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Diversity of Bacterial Communities in a Profile of a Winter Wheat Field: Known and Unknown Members
Stroobants, Aurore; Degrune, Florine; Olivier, Claire et al.
2014In Microbial Ecology
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Keywords :
bacterial diversity; 16S rRNA gene; agricultural soil; pyrosequencing; depth; RDP classifier
Abstract :
[en] In soils, bacteria are very abundant and diverse. They are involved in various agro-ecosystem processes such as the nitrogen cycle, organic matter degradation, and soil formation. Yet, little is known about the distribution and composition of bacterial communities through the soil profile, particularly in agricultural soils, as most studies have focused only on topsoils or forest and grassland soils. In the present work, we have used bar-coded pyrosequencing analysis of the V3 region of the 16S rRNA gene to analyze bacterial diversity in a profile (depths 10, 25, and 45 cm) of a well-characterized field of winter wheat. Taxonomic assignment was carried out with the Ribosomal Database Project (RDP) Classifier program with three bootstrap scores: a main run at 0.80, a confirmation run at 0.99, and a run at 0 to gain information on the unknown bacteria. Our results show that biomass and bacterial quantity and diversity decreased greatly with depth. Depth also had an impact, in terms of relative sequence abundance, on 81 % of the most represented taxonomic ranks, notably the ranks Proteobacteria, Bacteroidetes, Actinobacteridae, and Acidobacteria. Bacterial community composition differed more strongly between the topsoil (10 and 25 cm) and subsoil (45 cm) than between levels in the topsoil, mainly because of shifts in the carbon, nitrogen, and potassium contents. The subsoil also contained more unknown bacteria, 53.96 % on the average, than did the topsoil, with 42.06 % at 10 cm and 45.59 % at 25 cm. Most of these unknown bacteria seem to belong to Deltaproteobacteria, Actinobacteria, Rhizobiales, and Acidobacteria.
Disciplines :
Environmental sciences & ecology
Author, co-author :
Stroobants, Aurore ;  Université de Liège - ULiège > Chimie et bio-industries > Microbiologie et génomique
Degrune, Florine ;  Université de Liège - ULiège > Chimie et bio-industries > Microbiologie et génomique
Olivier, Claire
Muys, Céline
Roisin, Christian
Colinet, Gilles  ;  Université de Liège - ULiège > Sciences et technologie de l'environnement > Systèmes Sol-Eau
Bodson, Bernard ;  Université de Liège - ULiège > Sciences agronomiques > Phytotechnie des régions tempérées
Portetelle, Daniel ;  Université de Liège - ULiège > Chimie et bio-industries > Microbiologie et génomique
Vandenbol, Micheline ;  Université de Liège - ULiège > Chimie et bio-industries > Microbiologie et génomique
Language :
English
Title :
Diversity of Bacterial Communities in a Profile of a Winter Wheat Field: Known and Unknown Members
Publication date :
10 July 2014
Journal title :
Microbial Ecology
ISSN :
0095-3628
eISSN :
1432-184X
Publisher :
Springer Verlag, New York, United States - New York
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBi :
since 10 August 2014

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