Agricultural and Other Biotechnological Applications Resulting from Trophic Plant-Endophyte Interactions

Variations in the structure and function of the soil fungal communities in the traditional cropping systems from Madeira Island

Agricultural soils are responsible for ecological functions and services that include primary production of food, fiber and fuel, nutrient cycling, carbon cycling and storage, water infiltration and purification, among others. Fungi are important drivers of most of those ecosystem services. Given the importance of fungi in agricultural soils, in this study, we aimed to characterize and analyse the changes of the soil fungal communities of three cropping systems from Madeira Island, where family farming is predominant, and investigate the response of fungi and its functional groups to soil physicochemical properties. To achieve that, we sequenced amplicons targeting the internal transcribed spacer 1 (ITS1) of the rRNA region, to analyse soil samples from 18 agrosystems: 6 vineyards (V), 6 banana plantations (B) and 6 vegetable plantations (H). Our results showed that alpha diversity indices of fungal communities are similar in the three cropping systems, but fungal composition and functional aspects varied among them, with more pronounced differences in B. Ascomycota, Basidiomycota, and Mortierellomycota were the main phyla found in the three cropping systems. Agaricomycetes and Sordariomycetes are the predominant classes in B, representing 23.8 and 22.4%, respectively, while Sordariomycetes (27.9%) followed by Eurotiomycetes (12.3%) were the predominant classes in V and Sordariomycetes (39.2%) followed by Tremellomycetes (8.9%) in the H. Saprotrophs are the fungal group showing higher relative abundance in the three cropping systems, followed by plant pathogens. Regarding symbionts, endophytes were highly observed in B, while mycorrhizal fungi was predominant in V and H. The structure of fungal communities was mainly correlated with soil content of P, K, N, Fe, and Cu. In addition, we identified bioindicators for each cropping system, which means that cultivated crops are also drivers of functional groups and the composition of communities. Overall, the three cropping systems favored diversity and growth of taxa that play important roles in soil, which highlights the importance of conservative management practices to maintain a healthy and resilient agrosystem.

Low microbial diversity, yeast prevalence, and nematode-trapping fungal presence in fungal colonization and leaf microbiome of Serjania erecta

Medicinal plant microbiomes undergo selection due to secondary metabolite presence. Resident endophytic/epiphytic microorganisms directly influence plant's bioactive compound synthesis. Hypothesizing low microbial diversity in Serjania erecta leaves, we assessed leaf colonization by epiphytic and endophytic fungi. Given its traditional medicinal importance, we estimated diversity in the endophytic fungal microbiome. Analyses included scanning electron microscopy (SEM), isolation of cultivable species, and metagenomics. Epiphytic fungi interacted with S. erecta leaf tissues, horizontally transmitted via stomata/trichome bases, expressing traits for nematode trapping. Cultivable endophytic fungi, known for phytopathogenic habits, didn't induce dysbiosis symptoms. This study confirms low leaf microbiome diversity in S. erecta, with a tendency towards more fungal species, likely due to antibacterial secondary metabolite selection. The classification of Halicephalobus sp. sequence corroborated the presence of nematode eggs on the epidermal surface of S. erecta by SEM. In addition, we confirmed the presence of methanogenic archaea and a considerable number of methanotrophs of the genus Methylobacterium. The metagenomic study of endophytic fungi highlighted plant growth-promoting yeasts, mainly Malassezia, Leucosporidium, Meyerozyma, and Hannaella. Studying endophytic fungi and S. erecta microbiomes can elucidate their impact on beneficial bioactive compound production, on the other hand, it is possible that the bioactive compounds produced by this plant can recruit specific microorganisms, impacting the biological system.

A review on endophytic fungi: a potent reservoir of bioactive metabolites with special emphasis on blight disease management

Phytopathogenic microorganisms have caused blight diseases that present significant challenges to global agriculture. These diseases result in substantial crop losses and have a significant economic impact. Due to the limitations of conventional chemical treatments in effectively and sustainably managing these diseases, there is an increasing interest in exploring alternative and environmentally friendly approaches for disease control. Using endophytic fungi as biocontrol agents has become a promising strategy in recent years. Endophytic fungi live inside plant tissues, forming mutually beneficial relationships, and have been discovered to produce a wide range of bioactive metabolites. These metabolites demonstrate significant potential for fighting blight diseases and provide a plentiful source of new biopesticides. In this review, we delve into the potential of endophytic fungi as a means of biocontrol against blight diseases. We specifically highlight their significance as a source of biologically active compounds. The review explores different mechanisms used by endophytic fungi to suppress phytopathogens. These mechanisms include competing for nutrients, producing antifungal compounds, and triggering plant defense responses. Furthermore, this review discusses the challenges of using endophytic fungi as biocontrol agents in commercial applications. It emphasizes the importance of conducting thorough research to enhance their effectiveness and stability in real-world environments. Therefore, bioactive metabolites from endophytic fungi have considerable potential for sustainable and eco-friendly blight disease control. Additional research on endophytes and their metabolites will promote biotechnology solutions.

Functional differences of cultivable leaf-associated microorganisms in the native Andean tree Gevuina avellana Mol. (Proteaceae) exposed to atmospheric contamination

AIMS

This study aimed to evaluate and describe the functional differences of cultivable bacteria and fungi inhabiting the leaves of Gevuina avellana Mol. (Proteaceae) in an urban area with high levels of air pollution and in a native forest in the southern Andes.

METHODS AND RESULTS

Phyllosphere microorganisms were isolated from the leaves of G. avellana, their plant growth-promoting capabilities were estimated along with their biocontrol potential and tolerance to metal(loid)s. Notably, plants from the urban area showed contrasting culturable leaf-associated microorganisms compared to those from the native area. The tolerance to metal(loid)s in bacteria range from 15 to 450 mg l-1 of metal(loid)s, while fungal strains showed tolerance from 15 to 625 mg l-1, being especially higher in the isolates from the urban area. Notably, the bacterial strain Curtobacterium flaccumfaciens and the fungal strain Cladosporium sp. exhibited several plant-growth-promoting properties along with the ability to inhibit the growth of phytopathogenic fungi.

CONCLUSIONS

Overall, our study provides evidence that culturable taxa in G. avellana leaves is directly influenced by the sampling area. This change is likely due to the presence of atmospheric pollutants and diverse microbial symbionts that can be horizontally acquired from the environment.

Changes of microbiome in response to supplements with silver nanoparticles in cotton rhizosphere

The current study focuses on analyzing the effects of supplements containing silver nanoparticles (AgNPs) on plant growth and rhizospheric bacterial communities. Specifically, the impact of AgNP supplements was assessed on both plant growth promoting traits and bacterial communities in the soil. To do this, a screening process was conducted to select bacteria capable of synthesizing AgNPs through extracellular biosynthesis. UV-Visible spectrophotometer, Fourier transform infrared, X-ray diffraction, scanning electron microscope, and field emission scanning electron microscopy all confirmed, produced AgNPs is in agglomerates form. The resulting AgNPs were introduced into soil along with various supplements and their effects were evaluated after 10 days using next generation sequencing (Illumina-16S rDNA V3-V4 region dependent) to analyze changes in bacterial communities. Seed germination, root-shoot biomass and chlorophyll content were used to assess the growth of the cotton plant, whereas the bacterial ability to promote growth was evaluated by measuring its culturable diversity including traits like phosphate solubilization and indole acetic acid production. The variance in Bray-Curtis β diversity among six selected combinations including control depends largely on the type of added supplements contributing to 95%-97% of it. Moreover, seed germination improves greatly between 63% and 100% at a concentration range of 1.4 to 2.8 mg/L with different types of supplements. Based on the results obtained through this study, it is evident that using AgNPs along with fructose could be an effective tool for promoting Gossypium hirsutum growth and enhancing plant growth traits like profiling rhizospheric bacteria. The results that have been obtained endorse the idea of boosting the growth of rhizospheric bacteria in a natural way when AgNPs are present. Using these supplements in fields that have been contaminated will lead to a better understanding of how ecological succession occurs among rhizospheric bacteria, and what effect it has on the growth of plants.

Plant growth-promoting traits of culturable seed microbiome of citrus species from Purvanchal Himalaya

Despite Northeastern India being "Treasure House of Citrus Genetic Wealth," genetic erosion of citrus diversity poses severe concern with a corresponding loss in seed microbial diversity. The seed microbiome of citrus species unique to the Purvanchal Himalaya is seldom explored for their use in sustainable orchard management. Isolation and characterization of culturable seed microbiomes of eight citrus species, namely, Citrus reticulata Blanco, C. grandis (L.) Osbeck, C. latipes Tanaka, C. megaloxycarpa Lushaigton, C. jambhiri Lush, C. sinensis (L.) Osbeck, C. macroptera Montr, and C. indica Tanaka collected from NE India were carried out. The isolates were then screened for an array of plant growth-promoting (PGP) traits [indole acetic acid (IAA) production, N₂ fixation, phosphate and zinc complex dissolution, siderophores, and Hydrogen Cyanide (HCN) production]. The pure culture isolates of seed microbiomes were capable of dissolving insoluble Ca₃(PO₄)₂ (1.31-4.84 µg Pi ml^-1 h^-1), Zn₃(PO₄)₂ (2.44-3.16 µg Pi ml^-1 h^-1), AlPO₄ (1.74-3.61 µg Pi ml^-1 h^-1), and FePO₄ (1.54-4.61µg Pi ml^-1 h^-1), mineralized phytate (12.17-18.00 µg Pi ml^-1 h^-1) and produced IAA-like substances (4.8-187.29 µg ml^-1 h^-1). A few isolates of the seed microbiome were also able to fix nitrogen, secrete siderophore-like compounds and HCN, and dissolve ZnSO₄ and ZnO. The 16S ribosomal Ribonucleic Acid (rRNA)-based taxonomic findings revealed that Bacillus was the most dominant genus among the isolates across citrus species. Isolates CG2-1, CME6-1, CME6-4, CME6-5, CME6-9, CJ7-1, CMA10-1, CI11-3, and CI11-4 were identified as promising bioinoculants for development of microbial consortium having multifaceted PGP traits for nutritional benefits of nitrogen, phosphorus and zinc, and IAA hormonal benefits to citrus crops for better fitness in acid soils.

Microbial Endophytes: Emerging Trends and Biotechnological Applications

A plethora of knowledge on the role of endophytic microorganisms has been reported in recent years. The cooperative chemistry between the endophytes and the internal host tissue has turned them into a crucial aid for biotechnological applications. Microbial endophytes are ubiquitous among most plant species on earth and contribute to the benefit of host plants by generating a wide range of metabolites that provide the plant with survival value. Endophytes can either directly stimulate plant growth by producing phytohormones or indirectly stimulate plant growth by increasing the availability of soil nutrients to plants. Endophytes may also help suppress diseases in plants directly by neutralizing environmental toxic elements, and by inhibiting plant pathogens by antagonistic action, or indirectly by stimulating induced plant systemic resistance. Several natural compounds produced by endophytes as secondary metabolites are beneficial to both plants and humans. This is why endophytes are regarded as a significant source of novel natural products of value in modern medicine, agriculture, and industry. Endophytes are known for producing pigments, bioactive compounds, and industrially important enzymes, like glucanase, amylase, laccase, etc. Some endophytes can also produce nanoparticles that potentially have numerous applications in a variety of fields. They also play an important role in biodegradation and bioremediation, both of which are beneficial to the environment and ecology. In this review, we highlighted potential biotechnological applications of endophytic microbes, as well as their diverse importance in plant growth and public health.

Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria

This review evaluates oilseed crop soybean endophytic bacteria, their prospects, and challenges for sustainable agriculture. Soybean is one of the most important oilseed crops with about 20-25% protein content and 20% edible oil production. The ability of soybean root-associated microbes to restore soil nutrients enhances crop yield. Naturally, the soybean root endosphere harbors root nodule bacteria, and endophytic bacteria, which help increase the nitrogen pool and reclamation of another nutrient loss in the soil for plant nutrition. Endophytic bacteria can sustain plant growth and health by exhibiting antibiosis against phytopathogens, production of enzymes, phytohormone biosynthesis, organic acids, and secondary metabolite secretions. Considerable effort in the agricultural industry is focused on multifunctional concepts and bioprospecting on the use of bioinput from endophytic microbes to ensure a stable ecosystem. Bioprospecting in the case of this review is a systemic overview of the biorational approach to harness beneficial plant-associated microbes to ensure food security in the future. Progress in this endeavor is limited by available techniques. The use of molecular techniques in unraveling the functions of soybean endophytic bacteria can explore their use in integrated organic farming. Our review brings to light the endophytic microbial dynamics of soybeans and current status of plant microbiome research for sustainable agriculture.

Plant Growth-Promoting Fungi as Biocontrol Tool against Fusarium Wilt Disease of Tomato Plant

Plant growth-promoting fungi (PGPF) improve plant health and resist plant pathogens. The present study was carried out to biocontrol tomato Fusarium wilt using PGPF through antifungal activity and enhance tomato plant immune response. Four PGPF were identified genetically as Aspergillus flavus, Aspergillus niger, Mucor circinelloides and Pencillium oxalicum. In vitro antagonistic activity assay of PGPF against Fusariumoxysporum was evaluated, where it exhibited promising antifungal activity where MIC was in the range 0.25-0.5 mg/mL. Physiological markers of defense in a plant as a response to stimulation of induced systemic resistance (ISR) were recorded. Our results revealed that A. niger, M. circinelloides, A. flavus and P. oxalicum strains significantly reduced percentages of disease severity by 16.60% and 20.83% and 37.50% and 45.83 %, respectively. In addition, they exhibited relatively high protection percentages of 86.35%, 76.87%, 56.87% and 59.06 %, respectively. With concern to the control, it is evident that the percentage of disease severity was about 87.50%. Moreover, the application of M. circinelloides, P. oxalicum, A. niger and A. flavus successfully recovered the damage to morphological traits, photosynthetic pigments' total carbohydrate and total soluble protein of infected plants. Moreover, the application of tested PGPF enhanced the growth of healthy and infected tomato plants.

Metagenomic study of the communities of bacterial endophytes in the desert plant Senna Italica and their role in abiotic stress resistance in the plant

Abstract Plant leaves and roots are home to diverse communities of bacteria, which play a significant role in plant health and growth. Although one of the most unfriendly environments for plant growth is deserts, desert plants can influence their surrounding microbial population and choose favorable bacteria that encourage their growth under these severe circumstances. Senna italica is known for its excellent medicinal values as a traditional medical plant, but little is known about its associated endophytic bacterial community under extreme conditions. In the present study, metagenomic sequencing of 16S rRNA was used to report the diversity of endophytic bacterial communities associated with the leaves and roots of the desert medicinal plant Senna italica that was collected from the Asfan region in northeast Jeddah, Saudi Arabia. Analyses of the 16S rRNA sequences at the taxonomic phylum level revealed that bacterial communities in the roots and leaves samples belonged to five phyla, including Cyanobacteria, Proteobacteria, Actinobacteria, Firmicutes, and unclassified phyla. Results indicated that the most common phyla were Cyanobacteria/Chloroplast and Actinobacteria. Analysis of the 16S rRNA sequences at the taxonomic phylum level revealed that bacterial communities in the roots and leaves samples belonged to twelve genera at the taxonomic genus level. The most abundant ones were highlighted for further analysis, including Okibacterium and Streptomyces found in Actinobacteria, which were the dominant genus in roots samples. However, Streptophyta found in Cyanobacteria/Chloroplast was the dominant genus in leaf samples. Metagenomic analysis of medicinal plants leads to identifying novel organisms or genes that may have a role in abiotic stress resistance in the plant. The study of endophytic microbiome taxonomic, phylogenetic, and functional diversity will better know innovative candidates that may be selected as biological agents to enhance agricultural and industrial processes, especially for crop desert agricultural improvement.

Dual inoculation of dark septate endophytes and Trichoderma viride drives plant performance and rhizosphere microbiome adaptations of Astragalus mongholicus to drought

Rhizosphere microbiome adapts their structural compositions to water scarcity and have the potential to mitigate drought stress of plants. To unlock this potential, it is crucial to understand community responses to drought in the interplay between soil properties, water management and exogenous microbes interference. Inoculation with dark septate endophytes (DSE) (Acrocalymma vagum, Paraboeremia putaminum) and Trichoderma viride on Astragalus mongholicus grown in the non-sterile soil was exposed to drought. Rhizosphere microbiome were assessed by Illumina MiSeq sequencing of the 16S and ITS2 rRNA genes. Inoculation positively affected plant growth depending on DSE species and water regime. Ascomycota, Proteobacteria, Actinobacteria, Chloroflexi and Firmicutes were the dominant phyla. The effects of dual inoculation on bacterial community were greater than those on fungal community, and combination of P. putaminum and T. viride exerted a stronger impact on the microbiome under drought stress. The observed changes in soil factors caused by inoculation could be explained by the variations in microbiome composition. Rhizosphere microbiome mediated by inoculation exhibited distinct preferences for various growth parameters. These findings suggest that dual inoculation of DSE and T. viride enriched beneficial microbiota, altered soil nutrient status and might contribute to enhance the cultivation of medicinal plants in dryland agriculture.

Rhytidhylides A and B, Two New Phthalide Derivatives from the Endophytic Fungus Rhytidhysteron sp. BZM-9

Two new phthalide derivatives, rhytidhylides A (1) and B (2), together with ten known compounds (3–12) were isolated from cultures of Rhytidhysteron sp. BZM-9, an endophyte isolated from the leaves of Leptospermum brachyandrum. Their structures were identified by an extensive analysis of NMR, HRESIMS, ECD, and through comparison with data reported in the literature. In addition, the cytotoxic activities against two human hepatoma cell lines (HepG2 and SMMC7721) and antibacterial activities against MRSA and E. coli were evaluated.

Mycotoxins Biocontrol Methods for Healthier Crops and Stored Products

Contamination of crops with phytopathogenic genera such as Fusarium, Aspergillus, Alternaria, and Penicillium usually results in mycotoxins in the stored crops or the final products (bread, beer, etc.). To reduce the damage and suppress the fungal growth, it is common to add antifungal substances during growth in the field or storage. Many of these antifungal substances are also harmful to human health and the reduction of their concentration would be of immense importance to food safety. Many eminent researchers are seeking a way to reduce the use of synthetic antifungal compounds and to implement more eco-friendly and healthier bioweapons against fungal proliferation and mycotoxin synthesis. This paper aims to address the recent advances in the effectiveness of biological antifungal compounds application against the aforementioned fungal genera and their species to enhance the protection of ecological and environmental systems involved in crop growing (water, soil, air) and to reduce fungicide contamination of food derived from these commodities.

A Comprehensive Analysis Using Colorimetry, Liquid Chromatography-Tandem Mass Spectrometry and Bioassays for the Assessment of Indole Related Compounds Produced by Endophytes of Selected Wheat Cultivars

Liquid chromatography–tandem mass spectrometry (LC–MS/MS), colorimetry, and bioassays were employed for the evaluation of the ability of endophytic bacterial strains to synthesize indole-related compounds (IRCs) and in particular indole-3-acetic acid (IAA). A total of 54 endophytic strains belonging to seven bacterial genera isolated from tissues of common and spelt wheat cultivars were studied. The endophytic bacteria isolated from different tissues of the tested wheat types were capable of IRCs production, including IAA, which constituted from 1.75% to 52.68% of all IRCs, in in vitro conditions via the tryptophan dependent pathway. The selected post-culture medium was also examined using a plant bioassay. Substantial growth of wheat coleoptile segments treated with the bacterial post-culture medium was observed in several cases. Our data suggest that the studied endophytic bacteria produce auxin-type compounds to support plant development. Summarizing, our approach to use three complementary methods for estimation of IRCs in different endophytic strains provides a comprehensive picture of their effect on wheat growth.

Climatic Aridity Gradient Modulates the Diversity of the Rhizosphere and Endosphere Bacterial Microbiomes of Opuntia ficus-indica

Recent microbiome research has shown that soil fertility, plant-associated microbiome, and crop production can be affected by abiotic environmental parameters. The effect of aridity gradient on rhizosphere-soil (rhizosphere) and endosphere-root (endosphere) prokaryotic structure and diversity associated with cacti remain poorly investigated and understood. In the current study, next-generation sequencing approaches were used to characterize the diversity and composition of bacteria and archaea associated with the rhizosphere and endosphere of Opuntia ficus-indica spineless cacti in four bioclimatic zones (humid, semi-arid, upper-arid, and lower-arid) in Tunisia. Our findings showed that bacterial and archaeal cactus microbiomes changed in inside and outside roots and along the aridity gradient. Plant compartment and aridity gradient were the influencing factors on the differentiation of microbial communities in rhizosphere and endosphere samples. The co-occurrence correlations between increased and decreased OTUs in rhizosphere and endosphere samples and soil parameters were determined according to the aridity gradient. Blastococcus, Geodermatophilus, Pseudonocardia, Promicromonospora, and Sphingomonas were identified as prevailing hubs and were considered as specific biomarkers taxa, which could play a crucial role on the aridity stress. Overall, our findings highlighted the prominence of the climatic aridity gradient on the equilibrium and diversity of microbial community composition in the rhizosphere and endosphere of cactus.

Fusarium Head Blight, Mycotoxins and Strategies for Their Reduction

Mycotoxins are secondary metabolites of microscopic fungi, which commonly contaminate cereal grains. Contamination of small-grain cereals and maize with toxic metabolites of fungi, both pathogenic and saprotrophic, is one of the particularly important problems in global agriculture. Fusarium species are among the dangerous cereal pathogens with a high toxicity potential. Secondary metabolites of these fungi, such as deoxynivalenol, zearalenone and fumonisin B1 are among five most important mycotoxins on a European and world scale. The use of various methods to limit the development of Fusarium cereal head diseases and grain contamination with mycotoxins, before and after harvest, is an important element of sustainable agriculture and production of safe food. The applied strategies utilize chemical and non-chemical methods, including agronomic, physical and biological treatments. Biological methods now occupy a special place in plant protection as an element of biocontrol of fungal pathogens by inhibiting their development and reducing mycotoxins in grain. According to the literature, Good Agricultural Practices are the best line of defense for controlling Fusarium toxin contamination of cereal and maize grains. However, fluctuations in weather conditions can significantly reduce the effectiveness of plants protection methods against infection with Fusarium spp. and grain accumulation of mycotoxins.