1 Introduction: Alkaliphiles in the Metagenomics Era
Alkaliphiles are a diverse group of microorganisms that are defined as being able to
grow in high pH environments (!9). These organisms reside in a range of extreme
environments in which high alkalinity has been established through geological
processes, such as the accumulation of CO 2 and subsequent production of carbonate-/bicarbonate-rich solutions in soda lakes, as well as transient biological events
such as ammonification and sulphate reduction in soils [1]. In these extreme niches,
microbial communities are not only well adapted to alkalinity, but they must also
cope with a range of other environmental stresses, including high salinity, low or
high temperatures, and oxygen deprivation [2]. Consequently, alkaliphiles are of
great scientific and biotechnological interest due to their highly selective niche
specialization and their ability to produce proteins that are stable across a wide
range of extreme conditions [1].
Since the first report of an alkaliphile genome sequence in 2000 [3], the number of
sequenced genomes of alkaliphilic microorganisms has increased exponentially due
to advances in next-generation sequencing technologies [4]. Currently, the JGI
genome portal [5] lists the sequences of 288 genomes from isolated microorganisms
that have been characterized to grow in alkaline conditions. These genomes are
distributed across ten different phyla (Fig. 1a) and are highly variable in terms of GC
content (from 26 to 74%) and genome size (from 1.6 to 11 Mb) (Fig. 1b). This
high genetic variability, together with the range of habitats from which alkaliphiles
have been isolated, reflects the functional diversity of alkaliphilic microorganisms.
As such, no obvious trends can be found between the alkaliphilic phenotype and
particular genetic features. The phylum Firmicutes, which includes the historically
relevant species Bacillus halodurans C-125 and B. pseudofirmus OF-4 [3, 6],
represents the second largest fraction of sequenced genomes (83 genomes), most
of which have a GC content below 50%. By comparison, the JGI lists 114 genomes
of alkaliphile Proteobacteria, the majority of which have a high GC content
(!50%). These include Halomonas sp. GFAJ-1, which is capable of thriving in
arsenic-rich environments and has been associated with arsenate detoxification
[7]. To date, only two genomes of alkaliphilic Cyanobacteria have been listed in
the JGI database, despite the fact that members of this phylum play a crucial role as
primary photoautotrophic producers in many alkaline environments [8]. The two
genomes belong to the desiccation-tolerant Chroococcidiopsis thermalis PCC 7203,
and Arthrospira platensis C1, which is cultivated at large industrial scale as a food
product for both humans and animals [9]. All 16 publicly available alkaliphilic
archaeal genomes belong to the Euryarchaeota phylum, and the majority of these
organisms have been isolated from highly saline fresh water environments. Genome
sizes for these archaea vary between 1.8 and 4.9 Mb, and 12 have a very high GC
content (!60%). High genomic GC content is a common feature of halophiles and
has been associated with adaptation mechanisms against UV-induced thymidine
dimer formation and the consequent accumulation of mutations [10]. Ten other
Genomics of Alkaliphiles
137
Alkaliphiles are a diverse group of microorganisms that are defined as being able to
grow in high pH environments (!9). These organisms reside in a range of extreme
environments in which high alkalinity has been established through geological
processes, such as the accumulation of CO 2 and subsequent production of carbonate-/bicarbonate-rich solutions in soda lakes, as well as transient biological events
such as ammonification and sulphate reduction in soils [1]. In these extreme niches,
microbial communities are not only well adapted to alkalinity, but they must also
cope with a range of other environmental stresses, including high salinity, low or
high temperatures, and oxygen deprivation [2]. Consequently, alkaliphiles are of
great scientific and biotechnological interest due to their highly selective niche
specialization and their ability to produce proteins that are stable across a wide
range of extreme conditions [1].
Since the first report of an alkaliphile genome sequence in 2000 [3], the number of
sequenced genomes of alkaliphilic microorganisms has increased exponentially due
to advances in next-generation sequencing technologies [4]. Currently, the JGI
genome portal [5] lists the sequences of 288 genomes from isolated microorganisms
that have been characterized to grow in alkaline conditions. These genomes are
distributed across ten different phyla (Fig. 1a) and are highly variable in terms of GC
content (from 26 to 74%) and genome size (from 1.6 to 11 Mb) (Fig. 1b). This
high genetic variability, together with the range of habitats from which alkaliphiles
have been isolated, reflects the functional diversity of alkaliphilic microorganisms.
As such, no obvious trends can be found between the alkaliphilic phenotype and
particular genetic features. The phylum Firmicutes, which includes the historically
relevant species Bacillus halodurans C-125 and B. pseudofirmus OF-4 [3, 6],
represents the second largest fraction of sequenced genomes (83 genomes), most
of which have a GC content below 50%. By comparison, the JGI lists 114 genomes
of alkaliphile Proteobacteria, the majority of which have a high GC content
(!50%). These include Halomonas sp. GFAJ-1, which is capable of thriving in
arsenic-rich environments and has been associated with arsenate detoxification
[7]. To date, only two genomes of alkaliphilic Cyanobacteria have been listed in
the JGI database, despite the fact that members of this phylum play a crucial role as
primary photoautotrophic producers in many alkaline environments [8]. The two
genomes belong to the desiccation-tolerant Chroococcidiopsis thermalis PCC 7203,
and Arthrospira platensis C1, which is cultivated at large industrial scale as a food
product for both humans and animals [9]. All 16 publicly available alkaliphilic
archaeal genomes belong to the Euryarchaeota phylum, and the majority of these
organisms have been isolated from highly saline fresh water environments. Genome
sizes for these archaea vary between 1.8 and 4.9 Mb, and 12 have a very high GC
content (!60%). High genomic GC content is a common feature of halophiles and
has been associated with adaptation mechanisms against UV-induced thymidine
dimer formation and the consequent accumulation of mutations [10]. Ten other
Genomics of Alkaliphiles
137