Microbial communities control many biogeochemical processes. Many of these processes are impractical or expensive to measure directly.

Sulfate-reducing bacteria (SRB) are one of the main sources of biogenic H 2 S generation in oil reservoirs. Excess H 2 S production in these systems leads to oil biosouring, which causes operational risks, health hazards and can increase the cost of refining crude oil. Nitrate salts are often added to the system to suppress sulfidogenesis. Because SRB populations can persist in biofilms even after nitrate treatment, identifying shifts in the sessile community is crucial for successful mitigation. However, sampling the sessile community is hampered by its inaccessibility. Here we use the results of a long-term (148 days) ex situ experiment to identify particular sessile community members from observations of the sample waste stream. Microbial community structure was determined for 731 samples across twenty bioreactors using 16S rRNA gene sequencing. By associating microbial community structure with specific steps in the mitigation process, we could distinguish between taxa associated with H 2 S production and mitigation. After initiation of nitrate treatment, certain SRB populations increased in the planktonic community during critical time points, indicating the dissociation of SRBs from the biofilm. Predicted relative abundances of the dissimilatory sulfate reduction pathway also increased during the critical time points. Here, by analyzing the planktonic community structure, we describe a general method that uses high-throughput amplicon sequencing, metabolic inferences, and cell abundance data to identify successful biofilm mitigation. We anticipate that our approach is also applicable to other systems where biofilms must be mitigated but cannot be easily sampled. Importance Microbial biofilms are commonly present in many industrial processes and can negatively impact performance and safety. Within the oil industry, subterranean biofilms cause biosouring with implications for oil quality, cost, occupational health, and the environment. Because these biofilms cannot be directly sampled, methods are needed to indirectly assess the success of mitigation measures. This study demonstrates how the planktonic microbial community can be used to assess the dissociation of SRB-containing biofilms. We found that an increase in the abundance of a specific SRB population in the effluent after nitrate treatment can be used as a potential indicator for the successful mitigation of biofilm-forming SRBs. Moreover, a method for determining critical time points for detecting potential indicators is suggested. This study expands our knowledge in improving mitigation strategies for biosouring and could have broader implications in other systems where biofilms lead to adverse consequences.