DATASET BRIEF Structure and function of the symbiosis partners of the lung lichen (Lobaria pulmonaria L. Hoffm.) analyzed by metaproteomics Thomas Schneider 1 , Emanuel Schmid 2 , Joa ˜o V. de Castro Jr. 3 , Massimiliano Cardinale 3 , Leo Eberl 1 , Martin Grube 4 , Gabriele Berg 3 and Kathrin Riedel 5,6 1 University of Zurich, Institute of Plant Biology, Z . urich, Switzerland 2 ETH Zurich, Institute of Molecular Systems Biology, Z . urich, Switzerland 3 Graz University of Technology, Institute of Environmental Biotechnology, Graz, Austria 4 Karl-Franzens University of Graz, Institute of Plant Sciences, Graz, Austria 5 Braunschweig University of Technology, Institute of Microbiology, Braunschweig, Germany 6 Helmholtz-Centre of Infection Research, Braunschweig, Germany Received: October 22, 2010 Revised: February 11, 2011 Accepted: April 11, 2011 Environmental proteomics, also referred to as metaproteomics, is an emerging technology to study the structure and function of microbial communities. Here, we applied semi-quanti- tative label-free proteomics using one-dimensional gel electrophoresis combined with LC-MS/MS and normalized spectral counting together with fluorescence in situ hybridization and confocal laser scanning microscopy to characterize the metaproteome of the lung lichen symbiosis Lobaria pulmonaria. In addition to the myco- and photobiont, L. pulmonaria harbors proteins from a highly diverse prokaryotic community, which is dominated by Proteobacteria and including also Archaea. While fungal proteins are most dominant (75.4% of all assigned spectra), about the same amount of spectra were assigned to prokaryotic proteins (10%) and to the green algal photobiont (9%). While the latter proteins were found to be mainly asso- ciated with energy and carbohydrate metabolism, a major proportion of fungal and bacterial proteins appeared to be involved in PTMs and protein turnover and other diverse functions. Keywords: Lichens / Metaproteomics / Microbial ecology / Microbiology Lichens are ecologically obligate, self-sustaining symbioses between a fungal partner (the mycobiont) and an inhabitant population of extracellularly located unicellular or fila- mentous algal or cyanobacterial cells (the photobiont) [1]. The emergence of the lichen habit coincides with a substantial primary evolutionary radiation of ascomycetous fungi and allows both partners to develop complex and exposed thallus structures under environmental situations that would usually not be favorable for them in biological solitude [2]. Even under rather hostile circumstances, the composite organisms or thalli can take thousands of years to develop [3]. In the last years it was shown that lichens form mini- ecosystems, which harbor in addition highly abundant and diverse bacterial communities [4–6]. They form biofilm-like structures and show a high degree of species specificity [7]. Although the structure and composition of lichen-associated bacterial communities have been studied by molecular tools (reviewed in [8]) it is difficult to analyze their function. Investigations on bacterial isolates and functional genes suggested that they are involved in nitrogen fixation and nutrient cycling [6]. For a deeper understanding of the Colour Online: See the article online to view Figs. 1 and 2 in colour. Abbreviation: FISH-CLSM, fluorescent in situ hybridization confocal laser scanning microscopy Correspondence: Professor Kathrin Riedel, Institute of Micro- biology, Braunschweig University of Technology, Inhoffen- strasse 7, D-38124 Braunschweig, Germany E-mail: ak.riedel@tu-bs.de Fax: 143-531-391-5854 & 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com 2752 Proteomics 2011, 11, 2752–2756 DOI 10.1002/pmic.201000679