Rothschild, L. J. & Mancinelli, R. L. Life in extreme environments. Nature 409, 1092–1101 (2001).
Google Scholar
Schmid, A. K., Allers, T. & DiRuggiero, J. Snapshot: microbial extremophiles. Cell 180, 818–818.e1 (2020).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Oren, A. Halophilic microbial communities and their environments. Curr. Opin. Microbiol. 33, 119–124 (2015).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Huber, J. A. et al. Microbial population structures in the deep marine biosphere. Science 318, 97–100 (2007).
Google Scholar
Kuang, J. L. et al. Contemporary environmental variation determines microbial diversity patterns in acid mine drainage. ISME J. 7, 1038–1050 (2013).
Google Scholar
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.
Google Scholar
Podell, S. et al. Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME J. 8, 979–990 (2014).
Google Scholar
Chen, L. X. et al. Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage. ISME J. 9, 1579–1592 (2015).
Google Scholar
Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013).
Google Scholar
Brown, C. T. et al. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523, 208–211 (2015).
Google Scholar
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.
Google Scholar
Sharp, C. E. et al. Humboldt’s spa: microbial diversity is controlled by temperature in geothermal environments. ISME J. 8, 1166–1174 (2014).
Google Scholar
Hedlund, B. P. et al. Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’. Curr. Opin. Microbiol. 25, 136–145 (2015).
Google Scholar
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).
Google Scholar
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.
Google Scholar
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).
Google Scholar
Chen, L. X. et al. Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota. ISME J. 12, 756–775 (2018).
Google Scholar
Baker, B. J. et al. Enigmatic, ultrasmall, uncultivated Archaea. Proc. Natl Acad. Sci. USA 107, 8806–8811 (2010).
Google Scholar
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).
Google Scholar
Brock, T. D. Life at high temperatures. Science 158, 1012–1019 (1967).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Ward, D. M. et al. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345, 63–65 (1990).
Google Scholar
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).
Google Scholar
Ward, L. et al. Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring. ISME J. 11, 1158–1167 (2017).
Google Scholar
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).
Google Scholar
Takai, K. & Yoshihiko, S. A molecular view of archaeal diversity in marine and terrestrial hot water environments. FEMS Microbiol. Ecol. 28, 177–188 (1999).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Hua, Z. S. et al. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat. Commun. 9, 2832 (2018).
Google Scholar
Takami, H. et al. A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem. PLoS ONE 7, e30559 (2012).
Google Scholar
Colman, D. R. et al. Novel, deep-branching heterotrophic bacterial populations recovered from thermal spring metagenomes. Front. Microbiol. 7, 304 (2016).
Google Scholar
Nobu, M. et al. Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics. ISME J. 10, 273–286 (2016).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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.
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Dick, G. J. et al. The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally. Nat. Rev. Microbiol. 17, 271–283 (2019).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Takai, K., Komatsu, T., Inagaki, F. & Horikoshi, K. Distribution of archaea in a black smoker chimney structure. Appl. Environ. Microbiol. 67, 3618–3629 (2001).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Huber, H. et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417, 63–67 (2002).
Google Scholar
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).
Google Scholar
Casanueva, A. et al. Nanoarchaeal 16S rRNA gene sequences are widely dispersed in hyperthermophilic and mesophilic halophilic environments. Extremophiles 12, 651–656 (2008).
Google Scholar
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.
Google Scholar
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.
Google Scholar
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).
Google Scholar
Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017).
Google Scholar
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.
Google Scholar
Margesin, R. & Collins, T. Microbial ecology of the cryosphere (glacial and permafrost habitats): current knowledge. Appl. Microbiol. Biotechnol. 103, 2537–2549 (2019).
Google Scholar
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).
Google Scholar
Hoham, R. W. & Duval, B. in Snow Ecology (eds Jones, H. et al.) 168–228 (Cambridge Univ. Press, 2001).
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).
Google Scholar
Jungblut, A. D., Lovejoy, C. & Vincent, W. F. Global distribution of cyanobacterial ecotypes in the cold biosphere. ISME J. 4, 191–202 (2010).
Google Scholar
Franzetti, A. et al. Temporal variability of bacterial communities in cryoconite on an alpine glacier. Environ. Microbiol. Rep. 9, 71–78 (2017).
Google Scholar
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).
Christner, B. C. et al. A microbial ecosystem beneath the West Antarctic ice sheet. Nature 512, 310–313 (2014).
Google Scholar
Hultman, J. et al. Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521, 208–212 (2015).
Google Scholar
Mackelprang, R. et al. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480, 368–371 (2011).
Google Scholar
Frey, B. et al. Microbial diversity in European alpine permafrost and active layers. FEMS Microbiol. Ecol. 92, fiw018 (2016).
Google Scholar
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).
Google Scholar
Ventosa, A. et al. Microbial diversity of hypersaline environments: a metagenomic approach. Curr. Opin. Microbiol. 25, 80–87 (2015).
Google Scholar
Emerson, J. B. et al. Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia. Archaea 2013, 370871 (2013).
Google Scholar
Ley, R. E. et al. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl. Environ. Microbiol. 72, 3685–3695 (2006).
Google Scholar
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.
Google Scholar
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).
Google Scholar
Hamm, J. N. et al. Unexpected host dependency of Antarctic Nanohaloarchaeota. Proc. Natl Acad. Sci. USA. 116, 14661–14670 (2019).
Google Scholar
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).
Google Scholar
Vavourakis, C. D. et al. A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. Microbiome 6, 168 (2018).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Starnawski, P. et al. Microbial community assembly and evolution in subseafloor sediment. Proc. Natl Acad. Sci. USA 114, 2940–2945 (2017).
Google Scholar
Ciobanu, M. C. et al. Microorganisms persist at record depths in the subseafloor of the Canterbury Basin. ISME J. 8, 1370–1380 (2014).
Google Scholar
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).
Google Scholar
D’Hondt, S., Pockalny, R., Fulfer, V. M. & Spivack, A. J. Subseafloor life and its biogeochemical impacts. Nat. Commun. 10, 3519 (2019).
Google Scholar
Petro, C., Starnawski, P., Schramm, A. & Kjeldsen, K. U. Microbial community assembly in marine sediments. Aquat. Microb. Ecol. 79, 177–195 (2017).
Teske, A. & Sørensen, K. B. Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J. 2, 3–18 (2008).
Google Scholar
Orsi, W. D. Ecology and evolution of seafloor and subseafloor microbial communities. Nat. Rev. Microbiol. 16, 671–683 (2018).
Google Scholar
Sørensen, K. B. & Teske, A. Stratified communities of active Archaea in deep marine subsurface sediments. Appl. Environ. Microbiol. 72, 4596–4603 (2006).
Google Scholar
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).
Google Scholar
Petro, C. et al. Marine deep biosphere microbial communities assemble in near-surface sediments in Aarhus Bay. Front. Microbiol. 10, 758 (2019).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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.
Google Scholar
Bar-On, Y. M., Phillips, R. & Milo, R. The biomass distribution on Earth. Proc. Natl Acad. Sci. USA 115, 6506–6511 (2018).
Google Scholar
Nyyssönen, M. et al. Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield. ISME J. 8, 126–138 (2014).
Google Scholar
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).
Google Scholar
Osburn, M. R. et al. Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA. Front. Microbiol. 5, 610 (2014).
Google Scholar
Magnabosco, C. et al. The biomass and biodiversity of the continental subsurface. Nat. Geosci. 11, 707–717 (2018).
Google Scholar
Navarro-Noya, Y. E. et al. Pyrosequencing analysis of the bacterial community in drinking water wells. Microb. Ecol. 66, 19–29 (2013).
Google Scholar
Wrighton, K. C. et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 337, 1661–1665 (2012).
Google Scholar
Bagnoud, A. et al. Reconstructing a hydrogen driven microbial metabolic network in Opalinus Clay rock. Nat. Commun. 7, 12770 (2016).
Google Scholar
Magnabosco, C. et al. A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust. ISME J. 10, 730–741 (2016).
Google Scholar
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).
Google Scholar
Anantharaman, K. et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat. Commun. 7, 13219 (2016).
Google Scholar
Kantor, R. S. et al. Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. mBio 4, e00708–e00713 (2013).
Google Scholar
Wrighton, K. C. et al. Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer. ISME J. 8, 1452–1463 (2014).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Golyshina, O. V. et al. ‘ARMAN’ archaea depend on association with euryarchaeal host in culture and in situ. Nat. Commun. 8, 60 (2017).
Google Scholar
Antony, C. P. et al. Microbiology of Lonar Lake and other soda lakes. ISME J. 7, 468–476 (2013).
Google Scholar
Sorokin, D. Y. et al. Microbial diversity and biogeochemical cycling in soda lakes. Extremophiles 18, 791–809 (2014).
Google Scholar
Reynolds, J. F. et al. Global desertification: building a science for dryland development. Science 316, 847–851 (2007).
Google Scholar
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).
Google Scholar
Makhalanyane, T. P. et al. Microbial ecology of hot desert edaphic systems. FEMS Microbiol. Rev. 39, 203–221 (2015).
Google Scholar
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).
Google Scholar
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).
DeLong, E. F. et al. Community genomics among stratified microbial assemblages in the ocean’s interior. Science 311, 496–503 (2006).
Google Scholar
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).
Google Scholar
Karner, M. B., DeLong, E. F. & Karl, D. M. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409, 507–510 (2001).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Klatt, C. G. et al. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Front. Microbiol. 4, 106 (2013).
Google Scholar
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).
Google Scholar
Swingley, W. D. et al. Coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem. PLoS ONE 7, e38108 (2012).
Google Scholar
Liu, Z. et al. Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat. ISME J. 5, 1279–1290 (2011).
Google Scholar
Woodcroft, B. J. et al. Genome-centric view of carbon processing in thawing permafrost. Nature 560, 49–54 (2018).
Google Scholar
Ghai, R. et al. New abundant microbial groups in aquatic hypersaline environments. Sci. Rep. 1, 135 (2011).
Google Scholar
Uritskiy, G. et al. Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert. ISME J. 13, 2737–2749 (2019).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Mueller, R. S. et al. Ecological distribution and population physiology defined by proteomics in a natural microbial community. Mol. Syst. Biol. 6, 374 (2010).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Mosier, A. C. et al. Elevated temperature alters proteomic responses of individual organisms within a biofilm community. ISME J. 9, 180–194 (2015).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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.
Google Scholar
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).
Google Scholar
Nelson-Sathi, S. et al. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517, 77–80 (2015).
Google Scholar
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).
Google Scholar
Lo, I. et al. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446, 537–541 (2007).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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.
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Baker, B. J. et al. Diversity, ecology and evolution of archaea. Nat. Microbiol. 5, 887–900 (2020).
Google Scholar
Paul, B. G. et al. Targeted diversity generation by intraterrestrial archaea and archaeal viruses. Nat. Commun. 6, 6585 (2015).
Google Scholar
Paul, B. G. et al. Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea. Nat. Microbiol. 2, 17045 (2017).
Google Scholar
Burstein, D. et al. New CRISPR-Cas systems from uncultivated microbes. Nature 542, 237–241 (2017).
Google Scholar
Anderson, R. E. et al. Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents. Nat. Commun. 8, 1114 (2017).
Google Scholar
Brazelton, W. J. & Baross, J. A. Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm. ISME J. 3, 1420–1424 (2009).
Google Scholar
Jansson, J. K. & Taş, N. The microbial ecology of permafrost. Nat. Rev. Microbiol. 12, 414–425 (2014).
Google Scholar
Kuang, J. et al. Predicting taxonomic and functional structure of microbial communities in acid mine drainage. ISME J. 10, 1527–1539 (2016).
Google Scholar
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).
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).
Google Scholar
Wilkins, D. et al. Key microbial drivers in Antarctic aquatic environments. FEMS Microbiol. Rev. 37, 303–335 (2013).
Google Scholar
Cavicchioli, R. Microbial ecology of Antarctic aquatic systems. Nat. Rev. Microbiol. 13, 691–706 (2015).
Google Scholar
López-Bueno, A. et al. High diversity of the viral community from an Antarctic lake. Science 326, 858–861 (2009).
Google Scholar
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).
Google Scholar
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.
Google Scholar
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.
Google Scholar
Tschitschko, B. et al. Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation. ISME J. 9, 2094–2107 (2015).
Google Scholar
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).
Google Scholar
Quemener, M. et al. Meta-omics highlights the diversity, activity and adaptations of fungi in deep oceanic crust. Environ. Microbiol. 22, 3950–3967 (2020).
Google Scholar
Fredrickson, J. K. Ecological communities by design. Science 348, 1425–1427 (2015).
Google Scholar
Fuhrman, J. A. et al. Annually reoccurring bacterial communities are predictable from ocean conditions. Proc. Natl Acad. Sci. USA 103, 13104–13109 (2006).
Google Scholar
Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015).
Google Scholar
Lozupone, C. A. & Knight, R. Global patterns in bacterial diversity. Proc. Natl Acad. Sci. USA 104, 11436–11440 (2007).
Google Scholar
Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl Acad. Sci. USA 103, 626–631 (2006).
Google Scholar
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).
Google Scholar
Altshuler, I., Goordial, J. & Whyte, L. G. in Psychrophiles: From Biodiversity to Biotechnology (ed. Margesin, R.) 153–180 (Springer International Publishing, 2017).
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).
Google Scholar
Klatt, C. G. et al. Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential. ISME J. 5, 1262–1278 (2011).
Google Scholar
Menzel, P. et al. Comparative metagenomics of eight geographically remote terrestrial hot springs. Microb. Ecol. 70, 411–424 (2015).
Google Scholar
Stokke, R. et al. Functional interactions among filamentous Epsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm. Environ. Microbiol. 17, 4063–4077 (2015).
Google Scholar
Zeng, Y. et al. Potential rhodopsin- and bacteriochlorophyll-based dual phototrophy in a High Arctic glacier. mBio 11, e02641–20 (2020).
Google Scholar
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).
Google Scholar
Lipson, D. A. et al. Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile. PLoS ONE 8, e64659 (2013).
Google Scholar
Podell, S. et al. Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS ONE 8, e61692 (2013).
Google Scholar
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).
Google Scholar
Smith, A. R. et al. Carbon fixation and energy metabolisms of a subseafloor olivine biofilm. ISME J. 13, 1737–1749 (2019).
Google Scholar
Zhao, R. et al. Geochemical transition zone powering microbial growth in subsurface sediments. Proc. Natl Acad. Sci. USA. 117, 32617–32626 (2020).
Google Scholar
Luo, Z. H. et al. Diversity and genomic characterization of a novel Parvarchaeota family in acid mine drainage sediments. Front. Microbiol. 11, 612257 (2020).
Google Scholar
Lewin, A., Wentzel, A. & Valla, S. Metagenomics of microbial life in extreme temperature environments. Curr. Opin. Biotechnol. 24, 516–525 (2013).
Google Scholar
Schlesinger, M. J. Heat-shock proteins. J. Biol. Chem. 265, 12111–12114 (1990).
Google Scholar
D’Amico, S., Collins, T., Marx, J.-C., Feller, G. & Gerday, C. Psychrophilic microorganisms: challenges for life. EMBO Rep. 7, 385–389 (2006).
Google Scholar
Bakermans, C., Bergholz, P. W., Ayala-del-Río, H. & Tiedje, J. in Permafrost Soils (ed. Margesin, R.) 159–168 (Springer, 2009).
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).
Google Scholar
Baker-Austin, C. & Dopson, M. Life in acid: pH homeostasis in acidophiles. Trends Microbiol. 15, 165–171 (2007).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Allen, E. E. & Banfield, J. F. Community genomics in microbial ecology and evolution. Nat. Rev. Microbiol. 3, 489–498 (2005).
Google Scholar
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).
Google Scholar
Lima-Mendez, G. et al. Determinants of community structure in the global plankton interactome. Science 348, 1262073 (2015).
Google Scholar
Source: Ecology - nature.com