Aridity modulates belowground bacterial community dynamics in olive tree

Rhizosphere bacterial communities of Namib Desert plant species: Evidence of specialised plant-microbe associations

Rhizosphere microbial communities are intimately associated with plant root surfaces. The rhizosphere microbiome is recruited from the surrounding soil and is known to impact positively on the plant host via enhanced resistance to pathogens, increased nutrient availability, growth stimulation and increased resistance to desiccation. Desert ecosystems harbour a diversity of perennial and annual plant species, generally exhibiting considerable physiological adaptation to the low-water environment. In this study, we explored the rhizosphere bacterial microbiomes associated with selected desert plant species. The rhizosphere bacterial communities of 11 plant species from the central Namib Desert were assessed using 16S rRNA gene-dependent phylogenetic analyses. The rhizosphere microbial community of each host plant species was compared with control soils collected from their immediate vicinity, and with those of all other host plants. Rhizosphere and control soil bacterial communities differed significantly and were influenced by both location and plant species. Rhizosphere-associated genera included 67 known plant growth-promoting taxa, including Rhizobium, Bacillus, Microvirga, Kocuria and Paenibacillus. Other than Kocuria, these genera constituted the 'core' rhizosphere bacterial microbiome, defined as being present in > 90 % of the rhizosphere communities. Nine of the 11 desert plant species harboured varying numbers and proportions of species-specific microbial taxa. Predictive analyses of functional pathways linked to rhizosphere microbial taxa showed that these were significantly enriched in the biosynthesis or degradation of a variety of substances such as sugars, secondary metabolites, phenolic compounds and antimicrobials. Overall, our data suggest that plant species in the Namib Desert recruit unique taxa to their rhizosphere bacterial microbiomes that may contribute to their resilience in this extreme environment.

Unravelling Changes in the Pinus radiata Root and Soil Microbiomes as a Function of Aridity

Increased aridity is emerging as a key impact of climate change in terrestrial ecosystems globally. Forest biomes are particularly vulnerable to the impacts of changing environmental conditions due to their long-lived and sessile nature. Microbiomes have coevolved with plants under changing environmental conditions with shared fitness outcomes. However, both the movement of plants via domestication and rapid pace of environmental change may impact the ability of plants to recruit microbial symbionts that support environmental stress tolerance. This study investigates the effects of aridity on tree-root microbiome symbiosis, focusing on the widely planted Pinus radiata. By sampling a broad geographic range and diverse environmental gradients, we reveal how aridity, soil and climatic variables shape microbial communities in P. radiata roots and soils. Our findings highlight that while aridity significantly predicts microbial community assembly, other environmental variables such as soil pH and organic carbon, strongly influence bacterial diversity. Groups of both bacterial and fungal taxa were identified as conditionally present with aridity, underscoring their importance in P. radiata resilience under increasingly environmental stress. Based on the transition of current mesic ecosystems to arid conditions under climate change, we found these arid associated taxa vary in their frequency in bulk soils projected to become arid. These results highlight the risk that these taxa will need to be recruited by other means. Ecological filtering by the host and environmental conditions fosters a "friends with benefits" relationship, wherein certain microbial taxa provide key benefits, such as extension of phenotypic tolerance to water limitation, to the host. Both bacterial and fungal communities are shaped more by stochastic than deterministic assembly processes, suggesting a complex interplay of host and environmental factors in community structure formation. The insights gained have implications for understanding the resilience of tree species and the ecosystem services they provide under future climate scenarios.

Desert-adapted plant growth-promoting pseudomonads modulate plant auxin homeostasis and mitigate salinity stress

By providing adaptive advantages to plants, desert microorganisms are emerging as promising solutions to mitigate the negative and abrupt effects of climate change in agriculture. Among these, pseudomonads, commonly found in soil and in association with plants' root system, have been shown to enhance plant tolerance to salinity and drought, primarily affecting root system architecture in various hosts. However, a comprehensive understanding of how these bacteria affect plant responses at the cellular, physiological and molecular levels is still lacking. In this study, we investigated the effects of two Pseudomonas spp. strains, E102 and E141, which were previously isolated from date palm roots and have demonstrated efficacy in promoting drought tolerance in their hosts. These strains colonize plant roots, influencing root architecture by inhibiting primary root growth while promoting root hair elongation and lateral root formation. Strains E102 and E141 increased auxin levels in Arabidopsis, whereas this effect was diminished in IAA-defective mutant strains, which exhibited reduced IAA production. In all cases, the effectiveness of the bacteria relies on the functioning of the plant auxin response and transport machinery. Notably, such physiological and morphological changes provide an adaptive advantage to the plant, specifically under stress conditions such as salinity. Collectively, this study demonstrates that by leveraging the host's auxin signalling machinery, strains E102 and E141 significantly improve plant resilience to abiotic stresses, positioning them as potential biopromoters/bioprotectors for crop production and ecosystem restoration in alignment with Nature-based Solution approaches.

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.

Effects of different dwarfing interstocks on the rhizosphere, endophytic bacteria, and drought resistance of apple trees

Rootstock is commonly used to enhance plant resistance to drought stress. However, it is necessary to investigate the effects of different rootstock, interstock, and scion combinations on rhizosphere and root endophytic bacteria under drought stress. We conducted a pot experiment to investigate how interstock [SH40, Jizhen 1 (J1), and Jizhen 2 (J2)] affects the drought tolerance and nitrogen (N) uptake and utilization of apple trees under drought stress. The results showed that the total dry weight, total chlorophyll content, carotenoid content, photosynthesis rate, and N absorption and utilization efficiency of apple trees decreased significantly, whereas relative electrolyte leakage increased significantly under drought stress. Membership function analysis showed that the apple plants with the J1 interstock had the greatest drought resistance. In addition, drought treatment significantly affected the diversity and composition of rhizosphere and root endophytic communities in all three rootstock/interstock/scion combinations. Further analysis revealed that the relative abundance of the plant pathogen Ralstonia was significantly increased in J2 drought-treated roots, compared to the other groups, whereas those of some potentially beneficial bacteria (0134_terrestrial_group, Phenylobacterium, Ellin6067, Kribbella, Chloronema, and Streptomyces) increased significantly in the J1 drought-treated sample. Co-occurrence network analysis showed that some potentially beneficial bacteria (Ellin6067, S0134_terrestrial_group, Pedomicrobium, and Subgroup_10) were significantly positively correlated with N content. These modifications of the rhizosphere and endophytic bacterial communities may influence the drought resilience and N uptake efficiency of different combinations of interstocks and scions. This study is a much-needed step towards understanding the stress response mechanism of scion-rootstock combinations.

Determination of Bacterial Community Structure of Table Olive via Metagenomic Approach in Şarköy

One of the most popular pickled foods created worldwide is table olives. The aim was to identify the bacterial microbiota of table olive samples collected from Şarköy, Tekirdağ-Türkiye using next generation sequencing and 16S metagenomic analysis. Samples were studied as non-pre-enriched (n : 10) and after pre-enrichment (n : 10) to compare the effects of the enrichment process on the bacterial diversity. In non-pre-enriched, the most common genus found was Sphingomonas, followed by Altererythrobacter and Lysobacter. The most common phylum found was Proteobacteria, followed by Bacteroidota and Actinobacteria. In pre-enriched, Bacillus was the most commonly detected genus, followed by Pantoea and Staphylococcus. The most frequently found phylum was Firmicutes, followed by Proteobacteria and Cyanobacteria. This study is the first study for Şarköy, which is the only table olive production place in the Tekirdağ region due to its microclimate feature. Further studies are needed in more table olive samples from different geographical areas to confirm and develop current findings.

Confronting stresses affecting olive cultivation from the holobiont perspective

The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.

Pseudomonas and Curtobacterium Strains from Olive Rhizosphere Characterized and Evaluated for Plant Growth Promoting Traits

Plant growth promoting (PGP) bacteria are known to enhance plant growth and protect them from environmental stresses through different pathways. The rhizosphere of perennial plants, including olive, may represent a relevant reservoir of PGP bacteria. Here, seven bacterial strains isolated from olive rhizosphere have been characterized taxonomically by 16S sequencing and biochemically, to evaluate their PGP potential. Most strains were identified as Pseudomonas or Bacillus spp., while the most promising ones belonged to genera Pseudomonas and Curtobacterium. Those strains have been tested for their capacity to grow under osmotic or salinity stress and to improve the germination and early development of Triticum durum subjected or not to those stresses. The selected strains had the ability to grow under severe stress, and a positive effect has been observed in non-stressed seedlings inoculated with one of the Pseudomonas strains, which showed promising characteristics that should be further evaluated. The biochemical and taxonomical characterization of bacterial strains isolated from different niches and the evaluation of their interaction with plants under varying conditions will help to increase our knowledge on PGP microorganisms and their use in agriculture.