RESEARCH ARTICLE Contribution of deep dark fixation processes to overall CO 2 incorporation and large vertical changes of microbial populations in stratified karstic lakes Emilio O. Casamayor • Marc Lliro ´s • Antonio Picazo • Albert Barbera ´n • Carles M. Borrego • Antonio Camacho Received: 20 September 2010 / Accepted: 3 March 2011 / Published online: 17 March 2011 Ó Springer Basel AG 2011 Abstract We carried out a detailed study in five stratified lakes in the karstic regions of NE Spain along a redox gradient combining vertical profiles of inorganic carbon dioxide fixation and analysis of microbial (bacteria and archaea) community composition determined by 16S rRNA gene fingerprinting (DGGE), microscopic counts, and pigment analysis. High rates of non-photosynthetic (i.e., ‘‘dark’’) inorganic carbon incorporation were detected mostly at deeper layers after short-term in situ incubations at noon. Significant contribution of dark CO 2 incorporation was observed at the whole lake level for the single time sampling, ranging between 4 and 19% of total carbon fixation measured, and up to 31% in the case of a mero- mictic basin. Good agreement was found between vertical patterns in redox conditions and the different microbial diversity descriptors (DGGE band sequencing, microscopic analysis, and pigment data), showing large vertical changes in microbial community composition covering a wide range of phylogenetic diversity. Cyanobacteria, Alpha and Beta-Proteobacteria, Actinobacteria, Flavobacteria and Flectobacillaceae were the most frequently recovered groups in the DGGE from oxygenated water masses. In anoxic waters, we found Beta-Proteobacteria mostly of the Rhodoferax group, Gamma-Proteobacteria (Chromatia- ceae), Delta-Proteobacteria related to different sulfate reducing bacteria, Chlorobiaceae, and anaerobic Bacteroi- detes spread among the Bacteroidales, Flavobacteriales and Saprospiraceae. However, as a whole, we did not find any significant correlation between dark fixation rates and either nutrient distribution and microbial community composition in the study lakes. All of this suggests that (1) different physiologies and ecologies are simultaneously contributing to the process (2) more sensitive methods are needed and more specific compounds measured and (3) some of the non-specialist microbial populations detected may carry out carbon dioxide assimilation in the dark under in situ conditions. Keywords Primary production Á Dark carbon fixation Á Photosynthetic sulfur bacteria Á Bacteria Á Archaea Á Karstic lakes Á 16S rRNA Á DGGE Introduction Karstic lakes are freshwater ecosystems that develop on sedimentary rocks consisting mainly of calcium Electronic supplementary material The online version of this article (doi:10.1007/s00027-011-0196-5) contains supplementary material, which is available to authorized users. E. O. Casamayor (&) Á A. Barbera ´n Department of Continental Ecology-Biogeodynamics and Biodiversity Interactions, Centre d’Estudis Avanc ¸ats de Blanes, CEAB-CSIC, Blanes, Spain e-mail: casamayor@ceab.csic.es M. Lliro ´s Á C. M. Borrego Group of Molecular Microbial Ecology, Institut d’Ecologia Aquatica, University of Girona, Girona, Spain Present Address: M. Lliro ´s Laboratory of Freshwater Ecology-URBO, Faculte Universitaires Notre Dame de la Paix, University of Namur, Namur, Belgium A. Picazo Á A. Camacho Department of Microbiology and Ecology, Instituto Cavanilles de Biodiversidad y Biologı ´a Evolutiva, University of Valencia, Burjassot, Spain Aquat Sci (2012) 74:61–75 DOI 10.1007/s00027-011-0196-5 Aquatic Sciences 123