Abstract Wetlands are among the most important ecosystems on Earth both in terms of productivity and biodiversity, but also as a source of the greenhouse gas CH 4 . Microbial processes catalyzing nutrient recycling and CH 4 production are controlled by sediment phys- ico-chemistry, which is in turn affected by plant activity and the foraging behaviour of herbivores. We per- formed field and laboratory experiments to evaluate the direct effect of herbivores on soil microbial activity and their indirect effects as the consequence of reduced macrophyte density, using migratory Bewick’s swans (Cygnus columbianus bewickii Yarrell) feeding on fennel pondweed (Potamogeton pectinatus L.) tu- bers as a model system. A controlled foraging experi- ment using field enclosures indicated that swan bioturbation decreases CH 4 production, through a de- crease in the activity of methanogenic Archaea and an increased rate of CH 4 oxidation in the bioturbated sediment. We also found a positive correlation be- tween tuber density (a surrogate of plant density dur- ing the previous growth season) and CH 4 production activity. A laboratory experiment showed that sedi- ment sterilization enhances pondweed growth, proba- bly due to elimination of the negative effects of microbial activity on plant growth. In summary, the bioturbation caused by swan grazing modulates CH 4 cycling by means of both direct and indirect (i.e. plant- mediated) effects with potential consequences for CH 4 emission from wetland systems. Keywords Multitrophic interactions Æ Methane cycling Æ Shallow lakes Æ Bewick’s swans Æ Fennel pondweed 1 Introduction Wetlands are among the most productive ecosystems on Earth, mainly due to the rapid recycling of nutri- ents mediated by the hydrological regime and the coupled activity of water and soil bacteria (Mitsch and Gosselink 2000). Wetlands are also among the most prominent sources of atmospheric CH 4 , con- tributing 55% to the annual global CH 4 emission to the atmosphere (Houghton et al. 2001; LeMer and Communicated by Christian Ko ¨ rner Electronic supplementary material Supplementary material is available in the online version of this article athttp://dx.doi.org/ 10.1007/s00442-006-0445-9 and is accessible for authorized users. P. L. E. Bodelier (&) Æ M. Stomp Æ H. J. Laanbroek Department of Microbial Wetland Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Centre for Limnology, Rijksstraatweg 6, 3631AC, Nieuwersluis, The Netherlands e-mail: p.bodelier@nioo.knaw.nl M. Stomp Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Nieuwe Achtergracht 127, 1018 WS Amsterdam, The Netherlands L. Santamaria Æ M. Klaassen Department of Plant–Animal Interactions, Netherlands Institute of Ecology (NIOO-KNAW), Centre for Limnology, Rijksstraatweg 6, 3631AC, Nieuwersluis, The Netherlands L. Santamaria Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Miquel Marque `s 21, 07190, Esporles, Mallorca, Illes Balears, Spain Oecologia (2006) 149:233–244 DOI 10.1007/s00442-006-0445-9 123 PLANT ANIMAL INTERACTIONS Animal–plant–microbe interactions: direct and indirect effects of swan foraging behaviour modulate methane cycling in temperate shallow wetlands Paul L. E. Bodelier Æ Maayke Stomp Æ Luis Santamaria Æ Marcel Klaassen Æ Hendrikus J. Laanbroek Received: 14 September 2005 / Accepted: 26 April 2006 / Published online: 31 May 2006 Ó Springer-Verlag 2006