Diversity analysis of magnetotactic bacteria in Lake Miyun, northern China, by restriction fragment length polymorphism

Abstract

Magnetotactic bacteria (MTB) synthesize intracellular nano-scale crystals of magnetite or greigite within magnetosomes. MTB are ubiquitous in limnic and marine environments. In order to understand the diversity of MTB better, sediment samples were examined from Lake Miyun near Beijing by restriction fragment length polymorphism (RFLP). First, in silico analysis was used to evaluate the effectiveness of 12 sets of restriction endonucleases for distinguishing MTB sequences retrieved from the GenBank database. It was found that the tested restriction endonucleases had different power in the ability to differentiate the operational taxonomic units (OTUs) of MTB. Specifically, of the 12 sets of enzymes, MspI plus RsaI was found to be the most effective for correctly differentiating the OTUs of selected MTB sequences and it could detect 16 OTUs with appropriate OTUmin and OTUmax values (96.7% and 97.7%, respectively). The MspI plus RsaI RFLP analysis was then utilized to investigate the diversity of MTB in Lake Miyun sediment and it identified 8 OTUs (74.5% of the whole library) as MTB. Among these, 5 were affiliated to Alphaproteobacteria, while the rest belonged to the Nitrospira phylum. Interestingly, OTUs C, D and I displayed 91.8–98.4% similarity to “ Magnetobacterium bavaricum”. Together, these results demonstrated that the MspI plus RsaI RFLP analysis was useful for studying the diversity and change in community composition of uncultivated MTB from environmental samples.