ABSTRACT
Magnetotactic bacteria (MTB) belong to different taxonomic groups according to 16S rRNA or whole-genome phylogeny. Magnetotactic representatives of the class Alphaproteobacteria and the order Magnetococcales are the most frequently isolated MTB in environmental samples. This bias is due in part to limitations of currently available methods to isolate MTB. Here we describe a new approach for isolation of MTB cells that does not depend on cell motility and will allow collecting bacteria both south- and north-seeking movement. We also designed a specific primer system for the gene encoding the MamK protein that effectively detects diverse MTB phylogenetic groups in any sample type. The combination of these two approaches allowed the identification of a novel MTB belonging to the family Syntrophaceae of the class Deltaproteobacteria. Moreover, we found that Nitrospirae bacteria predominated in the MTB fraction of a sample taken from Lake Beloe Bordukovskoe near Moscow, Russia. We describe the novel dominant Nitrospirae bacterium ‘Candidatus Magnetomonas plexicatena’ and propose its taxonomic name.
IMPORTANCE Among magnetotactic bacteria (MTB), the members of phyla Proteobacteria, Nitrospirae and ‘Ca. Omnitrophica’ have been studied extensively using the existing approaches. However, in recent years, analyses of the metagenomic databases have revealed the presence of MTB in phylogenetic groups, which had not been previously detected using standard approaches. This finding indicates that the biodiversity of MTB is much broader than is currently known. The difficulty of identifying MTB based on comparative analysis of 16S rRNA genes lies in the existence of closely related species of non-magnetotactic bacteria. Moreover, there is an absence of 16S rRNA MTB sequences from such taxonomic groups as ‘Latescibacteria’ and Planctomycetes. In addition, the standard methods of separating MTB can benefit bacteria with high motility. Developing novel strategies for investigation offers great promise towards identifying MTB groups. We have proposed new approach to separate MTB cells from environmental samples and have also proposed a specific primer system for the MTB identification.