T. & DeLong, E. F. Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre. Environ. Microbiol. 10, 2313–2330 (2008).

    CAS  PubMed  Google Scholar 

  125. 125.

    Karner, M. B., DeLong, E. F. & Karl, D. M. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409, 507–510 (2001).

    CAS  PubMed  Google Scholar 

  126. 126.

    Ziegler, S. et al. Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria. ISME J. 7, 1725–1737 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  127. 127.

    Méndez-García, C. et al. Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage. ISME J. 8, 1259–1274 (2014).

    PubMed  PubMed Central  Google Scholar 

  128. 128.

    Klatt, C. G. et al. Temporal metatranscriptomic patterning in phototrophic Chloroflexi inhabiting a microbial mat in a geothermal spring. ISME J. 7, 1775–1789 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  129. 129.

    Klatt, C. G. et al. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Front. Microbiol. 4, 106 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  130. 130.

    Inskeep, W. P. et al. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PLoS ONE 5, e9773 (2010).

    PubMed  PubMed Central  Google Scholar 

  131. 131.

    Swingley, W. D. et al. Coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem. PLoS ONE 7, e38108 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  132. 132.

    Liu, Z. et al. Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat. ISME J. 5, 1279–1290 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  133. 133.

    Woodcroft, B. J. et al. Genome-centric view of carbon processing in thawing permafrost. Nature 560, 49–54 (2018).

    CAS  PubMed  Google Scholar 

  134. 134.

    Ghai, R. et al. New abundant microbial groups in aquatic hypersaline environments. Sci. Rep. 1, 135 (2011).

    PubMed  PubMed Central  Google Scholar 

  135. 135.

    Uritskiy, G. et al. Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert. ISME J. 13, 2737–2749 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  136. 136.

    Uritskiy, G. et al. Cellular life from the three domains and viruses are transcriptionally active in a hypersaline desert community. Environ. Microbiol. 23, 3401–3417 (2021).

    CAS  PubMed  Google Scholar 

  137. 137.

    Herrmann, M. et al. Large fractions of CO2-fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds. Appl. Environ. Microbiol. 81, 2384–2394 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  138. 138.

    Probst, A. J. et al. Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nat. Microbiol. 3, 328–336 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  139. 139.

    Mueller, R. S. et al. Ecological distribution and population physiology defined by proteomics in a natural microbial community. Mol. Syst. Biol. 6, 374 (2010).

    PubMed  PubMed Central  Google Scholar 

  140. 140.

    Chen, L. X. et al. Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings. Environ. Microbiol. 15, 2431–2444 (2013).

    CAS  PubMed  Google Scholar 

  141. 141.

    Mueller, R. S. et al. Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community. Environ. Microbiol. 13, 2279–2292 (2011).

    CAS  PubMed  Google Scholar 

  142. 142.

    Mosier, A. C. et al. Elevated temperature alters proteomic responses of individual organisms within a biofilm community. ISME J. 9, 180–194 (2015).

    CAS  PubMed  Google Scholar 

  143. 143.

    Papke, R. T., Koenig, J. E., Rodriguez-Valera, F. & Doolittle, W. F. Frequent recombination in a saltern population of Halorubrum. Science 306, 1928–1929 (2004).

    CAS  PubMed  Google Scholar 

  144. 144.

    Whitaker, R. J., Grogan, D. W. & Taylor, J. W. Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. Mol. Biol. Evol. 22, 2354–2361 (2005).

    CAS  PubMed  Google Scholar 

  145. 145.

    Naor, A., Lapierre, P., Mevarech, M., Papke, R. T. & Gophna, U. Low species barriers in halophilic archaea and the formation of recombinant hybrids. Curr. Biol. 22, 1444–1448 (2012).

    CAS  PubMed  Google Scholar 

  146. 146.

    Reno, M. L., Held, N. L., Fields, C. J., Burke, P. V. & Whitaker, R. J. Biogeography of the Sulfolobus islandicus pan-genome. Proc. Natl Acad. Sci. USA 106, 8605–8610 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  147. 147.

    Mongodin, E. F. et al. The genome of Salinibacter Ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc. Natl Acad. Sci. USA 102, 18147–18152 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  148. 148.

    Nelson-Sathi, S. et al. Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proc. Natl Acad. Sci. USA 109, 20537–20542 (2012). Comparative genomics provides evidence that massive amounts of gene influx from bacterial sources may have led to the drastic change in lifestyle in the extremely salt tolerant Haloarchaea.

    CAS  PubMed  PubMed Central  Google Scholar 

  149. 149.

    Wolf, Y. I., Makarova, K. S., Yutin, N. & Koonin, E. V. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol. Direct 7, 46 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  150. 150.

    Nelson-Sathi, S. et al. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517, 77–80 (2015).

    CAS  PubMed  Google Scholar 

  151. 151.

    Simmons, S. L. et al. Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol. 6, e177 (2008).

    PubMed  PubMed Central  Google Scholar 

  152. 152.

    Lo, I. et al. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446, 537–541 (2007).

    CAS  PubMed  Google Scholar 

  153. 153.

    Denef, V. J. et al. Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environ. Microbiol. 11, 313–325 (2009).

    CAS  PubMed  Google Scholar 

  154. 154.

    Denef, V. J. et al. Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc. Natl Acad. Sci. USA 107, 2383–2390 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  155. 155.

    Denef, V. J. & Banfield, J. F. In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids. Science 336, 462–466 (2012). This study provides a time-series population metagenomic analysis of microorganisms in exceptionally low diversity AMD biofilms, allowing for the first time measurement of evolutionary rates for wild populations.

    CAS  PubMed  Google Scholar 

  156. 156.

    Brochier-Armanet, C., Boussau, B., Gribaldo, S. & Forterre, P. Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat. Rev. Microbiol. 6, 245–252 (2008).

    CAS  PubMed  Google Scholar 

  157. 157.

    Kelly, S., Wickstead, B. & Gull, K. Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes. Proc. Biol. Sci. 278, 1009–1018 (2011).

    CAS  PubMed  Google Scholar 

  158. 158.

    Sorokin, D. Y. et al. Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis. Nat. Microbiol. 2, 17081 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  159. 159.

    Baker, B. J. et al. Diversity, ecology and evolution of archaea. Nat. Microbiol. 5, 887–900 (2020).

    CAS  PubMed  Google Scholar 

  160. 160.

    Paul, B. G. et al. Targeted diversity generation by intraterrestrial archaea and archaeal viruses. Nat. Commun. 6, 6585 (2015).

    CAS  PubMed  Google Scholar 

  161. 161.

    Paul, B. G. et al. Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea. Nat. Microbiol. 2, 17045 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  162. 162.

    Burstein, D. et al. New CRISPR-Cas systems from uncultivated microbes. Nature 542, 237–241 (2017).

    CAS  PubMed  Google Scholar 

  163. 163.

    Anderson, R. E. et al. Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents. Nat. Commun. 8, 1114 (2017).

    PubMed  PubMed Central  Google Scholar 

  164. 164.

    Brazelton, W. J. & Baross, J. A. Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm. ISME J. 3, 1420–1424 (2009).

    CAS  PubMed  Google Scholar 

  165. 165.

    Jansson, J. K. & Taş, N. The microbial ecology of permafrost. Nat. Rev. Microbiol. 12, 414–425 (2014).

    CAS  PubMed  Google Scholar 

  166. 166.

    Kuang, J. et al. Predicting taxonomic and functional structure of microbial communities in acid mine drainage. ISME J. 10, 1527–1539 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  167. 167.

    Clark, D. R. et al. Biogeography at the limits of life: do extremophilic microbial communities show biogeographical regionalization? Glob. Ecol. Biogeogr. 26, 1435–1446 (2017).

    Google Scholar 

  168. 168.

    Atanasova, N. S., Roine, E., Oren, A., Bamford, D. H. & Oksanen, H. M. Global network of specific virus-host interactions in hypersaline environments. Environ. Microbiol. 14, 426–440 (2012).

    CAS  PubMed  Google Scholar 

  169. 169.

    Wilkins, D. et al. Key microbial drivers in Antarctic aquatic environments. FEMS Microbiol. Rev. 37, 303–335 (2013).

    CAS  PubMed  Google Scholar 

  170. 170.

    Cavicchioli, R. Microbial ecology of Antarctic aquatic systems. Nat. Rev. Microbiol. 13, 691–706 (2015).

    CAS  PubMed  Google Scholar 

  171. 171.

    López-Bueno, A. et al. High diversity of the viral community from an Antarctic lake. Science 326, 858–861 (2009).

    PubMed  Google Scholar 

  172. 172.

    Aguirre de Cárcer, D., López-Bueno, A., Pearce, D. A. & Alcamí, A. Biodiversity and distribution of polar freshwater DNA viruses. Sci. Adv. 1, e1400127 (2015).

    PubMed  PubMed Central  Google Scholar 

  173. 173.

    Yau, S. et al. Virophage control of Antarctic algal host–virus dynamics. Proc. Natl Acad. Sci. USA 108, 6163–6168 (2011). This is the first study to reveal the important ecological roles of virophages and their regulation of host–virus interactions.

    CAS  PubMed  PubMed Central  Google Scholar 

  174. 174.

    Al-Shayeb, B. et al. Clades of huge phages from across Earth’s ecosystems. Nature 578, 425–431 (2020). Analysis of massive metagenomic datasets revealed clades of huge phages from diverse habitats, including extreme environments.

    CAS  PubMed  PubMed Central  Google Scholar 

  175. 175.

    Tschitschko, B. et al. Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation. ISME J. 9, 2094–2107 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  176. 176.

    Mosier, A. C. et al. Fungi contribute critical but spatially varying roles in nitrogen and carbon cycling in acid mine drainage. Front. Microbiol. 7, 238 (2016).

    PubMed  PubMed Central  Google Scholar 

  177. 177.

    Quemener, M. et al. Meta-omics highlights the diversity, activity and adaptations of fungi in deep oceanic crust. Environ. Microbiol. 22, 3950–3967 (2020).

    CAS  PubMed  Google Scholar 

  178. 178.

    Fredrickson, J. K. Ecological communities by design. Science 348, 1425–1427 (2015).

    CAS  PubMed  Google Scholar 

  179. 179.

    Fuhrman, J. A. et al. Annually reoccurring bacterial communities are predictable from ocean conditions. Proc. Natl Acad. Sci. USA 103, 13104–13109 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  180. 180.

    Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015).

    PubMed  Google Scholar 

  181. 181.

    Lozupone, C. A. & Knight, R. Global patterns in bacterial diversity. Proc. Natl Acad. Sci. USA 104, 11436–11440 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  182. 182.

    Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl Acad. Sci. USA 103, 626–631 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  183. 183.

    López-Pérez, M., Haro-Moreno, J. M., Coutinho, F. H., Martinez-Garcia, M. & Rodriguez-Valera, F. The evolutionary success of the marine bacterium SAR11 analyzed through a metagenomic perspective. mSystems 5, e00605-20 (2020).

    PubMed  PubMed Central  Google Scholar 

  184. 184.

    Altshuler, I., Goordial, J. & Whyte, L. G. in Psychrophiles: From Biodiversity to Biotechnology (ed. Margesin, R.) 153–180 (Springer International Publishing, 2017).

  185. 185.

    Huang, L. N., Kuang, J. L. & Shu, W. S. Microbial ecology and evolution in the acid mine drainage model system. Trends Microbiol. 24, 581–593 (2016).

    CAS  PubMed  Google Scholar 

  186. 186.

    Klatt, C. G. et al. Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential. ISME J. 5, 1262–1278 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  187. 187.

    Menzel, P. et al. Comparative metagenomics of eight geographically remote terrestrial hot springs. Microb. Ecol. 70, 411–424 (2015).

    PubMed  Google Scholar 

  188. 188.

    Stokke, R. et al. Functional interactions among filamentous Epsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm. Environ. Microbiol. 17, 4063–4077 (2015).

    CAS  PubMed  Google Scholar 

  189. 189.

    Zeng, Y. et al. Potential rhodopsin- and bacteriochlorophyll-based dual phototrophy in a High Arctic glacier. mBio 11, e02641–20 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  190. 190.

    Simon, C., Wiezer, A., Strittmatter, A. W. & Daniel, R. Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome. Appl. Environ. Microbiol. 75, 7519–7526 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  191. 191.

    Lipson, D. A. et al. Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile. PLoS ONE 8, e64659 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  192. 192.

    Podell, S. et al. Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS ONE 8, e61692 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  193. 193.

    DeMaere, M. Z. et al. High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Proc. Natl Acad. Sci. USA. 110, 16939–16944 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  194. 194.

    Smith, A. R. et al. Carbon fixation and energy metabolisms of a subseafloor olivine biofilm. ISME J. 13, 1737–1749 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  195. 195.

    Zhao, R. et al. Geochemical transition zone powering microbial growth in subsurface sediments. Proc. Natl Acad. Sci. USA. 117, 32617–32626 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  196. 196.

    Luo, Z. H. et al. Diversity and genomic characterization of a novel Parvarchaeota family in acid mine drainage sediments. Front. Microbiol. 11, 612257 (2020).

    PubMed  PubMed Central  Google Scholar 

  197. 197.

    Lewin, A., Wentzel, A. & Valla, S. Metagenomics of microbial life in extreme temperature environments. Curr. Opin. Biotechnol. 24, 516–525 (2013).

    CAS  PubMed  Google Scholar 

  198. 198.

    Schlesinger, M. J. Heat-shock proteins. J. Biol. Chem. 265, 12111–12114 (1990).

    CAS  PubMed  Google Scholar 

  199. 199.

    D’Amico, S., Collins, T., Marx, J.-C., Feller, G. & Gerday, C. Psychrophilic microorganisms: challenges for life. EMBO Rep. 7, 385–389 (2006).

    PubMed  PubMed Central  Google Scholar 

  200. 200.

    Bakermans, C., Bergholz, P. W., Ayala-del-Río, H. & Tiedje, J. in Permafrost Soils (ed. Margesin, R.) 159–168 (Springer, 2009).

  201. 201.

    Gunde-Cimerman, N., Plemenitaš, A. & Oren, A. Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations. FEMS Microbiol. Rev. 42, 353–375 (2018).

    CAS  PubMed  Google Scholar 

  202. 202.

    Baker-Austin, C. & Dopson, M. Life in acid: pH homeostasis in acidophiles. Trends Microbiol. 15, 165–171 (2007).

    CAS  PubMed  Google Scholar 

  203. 203.

    Dopson, M., Baker-Austin, C., Koppineedi, P. R. & Bond, P. L. Growth in sulfidic mineral environments: metal resistance mechanisms in acidophilic micro-organisms. Microbiology 149, 1959–1970 (2003).

    CAS  PubMed  Google Scholar 

  204. 204.

    Dopson, M., Ossandon, F. J., Lövgren, L. & Holmes, D. S. Metal resistance or tolerance? Acidophiles confront high metal loads via both abiotic and biotic mechanisms. Front. Microbiol. 5, 157 (2014).

    PubMed  PubMed Central  Google Scholar 

  205. 205.

    Allen, E. E. & Banfield, J. F. Community genomics in microbial ecology and evolution. Nat. Rev. Microbiol. 3, 489–498 (2005).

    CAS  PubMed  Google Scholar 

  206. 206.

    Sakowski, E. et al. Current state of and future opportunities for prediction in microbiome research: report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019. mSystems 4, e00392–19 (2019).

    PubMed  PubMed Central  Google Scholar 

  207. 207.

    Lima-Mendez, G. et al. Determinants of community structure in the global plankton interactome. Science 348, 1262073 (2015).

    PubMed  Google Scholar 

Download references

Acknowledgements

Support was received from the National Natural Science Foundation of China (grant no. 41830318 to W.-S.S. and grant nos 31570500 and 31870111 to L.-N.H.). The contributions of Z. Luo and other students and postdoctoral scientists in the authors’ team are gratefully acknowledged. The authors thank Z. Hua and Z. Luo for helpful discussions, and K. Anantharaman and J. F. Banfield for providing metagenome-derived taxon abundance data for the analysis of the microbial composition of the Colorado River aquifer communities (Fig. 2).

Author information

Affiliations

Authors

Contributions

The authors contributed equally to all aspects of the article.

Corresponding authors

Correspondence to Wen-Sheng Shu or Li-Nan Huang.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information

Nature Reviews Microbiology thanks J. DiRuggiero and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Glossary

16S ribosomal RNA (rRNA) gene clone library analysis

The cloning and Sanger sequencing of 16S ribosomal RNA (rRNA) genes PCR-amplified from total DNA extracted from an environmental sample, resolving the composition and diversity of the microbial community.

Metagenomic analysis

The sequencing and genomic analysis of total community DNA directly recovered from the environment.

16S rRNA amplicon sequencing

High-throughput (next-generation) sequencing of 16S ribosomal RNA (rRNA) gene fragments PCR-amplified from total community genomic DNAs, allowing sampling and analysis of microbial diversity on an unprecedented scale.

Thermophily

The ability of a microorganism (that is, a thermophile) to grow at a high temperature.

Whole-genome shotgun sequencing

A process in which the genomic DNA from a pure culture is randomly fragmented and sequenced, and the sequences obtained are then assembled through bioinformatics to a whole microbial genome.

Genome bins

The population genomes (also called ‘metagenome-assembled genomes’) assembled from metagenomic sequence data based on G+C content, k-mer frequency and/or read coverage.

Circumneutral

Near neutral.

Cryoconite holes

Small holes on the surface of a glacier. The deposited cryoconite (windblown dust comprising both mineral and biological material, including microorganisms) absorbs solar radiation, melting the snow and ice beneath.

Ectosymbiotic lifestyle

A form of symbiotic behaviour in which an ectosymbiont lives on the surface of its host.

Thalassohaline salt lake

Hypersaline lake of marine origin where salt ratios are similar to those of seawater and pH is near neutral to slightly alkaline.

Biomining

The application of microorganisms to recover metals from ores or mining waste.

Tailings

The finely ground residues from mined ores after extraction of valuable minerals and metals.

Evapotranspiration

The combined loss of water from the land both by evaporation from the soil surface and by transpiration from the plants growing thereon.

Diel cycle

A 24-h period comprising a day and a consecutive night, or a regular day–night cycle of physiology or behaviour of an organism.

Multilocus sequence typing

A molecular typing technique in which multiple targeted housekeeping genes (loci) are sequenced, often partially.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Shu, WS., Huang, LN. Microbial diversity in extreme environments. Nat Rev Microbiol (2021). https://doi.org/10.1038/s41579-021-00648-y

Download citation

Search

Quick links