Selective DNA and Protein Isolation From Marine Macrophyte Surfaces

Author(s)
Marino Korlević, Marsej Markovski, Zihao Zhao, Gerhard J Herndl, Mirjana Najdek
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.

Organisation(s)
Functional and Evolutionary Ecology, Research Platform Vienna Metabolomics Center
External organisation(s)
Institute Ruder Boskovic (RBI), Royal Netherlands Institute for Sea Research
Journal
Frontiers in Microbiology
Volume
12
ISSN
1664-302X
DOI
https://doi.org/10.3389/fmicb.2021.665999
Publication date
05-2021
Peer reviewed
Yes
Austrian Fields of Science 2012
106021 Marine biology
Portal url
https://ucris.univie.ac.at/portal/en/publications/selective-dna-and-protein-isolation-from-marine-macrophyte-surfaces(4c9121b8-77fd-4555-b9e4-331e9aab6021).html