Interlaboratory quantification of Bacteria and Archaea in deeply buried sediments of the Baltic Sea (IODP Expedition 347)

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doi: 10.1093/femsec/fix007
Author(s): Buongiorno, Joy; Turner, Stephanie; Webster, Gordon; Asai, Masanori; Shumaker, Alexander K.; Roy, Taylor; Weightman, Andrew; Schippers, Axel; Lloyd, Karen G.
Author Affiliation(s): Primary:
University of Tennessee, Department of Microbiology, Knoxville, TN, United States
Other:
Federal Institute for Geosciences and Natural Resources, Germany
Cardiff University, United Kingdom
Volume Title: FEMS Microbiology. Ecology
Source: FEMS Microbiology. Ecology, 93(3), 16p. Publisher: Blackwell Publishing, Amsterdam, Netherlands. ISSN: 0168-6496
Note: In English. 59 refs.; illus., incl. 4 tables, sketch map
Summary: Two common quantification methods for subseafloor microorganisms are catalyzed reporter deposition fluorescence in situ 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 interlaboratory 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 x 107 cells cm-3. 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 x 106 - 2.34 x 109 16S rRNA gene copies cm-3 vs. 1.39 x 107 - 1.87 x 109 total cells cm-3. 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.
Year of Publication: 2017
Research Program: IODP Integrated Ocean Drilling Program
Key Words: 07 Marine Geology and Oceanography; Archaea; Atlantic Ocean; Bacteria; Baltic Sea; Biota; Communities; DNA; Denmark; Europe; Expedition 347; Genetics; IODP Site M0059; IODP Site M0060; IODP Site M0063; IODP Site M0065; Integrated Ocean Drilling Program; Interlaboratory comparison; Kattegat; Living taxa; Marine sediments; North Atlantic; North Sea; Nucleic acids; Quantitative analysis; Scandinavia; Sediments; Western Europe
Coordinates: N550000 N625725 E0181530 E0094800
Record ID: 2018086709
Copyright Information: GeoRef, Copyright 2019 American Geosciences Institute.