Does capillary racetrack-based enrichment reflect the diversity of uncultivated magnetotactic cocci in environmental samples?
The racetrack-based PCR approach is widely used in phylogenetic analysis of magnetotactic bacteria (MTB), which are isolated from environmental samples using the capillary racetrack method. To evaluate whether the capillary racetrack-based enrichment can truly reflect the diversity of MTB in the targeted environmental sample, phylogenetic diversity studies of MTB enriched from the Miyun lake near Beijing were carried out, using both the capillary racetrack-based PCR and a modified metagenome-based PCR approach. Magnetotactic cocci were identified in the studied sample using both approaches. Comparative studies showed that three clusters of magnetotactic cocci were revealed by the modified metagenome-based PCR approach, while only one of them (e.g. MYG-22 sequence) was detected by the racetrack-based PCR approach from the studied sample. This suggests that the result of capillary racetrack-based enrichment might have been biased by the magnetotaxis of magnetotactic bacteria. It appears that the metagenome-based PCR approach better reflects the original diversity of MTB in the environmental sample.
Lin
Wei
W
Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, State Key Laboratory of Lithospheric Evolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, 19 Bei Tu Cheng Xi Road, Beijing, China.
Tian
Lanxiang
L
Li
Jinhua
J
Pan
Yongxin
Y
D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D001431:Bacteriological Techniques / Q000379:methods*; D002681:China; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D014871:Water Microbiology
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S