ena-STUDY-University Hospital Bonn-18-03-2021-12:04:56:281-12
Dissecting biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits
PREMISE: Within a larger study on leaf fossilization, little is known about the association between decay, preservation, and bacterial biofilms. Here water lily leaves are employed as a study model to investigate how bacterial microbiomes relate to decay and preservation. To reduce bias, DNA extraction protocols should be tested for the efficacy of kits prior to major experimentation.METHODS: We extracted surface-associated DNA from Nymphaea leaves in early stages of decay at two water depths levels with four commercially available kits to identify the protocol most suitable for bacterial extraction. A mock microbial community standard enabled a reliable comparison of the kits.RESULTS: Kit 4, the FastDNA Spin Kit for Soil (MP Biomedicals, USA), resulted in high DNA concentrations with better quality and yielded the most accurate depiction of the mock community. Comparison of the leaves at two water depths showed no significant differences in community composition.DISCUSSION: The success of Kit 4 may be attributed to bead beating with a homogenizer, which was more efficient in the lysis of Gram-positive bacteria than the manual vortexing protocols of the other kits. Hence, microbial composition on leaves during early decay may remain comparable and change only during further stages of decomposition.
PREMISE: Within a larger study on leaf fossilization, little is known about the association between decay, preservation, and bacterial biofilms. Here water lily leaves are employed as a study model to investigate how bacterial microbiomes relate to decay and preservation. To reduce bias, DNA extraction protocols should be tested for the efficacy of kits prior to major experimentation.METHODS: We extracted surface-associated DNA from Nymphaea leaves in early stages of decay at two water depths levels with four commercially available kits to identify the protocol most suitable for bacterial extraction. A mock microbial community standard enabled a reliable comparison of the kits.RESULTS: Kit 4, the FastDNA Spin Kit for Soil (MP Biomedicals, USA), resulted in high DNA concentrations with better quality and yielded the most accurate depiction of the mock community. Comparison of the leaves at two water depths showed no significant differences in community composition.DISCUSSION: The success of Kit 4 may be attributed to bead beating with a homogenizer, which was more efficient in the lysis of Gram-positive bacteria than the manual vortexing protocols of the other kits. Hence, microbial composition on leaves during early decay may remain comparable and change only during further stages of decomposition.