Effect of Soil Ammonium Concentration on N ₂ O Release and on the Community Structure of Ammonia Oxidizers and Denitrifiers

Abstract

The effect of ammonium addition (6.5, 58, and 395 g of NH 4 ؉ -N g [dry weight] of soil ؊1 ) on soil microbial communities was explored. For medium and high ammonium concentrations, increased N 2 O release rates and a shift toward a higher contribution of nitrification to N 2 O release occurred after incubation for 5 days at 4°C. Communities of ammonia oxidizers were assayed after 4 weeks of incubation by denaturant gradient gel electrophoresis (DGGE) of the amoA gene coding for the small subunit of ammonia monooxygenase. The DGGE fingerprints were invariably the same whether the soil was untreated or incubated with low, medium, or high ammonium concentrations. Phylogenetic analysis of cloned PCR products from excised DGGE bands detected amoA sequences which probably belonged to Nitrosospira 16S rRNA clusters 3 and 4. Additional clones clustered with Nitrosospira sp. strains Ka3 and Ka4 and within an amoA cluster from unknown species. A Nitrosomonas-like amoA gene was detected in only one clone. In agreement with the amoA results, community profiles of total bacteria analyzed by terminal restriction fragment length polymorphism (T-RFLP) showed only minor differences. However, a community shift occurred for denitrifier populations based on T-RFLP analysis of nirK genes encoding copper-containing nitrite reductase with incubation at medium and high ammonia concentrations. Major terminal restriction fragments observed in environmental samples were further described by correspondence to cloned nirK genes from the same soil. Phylogenetic analysis grouped these clones into clusters of soil nirK genes. However, some clones were also closely related to genes from known denitrifiers. The shift in the denitrifier community was probably the consequence of the increased supply of oxidized nitrogen through nitrification. Nitrification activity increased upon addition of ammonium, but the community structure of ammonium oxidizers did not change.

Responses of soil nitrous oxide production and abundances and composition of associated microbial communities to nitrogen and water amendment

“…In the N treatment, the AOB community composition was significantly altered by ammonium addition in both soils. However, our result was inconsistent with previous study of Avrahami et al (2002) who reported that agricultural soils did not show any AOB community shifts under ammonium treatment with 4-6 weeks of incubation. This inconsistency might be attributed to higher ammonium level in our study, which could promote the growth of AOB in soils (Jia and Conrad 2009;Cui et al 2013).…”

Bacteria, not archaea, restore nitrification in a zinc-contaminated soil

“…However, at T2, bands 'h' and 'i 0 were most prominent in the AOB amoA community profile (Figure 3c). Sequence analysis revealed that all detected AOB amoA bands were affiliated with several sequence clusters within Nitrification in zinc-contaminated soil J Mertens et al the Nitrosospira lineage (Avrahami et al, 2002), and no clustering of sequences was observed with respect to the Zn tolerance of the community (Supplementary Figure 2).…”

Effect of pyrene on denitrification activity and abundance and composition of denitrifying community in an agricultural soil

“…Previous studies also showed that ammonium, fertilization, plant species, sampling time, water logging and temperature all temporarily altered the structure of nirK-harboring denitrifying community (Avrahami et al, 2002;Braker et al, 2010;Bremer et al, 2007;Wolsing and Priemé, 2004;Yoshida et al, 2009). The genetic shifts of the denitrifying community due to PAHs perturbation could be attributed to the inhibition of sensitive and the development of tolerant species (Leahy and Colwell, 1990;Ford, 1993;Whittaker, 1975).…”