Antifungal peptides produced by Bacillus amyloliquefaciens AG1 active against grapevine fungal pathogens

Isolation and characterization of an antimicrobial Bacillus subtilis strain O-741 against Vibrio parahaemolyticus

Vibrio parahaemolyticus is a marine bacterium that can infect and cause the death of aquatic organisms. V. parahaemolyticus can also cause human foodborne infection via contaminated seafood, with clinical syndromes which include diarrhea, abdominal cramps, nausea and so on. Since controlling V. parahaemolyticus is important for aquaculture and human health, various strategies have been explored. This study investigates the application of antagonistic microorganisms to inhibit the growth of V. parahaemolyticus. We screened aquaculture environment samples and identified a Bacillus subtilis strain O-741 with potent antimicrobial activities. This strain showed a broad spectrum of antagonistic activities against V. parahaemolyticus and other Vibrio species. Application of the O-741 bacterium significantly increased the survival of Artemia nauplii which were infected with V. parahaemolyticus. Furthermore, the cell-free supernatant (CFS) of O-741 bacterium exhibited inhibitory ability against V. parahaemolyticus, and its activity was stable to heat, acidity, UV, enzymes, and organic solvents. Next, the O-741 CFS was extracted by ethyl acetate, and analyzed by ultra-performance liquid chromatography-mass-mass spectrometry (UPLC-MS/MS), and the functional faction was identified as an amicoumacin A compound. The organic extracts of CFS containing amicoumacin A had bactericidal effects on V. parahaemolyticus, and the treated V. parahaemolyticus cells showed disruption of the cell membrane and formation of cell cavities. These findings indicate that B. subtilis strain O-741 can inhibit the V. parahaemolyticus in vitro and in vivo, and has potential for use as a biocontrol agent for preventing V. parahaemolyticus infection.

The Prospect of Hydrolytic Enzymes from Bacillus Species in the Biological Control of Pests and Diseases in Forest and Fruit Tree Production

Plant diseases and insect pest damage cause tremendous losses in forestry and fruit tree production. Even though chemical pesticides have been effective in the control of plant diseases and insect pests for several decades, they are increasingly becoming undesirable due to their toxic residues that affect human life, animals, and the environment, as well as the growing challenge of pesticide resistance. In this study, we review the potential of hydrolytic enzymes from Bacillus species such as chitinases, β-1,3-glucanases, proteases, lipases, amylases, and cellulases in the biological control of phytopathogens and insect pests, which could be a more sustainable alternative to chemical pesticides. This study highlights the application potential of the hydrolytic enzymes from different Bacillus sp. as effective biocontrol alternatives against phytopathogens/insect pests through the degradation of cell wall/insect cuticles, which are mainly composed of structural polysaccharides like chitins, β-glucans, glycoproteins, and lipids. This study demonstrates the prospects for applying hydrolytic enzymes from Bacillus sp. as effective biopesticides in forest and fruit tree production, their mode of biocidal activity and dual antimicrobial/insecticidal potential, which indicates a great prospect for the simultaneous biocontrol of pests/diseases. Further research should focus on optimizing the production of hydrolytic enzymes, and the antimicrobial/insecticidal synergism of different Bacillus sp. which could facilitate the simultaneous biocontrol of pests and diseases in forest and fruit tree production.

MALDI mass spectrometry-based identification of antifungal molecules from endophytic Bacillus strains with biocontrol potential of Lasiodiplodia theobromae, a grapevine trunk pathogen in Peru

Lasiodiplodia theobromae, a grapevine trunk pathogen, is becoming a significant threat to vineyards worldwide. In Peru, it is responsible for Botryosphaeria dieback in many grapevine-growing areas and it has spread rapidly due to its high transmissibility; hence, control measures are urgent. It is known that some endophytic bacteria are strong inhibitors of phytopathogens because they produce a wide range of antimicrobial molecules. However, studies of antimicrobial features from endophytic bacteria are limited to traditional confrontation methods. In this study, a MALDI mass spectrometry-based approach was performed to identify and characterize the antifungal molecules from Bacillus velezensis M1 and Bacillus amyloliquefaciens M2 grapevine endophytic strains. Solid medium antagonism assays were performed confronting B. velezensis M1 - L. theobromae and B. amyloliquefaciens M2 - L. theobromae for antifungal lipopeptides identification. By a MALDI TOF MS it was possible identify mass spectra for fengycin, iturin and surfactin protoned isoforms. Masses spectrums for mycobacillin and mycosubtilin were also identified. Using MALDI Imaging MS we were able to visualize and relate lipopeptides mass spectra of fengycin (1463.9 m/z) and mycobacillin (1529.6 m/z) in the interaction zone during confrontations. The presence of lipopeptides-synthesis genes was confirmed by PCR. Liquid medium antagonism assays were performed for a proteomic analysis during the confrontation of B. velezensis M1 - L. theobromae. Different peptide sequences corresponding to many antifungal proteins and enzymes were identified by MALDI TOF MS/MS. Oxalate decarboxylase bacisubin and flagellin, reported as antifungal proteins, were identified at 99 % identity through peptide mapping. MALDI mass spectrometry-based identification of antifungal molecules would allow the early selection of endophytic bacteria with antifungal features. This omics tool could lead to measures for prevention of grapevine diseases and other economically important crops in Peru.

Microbial Biological Control of Fungi Associated with Grapevine Trunk Diseases: A Review of Strain Diversity, Modes of Action, and Advantages and Limits of Current Strategies

Grapevine trunk diseases (GTDs) are currently among the most important health challenges for viticulture in the world. Esca, Botryosphaeria dieback, and Eutypa dieback are the most current GTDs caused by fungi in mature vineyards. Their incidence has increased over the last two decades, mainly after the ban of sodium arsenate, carbendazim, and benomyl in the early 2000s. Since then, considerable efforts have been made to find alternative approaches to manage these diseases and limit their propagation. Biocontrol is a sustainable approach to fight against GTD-associated fungi and several microbiological control agents have been tested against at least one of the pathogens involved in these diseases. In this review, we provide an overview of the pathogens responsible, the various potential biocontrol microorganisms selected and used, and their origins, mechanisms of action, and efficiency in various experiments carried out in vitro, in greenhouses, and/or in vineyards. Lastly, we discuss the advantages and limitations of these approaches to protect grapevines against GTDs, as well as the future perspectives for their improvement.

Transcriptome profiling reveals the underlying mechanism of grape post-harvest pathogen Penicillium olsonii against the metabolites of Bacillus velezensis

Introduction

Pathogen infection influences the post-harvest shelf life of grape berries. In a preliminary study, metabolites produced by Bacillus velezensis significantly inhibited the growth of the grape postharvest pathogen Penicillium olsonii.

Methods

To investigate the mechanism of interaction between B. velezensis and P. olsonii, a draft genome was generated for P. olsonii WHG5 using the Illumina NovaSeq platform, and the transcriptomic changes in WHG5 were analyzed in response to the exposure to B. velezensis metabolites (10% v/v).

Results

The expression levels of genes associated with sporulation, including GCY1, brlA, and abaA, were down-regulated compared with those of the control. In addition, spore deformation and abnormal swelling of the conidiophore were observed. The expression of crucial enzymes, including fructose 2,6-bisphosphate and mannitol-2-dehydrogenase, was down-regulated, indicating that the glycolytic pathway of WHG5 was adversely affected by B. velezensis metabolites. The KEGG pathway enrichment analysis revealed that glutathione metabolism and the antioxidant enzyme system were involved in the response to B. velezensis metabolites. The down-regulation of the pathogenesis-related genes, PG1 and POT1, suggested that B. velezensis metabolites decreased the pathogenicity of P. olsonii. B. velezensis metabolites disrupted the homeostasis of reactive oxygen species in P. olsonii by affecting glucose metabolism, resulting in spore deformation and disruption of growth. In addition, the expression of key pathogenesis-related genes was down-regulated, thereby reducing the pathogenicity of P. olsonii.

Disscusion

This study provides insights into the responses of P. olsonii to B. velezensis metabolites and identifies potential target genes that may be useful in biocontrol strategies for the suppression of post-harvest spoilage in grapes.

Characterization of Bacillus velezensis E2 with abilities to degrade ochratoxin A and biocontrol against Aspergillus westerdijkiae fc-1

Ochratoxin A (OTA), primarily produced by the fungi belonging to the species of Aspergillus and Penicillium, is one of the most common mycotoxins found in cereals and fruits. In addition to resulting in huge economic losses, OTA contamination also poses considerable threat to human and livestock health. Microbial degradation of mycotoxins has been considered with great potential in mycotoxins decontamination. In a previous study, Bacillus velezensis E2 was isolated by our laboratory and showed appreciable inhibitory effect on Aspergillus flavus growth and aflatoxin production in rice grains. In this study, B. velezensis E2 was investigated for its ability to remove OTA and biocontrol against the ochratoxigenic Aspergillus westerdijkiae fc-1. The results revealed that B. velezensis E2 has considerable inhibitory effect on A. westerdijkiae fc-1 both on PDA medium and pear fruits, with inhibitory rate of 51.7% and 73.9%, respectively. In addition, its ability to remove OTA was evaluated in liquid medium and the results showed that more than 96.1% of OTA with an initial concentration of 2.5 μg/mL could be removed by B. velezensis E2 in 48 h. Further experiments revealed that enzymatic transformation and alkaline hydrolysis might be the main mechanisms related to OTA degradation by B. velezensis E2, with ring open ochratoxin α (OP-OTα) as a possible degradation product. Our study indicated that the B. velezensis E2 strain could be a potential bacterial candidate in biodegradation of OTA and biocontrol against A. westerdijkiae fc-1.

The effect of adding Bacillus amyloliquefaciens LSG2-8 in diets on the growth, immune function, antioxidant capacity, and disease resistance of Rhynchocypris lagowskii

The purpose of this study was to investigate the effect of Bacillus amyloliquefaciens LSG2-8 on the growth performance, immune function, antioxidant capacity, and disease resistance of Rhynchocypris lagowskii. Fish were fed with the feed containing five levels such as 0, 1.0 × 10⁶, 1.0 × 10⁷, 1.0 × 10^8, and 1.0 × 10⁹ CFU/g of the B. amyloliquefaciens LSG2-8 for 56 days. After 56 days of feeding, twenty four fish were randomly selected to test various growth, immune and antioxidant parameters. Ten fish were challenged with Aeromonas hydrophila for 14 days; the mortality rate was recorded 14 days after infection. The results showed that B. amyloliquefaciens LSG2-8 could significantly increase the growth parameters of R. lagowskii's, such as final body weight, weight gain rate, specific growth rate, and feed efficiency (p < 0.05). Further examination revealed the activity of antioxidant enzymes, Nrf-2 mRNA, and Keap-1 mRNA gene expression in the intestine and liver, and the serum immune index of R. lagowskii in the 1.0 × 108 CFU/g were all significantly higher compared to the other groups. Furthermore, fish fed a diet supplemented with B. amyloliquefaciens LSG2-8 had a significantly lower (p < 0.05) post-challenge mortality rate than the control fish. In summary, the research results showed that B. amyloliquefaciens LSG2-8 could improve the growth performance, immune function, antioxidant capacity, and disease resistance of R. lagowskii and be used in aquaculture.

Root-Associated Bacteria Are Biocontrol Agents for Multiple Plant Pests

Biological control is an important process for sustainable plant production, and this trait is found in many plant-associated microbes. This study reviews microbes that could be formulated into pesticides active against various microbial plant pathogens as well as damaging insects or nematodes. The focus is on the beneficial microbes that colonize the rhizosphere where, through various mechanisms, they promote healthy plant growth. Although these microbes have adapted to cohabit root tissues without causing disease, they are pathogenic to plant pathogens, including microbes, insects, and nematodes. The cocktail of metabolites released from the beneficial strains inhibits the growth of certain bacterial and fungal plant pathogens and participates in insect and nematode toxicity. There is a reinforcement of plant health through the systemic induction of defenses against pathogen attack and abiotic stress in the plant; metabolites in the beneficial microbial cocktail function in triggering the plant defenses. The review discusses a wide range of metabolites involved in plant protection through biocontrol in the rhizosphere. The focus is on the beneficial firmicutes and pseudomonads, because of the extensive studies with these isolates. The review evaluates how culture conditions can be optimized to provide formulations containing the preformed active metabolites for rapid control, with or without viable microbial cells as plant inocula, to boost plant productivity in field situations.

Activity of Trichoderma asperellum Strain ICC 012 and Trichoderma gamsii Strain ICC 080 Toward Diseases of Esca Complex and Associated Pathogens

Grapevine trunk diseases are widespread in all grape-growing countries. The diseases included in the Esca complex of diseases are particularly common in European vineyards. Their distinctive foliar symptoms are well known to be associated not only with losses in quantity, as with all grapevine wood diseases, but also with losses in the quality of the crop. Protection of pruning wounds is known to reduce infections in artificial inoculations and, to some extent, reduce the external leaf symptoms. The application of biological control agents in the field is typically started at the first appearance of symptoms. In this article, the two strains belonging to two different species, Trichoderma asperellum ICC 012 and T. gamsii ICC 080, which are present in a commercial formulation, were tested in vitro, in vivo in artificial inoculation, and in the field in long-term experiments where the wounds on four young asymptomatic vineyards were protected since 1 or 2 years after planting. The in vitro trials highlighted the different temperature requirements of the two strains, the direct mycoparasitizing activity of T. asperellum, and the indirect activity shown by both Trichoderma strains. The in vivo trials confirmed the ability of the two strains to reduce the colonization following artificial inoculations with the high, unnatural concentration of spores used in artificial infections, even if with variable efficacy, and with long persistence as they could be reisolated 7 months post-application. The preventive applications carried out over 9 years showed a very high reduction in symptom development in the treated vines, on annual and cumulated incidence and on the death of vines, with disease reduction varying from 66 to almost 90%. Early and annual application of protection to the pruning wounds appears to be the best method for reducing damages caused by grapevine leaf stripe disease (a disease of the Esca complex of diseases). Trichoderma appears to offer an efficient, environmentally friendly, and long-lasting protection in the presence of a natural inoculum concentration.

Potential of an endophytic bacteria Bacillus amyloliquefaciens 3-5 as biocontrol agent against potato scab

To obtain a potential biocontrol agent for potato scab, 75 endophytic bacteria were isolated from the healthy potato tubers and strain 3-5 was selected as an optimal antagonistic bacterium against Streptomyces griseoplanus (Streptacidiphilus griseoplanus) causing potato scab. Strain 3-5 was identified as Bacillus amyloliquefaciens based on its morphological characteristics, 16S rDNA and gyrB gene sequence analysis. B. amyloliquefaciens 3-5 has biological functions of indole-3-acetic acid (IAA) production and nitrogen fixation. Polymerase chain reaction (PCR) detection revealed that B. amyloliquefaciens 3-5 had 6 diverse antibacterial substance synthesis genes, named bacD, bacAB, ituD, ituC, sfP and albF, which resulted in the production of bacilysin, iturin, surfactin and subtilosin. Field efficacy evaluation revealed that B. amyloliquefaciens 3-5 (solid fermentation) was successful in controlling potato scab with a 38.90 ± 3.2140% efficiency which is higher than other chemical bactericides except zhongshengmycin·oligosaccharins and kasugamycin·zhongshengmycin. The endophytic bacterium B. amyloliquefaciens 3-5 could be used as a biocontrol agent against potato scab due its control efficacy and environmental safety.

Antibacterial potential of hive bees honey from Himachal Pradesh, India

This paper presents a pioneer study on the microbial diversity and antibacterial potential of hive bees (Apis cerana and A. mellifera) honey collected from Himachal Pradesh. In total, 26 bacteria (14 from A. cerana and 12 from A. mellifera) but no fungal isolate were recovered. Bee species and locations comparison in terms of bacterial load (log CFU/g) revealed maximum loads of 3.74 and 3.99 in the honey from A. cerana and Mandi location, respectively. The most prevalent strains (HC3, HC5, HC6, HC8 and HM2) were identified (16S rRNA ribotyping) as Staphylococcus haemolyticus (MT742636), "Bacillus subtilis subsp. stecoris" (MT742637), Bacillus safensis subsp. safensis (MT742638), "Bacillus zanthoxyli" (MT742639) and Bacillus safensis subsp. safensis (MT938911). The apiary honey displayed good to excellent inhibitory activity against Escherichia coli ATCC1041 whereas, fair to good against Bacillus subtilis ATCC6633, Pseudomonas aeruginosa ATCC10662, Salmonella typhi NCTC786 and Klebsiella pneumoniae ATCC13883, highlighting its use as a therapeutic agent. Furthermore, it can be effective in minimizing numerous side effects associated with the consumption of synthetic drugs for treating bacterial infections thereby signifying the role of honey as a healthier substitute for synthetic drugs.

Development and Application of Low-Cost and Eco-Sustainable Bio-Stimulant Containing a New Plant Growth-Promoting Strain Kosakonia pseudosacchari TL13

The use of beneficial microbes as inoculants able to improve fitness, growth and health of plants also in stress conditions is an attractive low-cost and eco-friendly alternative strategy to harmful chemical inputs. Thirteen potential plant growth-promoting bacteria were isolated from the rhizosphere of wheat plants cultivated under drought stress and nitrogen deficiency. Among these, the two isolates TL8 and TL13 showed multiple plant growth promotion activities as production of indole-3-acetic acid (IAA), siderophores, ammonia, and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase production, the ability to solubilize phosphate as well as exerted antimicrobial activity against plant pathogens as Botrytis spp. and Phytophthora spp. The two selected strains were identified as Kosakonia pseudosacchari by sequencing of 16S rRNA gene. They resulted also tolerant to abiotic stress and were able to efficiently colonize plant roots as observed in vitro assay under fluorescence microscope. Based on the best PGP properties, the strain K. pseudosacchari TL13 was selected to develop a new microbial based formulate. A sustainable and environmentally friendly process for inoculant production was developed using agro-industrial by-products for microbial growth. Moreover, the application of K. pseudosacchari TL13- based formulates in pot experiment improved growth performance of maize plants.

P-Solubilizing Streptomyces roseocinereus MS1B15 With Multiple Plant Growth-Promoting Traits Enhance Barley Development and Regulate Rhizosphere Microbial Population

Phosphate-solubilizing bacteria (PSB) have been reported to increase phosphate (P) content and plant growth. Their application in agricultural systems is an eco-friendly alternative strategy for limiting negative environmental impact of chemical fertilizers and increasing costs. Therefore, the aim of this study was to isolate and characterize new putative PSB to use as inoculum to enhance plant growth and increase P bioavailability in soil. Sixteen bacteria were isolated from Moroccan oat rhizosphere and were screened for their putative P-solubilization by semi-quantitative agar spot method. The two strains MS1B15 and MS1B13, identified as Streptomyces roseocinereus and Streptomyces natalensis, respectively, showed the maximum phosphate solubilization index (PSI = 1.75 and PSI = 1.63). After quantitative assay to determine phosphate solubilization activity, S. roseocinereus MS1B15 was selected for evaluating its putative plant growth promotion activities including production of siderophores, indole-3-acetic acid (IAA) and amino-cyclopropane-1-carboxylate (ACC) deaminase, nitrogen fixation and antimicrobial activity against soil-borne plant pathogens. Under greenhouse condition, barley plants inoculated with S. roseocinereus MS1B15 significantly increased shoot and ear length as well as available phosphorus in ears and leaves and P and N contents in the soil. Overall results showed that the selected strain S. roseocinereus MS1B15 could represent a potential candidate as biofertilizer to increase plant growth as well as P uptake.

Methyl t-butyl ether-degrading bacteria for bioremediation and biocontrol purposes

A total of fifteen potential methyl t-butyl ether (MtBE)-degrading bacterial strains were isolated from contaminated soil. They have been identified as belonging to the genera Bacillus, Pseudomonas, Kocuria, Janibacter, Starkeya, Bosea, Mycolicibacterium, and Rhodovarius. Bacillus aryabhattai R1B, S. novella R8b, and M. mucogenicum R8i were able to grow using MtBE as carbon source, exhibiting different growth behavior and contaminant degradation ability. Their biocontrol ability was tested against various fungal pathogens. Both S. novella R8b and B. aryabhattai were effective in reducing the development of necrotic areas on leaves within 48 hours from Botritys cinerea and Alternaria alternata inoculation. Whereas, M. mucogenicum effectively controlled B. cinerea after 72 hours. Similar results were achieved using Pythium ultimum, in which the application of isolated bacteria increased seed germination. Only M. mucogenicum elicited tomato plants resistance against B. cinerea. This is the first report describing the occurrence of bioremediation and biocontrol activities in M. mucogenicum, B. aryabhattai and S. novella species. The production of maculosin and its antibiotic activity against Rhizoctonia solani has been reported for first time from S. novella. Our results highlight the importance of multidisciplinary approaches to achieve a consistent selection of bacterial strains useful for plant protection and bioremediation purposes.

Epicoccum layuense a potential biological control agent of esca-associated fungi in grapevine

Epicoccum is a genus of ascomycetes often associated with the mycobiome of grapevines (Vitis vinifera). Epicoccum spp. are found in the soil, phyllosphere, as well as in the wood, where they interact both with the plant and with other endophytes and pathogens. Wood pathogens involved in the esca disease complex, a grapevine trunk disease, are particularly concerning in viticulture, as current control strategies have proven unsatisfactory. This study investigated the interaction among Epicoccum spp. and three esca-associated fungi, with the aim of establishing whether they are suitable candidates for biological control.A screening conducted in vitro, by means of dual culture, revealed that all tested Epicoccum spp. inhibited the growth of pathogens Phaeomoniella chlamydospora and Fomitiporia mediterranea, while only some of them inhibited Phaeoacremonium minimum. Epicoccum layuense E24, identified as the most efficient antagonist, was tested in rooted grapevine cuttings of cultivars Cabernet Sauvignon and Touriga Nacional, under greenhouse conditions, against P. chlamydospora and P. minimum. This study revealed that the inoculation of E. layuense E24 produced a successful colonization of the wood of grapevines; in addition it did not impair the growth of the plants or induce the appearance of symptoms in leaves or in wood. Moreover, grapevines colonized by E. layuense E24 showed a considerable decrease in the wood symptomatology caused by the inoculated pathogens (by 31-82%, depending on the pathogen/grapevine cultivar), as well as a reduction in their frequency of re-isolation (60-74%).Our findings suggest that E. layuense E24 is a promising candidate for its application in biological control, due to its antagonistic interaction with some esca-associated fungal pathogens.

Identification of a small antimycotic peptide produced by Bacillus amyloliquefaciens 6256

Bacillus sp. 6256 is a good biocontrol agent against Botrytis cinerea which caused tomato gray mold disease. Strain 6256 was identified as B. amyloliquefaciens by analysis of its partial gyrB gene sequence. To identify and characterize the antimycotic peptides from the culture broth of the bacterium, the antimicrobial substances produced by B. amyloliquefaciens 6256 were isolated by ammonium sulfate precipitation, Superdex 200 gel filtration chromatography and DEAE anion exchange chromatography. The purified compound was designated as P657. The biological activity of P657 was stable at as high as 100 °C for 20 min and in pH value ranged from 5 to 10. The antimycotic compound was resistant to trypsin and proteinase K, and could completely inhibit spore germination of Botrytis cinerea in vitro. MALDI-TOF-MS analysis results showed the presence of fengycins A (C₁₆-C₁₇) and fengycins B (C₁₅-C₁₇) isoforms in P657.

Isolation and identification of antifungal peptides from Bacillus amyloliquefaciens W10

Antifungal metabolites produced by Bacillus sp. W10, which was previously isolated from the tomato rhizosphere, were investigated. Strain W10 was identified as Bacillus amyloliquefaciens by analysis of its 16S rDNA and gyrB gene partial sequences. PCR analysis showed the presence of fenB, sfp, and ituD genes, coding for fengycin, surfactin, and iturin, respectively. A novel small antifungal peptide, designated 5240, produced by this strain was isolated by ammonium sulfate precipitation and Superdex 200 gel filtration chromatography. The 5240 peptide was stable at 100 °C for 20 min and remained active throughout a wide pH range (4-10). The antagonistic activity was not affected by protease K and trypsin. The purified 5240 peptide exhibited a broad inhibitory spectrum against various plant pathogenic fungi and was identified as iturin A (C₁₄-C₁₆). Moreover, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry indicated the presence of fengycin A (C₁₄-C₁₅), fengycin B (C₁₆-C₁₇), and surfactin (C₁₃-C₁₆) isoforms in supernatants from strain W10. These results suggest that B. amyloliquefaciens W10 has significant potential as a biocontrol agent.

The Microbial Community Dynamics during the Vitex Honey Ripening Process in the Honeycomb

The bacterial and fungal communities of vitex honey were surveyed by sequencing the 16S rRNA gene and the internal transcribed spacer region of ribosomal DNA. Vitex honey samples were analyzed at different stage of ripening; the vitex flower was also analyzed, and the effect of the chemical composition in the experimental setup was assessed. The results confirmed the presence of dominant Bacillus spp. as the dominant bacterial in honey, and yeast related genera was the main fungal in the honey, respectively. Lactococcus and Enterococcus were detected for the first time in honey. The proportion of most of the fungal community decreased during the honey ripening process. Multivariate analyses also showed that the fungal community of 5, 10, and 15 days honey samples tended to cluster together and were completely separated from the 1 day honey sample. The change in the fungal community showed a correlation with the variation in the chemical components, such as moisture and phenolic compounds. Together, these results suggest that ripening of honey could change its microbial composition, and decrease the potential risk of microbiology.

Impact of Alternative Fungicides on Grape Downy Mildew Control and Vine Growth and Development

Grapevine downy mildew (GDM) is one of the most serious diseases of grapevines. With limitations in the use of copper-based products imposed for organic agriculture by the European Union, research for alternatives is encouraged. The aim of this research was to follow a 2-year trial to evaluate the control of GDM using some alternative compounds, and to determine their effects on shoot growth, plant photosynthesis, and grape quality and quantity. Under low disease pressure, Bordeaux mixture, copper hydroxide, laminarin combined with low copper, and 0.5 and 0.8% chitosan had the lowest GDM incidence, reduced on leaves by 96, 95, 75, 56, and 81%, respectively, compared with the untreated control in the last survey. With high disease pressure, Bordeaux mixture, laminarin combined with Saccharomyces extracts, and 0.5 and 0.8% chitosan had the lowest GDM incidence, reduced on grape by 86, 37, 66, and 75%, respectively, compared with the untreated control in the survey of mid-July. Chitosan at 0.8% lowered net photosynthesis, due to reduced stomatal conductance, leaf area, and dry weight, with no negative effects observed on the quantity of the grape berries and the quality parameters of their juice. Among the alternatives to copper, chitosan provided the best GDM protection and reduced the vigor of the vegetation, inducing physiological changes without negative effects on grape production.

Exploring the microbiota dynamics related to vegetable biomasses degradation and study of lignocellulose-degrading bacteria for industrial biotechnological application

The aims of this study were to evaluate the microbial diversity of different lignocellulosic biomasses during degradation under natural conditions and to isolate, select, characterise new well-adapted bacterial strains to detect potentially improved enzyme-producing bacteria. The microbiota of biomass piles of Arundo donax, Eucalyptus camaldulensis and Populus nigra were evaluated by high-throughput sequencing. A highly complex bacterial community was found, composed of ubiquitous bacteria, with the highest representation by the Actinobacteria, Proteobacteria, Bacteroidetes and Firmicutes phyla. The abundances of the major and minor taxa retrieved during the process were determined by the selective pressure produced by the lignocellulosic plant species and degradation conditions. Moreover, cellulolytic bacteria were isolated using differential substrates and screened for cellulase, cellobiase, xylanase, pectinase and ligninase activities. Forty strains that showed multienzymatic activity were selected and identified. The highest endo-cellulase activity was seen in Promicromonospora sukumoe CE86 and Isoptericola variabilis CA84, which were able to degrade cellulose, cellobiose and xylan. Sixty-two percent of bacterial strains tested exhibited high extracellular endo-1,4-ß-glucanase activity in liquid media. These approaches show that the microbiota of lignocellulosic biomasses can be considered an important source of bacterial strains to upgrade the feasibility of lignocellulose conversion for the ‘greener' technology of second-generation biofuels.

Methylobacterium populi VP2: plant growth-promoting bacterium isolated from a highly polluted environment for polycyclic aromatic hydrocarbon (PAH) biodegradation

The use of microorganisms to accelerate the natural detoxification processes of toxic substances in the soil represents an alternative ecofriendly and low-cost method of environmental remediation compared to harmful incineration and chemical treatments. Fourteen strains able to grow on minimal selective medium with a complex mixture of different classes of xenobiotic compounds as the sole carbon source were isolated from the soil of the ex-industrial site ACNA (Aziende Chimiche Nazionali Associate) in Cengio (Savona, Italy). The best putative degrading isolate, Methylobacterium populi VP2, was identified using a polyphasic approach on the basis of its phenotypic, biochemical, and molecular characterisation. Moreover, this strain also showed multiple plant growth promotion activities: it was able to produce indole-3-acetic acid (IAA) and siderophores, solubilise phosphate, and produce a biofilm in the presence of phenanthrene and alleviate phenanthrene stress in tomato seeds. This is the first report on the simultaneous occurrence of the PAH-degrading ability by Methylobacterium populi and its multiple plant growth-promoting activities. Therefore, the selected indigenous strain, which is naturally present in highly contaminated soils, is good candidate for plant growth promotion and is capable of biodegrading xenobiotic organic compounds to remediate contaminated soil alone and/or soil associated with plants.

Expression analysis of the impact of culture filtrates from the biocontrol agent, Phlebiopsis gigantea on the conifer pathogen, Heterobasidion annosum s.s. Transcriptome

Phlebiopsis gigantea has been routinely used as the biological control agent for the conifer pathogen Heterobasidion annosum sensu lato, but the actual mechanism for the biocontrol process is not known. To investigate the effect of secreted molecules from culture filtrate produced by P. gigantea on the gene expression profile of H. annosum s.s., microarray analysis was used. Analysis of the differentially expressed genes led to the identification of genes with diverse functions. A major proportion of the up- and downregulated genes were either uncharacterized or genes whose functions were not known. A number of genes coding for proteins involved in metabolism, transport, and signal transduction were differentially downregulated; comparatively lower number of such genes were upregulated. Some genes involved in transport (polyamine transporters, 2573-fold, P = 0.002) and metabolism (endoglucanase, 622.5-fold, P = 0.002, cytochrome P450, 133.2-fold, P = 0.05) showed high transcript fold changes and were statistically significantly upregulated. Genes encoding defense-related proteins such as hydrophobins were either downregulated or expressed at relatively low levels. Further analysis of the effect of the culture filtrate on glucose metabolism showed downregulation of some key enzymes at the early stage of the glycolytic pathway while some genes were upregulated at the later stage of the pathway. A subset of the genes were selected and used to validate the micro-array result by quantitative real time polymerase chain reaction (qPCR) method. Generally, the high transcript levels of genes encoding several biochemically important genes (protein kinases, major facilitator superfamily polyamine transporters, endoglucanase, cytochrome P450, endoglucanase) suggests their potential functional relevance in signal perception, stress tolerance, cell defenses, and detoxification of toxic molecules during competitive interaction. These results have provided further insights into possible molecular and genetic factors underlying the response of H. annosum to metabolites from P. gigantea during interspecific interaction.

Cultivable microorganisms associated with honeys of different geographical and botanical origin

In this study, the composition of the cultivable microbial populations of 38 nectar honey and honeydew honey samples of different botanical and geographical origin were assessed. After growth in specific media, various colonies with different appearance were isolated and purified before phenotypic (morphological, physiological and biochemical traits) and genotypic [randomly amplified polymorphic DNA (RAPD), repetitive DNA elements-PCR (rep-PCR) and restriction fragment length polymorphism (RFLP)] differentiation. The identification was carried out by 16S rRNA gene sequencing for bacteria and, in addition to RFLP, by sequencing the D1/D2 region of the 26S rRNA gene for yeasts and the 5.8S-ITS rRNA region for filamentous fungi. The results showed the presence of 13 species of bacteria, 5 of yeasts and 17 of filamentous fungi; the species most frequently isolated were Bacillus amyloliquefaciens, Zygosaccharomyces mellis and Aspergillus niger for the three microbial groups, respectively. The highest microbial diversity was found in multifloral honeys. No correlation among the microbial species and the botanical/geographical origin was found, but some strains were highly adapted to these matrices since they were found in several samples of different origin.