Functional genomics analysis of a phyllospheric Pseudomonas spp with potential for biological control against coffee rust

Abstract

Background Pseudomonas spp. promotes plant growth and colonizes a wide range of environments. During the annotation of a Coffea arabica ESTs database, we detected a considerable number of contaminant Pseudomonas sequences, specially associated with leaves. The genome of a Pseudomonas isolated from coffee leaves was sequenced to investigate in silico information that could offer insights about bacterial adaptation to coffee phyllosphere. In parallel, several experiments were performed to confirm certain physiological characteristics that could be associated with phyllospheric behavior. Finally, in vivo and in vitro experiments were carried out to verify whether this isolate could serve as a biocontrol agent against coffee rust and how the isolate could act against the infection. Results The isolate showed several genes that are associated with resistance to environmental stresses, such as genes encoding heat/cold shock proteins, antioxidant enzymes, carbon starvation proteins, proteins that control osmotic balance and biofilm formation. There was an increase of exopolysaccharides synthesis in response to osmotic stress, which may protect cells from dessication on phyllosphere. Metabolic pathways for degradation and incorporation into citrate cycle of phenolic compounds present in coffee were found, and experimentally confirmed. In addition, MN1F was found to be highly tolerant to caffeine. The experiments of biocontrol against coffee leaf rust showed that the isolate can control the progress of the disease, most likely through competition for resources. Conclusion Genomic analysis and experimental data suggest that there are adaptations of this Pseudomonas to live in association with coffee leaves and to act as a biocontrol agent.

Pan-metagenome reveals the abiotic stress resistome of cigar tobacco phyllosphere microbiome

“…In a recent study by de Sousa et al. ( de Sousa et al., 2022 ), it was demonstrated that Pseudomonas spp. rely on increased synthesis of exopolysaccharides (EPSs) to cope with osmotic stress and protect cells from desiccation in the phyllosphere.…”

“…The biosynthesis of osmoprotectants and the production of EPS enriched in the tested metagenome may reflect adaptations of microbial inhabitants by enhancing attachment to surfaces and offering resistance to environmental pressures and plant defenses (Rastogi et al, 2013). In a recent study by de Sousa et al (de Sousa et al, 2022), it was demonstrated that Pseudomonas spp. rely on increased synthesis of exopolysaccharides (EPSs) to cope with osmotic stress and protect cells from desiccation in the phyllosphere.…”

Essential Oils and Antagonistic Microorganisms as Eco-Friendly Alternatives for Coffee Leaf Rust Control

“…Biocontrol has been proposed in organic coffee cultivations as an alternative to CLR control. The bacteria of the genus Pseudomonas have generated a great interest in this field because of their benefits for the host plant by producing auxins and siderophores that improve plant development and growth as well as protecting them against phytopathogens [84]. Studies have discovered that Bacillus subtilis and Pseudomonas fluorescens inhibit urediniospore germination and reduce disease incidence and severity.…”

Diseases affecting the coffee crop: Elucidating the life cycle of Rust,Thread Blight and Cercospora Leaf Spot

“…En dicho experimento se evaluaron un total de 234 bacterias endófitas (217) y hongos (17) aislados de tejidos de café. Aunque especies de Pseudomonas también promueven el crecimiento de las plantas y coloniza una amplia gama de ambientes, puede ser un excelente biocontrolador contra la Roya en cafetos ( de Sousa et al, 2022). La creciente preocupación por evitar o reducir el uso de plaguicidas y fertilizantes inorgánicos en el cultivo de café, y optar por alternativas sostenibles y respetuosas con el medio ambiente, ha hecho que entre las investigaciones más demandadas estén el uso de microorganismos y sus compuestos en el manejo de enfermedades como la Roya (Castillo et al, 2022).…”