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An optimized metaproteomics protocol for a holistic taxonomic and functional characterization of microbial communities from marine particles
Author(s) -
Schultz Doreen,
Zühlke Daniela,
Bernhardt Jörg,
Francis Thomas Ben,
Albrecht Dirk,
Hirschfeld Claudia,
Markert Stephanie,
Riedel Katharina
Publication year - 2020
Publication title -
environmental microbiology reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.229
H-Index - 69
ISSN - 1758-2229
DOI - 10.1111/1758-2229.12842
Subject(s) - metaproteomics , biology , metagenomics , bacteria , cyanobacteria , proteobacteria , computational biology , microbiology and biotechnology , biochemistry , 16s ribosomal rna , gene , genetics
Summary This study aimed to establish a robust and reliable metaproteomics protocol for an in‐depth characterization of marine particle‐associated (PA) bacteria. To this end, we compared six well‐established protein extraction protocols together with different MS‐sample preparation techniques using particles sampled during a North Sea spring algae bloom in 2009. In the final optimized workflow, proteins are extracted using a combination of SDS‐containing lysis buffer and cell disruption by bead‐beating, separated by SDS‐PAGE, in‐gel digested and analysed by LC–MS/MS, before MASCOT search against a metagenome‐based database and data processing/visualization with the in‐house ‐developed bioinformatics tools Prophane and Paver . As an application example, free‐living (FL) and particulate communities sampled in April 2009 were analysed, resulting in an as yet unprecedented number of 9354 and 5034 identified protein groups for FL and PA bacteria, respectively. Our data suggest that FL and PA communities appeared similar in their taxonomic distribution, with notable exceptions: eukaryotic proteins and proteins assigned to Flavobacteriia , Cyanobacteria , and some proteobacterial genera were found more abundant on particles, whilst overall proteins belonging to Proteobacteria were more dominant in the FL fraction. Furthermore, our data points to functional differences including proteins involved in polysaccharide degradation, sugar‐ and phosphorus uptake, adhesion, motility, and stress response.