Endogeic earthworms shape bacterial functional communities and affect organic matter mineralization in a tropical soil

The ISME Journal (2012) 6, 213–222 & 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12 www.nature.com/ismej ORIGINAL ARTICLE Endogeic earthworms shape bacterial functional communities and affect organic matter mineralization in a tropical soil Laetitia Bernard1, Lydie Chapuis-Lardy2, Tantely Razafimbelo3, Malalatiana Razafindrakoto3, Anne-Laure Pablo1, Elvire Legname1, Julie Poulain4, Thomas Brüls4, Michael O’Donohue5, Alain Brauman1, Jean-Luc Chotte1 and Eric Blanchart1 1 Institut de Recherche pour le Développement (IRD), UMR Eco&Sols, Montpellier Cedex, France; 2Institut de Recherche pour le Développement (IRD), UMR Eco&Sols, Antananarivo, Madagascar; 3Université d’Antananarivo, Laboratoire des Radio-Isotopes (LRI), Antananarivo, Madagascar; 4Institut de Génomique, Genoscope, UMR8030 (CNRS, CEA, Université d’Evry), Evry, France and 5INSA, LISBP, Toulouse Cedex, France Priming effect (PE) is defined as a stimulation of the mineralization of soil organic matter (SOM) following a supply of fresh organic matter. This process can have important consequences on the fate of SOM and on the management of residues in agricultural soils, especially in tropical regions where soil fertility is essentially based on the management of organic matter. Earthworms are ecosystem engineers known to affect the dynamics of SOM. Endogeic earthworms ingest large amounts of soil and assimilate a part of organic matter it contains. During gut transit, microorganisms are transported to new substrates and their activity is stimulated by (i) the production of readily assimilable organic matter (mucus) and (ii) the possible presence of fresh organic residues in the ingested soil. The objective of our study was to see (i) whether earthworms impact the PE intensity when a fresh residue is added to a tropical soil and (ii) whether this impact is linked to a stimulation/inhibition of bacterial taxa, and which taxa are affected. A tropical soil from Madagascar was incubated in the laboratory, with a 13C wheat straw residue, in the presence or absence of a peregrine endogeic tropical earthworm, Pontoscolex corethrurus. Emissions of 12CO2 and 13CO2 were followed during 16 days. The coupling between DNA-SIP (stable isotope probing) and pyrosequencing showed that stimulation of both the mineralization of wheat residues and the PE can be linked to the stimulation of several groups especially belonging to the Bacteroidetes phylum. The ISME Journal (2012) 6, 213–222; doi:10.1038/ismej.2011.87; published online 14 July 2011 Subject Category: microbial ecology and functional diversity of natural habitats Keywords: Bacteroidetes; DNA-SIP; Madagascar; Pontoscolex corethrurus; priming effect; pyrosequencing Introduction Soil microorganisms convert fresh organic matter (FOM) entering the soil into chemically stable, biologically inactive organic matter via the so-called humification process (Brookes et al., 2008). This process is comprised of discrete steps, during which the organic matter is exposed to microbial activity. At each successive step, more energy is required to breakdown the structures, which become progressively more complex and disordered, but richer in organic N and P. Moreover, microorganisms usually mineralize 40–60% of the carbon contained within Correspondence: L Bernard, Institut de Recherche pour le Développement (IRD), UMR Eco&Sols, 2 place Viala Bt12, Montpellier Cedex 1, F-34060, France. E-mail: Received 7 March 2011; revised 6 June 2011; accepted 6 June 2011; published online 14 July 2011 the organic matter as CO2. Therefore, soil organic matter (SOM) is a continuum of organic molecules, corresponding to the various intermediates of the FOM to biologically inactive organic matter conversion process. The apparent linearity of the humification process is sometimes disturbed by a mechanism called priming effect (PE). PE is defined as a change in the decomposition rate of the SOM provoked by the addition of FOM (Jenkinson, 1966; Blagodatskaya and Kuzyakov, 2008). The positive PE (stimulation of the SOM mineralization rate) leads to the recycling of the nutrients (organic N and P) trapped in the SOM and benefits the primary production (Kuzyakov et al., 2000). On the other hand, when the PE is unbalanced by the humification process, the decrease in SOM content may render the soil more sensitive to erosion processes. The PE was first described many years ago by Löhnis (1926), but Tropical earthworms and priming effect L Bernard et al 214 nevertheless this process is still poorly understood (Guenet et al., 2010). Understanding and controlling this process is a key concern in developing countries, where organic matter of local origin is used to reduce mineral fertilizer input (Beare et al., 1997) and where high temperatures accelerate microbial metabolism and C turnover rates. Two different mechanisms have been proposed to explain the true positive PE. The first one describes the PE as an indirect result of an increase in extracellular FOM-degrading enzymes produced by microorganisms (Kuzyakov et al., 2000). The second, proposed by Fontaine et al. (2003), suggests that the SOM-degrading microbial population might out-compete the FOM decomposers with regard to the metabolism of polymeric FOM compounds. Likewise, using the energy-rich FOM, SOM feeders would increase the decomposition rate of the nutrient-rich SOM in a co-metabolism process, which would allow them to assimilate N and P. These authors concluded that any disturbances affecting the relative proportions of the two functional groups (FOM and SOM feeders) would impact the intensity of the PE. However, the identity of microorganisms that form part of the SOM-feeder group remains more or less unknown (Bernard et al., 2009; Kuzyakov, 2010). Ecosystem engineers are organisms that modulate the availability of resources to other species, by causing physical changes in biotic or abiotic material (Jones et al., 1994). It is well known that earthworms modify the environment of soil microorganisms (Lavelle, 1997). Earthworms provide labile FOM, present in their mucus, and increase decomposition by favoring the contact between microorganisms and their substrates, via the mixing effect of gut transit. Moreover, earthworms alter edaphic parameters, such as soil structure, pH, O2, water regime etc. Basically, from a short-term perspective, earthworms have been shown to stimulate the rates of decomposition and mineralization of SOM (Speratti and Whalen, 2008), while in the longer term they increase the incorporation of fresh residues into newly formed stable microaggregates within casts, thus promoting carbon storage (Bossuyt et al., 2004, 2006; Coq et al., 2007; and for review see Brown et al., 2000). Additionally, it has been shown that while earthworms are unlikely to possess an indigenous microbial community, they significantly impact the structure of the soil microbial community (Egert et al., 2004) (...truncated)