The soil microbiome links plant, animal, and human health along the soil–plant–food–human continuum. This review examines how soil- and plant-associated microbiomes, particularly the rhizosphere, influence nutrient cycling, plant disease suppression, pathogen persistence, and antimicrobial resistance. Rhizosphere communities can contribute to plant immunity, whereas intensive inputs, simplified agroecosystems, or pathogen manipulation may cause dysbiosis and weaken colonisation resistance. Disease-suppressive soils can limit plant pathogens, while diverse resident microbiota may also contribute to reduced invasion or persistence of enteric pathogens through related but not necessarily equivalent ecological processes. Synthetic plant protection products (PPPs), microbial active substances, and non-microbial natural substances used for plant protection can alter microbial communities and symbioses. Laboratory exposure to selected pesticide formulations, particularly herbicide formulations, can alter bacterial antibiotic susceptibility, whereas agricultural azole fungicides can select cross-resistance to clinical azoles; however, complete environmental-to-clinical pathways are not established for all such effects. EU PPP assessment relies mainly on standardised functional endpoints, particularly nitrogen transformation, while the Organisation for Economic Co-operation and Development (OECD) framework also includes carbon transformation; these tests incompletely capture community, genomic, and resistome responses. Complementary microbiome and resistome metrics could therefore be incorporated into PPP risk assessment, provided that sampling, quantification, background variability, persistence, and recovery are standardised. Integrating mechanistic evidence, microbiome-informed management, and regulatory assessment is needed to identify persistent effects across plant, animal, human, and environmental health—the core principle of One Health—and to support productive, microbiologically safe cropping systems.
Bacterial blight (BLB) of rice, caused by Xanthomonas oryzae pv. oryzae, is a major constraint to rice production and is difficult to manage using conventional bactericides. Quorum sensing (QS), particularly the diffusible signal factor-mediated system, plays a central role in regulating virulence traits of X. oryzae pv. oryzae such as motility, exopolysaccharide (EPS) production, and biofilm formation. The present study evaluated the anti-QS potential of selected medicinal plant extracts as an eco-friendly strategy to attenuate X. oryzae pv. oryzae virulence. Methanolic leaf extracts of fifteen medicinal plants were initially screened for QS inhibition using Chromobacterium violaceum MTCC 2656 as a biosensor. Six extracts inhibited violacein production, of which four namely Acorus calamus, Lawsonia inermis, Aloe barbadensis, and Ocimum basilicum showed antibacterial activity against X. oryzae pv. oryzae and were selected for detailed studies. Among them, A. calamus exhibited the lowest minimum inhibitory concentration and the strongest suppression of QS-regulated traits in X. oryzae pv. oryzae, including swarming, swimming and twitching motility, EPS production, and biofilm formation. Quantitative assays revealed maximum inhibition of swarming (57.69%), swimming (60.31%), twitching (48.14%) motilities, EPS production (66.67%), and biofilm formation (71.73%) by A. calamus. LC-MS/MS profiling of active extracts identified diverse bioactive phytoconstituents, including flavonoids, phenolics, alkaloids, terpenoids, and fatty acid derivatives, which may collectively contribute to QS interference. The findings demonstrate that medicinal plants, particularly A. calamus, are promising sources of natural QSIs and offer a sustainable, anti-virulence approach for the management of BLB of rice.
Coffee berry rot is an important fungal disease of coffee, yet the identity and pathogenic significance of associated fungi remain poorly documented in Malaysia. From December 2023 to May 2024, symptomatic berries of Coffea arabica, C. canephora, and C. liberica were collected from eight plantations across five states in Peninsular Malaysia. Twenty-one Lasiodiplodia isolates were recovered from 93 symptomatic berries. Morphological characterization and multilocus phylogenetic analyses of the internal transcribed spacer (ITS), translation elongation factor 1-alpha (tef1-α), β-tubulin (tub2), and RNA polymerase II second largest subunit (rpb2) gene regions identified 18 isolates as L. theobromae and three as L. pseudotheobromae. Lasiodiplodia theobromae was recovered more frequently than L. pseudotheobromae across the surveyed plantations. In detached-berry pathogenicity assays, both species produced rot symptoms comparable with those observed in the field, whereas control berries remained symptomless. Lesion development differed significantly among coffee species, but no significant effect of Lasiodiplodia species or fungus × host interaction was detected under the tested conditions. These findings demonstrate the pathogenicity of L. theobromae and L. pseudotheobromae on coffee berries and provide morphological and multilocus evidence of their association with coffee berry rot in Malaysia. The results also indicate that host species contributes substantially to variation in lesion development in detached berries.
Macrophomina phaseolina, the causal agent of charcoal rot disease, poses a major threat to Phaseolus vulgaris production, particularly under climate change. Climate-induced environmental extremes, in which elevated temperatures and drought conditions favour disease development and pathogen aggressiveness, pose a major challenge to agricultural productivity globally. This study assessed the plant growth-promoting and biocontrol potential of six bacterial endophytic isolates against M. phaseolina in P. vulgaris, using an integration of biochemical, physiological antifungal, and seed germination assays. All the isolates show significant potential (p < 0.05) for producing ammonia and indole-3-acetic acid (IAA), solubilising nutrients, exhibiting hydrolytic enzyme activity, and demonstrating biocontrol traits. Of the six isolates, Serratia marcescens (PR1AI2) showed the highest IAA production and zinc solubilization activity, whereas Enterobacter sp. L1I9 showed enhanced phosphate solubilization. Protease activity was highest in PR1AI2, while Pseudomonas rhodesiae strain MSG-15 (L3I2) exhibited the strongest amylase activity. Dual culture assays demonstrated significant inhibition (p < 0.05) of M. phaseolina mycelial growth and reduction in sporulation by the endophytic bacterial isolates. Among the isolates, L3I2 had the highest inhibition of mycelial growth (75.93%), whereas PR1AI2 qualitatively showed the greatest sporulation reduction. Seed germination assays further showed variable responses under M. phaseolina, with Streptomyces bikiniensis strain SBM (L2I3) and Enterobacter kobei strain V51 (PR5AI1) showing germination percentages of 80.00% and 75.56%, respectively, compared with 76.67% in the M. phaseolina-treated control. These isolates therefore represent promising candidates for sustainable biological management of charcoal rot disease in P. vulgaris, as they possess multiple traits associated with pathogen suppression and improved plant development.
Fungal pathogens, particularly Colletotrichum falcatum and Fusarium sacchari, are major constraints to sugarcane productivity worldwide. Chitinases constitute an important component of the plant innate immune system by hydrolyzing chitin, a principal structural polysaccharide of fungal cell walls. In this study, comparative proteomic analysis of sugarcane following Colletotrichum falcatum challenge revealed temporal differences in protein abundance, including changes in proteins associated with chitinase-mediated defense. The observed abundance patterns suggest potential alterations in chitinase-associated defense responses during the early stages of pathogen challenge. However, because the infected samples collected at 3, 6, and 24 h post-inoculation were compared with mock-inoculated samples collected only at 0 h, the contributions of pathogen challenge and time-dependent changes cannot be fully distinguished. Therefore, the observed patterns should be interpreted as changes associated with pathogen challenge rather than definitive evidence of infection-induced suppression of chitinase-mediated immunity. Notably, Chitinase 6 accumulated significantly in the resistant cultivar, whereas Chitinase 5 showed enhanced abundance in the susceptible cultivar. Quantitative real-time PCR (qRT-PCR) analysis revealed predominantly reduced transcript abundance for most chitinases, but also showed strong isoform- and cultivar-specific responses that did not directly correspond to the proteomic patterns. On the other hand, Chitinase 5 showed pronounced transcript induction in BO91, whereas Chitinase 6 showed strong transcript induction in CoJ64. To explore whether chitinase transcriptional responses also occur following challenge with another fungal pathogen, the seven chitinase genes were examined in Fusarium sacchari-infected leaves of the susceptible cultivar Co-7717. The F. sacchari experiment revealed marked changes in chitinase transcript abundance, including pronounced induction of Chitinase 5. Collectively, the findings demonstrate extensive isoform- and cultivar-dependent regulation of sugarcane chitinases during fungal infection and highlight the importance of integrating protein- and transcript-level analyses.
