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Bitte verwenden Sie diesen Link, wenn Sie dieses Dokument zitieren oder verlinken wollen: https://nbn-resolving.org/urn:nbn:de:gbv:9-opus-41624

An optimized metaproteomics protocol for a holistic taxonomic and functional characterization of microbial communities from marine particles

  • 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.

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Metadaten
Author: Doreen Schultz, Daniela Zühlke, Jörg Bernhardt, Thomas Ben Francis, Dirk Albrecht, Claudia Hirschfeld, Stephanie Markert, Katharina Riedel
URN:urn:nbn:de:gbv:9-opus-41624
DOI:https://doi.org/10.1111/1758-2229.12842
Parent Title (English):Environmental Microbiology Reports
Publisher:John Wiley & Sons, Inc.
Place of publication:Hoboken, USA
Document Type:Article
Language:English
Date of first Publication:2020/07/10
Release Date:2021/02/06
GND Keyword:-
Volume:12
Issue:4
First Page:367
Last Page:376
Faculties:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Mikrobiologie - Abteilung für Genetik & Biochemie
Licence (German):License LogoCreative Commons - Namensnennung