Article (Scientific journals)
A novel sub-phylum method discriminates better the impact of crop management on soil microbial community
Degrune, Florine; Dufrêne, Marc; Colinet, Gilles et al.
2015In Agronomy for Sustainable Development
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Keywords :
microbial diversity; microbial community composition; taxonomic level; pyrosequencing; conservation agriculture
Abstract :
[en] 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, 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. Whereas 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.
Research center :
AgricultureIsLife , TERRA Teaching and Research Centre - TERRA
Disciplines :
Agriculture & agronomy
Microbiology
Author, co-author :
Degrune, Florine ;  Université de Liège - ULiège > Chimie et bio-industries > Microbiologie et génomique
Dufrêne, Marc  ;  Université de Liège - ULiège > Forêts, Nature et Paysage > Biodiversité et Paysage
Colinet, Gilles  ;  Université de Liège - ULiège > Sciences et technologie de l'environnement > Systèmes Sol-Eau
Massart, Sébastien  ;  Université de Liège - ULiège > Sciences agronomiques > Phytopathologie
Taminiau, Bernard  ;  Université de Liège - ULiège > Département de sciences des denrées alimentaires (DDA) > Microbiologie des denrées alimentaires
Bodson, Bernard ;  Université de Liège - ULiège > Sciences agronomiques > Phytotechnie des régions tempérées
Hiel, Marie-Pierre ;  Université de Liège - ULiège > Sciences agronomiques > Phytotechnie des régions tempérées
Daube, Georges  ;  Université de Liège - ULiège > Département de sciences des denrées alimentaires (DDA) > Microbiologie des denrées alimentaires
Vandenbol, Micheline ;  Université de Liège - ULiège > Chimie et bio-industries > Microbiologie et génomique
Other collaborator :
Nezer, Carine
Language :
English
Title :
A novel sub-phylum method discriminates better the impact of crop management on soil microbial community
Publication date :
23 January 2015
Journal title :
Agronomy for Sustainable Development
ISSN :
1774-0746
eISSN :
1773-0155
Publisher :
EDP Sciences, Les Ulis, France
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBi :
since 05 April 2015

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