Journal of Soils and Sediments (2019) 19:1416–1426 https://doi.org/10.1007/s11368-018-2109-x SOILS, SEC 5 • SOIL AND LANDSCAPE ECOLOGY • RESEARCH ARTICLE The relative contribution of nitrifiers to autotrophic nitrification across a pH-gradient in a vegetable cropped soil Yaying Li1,2 & Ruijiao Xi1,2,3 & Weijin Wang4 & Huaiying Yao1,2,5 Received: 1 June 2018 /Accepted: 9 August 2018 /Published online: 15 August 2018 # Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Purpose Microbial nitrification plays an important role in nitrogen cycling in ecosystems. Nitrification is performed by ammonia- oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) including complete ammonia oxidizers. However, the relative importance of nitrifiers in autotrophic nitrification in relation to soil pH is still unclear. Materials and methods Combining DNA-based stable isotope probing (SIP) and molecular biological techniques, we investigated the abundance, structure, and activity of AOA, AOB, and NOB along a pH-gradient (3.97–7.04) in a vegetable cropped soil. Results and discussion We found that AOA abundance outnumbered AOB abundance and had a significantly negative relation- ship with soil pH. The abundances of NOB Nitrospira 16S rRNA, nxrB gene, and Nitrobacter nxrA gene were affected by soil 13 13 pH. Incubation of soil with CO2 and DNA-SIP analysis demonstrated that significant CO2 assimilation by AOA rather than by AOB occurred in the acidic soils, whereas the labeled 13C level of AOA was much less in the neutral soil than in the acidic 13 soils. There was no evidence of CO2 assimilation by NOB except for Nitrobacter with NxrB gene at pH 3.97. Phylogenetic analysis of AOA amoA gene in the 13C- and 12C-labeled treatments showed that the active AOA mainly belonged to Nitrososphaera in the acidic soils. Conclusions These results suggested that the main performer of nitrification was AOA in the acidic soils, but both AOA and AOB participated in nitrification in the neutral soil with low nitrification activity. NOB Nitrospira and Nitrobacter did not grow in the soils with pH 4.82–7.04 and other populations of NOB were probably involved in nitrite oxidation in the vegetable cropped soil. Keywords Nitrifiers . Soil pH . Stable isotope probing . Vegetable soil 1 Introduction denitrification (Gruber and Galloway 2008). Among these steps, nitrification is very important in biogeochemical cycles, The processes of nitrogen cycling driven by microorganisms leading to nitrate loss and pollution (Zhao et al. 2010). include nitrogen fixation, ammoniation, nitrification, and Aerobic autotrophic nitrification is a two-step process driven Responsible editor: Yuan Ge Yaying Li and Ruijiao Xi contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11368-018-2109-x) contains supplementary material, which is available to authorized users. * Huaiying Yao 3 University of Chinese Academy of Sciences, Beijing 100049, [email protected] People’s Republic of China 1 Key Laboratory of Urban Environment and Health, Institute of Urban 4 Department of Science, Information Technology and Innovation, Environment, Chinese Academy of Sciences, Xiamen 361021, GPO Box 5078, Brisbane, QLD 4001, Australia People’s Republic of China 2 Ningbo Key Laboratory of Urban Environmental Processes and 5 Research Center for Environmental Ecology and Engineering, Pollution Control, Ningbo Urban Environment Observation and School of Environmental Ecology and Biological Engineering, Research Station—NUEORS, Chinese Academy of Sciences, Wuhan Institute of Technology, Wuhan 430073, People’sRepublic Ningbo 315800, People’s Republic of China of China J Soils Sediments (2019) 19:1416–1426 1417 by ammonia oxidizers and nitrite oxidizers, respectively. studies showed that AOA accounts for about 10% of the total However, recent studies suggested that some species of quantity of soil microorganisms, and that AOA amoA gene Nitrospira can conduct complete ammonia oxidation copies were up to 3000-fold more abundant than AOB amoA (comammox) (Hu and He 2017). Ammonia oxidation is the gene copies (Leininger et al. 2006). Nonetheless, these obser- first step in which ammonia is oxidized to nitrite, also the vations do not definitively mean that ammonia oxidation is rate-limiting step of nitrification. It is carried out by exclusively or mainly governed by AOA as implied by the chemolithoautotrophic AOB and AOA by the key enzyme, extremely high abundance (Jia and Conrad 2009;Souza ammonia mono-oxygenase (AMO). AOB was previously be- 2009). A previous study on agricultural soil found close cor- lieved to be the exclusive performer in microbial ammonia ox- relation between the activity of ammonia oxidation and AOB idation until the discovery of AOA and archaeal amoA gene (de amoA gene abundance, and observed incorporation of 13C- Boer and Kowalchuk 2001; Venter et al. 2004). Recent investi- CO2 into the AOB amoA gene, but not AOA (Jia and gation into the amoA gene revealed that this gene encodes the Conrad 2009). In addition, a study of long-term field experi- first subunit of AMO enzyme, and that AOA, in addition to mental plots revealed that AOA had higher abundance com- AOB, play a main role in ammonia oxidation in acidic soil or pared with AOB in all the treatments. However, the two types infertile soil (Leininger et al. 2006;Heetal.2007). of ammonia oxidizers had significant positive relationships AOA and AOB are widely distributed in terrestrial systems. with potential nitrification rates, demonstrating that both They are found in paddy soil, vegetable soil, seawater, sedi- AOA and AOB drove the process of autotrophic ammonia ment, wetland, rhizosphere soil, and hot spring (Francis et al. oxidation (He et al. 2007). 2005;Chenetal.2008; Santoro and Casciotti 2011;Zhanget The second step of nitrification is nitrite oxidation. In this al. 2011; Lee et al. 2014). The two groups of ammonia oxi- step, nitrite is oxidized to nitrate by enzyme nitrite oxidoreduc- dizers are different in cellular biochemistry and physiology, tase (NXR), which is mediated by nitrite-oxidizing bacteria which cause the differential of abundance and community (NOB). Because ammonia oxidation is the rate-limiting step, structure of ammonia oxidizers in different agroecosystems the second step is often given little attention. NOB are classified (Shen et al. 2008; Yao et al. 2011;Heetal.2012). Many factors into four genera, namely Nitrobacter, Nitrospira, Nitrococcus, can affect ammonia oxidizers, such as soil pH, oxygen and and Nitrospina. Among them, research into Nitrobacter and substrate concentration, temperature, etc. (Santoro et al. 2008; Nitrospira has dominated (Bartosch et al. 2002; Freitag et al. Shen et al. 2008; Morimoto et al. 2011). Among them, soil pH 2005). Unlike ammonia oxidizers, target-specific 16S rRNA is an important driver of ammonia oxidizer activity, abundance, primers to NOB are not available for complicated environment and community structure (Stephen et al. 1998; Nicol et al. systems (Freitag et al. 2005,Lietal.2018). In contrast, 16S 2008). Hu et al. (2013) confirmed that the distribution of rRNA primers and nxrB primers can be successfully used to AOA and AOB was driven by soil pH, and the AOA/AOB target Nitrospira strains (Pester et al. 2014), and nxrA (Poly et ratio decreased with an increase in soil pH. They used 65 soil al. 2008)ornxrB (Pester et al. 2014) is widely used for studying samples collected from different regions and found that AOA Nitrobacter groups in soil. The NXR active site in Nitrobacter had a competitive advantage over AOB. Nicol et al. (2008) is cytoplasmic-orientated, whereas the NXR active site in found that the AOA amoA gene abundance decreased with Nitrospira faces the periplasm (Spieck and Bock 2005; increasing soil pH, while AOB amoA gene abundance gener- Sorokin et al. 2012). The difference of adaptation and niche ally increased with increasing pH. Generally, the quantity of differentiation among NOB species could be due to the differ- AOA is greater than the quantity of AOB in acidic soils, dem- ent membrane orientations of the active site of NXR (Spieck onstrating that AOA has a stronger ability to adapt to low pH and Bock 2005). Previously, most of the researches focused on habitats (Leininger et al. 2006). Nitrobacter and suggested that Nitrobacter played a main role Relative contribution of AOA and AOB to ammonia oxi- in nitrite oxidation, but recent studies suggest Nitrospira may dation depends on soil conditions and ecosystems (Prosser be of significant importance as well. and Nicol 2008). Autotrophic AOB has been adjudged the DNA-SIP technique has been successfully used to link mi- foremost contributor to ammonia oxidation before (Purkhold croorganisms to specific functions within different ecosystems 13 et al. 2000;Bocketal.2006). However, the contribution of (Radajewski et al. 2000; Uhlík et al. 2009). Lately, CO2- AOA to autotrophic nitrification should not be underestimated DNA-SIP experiments persuasively linked autotrophic nitrifi- in light of amoA gene and AOA research (Yao et al. 2011; cation activity and ammonia oxidizers together in an acidic Zhang et al. 2011 ). Yao et al. (2011) found that AOAwas more soil (Lehtovirta-Morley et al. 2011), whereas previously, this abundant than AOB in Chinese tea orchard soils. In addition, was only shown in the neutral sediment of lakes (Whitby et al. soil nitrification potential and AOA abundance