spermidine, a large cluster of 11 genes coding for putative gas vesicle proteins that
would allow for better access to surface oxygen, and genes encoding for metal
transport proteins, which would may be involved in metal homeostasis in
hypersaline environments [18, 19].
The genus Arthrospira comprises a group of non-N 2 -fixing cyanobacteria that
grow in carbonate/bicarbonate-rich alkaline lakes and are economically important as
food sources. The draft genome of one of the two alkaliphilic cyanobacterial
genomes listed in the JGI database, Arthrospira platensis C1, was published in
2012 [9]. This genome shares between 94.93 and 97.43% sequence identities with
the other five sequenced Arthrospira sp., which together share a highly conserved
core genome. As with many other genomes from alkaliphilic prokaryotes,
A. platensis C1 contains several genes encoding Na
+
/H
+ antiporters, particularly
one NapA-type Na
+
/H
+ antiporter homolog that has been associated with salt and pH
homeostasis in alkaline conditions [9]. Analysis of the genome of A. platensis
NIS-39 showed that it contained a large number of genes with adenylate and
guanylate cyclase domains that are involved in cAMP and c-di-GMP signal transduction and response to external stimuli. In addition, this genome also contained
seven genes for putative Na
+ /H
+ antiporters, as well as seven σ factors from groups
2 and 3, which are involved in responses to environmental stress [20].
Despite the limited information on the genomics of eukaryotic alkaliphiles,
several biodiversity studies have depicted a large diversity of eukaryotes in alkaline
environments, including plankton diatoms, green algae, cryptophytes, and
haptophytes [12, 21–23]. Two recently sequenced genomes from the closely related
alkaliphilic fungi Acremonium alcalophilum ATCC 90507 and Sodiomyces
alkalinus F11 provide a glimpse into the genetic basis of alkaliphily in eukaryotes
[24, 25]. The genomes are 54.42 Mb and 43.45 Mb in size, respectively, and encode
a comparable number of genes for hydrogen/solute symporters (25 in S. alkalinus vs
33 in A. alcalophilum), sodium/solute symporters (5 in both cases), and solute/
hydrogen antiporters (10 in S. alkalinus vs 15 in A. alcalophilum). Comparison of
these genomes in the JGI MycoCosm fungal genomic resource (https://genome.jgi.
doe.gov/programs/fungi/index.jsf) shows that more neutrophilic fungi such as
Aspergillus oryzae and Plectosphaerella cucumerina also contain comparable
numbers of sodium and hydrogen transporters, and therefore these genes cannot be
used as hallmarks for alkaliphily in fungi (Table 1). Instead, both A. alcalophilum
and S. alkalinus show an enrichment of halotolerance proteins with FAD domains,
which suggests a strong correlation between halotolerance and alkaliphily in the
environments from where these fungi were isolated.
In addition to their genomic heterogeneity, several alkaliphiles have been shown
to harbour extrachromosomal plasmids containing resistance genes and other genetic
elements that provide an adaptive edge in the extreme environments where these
organisms inhabit (Table 2). For instance, B. pseudofirmus OF4 contains two
plasmids, pBpOF4-01 (0.28 Mb) and pBpOF4-02 (0.10 Mb), that code for genes
involved in resistance to heavy metals such as cadmium, copper, and mercury
[6]. Similarly, pCHRO.01 (0.37 Mb) from the alkali-tolerant Chroococcidiopsis
thermalis PCC7203 codes for several metal efflux transporters and multicopper
oxidases in addition to toxin-antitoxin systems and DNA translocation proteins. In
Genomics of Alkaliphiles
141
would allow for better access to surface oxygen, and genes encoding for metal
transport proteins, which would may be involved in metal homeostasis in
hypersaline environments [18, 19].
The genus Arthrospira comprises a group of non-N 2 -fixing cyanobacteria that
grow in carbonate/bicarbonate-rich alkaline lakes and are economically important as
food sources. The draft genome of one of the two alkaliphilic cyanobacterial
genomes listed in the JGI database, Arthrospira platensis C1, was published in
2012 [9]. This genome shares between 94.93 and 97.43% sequence identities with
the other five sequenced Arthrospira sp., which together share a highly conserved
core genome. As with many other genomes from alkaliphilic prokaryotes,
A. platensis C1 contains several genes encoding Na
+
/H
+ antiporters, particularly
one NapA-type Na
+
/H
+ antiporter homolog that has been associated with salt and pH
homeostasis in alkaline conditions [9]. Analysis of the genome of A. platensis
NIS-39 showed that it contained a large number of genes with adenylate and
guanylate cyclase domains that are involved in cAMP and c-di-GMP signal transduction and response to external stimuli. In addition, this genome also contained
seven genes for putative Na
+ /H
+ antiporters, as well as seven σ factors from groups
2 and 3, which are involved in responses to environmental stress [20].
Despite the limited information on the genomics of eukaryotic alkaliphiles,
several biodiversity studies have depicted a large diversity of eukaryotes in alkaline
environments, including plankton diatoms, green algae, cryptophytes, and
haptophytes [12, 21–23]. Two recently sequenced genomes from the closely related
alkaliphilic fungi Acremonium alcalophilum ATCC 90507 and Sodiomyces
alkalinus F11 provide a glimpse into the genetic basis of alkaliphily in eukaryotes
[24, 25]. The genomes are 54.42 Mb and 43.45 Mb in size, respectively, and encode
a comparable number of genes for hydrogen/solute symporters (25 in S. alkalinus vs
33 in A. alcalophilum), sodium/solute symporters (5 in both cases), and solute/
hydrogen antiporters (10 in S. alkalinus vs 15 in A. alcalophilum). Comparison of
these genomes in the JGI MycoCosm fungal genomic resource (https://genome.jgi.
doe.gov/programs/fungi/index.jsf) shows that more neutrophilic fungi such as
Aspergillus oryzae and Plectosphaerella cucumerina also contain comparable
numbers of sodium and hydrogen transporters, and therefore these genes cannot be
used as hallmarks for alkaliphily in fungi (Table 1). Instead, both A. alcalophilum
and S. alkalinus show an enrichment of halotolerance proteins with FAD domains,
which suggests a strong correlation between halotolerance and alkaliphily in the
environments from where these fungi were isolated.
In addition to their genomic heterogeneity, several alkaliphiles have been shown
to harbour extrachromosomal plasmids containing resistance genes and other genetic
elements that provide an adaptive edge in the extreme environments where these
organisms inhabit (Table 2). For instance, B. pseudofirmus OF4 contains two
plasmids, pBpOF4-01 (0.28 Mb) and pBpOF4-02 (0.10 Mb), that code for genes
involved in resistance to heavy metals such as cadmium, copper, and mercury
[6]. Similarly, pCHRO.01 (0.37 Mb) from the alkali-tolerant Chroococcidiopsis
thermalis PCC7203 codes for several metal efflux transporters and multicopper
oxidases in addition to toxin-antitoxin systems and DNA translocation proteins. In
Genomics of Alkaliphiles
141