Multi-method keystone screening reveals distributed ecological resilience in aquaponic microbiomes

Background Aquaponic systems couple aquaculture and crop production with microbial communities underpinning both the waste removal needs of the fish and nutrient supply needs of the plants. Keystone taxa, organisms whose removal disproportionately restructures the community, are well-documented in macroecological food webs (1), yet their existence in aquaponic microbiomes and the practical implications for system monitoring remain untested. We applied a multi-method consensus framework for keystone identification to 16S rRNA gene amplicon data from a research-scale aquaponic facility operating both coupled and decoupled hydraulic configurations. Results 88 amplicon libraries from three compartments (clarifier, fish tank, grow bed) in four treatment configurations (coupled/decoupled × light/dark conditions in the fish tank) across six sampling dates were processed with DADA2, yielding 825 ASVs after prevalence filtering. Three independent keystone screens were applied: leave-one-out PERMANOVA (67 taxa with FDR < 0.05 and R² > 0.02), co-occurrence network hub analysis (four hubs), and LASSO regression on temporal turnover (no individual predictors retained). No taxon was supported by more than one method. Cetobacterium sp. ( Fusobacteriota ) ranked highest in the presence-impact screen (R² up to 0.11) and was strongly enriched in fish tank samples, consistent with its gut-associated ecology; network hubs were environmental biofilm-associated Proteobacteria and Planctomycetota . Conclusions The absence of cross-method convergence is consistent with a distributed ecological architecture in which community function is spread across habitats and functional guilds rather than concentrated in any single taxon. Aquaponic microbiome monitoring should therefore target compartment-specific indicators and operating conditions rather than universal keystone candidates. Cetobacterium nonetheless stood out as a useful fish-tank community marker, but its influence does not extend system-wide. In practice, monitoring compartment-specific assemblages, especially Cetobacterium in fish tanks and Chitinophagaceae in biofilm fractions, is more tractable than targeting a single universal keystone organism.