The prokaryotes consist of two subdivisions which are biochemically and physiologically distinct. The archea represent species which are mostly known from extreme environments. In the anaerobic environment of submerged rice fields, the methanogens are significant contributors to methane emissions. Archea are also found near deep-sea thermal vents or in other hot environments where other prokaryote and eukaryote species cannot tolerate the temperatures. They also occur in extreme acid or saline environments. There are about 40 genera of archea, but we will not discuss these taxa further. Most prokaryotes belong to the bacteria subdivision, which contains >480 genera, plus the Cyanobacteria, in 17 main lineages, to which we will refer as phyla (Table 1.5). For general reference on the biology of bacteria, the ecolo-gist is directed to Schlegel (1993) which contains sufficient natural history, and to Lengeler et al. (1999) for their cellular biochemistry. Two further texts deal with soil bacteriology specifically and in great detail (Paul and Clark 1998; Tate, 2000).
Table 1.5. Organization of the kingdom bacteria according to Cavalier-Smith (1998).
No. of genera
Lipobacteria Heliobacteria Hadobacteria
Chlorobacteria Deinobacteria Euspirochaetae Leptospirae
Glycobacteria Sphingobacteria Chlorobibacteria
Flavobacteria Eurybacteria Selenobacteria Fusobacteria Fibrobacteria Gloeobacteria Phycobacteria Rhodobacteria
Planctobacteria Posibacteria Posibacteria
Alphabacteria, Betabacteria, Gammabacteria, Deltabacteria
Clostridea, Mollicutes Actinobacteria
Chloroflexus, Heliothrix 6
Deinococcus, Thermus 3
Cytophaga, Flavobacterium Selenomonas, Sporomusa 4
Fusobacterium, Leptotrichia Fibrobacter 1
Anabaena, Nostoc, Prochloron
Agrobacterium, Rickettsia, Rhodospirillum -270
Chromatium, Escherichia, Spirillum
'Myxobacteria ', Desulfovibrio, Thiovulum
Chlamydiae, Planctobacteria, 5
Bacillus, Clostridea, Mycoplasma -172 Corynebacterium, Streptomyces Aquifex, Thermotogales 3
Data compiled from Cavalier-Smith (1998), Lengeler et al. (1999) and other sources.
Bacteria are simpler in their structure and physiology than eukary-otes. The cell is composed of a relatively small number of molecules (Table 1.6). Most bacteria have a cross-sectional diameter of 0.6-1.2 ^m, with length varying between 1 and 2 ^m. The length is more variable, with some genera having species of about 10 ^m long. Many are characterized morphologically as cocci (spherical), rods (box shaped) or filamentous (cells remain attached) (Fig. 1.29). Growth of bacteria by successive cell divisions results in aggregated cells, called colonies. Many species naturally secrete a layer of slime or gelatinous sheath. In some species, it provides an environment for gliding, or for keeping the colony together. In other species, it is secreted as protection against desiccation or during physiological stress. The slime or capsule helps absorb moisture from the habitat, and provides a protective covering after desiccation. In general, the more motile the species, the less aggregated the colony. Motility is the result of gliding on the substrate, or propulsion by one or more flagella. The flagellum consists
Table 1.6. Number of macromolecules estimated in one cell of the bacterium Escherichia coli.
No. of molecule types No. of molecules
Outer membrane >50 proteins 106 molecules
5 phospholipids 106 molecules 1 lipopolysaccharide 107 molecules
Cell membrane >200 proteins 105 molecules
Ribosome 55 proteins One set for 104-105 ribosomes
3 rRNA One set/ribosome
>103 mRNA Variable
60 tRNA 105 molecules
Chromosome One 4.2 kb
Data from Lengeler et a/., 1999.
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