Nitrification–denitrification dynamics and community structure of ammonia oxidizing bacteria in a high yield irrigated Philippine rice field

Abstract

Nitrogen is the single most limiting factor for rice production. Detailed knowledge on nitrogen dynamics in rice fields is therefore of major importance for developing sustainable rice production. A combination of state-of-the-art microsensor, stable isotope tracer, and molecular techniques was used to evaluate coupled nitrification-denitrification potentials and community structure of ammonia-oxidizing bacteria in a high yield irrigated rice cropping system in the Philippines, without the use of microcosm incubations. The multiple approaches showed a high degree of concordance among methods and thereby clarified the investigated processes. Numbers and potential activity of ammonia-oxidizing bacteria in the system reflected the availability of substrate in three defined soil factions with a ranking of: surface soil > rhizosphere > bulk soil. No nitrification activity was measured between spit applications of N fertilizer. However, nitrification was induced upon nitrogen amendment in intact soil cores. Despite induction by nitrogen amendment, the loss of nitrogen through coupled nitrification-denitrification was less than 10% of the plant nitrogen uptake. Denaturant gradient gel electrophoresis of amoA fragments revealed no differences in diversity profiles between the soil fractions, and phylogenetic analysis, based on amoA genes retrieved from the rice paddy soil, identified a set of mutually very similar sequences related to Nitrosomonas nitrosa.

Effect of Different Ammonia Concentrations on Community Succession of Ammonia-oxidizing Microorganisms in a Simulated Paddy Soil Column

“…In the present study, the highest ratio of AOA/AOB was found to be 12.96 in the second stage in the surface layer. The growth and ammonia oxidation activity of Nitrosopumilus maritimus were inhibited at an ammonia concentration of 28 mg/L [28] which was lower than the inhibitory concentrations (7000–14000 mg/L) of ammonia found for AOB [47]. Therefore, it was expected that the numbers of bacterial amoA gene copies would exceed the archaeal amoA gene copy numbers in the surface layer during the last stage, where the ammonia concentration was the highest.…”

pH regulates ammonia-oxidizing bacteria and archaea in paddy soils in Southern China

“…In addition, Nitrosomonas were detected only in GL, GZ, HB, SC, and TY soils, although in some cases, the Nitrosomonas are predominant over Nitrosospira (Nicolaisen et al 2004;Wang et al 2009). This might be due to the increase of pH value ) as described previously.…”

pH regulates key players of nitrification in paddy soils

“…For instance, it has been reported that net nitrification was about 18 mg N kg À1 d À1 for a paddy soil with a pH of 8.3, but a lower range from 3 to 6 mg N kg À1 d À1 for an acidic paddy soil with a pH of 6.2 (Lan et al, 2014). In fact, nitrification in rice fields have shown a wide range from 6 to 10 mg N kg À1 d À1 in Japan (Nishio et al, 1994), and 9.4e18 mg N kg À1 d À1 (Nicolaisen et al, 2004) in Europe. Nitrification activities in paddy fields are usually higher than in wetlands from 1.0 to 4.5 mg N kg À1 d À1 (BedardHaughn et al, 2006), in part due to intensive fertilization of the paddy fields.…”