The Role of Microbial Inoculants on Plant Protection, Growth Stimulation, and Crop Productivity of the Olive Tree (Olea europea L.)

Unraveling the spatio-temporal dynamics of soil and root-associated microbiomes in Texas olive orchards

Understanding the structure and diversity of microbiomes is critical to establishing olives in non-traditional production areas. Limited studies have investigated soil and root-associated microbiota dynamics in olives across seasons or locations in the United States. We explored the composition and spatiotemporal patterns of the olive-associated microbial communities and specificity in two niches (rhizosphere and root endosphere), seasons (spring, summer, and fall), and domains (bacteria and fungi) in the microbiome of the olive cultivar Arbequina across three olive orchards in Texas. Phylum Proteobacteria, followed by Actinobacteriota, dominated the bacterial populations in the rhizosphere and endosphere. Rubrobacter and Actinophytocola were dominant taxa in the rhizosphere and root endosphere at the genus level. Among fungal communities, phylum Ascomycota was prevalent in the rhizosphere and endosphere, while members of the Chaetomiaceae family outnumbered other taxa in the root endosphere. As per the alpha diversity indices, the rhizosphere at Moulton showed much higher richness and diversity than other places, which predicted a significant difference in rhizosphere between locations for bacterial diversity and richness. There was no significant variation in the bacterial diversity in the niches and the fungal diversity within the root endosphere between locations. Beta diversity analysis confirmed the effect of compartments-in influencing community differences. Microbial diversity was apparent within the endosphere and rhizosphere. The seasons influenced only the rhizosphere fungal diversity, contrasting the bacterial diversity in either niche. The research provided a comprehensive overview of the microbial diversity in olive trees' rhizosphere and root endosphere. The abundance and composition of OTUs associated with the rhizosphere soil of Arbequina suggest its role as a source reservoir in defining the potential endophytes.

Olive Tree Belowground Microbiota: Plant Growth-Promoting Bacteria and Fungi

The olive tree is one of the most significant crops in the Mediterranean region. Its remarkable adaptability to various environments has facilitated olive cultivation across diverse regions and agricultural scenarios. The rising global demand for olive products, coupled with climate challenges, is driving changes in cultivation methods. These changes are altering the traditional landscape and may potentially reshape the structure and composition of orchard microbial communities, which can impact productivity and stress tolerance. Bacterial and fungal communities naturally associated with plants have long been recognized as crucial for plant growth and health, serving as a vital component of sustainable agriculture. In this review, we aim to highlight the significance of olive cultivation and the impact of abiotic stresses. We update the current knowledge on the profiles of rhizosphere and root fungal and bacterial communities in olive orchards and examine how (a)biotic factors influence these communities. Additionally, we explore the potential of plant growth-promoting bacteria and fungi in enhancing olive physiological performance and stress tolerance. We identify knowledge gaps and emphasize the need for implementing new strategies. A comprehensive understanding of olive-associated microbiota will aid in developing sustainable agronomic practices to address climatic challenges and meet the growing demand for olive products.

Evaluation of Biological Plant Protection Products for Their Ability to Induce Olive Innate Immune Mechanisms and Control Colletotrichum acutatum, the Causal Agent of Olive Anthracnose

Olive anthracnose is the most important fungal disease of the olive fruit worldwide, with the fungus Colletotrichum acutatum as the main cause of the disease in Greece. A total of 11 commercial biological plant protection products (bioPPPs) (Amylo-X®, Botector®, FytoSave®, LBG 01F34®, Mevalone®, Polyversum®, Remedier®, Serenade® ASO, Sonata®, Trianum-P®, Vacciplant®), with various modes of action against the fungus C. acutatum, were evaluated by bioassays using detached fruits of two important olive Greek varieties, cv. Koroneiki and cv. Kalamon. Subsequently, the most effective bioPPPs were evaluated for their ability to induce plant defense mechanisms, by determining the expression levels of ten Olea europaea defense genes (Pal, CuaO, Aldh1, Bglu, Mpol, Lox, Phely, CHI-2, PR-10, PR-5). Remedier®, Trianum-P®, Serenade® ASO, Sonata®, and Mevalone® were the most effective in reducing disease severity, and/or inhibiting the conidia production by the fungus at high rates. Post bioPPPs application, high expression levels of several olive plant defense genes were observed. This study provides insights into commercial bioPPPs' effectiveness in controlling olive anthracnose, as well as biocontrol-agents-mediated modulation of olive defense mechanisms.

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.

Decoding the guardians of cotton resilience: A comprehensive exploration of the βCA genes and its role in Verticillium dahliae resistance

Plant Carbonic anhydrases (Cas) have been shown to be stress-responsive enzymes that may play a role in adapting to adverse conditions. Cotton is a significant economic crop in China, with upland cotton (Gossypium hirsutum) being the most widely cultivated species. We conducted genome-wide identification of the βCA gene in six cotton species and preliminary analysis of the βCA gene in upland cotton. In total, 73 βCA genes from six cotton species were identified, with phylogenetic analysis dividing them into five subgroups. GHβCA proteins were predominantly localized in the chloroplast and cytoplasm. The genes exhibited conserved motifs, with motifs 1, 2, and 3 being prominent. GHβCA genes were unevenly distributed across chromosomes and were associated with stress-responsive cis-regulatory elements, including those responding to light, MeJA, salicylic acid, abscisic acid, cell cycle regulation, and defence/stress. Expression analysis indicated that GHβCA6, GHβCA7, GHβCA10, GHβCA15, and GHβCA16 were highly expressed under various abiotic stress conditions, whereas GHβCA3, GHβCA9, GHβCA10, and GHβCA18 had higher expression patterns under Verticillium dahliae infection at different time intervals. In Gossypium thurberi, GthβCA1, GthβCA2, and GthβCA4 showed elevated expression across stress conditions and tissues. Silencing GHβCA10 through VIGS increased Verticillium wilt severity and reduced lignin deposition compared to non-silenced plants. GHβCA10 is crucial for cotton's defense against Verticillium dahliae. Further research is needed to understand the underlying mechanisms and develop strategies to enhance resistance against Verticillium wilt.

Co-occurrence network analysis unveils the actual differential impact on the olive root microbiota by two Verticillium wilt biocontrol rhizobacteria

BACKGROUND

Verticillium wilt of olive (VWO), caused by Verticillium dahliae Kleb, is one of the most threatening diseases affecting olive cultivation. An integrated disease management strategy is recommended for the effective control of VWO. Within this framework, the use of biological control agents (BCAs) is a sustainable and environmentally friendly approach. No studies are available on the impact that the introduction of BCAs has on the resident microbiota of olive roots. Pseudomonas simiae PICF7 and Paenibacillus polymyxa PIC73 are two BCAs effective against VWO. We examined the effects of the introduction of these BCAs on the structure, composition and co-occurrence networks of the olive (cv. Picual) root-associated microbial communities. The consequences of the subsequent inoculation with V. dahliae on BCA-treated plants were also assessed.

RESULTS

Inoculation with any of the BCAs did not produce significant changes in the structure or the taxonomic composition of the 'Picual' root-associated microbiota. However, significant and distinctive alterations were observed in the topologies of the co-occurrence networks. The introduction of PIC73 provoked a diminution of positive interactions within the 'Picual' microbial community; instead, PICF7 inoculation increased the microbiota's compartmentalization. Upon pathogen inoculation, the network of PIC73-treated plants decreased the number of interactions and showed a switch of keystone species, including taxa belonging to minor abundant phyla (Chloroflexi and Planctomycetes). Conversely, the inoculation of V. dahliae in PICF7-treated plants significantly increased the complexity of the network and the number of links among their modules, suggestive of a more stable network. No changes in their keystone taxa were detected.

CONCLUSION

The absence of significant modifications on the structure and composition of the 'Picual' belowground microbiota due to the introduction of the tested BCAs underlines the low/null environmental impact of these rhizobacteria. These findings may have important practical consequences regarding future field applications of these BCAs. Furthermore, each BCA altered the interactions among the components of the olive belowground microbiota in idiosyncratic ways (i.e. PIC73 strongly modified the number of positive relations in the 'Picual' microbiota whereas PICF7 mostly affected the network stability). These modifications may provide clues on the biocontrol strategies used by these BCAs.

Microbiome Associated with Olive Cultivation: A Review

International research has devoted much effort to the study of the impacts caused to the soil by different management practices applied to olive cultivation. Such management involves techniques considered conventional, including the control of spontaneous plants with herbicides or machines, inorganic fertilizers, and pesticides to control pests and diseases. Equally, some producers use sustainable techniques, including drastic pruning, the use of cultivars that are tolerant to diseases and adverse climates, the use of organic conditioners in the soil, the maintenance of vegetation cover with spontaneous plants, and the use of inoculants, among others. In both conventional and sustainable/organic management, the effects on soil quality, crop development, and production are accessed through the presence, activity, and/or behavior of microorganisms, microbial groups, and their processes in the soil and/or directly in the crop itself, such as endophytes and epiphytes. Thus, our present review seeks to assemble research information, not only regarding the role of microorganisms on growth and development of the olive tree (Olea europaea L.). We looked mainly for reviews that reveal the impacts of different management practices applied in countries that produce olive oil and olives, which can serve as a basis and inspiration for Brazilian studies on the subject.

Funneliformis mosseae Inoculation Enhances Cucurbita pepo L. Plant Growth and Fruit Yield by Reshaping Rhizosphere Microbial Community Structure

Arbuscular mycorrhizal fungi (AMF) are essential components of the soil microbiome that can facilitate plant growth and enhance abiotic and biotic stress resistance. However, the mechanisms via which AMF inoculation influences Cucurbita pepo L. plant growth and fruit yield remain unclear. Here, we conducted pot experiments to investigate bacterial and fungal community structure in the rhizosphere of C. pepo plants inoculated with Funneliformis mosseae (Nicoll. & Gerd.) Gerd. & Trappe based on 16S ribosomal RNA and internal transcribed spacer gene sequencing. The α-diversity of bacteria increased significantly following F. mosseae inoculation, whereas the α-diversity of fungi exhibited an opposite trend (p < 0.01). The relative abundances of major bacterial phyla, Actinobacteria, Acidobacteria, and Chloroflexi, together with the fungal phylum Ascomycota, were all higher in inoculated samples than in uninoculated controls. F. mosseae inoculation led to remarkable enrichment of potentially beneficial taxa (e.g., Streptomyces, Sphingomonas, Lysobacter, and Trichoderma), in stark contrast to depletion of fungal pathogens (e.g., Botryotrichum, Acremonium, Fusarium, and Plectosphaerella). Pathways related to amino acid metabolism and antibiotic biosynthesis were upregulated by F. mosseae inoculation, whereas pathways involved in infectious diseases were downregulated. The results suggest that F. mosseae inoculation reshapes the rhizosphere microbiome, thereby augmenting C. pepo plant growth and fruit yield.

Potential for Biological Control of Pythium schmitthenneri Root Rot Disease of Olive Trees (Olea europaea L.) by Antagonistic Bacteria

Several diseases affect the productivity of olive trees, including root rot disease caused by Pythium genera. Chemical fungicides, which are often used to manage this disease, have harmful side effects on humans as well as environmental components. Biological management is a promising control approach that has shown its great potential as an efficient eco-friendly alternative to treating root rot diseases. In the present study, the antagonistic activity of ten bacterial isolates was tested both in vitro and in planta against Pythium schmitthenneri, the causal agent of olive root rot disease. These bacterial isolates belonging to the genera Alcaligenes, Pantoea, Bacillus, Sphingobacterium, and Stenotrophomonas were chosen for their potential antimicrobial effects against many pathogens. Results of the in vitro confrontation bioassay revealed a high reduction of mycelial growth exceeding 80%. The antifungal effect of the volatile organic compounds (VOCs) was observed for all the isolates, with mycelial inhibition rates ranging from 28.37 to 70.32%. Likewise, the bacterial cell-free filtrates showed important inhibition of the mycelial growth of the pathogen. Overall, their efficacy was substantially affected by the nature of the bacterial strains and their modes of action. A greenhouse test was then carried out to validate the in vitro results. Interestingly, two bacterial isolates, Alcaligenes faecalis ACBC1 and Bacillus amyloliquefaciens SF14, were the most successful in managing the disease. Our findings suggested that these two antagonistic bacterial isolates have promising potential as biocontrol agents of olive root rot disease.

Role of Combined Inoculation with Arbuscular Mycorrhizal Fungi, as a Sustainable Tool, for Stimulating the Growth, Physiological Processes, and Flowering Performance of Lavender

Arbuscular mycorrhizal fungi (AMF) are essential soil microorganisms for terrestrial ecosystems and form beneficial symbioses with the root systems of most agricultural plants. The purpose of this paper was to examine the effect of the community of six AMF on the growth, physiological response, and flowering performance in organic potted lavender culture. The mixture of AMF containing Rhizophagus irregularis, Claroideoglomus claroideum, Funneliformis mosseae, Funneliformis geosporum, Claroideoglomus etunicatum, and Glomus microaggregatum was added in a pot with peat, volcanic rock, and coconut bark. We analyzed the fresh shoot biomass, root biomass, total plant biomass, leaf area, flowering performance, photosynthesis rate, and photosynthetic pigment content. Pearson’s correlation coefficient was performed to get a better understanding of the relationships between the studied variables. The total plant biomass was more pronounced in plants with AMF-S20g (212.01 g plant−1) and AMF-S30g (220.25 g plant−1) than with AMF-S10g (201.96 g plant−1) or in untreated plants (180.87 g plant−1). A statistically significant increase for Chl a, Chl b, and Car was found for AMF-S20g and AMF-S30. Our findings suggest that the AMF mixture application in a growing substrate with peat, coconut bark, and volcanic rock improved plant growth, physiological processes, and ornamental value in mycorrhizal lavender plants. This environmentally friendly agricultural practice could be used for the sustainable production of lavender.

Effect of Aspergillus and Bacillus Concentration on Cotton Growth Promotion

There are no studies in literature on the effect of inoculant concentrations on plant growth promotion. Therefore, in the present study, two experiments were carried out, one under pot conditions and the other in the field with cotton crop, in order to verify the effect of Aspergillus and Bacillus concentrations on the biometric and nutritional parameters of plant and soil, in addition to yield. The pot experiment evaluated the effect of different concentrations, ranging from 1 × 10⁴ to 1 × 10¹⁰ colony-forming units per milliliter (CFU mL^–1) of microorganisms Bacillus velezensis (Bv188), Bacillus subtilis (Bs248), B. subtilis (Bs290), Aspergillus brasiliensis (F111), Aspergillus sydowii (F112), and Aspergillus sp. versicolor section (F113) on parameters plant growth promotion and physicochemical and microbiological of characteristics soil. Results indicated that the different parameters analyzed are influenced by the isolate and microbial concentrations in a different way and allowed the selection of four microorganisms (Bs248, Bv188, F112, and F113) and two concentrations (1 × 10⁴ and 1 × 10¹⁰ CFU mL^–1), which were evaluated in the field to determine their effect on yield. The results show that, regardless of isolate, inoculant concentrations promoted the same fiber and seed cotton yield. These results suggest that lower inoculant concentrations may be able to increase cotton yield, eliminating the need to use concentrated inoculants with high production cost.

Nitrogen absorption efficiency and mechanism in Arbuscular mycorrhizal fungi - Canna indica symbiosis

Arbuscular mycorrhizal fungi (AMF) and its symbiosis with Canna indica on nitrogen (N) absorption was investigated for the remediation of contaminated soil. Canna indica plants with rhizome and leaf integrity intact were collected in spring and autumn seasons. To maintain the ideal nutrient composition, Hoagland concentrated nutrient solution was diluted with deionized water and additional nutrient solution was added periodically. Treated root samples were observed with an optical microscope and the number of hyphae and intersections as well as inoculation status were examined. High-throughput sequencing experiment was conducted to quantify AMF inoculation. Alpha diversity study was used to characterize abundance and diversity of the symbiosis. Hydroponic experiments were conducted to explore the absorption effectiveness of AMF-Canna symbiosis under different NH₄⁺-N and NO₃^--N combinations. Hyphal colonization rate was only about 5.66 ± 1.08% in seedling stage in spring, but enhanced in the adult stage in autumn (53.89 ± 1.43%). Results revealed that AMF had no significant impact on NO₃^--N absorption by Canna roots, however, absorption of NH₄⁺-N was improved by 63% under low concentration. Results revealed that when NH₄⁺-N and NO₃^--N were applied combinedly in a 1:1 ratio, their respective absorption rates were enhanced to 99.63% and 99.50%. Compared with the case of NH₄⁺-N as N source alone, synergistic effect of NH₄⁺-N and NO₃^--N significantly changed the absorption of NH₄⁺-N by C. indica, but its correlation with AMF inoculation was still not significant. Current findings could enhance understanding for effective N uptake and resource recovery.

Plant Tolerance to Drought Stress in the Presence of Supporting Bacteria and Fungi: An Efficient Strategy in Horticulture

Increasing temperature leads to intensive water evaporation, contributing to global warming and consequently leading to drought stress. These events are likely to trigger modifications in plant physiology and microbial functioning due to the altered availability of nutrients. Plants exposed to drought have developed different strategies to cope with stress by morphological, physiological, anatomical, and biochemical responses. First, visible changes influence plant biomass and consequently limit the yield of crops. The presented review was undertaken to discuss the impact of climate change with respect to drought stress and its impact on the performance of plants inoculated with plant growth-promoting microorganisms (PGPM). The main challenge for optimal performance of horticultural plants is the application of selected, beneficial microorganisms which actively support plants during drought stress. The most frequently described biochemical mechanisms for plant protection against drought by microorganisms are the production of phytohormones, antioxidants and xeroprotectants, and the induction of plant resistance. Rhizospheric or plant surface-colonizing (rhizoplane) and interior (endophytic) bacteria and fungi appear to be a suitable alternative for drought-stress management. Application of various biopreparations containing PGPM seems to provide hope for a relatively cheap, easy to apply and efficient way of alleviating drought stress in plants, with implications in productivity and food condition.

Selection of Bacterial Strains for Control of Root-Knot Disease Caused by Meloidogyne incognita

Root-knot disease caused by Meloidogyne incognita leads to significant crop yield losses that may be aggravated by the association with pathogenic fungi and bacteria. Biological agents can be effectively used against the complex disease of root-knot nematode and pathogenic fungi. In this study, 35 bacterial strains were analyzed for their in vitro nematicidal, antagonistic and growth stimulation activities. Based on results from the in vitro assays, grow-box experiments on tomato and cucumber were carried out with the strain BZR 86 of Bacillus velezensis applied at different concentrations. Effects of B. velezensis BZR 86 on the development of root-knot disease were evaluated by recording root gall index, number of galls and number of eggs in egg masses. Application of B. velezensis BZR 86 noticeably decreased the development of root-knot disease on tomato and cucumber plants, as well as significantly increased growth and biomass of cucumber plants in accordance with bacterial concentration. This study seems to demonstrate that strain B. velezensis BZR 86 could be an additional tool for an environmentally safe control of root-knot disease on horticultural crops.

Assessing the Involvement of Selected Phenotypes of Pseudomonas simiae PICF7 in Olive Root Colonization and Biological Control of Verticillium dahliae

Pseudomonas simiae PICF7 is an indigenous inhabitant of the olive (Olea europaea L.) rhizosphere/root endosphere and an effective biocontrol agent against Verticillium wilt of olive (VWO), caused by the soil-borne fungus Verticillium dahliae. This study aimed to evaluate the potential involvement of selected phenotypes of strain PICF7 in root colonization ability and VWO biocontrol. Therefore, a random transposon-insertion mutant bank of P. simiae PICF7 was screened for the loss of phenotypes likely involved in rhizosphere/soil persistence (copper resistance), root colonization (biofilm formation) and plant growth promotion (phytase activity). Transposon insertions in genes putatively coding for the transcriptional regulator CusR or the chemotaxis protein CheV were found to affect copper resistance, whereas an insertion in fleQ gene putatively encoding a flagellar regulatory protein hampered the ability to form a biofilm. However, these mutants displayed the same antagonistic effect against V. dahliae as the parental strain. Remarkably, two mutants impaired in biofilm formation were never found inside olive roots, whereas their ability to colonize the root exterior and to control VWO remained unaffected. Endophytic colonization of olive roots was unaltered in mutants impaired in copper resistance and phytase production. Results demonstrated that the phenotypes studied were irrelevant for VWO biocontrol.

Endophytic Fungi of Olive Tree

In addition to the general interest connected with investigations on biodiversity in natural contexts, more recently the scientific community has started considering occurrence of endophytic fungi in crops in the awareness of the fundamental role played by these microorganisms on plant growth and protection. Crops such as olive tree, whose management is more and more frequently based on the paradigm of sustainable agriculture, are particularly interested in the perspective of a possible applicative employment, considering that the multi-year crop cycle implies a likely higher impact of these symbiotic interactions. Aspects concerning occurrence and effects of endophytic fungi associated with olive tree (Olea europaea) are revised in the present paper.