In this paper the authors look at how anthropogenic perturbation (e.g. addition of new electron acceptors and donors and new microbes) influences a deep subsurface oil reservoir. The oil reservoir studied was subjected to both seawater and nitrite injections, which induced a shift in the microbial communities from slow growing anaerobic bacteria (Thermotogae and Clostridiales) to fast growing opportunists (Deferribacteres, Delta-, Epsilon- and Gammaproteobacteria). Interestingly, the analysis of the primary production wells, which have the least anthropogenic input, suggested that the formation water-chemical composition influences the structure of the indigenous communities and that different indigenous communities can co-occur within an oil reservoir.