Aug 2026· Microorganisms· Vol 14, pp. 1850· 0 citations· 47 references
Medicine
TL;DR
Evidence is provided linking bacterial colonization, host transcriptomic regulation, carbon allocation, and biomass production in duckweed, offering a basis for engineering high-performance duckweed–microbiome systems for sustainable biomass production.
Abstract
Duckweed-associated plant growth-promoting bacteria have attracted attention for their potential to enhance duckweed biomass production. However, the mechanisms underlying isolate-specific growth promotion are unclear. This study compared the effects of two duckweed-associated bacterial isolates, Terrimicrobium sp. PS02 and Aeromicrobium sp. PS05, on the growth, biomass composition, colonization behavior, and transcriptomic responses of Spirodela polyrhiza. Biomass composition and transcriptome analyses were performed to characterize the host responses. Both isolates enhanced duckweed biomass; PS02 increased it 1.2-fold, whereas PS05 induced a significant 1.4-fold increase compared to the uninoculated control. PS05 established bacterial populations approximately one order of magnitude higher than those of PS02 and formed dense extracellular polymeric substance-mediated microcolonies on the surface. Transcriptome analysis revealed that PS05 induced 1108 differentially expressed genes, compared with 454 in PS02, indicating greater host transcriptomic reprogramming. Functional enrichment of transcriptome responses showed that PS05 preferentially regulates carbohydrate biosynthesis, central carbon metabolism, and starch biosynthesis, significantly enhancing starch accumulation and turion formation without reducing protein or photosynthetic pigment content. This study provides evidence linking bacterial colonization, host transcriptomic regulation, carbon allocation, and biomass production in duckweed, offering a basis for engineering high-performance duckweed–microbiome systems for sustainable biomass production.
This study introduces L. aquatilis strain MC3 as an emerging candidate for bioinoculant development and one of the first reports for identification of L. aquatilis as multifunctional PGPR from Himalayan ecosystems.
S. Devi, Riya Chandel, D. Thakur et al.· Frontiers in Systems Biology· 0 citations
Endophytic bacteria play an important role in plant growth promotion and stress tolerance, offering sustainable alternatives to chemical inputs in agriculture. In this study, an endophytic bacterial strain P1 was isolated and identified as
Pseudomonas stutzeri
, a plant-associated bacterium exhibiting multiple plant growth–promoting traits (PGPTs). Biochemical (qualitative and quantitative) and
in vitro
analyses demonstrated nitrogen fixation, phosphate solubilization, ammonia production, indole-3-acetic acid (IAA) production, biofilm formation, and tolerance to abiotic stresses, including salinity and drought. Furthermore, the P1 strain displayed strong biocontrol activity against the fungal pathogen
Fusarium oxysporum
f. sp.
cumini,
indicating its potential to mitigate biotic stress. Whole-genome sequencing generated a high-quality complete genome of 4,758,235 bp. Functional annotation showed enrichment of metabolic pathways associated with plant-microbe interactions and environmental adaptation. Further analyses using KEGG and PGPT-pred data confirmed the presence of genes associated with direct and indirect PGPT, such as nitrogen fixation, phosphate solubilization, biofilm formation, and stress tolerance. The genome also contained genes related to CAZymes, adhesion, and motility, highlighting a strong plant association, whereas the genome lacked major virulence factors and antimicrobial traits, supporting the non-pathogenic nature of the P1 strain. Overall, these findings demonstrate the potential of P1 as a promising bioinoculant candidate for sustainable agriculture in the potato sector.
Poonam Patel, K. Raval, Satyamitra Shekh et al.· Frontiers in Microbiology· 0 citations
Seed-associated microbiota are emerging as key determinants of early plant establishment and resilience, yet their functional potential in wheat remains underexplored. Here, we isolated and functionally characterized culturable bacterial endophytes from seeds of Triticum aestivum cvs. Saekeumkang, Baeggang, and Ariheuk to assess plant growth promotion and pathogen suppression. Sixteen bacterial strains, belonging to Pseudomonadota, Actinomycetota, and Bacillota, were identified using 16S rRNA gene sequencing. Functional assays revealed the high prevalence of plant growth-promoting traits, with all isolates producing indole-3-acetic acid and 56.25% exhibiting phosphate-solubilizing activity, whereas siderophore production was restricted to Pseudomonas poae WSSR12. Despite this apparent functional redundancy, in planta assays demonstrated strong strain-specific effects on seedling biomass. Neobacillus cucumis WSSR17 consistently induced the highest increase in fresh weight. In parallel, dual culture assays against multiple Fusarium pathogens revealed that only one isolate, Calidifontibacillus erzurumensis WSSR11, showed consistent antifungal activity across all tested Fusarium strains. Notably, isolates combining multiple functional traits did not always correspond to the strongest growth promotion, underscoring the importance of host-microbe compatibility and trait expression in planta. Collectively, these findings reveal a functionally diverse seed endophytic community with complementary roles in plant growth and disease suppression. We propose that rational selection and combination of complementary strains, particularly N. cucumis WSSR17 (growth promotion), C. erzurumensis WSSR11 (biocontrol), and P. poae WSSR12 (multifunctional nutrient mobilization) could enable the development of targeted, multi-strain bioinoculant strategies for wheat. This study advances our understanding of seed microbiome functionality and provides a foundation for microbiome-informed crop improvement.
Management of Myzus persicae in pepper still depends largely on insecticides, but resistance limits the long-term effectiveness of chemical control. Here, we used a microbiome-guided approach to identify rhizosphere bacteria associated with aphid infestation and to evaluate their potential for aphid suppression. Pepper plants were grown in soil collected from nine field sites, and rhizosphere bacterial communities were profiled using full-length 16S rRNA gene sequencing. After excluding soils with extreme physicochemical profiles, aphid-infested plants exhibited distinct rhizosphere bacterial communities characterized by the enrichment of Massilia, Rhizobium, and Chujaibacter. To further investigate these community-level patterns, culture-dependent isolation from aphid-associated rhizosphere soils yielded five strains assigned to the genera Telluria and Massilia. Among them, Telluria sp. 100-57A consistently reduced the estimated aphid population growth rate by 36.2% and 41.5% at the 500- and 1,000-fold dilutions, respectively, compared with the negative control. This strain also induced credible avoidance of treated leaves in detached-leaf choice assays. Transcriptome analysis of pepper plants treated with strain 100-57A showed enrichment of defense-related, jasmonic acid-related, and wound-response categories during the early response period relative to the negative control. Compared with acibenzolar-S-methyl (ASM), strain 100-57A showed stronger enrichment of photosynthesis-related categories, suggesting a defense-associated transcriptional response distinct from ASM treatment. These findings support microbiome-informed strategies for identifying aphid-suppressive bacteria and highlight Telluria sp. 100-57A as a promising candidate for microbiome-based aphid management in pepper.
Jun Su Noh, Gyeongjun Cho, Jihye Jung et al.· Frontiers in Plant Science· 0 citations
Root exudates from Oryza rufi pogon elicit stronger transcriptional responses in benefi cial bacterial endophytes and, together with bacterial inoculation, reveal distinct plant responses compared with cultivated rice, suggesting that microbiome-associated traits altered during domestication could be exploited for sustainable rice breeding. Beneficial interactions between plants and microorganisms strongly influence plant health and productivity, and root exudates play a central role in shaping these associations. In this study, we analyzed the transcriptional responses of the bacterial endophytes Enterobacter asburiae RCA24 and Kosakonia sacchari RCA25 to root exudates from two commercial Italian rice accessions (Oryza sativa Baldo and Vialone Nano) and from an accession of the wild progenitor of tropical rice, Oryza rufipogon. Transcriptome analysis showed that RCA24 displayed distinct responses to the two O. sativa varieties, whereas RCA25 exhibited more extensive transcriptional changes in response to O. rufipogon root exudates. Differentially expressed genes were mainly associated with central metabolism, stress response, and signal transduction, suggesting distinct patterns of bacterial adaptation to the different exudate profiles. Transcriptome analysis of inoculated rice further indicated broader transcriptional changes in plants colonized by RCA24 than in those colonized by RCA25. Differentially expressed genes, particularly in shoots, were associated with defense responses, hormone-mediated signaling pathways, and ribosome biogenesis, consistent with genotype-dependent plant responses to different bacterial strains. Overall, these findings indicate that wild and cultivated rice accessions differ in their interaction with beneficial bacterial endophytes at the transcriptional level. Traits associated with plant–microbiota interactions in O. rufipogon, which are lost during domestication and diversification, may represent valuable targets for future studies aimed at enhancing beneficial microbial associations in cultivated rice.
Francesca A. Vaccaro, Maria Laura Amenta, Iacopo Passeri et al.· Plant Cell Reports· 0 citations
Stem rot disease frequently occurs during the artificial cultivation of Dendrobium officinale Kimura et Migo, which has adverse effects on its yield and quality. Endophytic bacteria present in plants represented potential sources of biocontrol agents. This study isolated 43 distinct microbial strains from wild Dendrobium moniliforme (L.) Sw., among which strain MEPP0209 exhibited significant inhibition of Lasiodiplodia theobromae hyphal growth. Based on the 16S rDNA sequences, the strain was identified as Streptomyces sp. MEPP0209. The cell-free supernatant (CFS) of MEPP0209 significantly inhibited L. theobromae growth, and effectively reduced the disease index of stem rot in D. officinale tissue-cultured seedlings. Transcriptome analysis showed that differentially expressed genes (DEGs) related to cell division and cell cycle were significantly downregulated in L. theobromae hyphae after MEPP0209 CFS treatment, such as MCM2/3/4/5/6/7, NDT80, POLA1, and MBP1, while DEGs related to energy metabolism and oxidative stress were significantly upregulated. Metabolomics analysis and in vitro antagonistic assays indicated that the candidate antagonistic substances, 5,6-dimethylbenzimidazole and pyrrole-2-carboxylic acid, can effectively inhibit the growth of L. theobromae. And qRT-PCR results obtained from the pathogen treated with these two metabolites further indicated the downregulation of genes implicated in cell division and cell cycle. Overall, our findings suggested that the inhibition of fungal growth by MEPP0209 may be associated with the downregulation of genes related to cell division and proliferation in L. theobromae. The metabolites produced by MEPP0209, including 5,6-dimethylbenzimidazole and pyrrole-2-carboxylic acid, likely contributed to this inhibitory effect. This study provides a theoretical basis for future investigations into the role of MEPP0209 in biological control of D. officinale stem rot.
Zhi-Li Jiang, Hailan Fu, Yujie Chen et al.· Applied Microbiology and Bio...· 0 citations
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