Methanotrophic abundance and community fingerprint in pine and tea plantation soils as revealed by molecular methods

Abstract

Understanding the community structure of methane-oxidizing bacteria (methanotrophs) is important to assess the microbial oxidation of the greenhouse gas methane (CH₄) in soil under different land uses. Soil samples were collected from two plantation plots of pine and tea in southern China. Methanotrophic abundance was quantified with quantitative real-time polymerase chain reaction (qPCR) based on the 16S rRNA and pmoA genes, and the community fingerprint was characterized with denaturing gradient gel electrophoresis (DGGE) targeting the pmoA gene. No significant difference in the gene copy numbers of methanotrophs was found between the pine and tea land-use, regardless of 16S rRNA and pmoA genes. Higher abundance of type I (1.35 vs 1.66×108 copie g-1 soil) over type II methanotrophs (8.59 vs 10.9 × 107) were found both in pine and tea plantation soils. Apparent differences in methanotrophic community fingerprint were observed between the pine and tea treatments. Correlations analysis between methanotrophic abundance and soil characteristics, combining with canonial correspondence analysis (CCA) regarding community fingerprint and environmental parameters indicated that soil pH and available phosphorus were the most important factors potentially affecting the methanotrophic community diversity in the acidic red soil.

Key words: Denaturing gradient gel electrophoresis (DGGE), land use, methanotrophs, pmoA gene, quantitative real-time PCR (qPCR).