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Applied and Environmental Microbiology, October 2008, p. 6417-6426, Vol. 74, No. 20
0099-2240/08/$08.00+0     doi:10.1128/AEM.00843-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Global Occurrence of Archaeal amoA Genes in Terrestrial Hot Springs

Chuanlun L. Zhang,^1,* Qi Ye,¹ Zhiyong Huang,¹ WenJun Li,² Jinquan Chen,² Zhaoqi Song,² Weidong Zhao,¹ Christopher Bagwell,³ William P. Inskeep,⁴ Christian Ross,⁵ Lei Gao,⁶ Juergen Wiegel,⁷ Christopher S. Romanek,⁸ Everett L. Shock,⁹ and Brian P. Hedlund^5,

Department of Marine Sciences, University of Georgia, Athens, Georgia 30602,¹ Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, China,² Savannah River National Laboratory, Aiken, South Carolina 29802,³ Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana 59717,⁴ School of Life Sciences, University of Nevada, Las Vegas, Nevada 89154,⁵ T-Life Research Center, Fudan University, Shanghai 200433, China,⁶ Department of Microbiology, University of Georgia, Athens, Georgia 30605,⁷ Department of Geology, University of Georgia, Athens, Georgia 30605,⁸ School of Earth & Space Exploration and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287⁹

Received 13 April 2008/ Accepted 21 July 2008

Despite the ubiquity of ammonium in geothermal environments and the thermodynamic favorability of aerobic ammonia oxidation, thermophilic ammonia-oxidizing microorganisms belonging to the crenarchaeota kingdom have only recently been described. In this study, we analyzed microbial mats and surface sediments from 21 hot spring samples (pH 3.4 to 9.0; temperature, 41 to 86°C) from the United States, China, and Russia and obtained 846 putative archaeal ammonia monooxygenase large-subunit (amoA) gene and transcript sequences, representing a total of 41 amoA operational taxonomic units (OTUs) at 2% identity. The amoA gene sequences were highly diverse, yet they clustered within two major clades of archaeal amoA sequences known from water columns, sediments, and soils: clusters A and B. Eighty-four percent (711/846) of the sequences belonged to cluster A, which is typically found in water columns and sediments, whereas 16% (135/846) belonged to cluster B, which is typically found in soils and sediments. Although a few amoA OTUs were present in several geothermal regions, most were specific to a single region. In addition, cluster A amoA genes formed geographic groups, while cluster B sequences did not group geographically. With the exception of only one hot spring, principal-component analysis and UPGMA (unweighted-pair group method using average linkages) based on the UniFrac metric derived from cluster A grouped the springs by location, regardless of temperature or bulk water pH, suggesting that geography may play a role in structuring communities of putative ammonia-oxidizing archaea (AOA). The amoA genes were distinct from those of low-temperature environments; in particular, pair-wise comparisons between hot spring amoA genes and those from sympatric soils showed less than 85% sequence identity, underscoring the distinctness of hot spring archaeal communities from those of the surrounding soil system. Reverse transcription-PCR showed that amoA genes were transcribed in situ in one spring and the transcripts were closely related to the amoA genes amplified from the same spring. Our study demonstrates the global occurrence of putative archaeal amoA genes in a wide variety of terrestrial hot springs and suggests that geography may play an important role in selecting different assemblages of AOA.

Published ahead of print on 1 August 2008.

These authors contributed equally to the writing of the paper.