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Ammonia-oxidizing archaea and bacteria are structured by geography in biological soil crusts across North American arid lands

Yevgeniy Marusenko1, Scott T Bates2, Ian Anderson1, Shannon L Johnson3, Tanya Soule4 and Ferran Garcia-Pichel1*

Author Affiliations

1 School of Life Sciences, Arizona State University, P.O. Box 874501, Tempe, AZ 85287-4501, USA

2 Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA

3 Bioscience Division, B-11, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

4 Department of Biology, Indiana University-Purdue University, Fort Wayne, IN, USA

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Ecological Processes 2013, 2:9  doi:10.1186/2192-1709-2-9

Published: 26 April 2013

Abstract

Introduction

Biological soil crusts (BSCs) can dominate surface cover in dry lands worldwide, playing an integral role in arid land biogeochemistry, particularly in N fertilization through fixation and cycling. Nitrification is a characteristic and universal N transformation in BSCs that becomes important for the export of N beyond the microscopic bounds of the crust itself. The contribution of ammonia-oxidizing bacteria (AOB) in BSCs has been shown, but the role and extent of the recently discovered ammonia-oxidizing archaea (AOA) have not.

Methods

We sampled various types of crusts in four desert regions across the western United States and characterized the composition and size of ammonia-oxidizing communities using clone libraries and quantitative PCR targeting the amoA gene, which codes for the ammonia monooxygenase enzyme, universally present in ammonia-oxidizing microbes.

Results

All archaeal amoA sequences retrieved from BSCs belonged to the Thaumarchaeota (Nitrososphaera associated Group I.1b). Sequences from the Sonoran Desert, Colorado Plateau, and Great Basin were indistinguishable from each other but distinct from those of the Chihuahuan Desert. Based on amoA gene abundances, archaeal and bacterial ammonia oxidizers were ubiquitous in our survey, but the ratios of archaeal to bacterial ammonia oxidizers shifted from bacterially dominated in northern, cooler deserts to archaeally dominated in southern, warmer deserts.

Conclusions

Archaea are shown to be potentially important biogeochemical agents of biological soil crust N cycling. Conditions associated with different types of BSCs and biogeographical factors reveal a niche differentiation between AOA and AOB, possibly driven by temperature.

Keywords:
Biological soil crust; Desert; Arid; amoA; Ammonia oxidation; Nitrification; Nitrogen cycle; Thaumarchaeota