amoA‐based consensus phylogeny of ammonia‐oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions

Wiley - Tập 14 Số 2 - Trang 525-539 - 2012
Michael Pester1, Thomas Rattei2, Stefan Flechl1, Alexander Gröngröft3, Andreas Richter4, Jörg Overmann5, Barbara Reinhold‐Hurek6, Alexander Loy1, Michael Wagner1
1Departments of Microbial Ecology,
2Computational Systems Biology
3Institute of Soil Science, University of Hamburg, Allende-Platz 2, D 20146 Hamburg, Germany
4Chemical Ecology and Ecosystem Research, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria.
5Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, D‐38124 Braunschweig, Germany.
6Department of Microbe-Plant Interactions, University of Bremen, Postfach 330440, D-28334 Bremen, Germany

Tóm tắt

SummaryAmmonia‐oxidizing archaea (AOA) play an important role in nitrification and many studies exploit their amoA genes as marker for their diversity and abundance. We present an archaeal amoA consensus phylogeny based on all publicly available sequences (status June 2010) and provide evidence for the diversification of AOA into four previously recognized clusters and one newly identified major cluster. These clusters, for which we suggest a new nomenclature, harboured 83 AOA species‐level OTU (using an inferred species threshold of 85% amoA identity). 454 pyrosequencing of amoA amplicons from 16 soils sampled in Austria, Costa Rica, Greenland and Namibia revealed that only 2% of retrieved sequences had no database representative on the species‐level and represented 30–37 additional species‐level OTUs. With the exception of an acidic soil from which mostly amoA amplicons of the Nitrosotalea cluster were retrieved, all soils were dominated by amoA amplicons from the Nitrososphaera cluster (also called group I.1b), indicating that the previously reported AOA from the Nitrosopumilus cluster (also called group I.1a) are absent or represent minor populations in soils. AOA richness estimates on the species level ranged from 8–83 co‐existing AOAs per soil. Presence/absence of amoA OTUs (97% identity level) correlated with geographic location, indicating that besides contemporary environmental conditions also dispersal limitation across different continents and/or historical environmental conditions might influence AOA biogeography in soils.

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Wiley

Tập 14 Số 2

525-539

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