Phyllum verrucomicrobia

Prokaryotes (2006) 7:881–896 DOI: 10.1007/0-387-30747-8_37

CHAPTER 11.1
eh T m l yh u P : a i b r c i ocur re o m V A y l l ac i t enego l yh P su enegore t e o H l a i re t ca B p or uG

The Phylum Verrucomicrobia: A Phylogenetically Heterogeneous Bacterial Group
HEINZ SCHLESNER, CHERYL JENKINS AND JAMES T. STALEY

Introduction
General Phylogeny and Taxonomy
The Verrucomicrobia wereproposed 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), Opitutusand 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 andProsthecobacter 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 relativelyfew 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 varioushabitats. 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 “CandidatusXiphinematobacter” 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, Victivallis vadensis, is placed in subdivision7. Only a few other strains have been isolated. Janssen et al. (2002) were able to cultivate strain Ellin 428 from Australian pasture soil (which could be grouped in subdivision 2), and Sakai et al. (2003) reported of a fucoidan-degrading marine bacterium (provisional name “Fucophilus fucoidanolyticus”) from the gut contents of the sea cucumber Stichopus japonicus.

Ecology
Verrucomicrobiawere first observed in aquatic habitats (Henrici and Johnson, 1935) but are now known to exist in many other habitats, the majority of which are eutrophic or even heavily polluted (Table 2). They were found not only at moderate temperatures but also at cold temperatures in the deep sea and in Antarctica. A member of the Verrucomicrobia was also identified from a hot spring (75–95∞C). Several reports...