Understanding the Responses of Soil Bacterial Communities to Long-Term Fertilization Regimes Using DNA and RNA Sequencing

Abstract

Studies of soil DNA-based and RNA-based bacterial communities under contrasting long-term fertilization regimes can provide valuable insights into how agricultural management affects soil microbial structure and functional diversity. In this study, soil bacterial communities subjected to six fertility treatments in an alkaline soil over 27 years were investigated by 454 pyrosequencing based on 16S rDNA and 16S rRNA. Long-term fertilization showed significant influences on the diversity of the soil DNA-based bacteria, as well as on their RNA-based members. The top five phyla (Proteobacteria, Acidobacteria, Chloroflexi, Actinobacteria, and Planctomycetes) were found in both the DNA- and RNA-based samples. However, the relative abundances of these phyla at both DNA and RNA levels were showed significantly different. Analysis results showed that the diversity of the 16S rRNA samples was consistently lower than that of the rDNA samples, however, 16S rRNA samples had higher relative abundance. PICRUSt analysis indicated that glycan biosynthesis and metabolism were detected mainly in the DNA samples, while metabolism and degradation of xenobiotics and the metabolism of amino acids, terpenoids and polyketides were relatively higher in the RNA samples. Bacilli were significantly more abundant in all the OM-fertilized soils. Redundancy analysis indicated that the relative abundances of both DNA- and RNA-based bacterial groups were correlated with soil total organic carbon content, nitrogen content, Olsen-P, and soil pH. Moreover, the RNA-based Bacilli were positively correlated with available phosphorus (Olsen-P).

Keywords

• bacterial community
• diversity
• 16S rDNA and 16S rRNA sequencing
• long-term fertilization regime
• labile organic carbon fractions