We compared the spatial distribution and diversity of autotrophic microbial communities among four permanently ice-covered, chemically stratified lakes located in the Taylor (Lakes Bonney-east and west lobes, Fryxell), and Wright (Lake Vanda) Valleys of the McMurdo Dry Valleys (Victoria Land, Antarctica). Clone libraries were constructed for major carbon fixation genes (rbcL isoforms IA/B and ID; cbbM; nifJ). Real time quantitative polymerase chain reaction assays were also developed for each of these markers of autotrophy to assess the influence of lake physicochemical factors on spatial trends in major photosynthetic and chemolithoautotrophic groups. Both lobes of Lake Bonney were dominated by Ribulose-1, 5-bisphosphate carboxylase oxygenase (RubisCO) form ID rbcL (haptophytes and stramenopiles), while Lake Fryxell was dominated by rbcL form ID-harboring cryptophytes. Lake Vanda was the least productive lake and was dominated by form IA/B rbcL (cyanobacteria and chlorophytes) and form ID rbcL (stramenopiles). Autotrophic carbon fixation genes from photosynthetic organisms were generally positively correlated with light availability. Chemolithoautotrophic organisms harboring form II RubisCO were detected in only two of the four lakes (west lobe Lake Bonney and Fryxell) and were associated with the presence of either sulfide (Fryxell) or dimethylated sulfur compounds (west lobe Lake Bonney).

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