Magnetotactic bacteria (MTB) are able to synthesize membrane-bound, nano-sized, and single-domain magnetite or greigite magnetosomes. These particles allow MTB to sense the Earth’s magnetic field and to locate the oxic-anoxic interface in chemically stratified environments. MTB are broadly distributed throughout freshwater and marine environments and have been considered to play major roles in iron cycling and in the bulk magnetism of sediments.

Specific primers (FMTCf and FMTCr) were developed in this study in order to effectively investigate the diversity and distribution of freshwater alphaproteobacterial magnetotactic cocci. Their specificity, applicability, and effectiveness were evaluated theoretically and empirically. The new primers provide a viable method to sensitively detect these magnetotactic cocci in sediment without prior magnetic enrichment. A combination of the specific primers FMTCf and FMTCr with other approaches, e.g., classical magnetic enrichment methods, transmission electron microscopy, and fluorescence in situ hybridization, will improve our understanding of the diversity, distribution, and ecological role of freshwater alphaproteobacterial magnetotactic cocci.