Linking microbial taxa and the effect of mineral nitrogen forms on residue decomposition at the early stage in arable soil by DNA-qSIP

Abstract The decomposition of crop residues represents the largest organic carbon (C) input into agricultural ecosystems, and plays an important role in soil C sequestration and soil fertility. However, how different forms of mineral nitrogen (N) influence the decomposition of these residues, or their associated active microbes, is poorly understood. In this study, we investigated the impacts of ammonium ((NH4)2SO4) and nitrate (KNO3) on the early stages (14 days) of decomposition of highly enriched 13C-labeled (13C atom% = 77.0%) maize residues. Further, we characterized the contributions of various bacterial and archaeal taxa using quantitative stable isotope probing (qSIP). To our surprise, we found that the majority of measured parameters including 13C soil respiration, total 13C microbial assimilation in soil DNA, as well as the diversity and structure of these microbial communities, were not significantly different between these two N forms during our 2-week incubation. Slight differences were observed however, in the activity of straw-metabolizing microbes. The qSIP revealed variability in 13C assimilation (excess atom fraction, EAF) among different microbial taxa at the operational taxonomic unit (OTU) level, with Proteobacteria, Bacteroidetes, and Verrucomicrobia being the most intensively 13C-labeled phyla, suggesting their potentially dominant roles in residue decomposition. However, only the 13C EAF of Thaumarchaeota (genus Nitrososphaera) was significantly higher in the ammonium treatment than in the nitrate treatment. The Nitrososphaera might indirectly participate in the decomposition of residues by fixing CO2 or by directly incorporate 13C from organic matter. These results reveal a quantitative overview of the contribution of bacteria and archaea to residue decomposition. Further, we document that the similar effect of nitrate and ammonium on residue decomposition at the early stages is likely due to the unchanged activity of predominant bacterial taxa with the two N forms.