Abstract
In the last years, archaea have been identified as key players in global N cycling, especially in nitrification. Ammonia-oxidizing archaea (AOA) are postulated to belong to the new phylum Thaumarchaeota for which the lipid crenarchaeol should be specific. The ratios between two independent markers for AOA, the ammonia monooxygenase gene and crenarchaeol have been studied in different aerated soils, but so far not in flooded soils. This study investigated ammonia-oxidizing archaea in four paddy soils and a tidal wetland. Ratios were significantly higher in the paddy soils compared to the tidal wetland and in general higher as in upland soils, leading to the assumption that archaeal ammonia oxidizers different from crenarchaeol-containing Thaumarchaeota may play an important role in paddy soils.
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References
Chen S, Huang Y, Zou J (2008) Relationship between nitrous oxide emission and winter wheat production. Biol Fertil Soils 44:985–989
Cheng Y-Q, Yang L-Z, Cao Z-H, Ci E, Yin S (2009) Chronosequential changes of selected pedogenic properties in paddy soils as compared with non-paddy soils. Geoderma 151:31–41
De Rosa M, Gambacorta A (1988) The lipids of Archaebacteriaea. Prog Lipid Res 27:153–175
Erguder TH, Boon N, Wittebolle L, Marzorati M, Verstraete W (2009) Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiol Rev 33:855–869
Gattinger A, Bausenwein U, Bruns C (2004) Microbial biomass and activity in composts of different composition and age. J Plant Nutr Soil Sci Z Pflanzenernahrung Bodenkunde 167:556–561
Gubry-Rangin C, Nicol GW, Prosser JI (2010) Archaea rather than bacteria control nitrification in two agricultural acidic soils. FEMS Microbiol Ecol 74:566–574
Harvey HR, Macko SA (1997) Kinetics of phytoplankton decay during simulated sedimentation: changes in lipids under oxic and anoxic conditions. Org Geochem 27:129–140
Kuypers MMM, Blokker P, Erbacher J, Kinkel H, Pancost RD, Schouten S, Damste JSS (2001) Massive expansion of marine archaea during a mid-Cretaceous oceanic anoxic event. Science 293:92–94
Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806–809
Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362:709–715
Neue HU, Gaunt JL, Wang ZP, BeckerHeidmann P, Quijano C (1997) Carbon in tropical wetlands. Geoderma 79:163–185
Nicol GW, Leininger S, Schleper C, Prosser JI (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microb 10:2966–2978
Pietramellara G, Ascher J, Borgogni F, Ceccherini M, Guerri G, Nannipieri P (2009) Extracellular DNA in soil and sediment: fate and ecological relevance. Biol Fertil Soils 45:219–235
Poinar HN, Hoss M, Bada JL, Paabo S (1996) Amino acid racemization and the preservation of ancient DNA. Science 272:864–866
Reigstad LJ, Richter A, Daims H, Urich T, Schwark L, Schleper C (2008) Nitrification in terrestrial hot springs of Iceland and Kamchatka. FEMS Microbiol Ecol 64:167–174
Schleper C, Jurgens G, Jonuscheit M (2005) Genomic studies of uncultivated archaea. Nat Rev Microbiol 3:479–488
Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P, Spieck E, Streit W, Stahl DA, Wagner M, Schleper C (2010) Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol 18:331–340
Töwe S, Albert A, Kleineidam K, Brankatschk R, Dümig A, Welzl G, Munch J, Zeyer J, Schloter M (2010) Abundance of microbes involved in nitrogen transformation in the rhizosphere of Leucanthemopsis alpina (L.) heywood grown in soils from different sites of the Damma Glacier Forefield. Microb Ecol 60:762–770
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu DY, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74
Willerslev E, Hansen AJ, Poinar HN (2004) Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends Ecol Evol 19:141–147
Wrage N, Velthof GL, van Beusichem ML, Oenema O (2001) Role of nitrifier denitrification in the production of nitrous oxide. Soil Biol Biochem 33:1723–1732
Zhang M, Lu H, Zhao X, Li R (2004) A comparative study of fertility change of upland soil in Cixi County. Chin J Soil Sci 35:91–93
Zou P, Fu J, Cao Z (2011) Chronosequence of paddy soils and phosphorus sorption–desorption properties. J Soils Sediments 11:249–259
Acknowledgments
We thank Gudrun Hufnagel for excellent technical support in measuring ammonium and nitrate concentrations. Dr. Kai Mangelsorf, GFZ Potsdam is thanked for access to LC/MS/MS instrumentation. Many thanks also to Adrian Ho and Peter Frenzel for their help during soil sampling. We also thank the reviewers of the manuscript and the editor of Biol Fertil Soils for their valuable input. Financial support was provided by the German Research Foundation DFG. This paper represents a contribution to the DFG FOR 995 Biogeochemistry of paddy soil evolution.
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Bannert, A., Mueller-Niggemann, C., Kleineidam, K. et al. Comparison of lipid biomarker and gene abundance characterizing the archaeal ammonia-oxidizing community in flooded soils. Biol Fertil Soils 47, 839–843 (2011). https://doi.org/10.1007/s00374-011-0552-6
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DOI: https://doi.org/10.1007/s00374-011-0552-6