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Bacteria on and inside leaves can influence forest tree health and resilience. The distribution and limits of a tree species' range can be influenced by various factors, with biological interactions among the most significant. We investigated the processes shaping the bacterial needle community across the species distribution of limber pine, a widespread Western conifer inhabiting a range of extreme habitats. We tested four hypotheses: (i) Needle community structure varies across sites, with site-specific factors more important to microbial assembly than host species selection; (ii) dispersal limitation structures foliar communities across the range of limber pine; (iii) the relative significance of dispersal and selection differs across sites in the tree species range; and (iv) needle age structures bacterial communities. We characterized needle communities from the needle surface and tissue of limber pine and co-occurring conifers across 16 sites in the limber pine distribution. Our findings confirmed that site characteristics shape the assembly of bacterial communities across the host species range and showed that these patterns are not driven by dispersal limitation. Furthermore, the strength of selection by the host varied by site, possibly due to differences in available microbes. Our study, by focusing on trees in their natural setting, reveals real needle bacterial dynamics in forests, which is key to understanding the balance between stochastic and deterministic processes in shaping forest tree-microbe interactions. Such understanding will be necessary to predict or manipulate these interactions to support forest ecosystem productivity or assist plant migration and adaptation in the face of global change.

Variovorax species catabolize a wide range of natural and industrial products and have been shown to be integral rhizosphere inhabitants. Here, we report the complete genomes of V. paradoxus 2u118 and V. sp. SPNA7, which were isolated from alfalfa root nodules and possess plant growth-promoting properties.

Producción Científica, Endophytic fungi offer promising alternatives for sustainable plant disease management strategies, often through the production of bioactive secondary metabolites. This study investigated the biocontrol potential of filtrates and extracts, produced under controlled conditions, from Alternaria leptinellae E138 against Pseudomonas syringae in tomato plants under greenhouse conditions. To understand the main mechanisms involved in biocontrol, the direct inhibition of bacterial growth and disruption of quorum sensing activity caused by metabolites were studied in vitro, as well as indirect mechanisms, such as their capacity to produce phytohormone-like substances, nutrient mobilization, and antioxidant activity, which can enhance plant growth and fitness. Moreover, a mass spectrometry analysis was used to tentatively identify the secondary metabolites present in the extract with antimicrobial properties, which could explain the biocontrol effects observed. Mycopriming assays, involving the direct treatment of tomato seeds with the fungal A. leptinellae E138 extracts, produced increased germination rates and seedling vigor in tomato seeds. As another treatment, postemergence application of the extracts in greenhouse conditions significantly improved plant health and resulted in a 41% decrease in disease severity. Overall, this study underscores the potential of A. leptinellae E138 extract as a plant growth promoter with biocontrol capabilities, offering promising avenues for sustainable plant disease management., Junta de Extremadura y Fondo Social Europeo - (grant PD18037)

The model moss species Physcomitrium patens has long been used for studying divergence of land plants spanning from bryophytes to angiosperms. In addition to its phylogenetic relationships, the limited number of differential tissues, and comparable morphology to the earliest embryophytes provide a system to represent basic plant architecture. Based on plant-fungal interactions today, it is hypothesized these kingdoms have a long-standing relationship, predating plant terrestrialization. Mortierellaceae have origins diverging from other land fungi paralleling bryophyte divergence, are related to arbuscular mycorrhizal fungi but are free-living, observed to interact with plants, and can be found in moss microbiomes globally. Due to their parallel origins, we assess here how two Mortierellaceae species, Linnemannia elongata and Benniella erionia, interact with P. patens in coculture. We also assess how Mollicute-related or Burkholderia-related endobacterial symbionts (MRE or BRE) of these fungi impact plant response. Coculture interactions are investigated through high-throughput phenomics, microscopy, RNA-sequencing, differential expression profiling, gene ontology enrichment, and comparisons among 99 other P. patens transcriptomic studies. Here we present new high-throughput approaches for measuring P. patens growth, identify novel expression of over 800 genes that are not expressed on traditional agar media, identify subtle interactions between P. patens and Mortierellaceae, and observe changes to plant-fungal interactions dependent on whether MRE or BRE are present. Our study provides insights into how plants and fungal partners may have interacted based on their communications observed today as well as identifying L. elongata and B. erionia as modern fungal endophytes with P. patens.

Meristematic fungi are mainly defined as having aggregates of thick-walled, melanised cells enlarging and reproducing by isodiametric division. Dothideomycetes black meristematic and meristematic-like fungi have been allied to Myriangiales, which currently has two accepted families, Myriangiaceae and Elsinoaceae, with fungi mainly regarded as pathogens, parasites, saprobes and epiphytes of different plant species. This study aimed to verify the phylogenetic position using four nuclear markers (SSU, LSU, ITS and RPB2) of the incertae sedis genera associated with Myriangiales, namely Endosporium, Gobabebomyces, Lembosiniella and Phaeosclera, and the new genus, Endophytium gen. nov. (including E. albocacti sp. nov. and E. cacti sp. nov.), established for endophytic fungi occurring in cacti in Brazil. Based on morphology, lifestyle and phylogenetic inferences, these black meristematic and meristematic-like fungi cannot be accommodated in Myriangiales. Combining these results, three new orders and two new families are introduced: Endophytiales ord. nov. (including Endophytiaceae fam. nov. for Endophytium gen. nov.), Endosporiales ord. nov. (including Endosporiaceae for Endosporium) and Phaeosclerales ord. nov. (including Phaeoscleraceae fam. nov. for Phaeosclera). Gobabebomyces and Lembosiniella remained incertae sedis due to their disposition in the phylogenetic tree, that moved among clades accordingly with the gene analysed. Our results show that the inclusion of endophytic fungi obtained from plants in dry forests can contribute to the discovery of new taxa,clarify the phylogenetic position of allied taxa and confer information to the estimation of national and global fungal diversity.

Many plants possess immense pharmacological properties because of the presence of various therapeutic bioactive secondary metabolites that are of great importance in many pharmaceutical industries. Therefore, to strike a balance between meeting industry demands and conserving natural habitats, medicinal plants are being cultivated on a large scale. However, to enhance the yield and simultaneously manage the various pest infestations, agrochemicals are being routinely used that have a detrimental impact on the whole ecosystem, ranging from biodiversity loss to water pollution, soil degradation, nutrient imbalance and enormous health hazards to both consumers and agricultural workers. To address the challenges, biological eco-friendly alternatives are being looked upon with high hopes where endophytes pitch in as key players due to their tight association with the host plants. The intricate interplay between plants and endophytic microorganisms has emerged as a captivating subject of scientific investigation, with profound implications for the sustainable biosynthesis of pharmaceutically important secondary metabolites. This review delves into the hidden world of the "secret wedlock" between plants and endophytes, elucidating their multifaceted interactions that underpin the synthesis of bioactive compounds with medicinal significance in their plant hosts. Here, we briefly review endophytic diversity association with medicinal plants and highlight the potential role of core endomicrobiome. We also propose that successful implementation of in situ microbiome manipulation through high-end techniques can pave the way towards a more sustainable and pharmaceutically enriched future., Correction in: Microbial Cell Factories, vol. 23, issue 1, DOI:10.1186/s12934-023-02281-1QC 20231116

The biological management of plant diseases has developed into a separate scientific and technological discipline, and in recent years, this change has happened quickly. A fonn of bacterium known as a bacterial endophyte may colonize any portion of a plant without causing any symptoms or harm to the host plant. Endophytic bacteria have been discovered by several researchers, and there is growing evidence that they can stop a variety of plant diseases from growing and functioning. Endophytes have a variety of benefits including growth-increasing and disease-hampering properties. Researchers’ interest in this field is growing as a result of its potentially to be utilized as an alternative to synthetic fungicides. This review’s main objectives are to chart the development of endophytic bacterial research and give scientists access to current knowledge that will spur further investigation. Endophytic bacteria are employed to control plant diseases including wilt, rot and post-harvest damage, as well as nematode infestation. Endophytic bacteria are also used to control nematodes and postharvest diseases. With an emphasis on endophytic bacteria, this review explains the diverse mechanisms of bacterial endophytes to shield the plant from biotic infection.

Extreme Wetterereignisse wie Dürre werden laut Prognosen aufgrund des Klimawandels in ihrer Häufigkeit und Intensität in Zukunft zunehmen (Compant et al., 2010; Naylor & Coleman-Derr, 2018). Durch die enge Korrelation von Klima und Landwirtschaft werden durch den Klimawandel auch die Ernteerträge beeinflusst. Bei Pflanzen löst Dürrestress unter anderem eine Verringerung der Produktivität der Kulturpflanzen und geringere Ernteerträge aus (Bogati & Walczak, 2022). Die Gerste (Hordeum vulgare) gilt nach Weizen, Mais und Reis als vierthäufigstes angebautes Getreide weltweit (Newton et al., 2011). Hitzestress führt beispielsweise bei der Gerste zu einem verringerten Ertrag, es kommt zu einer Verschlechterung der Malzqualität, was auf hohe Proteinkonzentrationen und geringe Akkumulation von Kohlenhydraten zurückzuführen ist (Mahalingam & Bergitzer, 2019). Aber auch Bodenbakterien, die Schlüsselrollen bei der Regulation des Nährstoffkreislaufs, der Mineralisierung, der Stickstofffixierung und der Umwandlung von Ammoniak in pflanzenverfügbares Nitrat spielen, können von erhöhten Bodentemperaturen ebenfalls negativ beeinflusst werden (Younas et al., 2022). Endophytische Mikroben (Bakterien und Pilze) besiedeln das Innere der Pflanzen und können positive Auswirkungen auf die Wirtspflanze haben (Hardoim et al., 2015). In dieser Arbeit wurden die Auswirkungen einer vierwöchigen Dürre auf die Bodenmikrobiologie und die Diversität und Abundanz endophytischer Mikroben in den Wurzeln der Gerste untersucht. Hierfür wurden Felder am Forschungsbauernhof in Imst in vier Parzellen eingeteilt und für einen kontrollierten Wassereintrag überdacht. Es wurde ein genaues Bewässerungsregime berechnet, bei dem zwei Parzellen kaum bewässert (=unbewässert) wurden und Dürre simulierten. Die Bewässerung der anderen 2 Parzellen glich einer normalen Dotation während der Vegetationszeit der Sommergerste und sollte dem natürlichen Niederschlag in dieser Region entsprechen (=bewässert). Es wurden zwei v, Extreme weather events such as drought are predicted to increase in frequency and intensity in the future due to climate change (Compant et al., 2010; Naylor & Coleman-Derr, 2018). Due to the close correlation between climate and agriculture, crop yields will also be affected by climate change. With the rise of air temperature, it must be assumed that soil temperature will also increase in the future. In plants, drought stress triggers, among other things, a reduction in crop productivity and lower crop yields (Bogati & Walczak, 2022). Barley (Hordeum vulgare) is considered the fourth most widely grown cereal in the world after wheat, corn and rice (Newton et al., 2011). Drought and heat stress was shown to lead to reduced yields of barley, for example, and there is also a deterioration in malt quality, which is due to high protein concentrations and low accumulation of carbohydrates (Mahalingam & Bergitzer, 2019). However, soil bacteria, which play key roles in nutrient cycling regulation, mineralization, nitrogen fixation, and the conversion of ammonia to plant-available nitrate, can also be negatively affected by elevated soil temperature and reduced water availability (Younas et al., 2022). Endophytic microbes (bacteria and fungi) colonize the interior of plants and can have beneficial effects on the host plant (Hardoim et al., 2015). To test the effect of drought on soil microbiology and the diversity and abundance of endophytic microbes, the current study was performed on barley fields and with barley roots. For this purpose, a part of the research field in Imst was divided into four plots and covered for controlled water input. Of these, two plots were hardly irrigated (=unirrigated), the irrigation of the other two plots corresponded to a natural precipitation amount during the growing season of spring barley in this region (=irrigated). Two different varieties of spring barley were grown. On the one hand the Alpina barley and on the other hand the Montafone, Masterarbeit Universität Innsbruck 2023

Despite evidence that the microbiome extends host genetic and phenotypic traits, information on how the microbiome is transmitted and maintained across generations remains fragmented. For seed-bearing plants, seeds harbor a distinct microbiome and play a unique role by linking one generation to the next. Studies on microbial inheritance, a process we suggest including both vertical transmission and the subsequent migration of seed microorganisms to the new plant, thus become essential for our understanding of host evolutionary potential and host–microbiome coevolution. We propose dividing the inheritance process into three stages: (i) plant to seed, (ii) seed dormancy, and (iii) seed to seedling. We discuss the factors affecting the assembly of the microbiome during the three stages, highlight future research directions, and emphasize the implications of microbial inheritance for fundamental science and society.

Dutch elm disease (DED) is causing extensive mortality of ecologically and culturally valuable elm trees (Ulmus spp.). Treatment of elms with the biological vaccine Dutch Trig((R)) has been found to provide effective protection against DED by stimulating the defensive mechanisms of the trees. We hypothesized that the same mechanisms could also affect non-target organisms associated with elms. We explored the possible effects of vaccination on epiphytes (mainly lichens) and fungal endophytes living in the bark and young xylem of treated elms. Epiphyte cover percentage was assessed visually using a grid placed on the trunks, and a culture-based approach was used to study endophytes. Epiphyte cover was lower on the trunks of vaccinated trees as compared with unvaccinated trees, but the difference was not statistically significant. The presence of slow-growing and uncommon endophytes seemed to be reduced in continuously vaccinated elms; however, the highest endophyte diversity was found in elms four years after cessation of the vaccination treatments. Our findings suggest that although vaccination may shape epiphyte and endophyte communities in elms, its impacts are not straightforward. More detailed studies are, therefore, needed to inform the sustainable application of the vaccine as a part of the integrated management of DED.

According to the EU, the global consumption of biomass, fossil fuels, metals, and minerals is expected to double by 2050, while waste will increase by 70%. In this context, the Circular Economy Action Plan (CEAP) intends to integrate development and sustainability. In this regard, tailored biofertilizers based on plant growth-promoting bacteria (PGPB) can improve plant yield with fewer inputs. In our project, an autochthonous halophyte of the Andalusian marshes, namely Mesembryanthemum crystallinum, was selected for its interest as a source of pharmaceuticals and nutraceuticals. The aim of this work was to use a culturomics approach for the isolation of specific PGPB and endophytes able to promote plant growth and, eventually, modulate the metabolome of the plant. For this purpose, a specific culture medium based on M. crystallinum biomass, called Mesem Agar (MA), was elaborated. Bacteria of three compartments (rhizosphere soil, root endophytes, and shoot endophytes) were isolated on standard tryptone soy agar (TSA) and MA in order to obtain two independent collections. A higher number of bacteria were isolated on TSA than in MA (47 vs. 37). All the bacteria were identified, and although some of them were isolated in both media (Pseudomonas, Bacillus, Priestia, Rosellomorea, etc.), either medium allowed the isolation of specific members of the M. crystallinum microbiome such as Leclercia, Curtobacterium, Pantoea, Lysinibacillus, Mesobacillus, Glutamicibacter, etc. Plant growth-promoting properties and extracellular degrading activities of all the strains were determined, and distinct patterns were found in both media. The three best bacteria of each collection were selected in order to produce two different consortia, whose effects on seed germination, root colonization, plant growth and physiology, and metabolomics were analyzed. Additionally, the results of the plant metabolome revealed a differential accumulation of several primary and secondary metabolites with

A rapidly increasing human population coupled with climate change and several decades of over-reliance on synthetic fertilizers has led to two pressing global challenges: food insecurity and land degradation. Therefore, it is crucial that practices enabling both soil and plant health as well as sustainability be even more actively pursued. Sustainability and soil fertility encompass practices such as improving plant productivity in poor and arid soils, maintaining soil health, and minimizing harmful impacts on ecosystems brought about by poor soil management, including run-off of agricultural chemicals and other contaminants into waterways. Plant growth promoting bacteria (PGPB) can improve food production in numerous ways: by facilitating resource acquisition of macro- and micronutrients (especially N and P), modulating phytohormone levels, antagonizing pathogenic agents and maintaining soil fertility. The PGPB comprise different functional and taxonomic groups of bacteria belonging to multiple phyla, including Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, among others. This review summarizes many of the mechanisms and methods these beneficial soil bacteria use to promote plant health and asks whether they can be further developed into effective, potentially commercially available plant stimulants that substantially reduce or replace various harmful practices involved in food production and ecosystem stability. Our goal is to describe the various mechanisms involved in beneficial plant-microbe interactions and how they can help us attain sustainability.

The citrus root and rhizosphere microbiomes have been relatively well described in the literature, especially in the context of Huanglonbing disease. Yet questions addressing the assembly of root microbial endophytes have remained unanswered. In the above ground tree tissues, leaves and stems have been the research focus point, while flush and flower microbiomes, two important tissues in the vegetative and reproductive cycles of the tree, are not well described. In this study, the fungal and bacterial taxa in five biocompartments (bulk soil, rhizosphere, root endosphere, flower and flush) of citrus trees grown in a single California orchard were profiled using an amplicon-based metagenomic Illumina sequencing approach. Trees with no observable signs of abiotic or biotic stresses were sampled for two consecutive years during the floral development phase. The rhizosphere was the most biodiverse compartment compared to bulk soil, root endosphere, flower and flush microbiomes. In addition, the belowground bacteriome was more diverse than the mycobiome. Microbial richness decreased significantly from the root exosphere to the endosphere and was overall low in the above ground tissues. Root endophytic microbial community composition shared strong similarities to the rhizosphere but also contained few taxa from above ground tissues. Our data indicated compartmentalization of the microbiome with distinct profiles between above and below ground microbial communities. However, several taxa were present across all compartments suggesting the existence of a core citrus microbiota. These findings highlight key microbial taxa that could be engineered as biopesticides and biofertilizers for citriculture.

Bacterial and fungal root endophytes can impact the fitness of their host plants, but the relative importance of drivers for root endophyte communities is not well known. Host plant species, the composition and density of the surrounding plants, space, and abiotic drivers could significantly affect bacterial and fungal root endophyte communities. We investigated their influence in endophyte communities of alpine plants across a harsh high mountain landscape using high-throughput sequencing. There was less compositional overlap between fungal than bacterial root endophyte communities, with four 'cosmopolitan' bacterial OTUs found in every root sampled, but no fungal OTUs found across all samples. We found that host plant species, which included nine species from three families, explained the greatest variation in root endophyte composition for both bacterial and fungal communities. We detected similar levels of variation explained by plant neighborhood, space, and abiotic drivers on both communities, but the plant neighborhood explained less variation in fungal endophytes than expected. Overall, these findings suggest a more cosmopolitan distribution of bacterial OTUs compared to fungal OTUs, a structuring role of the plant host species for both communities, and largely similar effects of the plant neighborhood, abiotic drivers, and space on both communities.

Increased soil salinity has numerous negative effects on plant growth and poses a significant threat to agricultural productivity worldwide. The diversity of endophytic bacterial communities found in various indigenous halophytes such as Salicornia europaea, Suaeda maritima, and Camphorosma annua, may reveal beneficial bacteria with various plant growthpromoting (PGP) properties. Members of Halomonas, the largest genus of the family Halomonadaceae, are rod-shaped, gram-negative, moderately halophilic bacteria that have been increasingly isolated from various saline environments, including halophyte tissues. As part of the halophytic microbiota, halotolerant plant growth-promoting endophytic bacteria can contribute to plant host growth, productivity, and fitness under abiotic and biotic stresses. The use of halotolerant PGP bacteria represents a good alternative strategy to mitigate the effects of salt stress in crops and to recover saline soils. The aim of this study was to isolate halotolerant bacteria from halophyte roots, and evaluate their PGP ability and their effect on germination parameters of selected crops. The endophytic bacterial communities in the roots of halophytes from natural saline soil in Slano Kopovo (Serbia) were analyzed using culture-dependent techniques. The genus Halomonas was the predominant among the halotolerant root-associated bacteria of analyzed halophytes. We have isolated seven Halomonas sp. strains, six of which were closely related (>99,86% similarity) to Halomonas songnenensis, a moderately halophilic bacterium from saline and alkaline soils. Obtained isolates were tested at different sodium chloride concentrations for a range of PGP traits at different concentrations of sodium chloride. The selected strains were used to inoculate seeds iand monitor of the germination process of barley, sunflower, and wheat under conditions of elevated salinity. Most of the isolates tolerate the NaCl concentration up to 18% and showed multiple PGP

Although plant genotypes are known to be a determinant of microbiome composition, the genetic mechanisms underlying how genotypes affect the microbiome are poorly understood. Citrus is an important, perennial fruit crop that normally contains scion grafted on the rootstock. Here, we investigated the genetic traits underlying the citrus microbiome. We sequenced the metagenome of leaf, root, and rhizosphere soil samples and the genome of corresponding citrus genotypes, which included 66 unique rootstock-scion combinations (56 scion genotypes and 9 rootstock genotypes) from one location using deep shotgun sequencing. Using a genome-wide association study (GWAS) analysis, we identified significant associations between citrus genes and a subset of genera and functional traits of the microbiome. Intriguingly, we found that bacterial secretion systems and mobility-related genes were present in single-nucleotide polymorphism-associated microbial functional traits of leaf and root microbiomes but not in the rhizosphere microbiome, indicating that they are important factors for bacteria to colonize inside or on leaf and root tissues but less so in the rhizosphere. We also discovered that chemotaxis and flagella genes play critical roles for bacteria colonizing leaf tissues but not in root tissues and the rhizosphere. Microbiome-associated host genes were mainly involved in plant immunity, transporters, hormones, cell walls, and the metabolism of carbohydrates, amino acids, and nitrogen. We identified genetic determinants that are associated with the abundance of Bacillus, Bradyrhizobium, Burkholderia, and Cellvibrio, genera that are known to comprise many beneficial bacteria for citrus. This study unraveled the genetic traits underneath the mutual selection of citrus and microbes via GWAS analyses. This study provides useful information that aids the utilization of genotypes and key members of a healthy microbiota for microbiome engineering as well as the editin

Endophytes are the microorganisms that are present in living tissue of various plant parts (roots, fruits, stem, seed, leaf etc,). Endophytic microorganisms are good source of antibiotics. Endophytic antagonists were isolated from the roots of healthy acid lime plants collected from major acid lime growing areas of Andhra Pradesh. A total of 8 fungal and 10 bacterial endophytic antagonists were isolated. The antagonists were further subjected to preliminary screening, out of which only 6 endophytic fungal antagonists (EFA 1-6) and 8 endophytic bacterial antagonists (EBA 1-8) isolates showed good inhibitory effect on radial growth of Fusarium solani causing dry root rot in acid lime in vitro. Among them the one of the best fungal and bacterial antagonists that were found to be extremely efficient against Fusarium solani in dual culture assay were selected for further molecular identification. The BLAST results revealed that one of the fungal isolate had shown 100% similarity with Aspergillus fumigatus and one of the bacterial isolate had shown 95.56% similarity with Pseudomonas aeruginosa.

The determinants of phyllosphere microbial communities are drawing much attention given their functional importance for their plant host fitness and health. Identifying these determinants remains challenging in neotropical forests, considering the diversity of the tree hosts and the strong vertical heterogeneity of abiotic conditions within the canopy and at the scale of the leaf. Here, we studied fungal and bacterial communities living in the endophytic and epiphytic phyllosphere in tree species across vertical gradients, from the top of the canopy to the ground. We used DNA metabarcoding to characterize microbial communities and measured abiotic variables and foliar traits to characterize environmental heterogeneity. The assembly of fungal communities was more driven by deterministic processes compared with bacteria, with endo- and epiphytic communities being similarly shaped by the host identity and unmeasured parameters. In contrast, in bacterial communities, the relative importance of deterministic processes decreased from endophytic to epiphytic communities. Bacterial epi- and endophytic communities were partly and differently determined by the position within the canopy, the host identity, and leaf traits, suggesting an effect of the vertical gradient and a stronger selection in the inner tissues of the leaf than on its surface. The tree host exerts a selective pressure on microbial communities but the leaf as microhabitat also contributes significantly to the assembly of microbial communities. Discrepancies exist between fungi and bacteria that probably reflect different life-history traits and ecological strategies, emphasizing the need to study these communities jointly if we are to fully understand plant–phyllosphere interactions.

Oats (Avena sativa) is a versatile crop grown worldwide for animal feed and human consumption. Humanoat consumption has recently risen due to its various health benefits. However, oats are susceptible toFusarium head blight (FHB) caused by various Fusarium fungi. FHB reduces yield and leads to mycotoxinaccumulation. The most commonly reported mycotoxins in oat are trichothecenes deoxynivalenol (DON)and T-2/HT-2 toxins. Trichothecenes inhibit eukaryotic protein biosynthesis and cause acute and chronictoxicoses in human and animals. Effective control of FHB is important for ensuring safety and quality ofoats. This thesis examines various aspects of FHB in oats, relevant to the development of better FHBcontrol strategies.Accurate FHB symptom identification is crucial for breeding resistant oats, but the symptoms of FHB arecryptic, causing errors in scoring the disease during trials. This work presents an affordable method forassessing FHB symptoms in oats by de-hulling mature seeds. Symptoms of blackening and discolorationof the oat kernels significantly correlate with Fusarium DNA and mycotoxin accumulation and thus canbe used as quantitative disease indicators.To enhance pathogen resistance, identifying and characterizing plant resistance genes is key. In thiswork two oat genes coding for DON-detoxifying UDP-glucosyltransferases (UGTs) were identified andcharacterised. Transcripts of two oat UGTs were highly upregulated in response to DON treatment andF.graminearum infection. The genes conferred resistance to several trichothecenes when expressed inyeast. Both UGTs, recombinantly expressed in E.coli were confirmed for their ability to detoxify DON.These genes could potentially be used for developing genetic markers for FHB resistance in oat.Further in this thesis, biocontrol possibilities for FHB in oats are investigated. The fungal BCAClonostachys rosea's potential against FHB is examined. Treating oat spikelets with C. rosea reducedFusarium DNA and DON content in m

Farmers use excessive chemical fertilizers to boost crop productivity to meet growing agricultural demands. However, this practice is costly and environmentally hazardous. Sustainable increase in crop yield can be achieved through alternatives like microbial-based fertilizers. In the quest to identify plant growth-promoting endophytic bacteria, the present study was carried out and selected unexplored halophytic plant Heliotropium curassavicum L. Thirteen endophytic bacterial strains were isolated from both aerial and root portions of H.curassavicum. These isolates were tested for salt tolerance, enzyme production, and synthesis of growth-promoting secondary metabolites, like Indole-3-acetic acid (IAA) and phosphate solubilization . Most of the isolates belonged to the Bacillus family, exhibiting varying Gram staining and biochemical reactions. The majority are Gram-positive bacteria, non-motile, spore formers, and exist in two cells or chains. All isolates could tolerate up to 10% NaCl concentration and a temperature of 42°C. Based on phenotypic, bio-chemical characteristics, isolate HCR3 showed promising properties in synthesizing IAA and phosphate solubilization abilities. The isolate HCR3 grew well upto 10% NaCl concentration and also 42°C temperature. Based on molecular characterization by using 16S rRNA gene-based analysis HCR3 isolate was identified and belonged to the Genus Pseudomonas with the highest similarity index with Pseudomonas khazarica sp. HCR3 showed IAA production of 37µg ml-1, had a phosphate solubilization ability of 3.5 ppm, and recorded protease activity on gelatin medium. The findings highlight the potential of HCR3 and other strains from halophytic H. curassavicum L. to enhance plant growth through secondary bioactive metabolites, offering eco-friendly solutions for sustainable agriculture.

Tall fescue (Schedonorus arundinaceous (Schreb.) Dumort. nom. cons. Lolium arundinaceum (Schreb.) Darbysh.) toxicosis results from the consumption of alkaloids released by wild-type endophytes (Epichloe coenophiala) that live in symbiosis with the plant. Alkaloid consumption causes significant production and reproductive losses which cost the U.S. beef industry approximately $2 billion every year. Incorporating species that contain condensed tannins (CTs) into forage systems may be an effective strategy to reduce the effects of fescue toxicosis in livestock. It has been hypothesized that stable complexes formed between CTs and toxic alkaloids could help reduce their absorption through the gastrointestinal epithelia, thus reducing their toxic effects. However, it is not yet clear whether CTs are effective in reducing the effects of fescue toxicosis in grazing systems. A comprehensive literature search was carried out using Google Scholar to identify studies relevant to the research question, from which the cited articles were selected. This review covers the value and issues of tall fescue employed as useful forage, summarizes the impact endophyte-infected tall fescue can have on cattle, and sets out the current management strategies implemented to minimize fescue toxicosis. The review continues with a brief summary of tannin structure and the well-documented benefits that CT-containing forages can contribute to the productivity and sustainability of ruminant agriculture. Finally, a summary of the potential forage sources, mechanisms, and benefits of CTs in reducing the negative post-ingestion effects of fescue alkaloids in livestock is provided.

Endophytic fungal communities living in leaves of trees can have a significant impact on their hosts,showing both beneficial and detrimental effects. Some mutualistic fungal species protect the host against pathogens or herbivores, while pathogenic species can increase the vulnerability of the host against biotic and abiotic stresses. The Swedish forestry model consists of planting nursery-produced seedlings after final felling. In the nurseries, the seedlings are grown densely in containers under greenhouse conditions and for disease prevention the Integrated Pest Management strategy is followed, where fungicides are applied to protect the plants. It is known that the intensive nursery production system affect the fungal communities present in the roots of seedlings by making them less diverse, but the effect in the foliar fungi is still unknown. The main objective of this study was to investigate the diversity of foliar fungal communities in Scots pine (Pinus sylvestris) seedlings produced in the nursery after their transplantation to the forest clear-cuts and to compare them with naturally regenerated seedlings. Needle samples of both types of seedlings were collected from three different forest clear-cut sites in Uppland, Sweden. The time scale and the exposure time of the needle were taken into account by sampling at 8-time points of the seasonal period and taking one-year old needles and current-year needles. Fungal communities were characterised by high- throughput sequencing of the ITS2 rRNA region of healthy-looking needles. Sequences were filtered and grouped into operational taxonomic units (OTU). The taxonomic classification of each OTU was determined using the PROTAX-fungi and massBLASTer databases and fungal lifestyle was assigned using the FungalTraits database. Results show that exposure time and needle age are the main factors affecting fungal diversity in needles, irrespective of whether seedlings are from nurseries or natural regeneration. Overall

Mangroves harbour many beneficial microorganisms in their rhizosphere, phyllosphere and endophytically, which forms an ideal ecological habitation for isolating halotolerant endophytic bacteria with unique characteristics. Endophytes can produce numerous bioactive secondary metabolites and phytohormones, which may be directly or in some way beneficial to the host plant. The present study aimed to identify novel endophytes capable of producing plant growth-promoting substances. The mangrove plants Acanthus ilicifolius L. at Corangi Wildlife Sanctuary were selected, and their leaves and roots were collected for endophyte isolation. Eight isolates from the leaves and roots were collected, purified and preserved. All these isolates were subjected to morphological, phenotypical and biochemical studies. Isolates were grown best at 3% NaCl nutrient agar and could tolerate salinity upto 8%NaCl. Most of them could grow upto 42°C. The majority were gram’s positive, motile, aerobic, rod-shaped and some were gram’s negative, rod-shaped organisms. Many of the endophytic organisms had the ability to synthesize Indole-3-acetic acid(IAA) varied from 0.7 µg/ml (AIL1) to 51.0 µg/ml (AIL2) and the highest phosphate solubilizing ability was recorded with AIR3 (3.71 ppm) followed by AIR4 (3.00 ppm) and lowest was recorded by AIL4 (1.80 ppm). Among total isolates, AIL2 (51µg/ml) showed promising potential in producing IAA and had phosphate solubilization ability. Based on 16S ribosomal RNA molecular method the isolate AIL2 was identified as Bacillus altitudinis. This is the first to report that B.altitudinis strain AIL2 isolated from A.ilicifolius L. could produce IAA, which can be used as a bioinoculant in agriculture and allied sector.

The adaptability of halophytes to increased soil salinity is related to complex rhizosphere interactions. In this study, an integrative approach, combining culture-independent and culture-dependent techniques was used to analyze the bacterial communities in the endorizosphere of indigenous succulent halophytes Salicornia europaea, Suaeda maritima, and Camphorosma annua from the natural salt marshes of Slano Kopovo (Serbia). The 16 S rDNA analyses gave, for the first time, an insight into the composition of the endophytic bacterial communities of S. maritima and C. annua. We have found that the composition of endophyte microbiomes in the same habitat is to some extent influenced by plant species. A cultivable portion of the halophyte microbiota was tested at different NaCl concentrations for the set of plant growth promoting (PGP) traits. Through the mining of indigenous halotolerant endophytes, we obtained a collection representing a core endophyte microbiome conferring desirable PGP traits. The majority (65%) of the selected strains belonged to the common halotolerant/halophilic genera Halomonas, Kushneria, and Halobacillus, with representatives exhibiting multiple PGP traits, and retaining beneficial traits in conditions of the increased salinity. The results suggest that the root endosphere of halophytes is a valuable source of PGP bacteria supporting plant growth and fitness in salt-affected soils. © 2023, The Author(s).

Introduction. The use of plant growth-promoting bacteria can be an alternative to be integrated as a management strategy of cape gooseberry crop through their incorporation in seedling stages, allowing to obtain more vigorous seedlings that can tolerate biotic and abiotic stress at the time of transplant. Objective. To evaluate the plant growth promoting activity and endophytic capacity of Bacillus amyloliquefaciens Bs006 and Pseudomonas migulae Pf014 inoculated during the seedling stage of cape gooseberry (Physalis peruviana L.). Materials and methods. In a randomized complete block design with three replications, an experiment was carried out from April to May 2018 in a greenhouse located at the Tibaitatá Research Center, Mosquera, Colombia. Bacteria were inoculated separately in the substrate at 1 x 108 UFC mL-1. Physiological variables such as dry biomass of the root, stem, and leaves (g), final length (cm), leaf area (cm2), and the number of leaves were analyzed; additionally, its endophytism was verified by evaluating the colonization of the plant tissue. Results. B. amyloliquefaciens Bs006 stimulated seedling growth at different levels, exhibiting greater promotion capacity than P. migulae Pf014, since it increased plant length by 34 %, and stem and root growth by 59 % and 16 %, respectively; also, increase in dry root biomass by 178 %, stem by 161 %, and leaves by 96 % was found. In addition, bacteria were isolated from the interior of plant tissues, demonstrating their endophytic behavior. Conclusions. The positive response in all the agronomic variables evaluated with the application of B. amyloliquefaciens Bs006, indicates that this rhizobacterium can be integrated into the cape gooseberry production scheme, helping to enhance crop production., Introducción. El uso de bacterias promotoras de crecimiento vegetal puede ser una alternativa a integrar en estrategias de manejo del cultivo de uchuva mediante su incorporación en etapas de semillero, permitiendo obtener plántulas de mayor vigor que puedan tolerar el estrés biótico y abiótico al momento del trasplante. Objetivo. Evaluar la actividad promotora de crecimiento vegetal y capacidad endofítica de las bacterias Bacillus amyloliquefaciens Bs006 y Pseudomonas migulae Pf014 inoculadas durante la etapa de semillero de uchuva (Physalis peruviana L.). Materiales y métodos. Se realizó un experimento de abril a mayo de 2018 en invernadero ubicado en el Centro de Investigación Tibaitatá, Mosquera, Colombia, en un diseño de bloques completos al azar con tres repeticiones. Se inocularon rizobacterias por separado en el sustrato 1 x 108 UFC mL-1 y se analizaron las variables fisiológicas biomasa seca (g) de raíz, tallo y hojas, la longitud final (cm), el área foliar (cm2) y número de hojas, adicionalmente se comprobó su endofitismo mediante la evaluación de la colonización del tejido vegetal. Resultados. B. amyloliquefaciens Bs006 estimuló el crecimiento de plántulas a diferentes niveles, exhibiendo mayor capacidad de promoción que P. migulae Pf014, ya que aumentó la longitud de la planta en 34 %, y el crecimiento en tallo y raíz en 59 % y 16 % respectivamente; aumento de la biomasa seca de la raíz en 178 %, el tallo en 161 %, y de las hojas en 96 %. Las bacterias se aislaron del interior de los tejidos vegetales demostrando su comportamiento endofítico. Conclusiones. La respuesta positiva en todas las variables agronómicas evaluadas con la aplicación de B. amyloliquefaciens Bs006, indica que esta bacteria puede ser integrada al esquema de producción de la uchuva contribuyendo a potenciar la producción del cultivo.

Vascular pathogens are the causal agents of some of the most devastating plant diseases in the world, which can cause, under specific conditions, the destruction of entire crops. These plant pathogens activate a range of physiological and immune reactions in the host plant following infection, which may trigger the proliferation of a specific microbiome to combat them by, among others, inhibiting their growth and/or competing for space. Nowadays, it has been demonstrated that the plant microbiome can be modified by transplanting specific members of the microbiome, with exciting results for the control of plant diseases. However, its practical application in agriculture for the control of vascular plant pathogens is hampered by the limited knowledge of the plant endosphere, and, in particular, of the xylem niche. In this review, we present a comprehensive overview of how research on the plant microbiome has evolved during the last decades to unravel the factors and complex interactions that affect the associated microbial communities and their surrounding environment, focusing on the microbial communities inhabiting the xylem vessels of olive trees (Olea europaea subsp. europaea), the most ancient and important woody crop in the Mediterranean Basin. For that purpose, we have highlighted the role of xylem composition and its associated microorganisms in plants by describing the methodological approaches explored to study xylem microbiota, starting from the methods used to extract xylem microbial communities to their assessment by culture-dependent and next-generation sequencing approaches. Additionally, we have categorized some of the key biotic and abiotic factors, such as the host plant niche and genotype, the environment and the infection with vascular pathogens, that can be potential determinants to critically affect olive physiology and health status in a holobiont context (host and its associated organisms). Finally, we have outlined future directions and challe

Postharvest pathogens cause diseases that reduce the shelf-life of fresh produce, resulting in losses that can reach 50% of the production. Therefore it is necessary to investigate new strategies to reduce the damage caused by these pathogens. Endophytic fungi are microorganisms, including a wide range of filamentous fungi and yeasts, that live in association with host plant tissues or organs without generating disease symptoms. These microorganisms can promote plant growth, increase tolerance to abiotic stresses, or be a source of important chemical compounds for industry. Furthermore, endophytic fungi stand out as important biological control agents (BCAs) of phytopathogens, due to mechanisms such as direct parasitism, production of diffusible or volatile antimicrobial secondary metabolites, lytic enzymes, competition for space and nutrients and/or the activation of plant defenses. In recent decades, several studies have proposed the application of endophytic fungi as BCAs in postharvest diseases in fresh produce, both through direct application and through the use of their secondary metabolites.

Nodule endophytes and associated bacteria are non-symbiotic bacteria that colonize legume nodules. They accompany nodulating rhizobia and can form beneficial associations, as some of them are plant growth-promoting rhizobacteria (PGPR) that are able to promote germination and plant growth and increase tolerance to biotic and abiotic stress. White lupin (Lupinus albus) is a legume crop that is gaining relevance as a suitable alternative to soybean as a plant protein source. Eleven nodule-associated bacteria were isolated from white lupin nodules grown in a Tunisian soil. They belonged to the genera Rhizobium, Ensifer, Pseudomonas and Bacillus. Their plant growth-promoting (PGP) and enzymatic activities were tested in vitro. Strains Pseudomonas sp., L1 and L12, displayed most PGP activities tested, and were selected for in planta assays. Inoculation with strains L1 or L12 increased seed germination and had the same positive effects on all plant growth parameters as did inoculation with symbiotic Bradyrhizobium canariense, with no significant differences among treatments. Inoculation with efficient nitrogen-fixing rhizobia must compete with rhizobia present in the soil that sometimes nodulate efficiently but fix nitrogen poorly, leading to a low response to inoculation. In such cases, inoculation with highly effective PGPR might represent a feasible alternative to boost crop productivity.

Members of the fungal genus Phyllosticta can colonize a variety of plant hosts, including several Citrus species such as Citrus sinensis (orange), Citrus limon (lemon), and Citrus maxima (pomelo). Some Phyllosticta species have the capacity to cause disease, such as Citrus Black Spot, while others have only been observed as endophytes. Thus far, genomic differences underlying lifestyle adaptations of Phyllosticta species have not yet been studied. Furthermore, the lifestyle of Phyllosticta citrichinaensis is ambiguous, as it has been described as a weak pathogen but Koch's postulates may not have been established and the presence of this species was never reported to cause any crop or economic losses. Here, we examined the genomic differences between pathogenic and endophytic Phyllosticta spp. colonizing Citrus and specifically aimed to elucidate the lifestyle of Phyllosticta citrichinaensis. We found several genomic differences between species of different lifestyles, including groups of genes that were only present in pathogens or endophytes. We also observed that species, based on their carbohydrate active enzymes, group independent of their phylogenetic association, and this clustering correlated with trophy prediction. Phyllosticta citrichinaensis shows an intermediate lifestyle, sharing genomic and phenotypic attributes of both pathogens and endophytes. We thus present the first genomic comparison of multiple citrus-colonizing pathogens and endophytes of the genus Phyllosticta, and therefore provide the basis for further comparative studies into the lifestyle adaptations within this genus.

Pasture dieback causes unhealthy growth and death in a range of introduced and native grasses across Queensland and into northern New South Wales, resulting in large losses in beef production areas. Pasture mealybug, Heliococcus summervillei Brookes, has been identified as the leading cause of pasture dieback. Possible management strategies include the identification of resistant or tolerant pasture varieties, and the use of endophytic fungi (both seed born and facultative) to protect pasture grasses possibly in association with pasture mixes including legumes. In New Zealand, pasture dieback in rye grass caused by the mealybug Balanococcus poae has been effectively managed by selection of endophytic fungi and incorporation into commercial pasture varieties. Fungal endophytes may be transferred in seed, while others are acquired from healthy soils, primarily by colonising the roots. Assay methods were developed and used. The relative susceptibility of 15 selected grass varieties to pasture mealybug was determined in screenhouse assays by infestation with the mealybug H. summervillei. Significant differences in susceptibility were detected. Mekong brizantha, Argentina bahia, curly Mitchel grass, Biloela buffel and Gatton panic were all less susceptible to mealybug than American buffel. Callide and Katambora Rhodes, Paspalum nicorae, green panic, and Gayndah buffel were all similar in susceptibility to American buffel. In sensitive, rapid and statistically robust laboratory assays, mealybugs on Gatton panic and Mekong brizantha died more rapidly and in higher proportions, and were less able to develop to maturity than on American Buffel. Assays demonstrated that the seed-born fungal endophyte Epichloë festucae reduced the susceptibility of perennial ryegrass to the Australian pasture mealybug H. summervillei, and reduced the severity of dieback symptoms. This result provides ‘proof of concept’ of the use of endophytes, as used commercially in New Zealand

Plants evolved in association with a diverse community of microorganisms. The effect of plant phylogeny and domestication on host-microbiome co-evolutionary dynamics are poorly understood. Here we examined the effect of domestication and plant lineage on the composition of the endophytic microbiome of 11 Malus species, representing three major groups: domesticated apple (M. domestica), wild apple progenitors, and wild Malus species. The endophytic community of M. domestica and its wild progenitors showed higher microbial diversity and abundance than wild Malus species. Heirloom and modern cultivars harbored a distinct community composition, though the difference was not significant. A community-wide Bayesian model revealed that the endophytic microbiome of domesticated apple is an admixture of its wild progenitors, with clear evidence for microbiome introgression, especially for the bacterial community. We observed a significant correlation between the evolutionary distance of Malus species and their microbiome. This study supports co-evolution between Malus species and their microbiome during domestication. This finding has major implications for future breeding programs and our understanding of the evolution of plants and their microbiomes.

High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number of environmental samples. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes sampled across the growing season, and consequently varying in phenolic composition and in the abundance of endo- and epiphytic fungal species. We optimized the DNA extraction protocol by comparing commercial kits and evaluating five fungal ribosomal specific primers (Ps) alone, and with extended primers that allow binding to sample-specific index primers, and we then optimized the amplification with these composite Ps for 380 samples. The fungal DNA concentration in the samples varied from 561 ng/µL to 1526 ng/µL depending on the DNA extraction kit used. However, binding to phenolic compounds affected DNA quality as assessed by Nanodrop measurements (0.63–2.04 and 0.26–2.00 absorbance ratios for 260/280 and 260/230, respectively), and this was judged to be more important in making our choice of DNA extraction kit. We initially modified the PCR conditions after determining the concentration of DNA extract in a few subsamples and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required amplification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected amplicon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully amplified this region for every sample (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of sample-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to success

Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Overall, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.

Microorganisms have the potential to affect plant seed germination and seedling fitness, ultimately impacting plant health and community dynamics. Because seed-associated microbiota are highly variable across individual plants, plant species, and environments, it is challenging to identify the dominant processes that underlie the assembly, composition, and influence of these communities. We propose here that metacommunity ecology provides a conceptually useful framework for studying the microbiota of developing seeds, by the application of metacommunity principles of filtering, species interactions, and dispersal at multiple scales. Many studies in seed microbial ecology already describe individual assembly processes in a pattern-based manner, such as correlating seed microbiome composition with genotype or tracking diversity metrics across treatments in dispersal limitation experiments. But we see a lot of opportunities to examine understudied aspects of seed microbiology, including trait-based research on mechanisms of filtering and dispersal at the micro-scale, the use of pollination exclusion experiments in macro-scale seed studies, and an in-depth evaluation of how these processes interact via priority effect experiments and joint species distribution modeling.

Biotic and abiotic stresses severely affect agriculture by affecting crop productivity, soil fertility, and health. These stresses may have significant financial repercussions, necessitating a practical, cost-effective, and ecologically friendly approach to lessen their negative impacts on plants. Several agrochemicals, such as fertilizers, pesticides, and insecticides, are used to improve plant health and protection; however, these chemical supplements have serious implications for human health. Plants being sessile cannot move or escape to avoid stress. Therefore, they have evolved to develop highly beneficial interactions with endophytes. The targeted use of beneficial plant endophytes and their role in combating biotic and abiotic stresses are gaining attention. Therefore, it is important to experimentally validate these interactions and determine how they affect plant fitness. This review highlights research that sheds light on how endophytes help plants tolerate biotic and abiotic stresses through plant–symbiont and plant–microbiota interactions. There is a great need to focus research efforts on this vital area to achieve a system-level understanding of plant–microbe interactions that occur naturally.

Grapevine trunk diseases (GTDs) are caused by multiple unrelated fungal pathogens, and their management remains difficult worldwide. Biocontrol is an attractive and sustainable strategy given the current need for a cleaner viticulture. In this study, twenty commercial vineyards were sampled across California to isolate endophytic and rhizospheric bacteria from different grapevine cultivars with the presence and absence of GTD symptoms. A collection of 1344 bacterial isolates were challenged in vitro against Neofusicoccum parvum and Diplodia seriata, from which a subset of 172 isolates exerted inhibition levels of mycelial growth over 40%. Bacterial isolates were identified as Bacillus velezensis (n = 154), Pseudomonas spp. (n = 12), Serratia plymuthica (n = 2) and others that were later excluded (n = 4). Representative isolates of B. velezensis, P. chlororaphis, and S. plymuthica were challenged against six other fungal pathogens responsible for GTDs. Mycelial inhibition levels were consistent across bacterial species, being slightly higher against slow-growing fungi than against Botryosphaeriaceae. Moreover, agar-diffusible metabolites of B. velezensis strongly inhibited the growth of N. parvum and Eutypa lata, at 1, 15, and 30% v/v. The agar-diffusible metabolites of P. chlororaphis and S. plymuthica, however, caused lower inhibition levels against both pathogens, but their volatile organic compounds showed antifungal activity against both pathogens. These results suggest that B. velezensis, P. chlororaphis and S. plymuthica constitute potential biocontrol agents (BCAs) against GTDs and their application in field conditions should be further evaluated.

Plant microbiomes are an essential component of the plant host and are widely known to ameliorate environmental stress response. In the California Sierra Nevada, the endemic cutleaf monkeyflower (Mimulus laciniatus) is experiencing and adapting to various levels of stress associated with climate change, however, it is unclear to what extent the M. laciniatus microbiome is engaged in responding to this stress. This thesis aims to determine the monkeyflower microbiome along with their growing substrate (moss or soil) across a steep elevation gradient in the species range during the 2019 growing season. Specifically, we collected monkeyflower plants and divided those collections into compartment subsamples (roots, shoots, soil, and moss substrate) to assess the bacterial communities of each compartment by 16S rRNA gene sequencing to answer the following: (i) Do the M. laciniatus endophyte communities differ in composition and diversity across the M. laciniatus species range, and does this composition vary by elevation? (ii) Does the M. laciniatus endophyte community differ between plant compartments (e.g. root and shoot)? (iii) Do soil and moss, from which M. laciniatus grows, serve as a source of M. laciniatus endophytes, and do soil and moss communities vary in structure across the M. laciniatus species range? We found that the bacterial community structure of both plant compartments (roots and shoots) and the substrate (soil, and moss) differed across the range of M. laciniatus. Compartment strongly influenced bacterial communities, supporting the idea that plant compartments provide micro-habitats for bacterial communities. Elevation played a role in community variation when all samples were analyzed together. When compartment subsets were analyzed separately, population and site (nested in population) were significant drivers of variation in all four compartments. The differences between sites and population may be explained by the effect on bacterial communities by local climate, which could in turn reflect that the plant host selects beneficial microbes to support plant responses to the local environment, leading to habitat-adapted symbiosis. Alternatively, differences in bacterial community structure across the M. laciniatus species range could be due to differences in the metacommunity of locally available bacterial taxa to colonize compartments. This thesis highlights the importance of plant compartment and local climate or metacommunity in shaping bacterial communities along the elevation gradient of plant species.

Recently, a new annotation tool “FungalTraits” was created based on the previous FUNGuild and FunFun databases, which has attracted high attention in the scientific community. These databases were widely used to gain more information from fungal sequencing datasets by assigning fungal functional traits. More than 1500 publications so far employed FUNGuild and the aim of this study is to compare this successful database with the recent FungalTraits database. Quality and quantity of the assignment by FUNGuild and FungalTraits to a fungal internal transcribed spacer (ITS)–based amplicon sequencing dataset on amplicon sequence variants (ASVs) were addressed. Sequencing dataset was derived from leaves and needles of 12 temperate broadleaved and coniferous tree species. We found that FungalTraits assigned more functional traits than FUNGuild, and especially the coverage of saprotrophs, plant pathogens, and endophytes was higher while lichenized fungi revealed similar findings. Moreover, ASVs derived from leaves and needles of each tree species were better assigned to all available fungal traits as well as to saprotrophs by FungalTraits compared to FUNGuild in particular for broadleaved tree species. Assigned ASV richness as well as fungal functional community composition was higher and more diverse after analyses with FungalTraits compared to FUNGuild. Moreover, datasets of both databases showed similar effect of environmental factors for saprotrophs but for endophytes, unidentical patterns of significant corresponding factors were obtained. As a conclusion, FungalTraits is superior to FUNGuild in assigning a higher quantity and quality of ASVs as well as a higher frequency of significant correlations with environmental factors.

Les aulnes, des arbustes rustiques indigènes au Canada, peuvent coloniser des environnements perturbés grâce en partie à leurs symbioses avec des microorganismes bénéfiques. Les bactéries filamenteuses du genre Frankia, par exemple, forment des structures spécialisées appelées nodules sur les racines d'aulnes qui permettent une fixation d'azote atmosphérique suffisante pour combler les besoins en cet élément essentiel pour la plante, un phénomène nommé symbiose actinorhizienne. Ces caractéristiques font des aulnes crispés et rugueux des candidats de choix pour la revégétalisation de sites anthropisés comme des sites miniers au Québec. D’autres bactéries que Frankia ont été retrouvées dans des nodules de diverses plantes actinorhiziennes, mais cette exploration n'a pas à ce jour été effectuée chez les aulnes crispés et rugueux de l'Amérique du Nord. L'objectif de cette thèse est donc d'isoler et caractériser des souches bactériennes endophytes des nodules de ces deux espèces végétales. Une diversité microbienne surprenante a été isolée d'aulnes gnotobiotiques inoculés avec des échantillons environnementaux provenant de la mine Sigma à Val-d'Or, Qc, et des traits associés à une promotion de la croissance végétale ont été détectés parmi les isolats. Plusieurs isolats peuvent sécréter des hormones végétales auxiniques, solubiliser des phosphates inorganiques et mobiliser le fer à l'aide de sidérophores. Le séquençage génomique d'une sélection d'isolats a aussi révélé une grande diversité de capacités métaboliques, dont des gènes associés à la promotion de la croissance végétale. Des gènes liés à la synthèse et manipulation de niveaux d'hormones végétales ont été répertoriés, tout comme des gènes de synthèse de nombreux métallophores et des gènes associés à la solubilisation et la mobilisation de sources de phosphore. Des gènes de résistance aux métaux lourds, xénobiotiques organiques et espèces réactives de l'oxygène ont été retrouvés chez bon nombre d'isolats et quelqu

In the last 30 years, quinoa started to be tested and produced in more than 100 countries outside the Andes, its region of origin. Nowadays, quinoa is found in more than 120 countries around the globe. During this time, biotechnology has become an important tool for different areas of research in quinoa, especially with the use of genetic markers. Biotechnology applications in this underutilized grain started in the United States, and their use has been more intensive in countries where quinoa was recently introduced. Biotechnology benefitted the quinoa sector with numerous studies on the species evolution, responses to abiotic stress, and assisted methods for faster genetic improvement. The recent quinoa genome description enables an exponential development with the complementation from novel areas, techniques, and tools such as omics and bioinformatics. Despite this, biotechnology applications in the Andean countries have been more limited due to economic and politic contexts. Nevertheless, biotechnology has been used to characterize the rich Andean germplasm, improve conservation systems, and develop bioinput. In this sense, since biotechnology should keep providing solutions for food security under healthy, sustainable, and reasonable principles, its use can be highly recommended. Biotechnology has the great potential to accelerate conventional breeding processes commonly applied to this crop, as well as to generate alternative options to enhance the production system and as model to improve other crops. With an integrative view and collaboration between different countries, biotechnology can provide tangible benefits to different stakeholders.

Understanding the unique and unexplored microbial environment of xylem sap is starting to be of relevant importance for plant health, as it could include microbes that may protect plants against xylem-limited pathogens, such as Verticillium dahliae and Xylella fastidiosa. In this study, we evaluated the effects that the method for extracting the xylem bacterial communities, the plant age and the PCR primers may have on characterizing the xylem-bacterial-community composition by using an NGS approach. Xylem sap was extracted from xylem vessels by using a Scholander pressure chamber, or by macerating wood shavings that were obtained from xylem tissues by using branches from 10-year-old olive trees, or the entire canopy of 1-year-old olive plantlets. Additionally, we compared four different PCR-primer pairs that target 16S rRNA for their efficacy to avoid the coamplification of mitochondria and chloroplast 16S rRNA, as this represents an important drawback in metabarcoding studies. The highest amplifications in the mitochondria and chloroplast reads were obtained when using xylem woody chips with the PCR1-799F/1062R (76.05%) and PCR3-967F/1391R (99.96%) primer pairs. To the contrary, the PCR2-799F/1115R and PCR4-799F/1193R primer pairs showed the lowest mitochondria 16S rRNA amplification (<27.48%), no chloroplast sequences and the highest numbers of bacterial OTUs identified (i.e., 254 and 266, respectively). Interestingly, only 73 out of 172 and 46 out of 181 genera were shared between the xylem sap and woody chips after amplification with PCR2 or PCR4 primers, respectively, which indicates a strong bias of the bacterial-community description, depending on the primers used. Globally, the most abundant bacterial genera (>60% of reads) included Anoxybacillus, Cutibacterium, Pseudomonas, Spirosoma, Methylobacterium-Methylorubrum and Sphingomonas; however, their relative importance varied, depending on the matrix that was used for the DNA extraction and the primer pairs

Environmental stresses can compromise the interactions of plants with beneficial microbes. In the present review, experimental results showing that stresses negatively affect the abundance and/or functionality of plant beneficial microbes are summarized. It is proposed that the environmental interference of these plant-microbe interactions is explained by the stress-mediated induction of plant signalling pathways associated with defence hormones and reactive oxygen species. These plant responses are recognized to regulate beneficial microbes within plants. The direct negative effect of stresses on microbes may also contribute to the environmental regulation of these plant mutualisms. It is also posited that, in stress situations, beneficial microbes harbour mechanisms that contribute to maintain the mutualistic associations. Beneficial microbes produce effector proteins and increase the antioxidant levels in plants that counteract the detrimental effects of plant stress responses on them. In addition, they deliver specific stress-protective mechanisms that assist to their plant hosts to mitigate the negative effects of stresses. Our study contributes to understanding how environmental stresses affect plant-microbe interactions and highlights why beneficial microbes can still deliver benefits to plants in stressful environments.

Cactus are among the most drought tolerant plants. As Opuntia is able to grow under the stress of drought, this study aims to check if endophytic bacteria isolated from cactus roots have beneficial potential for crops such as wheat during drought. Two endophytic bacterial isolates were isolated from the roots of the cactus and screened for their plant growth promoting characteristics, such as N-free growth and auxin production. These bacteria have demonstrated their potential to promote the growth of durum wheat under in-vitro conditions and have been identified as Pseudomonas putida and P.brassicacearum, following the sequencing of the 16S rRNA gene and phylogenetic analysis, and significantly improved growth parameters such as seeding length compared to the unobstructed control. After 05 days of contact of the two bacteria, P.putida and P.brassicacearum, with sprouted wheat seeds, a root growth rate of (39.88% and 62.14%, respectively) was recorded. The same effect on the growth of wheat roots is caused by the volatile substances of these bacteria deposited separately, with a rate of (53.30% and 24.18%) respectively. Symptoms of drought stress were visibly reduced on seedlings inoculated with P.putida and P.brassicacearum bacteria, a result supported by a growth rate of root parameters in length (260.83% and 179.60%), surface (21.98% and 60.17%) and scope (59.46% and 62.67%), respectively. This work opens up many perspectives for the characterization and selection of endophyte bacteria of under-used drought-tolerant species such as cacti for the improvement of the growth of field crops. These results promote the deployment of Pseudomonas sp as an effective biofertilizer in wheat.

Beneficial plant–microbe interactions lead to physiological and biochemical changes that may result in plant-growth promotion. This study evaluated the effect of the interaction between sugarcane and endophytic bacterial strains on plant physiological and biochemical responses under two levels of nitrogen (N) fertilization. Six strains of endophytic bacteria, previously selected as plant growth-promoting bacteria (PGPB), were used to inoculate sugarcane mini stalks, with and without N fertilization. After 45 days, biomass production; shoot nutrient concentrations; foliar polyamine and free amino acid profiles; activities of nitrate reductase and glutamine synthase; and the relative transcript levels of the GS1, GS2, and SHR5 genes in sugarcane leaves were determined. All six endophytic strains promoted sugarcane growth, increasing shoot and root biomass, plant nutritional status, and the use efficiency of most nutrients. The inoculation-induced changes at the biochemical level altered the foliar free amino acid and polyamine profiles, mainly regarding the relative concentrations of citrulline, putrescine, glycine, alanine, glutamate, glutamine, proline, and aspartate. The transcription of GS1, GS2, and SHR5 was higher in the N fertilized seedlings, and almost not altered by endophytic bacterial strains. The endophytic strains promoted sugarcane seedlings growth mainly by improving nutrient efficiency. This improvement could not be explained by their ability to induce the production of amino acid and polyamine composts, or GS1, GS2, and SHR5, showing that complex interactions may be associated with enhancement of the sugarcane seedlings’ performance by endophytic bacteria. The strains demonstrated biotechnological potential for sugarcane seedling production.

In natural and agricultural ecosystems, survival and growth of plants depend substantially on residing microbes in the endosphere and rhizosphere. Although numerous studies have reported the presence of plant-growth promoting bacteria and fungi in below-ground biomes, it remains a major challenge to understand how sets of microbial species positively or negatively affect plants’ performance. By conducting a series of single- and dual-inoculation experiments of 13 plant-associated fungi targeting a Brassicaceae plant species (Brassica rapa var. perviridis), we here systematically evaluated how microbial effects on plants depend on presence/absence of co-occurring microbes. The comparison of single- and dual-inoculation experiments showed that combinations of the fungal isolates with the highest plant-growth promoting effects in single inoculations did not have highly positive impacts on plant performance traits (e.g., shoot dry weight). In contrast, pairs of fungi with small/moderate contributions to plant growth in single-inoculation contexts showed the greatest effects on plants among the 78 fungal pairs examined. These results on the offset and synergistic effects of pairs of microbes suggest that inoculation experiments of single microbial species/isolates can result in the overestimation or underestimation of microbial functions in multi-species contexts. Because keeping single-microbe systems under outdoor conditions is impractical, designing sets of microbes that can maximize performance of crop plants is an important step for the use of microbial functions in sustainable agriculture.

A thesis submitted in fulfillment of the requirements for the Degree of Master of Science, Endophytic microorganisms are symbionts found inside host tissue without eliciting disease, symptoms or causing any damage. They play an integral role in spermatophyte life cycles and are endowed with multi-functional traits that promote the host’s health, growth and yield. Cleome gynandra L. (C. gynandra), is an unexplored “orphan” plant that has a diverse array of such endophytic microbial populations. C. gynandra (Ombidi in Oshiwambo; Ombowa in Herero; Gomabeb in Damara/Nama) is a neglected droughttolerant wild annual crop spread in semi-arid regions of Northern Namibia. This plant has shown great potential in agronomy, climate adaptation, economy and traditional medicine, making it stand out as a prominent contender among climate-adapted future crops. Little, however, is known about C. gynandra plant growth promoting (PGP) seed endophytes. The study aimed to isolate and identify endophytic bacteria associated with C. gynandra spermatophyte and characterize their functional plant growth promoting potential which could be used to improve plant growth and yield. Twenty morphologically distinct isolates were assessed. They exhibited various abilities to produce growth regulators that contribute to ammonia production (85%), atmospheric nitrogen fixation (40%), fluorescence production (10%), hydrogen cyanide production (30%), indole acetic acid (IAA) production (100%), phosphate solubilization (15%) and siderophore production (80%). Phylogenetic analysis showed that all the isolates (excluding Phytobacter ursingii) belonged to the Proteobacteria phylum. The application of endophytic plant growth promoting bacteria (PGPB) is considered to have the potential for improving plant growth in extreme environments. Three best PGP producing isolates, namely Enterobacter cloacae, Klebsiella pneumoniae and Kluyvera cryocrescens were selected for greenhouse trials using Brassica napus L. (Rape English Giant) seeds. In comparison to the control groups, there was a statistically si