Contrasting genome patterns of two pseudomonas strains isolated from the date palm rhizosphere to assess survival in a hot arid environment

Investigating the genomic and metabolic abilities of PGPR Pseudomonas fluorescens in promoting plant growth and fire blight management

Pseudomonas fluorescens is commonly found in diverse environments and is well known for its metabolic and antagonistic properties. Despite its remarkable attributes, its potential role in promoting plant growth remains unexplored. This study examines these traits across 14 strains residing in diverse rhizosphere environments through pangenome and comparative genome analysis, alongside molecular docking studies against Erwinia amylovora to combat fire blight. Whole genome analysis revealed circular chromosome (6.01-7.07 Mb) with GC content averaging 59.95-63.39%. Predicted genes included 16S rRNA and protein-coding genes ranging from 4435 to 6393 bp and 1527 to 1541 bp, respectively. Pangenome analysis unveiled an open pangenome, shedding light on genetic factors influencing plant growth promotion and biocontrol, including nitrogen fixation, phosphorus solubilization, siderophore production, stress tolerance, flagella biosynthesis, and induced systemic resistance. Furthermore, pyrrolnitrin, phenazine-1-carboxylic acid, pyoluteorin, lokisin, 2,4-diacetylpholoroglucinol and pseudomonic acid were identified. Molecular docking against key proteins of E. amylovora highlighted the high binding affinities of 2,4-diacetylphloroglucinol, pseudomonic acid, and lokisin. These findings underscore the multifaceted role of P. fluorescens in plant growth promotion and biocontrol, with key biomolecules showing promising applications in plant growth and defense against pathogens.

Juvenile Plant-Microbe Interactions Modulate the Adaptation and Response of Forest Seedlings to Rapid Climate Change

The negative impacts of climate change on native forest ecosystems have created challenging conditions for the sustainability of natural forest regeneration. These challenges arise primarily from abiotic stresses that affect the early stages of forest tree development. While there is extensive evidence on the diversity of juvenile microbial symbioses in agricultural and fruit crops, there is a notable lack of reports on native forest plants. This review aims to summarize the critical studies conducted on the diversity of juvenile plant-microbe interactions in forest plants and to highlight the main benefits of beneficial microorganisms in overcoming environmental stresses such as drought, high and low temperatures, metal(loid) toxicity, nutrient deficiency, and salinity. The reviewed studies have consistently demonstrated the positive effects of juvenile plant-microbiota interactions and have highlighted the potential beneficial attributes to improve plantlet development. In addition, this review discusses the beneficial attributes of managing juvenile plant-microbiota symbiosis in the context of native forest restoration, including its impact on plant responses to phytopathogens, promotion of nutrient uptake, facilitation of seedling adaptation, resource exchange through shared hyphal networks, stimulation of native soil microbial communities, and modulation of gene and protein expression to enhance adaptation to adverse environmental conditions.

Multifaceted Impacts of Plant-Beneficial Pseudomonas spp. in Managing Various Plant Diseases and Crop Yield Improvement

The modern agricultural system has issues with the reduction of agricultural productivity due to a wide range of abiotic and biotic stresses. It is also expected that in the future the entire world population may rapidly increase and will surely demand more food. Farmers now utilize a massive quantity of synthetic fertilizers and pesticides for disease management and to increase food production. These synthetic fertilizers badly affect the environment, the texture of the soil, plant productivity, and human health. However, agricultural safety and sustainability depend on an ecofriendly and inexpensive biological application. In contrast to synthetic fertilizers, soil inoculation with plant-growth-promoting rhizobacteria (PGPR) is one of the excellent alternative options. In this regard, we focused on the best PGPR genera, Pseudomonas, which exists in the rhizosphere as well as inside the plant's body and plays a role in sustainable agriculture. Many Pseudomonas spp. control plant pathogens and play an effective role in disease management through direct and indirect mechanisms. Pseudomonas spp. fix the amount of atmospheric nitrogen, solubilize phosphorus and potassium, and also produce phytohormones, lytic enzymes, volatile organic compounds, antibiotics, and secondary metabolites during stress conditions. These compounds stimulate plant growth by inducing systemic resistance and by inhibiting the growth of pathogens. Furthermore, pseudomonads also protect plants during different stress conditions like heavy metal pollution, osmosis, temperature, oxidative stress, etc. Now, several Pseudomonas-based commercial biological control products have been promoted and marketed, but there are a few limitations that hinder the development of this technology for extensive usage in agricultural systems. The variability among the members of Pseudomonas spp. draws attention to the huge research interest in this genus. There is a need to explore the potential of native Pseudomonas spp. as biocontrol agents and to use them in biopesticide development to support sustainable agriculture.

Comparative Functional Genome Analysis Reveals the Habitat Adaptation and Biocontrol Characteristics of Plant Growth-Promoting Bacteria in NCBI Databases

Plant growth-promoting bacteria (PGPB) are a group of beneficial microorganisms that include 60 bacterial genera, such as Bacillus, Pseudomonas, and Burkholderia, which widely colonize plant leaves and soil, promote plant growth, and/or inhibit pathogen infection. However, the genetic factors underpinning adaptation of PGPB to plant leaves and soil remain poorly understood. In this study, we performed a comparative functional genome analysis approach to investigate the functional genes of 195 leaf-associated (LA) and 283 soil-associated (SA) PGPB strains and their roles in adapting to their environment, using 95 strains from other-associated (OA) environmental habitats with growth-promoting or antimicrobial functions as negative controls. Comparison analysis of the enrichment of nonredundant (NR) protein sequence databases showed that cytochrome P450, DNA repair, and motor chemotaxis genes were significantly enriched in LA PGPB strains related to environmental adaptation, while cell wall-degrading enzymes, TetR transcriptional regulatory factors, and sporulation-related genes were highly enriched in SA PGPB strains. Additionally, analysis of carbohydrate-active enzymes demonstrated that glycosyltransferases (GTs) and glycoside hydrolases (GHs) were abundant families in all PGPB strains, which is in favor of plant growth, and enriched in SA PGPB strains. Except for most Bacillus strains, SA PGPB genomes contained significantly more secondary metabolism clusters than LA PGPB. Most LA PGPB contained hormone biosynthesis genes, which may contribute to plant growth promotion, while SA PGPB harbored numerous carbohydrate and antibiotic metabolism genes. In summary, this study further deepens our understanding of the habitat adaptation and biocontrol characteristics of LA and SA PGPB strains. IMPORTANCE Plant growth-promoting bacteria (PGPB) are essential for the effectiveness of biocontrol agents in plant phyllosphere and rhizosphere. However, little is known about the ecological adaptation of PGPB to different habitats. In this study, comparative functional genome analysis of leaf-associated (LA), soil-associated (SA), and other-associated (OA) PGPB strains was performed. We found that genes related to the metabolism of hormones were enriched in LA PGPB. Carbohydrate and antibiotic metabolism genes were enriched in SA PGPB, which likely facilitated their adaptation to the plant growth environment. Our findings provide genetic insights on LA and SA PGPB strains' ecological adaptation and biocontrol characteristics.