Ecological dynamics and vertical transmission of rice seed endophytes: Implications for phytomanagement and biomass production on heavy metal–contaminated farmland
Description
Heavy metal contamination of agricultural soils threatens food security while constraining biomass-based industrial development. Rice (Oryza sativa), one of the world’s highest biomass-producing cereals, holds dual potential for safe grain production and phytomanagement of cadmium (Cd)-contaminated farmland. However, the role of heritable seed endophytic fungi in regulating Cd accumulation and biomass performance remains unclear. We investigated three low-Cd-accumulating and two high-Cd-accumulating rice cultivars to characterize the composition, functional potential, and vertical transmission of seed endophytic fungi. A total of 895 fungal OTUs were identified, forming genotype-dependent communities. A pronounced richness–abundance decoupling pattern was observed: core OTUs accounted for <17.5% of richness but contributed >75.5% of community abundance, whereas rare taxa represented >52.2% of OTUs yet <0.9% of abundance. Community reinoculation and representative strain assays confirmed that seed endophytes significantly promoted plant growth and enhanced Cd tolerance, with evidence of both functional redundancy and complementarity among strains. Vertical transmission analysis revealed strong host filtering, with <15.0% of seed-derived OTUs colonizing progeny tissues. Rare taxa exhibited higher transmission rates (>46.3%) than abundant (<40.5%) and intermediate taxa (<18%), and certain ultra-rare OTUs undetected in parental seeds emerged as dominant taxa in offspring, indicating marked ecological plasticity. These findings demonstrate that seed endophytes combine a stable core with a plastic rare biosphere, providing heritable microbial resources for engineering synthetic consortia and enhancing phytomanagement-based industrial utilization of contaminated farmland.
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Figure 3: The plants were cultivated in a greenhouse for 60 days under natural light conditions (15-30 °C), with soil moisture maintained at 70% water-holding capacity by weight. Prior to harvest, plant height, tiller number, and SPAD chlorophyll content (SPAD-502 Plus, Konica Minolta, Japan) were measured. Plant samples and soil samples were digested using a mixture of HNO3-HClO4 (4:1, v/v) for plant tissues, and HNO3-HClO4-HF (5:1:2, v/v) for soil samples. The total metal concentrations were then measured using a flame atomic absorption spectrometer (Hitachi, FAAS ZA-3000, Japan). The bioavailability of heavy metals in the soils was evaluated through extraction using a diethylenetriaminepentaacetic acid (DTPA) extraction solution. BCF and TF were calculated as: BCF = Croot / Csoil and TF = Cshoot / Croot (Croot, Cshoot, Csoil: total heavy metal concentrations in roots, shoots, and soil). Figure 4: Phosphate solubilization was tested in PVK medium (5 g/L tricalcium phosphate) after 7 d at 28 °C, with measurements of filtrate pH, mycelial dry weight, and soluble phosphate. Siderophore production was examined on CAS agar (halo formation after 6 d) and quantified in iron-deficient MMN broth by CAS assay at 680 nm. Cd tolerance was evaluated on MMN agar containing 1 mM Cd2+ by colony diameter and tolerance index (TI). ACC deaminase activity and jasmonic acid levels were determined from 7-d culture supernatants using ELISA kits at 450 nm. Figure S3: Detection methods for rice biomass, plant heught, chlorophyll content, total plant Cd accumulation, heavy metal and DTPA-Cd concentrations, as well as BCF and TF, are referenced in Figure 3.