In the early 21st century, agriculture faces a new challenge: to meet the demand for food production of the ever-growing world population while preventing environmental damage. To meet this challenge, an agroecological approach seems promising, but to develop the agriculture of tomorrow will require a multi- and inter-disciplinary strategy in order to build knowledge and create innovative tools. The AgricultureIsLife research platform was initiated in 2013 to facilitate collaborative research between different scientific domains and to explore various aspects of the agroecosystem around five key innovation themes. Among these, the management of organic residues through different tillage regimes is of primary interest, as crop residues can influence physical, chemical, and biological soil properties that in turn may influence soil health and quality. Bacteria and fungi, key components of agroecosystem functioning, mediate most soil processes, such as those linked to essential plant nutrients.

In our study, we have employed high-throughput 454 pyrosequencing technology to explore soil microbial α- and β-diversity under different soil treatments combining one tillage regime (conventional or reduced tillage) with one crop residue management practice (retention or removal). We have explored the effects of these soil treatments at two depth ranges along the soil profile, 0 to 5 cm and 15 to 20 cm and over the growing seasons of two crops: Vicia faba (fababean) and Triticum aestivum (wheat).

Our work has clearly demonstrated differences in microbial α- and β-diversity between conventional and reduced tillage, but no variation linked to crop residue management. The observed differences appear associated with tillage-regime-related differences in physical (e.g. structure and moisture), chemical (nutrient status), and biological (e.g. root system) soil properties. The nutrient status and moisture were higher under conventional tillage, with crop residues mixed through the soil profile, while under reduced tillage, severe soil compaction occurred through the soil profile, with crop residues concentrated in the top soil. Overall α-diversity indexes indicated a higher richness and a lower evenness under conventional than under reduced tillage. To explore β-diversity, we used an original method considering the tillage-related patterns occurring at different levels of taxonomic resolution (from phylum to genus). We improved our method by using innovative tools, including a taxonomic tree, to better visualize microbial diversity as a whole and the tillage-related patterns at each level of resolution. With these innovative tools, analysis of β-diversity revealed some taxa to be more abundant under conventional tillage, while others appeared more abundant under reduced tillage. On the basis of the literature, we were able to associate ecological meanings with the observed microbial patterns. For example, we identified major groups of bacteria (e.g. Bacteroidetes and β-Proteobacteria) previously categorized as copiotrophs, i.e. as thriving under conditions of high-nutrient availability, to be more abundant under conventional tillage, while other major groups (e.g. Acidobacteria), previously categorized as oligotrophs, i.e. as thriving better under condition of low nutrient availability, were more abundant under reduced tillage. We also identified taxa associated with particular ecological roles, such as the phylum Glomeromycota, which contains arbuscular mycorrhizal fungi (AMF), an economically and ecologically important group of fungi forming symbiotic relationships with most plants. However, the large majority of bacteria and fungi are still poorly undescribed as regards their physiology and metabolism, which are linked to lifestyle strategies and ecological roles. We further found the responses of soil microbial α- and β-diversity to the tillage regime to be influenced strongly by soil depth and moderately by the growth stage. In addition, bacteria and fungi showed different patterns. For example, fungal β-diversity was influenced mostly by soil depth, and bacterial β-diversity mostly by the tillage regime. Concerning the interaction between tillage regime and growth stage, different patterns were again identified for bacteria and fungi. Bacteria were more resilient, i.e. less influenced by tillage at later growth stages, while fungi were less resilient, i.e. influenced by tillage throughout the growing season.

Our study was a pioneer in exploring microbial diversity under different soil treatments in the specific pedological and climate context found in central Belgium. Our exploratory study raises new questions regarding the impacts of α- and β-diversity changes on agroecosystem functioning. We encourage researchers to undertake further research into the functional roles of microbial communities, using complementary methods such as the functional-trait-based approach, in order to improve our understanding of agroecosystem functioning.

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