The endosphere microbial communities, a great promise in agriculture

Microbial allies: exploring fungal endophytes for biosynthesis of terpenoid indole alkaloids

Terpenoid indole alkaloids (TIAs) are natural compounds found in medicinal plants that exhibit various therapeutic activities, such as antimicrobial, anti-inflammatory, antioxidant, anti-diabetic, anti-helminthic, and anti-tumor properties. However, the production of these alkaloids in plants is limited, and there is a high demand for them due to the increasing incidence of cancer cases. To address this research gap, researchers have focused on optimizing culture media, eliciting metabolic pathways, overexpressing genes, and searching for potential sources of TIAs in organisms other than plants. The insufficient number of essential genes and enzymes in the biosynthesis pathway is the reason behind the limited production of TIAs. As the field of natural product discovery from biological species continues to grow, endophytes are being investigated more and more as potential sources of bioactive metabolites with a variety of chemical structures. Endophytes are microorganisms (fungi, bacteria, archaea, and actinomycetes), that exert a significant influence on the metabolic pathways of both the host plants and the endophytic cells. Bio-prospection of fungal endophytes has shown the discovery of novel, high-value bioactive compounds of commercial significance. The discovery of therapeutically significant secondary metabolites has been made easier by endophytic entities' abundant but understudied diversity. It has been observed that fungal endophytes have better intermediate processing ability due to cellular compartmentation. This paper focuses on fungal endophytes and their metabolic ability to produce complex TIAs, recent advancements in this area, and addressing the limitations and future perspectives related to TIA production.

Promoting sustainable agriculture by exploiting plant growth-promoting rhizobacteria (PGPR) to improve maize and cowpea crops

Maize and cowpea are among the staple foods most consumed by most of the African population, and are of significant importance in food security, crop diversification, biodiversity preservation, and livelihoods. In order to satisfy the growing demand for agricultural products, fertilizers and pesticides have been extensively used to increase yields and protect plants against pathogens. However, the excessive use of these chemicals has harmful consequences on the environment and also on public health. These include soil acidification, loss of biodiversity, groundwater pollution, reduced soil fertility, contamination of crops by heavy metals, etc. Therefore, essential to find alternatives to promote sustainable agriculture and ensure the food and well-being of the people. Among these alternatives, agricultural techniques that offer sustainable, environmentally friendly solutions that reduce or eliminate the excessive use of agricultural inputs are increasingly attracting the attention of researchers. One such alternative is the use of beneficial soil microorganisms such as plant growth-promoting rhizobacteria (PGPR). PGPR provides a variety of ecological services and can play an essential role as crop yield enhancers and biological control agents. They can promote root development in plants, increasing their capacity to absorb water and nutrients from the soil, increase stress tolerance, reduce disease and promote root development. Previous research has highlighted the benefits of using PGPRs to increase agricultural productivity. A thorough understanding of the mechanisms of action of PGPRs and their exploitation as biofertilizers would present a promising prospect for increasing agricultural production, particularly in maize and cowpea, and for ensuring sustainable and prosperous agriculture, while contributing to food security and reducing the impact of chemical fertilizers and pesticides on the environment. Looking ahead, PGPR research should continue to deepen our understanding of these microorganisms and their impact on crops, with a view to constantly improving sustainable agricultural practices. On the other hand, farmers and agricultural industry players need to be made aware of the benefits of PGPRs and encouraged to adopt them to promote sustainable agricultural practices.

Selection of the Dominant Endophytes Based on Illumina Sequencing Analysis for Controlling Bacterial Wilt of Patchouli Caused by Ralstonia solanacearum

Bacterial wilt caused by Ralstonia solanacearum (RS) is one of the most devastating diseases in patchouli (Pogostemon cablin [Blanco] Benth.), which results in low yield and quality of patchouli. However, no stable and effective control methods have been developed yet. To evaluate the potential of dominant bacterial endophytes in biocontrol, the endophytic bacterial diversity of patchouli was investigated based on Illumina sequencing analysis, and the ability of isolates belonging to the dominant bacterial genera to control RS wilt of patchouli was explored in pot experiments. A total of 245 bacterial genera were detected in patchouli plants, with the highest relative abundance of operational taxonomic units belonging to the genus Pseudomonas detected in roots, leaves, and stems. The Pseudomonas isolates S02, S09, and S26 showed antagonistic activity against RS in vitro and displayed many plant growth-promoting characteristics, including production of indole-3-acetic acid, siderophores, and 1-aminocyclopropane-1-carboxylic acid deaminase and phosphate- and potassium-solubilizing capability. Inoculation of patchouli plants with the isolates S02, S09, and S26 significantly improved shoot growth and decreased the incidence of bacterial wilt caused by RS. The results suggest that screening of dominant bacterial endophytes for effective biocontrol agents based on Illumina sequencing analysis is more efficient than random isolation and screening procedures.

Fusarium Wilt Invasion Results in a Strong Impact on Strawberry Microbiomes

Plant-endophytic microbes affect plant growth, development, nutrition, and resistance to pathogens. However, how endophytic microbial communities change in different strawberry plant compartments after Fusarium pathogen infection has remained elusive. In this study, 16S and internal transcribed spacer rRNA amplicon sequencing were used to systematically investigate changes in the bacterial and fungal diversity and composition in the endophytic compartments (roots, stems, and leaves) of healthy strawberries and strawberries with Fusarium wilt, respectively. The analysis of the diversity, structure, and composition of the bacterial and fungal communities revealed a strong effect of pathogen invasion on the endophytic communities. The bacterial and fungal community diversity was lower in the Fusarium-infected endophytic compartments than in the healthy samples. The relative abundance of certain bacterial and fungal genera also changed after Fusarium wilt infection. The relative abundance of the beneficial bacterial genera Bacillus, Bradyrhizobium, Methylophilus, Sphingobium, Lactobacillus, and Streptomyces, as well as fungal genera Acremonium, Penicillium, Talaromyces, and Trichoderma, were higher in the healthy samples than in the Fusarium wilt samples. The relative abundance of Fusarium in the infected samples was significantly higher than that in the healthy samples, consistent with the field observations and culture isolation results for strawberry wilt. Our findings provide a theoretical basis for the isolation, identification, and control of strawberry wilt disease.

Endosphere microbial communities and plant nutrient acquisition toward sustainable agriculture

Endophytic microbial communities have essential information for scientists based on their biological contribution to agricultural practices. In the external plant environment, biotic and abiotic factors affect microbial populations before getting into plant tissues. Endophytes are involved in mutualistic and antagonistic activities with the host plant. Microbial communities inhabiting the internal tissues of plant roots depend on their ability to live and contend with other plant microflora. The advantageous ones contribute to soil health and plant growth either directly or indirectly. The microbial communities move via soil-root environment into the endosphere of plants promoting plant growth features like antibiosis, induced systemic resistance, phytohormone synthesis, and bioremediation. Therefore, the existence of these microorganisms contributes to plant genomes, nutrient availability in the soil, the presence of pathogens, and abiotic factors. This review aims at how endophytic microorganisms have displayed great interest in contributing to abundant crop production and phytopathogen inhibition.

The seed microbiomes of staple food crops

The scientific community increasingly recognized that seed microbiomes are important for plant growth and nutrition. The versatile roles and modulating properties that microbiomes hold in the context of seeds seem to be an inherited approach to avert adverse conditions. These discoveries attracted extensive interest, especially in staple food crops (SFCs) where grain was consumed as food. Along with the rapid expansion of population and industrialization that posed a severe challenge to the yield of SFCs, microbiologists and botanists began to explore and engineer seed microbiomes, for safer and more fruitful grain production. To utilize seed microbiomes, we present an overall review of the most updated scientific literature on three representative SFCs (wheat, rice and maize) using the 5W1H (Which, Where, What, Why, When and How) method that provides a comprehensive understanding of the issue. These include which factors determine the composition of seed microbiomes? Where do seed microbiomes come from? What are these seed microbes? Why do these microbes choose seeds as their destination and when do microbes settle down and become seed communists? In addition, how do seed microbiomes work and can be manipulated effectively? Therefore, answering the aforementioned questions regarding SFCs seed microbiomes remain fundamental in bridging endophytic research gaps and harnessing their ecological services.

Genomic Characteristics and Comparative Genomics Analysis of the Endophytic Fungus Paraphoma chrysanthemicola DS-84 Isolated from Codonopsis pilosula Root

Paraphoma chrysanthemicola is a newly identified endophytic fungus. The focus of most studies on P. chrysanthemicola has been on its isolation, identification and effects on plants. However, the limited genomic information is a barrier to further research. Therefore, in addition to studying the morphological and physiological characteristics of P. chrysanthemicola, we sequenced its genome and compared it with that of Paraphoma sp. The results showed that sucrose, peptone and calcium phosphate were suitable sources of carbon, nitrogen and phosphorus for this strain. The activities of amylase, cellulase, chitosanase, lipase and alkaline protease were also detected. Sequencing analysis revealed that the genome of P. chrysanthemicola was 44.1 Mb, with a scaffold N50 of 36.1 Mb and 37,077 protein-coding genes. Gene Ontology (GO) annotation showed that mannose-modified glycosylation was predominant in monosaccharide utilisation. The percentage of glycoside hydrolase (GH) modules was the highest in the carbohydrate-active enzymes database (CAZy) analysis. Secondary metabolite-associated gene cluster analysis identified melanin, dimethylcoprogen and phyllostictine A biosynthetic gene clusters (>60% similarity). The results indicated that P. chrysanthemicola had a mannose preference in monosaccharide utilisation and that melanin, dimethylcoprogen and phyllostictine A were important secondary metabolites for P. chrysanthemicola as an endophytic fungus.

Biodiversity of Endophytic Microbes in Diverse Tea Chrysanthemum Cultivars and Their Potential Promoting Effects on Plant Growth and Quality

The endophytic microbiomes significantly differed across tea chrysanthemum cultivars and organs (stems and leaves). The most abundant endophytic bacterial genera were Pseudomonas, Masillia, and Enterobacter in the leaves and Sphingomonas and Curtobacterium in the stems of the five cultivars. Meanwhile, the most abundant endophytic fungal genera in the leaves and stems of the five tea chrysanthemums were Alternaria, Cladosporium, and Sporobolomyces. Specifically, Rhodotorula was dominant in the leaves of 'Jinsi huangjv' and Paraphoma was dominant in the stems of 'Jinsi huangjv'. In all cultivars, the diversity and richness of endophytic bacteria were higher in leaves than in stems (p < 0.05). The highest diversity and richness of endophytic bacteria were recorded in 'Chujv', followed by 'Jinsi huangjv', 'Fubai jv', 'Nannong jinjv', and 'Hangbai jv'. Meanwhile, endophytic fungi were less pronounced. Twenty-seven and 15 cultivable endophytic bacteria and fungi were isolated, four isolated endophytic bacteria, namely, CJY1 (Bacillus oryzaecorticis), CY2 (Pseudomonas psychrotolerans), JSJ7, and JSJ17 (Enterobacter cloacae) showed higher indole acetic acid production ability. Further field studies indicated that inoculation of these four endophytic bacteria not only promoted plant growth and yield but also increased total flavonoids, chlorogenic acid, luteolin, and 3,5-dicoffeylquinic acid levels in the dry flowers of tea chrysanthemums.

A Pipeline to Investigate Fungal-Fungal Interactions: Trichoderma Isolates against Plant-Associated Fungi

Soil fungi play essential roles in ecosystems, forming complex interaction networks with bacteria, yeasts, other fungi, or plants. In the framework of biocontrol strategies, Trichoderma-based fungicides are at the forefront of research as an alternative to synthetic ones. However, the impact of introducing new microbial strain(s) on the soil microbiome of a habitat is not well-explored. Aiming to identify a quantitative method to explore the complex fungal interactions, we isolated twelve fungi from three Italian vineyards and identified three strains of the Trichoderma genus in addition to nine more plant-associated fungi of different genera. Investigating in dual nucleation assay fungal-fungal interactions, we recognised two types of interaction: neutral or antagonistic. All three Trichoderma strains displayed a slight inhibitory behaviour against themselves. Trichoderma strains showed a mutually intermingling growth with Aspergillus aculeatus and Rhizopus arrhizus but antagonistic behaviour against the plant pathogens Alternaria sp., Fusarium ramigenum, and Botrytis caroliniana. Yet, in some cases, antagonistic behaviour by Trichoderma fungi was also observed against plant-promoting fungi (e.g., Aspergillus piperis and Penicillium oxalicum). Our study highlights the importance of studying the interactions between fungi, aiming to clarify better the impact of fungal-based biological fungicides in the soil communities, and offers a pipeline for further applications.

Chemical Characterization and Metagenomic Identification of Endophytic Microbiome from South African Sunflower (Helianthus annus) Seeds

Helianthus annus (sunflower) is a globally important oilseed crop whose survival is threatened by various pathogenic diseases. Agrochemical products are used to eradicate these diseases; however, due to their unfriendly environmental consequences, characterizing microorganisms for exploration as biocontrol agents are considered better alternatives against the use of synthetic chemicals. The study assessed the oil contents of 20 sunflower seed cultivars using FAMEs-chromatography and characterized the endophytic fungi and bacteria microbiome using Illumina sequencing of fungi ITS 1 and bacteria 16S (V3-V4) regions of the rRNA operon. The oil contents ranged between 41-52.8%, and 23 fatty acid components (in varied amounts) were found in all the cultivars, with linoleic (53%) and oleic (28%) acids as the most abundant. Ascomycota (fungi) and Proteobacteria (bacteria) dominated the cultivars at the phyla level, while Alternaria and Bacillus at the genus level in varying abundance. AGSUN 5102 and AGSUN 5101 (AGSUN 5270 for bacteria) had the highest fungi diversity structure, which may have been contributed by the high relative abundance of linoleic acid in the fatty acid components. Dominant fungi genera such as Alternaria, Aspergillus, Aureobasidium, Alternariaste, Cladosporium, Penicillium, and bacteria including Bacillus, Staphylococcus, and Lactobacillus are established, providing insight into the fungi and bacteria community structures from the seeds of South Africa sunflower.

Enhanced legume growth and adaptation to degraded estuarine soils using Pseudomonas sp. nodule endophytes

The joint estuary of Tinto and Odiel rivers (SW Spain) is one of the most degraded and polluted areas in the world and its recovery is mandatory. Legumes and their associated bacteria are recommended sustainable tools to fight against soils degradation and loss of fertility due to their known positive impacts on soils. The aim of this work was to isolate and characterize plant growth promoting nodule endophytes (PGPNE) from inside nodules of Medicago spp. naturally growing in the estuary of the Tinto and Odiel Rivers and evaluate their ability to promote legume adaptation in degraded soils. The best rhizobia and non-rhizobia among 33 endophytes were selected based on their plant growth promoting properties and bacterial enzymatic activities. These strains, identified as Pseudomonas sp. N4, Pseudomonas sp. N8, Ensifer sp. N10 and Ensifer sp. N12, were used for in vitro studies using Medicago sativa plants. The effects of individual or combined inoculation on seed germination, plant growth and nodulation were studied, both on plates and pots containing nutrient-poor soils and moderately contaminated with metals/loids from the estuary. In general, inoculation with combinations of rhizobia and Pseudomonas increased plant biomass (up to 1.5-fold) and nodules number (up to 2-fold) compared to single inoculation with rhizobia, ameliorating the physiological state of the plants and helping to regulate plant stress mechanisms. The greatest benefits were observed in plants inoculated with the consortium containing the four strains. In addition, combined inoculation with Ensifer and Pseudomonas increased As and metals accumulation in plant roots, without significant differences in shoot metal accumulation. These results suggest that PGPNE are useful biotools to promote legume growth and phytostabilization potential in nutrient-poor and/or metals contaminated estuarine soils.

Colonization characteristics of fungi in Polygonum hydropipe L. and Polygonum lapathifolium L. and its effect on the content of active ingredients

Polygonum hydropiper, is a plant of the Persicaria genus, which is commonly used to treat various diseases, including gastrointestinal disorders, neurological disorders, inflammation, and diarrhea. However, because of different local standards of P. hydropiper, people often confuse it with Polygonum lapathifolium L. and other closely related plants. This poses a serious threat to the safety and efficacy of the clinical use of P. hydropiper. This study aims to determine the six active ingredients of P. hydropiper and P. lapathifolium. Then the endophytic fungi and rhizosphere soil of the two species were sequenced by Illumina Miseq PE300. The results show significant differences between the community composition of the leaves, stems, and roots of the P. hydropiper and the P. lapathifolium in the same soil environment. Of the six secondary metabolites detected, five had significant differences between P. hydropiper and P. lapathifolium. Then, we evaluated the composition of the significantly different communities between P. hydropiper and P. lapathifolium. In the P. hydropiper, the relative abundance of differential communities in the leaves was highest, of which Cercospora dominated the differential communities in the leaves and stem; in the P. lapathifolium, the relative abundance of differential community in the stem was highest, and Cladosporium dominated the differential communities in the three compartments. By constructing the interaction network of P. hydropiper and P. lapathifolium and analyzing the network nodes, we found that the core community in P. hydropiper accounted for 87.59% of the total community, dominated by Cercospora; the core community of P. lapathifolium accounted for 19.81% of the total community, dominated by Sarocladium. Of these core communities, 23 were significantly associated with active ingredient content. Therefore, we believe that the community from Cercospora significantly interferes with recruiting fungal communities in P. hydropiper and affects the accumulation of secondary metabolites in the host plant. These results provide an essential foundation for the large-scale production of P. hydropiper. They indicate that by colonizing specific fungal communities, secondary metabolic characteristics of host plants can be helped to be shaped, which is an essential means for developing new medicinal plants.

Biocontrol of early blight disease of eggplant using endophytic Aspergillus terreus: improving plant immunological, physiological and antifungal activities

BACKGROUND

The eggplant suffers from many biotic stresses that cause severe damage to crop production. One of the most destructive eggplant pathogens is Alternaria solani, which causes early blight disease. A pot experiment was conducted to evaluate the role of fungal endophytes in protecting eggplant against early blight as well as in improving its growth performance.

RESULTS

Endophytic Aspergillus terreus was isolated from Ocimum basilicum leaves and identified morphologically and genetically. In vitro, crude extract of endophytic A. terreus exhibited promising antifungal activity against A. solani where minimum inhibitory concentration (MIC) was 1.25 mg/ml. Severity of the disease and rate of protection from the disease were recorded. Vegetative growth indices, physiological resistance signs (photosynthetic pigments, carbohydrates, proteins, phenols, proline, malondialdehyde (MDA), antioxidant enzymes), and isozymes were estimated. Alternaria solani caused a highly disease severity (87.5%) and a noticeable decreasing in growth characteristics and photosynthetic pigments except for carotenoids. Also, infection with A. solani caused significant decreases in the contents of carbohydrate and protein by 29.94% and 10.52%, respectively. Infection with A. solani caused enhancement in phenolics (77.21%), free proline (30.56%), malondialdehyde (30.26%), superoxide dismutase (SOD) (125.47%), catalase (CAT) (125.93%), peroxidase (POD) (25.07%) and polyphenol oxidase (PPO) (125.37%) compared to healthy plants. In contrast, the use of A. terreus on infected plants succeeded in recovering eggplants from the disease, as the disease severity was recorded (caused protection by 66.67%). Application of A. terreus either on healthy or infected eggplants showed several responses in number and density of peroxidase (POD) and polyphenol oxidase (PPO) isozymes.

CONCLUSION

It is necessary for us to address the remarkable improvement in the photosynthetic pigments, protein, carbohydrates, and enzymatic activity compared to infected control, which opens the way for more studies on the use of biocides as safe alternatives against fungal diseases.

Is Endophytic Colonization of Host Plants a Method of Alleviating Drought Stress? Conceptualizing the Hidden World of Endophytes

In the wake of changing climatic conditions, plants are frequently exposed to a wide range of biotic and abiotic stresses at various stages of their development, all of which negatively affect their growth, development, and productivity. Drought is one of the most devastating abiotic stresses for most cultivated crops, particularly in arid and semiarid environments. Conventional breeding and biotechnological approaches are used to generate drought-tolerant crop plants. However, these techniques are costly and time-consuming. Plant-colonizing microbes, notably, endophytic fungi, have received increasing attention in recent years since they can boost plant growth and yield and can strengthen plant responses to abiotic stress. In this review, we describe these microorganisms and their relationship with host plants, summarize the current knowledge on how they “reprogram” the plants to promote their growth, productivity, and drought tolerance, and explain why they are promising agents in modern agriculture.

Bacterial Community with Plant Growth-Promoting Potential Associated to Pioneer Plants from an Active Mexican Volcanic Complex

Microorganisms in extreme volcanic environments play an important role in the development of plants on newly exposed substrates. In this work, we studied the structure and diversity of a bacterial community associated to Andropogon glomeratus and Cheilanthes aemula at El Chichón volcano. The genetic diversity of the strains was revealed by genomic fingerprints and by 16S rDNA gene sequencing. Furthermore, a metagenomic analysis of the rhizosphere samples was carried out for pioneer plants growing inside and outside the volcano. Multifunctional biochemical tests and plant inoculation assays were evaluated to determine their potential as plant growth-promoting bacteria (PGPB). Through metagenomic analysis, a total of 33 bacterial phyla were identified from A. glomeratus and C. aemula rhizosphere samples collected inside the volcano, and outside the volcano 23 bacterial phyla were identified. For both rhizosphere samples, proteobacteria was the most abundant phylum. With a cultivable approach, 174 bacterial strains were isolated from the rhizosphere and tissue of plants growing outside the volcanic complex. Isolates were classified within the genera Acinetobacter, Arthrobacter, Bacillus, Burkholderia, Cupriavidus, Enterobacter, Klebsiella, Lysinibacillus, Pantoea, Pseudomonas, Serratia, Stenotrophomonas and Pandoraea. The evaluated strains were able to produce indole compounds, solubilize phosphate, synthesize siderophores, showed ACC deaminase and nitrogenase activity, and they had a positive effect on the growth and development of Capsicum chinense. The wide diversity of bacteria associated to pioneer plants at El Chichón volcano with PGPB qualities represent an alternative for the recovery of eroded environments, and they can be used efficiently as biofertilizers for agricultural crops growing under adverse conditions.

The Effects of Plant Health Status on the Community Structure and Metabolic Pathways of Rhizosphere Microbial Communities Associated with Solanum lycopersicum

Powdery mildew disease caused by Oidium neolycopersici is one of the major diseases affecting tomato production in South Africa. Interestingly, limited studies exist on how this disease affects the community structure microbial communities associated with tomato plants employing shotgun metagenomics. In this study, we assess how the health status of a tomato plant affects the diversity of the rhizosphere microbial community. We collected soil samples from the rhizosphere of healthy (HR) and diseased (DR; powdery mildew infected) tomatoes, alongside bulk soil (BR), extracted DNA, and did sequencing using shotgun metagenomics. Our results demonstrated that the rhizosphere microbiome alongside some specific functions were abundant in HR followed by DR and bulk soil (BR) in the order HR > DR > BR. We found eighteen (18) bacterial phyla abundant in HR, including Actinobacteria, Acidobacteria, Aquificae, Bacteroidetes, etc. The dominant fungal phyla include; Ascomycota and Basidiomycota, while the prominent archaeal phyla are Thaumarchaeota, Crenarchaeota, and Euryarchaeota. Three (3) bacteria phyla dominated the DR samples; Bacteroidetes, Gemmatimonadetes, and Thermotoga. Our result also employed the SEED subsystem and revealed that the metabolic pathways involved were abundant in HR. The α-diversity demonstrates that there is no significant difference among the rhizosphere microbiomes across the sites, while β-diversity demonstrated a significant difference.

Bacterial community structure of the sunflower (Helianthus annuus) endosphere

Agrochemical applications on farmland aim to enhance crop yield; however, the consequence of biodiversity loss has caused a reduction in ecological functions. The positive endosphere interactions and crop rotation systems may function in restoring a stable ecosystem. Employing culture-independent techniques will help access the total bacteria community in the sunflower endosphere. Limited information is available on the bacteria diversity in sunflower plants cultivated under different agricultural practices. Hence, this study was designed to investigate the endophytic bacterial community structure of sunflower at the growing stage. Plant root and stem samples were sourced from two locations (Itsoseng and Lichtenburg), for DNA extraction and sequenced on the Illumina Miseq platform. The sequence dataset was analyzed using online bioinformatics tools. Saccharibacteria and Acidobacteria were dominant in plant roots, while the stem is dominated by Proteobacteria, Bacteriodetes, and Gemmatimonadetes across the sites. Bacterial genera, Acidovorax, Flavobacterium, Hydrogenophaga, and Burkholderia-Paraburkhoderia were found dominant in the root, while the stem is dominated by Streptomyces. The diverse bacterial community structure at phyla and class levels were significantly different in plant organs across the sites. The influence of soil physical and chemical parameters analyzed was observed to induce bacterial distribution across the sites. This study provides information on the dominant bacteria community structure in sunflowers at the growing stage and their predictive functions, which suggest their future exploration as bioinoculants for improved agricultural yields.

Genomic assessment of Stenotrophomonas indicatrix for improved sunflower plant

Diverse agriculturally important microbes have been studied with known potential in plant growth promotion. Providing several opportunities, Stenotrophomonas species are characterized as promising plant enhancers, inducers, and protectors against environmental stressors. The S. indicatrix BOVIS40 isolated from the sunflower root endosphere possessed unique features, as genome insights into the Stenotrophomonas species isolated from oilseed crops in Southern Africa have not been reported. Plant growth-promotion screening and genome analysis of S. indicatrix BOVIS40 were presented in this study. The genomic information reveals various genes underlining plant growth promotion and resistance to environmental stressors. The genome of S. indicatrix BOVIS40 harbors genes involved in the degradation and biotransformation of organic molecules. Also, other genes involved in biofilm production, chemotaxis, and flagellation that facilitate bacterial colonization in the root endosphere and phytohormone genes that modulate root development and stress response in plants were detected in strain BOVIS40. IAA activity of the bacterial strain may be a factor responsible for root formation. A measurable approach to the S. indicatrix BOVIS40 lifestyle can strategically provide several opportunities in their use as bioinoculants in developing environmentally friendly agriculture sustainably. The findings presented here provide insights into the genomic functions of S. indicatrix BOVIS40, which has set a foundation for future comparative studies for a better understanding of the synergism among microbes inhabiting plant endosphere. Hence, highlighting the potential of S. indicatrix BOVIS40 upon inoculation under greenhouse experiment, thus suggesting its application in enhancing plant and soil health sustainably.

The plant endosphere-hidden treasures: a review of fungal endophytes

The endosphere represents intracellular regions within plant tissues colonize by microbial endophytes without causing disease symptoms to host plants. Plants harbor one or two endophytic microbes capable of synthesizing metabolite compounds. Environmental factors determine the plant growth and survival as well as the kind of microorganisms associated with them. Some fungal endophytes that symbiotically colonize the endosphere of medicinal plants with the potential of producing biological products have been employed in traditional and modern medicine. The bioactive resources from endophytic fungi are promising; biotechnologically to produce cheap and affordable commercial bioactive products as alternatives to chemical drugs and other compounds. The exploration of bioactive metabolites from fungal endophytes has been found applicable in agriculture, pharmaceutical, and industries. Thus, fungal endophytes can be engineered to produce a substantive quantity of pharmacological drugs through the biotransformation process. Hence, this review shall provide an overview of fungal endophytes, ecology, their bioactive compounds, and exploration with the biosystematics approach.

Genomic Analysis of Endophytic Bacillus cereus T4S and Its Plant Growth-Promoting Traits

Insights into plant endophytic microbes and their exploration in agriculture have provided opportunities for sustainable plant health and food safety. Notable endophytic Bacillus species with plant growth-promoting traits have been documented; nevertheless, information on genome analysis of B. cereus associated with the sunflower in South Africa has not been studied. Therefore, we present whole-genome sequence of agriculturally important B. cereus strain T4S isolated from sunflower plants. The NextSeq Illumina sequencing yielded 7,255,762 bp sequence reads, 151 bp average read length, 5,945,881 bp genome size, 56 tRNA, 63 rRNA, and G + C content of 34.8%. The phylogeny analysis of strain T4S was similar to B. cereus NJ-W. Secondary metabolites, such as petrobactin, bacillibactin, bacitracin, molybdenum factor, zwittermicin, and fengycin underlining bacterial biocontrol efficacy against phytopathogens were found in the T4S genome. The predicted novel genes in the bacterial genome mediating the complex metabolic pathways can provide a genetic basis in understanding endosphere biology and their multiple functions thereof in crop improvement. Interestingly, seed and root inoculation with strain T4S contributed to sunflower yield under greenhouse experiments. Hence, the detection of notable genes specific for plant growth promotion as validated under in vitro screening, promisingly, suggests the relevance of strain T4S in agricultural biotechnology.

Whole Genome Sequencing of Sunflower Root-Associated Bacillus cereus

In recent times, diverse agriculturally important endophytic bacteria colonizing plant endosphere have been identified. Harnessing the potential of Bacillus species from sunflower could reveal their biotechnological and agricultural importance. Here, we present genomic insights into B. cereus T4S isolated from sunflower sourced from Lichtenburg, South Africa. Genome analysis revealed a sequence read count of 7 255 762, a genome size of 5 945 881 bp, and G + C content of 34.8%. The genome contains various protein-coding genes involved in various metabolic pathways. The detection of genes involved in the metabolism of organic substrates and chemotaxis could enhance plant-microbe interactions in the synthesis of biological products with biotechnological and agricultural importance.

Microbial-Assisted Wheat Iron Biofortification Using Endophytic Bacillus altitudinis WR10

Microbial-assisted biofortification attracted much attention recently due to its sustainable and eco-friendly nature for improving nutrient content in wheat. An endophytic strain Bacillus altitudinis WR10, which showed sophistical regulation of iron (Fe) homeostasis in wheat seedlings, inspired us to test its potential for enhancing Fe biofortification in wheat grain. In this study, assays in vitro indicated that WR10 has versatile plant growth-promoting (PGP) traits and bioinformatic analysis predicted its non-pathogenicity. Two inoculation methods, namely, seed soaking and soil spraying, with 10⁷ cfu/ml WR10 cells were applied once before sowing of wheat (Triticum aestivum L. cv. Zhoumai 36) in the field. After wheat maturation, evaluation of yield and nutrients showed a significant increase in the mean number of kernels per spike (KPS) and the content of total nitrogen (N), potassium (K), and Fe in grains. At the grain filling stage, the abundance of Bacillus spp. and the content of N, K, and Fe in the root, the stem, and the leaf were also increased in nearly all tissues, except Fe in the stem and the leaf. Further correlation analysis revealed a positive relationship between the total abundance of Bacillus spp. and the content of N, K, and Fe in grains. Seed staining confirmed the enhanced accumulation of Fe, especially in the embryo and the endosperm. Finally, using a hydroponic coculture model, qPCR quantification indicated effective colonization, internalization, translocation, and replication of strain WR10 in wheat within 48 h. Collectively, strain WR10 assisted successful Fe biofortification in wheat in the field, laying a foundation for further large-scale investigation of its applicability and effectiveness.

Leaf infiltration in plant science: old method, new possibilities

The penetration of substances from the surface to deep inside plant tissues is called infiltration. Although various plant tissues may be effectively saturated with externally applied fluid, most described infiltration strategies have been developed for leaves. The infiltration process can be spontaneous (under normal atmospheric pressure) or forced by a pressure difference generated between the lamina surface and the inside of the leaf. Spontaneous infiltration of leaf laminae is possible with the use of liquids with sufficiently low surface tension. Forced infiltration is most commonly performed using needle-less syringes or vacuum pumps.Leaf infiltration is widely used in plant sciences for both research and application purposes, usually as a starting technique to obtain plant material for advanced experimental procedures. Leaf infiltration followed by gentle centrifugation allows to obtain the apoplastic fluid for further analyses including various omics. In studies of plant-microorganism interactions, infiltration is used for the controlled introduction of bacterial suspensions into leaf tissues or for the isolation of microorganisms inhabiting apoplastic spaces of leaves. The methods based on infiltration of target tissues allow the penetration of dyes, fixatives and other substances improving the quality of microscopic imaging. Infiltration has found a special application in plant biotechnology as a method of transient transformation with the use of Agrobacterium suspension (agroinfiltration) enabling genetic modifications of mature plant leaves, including the local induction of mutations using genome editing tools. In plant nanobiotechnology, the leaves of the target plants can be infiltrated with suitably prepared nanoparticles, which can act as light sensors or increase the plant resistance to environmental stress. In addition the infiltration has been also intensively studied due to the undesirable effects of this phenomenon in some food technology sectors, such as accidental contamination of leafy greens with pathogenic bacteria during the vacuum cooling process.This review, inspired by the growing interest of the scientists from various fields of plant science in the phenomenon of infiltration, provides the description of different infiltration methods and summarizes the recent applications of this technique in plant physiology, phytopathology and plant (nano-)biotechnology.

Genomic assessment of Stenotrophomonas indicatrix for improved sunflower plant

Diverse agriculturally important microbes have been studied with known potential in plant growth promotion. Providing several opportunities, Stenotrophomonas species are characterized as promising plant enhancers, inducers, and protectors against environmental stressors. The S. indicatrix BOVIS40 isolated from the sunflower root endosphere possessed unique features, as genome insights into the Stenotrophomonas species isolated from oilseed crops in Southern Africa have not been reported. Plant growth-promotion screening and genome analysis of S. indicatrix BOVIS40 were presented in this study. The genomic information reveals various genes underlining plant growth promotion and resistance to environmental stressors. The genome of S. indicatrix BOVIS40 harbors genes involved in the degradation and biotransformation of organic molecules. Also, other genes involved in biofilm production, chemotaxis, and flagellation that facilitate bacterial colonization in the root endosphere and phytohormone genes that modulate root development and stress response in plants were detected in strain BOVIS40. IAA activity of the bacterial strain may be a factor responsible for root formation. A measurable approach to the S. indicatrix BOVIS40 lifestyle can strategically provide several opportunities in their use as bioinoculants in developing environmentally friendly agriculture sustainably. The findings presented here provide insights into the genomic functions of S. indicatrix BOVIS40, which has set a foundation for future comparative studies for a better understanding of the synergism among microbes inhabiting plant endosphere. Hence, highlighting the potential of S. indicatrix BOVIS40 upon inoculation under greenhouse experiment, thus suggesting its application in enhancing plant and soil health sustainably.

Rhizosphere Microbiome Cooperations: Strategies for Sustainable Crop Production

Interactions between microorganisms and host plants determine the growth and development as well as the health of the host plant. Various microbial groups inhabit the rhizosphere, each with its peculiar function. The survival of each microbial group depends to a large extent on its ability to colonize the plant root and outcompete the native organisms. The role of the rhizospheric microbiome in enhancing plant growth has not been fully maximized. An understanding of the complexities of microbial interactions and factors affecting their assembly in the community is necessary to benefit maximally from the cooperations of various microbial communities for sustainable crop production. In this review, we outline the various organisms associated with the plant rhizosphere with emphasis on their interactions and mechanisms used in plant growth promotion.

Pharmacological Potential of Fungal Endophytes Associated with Medicinal Plants: A Review

Endophytic microbes are microorganisms that colonize the intracellular spaces within the plant tissues without exerting any adverse or pathological effects. Currently, the world population is facing devastating chronic diseases that affect humans. The resistance of pathogens to commercial antibiotics is increasing, thus limiting the therapeutic potential and effectiveness of antibiotics. Consequently, the need to search for novel, affordable and nontoxic natural bioactive compounds from endophytic fungi in developing new drugs with multifunction mechanisms to meet human needs is essential. Fungal endophytes produce invaluable bioactive metabolic compounds beneficial to humans with antimicrobial, anticancer, antidiabetic, anti-inflammatory, antitumor properties, etc. Some of these bioactive compounds include pestacin, taxol, camptothecin, ergoflavin, podophyllotoxin, benzopyran, isopestacin, phloroglucinol, tetrahydroxy-1-methylxanthone, salidroside, borneol, dibenzofurane, methyl peniphenone, lipopeptide, peniphenone etc. Despite the aforementioned importance of endophytic fungal metabolites, less information is available on their exploration and pharmacological importance. Therefore, in this review, we shall elucidate the fungal bioactive metabolites from medicinal plants and their pharmacological potential.

Plant-microbiome interactions for sustainable agriculture: a review

Plant-microbiome interactions are significant determinant for plant growth, fitness and productivity. Depending upon the specific habitat, plants' microbial communities are classified as the rhizo-, phyllo-, and endospheric regions. Understanding the plant microbiome interactions could provide an opportunity to develop strategies for sustainable agricultural practices. There is a necessity to decipher the complex structural and functional diversity within plant microbiomes to reveal its immense potential in agriculture. The plant microbiota harbors enormous microbial communities that defy analytical methodologies to study dynamics underlying plant microbiome interactions. Findings based on conventional approaches have ignored many beneficial microbial strains, which creates a serious gap in understanding the microbial communications along with the genetic adaptations, which favors their association with host plant. The new era of next generation sequencing techniques and modern cost-effective high-throughput molecular approaches can decipher microbial community composition and function. In this review, we have presented the overview of the various compartments of plants, approaches to allow the access to microbiome and factors that influence microbial community composition and function. Next, we summarize how plant microbiome interactions modulate host beneficial properties particularly nutrient acquisition and defense, along with future agricultural applications.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at. 10.1007/s12298-021-00927-1.

Plant Disease Management: Leveraging on the Plant-Microbe-Soil Interface in the Biorational Use of Organic Amendments

Agriculture is faced with many challenges including loss of biodiversity, chemical contamination of soils, and plant pests and diseases, all of which can directly compromise plant productivity and health. In addition, inadequate agricultural practices which characterize conventional farming play a contributory role in the disruption of the plant-microbe and soil-plant interactions. This review discusses the role of organic amendments in the restoration of soil health and plant disease management. While the use of organic amendments in agriculture is not new, there is a lack of knowledge regarding its safe and proper deployment. Hence, a biorational approach of organic amendment use to achieve sustainable agricultural practices entails the deployment of botanicals, microbial pesticides, and organic minerals as organic amendments for attaining plant fitness and disease suppression. Here, the focus is on the rhizosphere microbial communities. The role of organic amendments in stimulating beneficial microbe quorum formation related to the host-plant-pathogen interactions, and its role in facilitating induced systemic resistance and systemic-acquired resistance against diseases was evaluated. Organic amendments serve as soil conditioners, and their mechanism of action needs to be further elaborated to ensure food safety.