Effort Versus Reward: Preparing samples for fungal community characterization in high-throughput sequencing surveys of soils

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http://dx.doi.org/10.13020/D6301Q
http://hdl.handle.net/11299/170817

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Keywords

fungi

sample preparing

high-throughput sequencing

soil

Collection period

2013
2014

Date completed

2014

Date updated

Time period coverage

Geographic coverage

Source information

Journal Title

Journal ISSN

Volume Title

Title

Effort Versus Reward: Preparing samples for fungal community characterization in high-throughput sequencing surveys of soils

Published Date

2015-03-25

Authors

Song, Zewei

Schlatter, Dan

Kennedy, Peter

Kinkel, Linda

Kistler, H.Corby

Nguyen, Nhu

Bates, Scott

Group

Author Contact

Song, Zewei
songx208@umn.edu

Type

Dataset
Experimental Data
Genomics Data

Abstract

Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modifications to library preparation for high-throughput sequencing (HTS). The following treatments were considered: 1) the amount of soil used in DNA extraction, 2) the inclusion of additional steps (freeze/thaw cycles, sonication, or hot water bath incubation) in the extraction procedure, 3) the amount of DNA template used in polymerase chain reaction (PCR), and 4) the effect of sample pooling, either physically or computationally. Soils from two different ecosystems in Minnesota, USA, one prairie and one forest site, were used to assess the generality of our results. The first three treatments did not significantly influence observed fungal operational taxonomic unit (OTU) richness or community structure at either site. Physical pooling captured more OTU richness compared to individual samples, but total OTU richness at each site was highest when individual samples were computationally combined. We conclude that standard extraction kit protocols are well optimized for fungal HTS surveys, but because sample pooling can significantly influence OTU richness estimates, it is important to carefully consider the study aims when planning sampling procedures.

Description

This data set consists of four data files. The FASTA file, Representative OTU sequences.fa, contains representative sequences from the operational taxonomic units (OTUs) shown in the OTU table. FASTA files can be opened in simple text editors, and sequences can be aligned using the BLAST tool (http://blast.ncbi.nlm.nih.gov/Blast.cgi) or open source software, like AliView (http://www.ormbunkar.se/aliview/). There are two Excel data files: OTU table and heatmaps.xlsx and Diversity Indexes.xlsx. The former contains the raw abundance data for the observed OTUs from the different experimental sites. The latter is a breakdown of various diversity indices that are grouped based on experimental characteristics, such as extraction volume, extraction method, etc. Excel_Archive.zip is a compressed version of the two Excel data files that have been converted to more archival-friendly formats using Excel Archival Tool.

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License

CC0 1.0 Universal - Public Domain Dedication
http://creativecommons.org/publicdomain/zero/1.0/

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Data Repository for U of M (DRUM)

Funding information

USDA 2011-67019-30200
University of Minnesota MnDrive
NSF Grants EF 12-41895
NSF Long-Term Ecological Research Network 0620652

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Previously Published Citation

Suggested citation

Song, Zewei; Schlatter, Dan; Kennedy, Peter; Kinkel, Linda; Kistler, H.Corby; Nguyen, Nhu; Bates, Scott. (2015). Effort Versus Reward: Preparing samples for fungal community characterization in high-throughput sequencing surveys of soils. Retrieved from the University Digital Conservancy, http://dx.doi.org/10.13020/D6301Q.

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