Competition for iron drives phytopathogen control by natural rhizosphere microbiomes

Low-dose natural clay Kaolin promotes the growth of submerged macrophytes and alters the rhizosphere microorganism community: Implications for lake restoration

Sediment properties have a crucial effect on the growth and recovery of aquatic plants in lakes. Addition of various chemical substances has been proposed to reinforce the recovery of plants after a nutrient loading reduction. However, the effects of such sediment amendments on plant growth, especially those from rhizosphere microorganisms, is limited. We added Kaolin clay to sediments in different concentrations to explore its impact on the growth of Vallisneria natans and Ottelia acuminate and the concurrent shift in rhizosphere microorganisms using high-throughput sequencing technology. We found that the addition of low doses (10 % and 20 % in mass ratio) of Kaolin significantly modified sediment conditions (oxidation reduction potential and pH), with implications also for the composition, diversity, and stability of rhizosphere microorganisms. LEfSe analysis revealed that low-dose addition of Kaolin increased the abundances of functional microbial groups that benefit plant nutrient absorption and enhance plant stress resistance, such as Spirillaceae, Rhodocyclaceae, and Burkholderiales. Moreover, low doses of Kaolin significantly promoted the photosynthesis and nutrient absorption of submerged macrophytes, thereby facilitating plant growth. A structural equation model (SEM) indicated that the direct impact of Kaolin on the growth of submerged plants was relatively minor, while the indirect effect through modulation of rhizosphere microorganisms was important. Our study suggests that low doses of Kaolin may be used to promote the growth of submerged macrophytes when lakes with a high organic content in the sediment are recovering after nutrient loading reduction.

Interactions with native microbial keystone taxa enhance the biocontrol efficiency of Streptomyces

BACKGROUND

Streptomyces spp. are known for producing bioactive compounds that suppress phytopathogens. However, previous studies have largely focused on their direct interactions with pathogens and plants, often neglecting their interactions with the broader soil microbiome. In this study, we hypothesized that these interactions are critical for effective pathogen control. We investigated a diverse collection of Streptomyces strains to select those with strong protective capabilities against tomato wilt disease caused by Ralstonia solanacearum. Leveraging a synthetic community (SynCom) established in our lab, alongside multiple in planta and in vitro co-cultivation experiments, as well as transcriptomic and metabolomic analyses, we explored the synergistic inhibitory mechanisms underlying bacterial wilt resistance facilitated by both Streptomyces and the soil microbiome.

RESULTS

Our findings indicate that direct antagonism by Streptomyces is not sufficient for their biocontrol efficacy. Instead, the efficacy was associated with shifts in the rhizosphere microbiome, particularly the promotion of two native keystone taxa, CSC98 (Stenotrophomonas maltophilia) and CSC13 (Paenibacillus cellulositrophicus). In vitro co-cultivation experiments revealed that CSC98 and CSC13 did not directly inhibit the pathogen. Instead, the metabolite of CSC13 significantly enhanced the inhibition efficiency of Streptomyces R02, a highly effective biocontrol strain in natural soil. Transcriptomic and metabolomic analyses revealed that CSC13's metabolites induced the production of Erythromycin E in Streptomyces R02, a key compound that directly suppressed R. solanacearum, as demonstrated by our antagonism tests.

CONCLUSIONS

Collectively, our study reveals how beneficial microbes engage with the native soil microbiome to combat pathogens, suggesting the potential of leveraging microbial interactions to enhance biocontrol efficiency. These findings highlight the significance of intricate microbial interactions within the microbiome in regulating plant diseases and provide a theoretical foundation for devising efficacious biocontrol strategies in sustainable agriculture. Video Abstract.

Rhizosphere microbes facilitate the break of chlamydospore dormancy and root colonization of rice false smut fungi

Dormant chlamydospore germination of fungal pathogens directly affects disease occurrence and severity. The rice false smut (RFS) fungus Ustilaginoidea virens produces abundant chlamydospores, but their germination process and roles in plant infection remain unclear. Here, we found that soil-borne chlamydospores are a major source of U. virens inoculum and impact RFS development. Rhizosphere microbiome analysis of high-susceptibility (HS) and low-susceptibility (LS) rice varieties revealed that HS varieties recruited bacteria from the Sphingomonadaceae family, thereby facilitating the breakdown of chlamydospore dormancy through secreted exopolysaccharides. Hyphae formed by germinating chlamydospores grew on the root surfaces, invaded the root cortex, and grew intercellularly, potentially spreading further to aboveground plant parts. Furthermore, field experiments confirmed that treating the root with 30% prothioconazole and 20% zinc thiazole effectively reduced RFS incidence. Overall, these findings enhance our understanding of chlamydospore germination in natural environments and inform strategies for disease control.

Biocontrol of Bacterial Wilt Disease Using Plant-Associated Bacterial Communities in Tomato

Host-protective or disease-suppressive microorganisms are emerging as sustainable solutions for controlling crop diseases, such as bacterial wilt. However, the efficacy of biocontrol strategies is often constrained by limited resilience under varying environmental conditions and interactions with native microbial communities in the field. One major challenge is that introduced biocontrol microbes often face suppression by indigenous microbes due to competitive interactions. Synthetic communities (SynComs) offer a promising alternative strategy. However, conventional approaches to assembling SynComs by combining different microbial isolates often result in antagonism and competition among strains, leading to ineffective and inconsistent outcomes. In this study, we assembled a bacterial wilt-suppressive SynCom for tomato, composed of bacterial isolates derived from co-cultured microbial complexes associated with healthy plants. This SynCom demonstrates significant disease-suppressive effects against Ralstonia pseudosolanacearum in tomato seedlings under both axenic and soil conditions. Additionally, our findings suggest the presence of an optimal SynCom colonization level in plants, which is crucial for effective disease suppression. The SynCom also exhibits direct antibiotic activity and modulates the plant-associated microbiome. Our results provide an effective approach to constructing SynComs with consistent and effective disease-suppressive properties within microbial community contexts. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation

Microbial communities play a crucial role in supporting plant health and productivity. Reproducible, natural plant-associated microbiomes can help disentangle microbial dynamics across time and space. Here, using a sequential propagation strategy, we generated a complex and reproducible wheat rhizosphere microbiome (RhizCom) to study successional dynamics and interactions between the soil and heritable seed-borne rhizosphere microbiomes (SbRB) in a microcosm. Using 16S rRNA sequencing and genome-resolved shotgun metagenomics, we find that SbRB surpassed native soil microbes as the dominant rhizosphere-associated microbiome source. SbRB genomes were enriched in host-associated traits including degradation of key saccharide (niche partitioning) and cross-feeding interactions that supported partner strains (niche facilitation). In vitro co-culture experiments confirmed that helper SbRB strains facilitated the growth of partner bacteria on disaccharides as sole carbon source. These results reveal the importance of seed microbiota dynamics in microbial succession and community assembly, which could inform strategies for crop microbiome manipulation.

Cultivable and Non-Cultivable Approach to Bacteria from Undisturbed Soil with Plant Growth-Promoting Capacity

Undisturbed soils are essential ecosystems with high microbial diversity. Microorganisms present in the soil can regulate biogeochemical cycles, making available and transforming different minerals in the soil, such as nitrogen, phosphorus and sulfur. In this study, the microbiota of undisturbed soils was characterized using an integrated approach of 16S rRNA ribosomal gene amplicon analysis and classical microbiology techniques. Phylum-level analyses revealed a high abundance of Proteobacteria, Acidobacteria, Verrucomicrobia and Actinobacteria, key groups in nutrient recycling, organic matter decomposition and plant-microorganism interaction. In the genus analysis, Nitrospira spp., Candidatus Koribacter spp., Burkholderia spp., Bacillus spp., Flavobacterium spp. and Pedomicrobium spp. were identified, with important functions in nitrification, plant growth promotion, organic matter degradation, and recovery of degraded soils. On the other hand, by using selective and differential media, it was possible to demonstrate the presence of microorganisms such as Enterobacter spp. and Hafnia spp., with the ability to solubilize phosphorus and potassium and produce siderophores, which are likely contributing to the biogeochemical cycles and plant growth within the soil studied.

Synergic interactions between Trichoderma and the soil microbiomes improve plant iron availability and growth

Iron bioavailability is often limited especially in calcareous soils. Trichoderma harzianum strongly improves plant iron uptake and growth in calcareous soils. However, little is known about the mechanisms by which T. harzianum mobilizes iron in calcareous soils. Here, the model strain T. harzianum NJAU4742 and a synthetic microbial community (SynCom) was used to show that the efficacy of T. harzianum in enhancing plant iron nutrition in calcareous soils depends on the soil microbiome. Enhanced iron-mobilization functions of the SynCom were observed in the presence of T. harzianum NJAU4742. Concurrently, T. harzianum NJAU4742 improved the iron-mobilization capacity of the SynCom by enriching strains that are able to do so. Finally, Chryseobacterium populi was identified as a key driver of iron mobilization, while their synergistic colonization further enhances this process. This study unveils a pivotal mechanism by which T. harzianum NJAU4742-mediated re-structuring of the soil microbiome and ameliorates plant iron nutrition.

Antibacterial Siderophores of Pandoraea Pathogens and Their Impact on the Diseased Lung Microbiota

Antibiotic-resistant bacteria of the genus Pandoraea, frequently acquired from the environment, are an emerging cause of opportunistic respiratory infections, especially in cystic fibrosis (CF) patients. However, their specialized metabolites, including niche and virulence factors, remained unknown. Through genome mining of environmental and clinical isolates of diverse Pandoraea species, we identified a highly conserved biosynthesis gene cluster (pan) that codes for a nonribosomal peptide synthetase (NRPS) assembling a new siderophore. Using bioinformatics-guided metabolic profiling of wild type and a targeted null mutant, we discovered the corresponding metabolites, pandorabactin A and B. Their structures and chelate (gallium) complexes were elucidated by a combination of chemical degradation, derivatization, NMR, and MS analysis. Metagenomics and bioinformatics of sputum samples of CF patients indicated that the presence of the pan gene locus correlates with the prevalence of specific bacteria in the lung microbiome. Bioassays and mass spectrometry imaging showed that pandorabactins have antibacterial activities against various lung pathogens (Pseudomonas, Mycobacterium, and Stenotrophomonas) through depleting iron in the competitors. Taken together, these findings offer first insight into niche factors of Pandoraea and indicate that pandorabactins shape the diseased lung microbiota through the competition for iron.

Iron-based driven chitosan quaternary ammonium salt self-gelling powder: Sealing uncontrollable bleeding and promoting wound healing

Uncontrollable bleeding poses a significant risk of death and cost in wars, vehicle accidents, and first aid. Hence, in order to seal uncontrollable bleeding and promote wound healing, the Fe3+-driven chitosan quaternary ammonium salt self-gelling powder (QPF) was prepared using 5%QCS/AA/Fe3+ with the 52.72 % ± 0.30 % yield. As demonstrated by the results, the QPF had a high liquid absorption rate, mechanical properties, reactive oxygen species scavenging capacity, and bacteriostatic ability. Furthermore, QPF has excellent self-healing characteristics and underwater adherence, making it appropriate for a wide range of wound types. Importantly, this property is influenced by variations in Fe3+ concentration. In the in vitro coagulation experiment, QPF can rapidly capture blood cells, resulting in coagulation within 30s. After applying the QPF to different bleeding models, it immediately formed the self-gel (<2 s) that adheres securely to the hemorrhage site. Subsequently, the bleeding site could be promptly closed within 30s, and no blood leaking occurred within 10 min. Compared to CS, QPF (200 mg) improves wound healing by closing the wound gap, activating M2-type macrophage polarization, increasing neovascularization, and hastening granulation tissue proliferation (1046.0 μm ± 41.9 μm). In conclusion, iron-based driven self-gelling powders offer significant promise for limiting uncontrolled bleeding and promoting wound healing.

Continuous Rice Cultivation Increases Celery Yield by Enhancing Plant Beneficial Bacteria in Rice-Celery Rotations

The sustainable management of crops is a fundamental challenge as the human population and demand for food increase. Crop rotation, a practice that has been used for centuries, offers a sustainable solution with minimal environmental impact. However, our understanding of how microbial diversity changes during rotation and how microbially mediated functions enhance plant production remains limited. In our study, we combined field surveys of rice-celery rotations with greenhouse experiments. We found that crop rotation increased yield by increasing the presence of plant-beneficial bacteria, including a novel strain named Acinetobacter bohemicus HfQ1. Bacteria that promote plant growth are enriched under crop rotation, leading to increased ammonia oxidation, siderophore production and indole-3-acetic acid synthesis. These beneficial ecological consequences of crop rotation were consistent across various crops during our metadata analysis. Our study provides new insights into the development of innovative crop rotation models and effective strategies to safeguard food production and advance sustainable agriculture. Additionally, the Acinetobacter strain may serve as a potential microbial agent to replace chemical fertilisers, further supporting sustainable agricultural practices.

Genomic Insights into Cobweb Disease Resistance in Agaricus bisporus: A Comparative Analysis of Resistant and Susceptible Strains

Agaricus bisporus, a globally cultivated edible fungus, faces significant challenges from fungal diseases like cobweb disease caused by Cladobotryum mycophilum, which severely impacts yield. This study aimed to explore the genetic basis of disease resistance in A. bisporus by comparing the genomes of a susceptible strain (AB7) and a resistant strain (AB58). Whole-genome sequencing of AB7 was performed using PacBio Sequel SMRT technology, and comparative genomic analyses were conducted alongside AB58 and other fungal hosts of C. mycophilum. Comparative genomic analyses revealed distinct resistance features in AB58, including enriched regulatory elements, specific deletions in AB7 affecting carbohydrate-active enzymes (CAZymes), and unique cytochrome P450 (CYP) profiles. Notably, AB58 harbored more cytochrome P450 genes related to fatty acid metabolism and unique NI-siderophore synthetase genes, contributing to its enhanced environmental adaptability and disease resistance. Pan-genome analysis highlighted significant genetic diversity, with strain-specific genes enriched in pathways like aflatoxin biosynthesis and ether lipid metabolism, suggesting distinct evolutionary adaptations. These findings provide valuable insights into the genetic basis underlying disease resistance in A. bisporus, offering a foundation for future breeding strategies to improve fungal crop resilience.

Combating plant diseases through transition metal allocation

Understanding how plants fend-off invading microbes is essential for food security and the economy of large parts of the world. Consequently, a sustained and dedicated effort has been directed at unveiling how plants protect themselves from invading microbes. Major defense hormone signaling pathways have been characterized, the identity of many immune response-triggering molecules as well as many of their receptors have been determined, and the mechanisms of pathogen-host arms race are being studied. In recent years, evidence for a new layer of plant innate immunity involving transition metals has been brought forward. This would link plant metal nutrition with plant immune responses and open up possible new strategies for pathogen control involving metal fertilizers instead of pesticides. In this review, we outline our current understanding of metal-mediated plant immune response and indicate the future avenues of exploration of this topic.

Allelochemicals degradation and multifarious plant growth promoting potential of two Bacillus spp.: Insights into genomic potential and abiotic stress alleviation

The deposition of allelochemicals poses a challenge to continuous cropping. Microbial degradation is an efficient approach to degrade these hazardous compounds. The current study employed an integrated approach to explore the allelochemical degradation potential of Bacillus subtilis RS10 and Bacillus pumilus SF-4 and concurrently validate their capabilities to enhance plant growth and alleviate abiotic stress in pot experiments. During initial in vitro screening, both strains utilized more than 45% of benzoic acid within 60 h of incubation and showed maximum growth after 72 h. Meanwhile, the wheat seed germination rate was increased by 34.33% and 30% when treated with strain RS10 and SF-4, respectively. In addition, both strains demonstrated the capacity to promote wheat growth in terms of root length, shoot length, and plant weight in soil contaminated with p-hydroxybenzoic acid. To determine the associated mechanism of plant growth-promoting and allelochemical degradation, the culture extract of RS10 and SF-4 were analyzed using gas chromatography-mass spectrometry, which showed several plant growth-promoting volatile organic compounds, including propanediol and butanone. Genome-wide analysis unveiled several genetic loci associated with plant growth-promoting traits such as siderophore synthesis, phosphate solubilization, and biosynthesis of biocontrol compounds. Moreover, the in-depth comparative genome analysis, horizontal gene transfer, and strain-specific genes unveiled intriguing insight into the evolutionary dynamics of these strains and constraints driven by natural selection. In conclusion, the current study revealed the multifarious plant growth-promoting traits of strains RS10 and SF-4 and suggested an application of these strains as plant growth stimulators in soil contaminated with allelochemicals.

Ion Mobility-Coupled Mass Spectrometry for Metallophore Detection

Metal chelating small molecules (metallophores) play significant roles in microbial interactions and bacterial survival; however, current methods to identify metallophores are limited by low sensitivity, a lack of metal selectivity, and/or complicated data analysis. To overcome these limitations, we developed a novel approach for detecting metallophores in natural product extracts using ion mobility-coupled mass spectrometry (IM-MS). As a proof of concept, marine bacterial extracts containing known metallophores were analyzed by IM-MS with and without added metals, and the data were compared between conditions to identify metal-binding metabolites. Ions with changes in both mass and mobility were specific to metallophores, enabling their identification within these complex extracts. Additionally, we compared the use of direct infusion (DI) and liquid chromatography (LC) separation with IM-MS. For most samples, DI outperformed LC by minimizing the time required for data collection and simplifying analysis. However, for some samples, LC improved the detection of metallophores likely by reducing ion suppression. IM-MS was then used to identify 10 metallophores in an extract from a marine Micromonospora sp. Overall, incorporating IM-MS facilitated the rapid detection of metal-binding natural products in complex bacterial extracts through the comparison of mass and mobility data in the presence and absence of metals.

Lactobacillus reuteri metabolites alleviate apple replant disease (ARD) by driving beneficial bacteria to reshape the core root microbiome

Previous studies have shown that the bacterial fertilizer Lactobacillus reuteri (LBR) significantly alleviates apple replant disease (ARD), but the mechanism behind its effectiveness remains unclear. This study investigated the effects of key LBR metabolites on the rhizosphere microbial community. The biocontrol function of extracellular polysaccharides (EPS) was examined and shown to be further enhanced after optimizing the fermentation conditions. The optimized fermentation conditions were found to generate intermediates involved in various plant metabolic pathways, leading to plant growth promotion, increased abundance of beneficial bacteria like Bacillus and Pseudomonas in the rhizosphere soil, and decreased abundance of pathogenic fungi. Through the isolation and identification of rhizosphere microorganisms, a strain of Pseudomonas monteilii with chemotaxis to EPS was isolated, which had growth promotion ability and effectively improved plant resistance and relieves ARD. To further understand the mechanism underlying the inhibitory effect on soil pathogens of microbial aggregations and development in the rhizosphere driven by beneficial bacteria metabolites. These findings offer valuable technical insights for utilizing biocontrol bacteria metabolites in ARD management.

The phospho-ferrozine assay: a tool to study bacterial redox-active metabolites produced at the plant root

Soil microbial communities are pivotal to plant health and nutrient acquisition. It is becoming increasingly clear that many interactions, both among and between microbes and plants, are governed by small bioactive molecules or "secondary metabolites" that can aid in communication, competition, and nutrient uptake. Yet, secondary metabolite biogeography - who makes what, where, and why-is in its infancy. Further, secondary metabolite biosynthesis genes are often silent or weakly expressed under standard laboratory conditions, making it incredibly difficult to study these small molecules. To begin to address these dual challenges, we focused on redox-active metabolites (RAMs), a specific class of small molecules, and took advantage of recent findings that many RAMs aid in acquiring phosphorus and that their production is frequently stimulated by stress for this macronutrient. We developed a screen for RAM-producing bacteria that leverages phosphorus limitation to stimulate metabolite biosynthesis and uses a colorimetric (ferrozine) iron-reduction assay to identify redox activity. We isolated 557 root-associated bacteria from grasses collected at sites across the United States (Santa Rita Experimental Range [AZ], Konza Prairie Biological Station [KS], and Harvard Forest [MA]) and from commercial tomato plants and screened them for RAM production. We identified 128 soil isolates of at least 19 genera across Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes that produced RAMs under phosphorus stress. Our work reveals that the production of RAMs under phosphorus stress is common across diverse soil bacteria and provides an approach to screen for these small molecules rapidly.IMPORTANCEBy secreting secondary metabolites, bacteria at the plant root can defend against diseases and help acquire essential nutrients. However, the genes that synthesize secondary metabolites are typically inactive or are weakly expressed under standard laboratory conditions. This fact makes it difficult to study these small molecules and hinders the discovery of novel small molecules that may play crucial roles in agricultural and biomedical settings. Here, we focus on redox-active metabolites (RAMs), a class of secondary metabolites that can help bacteria solubilize phosphorus and are often produced when phosphorus is limited. We developed a screen that rapidly identifies RAM-producing bacteria by utilizing a colorimetric iron-reduction assay in combination with phosphorus limitation to stimulate biosynthesis. The screen reveals that RAM-producing bacteria are far more prevalent in soil than previously appreciated and that this approach can be used to identify RAM producers.

Alternaria alternata JTF001 Metabolites Recruit Beneficial Microorganisms to Reduce the Parasitism of Orobanche aegyptiaca in Tomato

Orobanche aegyptiaca is a holoparasitic weed that extracts water, nutrients, and growth regulators from host plants, leading to significant yield and quality losses. Biocontrol microbial metabolites have been shown to enhance plant resistance against parasitic plants, yet the underlying microbial mechanisms remain poorly understood. In this study, we investigated the role of Alternaria alternata JTF001 (J1) microbial metabolites in recruiting beneficial microbes to the tomato rhizosphere and promoting the establishment of a disease-suppressive microbiome. Pot experiments revealed that J1 metabolite application significantly reduced O. aegyptiaca parasitism. High-throughput sequencing of full-length 16S rRNA genes and ITS regions, along with in vitro culture assays, demonstrated an increase in the abundance of plant-beneficial bacteria, particularly Pseudomonas spp. The three candidate beneficial strains (zOTU_388, zOTU_533, and zOTU_2335) showed an increase of 5.7-fold, 5.4-fold, and 4.7-fold, respectively. These results indicate that J1 metabolites induce the recruitment of a disease-suppressive microbiome in tomato seedlings, effectively inhibiting O. aegyptiaca parasitism. Our findings suggest that microbial metabolites represent a promising strategy for managing parasitic plant infestations through microbial community modulation, offering significant implications for sustainable agricultural practices.

Siderophore synthetase-receptor gene coevolution reveals habitat- and pathogen-specific bacterial iron interaction networks

Bacterial social interactions play crucial roles in various ecological, medical, and biotechnological contexts. However, predicting these interactions from genome sequences is notoriously difficult. Here, we developed bioinformatic tools to predict whether secreted iron-scavenging siderophores stimulate or inhibit the growth of community members. Siderophores are chemically diverse and can be stimulatory or inhibitory depending on whether bacteria have or lack corresponding uptake receptors. We focused on 1928 representative Pseudomonas genomes and developed an experimentally validated coevolution algorithm to match encoded siderophore synthetases to corresponding receptor groups. We derived community-level iron interaction networks to show that siderophore-mediated interactions differ across habitats and lifestyles. Specifically, dense networks of siderophore sharing and competition were observed among environmental and nonpathogenic species, while small, fragmented networks occurred among human-associated and pathogenic species. Together, our sequence-to-ecology approach empowers the analyses of social interactions among thousands of bacterial strains and offers opportunities for targeted intervention to microbial communities.

Trichoderma virens XZ11-1 producing siderophores inhibits the infection of Fusarium oxysporum and promotes plant growth in banana plants

BACKGROUND

Banana Fusarium wilt caused by Fusarium oxysporum f. sp. cubense is a soil-borne fungal disease. Especially, tropical Race 4 (Foc TR4) can infect almost Cavendish subgroup and has a fatal threat to banana industry. Use of antagonistic microbes to manage soil-borne pathogen is viewed as a promising strategy.

RESULTS

Strain XZ11-1 isolated from tropical rainforest has the production ability of high siderophore. By the analysis of physiological and biochemical profiles, construction of phylogenetic tree, and comparative results from the NR database, strain XZ11-1 was identified as Trichoderma virens. A relative content of 79.45% siderophores was produced in the optimized fermentation solution, including hydroxamate and carboxylate-type siderophores. Siderophores were key for inhibiting the growth of Foc TR4 by competing for environmental iron. Similarly, T. virens XZ11-1 also had antagonistic activities against 10 phytopathogenic fungi. Pot experiments demonstrated that T. virens XZ11-1 could colonize in the root system of banana plants. The symbiotic interaction not only improve plant resistance to Foc TR4, but also enhance iron absorption of roots to promote plant growth by secreting siderophores.

CONCLUSIONS

T. virens XZ11-1 with the high-yield siderophores was isolated and identified. The strain could effectively inhibit the infection of Foc TR4 in banana roots and promote plant growth. It is a promising biocontrol agent for controlling fungal disease.

Host Metabolic Alterations Mediate Phyllosphere Microbes Defense upon Xanthomonas oryzae pv oryzae Infection

Rice bacterial leaf blight, caused by Xanthomonas oryzae pv oryzae (Xoo), is a significant threat to global food security. Although the microbiome plays an important role in protecting plant health, how the phyllosphere microbiome is recruited and the underlying disease resistance mechanism remain unclear. This study investigates how rice phyllosphere microbiomes respond to pathogen invasion through a comprehensive multiomics approach, exploring the mechanisms of microbial defense and host resistance. We discovered that Xoo infection significantly reshapes the physicosphere microbial community. The bacterial network became more complex, with increased connectivity and interactions following infection. Metabolite profiling revealed that l-ornithine was a key compound to recruiting three keystone microbes, Brevundimonas (YB12), Pantoea (YN26), and Stenotrophomonas (YN10). These microbes reduced the disease index by up to 67.6%, and these microbes demonstrated distinct defense mechanisms. Brevundimonas directly antagonized Xoo by disrupting cell membrane structures, while Pantoea and Stenotrophomonas enhanced plant immune responses by significantly increasing salicylic acid and jasmonic acid levels and activating defense-related enzymes. Our findings provide novel insights into plant-microbe interactions, demonstrating how host metabolic changes recruit and activate beneficial phyllosphere microbes to combat pathogenic invasion. This research offers promising strategies for sustainable agricultural practices and disease management.

Applying microbial biostimulants and drought-tolerant genotypes to enhance barley growth and yield under drought stress

With climate change, the frequency of regions experiencing water scarcity is increasing annually, posing a significant challenge to crop yield. Barley, a staple crop consumed and cultivated globally, is particularly susceptible to the detrimental effects of drought stress, leading to reduced yield production. Water scarcity adversely affects multiple aspects of barley growth, including seed germination, biomass production, shoot and root characteristics, water and osmotic status, photosynthesis, and induces oxidative stress, resulting in considerable losses in grain yield and its components. In this context, the present review aims to underscore the importance of selecting drought-tolerant barley genotypes and utilizing bio-inoculants constructed from beneficial microorganisms as an agroecological approach to enhance barley growth and production resilience under varying environmental conditions. Selecting barley genotypes with robust physiological and agronomic tolerance can mitigate losses under diverse environmental conditions. Plant Growth Promoting Rhizobacteria (PGPR) play a crucial role in promoting plant growth through nutrient solubilization, nitrogen fixation, phytohormone production, exopolysaccharide secretion, enzyme activity enhancement, and many other mechanisms. Applying drought-tolerant genotypes with bio-inoculants containing PGPR, improves barley's drought tolerance thereby minimizing losses caused by water scarcity.

Strain identity effects contribute more to Pseudomonas community functioning than strain interactions

Microbial communities can shape key ecological services, but the determinants of their functioning often remain little understood. While traditional research predominantly focuses on effects related to species identity (community composition and species richness), recent work increasingly explores the impact of species interactions on community functioning. Here, we conducted experiments with replicated small communities of Pseudomonas bacteria to quantify the relative importance of strain identity versus interaction effects on two important functions, community productivity and siderophore production. By combining supernatant and competition assays with an established linear model method, we show that both factors have significant effects on functioning, but identity effects generally outweigh strain interaction effects. These results hold irrespective of whether strain interactions are inferred statistically or approximated experimentally. Our results have implications for microbiome engineering, as the success of approaches aiming to induce beneficial (probiotic) strain interactions will be sensitive to strain identity effects in many communities.

Plant growth-promotion triggered by extracellular polymer is associated with facilitation of bacterial cross-feeding networks of the rhizosphere

Despite the critical role rhizosphere microbiomes play in plant growth, manipulating microbial communities for improved plant productivity remains challenging. One reason for this is the lack of knowledge on how complex substrates secreted in the microbiome ultimately shape the microbe-microbe and plant-microbe interaction in relation to plant growth. One such complex substrate is poly-γ-glutamic acid, which is a microbially derived extracellular polymer. While it has previously been linked with plant growth-promotion, the underlying mechanisms are not well understood. Here, we show that this compound benefits plants by fostering cross-feeding networks between rhizosphere bacteria. We first experimentally demonstrate that poly-γ-glutamic acid application increases potassium bioavailability for tomato plants by driving a shift in the rhizosphere bacterial community composition. Specifically, application of poly-γ-glutamic acid increased the relative abundance of Pseudomonas nitroreducens L16 and Pseudomonas monteilii L20 bacteria which both promoted tomato potassium assimilation by secreting potassium-solubilizing pyruvic acid and potassium-chelating siderophores, respectively. Although either Pseudomonas strain could not metabolize poly-γ-glutamic acid directly, the application of poly-γ-glutamic acid promoted the growth of Bacillus species, which in turn produced metabolites that could promote the growth of both P. nitroreducens L16 and P. monteilii L20. Moreover, the P. monteilii L20 produced 3-hydroxycapric acid, which could promote the growth of P. nitroreducens L16, resulting in commensal cross-feeding interaction between plant growth-promoting bacteria. Together, these results show that poly-γ-glutamic acid plays a crucial role in driving plant growth-promotion via bacterial cross-feeding networks, highlighting the opportunity for using microbially derived, complex substrates as catalysts to increase agricultural productivity.

Pseudomonas produce various metabolites displaying herbicide activity against broomrape

Pseudomonads are well-known for their plant growth-promoting properties and biocontrol capabilities against microbial pathogens. Recently, their potential to protect crops from parasitic plants has garnered attention. This study investigates the potential of different Pseudomonas strains to inhibit broomrape growth and to protect host plants against weed infestation. Four Pseudomonas strains, two P. fluorescens JV391D17 and JV391D10, one P. chlororaphis JV395B and one P. ogarae F113 were cultivated using various carbon sources, including fructose, pyruvate, fumarate, and malate, to enhance the diversity of potential Orobanche growth inhibition (OGI)-specialized metabolites produced by Pseudomonas strains. Both global and targeted metabolomic approaches were utilized to identify specific OGI metabolites. Both carbon sources and Pseudomonas genetic diversity significantly influenced the production of OGI metabolites. P. chlororaphis JV395B and P. ogarae F113 produced unique OGI metabolites belonging to different chemical families, such as hydroxyphenazines and phloroglucinol compounds, respectively. Additionally, metabolomic analyses identified an unannotated potential OGI ion, M375T65. This ion was produced by all Pseudomonas strains but was found to be over-accumulated in JV395B, which likely explains its superior OGI activity. Then, greenhouse experiments were performed to evaluate the biocontrol efficacy of selected strains: they showed the efficacy of these strains, particularly JV395B, in reducing broomrape infestation in rapeseed. These findings suggest that certain Pseudomonas strains, through their metabolite production, can offer a sustainable biocontrol strategy against parasitic plants. This biocontrol activity can be optimized by environmental factors, such as carbon amendments. Ultimately, this approach presents a promising alternative to chemical herbicides.

Antimicrobial activity of iron-depriving pyoverdines against human opportunistic pathogens

The global rise of antibiotic resistance calls for new drugs against bacterial pathogens. A common approach is to search for natural compounds deployed by microbes to inhibit competitors. Here, we show that the iron-chelating pyoverdines, siderophores produced by environmental Pseudomonas spp., have strong antibacterial properties by inducing iron starvation and growth arrest in pathogens. A screen of 320 natural Pseudomonas isolates used against 12 human pathogens uncovered several pyoverdines with particularly high antibacterial properties and distinct chemical characteristics. The most potent pyoverdine effectively reduced growth of the pathogens Acinetobacter baumannii, Klebsiella pneumoniae, and Staphylococcus aureus in a concentration- and iron-dependent manner. Pyoverdine increased survival of infected Galleria mellonella host larvae and showed low toxicity for the host, mammalian cell lines, and erythrocytes. Furthermore, experimental evolution of pathogens combined with whole-genome sequencing revealed limited resistance evolution compared to an antibiotic. Thus, pyoverdines from environmental strains have the potential to become a new class of sustainable antibacterials against specific human pathogens.

Gradient of acid mine drainage regulates microbial community assembly and the diversity of species associated with native plants

Acid mine drainage (AMD) is considered as one of the most important global environmental challenges. Therefore, understanding the impact of AMD on the diversity of microbial communities associated with native plants is important for phytoremediation. In this study, the community assembly and microbial diversity associated with native plants growing along an AMD impact gradient was investigated using metabarcoding and high throughput iChip technique. The study revealed that across both domains of bacteria and fungi, richness and species diversity decreased according to AMD impact. Bacterial species diversity was more stratified according to the pH gradient than fungi, and the AMD impact on the plant-associated microbial diversity decreased towards the plant roots. The microbial community composition of the undisturbed site was significantly different from the AMD impacted sites, and the communities in the AMD impacted sites were further stratified according to the degree of impact. The overall microbial diversity was mediated by the AMD impact, niche differences and plant species differences. Dispersal limitation was the most important community assembly process in the undisturbed site, while the homogenous selection of Burkholderia, Actinospica, Puia and Bradyrhizobium increased along the AMD impact gradient. Differential abundance analysis further revealed that Umbelopsis, Burkholderia and Sphingomonas were among the biomarkers of the AMD impacted sites. Several strains of some of these responsive genera were subsequently isolated using the iChip. Overall, this study presents novel insight into the ecology of plant-associated microbial communities that are relevant for environmental monitoring and for enhancing the revegetation of AMD impacted sites.

Characterization of Siderophores Produced by Bacillus velezensis YL2021 and Its Application in Controlling Rice Sheath Blight and Rice Blast

Bacillus velezensis YL2021 has extensive antimicrobial activities against phytopathogens, and its genome harbors a catechol-type siderophore biosynthesis gene cluster. Here, we describe the characterization of siderophores produced by strain YL2021 and its antimicrobial activity in vitro and in vivo. A few types of siderophores were detected by chrome azurol S plates coupled with Arnow's test, purified, and identified by reversed-phase high-performance liquid chromatography. We found that strain YL2021 can produce different antimicrobial compounds under low-iron M9 medium or iron-sufficient Luria-Bertani medium, although antimicrobial activities can be easily observed on the two media as described above in vitro. Strain YL2021 can produce at least three catechol-type siderophores in low-iron M9 medium, whereas no siderophores were produced in Luria-Bertani medium. Among them, the main antimicrobial siderophore produced by strain YL2021 was bacillibactin, with m/z 882, based on the liquid chromatography-tandem mass spectrometry analysis, which has broad-spectrum antimicrobial activities against gram-positive and gram-negative bacteria, the oomycete Phytophthora capsici, and phytopathogenic fungi. Moreover, the antifungal activity of siderophores, including bacillibactin, observed in vitro was correlated with control efficacies against rice sheath blight disease caused by Rhizoctonia solani and rice blast disease caused by Magnaporthe oryzae in vivo. Collectively, the results demonstrate that siderophores, including bacillibactin, produced by B. velezensis YL2021 are promising biocontrol agents for application in rice disease control.

Competition-driven phenotypic plasticity in Iron acquisition and aromatic utilization confers a fitness advantage to Pseudomonas putida in an Iron-limited rhizospheric environment

Iron scarcity poses a critical challenge for rhizospheric bacteria like Pseudomonas putida in the competitive rhizosphere. Despite its dependence on iron for essential functions such as root colonization, motility, and aromatic compound utilization, P. putida exhibits limited capability for heterologous siderophore utilization and primarily relies on the secretion of a single siderophore, pyoverdine. This study investigates the mechanisms by which P. putida acquires iron in an iron-limited, aromatic-rich, rhizosphere-like environment. Our findings demonstrate that P. putida exhibits significant phenotypic plasticity, dynamically modulating pyoverdine secretion in response to competitive pressures and substrate availability. This adaptive strategy optimizes energy expenditure and iron acquisition, providing a competitive advantage. Comparative gene expression analysis supports these observations, revealing the molecular underpinnings of this plasticity. Enhanced pyoverdine production driven by competition compensates for the bacterium's limited siderophore repertoire and facilitates rapid aromatic compound utilization, conferring a distinct fitness advantage in iron-deprived conditions. This study elucidates the complex interplay between competition, iron uptake, and aromatic compound utilization that underpins the rhizospheric success of P. putida.

The role of the rhizobiome recruited by root exudates in plant disease resistance: current status and future directions

Root exudates serve as a bridge connecting plant roots and rhizosphere microbes, playing a key role in influencing the assembly and function of the rhizobiome. Recent studies have fully elucidated the role of root exudates in recruiting rhizosphere microbes to enhance plant performance, particularly in terms of plant resistance to soil-borne pathogens; however, it should be noted that the composition and amount of root exudates are primarily quantitative traits regulated by a large number of genes in plants. As a result, there are knowledge gaps in understanding the contribution of the rhizobiome to soil-borne plant disease resistance and the ternary link of plant genes, root exudates, and disease resistance-associated microbes. Advancements in technologies such as quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS) offer opportunities for the identification of genes associated with quantitative traits. In the present review, we summarize recent studies on the interactions of plant and rhizosphere microbes through root exudates to enhance soil-borne plant disease resistance and also highlight methods for quantifying the contribution of the rhizobiome to plant disease resistance and identifying the genes responsible for recruiting disease resistance-associated microbes through root exudates.

Nitrogen fertilizers activate siderophore production by the common scab causative agent Streptomyces scabiei

Streptomyces scabiei is the causative agent of common scab on root and tuber crops. Life in the soil imposes intense competition between soil-dwelling microorganisms, and we evaluated here the antimicrobial properties of S. scabiei. Under laboratory culture conditions, increasing peptone levels correlated with increased growth inhibitory properties of S. scabiei. Comparative metabolomics showed that production of S. scabiei siderophores (desferrioxamines, pyochelin, scabichelin, and turgichelin) increased with the quantity of peptone, thereby suggesting that they participate in growth inhibition. Mass spectrometry imaging further confirmed that the zones of secreted siderophores and growth inhibition coincided. Moreover, either the repression of siderophore production or the neutralization of their iron-chelating activity led to increased microbial growth. Replacement of peptone by natural nitrogen sources regularly used as fertilizers such as ammonium nitrate, ammonium sulfate, sodium nitrate, and urea also triggered siderophore production in S. scabiei. The observed effect is not mediated by alkalinization of the medium as increasing the pH without providing additional nitrogen sources did not induce siderophore production. The nitrogen-induced siderophore production also inhibited the growth of important plant pathogens. Overall, our work suggests that not only the iron availability but also the nitrogen fertilizer sources could significantly impact the competition for iron between crop-colonizing microorganisms.

A Nonessential Sfp-Type Phosphopantetheinyl Transferase Contributes Significantly to the Pathogenicity of Ralstonia solanacearum

4'-Phosphopantetheinyl transferases (PPTases) play important roles in the posttranslational modifications of bacterial carrier proteins, which are involved in various metabolic pathways. Here, we found that RsacpS and RspcpS encoded a functional AcpS-type and Sfp-type PPTase, respectively, in Ralstonia solanacearum GMI1000, and both are capable of modifying R. solanacearum AcpP1, AcpP2, AcpP3, and AcpP5 proteins. RspcpS is located on the megaplasmid, which does not affect strain growth and fatty acid synthesis but significantly contributes to the virulence of R. solanacearum and preferentially participates in secondary metabolism. We found that deletion of RspcpS did not affect the abilities of cellulose degradation, biofilm formation, and resistance to NaCl, sodium dodecyl sulfate, and H2O2 and attenuated R. solanacearum pathogenicity only in the assay of soil-drenching infection but not stem injection of tomato. It is hypothesized that RsPcpS plays a role in cell viability in complex environments and in the process during which the strain recognizes and approaches plants. These results suggest that both RsAcpS and RsPcpS may be potential targets for controlling diseases caused by R. solanacearum.

Microhabitat influences on phage-bacteria dynamics in an abandoned mine for ecorestoration

Understanding the complex interactions between bacteriophages (phages) and bacteria within varied environmental niches is critical yet underexplored for improving microbe-assisted ecological restoration. This study investigates the influence of microhabitat heterogeneity within an abandoned mine on phage-bacteria interaction patterns, focusing on Pseudomonas-enriched bacterial communities. By isolating viral communities and purifying bacteria from soils of three distinct microhabitats, we assessed the regulatory role of environmental factors on these interactions, crucial for bacterial success in environmental applications. We characterized microhabitat variability by analyzing soil particle size fractions, minerals composition, and elemental content using X-ray diffraction and energy-dispersive X-ray analyses. 16S rRNA sequencing and cross-infection assays revealed that although bacterial communities across different microhabitats are taxonomically similar, their interaction patterns with phages are distinct. Phage communities showed nonselective infectivity across soil types, while bacterial communities exhibited selective adaptation, facilitating colonization across diverse microhabitats. Minerals such as mica, kaolinite, and hematite were found to increase phage infectivity, whereas mixed-layer clay correlated with early lysis. Additionally, higher levels of iron (Fe) and potassium (K) were linked to bacterial resistance strategies. Our findings highlight the importance of understanding asymmetric adaptive strategies between bacteria and phages, driven by microhabitat heterogeneity, for enhancing microbial-mediated nature-based restoration of degraded ecosystems.

Rhizobacterial Bacillus enrichment in soil enhances smoke tree resistance to Verticillium wilt

Verticillium wilt, caused by the soilborne fungus Verticillium dahliae, poses a serious threat to the health of more than 200 plant species worldwide. Although plant rhizosphere-associated microbiota can influence plant resistance to V. dahliae, empirical evidence underlying Verticillium wilt resistance of perennial trees is scarce. In this study, we systemically investigated the effect of the soil microbiota on the resistance of smoke trees (Cotinus coggygria) to Verticillium wilt using field, greenhouse and laboratory experiments. Comparative analysis of the soil microbiota in the two stands of smoke trees suggested that Bacillus represented the most abundant and key microbial genus related to potential disease suppression. Smoke tree seedlings were inoculated with isolated Bacillus strains, which exhibited disease suppressiveness and plant growth-promoting properties. Furthermore, repletion of Bacillus agents to disease conducive soil significantly resulted in reduced incidence of smoke tree wilt and increased resistance of the soil microbiota to V. dahliae. Finally, we explored a more effective combination of Bacillus agents with the fungicide propiconazole to combat Verticillium wilt. The results establish a foundation for the development of an effective control for this disease. Overall, this work provides a direct link between Bacillus enrichment and disease resistance of smoke trees, facilitating the development of green control strategies and measurements of soil-borne diseases.

Combating wheat yellow mosaic virus through microbial interactions and hormone pathway modulations

BACKGROUND

The rhizosphere microbiome is critical for promoting plant growth and mitigating soil-borne pathogens. However, its role in fighting soil-borne virus-induced diseases, such as wheat yellow mosaic virus (WYMV) transmitted by Polymyxa graminis zoospores, remains largely underexplored. In this study, we hypothesized that during viral infections, plant microbiomes engage in critical interactions with plants, with key microbes playing vital roles in maintaining plant health. Our research aimed to identify microbial taxa that not only suppress the disease but also boost wheat yield by using a blend of techniques, including field surveys, yield assessments, high-throughput sequencing of plant and soil microbiomes, microbial isolation, hydroponic experiments, and transcriptome sequencing.

RESULTS

We found that, compared with roots and leaves, the rhizosphere microbiome showed a better performance in predicting wheat yield and the prevalence of P. graminis and WYMV across the three WYMV-impacted regions in China. Using machine learning, we found that healthy rhizospheres were marked with potentially beneficial microorganisms, such as Sphingomonas and Allorhizobium-Neorhizobium-Parararhizobium-Rhizobium, whereas diseased rhizospheres were associated with a higher prevalence of potential pathogens, such as Bipolaris and Fusicolla. Structural equation modeling showed that these biomarkers both directly and indirectly impacted wheat yield by modulating the rhizosphere microbiome and P. graminis abundance. Upon re-introduction of two key healthy rhizosphere biomarkers, Sphingomonas azotifigens and Rhizobium deserti, into the rhizosphere, wheat growth and health were enhanced. This was attributed to the up-regulation of auxin and cytokinin signaling pathways and the regulation of jasmonic acid and salicylic acid pathways during infections.

CONCLUSIONS

Overall, our study revealed the critical role of the rhizosphere microbiome in combating soil-borne viral diseases, with specific rhizosphere microbes playing key roles in this process. Video Abstract.

Dynamic alterations and ecological implications of rice rhizosphere bacterial communities induced by an insect-transmitted reovirus across space and time

BACKGROUND

Cereal diseases caused by insect-transmitted viruses are challenging to forecast and control because of their intermittent outbreak patterns, which are usually attributed to increased population densities of vector insects due to cereal crop rotations and indiscriminate use of pesticides, and lack of resistance in commercial varieties. Root microbiomes are known to significantly affect plant health, but there are significant knowledge gaps concerning epidemics of cereal virus diseases at the microbiome-wide scale under a variety of environmental and biological factors.

RESULTS

Here, we characterize the diversity and composition of rice (Oryza sativa) root-associated bacterial communities after infection by an insect-transmitted reovirus, rice black-streaked dwarf virus (RBSDV, genus Fijivirus, family Spinareoviridae), by sequencing the bacterial 16S rRNA gene amplified fragments from 1240 samples collected at a consecutive 3-year field experiment. The disease incidences gradually decreased from 2017 to 2019 in both Langfang (LF) and Kaifeng (KF). BRSDV infection significantly impacted the bacterial community in the rice rhizosphere, but this effect was highly susceptible to both the rice-intrinsic and external conditions. A greater correlation between the bacterial community in the rice rhizosphere and those in the root endosphere was found after virus infection, implying a potential relationship between the rice-intrinsic conditions and the rhizosphere bacterial community. The discrepant metabolites in rhizosphere soil were strongly and significantly correlated with the variation of rhizosphere bacterial communities. Glycerophosphates, amino acids, steroid esters, and triterpenoids were the metabolites most closely associated with the bacterial communities, and they mainly linked to the taxa of Proteobacteria, especially Rhodocyclaceae, Burkholderiaceae, and Xanthomonadales. In addition, the greenhouse pot experiments demonstrated that bulk soil microbiota significantly influenced the rhizosphere and endosphere communities and also regulated the RBSDV-mediated variation of rhizosphere bacterial communities.

CONCLUSIONS

Overall, this study reveals unprecedented spatiotemporal dynamics in rhizosphere bacterial communities triggered by RBSDV infection with potential implications for disease intermittent outbreaks. The finding has promising implications for future studies exploring virus-mediated plant-microbiome interactions. Video Abstract.

Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways

Microbial secondary metabolites are a rich source for pharmaceutical discoveries and play crucial ecological functions. While tools exist to identify secondary metabolite clusters in genomes, precise sequence-to-function mapping remains challenging because neither function nor substrate specificity of biosynthesis enzymes can accurately be predicted. Here, we developed a knowledge-guided bioinformatic pipeline to solve these issues. We analyzed 1928 genomes of Pseudomonas bacteria and focused on iron-scavenging pyoverdines as model metabolites. Our pipeline predicted 188 chemically different pyoverdines with nearly 100% structural accuracy and the presence of 94 distinct receptor groups required for the uptake of iron-loaded pyoverdines. Our pipeline unveils an enormous yet overlooked diversity of siderophores (151 new structures) and receptors (91 new groups). Our approach, combining feature sequence with phylogenetic approaches, is extendable to other metabolites and microbial genera, and thus emerges as powerful tool to reconstruct bacterial secondary metabolism pathways based on sequence data.

Evaluation of Bacillus velezensis F9 for Cucumber Growth Promotion and Suppression of Fusarium wilt Disease

Cucumber wilt, caused by Fusarium oxysporum f. sp. cucumerinum (FOC), is a soilborne disease that poses a significant threat to cucumber production, resulting in substantial yield losses. This study aimed to evaluate the biocontrol and growth-promoting effects of Bacillus velezensis, a highly active bacterial strain. In vitro assays revealed that B. velezensis F9 exhibited broad-spectrum antifungal activity against eight plant pathogenic fungi, with inhibition ratio ranging from 62.66% to 88.18%. Additionally, the strain displayed the ability to produce IAA (5.97 ± 1.75 µg/mL), fix nitrogen, produce siderophores, and form biofilms. In vitro growth promotion assays demonstrated that different concentrations of B. velezensis F9 significantly promoted cucumber seedling growth. Furthermore, two pot experiments revealed that the strain exhibited biocontrol efficacy against cucumber wilt, with disease control rates ranging from 42.86% to 67.78%. Notably, the strain significantly increased the plant height, fresh weight, and dry weight, with increases ranging from 20.67% to 60.04%, 40.27% to 75.51%, and 22.07% to 52.54%, respectively. Two field trials confirmed the efficacy of B. velezensis F9 in controlling cucumber wilt, with disease control rates of 44.95% and 33.99%, respectively. The strain effectively alleviated the dwarfing and wilting symptoms caused by the pathogen. Compared with the FOC treatment, the F9 + FOC treatment significantly increased the plant height, fresh weight, and dry weight, with increases of 43.85% and 56.28%, 49.49% and 23.70%, and 36.25% and 73.63%, respectively. Enzyme activity assays indicated that inoculation significantly increased SOD activity in cucumber leaves and neutral phosphatase, sucrase, and urease activity in rhizosphere soil. Correlation analysis revealed a negative correlation between the disease index and plant height, fresh weight, dry weight, and peroxidase activity, with correlation coefficients of -0.53, -0.60, -0.38, and -0.45, respectively. These findings suggest that plant height, fresh weight, and dry weight are significantly negatively correlated with the cucumber disease index, highlighting their importance as indicators for evaluating the biocontrol efficacy of B. velezensis F9. In conclusion, B. velezensis F9 is a highly effective plant growth-promoting rhizobacterium with excellent biocontrol potential, showcasing promising applications in agricultural production.

Plant-Driven Assembly of Disease-Suppressive Soil Microbiomes

Plants have coevolved together with the microbes that surround them and this assemblage of host and microbes functions as a discrete ecological unit called a holobiont. This review outlines plant-driven assembly of disease-suppressive microbiomes. Plants are colonized by microbes from seed, soil, and air but selectively shape the microbiome with root exudates, creating microenvironment hot spots where microbes thrive. Using plant immunity for gatekeeping and surveillance, host-plant genetic properties govern microbiome assembly and can confer adaptive advantages to the holobiont. These advantages manifest in disease-suppressive soils, where buildup of specific microbes inhibits the causal agent of disease, that typically develop after an initial disease outbreak. Based on disease-suppressive soils such as take-all decline, we developed a conceptual model of how plants in response to pathogen attack cry for help and recruit plant-protective microbes that confer increased resistance. Thereby, plants create a soilborne legacy that protects subsequent generations and forms disease-suppressive soils.

Siderophore interactions drive the ability of Pseudomonas spp. consortia to protect tomato against

The soil-borne bacterial pathogen Ralstonia solanacearum causes significant losses in Solanaceae crop production worldwide, including tomato, potato, and eggplant. To efficiently prevent outbreaks, it is essential to understand the complex interactions between pathogens and the microbiome. One promising mechanism for enhancing microbiome functionality is siderophore-mediated competition, which is shaped by the low iron availability in the rhizosphere. This study explores the critical role of iron competition in determining microbiome functionality and its potential for designing high-performance microbiome engineering strategies. We investigated the impact of siderophore-mediated interactions on the efficacy of Pseudomonas spp. consortia in suppressing R. solanacearum , both in vitro and in vivo. Our findings show that siderophore production significantly enhances the inhibitory effects of Pseudomonas strains on pathogen growth, while other metabolites are less effective under iron-limited conditions. Moreover, siderophores play a crucial role in shaping interactions within the consortia, ultimately determining the level of protection against bacterial wilt disease. This study highlights the key role of siderophores in mediating consortium interactions and their impact on tomato health. Our results also emphasize the limited efficacy of other secondary metabolites in iron-limited environments, underscoring the importance of siderophore-mediated competition in maintaining tomato health and suppressing disease.

Influence of Drought Stress on the Rhizosphere Bacterial Community Structure of Cassava (Manihot esculenta Crantz)

Drought presents a significant abiotic stress that threatens crop productivity worldwide. Rhizosphere bacteria play pivotal roles in modulating plant growth and resilience to environmental stresses. Despite this, the extent to which rhizosphere bacteria are instrumental in plant responses to drought, and whether distinct cassava (Manihot esculenta Crantz) varieties harbor specific rhizosphere bacterial assemblages, remains unclear. In this study, we measured the growth and physiological characteristics, as well as the physical and chemical properties of the rhizosphere soil of drought-tolerant (SC124) and drought-sensitive (SC8) cassava varieties under conditions of both well-watered and drought stress. Employing 16S rDNA high-throughput sequencing, we analyzed the composition and dynamics of the rhizosphere bacterial community. Under drought stress, biomass, plant height, stem diameter, quantum efficiency of photosystem II (Fv/Fm), and soluble sugar of cassava decreased for both SC8 and SC124. The two varieties' rhizosphere bacterial communities' overall taxonomic structure was highly similar, but there were slight differences in relative abundance. SC124 mainly relied on Gamma-proteobacteria and Acidobacteriae in response to drought stress, and the abundance of this class was positively correlated with soil acid phosphatase. SC8 mainly relied on Actinobacteria in response to drought stress, and the abundance of this class was positively correlated with soil urease and soil saccharase. Overall, this study confirmed the key role of drought-induced rhizosphere bacteria in improving the adaptation of cassava to drought stress and clarified that this process is significantly related to variety.

Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition

Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.

The Phosphorus-Iron Nexus: Decoding the Nutrients Interaction in Soil and Plant

Phosphorus (P) and iron (Fe) are two essential mineral nutrients in plant growth. It is widely observed that interactions of P and Fe could influence their availability in soils and affect their homeostasis in plants, which has received significant attention in recent years. This review presents a summary of latest advances in the activation of insoluble Fe-P complexes by soil properties, microorganisms, and plants. Furthermore, we elucidate the physiological and molecular mechanisms underlying how plants adapt to Fe-P interactions. This review also discusses the current limitations and presents potential avenues for promoting sustainable agriculture through the optimization of P and Fe utilization efficiency in crops.

Plant growth promotion and biocontrol properties of a synthetic community in the control of apple disease

BACKGROUND

Apple Replant Disease (ARD) is common in major apple-growing regions worldwide, but the role of rhizosphere microbiota in conferring ARD resistance and promoting plant growth remains unclear.

RESULTS

In this study, a synthetic microbial community (SynCom) was developed to enhance apple plant growth and combat apple pathogens. Eight unique bacteria selected via microbial culture were used to construct the antagonistic synthetic community, which was then inoculated into apple seedlings in greenhouse experiments. Changes in the rhizomicroflora and the growth of aboveground plants were monitored. The eight strains, belonging to the genera Bacillus and Streptomyces, have the ability to antagonize pathogens such as Fusarium oxysporum, Rhizoctonia solani, Botryosphaeria ribis, and Physalospora piricola. Additionally, these eight strains can stably colonize in apple rhizosphere and some of them can produce siderophores, ACC deaminase, and IAA. Greenhouse experiments with Malus hupehensis Rehd indicated that SynCom promotes plant growth (5.23%) and increases the nutrient content of the soil, including soil organic matter (9.25%) and available K (1.99%), P (7.89%), and N (0.19%), and increases bacterial richness and the relative abundance of potentially beneficial bacteria. SynCom also increased the stability of the rhizosphere microbial community, the assembly of which was dominated by deterministic processes (|β NTI| > 2).

CONCLUSIONS

Our results provide insights into the contribution of the microbiome to pathogen inhibition and host growth. The formulation and manipulation of similar SynComs may be a beneficial strategy for promoting plant growth and controlling soil-borne disease.

Pseudomonas weihenstephanensis through the iron metabolism pathway promotes in situ spoilage capacity of prepared beef steaks during cold storage

In this study, we evaluated the histomorphology, reactive oxygen species (ROS), protein degradation, and iron metabolism characteristics and differential expression analysis of genes for siderophores synthesis and protease secretion in prepared beef steaks inoculated alone or co-inoculated with P. weihenstephanensis, B. thermotrichothrix and M. caseolyticus at 4 °C for 12 days. The results showed that the P. weihenstephanensis was the key bacteria that degraded protein in the process of prepared beef steaks spoilage, which led to protein oxidation by promoting ferritin degradation to release free iron and inducing ROS accumulation. The highest expression of FpvA and AprE was detected in the P. weihenstephanensis group by comparing qRT-PCR of the different inoculation groups. Both qRT-PCR and Western blot revealed that ferritin heavy polypeptide and ferritin light chain polypeptide gene and protein expressions were significantly higher in the P. weihenstephanensis inoculation group compared to the other inoculation groups. Results suggested that FpvA and AprE might play roles in meat spoilage and were potential positional, physiological and functional candidate genes for improving the quality traits of prepared beef steaks. This work may provide insights on controlling food quality and safety by intervening in spoilage pathways targeting iron carrier biosynthesis or protease secretion genes.

Genome Analysis of Multiple Polysaccharide-Degrading Bacterium Microbulbifer thermotolerans HB226069: Determination of Alginate Lyase Activity

Polysaccharide-degrading bacteria are key participants in the global carbon cycle and algal biomass recycling. Herein, a polysaccharide lyase-producing strain HB226069 was isolated from Sargassum sp. from Qingge Port, Hainan, China. Results of the phylogenetic of the 16S rRNA gene and genotypic analysis indicated that the isolate should be classified as Microbulbifer thermotolerans. The whole genome is a 4,021,337 bp circular chromosome with a G+C content of 56.5%. Analysis of the predicted genes indicated that strain HB226069 encoded 161 carbohydrate-active enzymes (CAZymes), and abundant putative enzymes involved in polysaccharide degradation were predicted, including alginate lyase, fucosidase, agarase, xylanase, cellulase, pectate lyase, amylase, and chitinase. Three of the putative polysaccharide lyases from PL7 and PL17 families were involved in alginate degradation. The alginate lyases of strain HB226069 showed the maximum activity of 117.4 U/mL at 50 °C, pH 7.0, and 0.05 M FeCl3, while exhibiting the best stability at 30 °C and pH 7.0. The Thin Layer Chromatography (TLC) and Electrospray Ionization Mass Spectrometry (ESI-MS) analyses indicated that the alginate oligosaccharides (AOSs) degraded by the partially purified alginate lyases contained oligosaccharides of DP2-DP5 and monosaccharide while reacting for 36 h. The complete genome of M. thermotolerans HB226069 enriches our understanding of the mechanism of polysaccharide lyase production and supports its potential application in polysaccharide degradation.

An overview of Parafrankia (Nod+/Fix+) and Pseudofrankia (Nod+/Fix-) interactions through genome mining and experimental modeling in co-culture and co-inoculation of Elaeagnus angustifolia

In many frankia, the ability to nodulate host plants (Nod+) and fix nitrogen (Fix+) is a common strategy. However, some frankia within the Pseudofrankia genus lack one or two of these traits. This phenomenon has been consistently observed across various actinorhizal nodule isolates, displaying Nod- and/or Fix- phenotypes. Yet, the mechanisms supporting the colonization and persistence of these inefficient frankia within nodules, both with and without symbiotic strains (Nod+/Fix+), remain unclear. It is also uncertain whether these associations burden or benefit host plants. This study delves into the ecological interactions between Parafrankia EUN1f and Pseudofrankia inefficax EuI1c, isolated from Elaeagnus umbellata nodules. EUN1f (Nod+/Fix+) and EuI1c (Nod+/Fix-) display contrasting symbiotic traits. While the prediction suggests a competitive scenario, the absence of direct interaction evidence implies that the competitive advantage of EUN1f and EuI1c is likely contingent on contextual factors such as substrate availability and the specific nature of stressors in their respective habitats. In co-culture, EUN1f outperforms EuI1c, especially under specific conditions, driven by its nitrogenase activity. Iron-depleted conditions favor EUN1f, emphasizing iron's role in microbial competition. Both strains benefit from host root exudates in pure culture, but EUN1f dominates in co-culture, enhancing its competitive traits. Nodulation experiments show that host plant preferences align with inoculum strain abundance under nitrogen-depleted conditions, while consistently favoring EUN1f in nitrogen-supplied media. This study unveils competitive dynamics and niche exclusion between EUN1f and EuI1c, suggesting that host plant may penalize less effective strains and even all strains. These findings highlight the complex interplay between strain competition and host selective pressure, warranting further research into the underlying mechanisms shaping plant-microbe-microbe interactions in diverse ecosystems.

IMPORTANCE

While Pseudofrankia strains typically lack the common traits of ability to nodulate the host plant (Nod-) and/or fix nitrogen (Fix-), they are still recovered from actinorhizal nodules. The enigmatic question of how and why these unconventional strains establish themselves within nodule tissue, thriving either alongside symbiotic strains (Nod+/Fix+) or independently, while considering potential metabolic costs to the host plant, remains a perplexing puzzle. This study endeavors to unravel the competitive dynamics between Pseudofrankia inefficax strain EuI1c (Nod+/Fix-) and Parafrankia strain EU1Nf (Nod+/Fix+) through a comprehensive exploration of genomic data and empirical modeling, conducted both in controlled laboratory settings and within the host plant environment.

The rhizosphere and root selections intensify fungi-bacteria interaction in abiotic stress-resistant plants

The microbial communities, inhabiting around and in plant roots, are largely influenced by the compartment effect, and in turn, promote the growth and stress resistance of the plant. However, how soil microbes are selected to the rhizosphere, and further into the roots is still not well understood. Here, we profiled the fungal, bacterial communities and their interactions in the bulk soils, rhizosphere soils and roots of eleven stress-resistant plant species after six months of growth. The results showed that the root selection (from the rhizosphere soils to the roots) was stronger than the rhizosphere selection (from the bulk soils to the rhizosphere soils) in: (1) filtering stricter on the fungal (28.5% to 40.1%) and bacterial (48.9% to 68.1%) amplicon sequence variants (ASVs), (2) depleting more shared fungal (290 to 56) and bacterial (691 to 2) ASVs measured by relative abundance, and (3) increasing the significant fungi-bacteria crosskingdom correlations (142 to 110). In addition, the root selection, but not the rhizosphere selection, significantly increased the fungi to bacteria ratios (f:b) of the observed species and shannon diversity index, indicating unbalanced effects to the fungal and bacteria communities exerted by the root selection. Based on the results of network analysis, the unbalanced root selection effects were associated with increased numbers of negative interaction (140 to 99) and crosskingdom interaction (123 to 92), suggesting the root selection intensifies the negative fungi-bacteria interactions in the roots. Our findings provide insights into the complexity of crosskingdom interactions and improve the understanding of microbiome assembly in the rhizosphere and roots.

Plant-microbe interactions through a lens: tales from the mycorrhizosphere

BACKGROUND

The soil microbiome plays a pivotal role in maintaining ecological balance, supporting food production, preserving water quality and safeguarding human health. Understanding the intricate dynamics within the soil microbiome necessitates unravelling complex bacterial-fungal interactions (BFIs). BFIs occur in diverse habitats, such as the phyllosphere, rhizosphere and bulk soil, where they exert substantial influence on plant-microbe associations, nutrient cycling and overall ecosystem functions. In various symbiotic associations, fungi form mycorrhizal connections with plant roots, enhancing nutrient uptake through the root and mycorrhizal pathways. Concurrently, specific soil bacteria, including mycorrhiza helper bacteria, play a pivotal role in nutrient acquisition and promoting plant growth. Chemical communication and biofilm formation further shape plant-microbial interactions, affecting plant growth, disease resistance and nutrient acquisition processes.

SCOPE

Promoting synergistic interactions between mycorrhizal fungi and soil microbes holds immense potential for advancing ecological knowledge and conservation. However, despite the significant progress, gaps remain in our understanding of the evolutionary significance, perception, functional traits and ecological relevance of BFIs. Here we review recent findings obtained with respect to complex microbial communities - particularly in the mycorrhizosphere - and include the latest advances in the field, outlining their profound impacts on our understanding of ecosystem dynamics and plant physiology and function.

CONCLUSIONS

Deepening our understanding of plant BFIs can help assess their capabilities with regard to ecological and agricultural safe-guarding, in particular buffering soil stresses, and ensuring sustainable land management practices. Preserving and enhancing soil biodiversity emerge as critical imperatives in sustaining life on Earth amidst pressures of anthropogenic climate change. A holistic approach integrates scientific knowledge on bacteria and fungi, which includes their potential to foster resilient soil ecosystems for present and future generations.

Rational management of the plant microbiome for the Second Green Revolution

The Green Revolution of the mid-20th century transformed agriculture worldwide and has resulted in environmental challenges. A new approach, the Second Green Revolution, seeks to enhance agricultural productivity while minimizing negative environmental impacts. Plant microbiomes play critical roles in plant growth and stress responses, and understanding plant-microbiome interactions is essential for developing sustainable agricultural practices that meet food security and safety challenges, which are among the United Nations Sustainable Development Goals. This review provides a comprehensive exploration of key deterministic processes crucial for developing microbiome management strategies, including the host effect, the facilitator effect, and microbe-microbe interactions. A hierarchical framework for plant microbiome modulation is proposed to bridge the gap between basic research and agricultural applications. This framework emphasizes three levels of modulation: single-strain, synthetic community, and in situ microbiome modulation. Overall, rational management of plant microbiomes has wide-ranging applications in agriculture and can potentially be a core technology for the Second Green Revolution.

Rhizosphere microbial markers (micro-markers): A new physical examination indicator for traditional Chinese medicines

Rhizosphere microorganisms, as one of the most important components of the soil microbiota and plant holobiont, play a key role in the medicinal plant-soil ecosystem, which are closely related to the growth, adaptability, nutrient absorption, stress tolerance and pathogen resistance of host plants. In recent years, with the wide application of molecular biology and omics technologies, the outcomes of rhizosphere microorganisms on the health, biomass production and secondary metabolite biosynthesis of medicinal plants have received extensive attention. However, whether or to what extent rhizosphere microorganisms can contribute to the construction of the quality evaluation system of Chinese medicinal materials is still elusive. Based on the significant role of rhizosphere microbes in the survival and quality formation of medicinal plants, this paper proposed a new concept of rhizosphere microbial markers (micro-markers), expounded the relevant research methods and ideas of applying the new concept, highlighted the importance of micro-markers in the quality evaluation and control system of traditional Chinese medicines (TCMs), and introduced the potential value in soil environmental assessment, plant pest control and quality assessment of TCMs. It provides reference for developing ecological planting of TCMs and ensuring the production of high quality TCMs by regulating rhizosphere microbial communities.