Characteristics of microbial habitats in a tropical soil subject to different fallow management Ndeye Yacine Badiane Ndour a,b , Wafa Achouak c , Richard Christen d , Thierry Heulin c , Alain Brauman e , Jean-Luc Chotte e, * a UR SeqBio, IRD Laboratoire d’Ecologie Microbienne des Sols et Agrosyste `mes Tropicaux, BP 1386 Dakar, Se ´ne ´gal b Institut Se ´ne ´galais de Recherche Agricole, Laboratoire National de Recherche sur les Productions Ve ´ge ´tales, Dakar, Se ´ne ´gal c DSV-DEVM, Laboratoire d’Ecologie Microbienne de la Rhizosphe `re et Environnements Extre ˆmes (LEMiRE), UMR 6191 CNRS-CEA-Universite ´ de la Me ´ diterrane ´e, CEA Cadarache, F-13108 Saint-Paul-lez-Durance, France d UMR 6543 CNRS-Universite ´ de Nice Sophia Antipolis, Centre de Biochimie, Parc Valrose, F-06108 Nice, France e UR SeqBio, IRD, SupAgro, 2 place Viala, Ba ˆ timent 12, 34060 Montpellier cedex 1, France 1. Introduction Microorganisms in soils are among the earth’s most diverse assemblages of living organisms. Thousands of species of bacteria colonize a single gram of soil (Torsvik et al., 1990). Microorganisms have traditionally been considered as ubi- quitous communities – ‘‘everything is everywhere’’ – with an immense range of functions. Despite their ecological importance, the diversity of soil microbial communities has only recently been studied, probably owing to the lack of efficient microbiological methods (cultivable bacteria, etc.) for accessing microbial diversity and functions and the extreme complexity of the soil environment. Many early soil microbial diversity studies used culture- based techniques. However, this method has proved to be inconsistent as it is too selective and not representative of the applied soil ecology 38 (2008) 51–61 article info Article history: Received 12 July 2006 Received in revised form 31 August 2007 Accepted 5 September 2007 Keywords: Tropics Fallows Microhabitats rrs sequences Telluria abstract Changes in land use affect soil properties. In most West-African farming systems forest- fallow management intended to restore soil fertility no longer functions efficiently because the duration of the fallow periods has been shortened and the fallow areas have been reduced. Alternative practices must, therefore, be adopted. This study tested the efficiency of short periods of improved fallows (Andropogon gayanus and Acacia holosericea) in regenerating soil microbial properties, compared to the efficiency of a natural long-term fallow. The microbial community was studied by cloning and sequen- cing 16S rDNA and by analyzing enzyme activities (alkaline phosphatase, b-glucosidase). The study was carried out at the soil aggregate scale to test how the microbial community in different micro-habitats reacted to the different fallow practices. The 4-year-old Acacia holosericea and Angropogon gayanus fallows did not regenerate soil properties as efficiently as the 21-year-old natural fallow. However, Andropogon gayanus could be used to restore soil properties quickly. Three different aggregate-size fractions were affected by fallow management: organic residues, the >2000 mm fraction and the 2–50 mm fraction. These microhabitats were enriched with bacteria belonging to the Telluria genus and more generally to b-Proteobacteria. Published by Elsevier B.V. * Corresponding author. Tel.: +33 4 99 61 21 17; fax: +33 4 99 31 21 19. E-mail address: Jean-Luc.Chotte@mpl.ird.fr (J.-L. Chotte). available at www.sciencedirect.com journal homepage: www.elsevier.com/locate/apsoil 0929-1393/$ – see front matter . Published by Elsevier B.V. doi:10.1016/j.apsoil.2007.09.001