{"id":12812,"date":"2018-08-15T12:22:46","date_gmt":"2018-08-15T19:22:46","guid":{"rendered":"https:\/\/www.darkenergybiosphere.org\/?post_type=publication&#038;p=12812"},"modified":"2018-09-04T13:16:49","modified_gmt":"2018-09-04T20:16:49","slug":"influence-of-commercial-dna-extraction-kit-choice-on-prokaryotic-community-metrics-in-marine-sediment","status":"publish","type":"publication","link":"https:\/\/www.darkenergybiosphere.org\/publication\/influence-of-commercial-dna-extraction-kit-choice-on-prokaryotic-community-metrics-in-marine-sediment\/","title":{"rendered":"Influence of commercial DNA extraction kit choice on prokaryotic community metrics in marine sediment"},"content":{"rendered":"<section id=\"section-1-en\" class=\"article-section article-section__abstract\" lang=\"en\" data-lang=\"en\">\n<div class=\"article-section__content en main\">\n<p>Commercial DNA extraction kits are widely used for cultivation\u2010free surveys of marine sediment. However, the consequences of popular extraction\u2010kit choices for sequence\u2010based 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<sup>\u00ae<\/sup>\u00a0DNA isolation kit and MP Biomedicals FastDNA<sup>TM<\/sup>\u00a0Spin Kit for Soil). We report comparisons of (1) total DNA yield, (2) extract purity, (3) gene\u2010targeted quantification, and (4) post\u2010sequencing ecological inferences in near\u2010seafloor (&lt; 1 meter below seafloor [mbsf]) and subsurface (&gt; 1 mbsf) marine sediment. In near\u2010seafloor sediment, the MP Biomedicals FastDNA<sup>TM<\/sup>\u00a0Spin 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<sup>\u00ae<\/sup>\u00a0DNA isolation kit generally co\u2010extracts less protein with the DNA in both near\u2010seafloor and subseafloor sediment. For samples from all depths, both kits exhibit similar depth\u2010dependent community richness patterns, taxonomic composition, and ordination\u2010based similarity trends. We conclude that, despite kit\u2010specific differences in extract yields, purity and reagent contaminant loads, ecological inferences based on next\u2010generation sequencing of DNA extracted using these popular commercial kits are robustly comparable, particularly for subseafloor sediment samples.<\/p>\n<\/div>\n<\/section>\n","protected":false},"template":"","tags":[],"publication_type":[19],"_links":{"self":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/publication\/12812"}],"collection":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/publication"}],"about":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/types\/publication"}],"wp:attachment":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/media?parent=12812"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/tags?post=12812"},{"taxonomy":"publication_type","embeddable":true,"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/publication_type?post=12812"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}