Search Results (55)

Walnut (Juglans regia L.) performance and sustainability are closely linked to soil–plant–microbe interactions; nowadays, the combined influence of edaphic context, plantation development and rootstock genotype on walnut-associated microbiomes remains insufficiently resolved. Here, we integrated soil physicochemical characterization, community-level physiological profiling and 16S rRNA gene amplicon sequencing across walnut plantations in four Spanish regions. The design included 14-year clonal stands (Galicia, Gerona, Toledo), an age gradient in Galicia (4, 9 and 14 years), and four rootstocks (MJ209, Vlach, own-rooted ‘Chandler’ and J. regia seedling) in the Córdoba plantation. At the community-level, rhizospheres exhibited higher overall metabolic activity, displaying substrate-specific functional fingerprints across regions. Regarding stand ages, a functional peak was observed at middle age, with a decline in richness and diversity with age. Moreover, rootstock genotype further modulated rhizosphere metabolic function. Sequencing supported compositional differences among regions, ages and rootstocks, identifying a bacterial core of Juglans spp. rhizosphere and detecting 36 putative Plant Growth-Promoting Rhizobacteria (PGPR) genera, suggesting a potential reservoir and possible uses in plant biotechnology. Overall, walnut-associated microbiomes are jointly structured by soil gradients, plantation development and rootstock genotype, supporting site and genotype-tailored microbiome management. Full article

Soil salinization threatens crop production; however, in multi-crop field systems, evidence for the effectiveness of waste biomass-functional microorganism composite amendments remains limited. Here, we developed a composite microbial soil conditioner (F2) using pine needles and crushed corn cobs as carriers combined with salt-tolerant strains Bacillus subtilis (K1), Azotobacter chroococcum (Y1), and Bacillus gelatinus (J3) to remediate moderately saline-alkali soil from central Gansu (pH 8.36 ± 0.18; EC 1658 ± 55.24 μS·cm⁻¹). Saturation screening identified an optimal carrier ratio of pine needles:corn cobs = 1:2 and an inoculum ratio of K1:Y1:J3 = 1:2:1. In pot experiments, F2 increased soil organic matter and water-holding capacity, enhanced alkaline phosphatase, urease, and sucrase activities, and significantly reduced soil pH and EC. Maize seedling height and chlorophyll content increased by 53.87% and 38.88%, respectively. Amplicon-based microbiome profiling indicated enrichment of beneficial microbial taxa and strengthened primary metabolic functions under F2. Field validation across five crops (flax, potato, edible sunflower, sorghum, and maize) showed consistent growth and yield-related improvements. Overall, these results demonstrate that the biomass–microbe composite amendment effectively alleviates saline-alkali constraints by jointly improving soil properties, microbial functions, and crop performance. Full article

Background: Overweight and obesity are currently a worldwide problem, with undesirable health consequences, such as type 2 diabetes. Therefore, much attention has been paid to preventing obesity through diet. Free fatty acids (FFAs) serve as signaling molecules in many biological processes, leading to increased energy expenditure and insulin secretion. Short-chain fatty acids (SCFAs) such as acetic, propionic and butyric acid are bioactive metabolites produced by gut microbes, and their beneficial effects on host metabolism are well studied. However, the effects of hexanoic acid on metabolism are poorly understood. Methods: Male C57BL/6J mice were fed a normal chow diet, a high-fat diet (HFD), an HFD containing 5% butyric acid or an HFD containing 5% hexanoic acid for 4 weeks, and the effects of hexanoic acid on their lipid and glucose metabolisms were examined. Results: Dietary supplementation of hexanoic acid or butyric acid for 4 weeks prevented HFD-induced obesity and fat accumulation in the white adipose tissues. Both FFAs also suppressed the elevated plasma non-esterified fatty acid (NEFA) levels and hepatic triglyceride content in the mice fed an HFD. In addition, butyric acid and hexanoic acid decreased the elevated expression of genes involved in fatty acid biosynthesis in the white adipose tissues under HFD conditions. Hyperinsulinemia induced by HFD feeding was attenuated by oral intake of butyric acid or hexanoic acid, whereas hyperglycemia under HFD feeding was improved only through oral administration of hexanoic acid. Hexanoic acid increased plasma glucagon-like peptide-1 (GLP-1) levels and the expression of genes associated with gluconeogenesis. The intraperitoneal glucose tolerance test (IPGTT) and the insulin tolerance test (ITT) revealed that the oral administration of hexanoic acid significantly enhanced glucose tolerance and insulin sensitivity. Conclusions: This study highlights the importance of hexanoic acid in improving lipid and glucose metabolisms. Hexanoic acid, as well as butyric acid, is a remarkable FFA with anti-obesity properties. Furthermore, hexanoic acid is more potent in maintaining glucose homeostasis than butyric acid. Thus, our findings provide insight into the development of functional foods which could prevent obesity-related diseases such as type 2 diabetes. Full article

Aerobic exercise mitigates age-related intestinal senescence through gut microbiota modulation, but the underlying mechanism has remained unclear. In this study, we performed 16S rRNA sequencing of gut contents from young, old, and old exercise C57BL/6J mice to assess exercise-induced alterations in microbiota community structure. Differential taxa analyses were applied to reveal age-associated bacterial signatures, gut barrier integrity, and systemic inflammation. Additionally, untargeted metabolomic profiling was employed to characterize gut metabolic profiles and reveal the key pathways through differential metabolite enrichment analyses. Aging significantly exacerbated the senescence-associated secretory phenotypes and the overgrowth of pathogenic bacteria in mice. However, aerobic exercise ameliorated these age-related deteriorations, restored gut microbial homeostasis, and reduced intestinal permeability. Notably, exercise intervention led to a significant increase in Akkermansia abundance in feces, establishing this mucin-degrading bacterium as a prominent exercise-responsive microbe. Metabolomic profiling identified eicosanoid metabolism as the most significantly perturbed pathway, and chronic exercise was found to regulate 14,15-Dhet levels. Our multi-omics integration confirmed that exercise is a potent modulator of the gut–microbiota–metabolite axis during aging. Elucidating the “Akkermansia–eicosanoid signaling” axis provided mechanistic insights into how exercise promotes healthy aging, identifying novel targets for anti-aging strategies via microbiota. Full article

Hepatitis A viral outbreaks continue to occur. It can be transmitted through aerosolized droplets and thus can contaminate surfaces and the environment. Ultraviolet light emitting diode (UV-C LED) systems are used for inactivation of microbes, though research is needed to determine optimal doses for aerosolized HAV inactivation. This study evaluates the UV-C LED doses for the inactivation of aerosolized hepatitis A virus (HAV) deposited on stainless-steel and glass discs. HAV was aseptically deposited onto stainless-steel or glass discs (1.27 cm diameter) using a nebulizer within a chamber followed by treatments for up to 1.5 min with 255 nm (surface dose = 0–76.5 mJ/cm²) or 279 nm (surface dose = 0–8.1 mJ/cm²) UV-C LED. Plaque assays were used to enumerate infectious titers of recovered viruses and data from three replicates were statistically analyzed. The calculated linear D₁₀-value (UV-C dose for a 1-log reduction in aerosolized deposits) for HAV by 255 nm UV-C LED was 47.39 ± 7.40 and 40.0 ± 2.94 mJ/cm² (R² = 0.94 and 0.91) and using 279 nm UV-C LED were 6.60 ± 0.27 and 5.57 ± 0.74 mJ/cm² (R² = 0.98 and 0.94) on stainless-steel and glass discs, respectively. The non-linear Weibull model showed δ (dose needed for a 1-log reduction in aerosolized HAV deposits) values for HAV of 29.69 ± 5.49 and 35.25 ± 15.01 mJ/cm² by 255 nm UV-C LED (R² = 0.99 and 0.92) and 6.67 ± 0.63 and 5.21 ± 1.25 mJ/cm² by 279 nm UV-C LED (R² = 0.98 and 0.95) on stainless-steel and glass discs, respectively. These data indicate that 279 nm UV-C LED showed higher efficiency for HAV inactivation than 255 nm UV-C LED, and that Weibull models were a better fit when tailing was observed. This study provides the inactivation data needed to aid in designing UV-C LED systems for delivering doses required to inactivate bio-aerosolized HAV deposits on stainless-steel and glass. Full article

The increasing demand for sustainable agricultural practises has sparked interest in microbes that promote plant immunity. Among these, Pseudomonas species have shown the potential to enhance induced systemic resistance (ISR) in crops. While type III secretion systems (T3SSs) in pathogenic bacteria have been widely studied for their role in local immunosuppression, their function in beneficial Pseudomonas species and on a systemic level remains largely unexplored. We show for the first time that the T3SS of a plant-beneficial Pseudomonas strain induces ISR by root colonisation. T3SS-positive Pseudomonas isolates were applied to the roots of sugar beet (Beta vulgaris L.) and systemic effects on plant immunity were assessed in leaves exposed to the pathogen P. syringae pv. aptata P21. Our results show that P. marginalis ORh26 reduced lesion size and pathogen proliferation in sugar beet leaves. ORh26 activated peroxidase and phenylalanine ammonia-lyase and upregulated NPR1 and MYC2 defence genes. Remarkably, a T3SS-deficient mutant of ORh26 failed to induce these effects. Genomic analysis identified T3SS structural genes and effector proteins, including a pectate lyase and an effector of the HopJ family, that may mediate these responses. This study reveals a previously uncharacterised role of T3SS in the induction of ISR and improves our understanding of plant–microbe interactions. Full article

Rhizosphere microbes, particularly bacteria, are essential for controlling plant-parasitic nematodes (PPNs) through various mechanisms. However, the plant’s age and the genetic composition of nematode populations can significantly influence the inhibitory effectiveness of these microbes against the beet cyst nematode Heterodera schachtii. In this study, rhizosphere microbes were isolated from 39-day-old and 69-day-old resistant oilseed radish plants to evaluate their impact on the penetration of the second-stage juveniles (J2s) originating from four genetically distinct H. schachtii populations. The suppression of J2s penetration by the attached microbes varied across the nematode populations, which displayed differing levels of aggressiveness toward the resistant oilseed radish. Furthermore, differences in the alpha and beta diversity of rhizosphere bacteria were observed between the 39-day-old and 69-day-old plants, leading to variations in the bacterial attachment among the four nematode populations. In summary, the effectiveness of resistant catch crops against H. schachtii is influenced by the pathogenicity of the nematode populations and their interactions with the rhizosphere microbial community shaped by the plant’s age. Full article

Orobanche aegyptiaca is a holoparasitic weed that extracts water, nutrients, and growth regulators from host plants, leading to significant yield and quality losses. Biocontrol microbial metabolites have been shown to enhance plant resistance against parasitic plants, yet the underlying microbial mechanisms remain poorly understood. In this study, we investigated the role of Alternaria alternata JTF001 (J1) microbial metabolites in recruiting beneficial microbes to the tomato rhizosphere and promoting the establishment of a disease-suppressive microbiome. Pot experiments revealed that J1 metabolite application significantly reduced O. aegyptiaca parasitism. High-throughput sequencing of full-length 16S rRNA genes and ITS regions, along with in vitro culture assays, demonstrated an increase in the abundance of plant-beneficial bacteria, particularly Pseudomonas spp. The three candidate beneficial strains (zOTU_388, zOTU_533, and zOTU_2335) showed an increase of 5.7-fold, 5.4-fold, and 4.7-fold, respectively. These results indicate that J1 metabolites induce the recruitment of a disease-suppressive microbiome in tomato seedlings, effectively inhibiting O. aegyptiaca parasitism. Our findings suggest that microbial metabolites represent a promising strategy for managing parasitic plant infestations through microbial community modulation, offering significant implications for sustainable agricultural practices. Full article

The increasing global population and the environmental consequences of meat consumption have led to the exploration of alternative sources of protein. Edible insects have gained attention as a sustainable and nutritionally rich meat alternative. We investigated the effects of two commonly consumed insects, Protaetia brevitarsis seulensis larva and Bombyx mori pupa, on beneficial gut microbiota growth, using whole 16s metagenome sequencing to assess diet-associated changes. Seven-week-old female C57BL/6J mice were administered the edible insects, along with fracto-oligosaccharide (FOS) as a positive control and sham (phosphate buffer saline (PBS)) as a negative control, to assess the relative abundance of insect-diet-associated gut microbes. In total, 567 genera and 470 species were observed, and among these, 15 bacterial genera were differentially abundant in all three groups. These results show that among the two insects, Bombyx mori pupa polysaccharides have a greater ability to regulate beneficial probiotics and next-generation probiotics. In particular, Lactococcus garvieae, which has promising effects on the gastrointestinal tracts of humans and animals, was significantly enriched in both Protaetia brevitarsis seulensis larva and Bombyx mori pupa polysaccharides, similar to fracto-oligosaccharide. The results suggest that the consumption of these insects, particularly polysaccharides, can enhance the growth of beneficial gut microbes, potentially leading to improved overall health in healthy populations. Full article

This paper presents the first in-depth research on the biological and genomic properties of lytic rhizobiophage AP-J-162 isolated from the soils of the mountainous region of Dagestan (North Caucasus), which belongs to the centers of origin of cultivated plants, according to Vavilov N.I. The rhizobiophage host strains are nitrogen-fixing bacteria of the genus Sinorhizobium spp., symbionts of leguminous forage grasses. The phage particles have a myovirus virion structure. The genome of rhizobiophage AP-J-162 is double-stranded DNA of 471.5 kb in length; 711 ORFs are annotated and 41 types of tRNAs are detected. The closest phylogenetic relative of phage AP-J-162 is Agrobacterium phage Atu-ph07, but no rhizobiophages are known. The replicative machinery, capsid, and baseplate proteins of phage AP-J-162 are structurally similar to those of Escherichia phage T4, but there is no similarity between their tail protein subunits. Amino acid sequence analysis shows that 339 of the ORFs encode hypothetical or functionally relevant products, while the remaining 304 ORFs are unique. Additionally, 153 ORFs are similar to those of Atu_ph07, with one-third of the ORFs encoding different enzymes. The biological properties and genomic characteristics of phage AP-J-162 distinguish it as a unique model for exploring phage–microbe interactions with nitrogen-fixing symbiotic microorganisms. Full article

The [ZnL(ONO₂)₂] 1 and [ZnL(NCS)₂] 2 complexes were synthesized using self-assembly of the s-triazine tridentate ligand (L) with Zn(NO₃)₂·6H₂O and Zn(ClO₄)₂·6H₂O/NH₄SCN, respectively. The Zn(II) is further coordinated by two nitrate and two isothiocyanate groups as monodentate ligands in 1 and 2, respectively. Both complexes have distorted square pyramidal coordination environments where the extent of distortion is found to be greater in 2 (τ₅ = 0.41) than in 1 (τ₅ = 0.28). Hirshfeld calculations explored the significant C···O, C···C, N···H, and O···H contacts in the molecular packing of both complexes. The energy framework analysis gave the total interaction energies of −317.8 and −353.5 kJ/mol for a single molecule in a 3.8 Å cluster of 1 and 2, respectively. The total energy diagrams exhibited a strong resemblance to the dispersion energy frameworks in both complexes. NBO charge analysis predicted the charges of the Zn(II) in complexes 1 and 2 to be 1.217 and 1.145 e, respectively. The electronic configuration of Zn1 is predicted to be [core] 4S^0.32 3d^9.98 4p^0.45 4d^0.02 5p^0.01 for 1 and [core] 4S^0.34 3d^9.97 4p^0.53 4d^0.02 for 2. The increased occupancy of the valence orbitals is attributed to the donor→acceptor interactions from the ligand groups to Zn(II). The Zn(II) complexes were examined for their cytotoxic and antimicrobial activities. Both 1 and 2 have good cytotoxic efficiency towards HCT-116 and A-549 cancerous cell lines. We found that 1 is more active (IC₅₀ = 29.53 ± 1.24 and 35.55 ± 1.69 µg/mL) than 2 (IC₅₀ = 41.25 ± 2.91 and 55.05 ± 2.87 µg/mL) against both cell lines. Also, the selectivity indices for the Zn(II) complexes are higher than one, indicating their suitability for use as anticancer agents. In addition, both complexes have broad-spectrum antimicrobial activity (IC₅₀ = 78–625 μg/mL) where the best result is found for 2 against P. vulgaris (IC₅₀ = 78 μg/mL). Its antibacterial activity is found to be good compared to gentamycin (5 μg/mL) as a positive control against this microbe. Full article

Streptococcus gordonii (S. gordonii, Sg) is one of the early colonizing, supragingival commensal bacterium normally associated with oral health in human dental plaque. MicroRNAs (miRNAs) play an important role in the inflammation-mediated pathways and are involved in periodontal disease (PD) pathogenesis. PD is a polymicrobial dysbiotic immune-inflammatory disease initiated by microbes in the gingival sulcus/pockets. The objective of this study is to determine the global miRNA expression kinetics in S. gordonii DL1-infected C57BL/6J mice. All mice were randomly divided into four groups (n = 10 mice/group; 5 males and 5 females). Bacterial infection was performed in mice at 8 weeks and 16 weeks, mice were euthanized, and tissues harvested for analysis. We analyzed differentially expressed (DE) miRNAs in the mandibles of S. gordonii-infected mice. Gingival colonization/infection by S. gordonii and alveolar bone resorption (ABR) was confirmed. All the S. gordonii-infected mice at two specific time points showed bacterial colonization (100%) in the gingival surface, and a significant increase in mandible and maxilla ABR (p < 0.0001). miRNA profiling revealed 191 upregulated miRNAs (miR-375, miR-34b-5p) and 22 downregulated miRNAs (miR-133, miR-1224) in the mandibles of S. gordonii-infected mice at the 8-week mark. Conversely, at 16 weeks post-infection, 10 miRNAs (miR-1902, miR-203) were upregulated and 32 miRNAs (miR-1937c, miR-720) were downregulated. Two miRNAs, miR-210 and miR-423-5p, were commonly upregulated, and miR-2135 and miR-145 were commonly downregulated in both 8- and 16-week-infected mice mandibles. Furthermore, we employed five machine learning (ML) algorithms to assess how the number of miRNA copies correlates with S. gordonii infections in mice. In the ML analyses, miR-22 and miR-30c (8-week), miR-720 and miR-339-5p (16-week), and miR-720, miR-22, and miR-339-5p (combined 8- and 16-week) emerged as the most influential miRNAs. Full article

Root-knot nematodes are the major diseases in protected cultivation around the world. Bio-organic fertilizer has become a research hotspot, with a variety of microorganisms that control various vegetable soil-borne diseases. This study screened nematocidal microorganisms from fresh vermicompost, explored the inhibitory substances produced by biocontrol agents, and evaluated their potential biocontrol ability in the pot and field under greenhouse conditions. The highly effective antagonistic microbes of Meloidogyne incognita (M. incognita) were screened. Strains YL1 and YL31 were identified as Peribacillus frigoritolerans, and strain YL6 was identified as Lysinibacillus fusiformis. The three strains all produced chitinase and protease, which prevented the normal development of eggs and the second-stage juveniles (J2) by destroying their appearance. The three strains all improved potassium-dissolving ability, and the strains YL1 and YL6 also enhanced phosphorus-dissolving ability. Pot experiments showed that tomato root knots were reduced, and plant growth improved. Field tests showed that the root-knot index and nematode population were reduced significantly, and cucumber growth and yield were enhanced. Strain YL1 had the best control effect with 70.6%, and the yield increased by 14.9% compared with the control. Overall, this study showed the ability of antagonistic bacteria YL1, YL6, and YL31 to control root-knot nematodes, and these antagonistic bacteria could be developed as biocontrol agents for sustainable agriculture. Full article

In recent years, CRISPR-Cas toolboxes for Streptomyces editing have rapidly accelerated natural product discovery and engineering. However, Cas efficiencies are oftentimes strain-dependent, and the commonly used Streptococcus pyogenes Cas9 (SpCas9) is notorious for having high levels of off-target toxicity effects. Thus, a variety of Cas proteins is required for greater flexibility of genetic manipulation within a wider range of Streptomyces strains. This study explored the first use of Acidaminococcus sp. Cas12j, a hypercompact Cas12 subfamily, for genome editing in Streptomyces and its potential in activating silent biosynthetic gene clusters (BGCs) to enhance natural product synthesis. While the editing efficiencies of Cas12j were not as high as previously reported efficiencies of Cas12a and Cas9, Cas12j exhibited higher transformation efficiencies compared to SpCas9. Furthermore, Cas12j demonstrated significantly improved editing efficiencies compared to Cas12a in activating BGCs in Streptomyces sp. A34053, a strain wherein both SpCas9 and Cas12a faced limitations in accessing the genome. Overall, this study expanded the repertoire of Cas proteins for genome editing in actinomycetes and highlighted not only the potential of recently characterized Cas12j in Streptomyces but also the importance of having an extensive genetic toolbox for improving the editing success of these beneficial microbes. Full article

Microorganisms associated with nematodes or enriched in galls have been reported previously to aid plant-parasitic nematodes (PPNs) in infecting and establishing parasitism in the host plants. However, the rhizosphere-associated microbiota, which strengthens the pathogenicity of PPNs, remains largely unknown. This study illustrated rhizosphere bacteria enhancing Meloidogyne incognita infection on Arabidopsis thaliana by comparing the gall numbers of the treatments between natural soil and the sterile soil or soils drenched with antibiotics. By culture-dependent and pot testing methods, sixteen bacterial combinations from rhizosphere soils of A. thaliana were demonstrated to enhance M. incognita pathogenicity, including the most effective Nocardioides. Single-strain inoculation from the Nocardioides combination significantly resulted in M. incognita forming more galls on roots than the control, in which N. nematodiphilus R-N-C8 was the most effective strain. Strain R-N-C8 could substantially facilitate the M. incognita second-stage juveniles (J2s) moving towards the roots of A. thaliana and infecting the roots by releasing chemoattractant to attract J2s. The chemoattractant from strain R-N-C8 was determined to be L-lysine. This study furnishes vital insights for understanding the infection of root-knot nematodes associated with rhizosphere microbes. Full article