Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0....

Full description

Bibliographic Details
Main Authors: Christopher Ryan Penton, V.S.R Gupta Vadakattu, Julian eYu, James M. Tiedje
Format: Article
Language:English
Published: Frontiers Media S.A. 2016-06-01
Series:Frontiers in Microbiology
Subjects:
Online Access:http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00824/full
id doaj-ff45d95dcd3c4a00a00a8d3a6443f10f
record_format Article
spelling doaj-ff45d95dcd3c4a00a00a8d3a6443f10f2020-11-25T01:30:06ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2016-06-01710.3389/fmicb.2016.00824202946Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene AmpliconsChristopher Ryan Penton0V.S.R Gupta Vadakattu1Julian eYu2James M. Tiedje3Arizona State UniversityCSIRO Agricultural FlagshipArizona State UniversityMichigan State UniversityWe examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5 and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00824/fullmicrobial ecologyMicrobial DiversitySample SizeDNA extractionfungal community
collection DOAJ
language English
format Article
sources DOAJ
author Christopher Ryan Penton
V.S.R Gupta Vadakattu
Julian eYu
James M. Tiedje
spellingShingle Christopher Ryan Penton
V.S.R Gupta Vadakattu
Julian eYu
James M. Tiedje
Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons
Frontiers in Microbiology
microbial ecology
Microbial Diversity
Sample Size
DNA extraction
fungal community
author_facet Christopher Ryan Penton
V.S.R Gupta Vadakattu
Julian eYu
James M. Tiedje
author_sort Christopher Ryan Penton
title Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons
title_short Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons
title_full Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons
title_fullStr Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons
title_full_unstemmed Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons
title_sort size matters: assessing optimum soil sample size for fungal and bacterial community structure analyses using high throughput sequencing of rrna gene amplicons
publisher Frontiers Media S.A.
series Frontiers in Microbiology
issn 1664-302X
publishDate 2016-06-01
description We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5 and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.
topic microbial ecology
Microbial Diversity
Sample Size
DNA extraction
fungal community
url http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00824/full
work_keys_str_mv AT christopherryanpenton sizemattersassessingoptimumsoilsamplesizeforfungalandbacterialcommunitystructureanalysesusinghighthroughputsequencingofrrnageneamplicons
AT vsrguptavadakattu sizemattersassessingoptimumsoilsamplesizeforfungalandbacterialcommunitystructureanalysesusinghighthroughputsequencingofrrnageneamplicons
AT julianeyu sizemattersassessingoptimumsoilsamplesizeforfungalandbacterialcommunitystructureanalysesusinghighthroughputsequencingofrrnageneamplicons
AT jamesmtiedje sizemattersassessingoptimumsoilsamplesizeforfungalandbacterialcommunitystructureanalysesusinghighthroughputsequencingofrrnageneamplicons
_version_ 1725093683215204352