Soil contamination by complex pesticide mixtures poses a systemic threat to ecosystem health, yet the mechanisms of microbial community assembly under the coexistence of legacy and modern pollutants remain insufficiently understood. This study evaluated the influence of legacy organochlorine pesticides (OCPs) versus current-use agrochemicals on the structure and inferred functional potential of soil bacterial communities in the Almaty Region, Kazakhstan, using high-throughput 16S rRNA gene sequencing and GC–MS/MS analysis of 217 compounds. Results revealed a clear contrast between contamination regimes: modern organophosphate insecticides and herbicides, such as simazine (up to 32.3 mg kg⁻¹ at the Amangeldy site), were associated with lower alpha diversity (Shannon ≈ 3.03) and enrichment of copiotrophic taxa such as Pseudomonas and Sphingobium. In contrast, persistent OCP residues, such as p,p′-DDE (up to 1.43 mg kg⁻¹ at the Kyzylkairat site), were associated with higher diversity (Shannon ≈ 5.46) and enrichment of more stress-tolerant oligotrophic lineages, including Acidobacteria and Vicinamibacteraceae. Procrustes analysis supported significant concordance between pesticide profiles and taxonomic structure (M² = 0.286, p < 0.001), indicating that pesticide residue composition was strongly associated with bacterial community structure across the studied soils. The observed shift in community balance, particularly the relative increase in Pseudomonas versus Acidobacteria, is proposed as a candidate compositional indicator of ecosystem instability in semi-arid agricultural soils and may inform future remediation-oriented studies.

This structured critical narrative review evaluates the bacterial transformation of six selected organophosphate pesticides—chlorpyrifos, methyl parathion, parathion, diazinon, malathion, and phosalone—in relation to chemical, mechanistic, and environmental evidence. Peer-reviewed literature was searched in Scopus and PubMed for the period from 1 January 2020 to 26 August 2026 and was supplemented by backward-reference screening and forward citation tracking of foundational studies. Evidence was assessed across eight domains spanning association, tolerance, controlled dissipation, product-resolved transformation, mechanistic attribution, non-sterile-soil validation, detoxification or ecological recovery, and field readiness. The selected compounds reveal substantial differences in pathway resolution: chlorpyrifos has the most developed parent–product evidence base, methyl parathion and parathion are comparatively well characterized at the hydrolytic and enzyme levels, diazinon and malathion retain important downstream uncertainties, and phosalone remains an unresolved evidence-gap comparator. The synthesis shows that credible soil bioremediation requires convergence among parent–product kinetics, catalytic attribution, transformation-product turnover, performance beyond natural attenuation, toxicity reduction, and recovery of relevant soil or plant functions.

Fusarium oxysporum-associated disease symptoms in rice (Oryza sativa L.) seedlings represent an experimentally tractable model for evaluating microbiome-mediated disease suppression under controlled conditions. Biological control of Fusarium-associated disease development in rice provides a promising ecological alternative to chemical fungicides. However, the mechanisms underlying the spatial reconfiguration of the host plant multicompartment microbiome in response to complex inoculants remain insufficiently understood. In this study, we investigated the ability of the monoculture Bacillus amyloliquefaciens Bn1 (B. amyloliquefaciens Bn) and phototrophic–heterotrophic consortia composed of Nostoc sp. J-1 and B. amyloliquefaciens Bn1 to suppress Fusarium oxysporum infection, with parallel profiling of bacterial and fungal communities in rhizosphere soil, the root endosphere, and the phyllosphere using 16S rRNA and ITS amplicon sequencing. Phenotypic screening showed that microbial inoculant application significantly reduced the disease index by up to 55% while maintaining plant dry weight. The protective phenotype was not primarily associated with shifts in alpha diversity, but rather with compartment-specific reorganization of microbial communities. These findings suggest that biological control efficacy was associated less with the overall taxonomic scale of microbiome disturbance than with the formation of a functionally balanced, compartment-specific holobiont architecture but by the formation of a functionally balanced, compartment-specific holobiont architecture, providing a conceptual basis for the targeted design of next-generation phototrophic–heterotrophic biopreparations.