Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil

Abstract

Nitrification is a fundamental component of the global nitrogen cycle and leads to significant fertilizer loss and atmospheric and groundwater pollution. Nitrification rates in acidic soils (pH < 5.5), which comprise 30% of the world's soils, equal or exceed those of neutral soils. Paradoxically, autotrophic ammonia oxidizing bacteria and archaea, which perform the first stage in nitrification, demonstrate little or no growth in suspended liquid culture below pH 6.5, at which ammonia availability is reduced by ionization. Here we report the discovery and cultivation of a chemolithotrophic, obligately acidophilic thaumarchaeal ammonia oxidizer, “ Candidatus Nitrosotalea devanaterra,” from an acidic agricultural soil. Phylogenetic analysis places the organism within a previously uncultivated thaumarchaeal lineage that has been observed in acidic soils. Growth of the organism is optimal in the pH range 4 to 5 and is restricted to the pH range 4 to 5.5, unlike all previously cultivated ammonia oxidizers. Growth of this organism and associated ammonia oxidation and autotrophy also occur during nitrification in soil at pH 4.5. The discovery of Nitrosotalea devanaterra provides a previously unsuspected explanation for high rates of nitrification in acidic soils, and confirms the vital role that thaumarchaea play in terrestrial nitrogen cycling. Growth at extremely low ammonia concentration (0.18 nM) also challenges accepted views on ammonia uptake and metabolism and indicates novel mechanisms for ammonia oxidation at low pH.

Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils

“…Growth of N. maritimus was observed at an ammonium substrate threshold below 10 nM at pH 7.5, which is significantly lower than the minimum concentration required by cultivated AOB (above 1 mM near neutral pH; Bollmann et al, 2002), indicating a higher substrate affinity than AOB in ammonialimited conditions. The recent cultivated thaumarchaeon, N. devanaterra, from an acidic soil could also autotrophically grow at remarkably low ammonia concentration (0.18 nM in liquid batch culture at pH 4.5) (Lehtovirta et al, 2011). Assuming ammonia rather than ammonium could serve as the direct substrate for ammonia oxidizers (Suzuki et al, 1974), strongly acidic soils might be perceived as ammonia-limited oligotrophic environments, due to exponential ionization of ammonia to ammonium with decreasing pH (NH 3 þ H þ 3NH 4 þ ; pK a ¼ 9.25) (De Boer and Kowalchuk, 2001).…”

“…Although the soil-isolated AOA strain, Nitrososphaera viennensis, revealed a relatively higher tolerance of ammonia substrates than marine isolate, it is still considerably lower than the reported maximum ammonia tolerance of AOB strains (Tourna et al, 2011). Very recently, an obligate acidophilic thaumarchaeal ammonia oxidizer was enriched from an acidic agricultural soil, demonstrating the autotrophic growth of ammoniaoxidizing thaumarchaea at extremely low ammonia concentration (Lehtovirta et al, 2011). These findings were supported by soil microcosm experiments where autotrophic ammonia oxidation was driven mainly by AOA rather than AOB under low ammonia conditions without external nitrogen supply (Offre et al, 2009;Zhang et al, 2010).…”

Abundance and community structure of ammonia oxidizing bacteria and archaea in a Sweden boreal forest soil under 19-year fertilization and 12-year warming

“…Microbial ammonia oxidation has been thought to be solely carried out by bacteria before an ammonia-oxidizing archaeon (AOA) was reported (Könneke et al 2005). More recently, two species of thaumarchaeota were isolated from a garden soil (Tourna et al 2011) and an acid soil (Lehtovirta-Morley et al 2011). To date, AOA have been found in various soils, where they outnumbered ammonia-oxidizing bacteria (AOB) (Leininger et al 2006;He et al 2007;Zhang et al 2010).…”

Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils

“…Strains of soil ammonia-oxidizing archaea (AOA) in the clade Thaumarchaeota, which were cultivated in laboratories, were shown to be capable of growing as autotrophic ammonia oxidizers (Jung et al, 2011;Lehtovirta-Morley et al, 2011;Kim et al, 2012). The thaumarchaeotal I.1a, I.1a-associated and I.1b clades are frequently recognized as the dominant ammonia-oxidizing organisms in terrestrial environments, possibly because of their high affinity for NH 3 (Jung et al, 2011;Kim et al, 2012).…”