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Journal : research of scientia naturalis

PLANT–SOIL–MICROBE INTERACTIONS REVISITED: MECHANISTIC INSIGHTS FROM BIOMOLECULAR AND ECOLOGICAL INTEGRATION Jihoon, Park; Siregar, Adelina; Tanaka, Kaito; Davis, Michael
Research of Scientia Naturalis Vol. 3 No. 1 (2026)
Publisher : Yayasan Adra Karima Hubbi

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.70177/scientia.v3i1.3468

Abstract

Plant–soil–microbe interactions underpin nutrient cycling, ecosystem productivity, and resilience under environmental change. Despite advances in rhizosphere ecology and molecular biology, integration between biomolecular processes and ecosystem-level dynamics remains fragmented. This study aims to develop and empirically validate a mechanistic framework linking gene expression, metabolite exchange, microbial functional traits, and ecological outcomes across controlled and field contexts. A multi-scale design combined greenhouse factorial experiments with field validation, integrating metagenomics, metatranscriptomics, metabolomics, soil nutrient assays, and ecological network modeling. Structural equation modeling and multivariate analyses were applied to identify causal pathways among root exudation, microbial functional gene abundance, nutrient availability, and plant biomass. Results demonstrate that functional gene abundance (? = 0.46, p < 0.001) and root metabolite diversity (? = 0.39, p < 0.01) significantly predict plant productivity, while network analysis identifies organic acids and nitrogen-fixing taxa as keystone interaction nodes. Drought treatments induced coordinated upregulation of stress-response genes and metabolite adjustments, partially buffering productivity losses. The study concludes that rhizosphere resilience emerges from tightly coupled biomolecular and ecological feedback mechanisms. Integrative multi-omics combined with ecological modeling enhances predictive understanding of ecosystem function under environmental variability.
BEYOND SPECIES RICHNESS: QUANTIFYING FUNCTIONAL BIODIVERSITY THROUGH MATHEMATICAL ECOLOGY Xiang, Yang; Tanaka, Kaito; Hoffmann, Lena
Research of Scientia Naturalis Vol. 3 No. 1 (2026)
Publisher : Yayasan Adra Karima Hubbi

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.70177/scientia.v3i1.3540

Abstract

Biodiversity has traditionally been assessed through species richness, yet this approach often fails to capture the functional roles that determine ecosystem processes and resilience. Increasing ecological evidence indicates that ecosystems with similar species counts may differ substantially in functional composition, leading to divergent ecological outcomes. This study aims to develop a mathematical ecology framework that quantifies functional biodiversity by integrating trait-based analysis with nonlinear modeling. The research employs a quantitative design combining secondary ecological datasets, multidimensional trait space construction, and computational modeling to evaluate relationships between functional diversity and ecosystem performance. Results demonstrate that functional richness, evenness, and divergence significantly predict ecosystem productivity and stability, while species richness shows limited explanatory power. Nonlinear analysis reveals threshold effects and complex interactions, indicating that functional trait composition governs ecosystem responses to environmental change. Functional diversity also shapes network structure, enhancing system resilience through redundancy and complementarity among traits. The study concludes that functional biodiversity provides a more comprehensive and predictive measure of ecological complexity than species richness alone. Integration of mathematical ecology with trait-based approaches offers a robust analytical framework for advancing biodiversity research and informing conservation strategies.