The tree was inferred from 1,381 aligned characters selleckbio [34,35] of the 16S rRNA gene sequence … To measure conflict between 16S rRNA data and taxonomic classification in detail, we followed a constraint-based approach as described recently in detail [41], conducting both unconstrained searches and searches constrained for the monophyly of both families and using our own re-implementation of CopyCat [42] in conjunction with AxPcoords and AxParafit [43] was used to determine those leaves (species) whose placement significantly deviated between the constrained and the unconstrained tree. The best-supported ML tree had a log likelihood of -12,191.55, whereas the best tree found under the constraint had a log likelihood of -12,329.92.

The constrained tree was significantly worse than the globally best one in the SH test as implemented in RAxML [37,44] (�� = 0.01). The best supported MP trees had a score of 1,926, whereas the best constrained trees found had a score of 1.982 and were also significantly worse in the KH test as implemented in PAUP [8,44] (�� < 0.0001). Accordingly, the current classification of the family as used in [45,46], on which the annotation of Figure 1 is based, is in significant conflict with the 16S rRNA data. Figure 1 also shows those species that cause phylogenetic conflict as detected using the ParaFit test (i.e., those with a p value > 0.05 because ParaFit measures the significance of congruence) in green font color. According to our analyses, the Hyphomonadaceae genera (Blastochloris and Prosthecomicrobium) nested within the Xanthobacteraceae display significant conflict.

In the constrained tree (data not shown), the Angulomicrobium-Methylorhabdus clade is placed at the base of the Xanthobacteraceae clade (forced to be monophyletic). For this reason, Angulomicrobium and Methylorhabdus were not detected as causing conflict (note that the ParaFit test essentially compares unrooted trees). A taxonomic revision of the group would probably need to start with the reassignment of these genera to different families. Morphology and physiology Cells of S. novella ATCC 8093T are non-motile, Gram-negative staining short rods or coccobacilli with a size of 0.4�C0.8 ��m �� 0.8�C2.0 ��m, occurring singly or in pairs (Figure 2, Table 1) [1].

Colonies grown on thiosulfate agar turn white with sulfur on biotin supplemented growth media [1], while in the presence of small amounts of yeast extract (DSMZ medium 69) the colonies have a pale pink appearance following growth on thiosulfate and no sulfur formation is observed. Cells grow on thiosulfate and tetrathionate under aerobic conditions, but not on sulfur or thiocyanate [1]. Ammonium salts, nitrates, urea and glutamate can serve as nitrogen sources [1]. Several surveys of substrates supporting heterotrophic growth have been published, and include glucose, formate, Dacomitinib methanol, oxalate [1,2,4,6].