Analysis of plant microbe interactions in the era of next generation sequencing technologies
- Institute of Crop Science and Resource Conservation—Molecular Biology of the Rhizosphere, Faculty of Agriculture, University of Bonn, Bonn, Germany
Next generation sequencing (NGS) technologies have impressively accelerated research in biological science during the last years by enabling the production of large volumes of sequence data to a drastically lower price per base, compared to traditional sequencing methods. The recent and ongoing developments in the field allow addressing research questions in plant-microbe biology that were not conceivable just a few years ago. The present review provides an overview of NGS technologies and their usefulness for the analysis of microorganisms that live in association with plants. Possible limitations of the different sequencing systems, in particular sources of errors and bias, are critically discussed and methods are disclosed that help to overcome these shortcomings. A focus will be on the application of NGS methods in metagenomic studies, including the analysis of microbial communities by amplicon sequencing, which can be considered as a targeted metagenomic approach. Different applications of NGS technologies are exemplified by selected research articles that address the biology of the plant associated microbiota to demonstrate the worth of the new methods.
Keywords: next generation sequencing, plant microbiota, phyllosphere, rhizosphere, metagenomics, amplicon sequencing
Citation: Knief C (2014) Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front. Plant Sci. 5:216. doi: 10.3389/fpls.2014.00216
Received: 15 February 2014; Accepted: 30 April 2014;
Published online: 21 May 2014.
Edited by:Ann E. Stapleton, University of North Carolina Wilmington, USA
Reviewed by:Xingyi Guo, Albert Einstein College of Medicine, USA
Ute Hentschel, University of Wuerzburg, Germany
Copyright © 2014 Knief. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Claudia Knief, Institute of Crop Science and Resource Conservation–Molecular Biology of the Rhizosphere, Faculty of Agriculture, Nussallee 13, 53115 Bonn, Germany e-mail: firstname.lastname@example.org