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

Juan Li,Xiangdong Yang,Yanchen Wen

doi:10.3390/agronomy11122425

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).

Highlights

The challenge of meeting the food consumption needs of a growing global population—while reducing the environmental impact of agriculture—has led to the emergence of the sustainable intensification paradigm, which aims to balance these two needs without the conversion of additional non-agricultural land [1]
The diversity and relative abundances of resident (DNA) and active (RNA)-based bacterial communities differed from those derived from DNA, with the taxa of the DM treatment standing out with a significantly different diversity and relative abundance of RNA-based bacteria
In soils established under 27-year fertilization regimes, lower relative abundance of DNA-based community were investigated and several RNA-based bacteria were found exclusively

Summary

Introduction

The challenge of meeting the food consumption needs of a growing global population—while reducing the environmental impact of agriculture—has led to the emergence of the sustainable intensification paradigm, which aims to balance these two needs without the conversion of additional non-agricultural land [1]. Previous reports have indicated that strategies in England and the EU encouraging well-managed animal manure application led to more environmentally sensitive farming methods, with reduced usage of mineral fertilizers [4,5]. Case reports have indicated that soil microbial biomass, diversity and activity can be altered by changes in the fertilization regime [3,9]. These differences were mainly attributed to variations in the levels of soil nitrogen, carbon, and pH among fertilization systems [10]. The change in coarse unprotected particulate organic matter (cPOM) has been indicated to be an important factor affecting soil microbial community (microbiome) composition [20]

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