Comparison between MICRO–CARD–FISH and 16 S 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: Wiley 2012
• Subjects: Arctic; Lesund
• Online Access: http://dx.doi.org/10.1111/1758-2229.12013; https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1758-2229.12013; https://onlinelibrary.wiley.com/doi/pdf/10.1111/1758-2229.12013; https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1758-2229.12013; http://onlinelibrary.wiley.com/wol1/doi/10.1111/1758-2229.12013/fullpdf

Summary We collected surface‐ and deep‐water samples (maximum depth 300 m) during the spring–summer transition in the coastal A rctic along a transect in the K ongsfjorden ( N y‐ Å lesund, S pitsbergen, N orway) to determine the structure of the active versus total marine bacterioplankton community using different approaches. Catalysed reporter deposition–fluorescence in situ hybridization combined with microautoradiography ( MICRO–CARD–FISH ) was used to determine the abundance and activity of different bacterial groups. The bacterial communities were dominated by members of A lphaproteobacteria followed by B acteroidetes, whereas G ammaproteobacteria were present at low abundance but exhibited a high percentage of active cells taking up leucine. The clone libraries of 16 S rRNA genes (16 S rDNA ) and 16 S rRNA from two different depths were used to decipher the bacterial community structure. Independently of the type of clone libraries analysed (16 S rDNA ‐ or 16 S 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 A lphaproteobacteria followed by G ammaproteobacteria. The R hodobacteriaceae were the most abundant members of the A lphaproteobacteria in both DNA and RNA clone libraries, followed by the SAR 11 clade, which was only detectable at the 16 S rDNA level. Moreover, there was a general agreement between the results obtained with both techniques, although some specific phylogenetic groups, such as SAR 11 and R oseobacter, deviated substantially from this relation. These discrepancies are most likely linked to different physiological states among members of the bacterioplankton community. Combined, MICRO–CARD–FISH 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.