Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression

Mitigating the vertical migration and leaching risks of antibiotic resistance genes through insect fertilizer application

The leaching and vertical migration risks of antibiotic resistance genes (ARGs) from fertilized soil to groundwater poses a significant threat to ecological and public safety. Insect fertilizer, particularly black soldier fly organic fertilizer (BOF), renowned for its minimal antibiotic resistance, emerge as a promising alternative for sustainable agricultural fertilization. This study employs soil-column leaching experiments to evaluate the impact of BOF on the leaching behavior of ARGs. Our results reveal that BOF significantly reduces the leaching risks of ARGs by 22.1 %-49.3 % compared to control organic fertilizer (COF). Moreover, BOF promotes the leaching of beneficial Bacillus and, according to random forest analysis, is the most important factor in predicting ARG profiles (3.02 % increase in the MSE). Further network analysis and mantel tests suggest that enhanced nitrogen metabolism in BOF leachates could foster Bacillus biofilm formation, thereby countering antibiotic-resistant bacteria (ARB) and mitigating antibiotic resistance. In addition, linear regression analysis revealed that Bacillus biofilm-associated genes pgaD (biofilm PGA synthesis protein), slrR (biofilm formation regulator), and kpsC (capsular polysaccharide export protein) were identified as pivotal in the elimination of ARGs, which can serve as effective indicators for assessing antibiotic resistance in groundwater. Collectively, this study demonstrates that BOF as an environmentally friendly fertilizer could markedly reduce the vertical migration risks of ARGs and proposes Bacillus biofilm formation related genes as reliable indicators for monitoring antibiotic resistance in groundwater.

Early inoculation and bacterial community assembly in plants: A review

The relationship between plants and early colonizing microbes is crucial for regulating agricultural ecosystems. Recent evidence strongly suggests that by introducing beneficial microbes during the seed or seedling stages, the diversity and assembly structure of the plant-related microbial community during later plant development can be altered, recruiting beneficial bacteria to enhance plant protection. However, the mechanisms of community assembly and their effects on plant growth are still not fully understood. To deepen our understanding of the importance of early inoculation for improving plant performance, this review comprehensively summarizes recent research advancements on the effects of early introduction on plant growth and adaptability. The mechanisms and ecological significance of early inoculation in the assembly of plant-related bacterial communities are discussed, with particular emphasis on the importance of seed endophytes, plant growth-promoting rhizobacteria (PGPR), and synthetic microbial consortia as microbial inoculants in enhancing plant health and productivity. Additionally, this review proposes a new strategy: sequential inoculation during the seed and seedling stages, aiming to maximize the effects of microbes.

Exploring the potential role of soil protists in predicting banana health

Fusarium wilt is increasingly threatening banana production around the world. Investigating soil microbial communities associated with healthy and diseased banana plants is the first step to understand the potential mechanisms involved in the disease suppression. Previous research has confirmed plant-beneficial bacterial and fungal communities are key determinants of banana health. However, to what extent protists, a key component of the soil microbiome, are linked to banana health on a large scale remains largely unknown. Here, we collected soil samples from healthy and diseased plants suffering from Fusarium wilt in multiple banana plantations within China and Laos, and examined holistic soil microbial communities including bacteria, fungi and protists using high-throughput sequencing. We explored the linkage between protists and Fusarium oxysporum and investigated the effects of biotic and abiotic factors on protists. Results showed the relative abundance of Fusarium oxysporum can be highly predicted by protists. Specifically, predatory protists revealed a negative correlation with F. oxysporum, which was confirmed in pot experiments. We found the putative plant growth-promoting bacteria, positively correlated with predatory protists, were also negatively correlated with F. oxysporum. In addition, both soil abiotic factors (i.e., soil pH and ammonia nitrogen) and biotic factors (soil bacteria) played crucial roles in determining predatory protists. We highlighted that soil predatory protists might contribute to banana health via directly inhibiting soil-borne pathogens or indirectly enriching plant beneficial bacteria.

Soil Microbial Mechanisms to Improve Pear Seedling Growth by Applying Bacillus and Trichoderma-Amended Biofertilizers

Bacillus velezensis SQR9 or Trichoderma harzianum NJAU4742-amended bioorganic fertilizers might significantly improve the soil microbial community and crop yields. However, the mechanisms these microorganisms act are far away from distinctness. We combined amplicon sequencing with culturable approaches to investigate the effects of these microorganisms on pear tree growth, rhizosphere nutrients and microbial mechanisms. The SQR9 and T4742 treatments increased the total biomass of pear trees by 68% and 84%, respectively, compared to the conventional organic fertilizer treatment (CK). SQR9 tends to increase soil organic matter and available phosphorus, while T4742 more effectively enhances nitrogen, potassium, iron and zinc levels. These effects were primarily linked to changes in the microbial community. T4742 treatment enriched twice as many differential microbes as SQR9. SQR9 significantly enriched Urebacillus, Streptomyces and Mycobacterium, while T4742 increased the abundance of Pseudomonas, Aspergillus and Penicillium. In vitro experiments revealed that secondary metabolites secreted by B. velezensis SQR9 and T. harzianum NJAU4742 stimulate the growth of key probiotics associated with their respective treatments, enhancing soil fertility and plant biomass. The study revealed the specific roles of these bioorganic fertilizers in agricultural applications, providing new insights for developing effective and targeted bioorganic fertilizer products and promoting sustainable agriculture.

Preparation of a novel economically efficient and environment friendly controlled release urea from liquefied corn straw and castor oil

Because of the renewable nature of castor oil, it has been widely used in the production of bio-based polyurethane (BPU) coated controlled-release fertilizer. However, although castor oil (CO) is a natural material, the polyurethane prepared from castor oil is still a product difficult to degrade. In order to further improve the degradability of castor oil-based polyurethane, six different BPU coated controlled-release urea were prepared using liquefied corn straw (LCS)-based polyols, castor oil, isocyanate as raw materials, glycerol and acrylamide as crosslinking agents. The surface morphology, hydrophobicity, thermal stability, release characteristic curve, degradation related functional groups, colony, soil micro plastic content and other indicators of controlled-release urea were determined, and then six different controlled-release urea were comprehensively evaluated. The results showed that the release time of LCS based polyurethane coated urea was shorter than that of CO based polyurethane coated urea, but the degradation was better. The crosslinking structure significantly improved the hydrophobicity of BPU and prolonged the release period of controlled-release fertilizer. When 30% castor oil was replaced by liquefied corn straw, the release period remained unchanged, but the degradability was improved, which made the content of microplastics in soil decreased. In a word, the partial replacement of castor oil with liquefied corn straw and its application in the production of coated controlled release fertilizer has high environmental benefits.

Using black soldier fly larval frass to restore soil health

The importance of sustainable solutions for restoring soil health amidst increasing soil degradation and organic waste accumulation has gained significant attention. Black soldier fly larval (BSFL) bioconversion offers a promising solution by converting organic wastes into value-added products, such as larval biomass and frass. BSFL frass, the main output of the bioconversion, is increasingly recognized for its potential to restore soil health. Here, this paper provides a comprehensive synthesis of BSFL frass production and properties, and explores its role in mitigating multiple problems related to soil degradation. Finally, this paper further discusses the challenges and future directions for the effective, safe, and sustainable use of BSFL frass. In summary, this paper revealed that BSFL frass, with its unique physicochemical properties and a variety of beneficial bioactive compounds and microorganisms, holds the potential to address problems such as soil acidification, fertility degradation, microbial dysbiosis, and soil-borne diseases, thereby restoring soil health.

The Effect of Selected Phosphate-Solubilizing Bacteria on the Growth of Cotton Plants in Salinized Farmlands

The utilization rate of phosphorus fertilizer is low in Xinjiang, China, due to the fact that phosphorus is easily fixed by the widely distributed lime soil, leading to the limited contribution of phosphorus fertilizer to crop yield and a decline in crop quality. Phosphate-soluble bacteria can convert insoluble phosphates in the soil into soluble phosphates, playing an important role in soil phosphorus circulation and plant growth. In this study, two bacteria with strong phosphate-solubilizing ability, Enterobacter hormaechei (P1) and Bacillus atrophaeus (P2), were selected from severely salinized soils in Xinjiang, China. The taxonomic status of the strains was determined by analyzing the colony morphology and 16S rRNA gene sequence similarity. Then, the content of organic acids and the activity of acid phosphatase and phytase in the P1 and P2 fermentation broths were measured. Finally, field experiments were conducted in 20 April-2 October 2023 in Wulanwusu, Xinjiang, China, to analyze the effects of phosphate-solubilizing bacterial agents (P1, P2, and P3 (P1 + P2)) on soil physicochemical properties, microbial diversity, and cotton yield. The results showed that both P1 and P2 could significantly solubilize phosphates and produce indole-3-acetic acid (IAA), lactic acid, and tartaric acid. In the cotton field under phosphorus fertilization, the cotton yield of P1, P2, and P3 treatments increased by 10.77%, 8.48%, and 14.00%, respectively, compared with no bacterial agent treatment (CK) (p < 0.05). In addition, the application of phosphate-solubilizing bacterial agents also significantly increased the content of available nutrients and the abundances of Acidobacteria, Bacteroidetes, Fusarium, Bacteroidetes, and Verrucobacteria in the soil compared with CK. In summary, inoculating with phosphate-solubilizing bacteria could promote cotton growth and yield formation by increasing soil available nutrients and altering soil microbial communities. This study will provide a basis for the efficient utilization of phosphorus resources and sustainable agricultural development.

Plant pathogens, microbiomes, and soil health

Healthy soil is vital for ecosystem sustainability and global food security. However, anthropogenic activities that promote intensive agriculture, landscape and biodiversity homogenization, and climate change disrupt soil health. The soil microbiome is a critical component of healthy soils, and increasing evidence suggests that soils with low diversity or homogenized microbial systems are more susceptible to soil pathogen invasion, but the extent and mechanisms that increase the threat of pathogen invasion (i.e., increase in prevalence of existing species and introduction of new species) remain unclear. This article aims to fill this knowledge gap by synthesizing the literature and providing novel insights for the scientific community and policy advisors. We also present the current and future global distribution of some dominant soil-borne pathogens. We argue that an improved understanding of the interplay between the soil microbiome, soil health, host, and pathogen distribution, and their responses to environmental changes is urgently needed to ensure the future of productive farms, safe food, sustainable environments, and holistic global well-being.

Bacillus velezensis TB918 mitigates garlic dry rot disease by forming consortia with Pseudomonas in the rhizosphere and bulb

Garlic dry rot (GDR), primarily caused by Fusarium proliferatum, is a significant postharvest disease that leads to substantial economic losses. Our previous research demonstrated that supplementing Bacillus-based biocontrol formulations with sucrose could boost its efficiency in protecting plants by building a hostile rhizomicrobiome for destructive soil-borne pathogens. B. velezensis TB918, previously isolated from pepper rhizosphere soil, exhibited a strong in vitro antifungal effect on Fusarium. In this study, we conducted a field experiment to investigate the efficacy of B. velezensis TB918 in controlling GDR, and explored the changes in microbial communities in garlic plants and rhizosphere soil following the application of TB918 with or without sucrose supplementation. Using 16S rRNA and ITS amplicon sequencing, we found that the introduction of TB918 significantly increased the abundance of Pseudomonas in garlic rhizosphere, especially when combined with sucrose. Three Pseudomonas strains were isolated from garlic tissues and rhizosphere soil treated with TB918 and sucrose, among which the GP2 strain exhibited antagonistic effects against pathogen ad planta. Co-culture and colonization assays showed that TB918 facilitated the biofilm formation of Pseudomonas strain by forming consortia. Interestingly, the abundance of potentially non-pathogenic Fusarium concentricum also increased, suggesting a potential niche exclusion effect. Our results demonstrated that TB918 in combination with sucrose effectively reduced the incidence of GDR during storage. This study provides valuable insights into the use of biocontrol agents and sucrose to modulate the garlic microbial community and suppress soil-borne pathogens.

Microbial diversity and interactions: Synergistic effects and potential applications of Pseudomonas and Bacillus consortia

Microbial diversity and interactions in the rhizosphere play a crucial role in plant health and ecosystem functioning. Among the myriads of rhizosphere microbes, Pseudomonas and Bacillus are prominent players known for their multifaceted functionalities and beneficial effects on plant growth. The molecular mechanism of interspecies interactions between natural isolates of Bacillus and Pseudomonas in medium conditions is well understood, but the interaction between the two in vivo remains unclear. This paper focuses on the possible synergies between Pseudomonas and Bacillus associated in practical applications (such as recruiting beneficial microbes, cross-feeding and niche complementarity), and looks forward to the application prospects of the consortium in agriculture, human health and bioremediation. Through in-depth understanding of the interactions between Pseudomonas and Bacillus as well as their application prospects in various fields, this study is expected to provide a new theoretical basis and practical guidance for promoting the research and application of rhizosphere microbes.

Digestate-based organic amendment substitution improves the red soil quality and pakchoi yield

This study investigated the effect of the partially substituting chemical fertilizers (CF) with digestate-based organic amendment (OA) on the amelioration of red soil and the growth of plant. OA with nitrogen substitution rates ranging from 10 % to 40 % were mixed with CF and applied to red soil in a pot experiment. The results indicated that plant growth was significantly enhanced in the treatment where 20 % of the CF was substituted with the OA (OA20) compared to other treatments (p < 0.05). Specifically, the OA20 treatment increased nutrient use efficiency by 54.76 %-100.42 % compared to the treatment using only CF. Furthermore, all OA treatments improved the quality of red soil, with the nutrient content significantly higher in the OA20 group than in the other treatments (p < 0.05). The parameters of total phosphorus (TP), available nitrogen (AN), available phosphorus (AP), and total potassium (TK) significantly affected the soil quality index and plant growth, serving as reliable indicators of soil quality and plant yield. Microbial analysis revealed that the bacterial Chao index and the abundance of microorganisms involved in C-N nutrient cycling, such as Chryseolinea and norank_f__norank_o__Actinomarinales, were highest in the OA20 group. Significant correlations were observed between soil nutrient content (AN, AP, and TK) and the abundance of norank_f__norank_o__Actinomarinales and Chryseolinea, indicating their close relationship with pakchoi growth. Consequently, digestate-based OA may positively affect plant growth in acidic ecosystems by enhancing soil properties, inducing shifts in microbial community composition, and promoting the enrichment of potentially beneficial bacteria. This study provides valuable insights for the enhancement of low-quality soils and the resource utilization of digestate.

Different active exogenous carbons improve the yield and quality of roses by shaping different bacterial communities

The application of exogenous organic carbon represents a significant strategy for enhancing soil fertility and promoting sustainable agricultural development. This approach modifies the physicochemical properties of soil and influences microbial community structures, consequently improving crop yield and quality. Nevertheless, the mechanisms underlying microbial community responses to various forms of active exogenous organic carbon remain poorly understood and require further investigation. A 1-year follow-up experiment was conducted to examine the effects of different carbon sources on the yield and quality of cut roses, along with the characteristics of the soil bacterial community. The results indicated that applying organic fertiliser and biochar significantly enhanced the productivity of cut roses, demonstrating a sustained growth-promoting effect. Organic fertiliser provides more active, readily oxidisable organic carbon to the soil compared to biochar. In contrast, biochar supplies stable organic carbon, including inert organic carbon that is difficult to oxidise, firm organic carbon (FOC), and total inert organic carbon, which has a high degree of humification that significantly exceeds that of organic fertiliser. The application of biochar and organic fertiliser not only altered the abundance, diversity, and composition of the rhizosphere microbial community but also enriched beneficial microorganisms. Redundancy analysis results indicated that FOC, available phosphorus, and soil organic matter were the primary factors influencing the bacterial community. The results of this study demonstrated that exogenous organic carbon exerted positive and indirect effects on crop yield by influencing soil properties and bacterial communities. These findings provide novel evidence supporting the rational application of biochar and organic fertilisers as a means to promote agricultural sustainability in red soil regions.

Multiwalled Carbon Nanotubes Promoted Biofilm Formation and Rhizosphere Colonization of Bacillus subtilis Tpb55

Plant growth-promoting bacteria (PGPB) achieve effective colonization by forming a biofilm on the root surface. However, the promoting effects and mechanisms of nanomaterials on PGPB biofilm formation and rhizosphere colonization are rarely studied. This study investigated the effects and the potential mechanism of multiwalled carbon nanotubes (MWCNTs) on biofilm formation and rhizosphere colonization of PGPB Bacillus subtilis. 10 and 100 mg/L MWCNTs increased biofilm biomass, extracellular polymeric substance components, live/dead cell ratio, and spores in biofilms. MWCNTs induced B. subtilis Tpb55 upregulated gene expressions of malL, sacX, tasA-tapA, and epsA-O correlated with carbohydrate metabolism and biofilm formation. MWCNTs first stimulated Tpb55 flagellar motility and then increased biofilm formation, thus promoting colonization in the tobacco rhizosphere. Greenhouse experiments showed that the combination of MWCNTs and Tpb55 reduced the occurrence of tobacco black shank. Therefore, MWCNTs have broad application potential in enhancing the effectiveness of PGPB in agricultural disease control and yield enhancement.

Bacterial Supplements Significantly Improve the Growth Rate of Cultured Asparagopsis armata

Seaweed aquaculture is an expanding industry with innovative applications beyond the traditional uses as human foods and phycocolloids. Asparagopsis armata, a red seaweed, is cultivated as a feed supplement to reduce methane emission from ruminants. The manipulation of microbiota with seaweed beneficial microorganisms (SBMs) has shown promise in enhancing disease resistance and growth in seaweeds and has potential to aid the cultivation of A. armata. In this study, we developed a growth assay for the rapid selection of bacteria that promote the growth of A. armata tetrasporophytes. We tested bacterial strains from the genera Phaeobacter and Pseudoalteromonas for their impact on the growth of A. armata, as these bacteria have been recognized for their beneficial traits in other seaweeds. All strains significantly enhanced the specific growth rate (SGR) of A. armata tetrasporophytes compared to controls without bacterial treatment. Bacterial 16S rRNA gene amplicon sequencing confirmed the presence of the inoculated growth-promoting SBMs (SBM-Gs) in A. armata cultures with no significant impacts on the resident microbial community. Co-occurrence network analysis of the resulting communities demonstrated that the inoculated Phaeobacter spp. formed distinct modules, exclusively interacting with resident Phaeobacter species, while the Pseudoalteromonas sp. was absent from the network. These results demonstrate that microbial inoculation is an effective strategy for incorporating SBM-Gs into the A. armata microbiota to promote growth. The tested SBM-Gs may exert their influence by interacting with specific resident species or by directly affecting host physiology, resulting in minimal undesired effects on the microbiome.

Bacteriophage-Bacteria Interactions Promote Ecological Multifunctionality in Compost-Applied Soils

Bacteriophages (phages) influence biogeochemical cycling in soil ecosystems by mediating bacterial metabolism. However, the participation of phages in soil's overall ecological functions (multifunctionality) remains unclear. Hence, this study investigated the potential for phages and bacterial communities to shape the multifunctionality of compost-applied soils. The findings revealed that cow compost and vermicompost applications enhanced the soil's multifunctionality; consequently, the highest multifunctionality was observed in the soil with vermicompost application (p < 0.05). The composition and diversity of bacteria and phages, as well as the abundance of functional genes of bacteria and phages related to carbon, nitrogen, phosphorus and sulphur metabolism, were dramatically altered following the application of both compost types. Moreover, the impact of phage diversity on soil multifunctionality is crucial for multi-threshold calculations. Structural equation modelling indicated that the effects of bacterial diversity on soil multifunctionality following compost application were paramount, with a path coefficient of 0.88 (p < 0.01). The rise in phage diversity and the enrichment of functional genes indirectly led to a dramatic increase in the soil's ecological multifunctionality by affecting the host bacteria's metabolic processes. These results offer a novel avenue to improve soil's functions and environmental services by transforming the phage community composition and functions of soils.

Efficacy of L-arabinose in managing cucumber Fusarium wilt and the underlying mechanism of action

BACKGROUND

Cucumber Fusarium wilt (CFW), triggered by Fusarium oxysporum f. sp. cucumerinum, leads to substantial yield reductions in global cucumber (Cucumis sativus L.) production. Common management strategies for CFW include soil fumigation, grafting, and crop rotation. However, these methods have limitations regarding safety and efficacy stability, necessitating the development of new, cost-effective, and eco-friendly control strategies. Our prior research demonstrated that L-arabinose, an inexpensive and safe sugar commonly used in food and beverages, effectively suppressed bacterial wilt in tomatoes. This study explores the potential of L-arabinose in managing CFW and investigates its mechanism of action.

RESULTS

Soil applications of L-arabinose, ranging from 0.00001 to 0.01%, effectively suppressed CFW. The most significant suppressive effect was observed at 0.01%, reducing the disease severity index by 67.5% compared to the control treatment. Microscopic examination of transverse root sections showed that pathogen hyphae colonized the epidermis but seldom penetrated the cortical layer of roots in L-arabinose-treated seedlings. In contrast, the entire root tissue of control seedlings was colonized by the pathogen. Quantitative real-time PCR revealed a significant increase in the expression of defense-related genes dependent on salicylic acid, jasmonic acid, and ethylene in L-arabinose-treated plants compared to control plants, 6 and 10 days post pathogen inoculation.

CONCLUSION

This study demonstrated that soil application of L-arabinose can effectively suppress CFW by priming root tissues for multiple defense signaling pathways. Therefore, L-arabinose holds potential as a new fungicide for managing CFW. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Biochar-based organic fertilizer application promotes the alleviation of tobacco (Nicotiana tabacum L.) continuous cropping obstacles by improving soil chemical properties and microbial community structure

BACKGROUND

Intensive monoculture poses a serious threat to agricultural sustainable development due to the phenomenon of continuous cropping obstacles. Although organic amendment has been considered an efficient and environmentally friendly solution to mitigate this tough issue, the associated mechanisms remain poorly understood. Here, a two-year field experiment was conducted with the application of four fertilizers, wood, rice straw, compound biochar-based organic fertilizers (WBF, RBF, CBF) and chemical fertilizer (CF) under tobacco rotation with broad bean and oilseed rape, respectively. This work aims to determine how BFs application alleviates tobacco CCO and to further reveal the underlying action mechanisms primarily focusing on the change of soil micro-ecology environments.

RESULTS

The results depicted that BFs addition decreased tobacco morbidity (by 15.7-85.0%), heavy metals (Cd, V, Cu, Zn) contents in tobacco, and improved tobacco leaf production yield (by 4.5-20.5%), economic value (by 14.6-34.4%) and chemical quality compared with CF. Rhizosphere soil chemical properties and the structure and diversity of microbial communities were enhanced under BFs treatments, reflecting in the growth of bacterial OTUs number, microbial alpha-diversity, the abundances of some beneficial genera (Arthrobacter, Pseudomonas, Gemmatimonas, Trichoderma, Mortierella, Penicillium, Chaetomium, etc.), and the reduction of the numbers of detrimental microbes (Alternaria, Phytophthora nicotianae and Fusarium oxysporum). Moreover, CBF amendment improved the stability and complexity of microbial co-occurrence networks. Soil total carbon, microbial structure, and diversity were the most important explanatory factors for the increase of tobacco leaf yield and economic value.

CONCLUSIONS

Collectively, BFs application under rotation regime showed the great potential as a practical and environmentally friendly strategy to alleviate tobacco CCO by providing an optimized soil environment.

Unraveling the Mechanism of the Endophytic Bacterial Strain Pseudomonas oryzihabitans GDW1 in Enhancing Tomato Plant Growth Through Modulation of the Host Transcriptome and Bacteriome

Endophytic Pseudomonas species from agricultural crops have been extensively studied for their plant-growth-promoting (PGP) potential, but little is known about their PGP potential when isolated from perennial trees. This study investigated the plant-growth-promoting (PGP) potential of an endophyte, Pseudomonas oryzihabitans GDW1, isolated from a healthy pine tree by taking tomato as a host plant. We employed multiomics approaches (transcriptome and bacteriome analyses) to elucidate the underlying PGP mechanisms of GDW1. The results of greenhouse experiments revealed that the application of GDW1 significantly improved tomato plant growth, increasing shoot length, root length, fresh weight, and biomass accumulation by up to 44%, 38%, 54%, and 59%, respectively, compared with control. Transcriptomic analysis revealed 1158 differentially expressed genes significantly enriched in the plant hormone signaling (auxin, gibberellin, and cytokinin) and stress response (plant-pathogen interaction, MAPK signaling pathway-plant, and phenylpropanoid biosynthesis) pathways. Protein-protein interaction network analysis revealed nine hub genes (MAPK10, ARF19-1, SlCKX1, GA2ox2, PAL5, SlWRKY37, GH3.6, XTH3, and NML1) related to stress tolerance, hormone control, and plant defense. Analysis of the tomato root bacteriome through 16S rRNA gene amplicon sequencing revealed that GDW1 inoculation dramatically altered the root bacterial community structure, enhancing the diversity and abundance of beneficial taxa (Proteobacteria and Bacteroidota). Co-occurrence network analysis showed a complex bacterial network in treated plants, suggesting increasingly intricate microbial relationships and improved nutrient absorption. Additionally, FAPROTAX and PICRUSt2 functional prediction analyses suggested the role of GDW1 in nitrogen cycling, organic matter degradation, plant growth promotion, and stress resistance. In conclusion, this study provides novel insights into the symbiotic relationship between P. oryzihabitans GDW1 and tomato plants, highlighting its potential as a biofertilizer for sustainable agriculture and a means of reducing the reliance on agrochemicals.

Effects of drought stress and Morchella inoculation on the physicochemical properties, enzymatic activities, and bacterial community of Poa pratensis L. rhizosphere soil

Background

Soil microorganisms are crucial for plant growth, and both plants and their associated rhizosphere microbes are impacted by changes in soil moisture. Inoculation with beneficial fungi can improve bacterial community structure and soil parameters.

Aim

Under drought stress conditions, the effects of inoculation with Morchella on the physicochemical properties, enzyme activity, and bacterial community structure of the rhizosphere soil of Poa pratensis were studied.

Methods

High-throughput sequencing was employed to study rhizosphere soil bacterial communities in both Morchella-inoculated and uninoculated Poa pratensis rhizosphere soil subjected to moderate (50% soil moisture) and severe (30% soil moisture) drought stress, as well as under normal water conditions (70% soil moisture).

Results

Morchella inoculation significantly increased the alkaline nitrogen (AN) and available phosphorus (AP) contents, protease activity (PA), and alkaline phosphatase activity (APA) of Poa pratensis rhizosphere soil. Both Morchella inoculation and drought stress significantly altered the abundance and diversity of the P. pratensis rhizosphere community. The Chao1, Shannon, and Pielou diversity indices decreased with increasing drought stress. The effect of Morchella inoculation was improved under moderate drought stress and unstressed conditions. In addition, Morchella inoculation may help to stabilize the rhizosphere bacterial community under various levels of soil moisture.

Deciphering the Distinct Associations of Rhizospheric and Endospheric Microbiomes with Capsicum Plant Pathological Status

Exploring endospheric and rhizospheric microbiomes and their associations can help us to understand the pathological status of capsicum (Capsicum annuum L.) for implementing appropriate management strategies. To elucidate the differences among plants with distinct pathological status in the communities and functions of the endospheric and rhizospheric microbiomes, the samples of healthy and diseased capsicum plants, along with their rhizosphere soils, were collected from a long-term cultivation field. The results indicated a higher bacterial richness in the healthy rhizosphere than in the diseased rhizosphere (P < 0.05), with rhizospheric bacterial diversity surpassing endospheric bacterial diversity. The community assemblies of both the endospheric and rhizospheric microbiomes were driven by a combination of stochastic and deterministic processes, with the stochastic processes playing a primary role. The majority of co-enriched taxa in the healthy endophyte and rhizosphere mainly belonged to bacterial Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal Ascomycota. Most of the bacterial indicators, primarily Alphaproteobacteria and Actinobacteria, were enriched in the healthy rhizosphere, but not in the diseased rhizosphere. In addition, most of the fungal indicators were enriched in both the healthy and diseased endosphere. The diseased endophyte constituted a less complex and stable microbial community than the healthy endophyte, and meanwhile, the diseased rhizosphere exhibited a higher complexity but lower stability than the healthy rhizosphere. Notably, only a microbial function, namely biosynthesis of other secondary metabolites, was higher in the healthy endophytes than in the diseased endophyte. These findings indicated the distinct responses of rhizospheric and endospheric microbiomes to capsicum pathological status, and in particular, provided a new insight into leveraging soil and plant microbial resources to enhance agriculture production.

Deep generative modeling of annotated bacterial biofilm images

Biofilms are critical for understanding environmental processes, developing biotechnology applications, and progressing in medical treatments of various infections. Nowadays, a key limiting factor for biofilm analysis is the difficulty in obtaining large datasets with fully annotated images. This study introduces a versatile approach for creating synthetic datasets of annotated biofilm images with employing deep generative modeling techniques, including VAEs, GANs, diffusion models, and CycleGAN. Synthetic datasets can significantly improve the training of computer vision models for automated biofilm analysis, as demonstrated with the application of Mask R-CNN detection model. The approach represents a key advance in the field of biofilm research, offering a scalable solution for generating high-quality training data and working with different strains of microorganisms at different stages of formation. Terabyte-scale datasets can be easily generated on personal computers. A web application is provided for the on-demand generation of biofilm images.

Synthetic Microbial Communities Enhance Pepper Growth and Root Morphology by Regulating Rhizosphere Microbial Communities

Synthetic microbial community (SynCom) application is efficient in promoting crop yield and soil health. However, few studies have been conducted to enhance pepper growth via modulating rhizosphere microbial communities by SynCom application. This study aimed to investigate how SynCom inoculation at the seedling stage impacts pepper growth by modulating the rhizosphere microbiome using high-throughput sequencing technology. SynCom inoculation significantly increased shoot height, stem diameter, fresh weight, dry weight, chlorophyll content, leaf number, root vigor, root tips, total root length, and root-specific surface area of pepper by 20.9%, 36.33%, 68.84%, 64.34%, 29.65%, 27.78%, 117.42%, 35.4%, 21.52%, and 39.76%, respectively, relative to the control. The Chao index of the rhizosphere microbial community and Bray-Curtis dissimilarity of the fungal community significantly increased, while Bray-Curtis dissimilarity of the bacterial community significantly decreased by SynCom inoculation. The abundances of key taxa such as Scedosporium, Sordariomycetes, Pseudarthrobacter, norankSBR1031, and norankA4b significantly increased with SynCom inoculation, and positively correlated with indices of pepper growth. Our findings suggest that SynCom inoculation can effectively enhance pepper growth and regulate root morphology by regulating rhizosphere microbial communities and increasing key taxa abundance like Sordariomycetes and Pseudarthrobacter, thereby benefiting nutrient acquisition, resistance improvement, and pathogen resistance of crops to ensure sustainability.

Evaluating a Soil Amendment for Cadmium Mitigation and Enhanced Nutritional Quality in Faba Bean Genotypes: Implications for Food Safety

Soil amendments combined with low cadmium (Cd)-accumulating crops are commonly used for remediating Cd contamination and ensuring food safety. However, the combined effects of soil amendments and the cultivation of faba beans (Vicia faba L.)-known for their high nutritional quality and low Cd accumulation-in moderately Cd-contaminated soils remain underexplored. This study investigates the impact of a soil amendment (SA) on agronomic traits, seed nutrition, and Cd accumulation in 11 faba bean genotypes grown in acidic soil (1.3 mg·kg-1 Cd, pH 5.39). The SA treatment increased soil pH to 6.0 (an 11.31% increase) and reduced DTPA-Cd by 37.1%. Although the average yield of faba beans decreased marginally by 8.74%, it remained within the 10% national permissible limit. Notably, SA treatment reduced Cd concentration in seeds by 60% and significantly mitigated Mn and Al toxicity. Additionally, SA treatment enhanced levels of essential macronutrients (Ca, Mg, P, S) and micronutrients (Mo, Cu) while lowering Phytate (Phy)/Ca, Phy/Mg, and Phy/P ratios, thus improving mineral nutrient bioavailability. Among the genotypes, F3, F5, and F6 showed the most favorable balance of nutrient quality, and yield following SA application. This study provides valuable insights into the effectiveness of SA for nutrient fortification and Cd contamination mitigation in Cd-contaminated farmland.

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.

Surfactin facilitates establishment of Bacillus subtilis in synthetic communities

Soil bacteria are prolific producers of a myriad of biologically active secondary metabolites. These natural products play key roles in modern society, finding use as anti-cancer agents, as food additives, and as alternatives to chemical pesticides. As for their original role in interbacterial communication, secondary metabolites have been extensively studied under in vitro conditions, revealing many roles including antagonism, effects on motility, niche colonization, signaling, and cellular differentiation. Despite the growing body of knowledge on their mode of action, biosynthesis, and regulation, we still do not fully understand the role of secondary metabolites on the ecology of the producers and resident communities in situ. Here, we specifically examine the influence of Bacillus subtilis-produced cyclic lipopeptides during the assembly of a bacterial synthetic community, and simultaneously, explore the impact of cyclic lipopeptides on B. subtilis establishment success in a synthetic community propagated in an artificial soil microcosm. We found that surfactin production facilitates B. subtilis establishment success within multiple synthetic communities. Although neither a wild type nor a cyclic lipopeptide non-producer mutant had a major impact on the synthetic community composition over time, both the B. subtilis and the synthetic community metabolomes were altered during co-cultivation. Overall, our work demonstrates the importance of surfactin production in microbial communities, suggesting a broad spectrum of action of this natural product.

Delineating the soil physicochemical and microbiological factors conferring disease suppression in organic farms

Organic farming utilizes farmyard manure, compost, and organic wastes as sources of nutrients and organic matter. Soil under organic farming exhibits increased microbial diversity, and thus, becomes naturally suppressive to the development of soil-borne pathogens due to the latter's competition with resident microbial communities. Such soils that exhibit resistance to soil-borne phytopathogens are called disease-suppressive soils. Based on the phytopathogen suppression range, soil disease suppressiveness is categorised as specific- or general- disease suppression. Disease suppressiveness can either occur naturally or can be induced by manipulating soil properties, including the microbiome responsible for conferring protection against soil-borne pathogens. While the induction of general disease suppression in agricultural soils is important for limiting pathogenic attacks on crops, the factors responsible for the phenomenon are yet to be identified. Limited efforts have been made to understand the systemic mechanisms involved in developing disease suppression in organically farmed soils. Identifying the critical factors could be useful for inducing disease suppressiveness in conducive soils as a cost-effective alternative to the application of pesticides and fungicides. Therefore, this review examines the soil properties, including microbiota, and assesses indicators related to disease suppression, for the process to be employed as a tactical option to reduce pesticide use in agriculture.

Thiophanate-methyl and its major metabolite carbendazim weaken rhizobacteria-mediated defense responses in cucumbers against Fusarium wilt

The effect of fungicides on the plant-rhizosphere microbiome is a subject of ongoing debate, but whether any alteration in the rhizosphere microbiome could affect plant health is an issue that has not been thoroughly investigated. To address this deficiency, we analyzed the rhizosphere microbiome of wilt disease-resistant and disease-susceptible cucumber cultivars to determine whether (and which) plant-associated microorganisms have a role in disease resistance. We further assessed whether the fungicides thiophanate-methyl and carbendazim affect the rhizosphere microbiome, which may contribute to the plant's immune response. Based on results acquired with both radicle-inoculation and soil-inoculation methods, cultivars Longyuanxiuchun (LYXC) and Shuyan2 (SY2) were identified as being disease resistant, whereas Zhongnong6 (ZN6) and Zhongnong38 (ZN38) were susceptible. The microbiome structure differed substantially between the resistant and susceptible plants, with LYXC and SY2 each having a significantly greater Shannon index than Zhongnong38. These results revealed that the disease-resistant cucumber cultivars recruited more beneficial bacteria, i.e., Bacillus, in their rhizosphere soil; as such, Bacillus was identified as a keystone genus in the microbial co-occurrence network. Thus, the presence of Bacillus may help cucumbers defend against fungal pathogens within the rhizosphere. Bacillus subtilis strain LD15, which was isolated from LYXC rhizosphere soil, could suppress pathogen growth, in vitro, and reduce disease severity in pot assays. Moreover, evidence also confirmed the accumulation of LD1 in the rhizosphere soil of resistant cucumber cultivars. For LYXC, application of thiophanate-methyl or carbendazim altered the microbiome structure, decreased bacterial diversity, and reduced the abundance of Bacillus species. Finally, pot assays verified that fungicide application decreased the proportion of LD15 in rhizosphere soil. From a microbial perspective, thiophanate-methyl and carbendazim may weaken the rhizobacteria-mediated defense response of cucumbers against cucumber Fusarium wilt disease. Our findings reveal a role for the rhizosphere microbiome in protecting plants from pathogens and constitute a reference for assessing the ecotoxicological risk of pesticides to non-target soil microorganisms.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-024-00181-5.

The Colonization of Synthetic Microbial Communities Carried by Bio-Organic Fertilizers in Continuous Cropping Soil for Potato Plants

Synthetic microbial communities (SynComs) play significant roles in soil health and sustainable agriculture. In this study, bacterial SynComs (SCBs) and fungal SynComs (SCFs) were constructed by selecting microbial species that could degrade the potato root exudates associated with continuous cropping obstacles. SCBs, SCFs, and SCB + SCF combinations were then inoculated into organic fertilizers (OFs, made from sheep manure) to produce three bio-organic fertilizers (BOFs), denoted by SBFs (BOFs of inoculated SCBs), SFFs (BOFs of inoculated SCFs), and SBFFs (BOFs of inoculated SCB + SCF combinations), respectively. The OF and three BOFs, with a chemical fertilizer (CK) as the control, were then used in pot experiments involving potato growth with soil from a 4-year continuous cropping field. Microbial diversity sequencing was used to investigate the colonization of SCBs and SCFs into the rhizosphere soil and the bulk soil, and their effects on soil microbial diversity were evaluated. Source Tracker analysis showed that SCBs increased bacterial colonization from the SBFs into the rhizosphere soil, but at a relatively low level of 1% of the total soil bacteria, while SCFs increased fungi colonization from the SFF into the bulk soil at a much higher level of 5-18% of the total soil fungi. In combination, SCB + SCF significantly increased fungi colonization from the SBFF into both the bulk soil and the rhizosphere soil. Overall, the soil fungi were more susceptible to the influence of the BOFs than the bacteria. In general, the application of BOFs did not significantly change the soil microbial alpha diversity. Correlation network analysis showed that key species of bacteria were stable in the soils of the different groups, especially in the rhizosphere soil, while the key species of fungi significantly changed among the different groups. LEfSe analysis showed that the application of BOFs activated some rare species, which were correlated with improvements in the function categories of the tolerance of stress, nitrogen fixation, and saprotroph functions. Mantel test analysis showed that the BOFs significantly affected soil physicochemical properties, influencing bacterial key species, and core bacteria, promoting potato growth. It was also noted that the presence of SynCom-inoculated BOFs may lead to a slight increase in plant pathogens, which needs to be considered in the optimization of SynCom applications to overcome continuous cropping obstacles in potato production.

Effects of cotton peanut rotation on crop yield soil nutrients and microbial diversity

Background and Aims Cotton-peanut rotation is a sustainable farming practice that enhances land utilization and promotes the sustainable development of agriculture. Crop rotation can reduce the occurrence of pests and diseases, as different crops have varying levels of resistance to such threats. Additionally, by alternating the types of crops grown, the soil environment is changed, which can lead to the elimination of favorable conditions for pathogens and pests, thereby alleviating the impact of these issues. Furthermore, cotton-peanut rotation can improve soil fertility.To investigate the effects of different crop rotation systems on crop yield, soil nutrients, and soil microbial communities.

METHODS

Using high-throughput sequencing technology, investigate the soil microbial diversity in the root zone after cotton-peanut rotation.Various planting patterns, including cotton continuous cropping (MC), peanut continuous cropping (HC), peanut-cotton-peanut rotation (HR), and fallow (X), were established to assess variations in crop yield, soil nutrients, and soil microbial diversity.

RESULTS

Significant differences were observed in crop yield, soil nutrients, and soil microbial community structure among different planting patterns. The HR system significantly increased the output compared with the HC and MC systems. Additionally, HR exhibited significantly lower total nitrogen (N) and basic nitrogen (BN) contents than HC and MC, whereas MC showed lower total potassium (K) and available potassium (AK) contents. HR led to a decrease in soil bacterial diversity but an increase in fungal diversity, with Ascomycota and Mortierellomycota being dominant. Various bacteria (Chloroflexi, Bacteroidota, and Actinobacteriota) associated with organic matter degradation and nutrient cycling were found across different planting systems, enhancing material cycling efficiency. Furthermore, Planctomycetota bacteria related to crop nutrient synthesis and Glomeromycota bacteria aiding plant nutrient absorption were significantly higher in the MC system than in the HR or HC systems. Redundancy analysis indicated a significant negative correlation between crop rotation and soil fungal community, whereas Ascomycota exhibited a significant negative correlation with organic matter.

CONCLUSION

Peanut-cotton rotation can mitigate soil nutrient loss, enhance beneficial microorganism diversity, suppress harmful bacterial populations, stabilize ecosystems, and boost crop yield.

Biocontrol Agents Inhibit Banana Fusarium Wilt and Alter the Rooted Soil Bacterial Community in the Field

Banana is an important fruit and food crop in tropical and subtropical regions worldwide. Banana production is seriously threatened by Fusarium wilt of banana (FWB), a disease caused by Fusarium oxysporum f. sp. cubense, and biological control is an important means of curbing this soil-borne disease. To reveal the effects of biocontrol agents on inhibiting FWB and altering the soil bacterial community under natural ecosystems, we conducted experiments at a banana plantation. The control efficiency of a compound microbial agent (CM), Paenibacillus polymyxa (PP), Trichoderma harzianum (TH), and carbendazim (CA) on this disease were compared in the field. Meanwhile, the alterations in structure and function of the rooted soil bacterial community in different treatments during the vigorous growth and fruit development stages of banana were analyzed by microbiomics method. The results confirmed that the different biocontrol agents could effectively control FWB. In particular, CM significantly reduced the incidence of the disease and showed a field control efficiency of 60.53%. In terms of bacterial community, there were no significant differences in the richness and diversity of banana rooted soil bacteria among the different treatments at either growth stage, but their relative abundances differed substantially. CM treatment significantly increased the ratios of Bacillus, Bryobacter, Pseudomonas, Jatrophihabitans, Hathewaya, and Chujaibacter in the vigorous growth stage and Jatrophihabitans, Occallatibacter, Cupriavidus, and 1921-3 in the fruit development stage. Furthermore, bacterial community function in the banana rooted soil was affected differently by the various biocontrol agents. CM application increased the relative abundance of multiple soil bacterial functions, including carbohydrate metabolism, xenobiotic biodegradation and metabolism, terpenoid and polyketide metabolism, lipid metabolism, and metabolism of other amino acids. In summary, our results suggest that the tested biocontrol agents can effectively inhibit the occurrence of banana Fusarium wilt and alter the soil bacterial community in the field. They mainly modified the relative abundance of bacterial taxa and the metabolic functions rather than the richness and diversity. These findings provide a scientific basis for the use of biocontrol agents to control banana Fusarium wilt under field conditions, which serves as a reference for the study of the soil microbiological mechanisms of other biocontrol agents.

Protorhabditis nematodes and pathogen-antagonistic bacteria interactively promote plant health

BACKGROUND

Fertilization practices control bacterial wilt-causing Ralstonia solanacearum by shaping the soil microbiome. This microbiome is the start of food webs, in which nematodes act as major microbiome predators. However, the multitrophic links between nematodes and the performance of R. solanacearum and plant health, and how these links are affected by fertilization practices, remain unknown.

RESULTS

Here, we performed a field experiment under no-, chemical-, and bio-organic-fertilization regimes to investigate the potential role of nematodes in suppressing tomato bacterial wilt. We found that bio-organic fertilizers changed nematode community composition and increased abundances of bacterivorous nematodes (e.g., Protorhabditis spp.). We also observed that pathogen-antagonistic bacteria, such as Bacillus spp., positively correlated with abundances of bacterivorous nematodes. In subsequent laboratory and greenhouse experiments, we demonstrated that bacterivorous nematodes preferentially preyed on non-pathogen-antagonistic bacteria over Bacillus. These changes increased the performance of pathogen-antagonistic bacteria that subsequently suppressed R. solanacearum.

CONCLUSIONS

Overall, bacterivorous nematodes can reduce the abundance of plant pathogens, which might provide a novel protection strategy to promote plant health. Video Abstract.

Taxonomy of Pseudomonas spp. determines interactions with Bacillus subtilis

Bacilli and pseudomonads are among the most well-studied microorganisms commonly found in soil and frequently co-isolated. Isolates from these two genera are frequently used as plant beneficial microorganisms; therefore, their interaction in the plant rhizosphere is relevant for agricultural applications. Despite this, no systematic approach has been employed to assess the coexistence of members from these genera. Here, we screened 720 fluorescent soil isolates for their effects on Bacillus subtilis pellicle formation in two types of media and found a predictor for interaction outcome in Pseudomonas taxonomy. Interactions were context-dependent, and both medium composition and culture conditions strongly influenced interactions. Negative interactions were associated with Pseudomonas capeferrum, Pseudomonas entomophila, and Pseudomonas protegens, and 2,4-diacetylphloroglucinol was confirmed as a strong (but not exclusive) inhibitor of B. subtilis. Non-inhibiting strains were closely related to Pseudomonas trivialis and Pseudomonas lini. Using such a non-inhibiting isolate, Pseudomonas P9_31, which increased B. subtilis pellicle formation demonstrated that the two species were spatially segregated in cocultures. Our study is the first one to propose an overall negative outcome from pairwise interactions between B. subtilis and fluorescent pseudomonads; hence, cocultures comprising members from these groups are likely to require additional microorganisms for coexistence.

IMPORTANCE

There is a strong interest in the microbial ecology field to predict interaction among microorganisms, whether two microbial isolates will promote each other's growth or compete for resources. Numerous studies have been performed based on surveying the available literature or testing phylogenetically diverse sets of species in synthetic communities. Here, a high throughput screening has been performed using 720 Pseudomonas isolates, and their impact on the biofilm formation of Bacillus subtilis was tested. The aim was to determine whether a majority of Pseudomonas will promote or inhibit the biofilms of B. subtilis in the co-cultures. This study reports that Pseudomonas taxonomy is a good predictor of interaction outcome, and only a minority of Pseudomonas isolates promote Bacillus biofilm establishment.

The structure and function of rhizosphere bacterial communities: impact of chemical vs. bio-organic fertilizers on root disease, quality, and yield of Codonopsis pilosula

Introduction

Long-term use of chemical fertilizers (CFs) can cause soil compaction and acidification. In recent years, bio-organic fertilizers (BOFs) have begun to replace CFs in some vegetables and cash crops, but the application of CFs or BOFs has resulted in crop quality and disease occurrence.

Methods

This study aimed to analyze the microbial mechanism of differences between CFs and BOFs in root disease, quality, and yield of tuber Chinese herbal medicine. We studied the effects of CFs, organic fertilizers, commercial BOFs, biocontrol bacteria BOFs, and biocontrol fungi BOFs on rhizosphere microbial community structure and function, root rot, quality, and yield of Codonopsis pilosula at different periods after application and analyzed the correlation.

Results and discussion

Compared to CFs, the emergence rate and yield in BOF treatments were increased by 21.12 and 33.65%, respectively, and the ash content, water content, and disease index in the BOF treatments were decreased by 17.87, 8.19, and 76.60%, respectively. The structural equation model showed that CFs promoted the quality and yield of C. pilosula by influencing soil environmental factors, while BOFs directly drove soil bacterial community to reduce disease index and improve the quality and yield of C. pilosula. There was a stronger interaction and stability of soil microbial networks after BOF treatments. Microlunatus, Rubrobacter, Luteitalea, Nakamurella, and Pedomicrobium were identified as effector bacteria, which were related to disease prevention and yield and quality increase of C. pilosula. Microbial functional analysis indicated that the signal transduction and amino acid metabolism of soil bacteria might play a major role in improving the quality and yield of C. pilosula in the early and middle growth stages. In conclusion, compared to CFs, BOFs obtained a lower disease index of root rot and a higher quality and yield of C. pilosula by changing the structure and function of the rhizosphere bacterial community.

The occurrence of banana Fusarium wilt aggravates antibiotic resistance genes dissemination in soil

The spread of antibiotic resistance genes (ARGs) and subsequent soil-borne disease outbreaks are major threats to soil health and sustainable crop production. However, the relationship between occurrences of soil-borne diseases and the transmission of soil ARGs remains unclear. Here, soil ARGs, mobile genetic elements and microbial communities from co-located disease suppressive and conducive banana orchards were deciphered using metagenomics and metatranscriptomics approaches. In total, 23 ARG types, with 399 subtypes, were detected using a metagenomics approach, whereas 23 ARG types, with 452 subtypes, were discovered using a metatranscriptomics method. Furthermore, the metagenomics analysis revealed that the ARG total abundance levels were greater in rhizospheres (0.45 ARGs/16S rRNA on average) compared with bulk (0.32 ARGs/16S rRNA on average) soils. Interestingly, metatranscriptomics revealed that the total ARG abundances were greater in disease-conducive (8.85 ARGs/16S rRNA on average) soils than disease suppressive (1.45 ARGs/16S rRNA on average) soils. Mobile genetic elements showed the same trends as ARGs. Network and binning analyses indicated that Mycobacterium, Streptomyces, and Blastomonas are the main potential hosts of ARGs. Furthermore, Bacillus was significantly and negatively correlated with Fusarium (P < 0.05, r = -0.84) and hosts of ARGs (i.e., Mycobacterium, Streptomyces, and Blastomonas). By comparing metagenomic and metatranscriptomic analyses，this study demonstrated that metatranscriptomics may be more sensitive in indicating ARGs activities in soil. Our findings enable the more accurate assessment of the transmission risk of ARGs. The data provide a new perspective for recognizing soil health, in which soil-borne disease outbreaks appear to be associated with ARG spread, whereas beneficial microbe enrichment may mitigate wilt disease and ARG transmission.

Enrichment of novel entomopathogenic Pseudomonas species enhances willow resistance to leaf beetles

BACKGROUND

Plants have evolved various defense mechanisms against insect herbivores, including the formation of physical barriers, the synthesis of toxic metabolites, and the activation of phytohormone responses. Although plant-associated microbiota influence plant growth and health, whether they play a role in plant defense against insect pests in natural ecosystems is unknown.

RESULTS

Here, we show that leaves of beetle-damaged weeping willow (Salix babylonica) trees are more resistant to the leaf beetle Plagiodera versicolora (Coleoptera) than those of undamaged leaves. Bacterial community transplantation experiments demonstrated that plant-associated microbiota from the beetle-damaged willow contribute to the resistance of the beetle-damaged willow to P. versicolora. Analysis of the composition and abundance of the microbiome revealed that Pseudomonas spp. is significantly enriched in the phyllosphere, roots, and rhizosphere soil of beetle-damaged willows relative to undamaged willows. From a total of 49 Pseudomonas strains isolated from willows and rhizosphere soil, we identified seven novel Pseudomonas strains that are toxic to P. versicolora. Moreover, re-inoculation of a synthetic microbial community (SynCom) with these Pseudomonas strains enhances willow resistance to P. versicolora.

CONCLUSIONS

Collectively, our data reveal that willows can exploit specific entomopathogenic bacteria to enhance defense against P. versicolora, suggesting that there is a complex interplay among plants, insects, and plant-associated microbiota in natural ecosystems.

Streptomyces-Secreted Fluvirucin B6 as a Potential Bio-Fungicide for Managing Banana Fusarium Wilt and Mycotoxins and Modulating the Soil Microbial Community Structure

Banana Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc TR4) is the most destructive soil-borne fungal disease. Until now, there has been a lack of effective measures to control the disease. It is urgent to explore biocontrol agents to control Foc TR4 and the secretion of mycotoxin. In this study, fluvirucin B6 was screened from Streptomyces solisilvae using an activity-guided method. Fluvirucin B6 exhibited strong antifungal activity against Foc TR4 (0.084 mM of EC50 value) and significantly inhibited mycelial growth and spore germination. Further studies demonstrated that fluvirucin B6 could cause the functional loss of mitochondria, the disorder of metabolism of Foc TR4 cells, and the decrease of enzyme activities in the tricarboxylic acid cycle and electron transport chain, ultimately inhibiting mycotoxin metabolism. In a pot experiment, the application of fluvirucin B6 significantly decreased the incidence of banana Fusarium wilt and the amount of Foc TR4 and controlled fungal toxins in the soil. Additionally, fluvirucin B6 could positively regulate the changes in the structure of the banana rhizosphere microbial community, significantly enriching beneficial microbes associated with disease resistance. In summary, this study identifies fluvirucin B6, which plays versatile roles in managing fungal diseases and mycotoxins.

OsPHR2-mediated recruitment of Pseudomonadaceae enhances rice phosphorus uptake

Plants can shape their root microbiome to promote growth and nutrient uptake. PHOSPHATE STARVATION RESPONSE 2 (OsPHR2) is a central regulator of phosphate signaling in rice, but whether OsPHR2 can shape the root microbiome to promote phosphorus uptake is unclear. Here, we investigate the role of OsPHR2 in recruiting microbiota for phosphorus uptake using high-throughput sequencing and metabolite analysis. OsPHR2-overexpressing (OsPHR2 OE) rice showed 69.8% greater shoot P uptake in natural soil compared with sterilized soil under high-phosphorus (HP) conditions, but there was only a 54.8% increase in the wild-type (WT). The abundance of the family Pseudomonadaceae was significantly enriched in OsPHR2 OE roots relative to those of WT rice. Compared with the WT, OsPHR2 OE rice had a relatively higher abundance of succinic acid and methylmalonic acid, which could stimulate the growth of Pseudomonas sp. (P6). After inoculation with P6, phosphorus uptake in WT and OsPHR2 OE rice was higher than that in uninoculated rice under low-phosphorus (LP) conditions. Taken together, our results suggest that OsPHR2 can increase phosphorus use in rice through root exudate-mediated recruitment of Pseudomonas. This finding reveals a cooperative contribution of the OsPHR2-modulated root microbiome, which is important for improving phosphorus use in agriculture.

Superiority of native soil core microbiomes in supporting plant growth

Native core microbiomes represent a unique opportunity to support food provision and plant-based industries. Yet, these microbiomes are often neglected when developing synthetic communities (SynComs) to support plant health and growth. Here, we study the contribution of native core, native non-core and non-native microorganisms to support plant production. We construct four alternative SynComs based on the excellent growth promoting ability of individual stain and paired non-antagonistic action. One of microbiome based SynCom (SC2) shows a high niche breadth and low average variation degree in-vitro interaction. The promoting-growth effect of SC2 can be transferred to non-sterile environment, attributing to the colonization of native core microorganisms and the improvement of rhizosphere promoting-growth function including nitrogen fixation, IAA production, and dissolved phosphorus. Further, microbial fertilizer based on SC2 and composite carrier (rapeseed cake fertilizer + rice husk carbon) increase the net biomass of plant by 129%. Our results highlight the fundamental importance of native core microorganisms to boost plant production.

Stimulating the biofilm formation of Bacillus populations to mitigate soil antibiotic resistome during insect fertilizer application

Antibiotic resistance in soil introduced by organic fertilizer application pose a globally recognized threat to human health. Insect organic fertilizer may be a promising alternative due to its low antibiotic resistance. However, it is not yet clear how to regulate soil microbes to reduce antibiotic resistance in organic fertilizer agricultural application. In this study, we investigated soil microbes and antibiotic resistome under black soldier fly organic fertilizer (BOF) application in pot and field systems. Our study shows that BOF could stimulate ARB (antibiotic resistant - bacteria) - suppressive Bacillaceae in the soil microbiome and reduce antibiotic resistome. The carbohydrate transport and metabolism pathway of soil Bacillaceae was strengthened, which accelerated the synthesis and transport of polysaccharides to form biofilm to antagonistic soil ARB, and thus reduced the antibiotic resistance. We further tested the ARB - suppressive Bacillus spp. in a microcosm assay, which resulted in a significant decrease in the presence of ARGs and ARB together with higher abundance in key biofilm formation gene (epsA). This knowledge might help to the development of more efficient bio-fertilizers aimed at mitigating soil antibiotic resistance and enhancing soil health, in particular, under the requirements of global "One Health".

Comparative Metagenomic Analysis Reveals Rhizosphere Microbiome Assembly and Functional Adaptation Changes Caused by Clubroot Disease in Chinese Cabbage

Clubroot is a major disease and severe threat to Chinese cabbage, and it is caused by the pathogen Plasmodiophora brassicae Woron. This pathogen is an obligate biotrophic protist and can persist in soil in the form of resting spores for more than 18 years, which can easily be transmitted through a number of agents, resulting in significant economic losses to global Chinese cabbage production. Rhizosphere microbiomes play fundamental roles in the occurrence and development of plant diseases. The changes in the rhizosphere microorganisms could reveal the severity of plant diseases and provide the basis for their control. Here, we studied the rhizosphere microbiota after clubroot disease infections with different severities by employing metagenomic sequencing, with the aim of exploring the relationships between plant health, rhizosphere microbial communities, and soil environments; then, we identified potential biomarker microbes of clubroot disease. The results showed that clubroot disease severity significantly affected the microbial community composition and structure of the rhizosphere soil, and microbial functions were also dramatically influenced by it. Four different microbes that had great potential in the biocontrol of clubroot disease were identified from the obtained results; they were the genera Pseudomonas, Gemmatimonas, Sphingomonas, and Nocardioides. Soil pH, organic matter contents, total nitrogen, and cation exchange capacity were the major environmental factors modulating plant microbiome assembly. In addition, microbial environmental information processing was extremely strengthened when the plant was subjected to pathogen invasion, but weakened when the disease became serious. In particular, oxidative phosphorylation and glycerol-1-phosphatase might have critical functions in enhancing Chinese cabbage's resistance to clubroot disease. This work revealed the interactions and potential mechanisms among Chinese cabbage, soil environmental factors, clubroot disease, and microbial community structure and functions, which may provide a novel foundation for further studies using microbiological or metabolic methods to develop disease-resistant cultivation technologies.

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.

Meta-analysis reveals the effects of microbial inoculants on the biomass and diversity of soil microbial communities

Microbial inoculation involves transplanting microorganisms from their natural habitat to new plants or soils to improve plant performance, and it is being increasingly used in agriculture and ecological restoration. However, microbial inoculants can invade and alter the composition of native microbial communities; thus, a comprehensive analysis is urgently needed to understand the overall impact of microbial inoculants on the biomass, diversity, structure and network complexity of native communities. Here we provide a meta-analysis of 335 studies revealing a positive effect of microbial inoculants on soil microbial biomass. This positive effect was weakened by environmental stress and enhanced by the use of fertilizers and native inoculants. Although microbial inoculants did not alter microbial diversity, they induced major changes in the structure and bacterial composition of soil microbial communities, reducing the complexity of bacterial networks and increasing network stability. Finally, higher initial levels of soil nutrients amplified the positive impact of microbial inoculants on fungal biomass, actinobacterial biomass, microbial biomass carbon and microbial biomass nitrogen. Together, our results highlight the positive effects of microbial inoculants on soil microbial biomass, emphasizing the benefits of native inoculants and the important regulatory roles of soil nutrient levels and environmental stress.

Synthetic community derived from grafted watermelon rhizosphere provides protection for ungrafted watermelon against Fusarium oxysporum via microbial synergistic effects

BACKGROUND

Plant microbiota contributes to plant growth and health, including enhancing plant resistance to various diseases. Despite remarkable progress in understanding diseases resistance in plants, the precise role of rhizosphere microbiota in enhancing watermelon resistance against soil-borne diseases remains unclear. Here, we constructed a synthetic community (SynCom) of 16 core bacterial strains obtained from the rhizosphere of grafted watermelon plants. We further simplified SynCom and investigated the role of bacteria with synergistic interactions in promoting plant growth through a simple synthetic community.

RESULTS

Our results demonstrated that the SynCom significantly enhanced the growth and disease resistance of ungrafted watermelon grown in non-sterile soil. Furthermore, analysis of the amplicon and metagenome data revealed the pivotal role of Pseudomonas in enhancing plant health, as evidenced by a significant increase in the relative abundance and biofilm-forming pathways of Pseudomonas post-SynCom inoculation. Based on in vitro co-culture experiments and bacterial metabolomic analysis, we selected Pseudomonas along with seven other members of the SynCom that exhibited synergistic effects with Pseudomonas. It enabled us to further refine the initially constructed SynCom into a simplified SynCom comprising the eight selected bacterial species. Notably, the plant-promoting effects of simplified SynCom were similar to those of the initial SynCom. Furthermore, the simplified SynCom protected plants through synergistic effects of bacteria.

CONCLUSIONS

Our findings suggest that the SynCom proliferate in the rhizosphere and mitigate soil-borne diseases through microbial synergistic interactions, highlighting the potential of synergistic effects between microorganisms in enhancing plant health. This study provides a novel insight into using the functional SynCom as a promising solution for sustainable agriculture. Video Abstract.

A smooth vetch (Vicia villosa var.) strain endogenous to the broad-spectrum antagonist Bacillus siamensis JSZ06 alleviates banana wilt disease

Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), poses a significant threat to banana production globally, thereby necessitating effective biocontrol methods to manage this devastating disease. This study investigates the potential of Bacillus siamensis strain JSZ06, isolated from smooth vetch, as a biocontrol agent against Foc TR4. To this end, we conducted a series of in vitro and in vivo experiments to evaluate the antifungal activity of strain JSZ06 and its crude extracts. Additionally, genomic analyses were performed to identify antibiotic synthesis genes, while metabolomic profiling was conducted to characterize bioactive compounds. The results demonstrated that strain JSZ06 exhibited strong inhibitory activity against Foc TR4, significantly reducing mycelial growth and spore germination. Moreover, scanning and transmission electron microscopy revealed substantial ultrastructural damage to Foc TR4 mycelia treated with JSZ06 extracts. Genomic analysis identified several antibiotic synthesis genes, and metabolomic profiling revealed numerous antifungal metabolites. Furthermore, in pot trials, the application of JSZ06 fermentation broth significantly enhanced banana plant growth and reduced disease severity, achieving biocontrol efficiencies of 76.71% and 79.25% for leaves and pseudostems, respectively. In conclusion, Bacillus siamensis JSZ06 is a promising biocontrol agent against Fusarium wilt in bananas, with its dual action of direct antifungal activity and plant growth promotion underscoring its potential for integrated disease management strategies.

Synthetic consortia of four strains promote Schisandra chinensis growth by regulating soil microbial community and improving soil fertility

MAIN CONCLUSION

Synthetic consortia performed better in promoting Schisandra chinensis growth than individual strains, and this result provides valuable information for the development of synthetic microbial fertilizers. Schisandra chinensis is an herbal medicine that can treat numerous diseases. However, the excessive reliance on chemical fertilizers during the plantation of S. chinensis has severely restricted the development of the S. chinensis planting industry. Plant growth-promoting rhizobacteria (PGPR) can promote the growth of a wide range of crops, and synthetic consortia of them are frequently superior to those of a single strain. In this study, we compared the effects of four PGPR and their synthetic consortia on S. chinensis growth. The pot experiment showed that compared with the control, synthetic consortia significantly increased the plant height, biomass, and total chlorophyll contents of S. chinensis, and their combined effects were better than those of individual strains. In addition, they improved the rhizosphere soil fertility (e.g., TC and TN contents) and enzyme activities (e.g., soil urease activity) and affected the composition and structure of soil microbial community significantly, including promoting the enrichment of beneficial microorganisms (e.g., Actinobacteria and Verrucomicrobiota) and increasing the relative abundance of Proteobacteria, a dominant bacterial phylum. They also enhanced the synergistic effect between the soil microorganisms. The correlation analysis between soil physicochemical properties and microbiome revealed that soil microorganisms participated in regulating soil fertility and promoting S. chinensis growth. This study may provide a theoretical basis for the development of synthetic microbial fertilizers for S. chinensis.

Effects of coastal saline-alkali soil on rhizosphere microbial community and crop yield of cotton at different growth stages

Soil salinization is a global constraint that significantly hampers agricultural production, with cotton being an important cash crop that is not immune to its detrimental effects. The rhizosphere microbiome plays a critical role in plant health and growth, which assists plants in resisting adverse abiotic stresses including soil salinization. This study explores the impact of soil salinization on cotton, including its effects on growth, yield, soil physical and chemical properties, as well as soil bacterial community structures. The results of β-diversity analysis showed that there were significant differences in bacterial communities in saline-alkali soil at different growth stages of cotton. Besides, the more severity of soil salinization, the more abundance of Proteobacteria, Bacteroidota enriched in rhizosphere bacterial composition where the abundance of Acidobacteriota exhibited the opposite trend. And the co-occurrence network analysis showed that soil salinization affected the complexity of soil bacterial co-occurrence network. These findings provide valuable insights into the mechanisms by which soil salinization affects soil microorganisms in cotton rhizosphere soil and offer guidance for improving soil salinization using beneficial microorganisms.

Difference in the Effect of Applying Bacillus to Control Tomato Verticillium Wilt in Black and Red Soil

In practical applications, the effectiveness of biological control agents such as Bacillus is often unstable due to different soil environments. Herein, we aimed to explore the control effect and intrinsic mechanism of Bacillus in black soil and red soil in combination with tomato Verticillium wilt. Bacillus application effectively controlled the occurrence of Verticillium wilt in red soil, reducing the incidence by 19.83%, but played a limited role in black soil. Bacillus colonized red soil more efficiently. The Verticillium pathogen decreased by 71.13% and 76.09% after the application of Bacillus combinations in the rhizosphere and bulk of the red soil, respectively, while there was no significant difference in the black soil. Additionally, Bacillus application to red soil significantly promoted phosphorus absorption. Furthermore, it significantly altered the bacterial community in red soil and enriched genes related to pathogen antagonism and phosphorus activation, which jointly participated in soil nutrient activation and disease prevention, promoting tomato plant growth in red soil. This study revealed that the shaping of the bacterial community by native soil may be the key factor affecting the colonization and function of exogenous Bacillus.

Customized plant microbiome engineering for food security

Plant microbiomes play a vital role in promoting plant growth and resilience to cope with environmental stresses. Plant microbiome engineering holds significant promise to increase crop yields, but there is uncertainty about how this can best be achieved. We propose a step-by-step approach involving customized direct and indirect methods to condition soils and to match plants and microbiomes. Although three approaches, namely the development of (i) 'plant- and microbe-friendly' soils, (ii) 'microbe-friendly' plants, and (iii) 'plant-friendly' microbiomes, have been successfully tested in isolation, we propose that the combination of all three may lead to a step-change towards higher and more stable crop yields. This review aims to provide knowledge, future directions, and practical guidance to achieve this goal via customized plant microbiome engineering.

Two microbes assisting Miscanthus floridulus in remediating multi-metal(loid)s-contaminated soil

Miscanthus has good tolerance to multi-metal(loid)s and has received increasing attention in remediated studies of metal(loid)s-contaminated soil. In this study, we conducted phytoextraction techniques to investigate the synergic effects of remediation of multi-metal(loid)s-contaminated soil by Miscanthus floridulus (Lab.) and two plant growth-promoting bacteria (PGPB), TS8 and MR2, affiliated to Enterobacteriaceae. The results exhibited a decrease of arsenic (15.27-21.50%), cadmium (8.64-15.52%), plumbum (5.92-12.76%), and zinc (12.84-24.20%) except for copper contents in the soil in bacterial inoculation groups, indicating that MR2 and TS8 could enhance the remediation of metal(loid)s. Moreover, increased fresh/dry weight and height indicated that inoculated bacteria could promote Miscanthus growth. Although the activities of antioxidant enzymes and the content of chlorophyll in the overground tissues showed no significant increase or even decrease, the activities of antioxidant enzymes in the underground tissues and soil were elevated by 48.95-354.17%, available P by 19.07-23.02%, and available K by 15.34-17.79% (p < 0.05). Bacterial inoculants could also decrease the soil pH. High-throughput sequencing analysis showed that the bacterial inoculant affected the rhizosphere bacterial community and reduced community diversity, but the relative abundance of some PGPB was found to increase. Phylogenetic molecular ecological networks indicated that bacterial inoculants reduced interactions between rhizosphere bacteria and thereby led to a simpler network structure but increased the proportion of positive-correlation links and enhanced the metabiosis and symbiosis of those bacteria. Spearman's test showed that OTUs affiliated with Enterobacteriaceae and soil nutrients were critical for metal(loid) remediation and Miscanthus growth. The results of this study provide a basis for the synergic remediation of multi-metal(loid)s-contaminated soils by Miscanthus and PGPB and provide a reference for the subsequent regulation of Miscanthus remediation efficiency by the other PGPB or critical bacteria.

Important soil microbiota's effects on plants and soils: a comprehensive 30-year systematic literature review

Clarifying the relationship between soil microorganisms and the plant-soil system is crucial for encouraging the sustainable development of ecosystems, as soil microorganisms serve a variety of functional roles in the plant-soil system. In this work, the influence mechanisms of significant soil microbial groups on the plant-soil system and their applications in environmental remediation over the previous 30 years were reviewed using a systematic literature review (SLR) methodology. The findings demonstrated that: (1) There has been a general upward trend in the number of publications on significant microorganisms, including bacteria, fungi, and archaea. (2) Bacteria and fungi influence soil development and plant growth through organic matter decomposition, nitrogen, phosphorus, and potassium element dissolution, symbiotic relationships, plant growth hormone production, pathogen inhibition, and plant resistance induction. Archaea aid in the growth of plants by breaking down low-molecular-weight organic matter, participating in element cycles, producing plant growth hormones, and suppressing infections. (3) Microorganism principles are utilized in soil remediation, biofertilizer production, denitrification, and phosphorus removal, effectively reducing environmental pollution, preventing soil pathogen invasion, protecting vegetation health, and promoting plant growth. The three important microbial groups collectively regulate the plant-soil ecosystem and help maintain its relative stability. This work systematically summarizes the principles of important microbial groups influence plant-soil systems, providing a theoretical reference for how to control soil microbes in order to restore damaged ecosystems and enhance ecosystem resilience in the future.