the case of Sinorhizobium medicae WSM419, two of its three plasmids, pSMED01
(1.57 Mb) and pSMED02 (1.24 Mb), represent a large proportion of the genome and
code for a broad range of functions in addition to stress adaptation, including
proteins involved in energy conversion and amino acid synthesis [26]. Alternatively,
the two plasmids from the alkalithermophile Natranaerobius thermophilus
JW/NM-WN-LF primarily code for DNA restriction and modification enzymes as
well as a growth inhibition regulator and are thus not directly involved in stress
adaptation [27]. Rather, the abundance of transposons, integrases, and other mobile
elements in the majority of the plasmids listed in Table 1 suggests they also play an
important role in both adaptive and non-adaptive plasticity of the genomes of
alkaliphiles.
3 Genomic Insights into the Metabolism of Alkaliphiles
Alkaliphilic microorganism are found in a wide range of bacterial, archaeal, and
eukaryotic phyla and constitute a functionally diverse group of organisms that play
vastly different but interdependent ecological roles in their native habitats. For
instance, communities in soda lakes are thought to be organized in a complex
multilayered structure, in which the by-products and dead matter from the primary
photoautotrophic cyanobacterial producers at the surface are initially used by a
second layer of heterotrophic bacteria from the Firmicutes and Proteobacteria
phyla. The metabolic products from these bacteria are subsequently used as
substrates for anaerobic organisms that degrade organic matter, producing gases
that support the growth of a fourth layer of lithotrophic organisms such
as homoacetogens, hydrogenotropic sulphidogens, and anoxygenic anaerobic
phototrophs [8, 28].
As primary producers, cyanobacteria play a crucial role in pioneering and
maintaining communities in many extreme environments. Sequence analysis of the
alkaliphilic A. platensis showed that it contains a full set of genes for photosystems I
and II, as well as variant genes such as cytochrome c550-like and cytochrome c 6
[20]. As a photoautotroph, A. platensis also contains the genes for the common
cyanobacterial metabolic pathways, including the pentose phosphate (PP) pathway
for primary metabolism of bicarbonate ions, as well as the Calvin cycle for CO 2
fixation, which depends on the activity of two enzymes, phosphoribulokinase
and RuBisCO. These two proteins are also specific to the PP pathway in light
energy conditions, while under dark conditions, the glucose-6-phosphate and
6-phosphogluconate dehydrogenases are used [29]. Cyanobacteria surviving in
alkaline conditions where CO 2 concentrations are limited rely on CO 2 -concentrating
mechanisms, which involved CO 2 and bicarbonate (HCO 3
À ) uptake by NAD(P)H
dehydrogenases and plasma membrane transporters, as well as HCO 3
À conversion
into CO 2 catalysed in RubisCO-containing carboxysome subcellular compartments
[30]. A comparative genomics study of all known alkaline cyanobacterial genomes
revealed that they all contained the same RubisCO variant, RubisCO B1 [11]. In
addition, all the strains analysed contained genes that encode CO 2 -concentrating
Genomics of Alkaliphiles
143
(1.57 Mb) and pSMED02 (1.24 Mb), represent a large proportion of the genome and
code for a broad range of functions in addition to stress adaptation, including
proteins involved in energy conversion and amino acid synthesis [26]. Alternatively,
the two plasmids from the alkalithermophile Natranaerobius thermophilus
JW/NM-WN-LF primarily code for DNA restriction and modification enzymes as
well as a growth inhibition regulator and are thus not directly involved in stress
adaptation [27]. Rather, the abundance of transposons, integrases, and other mobile
elements in the majority of the plasmids listed in Table 1 suggests they also play an
important role in both adaptive and non-adaptive plasticity of the genomes of
alkaliphiles.
3 Genomic Insights into the Metabolism of Alkaliphiles
Alkaliphilic microorganism are found in a wide range of bacterial, archaeal, and
eukaryotic phyla and constitute a functionally diverse group of organisms that play
vastly different but interdependent ecological roles in their native habitats. For
instance, communities in soda lakes are thought to be organized in a complex
multilayered structure, in which the by-products and dead matter from the primary
photoautotrophic cyanobacterial producers at the surface are initially used by a
second layer of heterotrophic bacteria from the Firmicutes and Proteobacteria
phyla. The metabolic products from these bacteria are subsequently used as
substrates for anaerobic organisms that degrade organic matter, producing gases
that support the growth of a fourth layer of lithotrophic organisms such
as homoacetogens, hydrogenotropic sulphidogens, and anoxygenic anaerobic
phototrophs [8, 28].
As primary producers, cyanobacteria play a crucial role in pioneering and
maintaining communities in many extreme environments. Sequence analysis of the
alkaliphilic A. platensis showed that it contains a full set of genes for photosystems I
and II, as well as variant genes such as cytochrome c550-like and cytochrome c 6
[20]. As a photoautotroph, A. platensis also contains the genes for the common
cyanobacterial metabolic pathways, including the pentose phosphate (PP) pathway
for primary metabolism of bicarbonate ions, as well as the Calvin cycle for CO 2
fixation, which depends on the activity of two enzymes, phosphoribulokinase
and RuBisCO. These two proteins are also specific to the PP pathway in light
energy conditions, while under dark conditions, the glucose-6-phosphate and
6-phosphogluconate dehydrogenases are used [29]. Cyanobacteria surviving in
alkaline conditions where CO 2 concentrations are limited rely on CO 2 -concentrating
mechanisms, which involved CO 2 and bicarbonate (HCO 3
À ) uptake by NAD(P)H
dehydrogenases and plasma membrane transporters, as well as HCO 3
À conversion
into CO 2 catalysed in RubisCO-containing carboxysome subcellular compartments
[30]. A comparative genomics study of all known alkaline cyanobacterial genomes
revealed that they all contained the same RubisCO variant, RubisCO B1 [11]. In
addition, all the strains analysed contained genes that encode CO 2 -concentrating
Genomics of Alkaliphiles
143