{"id":10630,"date":"2017-02-01T11:50:46","date_gmt":"2017-02-01T19:50:46","guid":{"rendered":"https:\/\/www.darkenergybiosphere.org\/?post_type=publication&#038;p=10630"},"modified":"2017-02-15T11:39:50","modified_gmt":"2017-02-15T19:39:50","slug":"inter-laboratory-quantification-of-bacteria-and-archaea-in-deeply-buried-sediments-of-the-baltic-sea-iodp-expedition-347","status":"publish","type":"publication","link":"https:\/\/www.darkenergybiosphere.org\/publication\/inter-laboratory-quantification-of-bacteria-and-archaea-in-deeply-buried-sediments-of-the-baltic-sea-iodp-expedition-347\/","title":{"rendered":"Inter-laboratory quantification of Bacteria and Archaea in deeply buried sediments of the Baltic Sea (IODP Expedition 347)"},"content":{"rendered":"<p>Two common quantification methods for subseafloor microorganisms are catalyzed reporter deposition fluorescence <em>in situ<\/em> hybridization (CARD-FISH) and quantitative PCR (qPCR). Using these methods, we quantified Bacteria and Archaea in Baltic Sea basin sediments (IODP Exp. 347) down to 90 mbsf, testing the following hypotheses in an inter-laboratory comparison: 1) proteinase K permeabilization of Archaeal cell walls increases CARD-FISH accuracy, and 2) qPCR varies by more than an order of magnitude between laboratories using similar protocols. CARD-FISH counts did not differ between permeabilization treatments, demonstrating that proteinase K did not increase accuracy of CARD-FISH counts. However, 91% of these counts were below the quantification limit of 1.3 \u00d7 10<sup>7<\/sup> cells cm<sup>\u22123<\/sup>. For qPCR, data varied between laboratories, but were largely within the same order of magnitude if the same primers were used, with 88% of samples being above the quantification limit. Copy number values were elevated by preparing a sediment slurry before DNA extraction: 3.88 \u00d710<sup>6<\/sup> to 2.34 \u00d710<sup>9<\/sup> 16S rRNA gene copies cm<sup>\u22123<\/sup> vs. 1.39 \u00d7 10<sup>7<\/sup> to 1.87 \u00d7 10<sup>9<\/sup> total cells cm<sup>\u22123<\/sup>. By qPCR, Bacteria were more abundant than Archaea, although they usually were within the same order of magnitude. Overall, qPCR is more sensitive than CARD-FISH, but both require optimization to consistently achieve both precision and accuracy.<\/p>\n","protected":false},"template":"","tags":[],"publication_type":[19],"_links":{"self":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/publication\/10630"}],"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=10630"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/tags?post=10630"},{"taxonomy":"publication_type","embeddable":true,"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/publication_type?post=10630"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}