Reservoir fluids versus produced water as proxies for oil reservoir microbiomes

Microbial communities influence key processes in oil reservoirs, including souring, corrosion, and hydrocarbon degradation, so characterizing them is important for reservoir management. Reliable characterization depends on obtaining a sample that represents the community living in the subsurface. As nucleic acids are difficult to recover from oil, produced water, the aqueous phase separated from reservoir fluids, is widely used as a convenient proxy for analyzing the reservoir microbiome. However, whether produced water faithfully represents that community, to our knowledge, has never been tested with paired samples. We addressed this question using 16S rRNA gene amplicon and metagenomic sequencing of reservoir fluids and produced water collected from the same production wells across four North Sea oil fields. The two sample types harbored markedly different microbial communities and functional profiles. This difference persisted after accounting for reservoir identity, and it was larger than the differences between reservoirs. Produced water was less diverse, more uniform across fields, and dominated by aerobic genera associated with seawater and aquifers. Reservoir fluids, in contrast, retained the thermophilic, halophilic, and anaerobic taxa characteristic of the deep subsurface. Only 41% of reservoir-fluid genera and 21% of their amplicon sequence variants were also detected in the paired produced water, indicating overlapping broad taxa but largely distinct populations. Notably, the putatively native reservoir community remained detectable in reservoir fluids even after decades of production, while produced water offered only an incomplete, directionally biased view. Reservoir fluids should therefore be sampled wherever feasible to characterize the in-situ microbiome.