Adv Biochem Eng Biotechnol (2020) 172: 135–156
DOI: 10.1007/10_2018_83
© Springer Nature Switzerland AG 2019
Published online: 23 February 2019
Genomics of Alkaliphiles
Pedro H. Lebre and Don A. Cowan
Contents
1 Introduction: Alkaliphiles in the Metagenomics Era . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
2 The Genomic Features of Alkaliphilic Microorganisms . . . . . . . . . . . . . . . . .. . . . . . . . . . . . .. . . . . . 139
3 Genomic Insights into the Metabolism of Alkaliphiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
4 The Bioenergetics of Alkaliphiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . 145
5 The Alkaliphilic Respiration Chain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
6 The Link Between Respiration and ATP Synthases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
6.1 NADH and Succinate Dehydrogenases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
6.2 Cytochromes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
7 Concluding Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
Abstract Alkalinicity presents a challenge for life due to a “reversed” proton
gradient that is unfavourable to many bioenergetic processes across the membranes
of microorganisms. Despite this, many bacteria, archaea, and eukaryotes, collectively termed alkaliphiles, are adapted to life in alkaline ecosystems and are of great
scientific and biotechnological interest due to their niche specialization and ability to
produce highly stable enzymes. Advances in next-generation sequencing technologies have propelled not only the genomic characterization of many alkaliphilic
microorganisms that have been isolated from nature alkaline sources but also our
understanding of the functional relationships between different taxa in microbial
communities living in these ecosystems. In this review, we discuss the genetics and
molecular biology of alkaliphiles from an “omics” point of view, focusing on how
metagenomics and transcriptomics have contributed to our understanding of these
extremophiles.
P. H. Lebre and D. A. Cowan (*)
Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and
Microbiology, University of Pretoria, Pretoria, South Africa
e-mail: don.cowan@up.ac.za
DOI: 10.1007/10_2018_83
© Springer Nature Switzerland AG 2019
Published online: 23 February 2019
Genomics of Alkaliphiles
Pedro H. Lebre and Don A. Cowan
Contents
1 Introduction: Alkaliphiles in the Metagenomics Era . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
2 The Genomic Features of Alkaliphilic Microorganisms . . . . . . . . . . . . . . . . .. . . . . . . . . . . . .. . . . . . 139
3 Genomic Insights into the Metabolism of Alkaliphiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
4 The Bioenergetics of Alkaliphiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . 145
5 The Alkaliphilic Respiration Chain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
6 The Link Between Respiration and ATP Synthases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
6.1 NADH and Succinate Dehydrogenases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
6.2 Cytochromes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
7 Concluding Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
Abstract Alkalinicity presents a challenge for life due to a “reversed” proton
gradient that is unfavourable to many bioenergetic processes across the membranes
of microorganisms. Despite this, many bacteria, archaea, and eukaryotes, collectively termed alkaliphiles, are adapted to life in alkaline ecosystems and are of great
scientific and biotechnological interest due to their niche specialization and ability to
produce highly stable enzymes. Advances in next-generation sequencing technologies have propelled not only the genomic characterization of many alkaliphilic
microorganisms that have been isolated from nature alkaline sources but also our
understanding of the functional relationships between different taxa in microbial
communities living in these ecosystems. In this review, we discuss the genetics and
molecular biology of alkaliphiles from an “omics” point of view, focusing on how
metagenomics and transcriptomics have contributed to our understanding of these
extremophiles.
P. H. Lebre and D. A. Cowan (*)
Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and
Microbiology, University of Pretoria, Pretoria, South Africa
e-mail: don.cowan@up.ac.za