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A selective procedure for DNA and protein isolation from marine macrophyte surfaces

To successfully apply methods such as 16S rRNA sequencing, metagenomics, and metaproteomics on microbial communities inhabiting surfaces of marine macrophytes, microbial DNA and proteins need to be selectively isolated with a minimum of disrupting the host tissue. Methods for separating microbial cells from the host such as shaking, scraping and ultrasonication have been shown to be insufficient. These methods do not provide a complete cell detachment and in the case of ultrasonication may also cause host tissue disruption. To circumvent these problems, two protocols for a selective extraction of DNA and proteins from epiphytic communities of two marine macrophytes, the seagrass Cymodocea nodosa and the macroalga Caulerpa cylindracea, were adapted. An almost complete removal of the epiphytic community regardless of the sampling season, location, settlement or host species was achieved. The extracted DNA was suitable for metagenomic and 16S rRNA sequencing, while isolated proteins could be identified by mass spectrometry. Low macrophyte DNA and protein presence indicated a high specificity of the protocols towards epiphytic communities. Furthermore, the procedures are based on universally available laboratory chemicals making them widely applicable. In conclusion, the adapted protocols ensure an almost complete removal of the surface associated microbial community, are highly selective for microbes inhabiting macrophyte surfaces and provide DNA and proteins suitable for 16S rRNA sequencing, metagenomics and metaproteomics.

selective isolation ; DNA ; proteins ; marine macrophytes ; Cymodocea nodosa ; Caulerpa cylindracea

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