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Chapter 23 : Environmental and Taxonomic Biodiversities of Gram-Positive Alkaliphiles

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Environmental and Taxonomic Biodiversities of Gram-Positive Alkaliphiles, Page 1 of 2

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Abstract:

This chapter focuses on the environmental and taxonomic distributions of gram-positive alkaliphiles. Garbeva et al. developed a polymerase chain reaction (PCR) system for studying the diversity of the species of and related taxa using DNA directly obtained from soil. Detection of by this procedure indicated that although the soil samples were slightly acidic, might be one of the major species in the soil samples used in that study. Microbial diversities of soda lakes in Africa, Europe, and North America have been detected on the basis of the analysis of DNA clone libraries produced by amplification of obtained DNA as well as from the isolation of microorganisms from the environments. The major gram-negative isolates are members of the gamma subdivision of . Indigo-reducing bacteria have been isolated by Takahara and Tanabe and identified as sp. they have been named . This is the only species that can grow at 5°C among the currently known alkaliphilic spp. The chapter provides facts that suggest that niches of patagoniensis are in soil and in rhizosphere of certain plants. Some of the strains in this group were formally classified as . In the next decade, the understanding of the distribution in the environment and of the taxonomic diversities of alkaliphiles will proceed further not only by isolation of novel species of alkaliphiles but also from results of analyses of DNA directly obtained from various environments.

Citation: Yumoto I. 2007. Environmental and Taxonomic Biodiversities of Gram-Positive Alkaliphiles, p 295-310. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch23

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Bacillus halodurans
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Bacillus pseudofirmus
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Bacillus subtilis
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Figures

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Figure 1.

Phylogenetic tree derived from 16S rRNA gene sequences of alkaliphilic spp., constructed using the neighbor-joining method. IAM 12118 and NCDO 1774 are used as a representative strain of group I species and outgroup of the phylogenetic tree, respectively. The two strains are not alkaliphiles. Origin of alkaliphiles: a, soil; b, bauxite-processing red mud tailing pond; c, soda lake; d, bottom sediment of soda lake; e, algal mat from mineral pool; f, soil and horse meadow; g, rhizosphere of shrub; h, hot spa. GenBank/EMBL/DDBJ accession numbers are given in parentheses. Numbers indicate bootstrap values greater than 500. Bar, 0.1 .

Citation: Yumoto I. 2007. Environmental and Taxonomic Biodiversities of Gram-Positive Alkaliphiles, p 295-310. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch23
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Image of Figure 2.
Figure 2.

Phylogenetic tree derived from 16S rRNA gene sequences of alkaliphiles that are high G+C and low G+C gram-positive bacteria. DSM 13738 is used as an outgroup of the phylogenetic tree, and the strain is not a gram-positive alkaliphile. Origin of alkaliphiles: a, muddy sample in salt lake; b, salt for soy source; c, sediment of littoral zone of soda lake; d, soda soil in soda lake; e, soil; f, sewage; g, soda deposits in soda lake; h, alkaline water pool in gold mine; i, mixture of mud and surface cyanobacterial mud; j, soda lake; k, water and soil sample; l, potato-processing effluent; m, unknown; n, manure; o, marine organisms; p, washwaters of edible olive; q, highly saline mud; r, hypersaline soil; s, mud from deep sea; t kitchen refuse; u, salt lake. GenBank/EMBL/DDBJ accession numbers are given in parentheses. Numbers indicate bootstrap values greater than 500. Bar, 0.1 .

Citation: Yumoto I. 2007. Environmental and Taxonomic Biodiversities of Gram-Positive Alkaliphiles, p 295-310. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch23
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89. Yumoto, I.,, K. Yamazaki,, M. Hishinuma,, Y. Nodasaka,, A. Suemori,, K. Nakajima,, N. Inoue, and, K. Kawasaki. 2001. Pseudomonas alcaliphila sp. nov., a novel facultatively psychrophilic alkaliphile isolated from seawater. Int. J. Syst. Evol. Microbiol. 51:349355.
90. Yumoto, I. 2002. Bioenergetics of alkaliphilic Bacillus spp. J. Biosci. Bioeng. 93:342353.
91. Yumoto, I.,, A. Nakamura,, H. Iwata,, K. Kojima,, K. Kusumoto,, Y. Nodasaka, and, H. Matsuyama. 2002. Dietzia psychralcaliphila sp. nov., a novel facultatively psychrophilic alkaliphile that grows on hydrocarbons. Int. J. Syst. Evol. Microbiol. 52:8590.
92. Yumoto, I. 2003. Electron transport system in alkaliphilic Bacillus spp. Recent Res. Dev. Bacteriol. 1:131149.
93. Yumoto, I.,, S. Yamaga,, Y. Sogabe,, Y. Nodasaka,, H. Matsuyama,, K. Nakajima, and, A. Suemori. 2003. Bacillus krulwichae sp. nov., a halotolerant obligate alkaliphile that utilizes benzoate and m-hydroxybenzoate. Int. J. Syst. Evol. Microbiol. 53:15311536.
94. Yumoto, I.,, M. Hishinuma-Narisawa,, K. Hirota,, T. Shingyo,, F. Takebe,, Y. Nodasaka,, H. Matsuyama, and, I. Hara. 2004a. Exiguobacterium oxidotolerans sp. nov., a novel alkaliphile exhibiting high catalase activity. Int. J. Syst. Evol. Microbiol. 54:20132017.
95. Yumoto, I.,, K. Hirota,, Y. Nodasaka,, Y. Yokota,, T. Hoshino and, K. Nakajima. 2004b. Alkalibacterium psychrotolerans sp. nov., a psychrotolerant obligate alkaliphile that reduces an indigo dye. Int. J. Syst. Evol. Microbiol. 54:23792383.
96. Yumoto, I.,, K. Hirota,, T. Goto,, Y. Nodasaka, and, K. Nakajima. 2005a. Bacillus oshimensis sp. nov., a moderately halophilic, nonmotile alkaliphile. Int. J. Syst. Evol. Microbiol. 55:935939.
97. Yumoto, I.,, K. Hirota,, Y. Nodasaka, and, K. Nakajima. 2005b. Oceanobacillus oncorhynchi sp. nov., a halotolerant obligate alkaliphile isolated from the skin of a rainbow trout (Oncorhynchus mykiss), and emended description of the genus Oceanobacillus. Int. J. Syst. Evol. Microbiol. 55:15211524.
98. Zhilina, T. N.,, E. N. Detkova,, F. A. Rainey,, G. A. Osipov,, A. M. Lysenko,, N. A. Kostrikina,, G. A. Zavarzin. 1998. Natronoincola histidinovorans gen. nov., sp. nov., a new alkaliphilic acetogenic anaerobe. Curr. Microbiol. 37:177185.
99. Zhilina, T. N.,, E. S. Garnova,, T. P. Tourova,, N. A. Kostrikina, and, G. A. Zavarzin. 2001. Amphibacillus fermentum sp. nov. and Amphibacillus tropicus sp. nov., new alkaliphilic, facultatively anaerobic, saccharolytic bacilli from Lake Magadi. Mikrobiologiia 70:825827.
100. Zhilina, T. N.,, R. Appel,, C. Probian,, E. L. Brossa,, J. Harder,, F. Widdel, and, G. A. Zavarzin. 2004. Alkaliflexus imshenetskii gen. nov., a new alkaliphilic gliding carbohydrate-fermenting bacterium with propionate formation from a soda lake. Arch. Microbiol. 182:244253.

Tables

Generic image for table
Table 1.

Characteristics of alkaliphilic spp.

Citation: Yumoto I. 2007. Environmental and Taxonomic Biodiversities of Gram-Positive Alkaliphiles, p 295-310. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch23
Generic image for table
Table 2.

Characteristics of alkaliphilic obligately anaerobic and lactic acid bacterial groups

Citation: Yumoto I. 2007. Environmental and Taxonomic Biodiversities of Gram-Positive Alkaliphiles, p 295-310. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch23
Generic image for table
Table 3.

Characteristics of alkaliphilic aerobic mesophiles other than spp. and thermophiles

Citation: Yumoto I. 2007. Environmental and Taxonomic Biodiversities of Gram-Positive Alkaliphiles, p 295-310. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch23
Generic image for table
Table 4.

Characteristics of alkaliphilic gram-positive high G+C bacteria

Citation: Yumoto I. 2007. Environmental and Taxonomic Biodiversities of Gram-Positive Alkaliphiles, p 295-310. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch23

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