Acknowledgements The authors wish to thank the University of Pretoria and the National
Research Foundation of South Africa for financial support.
References
1. Grant WD, Mwatha WE, Jones BE (1990) Alkaliphiles: ecology, diversity and applications.
FEMS Microbiol Rev 75:255–270
2. Yumoto I, Fukumori Y, Yamanaka T (1991) Stopped-flow and rapid-scan studies of the redox
behavior of cytochrome aco from facultative alkalophilic Bacillus. J Biol Chem 266
(2):14310–14316
3. Takami H, Takaki Y, Maeno G, Sasaki R, Masui N, Fumie F et al (2000) Complete genome
sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison
with Bacillus subtilis. Nucleic Acids Res 28(21):4317–4331
4. Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER (2013) The next-generation
sequencing revolution and its impact on genomics. Cell 155(1):27–38
5. Nordberg H, Cantor M, Dusheyko S, Hua S, Poliakov A, Shabalov I et al (2014) The genome
portal of the department of energy Joint Genome Institute: 2014 updates. Nucleic Acids Res 42:
D26–D31
6. Janto B, Ahmed A, Ito M, Liu J, Hicks DB, Pagnl S et al (2011) Genome of alkaliphilic Bacillus
pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range
from 7.5 to 11.4. Environ Microbiol 13(12):3289–3309
7. Wu S, Wang L, Gan R, Tong T, Bian H, Li Z et al (2018) Signature arsenic detoxification
pathways in Halomonas sp. strain GFAJ-1. MBio 9(3):e00515–e00518
8. Zavarzin GA, Zhilina TN, Kevbrin VV (1999) The alkaliphilic microbial community and its
functional diversity. Microbiology 68(5):503–521
9. Cheevadhanarak S, Paithoonrangsarid K, Prommeenate P, Kaewngam W, Musigkain A,
Tragoonrung S et al (2012) Draft genome sequence of Arthrospira platensis C1 (PCC9438).
Stand Genomic Sci 6:43–53
10. Paul S, Bag SK, Das S, Harvill ET, Dutta C (2008) Molecular signature of hypersaline
adaptation: insights from genome and proteome composition of halophilic prokaryotes.
Genome Biol 9:R70
11. Klanchui A, Cheevadhanarak S, Prommeenate P, Meechai A (2017) Exploring components of
the CO 2 -concentrating mechanism in alkaliphilic cyanobacteria through genome-based analysis. Comput Struct Biotechnol J 15:340–350
12. Amaral-Zettler LA (2012) Eukaryotic diversity at pH extremes. Front Microbiol 3:441
13. Takami H (2011) Genomic and evolution of alkaliphilic Bacillus species. In: Horikoshi H
(ed) Extremophiles handbook. Springer, Tokyo, pp 183–211
14. Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C et al (2017)
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Mol Biol Evol 34(8):2115–2122
15. Takami H, Takaki Y, Uchiyama I (2002) Genome sequence of Oceanobacillus iheyensis
isolated from the Iheya ridge and its unexpected adaptive capabilities to extreme environments.
Nucleic Acids Res 30(18):3927–3935
16. Schadewaldt P, Hummel W, Wendel U, Adelmeyer F (1995) Enzymatic method for determination of branched-chain amino acid aminotransferase activity. Anal Biochem 230(2):199–204
17. Cheng B, Meng Y, Cui Y, Li C, Tao F, Yin H et al (2016) Alkaline response of a halotolerant
alkaliphilic halomonas strain and functional diversity of its Na+(K+)/H+ antiporters. J Biol
Chem 291(50):26056–26065
18. Siddaramappa S, Challacombe JF, DeCastro RE, Pfeiffer F, Sastre DE, Gimenez MI et al (2012)
A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon
Natrialba magadii ATCC 43099
T . BMC Genomics 13:165
152
P. H. Lebre and D. A. Cowan
Research Foundation of South Africa for financial support.
References
1. Grant WD, Mwatha WE, Jones BE (1990) Alkaliphiles: ecology, diversity and applications.
FEMS Microbiol Rev 75:255–270
2. Yumoto I, Fukumori Y, Yamanaka T (1991) Stopped-flow and rapid-scan studies of the redox
behavior of cytochrome aco from facultative alkalophilic Bacillus. J Biol Chem 266
(2):14310–14316
3. Takami H, Takaki Y, Maeno G, Sasaki R, Masui N, Fumie F et al (2000) Complete genome
sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison
with Bacillus subtilis. Nucleic Acids Res 28(21):4317–4331
4. Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER (2013) The next-generation
sequencing revolution and its impact on genomics. Cell 155(1):27–38
5. Nordberg H, Cantor M, Dusheyko S, Hua S, Poliakov A, Shabalov I et al (2014) The genome
portal of the department of energy Joint Genome Institute: 2014 updates. Nucleic Acids Res 42:
D26–D31
6. Janto B, Ahmed A, Ito M, Liu J, Hicks DB, Pagnl S et al (2011) Genome of alkaliphilic Bacillus
pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range
from 7.5 to 11.4. Environ Microbiol 13(12):3289–3309
7. Wu S, Wang L, Gan R, Tong T, Bian H, Li Z et al (2018) Signature arsenic detoxification
pathways in Halomonas sp. strain GFAJ-1. MBio 9(3):e00515–e00518
8. Zavarzin GA, Zhilina TN, Kevbrin VV (1999) The alkaliphilic microbial community and its
functional diversity. Microbiology 68(5):503–521
9. Cheevadhanarak S, Paithoonrangsarid K, Prommeenate P, Kaewngam W, Musigkain A,
Tragoonrung S et al (2012) Draft genome sequence of Arthrospira platensis C1 (PCC9438).
Stand Genomic Sci 6:43–53
10. Paul S, Bag SK, Das S, Harvill ET, Dutta C (2008) Molecular signature of hypersaline
adaptation: insights from genome and proteome composition of halophilic prokaryotes.
Genome Biol 9:R70
11. Klanchui A, Cheevadhanarak S, Prommeenate P, Meechai A (2017) Exploring components of
the CO 2 -concentrating mechanism in alkaliphilic cyanobacteria through genome-based analysis. Comput Struct Biotechnol J 15:340–350
12. Amaral-Zettler LA (2012) Eukaryotic diversity at pH extremes. Front Microbiol 3:441
13. Takami H (2011) Genomic and evolution of alkaliphilic Bacillus species. In: Horikoshi H
(ed) Extremophiles handbook. Springer, Tokyo, pp 183–211
14. Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C et al (2017)
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Mol Biol Evol 34(8):2115–2122
15. Takami H, Takaki Y, Uchiyama I (2002) Genome sequence of Oceanobacillus iheyensis
isolated from the Iheya ridge and its unexpected adaptive capabilities to extreme environments.
Nucleic Acids Res 30(18):3927–3935
16. Schadewaldt P, Hummel W, Wendel U, Adelmeyer F (1995) Enzymatic method for determination of branched-chain amino acid aminotransferase activity. Anal Biochem 230(2):199–204
17. Cheng B, Meng Y, Cui Y, Li C, Tao F, Yin H et al (2016) Alkaline response of a halotolerant
alkaliphilic halomonas strain and functional diversity of its Na+(K+)/H+ antiporters. J Biol
Chem 291(50):26056–26065
18. Siddaramappa S, Challacombe JF, DeCastro RE, Pfeiffer F, Sastre DE, Gimenez MI et al (2012)
A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon
Natrialba magadii ATCC 43099
T . BMC Genomics 13:165
152
P. H. Lebre and D. A. Cowan