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Chapter 3 : Ecology of

Authors: Ines Mandic-Mulec1, Polonca Stefanic2, Jan Dirk van Elsas3
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Affiliations: 1: University of Ljubljana, Biotechnical Faculty, Department of Food Science and Technology, Vecna pot 111, 1000 Ljubljana, Slovenia; 2: University of Ljubljana, Biotechnical Faculty, Department of Food Science and Technology, Vecna pot 111, 1000 Ljubljana, Slovenia; 3: Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Linneausborg, Nijenborgh 7, 9747AG Groningen, Netherlands
Content Type: Monograph
Publication Year: 2016

Category: Bacterial Pathogenesis

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Ecology of , Page 1 of 2

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Abstract:

The most distinguishing feature of most members of the family (phylum ) is their ability to form endospores that provide high resistance to heat, radiation, chemicals, and drought, allowing these bacteria to survive adverse conditions for a prolonged period of time. are widely distributed in natural environments, and their habitats are as varied as the niches humans have thought to sample. Over the years of microbiological research, members of this family have been found in soil, sediment, and air, as well as in unconventional environments such as clean rooms in the Kennedy Space Center, a vaccine-producing company, and even human blood ( ). Moreover, members of the have been detected in freshwater and marine ecosystems, in activated sludge, in human and animal systems, and in various foods (including fermented foods), but recently also in extreme environments such as hot solid and liquid systems (compost and hot springs, respectively), salt lakes, and salterns ( ). Thus, thermophilic genera of the family dominate the high-temperature stages of composting and have also been found in hot springs and hydrothermal vents, while representatives of halophilic genera have mostly been isolated from aquatic habitats such as salt lakes and salterns, but less often from saline soils ( ). The isolates that have been obtained, in particular, from the varied extreme habitats, produce a wide range of commercially valuable extracellular enzymes, including those that are thermostable ( ).

Citation: Mandic-Mulec I, Stefanic P, van Elsas J. 2016. Ecology of , p 59-85. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0017-2013
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Ecology of Bacillaceae
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Citation: Mandic-Mulec I, Stefanic P, van Elsas J. 2016. Ecology of , p 59-85. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0017-2013
/content/10.1128/9781555819323.chap3.fig3-1
Figure 1

Occurrence of , their ecosystem function, biotic interactions, and applications. The illustration shows different environments from which have been isolated highlights their main ecosystem functions and biotic interactions, and illustrates selected existing and possible applications.

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10.1128/9781555819323/fig3-1.gif
Image of Figure 1
Figure 1

Occurrence of , their ecosystem function, biotic interactions, and applications. The illustration shows different environments from which have been isolated highlights their main ecosystem functions and biotic interactions, and illustrates selected existing and possible applications.

Citation: Mandic-Mulec I, Stefanic P, van Elsas J. 2016. Ecology of , p 59-85. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0017-2013
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Figure 2

Growth of in soil and morphology on LB agar media. (A) Growth of riverbank isolate PS-209 ( ) was grown in an autoclaved soil microcosm at 28°C, and CFU counts were performed at indicated times on Luria-Bertani (LB) medium. The experiment was performed in three replicates. Error bars represent 95% confidence intervals of means calculated from log10 transformed CFU counts (L. Pal, S. Vatovec, P. Stefanic, T. Danevčič, and I. Mandic-Mulec, unpublished data). (B) Colony morphotypes. Colony morphology was visually examined and photographed after incubation at 37°C for 48 h on LB agar medium. Riverbank microscale and desert macroscale strains are marked with green and yellow, respectively (Courtesy of P. Stefanic).

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10.1128/9781555819323/fig3-2.gif
Image of Figure 2
Figure 2

Growth of in soil and morphology on LB agar media. (A) Growth of riverbank isolate PS-209 ( ) was grown in an autoclaved soil microcosm at 28°C, and CFU counts were performed at indicated times on Luria-Bertani (LB) medium. The experiment was performed in three replicates. Error bars represent 95% confidence intervals of means calculated from log10 transformed CFU counts (L. Pal, S. Vatovec, P. Stefanic, T. Danevčič, and I. Mandic-Mulec, unpublished data). (B) Colony morphotypes. Colony morphology was visually examined and photographed after incubation at 37°C for 48 h on LB agar medium. Riverbank microscale and desert macroscale strains are marked with green and yellow, respectively (Courtesy of P. Stefanic).

Citation: Mandic-Mulec I, Stefanic P, van Elsas J. 2016. Ecology of , p 59-85. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0017-2013
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Figure 3

Phylogenetic and ecotype simulation analyses of the subclade and minimum evolution tree of sequences. (A) The phylogeny of isolates from riverbank microscale and desert soils is based on a maximum parsimony analysis of the recombination-free concatenation of , , and , rooted by strain C-125 of ( ). (B) Minimum evolution tree of sequences (, , and partial sequences, 1,402 bp) depicts four sequence clusters that correspond to previously identified pherotypes or communication groups within - clade. Strains are marked with a shape representing their putative ecotype (PE) and by color representing pherotype (yellow, pherotype ROH1/RO-B-2; green, pherotype RS-D-2 /NAF4; orange, pherotype RO-E-2; and blue, pherotype 168). Unmarked strains were used as additional reference strains for tree construction ( ).

10.1128/9781555819323/fig3-3_thmb.gif
10.1128/9781555819323/fig3-3.gif
Image of Figure 3
Figure 3

Phylogenetic and ecotype simulation analyses of the subclade and minimum evolution tree of sequences. (A) The phylogeny of isolates from riverbank microscale and desert soils is based on a maximum parsimony analysis of the recombination-free concatenation of , , and , rooted by strain C-125 of ( ). (B) Minimum evolution tree of sequences (, , and partial sequences, 1,402 bp) depicts four sequence clusters that correspond to previously identified pherotypes or communication groups within - clade. Strains are marked with a shape representing their putative ecotype (PE) and by color representing pherotype (yellow, pherotype ROH1/RO-B-2; green, pherotype RS-D-2 /NAF4; orange, pherotype RO-E-2; and blue, pherotype 168). Unmarked strains were used as additional reference strains for tree construction ( ).

Citation: Mandic-Mulec I, Stefanic P, van Elsas J. 2016. Ecology of , p 59-85. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0017-2013
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References

/content/book/10.1128/9781555819323.chap3
1. Vaishampayan P,, Probst A,, Krishnamurthi S,, Ghosh S,, Osman S,, McDowall A,, Ruckmani A,, Mayilraj S,, Venkateswaran K . 2010. Bacillus horneckiae sp. nov., isolated from a spacecraft-assembly clean room. Int J Syst Evol Microbiol 60 : 1031– 1037.[PubMed] [CrossRef]
2. Seiler H,, Wenning M,, Scherer S . 2013. Domibacillus robiginosus gen. nov., sp. nov., isolated from a pharmaceutical clean room. Int J Syst Evol Microbiol 63( Pt 6) : 2054– 2061.[PubMed] [CrossRef]
3. Bottone EJ . 2010. Bacillus cereus, a volatile human pathogen. Clin Microbiol Rev 23 : 382– 398.[PubMed] [CrossRef]
4. Marquez MC,, Sanchez-Porro C,, Ventosa A, . 2011. Hallophilic and haloakalophilic, aerobic endospore-forming bacteria in soil, p 309– 339. In Logan NA,, De Vos P (ed), Endospore-Forming Soil Bacteria. Springer, New York, NY. [CrossRef]
5. Schmidt TR,, Scott EJ 2nd,, Dyer DW . 2011. Whole-genome phylogenies of the family Bacillaceae and expansion of the sigma factor gene family in the Bacillus cereus species-group. BMC Genomics 12 : 430. doi:10.1186/1471-2164-12-430. [PubMed] [CrossRef]
6. 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 : 3– 13.[PubMed] [CrossRef]
7. Carrasco IJ,, Marquez MC,, Yanfen X,, Ma Y,, Cowan DA,, Jones BE,, Grant WD,, Ventosa A . 2006. Gracilibacillus orientalis sp. nov., a novel moderately halophilic bacterium isolated from a salt lake in Inner Mongolia, China. Int J Syst Evol Microbiol 56 : 599– 604.[PubMed] [CrossRef]
8. Chen YG,, Cui XL,, Zhang YQ,, Li WJ,, Wang YX,, Xu LH,, Peng Q,, Wen ML,, Jiang CL . 2008. Gracilibacillus halophilus sp. nov., a moderately halophilic bacterium isolated from saline soil. Int J Syst Evol Microbiol 58 : 2403– 2408.[PubMed] [CrossRef]
9. Bischoff KM,, Rooney AP,, Li XL,, Liu S,, Hughes SR . 2006. Purification and characterization of a family 5 endoglucanase from a moderately thermophilic strain of Bacillus licheniformis . Biotechnol Lett 28 : 1761– 1765.[PubMed] [CrossRef]
10. Margesin R,, Schinner F . 2001. Potential of halotolerant and halophilic microorganisms for biotechnology. Extremophiles 5 : 73– 83.[CrossRef]
11. Logan NA,, Vos PD, . 2009. Family I. Bacillaceae . In Vos P,, Garrity G,, Jones D,, Krieg NR,, Ludwig W,, Rainey FA,, Schleifer K-H,, Whitman W (ed), Bergey’s Manual of Systematic Bacteriology: Firmicutes, 2nd ed, vol 3. Springer, New York, NY.
12. Logan NA,, Halket G, . 2011. Developments in the taxonomy of aerobic, endospore-forming bacteria, p 1– 30. In Logan NA,, De Vos P (ed), Endospore-Forming Soil Bacteria. Springer, New York, NY. [CrossRef]
13. Banat IM,, Marchant R,, Rahman TJ . 2004. Geobacillus debilis sp. nov., a novel obligately thermophilic bacterium isolated from a cool soil environment, and reassignment of Bacillus pallidus to Geobacillus pallidus comb. nov. Int J Syst Evol Microbiol 54 : 2197– 2201.[PubMed] [CrossRef]
14. Minana-Galbis D,, Pinzon DL,, Loren JG,, Manresa A,, Oliart-Ros RM . 2010. Reclassification of Geobacillus pallidus (Scholz et al. 1988) Banat et al. 2004 as Aeribacillus pallidus gen. nov., comb. nov. Int J Syst Evol Microbiol 60 : 1600– 1604.[PubMed] [CrossRef]
15. Zhou Y,, Xu J,, Xu L,, Tindall BJ . 2009. Falsibacillus pallidus to replace the homonym Bacillus pallidus Zhou et al. 2008. Int J Syst Evol Microbiol 59 : 3176– 3180.[PubMed] [CrossRef]
16. Cohn F, . 1962. Studies on the biology of the bacilli., p 49– 56. In Dale T (ed), Brock Milestones in Microbiology. Prentice-Hall, Inc., Englewood Cliffs, NJ.
17. Logan NA,, Vos PD, . 2009. Genus Bacillus Cohn 1872, p 21– 128. In Vos P,, Garrity G,, Jones D,, Krieg NR,, Ludwig W,, Rainey FA,, Schleifer K-H,, Whitman W (ed), Bergey’s Manual of Systematic Bacteriology: Firmicutes, 2nd ed, vol 3. Springer, New York, NY.
18. Wang LT,, Lee FL,, Tai CJ,, Kasai H . 2007. Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the Bacillus subtilis group. Int J Syst Evol Microbiol 57 : 1846– 1850.[PubMed] [CrossRef]
19. Stefanic P,, Decorosi F,, Viti C,, Petito J,, Cohan FM,, Mandic-Mulec I . 2012. The quorum sensing diversity within and between ecotypes of Bacillus subtilis . Environ Microbiol 14 : 1378– 1389.[PubMed] [CrossRef]
20. 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 : 789– 797.[PubMed] [CrossRef]
21. Priest FG,, Barker M,, Baillie LW,, Holmes EC,, Maiden MC . 2004. Population structure and evolution of the Bacillus cereus group. J Bacteriol 186 : 7959– 7970.[PubMed] [CrossRef]
22. Daffonchio D,, Cherif A,, Brusetti L,, Rizzi A,, Mora D,, Boudabous A,, Borin S . 2003. Nature of polymorphisms in 16S-23S rRNA gene intergenic transcribed spacer fingerprinting of Bacillus and related genera. Appl Environ Microbiol 69 : 5128– 5137.[PubMed] [CrossRef]
23. Helgason E,, Okstad OA,, Caugant DA,, Johansen HA,, Fouet A,, Mock M,, Hegna I,, Kolsto AB . 2000. Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis--one species on the basis of genetic evidence. Appl Environ Microbiol 66 : 2627– 2630.[PubMed] [CrossRef]
24. Tourasse NJ,, Kolsto AB . 2008. SuperCAT: a supertree database for combined and integrative multilocus sequence typing analysis of the Bacillus cereus group of bacteria (including B. cereus, B. anthracis and B. thuringiensis). Nucleic Acids Res 36 : D461– D468.[PubMed] [CrossRef]
25. Rasko DA,, Altherr MR,, Han CS,, Ravel J . 2005. Genomics of the Bacillus cereus group of organisms. FEMS Microbiol Rev 29 : 303– 329.[PubMed]
26. Rasko DA,, Rosovitz MJ,, Okstad OA,, Fouts DE,, Jiang L,, Cer RZ,, Kolsto AB,, Gill SR,, Ravel J . 2007. Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus-group plasmids, including Bacillus anthracis pXO1. J Bacteriol 189 : 52– 64.[PubMed] [CrossRef]
27. Ehling-Schulz M,, Fricker M,, Grallert H,, Rieck P,, Wagner M,, Scherer S . 2006. Cereulide synthetase gene cluster from emetic Bacillus cereus: structure and location on a mega virulence plasmid related to Bacillus anthracis toxin plasmid pXO1. BMC Microbiol 6 : 20. doi:10.1186/1471-2180-6-20. [PubMed] [CrossRef]
28. Van der Auwera GA,, Andrup L,, Mahillon J . 2005. Conjugative plasmid pAW63 brings new insights into the genesis of the Bacillus anthracis virulence plasmid pXO2 and of the Bacillus thuringiensis plasmid pBT9727. BMC Genomics 6 : 103. doi:10.1186/1471-2164-6-103. [PubMed] [CrossRef]
29. Zwick ME,, Joseph SJ,, Didelot X,, Chen PE,, Bishop-Lilly KA,, Stewart AC,, Willner K,, Nolan N,, Lentz S,, Thomason MK,, Sozhamannan S,, Mateczun AJ,, Du L,, Read TD . 2012. Genomic characterization of the Bacillus cereus sensu lato species: backdrop to the evolution of Bacillus anthracis . Genome Res 22 : 1512– 1524.[PubMed] [CrossRef]
30. Setlow P . 2006. Spores of Bacillus subtilis: their resistance to and killing by radiation, heat and chemicals. J Appl Microbiol 101 : 514– 525.[PubMed] [CrossRef]
31. Baril E,, Coroller L,, Couvert O,, El Jabri M,, Leguerinel I,, Postollec F,, Boulais C,, Carlin F,, Mafart P . 2012. Sporulation boundaries and spore formation kinetics of Bacillus spp. as a function of temperature, pH and a(w). Food Microbiol 32 : 79– 86.[PubMed] [CrossRef]
32. Van Ness GB . 1971. Ecology of anthrax. Science 172 : 1303– 1307.[PubMed] [CrossRef]
33. Hugh-Jones M,, Blackburn J . 2009. The ecology of Bacillus anthracis . Mol Aspects Med 30 : 356– 367.[PubMed] [CrossRef]
34. Kellogg CA,, Griffin DW . 2006. Aerobiology and the global transport of desert dust. Trends Ecol Evol 21 : 638– 644.[PubMed] [CrossRef]
35. Smith DJ,, Timonen HJ,, Jaffe DA,, Griffin DW,, Birmele MN,, Perry KD,, Ward PD,, Roberts MS . 2013. Intercontinental dispersal of bacteria and archaea by transpacific winds. Appl Environ Microbiol 79 : 1134– 1139.[PubMed] [CrossRef]
36. Smith DJ,, Jaffe DA,, Birmele MN,, Griffin DW,, Schuerger AC,, Hee J,, Roberts MS . 2012. Free tropospheric transport of microorganisms from Asia to North America. Microb Ecol 64 : 973– 985.[PubMed] [CrossRef]
37. Horneck G,, Rettberg P,, Reitz G,, Wehner J,, Eschweiler U,, Strauch K,, Panitz C,, Starke V,, Baumstark-Khan C . 2001. Protection of bacterial spores in space, a contribution to the discussion on Panspermia. Orig Life Evol Biosph 31 : 527– 547.[PubMed] [CrossRef]
38. Fajardo-Cavazos P,, Schuerger AC,, Nicholson WL . 2007. Testing interplanetary transfer of bacteria between Earth and Mars as a result of natural impact phenomena and human spaceflight activities. Acta Astronautica 60 : 534– 540.[CrossRef]
39. Martin PA,, Travers RS . 1989. Worldwide abundance and distribution of Bacillus thuringiensis isolates. Appl Environ Microbiol 55 : 2437– 2442.[PubMed]
40. Roberts MS,, Cohan FM . 1995. Recombination and migration rates in natural populations of Bacillus subtilis and Bacillus mojavensis . Evolution 49 : 1081– 1094.[CrossRef]
41. Stefanic P,, Mandic-Mulec I . 2009. Social interactions and distribution of Bacillus subtilis pherotypes at microscale. J Bacteriol 191 : 1756– 1764.[PubMed] [CrossRef]
42. Hudson AJ,, Daniel RM,, Morgan HW . 1988. Isolation of a strain of Bacillus schlegelii from geothermally heated antarctic soil. FEMS Microbiol Lett 51 : 57– 60.[CrossRef]
43. Kampfer P,, Glaeser SP,, Busse HJ . 2013. Transfer of Bacillus schlegelii to a novel genus and proposal of Hydrogenibacillus schlegelii gen. nov. comb. nov. Int J Syst Evol Microbiol 63( Pt 5) : 1723– 1727.[PubMed] [CrossRef]
44. Ivanova N,, Sorokin A,, Anderson I,, Galleron N,, Candelon B,, Kapatral V,, Bhattacharyya A,, Reznik G,, Mikhailova N,, Lapidus A,, Chu L,, Mazur M,, Goltsman E,, Larsen N,, D’Souza M,, Walunas T,, Grechkin Y,, Pusch G,, Haselkorn R,, Fonstein M,, Ehrlich SD,, Overbeek R,, Kyrpides N . 2003. Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis . Nature 423 : 87– 91.[PubMed] [CrossRef]
45. Chattopadhyay A,, Bhatnagar NB,, Bhatnagar R . 2004. Bacterial insecticidal toxins. Crit Rev Microbiol 30 : 33– 54.[PubMed] [CrossRef]
46. Choudhary DK,, Johri BN . 2009. Interactions of Bacillus spp. and plants--with special reference to induced systemic resistance (ISR). Microbiol Res 164 : 493– 513.[PubMed] [CrossRef]
47. Waksman SA . 1932. Principles of Soil Microbiology, 2nd ed. The Williams & Wilkins Co., Baltimore, MD.
48. Siala A,, Hill IR,, Gray TRG . 1974. Populations of spore-forming bacteria in an acid forest soil, with special reference to Bacillus subtilis . J Gen Microbiol 81 : 183– 190.[CrossRef]
49. Toljander JF,, Artursson V,, Paul LR,, Jansson JK,, Finlay RD . 2006. Attachment of different soil bacteria to arbuscular mycorrhizal fungal extraradical hyphae is determined by hyphal vitality and fungal species. FEMS Microbiol Lett 254 : 34– 40.[PubMed] [CrossRef]
50. Tam NK,, Uyen NQ,, Hong HA,, Duc le H,, Hoa TT,, Serra CR,, Henriques AO,, Cutting SM . 2006. The intestinal life cycle of Bacillus subtilis and close relatives. J Bacteriol 188 : 2692– 2700.[PubMed] [CrossRef]
51. Soriano M,, Diaz P,, Pastor FI . 2005. Pectinolytic systems of two aerobic sporogenous bacterial strains with high activity on pectin. Curr Microbiol 50 : 114– 118.[PubMed] [CrossRef]
52. Ouattara HG,, Reverchon S,, Niamke SL,, Nasser W . 2011. Molecular identification and pectate lyase production by Bacillus strains involved in cocoa fermentation. Food Microbiol 28 : 1– 8.[PubMed] [CrossRef]
53. Soares FL Jr,, Melo IS,, Dias AC,, Andreote FD . 2012. Cellulolytic bacteria from soils in harsh environments. World J Microbiol Biotechnol 28 : 2195– 2203.[PubMed] [CrossRef]
54. Okeke BC,, Lu J . 2011. Characterization of a defined cellulolytic and xylanolytic bacterial consortium for bioprocessing of cellulose and hemicelluloses. Appl Biochem Biotechnol 163 : 869– 881.[PubMed] [CrossRef]
55. Maki ML,, Idrees A,, Leung KT,, Qin W . 2012. Newly isolated and characterized bacteria with great application potential for decomposition of lignocellulosic biomass. J Mol Microbiol Biotechnol 22 : 156– 166.[PubMed] [CrossRef]
56. Solanki MK,, Robert AS,, Singh RK,, Kumar S,, Pandey AK,, Srivastava AK,, Arora DK . 2012. Characterization of mycolytic enzymes of Bacillus strains and their bio-protection role against Rhizoctonia solani in tomato. Curr Microbiol 65 : 330– 336.[PubMed] [CrossRef]
57. Gomaa EZ . 2012. Chitinase production by Bacillus thuringiensis and Bacillus licheniformis: their potential in antifungal biocontrol. J Microbiol 50 : 103– 111.[PubMed] [CrossRef]
58. Xiao L,, Xie CC,, Cai J,, Lin ZJ,, Chen YH . 2009. Identification and characterization of a chitinase-produced bacillus showing significant antifungal activity. Curr Microbiol 58 : 528– 533.[PubMed] [CrossRef]
59. Pleban S,, Chernin L,, Chet I . 1997. Chitinolytic activity of an endophytic strain of Bacillus cereus . Lett Appl Microbiol 25 : 284– 288.[PubMed] [CrossRef]
60. Hallmann J,, Rodriguez-Kábana R,, Kloepper JW . 1999. Chitin-mediated changes in bacterial communities of the soil, rhizosphere and within roots of cotton in relation to nematode control. Soil Biol Biochem 31 : 551– 560.[CrossRef]
61. Sakurai M,, Suzuki K,, Onodera M,, Shinano T,, Osaki M . 2007. Analysis of bacterial communities in soil by PCR–DGGE targeting protease genes. Soil Biol Biochem 39 : 2777– 2784.[CrossRef]
62. Chu H,, Lin X,, Fujii T,, Morimoto S,, Yagi K,, Hu J,, Zhang J . 2007. Soil microbial biomass, dehydrogenase activity, bacterial community structure in response to long-term fertilizer management. Soil Biol Biochem 39 : 2971– 2976.[CrossRef]
63. Vilain S,, Luo Y,, Hildreth MB,, Brozel VS . 2006. Analysis of the life cycle of the soil saprophyte Bacillus cereus in liquid soil extract and in soil. Appl Environ Microbiol 72 : 4970– 4977.[PubMed] [CrossRef]
64. von der Weid I,, Duarte GF,, van Elsas JD,, Seldin L . 2002. Paenibacillus brasilensis sp. nov., a novel nitrogen-fixing species isolated from the maize rhizosphere in Brazil. Int J Syst Evol Microbiol 52 : 2147– 2153.[PubMed] [CrossRef]
65. Verbaendert I,, Boon N,, De Vos P,, Heylen K . 2011. Denitrification is a common feature among members of the genus Bacillus . Syst Appl Microbiol 34 : 385– 391.[PubMed] [CrossRef]
66. Ding Y,, Wang J,, Liu Y,, Chen S . 2005. Isolation and identification of nitrogen-fixing bacilli from plant rhizospheres in Beijing region. J Appl Microbiol 99 : 1271– 1281.[PubMed] [CrossRef]
67. Park SJ,, Yoon JC,, Shin KS,, Kim EH,, Yim S,, Cho YJ,, Sung GM,, Lee DG,, Kim SB,, Lee DU,, Woo SH,, Koopman B . 2007. Dominance of endospore-forming bacteria on a Rotating Activated Bacillus Contactor biofilm for advanced wastewater treatment. J Microbiol 45 : 113– 121.[PubMed]
68. Philippot L,, Hallin S,, Schloter M, . 2007. Ecology of denitrifying prokaryotes in agricultural soil, p 249– 305. In Donald LS (ed), Advances in Agronomy, vol 96. Elsevier, New York, NY.
69. Heylen K,, Gevers D,, Vanparys B,, Wittebolle L,, Geets J,, Boon N,, De Vos P . 2006. The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers. Environ Microbiol 8 : 2012– 2021.[PubMed] [CrossRef]
70. Albino U,, Saridakis DP,, Ferreira MC,, Hungria M,, Vinuesa P,, Andrade G . 2006. High diversity of diazotrophic bacteria associated with the carnivorous plant Drosera villosa var. villosa growing in oligotrophic habitats in Brazil. Plant Soil 287 : 199– 207.[CrossRef]
71. Beneduzi A,, Peres D,, da Costa PB,, Bodanese Zanettini MH,, Passaglia LM . 2008. Genetic and phenotypic diversity of plant-growth-promoting bacilli isolated from wheat fields in southern Brazil. Res Microbiol 159 : 244– 250.[PubMed] [CrossRef]
72. Beneduzi A,, Peres D,, Vargas LK,, Bodanese-Zanettini MH,, Passaglia LMP . 2008. Evaluation of genetic diversity and plant growth promoting activities of nitrogen-fixing bacilli isolated from rice fields in South Brazil. Appl Soil Ecol 39 : 311– 320.[CrossRef]
73. Różycki H,, Dahm H,, Strzelczyk E,, Li CY . 1999. Diazotrophic bacteria in root-free soil and in the root zone of pine ( Pinus sylvestris L.) and oak ( Quercus robur L.). Appl Soil Ecol 12 : 239– 250.[CrossRef]
74. Achouak W,, Normand P,, Heulin T . 1999. Comparative phylogeny of rrs and nifH genes in the Bacillaceae . Int J Syst Bacteriol 49( Pt 3) : 961– 967.[PubMed] [CrossRef]
75. Rodríguez H,, Fraga R . 1999. Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol Adv 17 : 319– 339.[PubMed] [CrossRef]
76. Mamta,, Rahi P,, Pathania V,, Gulati A,, Singh B,, Bhanwra RK,, Tewari R . 2010. Stimulatory effect of phosphate-solubilizing bacteria on plant growth, stevioside and rebaudioside-A contents of Stevia rebaudiana Bertoni. Appl Soil Ecol 46 : 222– 229.[CrossRef]
77. Whitelaw MA, . 1999. Growth promotion of plants inoculated with phosphate-solubilizing fungi, p 99– 151. In Donald LS (ed), Advances in Agronomy, vol 69. Academic Press, San Diego, CA.
78. Keneni A,, Assefa F,, Prabu PC . 2010. Isolation of phosphate solubilizing bacteria from the rhizosphere of faba bean of Ethiopia and their abilities on solubilizing insoluble phosphates. J Agric Sci Technol 12 : 79– 89.
79. Oliveira CA,, Alves VMC,, Marriel IE,, Gomes EA,, Scotti MR,, Carneiro NP,, Guimarães CT,, Schaffert RE,, Sá NMH . 2009. Phosphate solubilizing microorganisms isolated from rhizosphere of maize cultivated in an oxisol of the Brazilian Cerrado Biome. Soil Biol Biochem 41 : 1782– 1787.[CrossRef]
80. Chen YP,, Rekha PD,, Arun AB,, Shen FT,, Lai WA,, Young CC . 2006. Phosphate solubilizing bacteria from subtropical soil and their tricalcium phosphate solubilizing abilities. Appl Soil Ecol 34 : 33– 41.[CrossRef]
81. Sandeep C,, Venkat Raman R,, Radhika M,, Thejas MS,, Patra S,, Gowda T,, Suresh CK,, Mulla SR . 2011. Effect of inoculation of Bacillus megaterium isolates on growth, biomass and nutrient content of Peppermint. J Phytol 3 : 19– 24.
82. Pal SS . 1998. Interactions of an acid tolerant strain of phosphate solubilizing bacteria with a few acid tolerant crops. Plant Soil 198 : 169– 177.[CrossRef]
83. Kloepper JW,, Lifshitz R,, Zablotowicz RM . 1989. Free-living bacterial inocula for enhancing crop productivity. Trends Biotechnol 7 : 39– 44.[CrossRef]
84. Bhattacharyya PN,, Jha DK . 2012. Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture. World J Microbiol Biotechnol 28 : 1327– 1350.[PubMed] [CrossRef]
85. Hernandez J-P,, de-Bashan LE,, Rodriguez DJ,, Rodriguez Y,, Bashan Y . 2009. Growth promotion of the freshwater microalga Chlorella vulgaris by the nitrogen-fixing, plant growth-promoting bacterium Bacillus pumilus from arid zone soils. Eur J Soil Biol 45 : 88– 93.[CrossRef]
86. Gutiérrez-Mañero FJ,, Ramos-Solano B,, Probanza A,, Mehouachi J,, Tadeo FR,, Talon M . 2001. The plant-growth-promoting rhizobacteria Bacillus pumilus and Bacillus licheniformis produce high amounts of physiologically active gibberellins. Physiol Plant 111 : 206– 211.[CrossRef]
87. Sharma SK,, Sharma MP,, Ramesh A,, Joshi OP . 2012. Characterization of zinc-solubilizing Bacillus isolates and their potential to influence zinc assimilation in soybean seeds. J Microbiol Biotechnol 22 : 352– 359.[PubMed] [CrossRef]
88. Belimov AA,, Safronova VI,, Sergeyeva TA,, Egorova TN,, Matveyeva VA,, Tsyganov VE,, Borisov AY,, Tikhonovich IA,, Kluge C,, Preisfeld A,, Dietz KJ,, Stepanok VV . 2001. Characterization of plant growth promoting rhizobacteria isolated from polluted soils and containing 1-aminocyclopropane-1-carboxylate deaminase. Can J Microbiol 47 : 642– 652.[PubMed] [CrossRef]
89. Zhang H,, Sun Y,, Xie X,, Kim MS,, Dowd SE,, Pare PW . 2009. A soil bacterium regulates plant acquisition of iron via deficiency-inducible mechanisms. Plant J 58 : 568– 577.[PubMed] [CrossRef]
90. Li D-M,, Alexander M . 1988. Co-inoculation with antibiotic-producing bacteria to increase colonization and nodulation by rhizobia. Plant Soil 108 : 211– 219.[CrossRef]
91. Kloepper JW,, Ryu CM,, Zhang S . 2004. Induced systemic resistance and promotion of plant growth by Bacillus spp. Phytopathology 94 : 1259– 1266.[PubMed] [CrossRef]
92. Ryu CM,, Murphy JF,, Mysore KS,, Kloepper JW . 2004. Plant growth-promoting rhizobacteria systemically protect Arabidopsis thaliana against Cucumber mosaic virus by a salicylic acid and NPR1-independent and jasmonic acid-dependent signaling pathway. Plant J 39 : 381– 392.[PubMed] [CrossRef]
93. Banerjee MR,, Yesmin L,, Vessey JK, . 2006. Plant-growth-promoting Rhizobacteria as biofertilizers and biopesticides, p 137– 233. In Rai MK (ed), Handbook of Microbial Biofertilizers. The Haworth Press, Binghampton, NY.
94. Ongena M,, Jacques P . 2008. Bacillus lipopeptides: versatile weapons for plant disease biocontrol. Trends Microbiol 16 : 115– 125.[PubMed] [CrossRef]
95. Valenzuela-Soto JH,, Estrada-Hernandez MG,, Ibarra-Laclette E,, Delano-Frier JP . 2010. Inoculation of tomato plants ( Solanum lycopersicum) with growth-promoting Bacillus subtilis retards whitefly Bemisia tabaci development. Planta 231 : 397– 410.[PubMed] [CrossRef]
96. Vlamakis H,, Chai Y,, Beauregard P,, Losick R,, Kolter R . 2013. Sticking together: building a biofilm the Bacillus subtilis way. Nat Rev Microbiol 11 : 157– 168.[PubMed] [CrossRef]
97. Chen Y,, Yan F,, Chai Y,, Liu H,, Kolter R,, Losick R,, Guo JH . 2013. Biocontrol of tomato wilt disease by Bacillus subtilis isolates from natural environments depends on conserved genes mediating biofilm formation. Environ Microbiol 15 : 848– 864.[PubMed] [CrossRef]
98. Beauregard PB,, Chai Y,, Vlamakis H,, Losick R,, Kolter R . 2013. Bacillus subtilis biofilm induction by plant polysaccharides. Proc Natl Acad Sci USA 110 : E1621– E1630.[PubMed] [CrossRef]
99. Bais HP,, Fall R,, Vivanco JM . 2004. Biocontrol of Bacillus subtilis against infection of Arabidopsis roots by Pseudomonas syringae is facilitated by biofilm formation and surfactin production. Plant Physiol 134 : 307– 319.[PubMed] [CrossRef]
100. Debois D,, Jourdan E,, Smargiasso N,, Thonart P,, De Pauw E,, Ongena M . 2014. Spatiotemporal monitoring of the antibiome secreted by Bacillus biofilms on plant roots using MALDI mass spectrometry imaging. Anal Chem 86 : 4431– 4438.[PubMed] [CrossRef]
101. Oslizlo A,, Stefanic P,, Vatovec S,, Beigot Glaser S,, Rupnik M,, Mandic-Mulec I . Exploring ComQXPA quorum sensing diversity and biocontrol potential of Bacillus spp. isolates from tomato rhizoplane. Microb Biotechnol, in press. [PubMed]
102. Dogsa I,, Brloznik M,, Stopar D,, Mandic-Mulec I . 2013. Exopolymer diversity and the role of levan in Bacillus subtilis biofilms. PLoS One 8 : e62044. doi:10.1371/journal.pone.0062044. [PubMed] [CrossRef]
103. Ongena M,, Jourdan E,, Adam A,, Paquot M,, Brans A,, Joris B,, Arpigny JL,, Thonart P . 2007. Surfactin and fengycin lipopeptides of Bacillus subtilis as elicitors of induced systemic resistance in plants. Environ Microbiol 9 : 1084– 1090.[PubMed] [CrossRef]
104. Lakshmanan V,, Bais HP . 2013. Factors other than root secreted malic acid that contributes toward Bacillus subtilis FB17 colonization on Arabidopsis roots. Plant Signal Behav 8 : e27277. doi:10.4161/psb.27277. [PubMed] [CrossRef]
105. 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 : 504– 517.[PubMed] [CrossRef]
106. Anand AA,, Vennison SJ,, Sankar SG,, Prabhu DI,, Vasan PT,, Raghuraman T,, Geoffrey CJ,, Vendan SE . 2010. Isolation and characterization of bacteria from the gut of Bombyx mori that degrade cellulose, xylan, pectin and starch and their impact on digestion. J Insect Sci 10 : 107. doi:10.1673/031.010.10701. [PubMed] [CrossRef]
107. Visotto LE,, Oliveira MG,, Ribon AO,, Mares-Guia TR,, Guedes RN . 2009. Characterization and identification of proteolytic bacteria from the gut of the velvetbean caterpillar (Lepidoptera: Noctuidae). Environ Entomol 38 : 1078– 1085.[PubMed] [CrossRef]
108. Konig H . 2006. Bacillus species in the intestine of termites and other soil invertebrates. J Appl Microbiol 101 : 620– 627.[PubMed] [CrossRef]
109. Wenzel M,, Schonig I,, Berchtold M,, Kampfer P,, Konig H . 2002. Aerobic and facultatively anaerobic cellulolytic bacteria from the gut of the termite Zootermopsis angusticollis . J Appl Microbiol 92 : 32– 40.[PubMed] [CrossRef]
110. Gordon RE,, Haynes WC,, Pang H-NC . 1973. The Genus Bacillus . U.S. Department of Agriculture, Washington DC.
111. Roberts MS,, Nakamura LK,, Cohan FM . 1994. Bacillus mojavensis sp. nov., distinguishable from Bacillus subtilis by sexual isolation, divergence in DNA sequence, and differences in fatty acid composition. Int J Syst Bacteriol 44 : 256– 264.[PubMed] [CrossRef]
112. Sorokin A,, Candelon B,, Guilloux K,, Galleron N,, Wackerow-Kouzova N,, Ehrlich SD,, Bourguet D,, Sanchis V . 2006. Multiple-locus sequence typing analysis of Bacillus cereus and Bacillus thuringiensis reveals separate clustering and a distinct population structure of psychrotrophic strains. Appl Environ Microbiol 72 : 1569– 1578.[PubMed] [CrossRef]
113. Bizzarri MF,, Prabhakar A,, Bishop AH . 2008. Multiple-locus sequence typing analysis of Bacillus thuringiensis recovered from the phylloplane of clover ( Trifolium hybridum) in vegetative form. Microb Ecol 55 : 619– 625.[PubMed] [CrossRef]
114. Meintanis C,, Chalkou KI,, Kormas KA,, Lymperopoulou DS,, Katsifas EA,, Hatzinikolaou DG,, Karagouni AD . 2008. Application of rpoB sequence similarity analysis, REP-PCR and BOX-PCR for the differentiation of species within the genus Geobacillus . Lett Appl Microbiol 46 : 395– 401.[PubMed] [CrossRef]
115. Heyrman J,, Mergaert J,, Denys R,, Swings J . 1999. The use of fatty acid methyl ester analysis (FAME) for the identification of heterotrophic bacteria present on three mural paintings showing severe damage by microorganisms. FEMS Microbiol Lett 181 : 55– 62.[PubMed] [CrossRef]
116. Hotta Y,, Sato J,, Sato H,, Hosoda A,, Tamura H . 2011. Classification of the genus Bacillus based on MALDI-TOF MS analysis of ribosomal proteins coded in S10 and spc operons. J Agric Food Chem 59 : 5222– 5230.[PubMed] [CrossRef]
117. Balazova T,, Sedo O,, Stefanic P,, Mandic-Mulec I,, Vos M,, Zdrahal Z . 2014. Improvement in Staphylococcus and Bacillus strain differentiation by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling by using microwave-assisted enzymatic digestion. Rapid Commun Mass Spectrom 28 : 185– 1861.[PubMed] [CrossRef]
118. Prosser JI . 2012. Ecosystem processes and interactions in a morass of diversity. FEMS Microbiol Ecol 81 : 507– 519.[PubMed] [CrossRef]
119. Roesch LF,, Fulthorpe RR,, Riva A,, Casella G,, Hadwin AK,, Kent AD,, Daroub SH,, Camargo FA,, Farmerie WG,, Triplett EW . 2007. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1 : 283– 290.[PubMed]
120. Garbeva P,, van Veen JA,, van Elsas JD . 2003. Predominant Bacillus spp. in Agricultural soil under different management regimes detected via PCR-DGGE. Microb Ecol 45 : 302– 316.[PubMed] [CrossRef]
121. Felske A,, Wolterink A,, Van Lis R,, De Vos WM,, Akkermans AD . 2000. Response of a soil bacterial community to grassland succession as monitored by 16S rRNA levels of the predominant ribotypes. Appl Environ Microbiol 66 : 3998– 4003.[PubMed] [CrossRef]
122. Prosser JI,, Jansson JK,, Liu W-T, . 2010. Nucleic-acid-based characterization of community structure and function, p 65– 88. In Jansson JK,, Liu W-T (ed), Environmental Molecular Microbiology. Horizon Scientific, Norfolk, UK.
123. Kraigher B,, Stres B,, Hacin J,, Ausec L,, Mahne I,, van Elsas JD,, Mandic-Mulec I . 2006. Microbial activity and community structure in two drained fen soils in the Ljubljana Marsh. Soil Biol Biochem 38 : 2762– 2771.[CrossRef]
124. Felske AD,, Heyrman J,, Balcaen A,, de Vos P . 2003. Multiplex PCR screening of soil isolates for novel Bacillus-related lineages. J Microbiol Methods 55 : 447– 458.[PubMed] [CrossRef]
125. Janssen PH . 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72 : 1719– 1728.[PubMed] [CrossRef]
126. Brons JK,, van Elsas JD . 2008. Analysis of bacterial communities in soil by use of denaturing gradient gel electrophoresis and clone libraries, as influenced by different reverse primers. Appl Environ Microbiol 74 : 2717– 2727.[PubMed] [CrossRef]
127. Felske A,, Wolterink A,, Van Lis R,, Akkermans AD . 1998. Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Appl Environ Microbiol 64 : 871– 879.[PubMed]
128. Benizri E,, Baudoin E,, Guckert A . 2001. Root colonization by inoculated plant growth-promoting rhizobacteria. Biocontrol Sci Technol 11 : 557– 574.[CrossRef]
129. Rudrappa T,, Czymmek KJ,, Pare PW,, Bais HP . 2008. Root-secreted malic acid recruits beneficial soil bacteria. Plant Physiol 148 : 1547– 1556.[PubMed] [CrossRef]
130. Zeller SL,, Brandl H,, Schmid B . 2007. Host-plant selectivity of rhizobacteria in a crop/weed model system. PLoS One 2 : e846. doi:10.1371/journal.pone.0000846. [CrossRef]
131. Kremer RJ,, Souissi T . 2001. Cyanide production by rhizobacteria and potential for suppression of weed seedling growth. Curr Microbiol 43 : 182– 186.[PubMed] [CrossRef]
132. Åström B,, Gerhardson B . 1988. Differential reactions of wheat and pea genotypes to root inoculation with growth-affecting rhizosphere bacteria. Plant Soil 109 : 263– 269.[CrossRef]
133. Long HH,, Schmidt DD,, Baldwin IT . 2008. Native bacterial endophytes promote host growth in a species-specific manner; phytohormone manipulations do not result in common growth responses. PLoS One 3 : e2702. doi:10.1371/journal.pone.0002702. [CrossRef]
134. Berg G,, Roskot N,, Steidle A,, Eberl L,, Zock A,, Smalla K . 2002. Plant-dependent genotypic and phenotypic diversity of antagonistic rhizobacteria isolated from different Verticillium host plants. Appl Environ Microbiol 68 : 3328– 3338.[PubMed] [CrossRef]
135. da Silva KR,, Salles JF,, Seldin L,, van Elsas JD . 2003. Application of a novel Paenibacillus-specific PCR-DGGE method and sequence analysis to assess the diversity of Paenibacillus spp. in the maize rhizosphere. J Microbiol Methods 54 : 213– 231.[PubMed] [CrossRef]
136. Smalla K,, Wieland G,, Buchner A,, Zock A,, Parzy J,, Kaiser S,, Roskot N,, Heuer H,, Berg G . 2001. Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67 : 4742– 4751.[PubMed] [CrossRef]
137. Garbeva P,, van Elsas J,, van Veen J . 2008. Rhizosphere microbial community and its response to plant species and soil history. Plant Soil 302 : 19– 32.[CrossRef]
138. Inceoglu O,, Al-Soud WA,, Salles JF,, Semenov AV,, van Elsas JD . 2011. Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing. PLoS One 6 : e23321. doi:10.1371/journal.pone.0023321. [PubMed] [CrossRef]
139. Inceoglu O,, Falcao Salles J,, van Elsas JD . 2012. Soil and cultivar type shape the bacterial community in the potato rhizosphere. Microb Ecol 63 : 460– 470.[PubMed] [CrossRef]
140. Inceoglu O,, Salles JF,, van Overbeek L,, van Elsas JD . 2010. Effects of plant genotype and growth stage on the betaproteobacterial communities associated with different potato cultivars in two fields. Appl Environ Microbiol 76 : 3675– 3684.[PubMed] [CrossRef]
141. Fan B,, Borriss R,, Bleiss W,, Wu X . 2012. Gram-positive rhizobacterium Bacillus amyloliquefaciens FZB42 colonizes three types of plants in different patterns. J Microbiol 50 : 38– 44.[PubMed] [CrossRef]
142. Chowdhury SP,, Dietel K,, Randler M,, Schmid M,, Junge H,, Borriss R,, Hartmann A,, Grosch R . 2013. Effects of Bacillus amyloliquefaciens FZB42 on lettuce growth and health under pathogen pressure and its impact on the rhizosphere bacterial community. PLoS One 8 : e68818. doi:10.1371/journal.pone.0068818. [PubMed] [CrossRef]
143. Horner-Devine MC,, Carney KM,, Bohannan BJ . 2004. An ecological perspective on bacterial biodiversity. Proc Biol Sci 271 : 113– 122.[PubMed] [CrossRef]
144. Ramette A,, Tiedje JM . 2007. Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution. Microb Ecol 53 : 197– 207.[PubMed] [CrossRef]
145. Cohan FM,, Perry EB . 2007. A systematics for discovering the fundamental units of bacterial diversity. Curr Biol 17 : R373– R386.[PubMed] [CrossRef]
146. Cohan FM . 2006. Towards a conceptual and operational union of bacterial systematics, ecology, and evolution. Philos Trans R Soc Lond B Biol Sci 361 : 1985– 1996.[PubMed] [CrossRef]
147. Cohan FM . 2002. What are bacterial species? Annu Rev Microbiol 56 : 457– 487.[PubMed] [CrossRef]
148. Smith JM,, Szathmáry E . 1993. The origin of chromosomes I. selection for linkage. J Theor Biol 164 : 437– 446.[PubMed] [CrossRef]
149. Dubnau D,, Smith I,, Morell P,, Marmur J . 1965. Gene conservation in Bacillus species. I. Conserved genetic and nucleic acid base sequence homologies. Proc Natl Acad Sci USA 54 : 491– 498.[PubMed] [CrossRef]
150. Koeppel A,, Perry EB,, Sikorski J,, Krizanc D,, Warner A,, Ward DM,, Rooney AP,, Brambilla E,, Connor N,, Ratcliff RM,, Nevo E,, Cohan FM . 2008. Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proc Natl Acad Sci USA 105 : 2504– 2509.[PubMed] [CrossRef]
151. Nevo E . 1995. Asian, African and European biota meet at ‘Evolution Canyon’ Israel: local tests of global biodiversity and genetic diversity patterns. Proc Biol Sci 262 : 149– 155.[CrossRef]
152. 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 : 1349– 1358.[PubMed] [CrossRef]
153. von Stetten F,, Mayr R,, Scherer S . 1999. Climatic influence on mesophilic Bacillus cereus and psychrotolerant Bacillus weihenstephanensis populations in tropical, temperate and alpine soil. Environ Microbiol 1 : 503– 515.[PubMed] [CrossRef]
154. Tortosa P,, Logsdon L,, Kraigher B,, Itoh Y,, Mandic Mulec I,, Dubnau D . 2001. Specificity and genetic polymorphism of the Bacillus competence quorum sensing system. J Bacteriol 183 : 451– 460.[PubMed] [CrossRef]
155. Ansaldi M,, Dubnau D . 2004. Diversifying selection at the Bacillus Quorum sensing locus and determinants of modification specificity during synthesis of the ComX pheromone. J Bacteriol 186 : 15– 21.[CrossRef]
156. Ansaldi M,, Marolt D,, Stebe T,, Mandic Mulec I,, Dubnau D . 2002. Specific activation of the Bacillus quorum-sensing systems by isoprenylated pheromone variants. Mol Microbiol 44 : 1561– 1573.[PubMed] [CrossRef]
157. Magnuson R,, Solomon J,, Grossman AD . 1994. Biochemical and genetic characterization of a competence pheromone from B. subtilis . Cell 77 : 207– 216.[PubMed] [CrossRef]
158. Schneider KB,, Palmer TM,, Grossman AD . 2002. Characterization of comQ and comX, two genes required for production of ComX pheromone in Bacillus subtilis . J Bacteriol 184 : 410– 419.[CrossRef]
159. Dogsa I,, Oslizlo A,, Stefanic P,, Mandic-Mulec I . 2014. Social interactions and biofilm formation in Bacillus subtilis . Food Technol Biotechnol 52 : 149– 157.
160. Mandic Mulec I,, Kraigher B,, Cepon U,, Mahne I . 2003. Variability of the quorum sensing system in natural isolates of Bacillus sp. Food Technol Biotechnol 41 : 23– 28.
161. Tran PL-S,, Nagai T,, Itoh Y . 2000. Divergent structure of the ComQXPA quorum-sensing components: molecular basis of strain-specific communication mechanism in Bacillus subtilis . Mol Microbiol 37 : 1159– 1171.[CrossRef]
162. West SA,, Griffin AS,, Gardner A,, Diggle SP . 2006. Social evolution theory for microorganisms. Nat Rev Microbiol 4 : 597– 607.[PubMed] [CrossRef]
163. Eldar A . 2011. Social conflict drives the evolutionary divergence of quorum sensing. Proc Natl Acad Sci USA 108 : 13635– 13640.[PubMed] [CrossRef]
164. Diggle SP,, Griffin AS,, Campbell GS,, West SA . 2007. Cooperation and conflict in quorum-sensing bacterial populations. Nature 450 : 411– 414.[PubMed] [CrossRef]
165. Tortosa P,, Dubnau D . 1999. Competence for transformation: a matter of taste. Curr Opin Microbiol 2 : 588– 592.[PubMed] [CrossRef]
166. Dogsa I,, Choudhary KS,, Marsetic Z,, Hudaiberdiev S,, Vera R,, Pongor S,, Mandic-Mulec I . 2014. ComQXPA quorum sensing systems may not be unique to Bacillus subtilis: a census in prokaryotic genomes. PLoS One 9 : e96122. doi:10.1371/journal.pone.0096122. [PubMed] [CrossRef]
167. Oslizlo A,, Stefanic P,, Dogsa I,, Mandic-Mulec I . 2014. Private link between signal and response in Bacillus subtilis quorum sensing. Proc Natl Acad Sci USA 111 : 1586– 1591.[PubMed] [CrossRef]
168. Earl AM,, Losick R,, Kolter R . 2008. Ecology and genomics of Bacillus subtilis . Trends Microbiol 16 : 269– 275.[PubMed] [CrossRef]
169. Nakamura LK,, Roberts MS,, Cohan FM . 1999. Relationship of Bacillus subtilis clades associated with strains 168 and W23: a proposal for Bacillus subtilis subsp. subtilis subsp. nov. and Bacillus subtilis subsp. spizizenii subsp. nov. Int J Syst Bacteriol 49( Pt 3) : 1211– 1215.[PubMed] [CrossRef]
170. Earl AM,, Eppinger M,, Fricke WF,, Rosovitz MJ,, Rasko DA,, Daugherty S,, Losick R,, Kolter R,, Ravel J . 2012. Whole-genome sequences of Bacillus subtilis and close relatives. J Bacteriol 194 : 2378– 2379.[PubMed] [CrossRef]
171. Buscot F,, Varma A, . 2005. Microorganisms in soils: roles in genesis and functions, p 3– 16. In Buscot F,, Varma A (ed), Soil Biology, vol 3. Springer-Verlag, Berlin.
172. Grundmann GL . 2004. Spatial scales of soil bacterial diversity – the size of a clone. FEMS Microbiol Ecol 48 : 119– 127.[PubMed] [CrossRef]
173. Vos M,, Wolf AB,, Jennings SJ,, Kowalchuk GA . 2013. Micro-scale determinants of bacterial diversity in soil. FEMS Microbiol Rev 37 : 936– 954.[PubMed]
174. Cohn F . 1872. Untersuchungen uber Bakterien. Beitrage zur Biologie der Pflanzen 1. Heft II.
175. Jeon CO,, Lim JM,, Lee JM,, Xu LH,, Jiang CL,, Kim CJ . 2005. Reclassification of Bacillus haloalkaliphilus Fritze 1996 as Alkalibacillus haloalkaliphilus gen. nov., comb. nov. and the description of Alkalibacillus salilacus sp. nov., a novel halophilic bacterium isolated from a salt lake in China. Int J Syst Evol Microbiol 55 : 1891– 1896.[PubMed] [CrossRef]
176. Schmidt M,, Prieme A,, Johansen A,, Stougaard P . 2012. Alkalilactibacillus ikkensis, gen. nov., sp. nov., a novel enzyme-producing bacterium from a cold and alkaline environment in Greenland. Extremophiles 16 : 297– 305.[PubMed] [CrossRef]
177. Sheu SY,, Arun AB,, Jiang SR,, Young CC,, Chen WM . 2011. Allobacillus halotolerans gen. nov., sp. nov. isolated from shrimp paste. Int J Syst Evol Microbiol 61 : 1023– 1027.[PubMed] [CrossRef]
178. Didari M,, Amoozegar MA,, Bagheri M,, Schumann P,, Sproer C,, Sanchez-Porro C,, Ventosa A . 2012. Alteribacillus bidgolensis gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Bacillus persepolensis as Alteribacillus persepolensis comb. nov. Int J Syst Evol Microbiol 62 : 2691– 2697.[PubMed] [CrossRef]
179. Niimura Y,, Koh E,, Yanagida F,, Suzuki K-I,, Komagata K,, Kozaki M . 1990. Amphibacillus xylanus gen. nov., sp. nov., a facultatively anaerobic sporeforming xylan-digesting bacterium which lacks cytochrome, quinone, and catalase. Int J Syst Bacteriol 40 : 297– 301.[CrossRef]
180. Zavarzina DG,, Tourova TP,, Kolganova TV,, Boulygina ES,, Zhilina TN . 2009. Description of Anaerobacillus alkalilacustre gen. nov., sp. nov.—Strictly anaerobic diazotrophic bacillus isolated from soda lake and transfer of Bacillus arseniciselenatis, Bacillus macyae, and Bacillus alkalidiazotrophicus to Anaerobacillus as the new combinations A. arseniciselenatis comb. nov., A. macyae comb. nov., and A. alkalidiazotrophicus comb. nov. Microbiology 78 : 723– 731.[CrossRef]
181. Pikuta E,, Lysenko A,, Chuvilskaya N,, Mendrock U,, Hippe H,, Suzina N,, Nikitin D,, Osipov G,, Laurinavichius K . 2000. Anoxybacillus pushchinensis gen. nov., sp. nov., a novel anaerobic, alkaliphilic, moderately thermophilic bacterium from manure, and description of Anoxybacillus flavitherms comb. nov. Int J Syst Evol Microbiol 50( Pt 6) : 2109– 2117.[PubMed] [CrossRef]
182. Marquez MC,, Carrasco IJ,, Xue Y,, Ma Y,, Cowan DA,, Jones BE,, Grant WD,, Ventosa A . 2008. Aquisalibacillus elongatus gen. nov., sp. nov., a moderately halophilic bacterium of the family Bacillaceae isolated from a saline lake. Int J Syst Evol Microbiol 58 : 1922– 1926.[PubMed] [CrossRef]
183. Amoozegar MA,, Bagheri M,, Didari M,, Mehrshad M,, Schumann P,, Sproer C,, Sanchez-Porro C,, Ventosa A . 2014. Aquibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Virgibacillus koreensis as Aquibacillus koreensis comb. nov. and Virgibacillus albus as Aquibacillus albus comb. nov. Int J Syst Evol Microbiol 64( Pt 11) : 3616– 3623.[PubMed] [CrossRef]
184. Xue Y,, Zhang X,, Zhou C,, Zhao Y,, Cowan DA,, Heaphy S,, Grant WD,, Jones BE,, Ventosa A,, Ma Y . 2006. Caldalkalibacillus thermarum gen. nov., sp. nov., a novel alkalithermophilic bacterium from a hot spring in China. Int J Syst Evol Microbiol 56 : 1217– 1221.[PubMed] [CrossRef]
185. Coorevits A,, Dinsdale AE,, Halket G,, Lebbe L,, De Vos P,, Van Landschoot A,, Logan NA . 2012. Taxonomic revision of the genus Geobacillus: emendation of Geobacillus, G. stearothermophilus, G. jurassicus, G. toebii, G. thermodenitrificans and G. thermoglucosidans (nom. corrig., formerly ‘thermoglucosidasius’); transfer of Bacillus thermantarcticus to the genus as G. thermantarcticus comb. nov.; proposal of Caldibacillus debilis gen. nov., comb. nov.; transfer of G. tepidamans to Anoxybacillus as A. tepidamans comb. nov.; and proposal of Anoxybacillus caldiproteolyticus sp. nov. Int J Syst Evol Microbiol 62 : 1470– 1485.[PubMed] [CrossRef]
186. Moriya T,, Hikota T,, Yumoto I,, Ito T,, Terui Y,, Yamagishi A,, Oshima T . 2011. Calditerricola satsumensis gen. nov., sp. nov. and Calditerricola yamamurae sp. nov., extreme thermophiles isolated from a high-temperature compost. Int J Syst Evol Microbiol 61 : 631– 636.[PubMed] [CrossRef]
187. 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 : 1063– 1069.[PubMed] [CrossRef]
188. Seiler H,, Wenning M,, Scherer S . 2012. Domibacillus robiginosus gen. nov., sp. nov., isolated from a pharmaceutical clean room. Int J Syst Evol Microbiol 63( Pt 6) : 2054– 2061.[PubMed] [CrossRef]
189. Schlesner H,, Lawson PA,, Collins MD,, Weiss N,, Wehmeyer U,, Volker H,, Thomm M . 2001. Filobacillus milensis gen. nov., sp. nov., a new halophilic spore-forming bacterium with Orn-D-Glu-type peptidoglycan. Int J Syst Evol Microbiol 51 : 425– 431.[PubMed]
190. Glaeser SP,, Dott W,, Busse HJ,, Kampfer P . 2013. Fictibacillus phosphorivorans gen. nov. sp. nov. and proposal to reclassify Bacillus arsenicus, Bacillus barbaricus, Bacillus macauensis, Bacillus nanhaiensis, Bacillus rigui, Bacillus solisalsi and B. gelatini into the genus Fictibacillus . Int J Syst Evol Microbiol 63( Pt 8) : 2934– 2944.[PubMed] [CrossRef]
191. Lal D,, Khan F,, Gupta SK,, Schumann P,, Lal R . 2013. Edaphobacillus lindanitolerans gen. nov., sp. nov., isolated from hexachlorocyclohexane (HCH) contaminated soil. J Basic Microbiol 53 : 758– 765.[PubMed] [CrossRef]
192. Nazina TN,, Tourova TP,, Poltaraus AB,, Novikova EV,, Grigoryan AA,, Ivanova AE,, Lysenko AM,, Petrunyaka VV,, Osipov GA,, Belyaev SS,, Ivanov MV . 2001. Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th. Int J Syst Evol Microbiol 51 : 433– 446.[PubMed]
193. Waino M,, Tindall BJ,, Schumann P,, Ingvorsen K . 1999. Gracilibacillus gen. nov., with description of Gracilibacillus halotolerans gen. nov., sp. nov.; transfer of Bacillus dipsosauri to Gracilibacillus dipsosauri comb. nov., and Bacillus salexigens to the genus Salibacillus gen. nov., as Salibacillus salexigens comb. nov. Int J Syst Bacteriol 49( Pt 2) : 821– 831.[PubMed] [CrossRef]
194. Echigo A,, Fukushima T,, Mizuki T,, Kamekura M,, Usami R . 2007. Halalkalibacillus halophilus gen. nov., sp. nov., a novel moderately halophilic and alkaliphilic bacterium isolated from a non-saline soil sample in Japan. Int J Syst Evol Microbiol 57 : 1081– 1085.[PubMed] [CrossRef]
195. Spring S,, Ludwig W,, Marquez MC,, Ventosa A,, Schleifer K-H . 1996. Halobacillus gen. nov., with descriptions of Halobacillus litoralis sp. nov. and Halobacillus trueperi sp. nov., and transfer of Sporosarcina halophila to Halobacillus halophilus comb. nov. Int J Syst Bacteriol 46 : 492– 496.[CrossRef]