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

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.

Shifts in reclamation management strategies shape the role of exopolysaccharide and lipopolysaccharide‐producing bacteria during soil formation

“…This result indicates that the bacterial community grows in abundance, and eventually adapts and stabilizes with agricultural practices. This is in accordance with other studies showing a stable community under long‐term treatments (at least on the DNA level) (de Vries et al , ; Cania et al , ). Moreover, soil organic carbon concentrations peaked at RA6 and decreased at RA12 and RA24 (Pihlap et al , ), likely because organic fertilizers were applied only in the 4th and 7th year of the reclamation process.…”

Microbial community responses to soil tillage and crop rotation in a corn/soybean agroecosystem

“…While not measured, the no‐till fields appeared to have higher crop residue and did have marginally higher levels of organic carbon (Appendix Figure S4). High levels of Chitinophagaceae in soil has been associated with increased activity of β‐glucosidase (Bailey, Fansler, Stegen, & McCue, ), an important enzyme associated with the breakdown of cellulose; note, though, that another study (de Vries, Schöler, Ertl, Xu, & Schloter, ) did not find differences in cellulose degrading gene copy number in conventionally tilled versus no‐till soils. The higher copy number of genes associated with nitrogen fixation in no‐till soils (Figure ) may be associated with the high abundance of nitrogen‐fixing Rhizobiales .…”

Microbial energy and matter transformation in agricultural soils

“…In a comparison of conventional tillage versus reduced tillage cropping soil, tillage had no effect on the composition of GH families (de Vries et al, 2015). However, significantly higher activities of cellobiohydrolase and b-glucosidase occurred under reduced tillage, where TOC and N were greater (1.6% versus 1.1% and 0.2% versus 0.1% for C and N, respectively) after 13 years of tillage management (de Vries et al, 2015). Conversely, where TOC (%) does not change between management practices (conventional versus growth of N-fixing legumes during a fallow period) the activity of cellobiohydrolase and b-glucosidase does not change (Bossio et al, 2005).…”

“…Similarly, a comparison of conventional cropping versus low input management of a corn-soybean-winter wheat rotational cropping soil showed that where SOC (%) was significantly lower under conventional management, there was a loss in relative abundances of functional genes involved in the degradation of starch, hemicellulose, cellulose, aromatic C compounds and an endochitinase (Xue et al, 2012). In a comparison of conventional tillage versus reduced tillage cropping soil, tillage had no effect on the composition of GH families (de Vries et al, 2015). However, significantly higher activities of cellobiohydrolase and b-glucosidase occurred under reduced tillage, where TOC and N were greater (1.6% versus 1.1% and 0.2% versus 0.1% for C and N, respectively) after 13 years of tillage management (de Vries et al, 2015).…”

“…Conversely, where TOC (%) does not change between management practices (conventional versus growth of N-fixing legumes during a fallow period) the activity of cellobiohydrolase and b-glucosidase does not change (Bossio et al, 2005). In these examples, GHs could be predominantly associated to the potentially copiotrophic phyla Proteobacteria, Bacteroides and Actinobacteria, reflecting their dominance in agricultural systems (Uroz et al, 2013;de Vries et al, 2015;Manoharan et al, 2015). Thus the composition of the microbial community, the relative abundance of functional genes and the activity of C degrading enzymes closely follow SOM quantity and, presumably, availability.…”