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

Abstract

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrogen cycling. However, the effects of environmental factors on the activity, abundance, and diversity of AOA and AOB and the relative contributions of these two groups to nitrification in paddy soils are not well explained. In this study, potential nitrification activity (PNA), abundance, and diversity of amoA genes from 12 paddy soils in Southern China were determined by potential nitrification assay, quantitative PCR, and cloning. The results showed that PNA was highly variable between paddy soils, ranging from 4.05 ± 0.21 to 9.81 ± 1.09 mg NOx-N kg(-1) dry soil day(-1), and no significant correlation with soil parameters was found. The abundance of AOA was predominant over AOB, indicating that AOA may be the major members in aerobic ammonia oxidation in these paddy soils. Community compositions of AOA and AOB were highly variable among samples, but the variations were best explained by pH. AOA sequences were affiliated to the Nitrosopumilus cluster and Nitrososphaera cluster, and AOB were classified into the lineages of Nitrosospira and Nitrosomonas, with Nitrosospira being predominant over Nitrosomonas, accounting for 83.6 % of the AOB community. Moreover, the majority of Nitrosomonas was determined in neutral soils. Canonical correspondence analysis (CCA) analysis further demonstrated that AOA and AOB community structures were significantly affected by pH, soil total organic carbon, total nitrogen, and C/N ratio, suggesting that these factors exert strong effects on the distribution of AOB and AOA in paddy soils in Southern China. In conclusion, our results imply that soil pH was a key explanatory variable for both AOA and AOB community structure and nitrification activity.

Ammonia Oxidizing Archaea and Bacteria in East Asian Paddy Soils—A Mini Review

“…As Jing [27] observed, the increase in pH from 4.4 to 6.4 resulted in an increase of archaeal amoA gene abundance in paddy soil. These results were further supported by a study on paddy soils from southern China, showing that AOA abundance significantly increased with increasing pH in acidic and neutral paddy soils [25]. Taken together, however, these results seem to suggest that while both groups benefit from moderate conditions, relatively favorable edaphic conditions, i.e., neutral pH and an abundance of nutrients, seem to benefit bacteria disproportionately.…”

“…Finally, the third grouping includes the results of three studies with extremely high AOA/AOB ratios, above 300. As can be seen, two of these studies have acidic soils [10,25], whereas the other has a relatively alkaline soil with high levels of ammonium [23]. Table 1).…”

“…The effects of a wide range of factors on the nitrification processes in paddy soils have been discussed, such as soil types [23], availability of ammonium [15,16] and pH levels [24,25]. Although the importance of AOA and AOB in paddy soil has been extensively explored, microbial contribution to nitrification and microbial response to environmental factor are poorly understood [25,26]. Therefore, this mini-review summarizes some recent findings on the abundance, composition, relative importance, metabolic activity, and environmental factors that affect the distribution of AOA and AOB in East Asian paddy soils.…”

“…Numerous factors affect nitrification mechanisms and microbial communities associated with AOA and AOB in soil, such as habitat type, soil temperature, soil pH and the application of nitrogen fertilizers [17][18][19][20][21][22]. The effects of a wide range of factors on the nitrification processes in paddy soils have been discussed, such as soil types [23], availability of ammonium [15,16] and pH levels [24,25]. Although the importance of AOA and AOB in paddy soil has been extensively explored, microbial contribution to nitrification and microbial response to environmental factor are poorly understood [25,26].…”

pH rather than nitrification and urease inhibitors determines the community of ammonia oxidizers in a vegetable soil

“…Nicol et al (2008) confirmed that soil pH determined the phylotype distribution of bacterial and archaeal ammonia oxidizers. Li et al (2015) also reported that the ammonia oxidizers community structure and nitrification activity were significantly affected by soil pH. The aim of our work was to investigate the short-term effects of nitrapyrin and NBPT on nitrification and the abundance and community structure of AOA and AOB in a vegetable soil across a pH-gradient.…”