pH-dominated niche segregation of ammonia-oxidising microorganisms in Chinese agricultural soils

Abstract

Ammonia-oxidising archaea (AOA) are increasingly recognised as the primary mediators of soil ammonia oxidation, particularly in acidic soils. To explore the niche segregation of AOA and ammonia-oxidising bacteria (AOB) and the potential effect of this segregation on nitrification rates and the nitrogen cycle in Chinese agricultural soils, AOA and AOB amoA gene databases were established, and 454 high-throughput sequencing was used to investigate the key factors leading to the niche segregation of these two types of microorganisms. qPCR results demonstrated that there were more functional genes for AOA than for AOB in most of the soils. AOA diversity was higher than AOB diversity in most of the soils with AOA operational taxonomic units (OTU) numbers ranging from 40 to 169 and AOB OTU numbers ranging from 18 to 105. pH was the most important factor influencing the community structure of AOA (P < 0.01) and AOB (P < 0.05), and acidophilic AOA (i.e. Nitrosotalea-related sequences) were dominant in soils with pH values below 6.0. In addition, AOA amoA gene copy numbers were significantly positively correlated with pH (P < 0.05), the ratio of AOA OTU numbers/AOB OTU numbers was significantly negatively correlated with pH (P < 0.05), and the percentage of sequences represented by the Nitrosotalea cluster was significantly negatively correlated with pH (P < 0.01).

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

“…Archaeal amoA abundance and the ratio of AOA/archaeal 16S rRNA increased significantly with increasing pH, indicating that pH plays an important role in controlling AOA abundance in acidic and neutral paddy soils. Moreover, the ratio of AOA/ AOB amoA gene copy numbers ranged from 1.91 to 1048, which was consistent the ratio of AOA/AOB in previous studies (Leininger et al 2006;Shen et al 2008;Hu et al 2014), implying that indicating that AOA may be the major members in aerobic ammonia oxidation in these paddy soils. Zhang et al (2012) also indicated that AOA have more prominent role in ammonia oxidation in acidic soils, which means that acidic condition is more beneficial to AOA than AOB.…”

“…Further analysis via CCA also illustrated that soil SOC, TN, and the ratio of C/N were correlated with AOA abundance and consistent with the previous studies (Li et al 2014;Wu et al 2011). The abundance of AOA rather than AOB was influenced by soil properties in these paddy soils, especially pH, indicating that AOA were more sensitive to soil characteristics (Hu et al 2014;Chen et al 2011).…”

“…Among these factors, increasing lines of evidence has suggested that soil pH plays the most dominant role in controlling the abundance and distribution of AOA and shaping the distinct ecological niches of AOA and AOB. Diverse researches have elaborated the microbial community composition and abundance of AOA and their bacterial counterparts AOB in various ecosystems (Chen et al 2008(Chen et al , 2010(Chen et al , 2011He et al 2007;Yao et al 2011;Li et al 2011;Pester et al 2012;Shen et al 2012;Hu et al 2013Hu et al ,2014Long et al 2014;Wang et al 2015;Jiang et al 2015). However, most of these investigations focused on a locational samples or a limited number of soil samples.…”

“…However, most of these investigations focused on a locational samples or a limited number of soil samples. To our knowledge, rare researches have been carried out to directly compare the large-scale distribution patterns of AOA and AOB in China (Hu et al 2013(Hu et al , 2014, which are of significant importance to decipher the niche differentiation of these two microbial communities. Furthermore, no study has performed investigations on the activity together with the diversity of AOA and AOB in paddy soils in a large scale.…”

Potential correlated environmental factors leading to the niche seg- regation of ammonia-oxidizing archaea and ammonia-oxidizing bac- teria: A review

“…AOB, however, exhibited the opposite and the copy numbers and transcriptional abundance of AOB amoA genes were less than that of AOA by two orders of magnitudes . In most acid soils, the abundance of AOA was more than that of AOB, suggesting a greater adaptability of AOA to live in the acid environment (Gan et al, 2016;He et al, 2007;Hu et al, 2014;Leininger et al, 2006;Norman and Barrett, 2016;Stempfhuber et al, 2015). In a peaty soil with a pH value of 4.1, the abundance of AOB amoA genes was below the detection limit while the abundance of AOA increased as the incubation went on.…”