Contribution of deep dark fixation processes to overall CO2 incorporation and large vertical changes of microbial populations in stratified karstic lakes

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 CO2 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 meromictic 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 (Chromatiaceae), Delta-Proteobacteria related to different sulfate reducing bacteria, Chlorobiaceae, and anaerobic Bacteroidetes 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.