Dynamics of bacterial and archaeal amoA gene abundance after additions of organic inputs combined with mineral nitrogen to an agricultural soil

Dynamics of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) abundance was assayed in a tropical Humic Nitisol during two cropping seasons of a long-term field experiment situated in the central highlands of Kenya. Since 2002, soils were treated yearly with biochemically contrasting organic inputs (4 Mg C ha(-1) year(-1)) of Tithonia diversifolia (TD; C/N ratio: 13; lignin: 8.9 %; polyphenols: 1.7 %), Calliandra calothyrsus (CC; 13; 13; 9.4) and Zea mays (ZM; 59; 5.4; 1.2) combined with and without 120 kg CaNH4NO3 ha(-1) season(-1). In 2012 and 2013, soils (0-15 cm) were sampled at young growth (EC30) and flowering (EC60) stages of maize and subjected to DNA-based amoA gene quantification. ZM and TD increased AOB abundance by 9 and 19 %, respectively, compared to CC, while AOA remained unaffected. This was ascribed to high organic N in TD and lower lignin and polyphenol contents in ZM than in CC. In CC, formation of polyphenol-protein complexes limited microbial access to N. Sole use of mineral N or its combination with organic inputs decreased AOA abundance by 35 % but not AOB as a consequence of pH reduction by mineral N. Overall, AOB was more responsive than AOA to input quality that became most pronounced under optimal soil moisture conditions found in 2013 and at EC60 in 2012. We recommend prolonged study periods, considering also rRNA-based analyses to explore the dynamics of active nitrifying communities as a consequence of interrelations of contrasting organic inputs, crop growth stages and seasonality in agricultural soils.