Silvanigrella aquatica gen. nov., sp. nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., and reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales

Abstract

The unusual chemo-organoheterotrophic proteobacterial strain MWH-Nonnen-W8redT was isolated from a lake located in the Black Forest (Schwarzwald), Germany, by using the filtration-acclimatization method. Phylogenetic analyses based on the 16S rRNA gene sequence of the strain could not provide clear hints on classification of the strain in one of the current classes of the phylum Proteobacteria. Whole-genome sequencing resulted in a genome size of 3.5 Mbp and revealed a quite low DNA G+C content of 32.6 mol%. In-depth phylogenetic analyses based on alignments of 74 protein sequences of a phylogenetically broad range of taxa suggested assignment of the strain to a new order of the class Oligoflexia. These analyses also suggested that the order Bdellovibrionales should be transferred from the class Deltaproteobacteria to the class Oligoflexia, that this order should be split into two orders, and that the family Pseudobacteriovoracaceae should be transferred from the order Bdellovibrionales to the order Oligoflexales. We propose to establish for strain MWH-Nonnen-W8redT (=DSM 23856T=CCUG 58639T) the novel species and genus Silvanigrella aquatica gen. nov., sp. nov. to be placed in the new family Silvanigrellaceae fam. nov. of the new order Silvanigrellales ord. nov.

Fig. 1

Scanning electron microscopy images. Most visible bacteria show a filamentous morphology when growing in soft agar while some bacteria form spirals (arrows in A) with no visible constrictions or separations along the spirals (B).

Fig. 2

Frequency distribution of G+C values of Proteobacteria genomes available in the Integrated Microbial Genomes (IMG) system characterized by genome sizes of ≥ 3 Mbp. Only four and eight (including MWH-Nonnen-W8red^T) genomes possess G+C values in the range of 25-30 and 30-35 mol%, respectively.

Fig. 3

RAxML tree calculated with an alignment of 74 protein sequences extracted from 85 genome sequences. Taxa affiliated with the phylum Proteobacteria are shown by using colour codes. All proteobacterial classes (including ‘Zetaproteobacteria’) but Deltaproteobacteria are shown by colour-coded fonts. Deltaproteobacterial orders are highlighted by colour-coded areas. Furthermore, the two representatives of the phylum Acidobacteria are highlighted by red fonts. Bootstrap values obtained by the RAxML, MrBayes and Neighbour-Joining method are depicted. The coloured dots indicate nodes supported by different treeing methods.

Fig. 4

Revised taxonomy of the class Oligoflexia. The shown Neighbour-Joining tree was calculated with almost complete 16S rRNA sequences of bacteria proposed to be classified in the previously monotypic class Oligoflexia. Alignment positions with gaps in any sequence were completely omitted for the tree calculation, which resulted in an alignment length of 1343 positions. Phylogenetic distances were calculated by using the Tamura 3-parameter substitution model. Sequences of taxa not affiliated with the phylum Proteobacteria were used as outgroup (not shown). Bootstrap values obtained with the neighbour joining, the maximum likelihood and the maximum parsimony methods (1000, 100, 100 replications, respectively) are indicated. Note that this 16S rRNA tree differs regarding the position of the revised Bdellovibrionales from the calculated multi-protein trees (Fig. 4 and Suppl. Mat. Fig. S3), however the responsible node is only weakly supported in the 16S rRNA tree. The branching order of the calculated NJ and ML tree is identical.