The PVC superphylum: exceptions to the bacterial definition?
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The PVC superphylum is a grouping of distinct phyla of the domain bacteria proposed initially on the basis of 16S rRNA gene sequence analysis. It consists of a core of phyla Planctomycetes, Verrucomicrobia and Chlamydiae, but several other phyla have been considered to be members, including phylum Lentisphaerae and several other phyla consisting only of yet-to-be cultured members. The genomics-based links between Planctomycetes, Verrucomicrobia and Chlamydiae have been recently strengthened, but there appear to be other features which may confirm the relationship at least of Planctomycetes, Verrucomicrobia and Lentisphaerae. Remarkably these include the unique planctomycetal compartmentalized cell plan differing from the cell organization typical for bacteria. Such a shared cell plan suggests that the common ancestor of the PVC superphylum members may also have been compartmentalized, suggesting this is an evolutionarily homologous feature at least within the superphylum. Both the PVC endomembranes and the eukaryote-homologous membrane-coating MC proteins linked to endocytosis ability in Gemmata obscuriglobus and shared by PVC members suggest such homology may extend beyond the bacteria to the Eukarya. If so, either our definition of bacteria may have to change or PVC members admitted to be exceptions. The cases for and against considering the PVC superphylum members as exceptions to the bacteria are discussed, and arguments for them as exceptions presented. Recent critical analysis has favoured convergence and analogy for explaining eukaryote-like features in planctomycetes and other PVC organisms. The case is made for constructing hypotheses leaving the possibility of homology and evolutionary links to eukaryote features open. As the case of discovery of endocytosis-like protein uptake in planctomycetes has suggested, this may prove a strong basis for the immediate future of experimental research programs in the PVC scientific community.
KeywordsPVC superphylum Planctomycetes Verrucomicrobia Chlamydia Lentisphaerae Compartmentalization
- Choo YJ, Lee K et al (2007) Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum Verrucomicrobia. Int J Syst Evol Microbiol 57(Pt 3):532–537PubMedCrossRefGoogle Scholar
- Jenkins C, Kedar V et al (2002) Gene discovery within the planctomycete division of the domain bacteria using sequence tags from genomic DNA libraries. Genome Biol 3(6): RESEARCH0031Google Scholar
- Qiu YL, Muramatsu M et al (2013) Oligosphaera ethanolica gen. nov., sp. nov., an anaerobic, carbohydrate-fermenting bacterium isolated from methanogenic sludge, and description of Oligosphaeria classis nov. in the phylum Lentisphaerae. Int J Syst Evol Microbiol 63(Pt 2):533–539PubMedCrossRefGoogle Scholar
- Rinke C, Schwientek P et al (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499(7459):431–437Google Scholar
- Teeling H, Lombardot T et al (2004) Evaluation of the phylogenetic position of the planctomycete Rhodopirellula baltica SH 1 by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees. Int J Syst Evol Microbiol 54(Pt 3):791–801PubMedCrossRefGoogle Scholar
- Yoon J, Yasumoto-Hirose M et al (2007c) Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum Verrucomicrobia, isolated from seawater by in situ cultivation. Int J Syst Evol Microbiol 57(Pt 7):1377–1385PubMedCrossRefGoogle Scholar