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Aquatic Microbial Ecology

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AME 55:189-201 (2009)  -  DOI:

Diversity of Archaea and detection of crenarchaeotal amoA genes in the rivers Rhine and Têt

Lydie Herfort1,2,*, Jung-Hyun Kim1, Marco J. L. Coolen1,3, Ben Abbas1,4, Stefan Schouten1, Gerhard J. Herndl1, Jaap S. Sinninghe Damsté1

1Department of Marine Biogeochemistry and Toxicology, and Department of Biological Oceanography, Royal Netherlands Institute for Sea Research (NIOZ), PO Box 59, 1790 AB Den Burg, Texel, The Netherlands
2Present address: Center for Coastal Marine Observation & Prediction, Oregon Health & Science University, 20000 NW Walker Road, Beaverton, Oregon 97006, USA
3Present address:
Woods Hole Oceanographic Institution, Department of Marine Chemistry and Geochemistry, 360 Woods Hole Road, Massachusetts 02543, USA
4Present address: Department of Biotechnology, Delft University of Technology, 2628 BC Delft, The Netherlands

ABSTRACT: Pelagic archaeal phylogenetic diversity and the potential for crenarchaeotal nitrification of Group 1.1a were determined in the rivers Rhine and Têt by 16S rRNA sequencing, catalyzed reported deposition-fluorescence in situ hybridization (CARD–FISH) and quantification of 16S rRNA and functional genes. Euryarchaeota were, for the first time, detected in temperate river water even though a net predominance of crenarchaeotal phylotypes was found. Differences in phylogenic distribution were observed between rivers and seasons. Our data suggest that a few archaeal phylotypes (Euryarchaeota Groups RC-V and LDS, Crenarchaeota Group 1.1a) are widely distributed in pelagic riverine environments whilst others (Euryarchaeota Cluster Sagma-1) may only occur seasonally in river water. Crenarchaeota Group 1.1a has recently been identified as a major nitrifier in the marine environment and phylotypes of this group were also present in both rivers, where they represented 0.3% of the total pelagic microbial community. Interestingly, a generally higher abundance of Crenarchaeota Group 1.1a was found in the Rhine than in the Têt, and crenarchaeotal ammonia monooxygenase gene (amoA) was also detected in the Rhine, with higher amoA copy numbers measured in February than in September. This suggests that some of the Crenarchaeota present in river waters have the ability to oxidize ammonia and that riverine crenarchaeotal nitrification of Group 1.1a may vary seasonally.

KEYWORDS: Archaea · River · Diversity · Nitrification

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Cite this article as: Herfort L, Kim JH, Coolen MJL, Abbas B, Schouten S, Herndl GJ, Sinninghe Damsté JS (2009) Diversity of Archaea and detection of crenarchaeotal amoA genes in the rivers Rhine and Têt. Aquat Microb Ecol 55:189-201.

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