The contigs were manually cropped to roughly the same length using the Phred base quality scores of the ends of the contigs as a guide. The resulting same-length (about Protein Tyrosine Kinase inhibitor 1250 bp), good quality contiguous sequences were checked for chimeras using Bellerophon [46] through the online Greengenes interface [22]. The Rhodopirellula sp. strain P1 was sequenced in forward and reverse direction several times with different 16S rRNA gene primers. The individual sequence

reads were manually assembled into one full-length consensus IWP-2 price sequence. Phylogenetic tree reconstruction The near full-length sequences were aligned using the SINA web aligner, imported into ARB and edited as described in the previous section. Reference sequences that were closely related to the clone sequences from this study and sequences from cultured planctomycetes were selected from the SILVA database and were included in the tree calculations. Several tree calculation methods including neighbor joining (NJ), maximum likelihood (ML) and maximum parsimony (MP) were used in combination with different conservatory filters in ARB and the tree topologies compared to ensure a reliable result. The final ML tree was calculated in ARB with 175 sequences using PhyML [47] applying bootstrap analysis (1000 bootstraps) and no filter. Four Verrucomicrobia

sequences (accession numbers: AY271254, DQ302104, AB297805, AB297806) were used as an outgroup in the tree calculation. The tree was edited by removing AZD6738 supplier some of Selleck Docetaxel the reference sequences for clarity of presentation and the final result is shown in Figure 4. Acknowledgements The authors wish to thank Tomas Sørlie and Julia Storesund for sampling assistance, Friederike Hoffmann for valuable advice on FISH and Anders Lanzén for bioinformatics assistance. Kjersti Sjøtun, Antonio García Moyano, Jeffrey Keen, Tim Urich and three anonymous reviewers provided constructive comments that considerably improved

the manuscript. Funding for sampling and laboratory expenses was provided by FMC Biopolymer. The authors are funded by the University of Bergen. References 1. Lindsay MR, Webb RI, Strous M, Jetten MS, Butler MK, Forde RJ, Fuerst JA: Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell. Arch Microbiol 2001,175(6):413–429.PubMedCrossRef 2. Fuerst JA: Intracellular compartmentation in planctomycetes. Annual review of microbiology 2005, 59:299–328.PubMedCrossRef 3. Strous M, Fuerst JA, Kramer EHM, Logemann S, Muyzer G, van de Pas-Schoonen KT, Webb R, Kuenen JG, Jetten MSM: Missing lithotroph identified as new planctomycete. Nature 1999,400(6743):446–449.PubMedCrossRef 4.