Dynamics of ammonia-oxidizing communities in barley-planted bulk soil and rhizosphere following nitrate and ammonium fertilizer amendment

Abstract

Oxidation of ammonia by nitrifying microorganisms is a major pathway that fertilizer nitrogen (N) may take upon application to agricultural soils, but the relative roles of bacterial (AOB) vs. archaeal (AOA) ammonia oxidizers are controversial. We explored the effects of various forms of mineral N fertilizer on the AOB and AOA community dynamics in two different soils planted with barley. Ammonia oxidizers were monitored via real-time PCR and terminal restriction fragment length polymorphism analysis of bacterial and archaeal amoA genes following the addition of either [NH 4 ] 2 SO 4 , NH 4 NO 3 or KNO 3 . AOB and AOA communities were also studied specifically in the rhizospheres of two different barley varieties upon [NH 4 ] 2 SO 4 vs. KNO 3 addition. AOB changed in community composition and increased in abundance upon ammonium amendment in bulk soil and rhizosphere, with changes in bacterial amoA copy numbers lagging behind relative to changes in soil ammonium. In both soils, only T-RFs corresponding to phylotypes related to Nitrosospira clade 3a underwent significant community changes. Increases in AOB abundance were generally stronger in the bulk soil than in the rhizosphere, implying significant ammonia uptake by plant roots. AOA underwent shifts in the community composition over time and fluctuated in abundance in all treatments irrespective of ammonia availability. AOB were thus considered as the main agents responsible for fertilizer ammonium oxidation, while the functions of AOA in soil N cycling remain unresolved.

Relationships between ammonia-oxidizing communities, soil methane uptake and nitrous oxide fluxes in a subtropical plantation soil with nitrogen enrichment

“…These indicate that the effects on soil ammonia-oxidizer communities in the subtropical plantation are stronger by deposited NH 4 þ À N than by deposited NO 3 À À N. First, it is because NH 4 þ -N fertilization directly increases soil NH 4 þ À N levels, and NH 4 þ /NH 3 serves as the direct substrate to ammonia monooxygense in NH 3 oxidation [50]. On the contrary, several studies documented that both NH 4 þ À N and NO 3 À À N fertilizations increased soil AOB abundances in the alpine meadow [35], and the farmlands [32]. These inconsistent results could be attributed to the differences of climatic regions (warm-wet vs. colddry), soil pH (acid vs. alkaline), and initial status of soil mineral N (e.g., [40].…”

“…The effects of N additions on soil AOB abundance are controversial, including positive [30,34,35], negative [36], and neutral effects [27,28]. Moreover, few studies on the contrasting effects of soil NH 4 þ À N and NO 3 À À N enrichment on ammonia-oxidizer communities are available [37]. Few studies have investigated the relationships between ammonia-oxidizers and N 2 O emission in grassland [29,38] and agricultural soils [39].…”

Effect of chemical fertilization and green manure on the abundance and community structure of ammonia oxidizers in a paddy soil

“…They reported that the AOB abundance was more abundant in the N fertilization treatments than the control, AOA abundance decreased with increasing N fertilization rates. Glaser et al (2010) and Wu et al (2011) suggested that bacteria rather than archaea dominate ammonia oxidation in nearneutral or alkaline soils and in acidic soils, AOA play a more important role in ammonia oxidization (Zhang et al, 2012). From above literature reviews, it demonstrated that AOB and AOA may prefer to different ecological environments.…”

Impact of Short-Term Acidification on Nitrification and Nitrifying Bacterial Community Dynamics in Soilless Cultivation Media

“…Quantitative PCR (qPCR) targeting bacterial and archaeal amoA genes at selected time points of the incubation experiment was accomplished using an MX 3000 Real Time PCR system (Stratagene, La Jolla, CA). Amplification was carried out using the bacterial amoA primer set amoA1F/amoA2R and the archaeal amoA primer set Arch-amoAF/ Arch-amoAR (15). Standard curves for the archaeal and bacterial amoA genes were prepared by decimally diluting plasmids containing partial amoA amplicons to range from 10 9 to 100 copy numbers.…”