Community reconfiguration in hydrogen-driven denitrification under oxidized co-contaminants: Shift or shuffle

Low-carbon nitrogen removal requires H₂-driven microbiomes that remain stable under oxidized co-contaminant stress. We compared hydrogenotrophic communities exposed to Cr(VI), Se(VI), and As(V) + perfluorooctanoic acid (PFOA) in membrane biofilm reactors (MBfRs) and sequencing batch reactors (SBRs), using 16S rRNA profiling and compositional data analysis. Cr(VI) and Se(VI) served as single-inorganic-oxyanion references, while As(V) + PFOA represented a complex co-stress scenario to test backbone persistence under dual toxicity. We defined Shift as directional taxonomic turnover and Shuffle as abundance reweighting within a conserved core. Although α-diversity and genus-level dominance varied with dose, neither Bray-Curtis nor Aitchison ordination showed significant global separation among stressors (permutational multivariate analysis of variance, PERMANOVA: Bray-Curtis R² = 0.201, p = 0.356; Aitchison R² = 0.182, p = 0.796; Permutational analysis of multivariate dispersion, PERMDISP: p > 0.05 for both), a pattern consistent with shuffle-dominant change rather than wholesale community replacement. Set-overlap and Sankey analyses revealed conserved family- and phylum-level backbones centered on Comamonadaceae, Rhodocyclaceae, and Proteobacteria-centered routes. An integrated Stability-Ubiquity-Abundance (SUA) scoring framework with leave-one-sample-out sensitivity analysis prioritized ten candidate cross-contaminant generalists, including Pseudomonas, Stenotrophomonas, Azospira, Acinetobacter, Hydrogenophaga, Flavobacterium, Bradyrhizobium, Reyranella, Mycobacterium, and Sphingomonas. Localized shift signals were most evident under dichromate and in PFOA-sensitive niches. Reactor-configuration sensitivity analyses indicated that reactor configuration alone was unlikely to account for the conserved-backbone pattern. These findings support operating H₂-driven denitrification as a generalist-centered, shuffle-resilient process, with stepwise contaminant loading, stable H₂ supply, and early-warning monitoring of nitrate removal, oxyanion reduction, and conserved core taxa.