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Influence of commercial DNA extraction kit choice on prokaryotic community metrics in marine sediment
Author(s) -
Ramírez Gustavo A.,
Graham Dennis,
D'Hondt Steven
Publication year - 2018
Publication title -
limnology and oceanography: methods
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.898
H-Index - 72
ISSN - 1541-5856
DOI - 10.1002/lom3.10264
Subject(s) - sediment , dna extraction , extraction (chemistry) , environmental dna , seafloor spreading , environmental science , species richness , biology , oceanography , ecology , geology , polymerase chain reaction , biodiversity , chromatography , paleontology , chemistry , gene , genetics
Abstract Commercial DNA extraction kits are widely used for cultivation‐free surveys of marine sediment. However, the consequences of popular extraction‐kit choices for sequence‐based biological inferences about marine sedimentary communities have not previously been exhaustively assessed. To address this issue, we extracted DNA from multiple paired subsamples of marine sediment using two popular commercial extraction kits (MO BIO Laboratories PowerSoil ® DNA isolation kit and MP Biomedicals FastDNA TM Spin Kit for Soil). We report comparisons of (1) total DNA yield, (2) extract purity, (3) gene‐targeted quantification, and (4) post‐sequencing ecological inferences in near‐seafloor (< 1 meter below seafloor [mbsf]) and subsurface (> 1 mbsf) marine sediment. In near‐seafloor sediment, the MP Biomedicals FastDNA TM Spin Kit for Soil exhibits higher extraction yields, higher 16S rRNA gene loads, higher taxonomic diversity, and lower contaminant loads. In subseafloor sediment, both kits yield similar values for all of these parameters. The MO BIO Laboratories PowerSoil ® DNA isolation kit generally co‐extracts less protein with the DNA in both near‐seafloor and subseafloor sediment. For samples from all depths, both kits exhibit similar depth‐dependent community richness patterns, taxonomic composition, and ordination‐based similarity trends. We conclude that, despite kit‐specific differences in extract yields, purity and reagent contaminant loads, ecological inferences based on next‐generation sequencing of DNA extracted using these popular commercial kits are robustly comparable, particularly for subseafloor sediment samples.