Combining Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization and Microautoradiography To Detect Substrate Utilization by Bacteria and Archaea in the Deep Ocean

• Main Author: Gerhard J. Herndl
• Other Authors: The Pennsylvania State University CiteSeerX Archives
• Format: Text
• Language: English
• Published: 2004
• Subjects: North Atlantic
• Online Access: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.522.9117; http://www.microbial-oceanography.eu/pdf/Teira_AEM_2004.pdf

The recently developed CARD-FISH protocol was refined for the detection of marine Archaea by replacing the lysozyme permeabilization treatment with proteinase K. This modification resulted in about twofold-higher detection rates for Archaea in deep waters. Using this method in combination with microautoradiography, we found that Archaea are more abundant than Bacteria (42 % versus 32 % of 4,6-diamidino-2-phenylindole counts) in the deep waters of the North Atlantic and that a larger fraction of Archaea than of Bacteria takes up L-aspartic acid (19 % versus 10%). Over the past decade, our knowledge of the phylogenetic composition of marine prokaryotic communities, including those inhabiting the deep ocean, has increased considerably due to the application of molecular tools such as fingerprinting techniques, cloning, and sequencing (7, 9, 10, 12, 20, 21). Flu-orescence in situ hybridization (FISH) can directly assess the abundance of specific prokaryotes, but it frequently yields a very low recovery of Bacteria and Archaea compared to the total number of 4,6-diamidino-2-phenylindole (DAPI)-stain-