Interspecific plant interaction via root exudates structures the disease suppressiveness of rhizosphere microbiomes

Organic fertilizer mitigated the oxidative stress of tomato induced by nanoplastics through affecting rhizosphere soil microorganisms and bacteriophage functions

Nanoplastics (NPs), which are widely present in agricultural soils, are difficult to remove and are potentially harmful to plant growth and development. However, few studies have focused on how to mitigation the oxidative stress in plants induced by soil NPs exposure. Therefore, in this study, the effects of organic and chemical fertilizers on the oxidative stress of tomato under exposure to polystyrene nanoplastics (PS-NPs) in soil were investigated. Compared with chemical fertilizer under exposure to PS-NPs, the organic fertilizer reduced the reactive oxygen species (ROS) content by 25.63 % and the H2O2 content by 34.58 % in tomato stems, whereas no significant effects were observed with respect to the amount of PS-NP internalized in tomato. Additionally, organic fertilizer increased the accumulation of the phytohormones salicylic acid (SA) and abscisic acid (ABA) by 76.53 % and 22.54 %, respectively, and these factors are key for reducing the ROS and H2O2 contents in stems. In the rhizosphere microbiome of organic fertilizer group under exposure to PS-NPs, enrichment in Actinomycetes and an increased abundance of terpenoids and polyketides metabolism were the main factors affecting the accumulation of ABA and SA. Moreover, bacteriophage activity in the rhizosphere indirectly contributed to the increase in this function. These changes ultimately resulted in a reduction in oxidative stress in tomato stems and protected tomato growth. The results of this study will provide a better understanding of the interaction between plants and nanoplastics in soil and provide a new reference for alleviating the oxidative stress caused by nanoplastics in plants.

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.

Understanding the ternary interaction of crop plants, fungal pathogens, and rhizobacteria in response to global warming

Climate change is altering the equilibrium of the Earth's biosphere, imposing unpredictable survival dynamics on terrestrial organisms. This includes the intricate interactions between fungal pathogens and crop plants, which are pivotal for global food security. Rising temperatures are expected to exacerbate the prevalence of crop-pathogenic fungi worldwide, yet research on how crops respond to this imminent threat remains limited. Here, we identified predominant potential pathogens and antagonistic bacteria in vegetable fields in Shandong Province, China, revealing the near-ubiquitous presence of Fusarium oxysporum and Bacillus species in sampled soils of cucumber, tomato, chili, and ginger. Through simulated warming experiments within a temperature range of 20-40 °C and an experimental period of 3 days, we investigated the ternary interaction among vegetables and isolated F. oxysporum strain 05, and Bacillus sp. strain 31. Elevated temperatures enhanced F. oxysporum biomass and virulence, yet also stimulated vegetables to allocate more nutrients via root exudates. This enriched rhizospheric antagonistic Bacillus populations, it also boosted the expression of antifungal lipopeptide biosynthetic genes (bamb and ItuA) and auxin production in Bacillus sp. strain 31. This enrichment promoted plant growth and maintained a relatively stable level of pathogenic fungi. Our study unveiled a nuanced and complex interplay among crop plants, fungal pathogens, and rhizobacteria, that could inform future agricultural practices, and advance our understanding of crop survival strategies to bolster crop resilience and safeguard global food security under ongoing climate change.

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.

Nanoplastic and phthalate induced stress responses in rhizosphere soil: Microbial communities and metabolic networks

The widespread use of plastic products in agriculture has introduced micro-nano plastics (MNPs) and dibutyl phthalate (DBP) into soil ecosystems, disrupting microbial communities and altering metabolite profiles. However, their effects on the rhizosphere soil characteristics of medicinal plants like dandelion remain understudied. This study systematically examined the impact of PS NPs and DBP on rhizosphere microbial communities and metabolites by integrating high-throughput sequencing with liquid chromatography-mass spectrometry. Results demonstrated that individual and combined exposures to PS NPs and DBP decreased soil pH, organic matter content, and enzyme activities while reshaping the diversity, structure, and composition of rhizosphere bacteria and fungi. Notably, bacterial network stability and complexity increased under combined exposure, while fungal networks became more simplified, with a 33.72 % decrease in positive correlations. We identified potential PS NPs and DBP-degrading bacteria and biomarkers, including Nocardioides, Pseudarthrobacter, and Arenimonas. We revealed that co-exposure elevated differential soil metabolites associated with tyrosine metabolism and steroid biosynthesis. The significant positive associations between rhizosphere microorganisms and metabolites highlighted that metabolite accumulation was a key microbial response mechanism to stress. However, within the complex soil environment, the compensatory actions of microorganisms and metabolites were insufficient to mitigate the detrimental effects of PS NPs and DBP, resulting in continued inhibition of dandelion growth by 38.66 %. Consequently, these findings highlight that soil fungi and metabolism play key roles in responding to stress and influencing crop growth, providing novel insights into the impact of nanoparticle and plasticizer exposure on medicinal plant cultivation.

Strategy for enhanced soil lead passivation and mitigating lead toxicity to plants by biochar-based microbial agents

In the study, bone char (BC) backed biochemical composite coupling with phosphate-solubilizing bacteria (CFB1-P) was prepared to explore the passivation performance of lead (Pb) in soil and the mitigation effect on plant growth under Pb stress by measuring change of soil Pb speciation, plant growth parameters and physiological and biochemical indexes. After 30 d of remediation, addition of 1 % CFB1-P could effectively reduce 55.43 % of Pb labile fractions and converted them into Fe-Mn oxide and residual forms. Meanwhile, the bioavailability of Pb was not significantly affected by wetting-drying and freezing-thawing after 20 times cycles (the DTPA-Pb content only increased 6.91-7.35 mg/kg), which proved that the CFB1-P had an excellent prospect of passivating Pb. Moreover, the CFB1-P effectively increased soil fertility and improved soil enzyme activity. The application of CFB1-P could reshape the soil microbial community by recruiting beneficial microorganisms (Bacillus, Sulfurifustis, and Gaiella), which contributed to the improvement of Pb-contaminated soil quality. Furthermore, the fresh weight, photosynthetic pigment concentration, stems and roots length of cucumber seedings were significantly increased. Pb in the cucumber seedings and antioxidant enzyme activities of cucumber seedings were prominently decreased. Therefore, the study can offer a preferable comprehending for the advance of sustainable high-efficiency materials which microbial agent based on functional biochar remediated Pb-polluted soil.

Production performance in cultivated mixed-sown grasslands combining Poa pratensis L. and various Poaceae forage grasses

Kentucky bluegrass (Poa pratensis L.), a native grass species of the Qinghai-Tibetan Plateau, is widely used for ecological restoration due to its high growth rate and strong adaptability. However, monocultures of Poa pratensis are prone to rapid degradation and low productivity, limiting their suitability for animal husbandry. To address these challenges, this study evaluated the production performance and interspecific relationships of different mixed-sown and monoculture grasslands to identify optimal cultivation strategies. Field experiments were conducted over a six-year period, with three mixed-sown treatments-Poa pratensis combined with Siberian wildrye (Elymus sibiricus L.), Chinese fescue (Festuca sinensis Engler ex S.L.Lu), and alkali grass (Puccinellia tenuiflora (Griseb.) Scribn. & Merr.)-alongside their respective monocultures. LASSO regression (Least Absolute Shrinkage and Selection Operator Regression) and ROC curve analysis (Receiver Operating Characteristic Curve Analysis) were applied to identify key factors influencing production performance. The results indicated that the mixed-sown grassland of Elymus sibiricus and Poa pratensis significantly boosted forage yield by 216.88% to 323.06% in comparison with monoculture Poa pratensis. Additionally, the comprehensive evaluation index, which integrates forage yield and nutritional quality, was 16.41% higher for the Elymus sibiricus and Poa pratensis mixture than for the monoculture Poa pratensis grassland. These findings imply that the mixed-sown grassland of Elymus sibiricus and Poa pratensis effectively addresses the low productivity issue often seen in monoculture Poa pratensis grasslands. However, in terms of yield stability and interspecific compatibility, the mixed-sown grassland of Puccinellia tenuiflora and Poa pratensis demonstrated superior performance. Its relative total yield (RTY) consistently exceeded 1.0 from the third to the sixth year, reflecting higher interspecific compatibility and stable productivity over time. And the Poa pratensis and Puccinellia tenuiflora mixture showed the best performance, achieving the highest stability value of 3.12. Therefore, the combination of Poa pratensis and Puccinellia tenuiflora is recommended as the optimal strategy for achieving long-term yield stability and high productivity in cultivated grasslands.

Synergistic effect of grassland plants and beneficial rhizosphere bacteria helps plants cope with overgrazing stress

BACKGROUND

Overgrazing (OG) is an important driver of grassland degradation and productivity decline. Highly effective synergy between plants and rhizosphere growth-promoting rhizobacteria (PGPR) may be a major way for grassland plants to effectively cope with OG stress. There have been few reports providing solid evidence on how this synergy occurs.

RESULT

This study combined with multi-omics analysis and the interaction effect of specific root exudate with PGPR B68, aiming to reveal the synergistic effect and regulatory mechanism of L. chinensis and PGPR under overgrazing stress. The results showed that Leymus chinensis plants with OG history can recruit the beneficial Phyllobacterium sp. B68 by regulating specific root exudate compounds(such as amino acid L-leucyl-L-alanine and alkaloid cordycepin). These compounds enhanced B68 rhizosphere colonization by promoting B68 chemotaxis and biofilm formation. The pot study experiments indicated that the bacterial isolates used as bio inoculants increased L. chinensis growth (mainly including plant height and biomass) by significantly increasing the chlorophyll content, RuBisCO activity, soluble sugar, plant hormones and nutrient content. Metagenomics results show that B68 inoculation significantly altered rhizosphere soil bacterial community composition and function. Additionally, B68 systemically upregulated the expression level of genes involved in plant hormone signaling, nutrient and sugar transporters, nitrogen metabolism, cell division, cell wall modification and photosynthesis to promote plant growth. The above results indicate that the PGPR B68 recruited by the root exudates of L. chinensis under OG helps the plant adapt to stress by promoting nutrient uptake and transport, maintaining hormone homeostasis, and enhancing the expression of genes related to plant growth and nutrient metabolism.

CONCLUSION

This study provides new insights into the positive interactions between grassland plants and rhizosphere bacteria under OG stress, offering valuable knowledge for developing new fertilizers and better management practices for degraded rangeland restoration and sustainable agriculture development.

CLINICAL TRIAL NUMBER

Not applicable.

Nitrogen cycle induced by plant growth-promoting rhizobacteria drives "microbial partners" to enhance cadmium phytoremediation

BACKGROUND

Using plant growth-promoting rhizobacteria (PGPR) combined with hyperaccumulator is an ecologically viable way to remediate cadmium (Cd) pollution in agricultural soil. Despite recent advances in elucidating PGPR-enhanced phytoremediation, the response of plant-associated microbiota to PGPR remains unclear.

RESULTS

Here, we found that the effective colonization of PGPR reshaped the rhizosphere nutrient microenvironment, especially driving the nitrogen cycle, primarily mediated by soil nitrate reductase (S-NR). Elevated S-NR activity mobilized amino acid metabolism and synthesis pathways in the rhizosphere, subsequently driving a shift in life history strategies of the rhizosphere microbiota, and enriching specific rare taxa. The reconstructed synthetic community (SynCom3) confirmed that the inclusion of two crucial collaborators (Lysobacter and Microbacterium) could efficiently foster the colonization of PGPR and aid PGPR in executing phytoremediation enhancement. Finally, the multi-omics analysis highlighted the critical roles of phenylpropanoid biosynthesis and tryptophan metabolism pathways in inducing SynCom3 reorganization and PGPR-enhanced phytoremediation.

CONCLUSIONS

Our results underscore the significance of the rhizosphere microenvironment modification by PGPR for its colonization and efficacy, and highlight the collaborative role of rare microbiota in the context of PGPR-enhanced phytoremediation. Video Abstract.

Sorghum-peanut intercropping under salt stress mediates rhizosphere microbial community shaping in sorghum by affecting soil sugar metabolism pathways

Soil salinization is a substantial impediment to agricultural production, and investigating sustainable mitigation measures is essential for addressing food security. We conducted a two-year pot experiment to investigate the shaping mechanism of sorghum rhizosphere microbial community in sorghum-peanut intercropping system under salt stress. The experiment comprised four treatments: sole-cropped sorghum under normal soil conditions (NSS), intercropped sorghum under normal soil conditions (NIS), sole-cropped sorghum under salt-stress conditions (SSS), and intercropped sorghum under salt-stress conditions (SIS). The sorghum rhizosphere soil metabolites were examined using GC-MS, and the rhizosphere microbial community was characterized through metabolome sequencing. We identified 123 metabolites across treatments, with significant differences between normal and salt-stress soil conditions. The major metabolite classes included carbohydrates, alcohols, and acids. Key carbohydrates, including fructose and sucrose, were significantly reduced in the SIS than in SSS, NSS, and NIS treatments. Metabolic pathway analyses revealed that these differences were primarily associated with "Fructose and mannose metabolism," "Starch and sucrose metabolism" and "ABC transporter." Metabolome analyses revealed significant differences in microbial community structure across diverse soil conditions and cropping patterns. At phylum level, Proteobacteria, Gemmatimonadetes, and Verrucomicrobia predominated, with their relative abundance experiencing substantial changes under salt stress. SIS facilitated the enrichment of specific genera (Rhodanobacter), which were associated with soil health and stress tolerance. Additionally, the responses of rare microbial taxa to salt stress and intercropping varied, with specific rare microbial taxa (Rhizopus) exhibiting relative abundance under salt stress. Correlation analysis of metabolites and microbial taxa revealed that certain carbohydrates were significantly positively correlated with specific microbial phyla (Cyanobacteria and Nitrospirae) while demonstrating a significant negative correlation with Planctomycetota and Bacteroidota. These correlations indicate that sorghum intercropped with peanuts can promote the enrichment of microbial taxa under salt stress, thereby enhancing soil metabolic functions and stress tolerance by optimizing the rhizosphere microbial community. This study reveals the mechanism through which sorghum-peanut intercropping under salt stress influences the composition of sorghum's rhizosphere microbial community by modulating soil sugar metabolism pathways. This finding provides a new perspective on sustainable agricultural practices in saline soils and emphasizes the pivotal role of plant-metabolite-microbe interactions in abiotic stress mitigation.

Progressing towards eco-friendly agricultural management: Utilizing Ginkgo biloba leaf litter for potato common scab control

Soil ecological degradation intensifies soil-borne crop diseases. Employing eco-friendly and economical strategies to restore soil health is imperative for managing soil diseases. Here, we focused on potato common scab (PCS), a worldwide soil-borne disease caused by Streptomyces spp., and evaluated the suppression effects of Ginkgo leaf litter (GL) and its extract (GE), while elucidating their mechanisms. The results showed that both GL and GE significantly reduced the PCS disease index, with GL achieving over 50 % suppression in both pot and field trials. Both treatments effectively antagonized the PCS pathogen, reducing its relative abundance in bulk soil and geocaulosphere soil. The soil bacterial community was significantly correlated with the disease index, with the bacterial community in bulk soil making a particularly notable contribution to disease suppression, accounting for 52 % of the effect. Furthermore, GL and GE enhanced the stochastic processes in bacterial community assembly, and increased the complexity of bacterial co-occurrence networks. Notably, the microbial community restructured by GE significantly inhibited the expression of the pathogen's toxin gene, txtAB, decreasing its level from 104.5 copies per gram of soil to 102.1 copies, marking a decline exceeding two orders of magnitude. ASV339 (Aeromicrobium) and ASV932 (Achromobacter) were identified as key microbes, and their respective strains, Aeromicrobium OH2-5 and Achromobacter YD1-3, were isolated. The growth curve and biomass of these strains were positively influenced by GE, demonstrating Ginkgo leaves' enriching effect on beneficial microorganisms. These strains exhibited potent antagonistic activity against the PCS pathogen. Additionally, GE alleviated reactive oxygen species stress and up-regulated the defense-related gene PR1 in potato plants. This study validates the potential of Ginkgo leaf litter as a soil amendment additive for suppressing PCS and reveals its multifaceted mechanisms.

Arbuscular mycorrhizal fungi build a bridge for soybeans to recruit Pseudomonas putida

The assembly of the rhizosphere microbiome determines its functionality for plant fitness. Although the interactions between arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) play important roles in plant growth and disease resistance, research on the division of labor among the members of the symbionts formed among plants, AMF, and PGPR, as well as the flow of carbon sources, is still insufficient. To address the above questions, we used soybean (Glycine max), Funneliformis mosseae, and Pseudomonas putida KT2440 as research subjects to establish rhizobiont interactions and to elucidate the signal exchange and division of labor among these components. Funneliformis mosseae can attract P. putida KT2440 by secreting cysteine as a signaling molecule and can promote the colonization of P. putida KT2440 in the soybean rhizosphere. Colonized P. putida KT2440 can stimulate the l-tryptophan secretion of the host plant and can lead to the upregulation of genes involved in converting methyl-indole-3-acetic acid (Me-IAA) into IAA in response to l-tryptophan stimulation. Collectively, we decipher the tripartite mechanism of rhizosphere microbial community assembly via cross-kingdom interactions.

Biofertilizer Industry and Research Developments in China: A Mini-Review

Reliance on chemical fertilizers has significantly boosted food production in China, but it has also led to soil degradation, environmental pollution, and greenhouse gas emissions. To address these pressing issues, the Chinese government has launched various initiatives to reduce chemical fertilizer consumption and promote biofertilizers as effective alternatives to enhance soil fertility and mitigate environmental pollution. Biofertilizers promote crop growth by providing or activating essential nutrients, suppressing plant pathogens, improving soil health, and increasing resilience to abiotic stresses. The growing adoption of biofertilizers in China is reflected in the registration of more than 10,000 products, an annual production exceeding 35 million tons, and a market value of over US$5.5 billion, indicating a significant shift towards sustainable agricultural practices. Despite this progress, challenges such as the dominance of nitrogen fertilizers, inconsistent product performance, and the need for cultivar-specific microbial inoculants remain. Foundational research on the microbial genera utilised in biofertilizers, including nitrogen-fixing genera Rhizobium, Paenibacillus, and Pseudomonas, the widely used genus, Bacillus and Trichoderma, as well as multipurpose synthetic communities, is essential for overcoming these obstacles and enhancing the efficacy of biofertilizers. This review delves into the historical development of the biofertilizer industry and recent advancements in fundamental research on biofertilizers in China, highlighting the essential role of biofertilizers in promoting green agricultural development.

Intercropping of non-leguminous crops improves soil biochemistry and crop productivity: a meta-analysis

Plant species-rich systems tend to be more productive than depauperate ones. In agroecosystems, increasing crop plant diversity by including legumes often increases soil nitrogen (N) and improves soil fertility; however, such generality in outcomes of non-leguminous crop mixture is unknown. Here, through a meta-analysis of 174 individual cases, we explored the current global research trend of intercropping of exclusively non-leguminous crops (ICnl) and quantified its effect on agroecosystem productivity key metrics, for example crop plant health, soil chemistry, and microbial community under diverse experimental conditions. ICnl increased plant biomass and disease suppression and provided a notable yield advantage over monocultures. In addition to phosphorus and potassium, ICnl also increased plant-available soil N, which, along with increased soil microbial abundance, was positively associated with increased soil organic matter. These positive effects were more pronounced in experiments with long duration (> 1 yr), field soil conditions, and soil pH > 7. ICnl improves several crop productivity metrics, which could augment sustainable crop production, particularly when practiced for a long duration and in alkaline soils.

Chitooligosaccharide enhances plant resistance to P. nicotianae via sugar homeostasis and microorganism assembly

Phytophthora nicotianae is a highly destructive soil-borne plant pathogen that leads to significant economic losses in agriculture. Chitooligosaccharides (COS) are popular biostimulant which can promote plant growth and responses to biotic and abiotic stresses. However, the role of COS in resisting the black-shank disease (BSD, caused by P. nicotianae) through regulating plant root exudates and rhizosphere microecology remains unclear. An integrative analysis, based on the transcriptome analysis, root exudate metabolome, and biochemical tests, revealed the secretion of more sugar-related differential metabolites and differential gene expressions expressed under COS treatment during the disease resistance response. Furthermore, increased accumulation of trehalose and trehalose 6-phosphate as well as increased activity of trehalose 6-phosphate synthase was observed under COS treatment after inoculation with P. nicotianae. Additionally, sucrose and glucose, which positively regulate resistance to plant diseases, also exhibited elevated levels. Beneficial microorganisms, such as Bacillus were enriched in the rhizosphere soil during COS treatment. The isolated Bacillus velezensis T-2 strain exerted inhibitory activity on P. nicotianae, which was enhanced by the presence of trehalose. This multi-omics study of transcriptome, metabolome, and microbiomics revealed that COS enhances resistance to tobacco BSD by regulating sugar homeostasis and recruiting beneficial microorganisms.

The composite microbial agent controls tomato bacterial wilt by colonizing the root surface and regulating the rhizosphere soil microbial community

Introduction

Bacterial wilt caused by Ralstonia solanacearum seriously affects the healthy growth of tomato seedlings. Biocontrol microbes have been used to manage tomato bacterial wilt. Herein, we aim to investigate the behavior of the Enterobacter hormaechei Rs-5 and Bacillus subtilis SL-44 composite microbial agent (EB) in the rhizosphere soil, and assess its impact on both the soil microbial community and tomato plant growth in this study.

Methods

The plate confrontation experiment and the pot experiment were respectively used to explore the control ability of EB against Ralstonia solanacearum and bacterial wilt disease. The absolute quantitative PCR (AQ-PCR) was employed to investigate the migration ability of EB in the rhizosphere of tomatoes, and the chemotactic response of EB to tomato root exudates was analyzed by the swimming plate method. Scanning electron microscopy was utilized to study the biofilm formation of EB during its colonization on the root surface of tomatoes. Finally, high-throughput sequencing was adopted to analyze the impact of EB on the microbial community in the rhizosphere soil of tomatoes after being infected by Ralstonia solanacearum.

Results

The absolute quantitative PCR and scanning electron microscope showed that the EB could migrate and efficiently colonize the elongation zone of tomato roots to form a biofilm. In addition, the EB exhibits a chemotactic response to tomato root exudates like sucrose, leucine, glutamic acid, and aspartic acid. The pot experiment demonstrated that the EB can reduce the incidence of tomato bacterial wilt from 77.78% to 22.22%, and significantly increase the biomass, physicochemical properties, and rhizosphere soil nutrient contents of tomato seedlings. Besides, the relative abundance of beneficial bacteria such as Massilia, Pseudomonas, Bacillus, and Enterobacter increased, and the fungi community diversity was improved.

Conclusion

Overall, the EB can reduce the amount of Ralstonia solanacearum in rhizosphere soil, and then control tomato bacterial wilt directly. Besides, the EB can migrate to the root under the induction of tomato root exudates and colonize on the root surface efficiently, thereby indirectly regulating the soil microbial community structure and controlling tomato bacterial wilt.

Comparative analysis of the soil microbiome and carbohydrate content of Anthoxanthum nitens (Sweetgrass) and other Poaceae grass tissues and associated soils

Sweetgrass (Anthoxanthum nitens) is a culturally and environmentally significant perennial grass to many Indigenous Peoples; however, little is known about the potential of Sweetgrass as a contributor to soil health, biodiversity, and climate adaptation. Here, a team of transdisciplinary experts from academia, a non-governmental organization, and a First Nation community collaborated to investigate the structural composition of the rhizomes, stems, and leaves of greenhouse-grown Sweetgrass in comparison to other Poaceae grass members found in a nearby field. The data shows that the monosaccharide composition of A. nitens was evenly distributed throughout the three tissues, and that cellulose was the predominant polysaccharide followed by glucuronoararbinoxylans. There were lesser amounts of xyloglucans, mixed-linkage glucans, homogalacturonans, and rhamnogalacturonans as the hemicellulosic and pectic polysaccharides, respectively. The carbohydrate composition seen in A. nitens was consistent with the other Poaceae grasses evaluated in this study, with the exception of Setaria chondrachne, which contained elevated pectin levels in its stems and leaves. Additionally, the analysis of the carbohydrate content within the soil samples revealed a higher abundance of carbohydrates within greenhouse soil when compared to field soil samples, with significantly more mannose, galactose, and galacturonic acid. Further, there were structural differences in the microbial communities across sampling sites, including a significant increase in the abundance of Bacillus spp. in the greenhouse soil. Overall, this study provides the glycome and associated soil microbial community baseline for greenhouse-grown Sweetgrass.

Root exudates in controlled environment agriculture: composition, function, and future directions

Two decades of research has revealed an intricate network of root exudates in plants, which they use to interact with and mediate their surrounding environment, the rhizosphere. Prior research has been conducted mainly on model plants such as Arabidopsis or staple monoculture crops like maize, soybean, and rice, revealing crucial roles in plant growth, microbiota interaction, nutrient acquisition, and bioremediation. However, similar research has only begun to be conducted in Controlled Environment Agriculture (CEA) systems, leaving a considerable knowledge gap in the mechanisms, impacts, and uses of exudates in CEA. Exhaustive literature searches revealed less than two dozen articles with direct implications in CEA vegetable crop exudates. This review synthesizes the existing literature to examine the composition, functions, and influences of vegetable root exudates within CEA systems. The first section explores key compounds -including amino and organic acids, and sugars- along with mechanistic processes, and microbial interactions. The second section compares root exudates in soil-based versus hydroponic CEA systems based upon differences in substrate, (a)biotic stressors, microorganisms, and nutrient availability. By contrasting existing literature on both CEA soil-based and hydroponic systems, the section examines likely differences in exudate composition, mechanisms, and functions. The final section presents case studies from both hydroponic and soil based systems, highlighting how root exudates contribute to environmental stress mitigation, allelopathy, disease response, bio/phytoremediation, and pest control. It reveals major avenues for the use of exudates in CEA systems worldwide. Lastly, we ponder the future avenues of exploration for CEA root exudates, proposing the creation of a database for usage in smaller or organic farms and in urban agriculture settings. In conjunction, we emphasize the need for further investigation into the potential of exogenous applications of exudate-like compounds to positively impact yield, disease resistance, soil restoration, and land reclamation, especially in the context of climate change.

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.

Integrating 'cry for help' strategies for sustainable agriculture

Plants recruit specific soil microbes through a sophisticated 'cry for help' strategy to mitigate environmental stresses. Recent advances highlight the potential of leveraging this mechanism to develop microbe-based approaches for enhancing crop health, but challenges remain in refining the criteria and conceptual frameworks to effectively investigate and harness these plant-microbe interactions.

Enriched Flavonoid Compounds Confer Enhanced Resistance to Fusarium-Induced Root Rot in Oil Tea Plants

Root rot in Camellia oleifera complicates the development of targeted control measures owing to its complex aetiology. Although breeding resistant varieties of C. oleifera presents a promising solution, research into cultivation strategies and potential resistance mechanisms against root rot remains limited. In this study, we investigated six cultivars of C. oleifera that exhibit varying levels of resistance to root rot. We conducted transcriptome analysis, measurements of soil physicochemical properties and an analysis of the fungal microbiome to explore the relationship between Fusarium-induced root rot and flavonoid compounds in the rhizosphere. The resistant cultivar CL18 demonstrated superior performance concerning root rot incidence, root health status and the expression levels of genes associated with flavonoid biosynthesis in this study. Significant differences were observed in the composition and diversity of rhizosphere fungal communities among the various cultivars of C. oleifera. The abundance of Fusarium in the rhizosphere soil of CL18 was low, and a negative correlation was identified between the flavonoid content in the soil and the abundance of Fusarium. Our study uncovers the role of flavonoids in the resistance of C. oleifera to root rot, thereby offering new strategies for disease management and the breeding of resistant cultivars.

Neotrinia splendens (Liliopsida: Poaceae) Growth Influences Spatial Distribution of Soil Bacterial Community in a Degraded Temperate Grassland

Neotrinia splendens is widely distributed and is the dominant plant species of temperate degraded grassland in Inner Mongolia, showing a community growing habit forming a ring of individuals. However, there is a lack of attention to the soil microbial communities inside the ring (IN), outside the ring, and under the N. splendens ring (UN). This study investigated the soil bacterial community composition in three different zones of the N. splendens ring using amplicon sequencing technology, as well as soil environmental variables. The soil physicochemical properties, the composition of soil bacterial community, and the soil bacterial α-diversity varied significantly among the three zones. Especially, the growth of N. splendens promotes the soil bacterial diversity in the UN zone due to the interactions between plant and soil microbes. Soil NO3--N, TC, TN, and pH are the key factors causing the variations of soil bacterial community composition and bacterial diversity. Proteobacteria and Actinobacteria phyla of microorganisms accounted for the largest proportion in network analysis among the three zones. Overall, attention should be paid not only to the improvement of grassland vegetation and soil quality but also to the change in soil microorganisms during the formation and expansion of the N. splendens ring in the future.

A Simplified and Integrated View of Disease Control in Varietal Mixtures Using the Phytobiome Framework

Increasing intraspecific diversity within crop systems is a promising strategy to manage aerial diseases, particularly those caused by fungal aerial pathogens. This review examines how cultivar mixtures reduce disease incidence and severity using the phytobiome framework, identifying three major types of processes: (1) physical ones, which alter disease dynamics through dilution effects, barrier effects, and microclimate modifications; (2) processes that are mediated by microbial interactions, which influence disease severity via induced resistance and indirect plant-plant interactions mediated by the microbiome; and (3) processes involving direct plant-plant interactions, where danger signaling and signaling from healthy neighbors modulate plant physiology and immunity through resource management and molecular cues. This review provides a comprehensive understanding of how cultivar mixtures enhance disease resistance and emphasizes that direct plant-plant interactions are likely stronger contributors than so far considered. It highlights the need for further research into the roles of microbiomes and direct plant-plant interactions to optimize mixtures' performance.

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.

Root separation modulates AMF diversity and composition in tomato-potato onion intercropping systems

Plant-plant interactions shape arbuscular mycorrhizal fungi (AMF) communities in rhizosphere soil, with tomato/potato-onion intercropping emerging as a promising agro-ecological strategy to optimize resource utilization. However, the role of root separation methods in modulating AMF diversity within intercropping systems remains unclear. Specifically, whether the AMF community in the rhizosphere of tomato and potato-onion intercropping differs from monoculture and how root separation methods modulate these effects. This study evaluates the effects of various root separation methods (no separation, 0.45 μm nylon membrane, 38 μm nylon membrane, and solid separation) on AMF diversity and composition in tomato/potato-onion intercropping and monoculture systems. High-throughput Illumina MiSeq sequencing was used to assess AMF diversity indices (Ace, Chao1, Shannon, and Simpson), and Principal Coordinate Analysis evaluated community structure. Results showed that the non-separation mode achieved the highest Ace and Chao1 indices, indicating greater richness, while intercropping lowered Shannon and Simpson indices. Intercropping significantly reduced Glomerales but increased Paraglomerales, under the non-separation mode. Similarly, it decreased Glomus while increasing Paraglomus in the rhizosphere of both crops. Principal Coordinate Analysis revealed that root separation distinctly altered AMF community structure, reflecting specific barrier effects on AMF interactions. Intercropping increased AMF abundance in the tomato rhizosphere but reduced it in potato-onion as shown by 18S rRNA gene abundance. These findings emphasize that minimizing root separation in intercropping enhances AMF diversity and functionality, providing valuable insights for sustainable agricultural management. Understanding the role of root interactions in shaping AMF communities can help optimizing intercropping strategies to improve soil health and nutrient dynamics.

Root exudates and microbial metabolites: signals and nutrients in plant-microbe interactions

Plant roots meticulously select and attract particular microbial taxa from the surrounding bulk soil, thereby establishing a specialized and functionally diverse microbial community within the rhizosphere. Rhizosphere metabolites, including root exudates and microbial metabolites, function as both signals and nutrients that govern the assembly of the rhizosphere microbiome, playing crucial roles in mediating communications between plants and microbes. The environment and their feedback loops further influence these intricate interactions. However, whether and how specific metabolites shape plant-microbe interactions and facilitate diverse functions remains obscure. This review summarizes the current progress in plant-microbe communications mediated by chemical compounds and their functions in plant fitness and ecosystem functioning. Additionally, we raise some prospects on future directions for manipulating metabolite-mediated plant-microbe interactions to enhance crop productivity and health. Unveiling the biological roles of specific metabolites produced by plants and microbes will bridge the gap between fundamental research and practical applications.

Substrate preference triggers metabolic patterns of indigenous microbiome during initial composting stages

Composting organic waste is a sustainable recycling method in agricultural systems, yet the microbial preferences for different substrates and their influence on composting efficiency remain underexplored. Here, 210 datasets of published 16S ribosomal DNA amplicon sequences from straw and manure composts worldwide were analyzed, and a database of 278 bacterial isolates was compiled. Substrate-driven microbiome variations were most prominent during the initial composting stages. Indigenous synthetic communities exhibit substrate-specific adaptations, increasing compost temperatures by 2 %-10 %, microbial abundance by 44 %-233 %, and microbial activity by 26 %-60 %. Key dissolved substrates, such as choline and succinic acid in straw compost, and phloretin and uric acid in manure compost, drive these microbial preferences. These findings highlight how substrate-specific microbiomes can be engineered to enhance microbial activity, accelerate temperature rise, and extend the thermophilic phase, providing a targeted framework to improve composting efficiency and tailor strategies to different organic waste types.

Root exudate-mediated assemblage of rhizo-microbiome enhances Fusarium wilt suppression in chrysanthemum

Intercropping is emerging as a sustainable strategy to manage soil-borne diseases, yet the underlying mechanisms remain largely elusive. Here, we investigated how intercropping chrysanthemum (Chrysanthemum morifolium) with ginger (Zingiber officinale) suppressed Fusarium wilt and influenced the associated rhizo-microbiome. Chrysanthemum plants in intercropping systems exhibited a marked reduction in wilt severity and greater biomass compared to those grown in monoculture. In contrast, soil sterilization intensified wilt severity and abrogated the benefits of intercropping, highlighting the critical role of soil microbiota. 16S rRNA gene amplicon analysis revealed that intercropping significantly changed the composition and structure of rhizo-bacterial communities, particularly enriching Burkholderia species, which were closely associated with plant growth and disease resistance. Further investigation demonstrated that ginger root exudates, including sinapyl alcohol and 6-gingerol, greatly promoted the proliferation and colonization of Burkholderia sp. in chrysanthemum rhizosphere, conferring the enhanced disease suppression. Metabolomic profiling revealed that ginger root exudates stimulated the release of specific metabolites by chrysanthemum roots, which promoted the growth and biofilm formation of Burkholderia sp. Our findings uncovered the mechanism by which intercropping chrysanthemum with ginger plants modulated the rhizo-microbiome and thereby resulted in the enhanced disease suppression, offering insights into optimizing plant-microbe interactions for improving crop health and productivity.

Decomposition solutions from brassica and cereal residues suppress tomato bacterial wilt disease by regulating rhizosphere microbial communities

Cover crops can suppress the following crop diseases and alter soil microbial communities, but the mechanisms of such disease suppressive effects remain uncertain. Here, we studied the effects of brassica and cereal cover crops, along with decomposition solutions from these crop residues, on tomato growth and bacterial wilt. Moreover, tomato rhizosphere microorganisms were analyzed by qPCR and high-throughput sequencing. Rhizosphere transplant experiment was conducted to validate the disease suppressive potential of rhizosphere microorganisms mediated by decomposition solutions from these crop residues. Our findings revealed that brassica and cereal cover crops especially wheat, pakchoi and rape significantly enhanced tomato growth and inhibited bacterial wilt disease. Decomposition solutions from brassica and cereal residues had inhibitory effects on Ralstonia solanacearum and this disease. Moreover, such decomposition solutions can differently alter the abundances, compositions and diversities of tomato rhizosphere bacterial and fungal communities. Notably, decomposition solutions from wheat, pakchoi and rape residues increased the inverse Simpson diversity and the abundances of Bacillus spp. community. In addition, decomposition solutions from wheat and pakchoi residues significantly increased bacterial beta diversity, and decomposition solutions from rape residue significantly increased fungal beta diversity. Rhizosphere transplant experiment confirmed that the rhizosphere microbial changes induced by decomposition solutions contributed to the suppressiveness of tomato bacterial wilt disease. These suppressive effects were stronger in decomposition solutions from wheat, pakchoi and rape residues than those from oilseed rape, wild rocket and Indian mustard residues. Overall, our results demonstrated that decomposition solutions from brassica and cereal residues enhance disease suppression by shaping a beneficial rhizosphere microbiota, providing a promising strategy for sustainable management of bacterial wilt in tomato cultivation.

Small molecule metabolites drive plant rhizosphere microbial community assembly patterns

The assembly of rhizosphere microbial communities is essential for maintaining plant health, yet it is influenced by a wide range of biotic and abiotic factors. The key drivers shaping the composition of these communities, however, remain poorly understood. In this study, we analyzed 108 plant samples and evaluated root traits, plant growth characteristics, soil enzyme activities, rhizosphere metabolites, and soil chemical properties to identify the primary determinants of rhizosphere community assembly. Across 36 soil samples, we obtained 969,634 high-quality sequences, clustering into 6,284 ASVs predominantly classified into Proteobacteria (57.99%), Actinobacteria (30%), and Bacteroidetes (5.13%). Our findings revealed that rhizosphere metabolites accounted for more variance in microbial community composition compared to chemical properties (ANOVA, F = 1.53, p = 0.04), enzyme activities, or root traits (ANOVA, F = 1.04, p = 0.001). Seven small molecule metabolites, including glycerol, sorbitol, phytol, and alpha-ketoglutaric acid, were significantly correlated with βNTI, underscoring their role as critical drivers of microbial community assembly. The genus Rhizobium, significantly associated with βNTI (R = 0.25, p = 0.009), emerged as a keystone taxon shaping community structure. Soil culture experiments further validated that small molecule metabolites can modulate microbial community assembly. The ST treatment, enriched with these metabolites, produced 1,032,205 high-quality sequences and exhibited significant shifts in community composition (Adonis, p = 0.001, R = 0.463), with Rhizobium showing higher abundance compared to the control (CK). Variable selection (βNTI >2) drove phylogenetic turnover in ST, while stochastic processes (|βNTI| < 2) dominated in CK. This study provides quantitative insights into the role of rhizosphere metabolites in shaping microbial community assembly and highlights their potential for targeted modulation of rhizosphere microbiomes.

Composition and Biodiversity of Culturable Endophytic Fungi in the Roots of Alpine Medicinal Plants in Xinjiang, China

(1) Background: Endophytic fungi play an important role in plant growth and stress resistance. The presence of a special fungal taxon such as the dark septate endophytic (DSE) fungi in alpine environments is particularly important for plant resistance to environmental stresses. However, the composition of root endophytic fungi in different environments and between different host plants has not been well studied. (2) Results: A total of 408 culturable endophytic fungi were isolated from the roots of Saussurea involucrata and Rhodiola crenulata which were collected in 5 plots from the Tianshan and Karakoram Mountains of the Xinjiang region, belonging to 91 species, 54 genera, 31 families, and 3 phyla based on the morphological characteristics and molecular sequence. Among them, DSE fungi were the dominant group, accounting for 52.94%, and Leptodontidium orchidicola was the dominant species. In addition, we also compared the composition and diversity of root endophytic fungi from different plants and different sites, with emphasis on special fungal taxa such as DSE. (3) Conclusions: The composition and diversity of cultural endophytic fungi are significantly different in the two alpine medicinal plant species and across various locations. Some fungi showed the preferences of the host or environment. The endophytic fungal resources, especially DSE, were very rich in the two alpine medicinal plants, indicating that these fungi may play a crucial role in the ecological adaptation of host plants in harsh environments.

Plant interaction modifies effects of soil heterogeneity on seed germination, plant growth, and biomass of plant communities

Soil heterogeneity significantly impacts the structure and function of plant communities. However, most of the previous studies only focussed on the effects of soil heterogeneity on plant populations, while the joint effects of plant interaction and soil heterogeneity on plant communities remain unclear. Thus, a manipulation experiment was done to explore the effects of soil heterogeneity and species combination on the seed germination, plant height and plant biomass, where three soil heterogeneity levels were created by varying patch sizes (small, medium, and large), and 10 species combinations were generated by growing four typical forages on the Qinghai-Tibetan Plateau (Elymus nutans, Festuca sinensis, Poa pratensis, and Vicia unijuga) either in monocultures or in mixtures. Data were analysed at three scales (at the pot scale, at the monoculture, and at the mixture scale). Results showed that with decreasing patch size, (i) at the pot scale, the seed germination and plant height in both monocultures and mixtures decreased, while the plant biomass in mixtures first decreased and then increased, and the plant biomass in monocultures decreased; and (ii) at the monoculture scale and the mixture scale, the plant height of E. nutans in the monoculture first decreased and then increased, while the plant height of the other monocultures decreased. Furthermore, the plant biomass of E. nutans in the monoculture first decreased and then increased, while the plant biomass of the rest species combination decreased. This study provides insight into the future restoration of degraded grassland in alpine meadows and the healthy management of artificial grasslands.

The responses of root exudates and microbiome in the rhizosphere of main plant and aromatic intercrops to soil Cr stress

Soil chromium (Cr) stress has a well-recognized negative impact on plant growth, and intercropping is a commonly used method to mitigate heavy metal toxicity to main plants. However, the responses of root exudates-microbial and their interactions among soil zones to soil Cr stress are always in need of clarification in intercropping system. In this study, three intercropping patterns (CT, Malus only; TM, Malus × Mentha and TA, Malus × Ageratum) with different soil Cr addition levels (NCR, LCR, HCR) were applied, and the rhizosphere ecological traits in the main plant (FRS) and intercrop (ARS) were investigated. The results indicate that intercropping with either Mentha or Ageratum has a positive effect on main plants response to soil Cr stress, and intercropping with Ageratum showing a more significant effect. Importantly, we found that the rhizosphere of main plant tends to alleviate stress by accumulating organic acids and amino acids, while aromatic plants exhibit a broader accumulation of metabolites. Additionally, we identified five core differential microbial genera. Our findings provide novel insights into intercrop Cr detoxification in the main plant.

Intercropping improves the yield by increasing nutrient metabolism capacity and crucial microbial abundance in root of Camellia oleifera in purple soil

Intercropping system influences the endophytic microbial abundance, hormone balance, nutrient metabolism and yield, but the molecular mechanism of yield advantage in Camellia oleifera intercropping with peanut is not clear. In this study, the C. oleifera monoculture (CK) and C. oleifera-peanut intercropping (CP) treatments in purple soil were conducted, and the physicochemical properties, gene expressions, signal pathways and crucial microbial abundances were investigated to reveal the molecular mechanism of the yield advantage of intercropped C. oleifera. The results showed that the intercropping system increased in contents of pigment, carbohydrate, available nitrogen and phosphorus in leaf and root, as well as the abundances of Burkholderia, Ralstonia, Delftia, Pseudoalteromonas and Caulobacter, enhanced the relative expression levels of CoSPS, CoGBE, CoGlgP, CoGBSS/GlgA genes to promote sugar metabolism, decreased the relative expression levels of CoASA, CoTSB, CoPAI, CoTDC and CoCYP71A13 genes for inhibiting IAA biosynthesis and signal transduction, as well as microbial diversity, Fusarium, Albifimbria and Coniosporium abundances in root, ultimately improved the fruit yield of C. oleifera. These findings indicate that intercropping system improves the fruit yield by enhancing the nutrient metabolism capability and crucial microbial abundances in root of C. oleifera in purple soil.

Pepper root exudate alleviates cucumber root-knot nematode infection by recruiting a rhizobacterium

Root-knot nematodes (Meloidogyne spp.) have garnered significant attention from researchers owing to the substantial damage they cause to crops and their worldwide distribution. However, controlling these nematodes is challenging because a limited number of chemical pesticides and biocontrol agents are effective against them. Here, we demonstrate that pepper rotation markedly reduces Meloidogyne incognita infection in cucumber and diminishes the presence of p-hydroxybenzoic acid in the soil, a compound known to exacerbate M. incognita infection. Pepper rotation also restructures the rhizobacterial community, leading to the colonization of the cucumber rhizosphere by two Pseudarthrobacter oxydans strains (RH60 and RH97), facilitated by enrichment of palmitic acid in pepper root exudates. Both strains exhibit high nematocidal activity against M. incognita and have the ability to biosynthesize indoleacetic acid and biodegrade p-hydroxybenzoic acid. RH60 and RH97 also induce systemic resistance in cucumber plants and promote their growth. These data suggest that the pepper root exudate palmitic acid alleviates M. incognita infection by recruiting beneficial P. oxydans to the cucumber rhizosphere. Our analyses identify a novel chemical component in root exudates and reveal its pivotal role in crop rotation for disease control, providing intriguing insights into the keystone function of root exudates in plant protection against root-knot nematode infection.

Responses of fungal communities at different soil depths to grazing intensity in a desert steppe

Grazing can alter the physicochemical properties of soil and quickly influence the composition of microbial communities. However, the effects of grazing intensity on fungal community composition in different soil depth remain unclear. On the Inner Mongolia Plateau, we studied the effects of grazing intensity treatments including no grazing (NG), light grazing (LG), moderate grazing (MG), heavy grazing (HG), and over grazing (OG) on the physicochemical properties and fungal community composition of surface (0-20 cm) and subsurface (20-40 cm) soil layers. The α-diversity of fungi in subsurface soil decreased under the influence of grazing. The relative abundance of Ascomycota in the subsoil was higher than that in the topsoil, while the situation of Basidiomycota was the opposite. This was caused by the differences in the soil carbon (C) environment for the growth of oligotrophic and copiotrophic fungi. In the subsoil, grazing affected nutrient contents such as soil organic matter (SOM) and total nitrogen (TN), resulting in significantly lower relative abundance of Ortierellomycota under LG, HG, and OG than in the NG. HG showed much higher relative abundance of Glomeromycota. Results of a multiple regression tree (MRT) analysis revealed that TN and nitrate nitrogen affected the fungal α-diversity in top- and subsoils, respectively; the main driving factor regulating fungal community changes was soil water content (SWC) in the topsoil, while it was ammonium nitrogen and nitrate nitrogen in the subsoil. The results of our study indicate that grazing changes the soil environment by changing TN, SWC, nitrate nitrogen, ammonium nitrogen, and affects the diversity and community structure of soil fungi. This provides empirical support for coping with the impact of grazing on soil microbiomes in desert steppes.

Identification of stress-alleviating strains from the core drought-responsive microbiome of Arabidopsis ecotypes

Plant genetic and metabolic cues are involved in assembling their "core microbiome" under normal growth conditions. However, whether there is a core "stress responsive microbiome" among natural plant ecotypes remains elusive. Drought is the most significant abiotic stress worldwide. Characterizing conserved core root microbiome changes upon drought stress has the potential to increase plant resistance and resilience in agriculture. We screened the drought tolerance of 130 worldwide Arabidopsis ecotypes and chose the extremely drought tolerant and sensitive ecotypes for comparative microbiome studies. We detected diverse shared differentially abundant ASVs, network driver taxa among ecotypes, suggesting the existence of core drought-responsive microbiome changes. We previously identified 1479 microorganisms through high-throughput culturing, and successfully matched diverse core drought responsive ASVs. Our phenotypic assays validated that only those core drought responsive ASVs with higher fold changes in drought tolerant ecotypes were more likely to protect plants from stress. Transcriptome analysis confirmed that a keystone strain, Massilia sp. 22G3, can broadly reshape osmotic stress responses in roots, such as enhancing the expression of water up-taking, ROS scavenging, and immune genes. Our work reveals the existence of a core drought-responsive microbiome and demonstrates its potential role in enhancing plant stress tolerance. This approach helps characterize keystone "core drought responsive" microbes, and we further provided potential mechanisms underlying Massilia sp. 22G3 mediated stress protection. This work also provided a research paradigm for guiding the discovery of core stress-alleviating microbiomes in crops using natural ecotypes (cultivars).

Intercropping with Robinia pseudoacacia reduces soft rot incidence in konjac by modulating the root bacterial community

BACKGROUND

Soft rot (Pectobacterium aroidearum and Dickeya) is a devastating soil-borne bacterial disease that threatens konjac production. Intercropping with false acacia has been shown to significantly reduce soft rot incidence in konjac by shifting the microbial community. However, how intercropping shapes the root bacterial community and affects soft rot incidence remains unclear. To address this, we investigated three konjac intercropping systems (false acacia, paulownia, and maize) to explore the relationships among intercropping, soft rot incidence, root bacterial community, soil enzyme activity, and soil properties.

RESULTS

Konjac intercropped with false acacia exhibited the lowest soft rot incidence and the lowest abundance of pathogenic taxa. Soft rot incidence was negatively correlated with total soil nitrogen and potassium but positively correlated with total and available soil phosphorus. The bacterial community structure and function in konjac roots differed among intercropping types, mainly driven by available soil phosphorus. Beneficial microorganisms such as Bradyrhizobium and Variovorax were enriched under a false acacia intercropping system and were negatively correlated with soil-available phosphorus. Additionally, the stable bacterial community in healthy konjac roots under false acacia may make konjac less susceptible to pathogen invasion.

CONCLUSION

The study showed that intercropping reduced the soft rot incidence by regulating the structure and stability of the konjac root bacterial community, and soil-available phosphorus was the main factor affecting the difference in the konjac root bacterial community, which provided a basis for the management of soil fertilization in konjac cultivation. © 2024 Society of Chemical Industry.

Paenibacillus polymyxa J2-4 induces cucumber to enrich rhizospheric Pseudomonas and contributes to Meloidogyne incognita management under field conditions

BACKGROUND

Root knot nematodes (RKNs) pose a great threat to agricultural production worldwide. The bacterial nematocides have received increasing attention due to their safe and efficient control against RKNs. Here, we investigated the biocontrol efficacy of Paenibacillus polymyxa J2-4 against Meloidogyne incognita in the field and analyzed the rhizosphere microbiome of cucumber under nematode infection after application of the J2-4 strain. Furthermore, a biomarker strain of Pseudomonas spp. was isolated from the J2-4-inoculated rhizosphere soil, and its nematocidal activity and growth-promoting effect on host plants were determined. In addition, chemotaxis assay of P. fluroescens ZJ5 toward root exudates was carried out.

RESULTS

The field experiment demonstrated that P. polymyxa J2-4 could effectively suppressed gall formation in cucumber plants, with the galling index reduced by 67.63% in 2022 and 65.50% in 2023, respectively, compared with controls. Meanwhile, plant height and yield were significantly increased in J2-4 treated plants compared with controls. Metagenomic analysis indicated that J2-4 altered the rhizosphere microbial communities. The relative abundance of Pseudomonas spp. was notably enhanced in the J2-4 group, which was consistent with Linear discriminant analysis Effect Size results that Pseudomonas was determined as one of the biomarkers in the J2-4 group. Furthermore, the ZJ5 strain, one of the biomarker Pseudomonas strains, was isolated from the J2-4-inoculated rhizosphere soil and was identified as Pseudomonas fluorescens. In addition, P. fluorescens ZJ5 exhibited high nematicidal activity in vitro and in vivo, with 99.20% of the mortality rate of M. incognita at 24 h and 69.75% of gall index reduction. The biocontrol efficiency of the synthetic community of ZJ5 plus J2-4 was superior to that of any other single bacteria against M. incognita. Additionally, ZJ5 exhibited great chemotaxis ability toward root exudates inoculated with J2-4.

CONCLUSION

Paenibacillus polymyxa J2-4 has good potential in the biological control against M. incognita under field conditions. Enrichment of the beneficial bacteria Pseudomonas fluorescens ZJ5 in the J2-4-inoculated rhizosphere soil contributes to M. incognita management. © 2024 Society of Chemical Industry.

Exploring the link between soil health and crop productivity

Understanding the complex interactions of plants and soils in the face of global food security and environmental degradation challenges is critical to the future of sustainable agriculture. This review discusses the important link between soil health and crop productivity by providing and comprehensive assessment of soil properties and management methods. By examining the physical, chemical, and biological properties of soil, it uncovers the key limitations posed by the soil environment on crop growth. The review highlights how soil texture, nutrient availability, and moisture levels directly impact on root growth, water uptake, and nutrient use efficiencies, while also exploring how diverse cropping systems enhance soil ecology and biodiversity. By utilizing state-of-the-art bioinformatics, we offer an in-depth exploration of rhizosphere microbial communities, emphasizing the functions of phosphate-solubilizing and nitrogen-fixing bacteria in promoting vital nutrient cycles. The potential of using microbial fertilizers to increase crop resistance to disease and stress hold a major premise for future sustainability in agriculture. In this regard, this review highlights the long-term impacts of crop cultivation on soil microbial diversity, revealing intricate selection processes between crops and their microbial partners in shaping crop-soil-microbe interactions. In terms of soil management, practical nutrient management strategies are proposed based on soil testing, emphasizing the benefits of organic farming and conservation tillage for soil health. Modern precision agricultural tools and remote sensing technologies are encouraged to be refined for effective nutrient management. At the policy level, we evaluate international guidelines aimed at fostering agricultural sustainability, suggesting new research pathways for crop-soil dynamics and offering approaches for developing soil health indicators in the face of global environmental challenges.

Phlomoides rotata adapts to low-nitrogen environments by promoting root growth and increasing root organic acid exudate

Nitrogen (N) is one of the three major elements required for plant growth and development. It is of great significance to study the effects of different nitrogen application levels on the growth and root exudates of Phlomoides rotata, and can provide a theoretical basis for its scientific application of fertilizer to increase production. In this study, Phlomoides rotata were grown under different nitrogen conditions for two months. Soil and plant analyzer development (SPAD) values, bioaccumulation, root morphology, root exudate composition, nitrogen metabolism enzyme and antioxidant enzyme activity were evaluated. The results showed that compared with CK (no N fertilizer), N2 (CO(NH2)2 80 mg/kg) and N3 (CO(NH2)2 160 mg/kg) through significantly improved the activities of nitrogen metabolism enzyme nitrite reductase (NiR), glutamate dehydrogenase (GDH) and glutamine synthetase (GS), enhanced the nitrogen metabolism process, and increased the accumulation of plant soluble sugars (SS) and soluble protein (SP), thus improving Phlomoides rotata biomass yield. After 60 days of treatment, low nitrogen (N1, CO(NH2)2 40 mg/kg) increased root length, root volume, root surface area, average root diameter, significantly increased the diversity of organic acids in root exudates, and enhanced the activity of antioxidant enzymes to adapt the nitrogen deficiency environment. This study can provide new ideas for understanding the mechanism of nitrogen tolerance in Phlomoides rotata and developing scientific fertilization management strategies for plateau plants and medicinal plants.

Soil fungal networks exhibit sparser interactions than bacterial networks in diseased banana plantations

Soil microorganisms play a crucial role in suppressing soil-borne diseases. Although the composition of microbial communities in healthy versus diseased soils is somewhat understood, the interplay between microbial interactions and disease incidence remains unclear. This study used 16S rRNA and fungal internal transcribed spacer (ITS) sequencing to investigate the bacterial and fungal community composition in three soil types: forest soil (Z), soil from healthy banana plantations (H), and soil from diseased banana plantations (D). Principal coordinate analysis revealed significant differences among the bacterial and fungal community structures of the three soil types. Compared with those in forest soil, bacterial and fungal diversities significantly decreased in diseased banana soil. Key microorganisms, including the bacteria Chloroflexi and Pseudonocardia and the fungi Mortierellomycota and Moesziomyces, were significantly increased in soil from diseased banana plantations. Redundancy analysis revealed that total nitrogen and available phosphorus were the primary drivers of the soil microbial community structure. The neutral community model posited that the bacterial community assembly in banana plantations is predominantly governed by stochastic processes, whereas the fungal community assembly in banana plantations is primarily driven by deterministic processes. Furthermore, co-occurrence network analysis revealed that the proportion of positive edges in the fungal network of soil from diseased banana plantations was 5.92 times lower than that in soil from healthy banana plantations, and its fungal network structure was sparse and simple. In conclusion, reduced interactions within the fungal network were significantly linked to the epidemiology of Fusarium wilt. These findings underscore the critical role of soil fungal communities in modulating pathogens.

IMPORTANCE

Soil microorganisms are pivotal in mitigating soil-borne diseases. The intricate mechanisms underlying the interactions among microbes and their impact on disease occurrence remain enigmatic. This study underscores that a reduction in fungal network interactions correlates with the incidence of soil-borne Fusarium wilt.

Soybean nodulation shapes the rhizosphere microbiome to increase rapeseed yield

INTRODUCTION

Crop rotation, a crucial agricultural practice that enhances soil health and crop productivity, is widely used in agriculture worldwide. Soybeans play a crucial role in crop rotation owing to their nitrogen-fixing ability, which is facilitated by symbiotic bacteria in their root systems. The soybean-rapeseed rotation is an effective agricultural practice in the Yangtze River Basin of China. However, the mechanism underlying the effectiveness of this system remains unknown.

OBJECTIVES

The aim of this study was to decipher the mechanisms by which previous soybean cultivation enhances the growth of subsequent rapeseed.

METHODS

Soybeans with three distinct nodulation genotypes were rotated with rapeseed, and the impact of previous soybean cultivation on subsequent rapeseed growth was evaluated by examining the soybean root secretome and soil rhizosphere microbiome.

RESULTS

Soybean-rapeseed rotation significantly enhanced subsequent rapeseed growth and yield, especially when supernodulating soybean plants were used, which released the most nitrogen into the soil rhizosphere. The differences in soybean nodulation capability led to variations in root exudation, which in turn influenced the bacterial communities in the rhizosphere. Notably, the supernodulating soybean plants promoted Sphingomonadaceae family of bacteria growth by secreting oleic acid and cis-4-hydroxy-D-proline, and further attracted them through cis-4-hydroxy-D-proline. Furthermore, the exogenous application of Sphingomonadaceae bacteria, either alone or in combination with rhizobia, significantly enhanced the growth of rapeseed.

CONCLUSION

Our data definitively demonstrated the crucial role of previous soybean cultivation in enhancing the yield of rapeseed, with the assistance of Sphingomonadaceae bacteria and rhizobia. This study elucidates the role of soybean nodulation in rhizosphere bacterial dynamics, highlighting its importance in sustainable agricultural practices.

Harnessing biosynthesized selenium nanoparticles for recruitment of beneficial soil microbes to plant roots

Root exudates can benefit plant growth and health by reshaping the rhizosphere microbiome. Whether nanoparticles biosynthesized by rhizosphere microbes play a similar role in plant microbiome manipulation remains enigmatic. Herein, we collect elemental selenium nanoparticles (SeNPs) from selenobacteria associated with maize roots. In vitro and soil assays show that the SeNPs enhanced plant performance by recruiting plant growth-promoting bacteria (e.g., Bacillus) in a dose-dependent manner. Multiomic profilings unravel a cross-kingdom-signaling cascade that mediates efficient biosynthesis of SeNPs by selenobacteria. Specifically, maize roots perceive histamine signaling from Bacillus spp., which stimulates the plant to produce p-coumarate via root exudation. The rpoS gene in selenobacteria (e.g., Pseudomonas sp. ZY71) responds to p-coumarate signaling and positively regulates the biosynthesis of SeNPs. This study demonstrates a novel mechanism for recruiting host-beneficial soil microbes by microbially synthesized nanoparticles and unlocks promising possibilities for plant microbiome manipulation.

The impact of Ricinus straw on tomato growth and soil microbial community

Returning straw can alter the soil microbial community, reduce the occurrence of soilborne diseases, and promote plant growth. In this study, we aimed to evaluate the effects of Ricinus straw on tomato growth and rhizosphere microbial community. We carried out microcosm experiments to investigate the effects of Ricinus straw with different dosages (0, 1, and 3%) on tomato dry biomass and rhizosphere bacterial and fungal communities. The results indicated that the dry biomass of tomato seedlings with 1% addition of Ricinus straw increased by 53.98%. In addition, Ricinus straw also changed the abundance, diversities, and composition of tomato rhizosphere microbial communities. In detail, the addition of 1% Ricinus straw increased the relative abundance of putative beneficial bacteria and fungi in straw decomposition, such as Ramlibacter sp., Azohydromonas sp., Schizothecium sp., and Acaulium sp., and decreased the relative abundance of Fusarium sp. Meanwhile, Ricinus straw inhibited the growth of putative pathogenic microorganisms. The correlation analysis showed that the changes in fungal community operational taxonomic units stimulated by the addition of Ricinus straw may play a crucial positive regulatory role in tomato growth. Finally, the representative fungal strain Fusarium oxysporum f. sp. Lycopersici (FOL), named TF25, was isolated and cultured. We found that Ricinus straw extract inhibited the growth of TF25 in an in vitro experiment with an inhibition rate of 34.95-51.91%. Collectively, Ricinus straw promoted plant growth by changing the rhizosphere microbial community composition and inhibiting FOL growth, which provides new evidence for understanding the improvement of key microorganism composition in improving crop growth and the sustainability of agriculture.

Metagenomic insights into nitrogen cycling functional gene responses to nitrogen fixation and transfer in maize-peanut intercropping

The fixation and transfer of biological nitrogen from peanuts to maize in maize-peanut intercropping systems play a pivotal role in maintaining the soil nutrient balance. However, the mechanisms through which root interactions regulate biological nitrogen fixation and transfer remain unclear. This study employed a 15N isotope labelling method to quantify nitrogen fixation and transfer from peanuts to maize, concurrently elucidating key microorganisms and genera in the nitrogen cycle through metagenomic sequencing. The results revealed that biological nitrogen fixation in peanut was 50 mg and transfer to maize was 230 mg when the roots interacted. Moreover, root interactions significantly increased nitrogen content and the activities of protease, dehydrogenase (DHO) and nitrate reductase in the rhizosphere soil. Metagenomic analyses and structural equation modelling indicated that nrfC and nirA genes played important roles in regulating nitrogen fixation and transfer. Bradyrhizobium was affected by soil nitrogen content and DHO, indirectly influencing the efficiency of nitrogen fixation and transfer. Overall, our study identified key bacterial genera and genes associated with nitrogen fixation and transfer, thus advancing our understanding of interspecific interactions and highlighting the pivotal role of soil microorganisms and functional genes in maintaining soil ecosystem stability from a molecular ecological perspective.

Soil microbiological assessment on diversified annual cropping systems in China

Recent studies have demonstrated that monocropping of flue-cured tobacco can lead to various issues, including nutrient deficiencies, accumulation of allelopathic substances, and disturbance in soil microbial flora. While diversification in cropping systems has proven effective in alleviating monocropping barriers, however, further exploration is needed to understand the potential microbial mechanisms involved in this process. In our study, we set five cropping systems (RR: rice monocropping; TR: tobacco-rice rotation over 20 years; TRA: tobacco-rice-astragalus rotation; TRW: tobacco-rice-wheat rotation; TRO: tobacco-rice-oilseed rape rotation) to explore the impact on crop yield and quality, soil chemical properties, and microbial diversity. The results showed that the yield and gross margin were significantly decreased. Following diversification in cropping systems, particularly after implementing the TRA treatment, the yield and gross margin increased by 27.35% and 38.67%, respectively, compared to the TR treatment. Additionally, the presence of tobacco in the soil resulted in acidification, reduced soil fertility, and suppression of soil microorganism diversity and metabolite abundance. With diversification in cropping systems, there was an increase in soil pH, carbon and nitrogen cycle enzyme activities, and the relative abundance of beneficial microorganisms (acidobacteria, nitrospirillum, and ascomycota) and soil metabolites. Diversification in cropping systems has the potential to increase crop biomass, soil fertility, and soil microbial environment. Our results suggest a scientific foundation for implementing effective nutrient management practices and rational crop rotation systems.

Rhizosphere microbiome regulation: Unlocking the potential for plant growth

Rhizosphere microbial communities are essential for plant growth and health maintenance, but their recruitment and functions are affected by their interactions with host plants. Finding ways to use the interaction to achieve specific production purposes, so as to reduce the use of chemical fertilizers and pesticides, is an important research approach in the development of green agriculture. To demonstrate the importance of rhizosphere microbial communities and guide practical production applications, this review summarizes the outstanding performance of rhizosphere microbial communities in promoting plant growth and stress tolerance. We also discuss the effect of host plants on their rhizosphere microbes, especially emphasizing the important role of host plant species and genes in the specific recruitment of beneficial microorganisms to improve the plants' own traits. The aim of this review is to provide valuable insights into developing plant varieties that can consistently recruit specific beneficial microorganisms to improve crop adaptability and productivity, and thus can be applied to green and sustainable agriculture in the future.

Root hair developmental regulators orchestrate drought triggered microbiome changes and the interaction with beneficial Rhizobiaceae

Drought is one of the most serious abiotic stresses, and emerging evidence suggest plant microbiome affects plant drought tolerance. However, there is a lack of genetic evidence regarding whether and how plants orchestrate the dynamic assembly of the microbiome upon drought. By utilizing mutants with enhanced or decreased root hair densities, we find that root hair regulators also affect drought induced root microbiome changes. Rhizobiaceae is a key biomarker taxa affected by root hair related mutants. We isolated and sequenced 1479 root associated microbes, and confirmed that several Rhizobium strains presented stress-alleviating activities. Metagenome, root transcriptome and root metabolome studies further reveal the multi-omic changes upon drought stress. We knocked out an ornithine cyclodeaminase (ocd) gene in Rhizobium sp. 4F10, which significantly dampens its stress alleviating ability. Our genetic and integrated multi-omics studies confirm the involvement of host genetic effects in reshaping a stress-alleviating root microbiome during drought, and provide mechanistic insights into Rhizobiaceae mediated abiotic stress protection.

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.