Use of CAS-agar plate modified to study the effect of different variables on the siderophore production by Aspergillus

Transcriptomic analysis and carbohydrate metabolism-related enzyme expression across different pH values in Rhizopus delemar

Introduction

pH is one of the important factors affecting the growth and performance of microorganisms.

Methods

We studied the pH response and plant growth-promoting (PGP) ability of Rhizopus delemar using cultivation experiments and transcriptomics, and verified the expression profiles using quantitative real-time PCR.

Results

pH affected the growth and PGP properties of R. delemar. At pH 7, the growth rate of R. delemar was rapid, whereas pH 4 and 8 inhibited mycelial growth and PGP ability, respectively. In the pot experiment, the plant height was the highest at pH 7, 56 cm, and the lowest at pH 4 and pH 5, 46.6 cm and 47 cm, respectively. Enzyme activities were highest at pH 6 to pH 7. Enzyme activities were highest at pH 6 to pH 7. Among the 1,629 differentially expressed genes (DEGs), 1,033 genes were up-regulated and 596 were down-regulated. A total of 1,623 DEGs were annotated to carbohydrate-active enzyme coding genes.

Discussion

The PGP characteristics, e.g., Phosphorus solubilization ability, of R. delemar were strongest at pH 7. The results provide useful information regarding the molecular mechanism of R. delemar pH response.

Microbacterium nymphoidis sp. nov. and Microbacterium festucae sp. nov., two novel species with high plant-promoting potential isolated from wetland plants in China

Two novel plant growth-promoting, rod-shaped, Gram-positive and non-motile rhizobacteria, W1NT and W2RT, were isolated from wetland plants Festuca elata and Nymphoides peltatum, respectively, in China. The results of the 16S rRNA sequence alignment analysis showed that they were related to Microbacterium, with the highest similarity to Microbacterium ketosireducens (98.7 %) and Microbacterium laevaniformans (98.5 %) for strain W1NT, and to Microbacterium terricola (98.1 %) and Microbacterium marinum (98.0 %) for strain W2RT. Phylogenetic analyses based on 16S rRNA gene sequences and 92 conserved concatenated proteins suggested that the two strains belong to the genus Microbacterium and were placed in two separate novel phylogenetic clades. The genome sizes of the two strains were 3.2 and 3.7 Mb, and the G+C contents were 71.7 and 68.5 mol%, respectively. The comparative genome results showed that the average nucleotide identity values between W1NT and W2RT and other species ranged from 73.5 to 83.6 %, and the digital DNA-DNA hybridization values ranged from 19.7 to 26.8 %. These two strains show physiological and biochemical features that differ from those of closely related species. Rhamnose, galactose and glucose were present in the characteristic sugar fractions of strains W1NT and W2RT. The peptidoglycan of strains W1NT and W2RT contained the amino acids ornithine, alanine and aspartic acid. C15 : 0 anteiso, C17 : 0 anteiso and C16 : 0 iso were the predominant cellular fatty acids in W1NT and W2RT. Phosphatidylglycerol and diphosphatidylglycerol are major polar lipid components. Strain W1NT not only formed bacterial biofilms but also had the ability to solubilize phosphorus and produce indole-3-acetic acid. Strain W2RT had siderophore-producing and lignin-degrading properties. Based on their genetic and phenotypic characteristics, strains W1NT and W2RT were classified as novel bacteria in the genus Microbacterium and designated as Microbacterium festucae sp. nov. (type strain W1NT=ACCC 61807T=GDMCC 1.2966T=JCM 35339T) and Microbacterium nymphoidis sp. nov. (type strain W2RT=ACCC 61808T=GDMCC 1.2967T=JCM 35340T).

Effects of Phosphorus-dissolving Dark Septate Endophytes on the Growth of Blueberry

Dark septate endophytes (DSEs) are widely distributed and improve plant growth. DSEs secrete large amounts of enzymes to mineralize insoluble phosphorus in soil and convert it into soluble phosphorus, promoting plant uptake of phosphorus. However, the effects of DSEs with phosphate-solubilizing ability on host plants need further study. In this study, phosphorus-dissolving DSEs were screened for growth-promoting effects. We isolated, identified and characterized three DSE species (Thozetella neonivea, Pezicula ericae and Hyaloscyphaceae sp.) showing phosphate-solubilizing ability. The impact of single, dual or triple inoculation of DSEs on blueberry plant characteristics was studied. Their effects on colonization intensity, seedling biomass, nutrients in plants and soil, and activities of plant resistance enzymes and soil enzymes were markedly upregulated relative to the control (P < 0.05). The available phosphorus and acid phosphatase levels in different combinations were significantly increased. These findings indicate that the application of the three DSEs may be valuable in facilitating the cultivation of blueberry with a higher biomass and improved plant quality.

The Gene paaZ of the Phenylacetic Acid (PAA) Catabolic Pathway Branching Point and ech outside the PAA Catabolon Gene Cluster Are Synergistically Involved in the Biosynthesis of the Iron Scavenger 7-Hydroxytropolone in Pseudomonas donghuensis HYS

The newly discovered iron scavenger 7-hydroxytropolone (7-HT) is secreted by Pseudomonas donghuensis HYS. In addition to possessing an iron-chelating ability, 7-HT has various other biological activities. However, 7-HT's biosynthetic pathway remains unclear. This study was the first to report that the phenylacetic acid (PAA) catabolon genes in cluster 2 are involved in the biosynthesis of 7-HT and that two genes, paaZ (orf13) and ech, are synergistically involved in the biosynthesis of 7-HT in P. donghuensis HYS. Firstly, gene knockout and a sole carbon experiment indicated that the genes orf17-21 (paaEDCBA) and orf26 (paaG) were involved in the biosynthesis of 7-HT and participated in the PAA catabolon pathway in P. donghuensis HYS; these genes were arranged in gene cluster 2 in P. donghuensis HYS. Interestingly, ORF13 was a homologous protein of PaaZ, but orf13 (paaZ) was not essential for the biosynthesis of 7-HT in P. donghuensis HYS. A genome-wide BLASTP search, including gene knockout, complemented assays, and site mutation, showed that the gene ech homologous to the ECH domain of orf13 (paaZ) is essential for the biosynthesis of 7-HT. Three key conserved residues of ech (Asp39, His44, and Gly62) were identified in P. donghuensis HYS. Furthermore, orf13 (paaZ) could not complement the role of ech in the production of 7-HT, and the single carbon experiment indicated that paaZ mainly participates in PAA catabolism. Overall, this study reveals a natural association between PAA catabolon and the biosynthesis of 7-HT in P. donghuensis HYS. These two genes have a synergistic effect and different functions: paaZ is mainly involved in the degradation of PAA, while ech is mainly related to the biosynthesis of 7-HT in P. donghuensis HYS. These findings complement our understanding of the mechanism of the biosynthesis of 7-HT in the genus Pseudomonas.

Antimicrobial Traits of Beauveria bassiana Against Rhizoctonia solani, the Causal Agent of Sheath Blight of Rice Under Field Conditions

Beauveria bassiana, an entomopathogenic fungus, has recently drawn attention worldwide not only as a potential biocontrol agent against insect pests but also for its other beneficial roles as plant disease antagonist, endophyte, plant growth promoter, and beneficial rhizosphere colonizer. In the present study, 53 native isolates of B. bassiana were screened for antifungal ability against Rhizoctonia solani, the causal agent of sheath blight of rice. Also, the mechanisms underlying such interaction and the responsible antimicrobial traits involved were studied. Following this, potential B. bassiana isolates were assayed against the reduction of sheath blight of rice under field conditions. The results showed that B. bassiana exhibited antagonistic behavior against R. solani with a percent mycelial inhibition recorded maximum of up to 71.15%. Mechanisms behind antagonism were the production of cell-wall-degrading enzymes, mycoparasitism, and the release of secondary metabolites. The study also deciphered several antimicrobial traits and the presence of virulent genes in B. bassiana as a determinant of potential plant disease antagonists. Under field conditions, combined application of the B. bassiana microbial consortium as a seed treatment, seedling root dip, and foliar sprays showed reduced sheath blight disease incidence and severity up to 69.26 and 60.50%, respectively, along with enhanced plant-growth-promoting attributes. This is one of the few studies investigating the antagonistic abilities of the entomopathogenic fungus B. bassiana against phytopathogen R. solani and the underlying mechanisms involved.

Differential Responses of Bacterial and Fungal Communities to Siderophore Supplementation in Soil Affected by Tobacco Bacterial Wilt (Ralstonia solanacearum)

Siderophores secreted by microorganisms can promote ecological efficiency and could be used to regulate the unbalanced microbial community structure. The influence of the siderophore activity of Trichoderma yunnanense strain 2-14F2 and Beauveria pseudobassiana strain (2-8F2) on the physiological/biochemical functions and community structure of soil microbes affected by tobacco bacterial wilt (TBW) was studied. DNS Colorimetry and Biolog-eco plates were used to quantify the impacts of strain siderophores on soil enzyme activities and microbial metabolism. Based on Illumina MiSeq high-throughput sequencing, the soil 16S rDNA and ITS sequences were amplified to dissect the response characteristics of alpha/beta diversity and the structure/composition of a soil microbial community toward siderophores. The KEGG database was used to perform the PICRUSt functional prediction of the microbial community. We found that siderophores of 2-14F2 and 2-8F2, at certain concentrations, significantly increased the activities of sucrase (S-SC) and urease (S-UE) in the TBW soil and enhanced the average well color development (AWCD, carbon source utilization capacity) of the microbial community. The metabolic capacity of the diseased soil to amino acids, carbohydrates, polymers, aromatics, and carboxylic acids also increased significantly. The response of the bacterial community to siderophore active metabolites was more significant in alpha diversity, while the beta diversity of the fungal community responded more positively to siderophores. The relative abundance of Actinobacteria, Chloroflexi, and Acidobacteria increased and was accompanied by reductions in Proteobacteria and Firmicutes. LEfSe analysis showed that Pseudonocardiaceae, Gemmatimonas, Castellaniella, Chloridiumand and Acrophialophora altered the most under different concentrations of siderophore active metabolites. The PICRUSt functional prediction results showed that siderophore increased the abundance of the redox-related enzymes of the microbial community in TBW soil. The BugBase phenotypic prediction results showed that the siderophore activity could decrease the abundance of pathogenic bacteria. The study concludes that siderophore activity could decrease the abundance of pathogenic bacteria and regulate the composition of the microbial community in TBW soil. The activities of sucrase (S-SC) and urease (S-UE) in TBW soil were significantly increased. Overall, the siderophore regulation of community structures is a sustainable management strategy for soil ecosystems.

AlgU controls environmental stress adaptation, biofilm formation, motility, pyochelin synthesis and antagonism potential in Pseudomonas protegens SN15-2

Pseudomonas protegens is a typical plant-growth-promoting rhizobacterium that can serve as an agricultural biocontrol agent. The extracytoplasmic function (ECF) sigma factor AlgU is a global transcription regulator controlling stress adaption and virulence in Pseudomonas aeruginosa and Pseudomonas syringae. Meanwhile, the regulatory role of AlgU in the biocontrol ability of P.protegens has been poorly studied. In this study, deletion mutations of algU and its antagonist coding gene mucA were constructed to investigate the function of AlgU in P.protegens SN15-2 via phenotypic experiment and transcriptome sequencing analysis. On the basis of phenotypic analyses, it was concluded that the AlgU whose transcription was induced by osmotic stress and oxidative stress positively regulated biofilm formation and tolerance towards osmotic, heat, and oxidation stresses, while it negatively regulated motility, pyochelin synthesis, and the ability to inhibit pathogens. On the basis of the RNA-seq analysis, compared to the wild-type strain, 12 genes were significantly upregulated and 77 genes were significantly downregulated in ΔalgU, while 407 genes were significantly upregulated and 279 genes were significantly downregulated in ΔmucA, indicating the involvement of AlgU in several cellular processes, mainly related to resistance, carbohydrate metabolism, membrane formation, alginate production, the type VI secretion system, flagella motility and pyochelin production. Our findings provide insights into the important role of AlgU of P.protegens in biocontrol, which is of value in improving the biocontrol ability of P.protegens.

Stress-Resistance and Growth-Promoting Characteristics and Effects on Vegetable Seed Germination of Streptomyces sp. Strains Isolated from Wetland Plant Rhizospheres

Wetlands are the most biologically diverse ecosystems on Earth. The isolation of Streptomyces strains from wetlands is helpful to study their diversity and functions in such habitats. In this study, six strains of Streptomyces were isolated from the rhizosphere soil of three plant species in the Huaxi Wetland at Guiyang and were identified as Streptomyces galilaeus, S. avidinii, S. albogriseolus, S. albidoflavus, S. spororaveus, and S. cellulosae, respectively. The six strains all solubilized phosphate, fixed nitrogen, and produced ACC deaminase and siderophores, and four strains also secreted indole-3-acetic acid. The six strains had the ability to resist to certain degrees of salinity, drought, and acidic/alkaline pH stress. In addition, the S. avidinii WL3 and S. cellulosae WL9 strains significantly promoted seed germination of mung bean, pepper, and cucumber, especially the WL3 strain. A pot experiment further showed that WL3 significantly promoted the growth of cucumber seedlings. Thus, strains of six species of Streptomyces with multiple plant growth-promoting characteristics were isolated from the wetland. These results lay a foundation for their potential use as microbial agents for seed-coating treatments.

A Feasibility Study on the Recall of Metallophilic Fungi from Fe(III)-Contaminated Soil and Evaluating Their Mycoremediation Capacity: Experimental and Theoretical Study

Mycoremediation is one of the most attractive, eco-friendly, and sustainable methods to mitigate the toxic effects of heavy metals. This study aimed to determine the mycoremediation capacity of metallophilic fungi isolated from heavy-metal-contaminated soil containing a high Fe(III) concentration (118.40 mg/kg). Four common fungal strains were isolated, including Curvularia lunata, Fusarium equiseti, Penicillium pinophilum, and Trichoderma harzianum. These fungal strains were exposed to gradually increasing concentrations of Fe(III) of 100, 200, 300, 400, 500, 600, 700, 800, 900, and 1000 mg/L. Sophisticated techniques and tests were employed to investigate the mycoremediation capability, including tolerance index (TI), scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), and adsorption isotherm. Furthermore, the impacts of initial concentration, pH, and temperature on the Fe(III) removal (%) and uptake capacity (mg/g) of the studied samples were investigated. The results were validated by statistical analysis using one-way ANOVA. It was found that the Fe(III) uptake with different ratios triggered alterations in the Fe(III) tolerance (TI) morphological (SEM), chemical (FTIR), and adsorption capacity properties. The highest Fe(III) tolerance for all studied fungal strains was achieved at 100 mg/L. Moreover, the optimum conditions of Fe(III) removal (%) for all studied fungal strains were within pH 7 and 28 °C, with similar performance at the initial Fe(III) concentration ranging from 50-200 mg/L. At the same time, the maximum Fe(III) uptake was achieved at pH 7, 20 °C, and 200 mg/L. Compared to other strains, the Fe(III) tolerance of T. harzianum was rise in the Fe(III) concentration. The Fe(III) uptake reaction was corroborated by best fitting with the Langmuir model, achieving optimum adsorption capacities of 61.34, 62.90, 63.30, and 72.46 mg/g for C.lunata, F. equiseti, P. pinophilum, T. harzianum, respectively. It can be deduced that the addressed fungi species can be applied in mycoremediation according to the utilized Fe(III) concentrations with more superiority for live T. harzianum.

Growth and genome-based insights of Fe(III) reduction of the high-temperature and NaCl-tolerant Shewanella xiamenensis from Changqing oilfield of China

Introduction

A facultative anaerobe bacterium Shewanella xiamenensis CQ-Y1 was isolated from the wastewater of Changqing oilfield in Shaanxi Province of China. Shewanella is the important dissimilatory metal-reducing bacteria. It exhibited a well potential application in biodegradation and bioremediation.

Methods

Genome sequencing, assembling and functional annotation were conducted to explore the genome information of CQ-Y1. The effect of temperatures and NaCl concentrations on the CQ-Y1 growth and Fe(III) reduction were investigated by UV visible spectrophotometry, SEM and XRD.

Results

Genomic analysis revealed its complete genome was a circular chromosome of 4,710,887 bp with a GC content of 46.50% and 4,110 CDSs genes, 86 tRNAs and 26 rRNAs. It contains genes encoding for Na⁺/H⁺ antiporter, K⁺/Cl^- transporter, heat shock protein associated with NaCl and high-temperature resistance. The presence of genes related to flavin, Cytochrome c, siderophore, and other related proteins supported Fe(III) reduction. In addition, CQ-Y1 could survive at 10% NaCl (w/v) and 45°C, and temperature showed more pronounced effects than NaCl concentration on the bacterial growth. The maximum Fe(III) reduction ratio of CQ-Y1 reached 70.1% at 30°C without NaCl, and the reduction reaction remained active at 40°C with 3% NaCl (w/v). NaCl concentration was more effective than temperature on microbial Fe(III) reduction. And the reduction products under high temperature and high NaCl conditions were characterized as Fe₃(PO₄)₂, FeCl₂ and Fe(OH)₂.

Discussion

Accordingly, a Fe(III) reduction mechanism of CQ-Y1 mediated by Cytochrome c and flavin was hypothesised. These findings could provide information for a better understanding of the origin and evolution of genomic and metabolic diversity of S. xiamenensis.

Siderophore Synthesis Ability of the Nitrogen-Fixing Bacterium (NFB) GXGL-4A is Regulated at the Transcriptional Level by a Transcriptional Factor (trX) and an Aminomethyltransferase-Encoding Gene (amt)

Kosakonia radicincitans GXGL-4A, a gram-negative nitrogen-fixing (NF) bacterial strain is coated with a thick capsulatus on the surface of cell wall, which becomes a physical barrier for exogenous DNA to enter the cell, so the operation of genetic transformation is difficult. In this study, an optimized Tn5 transposon mutagenesis system was established by using a high osmotic HO-1 medium combined with the electroporation transformation. Eventually, a mutant library containing a total of 1633 Tn5 insertional mutants were established. Of these mutants, the mutants M81 and M107 were found to have an enhanced capability to synthesize siderophore through the CAS agar plate assay and the spectrophotometric determination. The bacterial cells of two mutants were applied in cucumber growth-promoting experiment. Cucumber seedlings treated with M81 and M107 cells had a significant increase in biomass including seedling height, seedling fresh weight, root fresh weight, and root length. The whole genome sequencing of the mutants M81 and M107 showed that the integration sites of Tn5 transposon element were located in MmyB-like helix-turn-helix transcription regulator (locus tag: A3780_19720, trX) and aminomethyltransferase-encoding genes (locus tag: A3780_01680, amt) in the genome of GXGL-4A, respectively. The ability of siderophore synthesis of the target mutants was improved by Tn5 insertion mutagenesis, and the mutants obtained showed a good plant growth-promoting effect when applied to the cucumber seedlings. The results suggest that the identified functional genes regulates the biosynthesis of siderophore in azotobacter GXGL-4A, and the specific mechanism needs to be further investigated.

Acrophialophora jodhpurensis: an endophytic plant growth promoting fungus with biocontrol effect against Alternaria alternata

In this study, efficiency of the endophytic fungal isolate Msh5 was evaluated on promoting tomato plant growth and controlling Alternaria alternata, the causal agent of early blight in tomatoes. Morphological and molecular (ITS and tub2 sequences) analyses revealed that the fungal isolate, Msh5, was Acrophialophora jodhpurensis (Chaetomium jodhpurense Lodha). This beneficial fungus was capable of producing indole-3-acetic acid (IAA), urease, siderophore, extracellular enzymes, and solubilized phosphate. Under laboratory conditions, the Msh5 isolate of A. jodhpurensis inhibited A. alternata growth in dual culture, volatile and non-volatile metabolites assays. The supernatant of this endophytic fungus was capable of reducing spore germination and altering the hyphal structure of A. alternata and the spores produced germ tubes showed vacuolization and abnormal structure compared to the control. Also, the effect of A. jodhpurensis on plant growth parameters (such as shoot and root weight and length) and suppressing A. alternata was investigated in vivo via seed inoculation with spores of A. jodhpurensis using 1% sugar, 0.5% carboxymethyl cellulose (CMC) or 0.5% molasses solution as stickers. Colonization of tomato roots by the endophytic fungus resulted in significant increasing plant growth parameters and reduction in the progress of the diseases caused by A. alternata compared to the controls. Among the different coating materials used as stickers, sugar was found to be the most effective for enhancing plant growth parameters and decreasing the disease progress. Therefore, A. jodhpurensis isolate Msh5 can be suggested as a potential biofertilizer and biocontrol agent for protecting tomato plants against A. alternata.

Regulating Root Fungal Community Using Mortierella alpina for Fusarium oxysporum Resistance in Panax ginseng

Plant-associated microbes play important roles in plant health and disease. Mortierella is often found in the plant rhizosphere, and its possible functions are not well known, especially in medical plants. Mortierella alpina isolated from ginseng soil was used to investigate its effects on plant disease. The promoting properties and interactions with rhizospheric microorganisms were investigated in a medium. Further, a pot experiment was conducted to explore its effects on ginseng root rot disease. Physicochemical properties, high-throughput sequencing, network co-occurrence, distance-based redundancy analysis (db-RDA), and correlation analysis were used to evaluate their effects on the root rot pathogen. The results showed that Mortierella alpina YW25 had a high indoleacetic acid production capacity, and the maximum yield was 141.37 mg/L at 4 days. The growth of M. alpina YW25 was inhibited by some probiotics (Bacillus, Streptomyces, Brevibacterium, Trichoderma, etc.) and potential pathogens (Cladosporium, Aspergillus, etc.), but it did not show sensitivity to the soil-borne pathogen Fusarium oxysporum. Pot experiments showed that M. alpina could significantly alleviate the diseases caused by F. oxysporum, and increased the available nitrogen and phosphorus content in rhizosphere soil. In addition, it enhanced the activities of soil sucrase and acid phosphatase. High-throughput results showed that the inoculation of M. alpina with F. oxysporum changed the microbial community structure of ginseng, stimulated the plant to recruit more plant growth-promoting bacteria, and constructed a more stable microbial network of ginseng root. In this study, we found and proved the potential of M. alpina as a biocontrol agent against F. oxysporum, providing a new idea for controlling soil-borne diseases of ginseng by regulating rhizosphere microorganisms.

A new function of white-rot fungi Ceriporia lacerata HG2011: improvement of biological nitrogen fixation of broad bean (Vicia faba)

The inoculation of plant growth-promoting microbes with multifarious functions is a simple, economic, and effective way to improve nodulation and biological nitrogen fixation (BNF) of legumes. Broad bean (Vicia faba) is commonly grown in the winter in tropics and subtropics for increasing soil N and farmers' income. The new functions of Ceriporia lacerata HG2011, a white-rot fungus, in nodulation and BNF (measured by ¹⁵N natural abundance) were studied with the broad bean in liquid culture, soil incubation, and greenhouse pot experiments. The results showed that this fungus released IAA, GA, and Fe-binding ligands into culture solutions, increased lateral roots and root surfaces, and mobilized phosphorus and iron into bioavailable forms in the soil. These performances may be beneficial to nodulation and BNF. The indigenous rhizobia that infect broad been were long-lived in the experimental soil. The efficiency of exogenous rhizobium inoculation may be unsatisfactory in the soils for frequently growing broad beans because of fierce competition with native rhizobia. Compared with no inoculation, the fungal inoculant increased nutrient (nitrogen, phosphorus, and potassium) availability in the fertilized soil, nodule mass, and plant BNF and nutrient uptake, leading to higher plant biomass and grain yield. Thus, C. lacerata HG2011 provided more potential sites for rhizobia infection in nodulation, increased nodule size, and improved nodule mineral nutrient (particularly phosphorus and iron) and photosynthate acquisitions, resulting in better nodulation and increased plant BNF. These significant findings firstly proved a new function of C. lacerata HG2011 in improving the inoculation and BNF of legume plants.

Plant-beneficial functions and interactions of Bacillus subtilis SL-44 and Enterobacter cloacae Rs-2 in co-culture by transcriptomics analysis

The development of mixed microbial agents can reduce the use of pesticides and fertilizers in agriculture. However, most previous studies focused only on the overall effects of mixed microbial agents and ignored the interactions between bacteria in mixed systems. In this study, Bacillus subtilis SL-44 and Enterobacter cloacae Rs-2 were used to explore the interactions between two different functional plant growth-promoting rhizobacteria (PGPR). The plant growth-promotion properties and inhibition rate of Rhizoctonia solani were determined, and the mechanism of the interactions under single and co-culture conditions was elucidated via transcriptomics analysis under single and co-culture conditions. Results showed that the co-culture was not conducive to B. subtilis SL-44 growth. Furthermore, the differentially expressed genes related to B. subtilis SL-44 developmental process and cell differentiation were downregulated by 82.7% and 84.8% respectively. Moreover, among the properties, only siderophore production by the mixed culture was higher than that of single cultures because of the upregulation of the siderophore-related genes of B. subtilis SL-44. In addition, results revealed the altruistic relationship between the two strains, and the chemical and non-chemical signals of their interaction. This study provides unique insights into PGPR interactions and offers guidance for the development and application of mixed microbial agents.

Plant Growth-Promoting Rhizobacteria HN6 Induced the Change and Reorganization of Fusarium Microflora in the Rhizosphere of Banana Seedlings to Construct a Healthy Banana Microflora

Streptomyces aureoverticillatus HN6 was isolated in our previous study and effectively controlled banana Fusarium wilt. We explored the role of HN6 in constructing a healthy rhizosphere microflora of banana seedlings. The method of antibiotic resistance was used to determine the colonization ability of HN6. The effect of HN6 on the rhizosphere microbial communities was assessed using culture-dependent and high-throughput sequencing. The effect of HN6 on the infection process of the pathogen was evaluated using a pot experiment and confocal laser scanning microscopy. The results showed that HN6 could prevent pathogen infection; it increased the nutrient content and diversity of the bacterial community in the rhizosphere, promoted plant growth, and decreased the mycotoxin fusaric acid content and abundance of pathogens in the banana rhizosphere. Thus, HN6 decreased the relative abundance of Fusarium species, increased the diversity of fungi, and increased the relative abundance of bacteria in the rhizosphere. HN6 induced the change and reorganization of the microbial community dominated by Fusarium in the rhizosphere of banana seedlings, and it evolved into a community dominated that was not conducive to the occurrence of diseases, shaping the rhizosphere microflora and promoting the growth of banana.

Identification of a phosphorus-solubilizing Tsukamurella tyrosinosolvens strain and its effect on the bacterial diversity of the rhizosphere soil of peanuts growth-promoting

Phosphate solubilizing microorganisms widely exist in plant rhizosphere soil, but report about the P solubilization and multiple growth-promoting properties of rare actinomycetes are scarce. In this paper, a phosphate solubilizing Tsukamurella tyrosinosolvens P9 strain was isolated from the rhizosphere soil of tea plants. Phosphorus-dissolving abilities of this strain were different under different carbon and nitrogen sources, the soluble phosphorus content was 442.41 mg/L with glucose and potassium nitrate as nutrient sources. The secretion of various organic acids, such as lactic acid, maleic acid, oxalic acid, etc., was the main mechanism for P solubilization and pH value in culture was very significant negative correlation with soluble P content. In addition, this strain had multiple growth-promoting characteristics with 37.26 μg/mL of IAA and 72.01% of siderophore relative content. Under pot experiments, P9 strain improved obviously the growth of peanut seedlings. The bacterial communities of peanut rhizoshpere soil were assessed after inoculated with P9 strain. It showed that there was no significant difference in alpha-diversity indices between the inoculation and control groups, but the P9 treatment group changed the composition of bacterial communities, which increased the relative abundance of beneficial and functional microbes, which relative abundances of Chitinophagaceae at the family level, and of Flavihumibacter, Ramlibacter and Microvirga at the genus level, were all siginificant increased. Specially, Tsukamurella tyrosinosolvens were only detected in the rhizosphere of the inoculated group. This study not only founded growth-promoting properties of T. tyrosinosolvens P9 strain and its possible phosphate solublizing mechanism, but also expected to afford an excellent strain resource in biological fertilizers.

Diversity and functional characteristics of endophytic bacteria from two grass species growing on an oil-contaminated site in the Yellow River Delta, China

Phragmites australis and Chloris virgata are native, dominant, salt-tolerant grass species that grow in the Yellow River Delta, China, and have potential applications in the phytoremediation of petroleum-polluted saline soil. The characteristics of endophytic bacterial communities of Phragmites australis and Chloris virgata and their functions in hydrocarbon degradation and plant growth promotion have been studied using both high-throughput sequencing and conventional microbial techniques. Through 16S rRNA gene amplicon sequencing, we found five bacterial phyla that were dominant among the endophytic bacterial communities of the two grass species, including Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Tenericutes. The phylum Proteobacteria was common among the endophytic bacterial communities of the two grass species. The diversity in the endophytic bacterial community of Chloris virgata was generally higher than that in the community of Phragmites australis. Thirty-eight hydrocarbon-degrading endophytic bacteria were isolated from the two grasses via culturing techniques. Based on phylogenetic analyses, the bacterial isolates were classified into the phyla Proteobacteria, Firmicutes, and Actinobacteria. The majority of strains belonged to the genera Bacillus and Pseudomonas. More than 70% of the isolates of hydrocarbon-degrading endophytes exhibited the ability to stimulate plant growth. These isolates mainly belonged to Bacillus sp., Pseudomonas sp., Beijerinckia sp., Serratia sp., Acinetobacter sp., Microbacterium sp., and Rhizobium sp. Altogether, the present study revealed that Phragmites australis and Chloris virgata growing on petroleum-polluted saline soil in the Yellow River Delta harbor several diverse species of endophytic bacteria and serve as novel sources of beneficial bacteria and hydrocarbon degradation.

Bioprospecting of Rhizosphere-Resident Fungi: Their Role and Importance in Sustainable Agriculture

Rhizosphere-resident fungi that are helpful to plants are generally termed as 'plant growth promoting fungi' (PGPF). These fungi are one of the chief sources of the biotic inducers known to give their host plants numerous advantages, and they play a vital role in sustainable agriculture. Today's biggest challenge is to satisfy the rising demand for crop protection and crop yield without harming the natural ecosystem. Nowadays, PGPF has become an eco-friendly way to improve crop yield by enhancing seed germination, shoot and root growth, chlorophyll production, and fruit yield, etc., either directly or indirectly. The mode of action of these PGPF includes the solubilization and mineralization of the essential micro- and macronutrients needed by plants to regulate the balance for various plant processes. PGPF produce defense-related enzymes, defensive/volatile compounds, and phytohormones that control pathogenic microbes' growth, thereby assisting the plants in facing various biotic and abiotic stresses. Therefore, this review presents a holistic view of PGPF as efficient natural biofertilizers to improve crop plants' growth and resistance.

Skin bacteria of rainbow trout antagonistic to the fish pathogen Flavobacterium psychrophilum

Rainbow trout fry syndrome (RTFS) and bacterial coldwater disease (BCWD) is a globally distributed freshwater fish disease caused by Flavobacterium psychrophilum. In spite of its importance, an effective vaccine is not still available. Manipulation of the microbiome of skin, which is a primary infection gate for pathogens, could be a novel countermeasure. For example, increasing the abundance of specific antagonistic bacteria against pathogens in fish skin might be effective to prevent fish disease. Here, we combined cultivation with 16S rRNA gene amplicon sequencing to obtain insight into the skin microbiome of the rainbow trout (Oncorhynchus mykiss) and searched for skin bacteria antagonistic to F. psychrophilum. By using multiple culture media, we obtained 174 isolates spanning 18 genera. Among them, Bosea sp. OX14 and Flavobacterium sp. GL7 respectively inhibited the growth of F. psychrophilum KU190628-78 and NCIMB 1947^T, and produced antagonistic compounds of < 3 kDa in size. Sequences related to our isolates comprised 4.95% of skin microbial communities, and those related to strains OX14 and GL7 respectively comprised 1.60% and 0.17% of the skin microbiome. Comparisons with previously published microbiome data detected sequences related to strains OX14 and GL7 in skin of other rainbow trout and Atlantic salmon.

Biological characteristics and salt-tolerant plant growth-promoting effects of an ACC deaminase-producing Burkholderia pyrrocinia strain isolated from the tea rhizosphere

Plant growth-promoting rhizobacteria that produce 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase can promote plant growth and enhance abiotic stress tolerance. In this study, Burkholderia pyrrocinia strain P10, with an ACC deaminase activity of 33.01-µmol/h/mg protein, was isolated from the tea rhizosphere and identified based on morphological, biochemical, and molecular characteristics. In addition to its ACC deaminase activity at pH 5.0-9.0 and in response to 5% NaCl and 20% polyethylene glycol, strain P10 can also solubilize phosphorus compounds, produce indole-3-acetic acid, and secrete siderophores. Pot experiments revealed that strain P10 can significantly enhance peanut seedling growth under saline conditions (100- and 170-mmol/L NaCl). Specifically, it increased the fresh weight and root length of plants by 90.12% and 79.22%, respectively, compared with high-salt stress. These results provide new insights into the biological characteristics of Burkholderia pyrrocinia, which may be useful as a bio-fertilizer.

Mathematical modelling of fungi-initiated siderophore-iron interactions

Nearly all life forms require iron to survive and function. Microorganisms utilize a number of mechanisms to acquire iron including the production of siderophores, which are organic compounds that combine with ferric iron into forms that are easily absorbed by the microorganism. There has been significant experimental investigation into the role, distribution and function of siderophores in fungi but until now no predictive tools have been developed to qualify or quantify fungi-initiated siderophore-iron interactions. In this investigation, we construct the first mathematical models of siderophore function related to fungi. Initially, a set of partial differential equations are calibrated and integrated numerically to generate quantitative predictions on the spatio-temporal distributions of siderophores and related populations. This model is then reduced to a simpler set of equations that are solved algebraically giving rise to solutions that predict the distributions of siderophores and resultant compounds. These algebraic results require the calculation of zeros of cross products of Bessel functions and thus new algebraic expansions are derived for a variety of different cases that are in agreement with numerically computed values. The results of the modelling are consistent with experimental data while the analysis provides new quantitative predictions on the time scales involved between siderophore production and iron uptake along with how the total amount of iron acquired by the fungus depends on its environment. The implications to bio-technological applications are briefly discussed.

Mobilization of recalcitrant phosphorous and enhancement of pepper P uptake and yield by a new biocontrol and bioremediation bacterium Burkholderia cepacia CQ18

AIMS

Phosphorus (P) is a finite resource and inoculation of phosphorus-mobilizing bacteria (PMB) is a promising approach for the enhancement of soil P availability and plant P uptake. This drives scientists to search for the microbes effective in mobilizing legacy P in soils.

METHODS AND RESULTS

The current incubation and greenhouse pot experiments were conducted to investigate P mobilization and pepper P uptake as affected by a new biocontrol and bioremediation bacterium Burkholderia cepacia CQ18. This bacterium converted Ca₃ (PO₄ )₂ , FePO₄ , AlPO₄ , and lecithin into soluble inorganic P in the culture solutions and increased available P (including water-soluble P and Olsen P) in the soil. There were positive correlations between the soluble inorganic phosphorus and the exudates (protons, organic acids (oxalate and gluconate), siderophores and phosphatases) in culture solutions. Pepper plant biomass, fruit yield and P uptake changed in the sequence: chemical fertilizers plus bacterial inoculant >only chemical fertilizers >only bacterial inoculant >blank control.

CONCLUSIONS

Taking into account the wide spectrums of P mobilization and simultaneous production of acid, neutral and alkaline phosphatases at a given pH, B.cepacia CQ18 may be a potential PMB used in soils with wide pH ranges. The mechanisms employed by this bacterium in the solubilization of recalcitrant inorganic P could be the efflux of protons, organic acids (oxalate and gluconate) and siderophores. Phosphatases could be of utmost importance in the mineralization of the organic P. The production of siderophores and phosphatases by of B.cepacia CQ18 could thus be crucial for not only the antagonism against plant pathogens but also the mobilization of soil sparingly available P.

SIGNIFICANCE AND IMPACT OF THE STUDY

Burkholderia cepacia CQ18 could be potentially developed into a biofertilizer.

Quantitative high-throughput approach to chalkophore screening in freshwaters

There is an increasing need to study the effects of trace metal micronutrients on microorganisms in natural waters. For Fe, small Fe-binding ligands called siderophores, which are secreted from cells and bind Fe with high affinity, have been demonstrated to modulate bioavailability of this critical nutrient. Relatively little is known about secretion of strong Cu-binding ligands (chalkophores) that may help organisms navigate the divide between Cu nutrition and toxicity. A barrier to environmental chalkophore research is a lack of literature on chalkophore analysis. Here we report the development of a quantitative, high-throughput approach to chalkophore screening based on a popular competitive-ligand binding assay for siderophores wherein ligands compete for metal in a chromogenic ternary complex of chrome azurol sulfonate-metal-surfactant. We developed the assay for high-throughput analysis using a microplate reader. The method performance is slightly better than that of comparable screening approaches for siderophores. We find that levels of other metals in natural samples may be capable of causing matrix interferences (a neglected source of analytical uncertainty in siderophore screening) and that for our method this can be overcome by standard additions. In this respect the high-throughput nature of the technique is a distinct advantage. To demonstrate practical use, we tested samples from field mesocosm studies that were set up with and without Cu and Fe amendments; we find trends in results that are logical in the environmental context of our application. This approach will be useful in areas such as risk assessment for a rapid survey of metal speciation and bioavailability; investigators who perform structural studies might also benefit from this approach to rapidly screen and select samples with high Fe/Cu binding capacity for further study.

Isolation and selection of endophytic spore-forming bacteria with plant growth promoting properties isolated from Ilex paraguariensis St. Hil. (yerba mate)

Yerba mate (Ilex paraguariensis St. Hil.) is a species native to the subtropical regions of South America. Despite being an important crop for the region, there are few studies on the use of microorganisms to improve the growth of seedlings in the nursery stage. The objective of this study was to isolate spore-forming endophytic bacteria with plant growth promoting properties associated with yerba mate seedlings and determine their phytobeneficial effect under controlled laboratory conditions. Isolates were selected based on their sporulation capacity and evaluated for in vitro plant growth promoting properties (nitrogen fixation, phosphate solubilization, production of siderophores and synthesis of indolic compounds). Yerba mate seedlings were inoculated with the most promising isolates, which were identified via analyses of the sequence of their 16S rDNA gene as Bacillus circulans (12RS3) and Bacillus altitudinis (19RS3, T5S-T4). After 120 days plants showed higher root dry weight when inoculated with isolate 19RS3 and higher shoot dry weight with 19RS3 and T5S-T4. In conclusion, further studies to determine the ability of these isolates to adapt to the climatic conditions and to survive amidst the native soil microflora in yerba mate cultivated native soils, will be crucial for developing such strains as biofertilizer.

Molecular characterization of siderophore biosynthesis in Paracoccidioides brasiliensis

Iron is an essential nutrient for all organisms. For pathogenic fungi, iron is essential for the success of infection. Thus, these organisms have developed high affinity iron uptake mechanisms to deal with metal deprivation imposed by the host. Siderophore production is one of the mechanisms that fungal pathogens employ for iron acquisition. Paracoccidioides spp. present orthologous genes encoding the enzymes necessary for the biosynthesis of hydroxamates, and plasma membrane proteins related to the transport of these molecules. All these genes are induced in iron deprivation. In addition, it has been observed that Paracoccidioides spp. are able to use siderophores to scavenge iron. Here we observed that addition of the xenosiderophore ferrioxamine B FOB) to P. brasiliensis culture medium results in repression (at RNA and protein levels) of the SidA, the first enzyme of the siderophore biosynthesis pathway. Furthermore, SidA activity was reduced in the presence of FOB, suggesting that P. brasiliensis blocks siderophores biosynthesis and can explore siderophores in the environment to scavenge iron. In order to support the importance of siderophores on Paracoccidioides sp. life and infection cycle, silenced mutants for the sidA gene were obtained by antisense RNA technology. The obtained AsSidA strains displayed decreased siderophore biosynthesis in iron deprivation conditions and reduced virulence to an invertebrate model.

Bacillus telluris sp. nov. Isolated from Greenhouse Soil in Beijing, China

A novel Gram-stain-positive, rod-shaped, endospore-forming bacterium, which we designated as strain 03113T, was isolated from greenhouse soil in Beijing, China. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 03113T is in the genus Bacillus and had the highest similarity to Bacillus solani CCTCC AB 2014277T (98.14%). The strain grew at 4 °C-50 °C (optimum 37 °C), with 0-10% (w/v) NaCl (optimum 5%), and in the range of pH 3.0-12.0 (optimum pH 8.0). Menaquinone was identified as MK-7, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The main major cellular fatty acids detected were anteiso-C15:0 (51.35%) and iso-C15:0 (11.06%), which are the predominant cellular fatty acids found in all recognized members of the genus Bacillus. The 16S rRNA gene sequence and core-genome analysis, the average nucleotide identity (ANI), and in silico DNA-DNA hybridization (DDH) value between strain 03113T and the most closely related species were 70.5% and 22.6%, respectively, which supported our conclusion that 03113T represented a novel species in the genus Bacillus. We demonstrated that type strain 03113T (=ACCC 03113T=JCM 33017T) was a novel species in the genus Bacillus, and the name Bacillus telluris sp. nov. was proposed. Strain 03113T secreted auxin IAA and carried the nitrogenase iron protein (nifH) gene, which indicated that strain 03113T has the potential to fix nitrogen and promote plant growth. Bacillus telluris sp. nov. 03113T is a potential candidate for the biofertilizers of organic agriculture areas.

A multifunctional rhizobacterial strain with wide application in different ferns facilitates arsenic phytoremediation

Pteris vittata and Pteris multifida are widely studied As hyperaccumulators that absorb As mainly via roots. Hence, rhizobacteria exhibit promising potential in phytoextraction owing to their immense microbial diversity and interactions with plants. Pseudomonas vancouverensis strain m318 that contains aioA-like genes was screened from P. multifida's rhizosphere through the high As resistance (minimum inhibitory concentrations (MICs) against As(III): 16 mM; MICs against As(V): 320 mM), rapid As oxidation (98% oxidation by bacterial cultures (OD_600nm = 1) from 200 μL of 0.1 mM As(III) within 24 h), predominant secretion of IAA (12.45 mg L^-1) and siderophores (siderophore unit: 88%). Strain m318 showed significant chemotactic response and high colonization efficiency to P. vittata roots, which suggested its wide host affinity. Interestingly, inoculation with strain m318 enhanced the proportion of aioA-like genes in the rhizosphere. And in field trials, inoculation with strain m318 increased As accumulation in P. vittata by 48-146% and in P. multifida by 42-233%. Post-transplantation inoculations also increased As accumulation in both ferns. The abilities of the isolated multifunctional strain m318 and the increase in the rhizosphere microbial aioA-like genes are thus speculated to be involved in As transformation in the rhizospheres and roots of P. vittata and P. multifida.

A fungal ABC transporter FgAtm1 regulates iron homeostasis via the transcription factor cascade FgAreA-HapX

Iron homeostasis is important for growth, reproduction and other metabolic processes in all eukaryotes. However, the functions of ATP-binding cassette (ABC) transporters in iron homeostasis are largely unknown. Here, we found that one ABC transporter (named FgAtm1) is involved in regulating iron homeostasis, by screening sensitivity to iron stress for 60 ABC transporter mutants of Fusarium graminearum, a devastating fungal pathogen of small grain cereal crops worldwide. The lack of FgAtm1 reduces the activity of cytosolic Fe-S proteins nitrite reductase and xanthine dehydrogenase, which causes high expression of FgHapX via activating transcription factor FgAreA. FgHapX represses transcription of genes for iron-consuming proteins directly but activates genes for iron acquisition proteins by suppressing another iron regulator FgSreA. In addition, the transcriptional activity of FgHapX is regulated by the monothiol glutaredoxin FgGrx4. Furthermore, the phosphorylation of FgHapX, mediated by the Ser/Thr kinase FgYak1, is required for its functions in iron homeostasis. Taken together, this study uncovers a novel regulatory mechanism of iron homeostasis mediated by an ABC transporter in an important pathogenic fungus.

Essential element iron plays important roles in many cellular processes in all organisms. The function of an ATP-binding cassette (ABC) transporter Atm1 in iron homeostasis has been characterized in Saccharomyces cerevisiae. Our study found that FgAtm1 regulates iron homeostasis via the transcription factor cascade FgAreA-HapX in F. graminearum and the function of FgHapX is dependent on its interaction with FgGrx4 and phosphorylation by the Ser/Thr kinase FgYak1. This study reveals a novel regulatory mechanism of iron homeostasis in an important plant pathogenic fungus, and advances our understanding in iron homeostasis and functions of ABC transporters in eukaryotes.

Growth-promoting characteristics of potential nitrogen-fixing bacteria in the root of an invasive plant Ageratina adenophora

Root endophytic nitrogen-fixing bacteria (reNFB) have been proposed as important contributors to the invasiveness of exotic legumes; however, the reNFB of invasive nonlegumes has received less attention. In particular, the growth-promoting effect of reNFB on invasive plants remains unknown. In this study, 131 strains of potential nitrogen-fixing bacteria were isolated and purified from the roots of the invasive plant, Ageratina adenophora, in Southwest China. Phylogenetically, these reNFB were categorized into three phyla at 97% sequence identity that included Proteobacteria (92.4%), Actinobacteria (4.6%), and Firmicutes (3.1%). The dominant isolates ranked by number were Pseudomonas (80 isolates, 61.1%), Rhizobium (12 isolates, 9.2%), and Duganella (11 isolates, 8.4%). The community composition and diversity of A. adenophora reNFB were markedly different across study regions. The capacity of these reNFB to accumulate indolyl-3-acetic acid (IAA), solubilize phosphate, and produce siderophores was determined. All 131 isolates of reNFB accumulated IAA, 67 isolates solubilized phosphate, and 108 isolates produced siderophores. Among the three dominant genera of reNFB, Pseudomonas had the highest phosphorus solubilization and siderophore production, while the accumulation of IAA in the genus Duganella was the lowest. Interestingly, the calculated reNFB Shannon diversity index of each A. adenophora individual was negatively correlated with the capacity of reNFB to produce growth-promoting products. Six randomly selected isolates from three dominant genera were further used to conduct inoculation experiments, and all isolates showed significant positive growth-promoting effects on A. adenophora seedlings. The contribution of reNFB to the root biomass was higher than that to the shoot biomass. Our results suggest that reNFB, similar to soil or nodular nitrogen-fixing bacteria, can potentially promote plant growth and may play an important role in the invasion of nonleguminous plants. More detailed studies on the correlation between reNFB and invasive plants are necessary.

The influence of pH on Staphylococcus saprophyticus iron metabolism and the production of siderophores

Staphylococcus saprophyticus is a gram-positive coagulase negative bacteria which shows clinical importance due to its capability of causing urinary tract infections (UTI), as well as its ability to persist in this environment. Little is known about how S. saprophyticus adapts to the pH shift that occurs during infection. Thus, in this study we aim to use a proteomic approach to analyze the metabolic adaptations which occur as a response by S. saprophyticus when exposed to acid (5.5) and alkaline (9.0) pH environments. Proteins related to iron storage are overexpressed in acid pH, whilst iron acquisition proteins are overexpressed in alkaline pH. It likely occurs because iron is soluble at acid pH and insoluble at alkaline pH. To evaluate if S. saprophyticus synthesizes siderophores, CAS assays were performed, and the results confirmed their production. The chemical characterization of siderophores demonstrates that S. saprophyticus produces carboxylates derived from citrate. Of special note is the fact that citrate synthase (CS) is down-regulated during incubation at acid pH, corroborating this result. This data was also confirmed by enzymatic assay. Our results demonstrate that iron metabolism regulation is influenced by different pH levels, and show, for the first time, the production of siderophores by S. saprophyticus. Enzymatic assays suggest that citrate from the tricarboxylic acid cycle (TCA) is used as substrate for siderophore production.

Characterization and Initial Application of Endophytic Bacillus safensis Strain ZY16 for Improving Phytoremediation of Oil-Contaminated Saline Soils

Hydrocarbon-degrading and plant-growth-promoting bacterial endophytes have proven useful for facilitating the phytoremediation of petroleum-contaminated soils with high salinity. In this study, we identified Bacillus safensis strain ZY16 as an endophytic bacterium that can degrade hydrocarbons, produce biosurfactants, tolerate salt, and promote plant growth. The strain was isolated from the root of Chloris virgata Sw., a halotolerant plant collected from the Yellow River Delta. ZY16 survived in Luria-Bertani (LB) broth with 0–16% (w/v) sodium chloride (NaCl) and grew well in LB broth supplemented with 0–8% NaCl, indicating its high salt tolerance. The endophytic strain ZY16 effectively degraded C₁₂–C₃₂n-alkanes of diesel oil effectively, as well as common polycyclic aromatic hydrocarbons under hypersaline conditions. For example, in mineral salts (MS) liquid medium supplemented with 6% NaCl, ZY16 degraded n-undecane, n-hexadecane, n-octacosane, naphthalene, phenanthrene, and pyrene, with degradation percentages of 94.5, 98.2, 64.8, 72.1, 59.4, and 27.6%, respectively. In addition, ZY16 produced biosurfactant, as confirmed by the oil spreading technique, surface tension detection, and emulsification of para-xylene and paraffin. The biosurfactant production ability of ZY16 under hypersaline conditions was also determined. Moreover, ZY16 showed plant-growth-promoting attributes, such as siderophore and indole-3-acetic acid production, as well as phosphate solubilization. To assess the enhanced phytoremediation of saline soils polluted by hydrocarbons and the plant-growth-promotion ability of ZY16, a pot trial with and without inoculation of the endophyte was designed and performed. Inoculated and non-inoculated plantlets of C. virgata Sw. were grown in oil-polluted saline soil, with oil and salt contents of 10462 mg/kg and 0.51%, respectively. After 120 days of growth, significant enhancement of both the aerial and underground biomass of ZY16-inoculated plants was observed. The soil total petroleum hydrocarbon degradation percentage (a metric of phytoremediation) after incubation with ZY16 was 63.2%, representing an elevation of 25.7% over phytoremediation without ZY16 inoculation. Our study should promote the application of endophytic B. safensis ZY16 in phytoremediation by extending our understanding of the mutualistic interactions between endophytes and their host plants.

The Isoniazid Metabolites Hydrazine and Pyridoxal Isonicotinoyl Hydrazone Modulate Heme Biosynthesis

In a mouse model, rifampicin and isoniazid combination treatment results in cholestatic liver injury that is associated with an increase in protoporphyrin IX, the penultimate heme precursor. Both ferrochelatase (FECH/Fech) and aminolevulinic acid synthase 1 (ALAS1/Alas1) are crucial enzymes in regulating heme biosynthesis. Isoniazid has recently been reported to upregulate Alas1 but downregulate Fech protein levels in mice; however, the mechanism by which isoniazid mediates disruption of heme synthesis has been unclear. Two metabolites of isoniazid, pyridoxal isonicotinoyl hydrazone (PIH, the isoniazid-vitamin B6 conjugate) and hydrazine, have been detected in the urine of humans treated with isoniazid. Here we show that, in primary human hepatocytes and the human hepatocellular carcinoma cell line HepG2/C3A, (1) isoniazid treatment increases Alas1 protein levels but decreases Fech levels; (2) hydrazine treatment upregulates Alas1 protein and Alas1 mRNA levels; (3) PIH treatment decreases Fech protein levels, but not Fech mRNA levels; and (4) PIH is detected after isoniazid treatment, with levels increasing further when exogenous vitamin B6 analogs are coadministered. In addition, the PIH-mediated downregulation of human FECH is associated with iron chelation. Together, these data demonstrate that hydrazine upregulates ALAS1, whereas PIH downregulates FECH, suggesting that the metabolites of isoniazid mediate its disruption of heme biosynthesis by contributing to protoporphyrin IX accumulation.

Eukaryotic Acquisition of a Bacterial Operon

Operons are a hallmark of bacterial genomes, where they allow concerted expression of functionally related genes as single polycistronic transcripts. They are rare in eukaryotes, where each gene usually drives expression of its own independent messenger RNAs. Here, we report the horizontal operon transfer of a siderophore biosynthesis pathway from relatives of Escherichia coli into a group of budding yeast taxa. We further show that the co-linearly arranged secondary metabolism genes are expressed, exhibit eukaryotic transcriptional features, and enable the sequestration and uptake of iron. After transfer, several genetic changes occurred during subsequent evolution, including the gain of new transcription start sites that were sometimes within protein-coding sequences, acquisition of polyadenylation sites, structural rearrangements, and integration of eukaryotic genes into the cluster. We conclude that the genes were likely acquired as a unit, modified for eukaryotic gene expression, and maintained by selection to adapt to the highly competitive, iron-limited environment.

Isolation and characterization of halotolerant phosphate-solubilizing microorganisms from saline soils

Halotolerant phosphate-solubilizing microorganisms (PSMs) capable of producing plant-growth-promoting traits were grown on salt medium containing Ca₃(PO₄)₂ or egg yolk. The number of colonies on plates with Ca₃(PO₄)₂ was higher than that on plates with egg yolk. Further, a total of 42 PSM isolates were purified. The majority were Bacillus spp., while one Providencia rettgeri strain was confirmed, for the first time, as a PSM. All PSMs had a phosphate-solubilizing index (PSI) between 1.1 and 2.58 and a strong capacity for dissolving calcium phosphate between 2.25 and 442 mg·L^-1. In contrast, these PSMs were less effective when dissolving aluminum phosphate, ferric phosphate and lecithin. Isolates were also tested for growth-promoting substances. The results showed that all isolates were able to secrete indole-3-acetic acid in amounts ranging from 2.7 to 31.8 mg·L^-1 and exopolysaccharide within the range 74.3 and 225.7 mg·L^-1. Only 12 siderophore-producing strains with siderophore units of 1.9-42.1% were detected. Among them, ten isolates with solubilization rates greater than 200 mg·L^-1 and relatively high NaCl tolerance (1.5 M) were classified as candidate PSMs. Eight different organic acids with different contents were detected in the culture filtrates, and propionic and oxalic acids have been proposed as the main mechanisms for solubilization. The ten isolates have the potential for use as bioinoculants to protect plants in saline environments.

Putative Iron Acquisition Systems in Stenotrophomonas maltophilia

Iron has been shown to regulate biofilm formation, oxidative stress response and several pathogenic mechanisms in Stenotrophomonas maltophilia. Thus, the present study is aimed at identifying various iron acquisition systems and iron sources utilized during iron starvation in S. maltophilia. The annotations of the complete genome of strains K279a, R551-3, D457 and JV3 through Rapid Annotations using Subsystems Technology (RAST) revealed two putative subsystems to be involved in iron acquisition: the iron siderophore sensor and receptor system and the heme, hemin uptake and utilization systems/hemin transport system. Screening for these acquisition systems in S. maltophilia showed the presence of all tested functional genes in clinical isolates, but only a few in environmental isolates. NanoString nCounter Elements technology, applied to determine the expression pattern of the genes under iron-depleted condition, showed significant expression for FeSR (6.15-fold), HmuT (12.21-fold), Hup (5.46-fold), ETFb (2.28-fold), TonB (2.03-fold) and Fur (3.30-fold). The isolates, when further screened for the production and chemical nature of siderophores using CAS agar diffusion (CASAD) and Arnows's colorimetric assay, revealed S. maltophilia to produce catechol-type siderophore. Siderophore production was also tested through liquid CAS assay and was found to be greater in the clinical isolate (30.8%) compared to environmental isolates (4%). Both clinical and environmental isolates utilized hemoglobin, hemin, transferrin and lactoferrin as iron sources. All data put together indicates that S. maltophilia utilizes siderophore-mediated and heme-mediated systems for iron acquisition during iron starvation. These data need to be further confirmed through several knockout studies.

A Complex Mechanism Involving LysR and TetR/AcrR That Regulates Iron Scavenger Biosynthesis in Pseudomonas donghuensis HYS

7-Hydroxytropolone (7-HT) is a symmetrical seven-membered heteroatomic ring with a carboxyl group and two hydroxyl groups and was recently reported to be an iron scavenger of Pseudomonas donghuensis HYS. Cluster 1 includes 12 genes related to the synthesis of 7-HT; among these genes, those for two regulators, Orf1 and Orf12, were predicted to regulate 7-HT biosynthesis and to be LysR-type transcriptional regulators (LTTRs) and TetR/AcrR family transcriptional regulators, respectively. Data from real-time quantitative PCR and β-galactosidase and classical siderophore assays indicated that the transcription levels of orf1 and orf12, as well as those of crucial genes orf6 to orf9, were repressed under high-iron conditions. The deletion of orf1 and orf12 led to an absence of 7-HT and a decrease in orf6-orf9 expression. Orf1 and Orf12 were essential for the production of 7-HT through orf6-orf9 These two regulators are regulated by the Gac/Rsm system; Orf1 facilitates the expression of Orf12, and Orf12 concomitantly stimulates the expression of orf6-orf9 to synthesize 7-HT. The overexpression of Orf12 decreased 7-HT yields, possibly through decreased orf6-orf9 expression. This work thus outlines a complex mechanism regulating the biosynthesis of the iron scavenger 7-HT in P. donghuensis HYS. The synergy between Orf1 and Orf12 ensures that 7-HT acts as an iron chelator despite being toxic to bacteria and provides new ideas for the novel regulation of dual-functional secondary metabolism and research on 7-HT and its derivates in other bacteria.IMPORTANCE A complex regulation mechanism including two regulators, LysR and TetR/AcrR, in the biosynthesis of the novel iron scavenger 7-hydroxytropolone (7-HT) was verified in Pseudomonas donghuensis HYS. The coaction of LysR Orf1 and TetR/AcrR Orf12 may balance the toxicity and iron chelation of 7-HT in P. donghuensis HYS to overcome iron deficiency, as well as improve the bacterial competitiveness under iron-scarce conditions because of the toxicity of 7-HT toward other bacteria, making the accurate regulation of 7-HT biosynthesis indispensable. This regulation mechanism may be ubiquitous in the Pseudomonas putida group but may better explain the group's strong adaptability.

Pseudomonas aeruginosa L10: A Hydrocarbon-Degrading, Biosurfactant-Producing, and Plant-Growth-Promoting Endophytic Bacterium Isolated From a Reed (Phragmites australis)

Bacterial endophytes with the capacity to degrade petroleum hydrocarbons and promote plant growth may facilitate phytoremediation for the removal of petroleum hydrocarbons from contaminated soils. A hydrocarbon-degrading, biosurfactant-producing, and plant-growth-promoting endophytic bacterium, Pseudomonas aeruginosa L10, was isolated from the roots of a reed, Phragmites australis, in the Yellow River Delta, Shandong, China. P. aeruginosa L10 efficiently degraded C₁₀-C₂₆n-alkanes from diesel oil, as well as common polycyclic aromatic hydrocarbons (PAHs) such as naphthalene, phenanthrene, and pyrene. In addition, P. aeruginosa L10 could produce biosurfactant, which was confirmed by the oil spreading method, and surface tension determination of inocula. Moreover, P. aeruginosa L10 had plant growth-stimulating attributes, including siderophore and indole-3-acetic acid (IAA) release, along with 1-aminocyclopropane-1-carboxylic (ACC) deaminase activity. To explore the mechanisms underlying the phenotypic traits of endophytic P. aeruginosa L10, we sequenced its complete genome. From the genome, we identified genes related to petroleum hydrocarbon degradation, such as putative genes encoding monooxygenase, dioxygenase, alcohol dehydrogenase, and aldehyde dehydrogenase. Genome annotation revealed that P. aeruginosa L10 contained a gene cluster involved in the biosynthesis of rhamnolipids, rhlABRI, which should be responsible for the observed biosurfactant activity. We also identified two clusters of genes involved in the biosynthesis of siderophore (pvcABCD and pchABCDREFG). The genome also harbored tryptophan biosynthetic genes (trpAB, trpDC, trpE, trpF, and trpG) that are responsible for IAA synthesis. Moreover, the genome contained the ACC deaminase gene essential for ACC deaminase activity. This study will facilitate applications of endophytic P. aeruginosa L10 to phytoremediation by advancing the understanding of hydrocarbon degradation, biosurfactant synthesis, and mutualistic interactions between endophytes and host plants.

Additional oxidative stress reroutes the global response of Aspergillus fumigatus to iron depletion

BACKGROUND

Aspergillus fumigatus has to cope with a combination of several stress types while colonizing the human body. A functional interplay between these different stress responses can increase the chances of survival for this opportunistic human pathogen during the invasion of its host. In this study, we shed light on how the H2O2-induced oxidative stress response depends on the iron available to this filamentous fungus, using transcriptomic analysis, proteomic profiles, and growth assays.

RESULTS

The applied H2O2 treatment, which induced only a negligible stress response in iron-replete cultures, deleteriously affected the fungus under iron deprivation. The majority of stress-induced changes in gene and protein expression was not predictable from data coming from individual stress exposure and was only characteristic for the combination of oxidative stress plus iron deprivation. Our experimental data suggest that the physiological effects of combined stresses and the survival of the fungus highly depend on fragile balances between economization of iron and production of essential iron-containing proteins. One observed strategy was the overproduction of iron-independent antioxidant proteins to combat oxidative stress during iron deprivation, e.g. the upregulation of superoxide dismutase Sod1, the thioredoxin reductase Trr1, and the thioredoxin orthologue Afu5g11320. On the other hand, oxidative stress induction overruled iron deprivation-mediated repression of several genes. In agreement with the gene expression data, growth studies underlined that in A. fumigatus iron deprivation aggravates oxidative stress susceptibility.

CONCLUSIONS

Our data demonstrate that studying stress responses under separate single stress conditions is not sufficient to understand how A. fumigatus adapts in a complex and hostile habitat like the human body. The combinatorial stress of iron depletion and hydrogen peroxide caused clear non-additive effects upon the stress response of A. fumigatus. Our data further supported the view that the ability of A. fumigatus to cause diseases in humans strongly depends on its fitness attributes and less on specific virulence factors. In summary, A. fumigatus is able to mount and coordinate complex and efficient responses to combined stresses like iron deprivation plus H2O2-induced oxidative stress, which are exploited by immune cells to kill fungal pathogens.

Modified microplate method for rapid and efficient estimation of siderophore produced by bacteria

In this study, siderophore production by various bacteria amongst the plant-growth-promoting rhizobacteria was quantified by a rapid and efficient method. In total, 23 siderophore-producing bacterial isolates/strains were taken to estimate their siderophore-producing ability by the standard method (chrome azurol sulphonate assay) as well as 96 well microplate method. Production of siderophore was estimated in percent siderophore unit by both the methods. It was observed that data obtained by both methods correlated positively with each other proving the correctness of microplate method. By the modified microplate method, siderophore production by several bacterial strains can be estimated both qualitatively and quantitatively at one go, saving time, chemicals, making it very less tedious, and also being cheaper in comparison with the method currently in use. The modified microtiter plate method as proposed here makes it far easier to screen the plant-growth-promoting character of plant-associated bacteria.

Clonality, virulence determinants, and profiles of resistance of clinical Acinetobacter baumannii isolates obtained from a Spanish hospital

INTRODUCTION

Acinetobacter baumannii is a nosocomial pathogen that is showing increasing rates of carbapenem resistance. Multi-Drug Resistant (MDR) International Clones (ICs), associated with certain oxacillinases, are being reported globally. This organism also harbors numerous virulence determinants. In this study, we aim at characterizing A. baumannii isolated from a Spanish hospital in terms of antimicrobial susceptibility, clonality, carbapenemase genes harbored, and virulence determinants expressed.

MATERIALS AND METHODS

Fifty nine clinical bloodstream isolates were obtained from 2009 until 2013. Antimicrobial Susceptibility Testing was performed according to the CLSI guidelines. PFGE and tri-locus PCR typing were then performed in order to determine local and international clonality. PCRs for the detection of common carbapenemases were also performed. Production of hemolysis, biofilms, siderophores, surface motility, and proteolysis were determined phenotypically. Doubling times for selected strains were also calculated. Finally, statistical analysis for detecting associations between these factors was conducted.

RESULTS AND DISCUSSION

Carbapenem non-susceptibility was 84.75%, suggesting the immediate need for intervention. PFGE showed the distribution of the majority of the isolates among 7 clusters. Although all three ICs were detected, IC II was predominant at 71.19%. blaOXA-24-like was the most prevalent carbapenemase (62.71%), followed by blaOXA-58-like (13.56%), and blaOXA-23-like (11.86%). Strains pertaining to IC II, and those harboring blaOXA-24-like, were positively associated with α-hemolysis, production of strong biofilms, and siderophore production. Harboring blaOXA-23-like and blaOXA-58-like was associated with attenuated virulence. These associations suggest that an interplay exists between these factors that could be locally exploited.

CONCLUSIONS

An alarmingly high rate of carbapenem non-susceptibility has been detected in this study. There was a predominance of IC II and blaOXA-24-like, and those factors were associated with heightened expression of virulence determinants. This association could be exploited for modifying treatment regimens and for improving on infection control protocols in this hospital.

Acinetobacter baumannii Isolated from Lebanese Patients: Phenotypes and Genotypes of Resistance, Clonality, and Determinants of Pathogenicity

Introduction:Acinetobacter baumannii is a nosocomial pathogen that usually affects critically ill patients. High mortality rates have been associated with MDR A. baumannii infections. Carbapenem resistance among these isolates is increasing worldwide and is associated with certain International Clones (ICs) and oxacillinases (OXAs). Moreover, this organism possesses a wide range of virulence factors, whose expression is not yet fully understood. In this study, clinical A. baumannii isolates are characterized in terms of antibiotic resistance, mechanisms of carbapenem resistance, clonality, and virulence.

Materials and Methods:A. baumannii clinical isolates (n = 90) where obtained from a tertiary care center in Beirut, Lebanon. API 20NE strips in addition to the amplification of bla_{OXA−51−like} were used for identification. Antibiotic susceptibility testing by disk diffusion was then performed in addition to PCRs for the detection of the most commonly disseminated carbapenemases. Clonality was determined by tri-locus PCR typing and doubling times were determined for isolates with varying susceptibility profiles. Biofilm formation, hemolysis, siderophore production, proteolytic activity, and surface motility was then determined for all the isolates. Statistical analysis was then performed for the determination of associations.

Results and Discussion: 81 (90%) of the isolates were resistant to carbapenems. These high rates are similar to other multi-center studies in the country suggesting the need of intervention on a national level. 74 (91.3%) of the carbapenem resistant isolates harbored bla_{OXA−23−like} including two that also harbored bla_{OXA−24−like}. 88.9% of the A. baumannii isolates pertained to ICII and three other international clones were detected, showing the wide dissemination of clones into geographically distinct locations. Virulence profiles were highly diverse and no specific pattern was observed. Nevertheless, an association between motility, siderophore production, and biofilm formation was detected (p < 0.05).

Conclusions: A very high rate of carbapenem resistance was detected, showing the need for immediate intervention. IC II and OXA-23-like were the most disseminated, reflecting their international dissemination. No specific associations were made between virulence and resistance, but instead associations among certain virulence factors were found. Investigating a more clonally diverse pool of isolates could help in the determination of associations between virulence and resistance.

Comparative Genomic Analysis of Delftia tsuruhatensis MTQ3 and the Identification of Functional NRPS Genes for Siderophore Production

Plant growth-promoting rhizobacteria (PGPR) are a group of rhizosphere bacteria that promote plant growth. Delftia tsuruhatensis MTQ3 is a member of PGPR that produces siderophores. The draft genome sequence of MTQ3 has been reported. Here, we analyzed the genome sequence of MTQ3 and performed a comparative genome analysis of four sequenced Delftia strains, revealing genetic relationships among these strains. In addition, genes responsible for bacteriocin and nonribosomal peptide synthesis were detected in the genomes of each strain. To reveal the functions of NRPS genes in siderophore production in D. tsuruhatensis MTQ3, three NRPS genes were knocked out to obtain the three mutants MTQ3-Δ1941, MTQ3-Δ1945, and MTQ3-Δ1946, which were compared with the wild-type strain. In qualitative and quantitative analyses using CAS assay, the mutants failed to produce siderophores. Accordingly, the NRPS genes in MTQ3 were functionally related to siderophore production. These results clarify one mechanism by which plant growth is promoted in MTQ3 and have important applications in agricultural production.

HapX Mediates Iron Homeostasis in the Pathogenic Dermatophyte Arthroderma benhamiae but Is Dispensable for Virulence

For many pathogenic fungi, siderophore-mediated iron acquisition is essential for virulence. The process of siderophore production and further mechanisms to adapt to iron limitation are strictly controlled in fungi to maintain iron homeostasis. Here we demonstrate that the human pathogenic dermatophyte Arthroderma benhamiae produces the hydroxamate siderophores ferricrocin and ferrichrome C. Additionally, we show that the iron regulator HapX is crucial for the adaptation to iron starvation and iron excess, but is dispensable for virulence of A. benhamiae. Deletion of hapX caused downregulation of siderophore biosynthesis genes leading to a decreased production of siderophores during iron starvation. Furthermore, HapX was required for transcriptional repression of genes involved in iron-dependent pathways during iron-depleted conditions. Additionally, the ΔhapX mutant of A. benhamiae was sensitive to high-iron concentrations indicating that HapX also contributes to iron detoxification. In contrast to other pathogenic fungi, HapX of A. benhamiae was redundant for virulence and a ΔhapX mutant was still able to infect keratinized host tissues in vitro. Our findings underline the highly conserved role of the transcription factor HapX for maintaining iron homeostasis in ascomycetous fungi but, unlike in many other human and plant pathogenic fungi, HapX of A. benhamiae is not a virulence determinant.