Advertisement

Evolutionary Success of Prokaryotes

  • Jean-Claude BertrandEmail author
  • Patricia Bonin
  • Bernard Ollivier
  • Karine Alain
  • Anne Godfroy
  • Nathalie Pradel
  • Philippe Normand
Chapter

Abstract

How can the evolutionary success of prokaryotes be explained? How did they manage to survive conditions that have fluctuated, with drastic events over 3.5 billion years? Which significant metabolisms and mechanisms have appeared over the course of evolution that have permitted them to survive the most inhospitable conditions from the physicochemical point of view? In a “Red Queen Race,” prokaryotes have always run sufficiently fast to adapt to constraints imposed by the environment and the other living species with which they have established interactions. If the criterion retained to define the level of evolution of an organism is its capacity to survive and to yield the largest number of offsprings, prokaryotes must be considered highly evolved organisms.

Keywords

Artificial minimal cell Biogeochemical cycles Carbon cycle Dormancy Extremophilic microorganisms Horizontal gene transfers Hypermutators Minimal bacterial gene set Mutations Nitrogen cycle Spores Starvation Storage of organic and inorganic compounds Theories of evolution Ultramicrobacteria Universal tree of life Viable but nonculturable state Viable prokaryotes in geological formations 

References

  1. Aanderud Z, Jones S, Fierer N, Lennon J (2015) Resuscitation of the rare biosphere contributes to pulses of ecosystem activity. Front Microbiol 6:24PubMedPubMedCentralCrossRefGoogle Scholar
  2. Abe A, Ohashi E, Ren H, Hayashi T, Endo H (2007) Isolation and characterization of a cold-induced nonculturable suppression mutant of Vibrio vulnificus. Microbiol Res 162:130–138PubMedCrossRefGoogle Scholar
  3. Abe F (2013) Dynamic structural changes in microbial membranes in response to high hydrostatic pressure analyzed using time-resolved fluorescence anisotropy measurement. Biophy Chemistry 183:3–8CrossRefGoogle Scholar
  4. Aguilera A (2013) Eukaryotic organisms in extreme acidic environments, the Rio Tinto case. Life (Basel) 3:363–374Google Scholar
  5. Aigle A, Bonin P, Iobbi-Nivol C, Méjean V, Michotey V (2017) Physiological and transcriptional approaches reveal connection between nitrogen and manganese cycles in Shewanella algae C6G3. Sci Rep 7:44725PubMedPubMedCentralCrossRefGoogle Scholar
  6. Al-Hinai M, Jones S, Papoutsakis E (2015) The Clostridium sporulation programs: diversity and preservation of endospore differentiation. Microbiol Mol Biol Rev 79:19–37PubMedPubMedCentralCrossRefGoogle Scholar
  7. Alazard D, Joseph M, Battaglia-Brunet F, Cayol J, Ollivier B (2010) Desulfosporosinus acidiphilus sp. nov.: a moderately acidophilic sulfate-reducing bacterium isolated from acid mining drainage sediments : New taxa: Firmicutes (Class Clostridia, Order Clostridiales, Family Peptococcaceae). Extremophiles 14:305–312PubMedCrossRefGoogle Scholar
  8. Allen E, Bartlett D (2004) Piezophiles: microbial adaptation to the deep-sea environment. In: Gerday C, Glansdorff N (eds) Extremophiles, vol 3. Eolss Publishers Co Ltd., Oxford, pp 231–255Google Scholar
  9. Alvarez C, Alvarez R, Grigera M, Lavado R (1998) Associations between organic matter fractions and the active soil microbial biomass. Soil Biol Biochem 30:767–773CrossRefGoogle Scholar
  10. Amato P, Ménager M, Sancelme M, Laj P, Mailhot G, Delort A-M (2005) Microbial population in cloud water at the Puy de Dôme: implications for the chemistry of clouds. Atmos Environ 39:4143–4153CrossRefGoogle Scholar
  11. Amato P, Demeer F, Melaouhi A, Fontanella S, Martin-Biesse A-S, Sancelme M, Laj P, Delort A-M (2007a) A fate for organic acids, formaldehyde and methanol in cloud water: their biotransformation by microorganisms. Atmos Chem Phys 7:4159–4169CrossRefGoogle Scholar
  12. Amato P, Parazols M, Sancelme M, Laj P, Mailhot G, Delort AM (2007b) Microorganisms isolated from the water phase of tropospheric clouds at the Puy de Dome: major groups and growth abilities at low temperatures. FEMS Microbiol Ecol 59:242–254PubMedCrossRefGoogle Scholar
  13. Amato P, Parazols M, Sancelme M, Mailhot G, Laj P, Delort A-M (2007c) An important oceanic source of micro-organisms for cloud water at the puy de Dôme (France). Atmos Environ 41:8253–8263CrossRefGoogle Scholar
  14. Amel B-N, Amine B, Amina B (2008) Survival of Vibrio fluvialis in seawater under starvation conditions. Microbiol Res 163:323–328PubMedCrossRefGoogle Scholar
  15. Amrani A, Bergon A, Holota H, Tamburini C, Garel M, Ollivier B, Imbert J, Dolla A, Pradel N (2014) Transcriptomics reveal several gene expression patterns in the piezophile Desulfovibrio hydrothermalis in response to hydrostatic pressure. PLoS ONE 9:e106831PubMedPubMedCentralCrossRefGoogle Scholar
  16. Amrani A, van Helden J, Bergon A, Aouane A, Ben Hania W, Tamburini C, Loriod B, Ollivier B, Imbert J, Ollivier B et al (2016) Deciphering the adaptation strategies of Desulfovibrio piezophilus to hydrostatic pressure through metabolic and transcriptional analyses. Environ Microbiol Rep 8:520–526.  https://doi.org/10.1111/1758-2229.12427 CrossRefPubMedGoogle Scholar
  17. Anderson I, Rodriguez J, Susanti D, Porat I, Reich C, Ulrich L, Elkins J, Mavromatis K, Lykidis A, Kim E et al (2008) Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. J Bacteriol 190:2957–2965PubMedPubMedCentralCrossRefGoogle Scholar
  18. Anderson I et al (2009) The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. BMC Genomics 10:145PubMedPubMedCentralCrossRefGoogle Scholar
  19. Anderson I et al (2010) Complete genome sequence of Methanothermus fervidus type strain (V24ST). Stand Genomic Sci 3:315–324PubMedPubMedCentralCrossRefGoogle Scholar
  20. Angert ER, Clements KD, Pace NR (1993) The largest bacterium. Nature 362:239–241PubMedCrossRefGoogle Scholar
  21. Aono E, Baba T, Ara T, Nishi T, Nakamichi T, Inamoto E, Toyonaga H, Hasegawa M, Takai Y, Okumura Y et al (2010) Complete genome sequence and comparative analysis of Shewanella violacea, a psychrophilic and piezophilic bacterium from deep-sea floor sediments. Mol Biosyst 6:1216–1226PubMedCrossRefGoogle Scholar
  22. Arana I, Seco C, Epelde K, Muela A, Fernández-Astorga A, Barcina I (2004) Relationships between Escherichia coli cells and the surrounding medium during survival processes. Antonie Van Leeuwenhoek 86:189–199PubMedCrossRefGoogle Scholar
  23. Arsene F, Tomoyasu T, Bukau B (2000) The heat shock response of Escherichia coli. Int J Food Microbiol 55:3–9PubMedCrossRefGoogle Scholar
  24. Avery OT, MacLeod CM, McCarty M (1944) Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Induction of transformation by a desoxyribosenucleic acid fraction isolated from pneumococcus type III. J Exp Med 79:137–158PubMedPubMedCentralCrossRefGoogle Scholar
  25. Ayrapetyan M, Oliver JD (2016) The viable non-culturable state and its relevance in food safety. COFS.  https://doi.org/10.1016/j.cofs.2016.1004.1010
  26. Babic A, Lindner A, Vulic M, Stewart E, Radman M (2008) Direct visualization of horizontal gene transfer. Science 319:1533–1536PubMedCrossRefGoogle Scholar
  27. Baharoglu Z, Mazel D (2014) SOS, the formidable strategy of bacteria against aggressions. FEMS Microbiol Rev 38:1126–1145PubMedCrossRefGoogle Scholar
  28. Baker-Austin C, Dopson M (2007) Life in acid: pH homeostasis in acidophiles. Trends Microbiol 15:165–171PubMedCrossRefGoogle Scholar
  29. Baker BJ et al (2010) Enigmatic, ultrasmall, uncultivated Archaea. Proc Natl Acad Sci U S A 107:8806–8811PubMedPubMedCentralCrossRefGoogle Scholar
  30. Bale S, Goodman K, Rochelle P, Marchesi J, Fry J, Weightman A, Parkes R (1997) Desulfovibrio profundus sp. nov., a novel barophilic sulphate-reducing bacterium from deep sediment layers in the Japan Sea. Int J Syst Bacteriol 47:515–521PubMedCrossRefGoogle Scholar
  31. Bapteste E, O’Malley M, Beiko R, Ereshefsky M, Gogarten J, Franklin-Hall L, Lapointe F, Dupré J, Dagan T, Boucher Y et al (2009) Prokaryotic evolution and the tree of life are two different things. Biol Direct 4:34PubMedPubMedCentralCrossRefGoogle Scholar
  32. Barabote RD, Xie G, Leu DH, Normand P, Necsulea A, Daubin V, Medigue C, Adney WS, Xu XC, Lapidus A et al (2009) Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations. Genome Res 19:1033–1043PubMedPubMedCentralCrossRefGoogle Scholar
  33. Bassham JA, Benson AA, Calvin M (1950) The path of carbon in photosynthesis. J Biol Chem 185:781–787PubMedGoogle Scholar
  34. Beal E, House C, Orphan V (2009) Manganese- and iron-dependent marine methane oxidation. Science 325:184–187PubMedCrossRefGoogle Scholar
  35. Ben Aissa F, Postec A, Erauso G, Payri C, Pelletier B, Hamdi M, Fardeau M, Ollivier B (2015) Characterization of Alkaliphilus hydrothermalis sp. nov., a novel alkaliphilic anaerobic bacterium, isolated from a carbonaceous chimney of the Prony hydrothermal field, New Caledonia. Extremophiles 19:183–181PubMedCrossRefGoogle Scholar
  36. Bennett GM, Abbà S, Kube M, Marzachì C (2016) Complete genome sequences of the obligate symbionts “Candidatus Sulcia muelleri” and “Ca. Nasuia deltocephalinicola” from the Pestiferous Leafhopper Macrosteles quadripunctulatus (Hemiptera: Cicadellidae). Genome Announc 4(1):e1604–e1615CrossRefGoogle Scholar
  37. Berg I (2011) Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Appl Environ Microbiol 77:1925–1936PubMedPubMedCentralCrossRefGoogle Scholar
  38. Berg I, Kockelkorn D, Buckel W, Fuchs GA (2007) 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 31:1782–1786CrossRefGoogle Scholar
  39. Berger S, David M, Vogel TM, Simonet P (2015) Involvement of horizontal gene transfer in chlorinated compounds biological degradation: example of the biological degradation of lindane. In: Bertrand J, Caumette P, Lebaron P, Matheron R, Normand P, Sime-Ngando T (eds) Environmental microbiology: fundamentals and applications. Springer, Dordrecht/Heidelberg/New York/London, pp 705–707Google Scholar
  40. Berleman J, Auer M (2013) The role of bacterial outer membrane vesicles for intra- and interspecies delivery. Environ Microbiol 15:347–354PubMedCrossRefGoogle Scholar
  41. Berner RA (2006) GEOCARBSULF: a combined model for Phanerozoic atmospheric O2 and CO2. Geochim Cosmochim Acta 70:5653–5664CrossRefGoogle Scholar
  42. Bernhardt HS, Tate WP (2012) Primordial soup or vinaigrette: did the RNA world evolve at acidic pH? Biol Direct 7:4PubMedPubMedCentralCrossRefGoogle Scholar
  43. Berry AM, Harriott OT, Moreau RA, Osman SF, Benson DR, Jones AD (1993) Hopanoid lipids compose the Frankia vesicle envelope, presumptive barrier of oxygen diffusion to nitrogenase. Proc Natl Acad Sci U S A 90:6091–6094PubMedPubMedCentralCrossRefGoogle Scholar
  44. Bes M, Merrouch M, Joseph M, Quéméneur M, Payri C, Pelletier B, Ollivier B, Fardeau M, Erauso G, Postec A (2015) Acetoanaerobium pronyense sp. nov., an anaerobic alkaliphilic bacterium isolated from a carbonate chimney of the Prony Hydrothermal Field (New Caledonia). Int J Syst Evol Microbiol 65:2574–2580PubMedCrossRefGoogle Scholar
  45. Biddle J, Sylvan J, Brazelton W, Tully B, Edwards K, Moyer C, Heidelberg J, Nelson W (2012) Prospects for the study of evolution in the deep biosphere. Front Microbiol 2:285PubMedPubMedCentralCrossRefGoogle Scholar
  46. Biller SJ, Schubotz F, Roggensack SE, Thompson AW, Summons RE, Chisholm SW (2014) Bacterial vesicles in marine ecosystems. Science 343:183–186PubMedCrossRefGoogle Scholar
  47. Blöchl E, Rachel R, Burggraf S, Hafenbradl D, Jannasch H, Stetter K (1997) Pyrolobus fumarii, gen. and sp. nov., represents a novel group of archaea, extending the upper temperature limit for life to 113°C. Extremophiles 1:14–21PubMedCrossRefGoogle Scholar
  48. Boaretti M, Lleò MM, Bonato B, Signoretto C, Canepari P (2003) Involvement of rpoS in the survival of Escherichia coli in the viable but non-culturable state. Environ Microbiol 5:986–996PubMedCrossRefGoogle Scholar
  49. Bogosian G, Morris P, O’Neil J (1998) A mixed culture recovery method indicates that enteric bacteria do not enter the viable but nonculturable state. Appl Environ Microbiol 64:1736–1742PubMedPubMedCentralGoogle Scholar
  50. Boto L (2010) Horizontal gene transfer in evolution: facts and challenges. Proc R Soc Lond B Biol Sci 277:819–827CrossRefGoogle Scholar
  51. Bottos E, Woo A, Zawar-Reza P, Pointing S, Cary S (2014) Airborne bacterial populations above desert soils of the McMurdo Dry Valleys, Antarctica. Microb Ecol 67:120–128PubMedCrossRefGoogle Scholar
  52. Braun M, Mayer F, Gottschalk G (1981) Clostridium aceticum (Wieringa), a microorganism producing acetic acid from molecular hydrogen and carbon dioxide. Arch Microbiol 128:288–293PubMedCrossRefGoogle Scholar
  53. Brazelton W, Ludwig K, Sogin M, Andreishcheva E, Kelley D, Shen C, Edwards R, Baross J (2010) Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys. Proc Natl Acad Sci U S A 107:1612–1617PubMedPubMedCentralCrossRefGoogle Scholar
  54. Brochier C, Philippe H, Moreira D (2000) The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. Trends Genet 16:529–533PubMedCrossRefGoogle Scholar
  55. Brochier-Armanet C, Moreira D (2015) Horizontal gene transfer in microbial ecosystems. In: Bertrand J, Caumette P, Lebaron P, Matheron R, Normand P, Sime-Ngando T (eds) Environmental microbiology: fundamentals and applications. Springer, Dordrecht/Heidelberg/New York/London, pp 471–512Google Scholar
  56. Brzuszkiewicz E, Brüggemann H, Liesegang H, Emmerth M, Olschläger T, Nagy G, Albermann K, Wagner C, Buchrieser C, Emody L et al (2006) How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc Natl Acad Sci U S A 103:12879–12884PubMedPubMedCentralCrossRefGoogle Scholar
  57. Bult CJ et al (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058–1073PubMedCrossRefGoogle Scholar
  58. Buchanan B, Arnon D (1990) Reverse KREBS cycle in photosynthesis: consensus at last. Photosynth Res 24:47–53PubMedCrossRefGoogle Scholar
  59. Burrows S, Butler T, Jöckel P, Tost H, Kerkweg A, Pöschl U, Lawrence M (2009) Bacteria in the global atmosphere – Part 2: Modeling of emissions and transport between different ecosystems. Atmos Chem Phys 9:9281–9297CrossRefGoogle Scholar
  60. Campanaro S, Treu L, Valle G (2008) Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates. BMC Evol Biol 8:313PubMedPubMedCentralCrossRefGoogle Scholar
  61. Campanaro S, Vezzi A, Vitulo N, Lauro F, D’Angelo M, Simonato F, Cestaro A, Malacrida G, Bertoloni G, Valle G et al (2005) Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains. BMC Genomics 6:122PubMedPubMedCentralCrossRefGoogle Scholar
  62. Campbell B, Engel A, Porter M, Takai K (2006) The versatile ɛ-proteobacteria: key players in sulphidic habitats. Nat Rev Microbiol 4:458–468PubMedCrossRefGoogle Scholar
  63. Canfield D, Glazer A, Falkowsli P (2010) The evolution and future of Earth’s nitrogen cycle. Sciences 330:192–196CrossRefGoogle Scholar
  64. Cano R, Borucki M (1995) Revival and identification of bacterial spores in 25- to 40 million-year-old Dominican amber. Science 268:1060–1064PubMedCrossRefGoogle Scholar
  65. Capone DG, Zehr JP, Paerl HW, Bergman B, Carpenter EJ (1997) Trichodesmium, a globally significant marine cyanobacterium. Science 276:1221–1229CrossRefGoogle Scholar
  66. Caron B, Mark A, Poger D (2014) Some like it hot: the effect of sterols and hopanoids on lipid ordering at high temperature. J Phys Chem Lett 5:3953–3957PubMedCrossRefGoogle Scholar
  67. Carpenter EJ (1983) Nitrogen fixation by marine Oscillatoria (Trichodesmium) in the world’s oceans. In: Carpenter EJ, Capone DG (eds) Nitrogen in the marine environment. Academic, NY, pp 65–104CrossRefGoogle Scholar
  68. Cavalier-Smith T (2002) The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 52:7–76PubMedCrossRefGoogle Scholar
  69. Cavicchioli R (2016) On the concept of a psychrophile. ISME J 10:793–795PubMedCrossRefGoogle Scholar
  70. Cayol J, Ollivier B, Patel B, Ageron E, Grimont P, Prensier G, Garcia J (1995) Haloanaerobium lacusroseus sp. nov., an extremely halophilic fermentative bacterium from the sediments of a hypersaline lake. Int J Syst Bacteriol 45:790–797PubMedCrossRefGoogle Scholar
  71. Cayol J-L, Ollivier B, Alazard D, Amils R, Godfroy A, Piette F, Prieur D (2015) The extreme conditions of life on the planet and exobiology. In: Bertrand J-C, Caumette P, Lebaron P, Matheron R, Normand P, Sime-Ngando T (eds) Environmental microbiology: fundamentals and applications: microbial ecology. Springer, Dordrecht, pp 353–394Google Scholar
  72. Chaiyanan S, Chaiyanan S, Grim C, Maugel T, Huq A, Colwell R (2007) Ultrastructure of coccoid viable but non-culturable Vibrio cholerae. Environ Microbiol 9:393–402PubMedCrossRefGoogle Scholar
  73. Chan C, Beiko R, Ragan M (2017) Scaling up the phylogenetic detection of lateral gene transfer events. In: Keith J (ed) Method in molecular biology bioinformatic, data, sequence analysis, and evolution, vol 1. Springer, New YorkGoogle Scholar
  74. Chatterjee S, Rothenberg E (2012) Interaction of bacteriophage l with its E. coli receptor, LamB. Viruses 4:3162–3178PubMedPubMedCentralCrossRefGoogle Scholar
  75. Chattopadhyay S, Weissman SJ, Minin VN, Russo TA, Dykhuizen DE, Sokurenko EV (2009) High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection. Proc Natl Acad Sci U S A 106:12412–12417PubMedPubMedCentralCrossRefGoogle Scholar
  76. Chen G-Q (2009) A microbial polyhydroxyalkanoates (PHA) based bio- and materials industry. Chem Soc Rev 38:2434–2446PubMedCrossRefGoogle Scholar
  77. Chen I, Dubnau D (2004) DNA uptake during bacterial transformation. Nat Rev Microbiol 2:241–249PubMedCrossRefGoogle Scholar
  78. Chiarabelli C, Stano P, Luisi P (2009) Chemical approaches to synthetic biology. Curr Opin Biotechnol 20:492–497PubMedCrossRefGoogle Scholar
  79. Christman MF, Storz G, Ames BN (1989) OxyR, a positive regulator of hydrogen peroxide-inducible genes in Escherichia coli and Salmonella typhimurium, is homologous to a family of bacterial regulatory proteins. Proc Natl Acad Sci U S A 86:3484–3488PubMedPubMedCentralCrossRefGoogle Scholar
  80. Colwell FS, D’Hondt S (2013) Nature and extent of the deep biosphere. In: Hazen RM, Jones AP, Baross JA (eds) Reviews in mineralogy and geochemistry. Mineralogical Society of America, Chantilly, pp 547–574Google Scholar
  81. Colwell R, Brayton P, Herrington D, Tall B, Huq A, Levine M (1996) Viable but non-culturable Vibrio cholerae 01 revert to a cultivable state in the human intestine. World J Microbiol Biotechnol 12:28–31PubMedCrossRefGoogle Scholar
  82. Colwell RR (2000) Viable but nonculturable bacteria: a survival strategy. J Infect Chemother 6:121–125PubMedCrossRefGoogle Scholar
  83. Comolli L, Baker B, Downing K, Siegerist C, Banfield J (2009) Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon. Isme J 3:159–167PubMedCrossRefGoogle Scholar
  84. Conrad R (1996) Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microb Rev 60:609–640Google Scholar
  85. Cox M (2003) The bacterial RecA protein as a motor protein. Annu Rev Microbiol 57:551–577PubMedCrossRefGoogle Scholar
  86. Cuny C, Dukan L, Fraysse L, Ballesteros M, Dukan S (2005) Investigation of the first events leading to loss of culturability during Escherichia coli starvation: future nonculturable bacteria form a subpopulation. J Bacteriol 187:2244–2248PubMedPubMedCentralCrossRefGoogle Scholar
  87. d’Ari R (1985) The SOS system. Biochimie 67:343–347PubMedCrossRefGoogle Scholar
  88. D’Amico S, Collins T, Marx J, Feller G, Gerday C (2006) Psychrophilic microorganisms: challenges for life. EMBO Rep 7:385–389PubMedPubMedCentralCrossRefGoogle Scholar
  89. Damsté J, Rijpstra W, Hopmans E, Schouten S, Balk M, Stams A (2007) Structural characterization of diabolic acid-based tetraester, tetraether and mixed ether/ester, membrane-spanning lipids of bacteria from the order Thermotogales. Arch Microbiol 188:629–641PubMedPubMedCentralCrossRefGoogle Scholar
  90. Darcan C, Özkanca R, Idil O, Ken P, Flint K (2009) Viable but non-culturable state (VBNC) of Escherichia coli related to EnvZ under the effect of pH, starvation and osmotic stress in sea water. Pol J Microbiol 58:307–317PubMedGoogle Scholar
  91. Darwin C (1859) The origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. John Murray, LondonGoogle Scholar
  92. DasSarma S, Arora P (2001) Halophiles. In: Encyclopedia of life sciences. Nature Publishing Group, London, pp 1–9Google Scholar
  93. Daubin V, Szöllősi G (2016) Horizontal gene transfer and the history of life. Cold Spring Harb Perspect Biol 8:a018036PubMedPubMedCentralCrossRefGoogle Scholar
  94. Davis C (2014) Enumeration of probiotic strains: review of culture-dependent and alternative techniques to quantify viable bacteria. J Microbiol Methods 103:9–17PubMedCrossRefGoogle Scholar
  95. Dawkins R (1976) The selfish gene. Oxford University Press, LondonGoogle Scholar
  96. Day A, Oliver J (2004) Changes in membrane fatty acid composition during entry of Vibrio vulnificus into the viable but nonculturable state. J Microbiol 42:69–73PubMedGoogle Scholar
  97. De Maayer P, Anderson D, Cary C, Cowan D (2014) Some like it cold: understanding the survival strategies of psychrophiles. EMBO Rep 15:508–517PubMedPubMedCentralCrossRefGoogle Scholar
  98. Delort A-M, Vaïtilingom M, Amato P, Sancelme M, Parazols M, Mailhot G, Laj P, Deguillaume L (2010) A short overview of the microbial population in clouds: potential roles in atmospheric chemistry and nucleation processes. Atmos Res 98:249–260CrossRefGoogle Scholar
  99. Denamur E, Matic I (2006) Evolution of mutation rates in bacteria. Mol Microbiol 60:820–827PubMedCrossRefGoogle Scholar
  100. Derelle E, Ferraz C, Rombauts S, Rouzé P, Worden AZ, Robbens S, Partensky F, Degroeve S, Echeynié S, Cooke R et al (2006) Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci U S A 103:11647–11652PubMedPubMedCentralCrossRefGoogle Scholar
  101. Deutsch C, Sarmiento J, Sigman DM, Gruber N, Dunne JP (2007) Spatial coupling of nitrogen inputs and losses in the ocean. Nature 445:163PubMedCrossRefGoogle Scholar
  102. Di Giulio M (2005) A comparison of proteins from Pyrococcus furiosus and Pyrococcus abyssi: barophily in the physicochemical properties of amino acids and in the genetic code. Gene 346:1–6PubMedCrossRefGoogle Scholar
  103. Ding T, Suo Y, Xiang Q, Zhao X, Chen S, Ye X, Liu D (2017) Significance of viable but nonculturable Escherichia coli: induction, detection, and control. J Microbiol Biotechnol 27:417–428PubMedCrossRefGoogle Scholar
  104. Dobrindt U, Hochhut B, Hentschel U, Hacker J (2004) Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2:414–424PubMedCrossRefGoogle Scholar
  105. Dobzhansky T (1937) Genetics and the origin of species. Columbia University Press, New YorkGoogle Scholar
  106. Dombrowski H (1963) Bacteria from paleozoic salt deposits. Ann N Y Acad Sci 108:453–460CrossRefGoogle Scholar
  107. Doolittle W (1999) Phylogenetic classification and the universal tree. Science 284:2124–2129PubMedCrossRefGoogle Scholar
  108. Dopson M, Holmes D (2014) Metal resistance in acidophilic microorganisms and its significance for biotechnologies. Appl Microbiol Biotechnol 98:8133–8144PubMedCrossRefGoogle Scholar
  109. Driks A (2002) Overview: development in bacteria: spore formation in Bacillus subtilis. Cell Mol Life Sci 59:389–391PubMedCrossRefGoogle Scholar
  110. Dubey G, Ben-Yehuda S (2011) Intercellular nanotubes mediate bacterial communication. Cell 144:590–600PubMedCrossRefPubMedCentralGoogle Scholar
  111. Dufresne A, Salanoubat M, Partensky F, Artiguenave F, Axmann I, Barbe V, Duprat S, Galperin M, Koonin E, Le Gall F et al (2003) Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A 100:10020–10025PubMedPubMedCentralCrossRefGoogle Scholar
  112. Dufresne A, Garczarek L, Partensky F (2005) Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biology 6:R14PubMedPubMedCentralCrossRefGoogle Scholar
  113. El-Hajj ZW, Newman EB (2015) How much territory can a single E. coli cell control? Front Microbiol 6:309PubMedPubMedCentralCrossRefGoogle Scholar
  114. Eldredge N, Gould S (1973) Punctuated equilibria: An alternative to phyletic gradualism. In: Schopf TJM (ed) Models in paleobiology. Freeman, Cooper & Co, San FranciscoGoogle Scholar
  115. Elkins J, Kunin V, Anderson I, Barry K, Goltsman E, Lapidus A, Hedlund B, Hugenholtz P, Kyrpides N, Graham D et al (2008) A korarchaeal genome reveals insights into the evolution of archaea. Proc Natl Acad Sci U S A 105:8102–8107PubMedPubMedCentralCrossRefGoogle Scholar
  116. Ellis RJ (1979) The most abundant protein on. Earth Trends Biochem Sci 4:241–244CrossRefGoogle Scholar
  117. Empadinhas N, DaCosta M (2008) Osmoadaptation mechanisms in prokaryotes: distribution of compatible solutes. Int J Microbiol 11:151–161Google Scholar
  118. Erill I, Campoy S, Barbé J (2007) Aeons of distress: an evolutionary perspective on the bacterial SOS response. FEMS Microbiol Rev 31:637–656PubMedCrossRefGoogle Scholar
  119. Erill I, Campoy S, Mazon G, Barbe J (2006) Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain. Nucleic Acids Res 34:66–77PubMedPubMedCentralCrossRefGoogle Scholar
  120. Ettwig K, Butler M, Le PD, Pelletier E, Mangenot S, Kuypers M, Schreiber F, Dutilh B, Zedelius J, de Beer D et al (2010) Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464:543–548PubMedCrossRefGoogle Scholar
  121. Fegatella F, Cavicchioli R (2000) Physiological responses to starvation in the marine oligotrophic ultramicrobacterium Sphingomonas sp. strain RB2256. Appl Environ Microbiol 66:2037–2044PubMedPubMedCentralCrossRefGoogle Scholar
  122. Fergus CL (1967) Resistance of spores of some thermlophilic actinomycetes to high temperature. Mycopathol Mycol Appl 32:205–208PubMedCrossRefGoogle Scholar
  123. Fernandes SO, Javanaud C, Aigle A, Michotey V, Guasco S, Deborde J, Deflandre B, Anschutz P, Bonin PC (2015) Anaerobic nitrification–denitrification mediated by Mn-oxides in meso-tidal sediments: implications for N2 and N2O production. Journal of Marine Systems 144:1–8CrossRefGoogle Scholar
  124. Fernández-Delgado M, García-Amado M, Contreras M, Incani R, Chirinos H, Rojas H, Suárez P (2015) Survival, induction and resuscitation of Vibrio cholerae from the viable but non-cultivable state in the Southern Caribbean sea. Rev Inst Med Trop Sao Paulo 57:21–26PubMedPubMedCentralCrossRefGoogle Scholar
  125. Ferry J (2010) How to make a living by exhaling methane. Annu Rev Microbiol 64:453–473PubMedCrossRefPubMedCentralGoogle Scholar
  126. Fisher RA (1930) The genetical theory of natural selection. Clarendon Press, OxfordCrossRefGoogle Scholar
  127. Fittipaldi M, Nocker A, Codony F (2012) Progress in understanding preferential detection of live cells using viability dyes in combination with DNA amplification. J Microbiol Methods 91:276–289PubMedCrossRefGoogle Scholar
  128. Forterre P, Bergerat A, Lopez-Garcia P (1996) The unique DNA topology and DNA topoisomerases of hyperthermophilic archaea. FEMS Microbiol Rev 18:237–248PubMedCrossRefGoogle Scholar
  129. Fraser C, Gocayne J, White O, Adams M, Clayton R, Fleischmann R, Bult C, Kerlavage A, Sutton G, Kelley J et al (1995) The minimal gene complement of Mycoplasma genitalium. Science 270:397–403PubMedCrossRefPubMedCentralGoogle Scholar
  130. Fröhlich-Nowoisky J, Kampf CJ, Weber B, Huffman JA, Pöhlker C, Andreae MO, Lang-Yona N, Burrows SM, Gunthee SS, Elbert W et al (2016) Bioaerosols in the Earth system: Climate, health, and ecosystem interactions. Atmospheric Res 182:346–376CrossRefGoogle Scholar
  131. Frost L, Leplae R, Summers A, Toussaint A (2005) Motile genetic elements : the agents of open source of evolution. Nat Rev Microbiol 3:722–732PubMedCrossRefGoogle Scholar
  132. Fuchs R, Fujii S, Wagner J (2004) Properties and functions of Escherichia coli: Pol IV and PolV. Adv Protein Chem 69:229–264PubMedCrossRefGoogle Scholar
  133. Galagan J, Nusbaum C, Roy A, Endrizzi M, Macdonald P, FitzHugh W, Calvo S, Engels R, Smirnov S, Atnoor D et al (2002) The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res 12:532–542PubMedPubMedCentralCrossRefGoogle Scholar
  134. Galperin MY, Mekhedov SL, Puigbo P, Smirnov S, Wolf YI, Rigden DJ (2012) Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. Environ Microbiol 14:2870–2890PubMedPubMedCentralCrossRefGoogle Scholar
  135. García M, Jones S, Pelaz C, Millar R, Abu Kwaik Y (2007) Acanthamoeba polyphaga resuscitates viable non-culturable Legionella pneumophila after disinfection. Environ Microbiol 9:1267–1277PubMedCrossRefGoogle Scholar
  136. Gest H, Mandelstam J (1987) Longevity of microorganisms in natural environments. Microbiol Sci 4:69–71PubMedGoogle Scholar
  137. Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez-Valera F (2013) Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria. Sci Rep 3:2471PubMedPubMedCentralCrossRefGoogle Scholar
  138. Giaquinto L, Curmi P, Siddiqui K, Poljak A, DeLong E, DasSarma S, Cavicchioli R (2007) Structure and function of cold shock proteins in archaea. J Bacteriol 189:5738–5748PubMedPubMedCentralCrossRefGoogle Scholar
  139. Gibson D, Glass J, Lartigue C, Noskov V, Chuang R, Algire M, Benders G, Montague M, Ma L, Moodie M et al (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329:52–56PubMedCrossRefGoogle Scholar
  140. Gil R, Peretó J (2015) Small genomes and the difficulty to define minimal translation and metabolic machineries. Front Ecol Evol 3:123CrossRefGoogle Scholar
  141. Gil R, Silva F, Peretó J, Moya A (2004) Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 68:518–537PubMedPubMedCentralCrossRefGoogle Scholar
  142. Gil R et al (2003) The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes. Proc Natl Acad Sci U S A 100:9388–9393PubMedPubMedCentralCrossRefGoogle Scholar
  143. Gillings M (2017) Lateral gene transfer, bacterial genome evolution, and the Anthropocene. Ann N Y Acad Sci 1389:20–36PubMedCrossRefGoogle Scholar
  144. Giovannoni S (2017) SAR11 bacteria: the most abundant plankton in the oceans. Ann Rev Mar Sci 9:231–255PubMedCrossRefGoogle Scholar
  145. Giovannoni SJ, Hayakawa D, Tripp H, Stingl U, Givan S, Cho J-C et al (2008) The small genome of an abundant coastal ocean methylotroph. Environ Microbiol 10:1771–1782PubMedCrossRefGoogle Scholar
  146. Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, Baptista D, Bibbs L, Eads J, Richardson TH, Noordewier M et al (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309:1242–1245PubMedCrossRefGoogle Scholar
  147. Giraud E, Fardoux J, Fourrier N, Hannibal L, Genty B, Bouyer P, Dreyfus B, Vermeglio A (2002) Bacteriophytochrome controls photosystem synthesis in anoxygenic bacteria. Nature 417:202–205PubMedCrossRefGoogle Scholar
  148. Glass J, Merryman C, Wise K, Hutchison C, Smith H (2017) Minimal cells-real and imagined. Cold Spring Harb Perspect Biol 9:pii: a023861CrossRefGoogle Scholar
  149. Gogarten JP, Doolittle WF, Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19:2226–2238PubMedCrossRefGoogle Scholar
  150. Gonzàlez-Escalona N, Fey A, Höfle M, Espejo R, Guzmán C (2006) Quantitative reverse transcription polymerase chain reaction analysis of Vibrio cholerae cells entering the viable but non-culturable state and starvation in response to cold shock. Environ Microbiol 8:658–666PubMedCrossRefGoogle Scholar
  151. Gonzalez-Toril E, Liobet-Brossa E, Casamayor E, Amann R, Amils R (2003) Microbial ecology of an extreme acidic environment, the Tinto river. Appl Environ Microbiol 69:4853–4865PubMedPubMedCentralCrossRefGoogle Scholar
  152. Gottschal J, Prins R (1991) Thermophiles – a life at elevated temperatures. Trends Ecol Evol 6:157–162PubMedCrossRefGoogle Scholar
  153. Gould G (2006) History of science – spores. In Lewis B Perry Memorial Lecture 2005PubMedCrossRefGoogle Scholar
  154. Grage K, Jahns A, Parlane N, Palanisamy R, Rasiah I, Atwood J, Rehm B (2009) Bacterial polyhydroxyalkanoate granules: biogenesis, structure, and potential use as nano-/micro-beads in biotechnological and biomedical applications. Biomacromolecules 10:660–669PubMedCrossRefGoogle Scholar
  155. Grant W (1992) Alkaline environments. In: Lederberg J (ed) Encyclopedia of microbiology, vol 2. Academic Press, New York, pp 73–84Google Scholar
  156. Grant W (2004) Life at low water activity. Philos Trans Roy Soc B 359:1249–1267CrossRefGoogle Scholar
  157. Grant W, Gemmell R, McGenity T (1998) Halobacteria: the evidence for longevity. Extremophiles 2:279–287PubMedCrossRefGoogle Scholar
  158. Grant W, Sorokin D (2011) Distribution and diversity of soda lake alkaliphiles. In: Horikoshi K (ed) Extremophiles handbook. Springer, New York, pp 28–54Google Scholar
  159. Graur D, Pupko T (2001) The Permian bacterium that isn’t. Mol Biol Evol 18:1143–1146PubMedCrossRefGoogle Scholar
  160. Griffith F (1928) The significance of pneumococcal types. Journal of Hygiene 27:113–159PubMedCrossRefGoogle Scholar
  161. Grote J, Thrash JC, Huggett MJ, Landry ZC, Carini P, Giovannoni SJ, Rappe SJ (2012) Streamlining and core genome conservation among highly divergent members of the SAR11 Clade. MBio 3:e00252–e00212PubMedPubMedCentralCrossRefGoogle Scholar
  162. Guerrero R, Berlanga M (2007) The hidden side of the prokaryotic cell: rediscovering the microbial world. Int Microbiol 10:157–168PubMedGoogle Scholar
  163. Gutiérrez G, Martin A (1998) The most ancient DNA recovered from amber-preserved specimen may not be as ancient as It seems. Mol Biol Evol 15:926–929PubMedCrossRefGoogle Scholar
  164. Hacker J, Kaper J (2000) Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol 54:641–679PubMedCrossRefGoogle Scholar
  165. Hagen C, Hawrylewicz E, Ehrlich R (1964) Survival of microorganisms in a simulated martian environment. I. Bacillus subtilis var. globigii. Appl Microbiol 12:215–218PubMedPubMedCentralGoogle Scholar
  166. Hahn M (2003) Isolation of strains belonging to the cosmopolitan Polynucleobacter necessarius cluster from freshwater habitats located in three climatic zones. Appl Environ Microbiol 69:5248–5254PubMedPubMedCentralCrossRefGoogle Scholar
  167. Haldane JBS (1932) The causes of evolution. Princeton University Press, PrincetonGoogle Scholar
  168. Hallatschek O, Hersen P, Ramanathan S, Nelson DR (2007) Genetic drift at expanding frontiers promotes gene segregation. Proc Natl Acad Sci U S A 104:19926–19930PubMedPubMedCentralCrossRefGoogle Scholar
  169. Hammerstrom T, Beabout K, Clements T, Saxer G, Shamoo Y (2015) Acinetobacter baumannii repeatedly evolves a hypermutator phenotype in response to tigecycline that effectively surveys evolutionary trajectories to resistance. PLoS One 10:e0140489PubMedPubMedCentralCrossRefGoogle Scholar
  170. Han K, Li Z, Peng R, Zhu L, Zhou T, Wang L, Li S, Zhang X, Hu W, Wu Z et al (2013) Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu. Sci Rep 3:2101PubMedPubMedCentralCrossRefGoogle Scholar
  171. Hanczyc M, Fujikawa S, Szostak J (2003) Experimental models of primitive cellular compartments: encapsulation, growth, and division. Science 302:618–622PubMedPubMedCentralCrossRefGoogle Scholar
  172. Haroon M, Hu S, Shi Y, Imelfort M, Keller J, Hugenholtz P, Yuan Z, Tyson G (2013) Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500:567–567PubMedCrossRefGoogle Scholar
  173. Hedlund B, Murugapiran S, Alba T, Levy A, Dodsworth J, Goertz G, Ivanova N, Woyke T (2015) Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’. Curr Opin Microbiol 25:136–145PubMedCrossRefGoogle Scholar
  174. Heim S, Lleo M, Bonato B, Guzman C, Canepari P (2002) The viable but nonculturable state and starvation are different stress responses of Enterococcus faecalis, as determined by proteome analysis. J Bacteriol 184:6739–6745PubMedPubMedCentralCrossRefGoogle Scholar
  175. Herbert RA (1999) Nitrogen cycling in coastal marine ecosystems. FEMS Microbiol Rev 23:563–590PubMedCrossRefGoogle Scholar
  176. Hoelher TM, Jørgensen BB (2013) Microbial life under extreme energy conditions. Nature Rev Microbiol 11:83–94Google Scholar
  177. Hoff M (2009) Surviving salt: how do extremophiles do it? PLoS Biol 7:e1000258PubMedPubMedCentralCrossRefGoogle Scholar
  178. Hood M, Macdonell M (1987) Distribution of ultramicrobacteria in a gulf coast estuary and induction of ultramicrobacteria. Microb Ecol 14:113–127PubMedCrossRefGoogle Scholar
  179. Hoshino T, Toki T, Ijiri A, Morono Y, Machiyama H, Ashi J, Okamura K, Inagaki F (2017) Atribacteria from the subseafloor sedimentary biosphere disperse to the hydrosphere through submarine mud volcanoes. Front Microbiol 8:1135PubMedPubMedCentralCrossRefGoogle Scholar
  180. Huber H, Gallenberger M, Jahn U, Eylert E, Berg I, Kockelkorn D, Eisenreich W, Fuchs G (2008) A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis. Proc Natl Acad Sci U S A 105:7851–7856PubMedPubMedCentralCrossRefGoogle Scholar
  181. Huber H, Thomm M, Konig H, Thies G, Stetter K (1982) Methanococcus thermolithotrophicus, a novel thermophilic lithotrophic methanogen. Arch Microbiol 132:47–50CrossRefGoogle Scholar
  182. Huber R, Wilharm T, Huber D, Trincone A, Burggraf S, König H, Rachel R, Rockinger I, Fricke H, Stetter K (1992) Aquifex pyrophilus gen. nov., sp. nov., represents a novel group of marine hyperthermophilic hydrogen-oxidizing bacteria. System Appl Microbiol 15:340–351CrossRefGoogle Scholar
  183. Huggett MJ, Hayakawa DH, Rappé MS (2012) Genome sequence of strain HIMB624, a cultured representative from the OM43 clade of marine Betaproteobacteria. Stand Genomic Sci 6:11–20PubMedPubMedCentralCrossRefGoogle Scholar
  184. Hügler M, Sievert S (2011) Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. Ann Rev Mar Sci 3:261–289PubMedCrossRefGoogle Scholar
  185. Hutchison C 3rd., Chuang R, Noskov V, Assad-Garcia N, Deerinck T, Ellisman M, Gill J, Kannan K, Karas B, Ma L et al (2016) Design and synthesis of a minimal bacterial genome. Science 351:aad6253PubMedCrossRefGoogle Scholar
  186. Huxley J (1948) Evolution: the modern synthesis. MIT Press, Cambridge, MAGoogle Scholar
  187. Inagaki F, Hinrichs K, Kubo Y, Bowles M, Heuer V, Hong W, Hoshino T, Ijiri A, Imachi H, Ito M et al (2015) DEEP BIOSPHERE. Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor. Science 349:420–442PubMedCrossRefGoogle Scholar
  188. Ioannidis P, Johnston K, Riley D, Kumar N, White J, Olarte K, Ott S, Tallon L, Foster J, Taylor M et al (2013) Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi. BMC Genomics 14:639PubMedPubMedCentralCrossRefGoogle Scholar
  189. Itoh T, Onishi M, Kato S, Iino T, Sakamoto M, Kudo T, Takashina T, Ohkuma M (2016) Athalassotoga saccharophila gen. nov., sp. nov., isolated from an acidic terrestrial hot spring, and proposal of Mesoaciditogales ord. nov. and Mesoaciditogaceae fam. nov. in the phylum Thermotogae. Int J Syst Evol Microbiol 66:1045–1051PubMedCrossRefGoogle Scholar
  190. Jacotot R, Virat B (1954) Longévité des spores de B. anthrasis (premier vaccin de Pasteur). Ann Inst Pasteur 87:215–217Google Scholar
  191. Jannasch H (1967) Enrichments of aquatic bacteria in continous culture. Arch Mikrobiol 59:165–173PubMedCrossRefGoogle Scholar
  192. Jannasch HW (1969) Estimations of bacterial growth rates in natural waters. J Bacteriol 99:156–160PubMedPubMedCentralGoogle Scholar
  193. Janto B, Ahmed A, Ito M, Liu J, Hicks DB, Pagni S, Fackelmayer OJ, Smith TA, Earl J, Elbourne LD et al (2011) Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4. Environ Microbiol 13:3289–3309PubMedPubMedCentralCrossRefGoogle Scholar
  194. Jayarama R (2009) Mutators and hypermutability in bacteria : the Escherichia coli paradigm. J Genet 88:379–391CrossRefGoogle Scholar
  195. Johnsborg O, Eldholm V, Håvarstein L (2007) Natural genetic transformation: prevalence, mechanisms and function. Res Microbiol 158:767–778PubMedCrossRefGoogle Scholar
  196. Johnson D (1998) Biodiversity and ecology of acidophilic microorganisms. FEMS Microbiol Ecol 27:307–317CrossRefGoogle Scholar
  197. Johnson D (2012) Geomicrobiology of extremely acidic subsurface environments. FEMS Microbiol Ecol 81:2–12PubMedCrossRefGoogle Scholar
  198. Jones E, Grant W, Duckworth A, Owenson G (1998) Microbial diversity of soda lakes. Extremophiles 2:191–200PubMedCrossRefGoogle Scholar
  199. Jones S, Lennon J (2010) Dormancy contributes to the maintenance of microbial diversity. Proc Natl Acad Sci U S A 107:5881–5886PubMedPubMedCentralCrossRefGoogle Scholar
  200. Jones W, Leigh J, Mayer F, Woese C, Wolfe R (1983) Methanococcus jannaschii sp. nov., an extremely thermophilic methanogen from a submarine hydrothermal vent. Arch Microbiol 136:254–261CrossRefGoogle Scholar
  201. Jørgensen B, Boetius A (2007) Feast and famine – microbial life in the deep-sea bed. Nat Rev Microbiol 5:770–781PubMedCrossRefGoogle Scholar
  202. Jørgensen BB (2011) Deep subseafloor microbial cells on physiological standby. Proc Natl Acad Sci U S A 108:18193–18194PubMedPubMedCentralCrossRefGoogle Scholar
  203. Jørgensen BB, D’Hondt S (2006) Ecology. A starving majority deep beneath the seafloor. Science 314:932–934PubMedCrossRefGoogle Scholar
  204. Joux F, Lebaron P (1997) Ecological implications of an improved direct viable count method for aquatic bacteria. Appl Environ Microbiol 63:3643–3647PubMedPubMedCentralGoogle Scholar
  205. Joye SB (2012) Microbiology: a piece of the methane puzzle. Nature 491:538–539PubMedCrossRefGoogle Scholar
  206. Juhas M (2016) On the road to synthetic life: the minimal cell and genome-scale engineering. Crit Rev Biotechnol 36:416–423PubMedGoogle Scholar
  207. Juhas M, van der Meer J, Gaillard M, Harding R, Hood D, Crook DW (2009) Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev 33:376–393PubMedCrossRefGoogle Scholar
  208. Kallmeyer J, Pockalny R, Adhikari RR, Smith DC, D’Hondt S (2012) Global distribution of microbial abundance and biomass in subseafloor sediment. Proc Natl Acad Sci U S A 109:16213–16236PubMedPubMedCentralCrossRefGoogle Scholar
  209. Kaneko R, Hayashi T, Tanahashi M, Naganuma T (2007) Phylogenetic diversity and distribution of dissimilatory sulfite reductase genes from deep-sea sediments cores. Mar Biotechnol (NY) 9:429–436CrossRefGoogle Scholar
  210. Kaneko T, Nakamura Y, Sato S, Asamizu E, Kato T, Sasamoto S, Watanabe A, Idesawa K, Ishikawa A, Kawashima K et al (2000) Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res 7:331–338PubMedCrossRefGoogle Scholar
  211. 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–e00713PubMedPubMedCentralCrossRefGoogle Scholar
  212. Kaprelyants A, Gottschal J, Kell D (1993) Dormancy in non-sporulating bacteria. FEMS Microbiol Rev 104:271–286CrossRefGoogle Scholar
  213. Kaprelyants A, Mukamolova G, Davey H, Kell D (1996) Quantitative analysis of the physiological heterogeneity within starved cultures of Micrococcus luteus by flow cytometry and cell sorting. Appl Environ Microbiol 62:1311–1316PubMedPubMedCentralGoogle Scholar
  214. Kashefi K, Holmes DE, Reysenbach AL, Lovley DR (2002) Use of Fe(III) as an electron acceptor to recover previously uncultured hyperthermophiles: isolation and characterization of Geothermobacterium ferrireducens gen. nov., sp. nov. Appl Environ Microbiol 68:1735–1742PubMedPubMedCentralCrossRefGoogle Scholar
  215. Kasting JF (1982) Stability of ammonia in the primitive terrestrial atmosphere. J Geophys Res: Oceans 87:3091–3098CrossRefGoogle Scholar
  216. Kasting JF (1993) Earth’s early atmosphere. Science 259:920–926PubMedCrossRefGoogle Scholar
  217. Kell D, Kaprelyants A, Weichart D, Harwood C, Barer M (1998) Viability and activity in readily culturable bacteria: a review and discussion of the practical issues. Antonie Van Leeuwenhoek 73:169–187PubMedCrossRefGoogle Scholar
  218. Kelley D, Karson J, Früh-Green G, Yoerger D, Shank T, Butterfield D, Hayes J, Schrenk M, Olson E, Proskurowski G et al (2005) A serpentinite-hosted ecosystem: the Lost City hydrothermal field. Science 307:1428–1434PubMedCrossRefGoogle Scholar
  219. Kennedy M, Reader S, Swiercznski L (1994) Preservation records of microorganisms : evidence of the tenacity of life. Microbiology 140:2514–2529Google Scholar
  220. Keyser HH, van Berkum P, Weber DF (1982) A comparative study of the physiology of symbioses formed by Rhizobium japonicum with Glycine max, Vigna unguiculata, and Macroptilium atropurpurem. Plant Physiol 70:1626–1630PubMedPubMedCentralCrossRefGoogle Scholar
  221. Khan M, Pyle B, Camper A (2010) Specific and rapid enumeration of viable but nonculturable and viable-culturable Gram-negative bacteria by using flow cytometry. Appl Environ Microbiol 76:5088–5096PubMedPubMedCentralCrossRefGoogle Scholar
  222. Kimura M (1986) DNA and the neutral theory. Philos Trans R Soc Lond B 312:343–354CrossRefGoogle Scholar
  223. Kimura M, Ohta T (1974) On some principles governing molecular evolution. Proc Natl Acad Sci U S A 71:2848–2852PubMedPubMedCentralCrossRefGoogle Scholar
  224. Kjelleberg S, Albertson N, Flärdh K, Holmquist L, Jouper-Jaan A, Marouga R, Östling J, Svenblad B, Weichart D (1993) How do non-differentiating bacteria adapt to starvation? Antonie Van Leeuwenhoek 63:333–341PubMedCrossRefGoogle Scholar
  225. Knittel K, Boetius A (2009) Anaerobic oxidation of methane: progress with an unknown process. Annu Rev Microbiol 63:311–334PubMedCrossRefPubMedCentralGoogle Scholar
  226. Kobayashi H, Takaki Y, Kobata K, Takami H, Inoue A (1998) Characterization of α-maltotetraohydrolase produced by Pseudomonas sp. MS300 isolated from the deepest site of the Mariana Trench. Extremophiles 2:401–407PubMedCrossRefGoogle Scholar
  227. Koch A (1971) The adaptative responses of Escherichia coli to feast existence. Adv Microb Physiol 6:147–217PubMedCrossRefGoogle Scholar
  228. Kogure K, Simidu U, Taga N (1979) A tentative direct microscopic method for counting living marine bacteria. Can J Microbiol 3:415–420CrossRefGoogle Scholar
  229. Konstantinidis KT, Tiedje JM (2004) Trends between gene content and genome size in prokaryotic species with larger genomes. Proc Natl Acad Sci U S A 101:3160–3165PubMedPubMedCentralCrossRefGoogle Scholar
  230. Koonin E (2016) Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions. F1000Res 5: F1000 Faculty Rev-1805Google Scholar
  231. Koonin E, Makarova K, Aravind L (2001) Horizontal gene transfer in Prokaryotes : quantification and classification. Annu Rev Microbiol 55:709–742PubMedPubMedCentralCrossRefGoogle Scholar
  232. Koonin EV, Wolf YI (2012) Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Front Cell Infect Microbiol 2:119PubMedPubMedCentralCrossRefGoogle Scholar
  233. Kourmentza C, Plácido J, Venetsaneas N, Burniol-Figols A, Varrone C, Gavala H, Reis M (2017) Recent advances and challenges towards sustainable polyhydroxyalkanoate (PHA) production. Bioengineering (Basel) 4:55CrossRefGoogle Scholar
  234. Kozak M (1999) Initiation of translation in prokaryotes and eukaryotes. Gene 234:187–208PubMedCrossRefGoogle Scholar
  235. Krimi Z, Petit A, Mougel C, Dessaux Y, Nesme X (2002) Seasonal fluctuations and long-term persistence of pathogenic populations of Agrobacterium spp. in soils. Appl Environ Microbiol 68:3358–3365PubMedPubMedCentralCrossRefGoogle Scholar
  236. Krulwich T, Liu J, Morino M, Fujisawa M, Ito M, Hicks D (2011a) Adaptative mechanisms of extreme alkaliphiles. In: Horikoshi K (ed) Extremophiles handbook. Springer, New York, pp 120–139Google Scholar
  237. Krulwich T, Sachs G, Padan E (2011b) Molecular aspects of bacterial pH sensing and homeostasis. Nat Rev Microbiol 9:330–343PubMedPubMedCentralCrossRefGoogle Scholar
  238. Kurland C, Canback B, Berg O (2003) Horizontal gene transfer: a critical view. Proc Natl Acad Sci U S A 100:9658–9662PubMedPubMedCentralCrossRefGoogle Scholar
  239. Kusumoto A, Asakura H, Kawamoto K (2012) General stress sigma factor RpoS influences time required to enter the viable but non-culturable state in Salmonella enterica. Microbiol Immunol 56:228–237PubMedCrossRefPubMedCentralGoogle Scholar
  240. Kuypers M, Lavik G, Woebken D, Schmid M, Fuchs B, Amann R, Jørgensen B, Jetten M (2005) Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Proc Natl Acad Sci U S A 102:6478–6483PubMedPubMedCentralCrossRefGoogle Scholar
  241. Lafond RE, Lukehart SA (2006) Biological basis for syphilis. Clin Microbiol Rev 19:29–49PubMedPubMedCentralCrossRefGoogle Scholar
  242. Land M, Hauser L, Jun S-R, Nookaew I, Leuze MR, Ahn T-H, Karpinets T, Lund O, Kora G, Wassenaar T et al (2015) Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics 15:141–161PubMedPubMedCentralCrossRefGoogle Scholar
  243. Langille M, Hsiao W, Brinkman F (2010) Detecting genomic islands using bioinformatics approaches. Nat Rev Microbiol 8:373–382PubMedCrossRefGoogle Scholar
  244. Lanyi J (1974) Salt-dependent properties of proteins from extremely halophilic bacteria. Bacteriol Rev 38:272–290PubMedPubMedCentralGoogle Scholar
  245. Lavire C, Normand P, Alekhina I, Bulat S, Prieur D, Birrien JL, Fournier P, Hanni C, Petit JR (2006) Presence of Hydrogenophilus thermoluteolus DNA in accretion ice in the subglacial Lake Vostok, Antarctica, assessed using rrs, cbb and hox. Environ Microbiol 8:2106–2114PubMedCrossRefGoogle Scholar
  246. Le Bihan T, Rayner J, Roy M, Spagnolo L (2013) Photobacterium profundum under pressure: a MS-based label-free quantitative proteomics study. PLoS ONE 8:e60897PubMedPubMedCentralCrossRefGoogle Scholar
  247. Lederberg J, Tatum EL (1946) Gene recombination in Escherichia coli. Nature 158:558PubMedCrossRefPubMedCentralGoogle Scholar
  248. Lennon J, Jones S (2011) Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat Rev Microbiol 9:119–130PubMedCrossRefGoogle Scholar
  249. Léonard L, Bouarab Chibane L, Ouled Bouhedda B, Degraeve P, Oulahal N (2016) Recent advances on multi-parameter flow cytometry to characterize antimicrobial treatments. Front Microbiol 7:1225PubMedPubMedCentralCrossRefGoogle Scholar
  250. Lepper BT, Frolking TA, Fisher DC, Goldstein G, Sanger JE, Wymer DA, Ogden JGI, Hooge PE (1991) Intestinal contents of a late Pleistocene mastodont from midcontinental North America. Quatern Res 36:120–125CrossRefGoogle Scholar
  251. Lerner A, Valverde A, Castro-Sowinski S, , Lerner H, Okon, Y, Burdman S (2010) Phenotypic variation in Azospirillum brasilense exposed to starvation. Environ Microbiol Rep 2: 577–586PubMedCrossRefPubMedCentralGoogle Scholar
  252. Li L, Mendis N, Trigui H, Oliver J, Faucher S (2014) The importance of the viable but non-culturable state in human bacterial pathogens. Front Microbiol 5:258PubMedPubMedCentralGoogle Scholar
  253. Licking E, Gorski L, Kaiser D (2000) A common step for changing cell shape in fruiting body and starvation-independent sporulation of Myxococcus xanthus. J Bacteriol 182:3553–3558PubMedPubMedCentralCrossRefGoogle Scholar
  254. Lindgren P, Higgins P, Seifert H, Cars O (2016) Prevalence of hypermutators among clinical Acinetobacter baumannii isolates. J Antimicrob Chemother 71:661–665CrossRefGoogle Scholar
  255. Lipscomb G, Hahn E, Crowley A, MWW A (2017) Reverse gyrase is essential for microbial growth at 95 °C. Extremophiles 21:603–608PubMedCrossRefGoogle Scholar
  256. Liu Y, Gilchrist A, Zhang J, Li X-F (2008) Detection of viable but nonculturable Escherichia coli O157:H7 bacteria in drinking water and river water. Appl Environ Microbiol 74:1502–1507PubMedPubMedCentralCrossRefGoogle Scholar
  257. Liu Y, Wang C, Fung C, Xing-Fang L (2010a) Quantification of viable but nonculturable Escherichia coli O157:H7 by targeting the rpoS mRNA. Anal Chem 82:2612–2615PubMedCrossRefGoogle Scholar
  258. Liu Y, Wang C, Tyrrell G, Li X-F (2010b) Production of Shiga-like toxins in viable but nonculturable Escherichia coli O157:H7. Water Res 44:711–718PubMedCrossRefGoogle Scholar
  259. Liu Y, Whitman W (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann N Y Acad Sci 1125:171–189PubMedCrossRefGoogle Scholar
  260. Ljungdahl L (1986) The autotrophic pathway of acetate synthesis in acetogenic bacteria. Annu Rev Microbiol 40:415–450PubMedCrossRefGoogle Scholar
  261. Lleò M, Pierobon S, Tafi M, Signoretto C, Canepari P (2000) mRNA detection by reverse transcription-PCR for monitoring viability over time in an Enterococcus faecalis viable but nonculturable population maintained in a laboratory microcosm. Appl Environ Microbiol 66:4564–4567PubMedCrossRefGoogle Scholar
  262. Lopez-Garcia P, Moreira D (2006) Selective forces for the origin of the eukaryotic nucleus. Bioessays 28:525–533PubMedCrossRefGoogle Scholar
  263. Lorenz M, Wackernagel W (1994) Bacterial gene transfer by natural genetic transformation in the environment. Microbiol Rev 58:563–602PubMedPubMedCentralGoogle Scholar
  264. Loveland-Curtze J, Miteva V, Brenchley J (2009) Herminiimonas glaciei sp. nov., a novel ultramicrobacterium from 3042 m deep Greenland glacial ice. Int J Syst Evol Microbiol 59:1272–1277PubMedCrossRefGoogle Scholar
  265. Luef B, Frischkorn KR, Wrighton KC, Holman HY, Birarda G, Thomas BC, Singh A, Williams KH, Siegerist CE, Tringe SG et al (2015) Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun 6:6372PubMedCrossRefGoogle Scholar
  266. Lulchev P, Klostermeier D (2014) Reverse gyrase – recent advances and current mechanistic understanding of positive DNA supercoiling. Nucleic Acids Res 42:8200–8213PubMedPubMedCentralCrossRefGoogle Scholar
  267. Luria SE, Delbruck M (1943) Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28:491–511PubMedPubMedCentralGoogle Scholar
  268. Lyons TW, Reinhard CT, Planavsky NJ (2014) The rise of oxygen in Earth’s early ocean and atmosphere. Nature 506:307–315PubMedCrossRefGoogle Scholar
  269. Ma Y, Galinski E, Grant W, Oren A, Ventosa A (2010) Halophiles 2010: life in saline environments. Appl Environ Microbiol 76:6971–6981PubMedPubMedCentralCrossRefGoogle Scholar
  270. Madigan M, Bender K, Buckley D, Sattley W, Stahl D (2015) Brock biology of microorganisms. Pearson, New YorkGoogle Scholar
  271. Mailloux BJ, Fuller ME (2003) Determination of in situ bacterial growth rates in aquifers and aquifer sediments. Appl Environ Microbiol 69:3798–3808PubMedPubMedCentralCrossRefGoogle Scholar
  272. Maki JS (2013) Bacterial intracellular sulfur globules: structure and function. J Mol Microbiol Biotechnol 23:270–280PubMedCrossRefGoogle Scholar
  273. Manina G, McKinney J (2013) A single-cell perspective on non-growing but metabolically active (NGMA) bacteria. Curr Top Microbiol Immunol 374:135–161PubMedGoogle Scholar
  274. Margesin R, Miteva V (2011) Diversity and ecology of psychrophilic microorganisms. Res Microbiol 162:346–361PubMedCrossRefGoogle Scholar
  275. Margulis L (1970) Origin of eukaryotic cells. Yale University Press, New YorkGoogle Scholar
  276. Maron D, Ames B (1983) Revised methods for the Salmonella mutagenicity test. Mutat Res 113:173–215PubMedCrossRefGoogle Scholar
  277. Marshall BJ, Barrett LJ, Prakash C, McCallum RW, Guerrant RL (1990) Urea protects Helicobacter (Campylobacter) pylori from the bactericidal effect of acid. Gastroenterology 99:697–702PubMedCrossRefGoogle Scholar
  278. Martin D, Bartlett D, Roberts M (2002) Solute accumulation in the deep-sea bacterium Photobacterium profundum. Extremophile 6:507–514CrossRefGoogle Scholar
  279. Martin W, Müller M (1998) The hydrogen hypothesis for the first eukaryote. Nature 392:37–41PubMedCrossRefGoogle Scholar
  280. Martínez-Cano D, Reyes-Prieto M, Martínez-Romero E, Partida-Martínez L, Latorre A, Moya A, Delaye L (2015) Evolution of small prokaryotic genomes. Front Microbiol 5:742PubMedPubMedCentralGoogle Scholar
  281. Martínez-García E, de Lorenzo V (2016) The quest for the minimal bacterial genome. Curr Opin Biotechnol 42:216–224PubMedCrossRefGoogle Scholar
  282. Mayr E (1942) Systematics and the origin of species, from the viewpoint of a zoologist. Harvard University Press, CambridgeGoogle Scholar
  283. McCutcheon JP, Moran NA (2010) Functional convergence in reduced genomes of bacterial symbionts spanning 200 my of evolution. Genome Biol Evol 2:708–718PubMedPubMedCentralCrossRefGoogle Scholar
  284. McCutcheon JP, Moran NA (2011) Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol 10:13–26PubMedCrossRefGoogle Scholar
  285. McCutcheon JP, von Dohlen CD (2011) An interdependent metabolic patchwork in the nested symbiosis of mealybugs. Curr Biol 21:1366–1372PubMedPubMedCentralCrossRefGoogle Scholar
  286. McGenity T, Gemmell R, Grant W, Stan-Lotter H (2000) Origins of halophilic microorganisms in ancient salt deposits. Environ Microbiol 2:243–250PubMedCrossRefGoogle Scholar
  287. McInerney MJ, Bryant MP, Hespell RB, Costerton JW (1981) Syntrophomonas wolfei gen. nov. sp. nov., an Anaerobic, Syntrophic, Fatty Acid-Oxidizing Bacterium. Appl Environ Microbiol 41:1029–1039PubMedPubMedCentralGoogle Scholar
  288. McKenney P, Driks A, Eichenberger P (2013) The Bacillus subtilis endospore: assembly and functions of the multilayered coat. Nature Rev Microbiol 11:33–44CrossRefGoogle Scholar
  289. McLeod MP et al (2006) The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A 103:15582–15587PubMedPubMedCentralCrossRefGoogle Scholar
  290. Mei N, Zergane N, Postec A, Erauso G, Ollier A, Payri C, Pelletier B, Fardeau M, Ollivier B, Quéméneur M (2014) Fermentative hydrogen production by a new alkaliphilic Clostridium sp. (strain PROH2) isolated from a shallow submarine hydrothermal chimney in Prony Bay, New Caledonia. Int J Hydrogen Energ 39:19465–19473CrossRefGoogle Scholar
  291. Mendell JE, Clements KD, Choat JH, Angert ER (2008) Extreme polyploidy in a large bacterium. Proc Natl Acad Sci U S A 105:6730–6734PubMedPubMedCentralCrossRefGoogle Scholar
  292. Mesbah N, Wiegel J (2008) Life at extreme limits: The anaerobic halophilic alkalithermophiles. Ann NY Acad Sci 1125:44–57PubMedCrossRefGoogle Scholar
  293. Mezzina M, Pettinari M (2016) Phasins, multifaceted polyhydroxyalkanoate granule associated proteins. Appl Environ Microbiol 82:5060–5067PubMedPubMedCentralCrossRefGoogle Scholar
  294. Michoud G, Jebbar M (2016) High hydrostatic pressure adaptive strategies in an obligate piezophile Pyrococcus yayanosii. Sci Rep 6:27289PubMedPubMedCentralCrossRefGoogle Scholar
  295. Miller SL, Schlesinger G (1983) The atmosphere of the primitive earth and the prebiotic synthesis of organic compounds. Adv Space Res 3:47–53PubMedCrossRefGoogle Scholar
  296. Milucka J, Ferdelman T, Polerecky L, Franzke D, Wegener G, Schmi M, Kuypers MM (2012) Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature 491:541PubMedCrossRefGoogle Scholar
  297. Moeller R, Schuerger A, Reitz G, Nicholson W (2012) Protective role of spore structural components in determining Bacillus subtilis spore resistance to simulated Mars surface conditions. Appl Environ Microbiol 78:8849–8853PubMedPubMedCentralCrossRefGoogle Scholar
  298. Moënne-Loccoz Y, Mavingui P, Combes C, Normand P, Steinberg C (2015) Micro-organisms and biotic interactions. In: Bertrand J, Caumette P, Lebaron P, Matheron R, Normand P, Sime-Ngando T (eds) Environmental microbiology: fundamentals and applications. Springer Verlag, Dordrecht, pp 395–444Google Scholar
  299. Mohanta TK, Bae H (2015) The diversity of fungal genome. Biol Proced Online 17:8PubMedPubMedCentralCrossRefGoogle Scholar
  300. Moran NA (1996) Accelerated evolution and Muller’s rachet in endosymbiotic bacteria. Proc Natl Acad Sci U S A 93:2873–2878PubMedPubMedCentralCrossRefGoogle Scholar
  301. Mori K, Kim H, Kakegawa T, Hanada S (2003) A novel lineage of sulfate-reducing microorganisms: Thermodesulfobiaceae fam. nov., Thermodesulfobium narugense, gen. nov., sp. nov., a new thermophilic isolate from a hot spring. Extremophiles 7:283–290PubMedCrossRefGoogle Scholar
  302. Morita R (1990) The starvation-survival state of microorganisms in nature and its relationship to bioavailable energy. Experientia 46:813–817CrossRefGoogle Scholar
  303. Moriyama M, Nikoh N, Hosokawa T, Fukatsu T (2015) Riboflavin Provisioning Underlies Wolbachia’s Fitness Contribution to Its Insect Host. MBio 6:e01732–e01715PubMedPubMedCentralCrossRefGoogle Scholar
  304. Morono Y, Terada T, Nishizawa M, Ito M, Hillion F, Takahata N, Sano Y, Inagaki F (2011) Carbon and nitrogen assimilation in deep subseafloor microbial cells. Proc Natl Acad Sci U S A 108:18295–18300PubMedPubMedCentralCrossRefGoogle Scholar
  305. Morris C, Conen F, Alex Huffman J, Phillips V, Pöschl U, Sands D (2014) Bioprecipitation: a feedback cycle linking earth history, ecosystem dynamics and land use through biological ice nucleators in the atmosphere. Glob Chang Biol 20:341–351PubMedCrossRefGoogle Scholar
  306. Morris RM, Rappé MS, Connon SA, Vergin KL, Siebold WA, Carlson C, Giovannoni S (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420:806–810PubMedCrossRefGoogle Scholar
  307. Moya A, Gil R, Latorre A, Peretó J, Pilar Garcillán-Barcia M, de la Cruz F (2009) Toward minimal bacterial cells: evolution vs. design. FEMS Microbiol Rev 33:225–235PubMedCrossRefGoogle Scholar
  308. Mukamolova G, Kaprelyants A, Kell D, Young M (2003) Adoption of the transiently non-culturable state – a bacterial survival strategy? Adv Microbiol Physiol 47:65–129CrossRefGoogle Scholar
  309. Muller HJ (1964) The relation of recombination to mutational advance. Mutat Res 106:2–9PubMedCrossRefGoogle Scholar
  310. Mushegian A, Koonin E (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci U S A 93:10268–10273PubMedPubMedCentralCrossRefGoogle Scholar
  311. Nakamura Y, Itoh T, Matsuda H, Gojobori T (2004) Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 36:760–766PubMedCrossRefGoogle Scholar
  312. Nicholson W, Schuerger A, Race M (2009) Migrating microbes and planetary protection. Trends Microbiol 17:389–392PubMedCrossRefGoogle Scholar
  313. Nilsson L, Oliver J, Kjelleberg S (1991) Resuscitation of Vibrio vulnificus from the viable but nonculturable state. J Bacteriol 173:5054–5059PubMedPubMedCentralCrossRefGoogle Scholar
  314. Nissen H (1987) Long term starvation of a marine bacterium, Alteromonas denitrificans, isolated from a Norwegian fjord. FEMS Microbiol Ecol 45:173–183CrossRefGoogle Scholar
  315. Nogva HK, Dromtorp S, Nissen H, Rudi K (2003) Ethidium monoazide for DNA-based differentiation of viable and dead bacteria by 5’-nuclease. PCR BioTechniques 810:812–813Google Scholar
  316. Nohmi T (2006) Environmental stress and lesion-bypass DNA polymerases. Annu Rev Microbiol 60:231–253PubMedCrossRefGoogle Scholar
  317. Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N et al (2007) Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res 17:7–15PubMedPubMedCentralCrossRefGoogle Scholar
  318. Novitsky J, Morita R (1977) Survival of a psychrophilic marine Vibrio under long-term nutrient starvation. Appl Environ Microbiol 33:635–641PubMedPubMedCentralGoogle Scholar
  319. Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299–304PubMedCrossRefGoogle Scholar
  320. Olendzenski L, Gogarten JP (2009) Evolution of genes and organisms: the tree/web of life in light of horizontal gene transfer. Ann N Y Acad Sci 1178:137–145PubMedCrossRefGoogle Scholar
  321. Oliver A (2005) Hypermutation in natural bacterial populations: consequences for medical microbiology. Rev Med Microbiol 16:25–32CrossRefGoogle Scholar
  322. Oliver A, Mena A (2010) Bacterial hypermutation in cystic fibrosis, not only for antibiotic resistance. Eur Soc Clin Microbiol Infect Dis 16:798–808CrossRefGoogle Scholar
  323. Oliver J (2010) Recent findings on the viable but nonculturable state in pathogenic bacteria. FEMS Microbiol Rev 34:415–425PubMedCrossRefGoogle Scholar
  324. Oliver J, Bockian R (1995) In vivo resuscitation, and virulence towards mice, of viable but nonculturable cells of Vibrio vulnificus. App Environ Microbiol 61:2620–2623Google Scholar
  325. Ollivier B, Caumette P, Garcia J, Mah R (1994) Anaerobic bacteria from hypersaline ecosystems. Microbiol Rev 58:27–38PubMedPubMedCentralGoogle Scholar
  326. Oren A (1999) Bioenergetic aspects of halophilism. Microbiol Mol Biol Rev 63:334–348PubMedPubMedCentralGoogle Scholar
  327. Oren A (2008) Microbial life at high salt concentration: phylogenetic and metabolic diversity. Saline Syst 4:2PubMedPubMedCentralCrossRefGoogle Scholar
  328. Oren A (2013) Life at high salt concentrations. The prokaryotes-prokaryotic communities and ecophysiology. Springer, Berlin/HeidelburgGoogle Scholar
  329. Orfaniotou F, Tzamalis P, Thanassoulas A, Stefanidi E, Zees A, Boutou E, Vlassi M, Nounesis G, Vorgias C (2009) The stability of the archaeal HU histone-like DNA-binding protein from Thermoplasma volcanium. Extremophiles 13:1–10PubMedCrossRefGoogle Scholar
  330. Padan E, Bibi E, Ito M, Krulwich T (2005) Alkaline pH homeostasis in bacteria: new insights. Biochim Biophys Acta 1717:67–88PubMedPubMedCentralCrossRefGoogle Scholar
  331. Paget E, Simonet P (1994) On the track of natural transformation in soil. FEMS Microbiol Ecol 15:109–117CrossRefGoogle Scholar
  332. Pais T, Lamosa P, Garcia-Moreno B, Turner D, Santos H (2009) Relationship between protein stabilization and protein rigidification induced by mannosylglycerate. J Mol Biol 394:237–250PubMedCrossRefGoogle Scholar
  333. Pál C, Papp B, Lercher M (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37:1372–1375PubMedCrossRefGoogle Scholar
  334. Pande S, Shitut S, Freund L, Westermann M, Bertels F, Colesie C, Bischofs I, Kost C (2015) Metabolic cross-feeding via intercellular nanotubes among bacteria. Nat Commun 6:6238PubMedCrossRefGoogle Scholar
  335. Parkes J (2000) A case of bacterial immortality? Nature 407:844–845PubMedCrossRefGoogle Scholar
  336. Parte A (2014) LPSN-list of prokaryotic names with standing in nomenclature. Nucl Acids Res 42:D613–D616PubMedCrossRefGoogle Scholar
  337. Paul K, Nonoh J, Mikulski L, Brune A (2012) “Methanoplasmatales,” Thermoplasmatales-related Archaea in termite guts and other environments, are the seventh order of methanogens. Appl Environ Microbiol 78:8245–8253PubMedPubMedCentralCrossRefGoogle Scholar
  338. Pernthaler J, Sattler B, Simek K, Schwarzenbacher A, Psenner R (1996) Top-down effects on the size-biomass distribution of a freshwater bacterioplankton community. Aquat Microb Ecol 10:255–263CrossRefGoogle Scholar
  339. Peters V, Rehm B (2005) In vivo monitoring of PHA granule formation using GFP-labeled PHA synthases. FEMS Microbiol Lett 248:93–100PubMedCrossRefGoogle Scholar
  340. Peterson C, Mandel M, Silhavy T (2005) Escherichia coli starvation diets: essential nutrients weigh in distinctly. J Bacteriol 187:7549–7553PubMedPubMedCentralCrossRefGoogle Scholar
  341. Phadtare S, Inouye M (2004) Genome-wide transcriptional analysis of the cold shock response in wild-type and cold-sensitive, quadruple-csp-deletion strains of Escherichia coli. J Bacteriol 186:7007–7014PubMedPubMedCentralCrossRefGoogle Scholar
  342. Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C et al (2013) Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science 341:281–286PubMedCrossRefGoogle Scholar
  343. Pinto D, Santos M, Chambel L (2015) Thirty years of viable but nonculturable state research: unsolved molecular mechanisms. Crit Rev Microbiol 41:61–76PubMedCrossRefGoogle Scholar
  344. Podar M, Anderson I, Makarova K, Elkins J, Ivanova N, Wall M, Lykidis A, Mavromatis K, Sun H, Hudson M et al (2008) A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol 9:R158PubMedPubMedCentralCrossRefGoogle Scholar
  345. Pöschl U, Shiraiwa M (2015) Multiphase chemistry at the atmosphere-biosphere interface influencing climate and public health in the anthropocene. Chem Rev 115:4440–4475PubMedCrossRefGoogle Scholar
  346. Postec A, Quéméneur M, Bes M, Mei N, Benaïssa F, Payri C, Pelletier B, Monnin C, Guentas-Dombrowsky L, Ollivier B et al (2015) Microbial diversity in a submarine carbonate edifice from the serpentinizing hydrothermal system of the Prony Bay (New Caledonia) over a 6-year period. Front Microbiol 6:857.  https://doi.org/10.3389/fmicb.2015.00857 CrossRefPubMedPubMedCentralGoogle Scholar
  347. Pötter M, Steinbüchel A (2005) Poly(3-hydroxybutyrate) granule-associated proteins: Impacts on poly(3-hydroxybutyrate) synthesis and degradation. Biomacromolecules 6:552–560PubMedCrossRefGoogle Scholar
  348. Poulsen M, Schwab C, Jensen B, Engberg R, Spang A (2013) Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. Nat Commun 4:1428PubMedCrossRefGoogle Scholar
  349. Pradel N, Ji B, Gimenez G, Talla E, Lenoble P, Garel M, Tamburini C, Fourquet P, Lebrun R, Bertin P et al (2013) The first genomic and proteomic characterization of a deep-sea sulfate reducer: insights into the piezophilic lifestyle of Desulfovibrio piezophilus. PLosOne 8:e55130CrossRefGoogle Scholar
  350. Preiss L, Hicks DB, Suziki S, Meier T, Krulwich TA (2015) Alkaliphilic bacteria with impact on industrial applications, concepts of early life forms, and bioenergetics of ATP synthesis. Front Bioeng Biotechnol 3:75PubMedPubMedCentralCrossRefGoogle Scholar
  351. Price P (2007) Microbial life in glacial ice and implications for a cold origin of life. FEMS Microbiol Ecol 59:217–231PubMedCrossRefGoogle Scholar
  352. Pucci F, Kwasigroch J, Rooman M (2017) SCooP: an accurate and fast predictor of protein stability curves as a function of temperature. Bioinformatics 33:3415–3422PubMedCrossRefGoogle Scholar
  353. Quayle J, Fuller R, Benson A, Calvin M (1957) Enzymatic carboxylation of ribulose diphosphate. J Am Chem Soc 76:3610–3612CrossRefGoogle Scholar
  354. Quéméneur M, Bes M, Postec A, Mei N, Hamelin J, Monnin C, Chavagnac V, Payri C, Pelletier B, Guentas-Dombrowsky L et al (2014) Spatial distribution of microbial communities in the shallow submarine alkaline hydrothermal field of the Prony Bay, New Caledonia. Environ Microbiol Rep 6:665–674PubMedCrossRefGoogle Scholar
  355. Radman M (1975) SOS repair hypothesis: phenomenology of an inducible DNA repair which is accompanied by mutagenesis. Basic Life Sci 5A:355–367PubMedGoogle Scholar
  356. Radman M (1999) Enzymes of evolutionary change. Nature 401:866–867PubMedCrossRefGoogle Scholar
  357. Raghoebarsing AA, Pol A, van de Pas-Schoonen KT, Smolders AJP, Ettwig KF, Rijpstra WIC (2006) A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 440:918–921PubMedCrossRefGoogle Scholar
  358. Rakhuba D, Kolomiets E, Dey E, Novik G (2010) Bacteriophage receptors, mechanisms of phage adsorption and penetration into host cell. Pol J Microbiol 59:145–155PubMedGoogle Scholar
  359. Ramamurthy T, Ghosh A, Pazhani G, Shinoda S (2014) Current perspectives on viable but non-culturable (VBNC) pathogenic bacteria. Front Public Health 2:103PubMedPubMedCentralCrossRefGoogle Scholar
  360. Ramírez-Arcos S, Fernández-Herrero L, Marín I, Berenguer J (1998) Anaerobic growth, a property horizontally transferred by an Hfr-like mechanism among extreme thermophiles. J Bacteriol 180:3137–3143PubMedPubMedCentralGoogle Scholar
  361. Rappe MS, Connon S, Vergin K, Giovannoni S (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633PubMedCrossRefGoogle Scholar
  362. Rasko D, Rosovitz M, Myers G, Mongodin E, Fricke W, Gajer P, Crabtree J, Sebaihia M, Thomson N, Chaudhuri R et al (2008) The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 190:6881–6893PubMedPubMedCentralCrossRefGoogle Scholar
  363. Rasmussen S, Chen L, Deamer D, Krakauer D, Packard N, Stadler P, Bedau M (2004) Evolution. Transitions from nonliving to living matter. Science 303:963–965PubMedCrossRefGoogle Scholar
  364. Ravagnani A, Finan CL, Young M (2005) A novel firmicute protein family related to the actinobacterial resuscitation-promoting factors by non-orthologous domain displacement. BMC Genomics 6:39PubMedPubMedCentralCrossRefGoogle Scholar
  365. Raven J (2009) Contributions of anoxygenic and oxygenic phototrophy and chemolithotrophy to carbon and oxygen fluxes in aquatic environments. Aquat Microb Ecol 56:177–192CrossRefGoogle Scholar
  366. Redfield R (2001) Do bacteria have sex ? Nat Rev Genet 2:634–639PubMedCrossRefGoogle Scholar
  367. Reeburgh W (2007) Oceanic methane biogeochemistry. Chem Rev 107:486–513PubMedCrossRefGoogle Scholar
  368. Rehm B (2003) Polyester synthases: natural catalysts for plastics. Biochem J 376:15–33PubMedPubMedCentralCrossRefGoogle Scholar
  369. Reysenbach A, Liu Y, Banta A, Beveridge T, Kirshtein J, Schouten S, Tivey M, Von Damm K, Voytek M (2006) A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents. Nature 442:444–447PubMedCrossRefPubMedCentralGoogle Scholar
  370. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA et al (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–437PubMedCrossRefPubMedCentralGoogle Scholar
  371. Rocap G, Larimer F, Lamerdin J, Malfatti S, Chain P, Ahlgren N, Arellano A, Coleman M, Hauser L, Hess W et al (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424:1042–1047PubMedCrossRefPubMedCentralGoogle Scholar
  372. Roszak D, Colwell R (1987) Survival strategies of bacteria in the natural environment. Microbiol Rev 51:365–379PubMedPubMedCentralGoogle Scholar
  373. Roszak D, Grimes D, Colwell R (1984) Viable but nonrecoverable stage of Salmonella enteritidis in aquatic systems. Can J Microbiol 30:334–338PubMedCrossRefPubMedCentralGoogle Scholar
  374. Røy H, Kallmeyer J, Adhikari R, Pockalny R, Jørgensen B, D’Hondt S (2012) Aerobic microbial respiration in 86-million-year-old deep-sea red clay. Science 336:922–925PubMedCrossRefGoogle Scholar
  375. Rudi K, Moen B, Drømtorp S, Holck A (2005) Use of ethidium monoazide and PCR in combination for quantification of viable and dead cells in complex samples. Appl Environ Microbiol 71:1018–1024PubMedPubMedCentralCrossRefGoogle Scholar
  376. Russell M, Barge L, Bhartia R, Bocanegra D, Bracher P, Branscomb E, Kidd R, MacGlynn S, Meier D, Nitscke W et al (2014) The drive to life on wet and, icy worlds. Astrobiol 14:308–343CrossRefGoogle Scholar
  377. Sagan L (1967) On the origin of mitosing cells. J Theor Biol 14:225–274CrossRefGoogle Scholar
  378. Samson J, Magadán A, Sabri M, Moineau S (2013) Revenge of the phages: defeating bacterial defences. Nat Rev Microbiol 11:675–687PubMedCrossRefGoogle Scholar
  379. Sanchez-Andrea I, Knittel K, Amann R, Amils R, Sanz J (2012) Quantification of Tinto River sediment microbial communities: Importance of sulfate-reducing bacteria and their role in attenuating acid mine drainage. Appl Environ Microbiol 78:4638–4645PubMedPubMedCentralCrossRefGoogle Scholar
  380. Santander R, Oliver J, Biosca E (2014) Cellular, physiological, and molecular adaptive responses of Erwinia amylovora to starvation. FEMS Microbiol Ecol 88:258–271PubMedCrossRefGoogle Scholar
  381. Santos CL, Tavares F, Thioulouse J, Normand P (2009) A phylogenomic analysis of bacterial helix-turn-helix transcription factors. FEMS Microbiol Rev 33:411–429PubMedCrossRefGoogle Scholar
  382. Scanlan D, Ostrowski M, Mazard S, Dufresne A, Garczarek L, Hess W, Post A, Hagemann M, Paulsen I, Partensky F (2009) Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev 73:249–299PubMedPubMedCentralCrossRefGoogle Scholar
  383. Schippers A, Neretin L, Kallmeyer J, Ferdelman T, Cragg B, Parkes R, Jørgensen B (2005) Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Nature 433:861–864PubMedCrossRefGoogle Scholar
  384. Schmidt O, Hink L, Horn M, Drake H (2016) Peat: home to novel syntrophic species that feed acetate- and hydrogen-scavenging methanogens. ISME J 10:1954–1966.  https://doi.org/10.1038/ismej.2015.256 CrossRefPubMedPubMedCentralGoogle Scholar
  385. Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer M, Bartels D, Bekel T, Beyer S, Bode E et al (2007) Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat Biotechnol 25:1281–1289PubMedCrossRefGoogle Scholar
  386. Schrenk M, Huber J, Edwards K (2010) Microbial provinces in the subseafloor. Ann Rev Mar Sci 2:279–304PubMedCrossRefGoogle Scholar
  387. Schulz H, Brinkhoff T, Ferdelman T, Mariné M, Teske A, Jorgensen B (1999) Dense populations of a giant sulfur bacterium in Namibian shelf sediments. Science 284:493–495PubMedCrossRefGoogle Scholar
  388. Senoh M, Ghosh-Banerjee J, Ramamurthy T, Hamabata T, Kurakawa T, Takeda M, Colwell R, Nair G, Takeda Y (2010) Conversion of viable but nonculturable Vibrio cholerae to the culturable state by co-culture with eukaryotic cells. Microbiol Immunol 54:502–507PubMedCrossRefGoogle Scholar
  389. Setlow P (2006) Spores of Bacillus subtilis: their resistance to and killing by radiation, heat and chemicals. J Appl Microbiol 101:514–525PubMedCrossRefGoogle Scholar
  390. Setlow P (2013) When the sleepers wake: the germination of spores of Bacillus species. J Appl Microbiol 115:1251–1268PubMedCrossRefGoogle Scholar
  391. Setlow P (2014a) Germination of spores of Bacillus species: what we know and do not know. J Bacteriol 196:1297–1305PubMedPubMedCentralCrossRefGoogle Scholar
  392. Setlow P (2014b) Spore resistance properties. Microbiol Spectr 2:1–15Google Scholar
  393. Sghaier H, Hezbri K, Ghodhbane-Gtari F, Pujic P, Sen A, Daffonchio D, Boudabous A, Tisa LS, Klenk HP, Armengaud J et al (2015) Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes. Isme J 10:21–29.  https://doi.org/10.1038/ismej.2015.108 CrossRefPubMedPubMedCentralGoogle Scholar
  394. Shivanand P, Mugeraya G (2011) Halophilic bacteria and their compatible solutes-osmoregulation and potential applications. Curr Sci 100:1516–1521Google Scholar
  395. Shoun H, Kim DH, Uchiyama H, Sugiyama J (1992) Denitrification by fungi. FEMS Microbiol Lett 94:277–281CrossRefGoogle Scholar
  396. Sieburth JM, Smetacek V, Lenz J (1978) Pelagic ecosystem structure: heterotrophic compartments of the plankton and their relationship to plankton size fractions. Limnol Oceanogr 23:1256–1263CrossRefGoogle Scholar
  397. Siliakus M, van der Oost J, Kengen S (2017) Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure. Extremophiles 21:651–670PubMedPubMedCentralCrossRefGoogle Scholar
  398. Silver WS, Postgate JR (1973) Evolution of asymbiotic nitrogen fixation. J Theor Biol 40:1–10PubMedCrossRefGoogle Scholar
  399. Simonato F, Campanaro S, Lauro F, Vezzi A, D’Angelo M, Vitulo N, Valle G, Bartlett D (2006) Piezophilic adaptation: a genomic point of view. J Biotechnol 126:11–25PubMedCrossRefGoogle Scholar
  400. Simpson GG (1944) Tempo and mode in evolution. Columbia University Press, New YorkGoogle Scholar
  401. Sinha RP, Hader DP (2002) UV-induced DNA damage and repair: a review. Photochem Photobiol Sci 1:225–236PubMedCrossRefGoogle Scholar
  402. Slepova T, Sokolova T, Lysenko T, Tourova T, Kolganova T, Kamzolkina O, Karpov G, Bonch-Osmolovskaya E (2006) Carboxydocella sporoproducens sp. nov., a novel anaerobic CO-utilizing/H2-producing thermophilic bacterium from a Kamchatka hot spring. Int J Syst Evol Microbiol 56:797–800PubMedCrossRefGoogle Scholar
  403. Slobodkin A, Reysenbach A, Slobodkina G, Kolganova T, Kostrikina N, Bonch-Osmolovskaya E (2013) Dissulfuribacter thermophilus gen. nov., sp. nov., a thermophilic, autotrophic, sulfur-disproportionating, deeply branching deltaproteobacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 63:1967–1971PubMedCrossRefGoogle Scholar
  404. Sneath P (1962) Longevity of micro-organisms. Nature 195:643–646PubMedCrossRefGoogle Scholar
  405. Sorokin D, Makarova K, Abbas B, Golyshin P, Galinski E, Ciordia S, Mena M, Merkel A, Wolf Y, van Loosdrecht M et al (2017) Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis. Nat Microbiol 2:17081PubMedPubMedCentralCrossRefGoogle Scholar
  406. Soulas G, Martin-Laurent F (2015) Pesticide biodegradation: genetic basis. The examples of hormone herbicides and s-triazines. In: Bertrand J, Caumette P, Lebaron P, Matheron R, Normand P, Sime-Ngando T (eds) Environmental microbiology: fundamentals and applications. Springer, Dordrecht/Heidelberg/New York/London, pp 693–697Google Scholar
  407. Spring S, Merkhoffer B, Weiss N, Kroppenstedt R, Hippe H, Stackebrandt E (2003) Characterization of novel psychrophilic clostridia from an Antarctic microbial mat: description of Clostridium frigoris sp. no., Clostridium lacusfryxellense sp. nov., Clostridium bowmanii sp. nov. and Clostridium psychrophilum sp. nov.and reclassification of Clostridium laramiense as Clostridium estertheticum subsp laramiense subsp. nov. Int J Syst Evol Microbiol 53:1019–1029PubMedCrossRefGoogle Scholar
  408. Stan-Lotter H, Pfaffenhuemer M, Legat A, Busse H-J, Radax C, Gruber C (2002) Halococcus dombrowskii sp. nov., an archaeal isolate from a Permian alpine salt deposit. Int J Syst Evol Microbiol 52:1807–1814PubMedGoogle Scholar
  409. Stanier RY, Ingraham JL, Wheelis ML, Painter PR (1986) The microbial world, 5th edn. Prentice-Hall, Englewood CliffsGoogle Scholar
  410. Steinbüchel A, Aerts K, Babel W, Follner C, Liebergesell M, Madkour M, Mayer F, Pieper-Furst U, Pries A, Valentin H (1995) Considerations on the structure and biochemistry of bacterial polyhydroxyalkanoic acid inclusions. Can J Microbiol 41:94–105PubMedCrossRefGoogle Scholar
  411. Steinbüchel A, Valentin H (1995) Diversity of bacterial polyhydroxyalkanoic acids. FEMS Microbiol Lett 128:219–228CrossRefGoogle Scholar
  412. Steinert M, Emödy L, Amann R, Hacker J (1997) Resuscitation of viable but nonculturable Legionella pneumophila Philadelphia JR32 by Acanthamoeba castellanii. Appl Environ Microbiol 63:2047–2053PubMedPubMedCentralGoogle Scholar
  413. Stenström J, Svensson K, Johansson M (2001) Reversible transition between active and dormant microbial states in soil. FEMS Microbiol Ecol 36:93–104PubMedCrossRefGoogle Scholar
  414. Stetter K (1999) Hyperthermophiles: isolation, classification, and properties. In: Horikoshi K, Grant W (eds) Extremophiles microbial life in extreme environments. Wiley, New York, pp 1–24Google Scholar
  415. Stetter K (2006) History of discovery of the first hyperthermophiles. Extremophiles 10:357–362PubMedCrossRefGoogle Scholar
  416. Stevenson L (1978) A case for bacterial dormancy in aquatic systems. Microbiol Ecol 4:127–133CrossRefGoogle Scholar
  417. Suzuki S, Ishii S, Wu A, Tenney A, Wanger G, Kuenen J, Nealson K (2013) Microbial diversity in The Cedars, an ultrabasic, ultrareducing, and low salinity serpentinizing ecosystem. Proc Natl Acad Sci U S A 110:15336–15341PubMedPubMedCentralCrossRefGoogle Scholar
  418. Suzuki S, Kuenen J, Schipper K, Van Der Velde S, Ishii S, Wu A, Sorokin D, Tenney A, Meng X, Morrill P et al (2014) Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site. Nature Com 5:3900CrossRefGoogle Scholar
  419. Swingley W, Chen M, Cheung P, Conrad A, Dejesa L, Hao J, Honchak B, Karbach L, Kurdoglu A, Lahiri S et al (2008) Niche, adaptation, and, genome, expansion, in, the, chlorophyll, d-producing, cyanobacterium, Acaryochloris, marina. Proc Natl Acad Sci U S A 105:2005–2010PubMedPubMedCentralCrossRefGoogle Scholar
  420. Taddei F, Radman M, Maynard-Smith J, Toupance B, Gouyon P, Godelle B (1997) Role of mutator alleles in adaptive evolution. Nature 387:700–702PubMedCrossRefGoogle Scholar
  421. Takai K, Nakamura K, Toki T, Tsunogai U, Miyazaki M, Miyazaki J, Hirayama H, Nakagawa S, Nunoura T, Horikoshi K (2008) Cell proliferation at 122 °C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation. Proc Natl Acad Sci U S A 105:10949–10954PubMedPubMedCentralCrossRefGoogle Scholar
  422. Takami H, Noguchi H, Takaki Y, Uchiyama I, Toyoda A, Nishi S, Chee G, Arai W, Nunoura T, Itoh T et al (2012) A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem. PLoS ONE 7:e30559PubMedPubMedCentralCrossRefGoogle Scholar
  423. Takano S, Pawlowska B, Gudelj I, Yomo T, Tsuru S (2017) Density-dependent recycling promotes the long-term survival of bacterial populations during periods of starvation. MBio 8:pii: e02336–02316Google Scholar
  424. Tamegai H, Ota Y, Haga M, Fujimori H, Kato C, Nogi Y, Kawamoto J, Kurihara T, Sambongi Y (2011) Piezotolerance of the respiratory terminal oxidase activity of the piezophilic Shewanella violacea DSS12 as compared with non-piezophilic Shewanella species. Biosci Biotechnol Biochem 75:919–924PubMedCrossRefGoogle Scholar
  425. Tan I, Ramamurthi K (2013) Spore formation in Bacillus subtilis. Environ Microbiol Rep 6:212–225PubMedPubMedCentralCrossRefGoogle Scholar
  426. Tenaillon O, Toupance B, Le Nagard H, Taddei F, Godelle B (1999) Mutators, population size, adaptive landscape and the adaptation of asexual populations of bacteria. Genetics 152:485–493PubMedPubMedCentralGoogle Scholar
  427. Thao M, Gullan P, Baumann P (2002) Secondary (gamma-Proteobacteria) endosymbionts infect the primary (beta-Proteobacteria) endosymbionts of mealybugs multiple times and coevolve with their hosts. Appl Environ Microbiol 68:3190–3197PubMedPubMedCentralCrossRefGoogle Scholar
  428. Thauer RK, Jungermann K, Deker K (1977) Energy conservation in chemotrophic anaerobic bacteria. Microbiol Mol Biol Rev 41:100–180Google Scholar
  429. Thauer R, Kaster A-K, Seedorf H, Buckel W, Hedderich R (2008) Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 6:579–591PubMedCrossRefGoogle Scholar
  430. Thiel T, Pratte B, Zhong J, Goodwin L, Copeland A, Lucas S, Han C, Pitluck S, Land M, Kyrpides N et al (2014) Complete genome sequence of Anabaena variabilis ATCC 29413. Stand Genomic Sci 9:562–573PubMedPubMedCentralCrossRefGoogle Scholar
  431. Thomas C, Nielsen K (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3:711–721PubMedCrossRefGoogle Scholar
  432. Tiago I, Chung A, Verissimo A (2004) Bacterial diversity in a non saline alkaline environment: heterotrophic aerobic populations. Appl Environ Microbiol 70:7378–7387PubMedPubMedCentralCrossRefGoogle Scholar
  433. Tiago I, Verissimo A (2013) Microbial and functional diversity of a subterrestrial high pH groundwater associated to serpentinization. Environ Microbiol 15:1687–1706PubMedCrossRefGoogle Scholar
  434. Tian J, Sinskey AJ, Stubbe J (2005) Kinetic studies of polyhydroxybutyrate granule formationin wautersia eutropha H16 by transmission electron microscopy. J Bacteriol 187:3814–3824PubMedPubMedCentralCrossRefGoogle Scholar
  435. Torrella F, Morlta RY (1981) Microcultural study of bacterial size changes and microcolony and ultramicrocolony formation by heterotrophic bacteria in seawater. Appl Environ Microbiol 41:518–527PubMedPubMedCentralGoogle Scholar
  436. Unsworth B, Cross T, Seaward M, Sims R (1977) The longevity of thermoactinomycete endospores in natural substrates. J Appl Bacteriol 42:45–52PubMedCrossRefGoogle Scholar
  437. Vaïtilingom M, Deguillaume L, Vinatier V, Sancelme M, Amato P, Chaumerliac N, Delort A-M (2013) Potential impact of microbial activity on the oxidant capacity and organic carbon budget in clouds. Proc Natl Acad Sci U S A 110:559–564PubMedCrossRefGoogle Scholar
  438. van Ditmarsch D, Xavier J (2014) Seeing is believing: what experiments with microbes reveal about evolution. Trends Microbiol 22:2–4PubMedCrossRefGoogle Scholar
  439. van Niftrik L, Jetten MS (2012) Anaerobic ammonium-oxidizing bacteria: unique microorganisms with exceptional properties. Microbiol Molec Biol Rev 76:585–596CrossRefGoogle Scholar
  440. Vanwonterghem I, Evans P, Parks D, Jensen P, Woodcroft B, Hugenholtz P, Tyson G (2016) Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nat Microbiol 1:16170PubMedCrossRefGoogle Scholar
  441. Venturi V, Weisbeek P, Koster M (1995) Gene regulation of siderophore-mediated iron acquisition in Pseudomonas: not only the Fur repressor. Mol Microbiol 17:603–610PubMedCrossRefGoogle Scholar
  442. Vreeland R, Rosenzweig W, Powers D (2000) Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal. Nature 407:897–900PubMedCrossRefGoogle Scholar
  443. Waite D, Vanwonterghem I, Rinke C, Parks D, Zhang Y, Takai K, Sievert S, Simon J, Campbell B, Hanson T et al (2017) Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol 8:682PubMedPubMedCentralCrossRefGoogle Scholar
  444. Wallace AR (1870) Contributions to the theory of natural selection. Macmillan and Company, New York/LondonGoogle Scholar
  445. Wang G, Mayes M, Gu L, Schadt C (2014a) Representation of dormant and active microbial dynamics for ecosystem modeling. PLoS ONE 9:e89252PubMedPubMedCentralCrossRefGoogle Scholar
  446. Wang HF, Zhang YG, Chen JY, Hozzein WN, Li L, Wadaan MA, Zhang YM, Li WJ (2014b) Nesterenkonia rhizosphaerae sp. nov., a novel alkaliphilic actinobacterium isolated from rhizosphere soil of Reaumuria soongorica in saline-alkaline desert. Int J Syst Evol Microbiol.  https://doi.org/10.1099/ijs.0.066894-0 CrossRefGoogle Scholar
  447. Wang Q, Cen Z, Zhao J (2015) The survival mechanisms of thermophiles at high temperatures: an angle of omics. Physiology 30:97–106PubMedCrossRefGoogle Scholar
  448. Waters E, Hohn M, Ahel I, Graham D, Adams M, Barnstead M, Beeson K, Bibbs L, Bolanos R, Keller M et al (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci U S A 100:12984–12988PubMedPubMedCentralCrossRefGoogle Scholar
  449. Werts C, Michel V, Hofnung M, Charbit A (1994) Adsorption of bacteriophage lambda on the LamB protein of Escherichia coli K-12: point mutations in gene J of lambda responsible for extended host range. J Bacteriol 176:941–947PubMedPubMedCentralCrossRefGoogle Scholar
  450. Westall F, Hickman-Lewis K, Hinman N, Gautret P, Campbell K, Bréhéret J, Foucher F, Hubert A, Sorieul S, Dass A et al (2018) A hydrothermal-sedimentary context for the origin of life. Astrobiology 18:1–35CrossRefGoogle Scholar
  451. Westberry T, Siegel DA (2006) Spatial and temporal distribution of Trichodesmium blooms in the world’s oceans. Glob Biogeochem Cycles 20:4CrossRefGoogle Scholar
  452. Whitesides M, Oliver J (1997) Resuscitation of Vibrio vulnificus from the viable but nonculturable state. App Environ Microbiol 63:1002–1005Google Scholar
  453. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95:6578–6583PubMedPubMedCentralCrossRefGoogle Scholar
  454. Wiegel J (2011) Anaerobic alkaliphiles and alkaliphilic poly-extremophiles. In: Horikoshi K (ed) Extremophiles handbook. Springer, New York, pp 82–97Google Scholar
  455. Wildman S (2002) Along the trail from Fraction I protein to Rubisco (ribulose bisphosphate carboxylase-oxygenase). Photosynth Res 73:243–250PubMedCrossRefGoogle Scholar
  456. Winogradsky SN (1949) Microbiologie du Sol. In: Problemes et Methodes: cinquante de recherches. Masson et Cie Eds, ParisGoogle Scholar
  457. Winters Y, Lowenstein T, Timofeeff M (2015) Starvation-survival in Haloarchaea. Life (Basel) 5:1587–1609Google Scholar
  458. Wirsen CO, Molyneaux SJ (1999) A study of deep-sea natural microbial populations and barophilic pure cultures using a high-pressure chemostat. Appl Environ Microbiol 65:5314–5321PubMedPubMedCentralGoogle Scholar
  459. Wolk CP (2000) Heterocyst formation in Anabaena. In: Brun YVS, Shimkets LJ (eds) Prokaryotic development. ASM Press, Washington, DC, pp 83–104Google Scholar
  460. Woodford N, Ellinton M (2006) The emergence of antibiotic resistance by mutation. Clin Microbiol Infect 13:5–18CrossRefGoogle Scholar
  461. Wright S (1931) Evolution in Mendelian populations. Genetics 16:97–159PubMedPubMedCentralGoogle Scholar
  462. Wu B, Liang W, Kan B (2016) Growth phase, oxygen, temperature, and starvation affect the development of viable but non-culturable state of Vibrio cholerae. Front Microbiol 7:404PubMedPubMedCentralGoogle Scholar
  463. Xu H, Roberts N, Singleton F, Attwell R, Grimes D, Colwell R (1982) Survival and viability of nonculturable Escherichia coli and Vibrio cholerae in the estuarine and marine environment. Microb Ecol 8:313–323PubMedCrossRefGoogle Scholar
  464. Yamamoto H (2000) Viable but nonculturable state as a general phenomenon of non-spore- forming bacteria, and its modeling. J Infect Chemother 6:112–114PubMedCrossRefGoogle Scholar
  465. Yaron S, Matthews K (2002) A reverse transcriptase-polymerase chain reaction assay for detection of viable Escherichia coli O157:H7: investigation of specific target genes. J Appl Microbiol 92:633–640PubMedCrossRefGoogle Scholar
  466. Yayanos AA, Dietz AS, Van Boxtel R (1981) Obligately barophilic bacterium from the Mariana trench. Proc Natl Acad Sci U S A 78:5212–5215PubMedPubMedCentralCrossRefGoogle Scholar
  467. Ye Y, Ma B, Dong C, Zhang H, Chen L, Guo FB (2016) A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network. Sci Rep 6:35082PubMedPubMedCentralCrossRefGoogle Scholar
  468. Young K (2006) The selective value of bacterial shape. Microbiol Mol Biol Rev 70:660–703PubMedPubMedCentralCrossRefGoogle Scholar
  469. Youssef N, Savage-Ashlock K, McCully A, Luedtke B, Shaw E, Hoff W, Elshahed M (2014) Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales. ISME J 8:636–649PubMedCrossRefGoogle Scholar
  470. Yu JS, Vargas M, Mityas C, Noll KM (2001) Liposome-mediated DNA uptake and transient expression in Thermotoga. Extremophiles 5:53–60PubMedCrossRefGoogle Scholar
  471. Yumoto I, Hirota K, Yoshimune K (2011) Environmental distribution and taxonomic diversity of alkaliphiles. In: Horikoshi K (ed) Extremophiles handbook. Springer, New York, pp 56–79Google Scholar
  472. Zahnle KJ (1986) Photochemistry of methan and the formation of hydrocyanide (HCN) in the earth’s early atmosphere. J Geophys Res 91:2819–2834CrossRefGoogle Scholar
  473. Zarzycki J, Brecht V, Müller M, Fuchs G (2009) Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus. Proc Natl Acad Sci U S A 106:21317–21322PubMedPubMedCentralCrossRefGoogle Scholar
  474. Žgur-Bertok D (2013) DNA damage repair and bacterial pathogens. PLoS Pathog 9:e1003711PubMedPubMedCentralCrossRefGoogle Scholar
  475. Zhang H, Fu H, Wang J, Sun L, Jiang Y, Zhang L, Gao H (2013) Impacts of nitrate and nitrite on physiology of Shewanella oneidensis. PLoS ONE 8:e62629PubMedPubMedCentralCrossRefGoogle Scholar
  476. Zhao X, Schwartz CL, Pierson J, Giovannoni SJ, McIntosh JR, Nicastro D (2017a) Three-dimensional structure of the ultraoligotrophic marine bacterium “Candidatus Pelagibacter ubique”. Appl Environ Microbiol:83, pii: e02807–02816.  https://doi.org/10.01128/AEM.02807-02816
  477. Zhao X, Zhong J, Wei C, Lin C-W, Ding T (2017b) Current perspectives on viable but non-culturable state in foodborne pathogens. Front Microbiol 8:580PubMedPubMedCentralGoogle Scholar
  478. Zhaxybayeva O, Swithers K, Lapierre P, Fournier G, Bickhart D, DeBoy R, Nelson K, Nesbø C, Doolittle W, Gogarten J et al (2009) On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc Natl Acad Sci U S A 106:5865–5870PubMedPubMedCentralCrossRefGoogle Scholar
  479. 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 4:79–87PubMedCrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Jean-Claude Bertrand
    • 1
    Email author
  • Patricia Bonin
    • 2
  • Bernard Ollivier
    • 2
  • Karine Alain
    • 3
  • Anne Godfroy
    • 4
  • Nathalie Pradel
    • 2
  • Philippe Normand
    • 5
  1. 1.Unité Mixte de Service, UMS 3470, OSU PythéasAix Marseille UniversitéMarseille CedexFrance
  2. 2.Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110MarseilleFrance
  3. 3.CNRS, Université de Bretagne Occidentale, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes – UMR6197, IfremerPlouzanéFrance
  4. 4.IFREMER, CNRS, Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes – UMR6197, IfremerPlouzanéFrance
  5. 5.Laboratoire d’Ecologie Microbienne, UMR 5557Université Claude Bernard Lyon 1VilleurbanneFrance

Personalised recommendations