Plant-microorganism Interactions Research Articles

Use of image analysis in the evaluation of radicular nodules in chickpeas

The use of advanced computational systems facilitates the application of a wide range of statistical techniques, available in open-source format, to perform analyses of substantial complexity in biological systems, particularly in the field of plant biology. The aim of this study is to demonstrate the application of image analysis in the evaluation of root nodules in Cicer arietinum plants. The research was conducted in the field, where roots were collected, subjected to rigorous cleaning protocols and subsequently photographed under precisely controlled studio conditions. This photographic process was performed using equipment configured with meticulous parameter settings. Subsequently, image analyses were performed using the statistical software package, R. Parameters of interest were quantified, including metrics such as root area, nodule area, the proportional representation of nodules in relation to the total root mass and the absolute count of nodules present. A critical comparison between the proposed analytical methodology and conventional approaches evidenced a substantial improvement in efficiency, thus highlighting the robustness and validity of this analytical framework for the outlined research objectives. Therefore, the developed methodology has significant potential to facilitate accurate and comprehensive analyses of nodules and root systems, thus making a notable contribution to fostering a deeper understanding and exploration of plant-microorganism interactions. Furthermore, this methodological advancement has the potential to contribute to reducing operational costs and optimizing the time spent on such meticulous evaluative undertakings.

Specification of Rhizospheric Characteristics of Some Bacteria Identified by MALDI TOF MS from Agricultural Soils in Kirsehir Province (Akçakent and Çiçekdağı) Districts

The rhizosphere are site of plant-microorganism interaction, and have critical impotance in events like nutrient supply, the production of compounds that support plant growth and phytopathogen protection. This study reports 52 bacteria isolated from 5 different plant rhizospheres (Hordeum vulgare, Avena sativa, Cicer arietinum, Helianthus annuus, and Phaseolus vulgaris) of two agricultural districts of Kırşehir (Akçakent and Çicekdağı regions) in Türkiye. Morphological, biochemical, plant growth-promoting characteristics (including production of indole-3-acetic acid, siderophore, nitrogen fixation, and phosphate solubilization) using MALDI-TOF-MS techniques were used to identify the isolates. Among all isolates, 33 isolate were Gram positive and 19 were Gram negative. Furthermore 40% of them were classified as Bacillus species, 10% belonged to Pseudomonas species, 7% were Acinetobacter species, 4% were Pantoeae species, and 39% other species (Blastomonas, Lysinibacillus, Comamonas, Alcaligenes, Bifidobacterium, Aromatoleum). It was seen that 12 isolates fixed nitrogen, 8 isolates produced dissolved inorganic phosphate, 12 isolates produced siderophores, 9 isolates were produced by IAA, and 14 isolates produced HCN during the screening of plant growth promoting properties. It is concluded that the culture of bacteria living in the rhizosphere are essential to promote soil fertility and sustainable agriculture. Therefore, there is a need to identify and use these strains with plant growth promoting properties in agriculture.

Strengthened plant-microorganism interaction after topsoil removal cause more deterministic microbial assembly processes and increased soil nitrogen mineralization

Topsoil removal, among other restoration measures, has been recognized as one of the most successful methods to restore biodiversity and ecosystem functioning in European grasslands. However, knowledge about how removal as well as other restoration methods influence interactions between plant and microbial communities is very limited. The aims of the current study were to understand the impact of topsoil removal on plant-microorganism interactions and on soil nitrogen (N) mineralization, as one example of ecosystem functioning. We examined how three different grassland restoration methods, namely ‘Harvest only’, ‘Topsoil removal’ and ‘Topsoil removal + Propagules (plant seed addition)’, affected i) the interactions between plants and soil microorganisms, ii) soil microbial community assembly processes, and iii) soil N mineralization. We compared the outcome of these three restoration methods to initial degraded and target semi-natural grasslands in the Canton of Zurich, Switzerland. We were able to show that ‘Topsoil removal’ and ‘Topsoil removal + Propagules’, but not ‘Harvest only’, reduced the soil total N pool and available N concentration, but increased soil N mineralization and strengthened the plant-microorganism interactions. Microbial community assembly processes shifted towards more deterministic after both topsoil removal treatments. These shifts could be attributed to an increase in dispersal limitation and selection due to stronger interactions between plants and soil microorganisms. The negative relationship between soil N mineralization and microbial community stochasticity indicated that microbial assembly processes, to some extent, can be incorporated into model predictions of soil functions. Overall, the results suggest that topsoil removal may change the microbial assembly processes and thus the functioning of grassland ecosystems by enhancing the interaction between plants and soil microorganisms.

Intercropping Systems: An Opportunity for Environment Conservation within Nut Production

Global population growth and intensive agriculture have both contributed negatively to the environment. As a result, there is increasing interest in the use of sustainable alternatives is increasing to promote better use of natural resources and create an equilibrium between agriculture and the environment. Intercropping, the simultaneous cultivation of multiple crops, aims to optimize land use economically while enhancing biodiversity through plant–microorganism interactions, thereby boosting crop productivity. This practice has particularly benefited nut production by combining the nutrient-sequestering capacity of trees with continuous annual crop production, improving soil nutrient and water utilization. Intercropping systems not only enhance nut yield and quality but also offer economic advantages to farmers. This review synthesized the existing literature with the aim of highlighting not only the positive aspects that intercropping brings to the production of nuts, but also the challenges and limitations faced in different regions when it comes to agricultural production.

Intensifying Cadmium remediation: the impact of synergy between Crambe abyssinica and plant growth-promoting microorganisms

Cd, a toxic metal, is naturally found in the environment and is exacerbated by human activities such as mining, agriculture, and industrial processes. Its contamination in soils poses serious risks to human health and ecosystems, prompting the need for effective remediation strategies. This study focuses on the use of Crambe abyssinica, an oilseed plant known for its tolerance to adverse environmental conditions, including Cd contamination, for phytoremediation of contaminated soils, associated with bioremediation through plant growth-promoting microorganisms. The study involved growing Crambe in vitro. Methods included seed asepsis, substrate contamination with various Cd concentrations, and inoculation with beneficial microorganisms such as Bradyrhizobium japonicum, Bacillus subtilis along with Bacillus megaterium, Azospirillum. brasilense, Pseudomonas fluorescens, and Trichoderma harzianum. Data such as plant length and root area were measured, and the nutrient and Cd content in the plants were assessed. Results indicated that inoculation with microorganisms significantly enhanced the nutrient content in Crambe plants, even under different Cd concentrations. Notably, A. brasilense and P. fluorescens were particularly effective, not only increasing nutrient uptake but also enhancing Cd accumulation in the plants, which is crucial for phytoremediation. The presence of these microorganisms also led to a significant reduction in the Cd concentration in the substrate, showcasing their potential in bioaugmentation. The study highlights the efficacy of using Crambe abyssinica in conjunction with specific microorganisms for the remediation of Cd-contaminated soils. The synergistic effects of these plant-microorganism interactions not only promote plant growth and health but also enhance the phytoextraction of Cd, offering a sustainable solution to soil contamination. Future research should focus on optimizing these interactions and exploring their applications in larger-scale environmental remediation projects.

The microbial-driven nitrogen cycle and its relevance for plant nutrition.

Nitrogen (N) is a vital nutrient and an essential component of biological macromolecules such as nucleic acids and proteins. Microorganisms are major drivers of N-cycling processes in all ecosystems, including the soil and plant environment. The availability of N is a major growth-limiting factor for plants and it is significantly affected by the plant microbiome. Plants and microorganisms form complex interaction networks resulting in molecular signaling, nutrient exchange, and other distinct metabolic responses. In these networks, microbial partners influence growth and N use efficiency of plants either positively or negatively. Harnessing the beneficial effects of specific players within crop microbiomes is a promising strategy to counteract the emerging threats to human and planetary health due to the overuse of industrial N fertilizers. However, in addition to N-providing activities (e.g. the well-known symbiosis of legumes and Rhizobium spp.), other plant-microorganism interactions must be considered to obtain a complete picture of how microbial-driven N transformations might affect plant nutrition. For this, we review recent insights into the tight interplay between plants and N-cycling microorganisms, focusing on microbial N-transformation processes representing N sources and sinks that ultimately shape plant N acquisition.

Reducing Heavy Metal Contamination in Soil and Water Using Phytoremediation.

The increase in industrialization has led to an exponential increase in heavy metal (HM) soil contamination, which poses a serious threat to public health and ecosystem stability. This review emphasizes the urgent need to develop innovative technologies for the environmental remediation of intensive anthropogenic pollution. Phytoremediation is a sustainable and cost-effective approach for the detoxification of contaminated soils using various plant species. This review discusses in detail the basic principles of phytoremediation and emphasizes its ecological advantages over other methods for cleaning contaminated areas and its technical viability. Much attention has been given to the selection of hyperaccumulator plants for phytoremediation that can grow on heavy metal-contaminated soils, and the biochemical mechanisms that allow these plants to isolate, detoxify, and accumulate heavy metals are discussed in detail. The novelty of our study lies in reviewing the mechanisms of plant-microorganism interactions that greatly enhance the efficiency of phytoremediation as well as in discussing genetic modifications that could revolutionize the cleanup of contaminated soils. Moreover, this manuscript discusses potential applications of phytoremediation beyond soil detoxification, including its role in bioenergy production and biodiversity restoration in degraded habitats. This review concludes by listing the serious problems that result from anthropogenic environmental pollution that future generations still need to overcome and suggests promising research directions in which the integration of nano- and biotechnology will play an important role in enhancing the effectiveness of phytoremediation. These contributions are critical for environmental scientists, policy makers, and practitioners seeking to utilize phytoremediation to maintain the ecological stability of the environment and its restoration.

Unveiling the Anatomical and Functional Attributes of Stipular Colleters in Palicourea tetraphylla Cham. & Schltdl. and Palicourea rudgeoides (Müll. Arg.) Standl. (Rubiaceae).

The characterization of colleters in Rubiaceae is crucial for understanding their role in plant function. Analyzing colleters in Palicourea tetraphylla and Palicourea rudgeoides aims to deepen the understanding of these structures morphoanatomical and functional characteristics. The study reveals colleters with palisade epidermis and a parenchymatic central axis, classified as standard type, featuring vascularization and crystals. Colleter secretion, abundant in acidic mucopolysaccharides, proteins, and phenolic compounds, protects against desiccation. The ontogenesis, development, and senescence of the colleters are quite rapid and fulfill their role well in biotic and abiotic protection because these structures are present at different stages of development in the same stipule. Pronounced protrusions on the colleters surface, coupled with the accumulation of secretion in the intercellular and subcuticular spaces, suggest that the secretory process occurs through the wall, driven by pressure resulting from the accumulation of secretion. The microorganisms in the colleters' secretion, especially in microbiota-rich environments such as the Atlantic Forest, provide valuable information about plant-microorganism interactions, such as resistance to other pathogens and organisms and ecological balance. This enhanced understanding of colleters contributes to the role of these structures in the plant and enriches knowledge about biological interactions within specific ecosystems and the family taxonomy.

Recent advances in research on phosphate starvation signaling in plants

Phosphorus is indispensable for plant growth and development, with its status crucial for determining crop productivity. Plants have evolved various biochemical, morphological, and developmental responses to thrive under conditions of low P availability, as inorganic phosphate (Pi), the primary form of P uptake, is often insoluble in soils. Over the past 25 years, extensive research has focused on understanding these responses, collectively forming the Pi starvation response system. This effort has not only expanded our knowledge of strategies to cope with Pi starvation (PS) but also confirmed their adaptive significance. Moreover, it has identified and characterized numerous components of the intricate regulatory network governing P homeostasis. This review emphasizes recent advances in PS signaling, particularly highlighting the physiological importance of local PS signaling in inhibiting primary root growth and uncovering the role of TORC1 signaling in this process. Additionally, advancements in understanding shoot-root Pi allocation and a novel technique for studying Pi distribution in plants are discussed. Furthermore, emerging data on the regulation of plant-microorganism interactions by the PS regulatory system, crosstalk between the signaling pathways of phosphate starvation, phytohormones and immunity, and recent studies on natural variation in Pi homeostasis are addressed.

Bacteria Associated with Spores of Arbuscular Mycorrhizal Fungi Improve the Effectiveness of Fungal Inocula for Red Raspberry Biotization

Intensive crop production leads to the disruption of the symbiosis between plants and their associated microorganisms, resulting in suboptimal plant productivity and lower yield quality. Therefore, it is necessary to improve existing methods and explore modern, environmentally friendly approaches to crop production. One of these methods is biotization, which involves the inoculation of plants with appropriately selected symbiotic microorganisms which play a beneficial role in plant adaptation to the environment. In this study, we tested the possibility of using a multi-microorganismal inoculum composed of arbuscular mycorrhizal fungi (AMF) and AMF spore-associated bacteria for biotization of the red raspberry. Bacteria were isolated from the spores of AMF, and their plant growth-promoting properties were tested. AMF inocula were supplemented with selected bacterial strains to investigate their effect on the growth and vitality of the raspberry. The investigations were carried out in the laboratory and on a semi-industrial scale in a polytunnel where commercial production of seedlings is carried out. In the semi-industrial experiment, we tested the growth parameters of plants and physiological response of the plant to temporary water shortage. We isolated over fifty strains of bacteria associated with spores of AMF. Only part of them showed plant growth-promoting properties, and six of these (belonging to the Paenibacillus genus) were used for the inoculum. AMF inoculation and co-inoculation of AMF and bacteria isolated from AMF spores improved plant growth and vitality in both experimental setups. Plant dry weight was improved by 70%, and selected chlorophyll fluorescence parameters (the contribution of light to primary photochemistry and fraction of reaction centre chlorophyll per chlorophyll of the antennae) were increased. The inoculum improved carbon assimilation, photosynthetic rate, stomatal conductance and transpiration after temporary water shortage. Raspberry biotization with AMF and bacteria associated with spores has potential applications in horticulture where ecological methods based on plant microorganism interaction are in demand.

Alleviation of cotton growth suppression caused by salinity through biochar is strongly linked to the microbial metabolic potential in saline-alkali soil

Biochar is a typical soil organic amendment; however, there is limited understanding of its impact on the metabolic characteristics of microorganisms in saline-alkaline soil microenvironment, as well as the advantages and disadvantages of plant-microorganism interactions. To elucidate the mechanisms underlying the impact of saline-alkali stress on cotton, a 6-month pot experiment was conducted, involving the sowing of cotton seedlings in saline-alkali soil. Three different biochar application levels were established: 0 % (C0), 1 % (C1), and 2 % (C2). Results indicated that biochar addition improved the biomass of cotton plants, especially under C2 treatment; the dry weight of cotton bolls were 8.15 times that of C0. Biochar application led to a rise in the accumulation of photosynthetic pigments by 8.30–51.89 % and carbohydrates by 7.4–10.7 times, respectively. Moreover, peroxidase (POD) activity, the content of glutathione (GSH), and ascorbic acid (ASA) were elevated by 23.97 %, 118.39 %, and 48.30 % under C2 treatment, respectively. Biochar caused a reduction in Na+ uptake by 8.21–39.47 %, relative electrical conductivity (REC) of plants, and improved K+/Na+ and Ca2+/Na+ ratio indicating that biochar alleviated salinity-caused growth reduction. Additionally, the application of biochar enhanced the absorption intensity of polysaccharide fingerprints in cotton leaves and roots. Two-factor co-occurrence analysis indicated that the key differential metabolites connected to several metabolic pathways were L-phenylalanine, piperidine, L-tryptophan, and allysine. Interestingly, biochar altered the metabolic characteristics of saline-alkali soil, especially related to the biosynthesis and metabolism of amino acids and purine metabolism. In conclusion, this study demonstrates that biochar may be advantageous in saline soil microenvironment; it has a favorable impact on how plants and soil microbial metabolism interact.

Long-term conservation tillage with reduced nitrogen fertilization intensity can improve winter wheat health via positive plant-microorganism feedback in the rhizosphere.

Microbiome-based solutions are regarded key for sustainable agroecosystems. However, it is unclear how agricultural practices affect the rhizosphere microbiome, plant-microorganism interactions and crop performance under field conditions. Therefore, we installed root observation windows in a winter wheat field cultivated either under long-term mouldboard plough (MP) or cultivator tillage (CT). Each tillage practice was also compared at two nitrogen (N) fertilization intensities, intensive (recommended N-supply with pesticides/growth regulators) or extensive (reduced N-supply, no fungicides/growth regulators). Shoot biomass, root exudates and rhizosphere metabolites, physiological stress indicators, and gene expression were analyzed together with the rhizosphere microbiome (bacterial/archaeal 16S rRNA gene, fungal ITS amplicon, and shotgun metagenome sequencing) shortly before flowering. Compared to MP, the rhizosphere of CT winter wheat contained more primary and secondary metabolites, especially benzoxazinoid derivatives. Potential copiotrophic and plant-beneficial taxa (e.g. Bacillus, Devosia, and Trichoderma) as well as functional genes (e.g. siderophore production, trehalose synthase, and ACC deaminase) were enriched in the CT rhizosphere, suggesting that tillage affected belowground plant-microorganism interactions. In addition, physiological stress markers were suppressed in CT winter wheat compared to MP. In summary, tillage practice was a major driver of crop performance, root deposits, and rhizosphere microbiome interactions, while the N-fertilization intensity was also relevant, but less important.

Extracellular niche establishment by plant pathogens.

The plant extracellular space, referred to as the apoplast, is inhabited by a variety of microorganisms. Reflecting the crucial nature of this compartment, both plants and microorganisms seek to control, exploit and respond to its composition. Upon sensing the apoplastic environment, pathogens activate virulence programmes, including the delivery of effectors with well-established roles in suppressing plant immunity. We posit that another key and foundational role of effectors is niche establishment - specifically, the manipulation of plant physiological processes to enrich the apoplast in water and nutritive metabolites. Facets of plant immunity counteract niche establishment by restricting water, nutrients and signals for virulence activation. The complex competition to control and, in the case of pathogens, exploit the apoplast provides remarkable insights into the nature of virulence, host susceptibility, host defence and, ultimately, the origin of phytopathogenesis. This novel framework focuses on the ecology of a microbial niche and highlights areas of future research on plant-microorganism interactions.

ДЕСТРУКЦИЯ ФИТОГОРМОНОВ БАКТЕРИЯМИ-СТИМУЛЯТОРАМИ РОСТА РАСТЕНИЙ

Phytohormones serve as regulators of plant growth and development, playing a fundamental role in the adaptation and survival of plants under different conditions. It is well-known that bacteria have the ability to influence plant physiology by producing phytohormones or decreasing their concentration in plant tissues and the surrounding environment through degradation or transformation. Studying these processes is crucial for a deeper comprehension of plant-microorganism interactions. This study presents the capability of bacteria that promote plant growth and development to degrade phytohormones (ABA, 6-BAP, and IAA) in a culture medium using them as the sole carbon and energy source. It was discovered that a significant portion of the selected strains could thrive on a medium containing ABA, 6-BAP, and IAA. However, the growth intensity varied significantly among different substrates. For instance, strains Pseudomonas plecoglossicida 2,4-D (2,4-D), Pseudomonas sp. RZ (RZ), and Pseudomonas plecoglossicida CH5%2 (CH5%2) exhibited equal growth rates on all substrates, but high-performance liquid chromatography (HPLC) results indicated that strain 2,4 D was the most efficient in the degradation of the aforementioned phytohormones. The extent of biodegradation of ABA, 6-BAP, and IAA by this strain during a 10-day cultivation period amounted to 33%, 70%, and 60%, respectively.

Effects of planting year of alfalfa on rhizosphere bacterial structure and function

In many areas across the world, alfalfa is still cultivated in the same place over many years, leading to gradually deplete the soil nutrients and increase plant disease and consequent decreases in the yield and quality. Agricultural management practices have been proved to affect largely soil microbial community structure and functions in many reports, but it remains unclear how planting year effects extend to the rhizosphere under a long-term cultivation practices of alfalfa. Exploring such impacts is of great importance to understand and develop plant-microorganism interactions for agricultural sustainability. A long-term field experiment was set up at Linze research station of Lanzhou University in Gansu province, where alfalfa was continuously planted for four years (Y4) and six years (Y6). Rhizosphere soils from two different planting years were collected to examine differences in the bacterial diversity, composition and co-occurrence patterns using 16S rRNA gene sequencing technologies as well as in functional profiles involved in nitrogen cycling predicted by FAPROTAX. We found that soil nutrients including soil organic carbon (SOC), AP (available phosphorus) and nitrate nitrogen (NO3−-N) differed significantly between planting years. Bacterial taxonomic diversity, composition and the relative abundance of functional groups involved in nitrogen cycling were significantly affected by planting years, sampling time and their interactions. Co-occurrence network analysis showed that keystone taxa in both planting years were affiliated to Proteobacteria and bacteria taxa had less complexity and more negative correlations in Y6 than in Y4. NO3−-N was a major factor affecting bacterial community diversity and composition across planting years. Together, our findings suggest that planting years of alfalfa can lead to large variations in soil nutrients and rhizosphere microbial community patterns. These results implies that in agricultural management practices, planting year effects can even extend to microorganisms in association with plant roots, which may affect crop growth given close linkages between rhizosphere processes and plant nutrition availability.

Generation and characterization of two new monoclonal antibodies produced by immunizing mice with plant fructans: New tools for immunolocalization of β-(2 → 1) and β-(2 → 6) fructans

Fructans are water-soluble polymers of fructose in which fructose units are linked by β-(2 → 1) and/or β-(2 → 6) linkages. In plants, they are synthesized in the vacuole but have also been reported in the apoplastic sap under abiotic stress suggesting that they are involved in plasmalemma protection and in plant-microbial interactions. However, the lack of fructan-specific antibodies currently prevents further study of their role and the associated mechanisms of action, which could be elucidated thanks to their immunolocalization. We report the production of two monoclonal antibodies (named BTM9H2 and BTM15A6) using mice immunization with antigenic compounds prepared from a mixture of plant inulins and levans conjugated to serum albumin. Their specificity towards fructans with β-(2 → 1) and/or β-(2 → 6) linkage has been demonstrated by immuno-dot blot tests on a wide range of carbohydrates. The two mAbs were used for immunocytolocalization of fructans by epifluorescence microscopy in various plant species. Fructan epitopes were specifically detected in fructan-accumulating plants, inside cells as well as on the surface of root tips, confirming both extracellular and intracellular localizations. The two mAbs provide new tools to identify the mechanism of extracellular fructan secretion and explore the roles of fructans in stress resistance and plant-microorganism interactions.

ISOLATION AND IDENTIFICATION OF BROAD-SPECTRUM ANTAGONIST BACTERIA AGAINST PATHOGENIC FUNGI OF MAIZE CROP

Fungal diseases may cause significant damage to crops worldwide, generating yield losses, poor grain quality, and health risks to humans and animals. Biological control using antagonistic bacteria offers innovative solutions for sustainable management aiming at plant protection. However, beneficial plant-microorganism interactions are particular, and few antagonists with broad-spectrum activity have been reported. In this work, two bacteria isolated from sorghum seeds were identified by partial sequencing of the 16S rRNA gene and tested in vitro for their capacity to control six important pathogenic fungi of maize: Fusarium verticillioides, Macrophomina phaseolina, Stenocarpella sp., Fusarium graminearum, Colletotrichum graminicola, and Bipolaris sp. The molecular identification revealed that the bacterial isolates belong to the genera Bacillus (strain LIS05) and Paenibacillus (strain LIS04). Both bacterial isolates inhibited the growth of all six phytopathogens by at least 49%. The isolate LIS05 showed the most significant antagonistic potential against the fungal pathogens tested, at an average of 73% inhibition. The highest antagonist activity (86.1% inhibition) was observed in the confrontation test between the isolate LIS05 and C. graminicola. In addition to the mycelial growth inhibition, the isolate LIS04 blocked the production of dark pigments by Bipolaris sp. This study showed that LIS05 and LIS04 are promising alternatives for developing integrated management strategies to control fungal diseases in maize and sorghum.

Changes in Diversity and Composition of Rhizosphere Bacterial and Fungal Community between Resistant and Susceptible Pakchoi under Plasmodiophora brassicae

Plasmodiophora brassicae (P. brassicae) is a soil-born pathogen worldwide and can infect most cruciferous plants, which causes great yield decline and economic losses. It is not well known how microbial diversity and community composition change during P. brassicae infecting plant roots. Here, we employed a resistant and a susceptible pakchoi cultivar with and without inoculation with P. brassicae to analyze bacterial and fungal diversity using 16S rRNA V3-V4 and ITS_V1 regions, respectively. 16S rRNA V3-V4 and ITS_V1 regions were amplified and sequenced separately. Results revealed that both fungal and bacterial diversity increased, and composition was changed in the rhizosphere soil of the susceptible pakchoi compared with the resistant cultivar. In the four groups of R_mock, S_mock, R_10d, and S_10d, the most relatively abundant bacterium and fungus was Proteobacteria, accounting for 61.92%, 58.17%, 48.64%, and 50.00%, respectively, and Ascomycota, accounting for 75.11%, 63.69%, 72.10%, and 90.31%, respectively. A total of 9488 and 11,914 bacteria were observed uniquely in the rhizosphere soil of resistant and susceptible pakchoi, respectively, while only 80 and 103 fungi were observed uniquely in the correlated soil. LefSe analysis showed that 107 and 49 differentially abundant taxa were observed in bacteria and fungi. Overall, we concluded that different pakchoi cultivars affect microbial diversity and community composition, and microorganisms prefer to gather around the rhizosphere of susceptible pakchoi. These findings provide a new insight into plant–microorganism interactions.

Biological denitrification inhibition (BDI) on nine contrasting soils: An unexpected link with the initial soil denitrifying community

Denitrification is considered the major pathway leading to soil gaseous (N) losses, affecting N availability for plants and consequently plant productivity. Biological denitrification inhibition (BDI) in Fallopia spp., a plant species complex with a high level of growth and competitiveness for mineral N, acts through procyanidin production. However, the soil factors governing BDI development are still unknown. Through a mesocosm experiment using two treatments – soil planted with Fallopia japonica and unplanted–, nine biologically and physically contrasting soils were studied with the aim to ascertain how each can affect BDI development. Microbial enzyme activities (respiration - SIR, denitrification - DEA), denitrifying functional gene abundance (nirK, nirS), total bacterial community abundance (rRNA 16S) and soil physicochemical parameters (N mineral forms, soil texture, moisture, pH) were measured before and after plant growth, and the DEA:SIR ratio was used as a BDI proxy. The DEA:SIR ratio decreased for six soils. BDI development is related to a small number of soil factors, mainly initial soil moisture and ammonium concentration, and unexpectedly, with the initial abundance of nirK(in), nirS(in) and rRNA 16S(in). The intensity of this decrease is positively correlated to the level of DEA in unplanted soil: the higher the DEA in unplanted soil, the more intense the BDI under F. japonica. The procyanidin concentration of the F. japonica belowground system was positively correlated to BDI intensity. These results suggest that a procyanidin assay from the plant belowground system could be a new proxy for measuring BDI intensity. Interestingly, this research shows that BDI is not systematic, and that few (a)biotic soil parameters influence its development. More importantly, this research is the first to highlight that biotic factors are relevant in explaining BDI. This paper also presents new perspectives on plant-microorganism interactions in terms of plant awareness of the soil microbial community.

Beneficial microbial consortium improves winter rye performance by modulating bacterial communities in the rhizosphere and enhancing plant nutrient acquisition.

The beneficial effect of microbial consortium application on plants is strongly affected by soil conditions, which are influenced by farming practices. The establishment of microbial inoculants in the rhizosphere is a prerequisite for successful plant-microorganism interactions. This study investigated whether a consortium of beneficial microorganisms establishes in the rhizosphere of a winter crop during the vegetation period, including the winter growing season. In addition, we aimed for a better understanding of its effect on plant performance under different farming practices. Winter rye plants grown in a long-time field trial under conventional or organic farming practices were inoculated after plant emergence in autumn with a microbial consortium containing Pseudomonas sp. (RU47), Bacillus atrophaeus (ABi03) and Trichoderma harzianum (OMG16). The density of the microbial inoculants in the rhizosphere and root-associated soil was quantified in autumn and the following spring. Furthermore, the influence of the consortium on plant performance and on the rhizosphere bacterial community assembly was investigated using a multidisciplinary approach. Selective plating showed a high colonization density of individual microorganisms of the consortium in the rhizosphere and root-associated soil of winter rye throughout its early growth cycle. 16S rRNA gene amplicon sequencing showed that the farming practice affected mainly the rhizosphere bacterial communities in autumn and spring. However, the microbial consortium inoculated altered also the bacterial community composition at each sampling time point, especially at the beginning of the new growing season in spring. Inoculation of winter rye with the microbial consortium significantly improved the plant nutrient status and performance especially under organic farming. In summary, the microbial consortium showed sufficient efficacy throughout vegetation dormancy when inoculated in autumn and contributed to better plant performance, indicating the potential of microbe-based solutions in organic farming where nutrient availability is limited.