Influence of commercial DNA extraction kit choice on prokaryotic community metrics in marine sediment

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 V R 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) postsequencing 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 V R 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 kitspecific 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.

Evaluation of primer pairs for microbiome profiling from soils to humans within the One Health framework

“…We could not demonstrate a significant effect of extraction kit on overall alpha diversity, and studies showing no effect or significant effect of DNA extraction kit on microbial alpha diversity are available in the literature (Fiedorova et al, 2019;Hallmaier-Wacker, Lueert, Roos, & Knauf, 2018;Mattei et al, 2019;Ramírez, Graham, & D'Hondt, 2018). Nevertheless, we observed that the tested extraction kits differentially detected less abundant taxa, a finding corroborated in previous DNA extraction kits comparisons (Liu, Xue, & Yang, 2019).…”

Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture

“…This suggests that there are likely to be taxon-specific variations in cell lysis between the kits, especially in the eukaryotic dataset. This finding is in agreement with other studies that have found a similar trend ( Carrigg et al, 2007 ; Lekang, Thompson & Troedsson, 2015 ; Ramírez, Graham & D’Hondt, 2018 ). This could be further tested by using positive extraction controls such as a known mock prokaryotic community, allowing for the assessment of lysis efficiencies amongst kits ( Hermans, Buckley & Lear, 2018 ).…”

Environmental factors shaping bacterial, archaeal and fungal community structure in hydrothermal sediments of Guaymas Basin, Gulf of California

“…This approach covered the available thermal range of cored sediment, while providing sufficient material for coordinated experiments with other cruise participants, and accommodating temperature fluctuations due to pulsating hydrothermal flows that impact surficial (5 to 10 cmbsf) sediments [ 14 ]. Total DNA was extracted using the FastDNA TM Spin Kit for Soil (MP Biomedicals), as recommended for marine sediment [ 35 ], following the manufacturer’s protocol. Bacterial and archaeal SSU rRNA hypervariable region 4–5 (V4-V5) amplicons were generated using the 515F-Y ( ) and 926R ( ) primers and customized thermocycling parameters [ 36 ].…”