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Combining catalyzed reporter deposition-fluorescence in situ hybridization and microautoradiography to detect substrate utilization by bacteria and archaea in the deep ocean

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Pernthaler,  A.
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Pernthaler,  J.
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Citation

Teira, E., Reinthaler, T., Pernthaler, A., Pernthaler, J., & Herndl, G. J. (2004). Combining catalyzed reporter deposition-fluorescence in situ hybridization and microautoradiography to detect substrate utilization by bacteria and archaea in the deep ocean. Applied and Environmental Microbiology, 70(7), 4411-4414.


Cite as: http://hdl.handle.net/21.11116/0000-0001-D121-D
Abstract
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). Fluorescence 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)-stainable cells (3). Only recently, the use of polynucleotide probes allowed the assessment of the abundance of Bacteria and Archaea in the meso- and bathypelagic waters of the Pacific (18) and in Antarctic marine waters (5). These authors found that the relative abundance of Crenarchaea increased significantly with depth, comprising up to 39% of total picoplankton cells down to 500 m, whereas the abundance of Euryarchaea was very low (<10%) throughout the water column. By contrast, very little is known about the metabolic function of specific prokaryotic groups in natural conditions (6, 23). The combination of fluorescence in situ techniques and microautoradiography has been used to determine the specific uptake of a given substrate in natural assemblages (6, 8, 14, 15, 19, 22, 23) but, to our knowledge, never in the deeper layers of the ocean (below 200 m).