Ammonia-oxidizing bacteria are more responsive than archaea to nitrogen source in an agricultural soil

Abstract

In the majority of agricultural soils, ammonium (NH +) is rapidly converted to nitrate (NO 3-) in the biological ammonia and nitrite oxidation processes known as nitrification. The often rate-limiting step of ammonia oxidation to nitrite is mediated by ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA). The response of AOA and AOB communities to organic and conventional nitrogen (N) fertilizers, and their relative contributions to the nitrification process were examined for an agricultural silage corn system using a randomized block design with 4 N treatments: control (no additional N), ammonium sulfate (AS) fertilizer at 100 and 200 kg N ha-1 , and steer-waste compost (200 kg total N ha-1) over four seasons. DNA was extracted from the soil, and real-time PCR and 454-pyrosequencing were used to evaluate the quantity and diversity of the amoA gene which encodes subunit A of ammonia monooxygenase. Soil pH, nitrate pools, and nitrification potentials were influenced by ammonium and organic fertilizers after the first fertilization, while changes in AOB abundance and community structure were not apparent until after the second fertilization or later. The abundance of AOA was always greater than AOB but was unaffected by N treatments. In contrast, AOB abundance and community structure were changed significantly by ammonium fertilizers. Specific inhibitors of nitrification were used to evaluate the relative contribution of AOA and AOB to nitrification. We found that AOB dominantly contributed to potential nitrification activity determined at 1 mM ammonium in soil slurries and nitrification potential activity was higher in soils treated with ammonium fertilizers relative to control soils. However, AOA dominated gross nitrification activity in moist soils. Our result suggests that AOB activity and community are more responsive to ammonium fertilizers than AOA but that in situ nitrification rate is controlled by ammonium availability in this agricultural soil. Understanding this response of AOA and AOB to N fertilizers may contribute to improving strategies for the management of nitrate production in agricultural soils.

Effects of dicyandiamide and acetylene on N2O emissions and ammonia oxidizers in a fluvo-aquic soil applied with urea

“…6), confirming similar results obtained from various agricultural soils (Phillips et al 2000;Chu et al 2007;Ouyang et al 2016). It has been suggested that Nitrosospira cluster 3 often outcompeted other Nitrosospira under fertile soil conditions (Tourna et al 2010).…”

Nitrogen fertiliser-induced changes in N2O emissions are attributed more to ammonia-oxidising bacteria rather than archaea as revealed using 1-octyne and acetylene inhibitors in two arable soils

“…However, by characterising the conserved amoA gene, which encodes a subunit of the ammonia monooxygenase (AMO), it has been observed that the populations of ammonia oxidisers are largely controlled by soil type, NH 4 + concentration, pH and water content (Nicol et al 2008;Di et al 2009;Chen et al 2010;Norton and Stark 2011). In ammoniumrich soils, AOB abundance and activity increased whereas AOA abudance is unaffected or inhibited in response to a high concentration of ammonium fertilisers (Jia and Conrad 2009;Di et al 2009;Di and Cameron 2011;Sterngren et al 2015;Ouyang et al 2016). In unfertilised or acidic soils, AOA abundance and metabolic activity are much higher than those of AOB (Offre et al 2009;GubryRangin et al 2010;Zhang et al 2012).…”

“…Recently, it has been shown that AOB is more sensitive to 1-octyne, a C8 alkine inhibitor, compared with AOA (Taylor et al 2013(Taylor et al , 2015. Moreover, Lu et al (2015) and Ouyang et al (2016) distinguished AOB and AOA contribution to nitrification by using 1-octyne in soil microcosm incubation and found that 1-octyne selectively inhibited AOB growth rather than AOA in forest and arable soils. Therefore, we could use 1-octyne to assess the relative contribution of AOB and AOA to N 2 O emission from two different arable soils.…”

Potential correlated environmental factors leading to the niche seg- regation of ammonia-oxidizing archaea and ammonia-oxidizing bac- teria: A review

“…A series of ecological researches verified that AOA were more suitable to live with low substrate concentrations in different habitat types. In an agricultural soil whose nitrification rate was dominated by AOA out of low ammonium availability, ammonium fertilizers stimulated AOB activity and community more strongly than AOA (Ouyang et al, 2016). In a temperate forest soil where AOA significantly contribute to ammonia oxidation, substrate availability limits nitrification by AOB.…”

“…Some evidences showed that those environmental factors might have interrelationship (Figure 2). Strong ecological coherence was reflected between phylogeny and pH, or phylogeny and organic matter content for terrestrial Thaumarchaeota (Oton et al, 2016). This implied that pH and organic matter content might have some internal direct or indirect connection.…”