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Selective DNA and protein isolation from marine macrophyte surfaces

Korlević, Marino; Markovski, Marsej; Zhao, Zihao; Herndl, Gerhard J.; Najdek-Dragić, Mirjana (2021) Selective DNA and protein isolation from marine macrophyte surfaces. Frontiers in microbiology, 12 . ISSN 1664-302X

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Abstract

Studies of unculturable microbes often combine methods, such as 16S rRNA sequencing, metagenomics, and metaproteomics. To apply these techniques to the microbial community inhabiting the surfaces of marine macrophytes, it is advisable to perform a selective DNA and protein isolation prior to the analysis to avoid biases due to the host material being present in high quantities. Two protocols for DNA and protein isolation were adapted for selective extractions of DNA and proteins from epiphytic communities inhabiting the surfaces of two marine macrophytes, the seagrass Cymodocea nodosa and the macroalga Caulerpa cylindracea. Protocols showed an almost complete removal of the epiphytic community regardless of the sampling season, station, settlement, or host species. The obtained DNA was suitable for metagenomic and 16S rRNA sequencing, while isolated proteins could be identified by mass spectrometry. Low presence of host DNA and proteins in the samples indicated a high specificity of the protocols. The procedures are based on universally available laboratory chemicals making the protocols widely applicable. Taken together, the adapted protocols ensure an almost complete removal of the macrophyte epiphytic community. The procedures are selective for microbes inhabiting macrophyte surfaces and provide DNA and proteins applicable in 16S rRNA sequencing, metagenomics, and metaproteomics.

Item Type: Article
Uncontrolled Keywords: selective isolation ; DNA ; proteins ; marine macrophytes ; Cymodocea nodosa ; Caulerpa cylindracea
Subjects: NATURAL SCIENCES > Biology
Divisions: Center for Marine Research
Projects:
Project titleProject leaderProject codeProject type
Analiza složenosti mikrobne dinamike u invadiranim livadama morskih cvjetnicaNajdek-Dragić, MirjanaIP-2016-06-7118HRZZ
Depositing User: Mirjana Najdek Dragić
Date Deposited: 31 May 2021 11:05
Last Modified: 06 Aug 2021 12:43
URI: http://fulir.irb.hr/id/eprint/6425
DOI: 10.3389/fmicb.2021.665999

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