The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks

To determine the optimal soil sample size for microbial community structure analysis, DNA extraction, microbial composition analysis, and diversity assessments were performed using soil sample sizes of 0.2, 1, and 5 g. This study focused on the relationship between soil amount and DNA extraction con...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Hiroki Morita, Satoshi Akao
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/99c2c07228074468ad2a6e38c46ffb78
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:99c2c07228074468ad2a6e38c46ffb78
record_format	dspace
spelling	oai:doaj.org-article:99c2c07228074468ad2a6e38c46ffb782021-11-25T06:19:40ZThe effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks1932-6203https://doaj.org/article/99c2c07228074468ad2a6e38c46ffb782021-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8601499/?tool=EBIhttps://doaj.org/toc/1932-6203To determine the optimal soil sample size for microbial community structure analysis, DNA extraction, microbial composition analysis, and diversity assessments were performed using soil sample sizes of 0.2, 1, and 5 g. This study focused on the relationship between soil amount and DNA extraction container volume and the alteration in microbial composition at different taxonomic ranks (order, class, and phylum). Horizontal (0.2 and 1 g) and vertical (5 g) shaking were applied during DNA extraction for practical use in a small laboratory. In the case of the 5 g soil sample, DNA extraction efficiency and the value of α-diversity index fluctuated severely, possibly because of vertical shaking. Regarding the 0.2 and 1 g soil samples, the number of taxa, Shannon–Wiener index, and Bray–Curtis dissimilarity were stable and had approximately the same values at each taxonomic rank. However, non-metric multidimensional scaling showed that the microbial compositions of these two sample sizes were different. The higher relative abundance of taxa in the case of the 0.2 g soil sample might indicate that cell wall compositions differentiated the microbial community structures in these two sample sizes due to high shear stress tolerance. The soil sample size and tube volume affected the estimated microbial community structure. A soil sample size of 0.2 g would be preferable to the other sample sizes because of the possible higher shearing force for DNA extraction and lower experimental costs due to smaller amounts of consumables. When the taxonomic rank was changed from order to phylum, some minor taxa identified at the order rank were integrated into major taxa at the phylum rank. The integration affected the value of the β-diversity index; therefore, the microbial community structure analysis, reproducibility of structures, diversity assessment, and detection of minor taxa would be influenced by the taxonomic rank applied.Hiroki MoritaSatoshi AkaoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hiroki Morita Satoshi Akao The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks
description	To determine the optimal soil sample size for microbial community structure analysis, DNA extraction, microbial composition analysis, and diversity assessments were performed using soil sample sizes of 0.2, 1, and 5 g. This study focused on the relationship between soil amount and DNA extraction container volume and the alteration in microbial composition at different taxonomic ranks (order, class, and phylum). Horizontal (0.2 and 1 g) and vertical (5 g) shaking were applied during DNA extraction for practical use in a small laboratory. In the case of the 5 g soil sample, DNA extraction efficiency and the value of α-diversity index fluctuated severely, possibly because of vertical shaking. Regarding the 0.2 and 1 g soil samples, the number of taxa, Shannon–Wiener index, and Bray–Curtis dissimilarity were stable and had approximately the same values at each taxonomic rank. However, non-metric multidimensional scaling showed that the microbial compositions of these two sample sizes were different. The higher relative abundance of taxa in the case of the 0.2 g soil sample might indicate that cell wall compositions differentiated the microbial community structures in these two sample sizes due to high shear stress tolerance. The soil sample size and tube volume affected the estimated microbial community structure. A soil sample size of 0.2 g would be preferable to the other sample sizes because of the possible higher shearing force for DNA extraction and lower experimental costs due to smaller amounts of consumables. When the taxonomic rank was changed from order to phylum, some minor taxa identified at the order rank were integrated into major taxa at the phylum rank. The integration affected the value of the β-diversity index; therefore, the microbial community structure analysis, reproducibility of structures, diversity assessment, and detection of minor taxa would be influenced by the taxonomic rank applied.
format	article
author	Hiroki Morita Satoshi Akao
author_facet	Hiroki Morita Satoshi Akao
author_sort	Hiroki Morita
title	The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks
title_short	The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks
title_full	The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks
title_fullStr	The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks
title_full_unstemmed	The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks
title_sort	effect of soil sample size, for practical dna extraction, on soil microbial diversity in different taxonomic ranks
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/99c2c07228074468ad2a6e38c46ffb78
work_keys_str_mv	AT hirokimorita theeffectofsoilsamplesizeforpracticaldnaextractiononsoilmicrobialdiversityindifferenttaxonomicranks AT satoshiakao theeffectofsoilsamplesizeforpracticaldnaextractiononsoilmicrobialdiversityindifferenttaxonomicranks AT hirokimorita effectofsoilsamplesizeforpracticaldnaextractiononsoilmicrobialdiversityindifferenttaxonomicranks AT satoshiakao effectofsoilsamplesizeforpracticaldnaextractiononsoilmicrobialdiversityindifferenttaxonomicranks
_version_	1718413880724553728

The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks

Ejemplares similares