Stratification of Diversity and Activity of Methanogenic and Methanotrophic Microorganisms in a Nitrogen-Fertilized Italian Paddy Soil

Abstract

Paddy fields are important ecosystems, as rice is the primary food source for about half of the world's population. Paddy fields are impacted by nitrogen fertilization and are a major anthropogenic source of methane. Microbial diversity and methane metabolism were investigated in the upper 60 cm of a paddy soil by qPCR, 16S rRNA gene amplicon sequencing and anoxic ¹³C-CH₄ turnover with a suite of electron acceptors. The bacterial community consisted mainly of <i>Acidobacteria, Chloroflexi, Proteobacteria, Planctomycetes,</i> and <i>Actinobacteria</i>. Among archaea, <i>Euryarchaeota</i> and <i>Bathyarchaeota</i> dominated over <i>Thaumarchaeota</i> in the upper 30 cm of the soil. <i>Bathyarchaeota</i> constituted up to 45% of the total archaeal reads in the top 5 cm. In the methanogenic community, <i>Methanosaeta</i> were generally more abundant than the versatile <i>Methanosarcina.</i> The measured maximum methane production rate was 444 nmol g_dwh^-1, and the maximum rates of nitrate-, nitrite-, and iron-dependent anaerobic oxidation of methane (AOM) were 57 nmol, 55 nmol, and 56 nmol g_dwh^-1, respectively, at different depths. qPCR revealed a higher abundance of '<i>Candidatus</i> Methanoperedens nitroreducens' than methanotrophic NC10 phylum bacteria at all depths, except at 60 cm. These results demonstrate that there is substantial potential for AOM in fertilized paddy fields, with '<i>Candidatus</i> Methanoperedens nitroreducens' archaea as a potential important contributor.