Fungal Root Microbiome from Healthy and Brittle Leaf Diseased Date Palm Trees (Phoenix dactylifera L.) Reveals a Hidden Untapped Arsenal of Antibacterial and Broad Spectrum Antifungal Secondary Metabolites

Abstract

In this study, we aimed to explore and compare the composition, metabolic diversity and antimicrobial potential of endophytic fungi colonizing internal tissues of healthy and brittle leaf diseased (BLD) date palm trees (Phoenix dactylifera L.) widely cultivated in arid zones of Tunisia. A total of 52 endophytic fungi were isolated from healthy and BLD roots of date palm trees, identified based on internal transcribed spacer-rDNA sequence analysis and shown to represent 13 species belonging to five genera. About 36.8% of isolates were shared between healthy and diseased root fungal microbiomes, whereas 18.4 and 44.7% of isolates were specific to healthy and BLD root fungal microbiomes, respectively. All isolates were able to produce at least two of the screened enzymes including amylase, cellulase, chitinase, pectinase, protease, laccase and lipase. A preliminary screening of the isolates using disk diffusion method for antibacterial activity against four Gram-positive and three Gram-negative bacteria and antifungal activities against three phytopathogenic fungi indicated that healthy and BLD root fungal microbiomes displayed interesting bioactivities against examined bacteria and broad spectrum bioactivity against fungal pathogens. Some of these endophytic fungi (17 isolates) were fermented and their extracts were evaluated for antimicrobial potential against bacterial and fungal isolates. Results revealed that fungal extracts exhibited antibacterial activities and were responsible for approximately half of antifungal activities against living fungi. These results suggest a strong link between fungal bioactivities and their secondary metabolite arsenal. EtOAc extracts of Geotrichum candidum and Thielaviopsis punctulata originating from BLD microbiome gave best results against Micrococcus luteus and Bacillus subtilis with minimum inhibitory concentration (MIC, 0.78 mg/mL) and minimum bactericidal concentration (6.25 mg/mL). G. candidum gave the best result against Rhizoctonia solani with MIC 0.78 mg/mL and minimum fungicidal concentration (MFC, 6.25 mg/mL). In conclusion, using plant microbiomes subjected to biotic stresses offers new endophytes with different bioactivities than those of healthy plants. Therefore, date palm endophytic fungi represent a hidden untapped arsenal of antibacterial and broad spectrum antifungal secondary metabolites and could be considered promising source of bioactive compounds with industrial and pharmaceutical applications.

Comparative Genomics of Bacillus amyloliquefaciens Strains Reveals a Core Genome with Traits for Habitat Adaptation and a Secondary Metabolites Rich Accessory Genome

“…As public pressure mounts to protect the environment, biological control strategies of phytopathogens including viruses, bacteria, fungi, and oomycetes (Lara and Belbahri, 2011 ; Olson et al, 2012 ; Luchi et al, 2013 ; Prospero et al, 2013 ; Abad et al, 2014 ) are more considered as ecologically sound and economically viable alternatives to pesticide usage strategies (Gurr and You, 2016 ; Mefteh et al, 2017 ). Plant-associated B. amyloliquefaciens strains colonize plant rhizosphere, promote plant growth and suppress competing phytopathogens.…”

“…Therefore, they have been widely used as biofertilizers and biopesticides (Wu et al, 2015 ). Abilities to compete with pathogens are linked to the production of secondary metabolites (Chen et al, 2007 ; Boottanun et al, 2017 ) that possess antimicrobial activity (Alenezi et al, 2015a , b ; Belbahri et al, 2015 ; Alenezi et al, 2016a , b , 2017 ; Mefteh et al, 2017 ) or host plant immune system stimulation (Chowdhury et al, 2015 ). Secondary metabolites have been widely documented in the fields of food processing (Chang et al, 2015 ; Chaves-Lopez et al, 2015 ), pharmaceuticals (Prazdnova et al, 2015 ) and environmental engineering (Alvarez et al, 2015 ; Mlaik et al, 2015 ; Sellami et al, 2016 ).…”

Increased Biological Activity of Aneurinibacillus migulanus Strains Correlates with the Production of New Gramicidin Secondary Metabolites

“…Producing pesticide-free food and maintaining a healthy environment are the main reasons to promote the development of environmentally sound approaches of disease control. Therefore, biological control agents (BCAs) that can suppress pathogen activities with less damage to the wider environment are increasingly used in agriculture (Roberts and Lohrke, 2003; Mefteh et al, 2017). …”

Potential antibiotic-producing fungal strains isolated from pharmaceutical waste sludge

“…Furthermore, in spite of a few reports about G. candidum metabolites with antibacterial property, they have been reported as important in cheesemaking [26]. However, two antimicrobial compounds were purified from G. candidum by Dieuleveux et al [27], while broad-spectrum antibacterial activity of ethyl acetate extracts of G. candidum from root biome of date palm trees has also been reported [28].…”