1887

Chapter 2 : Evolution in the

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

Evolution in the , Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555819323/9781555816759_Chap02-1.gif /docserver/preview/fulltext/10.1128/9781555819323/9781555816759_Chap02-2.gif

Abstract:

The family (domain Bacteria; kingdom ; phylum ; class ; order ) ( Fig. 1 ) is a globally dispersed and phenotypically heterogeneous group of bacteria ( ). It therefore follows that the family possesses a considerable evolutionary history for scientists to unravel. In recent years, the issue of evolution in the has been probed from two directions. Some researchers have taken an ecological approach to understand the organisms’ adaptive evolution to particular environmental niches; others have pursued a laboratory-based approach in which single laboratory strains are directed to evolve under particular conditions determined by the experimenter. Both approaches have yielded new insights. As in so many other facets of the biology of the , most of our knowledge has been derived from the intense study of relatively few members of the family, most notably ( ). Much less information has been obtained concerning the vast majority of the , prompting the present examination of diversity and evolution within this ubiquitous family. The present article builds upon previous reviews of the topic ( ). Additional information on the genomic diversity of spore-forming and on the ecology of the can be found in articles by Galperin ( ) and Mandic-Mulec et al. ( ).

Citation: Fajardo-Cavazos P, Maughan H, Nicholson W. 2016. Evolution in the , p 21-58. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0020-2014
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1
Figure 1

Taxonomic position of the reconstructed from 16S rDNA data posted in the Ribosomal Database Project Release 10 (http://rdp.cme.msu.edu/) ( ).

Citation: Fajardo-Cavazos P, Maughan H, Nicholson W. 2016. Evolution in the , p 21-58. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0020-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Plots of D value versus temperature for 168 spores suspended in water (open circles) or in saturated NaCl (filled circles). The lines are best-fit extrapolations of the data to ambient temperature (25°C; thick vertical line). Data are averages of triplicate determinations that varied by less than 5%.

Citation: Fajardo-Cavazos P, Maughan H, Nicholson W. 2016. Evolution in the , p 21-58. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0020-2014
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555819323.chap2
1. Ciccarelli FD,, Doerks T,, von Mering C,, Creevey CJ,, Snel B,, Bork P . 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311 : 12831287.[PubMed] [CrossRef]
2. Wu D,, Hugenholtz P,, Mavromatis K,, Pukall R,, Dalin E,, Ivanova NN,, Kunin V,, Goodwin L,, Wu M,, Tindall BJ,, Hooper SD,, Pati A,, Lykidis A,, Spring S,, Anderson IJ,, D’haeseleer P,, Zemla A,, Singer M,, Lapidus A,, Nolan M,, Copeland A,, Han C,, Chen F,, Cheng JF,, Lucas S,, Kerfeld C,, Lang E,, Gronow S,, Chain P,, Bruce D,, Rubin EM,, Kyrpides NC,, Klenk HP,, Eisen JA . 2009. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462 : 10561060.[PubMed] [CrossRef]
3. Graumann PE . 2007. Bacillus: Cellular and Molecular Biology. Caister Academic Press, Hethersett, UK.
4. Sonenshein AL,, Hoch JA,, Losick R (ed). 2002. Bacillus subtilis and Its Closest Relatives: From Genes to Cells. ASM Press, Washington, DC.
5. Nicholson WL . 2002. Roles of Bacillus endospores in the environment. Cell Mol Life Sci 59 : 410416.[PubMed] [CrossRef]
6. Nicholson WL, . 2004. Ubiquity, longevity, and ecological roles of Bacillus spores, p 115. In Ricca E,, Henriques AO,, Cutting SM (ed), Bacterial Spore Formers: Probiotics and Emerging Applications. Horizon Scientific Press, Norfolk, UK. [PubMed]
7. Priest FG, . 1993. Systematics and ecology of Bacillus , p 316. In Sonenshein AL,, Hoch JA,, Losick R (ed), Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology, and Molecular Genetics. ASM Press, Washington, DC.
8. Slepecky RA,, Leadbetter ER, . 1994. Ecology and relationships of endospore-forming bacteria: changing perspectives, p 195206. In Piggot PJ,, Moran CP Jr,, Youngman P (ed), Regulation of Bacterial Differentiation. American Society for Microbiology, Washington, DC.
9. Wiedenbeck J,, Cohan FM . 2011. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev 35 : 957976.[PubMed] [CrossRef]
10. Logan NA,, Halket G, . 2011. Developments in the taxonomy of aerobic, endospore-forming bacteria, p 131. In Logan NA,, De Vos P (ed), Endospore-Forming Soil Bacteria. Springer-Verlag, Heidelberg, Germany. [CrossRef]
11. Cohn F . 1872. Untersuchungen über Bacterien. I Beitr Biol Pfl 1 : 127224.
12. Koch R . 1876. Die Ätiologie der Milzbrand-krankheit, begründet auf die Entwicklungsgeschichte des Bacillus anthracis . Beitr Biologie Pflanz 2 : 277310.
13. Beierlein JM,, Anderson AC . 2011. New developments in vaccines, inhibitors of anthrax toxins, and antibiotic therapeutics for Bacillus anthracis . Curr Med Chem 18 : 50835094.[PubMed] [CrossRef]
14. Hudson MJ,, Beyer W,, Boehm R,, Fasanella A,, Garofolo G,, Golinski R,, Goossens PL,, Hahn U,, Hallis B,, King A,, Mock M,, Montecucco C,, Ozin A,, Tonello F,, Kaufmann SHE . 2008. Bacillus anthracis: balancing innocent research with dual-use potential. Int J Med Microbiol 298 : 345364.[PubMed] [CrossRef]
15. Graumann P . 2007. Bacillus: Cellular and Molecular Biology. Caister Academic Press, Hethersett, United Kingdom.
16. Winslow CE,, Broadhurst J,, Buchanan RE,, Krumwiede C,, Rogers LA,, Smith GH . 1920. The families and genera of the bacteria: final report of the Committee of the Society of American Bacteriologists on Characterization and Classification of Bacterial Types. J Bacteriol 5 : 191229.[PubMed]
17. Bergey DH,, Harrison FC,, Breed RS,, Hammer BW,, Huntoon FW . 1923. Bergey’s Manual of Determinative Bacteriology: A Key for the Identification of Organisms of the Class Schizomycetes. Williams & Wilkins, Baltimore, MD.
18. Woese CR,, Fox GE . 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74 : 50885090.[PubMed] [CrossRef]
19. Ash C,, Farrow JAE,, Wallbanks S,, Collins MD . 1991. Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small subunit ribosomal RNA sequences. Lett Appl Microbiol 13 : 202206.[CrossRef]
20. Priest FG, . 1993. Systematics and ecology of Bacillus , p 316. In Sonenshein AL,, Hoch JA,, Losick R (ed), Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology, and Molecular Genetics. American Society for Microbiology, Washington, DC.
21. Schloss PD,, Handelsman J . 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71 : 15011506.[PubMed] [CrossRef]
22. Stackebrandt E,, Goebel BM . 1994. A place for DNA-DNA reassociation and 16S ribosomal RNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44 : 846849.[CrossRef]
23. De Vos P,, Garrity GM,, Jones D,, Kreig NR,, Ludwig W,, Rainey FA,, Schleifer K-H,, Whitman WB (ed). 2009. Bergey’s Manual of Systematic Bacteriology , 2nd ed, vol 3. The Firmicutes. Springer-Verlag, New York, NY.
24. Maughan H,, Van der Auwera G . 2011. Bacillus taxonomy in the genomic era finds phenotypes to be essential though often misleading. Infect Genet Evol 11 : 789797.[PubMed] [CrossRef]
25. David LA,, Alm EJ . 2011. Rapid evolutionary innovation during an Archaean genetic expansion. Nature 469 : 9396.[PubMed] [CrossRef]
26. Moreno-Letelier A,, Olmedo G,, Eguiarte LE,, Martinez-Castilla L,, Souza V . 2011. Parallel evolution and horizontal gene transfer of the pst operon in Firmicutes from oligotrophic environments. Int J Evol Biol 2011 : 781642. doi:10.4061/2011/781642 [PubMed] [CrossRef]
27. Hobbs JK,, Shepherd C,, Saul DJ,, Demetras NJ,, Haaning S,, Monk CR,, Daniel RM,, Arcus VL . 2012. On the origin and evolution of thermophily: reconstruction of functional precambrian enzymes from ancestors of Bacillus . Mol Biol Evol 29 : 825835.[PubMed] [CrossRef]
28. Alcaraz LD,, Moreno-Hagelsieb G,, Eguiarte LE,, Souza V,, Herrera-Estrella L,, Olmedo G . 2010. Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics. BMC Genomics 11 : 332. doi:10.1186/1471-2164-11-332. [PubMed] [CrossRef]
29. Kobayashi K,, Ehrlich S,, Albertini A,, Amati G,, Andersen K,, Arnaud M,, Asai K,, Ashikaga S,, Aymerich S,, Bessieres P,, Boland F,, Brignell S,, Bron S,, Bunai K,, Chapuis J,, Christiansen L,, Danchin A,, Debarbouille M,, Dervyn E,, Deuerling E,, Devine K,, Devine S,, Dreesen O,, Errington J,, Fillinger S,, Foster S,, Fujita Y,, Galizzi A,, Gardan R,, Eschevins C,, Fukushima T,, Haga K,, Harwood C,, Hecker M,, Hosoya D,, Hullo M,, Kakeshita H,, Karamata D,, Kasahara Y,, Kawamura F,, Koga K,, Koski P,, Kuwana R,, Imamura D,, Ishimaru M,, Ishikawa S,, Ishio I,, Le Coq D,, Masson A,, Mauel C,, Meima R,, Mellado R,, Moir A,, Moriya S,, Nagakawa E,, Nanamiya H,, Nakai S,, Nygaard P,, Ogura M,, Ohanan T,, O’Reilly M,, O’Rourke M,, Pragai Z,, Pooley H,, Rapoport G,, Rawlins J,, Rivas L,, Rivolta C,, Sadaie A,, Sadaie Y,, Sarvas M,, Sato T,, Saxild H,, Scanlan E,, Schumann W,, Seegers J,, Sekiguchi J,, Sekowska A,, Seror S,, Simon M,, Stragier P,, Studer R,, Takamatsu H,, Tanaka T,, Takeuchi M,, Thomaides H,, Vagner V,, van Dijl J,, Watabe K,, Wipat A,, Yamamoto H,, Yamamoto M,, Yamamoto Y,, Yamane K,, Yata K,, Yoshida K,, Yoshikawa H,, Zuber U,, Ogasawara N . 2003. Essential Bacillus subtilis genes. Proc Natl Acad Sci USA 100 : 46784683.[PubMed] [CrossRef]
30. Baesman SM,, Stolz JF,, Kulp TR,, Oremland RS . 2009. Enrichment and isolation of Bacillus beveridgei sp. nov., a facultative anaerobic haloalkaliphile from Mono Lake, California, that respires oxyanions of tellurium, selenium, and arsenic. Extremophiles 13 : 695705.[PubMed] [CrossRef]
31. Mnif S,, Chamkha M,, Labat M,, Sayadi S . 2011. Simultaneous hydrocarbon biodegradation and biosurfactant production by oilfield-selected bacteria. J Appl Microbiol 111 : 525536.[PubMed] [CrossRef]
32. Chen Y-G,, Zhang Y-Q,, Liu Z-X,, Zhuang D-C,, Klenk H-P,, Tang S-K,, Cui X-L,, Li W-J . 2009. Halobacillus salsuginis sp nov., a moderately halophilic bacterium from a subterranean brine. Int J Syst Evol Microbiol 59 : 25052509.[PubMed] [CrossRef]
33. Taubel M,, Kampfer P,, Buczolits S,, Lubitz W,, Busse HA . 2003. Bacillus barbaricus sp. nov., isolated from an experimental wall painting. Int J Syst Evol Microbiol 53 : 725730.[PubMed] [CrossRef]
34. Batchelor MD . 1919. Aerobic spore-bearing bacteria in the intestinal tract of children. J Bacteriol 4 : 2334.[PubMed]
35. Vedder A . 1934. Bacillus alcalophilus n. sp.; benevens enkele ervaringen met sterk alcalische voedingsbodems. Antonie Leeuwenhoek 1 : 143147.
36. Hoyles L,, Honda H,, Logan NA,, Halket G,, La Ragione RM,, McCartney AL . 2012. Recognition of greater diversity of Bacillus species and related bacteria in human faeces. Res. Microbiol 163 : 313.[PubMed] [CrossRef]
37. Tamames J,, Abellán JJ,, Pignatelli M,, Camacho A,, Moya A . 2010. Environmental distribution of prokaryotic taxa. BMC Microbiol 10 : 85. doi:10.1186/1471-2180-10-85. [PubMed] [CrossRef]
38. Euzéby JP . 1997. List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47 : 590592.[PubMed] [CrossRef]
39. Philippot L,, Andersson SG,, Battin TJ,, Prosser JI,, Schimel JP,, Whitman WB,, Hallin S . 2010. The ecological coherence of high bacterial taxonomic ranks. Nat Rev Microbiol 8 : 523529.[PubMed] [CrossRef]
40. Lakay FM,, Botha A,, Prior BA . 2007. Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils. J Appl Microbiol 102 : 265273.[PubMed] [CrossRef]
41. Nicholson WL,, Munakata N,, Horneck G,, Melosh HJ,, Setlow P . 2000. Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments. Microbiol Mol Biol Rev 64 : 548572.[PubMed] [CrossRef]
42. Setlow P . 2006. Spores of Bacillus subtilis: their resistance to and killing by radiation, heat and chemicals. J Appl Microbiol 101 : 514525.[PubMed] [CrossRef]
43. Womack AM,, Bohannan BJ,, Green JL . 2010. Biodiversity and biogeography of the atmosphere. Philos Trans R Soc Lond B Biol Sci 365 : 36453653.[PubMed] [CrossRef]
44. DeSantis TZ,, Brodie EL,, Moberg JP,, Zubieta IX,, Piceno YM,, Andersen GL . 2007. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53 : 371383.[PubMed] [CrossRef]
45. Brodie EL,, DeSantis TZ,, Parker JP,, Zubietta IX,, Piceno YM,, Andersen GL . 2007. Urban aerosols harbor diverse and dynamic bacterial populations. Proc Natl Acad Sci USA 104 : 299304.[PubMed] [CrossRef]
46. Merrill L,, Dunbar J,, Richardson J,, Kuske CR . 2006. Composition of Bacillus species in aerosols from 11 U.S. cities. J Forensic Sci 51 : 559565.[PubMed] [CrossRef]
47. Sass AM,, McKew BA,, Sass H,, Fichtel J,, Timmis KN,, McGenity TJ . 2008. Diversity of Bacillus-like organisms isolated from deep-sea hypersaline anoxic sediments. Saline Syst 4 : 8. doi:10.1186/1746-1448-4-8. [PubMed] [CrossRef]
48. Nielsen KM,, Johnsen PJ,, Bensasson D,, Daffonchio D . 2007. Release and persistence of extracellular DNA in the environment. Environ Biosafety Res 6 : 3753.[PubMed] [CrossRef]
49. Earl AM,, Losick R,, Kolter R . 2008. Ecology and genomics of Bacillus subtilis . Trends Microbiol 16 : 269275.[PubMed] [CrossRef]
50. Ludwig W,, Schleifer K-H,, Whitman WB, . 2009. Revised road map to the phylum Firmicutes , p 113. In De Vos P,, Garrity GM,, Jones D,, Kreig NR,, Ludwig W,, Rainey FA,, Schleifer K-H,, Whitman WB (ed), Bergey’s Manual of Systematic Bacteriology, 2nd ed, vol 3. The Firmicutes. Springer, New York, NY.
51. Maughan H . 2007. Rates of molecular evolution in bacteria are relatively constant despite spore dormancy. Evolution 61 : 280288.[PubMed] [CrossRef]
52. Earl AM,, Losick R,, Kolter R . 2007. Bacillus subtilis genome diversity. J Bacteriol 189 : 11631170.[PubMed] [CrossRef]
53. Singh AH,, Wolf DM,, Wang P,, Arkin AP . 2008. Modularity of stress response evolution. Proc Natl Acad Sci USA 105 : 75007505.[PubMed] [CrossRef]
54. Nakamura K,, Haruta S,, Ueno S,, Ishii M,, Yokota A,, Igarashi Y . 2004. Cerasibacillus quisquiliarum gen. nov., sp. nov., isolated from a semi-continuous decomposing system of kitchen refuse. Int J Syst Evol Microbiol 54 : 10631069.[PubMed] [CrossRef]
55. Ajithkumar VP,, Ajithkumar B,, Mori K,, Takamizawa K,, Iriye R,, Tabata S . 2001. A novel filamentous Bacillus sp., strain NAF001, forming endospores and budding cells. Microbiology 147 : 14151423.[PubMed]
56. Thorne CB . 1968. Transducing bacteriophage for Bacillus cereus . J Virol 2 : 657662.[PubMed]
57. Lovett PS,, Bramucci D,, Bramucci MG,, Burdick BD . 1974. Some properties of the PBP1 transduction system in Bacillus pumilus . J Virol 13 : 8184.[PubMed]
58. Yasbin RE,, Young FE . 1974. Transduction in Bacillus subtilis by bacteriophage SPP1. J Virol 14 : 13431348.[PubMed]
59. Thorne CB . 1978. Transduction in Bacillus thuringiensis . Appl Environ Microbiol 35 : 11091115.[PubMed]
60. Vary PS,, Garbe JC,, Franzen M,, Frampton EW . 1982. MP13, a generalized transducing bacteriophage for Bacillus megaterium . J Bacteriol 149 : 11121119.[PubMed]
61. Ruhfel RE,, Robillard NJ,, Thorne CB . 1984. Interspecies transduction of plasmids among Bacillus anthracis, B. cereus, and B. thuringiensis . J Bacteriol 157 : 708711.[PubMed]
62. Welker NE . 1988. Transduction in Bacillus stearothermophilus . J Bacteriol 170 : 37613764.[PubMed]
63. Zahler SA, . 1993. Temperate bacteriophages, p 831842. In Sonenshein AL,, Hoch JA,, Losick R (ed.), Bacillus subtilis and Other Gram-positive Bacteria: Biochemistry, Physiology, and Molecular Genetics. American Society for Microbiology, Washington, DC.
64. Bertram J,, Strätz M,, Dürre P . 1991. Natural transfer of conjugative transposon Tn916 between gram-positive and gram-negative bacteria. J Bacteriol 173 : 443448.[PubMed]
65. Torres OR,, Korman RZ,, Zahler SA,, Dunny GM . 1991. The conjugative transposon Tn925: enhancement of conjugal transfer by tetracycline in Enterococcus faecalis and mobilization of chromosomal genes in Bacillus subtilis and E. faecalis . Mol Gen Genet 225 : 395400.[PubMed] [CrossRef]
66. Spizizen J . 1958. Transformation of biochemically deficient strains of Bacillus subtilis by deoxyribonucleate. Proc Natl Acad Sci USA 44 : 10721078. [PubMed] [CrossRef]
67. Anagnostopoulos C,, Spizizen J . 1961. Requirements for transformation in Bacillus subtilis . J Bacteriol 81 : 741746.[PubMed]
68. Bott KF,, Wilson GA . 1968. Metabolic and nutritional factors influencing the development of competence for transfection of Bacillus subtilis . Bacteriol Rev 32 : 370378.[PubMed]
69. van Sinderen D,, Luttinger A,, Kong L,, Dubnau D,, Venema G,, Hamoen L . 1995. comK encodes the competence transcription factor, the key regulatory protein for competence development in Bacillus subtilis . Mol Microbiol 15 : 455462.[PubMed] [CrossRef]
70. Finkel SE,, Kolter R . 2001. DNA as a nutrient: novel role for bacterial competence gene homologs. J Bacteriol 183 : 62886293.[PubMed] [CrossRef]
71. Redfield RJ . 2001. Do bacteria have sex? Nat Rev Genet 2 : 634639.[PubMed] [CrossRef]
72. Mirończuk AM,, Kovács Á,, Kuipers OP . 2008. Induction of natural competence in Bacillus cereus ATCC14579. Microb Biotechnol 1 : 226235.[PubMed] [CrossRef]
73. Duitman EH,, Wyczawski D,, Boven LG,, Venema G,, Kuipers OP,, Hamoen LW . 2007. Novel methods for genetic transformation of natural Bacillus subtilis isolates used to study the regulation of the mycosubtilin and surfactin synthetases. Appl Environ Microbiol 73 : 34903496.[PubMed] [CrossRef]
74. Nijland R,, Burgess JG,, Errington J,, Veening JW . 2010. Transformation of environmental Bacillus subtilis isolates by transiently inducing genetic competence. PLoS One 5 : e9724. doi:10.1371/journal.pone.0009724 [PubMed] [CrossRef]
75. Kennedy MJ,, Reader SL,, Swierczynski LM . 1994. Preservation records of microorganisms: evidence of the tenacity of life. Microbiology 140 : 25132529.[PubMed] [CrossRef]
76. Vreeland RH,, Rosenzweig WD,, Powers DW . 2000. Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal. Nature 407 : 897900.[PubMed] [CrossRef]
77. Cano RJ,, Borucki MK,, Higby-Schweitzer M,, Poinar HN,, Poinar GO,, Pollard KJ . 1994. Bacillus DNA in fossil bees: an ancient symbiosis. Appl Environ Microbiol 60 : 21642167.[PubMed]
78. Cano RJ,, Borucki MK . 1995. Revival and identification of bacterial spores in 25-million-year-old to 40-million-year-old Dominican amber. Science 268 : 10601064.[CrossRef]
79. Rosenzweig WD,, Woish J,, Peterson J,, Vreeland R . 2000. Development of a protocol to retrieve microorganisms from ancient salt crystals. Geomicrobiol J 17 : 185192.[CrossRef]
80. Vreeland RH,, Rosenzweig WD . 2002. The question of uniqueness of ancient bacteria. J Indust Microbiol Biotechnol 28 : 3241.[PubMed] [CrossRef]
81. Graur D,, Pupko T . 2001. The permian bacterium that isn’t. Mol Biol Evol 18 : 11431146.[PubMed] [CrossRef]
82. Lindahl T . 1993. Instability and decay of the primary structure of DNA. Nature 362 : 709715.[PubMed] [CrossRef]
83. Nicholson WL,, Schuerger AC,, Setlow P . 2005. The solar UV environment and bacterial spore UV resistance: considerations for Earth-to-Mars transport by natural processes and human spaceflight. Mutat Res 571 : 249264.[PubMed] [CrossRef]
84. Nicastro AJ,, Vreeland RH,, Rosenzweig WD . 2002. Limits imposed by ionizing radiation on the long-term survival of trapped bacterial spores: beta radiation. Int J Radiat Biol 78 : 891901.[PubMed] [CrossRef]
85. Kminek G,, Bada JL,, Pogliano K,, Ward JF . 2003. Radiation-dependent limit for the viability of bacterial spores in halite fluid inclusions and on Mars. Radiat Res 159 : 722729.[PubMed] [CrossRef]
86. Nicholson W . 2003. Using thermal inactivation kinetics to calculate the probability of extreme spore longevity: implications for paleomicrobiology and lithopanspermia. Orig Life Evol Biosph 33 : 621631.[PubMed] [CrossRef]
87. Maughan H,, Birky CW,, Nicholson WL,, Rosenzweig WD,, Vreeland RH . 2002. The paradox of the “ancient” bacterium which contains “modern” protein-coding genes. Mol Biol Evol 19 : 16371639.[PubMed] [CrossRef]
88. Nickle DC,, Learn GH,, Rain MW,, Mullins JI,, Mittler JE . 2002. Curiously modern DNA for a “250 million-year-old” bacterium. J Mol Evol 54 : 134137.[PubMed] [CrossRef]
89. Kuo CH,, Ochman H . 2009. Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. Biol Direct 4 : 10. doi:10.1186/1745-6150-4-35. [PubMed] [CrossRef]
90. Ochman H,, Elwyn S,, Moran NA . 1999. Calibrating bacterial evolution. Proc Natl Acad Sci USA 96 : 1263812643.[PubMed] [CrossRef]
91. Maughan H . 2007. Rates of molecular evolution in bacteria are relatively constant despite spore dormancy. Evolution 61 : 280288.[PubMed] [CrossRef]
92. Ochman H,, Selander RK . 1984. Evidence for clonal population structure in Escherichia coli . Proc Natl Acad Sci USA 81 : 198201.[PubMed] [CrossRef]
93. Selander RK,, Beltran P,, Smith NH, . 1991. Evolutionary genetics of Salmonella., p 2557. In Selander RK,, Clark AG,, Whittam TS (ed), Evolution at the Molecular Level. Sinauer Associates, Sunderland, MA.
94. Istock CA,, Duncan KE,, Ferguson N,, Zhou X . 1992. Sexuality in a natural population of bacteria-Bacillus subtilis challenges the clonal paradigm. Mol Ecol 1 : 95103.[PubMed] [CrossRef]
95. Sikorski J, . 2012. A glimpse into microevolution in nature: adaptation and speciation of Bacillus simplex from “Evolution Canyon,” p 225231. In Kolter R,, Maloy S (ed), Microbes and Evolution: The World That Darwin Never Saw. ASM Press, Washington, DC. [CrossRef]
96. Sikorski J,, Nevo E . 2005. Adaptation and incipient sympatric speciation of Bacillus simplex under microclimatic contrast at “Evolution Canyons” I and II, Israel. Proc Natl Acad Sci USA 102 : 1592415929.[PubMed] [CrossRef]
97. Sikorski J,, Nevo E . 2007. Patterns of thermal adaptation of Bacillus simplex to the microclimatically contrasting slopes of “Evolution Canyons” I and II, Israel. Environ Microbiol 9 : 71726.[PubMed] [CrossRef]
98. Connor N,, Sikorski J,, Rooney AP,, Kopac S,, Koeppel AF,, Burger A,, Cole SG,, Perry EB,, Krizanc D,, Field NC,, Slaton M,, Cohan FM . 2010. Ecology of speciation in the genus Bacillus . Appl Environ Microbiol 76 : 13491358.[PubMed] [CrossRef]
99. Lowry DB . 2012. Ecotypes and the controversy over stages in the formation of new species. Biol J Linnean Soc 106 : 241257.[CrossRef]
100. Shank EA,, Klepac-Ceraj V,, Collado-Torres L,, Powers GE,, Losick R,, Kolter R . 2011. Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. Proc Natl Acad Sci USA 108 : E1236E1243.[PubMed] [CrossRef]
101. Hooper SD,, Mavromatis K,, Kyrpides NC . 2009. Microbial co-habitation and lateral gene transfer: what transposases can tell us. Genome Biol 10 : R45. doi:10.1186/gb-2009-10-4-r45. [PubMed] [CrossRef]
102. Freilich S,, Kreimer A,, Meilijson I,, Gophna U,, Sharan R,, Ruppin E . 2010. The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Res 38 : 38573868.[PubMed] [CrossRef]
103. Mathew GM,, Ju YM,, Lai CY,, Mathew DC,, Huang CC . 2012. Microbial community analysis in the termite gut and fungus comb of Odontotermes formosanus: the implication of Bacillus as mutualists. FEMS Microbiol Ecol 79 : 504517.[PubMed] [CrossRef]
104. Stewart EJ . 2012. Growing unculturable bacteria. J Bacteriol 194 : 41514160.[PubMed] [CrossRef]
105. Kassen R . 2002. The experimental evolution of specialists, generalists, and the maintenance of diversity. J Evol Biol 15 : 173190.[CrossRef]
106. Elena SF,, Lenski RE . 2003. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet 4 : 457469.[PubMed] [CrossRef]
107. Graham JB,, Istock CA . 1978. Genetic exchange in Bacillus subtilis in soil. Mol Gen Genet 166 : 287290.[PubMed]
108. Graham JP,, Istock CA . 1979. Gene exchange and natural selection cause Bacillus subtilis to evolve in soil culture. Science 204 : 637639.[PubMed] [CrossRef]
109. Graham J,, Istock C . 1981. Parasexuality and microevolution in experimental populations of Bacillus subtilis . Evolution 35 : 954963.[CrossRef]
110. Maughan H,, Callicotte V,, Hancock A,, Birky CW,, Nicholson WL,, Masel J . 2006. The population genetics of phenotypic deterioration in experimental populations of Bacillus subtilis . Evolution 60 : 686695.[PubMed] [CrossRef]
111. Maughan H,, Nicholson WL . 2004. Stochastic processes influence stationary-phase decisions in Bacillus subtilis . J Bacteriol 186 : 22122214.[CrossRef]
112. Maughan H,, Masel J,, Birky C,, Nicholson W . 2007. The roles of mutation accumulation and selection in loss of sporulation in experimental populations of Bacillus subtilis . Genetics 177 : 937948.[PubMed] [CrossRef]
113. Masel J,, Maughan H . 2007. Mutations leading to loss of sporulation ability in Bacillus subtilis are sufficiently frequent to favor genetic canalization. Genetics 175 : 453457.[PubMed] [CrossRef]
114. Maughan H,, Birky CWJ,, Nicholson WL . 2009. Transcriptome divergence and the loss of plasticity in Bacillus subtilis after 6,000 generations of evolution under relaxed selection for sporulation. J Bacteriol 191 : 428433.[PubMed] [CrossRef]
115. Maughan H,, Nicholson WL . 2011. Increased fitness and alteration of metabolic pathways during Bacillus subtilis evolution in the laboratory. Appl Environ Microbiol 77 : 41054118.[PubMed] [CrossRef]
116. Brown CT,, Fishwick LK,, Chokshi BM,, Cuff MA,, Jackson JM,, Oglesby T,, Rioux AT,, Rodriguez E,, Stupp GS,, Trupp AH,, Woollcombe-Clarke JS,, Wright TN,, Zaragoza WJ,, Drew JC,, Triplett EW,, Nicholson WL . 2011. Whole-genome sequencing and phenotypic analysis of Bacillus subtilis mutants following evolution under conditions of relaxed selection for sporulation. Appl Environ Microbiol 77 : 68676877.[PubMed] [CrossRef]
117. Nicholson WL . 2012. Increased competitive fitness of Bacillus subtilis under nonsporulating conditions via inactivation of pleiotropic regulators AlsR, SigD, and SigW. Appl Environ Microbiol 78 : 35003503.[PubMed] [CrossRef]
118. Debora BN,, Vidales LE,, Ramírez R,, Ramírez M,, Robleto EA,, Yasbin RE,, Pedraza-Reyes M . 2011. Mismatch repair modulation of MutY activity drives Bacillus subtilis stationary-phase mutagenesis. J Bacteriol 193 : 236245.[PubMed] [CrossRef]
119. Pybus C,, Pedraza-Reyes M,, Ross CA,, Martin H,, Ona K,, Yasbin RE,, Robleto E . 2010. Transcription-associated mutation in Bacillus subtilis cells under stress. J Bacteriol 192 : 33213328.[PubMed] [CrossRef]
120. Vidales LE,, Cárdenas LC,, Robleto E,, Yasbin RE,, Pedraza-Reyes M . 2009. Defects in the error prevention oxidized guanine system potentiate stationary-phase mutagenesis in Bacillus subtilis . J Bacteriol 191 : 506513.[PubMed] [CrossRef]
121. Robleto EA,, Yasbin R,, Ross C,, Pedraza-Reyes M . 2007. Stationary phase mutagenesis in B. subtilis: a paradigm to study genetic diversity programs in cells under stress. Crit Rev Biochem Mol Biol 42 : 327339.[PubMed] [CrossRef]
122. Ross C,, Pybus C,, Pedraza-Reyes M,, Sung HM,, Yasbin RE,, Robleto E . 2006. Novel role of mfd: effects on stationary-phase mutagenesis in Bacillus subtilis . J Bacteriol 188 : 75127520.[PubMed] [CrossRef]
123. Pedraza-Reyes M,, Yasbin RE . 2004. Contribution of the mismatch DNA repair system to the generation of stationary-phase-induced mutants of Bacillus subtilis . J Bacteriol 186 : 64856491.[PubMed] [CrossRef]
124. Sung HM,, Yasbin RE . 2002. Adaptive, or stationary-phase, mutagenesis, a component of bacterial differentiation in Bacillus subtilis . J Bacteriol 184 : 56415653.[CrossRef]
125. Sung HM,, Yeamans G,, Ross CA,, Yasbin RE . 2003. Roles of YqjH and YqjW, homologs of the Escherichia coli UmuC/DinB or Y superfamily of DNA polymerases, in stationary-phase mutagenesis and UV-induced mutagenesis of Bacillus subtilis . J Bacteriol 185 : 21532160.[PubMed] [CrossRef]
126. McCutcheon JP,, Moran NA . 2012. Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol 10 : 1326.[PubMed]
127. Zeigler DR,, Prágai Z,, Rodriguez S,, Chevreux B,, Muffler A,, Albert T,, Bai R,, Wyss M,, Perkins JB . 2008. The origins of 168, W23, and other Bacillus subtilis legacy strains. J Bacteriol 190 : 69836995.[PubMed] [CrossRef]
128. Maughan H,, Birky CWJ,, Nicholson WL . 2009. Transcriptome divergence and the loss of plasticity in Bacillus subtilis after 6,000 generations of evolution under relaxed selection for sporulation. J Bacteriol 191 : 428433.[PubMed] [CrossRef]
129. McLoon AL,, Guttenplan SB,, Kearns DB,, Kolter R,, Losick R . 2011. Tracing the domestication of a biofilm-forming bacterium. J Bacteriol 193 : 20272034.[PubMed] [CrossRef]
130. Douglas GL,, Klaenhammer TR . 2010. Genomic evolution of domesticated microorganisms. Annu Rev Food Sci Technol 1 : 397414.[PubMed] [CrossRef]
131. Branda SS,, Gonzalez-Pastor JE,, Ben-Yehuda S,, Losick R,, Kolter R . 2001. Fruiting body formation by Bacillus subtilis . Proc Natl Acad Sci USA 98 : 1162111626.[PubMed] [CrossRef]
132. Gonzalez-Pastor JE, . 2012. Multicellularity and social behaviour in Bacillus subtilis , p 351375. In Graumann P (ed), Bacillus: Cellular and Molecular Biology, 2nd ed. Caister Academic Press, Wymondham, United Kingdom.
133. Yasbin RE,, Fields PI,, Andersen BJ . 1980. Properties of Bacillus subtilis 168 derivatives freed of their natural prophages. Gene 12 : 155159.[PubMed] [CrossRef]
134. Srivatsan A,, Han Y,, Peng J,, Tehranchi AK,, Gibbs R,, Wang JD,, Chen R . 2008. High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet 4 : e1000139. doi:10.1371/journal.pgen.1000139. [PubMed] [CrossRef]
135. Hosoi T,, Kiuchi K, . 2004. Production and probiotic effects of natto, p 143153. In Ricca E,, Henriques AO,, Cutting SM (ed), Bacterial Spore Formers: Probiotics and Emerging Applications. Horizon Bioscience, Wymondham, United Kingdom. [PubMed]
136. Kang SE,, Rhee JH,, Park C,, Sung MH,, Lee I . 2005. Distribution of poly-gamma-glutamate (gamma-PGA) producers in Korean fermented foods, Cheongkukjang, Doenjang, and Kochujang. Food Sci Biotechnol 14 : 704708.
137. Ouoba LII,, Thorsen L,, Varnam AH . 2008. Enterotoxins and emetic toxins production by Bacillus cereus and other species of Bacillus isolated from Soumbala and Bikalga, African alkaline fermented food condiments. Int J Food Microbiol 124 : 224230.[PubMed] [CrossRef]
138. Demain AL,, Solomon NA . 1981. Industrial microbiology. Sci Am 245 : 6775.[PubMed] [CrossRef]
139. Gupta R,, Gigras P,, Mohapatra H,, Goswami VK,, Chauhan B . 2003. Microbial alpha-amylases: a biotechnological perspective. Process Biochem 38 : 15991616.[CrossRef]
140. Gupta R,, Beg QK,, Lorenz P . 2002. Bacterial alkaline proteases: molecular approaches and industrial applications. Appl Microbiol Biotechnol 59 : 1532.[PubMed] [CrossRef]
141. Abbas CA,, Sibirny AA . 2011. Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers. Microbiol Mol Biol Rev 75 : 321360.[PubMed] [CrossRef]
142. Glick RG,, Pasternak JJ . 2003. Molecular Biotechnology: Principles and Applications of Recombinant DNA, 3rd ed. ASM Press, Washington, DC.
143. Harwood CR . 1992. Bacillus subtilis and its relatives: molecular biological and industrial workhorses. Trends Biotechnol 10 : 247256.[CrossRef]
144. Sun HY,, Zhao PJ,, Ge XY,, Xia YJ,, Hao ZK,, Liu JW,, Peng M . 2010. Recent advances in microbial raw starch degrading enzymes. Appl Biochem Biotechnol 160 : 9881003.[PubMed] [CrossRef]
145. Yoneda Y . 1980. Increased production of extracellular enzymes by the synergistic effect of genes introduced into Bacillus subtilis by stepwise transformation. Appl Environ Microbiol 39 : 274276.[PubMed]
146. Wohlgemuth R . 2009. The locks and keys to industrial biotechnology. N Biotechnol 25 : 204213.[PubMed] [CrossRef]
147. Liu YH,, Lu FP,, Li Y,, Yin XB,, Wang Y,, Gao C . 2008. Characterisation of mutagenised acid-resistant alpha-amylase expressed in Bacillus subtilis WB600. Appl Microbiol Biotechnol 78 : 8594.[PubMed] [CrossRef]
148. Santhanam N,, Vivanco JM,, Decker SR,, Reardon KF . 2011. Expression of industrially relevant laccases: prokaryotic style. Trends Biotechnol 29 : 480489.[PubMed] [CrossRef]
149. Gupta N,, Farinas ET . 2010. Directed evolution of CotA laccase for increased substrate specificity using Bacillus subtilis spores. Protein Eng Des Sel 23 : 679682.[PubMed] [CrossRef]
150. Sharma A,, Kawarabayasi Y,, Satyanarayana T . 2012. Acidophilic bacteria and archaea: acid stable biocatalysts and their potential applications. Extremophiles 16 : 119.[PubMed] [CrossRef]
151. Tu R,, Martinez R,, Prodanovic R,, Klein M,, Schwaneberg U . 2011. A flow cytometry-based screening system for directed evolution of proteases. J Biomol Screen 16 : 285294.[PubMed] [CrossRef]
152. Yao Y,, Li Y,, Hou S,, Li C,, Chen H,, Liao Y . 2011. Directed evolution of neutral endoglucanase gene by error-prone PCR. J Agric Biotechnol 19 : 11361143.
153. Qin J,, Gao W,, Li Q,, Li Y,, Zheng F,, Liu C,, Gu G . 2010. Improvement of thermostability of beta-1,3-1,4-glucanase from Bacillus amyloliquefaciens BS5582 through in vitro evolution. Sheng Wu Gong Cheng Xue Bao 26 : 12931301.[PubMed]
154. Joo JC,, Pack SP,, Kim YH,, Yoo YJ . 2011. Thermostabilization of Bacillus circulans xylanase: computational optimization of unstable residues based on thermal fluctuation analysis. J Biotechnol 151 : 5665.[PubMed] [CrossRef]
155. Van Arsdell SW,, Perkins JB,, Yocum RR,, Luan L,, Howitt CL,, Chatterjee NP,, Pero JG . 2005. Removing a bottleneck in the Bacillus subtilis biotin pathway: BioA utilizes lysine rather than S-adenosylmethionine as the amino donor in the KAPA-to-DAPA reaction. Biotechnol Bioeng 91 : 7583.[PubMed] [CrossRef]
156. Perkins JB,, Sloma A,, Hermann T,, Theriault K,, Zachgo E,, Erdenberger T,, Hannett N,, Chatterjee NP,, Williams V,, Rufo GA,, Hatch R,, Pero J . 1999. Genetic engineering of Bacillus subtilis for the commercial production of riboflavin. J Indust Microbiol Biotechnol 22 : 818.[CrossRef]
157. DeWulf P,, Vandamme EJ . 1997. Production of D-ribose by fermentation. Appl Microbiol Biotechnol 48 : 141148.[PubMed] [CrossRef]
158. Koglin A,, Doetsch V,, Bernhard F, . 2010. Molecular engineering aspects for the production of new and modified biosurfactants, p 158169. In Sen R (ed), Biosurfactants, vol 672. Springer-Verlag Berlin, Berlin, Germany. [PubMed] [CrossRef]
159. Shoda M . 2000. Bacterial control of plant diseases. J Biosci Bioeng 89 : 515521.[PubMed] [CrossRef]
160. Singh M,, Patel SKS,, Kalia VC . 2009. Bacillus subtilis as potential producer for polyhydroxyalkanoates. Microb Cell Fact 8 : 11. doi:10.1186/1475-2859-8-38. [PubMed] [CrossRef] </