Comparison between MICRO-CARD-FISH and 16S rRNA gene clone libraries to assess the active versus total bacterial community in the coastal Arctic

• Published in: Environmental Microbiology Reports
• Main Authors: de Corte, Daniele, Sintes, Eva, Yokokawa, Taichi, Herndl, Gerhard J.
• Format: Article in Journal/Newspaper
• Language: English
• Published: 2013
• Subjects: IN-SITU HYBRIDIZATION; GRADIENT GEL-ELECTROPHORESIS; MARINE BACTERIOPLANKTON; BIOMASS PRODUCTION; SINGLE CELLS; GROWTH-RATE; OCEAN; DIVERSITY; PHYTOPLANKTON; ECOLOGY; Arctic; Lesund; Norway; Kongsfjord*; Kongsfjorden; Phytoplankton; Spitsbergen
• Online Access: https://hdl.handle.net/11370/95b56fd2-c64a-4560-8e67-e12c1db28667; https://research.rug.nl/en/publications/95b56fd2-c64a-4560-8e67-e12c1db28667; https://doi.org/10.1111/1758-2229.12013; https://pure.rug.nl/ws/files/132365642/Comparison_between_MICRO_CARD_FISH_and_16S_rRNA_gene_clone_libraries_to_assess.pdf

We collected surface- and deep-water samples (maximum depth 300m) during the springsummer transition in the coastal Arctic along a transect in the Kongsfjorden (Ny-angstrom lesund, Spitsbergen, Norway) to determine the structure of the active versus total marine bacterioplankton community using different approaches. Catalysed reporter depositionfluorescence in situ hybridization combined with microautoradiography (MICROCARDFISH) was used to determine the abundance and activity of different bacterial groups. The bacterial communities were dominated by members of Alphaproteobacteria followed by Bacteroidetes, whereas Gammaproteobacteria were present at low abundance but exhibited a high percentage of active cells taking up leucine. The clone libraries of 16S rRNA genes (16S rDNA) and 16S rRNA from two different depths were used to decipher the bacterial community structure. Independently of the type of clone libraries analysed (16S rDNA- or 16S rRNA-based), four major and four minor taxonomic groups were detected. The bacterioplankton community was mainly dominated at both the DNA and the RNA levels by Alphaproteobacteria followed by Gammaproteobacteria. The Rhodobacteriaceae were the most abundant members of the Alphaproteobacteria in both DNA and RNA clone libraries, followed by the SAR11 clade, which was only detectable at the 16S rDNA level. Moreover, there was a general agreement between the results obtained with both techniques, although some specific phylogenetic groups, such as SAR11 and Roseobacter, deviated substantially from this relation. These discrepancies are most likely linked to different physiological states among members of the bacterioplankton community. Combined, MICROCARDFISH and DNA and RNA clone libraries, however, allowed for accurately quantifying different bacterial groups and their activity as well as a detailed phylogenetic insight into the fractions of present versus metabolically active bacterial groups.