Despite recent progress in understanding soil microbial responses to carbon (C) limitation, the functional shifts in microbial community structure associated with decreasing soil C availability and changes in organic matter chemistry remain poorly known. It has been proposed that Gram-negative (GN) bacteria use more plant-derived C sources that are relatively labile, while Gram-positive (GP) bacteria use C sources derived from soil organic matter that are more recalcitrant. Because these two groups may differ in how they influence the fate of different C forms in soils, it is important to understand how they vary across ecosystems that differ in their vegetation cover and ecosystem productivity or across environmental gradients. In this study, we used a 19-year plant functional group removal experiment across a long term post-fire chronosequence to assess how microbial community structure (assessed using phospholipids fatty acids; PLFAs) and the association of bacterial functional groups (specifically, the GP:GN ratio) responded to changes in organic matter chemistry (measured via nuclear magnetic resonance; NMR). We found that the GP:GN ratio increased upon removal of shrubs and tree roots and with decreasing ecosystem productivity along the chronosequence, thus showing the greater dependence of GN than GP bacteria on more labile plant-derived C. Overall, GN bacteria were associated with simple C compounds (alkyls) whereas GP bacteria were more strongly associated with more complex C forms (carbonyls). Therefore, we conclude that the GP:GN ratio has potential as a useful indicator of the relative C availability for soil bacterial communities in organic soils, and can be used as a coarse indicator of energy limitation in natural ecosystems.