High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure

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dc.contributor.author Darby, B. J.
dc.contributor.author Todd, Timothy C.
dc.contributor.author Herman, Michael A.
dc.date.accessioned 2014-06-12T20:16:14Z
dc.date.available 2014-06-12T20:16:14Z
dc.date.issued 2014-06-12
dc.identifier.uri http://hdl.handle.net/2097/17844
dc.description.abstract Nematodes are abundant consumers in grassland soils, but more sensitive and specific methods of enumeration are needed to improve our understanding of how different nematode species affect, and are affected by, ecosystem processes. High‐throughput amplicon sequencing is used to enumerate microbial and invertebrate communities at a high level of taxonomic resolution, but the method requires validation against traditional specimen‐based morphological identifications. To investigate the consistency between these approaches, we enumerated nematodes from a 25‐year field experiment using both morphological and molecular identification techniques in order to determine the long‐term effects of annual burning and nitrogen enrichment on soil nematode communities. Family‐level frequencies based on amplicon‐sequencing were not initially consistent with specimen‐based counts, but correction for differences in rRNA gene copy number using a genetic algorithm improved quantitative accuracy. Multivariate analysis of corrected sequence‐based abundances of nematode families was consistent with, but not identical to, analysis of specimen‐based counts. In both cases, herbivores, fungivores, and predator/omnivores generally were more abundant in burned than non‐burned plots, while bacterivores generally were more abundant in non-burned or nitrogen enriched plots. Discriminate analysis of sequence‐based abundances identified putative indicator species representing each trophic group. We conclude that high-throughput amplicon sequencing can be a valuable method for characterizing nematode communities at high taxonomic resolution as long as rRNA gene copy number variation is accounted for and accurate sequence databases are available. en_US
dc.language.iso en_US en_US
dc.relation.uri http://onlinelibrary.wiley.com/doi/10.1111/mec.12480/abstract en_US
dc.rights This is the peer reviewed version of the following article: Darby, B. J., Todd, T. C., & Herman, M. A. (2013). High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure. Molecular Ecology, 22(21), 5456–5471, which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/mec.12480/abstract en_US
dc.subject Tallgrass prairie en_US
dc.subject Nematodes en_US
dc.subject Konza prairie en_US
dc.subject Bar‐coding en_US
dc.subject Nitrogen enrichment en_US
dc.subject Burning en_US
dc.title High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure en_US
dc.type Article (author version) en_US
dc.date.published 2013 en_US
dc.citation.doi doi:10.1111/mec.12480 en_US
dc.citation.epage 5471 en_US
dc.citation.issue 21 en_US
dc.citation.jtitle Molecular Ecology en_US
dc.citation.spage 5456 en_US
dc.citation.volume 22 en_US
dc.contributor.authoreid nema en_US
dc.contributor.authoreid mherman en_US


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