Deciphering the mechanism of fungal pathogen-induced disease-suppressive soil.

One model of a disease-suppressive soil predicts that the confrontation of plant with a phytopathogen can lead to the recruitment and accumulation of beneficial microorganisms. However, more information needs to be deciphered regarding which beneficial microbes become enriched, and how the disease suppression is achieved. Here, we conditioned soil by continuously growing eight generations of cucumber inoculated with Fusarium oxysporum f.sp. cucumerinum in a split-root system. Disease incidence was found to decrease gradually upon pathogen infection accompanied with higher quantity of reactive oxygen species (ROS mainly OH• ) in roots and accumulation of Bacillus and Sphingomonas. These key microbes were proven to protect the cucumber from pathogen infection by inducing high ROS level in the roots through enrichment of pathways, including a two-component system, a bacterial secretion system, and flagellar assembly revealed by metagenomics sequencing. Untargeted metabolomics analysis combined with in vitro application assays suggested that threonic acid and lysine were pivotal to recruit Bacillus and Sphingomonas. Collectively, our study deciphered a 'cry for help' case, wherein cucumber releases particular compounds to enrich beneficial microbes that raise the ROS level of host to prevent pathogen attack. More importantly, this may be one of the fundamental mechanisms underpinning disease-suppressive soil formation.

A soil-borne Mn(II)-oxidizing bacterium of Providencia sp. exploits a strategy of superoxide production coupled to hydrogen peroxide consumption to generate Mn oxides.

Bacterial non-enzymatic Mn(II) oxidation involving reactive oxygen species (ROS) (i.e., indirect oxidation), initially discovered from a marine alpha-proteobacterium, is believed to be of importance in controlling biogeochemical cycles. For soil-borne bacteria, however, evidence of indirect Mn(II) oxidation remains unclear. In this study, the indirect Mn(II) oxidation was evidenced in a soil-borne bacterium, Providencia sp. LLDRA6. First, with and without 50 mM of Mn(II) exposure for LLDRA6, 300 differentially expressed genes were found to be linked to Mn(II) exposure via transcriptome sequencing. Among them, an operon, responsible for phenylacetic acid catabolism, was sharply upregulated in transcription, drawing us a special attention, since its transcriptional upregulation has recently shown to be important for withstanding ROS. Next, a fluorometric probe, 2',7'-Dichlorofluorescin diacetate (DCFDA), was used to qualitatively detect ROS from cells, showing a distinct increase in fluorescence intensities of ROS during Mn(II) exposure. Furthermore, concentrations of superoxide and hydrogen peroxide from cells were detected, respectively, with and without Mn(II) exposure, exhibiting that when Mn(II) oxidation occurred, superoxide concentration significantly increased but hydrogen peroxide concentration significantly decreased. Particularly, superoxide produced by LLDRA6 was proven to be the oxidant for Mn(II) in the formation of Mn oxides. Finally, we predicted links between phenylacetic acid metabolism pathway and ROS during Mn(II) exposure, proposing that the excessive ROS, generated in response to Mn(II) exposure, transcriptionally activate phenylacetic acid catabolism presumably by increasing concentrations of highly reactive oxepins.

Providencia manganoxydans sp. nov., a Mn(II)-oxidizing bacterium isolated from heavy metal contaminated soils in Hunan Province, China.

A facultatively anaerobic, Gram-negative, rod-shaped bacterial strain designated as LLDRA6T, was isolated from heavy metal contaminated soils collected near a ceased smelting factory at Zhuzhou, Hunan Province, China. Strain LLDRA6T has the ability to oxidize Mn(II) and generate biogenic manganese oxides. The strain can grow in a wide range of temperature from 10-42°C and pH from 5 to 10. Comparative analysis of its complete 16S rRNA gene sequence suggests that strain LLDRA6T is highly similar to species within the genus Providencia. The complete genome of LLDRA6T is 4 342 370 bp with 40.18 mol% of G+C content and contains no plasmids. In comparison to the genomes of type strains in Providencia, LLDRA6T shows average nucleotide identity values between 76.60 and 80.89 %, and digital DNA-DNA hybridization values in a range of 21.2-24.6 %. Both multilocus sequence analysis and genomic phylogenetics indicate a new taxonomic status for LLDRA6T in Providencia. Chemotaxonomic analyses for LLDRA6T show that the predominant cellular fatty acids are C16 : 0, C14 : 0 and cyclo-C17 : 0, accounting for 32.7, 16.1 and 10.3 % of total fatty acids, respectively. The polar lipids consist of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids, one unidentified phospholipid and three unidentified lipids. Within the cell wall, ribose and meso-diaminopimelic acid are the characteristic constituents for saccharides and amino acids, respectively. Respiratory quinones on cell membranes are composed of menaquinone (MK) and ubiquinone (coenzyme Q), including MK-8 (100.0 %), Q-7 (13.7 %) and Q-8 (86.3 %). Moreover, the positive results from d-lyxose and d-mannitol fermentation tests indicate that LLDRA6T is totally different from all the type strains within the genus Providencia. In summary, strain LLDRA6T represents a novel species in the genus Providencia, for which the name Providencia manganoxydans sp. nov. (type strain LLDRA6T=CCTCC AB 2021154T=KCTC 92091T) is proposed.

Inhibition of pathogenic microorganisms in solid organic waste via black soldier fly larvae-mediated management.

Inadequately managed solid organic waste generation poses a threat to the environment and human health globally. Biotransformation with the black soldier fly larvae (BSFL) is emerging as talent technology for solid waste management. However, there is a lack of understanding of whether BSFL can effectively suppress potential pathogenic microorganisms during management and the underlying mechanisms. In this study, we investigated the temporal variations of microorganisms in two common types of solid waste, i.e., kitchen waste (KW) and pig manure (PM). Natural composting and composting with BSFL under three different pH levels (pH 5, 7, and 9) were established to explore their impact on microbial communities in compost and the gut of BSFL. The results showed that the compost of kitchen waste and pig manure led to an increase in relative abundance of various potentially pathogenic bacteria. Temporal gradient analyses revealed that the most substantial reduction in the relative abundance and diversity of potentially pathogenic microorganisms occurred when the initial pH of both two wastes were adjusted to 7 upon the introduction of BSFL. Through network and pls-pm analysis, it was discovered that the gut microbiota of BSFL occupied an ecological niche in the compost, inhibiting the proliferation of potentially pathogenic microorganisms. This study has revealed the potential of BSFL in reducing public health risks during the solid waste management process, providing robust support for sustainable waste management.

Abiotic transformation of atrazine in aqueous phase by biogenic bixbyite-type Mn2O3 produced by a soil-derived Mn(II)-oxidizing bacterium of Providencia sp.

Recently, biogenic Mn oxides (BioMnOx) are considered as the promising degradation agents for environmental organic contaminants. However, little information is available for the degradation of atrazine by BioMnOx. In this work, BioMnOx, generated by a soil-derived Mn(II)-oxidizing bacterium, Providencia sp. LLDRA6, was explored to degrade atrazine. To begin with, collective results from mineral characterization analyses demonstrated that this BioMnOx was biogenic bixbyite-type Mn2O3. After that, purified biogenic Mn2O3 was found to exhibit a much higher removal efficiency for atrazine in aqueous phase, as compared to unpurified biogenic Mn2O3 and LLDRA6 biomass. During the atrazine removal by biogenic Mn2O3, six intermediate degradation products were discovered, comprising deethylatrazine (DEA), hydroxylatrazine (HA), deethylhydroxyatrazine (DEHA), ammeline, cyanuric acid, and 5-methylhexahydro-1,3,5-triazine-2-thione (MTT). Particularly, the intermediate, MTT, was considered as a new degradation product of atrazine, which was not described previously. Meanwhile, Mn(II) ions were released from biogenic Mn2O3, and on the surface of biogenic Mn2O3, the content of hydroxyl O species increased at the expense of that of lattice and water O species, but the fundamental crystalline structure of this Mn oxide remained unchanged. Additionally, no dissociative Mn(III) was found to involve in atrazine degradation. In summary, these results demonstrated that both the non-oxidative and oxidative reactions underlay the degradation of atrazine by biogenic Mn2O3.

Specific metabolites drive the deterministic assembly of diseased rhizosphere microbiome through weakening microbial degradation of autotoxin.

BACKGROUND: Process and function that underlie the assembly of a rhizosphere microbial community may be strongly linked to the maintenance of plant health. However, their assembly processes and functional changes in the deterioration of soilborne disease remain unclear. Here, we investigated features of rhizosphere microbiomes related to Fusarium wilt disease and assessed their assembly by comparison pair of diseased/healthy sequencing data. The untargeted metabolomics was employed to explore potential community assembly drivers, and shotgun metagenome sequencing was used to reveal the mechanisms of metabolite-mediated process after soil conditioning. RESULTS: Results showed the deterministic assembly process associated with diseased rhizosphere microbiomes, and this process was significantly correlated to five metabolites (tocopherol acetate, citrulline, galactitol, octadecylglycerol, and behenic acid). Application of the metabolites resulted in a deterministic assembly of microbiome with the high morbidity of watermelon. Furthermore, metabolite conditioning was found to weaken the function of autotoxin degradation undertaken by specific bacterial group (Bradyrhizobium, Streptomyces, Variovorax, Pseudomonas, and Sphingomonas) while promoting the metabolism of small-molecule sugars and acids initiated from another bacterial group (Anaeromyxobacter, Bdellovibrio, Conexibacter, Flavobacterium, and Gemmatimonas). Video Abstract CONCLUSION: These findings strongly suggest that shifts in a metabolite-mediated microbial community assembly process underpin the deterministic establishment of soilborne Fusarium wilt disease and reveal avenues for future research focusing on ameliorating crop loss due to this pathogen.

ggClusterNet: An R package for microbiome network analysis and modularity-based multiple network layouts.

The network analysis has attracted increasing attention and interest from ecological academics, thus it is of great necessity to develop more convenient and powerful tools. For that reason, we have developed an R package, named "ggClusterNet," to complete and display the network analysis in an easier manner. In that package, ten network layout algorithms are designed to better display the modules of microbiome network (randomClusterG, PolygonClusterG, PolygonRrClusterG, ArtifCluster, randSNEClusterG, PolygonModsquareG, PolyRdmNotdCirG, model_Gephi.2, model_igraph, and model_maptree). For the convenience of the users, many functions related to microbial network analysis, such as corMicor(), net_properties(), node_properties(), ZiPiPlot(), random_Net_compate(), are integrated to complete the network mining. Furthermore, the pipeline function named network.2() and corBionetwork() are also added for the quick achievement of the network or bipartite network analysis as well as their in-depth mining. The ggClusterNet is publicly available via GitHub (https://github.com/taowenmicro/ggClusterNet/) or Gitee (https://gitee.com/wentaomicro/ggClusterNet) for users' access. A complete description of the usages can be found on the manuscript's GitHub page (https://github.com/taowenmicro/ggClusterNet/wiki).

Metabolic Enhancement of Glycolysis and Mitochondrial Respiration Are Essential for Neuronal Differentiation.

Metabolic reactions provide energy and metabolic substance for cell function. It was recently shown that metabolic reprogramming is a key regulator of cell pluripotency and differentiation. Although many evidences point to a metabolic "switch" toward mitochondrial respiration, the importance of glycolysis and mitochondrial respiration is still controversial. In this study, we differentiated two different neuronal cells and compared the glycolytic and metabolic profile before and after differentiation. The results showed a significant increase in glycolysis (includes basal glycolysis and glycolytic capacity) and mitochondrial respiration (includes mitochondrial basal respiration, adenosine triphosphate production, and mitochondrial respiration capacity) of both SY5Y and neural stem cells (NSCs) during neuronal differentiation, whereas their mitochondrial DNA copies remain unchanged. Antimycin, a mitochondrial inhibitor, reduced cell density of differentiated SY5Y cells. However, for differentiated NSCs, antimycin dedifferentiated the cells, resulted in a significant increase in cell density, and lowered oxidative stress. In conclusion, this study demonstrated that metabolic enhancement of glycolysis and mitochondrial respiration (rather than a "switch") are both important for neuronal differentiation, although only the blocking of mitochondrial respiration reverses the differentiation process.

Blood Exosomes Have Neuroprotective Effects in a Mouse Model of Parkinson's Disease.

Parkinson's disease (PD) is a common and complex neurodegenerative disease; the pathogenesis of which is still uncertain. Exosomes, nanosized extracellular vesicles, have been suggested to participate in the pathogenesis of PD, but their role is unknown. Here, a metabolomic analysis of serum and brain exosomes showed differentially expressed metabolites between 1-Methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine hydrochloride- (MPTP-) induced PD mice and control mice, such as oxidized lipids, vitamins, and cholesterol. These metabolites were enriched in coenzyme, nicotinamide, and amino acid pathways related to PD, and they could be served as preclinical biomarkers. We further found that blood-derived exosomes from healthy volunteers alleviated impaired motor coordination in MPTP-treated mice. Results from immunohistochemistry and western blotting indicated that the loss of dopaminergic neurons in substantia nigra and striatum of PD model mice was rescued by the exosome treatment. The exosome treatment also restored the homeostasis of oxidative stress, neuroinflammation, and cell apoptosis in the model mice. These results suggest that exosomes are important mediators for PD pathogenesis, and exosomes are promising targets for the diagnosis and treatment of PD.

Removal of Pb(II) Ions from Aqueous Solutions by Spherical Nanocomposites Synthesized Through Immobilization of Paecilomyces lilacinus in Silica Nanoparticles Coated with Ca-Alginate.

In the present study, a novel microbial nanocomposite "Paecilomyces lilacinus-silica nanoparticlescalcium-alginate beads" (P. lilacinus-SN-Cal-Alg) were synthesized and their high efficiency for removing Pb(II) ions was demonstrated in aqueous solution. P. lilacinus-SN-Cal-Alg beads before and after the adsorption of Pb(II) were characterized by FT-IR, SEM-EDS, and XPS analyses. The adsorption capacity of Pb(II) by P. lilacinus-SN-Cal-Alg beads was analyzed in aqueous solution. For comparison, the adsorption capacity of Pb(II) by another type of microbial composites, namely, P. lilacinus-Cal-Alg beads, without addition of silica nanoparticles, was also studied in parallel. Lastly, the equilibrium data in adsorption process were examined by both Langmuir and Freundlich isotherm models to evaluate adsorption mechanism. The results showed that an excellent removal efficiency of Pb(II) in aqueous solution (85.54%) was obtained at initial concentration of 200 mg/L by using the P. lilacinus-SN-Cal-Alg beads. Meanwhile, they exhibited the better adsorption capacity for Pb(II) than P. lilacinus-Cal-Alg beads. The adsorption process by P. lilacinus-SN-Cal-Alg beads was best described by the Langmuir model indicating that monolayer adsorption of Pb(II) ions takes place on the beads surfaces and showed that its maximum adsorption capacity was 282.49 mg/g.

Discovery of a novel native bacterium of Providencia sp. with high biosorption and oxidation ability of manganese for bioleaching of heavy metal contaminated soils.

Heavy metal removal from contaminated soils is a long-term challenging problem important for global economics, environment, and human health. Marine and freshwater-originated Mn(II)-oxidizing bacteria are considered as the promising bioremediation agents for environmental applications. However, practical application of soil-originated Mn(II)-oxidizing bacteria remains to be developed for contaminated soil remediation. In this work, the Mn(II) biosorption/oxidation mechanism of a new soil-originated bacterium and its bioleaching efficiency of heavy metals from soils was studied in detail. First, we found, isolated and identified a new highly Mn(II)-tolerant bacterial strain Providencia sp. LLDRA6 from heavy metal-contaminated soils. Next, strain LLDRA6 demonstrated its high Mn(II) biosorption capacity in aqueous solution. Then, Mn(II) adsorption by LLDRA6 was largely proven to be a synergistic effect of (i) Mn(II) precipitation on the cell surface, (ii) oxidation of Mn(II) into BioMnOx on the cell surface, and (iii) intracellular accumulation of insoluble MnCO3. Finally, combination bioleaching by the bacterium of Providencia sp. LLDRA6 and its formed BioMnOx was proposed to develop a potential environment-friendly and cost-effective technique to remediate severely heavy metal-contaminated soils. The bioleaching tests demonstrated that the combination of Providencia sp. LLDRA6 and BioMnOx exhibited an excellent removal efficiency for heavy metals of Pb (81.72%), Cr (88.29%), Cd (90.34%), Cu (91.25%), Mn (56.13%), and Zn (59.83%) from contaminated soils, resulting in an increase of removal efficiency in the range of 1.68-26.4% compared to Providencia sp. LLDRA6 alone. Moreover, the bacterial leachate facilitated the residual fraction of metals to transform into the easily migratory fractions in soils. These findings have demonstrated that strain LLDRA6 has high adsorption ability to remove heavy metals from contaminated soils, thus providing a promising bio-adsorbent for environmental bioremediation.