Metagenomic analyses reveal no differences in genes involved in cellulose degradation under different tillage treatments.

Maria De Vries,Anne Schöler,Julia Ertl,Michael Schloter,Zhuofei Xu,Wietse De Boer

doi:10.1093/femsec/fiv069

Abstract

Incorporation of plant litter is a frequent agricultural practice to increase nutrient availability in soil, and relies heavily on the activity of cellulose-degrading microorganisms. Here we address the question of how different tillage treatments affect soil microbial communities and their cellulose-degrading potential in a long-term agricultural experiment. To identify potential differences in microbial taxonomy and functionality, we generated six soil metagenomes of conventional (CT) and reduced (RT) tillage-treated topsoil samples, which differed in their potential extracellular cellulolytic activity as well as their microbial biomass. Taxonomic analysis of metagenomic data revealed few differences between RT and CT, and a dominance of Proteobacteria and Actinobacteria, whereas eukaryotic phyla were not prevalent. Prediction of cellulolytic enzymes revealed glycoside hydrolase families 1, 3 and 94, auxiliary activity family 8 and carbohydrate-binding module 2 as the most abundant in soil. These were annotated mainly to the phyla of Proteobacteria, Actinobacteria and Bacteroidetes. These results suggest that the observed higher cellulolytic activity in RT soils can be explained by a higher microbial biomass or changed expression levels but not by shifts in the soil microbiome. Overall, this study reveals the stability of soil microbial communities and cellulolytic gene composition under the investigated tillage treatments.

Highlights

The most abundant organic polymer on earth is cellulose
We explored the influence of long-term conventional and reduced tillage on the taxonomic and functional diversity of soil microbial communities, which are involved in cellulose degradation
Reduced tillage leads to significantly higher microbial biomass compared to soil under conventional tillage, as measured by carbon analysis (0.28 ± 0.03 respectively 0.16 ± 0.02 mg g-1 dry weight (DW), P=0.004, Fig. 1a) and by Quantitative real-time PCR (qPCR) of both bacterial

Summary

Introduction

The most abundant organic polymer on earth is cellulose. As a key component of plant cell walls it is highly abundant in all plants mostly in combination with hemicellulose and xylan (Varner & Louis 1989). To clarify this question several long term agricultural experiments have been established to assess the adaptation of soils to different tillage treatments In this context it was shown that reduced tillage (RT) leads to a higher carbon content and higher microbial biomass in the topsoil compared to conventional tillage (CT) (van Groenigen et al 2011; Küstermann et al 2013; Alvarez et al 1995; Kandeler et al 1999). It is currently unclear how different tillage treatments influence the phylogenetic structure of the soil microbial community, in particular those which drive the degradation of polymers, like cellulose, which are major constituents of plant residues used to improve soil quality.

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Discussion

Methods