Raw data and metadata for: Genotypic diversity positively affects plant performance and soil properties but not bacterial communities

This study conducts a controlled salt-marsh mesocosm experiment to quantify how intraspecific (genotypic) diversity shapes plant performance, soil properties, and rhizosphere bacterial communities in the foundation sedge Scirpus mariqueter from the Yangtze River Estuary. The experiment integrates 96 pot-level experimental units (0.79 L pots, 10 cm × 10 cm; eight sprouted corms per pot) assembled from 16 genetically distinct, naturally occurring genotypes that were previously field-collected and clonally propagated to standardize plant material. The design combines monocultures and multi-genotype mixtures to disentangle genotype identity effects from genotypic richness effects: 48 monoculture pots (16 genotypes × 3 replicates) and 48 mixture pots composed of either 4-genotype mixtures (two corms per genotype) or 8-genotype mixtures (one corm per genotype). Mixtures were further structured to span different levels of genetic dissimilarity among component genotypes (e.g., low/medium/high genetic distance categories) so that responses could be evaluated along both genotypic richness and genetic distance gradients. All pots were filled with sieved marsh soil sourced from a Scirpus restoration area and were maintained in a common 2400-L outdoor cement pond to impose uniform abiotic conditions; after an initial freshwater saturation and acclimation period, salinity was adjusted stepwise (targeting 5‰ and then 10‰), and standardized nutrient additions were applied at regular intervals, with full water replacement and pot re-randomization prior to each addition to minimize spatial heterogeneity. The experiment ran from late March to late October 2018, concluding at seed maturity, and quantified responses across multiple trophic/compartment endpoints, including plant growth and reproduction (e.g., above- and belowground biomass, ramet density, corm production, inflorescence/seed metrics and tissue N), soil biogeochemistry (e.g., soil total N, soil organic C and available P), and rhizosphere bacterial communities characterized via 16S rRNA amplicon sequencing. To explicitly evaluate whether mixture performance was explainable by additive contributions of component genotypes or reflected emergent nonadditive processes, mixture outcomes were compared against null additive expectations generated from monoculture trait distributions using Monte Carlo resampling, producing simulation envelopes that classify mixture responses as additive versus nonadditive. Collectively, this integrative experimental design tests whether increasing genotypic diversity in a dominant marsh plant (i) enhances plant performance through complementarity or reduced intraspecific competition, (ii) alters soil nutrient pools and carbon storage, and (iii) modifies— or fails to modify—rhizosphere bacterial diversity and composition, thereby clarifying the pathways by which genetic diversity may influence ecosystem functioning in coastal wetlands. Our findings collectively reveal that genotypic diversity enhances plant productivity and soil nitrogen pools without restructuring microbial communities, providing mechanistic insights into how intraspecific variation stabilizes and promotes ecosystem functioning in salt-marsh.