Biogeochemical Cycles
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BACTERIA Michael Hoppert University of Göttingen, Göttingen, Germany
Synonyms Eubacteria (term abandoned) Definition Prokaryotes that constitute, besides Archaea and Eukarya, a domain of life. According to (old Greek) bakterion “small rod.” History During the nineteenth century, several fundamental discoveries defined the beginning of modern microbiology (cf. Schlegel, 1999). Louis Pasteur (1822–1895) found that growth of bacteria in nutrient broths is not due to spontaneous generation and that fermentation is caused by the growth of microorganisms. Ferdinand Cohn (1828–1898) could state that bacteria must belong to a phylogenetic group separated from other unicellular plants or animals, due to their size, shape, the mode of cell division, and their metabolic properties. Robert Koch (1842–1910) developed the concept of infectious diseases. The final proof that bacteria must be distinct from plants and animals could be shown not until the distinct compartmentation of bacterial cells was noticed by electron microscopy, in the 1960s. Especially, the absence of a nuclear membrane was a clear indicator for some fundamental differences in cellular processes. Hence, the term “prokaryote” for bacteria (including Archaea) was introduced. The separation of Archaea from Bacteria (as phylogenetic groups) was achieved by Woese and Fox (1977).
Besides the missing nuclear membrane as a common cytological feature, Bacteria and Archaea are structurally and physiologically distinct. The Bacteria are the phylogenetically most diverse domain, with a rapidly growing number of phyla. Currently, more than 80 phyla could be identified (Pace, 2009). About two-third of these phyla are just represented by rDNA sequences from environmental samples. Twenty-five phyla are represented by known species. Among them, twelve phyla contain the majority of currently known and well-characterized species. The well-known representatives of phyla, however, stand for an incomplete and subjective view on the bacterial domain. Human pathogenic species are, for example, overrepresented, because of their importance for human medicine. The significance of several groups relevant for environmental processes, such as Planctomycetes or the Roseobacter clade has just been addressed recently. General knowledge on the physiology of these groups is still limited. Most in-depth analyses on microbial physiology and molecular biology has been performed with selected species from a small number of phyla, such as Escherichia coli, Salmonella, and Pseudomonas species (Proteobacteria) or Bacillus (Firmicutes). Some organisms like Ralstonia (an aerobic hydrogen oxidizing Proteobacterium) or Rhodobacter (a photosynthetic bacterium) are model organisms for environmentally relevant processes. The phylogenetic tree (Figure 1), based upon 16SrDNA data shows an overview of these major, wellcharacterized lineages (Cole et al., 2009; Madigan et al., 2009). In-depth analysis based upon whole genomes may allow, in future, a more accurate positioning of genes and organisms in phylogen
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