Plant-associated Microorganisms Research Articles

Dimethylpolysulfides production as the major mechanism behind wheat fungal pathogen biocontrol, by Arthrobacter and Microbacterium actinomycetes.

Volatile organic compounds (VOCs) produced by plant-associated microorganisms could serve as natural biocontrol compounds. In this work, we investigate the potential of wheat rhizosphere Microbacterium and Arthrobacter actinomycetes to inhibit the growth of major wheat phytopathogenic fungi, Fusarium graminearum and Zymoseptoria tritici via production of antifungal VOCs. A correlative analysis between fungal-growth inhibition versus bacterial volatilomic profiles identified four dimethylpolysulfide (DMPS) VOCs as the main active compounds behind their biocontrol potential. Subsequent inhibition assays reveal that DMTriS (dimethyltrisulfide) exhibits the strongest inhibition effects, then dimethyldisulfide (DMDiS). Further investigation focuses on the mechanisms behind F. graminearum-growth inhibition by the most active strain Microbacterium JM188 in dual culture. Surprisingly, nine interaction-induced VOCs, including two fungal sesquiterpenes, were exclusively detected in dual cultures, suggesting a complex interplay between microbial VOC production and sensing. More importantly, all JM188 VOCs, including antifungal DMPS, were less abundant in dual cultures, suggesting an uptake of bacterial VOCs by the fungus. Quantification of pure DMPS after confrontation with F. graminearum confirmed complete and partial uptake by the fungus of DMTriS and DMDiS VOCs, respectively, suggesting a potential link between the fungal uptake level of bacterial VOCs and their toxicity. Finally, we demonstrated that F. graminearum growth inhibition leads to a complete depletion of DON (deoxynivalenol) carcinogenic mycotoxins, highlighting a significant modulation of fungal metabolism. Collectively, these results pinpoint DMPS as broad-range fungal-inhibiting VOCs produced by rhizosphere Microbacterium and Arthrobacter, and emphasize the extensive VOC-mediated interplay between bacterial biocontrol agents and fungal pathogens.IMPORTANCEAs the management of wheat fungal diseases becomes increasingly challenging, the use of bacterial agents with biocontrol potential against the two major wheat phytopathogens, Fusarium graminearum and Zymoseptoria tritici, may prove to be an interesting alternative to conventional pest management. Here, we have shown that dimethylpolysulfide volatiles are ubiquitously and predominantly produced by wheat-associated Microbacterium and Arthrobacter actinomycetes, displaying antifungal activity against both pathogens. By limiting pathogen growth and DON virulence factor production, the use of such DMPS-producing strains as soil biocontrol inoculants could limit the supply of pathogen inocula in soil and plant residues, providing an attractive alternative to dimethyldisulfide fumigant, which has many non-targeted toxicities. Notably, this study demonstrates the importance of bacterial volatile organic compound uptake by inhibited F. graminearum, providing new insights for the study of volatiles-mediated toxicity mechanisms within bacteria-fungus signaling crosstalk.

Plant endophytes: unveiling hidden applications toward agro-environment sustainability.

Endophytic microbes are plant-associated microorganisms that reside in the interior tissue of plants without causing damage to the host plant. Endophytic microbes can boost the availability of nutrient for plant by using a variety of mechanisms such as fixing nitrogen, solubilizing phosphorus, potassium, and zinc, and producing siderophores, ammonia, hydrogen cyanide, and phytohormones that help plant for growth and protection against various abiotic and biotic stresses. The microbial endophytes have attained the mechanism of producing various hydrolytic enzymes such as cellulase, pectinase, xylanase, amylase, gelatinase, and bioactive compounds for plant growth promotion and protection. The efficient plant growth promoting endophytic microbes could be used as an alternative of chemical fertilizers for agro-environmental sustainability. Endophytic microbes belong to different phyla including Euryarchaeota, Ascomycota, Basidiomycota, Mucoromycota, Firmicutes, Proteobacteria, and Actinobacteria. The most pre-dominant group of bacteria belongs to Proteobacteria including α-, β-, γ-, and δ-Proteobacteria. The least diversity of the endophytic microbes have been revealed fromBacteroidetes, Deinococcus-Thermus, and Acidobacteria. Among reported genera, Achromobacter, Burkholderia, Bacillus, Enterobacter, Herbaspirillum, Pseudomonas, Pantoea, Rhizobium, and Streptomyces were dominant in most host plants. The present review deals with plant endophytic diversity, mechanisms of plant growth promotion, protection, and their role for agro-environmental sustainability. In the future, application of endophytic microbes have potential role in enhancement of crop productivity and maintaining the soil health in sustainable manner.

Colonization potential of endophytes from halophytic plants growing in the "Runn of Kutch" salt marshes and their contribution to mitigating salt stress in tomato cultivation.

Increasing soil salinity depreciates the quantity of the crop produce. Looking at the tremendous potential of plant-associated microorganisms in salinity stress mitigation, it would be very useful in exploring and deciphering salt-tolerant microorganisms from halophytic plants and their utilization in cultivated plants. With this aim, in the present study, four halophytic plants were taken from Rann of Kutch, and bacterial endophytes were isolated from different plant organs. These endophytes were characterized by plant growth and health promotion features. The molecular identification was done based on 16 s rRNA sequence similarity. It was found that the endophytic bacteria isolated from 4 different halophytes found sharing phylogenetic relatedness. Four potential endophytes Alkalihalobacillus gibsonii 2H2, Achromobacter insuavis 2H18, Terribacillus halophilus 2H20, and Bacillus siamensis 4H1 were tested in tomato for salinity stress alleviation. Changes in the levels of antioxidants were analyzed. Total chlorophyll, total phenolics, malondialdehyde, and proline content indicated reduced damage in the plant system due to salinity by the application of endophytes. All the treatments exhibited low levels of electrolyte leakage. The accumulation of enzymatic reactive oxygen species scavengers was assessed from the levels of peroxidase, catalase, superoxide dismutase, phenylalanine ammonia-lyase, ascorbate peroxidase, and guiacol peroxidase. The NBT and DAB staining confirmed the findings. The reduction in the accumulation of Na+ ions in tomato leaves was visualized using Sodium Green probes under CSLM and found to be lowest in Terribacillus halophilus 2H20 and Bacillus siamensis 4H1 inoculated plants. The endophyte Terribacillus halophilus 2H20 was the most promising isolate. The colonization in tomato roots was confirmed using a cell tracker system. Results showed that the endophytes were found to have salinity stress mitigation traits. The efficiency could be further improved with the combination of other endophytes tested earlier.

Signatures of prescribed fire in the microbial communities of Cornus florida are largely undetectable five months post-fire.

Prescribed burn is a management tool that influences the physical structure and composition of forest plant communities and their associated microorganisms. Plant-associated microorganisms aid in host plant disease tolerance and increase nutrient availability. The effects of prescribed burn on microorganisms associated with native ecologically and economically important tree species, such as Cornus florida L. (flowering dogwood), are not well understood, particularly in aboveground plant tissues (e.g., leaf, stem, and bark tissues). The objective of this study was to use 16S rRNA gene and ITS2 region sequencing to evaluate changes in bacterial and fungal communities of five different flowering dogwood-associated niches (soil, roots, bark, stem, and leaves) five months following a prescribed burn treatment. The alpha- and beta-diversity of root bacterial/archaeal communities differed significantly between prescribed burn and unburned control-treated trees. In these bacterial/archaeal root communities, we also detected a significantly higher relative abundance of sequences identified as Acidothermaceae, a family of thermophilic bacteria. No significant differences were detected between prescribed burn-treated and unburned control trees in bulk soils or bark, stem, or leaf tissues. The findings of our study suggest that prescribed burn does not significantly alter the aboveground plant-associated microbial communities of flowering dogwood trees five months following the prescribed burn application. Further studies are required to better understand the short- and long-term effects of prescribed burns on the microbial communities of forest trees.

Molecular identification of endophytes from maize roots and their biocontrol potential against toxigenic fungi of Nigerian maize.

Plants benefit from plant-associated microorganisms, of which endophytes are of particular interest as they are transmitted from generation to generation. This study characterises endophytes from maize roots and determines their biocontrol potential against toxigenic fungi in Nigerian maize. Maize roots were collected from farms in Lafia, and stored grain samples were collected from the six Northern States of Nigeria, from which endophytes and toxigenic fungal strains were isolated. Molecular identification employing 16SrRNA/internal transcribed spacer (ITS) sequences for isolated fungal endophytes was carried out, and mycotoxins produced by fungi were determined by high-performance liquid chromatography analysis. Biocontrol activity of the endophytes was determined using the dual culture confrontation test. Aspergillus and Fusarium genera were the prevalent isolated fungal species. Eight fungal endophytes were identified of which Trichoderma harzianum, Dichotomopilus erectus and Burkholderia spp. were the isolates with biocontrol activities, while 12 Aspergillus spp. were found to produce varying amounts of ochratoxin A and aflatoxin B1, respectively. T. harzianum showed the best inhibition (74%), followed by D. erectus (50%) and Burkholderia spp. (48%). T. harzianum showed poor inhibition of Aspergillus flavus (B7) at 30%. However, results from the Pakdaman Biological Control Index showed that T. harzianum has the best antifungal biocontrol activity of the three endophytes. The study concludes that antifungal biocontrol agents can be sourced from endophytes to obtain indigenous control activities that can check mycotoxin contamination of food and livestock feed, as well as elucidate possible metabolites for agricultural and industrial applications, which will help improve plant performance, increase crop yield and sustainability.

Host-adaptive traits in the plant-colonizing Pseudomonas donghuensis P482 revealed by transcriptomic responses to exudates of tomato and maize

Pseudomonads are metabolically flexible and can thrive on different plant hosts. However, the metabolic adaptations required for host promiscuity are unknown. Here, we addressed this knowledge gap by employing RNAseq and comparing transcriptomic responses of Pseudomonas donghuensis P482 to root exudates of two plant hosts: tomato and maize. Our main goal was to identify the differences and the common points between these two responses. Pathways upregulated only by tomato exudates included nitric oxide detoxification, repair of iron-sulfur clusters, respiration through the cyanide-insensitive cytochrome bd, and catabolism of amino and/or fatty acids. The first two indicate the presence of NO donors in the exudates of the test plants. Maize specifically induced the activity of MexE RND-type efflux pump and copper tolerance. Genes associated with motility were induced by maize but repressed by tomato. The shared response to exudates seemed to be affected both by compounds originating from the plants and those from their growth environment: arsenic resistance and bacterioferritin synthesis were upregulated, while sulfur assimilation, sensing of ferric citrate and/or other iron carriers, heme acquisition, and transport of polar amino acids were downregulated. Our results provide directions to explore mechanisms of host adaptation in plant-associated microorganisms.

Holo-omic applications to unveil microbiome shaping sustainable horticultural production

Plant-associated microorganisms play a key role in the future sustainability of terrestrial ecosystems. In nature, plants and their associated microbiome can form an assemblage of species, considered interacting metaorganisms or holobionts. Horticultural plants, including vegetables, fruit and berries, and ornamentals live in intimate association with complex and diverse microbial communities that have evolved a myriad of cooperative and competitive interaction mechanisms that shape the holobiont fitness. Nonetheless, our understanding of these interactions in shaping more complex microbial horticulture communities, along with their relevance for host growth, fitness, stress resilience, and health in a more natural context remains sparse. In this perspective, the holo-omic landscape that requires careful consideration of study design and integrates multi-omic data from both host and microbiota domains is a promising approach to unveil the interplay between the two to advance horticultural production. The analysis of horticulture (meta)-omics and phenotyping, along with mechanistic experiments in model systems, is revolutionizing research by enhancing our ability to understand the structure and core function of the plant-associated microbiome. These advancements are complemented by improvements in the throughput and accuracy of DNA sequencing, enabling us to delve deeper into the genomes of microbial communities. Yet, many challenges remain. We focus this review on the potential for holo-omics to generate a more holistic perspective of molecular networks, and we further discuss the implementation and current limitations of the holo-omic approach within microbial horticulture. We argue that holo-omics will pave the way to improve, from a horticultural perspective, food security and safety, sustainability, breeding practices, development of microbiota- and host-tailored horticultural crops’ health treatments and increasing production efficiency.

Deciphering plant health status: The link between secondary metabolites, fungal community and disease incidence in olive tree.

Plant-associated microorganisms are increasingly recognized to play key roles in host health. Among several strategies, associated microorganisms can promote the production of specific metabolites by their hosts. However, there is still a huge gap in the understanding of such mechanisms in plant-microorganism interaction. Here, we want to determine whether different levels of olive leaf spot (OLS) disease incidence were related to differences in the composition of fungal and secondary metabolites (i.e. phenolic and volatile compounds) in leaves from olive tree cultivars with contrasting OLS susceptibilities (ranging from tolerant to highly susceptible). Accordingly, leaves with three levels of OLS incidence from both cultivars were used to assess epiphytic and endophytic fungal communities, by barcoding of cultivable isolates, as well as to evaluate leaf phenolic and volatile composition. Fungal and metabolite compositions variations were detected according to the level of disease incidence. Changes were particularly noticed for OLS-tolerant cultivars, opposing to OLS-susceptible cultivars, suggesting that disease development is linked, not only to leaf fungal and metabolite composition, but also to host genotype. A set of metabolites/fungi that can act as predictive biomarkers of plant tolerance/susceptibility to OLS disease were identified. The metabolites α-farnesene and p-cymene, and the fungi Fusarium sp. and Alternaria sp. were more related to disease incidence, while Pyronema domesticum was related to the absence of disease symptoms. Cultivar susceptibility to OLS disease is then suggested to be driven by fungi, volatile and phenolic host leaves composition, and above all to plant-fungus interaction. A deeper understanding of these complex interactions may unravel plant defensive responses.

Bacterial communities in the phyllosphere are distinct from those in root and soil, and sensitive to plant species changes in subtropical tree plantations.

Deciphering the local diversity and community composition of plant-associated microorganisms is crucial to predict their ecological functions in forest ecosystems. The differences in microbial diversity and community composition between the aboveground and belowground tree compartments remain largely unknown. Here we examined bacterial communities in the leaf surface (phyllosphere) and root-associated (root and rhizospheric soil) habitats of 13 tree species. Bacterial richness substantially differed across the three compartments, with the highest value observed in rhizospheric soil. Tree species exerted a significant effect on α-diversity of leaf- and soil- but not root-inhabiting bacteria. Bacterial communities were distinct across habitats and were significantly more divergent in leaf- than in root-associated habitats. Leaf nutrients and soil pH and NH4+-N were the main factors regulating leaf- and root-related community composition, respectively. This study highlights that host selection effects on bacterial community structure were more prominent in aboveground than in belowground habitats. Our findings contribute to a better understanding of the effect of compartments and subtropical tree species on microbial diversity, with crucial implications for sustainable forest plantation management.

Diseased-induced multifaceted variations in community assembly and functions of plant-associated microbiomes.

Plant-associated microorganisms are believed to be part of the so-called extended plant phenotypes, affecting plant growth and health. Understanding how plant-associated microorganisms respond to pathogen invasion is crucial to controlling plant diseases through microbiome manipulation. In this study, healthy and diseased (bacterial wilt disease, BWD) tomato (Solanum lycopersicum L.) plants were harvested, and variations in the rhizosphere and root endosphere microbial communities were subsequently investigated using amplicon and shotgun metagenome sequencing. BWD led to a significant increase in rhizosphere bacterial diversity in the rhizosphere but reduced bacterial diversity in the root endosphere. The ecological null model indicated that BWD enhanced the bacterial deterministic processes in both the rhizosphere and root endosphere. Network analysis showed that microbial co-occurrence complexity was increased in BWD-infected plants. Moreover, higher universal ecological dynamics of microbial communities were observed in the diseased rhizosphere. Metagenomic analysis revealed the enrichment of more functional gene pathways in the infected rhizosphere. More importantly, when tomato plants were infected with BWD, some plant-harmful pathways such as quorum sensing were significantly enriched, while some plant-beneficial pathways such as streptomycin biosynthesis were depleted. These findings broaden the understanding of plant-microbiome interactions and provide new clues to the underlying mechanism behind the interaction between the plant microbiome and BWD.

Application of Synthetic Consortia for Improvement of Soil Fertility, Pollution Remediation, and Agricultural Productivity: A Review

Climate change, inadequate possessions, and land degradation all pose obstacles to modern agriculture. In the current scenario, the agriculture industry is mainly dependent on the use of chemical-based pesticides and fertilizers that impact soil health and crop productivity. Moreover, water scarcity leads farmers in drastically affected regions to use heavy metal-enriched water sources mainly originating from industrial sources for field crops irrigation. Soil pollutants can be carried into the human body via dust and water, creating negative health effects varying from simple symptoms, e.g., nausea and diarrhea and reaching death in critical cases. Thus, to clean soil contaminants, and improve soil fertility and agricultural production, alternatives to chemical fertilizers must be developed. Therefore, using beneficial microbes found in plant-associated soil microorganisms offers an effective strategy to alleviate some of these challenges, improving soil fertility, and crop yield, and protecting plants from stress conditions. Through the use of synergistic interactions, the synthetic consortium strategy seeks to improve the stability of microbial communities. In this review, synthetic consortia and their potential use in agriculture were discussed. Further, engineering new effective synthetic consortia was suggested as an effective approach in the concept of environmental bioremediation of soil pollutants and contaminants.

Endophytic microbiota of floating aquatic plants: recent developments and environmental prospects.

Plant-associated microorganisms play a critical role in plant survival and functional attributes. There are many studies on the taxonomical and functional aspects of microorganisms associated with terrestrial plants. However, the microbiome of aquatic plants is not much explored. This work details the studies on microbiomes and diversity in microbial communities inhabiting the three common free-floating aquatic plants of tropical regions viz. duckweed, water hyacinth and water lettuce, widely implicated for their bioremediation potential. Studies conducted till date reveal the prevalence and dominance of different Bacillus sp. Other genera, including Rhodanobacter, Pseudomonas, Rhizobium, Achromobacter, Serratia, Actinobacteria, Proteobacter, Klebsiella and Acidobacteria, have also been prominently reported. This lesser explored niche offers great bioprospecting opportunities to obtain taxonomically diverse and functionally distinct microorganisms. Bacterial endophytes from these aquatic plants have been primarily studied for their ability to produce indole acetic acid and degrade phenol. Limited studies reveal some fungal endophytes to have promising herbicidal effect. Not much is known on other functional attributes and hence microbial studies on these plants holds much promise for obtaining novel isolates or isolates with novel functions that would impact both aquatic and terrestrial ecosystems. This study proposes the need for exploring the role of endophytes as biocontrol agents and their potential to provide a pragmatic and robust solution to the aquatic weed menace in freshwater bodies. Bioprospecting of this lesser studied ecological niche hence is a promising field of research that has both environmental and economic potential.

Seed priming by application of Microbacterium spp. strains for control of Botrytis cinerea and growth promotion of lettuce plants

The abusive use of chemical pesticides to control plant diseases has caused the loss of soil biodiversity as well as the emergence of resistance by plant pathogens. This effect has forced an urgent search for other environmentally sustainable alternatives that serve to control plant pathogens safely and efficiently. In this sense, the search for new biopesticides is currently a booming field within the field of agro-biotechnology. Volatile compounds produced by plant-associated microorganisms represent a diverse resource to promote plant growth and health. In this work, a collection of 29 strains of the genus Microbacterium from the composting of plant remains was studied. The objective was to determine whether the production of volatile compounds of microbial origin could contribute to the mitigation of symptoms caused by the fungus Botrytis cinerea (gray mold) as well as contribute to the lettuce plant growth in seedbeds. It should be noted that in both the B. cinerea inhibition and seed priming assays, the microorganisms did not come into direct contact with either the pathogen or the seeds. In all cases, incubation was carried out in a closed environment to expose the seeds to the microbial volatiles. Five strains capable of inhibiting the in vitro growth of B. cinerea at levels greater than 30% were pre-selected. Only 3 of these 5 strains, identified as M. aerolatum, M. foliorum and M. profundi showed positive results in the in vitro germination promotion test in lettuce seeds, increasing the radicle weight at levels close to 45%. These strains finally were tested in planta, showing two of them significant palliative effects of B. cinerea and promoting the development of lettuce seedlings both at aerial and root levels.

Bacterial biofilms as an essential component of rhizosphere plant-microbe interactions.

Most plant-associated microorganisms inhabit the rhizosphere, the thin, well-structured, dynamic and highly competitive biofilm located between the roots and the soil. Rhizosphere development progresses through stages in which soil bacteria are first recruited by root exudates and then proliferate within a protective matrix from within which they influence the nutritional status of the plant, its growth, and its ability to resist pathogens and abiotic stresses. To circumvent the challenges that make characterization of rhizosphere biofilms in soil difficult, experiments are often conducted with bacteria cultured in root exudates within controlled environments in devices such as microtiter plates, flow chambers, drip flow reactors and microfluidic platforms. When coupled with microscopy and metabolic analyses, such cultures have revealed intimate details of root development, rhizosphere establishment and biofilm spatiotemporal microheterogeneity. Studies in soil have shown that introduced microorganisms must compete aggressively with indigenous populations to establish themselves within the biofilm matrix and form dense populations capable of quorum sensing and other signalling activities that mediate plant growth promotion and disease suppression via antibiotic production. Healthy biofilm matrices rich in water-binding components also help to relieve drought stress in plants growing in arid parts of the world. The chapter includes sections that discuss the close resemblance between the processes of rhizosphere colonization and biofilm formation, provide an overview of experimental approaches for studying rhizosphere biofilms, and cover the practical importance of the rhizosphere microbiome.

Productivity and Nutrient Quality of Lemna minor as Affected by Microbiome, CO2 Level, and Nutrient Supply

Rising atmospheric carbon dioxide (CO2) levels can impact plant photosynthesis and productivity and threaten food security, especially when combined with additional environmental stressors. This study addresses the effects of elevated CO2 in combination with low nutrient supply on Lemna minor (common duckweed). We quantified plant growth rate and nutritional quality (protein content) and evaluated whether any adverse effects of elevated CO2, low nutrients, or the combination of the two could be mitigated by plant-microbe interaction. Plants were grown under controlled conditions and were either uninoculated or inoculated with microorganisms from a local pond that supported L. minor populations. Under low nutrients in combination with high CO2, growth (plant area expansion rate) decreased and biomass accumulation increased, albeit with lower nutritional quality (lower percentage of protein per plant biomass). Inoculation with plant-associated microorganisms restored area expansion rate and further stimulated biomass accumulation while supporting a high protein-to-biomass ratio and, thus, a high nutritional quality. These findings indicate that plant-microbe interaction can support a higher nutritional quality of plant biomass under elevated atmospheric CO2 levels, an important finding for both human and non-human consumers during a time of rapid environmental change.

Comparative study of the rhizosphere microbiome of Coffea arabica grown in different countries reveals a small set of prevalent and keystone taxa

Coffee (Coffea arabica) is a globally important crop and its cultivation demands the use of agrochemicals and pesticides. Recently, plant-associated microorganisms have emerged as an unexploited resource to enhance crop performance and sustainability. In particular, the rhizosphere microbiome has been identified as a hotspot for plant health, by providing tolerance to biotic and abiotic stresses as well as regulating phenological traits. However, its composition varies widely across crops and environmental conditions. Hence, the knowledge of the “common core” taxa, which are a subset of the microbiome that is persistently associated, across different environmental gradients and conditions, to a host species, represent valuable targets for the development of microbiome-based management approaches. This study aimed to characterize and determine the rhizosphere-inhabiting microbial groups (common core and most prevalent taxa), associated with the Coffea arabica plants in different geographical locations. To assess the structure of the coffee rhizosphere microbiome, we performed the 16 S rRNA amplicon analysis of samples collected across six locations spanning four countries and grown under different climate conditions, soil type, agroecosystem management, plant vegetative stage and age. Our findings allowed us to delineate and identify a robust set of six bacterial taxa, namely Sphingobium, Rhizobium group, Acidibacter, Sphingomonas, Burkholderia group and Amycolatopsis, which are likely to play an important role for the growth and health of coffee plants. Using network analysis, we observed that some of the six “common core” taxa were highly interconnected with the resident community, being also keystone taxa of the coffee rhizosphere microbiome. Furthermore, we performed a high-throughput targeted isolation resulting into 162 rhizosphere bacterial strains, some of them related to the most prevalent taxa. These isolates represent a working bacterial culture collection to be used in the future for the development of microbiome-based solutions for a more sustainable coffee farming.

The root signals in rhizospheric inter-organismal communications.

Root exudates play a key role in mediating plant-plant and plant-rhizomicrobiome interactions, including regulating biochemical/physiological aspects of plant-associated microorganisms, to enhance host plant growth and resilience. Root exudates can act as signals to reduce the competition from neighboring plants and recruiting/choreographing a wide range of diverse rhizomicrobiome members to make the host plant a good fit with its immediate environment. Root exudate production is a dynamic and key process, but there is a limited understanding of the metabolites or metabolic pathways involved in the inter-organismal communications facilitated by them. Given the well-known symbiotic relationships between plants and associated rhizomicrobiome members, adding root exudates to microbial isolation media may allow some of the large segments of rhizomicrobiome members that are not currently culturable to be grown in vitro. This will provide new insights into how root signals orchestrate associated microbes, will benefit agricultural production in the face of challenges posed by climate change, and will help to sustainably provide food for a growing global human population.

Simulated global warming affects endophytic bacterial and fungal communities of Antarctic pearlwort leaves and some bacterial isolates support plant growth at low temperatures

Antarctica is one of the most stressful environments for plant life and the Antarctic pearlwort (Colobanthus quitensis) is adapted to the hostile conditions. Plant-associated microorganisms can contribute to plant survival in cold environments, but scarce information is available on the taxonomic structure and functional roles of C. quitensis-associated microbial communities. This study aimed at evaluating the possible impacts of climate warming on the taxonomic structure of C. quitensis endophytes and at investigating the contribution of culturable bacterial endophytes to plant growth at low temperatures. The culture-independent analysis revealed changes in the taxonomic structure of bacterial and fungal communities according to plant growth conditions, such as the collection site and the presence of open-top chambers (OTCs), which can simulate global warming. Plants grown inside OTCs showed lower microbial richness and higher relative abundances of biomarker bacterial genera (Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Aeromicrobium, Aureimonas, Hymenobacter, Novosphingobium, Pedobacter, Pseudomonas and Sphingomonas) and fungal genera (Alternaria, Cistella, and Vishniacozyma) compared to plants collected from open areas (OA), as a possible response to global warming simulated by OTCs. Culturable psychrotolerant bacteria of C. quitensis were able to endophytically colonize tomato seedlings and promote shoot growth at low temperatures, suggesting their potential contribution to plant tolerance to cold conditions.

Nitrogen Fertilizer Application Alters the Root Endophyte Bacterial Microbiome in Maize Plants, but Not in the Stem or Rhizosphere Soil.

Plant-associated microorganisms that affect plant development, their composition, and their functionality are determined by the host, soil conditions, and agricultural practices. How agricultural practices affect the rhizosphere microbiome has been well studied, but less is known about how they might affect plant endophytes. In this study, the metagenomic DNA from the rhizosphere and endophyte communities of root and stem of maize plants was extracted and sequenced with the "diversity arrays technology sequencing," while the bacterial community and functionality (organized by subsystems from general to specific functions) were investigated in crops cultivated with or without tillage and with or without N fertilizer application. Tillage had a small significant effect on the bacterial community in the rhizosphere, but N fertilizer had a highly significant effect on the roots, but not on the rhizosphere or stem. The relative abundance of many bacterial species was significantly different in the roots and stem of fertilized maize plants, but not in the unfertilized ones. The abundance of N cycle genes was affected by N fertilization application, most accentuated in the roots. How these changes in bacterial composition and N genes composition might affect plant development or crop yields has still to be unraveled. IMPORTANCE We investigated the bacterial community structure in the rhizosphere, root, and stem of maize plants cultivated under different agricultural techniques, i.e., with or without N fertilization, and with or without tillage. We found that the bacterial community was defined mostly by the plant compartment and less by agricultural techniques. In the roots, N fertilizer application affected the bacterial community structure, the microbiome functionality, and the abundance of genes involved in the N cycle, but the effect in the rhizosphere and stem was much smaller. Contrary, tillage did not affect the maize microbiome. This study enriches our knowledge about the plant-microbiome system and how N fertilization application affected it.

The Growth-promoting and Antipathogenic Effects of Microorganisms Isolated from Solanum nigrum L. and Inoculated in Solanum lycopersicum L.

Background: In recent years, there has been a growing scientific interest in the biodiversity and function of endophytic bacteria, as well as the prospects for their practical use. Objective: The purpose of this work was to isolate endophytic microorganisms from generative organs of the European black nightshade (Solanum nigrum L.), assess their biological activity, and test their growth-promoting/protective effects in tomato (Solanum lycopersicum L.) plants. Methods: From the tissues of generative organs of S. nigrum plants, 14 strains of endophytic microorganisms were isolated. Most of them belonged to Bacillus sp. The physiological and biochemical properties and enzymatic and oxidative metabolism of some of them were studied. Sequence analysis of 16S rRNA fragments revealed 99,65% similarity of BA1s-OSN-0820 and BAXS-OSN-0820 isolates to B. amyloliquefaciens strains, while the ITS sequence of the RHC-OSN-0820 isolate showed 99,65% of similarity to Rhodotorula kratochvilovae. Results: The actions of these endophytes against tomato pathogenic bacteria and fungi were then tested. The isolates had a significant bacteriostatic effect against Xanthomonas campestris, the causative agent of black bacterial spotting of leaf, and Clavibacter michiganensis, the causative agent of bacterial wilt, with a lower effect against Pseudomonas syringae, the causative agent of bacterial spotting. Isolates also showed selectivity against micromycetes that cause mycosis in tomatoes grown indoors, such as Fusarium oxysporum, Alternaria solani, Botrytis cinerea, Sclerotinia sclerotiorum, and F. acuminatum. In particular, the highest antifungal activity was detected against S. sclerotiorum and fungi of the Fusarium genus. Inoculation of tomatoes with endophytic microorganisms revealed a positive effect on seed germination efficiency and the stimulation of seedling growth. Thus, the effectiveness of interspecific transfer of endophytic microorganisms from a wild, S. nigrum, to a cultivated Solanum species, S. lycopersicum, was reported. Conclusion: A consortium of plant-associated microorganisms isolated from a wild relative has a positive effect on the germination of tomato seeds, stimulating the formation of the root system and nutrition of seedlings. The antagonism of the isolates against phytopathogenic fungi and bacteria provides long-term protection during the most critical stages of plant development and has prospects for the development of microbial biologics for cultivated plants of the Solanaceae family.