The aim of this study was to inventory the types of plant growth-promoting rhizobacteria (PGPR) present in the rhizosphere of plants grown in soils contaminated with heavy metals, recalcitrant organics, petroleum sewage or salinity in China. We screened 1223 isolates for antifungal activity and about 24% inhibited Rhizoctonia solani or Sclerotinia sclerotiorum. Twenty-four strains inhibitory to R. solani, Gaeumannomyces graminis var. tritici and/or S. sclerotiorum and representing the dominant morphotypes were assayed for PGPR activity. Seven strains contained phlD, prnD, pltC or phzF genes and produced the antibiotics 2,4-diacetylphloroglucinol, pyrrolnitrin, pyoluteorin and phenazines respectively. Six strains contained acdS, which encodes 1-aminocyclopropane-1-carboxylic acid deaminase. Phylogenetic analysis of 16S rDNA and phlD, phzF and acdS genes demonstrated that some strains identified as Pseudomonas were similar to model PGPR strains Pseudomonas protegens Pf-5, Pseudomonas chlororaphis subsp. aureofaciens 30-84 and P. brassicacearum Q8r1-96. Pseudomonas protegens- and P. chlororaphis-like strains had the greatest biocontrol activity against Rhizoctonia root rot and take-all of wheat. Pseudomonas protegens and P. brassicacearum-like strains showed the greatest promotion of canola growth. Our results indicate that strains from contaminated soils are similar to well-described PGPR found in agricultural soils worldwide.

The agglomeration of silver nanoparticles (AgNPs) results in poor antibacterial performance, and the accumulation of silver in the human body threatens human health. Preparing a matrix is a technique worth considering as it not only prevents the aggregation of AgNPs but also reduces deposition of AgNPs in the human body. In this paper, carboxy-cellulose nanocrystals (CCNC) were prepared by a simple one-step acid hydrolysis method. Chito-oligosaccharides (CSos) were grafted onto the surface of CCNC to form CSos-CCNC composite nanoparticles. CCNC and CSos-CCNC were used as stabilizers for deposing AgNPs and two types of complexes-AgNPs-CCNC and AgNPs-CSos-CCNC-were obtained, respectively. The influence of the two stabilizer matrices-CCNC and CSos-CCNC-on the morphology, thermal behavior, crystal structure, antibacterial activity, and cell compatibility of AgNPs-CCNC and AgNPs-CSos-CCNC were examined. The results showed that the AgNPs deposited on the CSos-CCNC surface had a smaller average diameter and a narrower particle size distribution compared with the ones deposited on CCNC. The thermal stability of AgNPs-CSos-CCNC was better than that of AgNPs-CCNC. AgNPs did not affect the crystalline structure of CCNC and CSos-CCNC. The antibacterial activity of AgNPs-CSos-CCNC was better than that of AgNPs-CCNC based on antibacterial studies using Escherichia coli, Staphylococcus aureus, and Klebsiella pneumoniae. The cytotoxicity of AgNPs-CSos-CCNC was remarkably lower than that of AgNPs-CCNC.

Deep venous thrombosis (DVT) constitutes a major global disease burden. Endothelial progenitor cells (EPCs) have been described in association with recanalization of venous thrombus. Furthermore, emerging evidence suggests microRNAs are involved in this progression. The goal of this study was to investigate the influence of miR-150 on the behavior of EPCs and its potential contribution in venous thrombosis resolution.

Plants live in association with microorganisms that positively influence plant development, vigor, and fitness in response to pathogens and abiotic stressors. The bulk of the plant microbiome is concentrated belowground at the plant root-soil interface. Plant roots secrete carbon-rich rhizodeposits containing primary and secondary low molecular weight metabolites, lysates, and mucilages. These exudates provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. We addressed this gap by focusing on the molecular dialog between eight well-characterized beneficial strains of the Pseudomonas fluorescens group and Brachypodium distachyon, a model for economically important food, feed, forage, and biomass crops of the grass family. We collected and analyzed root exudates of B. distachyon and demonstrated the presence of multiple carbohydrates, amino acids, organic acids, and phenolic compounds. The subsequent screening of bacteria by Biolog Phenotype MicroArrays revealed that many of these metabolites provide carbon and energy for the Pseudomonas strains. RNA-seq profiling of bacterial cultures amended with root exudates revealed changes in the expression of genes encoding numerous catabolic and anabolic enzymes, transporters, transcriptional regulators, stress response, and conserved hypothetical proteins. Almost half of the differentially expressed genes mapped to the variable part of the strains' pangenome, reflecting the importance of the variable gene content in the adaptation of P. fluorescens to the rhizosphere lifestyle. Our results collectively reveal the diversity of cellular pathways and physiological responses underlying the establishment of mutualistic interactions between these beneficial rhizobacteria and their plant hosts.

The plant microbiota plays a crucial role in promoting plant health by facilitating the nutrient acquisition, abiotic stress tolerance, biotic stress resilience, and host immune regulation. Despite decades of research efforts, the precise relationship and function between plants and microorganisms remain unclear. Kiwifruit (Actinidia spp.) is a widely cultivated horticultural crop known for its high vitamin C, potassium, and phytochemical content. In this study, we investigated the microbial communities of kiwifruit across different cultivars (cvs. Deliwoong and Sweetgold) and tissues at various developmental stages. Our results showed that the microbiota community similarity was confirmed between the cultivars using principal coordinates analysis. Network analysis using both degree and eigenvector centrality indicated similar network forms between the cultivars. Furthermore, Streptomycetaceae was identified in the endosphere of cv. Deliwoong by analyzing amplicon sequence variants corresponding to tissues with an eigenvector centrality value of 0.6 or higher. Our findings provide a foundation for maintaining kiwifruit health through the analysis of its microbial community.

ire blight disease, caused by Erwinia amylovora, is a devastating affliction in apple cultivation worldwide. Chemical pesticides have exhibited limited effectiveness in controlling the disease, and biological control options for treating fruit trees are limited. Therefore, a relatively large-scale survey is necessary to develop microbial agents for apple trees. Here we collected healthy apple trees from across the country to identify common and core bacterial taxa. We analyzed the endophytic bacterial communities in leaves and twigs and discovered that the twig bacterial communities were more conserved than those in the leaves, regardless of the origin of the sample. This finding indicates that specific endophytic taxa are consistently present in healthy apple trees and may be involved in vital functions such as disease prevention and growth. Furthermore, we compared the community metabolite pathway expression rates of these endophyte communities with those of E. amylovora infected apple trees and discovered that the endophyte communities in healthy apple trees not only had similar community structures but also similar metabolite pathway expression rates. Additionally, Pseudomonas and Methylobacterium-Methylorobrum were the dominant taxa in all healthy apple trees. Our findings provide valuable insights into the potential roles of endophytes in healthy apple trees and inform the development of strategies for enhancing apple growth and resilience. Moreover, the similarity in cluster structure and pathway analysis between healthy orchards was mutually reinforcing, demonstrating the power of microbiome analysis as a tool for identifying factors that contribute to plant health.

The aim of this study was to investigate the regulation of lantipeptide production in Streptomyces globisporus SP6C4, which produces the novel antifungal lantipeptides conprimycin and grisin, and to identify the role of cytochrome P450 (P450) in tis regulation. To investigate the regulation of lantipeptide production, we created gene deletion mutants, including ΔP450, ΔtsrD, ΔlanM, ΔP450ΔtsrD, and ΔP450ΔlanM. These mutants were characterized in terms of their morphology, sporulation, attachment, and antifungal activity against Fusarium oxysporum. The gene deletion mutants showed distinct characteristics compared to the wild-type strain. Among them, the ΔP450ΔlanM double mutant exhibited a recovery of antifungal activity against F. oxysporum, indicating that P450 plays a significant role in regulating lantipeptide production in S. globisporus SP6C4. Our findings highlight the significant role of P450 in the regulation of lantipeptide production and morphological processes in S. globisporus. The results suggest a potential link between P450-mediated metabolic pathways and the regulation of growth and secondary metabolism in SP6C4, thereby highlighting P450 as a putative target for the development of new antifungal agents.

A modified coaxial electrospinning process was used to prepare composite nanofibrous mats from a poly(methyl methacrylate) (PMMA) solution with the addition of different cellulose nanocrystals (CNCs) as the sheath fluid and polyacrylonitrile (PAN) solution as the core fluid. This study investigated the conductivity of the as-spun solutions that increased significantly with increasing CNCs addition, which favors forming uniform fibers. This study discussed the effect of different CNCs addition on the morphology, thermal behavior, and the multilevel structure of the coaxial electrospun PMMA + CNCs/PAN composite nanofibers. A morphology analysis of the nanofibrous mats clearly demonstrated that the CNCs facilitated the production of the composite nanofibers with a core-shell structure. The diameter of the composite nanofibers decreased and the uniformity increased with increasing CNCs concentrations in the shell fluid. The composite nanofibrous mats had the maximum thermal decomposition temperature that was substantially higher than electrospun pure PMMA, PAN, as well as the core-shell PMMA/PAN nanocomposite. The BET (Brunauer, Emmett and Teller) formula results showed that the specific surface area of the CNCs reinforced core-shell composite significantly increased with increasing CNCs content. The specific surface area of the composite with 20% CNCs loading rose to 9.62 m²/g from 3.76 m²/g for the control. A dense porous structure was formed on the surface of the electrospun core-shell fibers.

Streptomyces griseus S4-7 was originally isolated from the strawberry rhizosphere as a microbial agent responsible for Fusarium wilt suppressive soils. S. griseus S4-7 shows specific and pronounced antifungal activity against Fusarium oxysporum f. sp. fragariae. In the Streptomyces genus, the whi transcription factors are regulators of sporulation, cell differentiation, septation, and secondary metabolites production. wblE2 function as a regulator has emerged as a new group in whi transcription factors. In this study, we reveal the involvement of the wblE2 transcription factor in the plant-protection by S. griseus S4-7. We generated ΔwblE, ΔwblE2, ΔwhiH, and ΔwhmD gene knock-out mutants, which showed less antifungal activity both in vitro and in planta. Among the mutants, wblE2 mutant failed to protect the strawberry against the Fusarium wilt pathogen. Transcriptome analyses revealed major differences in the regulation of phenylalanine metabolism, polyketide and siderophore biosynthesis between the S4-7 and the wblE2 mutant. The results contribute to our understanding of the role of streptomycetes wblE2 genes in a natural disease suppressing system.

We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45-52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire.

Members of the genus Paenibacillus are known for their production of useful substances, and some species of the genus are recognized to be plant growth-promoting rhizobacteria. Paenibacillus polymyxa TH2H2, isolated from a tomato flower, had antifungal activity. Here, the draft genome sequence of Paenibacillus polymyxa TH2H2 is reported. The 5,983,104-bp genome, with a G+C content of 45.31%, comprised 5,221 protein-coding genes, 64 ribosomal RNA and 100 transfer RNA. Three intact antibiotic biosynthesis gene clusters were identified using antiSMASH. These encoded the antifungal agent fusaricidin and two antibacterial agents, tridecaptin and polymyxin. Sequence data have been deposited in the DDBJ/ENA/GenBank database under the accession number RPDG01000000. The version described in this paper is RPDG00000000.1. The BioProject ID in the GenBank database is PRJNA505713.

Helicobacter pylori (H. pylori) infection can occur in early childhood, without eradication therapies such infection can persist throughout life and cause many different diseases. This study investigated the metabolic characteristics and explored the underlying mechanism of children with H. pylori infection, and identified potential biomarkers for evaluating the efficacy of H. pylori eradication therapies.

Lung cancer is the leading cause of cancer-related death worldwide. Therapies for lung cancer have relatively poor outcomes and need to be improved. Lung cancer immune cell infiltration associated RNA (LCIIAR) is a long noncoding RNA (lncRNA), which is overexpressed in human cancers. However, the clinical significance and functional role of LCIIAR in Lung Adenocarcinoma remain unclear. Here, we identified a novel long non-coding RNA (ENSG00000256802), termed LCIIAR (lung cancer immune cell infiltration associated lncRNA), up-regulated in lung cancer tissue and cell lines. We show that increase LCIIAR expression correlated with poor clinical stage and adverse clinical outcomes and that could also serve as an independent unfavorable prognostic factor in patients with Lung Adenocarcinima. GSEA analysis demonstrated that LCIIAR is mainly involved in the regulation of the immune response. We uncovered that elevate LCIIAR expression positively correlated with immune infiltration and immune modulator in Lung Adenocarcinoma. More importantly, we confirmed that silencing of LCIIAR expression significantly inhibits the proliferation, and migration abilities of these tumour cells. We also demonstrated that the LCIIAR/hsa-miR184/SLC16A3/CDCP1 network regulates SLC16A3/CDCP1 overexpression in and is associated with poor prognosis in this tumour. Therefore our findings revealed the critical role of LCIIAR in Lung Adenocarcinoma progression, which may also serve as a prognostic biomarker and novel therapeutic target.

Black soldier fly (BSF; Hermetia illucens L.) larvae can convert fresh pig manure into protein and fat-rich biomass, which can then be used as aquafeed for select species. Currently, BSF is the only approved insect for such purposes in Canada, USA, and the European Union. Pig manure could serve as a feed substrate for BSF; however, it is contaminated with zoonotic pathogens (e.g., Staphylococcus aureus and Salmonella spp.). Fortunately, BSF larvae inhibit many of these zoonotic pathogens; however, the mechanisms employed are unclear. We employed RNAi, qRT-PCR, and Illumina MiSeq 16S rDNA high-throughput sequencing to examine the interaction between two immune genes (Duox in Duox-reactive oxygen species [ROS] immune system and TLR3 in the Toll signaling pathway) and select pathogens common in pig manure to decipher the mechanisms resulting in pathogen suppression. Results indicate Bsf Duox-TLR3 RNAi increased bacterial load but decreased relative abundance of Providencia and Dysgonomonas, which are thought to be commensals in the BSF larval gut. Bsf Duox-TLR3 RNAi also inactivated the NF-κB signaling pathway, downregulated the expression of antimicrobial peptides, and diminished inhibitory effects on zoonotic pathogen. The resulting dysbiosis stimulated an immune response by activating BsfDuox and promoting ROS, which regulated the composition and structure of the gut bacterial community. Thus, BsfDuox and BsfTLR3 are important factors in regulating these key gut microbes, while inhibiting target zoonotic pathogens.

Herein, we explored the potential of the apple's core microbiota for biological control of Erwinia amylovora, which causes fire blight disease, and analyzed the structure of the apple's bacterial community across different tissues and seasons. Network analysis results showed distinct differences in bacterial community composition between the endosphere and rhizosphere of healthy apples, and eight taxa were identified as negatively correlated with E. amylovora, indicating their potential key role in a new control strategy against the pathogen. This study highlights the critical role of the apple's bacterial community in disease control and provides a new direction for future research in apple production. In addition, the findings suggest that using the composition of the apple's core taxa as a biological control strategy could be an effective alternative to traditional chemical control methods, which have been proven futile and environmentally harmful.

Plants pollination are conducted through various pollinators such as wind, animals, and insects. Recently, the necessity for artificial pollination is drawing attention as the proportion of natural pollinators involved is decreasing over the years. Likewise, the trade in pollen for artificial pollination is also increasing worldwide. Through these imported pollens, many unknown microorganisms can flow from foreign countries. Among them, spores of various fungi present in the particles of pollen can be dispersed throughout the orchard. Therefore, in this study, the composition of fungal communities in imported pollen was revealed, and potential ecological characteristics of the fungi were investigated in four types of imported pollen. Top 10 operational taxonomic unit (OTU) of fungi were ranked among the following groups: Alternaria sp., Cladosporium sp., and Didymella glomerata which belong to many pathogenic species. Through FUNGuild analysis, the proportion of OTUs, which is assumed to be potentially plant pathogens, was higher than 50%, except for apple pollen in 2018. Based on this study of fungal structure, this information can suggest the direction of the pollen quarantine process and contribute to fungal biology in pollen.

Plant-parasitic nematodes cause severe losses to crop production and economies all over the world. Bacillus aryabhattai MCCC 1K02966, a deep-sea bacterium, was obtained from the Southwest Indian Ocean and showed nematicidal and fumigant activities against Meloidogyne incognita in vitro. The nematicidal volatile organic compounds (VOCs) from the fermentation broth of B. aryabhattai MCCC 1K02966 were investigated further using solid-phase microextraction gas chromatography-mass spectrometry. Four VOCs, namely, pentane, 1-butanol, methyl thioacetate, and dimethyl disulfide, were identified in the fermentation broth. Among these VOCs, methyl thioacetate exhibited multiple nematicidal activities, including contact nematicidal, fumigant, and repellent activities against M. incognita. Methyl thioacetate showed a significant contact nematicidal activity with 87.90% mortality at 0.01 mg/mL by 72 h, fumigant activity in mortality 91.10% at 1 mg/mL by 48 h, and repellent activity at 0.01-10 mg/mL. In addition, methyl thioacetate exhibited 80-100% egg-hatching inhibition on the 7th day over the range of 0.5 mg/mL to 5 mg/mL. These results showed that methyl thioacetate from MCCC 1K02966 control M. incognita with multiple nematicidal modes and can be used as a potential biological control agent.

Plants in nature interact with other species, among which are mutualistic microorganisms that affect plant health. The co-existence of microbial symbionts with the host contributes to host fitness in a natural context. In turn, the composition of the plant microbiota responds to the environment and the state of the host, raising the possibility that it can be engineered to benefit the plant. However, technology for engineering the structure of the plant microbiome is not yet available.

Soybean is an important source of protein and for a wide range of agricultural, food, and industrial applications. Soybean is being affected by Xanthomonas citri pv. glycines, a causal pathogen of bacterial pustule disease, result in a reduction in yield and quality. Diverse microbial communities of plants are involved in various plant stresses is known. Therefore, we designed to investigate the microbial community differentiation depending on the infection of X. citri pv. glycines. The microbial community's abundance, diversity, and similarity showed a difference between infected and non-infected soybean. Microbiota community analysis, excluding X. citri pv. glycines, revealed that Pseudomonas spp. would increase the population of the infected soybean. Results of DESeq analyses suggested that energy metabolism, secondary metabolite, and TCA cycle metabolism were actively diverse in the non-infected soybeans. Additionally, Streptomyces bacillaris S8, an endophyte microbiota member, was nominated as a key microbe in the healthy soybeans. Genome analysis of S. bacillaris S8 presented that salinomycin may be the critical antibacterial metabolite. Our findings on the composition of soybean microbiota communities and the key strain information will contribute to developing biological control strategies against X. citri pv. glycines.

Nematodes feed mainly on bacteria and sense volatile signals through their chemosensory system to distinguish food from pathogens. Although nematodes recognizing bacteria by volatile metabolites are ubiquitous, little is known of the associated molecular mechanism. Here, we show that the antinematode bacterium Paenibacillus polymyxa KM2501-1 exhibits an attractive effect on Caenorhabditis elegans via volatile metabolites, of which furfural acetone (FAc) acts as a broad-spectrum nematode attractant. We show that the attractive response toward FAc requires both the G-protein-coupled receptors STR-2 in AWC neurons and SRA-13 in AWA and AWC neurons. In the downstream olfactory signaling cascades, both the transient receptor potential vanilloid channel and the cyclic nucleotide-gated channel are necessary for FAc sensation. These results indicate that multiple receptors and subsequent signaling cascades contribute to the attractive response of C. elegans to FAc, and FAc is the first reported ligand of SRA-13. Our current work discovers that P. polymyxa KM2501-1 exhibits an attractive effect on nematodes by secreting volatile metabolites, especially FAc and 2-heptanone, broadening our understanding of the interactions between bacterial pathogens and nematodes. IMPORTANCE Nematodes feed on nontoxic bacteria as a food resource and avoid toxic bacteria; they distinguish them through their volatile metabolites. However, the mechanism of how nematodes recognize bacteria by volatile metabolites is not fully understood. Here, the antinematode bacterium Paenibacillus polymyxa KM2501-1 is found to exhibit an attractive effect on Caenorhabditis elegans via volatile metabolites, including FAc. We further reveal that the attractive response of C. elegans toward FAc requires multiple G-protein-coupled receptors and downstream olfactory signaling cascades in AWA and AWC neurons. This study highlights the important role of volatile metabolites in the interaction between nematodes and bacteria and confirms that multiple G-protein-coupled receptors on different olfactory neurons of C. elegans can jointly sense bacterial volatile signals.