Abstract
High and low rates of ammonium supply are believed to favour ammonia-oxidising bacteria (AOB) and archaea (AOA), respectively. Although their contrasting affinities for ammonium are suggested to account for these differences, the influence of ammonia concentration on AOA and AOB has not been tested under environmental conditions. In addition, while both AOB and AOA contribute to nitrous oxide (N2O) emissions from soil, N2O yields (N2O–N produced per NO2−–N generated from ammonia oxidation) of AOA are lower, suggesting lower emissions when AOA dominate ammonia oxidation. This study tested the hypothesis that ammonium supplied continuously at low rates is preferentially oxidised by AOA, with lower N2O yield than expected for AOB-dominated processes. Soil microcosms were supplied with water, urea or a slow release, urea-based fertiliser and 1-octyne (inhibiting only AOB) was applied to distinguish AOA and AOB activity and associated N2O production. Low ammonium supply, from mineralisation of organic matter, or of the fertiliser, led to growth, ammonia oxidation and N2O production by AOA only, with low N2O yield. High ammonium supply, from free urea within the fertiliser or after urea addition, led to growth of both groups, but AOB-dominated ammonia oxidation was associated with twofold greater N2O yield than that dominated by AOA. This study therefore demonstrates growth of both AOA and AOB at high ammonium concentration, confirms AOA dominance during low ammonium supply and suggests that slow release or organic fertilisers potentially mitigate N2O emissions through differences in niche specialisation and N2O production mechanisms in AOA and AOB.
Highlights
IntroductionAttempts have been made to explain this by higher affinity for NH3 in AOA, based on reported lower Km values (0.13–0.69 μM total ammonia nitrogen (TAN, NH3 + NH4+) for cultured marine and soil AOA [19,20,21] than those for ammonia-oxidising bacteria (AOB), which are 2–4 orders of magnitude higher [22,23,24]
Microbes play central roles in global biogeochemical cycles but, despite evidence for niche differentiation, it is often difficult to identify and quantity the consequences of microbial community composition for rates of Electronic supplementary material The online version of this article contains supplementary material, which is available to authorised users.There is some evidence for niche differentiation between archaeal and bacterial NH3 oxidisers (AOA and ammonia-oxidising bacteria (AOB)), which are major players in soil NH3 oxidation [6, 7]
Evidence for this arose from correlations of AOA and AOB relative abundances in soils subjected to different fertiliser regimes [14,15,16,17], lack of stimulation of NH3 oxidation by supply of relatively high concentrations of inorganic NH4+, but stimulation by organic nitrogen in AOA-dominated soils [30, 49], and higher relative abundances of AOA where NH4+ is typically derived from mineralisation of native organic nitrogen [11, 30]
Summary
Attempts have been made to explain this by higher affinity for NH3 in AOA, based on reported lower Km values (0.13–0.69 μM total ammonia nitrogen (TAN, NH3 + NH4+) for cultured marine and soil AOA [19,20,21] than those for AOB, which are 2–4 orders of magnitude higher [22,23,24] While this provides a compelling explanation for numerical dominance of AOA in oceans, where TAN concentrations are in the nM range, it is less convincing in soil where bulk TAN concentrations are above the range of Km values for both AOA and AOB. An alternative explanation is greater sensitivity of AOA to inhibition by high NH4+ concentration, based on studies of relatively few cultured AOA, but the recently isolated and enriched AOA Candidatus Nitrosocosmicus species [27,28,29] can grow at NH3 concentrations that inhibit other cultured AOA, with Candidatus
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