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Microorganisms

Microorganisms is a scientific, peer-reviewed, open access journal of microbiology, published monthly online by MDPI. The Hellenic Society Mikrobiokosmos (MBK), the Spanish Society for Nitrogen Fixation (SEFIN) and the Society for Microbial Ecology and Disease (SOMED) are affiliated with Microorganisms, and their members receive a discount on the article processing charges.

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All Articles (19,449)

  • Article
  • Open Access

Plant growth-promoting rhizobacteria (PGPR) offer a sustainable alternative to chemical fertilizers in rice production, yet the mechanisms underlying multifunctional growth promotion by individual strains remain insufficiently characterized. In this study, strain ST2023006 was isolated from the sugarcane rhizosphere and systematically characterized through phenotypic assays and whole-genome sequencing. The strain was identified as Pseudomonas chlororaphis based on morphological, physiological, biochemical, and multilocus sequence analyses. It exhibited tolerance to temperature (25–37 °C), pH (5.0–9.0), and salinity (≤2% NaCl). 15N isotope dilution analysis revealed nitrogen fixation contribution rates of 13.4% and 9.72% to rice roots and shoots, respectively. Pot experiments demonstrated that inoculation significantly promoted growth in two rice varieties, increasing plant height by up to 86.6%, while enhancing root surface area, root volume, and biomass accumulation. In vitro antagonism against Rhizoctonia solani and quantitative IAA analysis (59.44 µg·mL−1 IAA equivalents) provided experimental support for genome-predicted in vitro antifungal potential and auxin-related traits. Whole-genome sequencing revealed genes potentially associated with nitrogen metabolism (nifU, fixI), nutrient mobilization (potassium/zinc solubilization, siderophores), phytohormone synthesis (IAA), stress tolerance (heavy metal resistance, heat/cold shock proteins), and complete biosynthetic gene clusters for the antifungal compounds pyrrolnitrin, phenazine, and hydrogen cyanide, predicting a genomic potential for antifungal activity. This potential was directly demonstrated by in vitro antagonism assays against Rhizoctonia solani. These findings indicate that P. chlororaphis ST2023006 is a promising multifunctional PGPR candidate with demonstrated plant growth-promoting effects at the seeding stage and experimentally supported genomic potential for in vitro antifungal activity.

Microorganisms

14 November 2026

Tolerances of the strain ST2023006 to temperature, pH, and NaCl (A) Temperature; (B) pH; (C) NaCl.
  • Article
  • Open Access

This in vitro study evaluated 48-h biofilm-associated viable cell recovery of Streptococcus salivarius BLIS K12 and M18 on conventionally heat polymerized (CV), CAD/CAM-milled (ML), and 3D-printed (PR) denture base materials and examined the associations between probiotic biofilm-associated viable CFU recovery, qualitatively visualized live/dead fluorescence patterns and material surface characteristics. Eighty-seven disc-shaped specimens were fabricated from three denture base materials and characterized for surface roughness (Ra), contact angle (CA; n = 20 per material), and surface morphology (n = 1). Following salivary pellicle formation, specimens (n = 14 per material–strain group) were inoculated separately with standardized suspensions of S. salivarius K12 or M18 and incubated for 48 h. After 48 h of incubation, biofilm-associated viable cells were quantified by CFU enumeration and expressed as log10 CFU/mm2, while live/dead fluorescence patterns and biofilm distribution were qualitatively assessed using confocal laser scanning microscopy (CLSM). The effects of denture base material, probiotic strain, and their interaction on biofilm-associated viable cell recovery were evaluated using a heteroscedasticity-robust factorial model with HC3 standard errors. Associations between surface properties and biofilm-associated viable cell recovery were assessed separately for each strain using Spearman’s rank correlation and multiple linear regression. Surface roughness and contact angle differed significantly among the three materials (p < 0.001 and p = 0.019, respectively). Biofilm-associated viable cell recovery was significantly affected by denture base material and probiotic strain, with a significant material × strain interaction (all p < 0.001). K12 recovery was significantly lower on CV than on ML and PR, whereas M18 recovery was significantly higher on ML than on CV and PR. K12 exhibited significantly greater recovery than M18 on PR (p < 0.001), while no significant strain-dependent differences were observed on CV or ML. Exploratory correlation analysis revealed a modest inverse association between K12 recovery and CA (ρ = −0.367, unadjusted p = 0.046), which was not statistically significant after Holm correction for multiple comparisons (adjusted p = 0.184). No significant correlations were observed between Ra and recovery for either strain or between CA and M18 recovery. Multiple regression models incorporating both surface characteristics were not statistically significant for either strain. Forty-eight-hour biofilm-associated viable cell recovery of S. salivarius K12 and M18 was material- and strain-dependent, with the most pronounced strain-specific difference observed on PR. Surface roughness and wettability alone did not consistently explain the observed differences in viable cell recovery. These findings highlight the importance of considering both probiotic strain and denture base material when investigating probiotic–denture interactions.

Microorganisms

14 November 2026

A graphical representation of the study flowchart.
  • Article
  • Open Access

Strong environmental gradients in arid salt lake wetlands are expected to reshape ecological relationships among plants, soil, and microorganisms; however, whether these relationships remain consistent with classical ecological principles under extreme stress remains poorly understood. Here, we investigated five typical ecosystems in the Ebinur Lake wetland, Xinjiang (soil EC: 1.81–12.69 mS cm−1; SWC: 5.73–19.53%), using plant community surveys, soil physicochemical analyses, and 16S rRNA and ITS amplicon sequencing to examine the relationships among plant diversity, soil environment, and bacterial and fungal communities. Bacteria and fungi responded differently along the environmental gradient. Bacterial α-diversity (Chao1 and Shannon indices) was significantly higher in EW and lowest in ALL (p < 0.05), with significant β-diversity habitat differentiation (PERMANOVA: R2 = 0.568, p = 0.002), whereas fungal communities remained stable with no significant α- or β-diversity differences. PLS-SEM further revealed that soil physicochemical properties were most strongly associated with bacterial diversity (β = −0.7266, p < 0.001), while plant diversity showed no significant direct effect. Thus, under persistent water–salinity stress and heterogeneous nutrient conditions, bacterial diversity was more strongly associated with soil physicochemical properties than with plant diversity. Overall, this study reveals a contrasting community assembly pattern of “strong bacterial response and weak fungal response” and highlights the strong association between plant–soil–microbe relationships and environmental filtering under extreme conditions.

Microorganisms

14 November 2026

Overview of the study area and sampling sites. (a) Location of Xinjiang in China; (b) Location of the Ebinur Lake wetland in Xinjiang, northwest China; (c) Distribution of sampling sites of the five ecosystem types in the Ebinur Lake wetland. Landscape photographs of the five ecosystem types: Lakeshore alluvium ecosystem (ALL), Mudflat wetland ecosystem (DLB), Estuarine wetland ecosystem (EW), Salt marsh ecosystem (SAS), and Sand dune ecosystem (SD).
  • Article
  • Open Access

Carotenoids play essential roles in insect physiology and are the primary determinants of cocoon color in the silkworm, Bombyx mori. While the host genetic mechanisms governing selective carotenoid transport are well characterized, how divergent host cocoon-color phenotypes relate to gut microbiome structure and assembly remains poorly understood. In this study, we compared the midgut microbiota of divergently selected yellow-cocoon silkworm lines (deep-yellow G101H and light-yellow G101L, derived from a common ancestral stock) and a white-cocoon reference strain (Jingsong, CK) reared under identical mulberry leaf dietary conditions. High-performance liquid chromatography (HPLC) analysis revealed that, relative to the β-carotene-to-lutein ratio in dietary mulberry leaves (0.25 ± 0.05), the relative fecal accumulation of β-carotene was significantly reduced in both CK (0.15 ± 0.04) and G101H (0.12 ± 0.03) groups (p < 0.05), with G101H exhibiting numerically lower mean residual fecal β-carotene levels than CK (0.69 ± 0.23 vs. 0.92 ± 0.29 mg/g dry weight, p > 0.05), coinciding with pronounced structural shifts in the midgut microbiota. Moreover, 16S rRNA gene amplicon sequencing of midgut contents (n = 3 biological replicates per group, 10 pooled larvae per replicate) demonstrated significant divergence in microbial community structure across strains (PERMANOVA R2 = 0.7781, p = 0.005; PERMDISP p = 0.052). Notably, relative to G101L, the G101H line exhibited significantly reduced alpha diversity (Shannon index = 1.24 ± 0.07, overall p = 0.0193; Simpson index = 0.55 ± 0.02, overall p = 0.0014), lower intra-strain genus distribution uniformity (Levins’ B), higher taxonomic turnover (RCbray), and a marked enrichment of Proteobacteria-affiliated taxa, particularly Methylobacterium (63.46 ± 1.89%) and Erwinia_B. Furthermore, complementary high-throughput in vitro screening across 280 parallel microcultures indicated that exogenous β-carotene supplementation under alkaline conditions lowered the bulk median community OD600 (p = 0.0001) and was associated with a compositional shift within Proteobacteria in the subcultured top-growing consortia. This shift reduced the relative abundance of Rhizobiales (from 42.45% to 7.90%, indicating no direct in vitro promotion of Methylobacterium) while enriching fast-growing Burkholderiales and Sphingomonadales. Collectively, these findings reveal a close association between host cocoon-color phenotypes and gut microbial community restructuring, offering new ecological insights into the interplay between host physiological traits and intestinal symbiont assembly.

Microorganisms

14 November 2026

Analysis of carotenoid content and composition in different samples. (A) Representative images of silk glands from the G101H, G101L, and CK strains. (B) Cocoon phenotypes of the corresponding silkworm strains. (C) HPLC quantification of lutein and β-carotene (mg/g dry weight, DW) in mulberry leaves (ML), G101H cocoons (G101H-C), G101H feces (G101H-F), and CK feces (CK-F). (D) The β-carotene/lutein ratio in different samples. Data are presented as mean ± SD (n = 3). In (C,D), ND indicates that β-carotene in G101H cocoons was below the limit of detection (LOD = 0.03 µg/mL) and was therefore excluded from parametric variance tests. Asterisks in (C) indicate statistical significance between lutein and β-carotene within quantifiable samples (** p &lt; 0.01, *** p &lt; 0.001; two-tailed Student’s t-test). Different lowercase letters in (D) denote statistically significant differences among groups (p &lt; 0.05; one-way ANOVA followed by Tukey’s post-hoc test).

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Microorganisms - ISSN 2076-2607