Distribution of methane production and methanogenic archaeal community structure across soil particle size fractions along a rice chronosequence

Methanogens, a phylogenetic group of archaea, are a key microbial community that mediate carbon (C) cycling and methane (CH₄) production in submerged soils. In this study, we analyzed the potential of CH₄ production and the archaeal community structure of different soil particle fractions in a chronosequence of rice (Oryza sativa L.) soil subjected to prolonged rice cultivation. The chronosequence of five age groups of a paddy soil formation was determined in a coastal area from East China, subjected to 50 to 700 years of rice cultivation. Undisturbed bulk soils were fractionated by low-energy ultra-sonication dispersion and centrifugation into four classes of particle size fractions (PSFs; coarse sand, fine sand, silt, and clay). The abundance and diversity of archaeal communities from each of the four fractions were analyzed by quantitative polymerase chain reaction and denaturing gradient gel electrophoresis, respectively. Among the size fractions, a high abundance of archaea and methanogens was found in both coarse sand- and clay-sized fractions. During prolonged rice cultivation, CH₄ production potential (MPP) and methanogenic gene abundance increased in the soil cultivated for 100 years, and thereafter changed more or less in the soils cultivated for longer periods. Moreover, marked changes in gene abundance and community diversity were observed in coarse sand- and clay-sized fractions, but not in fine sand- and silt-sized fractions. Sequencing analysis of 61 selected archaeal 16S rRNA genes revealed that Methanocellales was an abundant group of methanogens in all sized fractions of soils across the chronosequence, whereas Methanosarcinaceae and Methanosaetaceae were less widespread in the clay fractions across the soils. This study indicated that methanogens and their activities can be heterogeneously distributed among soil PSFs, and their distribution and activities change in response to years of paddy cultivation that affect PSFs formation.