alkaliphilic cyanobacterial genomes that are not listed in the JGI database have also
been sequenced, including five additional Arthrospira species [11].
Compared to prokaryotic alkaliphiles, there is a dearth of knowledge on the
genomics of alkaliphilic eukaryotes. Crucially, the recent drive for cultureindependent techniques such as metagenomics has led to in-depth studies into the
composition, functional capacities, and ecological impact of communities living
in alkaline environments, including eukaryote. To date, 153 metagenomes have
been obtained from alkaline environments, the majority of which were sourced
from saline and alkaline water (51 metagenomes), and serpentinite rock and fluid
(40 genomes). Members of the genera Frontania and Lacrymaria, both ciliates, were
reported to be found in four distinct alkaline environments, while diatoms of the
class Fragillariophyceae were found in both alkaline and acidic habitats [12].
2 The Genomic Features of Alkaliphilic Microorganisms
The increasing number of genomes for alkaliphiles allows for comparative genomic
studies that reveal the unique genetic features of these organisms. Historically,
bacteria from the genus Bacillus have been the target of substantial research on the
adaptation to alkaliphily, with the genomes of representative strains B. halodurans
C-125 and B. pseudofirmus OF4 being widely studied and characterized [13]. Both
genomes share a large percentage of genes (1,510 genes, 36.8% in B. pseudofirmus
OF4 and 38.2% in B. halodurans C-125), as well as 80% conserved synteny and
comparable origins of replication [6]. In turn, the genomes of B. halodurans C-125
and B. subtilis were found to share a high number of gene clusters involved in the
house-keeping functions such as motility and chemotaxis, sporulation, protein
secretion, main metabolic pathways, and DNA replication [3]. One big differential
factor between these genomes is the number and type of transposable elements.
B. halodurans contains 112 transposable elements divided into 27 distinct groups
compared to the ten transposable elements in B. subtilis, and all of this share
significant sequence similarity to transposases and recombinases from species such
as Rhodobacter capsulatus and Lactococcus lactis. In addition, B. halodurans C-125
contains ten unique extracytoplasmic function σ factors that might play a role in
adaptation to alkaline environments [3]. A distinct feature of B. pseudofirmus
OF4 is the presence of two resident plasmids that contain gene clusters for metal
acquisition and metal resistance, including P-type metal ATPases, copper chaperones, and cadmium resistance transporters [6]. Genomic differences between
B. pseudofirmus and B. halodurans further hint at the more alkaliphilic nature of
the former. For instance, B. pseudofirmus contains 13 cation/solute antiporters
compared to 5 in B. halodurans, which might contribute to increased capacity to
maintain pH homeostasis in the cytoplasm [6]. This enrichment in proton/cation
transporters can also be seen in genomes from other alkaliphiles (Fig. 2). Another
alkaliphilic bacillus, Oceanobacillus iheyensis HTE831, first isolated from deep-sea
sediments on the Iheya Ridge [15], is a strict aerobe that grows optimally at pH 9.5.
Genomics of Alkaliphiles
139
been sequenced, including five additional Arthrospira species [11].
Compared to prokaryotic alkaliphiles, there is a dearth of knowledge on the
genomics of alkaliphilic eukaryotes. Crucially, the recent drive for cultureindependent techniques such as metagenomics has led to in-depth studies into the
composition, functional capacities, and ecological impact of communities living
in alkaline environments, including eukaryote. To date, 153 metagenomes have
been obtained from alkaline environments, the majority of which were sourced
from saline and alkaline water (51 metagenomes), and serpentinite rock and fluid
(40 genomes). Members of the genera Frontania and Lacrymaria, both ciliates, were
reported to be found in four distinct alkaline environments, while diatoms of the
class Fragillariophyceae were found in both alkaline and acidic habitats [12].
2 The Genomic Features of Alkaliphilic Microorganisms
The increasing number of genomes for alkaliphiles allows for comparative genomic
studies that reveal the unique genetic features of these organisms. Historically,
bacteria from the genus Bacillus have been the target of substantial research on the
adaptation to alkaliphily, with the genomes of representative strains B. halodurans
C-125 and B. pseudofirmus OF4 being widely studied and characterized [13]. Both
genomes share a large percentage of genes (1,510 genes, 36.8% in B. pseudofirmus
OF4 and 38.2% in B. halodurans C-125), as well as 80% conserved synteny and
comparable origins of replication [6]. In turn, the genomes of B. halodurans C-125
and B. subtilis were found to share a high number of gene clusters involved in the
house-keeping functions such as motility and chemotaxis, sporulation, protein
secretion, main metabolic pathways, and DNA replication [3]. One big differential
factor between these genomes is the number and type of transposable elements.
B. halodurans contains 112 transposable elements divided into 27 distinct groups
compared to the ten transposable elements in B. subtilis, and all of this share
significant sequence similarity to transposases and recombinases from species such
as Rhodobacter capsulatus and Lactococcus lactis. In addition, B. halodurans C-125
contains ten unique extracytoplasmic function σ factors that might play a role in
adaptation to alkaline environments [3]. A distinct feature of B. pseudofirmus
OF4 is the presence of two resident plasmids that contain gene clusters for metal
acquisition and metal resistance, including P-type metal ATPases, copper chaperones, and cadmium resistance transporters [6]. Genomic differences between
B. pseudofirmus and B. halodurans further hint at the more alkaliphilic nature of
the former. For instance, B. pseudofirmus contains 13 cation/solute antiporters
compared to 5 in B. halodurans, which might contribute to increased capacity to
maintain pH homeostasis in the cytoplasm [6]. This enrichment in proton/cation
transporters can also be seen in genomes from other alkaliphiles (Fig. 2). Another
alkaliphilic bacillus, Oceanobacillus iheyensis HTE831, first isolated from deep-sea
sediments on the Iheya Ridge [15], is a strict aerobe that grows optimally at pH 9.5.
Genomics of Alkaliphiles
139