Successive DNA extractions improve characterization of soil microbial communities.
Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1-374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.
Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands; Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands.
Mauricio R
MR
Dimitrov
Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , Netherlands.
Annelies J
0000-0001-6286-7484
AJ
Veraart
Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , Netherlands.
Mattias
M
de Hollander
Laboratory of Microbiology, Wageningen University , Wageningen , Netherlands.
Hauke
H
Smidt
Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , Netherlands.
Johannes A
JA
van Veen
Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , Netherlands.
Eiko E
0000-0001-6701-8668
EE
Kuramae
454-pyrosequencing; Soil DNA extractions; Soil bacterial community; Soil fungal community; Soil microbial abundance; Soil microbial characterization; T-RFLP