The first report of a microdiverse anammox bacteria community in waters of Colombian Pacific, a transition area between prominent oxygen minimum zones of the eastern tropical Pacific M. Castro-González, 1 * V. Molina, 2 E. Rodríguez-Rubio 3,4 and O. Ulloa 5 1 Laboratorio de Ecología Microbiana, Universidad del Tolima, Ibagué, Colombia. 2 Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile. 3 Centro de Investigaciones Oceanográficas e Hidrográficas del Pacífico, Tumaco, Colombia. 4 Asesor, Instituto Colombiano del Petróleo, Piedecuesta, Colombia. 5 Departamento de Oceanografía, e Instituto Milenio de Oceanografía, Universidad de Concepción, Concepción, Chile. Summary Anaerobic ammonium oxidizers contribute to the removal of fixed nitrogen in oxygen-deficient marine ecosystems such as oxygen minimum zones (OMZ). Here we surveyed for the first time the occurrence and diversity of anammox bacteria in the Colombian Pacific, a transition area between the prominent South and North Pacific OMZs. Anammox bacteria were detected in the coastal and oceanic areas of the Colombian Pacific in low oxygen (< 22 μM), high nitrate (25–35 μM) and low nitrite (< 0.07 μM), and ammonium (< 1 μM) waters. In these waters, anammox bacteria were rich [∼ 7 operational taxo- nomic units (OTUs), 98% cut-off) and microdiverse (Shannon index H′< 1.24), in comparison with the observed at the prominent OMZ of the Eastern Tropical South Pacific, Arabian Sea and Black Sea. Anammox bacteria-like sequences from the Colom- bian Pacific were grouped together with sequences retrieved from the distinct OMZ’s marine subclu- sters (Peru, Northern Chile and Arabian Sea) within Candidatus ‘Scalindua spp’. Moreover, some anammox bacteria OTUs shared a low similarity with environmental phylotypes (86–94%). Our results indi- cated that a microdiverse anammox community inhabits the Colombian Pacific, generating new ques- tions about the ecological and biogeochemical differ- ences influencing its community structure. Introduction Anaerobic ammonium oxidation (Anammox) consists of a short circuit in the nitrogen gaseous formation of nitrogen cycling, providing an alternative pathway to the coupled nitrification–denitrification process (Mulder et al., 1995). The anammox process contributes to approximately 30–60% of the nitrogen loss in the ocean and has been estimated to account for between one-fifth and essentially all of the N 2 production in marine oxygen minimum zones (OMZ) (Dalsgaard et al., 2005; Kuypers et al., 2005). One of the most extensive surveys of anammox versus denitrification measurements recently carried out in the eastern south Pacific Ocean (ESPO) identified that anammox activity with maximum rates of 0.85 nmol N 2 L −1 h −1 was mainly centred in shallow anoxic depths (Dalsgaard et al., 2012). This was consistent with previous studies developed in the area (Hamersley et al., 2007; Galán et al., 2009; Lam et al., 2009; Ward et al., 2009). Anammox bacteria are phylogenetically constrained within a monophyletic deep branch in the order Planctomycetales, consisting of three Candidatus genera: Brocadia, Kuenenia and Scalindua. Scalindua-like anammox bacteria are the most commonly detected in many worldwide aquatic habitats such as OMZ and anoxic or suboxic marine waters (Dalsgaard et al., 2003; Kuypers et al., 2003; 2005; Hamersley et al., 2007; Lam et al., 2007; Woebken et al., 2008; Galán et al., 2009; 2012), marine and estuarine sediments (Dalsgaard and Thamdrup, 2002; Trimmer et al., 2003; Risgaard-Petersen et al., 2004; Rysgaard et al., 2004; Rich et al., 2008; Dale et al., 2009; Dang et al., 2010; Hirsh et al., 2011), and freshwater ecosystems (Penton et al., 2006; Schubert et al., 2006; Zhang et al., 2007; Hamersley et al., 2009; Wenk et al., 2013). However, anammox survey studies using 16S rRNA, ITS and the Received 8 July, 2013; accepted 1 April, 2014. *For correspondence. E-mail mcastro@ut.edu.co; Tel. 57(8)2772049; Fax 57(8)2772049. Environmental Microbiology Reports (2014) doi:10.1111/1758-2229.12165 © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd