ARTICLE pubs.acs.org/jpr Macromolecular Fingerprinting of Sulfolobus Species in Biofilm: A Transcriptomic and Proteomic Approach Combined with Spectroscopic Analysis Andrea Koerdt,†,‡ Alvaro Orell,†,‡ Trong Khoa Pham,§ Joy Mukherjee,§ Alexander Wlodkowski, Esther Karunakaran,§ Catherine A. Biggs,§ Phillip C. Wright,§ and Sonja-Verena Albers*,† † †Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg, Germany §ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheﬃeld, Mappin Street, Sheﬃeld, S1 3JD, United Kingdom bS Supporting Information ABSTRACT: Microorganisms in nature often live in surface- associated sessile communities, encased in a self-produced matrix, referred to as bioﬁlms. Bioﬁlms have been well studied in bacteria but in a limited way for archaea. We have recently character- ized bioﬁlm formation in three closely related hyperthermophi- lic crenarchaeotes: Sulfolobus acidocaldarius, S. solfataricus, and S. tokodaii. These strains form diﬀerent communities ranging from simple carpet structures in S. solfataricus to high density tower-like structures in S. acidocaldarius under static condition. Here, we combine spectroscopic, proteomic, and transcrip- tomic analyses to describe physiological and regulatory features associated with bioﬁlms. Spectroscopic analysis reveals that in comparison to planktonic life-style, bioﬁlm life-style has dis- tinctive inﬂuence on the physiology of each Sulfolobus spp. Proteomic and transcriptomic data show that bioﬁlm-forming life-style is strain speciﬁc (eg ca. 15% of the S. acidocaldarius genes were diﬀerently expressed, S. solfataricus and S. tokodaii had ∼3.4 and ∼1%, respectively). The -omic data showed that regulated ORFs were widely distributed in basic cellular functions, including surface modiﬁcations. Several regulated genes are common to bioﬁlm-forming cells in all three species. One of the most striking common response genes include putative Lrs14-like transcriptional regulators, indicating their possible roles as a key regulatory factor in bioﬁlm development. KEYWORDS: archaea, sulfolobus, bioﬁlm, proteomics, transcriptomics, FTIR, thermophilic, acidophilic ’ INTRODUCTION It is now broadly recognized that microorganisms in their natural environments are most often found in surface-associated sessile communities, known as bioﬁlms. This multicellular behavior oﬀers the community members beneﬁts, particularly with regard to increased resistance against environmental ﬂuctuations such as temperature, pH and nutrient availability.1 The underlying me- chanisms behind bioﬁlm formation and its importance for micro- bial survival in natural habitats have attracted increasing interest. Bacterial model bioﬁlm studies have identiﬁed many phenotypes and have provided information on numerous of factors that are important during bioﬁlm development and could be of widespread relevance beyond their importance in model systems. Among these factors are cell-to-cell communication, cell attachment mechan- isms, cell-to-cell interconnecting components, surface-associated spreading mechanisms, dispersion mechanisms and genetic ele- ments related to the regulation of bioﬁlm development. Although archaea are frequently detected in bioﬁlm commu- nities in a wide variety of environments,2,3 limited information is available describing bioﬁlm formation in this domain of life. The ﬁrst archaeal bioﬁlm was described for the hyperthermophilic euryarchaeon Thermococcus litoralis. The T. litoralis bioﬁlm developed in rich media on hydrophilic surfaces, for example, polycarbonate ﬁlters, and was accompanied by mannose-type extracellular polysaccharides production.4 The hyperthermo- phile Pyrococcus furiosus was shown to attach to surfaces of mica and carbon coated electron microscopy grids. During this process, the ﬂagella of the cells formed cablelike structures.5 Additionally, P. furiosus adherence to glass was only possible by cocolonization with Methanopyrus kandlerii by using its ﬂagella and establishing cell-to-cell contacts.6 For Archaeoglobus fulgidus, Received: April 1, 2011 Published: July 18, 2011 r 2011 American Chemical Society 4105 dx.doi.org/10.1021/pr2003006 | J. Proteome Res. 2011, 10, 4105–4119