Biocontrol of Diplodia bulgarica, the causal agent of apple canker, using Trichoderma zelobreve

Apple (Malus domestica Borkh) is one of the most consumed and nutritious fruits. Iran is one of the main producers of the apple in the world. Diplodia bulgarica is the major causal agent of apple tree decline in Iran. Biological control is a nature-friendly approach to plant disease management. Trichoderma zelobreve was isolated from apple trees infected with Diplodia bulgarica in West Azarbaijan province of Iran. The results showed that T. zelobreve strongly inhibited the colony growth of D. bulgarica. In vivo assay on detached branches of apple tree cv. Golden Delicious using T. zelobreve mycelial plug showed that canker length/stem length (CL/SL) and canker perimeter/stem perimeter (CP/SP) indices decreased by 76 and 69%, respectively, 21 days after inoculation. Additionally, wettable powder formulation (WPF) containing the antagonistic fungus "T. zelobreve" decreased CL and CP/SP by 75 and 67%, respectively, 6 months after inoculation. Moreover, canker progress curves and the area under the disease progress curve (AUDPC) supported these findings. The growth temperatures of the antagonist and pathogen were similar, indicating the adaptation of T. zelobreve for biocontrol of apple canker caused by D. bulgarica. The results also showed that T. zelobreve-based WPF stored at 25 °C assure excellent shelf life at least 4 months, allowing the bioproduct to be stored at room temperature, which is a great advantage and cost-effective option.

Phylogenetic analysis, molecular characterization and virulence profiling based on toxoflavin gene of an Indian BG1 strain of Burkholderia glumae causing panicle blight of rice

Bacterial panicle blight (BPB) caused by Burkholderia glumae (BG) has become significantly more prevalent in the rice-growing regions of North India. Based on virulence screening and in vitro quantification of toxoflavin, the BG strains were classified as hyper- (BG1 and BG3), moderate- (BG2, BG4, BG6, BG8, and BG9), and hypo- (BG5, BG7, and BG10) virulent. Plant inoculation assays with cell-free culture filtrate revealed strains with higher toxoflavin-producing ability had higher virulence. Based on 16S rRNA sequence, 6 isolates from Uttar Pradesh were grouped in clad C1; whereas, clad C2 exhibited 4 isolates, two each from Delhi and Uttar Pradesh. Strain BG1 being the most virulent Indian strain from Uttar Pradesh was further profiled for 11 tox genes. We found all the 11 tox genes present in strain BG1. In toxRABCDE cluster, all tox genes showed high similarity to B. glumae BGR1 except toxB, whereas in toxFGHIJ cluster toxF, toxG, toxH and toxI shared maximum similarity to B. glumae 336gr-1. tox genes of BG1 exhibited homology as well as divergence with B. gladioli. The domain prediction and protein association network analysis indicated the possible involvement of tox genes in the toxoflavin biosynthesis. As per our knowledge, this is the first report in India on characterization of tox genes cluster in B. glumae. Altogether, our study unravels a reliable method for identifying and characterizing B. glumae using tox genes and its relationship with disease production.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03660-6.

Isolation and characterization of endophytic bacteria from tomato foliage and their in vitro efficacy against root-knot nematodes

Fifteen endophytic bacteria were isolated from leaves and stems of Solanum lycopersicum and Solanum pimpinellifolium collected from different locations of the Jorhat district of Assam and characterized by morphological, cultural, biochemical and molecular approaches. An in vitro study was carried out to evaluate their potentiality as biological control agents against second stage juvenile of the root-knot nematode, Meloidogyne incognita race2. Thirty second stage juveniles (J₂) of M. incognita race 2 were exposed to cell free culture filtrates of all the 15 bacterial endophytes in a sterile cavity block at a concentration of S(100%), S/2(50%), S/4(25%), S/6(17%) and S/10(10%) for a duration of 6, 12, 24, and 48 hr. The results revealed that all the isolates had the potentiality to significantly increase the mortality of the second stage juveniles (J₂). The percent mortality was directly proportional to the duration of exposure time and the concentration of the culture filtrate. The isolate BETL2 showed the best result with 81.47% mortality of juveniles followed by isolates BETL4 (81.43%), BETLI (79.07%), BETS2 (78.87%), and BETL6 (78.17%). The 16S rRNA sequence amplification results indicated that these isolates were Bacillus marisflavi (BETL2), Bacillus altitudinis (BETL4), Microbacterium arborescens (BETL1), Exiguobacterium indicum (BETS2), and Bacillus marisflavi (BETL6). The four most efficient isolates were structurally analyzed using a scanning electron microscope and this revealed that the length and breadth of isolates—BETLI, BETL2, BETL4, and BETS2 were 701.70 nm × 348.30 nm, 954.10 nm × 303.10 nm, 984.10 nm × 332.90 nm and 1422.00 nm × 742.00 nm, respectively. The result of the present study indicated that the above four novel strains of endophytic bacterial isolates enhance the mortality of J₂ of M. incognita race2 and has the potentiality as biological control agents against M. incognita.

Extraction and Separation of Mycobacterial Proteins

The extraction and separation of native mycobacterial proteins remain necessary for antigen discovery, elucidation of enzymes to improve rational drug design, identification of physiologic mechanisms, use as reagents for diagnostics, and defining host immune responses. In this chapter, methods for the manipulation of whole mycobacterial cells and culture exudates are described in detail as these methods are the requisite first steps towards native protein isolation. Specifically, several methods for the inactivation of viable Mycobacterium tuberculosis along with qualification assays are provided, as this is key to safe manipulation of cell pastes for downstream processes. Next, the concentration of spent culture filtrate media in order to permit separation of soluble, secreted proteins is described followed by the separation of mycobacteria extracellular vesicles (MEV) from the remaining soluble proteins in spent media. We then describe the generation of whole-cell lysate and facile separation of lysate into subcellular fractions to afford cell wall, cell membrane, and cytosol-enriched proteins. Due to the hydrophobic nature of cell wall and cell membrane proteins, several extraction protocols to resolve protein subsets (such as extraction with urea and SDS) are also provided. Finally, methods for separation of hydrophobic and hydrophilic proteins from both whole-cell lysate and spent culture media are included. While these methods were optimized for the manipulation of Mycobacterium tuberculosis cells, they have been successfully applied to extract and isolate Mycobacterium leprae, Mycobacterium ulcerans, and Mycobacterium avium proteins.

Supplementation of sputum cultures with culture filtrate to detect tuberculosis in a cross-sectional study of HIV-infected individuals

While some healthcare systems have shifted to molecular diagnostics, culture still remains the gold standard for tuberculosis diagnosis, but it is limited by its long duration to a positive result. Methods to reduce time to culture positivity (TTP) are urgently required. We determined if growth factor supplementation in the mycobacterial growth indicator tube (MGIT) culture system reduces TTP. MGITs were supplemented with fresh culture filtrate (CF) as a source of growth stimulatory molecules from axenic Mycobacterium tuberculosis culture. Different volumes of CF and media components were tested. The performance of these modified MGITs was assessed with sputum from HIV-TB co-infected individuals. Reducing the volume of MGIT cultures and removal of detergent from cultures grown to generate CF had a marginal but significant benefit on reducing TTP. In a subset of specimens, CF inhibited growth. Following optimization of methods, a reduced TTP occurred in specimens with low bacillary load as measured by GeneXpert, smear microscopy and colony forming units. Three specimens that were negative under standard conditions flagged positive following CF supplementation. Our data provide preliminary evidence that addition of CF to MGIT cultures can enhance detection of M. tuberculosis in HIV-TB co-infected patients with low sputum bacillary loads.

Effect of an Arthrobotrys musiformis (Fungi: Orbiliales) culture filtrate on the population of gastrointestinal parasitic nematode eggs in faeces of grazing lambs

This study assessed the anthelmintic activity of the oral administration of a free-spore culture filtrate of the nematophagous fungus (NF) Arthrobotrys musiformis (M-10) on gastrointestinal parasitic nematodes (GIN) in naturally infected lambs. The fungus was grown on potato-dextrose agar plates (PDA) and transferred to a fermented rice medium (FRM). After 40-day incubation the total amount of FRM with the growing fungi was transferred to a flask shaker with distilled water for a 24 h period. The fungus was centrifuged and filtered. Three groups of six naturally-infected lambs (>1000 epg) each were treated once as follows: Group 1) 63.8 mg/kg A. musiformis culture filtrate (CF) (per os); Group 2) Levamisole 7.5 mg/ml (intramuscularly), Group 3) 15 ml of distilled water (per os). Faecal samples were individually collected on days -2, 0, 2, 4, 6, 8 and 10 after treatment. For each experimental group, mean egg shedding was calculated and transformed (log 10 [epg + 1]). Means between the fungal filtrate group and the negative control were analysed using a T-Student Test. The faecal egg count reduction test (FECRT) was performed in groups treated with CF and Levamisole in relation to the control group (water) were 36.8-57.4% and 89-95.4%, respectively., although due to the difference between groups, no statistical significance was found (p > 0.05). The use of A. musiformis CF appears to be a good alternative treatment, although, more studies should be performed to establish the use of these fungal products as potential tools for GIN control.

Effect of Bacillus pumilus CCIBP-C5 on Musa-Pseudocercospora fijiensis interaction

The effect of antifungal activity of culture filtrate (CF) of Bacillus pumilus strain CCIBP-C5, an isolate from a phyllosphere of banana (Musa) leaves, was determined on Pseudocercospora fijiensis challenged banana plants. The CF was shown to decrease the fungal biomass and induce changes in banana plant. In this sense, at 70 days post inoculation (dpi), a lower infection index as well as a decrease in fungal biomass after 6 dpi was obtained in treated plants with respect to control ones. At the same time, changes in the activities of several enzymes related to plant defense responses, such as phenylalanine ammonia lyase, chitinases, β-1,3-glucanases and peroxidases were observed. These results indicate that B. pumilus CCIBP-C5 has a potential role for biological control of P. fijiensis possibly due to the production of antifungal metabolites.

Nematicidal activity of Paecilomyces lilacinus 6029 cultured on Karanja cake medium

Antagonistic fungi parasitize root-knot nematodes through secretion of extracellular hydrolytic enzymes and secondary metabolites. In present study, in vitro bioassay showed that Paecilomyces lilacinus 6029 culture filtrate from Karanja cake medium killed 100% Meloidogyne incognita larvae while only 78.28% mortality was recorded by Czapeck-Dox filtrate within 12 h of exposure. The filtrate, irrespective of culture medium, was found to be more nematotoxic when incubated for 15 days. Fourier Transform infrared spectroscopy predicted the presence of phenolic and alcoholic compounds in the filtrate. Furthermore, the active metabolites in fungal filtrate were partially characterized. pH stability test revealed that nematotoxicity of the filtrate appeared at all range of pH with low pH filtrate possessing more toxicity against M. incognita. Interestingly, buffers of same pH value did not show any nematicidal effect. No significant difference in nematicidal activity was observed between boiled (98.2% mortality) and unboiled culture filtrate (100% mortality). Ethyl acetate and lyophilized aqueous extracts produced higher nematicidal activity than a hexane extract indicating polar nature of active compounds produced by P. lilacinus 6029.

Biological Control of Aphid Using Fungal Culture and Culture Filtrates of Beauveria bassiana

Aphids are one of the most destructive pests in crop production such as pepper, cucumber, and eggplants. The importance of entomopathogenic fungi as alternative pest control agents is increasing. Conidia of entomopathogenic fungi are influenced by environmental conditions, such as temperature and relative humidity, and cause slow and fluctuating mortality. These factors have prevented wider application and use of biocontrol agents. For investigation of means of mitigation of such problems, we conducted bioassays with 47 fungal culture filtrates in order to evaluate the potential of secondary metabolites produced by entomopathogenic fungi for use in aphid control. Among 47 culture filtrates cultured potato dextrose broth, filtrate of Beauveria bassiana Bb08 showed the highest mortality (78%) against green peach aphid three days after treatments. Filtrate of Bb08 cultured in Adamek's medium showed higher toxicity as 100% to third instar nymphs of the aphid compared with seven other filtrates cultured in different broths amended with colloidal chitin or oil. The culture filtrates and fungal cultures from media amended with colloidal chitin or oil had lower control efficacies than filtrates without these additives in three different media. These results indicate that the fungal culture fluid or culture filtrate of B. bassiana Bb08 cultured in Adamek's medium has potential for development as a mycopesticide for aphid control.