ENVIRONMENTAL BIOTECHNOLOGY Co-occurrence of nitrite-dependent anaerobic ammonium and methane oxidation processes in subtropical acidic forest soils Han Meng 1 & Yong-Feng Wang 2,3 & Ho-Wang Chan 1 & Ruo-Nan Wu 1 & Ji-Dong Gu 1 Received: 21 March 2016 /Revised: 24 April 2016 /Accepted: 27 April 2016 /Published online: 13 May 2016 # Springer-Verlag Berlin Heidelberg 2016 Abstract Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) are two new processes of recent discoveries linking the microbial nitrogen and carbon cycles. In this study, 16S ribosomal RNA (rRNA) gene of anammox bacteria and pmoA gene of n-damo bacteria were used to investigate their distribution and diversity in natural acidic and re-vegetated forest soils. The 16S rRNA gene sequences retrieved featured at least three species in two genera known anammox bacteria, namely Candidatus Brocadia anammoxidans, Candidatus Brocadia fulgida, and Candidatus Kuenenia stuttgartiensis while the pmoA gene amplified was affiliated with two species of known n-damo bacteria Candidatus Methylomirabilis oxyfera and a newly established Candidatus Methylomirabilis sp. According to the results, the diversity of anammox bacteria in natural forests was lower than in re-vegetated forests, but no significant difference was ob- served in n-damo community between them. Quantitative real- time PCR showed that both anammox and n-damo bacteria were more abundant in the lower layer (10–20 cm) than the surface layer (0–5 cm). The abundance of anammox bacteria varied from 2.21 × 10 5 to 3.90 × 10 6 gene copies per gram dry soil, and n- damo bacteria quantities were between 1.69 × 10 5 and 5.07 × 10 6 gene copies per gram dry soil in the two different layers. Both anammox and n-damo bacteria are reported for the first time to co-occur in acidic forest soil in this study, providing a more comprehensive information on more defined microbial processes contributing to C and N cycles in the ecosystems. Keywords Anammox bacteria . N-damo bacteria . pmoA gene . Forest soil . Carbon cycle . Nitrogen cycle Introduction Anaerobic ammonium oxidation (anammox) process, the ox- idation of ammonium to dinitrogen (N 2 ) gas using nitrite as an electron acceptor under anoxic conditions, was first discov- ered in a denitrifying fluid reactor nearly 20 years ago (Mulder et al. 1995; Van de Graaf et al. 1995). The discovery changes the traditional knowledge that oxidation of ammonium occurs only under aerobic conditions. Currently, five genera, Candidatus Kuenenia (Chamchoi and Nitisoravut 2007; Egli et al. 2001; Schmid et al. 2000; Strous et al. 2006), Candidatus Brocadia (Jetten 2001; Kartal et al. 2008), Candidatus Scalindua (Kindaichi et al. 2007 ), Candidatus Anammoxglobus (Kartal et al. 2007), and Candidatus Jettenia (Quan et al. 2008) and a total of 13 species of anammox bacteria, have been established through culture in- dependent approaches. All obtained anammox bacteria belong to the phylum of Planctomycetes (Strous et al. 1999). Since 1995, anammox bacteria have been reported as dis- tributed widely in various ecosystems, such as marine system (Dalsgaard et al. 2003; Dalsgaard et al. 2005); freshwater Electronic supplementary material The online version of this article (doi:10.1007/s00253-016-7585-6) contains supplementary material, which is available to authorized users. * Ji-Dong Gu jdgu@hku.hk 1 Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People’ s Republic of China 2 Guangdong Provincial Key Laboratory of Bio-control for the Forest Disease and Pest, Guangdong Academy of Forestry, No. 233, Guangshan 1st Road, Guangzhou, People’ s Republic of China 3 Laboratory of Microbial Ecology and Toxicology, Guangdong Academy of Forestry, No. 233, Guangshan 1st Road, Guangzhou, People’ s Republic of China Appl Microbiol Biotechnol (2016) 100:7727–7739 DOI 10.1007/s00253-016-7585-6