Dark biosphere research has been widely neglected, although by volume this biome comprises the lion’s share of habitats on our planet. In these systems the main metabolic strategies are of chemotrophic nature, leading to gradual depletion of redox gradients essential for sustaining life. Thus these environments are regarded more or less close to chemical equilibrium.Here, we use sequence data of whole community metagenomes and taxonomic marker approaches to study the ecology of environments close to the thermodynamic limit: deep terrestrial aquifers and aphotic systems impacted by petroleum- derived products. We show that these systems select for individuals with reduced genomes and cell sizes, likely as a mode to save energy. Due to genome reduction, these so called “streamlined” cells are reduced in the number of genes and metabolic pathways. This loss has led to community members sharing the metabolic burden of synthesizing in particular energy costly metabolites, creating tight interdependencies between the community members, as a consequence. In addition, we propose that cells scavenging anabolic products derived from detrital biomass and intermediate fermentation products are equally important in these systems. Hence, life at the thermodynamic limit involves a much more complex biological system than previously shown, that goes beyond traditionally described electron- and intermediate metabolite-transfer dependencies.This thesis furthermore includes ecological implications, demonstrating how species diversity and community metabolism are shaped by redox gradients and dispersal potential in the deep biosphere and contaminated sediments. This research is also relevant from a practical point of view, as it pinpoints new opportunities for enhanced bioremediation through metabolite additions in order to raise the efficiency of degradation processes.