Amplicon-based metabarcoding reveals temporal response of soil microbial community to fumigation-derived products Feng Wei, Thomas Passey, Xiangming Xu* NIAB East Malling Research, East Malling, Kent ME19 6BJ, UK A R T I C L E I N F O Article history: Received 11 August 2015 Received in revised form 19 January 2016 Accepted 15 March 2016 Available online xxx Keywords: Biofumigation Chemical fumigation Soil microbial community DNA metabarcoding A B S T R A C T The use of soil fumigation products to manage soilborne pathogens raises the question of whether it has undesirable effects on the soil ecosystem. Therefore, the aim of this study was to investigate the impacts of alternative fumigation products on soil microbial population structure. We characterised soil bacterial and fungal communities in response to the soil treatment with microencapsulated terpene, Brassica seedmeal (BioFence TM ) and chloropicrin in a field trial. The effect of soil treatments on the overall microbial population structure and relative abundance of individual microbial OTUs (operational taxonomic units) was assessed using an amplicon-based metabarcoding approach at three time points. Classifying representative OTU sequences into taxonomic groups was more uncertain for bacteria than for fungi. Chloropicrin dramatically altered both bacterial and fungal populations within four weeks of application. The effect on bacterial population structure is short-lived and became non-significant 16 weeks after treatment; however, fungal population structure was more persistently affected by chloropicrin. Neither terpene nor BioFence TM significantly affected soil microbiota. This study highlights the need for reliable algorithms in classifying sequences into taxonomic units and also the importance of identifying microbes into finer taxonomic groups for understanding soil microbiota and their effects on crop production. ã 2016 Elsevier B.V. All rights reserved. 1. Introduction Soil microbial communities represent the greatest reservoir of biological diversity known (Buee et al., 2009; Curtis et al., 2002; Gans et al., 2005). Microorganisms are vital to the soil ecosystem, being an integral part of important soil processes such as carbon and nitrogen cycles, decomposition of organic residues, formation of humic substance, and pollutant degradation. Microorganisms in soil are crucial for plant health (Berendsen et al., 2012) and crop yield (Xu et al., 2015), and shaped by numerous factors such as plant species and soil type. To maintain soil functions supporting the ecosystem, it is important to understand how soil micro- organisms respond to natural or human-mediated disturbance (Griffiths and Philippot, 2013). Sustainable crop production to secure food supply is vital, which depends critically on availability of high quality soils. Managing soilborne pathogens and pests is indispensable to food production worldwide, particularly for high-value horticul- ture crops. For instance, Verticillium wilt on strawberry, caused by the soilborne fungal pathogen Verticillium dahliae Kleb., is a major disease responsible for significant yield losses in commercial strawberry production (Maas, 1998). Without soil fumigation, it can result in 75% crop failure in susceptible strawberry cultivars (Wilhelm and Paulus, 1980). Pre-planting soil fumigation with broad-spectrum pesticides, e.g. methyl bromide and chloropicrin, have been indispensable for controlling soilborne pathogens on many crops for over 50 years (Martin, 2003). The broad-spectrum activities of these chemofumigants result in significant losses in soil microbial diversity (Dangi et al., 2015; Omirou et al., 2011; Spyrou et al., 2009). Because of the withdrawal of methyl bromide and the uncertain future of remaining chemicals (chloropicrin and dazomet) due to legislations, sustainable management of soilborne diseases has again become a major issue for production of many crops in soil. During the last two decades, much effort has been directed to search for alternative methods to manage soilborne diseases, including soil amendments by green or animal manures, bio- fumigation using Brassicaceae plants, disease suppressive crop rotations, anaerobic soil disinfestations and other non-chemical methods (e.g. soil solarisation and high-temperature steam treatment) (Colla et al., 2012; Goicoechea, 2009; Momma et al., 2013). However, use of these techniques to replace methyl bromide * Corresponding author. E-mail address: xiangming.xu@emr.ac.uk (X. Xu). http://dx.doi.org/10.1016/j.apsoil.2016.03.009 0929-1393/ ã 2016 Elsevier B.V. All rights reserved. Applied Soil Ecology 103 (2016) 83–92 Contents lists available at ScienceDirect Applied Soil Ecology journal homepage: www.elsevier.com/locate/apsoil