Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities

Abstract

. (2016) Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities. Molecular Ecology, 25 (21). pp. 5585-5602. Permanent WRAP URL:http://wrap.warwick.ac.uk/85060 Copyright and reuse:The Warwick Research Archive Portal (WRAP) makes this work by researchers of the University of Warwick available open access under the following conditions. Copyright © and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable the material made available in WRAP has been checked for eligibility before being made available.Copies of full items can be used for personal research or study, educational, or not-for profit purposes without prior permission or charge. Provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. Publisher's statement:This is the pre-peer reviewed version of the following article: Ray, J. L., Althammer, J., Skaar, K. S., Simonelli, P., Larsen, A., Stoecker, D., Sazhin, A., Ijaz, U. Z., Quince, C., Nejstgaard, J. C., Frischer, M., Pohnert, G. and Troedsson, C. (2016), Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities. Mol Ecol, 25: 5585-5602. doi:10.1111/mec.13844, which has been published in final form at http://dx.doi.org/10.1111/mec.13844 . This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving. A note on versions:The version presented here may differ from the published version or, version of record, if you wish to cite this item you are advised to consult the publisher's version. Please see the 'permanent WRAP url' above for details on accessing the published version and note that access may require a subscription. Current address: Jenabios GmbH, Orlaweg 2, 07743 Jena, Germany. 31 Abstract 32In order to characterize copepod feeding in relation to microbial plankton community dynamics, 33we combined metabarcoding and metabolome analyses during a 22-day seawater mesocosm 34 experiment. Nutrient amendment of mesocosms promoted the development of haptophyte- Introduction 52The trophic efficiency of the marine food web depends upon the pathway of carbon flow from 53 primary production to predatory fish -either through the classical food web (diatoms to 54 mesozooplankton), the microbial food web (flagellates/bacteria to ciliates to mesozooplankton) Nejstgaard et al. 1997; 2001b, and further discussion on methods in Nejstgaard et al. 2008). Amplicon library preparation 148The universal primers F-1183mod and R-1443mod (Table 1) (Table S1). Primer F- using distance matrices (PERMANOVA) was performed using the adonis function in "vegan". 214Constrained correspondence analysis (CCA) was performed using the cca f...

DNA metabarcoding unveils multiscale trophic variation in a widespread coastal opportunist

“…Furthermore, some of the DNA detected might come from secondary predation (taxa present in the stomach of preyed organisms; Berry et al., ; Kartzinel & Pringle, ). Cannibalism also imposes a specific problem in trophic molecular studies since it cannot be identified by means of metabarcoding (Berry et al., ; Ray et al., ). Large brown shrimps are known to be cannibalistic (Evans, ; Pihl & Rosenberg, ) but the removal of C. crangon sequence reads from our data set makes it impossible to gauge insights into the extent of cannibalism in this species.…”

“…Multiple stomachs were pooled prior to analysis and data were subjected to rigorous filtering to allow for a semiquantitative estimation of proportions of prey DNA (Deagle et al, 2005;Lejzerowicz et (Deagle et al, 2005). This study provides a significant addition to a growing body of studies in showing the applicability of semiquantitative estimations in molecular trophic ecology (e.g., Albaina et al, 2016;Deagle et al, 2018;Ray et al, 2016;Sakaguchi et al, 2017;Soininen et al, 2013).…”

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“…In fact, several field studies have shown that copepods can reject the most abundant phytoplankton, particularly certain PUA‐producing species (Leising et al ). On the other hand, Calanus finmarchicus fed on S. marinoi during its mesocosm bloom (Ray et al ). Predation had a stronger effect on the recruitment success of Calanus than diatom allelopathy throughout the spring bloom conditions (Pierson et al ).…”

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“…Mechanical lysis was achieved by bead beating in a FastPrep 24 5G (MP Biomedicals). Extracted DNA was amplified with primer pairs targeting the V4 region of the 16S rRNA gene [515f: 5′-GTGYCAGCMGCCGCGGTAA-3′, 806r: 5′-GGACTACNVGGGTWTCTAAT-3′ (Walters et al, 2016)] and the V7 region of the 18S rRNA gene [F-1183mod: 5′-AATTTGACTCAACRCGGG-3′, R-1443mod: 5′-GRGCATCACAGACCTG-3′ (Ray et al, 2016)] coupled to custom adaptor-barcode constructs. PCR amplification and Illumina MiSeq library preparation and sequencing (V3 chemistry) was carried out by LGC Genomics in Berlin.…”