Plant Compartments Research Articles

Divergent Assembly Processes of Phyllosphere and Rhizosphere Microbial Communities Along Environmental Gradient.

The underlying assembly processes of surface microbial communities are crucial for host plants and ecosystem functions. However, the relative importance of stochastic and deterministic processes in shaping epiphytic microbes remains poorly understood in both the phyllosphere and rhizosphere. Here, we compared the spatial variations in epiphytic microbial communities of two dominant grasses along a 1400 km transect on the Tibetan Plateau and assessed the assembly processes between the phyllosphere and rhizosphere. We found significant variations in epiphytic microbial community compositions between plant compartments and host species. Stochastic processes (drift and homogenizing dispersal) predominantly shaped microbial communities in both the phyllosphere and rhizosphere, with a greater contribution of stochastic processes in the phyllosphere. As environmental heterogeneity intensified, we found a transition from stochasticity to determinism in affecting the microbial assembly. This transition to homogeneous or variable selection depended on plant compartments and host species. Our study is among the first to compare the contribution of stochastic versus deterministic processes to epiphytic community assembly between the phyllosphere and rhizosphere on the Tibetan Plateau. These findings advance our knowledge of epiphytic microbial assembly and disentangle how host plants exploit the microbiome for improved performance and functioning in stressful alpine ecosystems.

Unravelling the microbiome of wild flowering plants: a comparative study of leaves and flowers in alpine ecosystems

BackgroundWhile substantial research has explored rhizosphere and phyllosphere microbiomes, knowledge on flower microbiome, particularly in wild plants remains limited. This study explores into the diversity, abundance, and composition of bacterial and fungal communities on leaves and flowers of wild flowering plants in their natural alpine habitat, considering the influence of environmental factors.MethodsWe investigated 50 wild flowering plants representing 22 families across seven locations in Austria. Sampling sites encompassed varied soil types (carbonate/silicate) and altitudes (450–2760 m). Amplicon sequencing to characterize bacterial and fungal communities and quantitative PCR to assess microbial abundance was applied, and the influence of biotic and abiotic factors assessed.ResultsOur study revealed distinct bacterial and fungal communities on leaves and flowers, with higher diversity and richness on leaves (228 fungal and 91 bacterial ASVs) than on flowers (163 fungal and 55 bacterial ASVs). In addition, Gammaproteobacteria on flowers and Alphaproteobacteria on leaves suggests niche specialization for plant compartments. Location significantly shaped both community composition and fungal diversity on both plant parts. Notably, soil type influenced community composition but not diversity. Altitude was associated with increased fungal species diversity on leaves and flowers. Furthermore, significant effects of plant family identity emerged within a subset of seven families, impacting bacterial and fungal abundance, fungal Shannon diversity, and bacterial species richness, particularly on flowers.ConclusionThis study provides novel insights into the specific microbiome of wild flowering plants, highlighting adaptations to local environments and plant–microbe coevolution. The observed specificity indicates a potential role in plant health and resilience, which is crucial for predicting how microbiomes respond to changing environments, ultimately aiding in the conservation of natural ecosystems facing climate change pressures.

Optimizing nitrogen fertilization in maize: the impact of nitrification inhibitors, phosphorus application, and microbial interactions on enhancing nutrient efficiency and crop performance.

Despite the essential role of nitrogen fertilizers in achieving high crop yields, current application practices often exhibit low efficiency. Optimizing nitrogen (N) fertilization in agriculture is, therefore, critical for enhancing crop productivity while ensuring sustainable food production. This study investigates the effects of nitrification inhibitors (Nis) such as Dimethyl Pyrazole Phosphate (DMPP) and Dimethyl Pyrazole Fulvic Acid (DMPFA), plant growth-promoting bacteria inoculation, and phosphorus (P) application on the soil-plant-microbe system in maize. DMPFA is an organic nitrification inhibitor that combines DMP and fulvic acid for the benefits of both compounds as a chelator. A comprehensive rhizobox experiment was conducted, employing varying levels of P, inoculant types, and Nis, to analyze the influence of these factors on various soil properties, maize fitness, and phenotypic traits, including root architecture and exudate profile. Additionally, the experiment examined the effects of treatments on the bacterial and fungal communities within the rhizosphere and maize roots. Our results showed that the use of Nis improved plant nutrition and biomass. For example, the use of DMPFA as a nitrification inhibitor significantly improved phosphorus use efficiency by up to 29%, increased P content to 37%, and raised P concentration in the shoot by 26%, compared to traditional ammonium treatments. The microbial communities inhabiting maize rhizosphere and roots were also highly influenced by the different treatments. Among them, the N treatment was the major driver in shaping bacterial and fungal communities in both plant compartments. Notably, Nis reduced significantly the abundance of bacterial groups involved in the nitrification process. Moreover, we observed that each experimental treatment employed in this investigation could select, promote, or reduce specific groups of beneficial or detrimental soil microorganisms. Overall, our results highlight the intricate interplay between soil amendments, microbial communities, and plant nutrient dynamics, suggesting that Nis, particularly DMPFA, could be pivotal in bolstering agricultural sustainability by optimizing nutrient utilization.

Ecological characteristics of tall fescue and spatially organized communities: Their contribution to mitigating cadmium damage

The threat of cadmium (Cd) stress to agricultural soil environments, as well as their productivity attracting growing global interest. Tall fescue (Festuca arundinacea Schreb.) is a strong candidate for the remediation of heavy metals in soil. However, the joint analysis of Cd tolerance, physiological responses, and multifaceted plant microbiomes in tall fescue fields has not been extensively researched. Therefore, this study employed microbial sequencing (i.e., 16S and ITS sequencing) to investigate the differences in microbial community structure among various plant compartments of Cd-resistant tall fescue (cv. ‘Arid3′) and Cd-sensitive tall fescue (cv. ‘Barrington’). Furthermore, we examined the mechanism of resistance to Cd by introducing three different bacteria and a fungus that were isolated from the ‘Arid3′ rhizosheath soil. It highlighted the potential application of enriched taxa such as Delftia, Novosphingobium, Cupriavidus and Torula in enhancing the activity of antioxidant defense systems, increasing the production of osmotic regulatory substances, and stimulating the expression of Cd-resistance genes. This ultimately promoted plant growth and enhanced phytoremediation efficiency. This study shed light on the response mechanism of the tall fescue microbiome to Cd stress and underscored the potential of tall fescue-microbe co-culture in the remediation of heavy metal-contaminated areas.

Thermochemical Transformation of Calcium during Biomass Burning and the Effects on Postfire Aqueous Dissolution of Macronutrients.

Calcium is commonly the most abundant element in fire residues and its speciation largely determines the geochemical properties of fire residues and their effects on postfire soil chemistry. To explore the effects of biomass composition and fire conditions on ash Ca speciation, this study characterizes the speciation of Ca in charcoal and ash samples that were derived from different plant compartments and thermal conditions, using Ca K-edge X-ray absorption near edge spectroscopy. Results showed that biomass contains abundant organic Ca complexes, which were mineralized into fairchildite and calcite after heating at 450 to 600 °C and then CaO, as temperature increased to 750 °C. Apatite could be an abundant Ca species in fire residues if the Ca/P molar ratio of the biomass is small (<2). The mineralization of organic Ca to the identified Ca minerals during burning was negligibly affected by the oxygen level. Calcium speciation in prescribed fire residues resembled that of biomass ash burned at 550 °C with similar Ca/P molar ratios. Batch experiments showed that macronutrients (Ca, Mg, K, and P) were differentially released, as a result of different solubility of minerals in ashes and reprecipitation of minerals. The aqueous solubility of Ca, Mg, and P decreased as pH increased from 5 to 9, while K showed no pH dependency and was almost completely soluble. Results from this study improve our understanding of the chemistry of fire residues and their geochemical behaviors, which can help evaluate the impact of fire on postfire soil properties and macronutrient cycling.

Bacillus species are core microbiota of resistant maize cultivars that induce host metabolic defense against corn stalk rot

BackgroundMicrobes colonizing each compartment of terrestrial plants are indispensable for maintaining crop health. Although corn stalk rot (CSR) is a severe disease affecting maize (Zea mays) worldwide, the mechanisms underlying host–microbe interactions across vertical compartments in maize plants, which exhibit heterogeneous CSR-resistance, remain largely uncharacterized.ResultsHere, we investigated the microbial communities associated with CSR-resistant and CSR-susceptible maize cultivars using multi-omics analysis coupled with experimental verification. Maize cultivars resistant to CSR reshaped the microbiota and recruited Bacillus species with three phenotypes against Fusarium graminearum including niche pre-emption, potential secretion of antimicrobial compounds, and no inhibition to alleviate pathogen stress. By inducing the expression of Tyrosine decarboxylase 1 (TYDC1), encoding an enzyme that catalyzes the production of tyramine and dopamine, Bacillus isolates that do not directly suppress pathogen infection induced the synthesis of berberine, an isoquinoline alkaloid that inhibits pathogen growth. These beneficial bacteria were recruited from the rhizosphere and transferred to the stems but not grains of the CSR-resistant plants.ConclusionsThe current study offers insight into how maize plants respond to and interact with their microbiome and lays the foundation for preventing and treating soil-borne pathogens.FCn65Jq_7Sh4F-UA4uQM99Video

Pupylation-Based Proximity-Tagging of FERONIA-Interacting Proteins in Arabidopsis

The plasma membrane-localized receptor kinase FERONIA (FER) plays critical roles in a remarkable variety of biological processes throughout the life cycle of Arabidopsis thaliana. Revealing the molecular connections of FER that underlie these processes starts with identifying the proteins that interact with FER. We applied pupylation-based interaction tagging (PUP-IT) to survey cellular proteins in proximity to FER, encompassing weak and transient interactions that can be difficult to capture for membrane proteins. We reproducibly identified 581, 115, and 736 specific FER-interacting protein candidates in protoplasts, seedlings, and flowers, respectively. We also confirmed fourteen previously characterized FER-interacting proteins. Protoplast transient gene expression expedited the testing of new gene constructs for PUP-IT analyses and the validation of candidate proteins. We verified the proximity labeling of five selected candidates that were not previously characterized as FER-interacting proteins. The PUP-IT method could be a valuable tool to survey and validate protein-protein interactions for targets of interest in diverse subcellular compartments in plants.

Mother trees of common ash (Fraxinus excelsior) disperse different sets of mycobiome through their seed wings

ObjectiveThe endophytic mycobiome is present in all studied plant compartments, including fruits and seeds. Here, we studied the mycobiome of seed wings as they are transferred with seeds in common ash and tested whether the mycobiome differs among trees. To achieve this, we used ITS1-based amplicon sequencing and two genotypes of F. excelsior as a model to compare the mycobiome of mother trees and their wings.ResultsWe compared the mycobiome of 57 seed wings to the seed stalks (57) collected from two genotypes of F. excelsior using three ramets of each genotype. Alpha diversity indices (ACE, Fisher and Observed OTUs) suggested a higher richness of the mycobiome associated with the seed wing than the seed stalk within each genotype. However, there were neither significant differences in Shannon diversity between the mycobiomes from the two tissue types nor the two genotypes. PERMANOVA revealed significant differences in the mycobiome composition between tissue types (P < 0.001). It also showed a significant difference between seed wings (P = 0.04), but not between seed stalks of the two genotypes. Our results suggest that Fraxinus excelsior mother trees disperse different sets of mycobiomes with their seed wings, which may be important for germination and seedling establishment—especially in the light of ash dieback.

Desert plants, arbuscular mycorrhizal fungi and associated bacteria: Exploring the diversity and role of symbiosis under drought.

Desert plants, such as Agave tequilana, A. salmiana and Myrtillocactus geometrizans, can survive harsh environmental conditions partly due to their symbiotic relationships with microorganisms, including arbuscular mycorrhizal fungi (AMF). Interestingly, some of these fungi also harbour endosymbiotic bacteria. Our research focused on investigating the diversity of these AMFs and their associated bacteria in these plants growing in arid soil. We found that agaves have a threefold higher AMF colonization than M. geometrizans. Metabarcoding techniques revealed that the composition of AMF communities was primarily influenced by the plant host, while the bacterial communities were more affected by the specific plant compartment or niche they inhabited. We identified both known and novel endofungal bacterial taxa, including Burkholderiales, and confirmed their presence within AMF spores using multiphoton microscopy. Our study also explored the effects of drought on the symbiosis between A. tequilana and AMF. We discovered that the severity of drought conditions could modulate the strength of this symbiosis and its outcomes for the plant holobiont. Severe drought conditions prevented the formation of this symbiosis, while moderate drought conditions promoted it, thereby conferring drought tolerance in A. tequilana. This research sheds light on the diversity of AMF and associated bacteria in Crassulacean Acid Metabolism (CAM) plants and underscores the crucial role of drought as a factor modulating the symbiosis between A. tequilana and AMF. Further research is needed to understand the role of endofungal bacteria in this response.

Unraveling the dynamic interplay of microbial communities associated to Lupinus angustifolius in response to environmental and cultivation conditions

Microorganisms form dynamic communities with plants, providing benefits such as nutrient acquisition and stress resilience. Understanding how these microorganisms are affected by environmental factors such as growth conditions and soil characteristics are essential for harnessing these communities for sustainable agriculture practices and their response to climate change. The microbiome associated to Lupinus angustifolius, a legume native in Europe, with a high protein value and stress resilience was characterized for the first time. Using 16S rRNA gene and ITS amplicon sequencing, we characterized the compositional and temporal changes of the bacterial and fungal communities associated to the soil, rhizosphere, and plant compartments where Lupinus angustifolius grows naturally. Our results suggest that the main difference in the soil microbial communities is related to the edaphic properties, although environmental factors such as temperature, humidity or rainfall also influenced the composition of the soil microbial communities. We also characterized the bacterial communities associated with the rhizosphere, roots, nodules, and leaves of wild plants collected in the field and compared them against plants obtained under greenhouse conditions. In the plant compartments, the bacterial composition appeared to be more affected by the growing conditions (field vs greenhouse), than by soil characteristics or location. These results can be used to identify key taxa that may play crucial roles in the development and adaptation of the host plant and its associated microbiota to environmental changes and highlight the importance of characterizing the plant microbiomes in their natural habitats. Soil, influenced by climatic seasons, shapes the plant microbiome assembly. Lupinus recruits a core microbiome across rhizosphere, roots, nodules, and leaves, that is stable across locations. However, cultivation conditions may alter microbiome dynamics, impacting the adaptability of its components. Wild plants show a resilient and adaptable microbiome while germination and cultivation in greenhouse conditions alter its composition and vulnerability.

Rhizosphere-xylem sap connections in the olive tree microbiome: implications for biostimulation approaches.

Climate change is endangering olive groves. Farmers are adapting by exploring new varieties of olive trees and examining the role of microbiomes in plant health.The main objectives of this work were to determine the primary factors that influence the microbiome of olive trees and to analyze the connection between the rhizosphere and endosphere compartments. The rhizosphere and xylem sap microbiomes of two olive tree varieties were characterized by next-generation 16S rRNA amplicon sequencing, and soil descriptors were analyzed. Bacterial communities in the rhizosphere of olive trees were more diverse than those found in the xylem sap. Pseudomonadota, Actinobacteriota, Acidobacteriota, and Bacillota were the dominant phyla in both compartments. At the genus level, only very few taxa were shared between soil and sap bacterial communities. The composition of the bacteriome was more affected by the plant compartment than by the olive cultivar or soil properties, and a direct route from the rhizosphere to the endosphere could not be confirmed. The large number of plant growth-promoting bacteria found in both compartments provides promising prospects for improving agricultural outcomes through microbiome engineering.

Abiotic stress reorganizes rhizosphere and endosphere network structure of Sorghum bicolor

Sorghum bicolor is a promising bioenergy feedstock with high biomass production and unusual tolerance for stresses such as water and nutrient limitation. While the membership of the sorghum microbiome in response to stress has been explored, relatively little is known about how microbe-microbe networks change under water- or nutrient-limited conditions. This is important because network changes can indicate impacts on the functionality and stability of microbial communities. We performed network-based analysis on the core bacterial and archaeal community of an agronomically promising high biomass bioenergy genotype, Grassl, grown under nitrogen and water stress. Stress caused relatively minor changes in bacterial abundances within soil, rhizosphere, and endosphere communities, but led to significant changes in bacterial network structure and modularity. We found a complete reorganization of network roles in all plant compartments as well as an increase in the modularity and proportion of positive associations which potentially could represent coexistence and cooperation in the sorghum bacterial/archaeal community under stress. While stressors are often believed to be destabilizing, we found stressed networks were as or more stable than non-stressed networks likely due to their redundancy and compartmentalization. Together, these findings support the idea that both sorghum and its bacterial/archaeal community can be resilient to future environmental stressors.

Changes in Endophyte Communities across the Different Plant Compartments in Response to the Rice Blast Infection.

The rice blast disease, caused by the fungal pathogen, Magnaporthe oryzae (syn. Pyricularia oryzae), poses a significant threat to the global rice production. Understanding how this disease impacts the plant's microbial communities is crucial for gaining insights into hostpathogen interactions. In this study, we investigated the changes in communities of bacterial and fungal endophytes inhabiting different compartments in healthy and diseased plants. We found that both alpha and beta diversities of endophytic communities do not change significantly by the pathogen infection. Rather, the type of plant compartment appeared to be the main driver of endophytic community structures. Although the overall structure seemed to be consistent between healthy and diseased plants, our analysis of differentially abundant taxa revealed the specific bacterial and fungal operational taxonomic units that exhibited enrichment in the root and leaf compartments of infected plants. These findings suggest that endophyte communities are robust to the changes at the early stage of pathogen infection, and that some of endophytes enriched in infected plants might have roles in the defense against the pathogen.

Superoxide Dismutase Premodulates Oxidative Stress in Plastids for Protection of Tobacco Plants from Cold Damage Ultrastructure Damage

ROS-dependent induction of oxidative damage can be used as a trigger initiating genetically determined non-specific protection in plant cells and tissues. Plants are potentially able to withstand various specific (toxic, osmotic) factors of abiotic effects, but do not have sufficient or specific sensitivity to form an adequate effective response. In this work, we demonstrate one of the possible approaches for successful cold acclimation through the formation of effective protection of photosynthetic structures due to the insertion of the heterologous FeSOD gene into the tobacco genome under the control of the constitutive promoter and equipped with a signal sequence targeting the protein to plastid. The increased enzymatic activity of superoxide dismutase in the plastid compartment of transgenic tobacco plants enables them to tolerate the oxidative factor of environmental stresses scavenging ROS. On the other hand, the cost of such resistance is quite high and, when grown under normal conditions, disturbs the arrangement of the intrachloroplastic subdomains leading to the modification of stromal thylakoids, probably significantly affecting the photosynthesis processes that regulate the efficiency of photosystem II. This is partially compensated for by the fact that, at the same time, under normal conditions, the production of peroxide induces the activation of ROS detoxification enzymes. However, a violation of a number of processes, such as the metabolism of accumulation, and utilization and transportation of sugars and starch, is significantly altered, which leads to a shift in metabolic chains. The expected step for further improvement of the applied technology could be both the use of inducible promoters in the expression cassette, and the addition of other genes encoding for hydrogen peroxide-scavenging enzymes in the genetic construct that are downstream in the metabolic chain.

Soil microbiota and herbivory drive the assembly of tomato plant-associated microbial communities through different mechanisms

Plant-associated microbial communities are key to shaping many aspects of plant biology. In this study, we tested whether soil microbial communities and herbivory influence the bacterial community of tomato plants and whether their influence in different plant compartments is driven by microbial spillover between compartments or whether plants are involved in mediating this effect. We grew our plants in soils hosting three different microbial communities and covered (or not) the soil surface to prevent (or allow) passive microbial spillover between compartments, and we exposed them (or not) to herbivory by Manduca sexta. Here we show that the soil-driven effect on aboveground compartments is consistently detected regardless of soil coverage, whereas soil cover influences the herbivore-driven effect on belowground microbiota. Together, our results suggest that the soil microbiota influences aboveground plant and insect microbial communities via changes in plant metabolism and physiology or by sharing microorganisms via xylem sap. In contrast, herbivores influence the belowground plant microbiota via a combination of microbial spillover and changes in plant metabolism. These results demonstrate the important role of plants in linking aboveground and belowground microbiota, and can foster further research on soil microbiota manipulation for sustainable pest management.

Root exudate-mediated plant–microbiome interactions determine plant health during disease infection

Understanding the interactions between plants and microbes during pathogen infection is crucial for plant health improvement. However, the integrated role of soil nutrients, root exudates, and plant microbiomes in plant health during disease outbreaks remains unclear. In this study, we hypothesized that root exudate-mediated healthy microbiomes (HealthyBiome) would facilitate the escape of soil-borne pathogen infection, whereas a root exudate-mediated disease-conductive microbiome (PathoBiome) would induce disease occurrence. Using watermelon wilt disease caused by Fusarium oxysporum as a model, we investigated these interactions and their implications in plant disease. We examined the pathogen load across plant compartments during the pathogen accumulation (AH) and disease outbreak periods. We analyzed the plant microbiomes and root exudates during the outbreak, which was associated with the emergence in both healthy (BH) and diseased (BD) plants. Compared with AH and BD plants, BH plants had the lowest F. oxysporum density in the root–soil system (0.74–0.84 times that of AH and BD plants). BD plants showed an elevated amino acid metabolism (2.84–3.38 times that of healthy plants), whereas BH plants showed a higher metabolism of phenolic compounds (1.73 times that of diseased plants). BH plants secreted more palmitic acid (1.53 times that of diseased plants) and recruited more nitrogen (N)-fixing bacteria (e.g., Paenarthrobacter, Sphingomonas), which potentially alleviated N scarcity in the soil, promoted plant growth, and improved the plant defense. Structural equation modeling highlighted the interactions among soil nutrients, root metabolites, and plant nutrients in recruiting pro-growth bacteria to the rhizosphere and roots for healthy plant growth. Our findings provide novel evidence of how root exudates influence plant–microbiome interactions during pathogen infections, highlighting the importance of a balanced root exudate profile and its associated “HealthyBiome” in promoting plant health and growth.

Comparative Transcriptome Analysis Reveals the Protective Role of Melatonin during Salt Stress by Regulating the Photosynthesis and Ascorbic Acid Metabolism Pathways in Brassica campestris.

Salinity stress is a type of abiotic stress which negatively affects the signaling pathways and cellular compartments of plants. Melatonin (MT) has been found to be a bioactive compound that can mitigate these adverse effects, which makes it necessary to understand the function of MT and its role in salt stress. During this study, plants were treated exogenously with 100 µM of MT for 7 days and subjected to 200 mM of salt stress, and samples were collected after 1 and 7 days for different indicators and transcriptome analysis. The results showed that salt reduced chlorophyll contents and damaged the chloroplast structure, which was confirmed by the downregulation of key genes involved in the photosynthesis pathway after transcriptome analysis and qRT-PCR confirmation. Meanwhile, MT increased the chlorophyll contents, reduced the electrolyte leakage, and protected the chloroplast structure during salt stress by upregulating several photosynthesis pathway genes. MT also decreased the H2O2 level and increased the ascorbic acid contents and APX activity by upregulating genes involved in the ascorbic acid pathway during salt stress, as confirmed by the transcriptome and qRT-PCR analyses. Transcriptome profiling also showed that 321 and 441 DEGs were expressed after 1 and 7 days of treatment, respectively. The KEGG enrichment analysis showed that 76 DEGs were involved in the photosynthesis pathway, while 35 DEGs were involved in the ascorbic acid metabolism pathway, respectively. These results suggest that the exogenous application of MT in plants provides important insight into understanding MT-induced stress-responsive mechanisms and protecting Brassica campestris against salt stress by regulating the photosynthesis and ascorbic acid pathway genes.

Accumulation of Atmospheric PAHs in White Mustard – Can the Seeds Be Affected?

Traffic-related particulate matter emissions have been considerably reduced due to stringent regulations in Europe. However, emission of diesel-powered vehicles still poses a significant environmental threat, affecting rural ecosystems and agriculture. Several studies have reported that polycyclic aromatic hydrocarbons (PAHs), a group of potentially toxic organic compounds, can accumulate in crops and vegetables. In our study, white mustard (Sinapis alba L.) plants were experimentally treated with an extract of diesel exhaust. PAH concentrations were measured in the different plant compartments (stems, leaves and seeds), bioconcentration factors (BCFs) were also calculated. Significant accumulation was measured in the leaves and seeds, stems showed lower accumulation potential. All plant matrices showed high tendency to accumulate higher molecular weight PAHs, BCF was the highest in the 6-ring group. The fact that considerable accumulation was experienced in the seeds might show the risk of cultivating crops nearby roads highly impacted by traffic-related emissions.

Disease-induced changes in bacterial and fungal communities from plant below- and aboveground compartments

The plant microbes are an integral part of the host and play fundamental roles in plant growth and health. There is evidence indicating that plants have the ability to attract beneficial microorganisms through their roots in order to defend against pathogens. However, the mechanisms of plant microbial community assembly from below- to aboveground compartments under pathogen infection remain unclear. In this study, we investigated the bacterial and fungal communities in bulk soil, rhizosphere soil, root, stem, and leaf of both healthy and infected (Potato virus Y disease, PVY) plants. The results indicated that bacterial and fungal communities showed different recruitment strategies in plant organs. The number and abundance of shared bacterial ASVs between bulk and rhizosphere soils decreased with ascending migration from below- to aboveground compartments, while the number and abundance of fungal ASVs showed no obvious changes. Field type, plant compartments, and PVY infection all affected the diversity and structures of microbial community, with stronger effects observed in the bacterial community than the fungal community. Furthermore, PVY infection, rhizosphere soil pH, and water content (WC) contributed more to the assembly of the bacterial community than the fungal community. The analysis of microbial networks revealed that the bacterial communities were more sensitive to PVY infection than the fungal communities, as evidenced by the lower network stability of the bacterial community, which was characterized by a higher proportion of positive edges. PVY infection further increased the bacterial network stability and decreased the fungal network stability. These findings advance our understanding of how microbes respond to pathogen infections and provide a rationale and theoretical basis for biocontrol technology in promoting sustainable agriculture.Key points• Different recruitment strategies between plant bacterial and fungal communities.• Bacterial community was more sensitive to PVY infection than fungal community.• pH and WC drove the microbial community assembly under PVY infection.

Going cresyl for plant cell imaging

The adventof fluorescent probesand the characterization of their photochemical properties in the past years allowed significant advances in the studies ofspatiotemporal cellular processes within complex and crowded systems.Dyesareindeedextremely useful tools forthe visualization ofcellular and subcellular structures present in living cells, as well asto studytheirdynamicand molecular composition or physiological changes. There are some areas of plant cell biology that have been more challenging to explore due to the physiology and organization of certain endomembrane compartments. In this study we characterize the labeling properties of cresyl violet as quick and inexpensive imaging agent for tracking endosomes, vacuole compartments which are usually very differentiated and categorized as more acidic as well as acidic plant compartments. Its photobleaching, labelling and cytotoxic properties are compared with other well-known and currently most used synthetic and molecular probes.