Insights into the microbial autotrophic potential of a shallow oligotrophic alpine pond

Carbon dioxide fixation is one of the most important biogeochemical processes worldwide, but our current understanding of the distribution of microbial autotrophy and its ecological significance in oligotrophic freshwater systems, and particularly in benthic habitats, is poor and limited primarily to photoautotrophic organisms. In this study we investigated the autotrophic microbial communities inhabiting the sediments of a high-elevation, oligotrophic freshwater pond in the north-western Italian Alps. The abundance and distribution of three different forms of the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) large-subunit gene (cbbLG, Form I green-like; cbbLR, Form I red-like; cbbM, Form II) were assessed in samples collected at different depths by quantitative polymerase chain reaction (qPCR); correlations with sediment geochemical properties and total bacterial abundance were also examined. RuBisCO forms cbbLG, cbbLR and cbbM were all detected, with abundances of 9.13–10.90, 6.93–8.77 and 6.75–7.93 log(copies) g–1 dry weight respectively. For all the RuBisCO genes, interannual variability overcame depth-related variability. The abundance of RuBisCO genes was strongly correlated with total bacterial abundance, and both were positively correlated with Ca2+ and Mg2+ concentrations. These observations provide some first indications of the distribution of photo- and chemolithoautotrophic bacteria relying on the Calvin–Benson–Bassham cycle for C fixation in alpine pond sediments, and suggest that they may represent an important component of the total benthic microbial community.