2.3 Soils
Another natural alkaline system where alkaliphiles live is soil, especially alkaline
soils. Soil is a highly heterogeneous mix of organic and mineral residues. Unlike soda
lakes or seawater, soils have complex chemical compositions which highly depend on
local geological background, inhabiting biota, and climatic features. Soils of all types
are rich reservoirs of different microorganisms, and no wonder that the first
alkaliphiles were isolated from soil, e.g., alkaliphilic strain of Bacillus circulans by
Horikoshi in the 1950s [2]. Surface layers of the soil are usually well-aerated and have
a low-water content which contributes to the survival of sporeformers. Because of
this, traditionally, soil samples serve as good source for the representatives of genus
Bacillus and bacilli-like organisms. Among various soil types classified in the World
Reference Base for soil resources, solonchak soils (“soils with limitations to root
growth and with high concentration of soluble salts” [56]) are the most likely habitat
for soil alkaliphiles. This soil has a high content of both sodium chloride and sodium
carbonates and, hence, an alkaline pH that supports the growth of alkaliphiles.
Solonchaks (or saline soda soils, or saline-alkaline soils, or Natracualf in Argentina)
are located in the arid zones and are found in southern Siberia (dry steppe), northeastern Mongolia, Northern China, Egypt, India, Pakistan, Hungary, Argentina, and
North American prairie. Interestingly, despite the fact that a lot of soil alkaliphilic
bacteria are known, not so many alkaliphiles have been isolated from solonchak soils
located far from the shallow soda lakes. The latter often accompany solonchaks on the
Asian continent, and, theoretically, alkaliphiles can migrate from alkaline water to
alkaline soil and back. Known alkaliphilic representatives include Actinobacteria
isolated from a solonchak soil sample of Xinjiang province in China: Lipingzhangella
halophila [57], Phytoactinopolyspora alkaliphila [58], haloalkaliphilic Egibacter
rhizosphaerae [59], and Bacillus tamaricis [60]. The latter two were isolated from
the soil of the rhizosphere of a tree Tamarix hispida Willd which tolerate salinealkaline conditions. Other rhizosphere-associated soil alkaliphiles include Bacillus
patagoniensis from a perennial shrub Atriplex lampa in Argentina [61] and Bacillus
kiskunsagensis from the bayonet grass Bolboschoenus maritimus in Hungary
[62]. The rhizosphere supplies nutrients to soil bacteria, as is well known for nodule
bacteria. Saline and alkaline soils have their own vegetation, so it was not surprising
to expect the isolation of alkaliphilic bacteria from the rhizosphere of such plants.
Metagenomic diversity in two physicochemically different soils from the coastal
region of Gujarat, India, were investigated using 16S rRNA gene clone libraries
[63]. The phylogenetic diversity of bacteria in a haloalkaline soil (pH 9.5) was
compared with a normal soil (pH 7.2). Clones representing phyla Proteobacteria,
Bacteroidetes, Chloroflexi, Firmicutes, Actinobacteria, Acidobacteria, and
Planctomycetes were found in both soils. Cyanobacteria, Verrucomicrobia, OP10,
and Bacteria incertae sedis were detected in normal soil, whereas Nitrospira was
found only in haloalkaline soil. The dominant phylum in the haloalkaline soil was
Bacteroidetes followed by Proteobacteria, whereas normal soil was dominated by
Proteobacteria and Actinobacteria. One third of the total sequences from both soil
Isolation and Cultivation of Alkaliphiles
61
Another natural alkaline system where alkaliphiles live is soil, especially alkaline
soils. Soil is a highly heterogeneous mix of organic and mineral residues. Unlike soda
lakes or seawater, soils have complex chemical compositions which highly depend on
local geological background, inhabiting biota, and climatic features. Soils of all types
are rich reservoirs of different microorganisms, and no wonder that the first
alkaliphiles were isolated from soil, e.g., alkaliphilic strain of Bacillus circulans by
Horikoshi in the 1950s [2]. Surface layers of the soil are usually well-aerated and have
a low-water content which contributes to the survival of sporeformers. Because of
this, traditionally, soil samples serve as good source for the representatives of genus
Bacillus and bacilli-like organisms. Among various soil types classified in the World
Reference Base for soil resources, solonchak soils (“soils with limitations to root
growth and with high concentration of soluble salts” [56]) are the most likely habitat
for soil alkaliphiles. This soil has a high content of both sodium chloride and sodium
carbonates and, hence, an alkaline pH that supports the growth of alkaliphiles.
Solonchaks (or saline soda soils, or saline-alkaline soils, or Natracualf in Argentina)
are located in the arid zones and are found in southern Siberia (dry steppe), northeastern Mongolia, Northern China, Egypt, India, Pakistan, Hungary, Argentina, and
North American prairie. Interestingly, despite the fact that a lot of soil alkaliphilic
bacteria are known, not so many alkaliphiles have been isolated from solonchak soils
located far from the shallow soda lakes. The latter often accompany solonchaks on the
Asian continent, and, theoretically, alkaliphiles can migrate from alkaline water to
alkaline soil and back. Known alkaliphilic representatives include Actinobacteria
isolated from a solonchak soil sample of Xinjiang province in China: Lipingzhangella
halophila [57], Phytoactinopolyspora alkaliphila [58], haloalkaliphilic Egibacter
rhizosphaerae [59], and Bacillus tamaricis [60]. The latter two were isolated from
the soil of the rhizosphere of a tree Tamarix hispida Willd which tolerate salinealkaline conditions. Other rhizosphere-associated soil alkaliphiles include Bacillus
patagoniensis from a perennial shrub Atriplex lampa in Argentina [61] and Bacillus
kiskunsagensis from the bayonet grass Bolboschoenus maritimus in Hungary
[62]. The rhizosphere supplies nutrients to soil bacteria, as is well known for nodule
bacteria. Saline and alkaline soils have their own vegetation, so it was not surprising
to expect the isolation of alkaliphilic bacteria from the rhizosphere of such plants.
Metagenomic diversity in two physicochemically different soils from the coastal
region of Gujarat, India, were investigated using 16S rRNA gene clone libraries
[63]. The phylogenetic diversity of bacteria in a haloalkaline soil (pH 9.5) was
compared with a normal soil (pH 7.2). Clones representing phyla Proteobacteria,
Bacteroidetes, Chloroflexi, Firmicutes, Actinobacteria, Acidobacteria, and
Planctomycetes were found in both soils. Cyanobacteria, Verrucomicrobia, OP10,
and Bacteria incertae sedis were detected in normal soil, whereas Nitrospira was
found only in haloalkaline soil. The dominant phylum in the haloalkaline soil was
Bacteroidetes followed by Proteobacteria, whereas normal soil was dominated by
Proteobacteria and Actinobacteria. One third of the total sequences from both soil
Isolation and Cultivation of Alkaliphiles
61