Soil DNA extraction procedure influences protist 18S rRNA gene community profiling outcome

TY - JOUR

T1 - Soil DNA extraction procedure influences protist 18S rRNA gene community profiling outcome

AU - Santos, Susana S.

AU - Nunes, Ines Marques

AU - Nielsen, Tue K.

AU - Jacquiod, Samuel Jehan Auguste

AU - Hansen, Lars H.

AU - Winding, Anne

PY - 2017/7

Y1 - 2017/7

N2 - Advances in sequencing technologies allow deeper studies of the soil protist diversity and function. However, little attention has been given to the impact of the chosen soil DNA extraction procedure to the overall results. We examined the effect of three acknowledged DNA recovery methods, two manual methods (ISOm-11063, GnS-GII) and one commercial kit (MoBio), on soil protist community structures obtained from different sites with different land uses. Results from 18S rRNA gene amplicon sequencing suggest that DNA extraction method significantly affect the replicate homogeneity, the total number of operational taxonomic units (OTUs) recovered and the overall taxonomic structure and diversity of soil protist communities. However, DNA extraction effects did not overwhelm the natural variation among samples, as the community data still strongly grouped by geographical location. The commercial DNA extraction kit was associated with the highest diversity estimates and with a corresponding higher retrieval of Excavata, Cercozoa and Amoebozoa-related taxa. Overall, our findings indicate that this extraction offers a compromise between rare and dominant taxa representation, while providing high replication reproducibility. A comprehensive understanding of the DNA extraction techniques impact on soil protist diversity can enable more accurate diversity assays.

AB - Advances in sequencing technologies allow deeper studies of the soil protist diversity and function. However, little attention has been given to the impact of the chosen soil DNA extraction procedure to the overall results. We examined the effect of three acknowledged DNA recovery methods, two manual methods (ISOm-11063, GnS-GII) and one commercial kit (MoBio), on soil protist community structures obtained from different sites with different land uses. Results from 18S rRNA gene amplicon sequencing suggest that DNA extraction method significantly affect the replicate homogeneity, the total number of operational taxonomic units (OTUs) recovered and the overall taxonomic structure and diversity of soil protist communities. However, DNA extraction effects did not overwhelm the natural variation among samples, as the community data still strongly grouped by geographical location. The commercial DNA extraction kit was associated with the highest diversity estimates and with a corresponding higher retrieval of Excavata, Cercozoa and Amoebozoa-related taxa. Overall, our findings indicate that this extraction offers a compromise between rare and dominant taxa representation, while providing high replication reproducibility. A comprehensive understanding of the DNA extraction techniques impact on soil protist diversity can enable more accurate diversity assays.

KW - Agriculture

KW - GnS-GII

KW - ISOm

KW - MoBio

KW - protist diversity

KW - taxonomic structure.

UR - http://www.scopus.com/inward/record.url?scp=85019001260&partnerID=8YFLogxK

U2 - 10.1016/j.protis.2017.03.002

DO - 10.1016/j.protis.2017.03.002

M3 - Journal article

C2 - 28477515

AN - SCOPUS:85019001260

SN - 1434-4610

VL - 168

SP - 283

EP - 293

JO - Protist

JF - Protist

IS - 3

ER -