A novel sub-phylum method discriminates better the impact of crop management on soil microbial community

Florine Degrune,Sébastien Massart,Gilles Colinet,Carine Nezer,Marie-Pierre Hiel,Micheline Vandenbol,Marc Dufrêne,Bernard Bodson,Georges Daube,Bernard Taminiau

doi:10.1007/s13593-015-0291-4

Abstract

Soil microorganisms such as mycorrhizae and plant-growth-promoting rhizobacteria have beneficial effects on crop productivity. Agricultural practices are known to impact soil microbial communities, but past studies examining this impact have focused mostly on one or two taxonomic levels, such as phylum and class, thus missing potentially relevant information from lower levels. Therefore, we propose here an original, sub-phylum method for studying how agricultural practices modify microbial communities. This method involves exploiting the available sequence information at the lowest taxonomic level attainable for each operational taxonomic unit. In order to validate this novel method, we assessed microbial community composition using 454 pyrosequencing of 16S and 28S rRNA genes, and then we compared the results with results of a phylum-level analysis. Agricultural practices included conventional tillage, reduced tillage, residue removal, and residue retention. Results show that, at the lowest taxonomic level attainable, tillage is the main factor influencing both bacterial community composition, accounting for 13 % of the variation, and fungal community composition, accounting for 18 % of the variation. On the other hand, phylum-level analysis failed to reveal any effect of soil practice on bacterial community composition and missed the fact that different members of the same phylum responded differently to tillage practice. For instance, the fungal phylum Chytridiomycota showed no impact of soil treatment, while sub-phylum-level analysis revealed an impact of tillage practice on the Chytridiomycota sub-groups Gibberella, which includes a notorious wheat pathogen, and Trichocomaceae. This clearly demonstrates the necessity of exploiting the information obtainable at sub-phylum level when assessing the effects of agricultural practice on microbial communities.

Highlights

Soil microorganisms are abundant and diverse and can have both beneficial and adverse effects on crop growth
With a view to achieving better discrimination power than is usual in such studies, we compared two methods of microbial community composition analysis applied to soils subjected to different tillage practices—conventional and reduced tillage—and different residue management practices—crop residue retention and removal
One approach was to limit our analysis to the phylum level, the second being to use the most precise taxonomic level reachable for each operational taxonomic unit

Summary

Introduction

Soil microorganisms are abundant and diverse and can have both beneficial and adverse effects on crop growth Some, such as plant-growth-promoting rhizobacteria and mycorrhizae, are well known to favor crop productivity and plant health (Siddiqui and Futai 2008; Berg 2009). Agricultural practices influence the physical and chemical properties of the soil and affect the abundance and diversity of soil microorganisms (Kladivko 2001; Helgason et al 2009; Lienhard et al 2013). This generates interest in studying the responses of microbial communities to agricultural practices. A central question in such studies remains: how to choose the taxonomic level used to detect microbial patterns?

Methods

Results

Conclusion