The Phylum Verrucomicrobia: A Phylogenetically Heterogeneous Bacterial Group
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The Phylum Verrucomicrobia: A Phylogenetically Heterogeneous Bacterial Group HEINZ SCHLESNER, CHERYL JENKINS AND JAMES T. STALEY
Introduction General Phylogeny and Taxonomy The Verrucomicrobia were proposed as a new division within the bacterial domain by Hedlund et al. (1997) and more recently ranked as a phylum (Garrity and Holt, 2001). They represent a distinct lineage within the phylogenetic trees and contain a number of environmental species as well as a small number of cultured species assigned to four genera (Table 1): Verrucomicrobium (Fig. 1a, b), Prosthecobacter (Fig. 2), Opitutus and Victivallis. Verrucomicrobia have shown a moderate degree of relationship to the Planctomycetes and Chlamydiae, but the significance of the common branching is low and the relationships among the three phyla may change as additional species are characterized. The comparative phylogenetic analyses of members of the order Planctomycetales and the type strains of Verrucomicrobium spinosum and Prosthecobacter fusiformis, as well as Prosthecobacter sp. strain FC-2, did not indicate a statistically significant phylogenetic relationship between the Planctomycetes and the Verrucomicrobia and further provided evidence that the Chlamydiae are no more related to both phyla than they are to members of other bacterial lineages. Knowledge of the phylum Verrucomicrobia is limited owing to the relatively few species that have been obtained in pure culture and characterized. However, through the application of molecular ecology techniques it has become apparent that the Verrucomicrobia are ubiquitous in a wide range of aquatic and terrestrial habitats. The phylogenetic tree based on sequence analyses of the 16S rDNA is dominated by sequences derived from the extraction of total DNA from various habitats. Hugenholtz et al. (1998a) recognized five subdivisions, of which three were characterized by clone sequences only. Since then the phylogenetic tree has been expanded to seven subdivisions, although only three contain validly described taxa (Fig. 3). The genera of the prosthecate bacteria Verrucomicrobium and Prosthecobacter are
grouped in subdivision 1. Bacteria designated “Candidatus Xiphinematobacter” are in subdivision 2. These bacteria are obligate endosymbionts of nematodes in the genus Xiphinema (Vandekerckhove et al., 2000). Another group of bacteria living in close connection to eukaryotes are the epixenosomes (Figs. 4 and 5), which are obligate ectosymbionts living on the dorsal surface of marine ciliates of the genus Euplotidium. They possess so-called “extrusomes,” harpoonlike organelles, and so provide their hosts with a weapon against predatory protozoa (Petroni et al., 2000; Chin et al., 2001). The epixenosomes are members of subdivision 4 together with Opitutus terrae (Chin et al., 2001) and three strains of ultramicrobacteria with dwarf cells isolated from anoxic rice paddy soil. The latest described organism,
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