Soil DNA extraction procedure influences protist 18S rRNA gene community profiling outcome
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Soil DNA extraction procedure influences protist 18S rRNA gene community profiling outcome. / Santos, Susana S.; Nunes, Ines Marques; Nielsen, Tue K.; Jacquiod, Samuel Jehan Auguste; Hansen, Lars H.; Winding, Anne.
In: Protist, Vol. 168, No. 3, 07.2017, p. 283-293.Research output: Contribution to journal › Journal article › Research › peer-review
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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
VL - 168
SP - 283
EP - 293
JO - Protist
JF - Protist
SN - 1434-4610
IS - 3
ER -
ID: 181413657