Carbon flow into ammonia-oxidizing bacteria and archaea during decomposition of 13C-labeled plant residues in soil

Abstract

Incorporation of plant residues into soil brings about nitrification when ammonification of organic nitrogen derived from plant residues proceeds. In the present study, we traced carbon flow into ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) during decomposition of plant residues in a soil, by isotope 13 carbon (13C)-DNA stable isotope probing and denaturing gradient gel electrophoresis (DGGE) analysis of amoA genes encoding ammonia monooxygenase subunit A. Unlabeled (12C) and 13C-labeled dried rice (Oryza sativa) callus (Oryza sativa L. cv. Yukihikari) was used as a model plant residue. The soil with or without the dried rice callus was aerobically incubated with 55% of maximum water holding capacity for 56 days. DGGE analysis of AOB and AOA communities showed that the band patterns of the callus-treated soil gradually changed during incubation and was distinctly different from the no-callus treatment (control) after 28 and 42 days of incubation, respectively. Subsequent analysis after isopycnic centrifugation of the soil DNA showed that 13C-enriched AOB clones were obtained at 14 and 28 days, whereas 13C-enriched AOA clones were found at 28 days of incubation. The AOB community consisted of members of clusters 1, 9 and 11 and other members of Nitrosospira spp., of which most of the 13C-enriched clones were affiliated with clusters 1 and 9. The AOA community mostly belonged to the clusters consisting of clones obtained mainly from terrestrial environments. The 13C-enriched AOA clones were all closely related to “Nitrososphaera viennensis” and Candidatus Nitrososphaera gargensis. Our study showed that carbon derived from the dried rice callus flowed into both the AOB and AOA communities in the aerobically incubated soil during decomposition.