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BMC Genomics Feb 2023Paenibacillus polymyxa WLY78 is a Gram-positive, endospore-forming and N-fixing bacterium. Our previous study has demonstrated that GlnR acts as both an activator and a...
BACKGROUND
Paenibacillus polymyxa WLY78 is a Gram-positive, endospore-forming and N-fixing bacterium. Our previous study has demonstrated that GlnR acts as both an activator and a repressor to regulate the transcription of the nif (nitrogen fixation) operon (nifBHDKENXhesAnifV) according to nitrogen availability, which is achieved by binding to the two GlnR-binding sites located in the nif promoter region. However, further study on the GlnR-mediated global regulation in this bacterium is still needed.
RESULTS
In this study, global identification of the genes directly under GlnR control is determined by using chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) and electrophoretic mobility shift assays (EMSA). Our results reveal that GlnR directly regulates the transcription of 17 genes/operons, including a nif operon, 14 nitrogen metabolism genes/operons (glnRA, amtBglnK, glnA1, glnK1, glnQHMP, nasA, nasD1, nasD2EF, gcvH, ansZ, pucR, oppABC, appABCDF and dppABC) and 2 carbon metabolism genes (ldh3 and maeA1). Except for the glnRA and nif operon, the other 15 genes/operons are newly identified targets of GlnR. Furthermore, genome-wide transcription analyses reveal that GlnR not only directly regulates the expression of these 17 genes/operons, but also indirectly controls the expression of some other genes/operons involved in nitrogen fixation and the metabolisms of nitrogen and carbon.
CONCLUSION
This study provides a GlnR-mediated regulation network of nitrogen fixation and the metabolisms of nitrogen and carbon.
Topics: Paenibacillus polymyxa; Nitrogen; Promoter Regions, Genetic; Bacterial Proteins; Binding Sites; Gene Expression Regulation, Bacterial
PubMed: 36823556
DOI: 10.1186/s12864-023-09147-1 -
Plants (Basel, Switzerland) Feb 2023Endophytes are primarily endosymbiotic bacteria and fungi that colonize the interior tissues of their host plant. They enhance the host plant's growth and attenuate...
Endophytes are primarily endosymbiotic bacteria and fungi that colonize the interior tissues of their host plant. They enhance the host plant's growth and attenuate adverse effects of biological stress. Endophytic species of many indigenous plants are an untapped resource of plant growth-promoting microorganisms that can mitigate abiotic stress effects. Thus, this study aimed to isolate endophytes from the roots and leaves of the medicinal plant to evaluate their in vitro growth-promoting capacities and drought tolerance and to characterize the most promising species. Twenty-six endophytes (fourteen bacteria and twelve fungi) were isolated and cultured from the roots and leaves of . All 26 endophytes produced flavonoids, and 14 strains produced phenolic compounds. Of the 11 strains that displayed good free radical scavenging capability (low IC) in the 1-1-diphenyl-1-picryhydrazyl radical scavenging assay, only three strains could not survive the highest drought stress treatment (40% polyethylene glycol). These 11 strains were all positive for ammonia and siderophore production and only one strain failed to produce hydrogen cyanide and solubilize phosphate. Seven isolates showed aminocyclopropane-1-carboxylate deaminase activity and differentially synthesized indole-3-acetic acid. Using molecular tools, two promising symbiotic, drought stress tolerant, and plant growth-enhancing endophytic species (EORB-2 and EOLF-5) were identified as and . The results of this study demonstrate that and should be further investigated for their drought stress mitigation and plant growth enhancement effects as they have the potential to be developed for use in sustainable agricultural practices.
PubMed: 36771720
DOI: 10.3390/plants12030638 -
Microbiology Spectrum Feb 2023Nematodes feed mainly on bacteria and sense volatile signals through their chemosensory system to distinguish food from pathogens. Although nematodes recognizing...
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. 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.
Topics: Animals; Acetone; Bacteria; Caenorhabditis elegans; Receptors, G-Protein-Coupled; Signal Transduction; Paenibacillus polymyxa
PubMed: 36511721
DOI: 10.1128/spectrum.02319-22 -
Frontiers in Microbiology 2022The multiple-sugar metabolism regulator (MsmR), a transcription factor belonging to the AraC/XylS family, participates in polysaccharide metabolism and virulence....
The multiple-sugar metabolism regulator (MsmR), a transcription factor belonging to the AraC/XylS family, participates in polysaccharide metabolism and virulence. However, the transcriptional regulatory mechanisms of MsmR1 in remain unclear. In this study, knocking out was found to reduce polymyxin synthesis by the SC2-M1 strain. Chromatin immunoprecipitation assay with sequencing (ChIP-seq) revealed that most enriched pathway was that of carbohydrate metabolism. Additionally, electromobility shift assays (EMSA) confirmed the direct interaction between MsmR1 and the promoter regions of , , , , , , , and . MsmR1 stimulates polymyxin biosynthesis by directly binding to the promoter regions of and , while also directly regulating and influencing the citrate cycle (TCA cycle). In addition, MsmR1 directly activates and was beneficial for spore and biofilm formation. These results indicated that MsmR1 could regulate carbohydrate and amino acid metabolism, and indirectly affect biological processes such as polymyxin synthesis, biofilm formation, and motility. Moreover, MsmR1 could be autoregulated. Hence, this study expand the current knowledge of MsmR1 and will be beneficial for the application of SC2 in the biological control against the certain pathogens in pepper.
PubMed: 36483206
DOI: 10.3389/fmicb.2022.1039806 -
Nutrients Nov 2022In the human intestinal tract, there are more than 100 trillion microorganisms classified into at least 1000 different species. The intestinal microbiota contributes to...
In the human intestinal tract, there are more than 100 trillion microorganisms classified into at least 1000 different species. The intestinal microbiota contributes to the regulation of systemic physiologic functions and the maintenance of homeostasis of the host. It has been reported that the alteration of the intestinal microbiota is involved in metabolic syndromes, including type II diabetes and dyslipidemia, inflammatory bowel disease, allergic disease, and cancer growth. It has been reported that a microbial product from AK, which was named Enzamin, ameliorated adipose inflammation with impaired adipocytokine expression and insulin resistance in db/db mice. In order to investigate the effect of Enzamin on the intestinal microbiota and inflammation induced by obesity, mice were fed with a high-fat diet and 1% Enzamin for 4 weeks. Enzamin improved the -to- ratio and altered the intestinal microbiota in mice fed the high-fat diet. In addition, Enzamin suppressed the decreased expression of claudin-4 and the increased serum LPS level in mice fed with the high-fat diet. Modulating the intestinal microbiota with Enzamin may cause a decrease in serum LPS level. Based on these results, Enzamin may improve inflammation and metabolic disorders by regulating the intestinal microbiota in obese mice.
Topics: Humans; Mice; Animals; Diet, High-Fat; Gastrointestinal Microbiome; Diabetes Mellitus, Type 2; Lipopolysaccharides; Mice, Obese; Inflammation
PubMed: 36432430
DOI: 10.3390/nu14224743 -
Frontiers in Microbiology 2022Soft rot caused by is an important bacterial disease affecting rice and other plants worldwide. In this study, Nanopore and Illumina sequencing platforms were used to...
Soft rot caused by is an important bacterial disease affecting rice and other plants worldwide. In this study, Nanopore and Illumina sequencing platforms were used to sequence the high-quality complete genome of a novel strain WH1 (size: 4.68 Mb; depth: 322.37x for Nanopore, 243.51x for Illumina; GC content: 53.59%), which was isolated from healthy rice root surface together with , a potential biocontrol bacterium against strain WH1. However, the pure WH1 culture presented severe pathogenicity. Multilocus sequence analysis (MLSA) indicated that strains WH1, EC1, and EC2 isolated from rice were grouped into a clade differentiated from other strains. The average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) analyses demonstrated that WH1 was phylogenetically closest to EC2. Furthermore, the pathogenicity determinants and virulence factors of WH1 were mainly analyzed through genomic comparison with complete genomes of other strains with high virulence (EC1, EC2, MS1, and MS2). The results revealed that plant cell wall-degrading extracellular enzymes (PCWDEs), flagellar and chemotaxis, and quorum sensing were highly conserved in all analyzed genomes, which were confirmed through phenotypic assays. Besides, WH1 harbored type I, II, III, and VI secretion systems (T1SS, T2SS, T3SS, and T6SS), but lost T4SS and T5SS. Like strains MS1 and MS2 isolated from bananas, WH1 harbored genes encoding both capsule polysaccharide (CPS) and exopolysaccharide (EPS) biosynthesis. The results of pathogenicity assays demonstrated that WH1 produced severe soft rot symptoms on potato tubers, carrots, radishes, and Chinese cabbage. Meanwhile, WH1 also produced phytotoxin(s) to inhibit rice seed germination with an 87% inhibitory rate in laboratory conditions. More importantly, we confirmed that phytotoxin(s) produced by WH1 are different from zeamines produced by EC1. Comparative genomics analyses and phenotypic and pathogenicity assays suggested that WH1 likely evolved through a pathway different from the other strains from rice, producing a new type of rice foot rot pathogen. These findings highlight the emergence of a new type of strain with high virulence, causing soft rot in rice and other plants.
PubMed: 36386707
DOI: 10.3389/fmicb.2022.997486 -
Foods (Basel, Switzerland) Sep 2022As bread is a very important staple food, its spoilage threatens global food security. Ropy bread spoilage manifests in sticky and stringy degradation of the crumb,... (Review)
Review
As bread is a very important staple food, its spoilage threatens global food security. Ropy bread spoilage manifests in sticky and stringy degradation of the crumb, slime formation, discoloration, and an odor reminiscent of rotting fruit. Increasing consumer demand for preservative-free products and global warming may increase the occurrence of ropy spoilage. , , , the group, , , , , , and were reported to cause ropiness in bread. Process hygiene does not prevent ropy spoilage, as contamination of flour with these species is unavoidable due to their occurrence as a part of the endophytic commensal microbiota of wheat and the formation of heat-stable endospores that are not inactivated during processing, baking, or storage. To date, the underlying mechanisms behind ropy bread spoilage remain unclear, high-throughput screening tools to identify rope-forming bacteria are missing, and only a limited number of strategies to reduce rope spoilage were described. This review provides a current overview on (i) routes of entry of endospores into bread, (ii) bacterial species implicated in rope spoilage, (iii) factors influencing rope development, and (iv) methods used to assess bacterial rope-forming potential. Finally, we pinpoint key gaps in knowledge and related challenges, as well as future research questions.
PubMed: 36230100
DOI: 10.3390/foods11193021 -
Frontiers in Plant Science 2022The root-knot nematode, , is a major pest in tomato production. , which is primarily found in soil and colonizing roots, is considered a successful biocontrol organism...
The root-knot nematode, , is a major pest in tomato production. , which is primarily found in soil and colonizing roots, is considered a successful biocontrol organism against many pathogens. To evaluate the biocontrol capacity of LMG27872 against in tomato, experiments were conducted both and . A dose-response effect [30, 50, and 100% (10 CFU/mL)] of bacterial suspensions (BSs) on growth and tomato susceptibility to with soil drenching as a mode of application was first evaluated. The results show that the biological efficacy of LMG27872 against parasitism in tomato was dose-dependent. A significantly reduced number of galls, egg-laying females (ELF), and second-stage juveniles (J2) were observed in BS-treated plants, in a dose-dependent manner. The effect of on tomato growth was also dose-dependent. A high dose of BSs had a negative effect on growth; however, this negative effect was not observed when the BS-treated plants were challenged with , indicating tolerance or a defense priming mechanism. In subsequent experiments, the direct effect of BSs was evaluated on J2 mortality and egg hatching of . The effect of BS on J2 mortality was observed from 12 to 24 h, whereby J2 was significantly inhibited by the BS treatment. The effect of on egg hatching was also dependent on the BS dose. The results show a potential of LMG27872 to protect plants from nematode parasitism and its implementation in integrated nematode management suitable for organic productions.
PubMed: 36186028
DOI: 10.3389/fpls.2022.961085 -
Scientific Reports Sep 2022Pectin is one of the main structural components in fruits and an indigestible fiber made of D-galacturonic acid units with α (1-4) linkage. This study investigates the...
Pectin is one of the main structural components in fruits and an indigestible fiber made of D-galacturonic acid units with α (1-4) linkage. This study investigates the microbial degradation of pectin in apple waste and the production of bioactive compounds. Firstly, pectin-degrading bacteria were isolated and identified, then pectinolytic activity was assessed by DNS. The products were evaluated by TLC and LC-MS-ESI. The antioxidative effects were investigated using DPPH and anti-cancer effects and cytotoxicity were analyzed by MTT and flow cytometry. In this study two new bacterial isolates, Alcaligenes faecalis AGS3 and Paenibacillus polymyxa S4 with the pectinolytic enzyme were introduced. Structure analysis showed that the products of enzymatic degradation include unsaturated mono, di, tri, and penta galacturonic acids with 74% and 69% RSA at 40 mg/mL for A. faecalis and P. polymyxa S4, respectively. The results of anti-tumor properties on MCF-7 cells by MTT assay, for products of AGS3 and S4 at 40 mg/mL after 48 h, showed 7% and 9% survival, respectively. In the flow cytometric assessment, the compounds of AGS3 at 40 mg/mL were 100% lethal in 48 h and regarding S4 isolate caused 98% death. Cytotoxicity evaluation on L-929 cells showed no significant toxicity on living cells.
Topics: Alcaligenes faecalis; Hexuronic Acids; Malus; Paenibacillus; Paenibacillus polymyxa; Pectins; Polygalacturonase
PubMed: 36138114
DOI: 10.1038/s41598-022-20011-2 -
Dissection of NSY50-Induced Defense in Cucumber Roots against f. sp. by Target Metabolite Profiling.Biology Jul 2022To gain insights into the roles of beneficial PGPR in controlling soil-borne disease, we adopted a metabolomics approach to investigate the beneficial impacts of NSY50...
To gain insights into the roles of beneficial PGPR in controlling soil-borne disease, we adopted a metabolomics approach to investigate the beneficial impacts of NSY50 on cucumber seedling roots under the pathogen of f. sp. (FOC). We found that NSY50 pretreatment (NSY50 + FOC) obviously reduced the production of reactive oxygen species (ROS). Untargeted metabolomic analysis revealed that 106 metabolites responded to NSY50 and/or FOC inoculation. Under FOC stress, the contents of root osmotic adjustment substances, such as proline and betaine were significantly increased, and dehydroascorbic acid and oxidized glutathione (GSH) considerably accumulated. Furthermore, the contents of free amino acids such as tryptophan, phenylalanine, and glutamic acid were also significantly accumulated under FOC stress. Similarly, FOC stress adversely affected glycolysis and the tricarboxylic acid cycles and transferred to the pentose phosphate pathway. Conversely, NSY50 + FOC better promoted the accumulation of α-ketoglutaric acid, ribulose-5-phosphate, and 7-phosphosodiheptanone compared to FOC alone. Furthermore, NSY50 + FOC activated GSH metabolism and increased GSH synthesis and metabolism-related enzyme activity and their encoding gene expressions, which may have improved redox homoeostasis, energy flow, and defense ability. Our results provide a novel perspective to understanding the function of NSY50, accelerating the application of this beneficial PGPR in sustainable agricultural practices.
PubMed: 36101409
DOI: 10.3390/biology11071028