Enrichment of beneficial cucumber rhizosphere microbes mediated by organic acid secretion

Allelopathic Effect of Osmanthus fragrans Changes the Soil Microbial Community and Increases the Soil Nutrients and the Aroma Quality of Tea Leaves

Intercropping is a sustainable agricultural practice that promotes the growth of tea plants. However, research on the effects of intercropping with aromatic plants on the soil environment and tea aroma quality remains limited. In this study, we conducted both greenhouse and field experiments to investigate the allelopathic effect of Osmanthus fragrans on soil properties, the soil microbial community, and tea aroma quality. The treatment with O. fragrans leaf litter or intercropping significantly increased soil pH and ammonium nitrogen content and changed soil enzyme activities. Both treatments enhanced the bacterial richness in rhizosphere soil and altered microbial communities, particularly increasing the relative and absolute abundance of beneficial Bacillus. The allelopathic effect of O. fragrans improved tea aroma quality, with five key volatile compounds (linalool oxide II, linalool, nonanal, methyl salicylate, and geraniol) consistently identified in both greenhouse and field treatments. Network analysis demonstrated that our treatments enhanced the correlation between soil bacterial communities and five volatile compounds in tea leaves. These findings provide a theoretical foundation for improving soil health and tea aroma in tea plantations.

Microbial Biotic Associations Dominated Adaptability Differences of Dioecious Poplar Under Salt Stress

How different stress responses by male and female plants are influenced by interactions with rhizosphere microbes remains unclear. In this study, we employed poplar as a dioecious model plant and quantified biotic associations between microorganisms to explore the relationship between microbial associations and plant adaptation. We propose a health index (HI) to comprehensively characterize the physiological characteristics and adaptive capacity of plants under stress. It was found that male poplars demonstrated higher salt stress tolerance than females, and root-secreted citric acid was significantly higher in the rhizospheres of male poplars. Positive biotic association among bacteria increased poplar HI significantly under salt stress, while fungal and cross-domain biotic association (bacteria-fungi) did not. We further identified a keystone bacterial taxon regulating bacterial biotic association, ASV_22706, which was itself regulated by citric acid and significantly positively correlated with host HI. The abundance of keystone fungal taxa was positively correlated with HI of male poplars and negatively correlated with HI of female poplars. Compared with female poplars, male poplars enriched more prebiotics and probiotics under stress. This work primarily reveals the relationship between adaptation differences and microbial interactions in dioecious plants, which suggests a microbial approach to improve plant adaptability to stress conditions.

Bioactive Metabolites from the Dusty Seeds of Gastrodia elata Bl., Based on Metabolomics and UPLC-Q-TOF-MS Combined with Molecular Network Strategy

Orchids produce tiny, light seeds (dust-like seeds without endosperm) that rely on specific symbiotic fungi for successful germination. Plant roots often release small signaling molecules or bioactive compounds to attract arbuscular mycorrhizal (AM) fungi, promoting fungal growth and hyphal branching. However, until now, no such bioactive or signaling molecules have been identified in orchids that help recruit fungi for seed germination. In this study, we used metabolomics and UPLC-Q-TOF-MS/MS, combined with a molecular network approach, to explore potential bioactive/signaling molecules in the seeds of the achlorophyllous orchid Gastrodia elata Bl. Our analysis revealed the presence of amino acids, nucleotides, lipids, organic acids, saccharides, phospholipids, and lignanamides. Specifically, organic acids, saccharides, and lignanamides were shown to promote the growth of Mycena osmundicola, a fungus important for seed germination. Additionally, lignanamides inhibited the plant pathogen Fusarium oxysporum and exhibited strong antioxidant and anti-inflammatory activities. This is the first systematic identification of bioactive/signaling molecules in G. elata Bl. seeds, providing new insights into the symbiotic relationship between orchids and fungi.

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.

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

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

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.

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 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.

Long-term garlic‒maize rotation maintains the stable garlic rhizosphere microecology

BACKGROUND

Crop rotation is a sophisticated agricultural practice that can modify the demographic structure and abundance of microorganisms in the soil, stimulate the growth and proliferation of beneficial microorganisms, and inhibit the development of harmful microorganisms. The stability of the rhizosphere microbiome is crucial for maintaining both soil ecosystem vitality and crop prosperity. However, the effects of extended garlic‒maize rotation on the physicochemical characteristics of garlic rhizosphere soil and the stability of its microbiome remain unclear. To investigate this phenomenon, soil samples from the garlic rhizosphere were collected across four different lengths of rotation in a garlic-maize rotation.

RESULTS

There were notable positive associations between the total nitrogen and total phosphorus contents in the soil and the duration of rotation. Prolonged rotation could increase the maintenance of microbiome α diversity. The number of years of rotation and the soil organic carbon (SOC) content emerged as principal determinants impacting the evolution of the bacterial community structure, with the SOC content playing a pivotal role in sculpting the species diversity within the garlic rhizosphere bacterial community. Additionally, SOC remains predominant in shaping the root-associated bacterial community's β-nearest taxon index. However, these factors do not have a notable effect on the fungal community inhabiting the garlic rhizosphere. In comparison with monoculture, rotation can amplify the interconnectivity and intricacy of microbial ecological networks. Long-term rotation can further maintain the stability of both microbial ecological networks and interactions between bacterial and fungal communities. It can enlist a plethora of beneficial Bacillus species microorganisms within the garlic rhizosphere to form a biological barricade that aids in safeguarding garlic against encroachment by the pathogenic fungus Fusarium oxysporum, consequently diminishing disease incidence. This study provides a theoretical foundation for the sustainable development of garlic through long-term crop rotation with maize.

CONCLUSIONS

Our research results indicate that long-term garlic‒maize rotation maintains stable garlic rhizosphere microecology. Our study provides compelling evidence for the role of long-term crop rotation in maintaining microbiota and community stability, emphasizing the importance of cultivating specific beneficial microorganisms to enhance rotation strategies for garlic farming, thereby promoting sustainability in agriculture.

Mechanisms of rhizosphere plant-microbe interactions: molecular insights into microbial colonization

The rhizosphere, as the "frontline" of plant life, connects plant roots, rhizosphere microorganisms, and surrounding soil, plays a crucial role in plant growth and health, particularly in sustainable agriculture. Despite the well-established contribution of plant-microbe interactions to plant health, the specific molecular mechanisms remain insufficiently understood. This review aims to summarize the physiological adjustments and signal modulation that both plants and microorganisms undergo within this unique ecological niche to ensure successful colonization. By analyzing key processes such as chemotaxis, root attachment, immune evasion, and biofilm formation, we uncover how plants precisely modulate root exudates to either recruit or repel specific microorganisms, thereby shaping their colonization patterns. These findings provide new insights into the complexity of plant-microbe interactions and suggest potential directions for future research in sustainable agriculture.

Distribution and characterization of endophytic and rhizosphere bacteriome of below-ground tissues in Chinese fir plantation

Plantations of Chinese fir, a popular woody tree species, face sustainable issues, such as nutrient deficiency and increasing disease threat. Rhizosphere and endophytic bacteria play important roles in plants' nutrient absorption and stress alleviation. Our understanding of the microbiome structure and functions is proceeding rapidly in model plants and some crop species. Yet, the spatial distribution and functional patterns of the bacteriome for the woody trees remain largely unexplored. In this study, we collected rhizosphere soil, non-rhizosphere soil, fine root, thick root and primary root samples of Chinese fir and investigated the structure and distribution of bacteriome, as well as the beneficial effects of endophytic bacterial isolates. We discovered that Burkholderia and Paraburkholderia genera were overwhelmingly enriched in rhizosphere soil, and the abundance of Pseudomonas genus was significantly enhanced in fine root. By isolating and testing the nutrient absorption and pathogen antagonism functions of representative endophytic bacteria species in Pseudomonas and Burkholderia, we noticed that phosphorus-solubilizing functional isolates were enriched in fine root, while pathogen antagonism isolates were enriched in thick root. As a conclusion, our study revealed that the endophytic and rhizosphere environments of Chinese fir hold distinct structure and abundance of bacteriomes, with potential specific functional enrichment of some bacterial clades. These findings assist us to further study the potential regulation mechanism of endophytic functional bacteria by the host tree, which will contribute to beneficial microbe application in forestry plantations and sustainable development.

Tomato Root Exudates Infected by Meloidogyne incognita Impact the Colonization of Nematicidal Proteus vulgaris

Root exudates play a pivotal role in shaping the microbial community in the rhizosphere and can impact the efficacy of bacteria in controlling nematode populations. This study identified Proteus vulgaris BX-1 as significantly effective in controlling Meloidogyne incognita. The infection of tomato plants with this nematode induced noticeable alterations in the composition of tomato root exudates and led to an increased colonization rate of strain BX-1. Further investigation into how strain BX-1 responded to changes in tomato root exudates revealed that specific metabolites, such as caffeic acid, coumarin, salicylic acid, sebacic acid, and butyric acid, strongly attracted strain BX-1. This attraction potentially contributed to its enhanced colonization and improved efficiency in controlling nematodes. Understanding the correlation between specific metabolites in root exudates and the response of antagonistic bacteria provides valuable insights for enhancing their effectiveness as biological control agents against plant-parasitic nematodes.

The epidemic occurrence of decline disease in bayberry trees altered plant and soil related microbiome and metabolome

BACKGROUND

In China, decline disease with unknown etiology appeared as an epidemic among bayberry trees in the southern area of the Yangtze River. Furthermore, the use of beneficial microbes has been reported to be able to reduce the incidence of this disease, emphasizing the association of this disease with microorganisms. Therefore, it has become critical to uncover the microbiome's function and related metabolites in remodeling the immunity of bayberry trees under biotic or abiotic stresses.

RESULTS

The amplicon sequencing data revealed that decline disease significantly altered bacterial and fungal communities, and their metabolites in the four distinct niches, especially in the rhizosphere soils and roots. Furthermore, the microbial communities in the four niches correlated with the metabolites of the corresponding niches of bayberry plants, and the fungal and bacterial networks of healthy trees were shown to be more complex than those of diseased trees. In addition, the role of microbiome in the resistance of bayberry trees to the occurrence of decline disease was justified by the isolation, identification, and characterization of important microorganisms such as significantly enriched Bacillus ASV804, Pseudomonas ASV815 in healthy plants, and significantly enriched Stenotrophomonas ASV719 in diseased plants.

CONCLUSION

Overall, our study revealed that the occurrence of decline disease altered the microbiome and its metabolites in four ecological niches in particular rhizosphere soils and roots of bayberry, which provides new insight into the control of bayberry decline disease.

Adaptation of rhizobacterial and endophytic communities in Citrus Grandis Exocarpium to long-term organic and chemical fertilization

Introduction

Organic fertilizers (OF) are crucial for enhancing soil quality and fostering plant growth, offering a more eco-friendly and enduring solution compared to chemical fertilizers (CF). However, few studies have systematically analyzed the effects of OF/CF on root microbiome of medicinal plants, especially in combination with active ingredients.

Methods

In this study, we investigated the composition and function of bacteria and fungi in the rhizosphere or within the root of traditional Chinese medicinal plants, Citri Grandis Exocarpium (Huajuhong), which were treated with OF or CF over 1, 3, and 5 years (starting from 2018). Additionally, we conducted metabolome analysis to evaluate the effects of different fertilizers on the medicinal properties of Huajuhong.

Results

The results indicated that extended fertilization could enhance the microbial population and function in plant roots. Notably, OF demonstrated a stronger influence on bacteria, whereas CF enhanced the cohesion of fungal networks and the number of fungal functional enzymes, and even potentially reduced the proliferation of harmful rhizosphere pathogens. By adopting distancebased redundancy analysis, we identified the key physicochemical characteristics that significantly influence the distribution of endophytes, particularly in the case of OF. In contrast, CF was found to exert a more pronounced impact on the composition of the rhizosphere microbiome. Although the application of OF resulted in a broader spectrum of compounds in Huajuhong peel, CF proved to be more efficacious in elevating the concentrations of flavonoids and polysaccharides in the fruit.

Discussion

Consequently, the effects of long-term application of OF or CF on medicinal plants is different in many ways. This research provides a guide for OF/CF selection from the perspective of soil microecology and aids us to critically assess and understand the effects of both fertilizers on the soil environment, and promotes sustainable development of organic agriculture.

Light stress elicits soilborne disease suppression mediated by root-secreted flavonoids in Panax notoginseng

Developing disease-suppressive soils is an effective approach for managing soilborne diseases, which can be achieved through crop metabolism and root secretion modification to recruit beneficial soil microbiota. Many factors, such as light, can elicit and modify plant metabolomic activities, resulting in disease suppression. To investigate the impact of light, Panax notoginseng was planted in a greenhouse and forest, conditioned with three levels of light intensities, including the optimal (15% light transmittance of full light), suboptimal low (5% light transmittance of full light) and suboptimal high (30% light transmittance of full light) intensities. We assessed the rhizosphere microbiota of P. notoginseng and root rot disease caused by soilborne pathogen Ilyonectria destructans, and elucidated the mechanism. Results showed that suboptimal light conditions alleviated root rot disease of P. notoginseng by enriching beneficial microbiota in the rhizosphere. Both low and high light stresses enhanced the secondary metabolism profile in favor of plant defense, particularly the flavonoid pathway. Notably, high light stress demonstrated a robust ability to promote flavonoid metabolism and secretion, resulting in the enrichment of more beneficial microorganisms that suppressed the soilborne pathogen I. destructans. These findings highlight the potential for adjusting canopy light intensities to improve soil health and promote sustainable agriculture.

Phosphorus availability influences disease-suppressive soil microbiome through plant-microbe interactions

BACKGROUND

Soil nutrient status and soil-borne diseases are pivotal factors impacting modern intensive agricultural production. The interplay among plants, soil microbiome, and nutrient regimes in agroecosystems is essential for developing effective disease management. However, the influence of nutrient availability on soil-borne disease suppression and associated plant-microbe interactions remains to be fully explored. T his study aims to elucidate the mechanistic understanding of nutrient impacts on disease suppression, using phosphorous as a target nutrient.

RESULTS

A 6-year field trial involving monocropping of tomatoes with varied fertilizer manipulations demonstrated that phosphorus availability is a key factor driving the control of bacterial wilt disease caused by Ralstonia solanacearum. Subsequent greenhouse experiments were then conducted to delve into the underlying mechanisms of this phenomenon by varying phosphorus availability for tomatoes challenged with the pathogen. Results showed that the alleviation of phosphorus stress promoted the disease-suppressive capacity of the rhizosphere microbiome, but not that of the bulk soil microbiome. This appears to be an extension of the plant trade-off between investment in disease defense mechanisms versus phosphorus acquisition. Adequate phosphorus levels were associated with elevated secretion of root metabolites such as L-tryptophan, methoxyindoleacetic acid, O-phosphorylethanolamine, or mangiferin, increasing the relative density of microbial biocontrol populations such as Chryseobacterium in the rhizosphere. On the other hand, phosphorus deficiency triggered an alternate defense strategy, via root metabolites like blumenol A or quercetin to form symbiosis with arbuscular mycorrhizal fungi, which facilitated phosphorus acquisition as well.

CONCLUSION

Overall, our study shows how phosphorus availability can influence the disease suppression capability of the soil microbiome through plant-microbial interactions. These findings highlight the importance of optimizing nutrient regimes to enhance disease suppression, facilitating targeted crop management and boosting agricultural productivity. Video Abstract.

Serendipita indica Drives Sulfur-Related Microbiota in Enhancing Growth of Hyperaccumulator Sedum alfredii and Facilitating Soil Cadmium Remediation

Endophytic fungus Serendipita indica can bolster plant growth and confer protection against various biotic and abiotic stresses. However, S. indica-reshaped rhizosphere microecology interactions and root-soil interface processes in situ at the submicrometer scale remain poorly understood. We combined amplicon sequencing and high-resolution nano X-ray fluorescence (nano-XRF) imaging of the root-soil interface to reveal cadmium (Cd) rhizosphere processes. S. indica can successfully colonize the roots of Sedum alfredii Hance, which induces a remarkable increase in shoot biomass by 211.32% and Cd accumulation by 235.72%. Nano-XRF images showed that S. indica colonization altered the Cd distribution in the rhizosphere and facilitated the proximity of more Cd and sulfur (S) to enter the roots and transport to the shoot. Furthermore, the rhizosphere-enriched microbiota demonstrated a more stable network structure after the S. indica inoculation. Keystone species were strongly associated with growth promotion and Cd absorption. For example, Comamonadaceae are closely related to the organic acid cycle and S bioavailability, which could facilitate Cd and S accumulation in plants. Meanwhile, Sphingomonadaceae could release auxin and boost plant biomass. In summary, we construct a mutualism system for beneficial fungi and hyperaccumulation plants, which facilitates high-efficient remediation of Cd-contaminated soils by restructuring the rhizosphere microbiota.

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.

Impact of Plant-Microbe Interactions with a Focus on Poorly Investigated Urban Ecosystems-A Review

The urbanization process, which began with the Industrial Revolution, has undergone a considerable increase over the past few decades. Urbanization strongly affects ecological processes, often deleteriously, because it is associated with a decrease in green spaces (areas of land covered by vegetation), loss of natural habitats, increased rates of species extinction, a greater prevalence of invasive and exotic species, and anthropogenic pollutant accumulation. In urban environments, green spaces play a key role by providing many ecological benefits and contributing to human psychophysical well-being. It is known that interactions between plants and microorganisms that occur in the rhizosphere are of paramount importance for plant health, soil fertility, and the correct functioning of plant ecosystems. The growing diffusion of DNA sequencing technologies and "omics" analyses has provided increasing information about the composition, structure, and function of the rhizomicrobiota. However, despite the considerable amount of data on rhizosphere communities and their interactions with plants in natural/rural contexts, current knowledge on microbial communities associated with plant roots in urban soils is still very scarce. The present review discusses both plant-microbe dynamics and factors that drive the composition of the rhizomicrobiota in poorly investigated urban settings and the potential use of beneficial microbes as an innovative biological tool to face the challenges that anthropized environments and climate change impose. Unravelling urban biodiversity will contribute to green space management, preservation, and development and, ultimately, to public health and safety.

Growth enhancement and changes in bacterial microbiome of cucumber plants exhibited by biopriming with some native bacteria

This study investigated the impact of a mixture of six endophytic bacterial strains isolated from cucumber plants on the growth and microbiome diversity of six cucumber traditional varieties and hybrids. Six bacterial species were isolated and identified by 16 s rRNA sequencing. All the bacteria showed plant growth promoting traits. Bacillus tequilensis showed 80 % inhibition of the mycelia growth of Fusarium oxysporum f.sp. cucumarinum (Foc). Mixed culture of all the bacteria was prepared and applied back to the varieties and hybrids of cucumber plants through seed soaking. Plant growth characteristics indicated that the treated plants showed increased plant growth in terms of plant height, number of leaves, vine length, male:female flower ratio, number of fruits and fruit length. Bacteria treated plants of hybrid HiVeg Chitra recorded 19 cm increase in vine length compared to control plants. The matataxonomic analysis of leaf samples by Illumina sequencing highlighted a diverse bacterial community shift in treated plants, with significant increases in genera like Bacillus and Staphylococcus. The core microbiome analysis identified key genera such as Bacillus, Staphylococcus, Sphingomonas, Methylobacterium, etc that could be pivotal in plant growth promotion. Bacillus and Staphylococcus showed increased abundance in treated varieties, correlating with the observed in plant growth parameters thus indicating their role in growth promotion of cucumber plants. Endophytic bacterial species identified from cucumber plants when re-applied by seed soaking, they promote the plant growth by modulating the microbiome. The bacterial species identified in the study could be potential candidates as microbial bioinputs for cucumber cultivation.

Extracellular niche establishment by plant pathogens

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

miR164-MhNAC1 regulates apple root nitrogen uptake under low nitrogen stress

Nitrogen is an essential nutrient for plant growth and serves as a signaling molecule to regulate gene expression inducing physiological, growth and developmental responses. An excess or deficiency of nitrogen may have adverse effects on plants. Studying nitrogen uptake will help us understand the molecular mechanisms of utilization for targeted molecular breeding. Here, we identified and functionally validated an NAC (NAM-ATAF1/2-CUC2) transcription factor based on the transcriptomes of two apple rootstocks with different nitrogen uptake efficiency. NAC1, a target gene of miR164, directly regulates the expression of the high-affinity nitrate transporter (MhNRT2.4) and citric acid transporter (MhMATE), affecting root nitrogen uptake. To examine the role of MhNAC1 in nitrogen uptake, we produced transgenic lines that overexpressed or silenced MhNAC1. Silencing MhNAC1 promoted nitrogen uptake and citric acid secretion in roots, and enhanced plant tolerance to low nitrogen conditions, while overexpression of MhNAC1 or silencing miR164 had the opposite effect. This study not only revealed the role of the miR164-MhNAC1 module in nitrogen uptake in apple rootstocks but also confirmed that citric acid secretion in roots affected nitrogen uptake, which provides a research basis for efficient nitrogen utilization and molecular breeding in apple.

Understanding the dynamic interactions of root-knot nematodes and their host: role of plant growth promoting bacteria and abiotic factors

Root-knot nematodes (Meloidogyne spp., RKN) are among the most destructive endoparasitic nematodes worldwide, often leading to a reduction of crop growth and yield. Insights into the dynamics of host-RKN interactions, especially in varied biotic and abiotic environments, could be pivotal in devising novel RKN mitigation measures. Plant growth-promoting bacteria (PGPB) involves different plant growth-enhancing activities such as biofertilization, pathogen suppression, and induction of systemic resistance. We summarized the up-to-date knowledge on the role of PGPB and abiotic factors such as soil pH, texture, structure, moisture, etc. in modulating RKN-host interactions. RKN are directly or indirectly affected by different PGPB, abiotic factors interplay in the interactions, and host responses to RKN infection. We highlighted the tripartite (host-RKN-PGPB) phenomenon with respect to (i) PGPB direct and indirect effect on RKN-host interactions; (ii) host influence in the selection and enrichment of PGPB in the rhizosphere; (iii) how soil microbes enhance RKN parasitism; (iv) influence of host in RKN-PGPB interactions, and (v) the role of abiotic factors in modulating the tripartite interactions. Furthermore, we discussed how different agricultural practices alter the interactions. Finally, we emphasized the importance of incorporating the knowledge of tripartite interactions in the integrated RKN management strategies.

Analysis of endophytic bacterial diversity in seeds of different genotypes of cotton and the suppression of Verticillium wilt pathogen infection by a synthetic microbial community

BACKGROUND

In agricultural production, fungal diseases significantly impact the yield and quality of cotton (Gossypium spp.) with Verticillium wilt posing a particularly severe threat.

RESULTS

This study is focused on investigating the effectiveness of endophytic microbial communities present in the seeds of disease-resistant cotton genotypes in the control of cotton Verticillium wilt. The technique of 16S ribosomal RNA (16S rRNA) amplicon sequencing identified a significant enrichment of the Bacillus genus in the resistant genotype Xinluzao 78, which differed from the endophytic bacterial community structure in the susceptible genotype Xinluzao 63. Specific enriched strains were isolated and screened from the seeds of Xinluzao 78 to further explore the biological functions of seed endophytes. A synthetic microbial community (SynCom) was constructed using the broken-rod model, and seeds of the susceptible genotype Xinluzao 63 in this community that had been soaked with the SynCom were found to significantly control the occurrence of Verticillium wilt and regulate the growth of cotton plants. Antibiotic screening techniques were used to preliminarily identify the colonization of strains in the community. These techniques revealed that the strains can colonize plant tissues and occupy ecological niches in cotton tissues through a priority effect, which prevents infection by pathogens.

CONCLUSION

This study highlights the key role of seed endophytes in driving plant disease defense and provides a theoretical basis for the future application of SynComs in agriculture.

Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis

Plant roots are functionally heterogeneous in cellular architecture, transcriptome profile, metabolic state, and microbial immunity. We hypothesized that axial differentiation may also impact spatial colonization by root microbiota along the root axis. We developed two growth systems, ArtSoil and CD-Rhizotron, to grow and then dissect Arabidopsis thaliana roots into three segments. We demonstrate that distinct endospheric and rhizosphere bacterial communities colonize the segments, supporting the hypothesis of microbiota differentiation along the axis. Root metabolite profiling of each segment reveals differential metabolite enrichment and specificity. Bioinformatic analyses and GUS histochemistry indicate microbe-induced accumulation of SWEET2, 4, and 12 sugar uniporters. Profiling of root segments from sweet mutants shows altered spatial metabolic profiles and reorganization of endospheric root microbiota. This work reveals the interdependency between root metabolites and microbial colonization and the contribution of SWEETs to spatial diversity and stability of microbial ecosystem.

Application Progress of Culturomics in the Isolated Culture of Rhizobacteria: A Review

Comprehending the structure and function of rhizobacteria components and their regulation are crucial for sustainable agricultural management. However, obtaining comprehensive species information for most bacteria in the natural environment, particularly rhizobacteria, presents a challenge using traditional culture methods. To obtain diverse and pure cultures of rhizobacteria, this study primarily reviews the evolution of rhizobacteria culturomics and associated culture methods. Furthermore, it explores new strategies for enhancing the application of culturomics, providing valuable insights into efficiently enriching and isolate target bacterial strains/groups from the environment. The findings will help improve rhizobacteria's culturability and enrich the functional bacterial library.

Recruitment of beneficial cucumber rhizosphere microbes mediated by amino acid secretion induced by biocontrol Bacillus subtilis isolate 1JN2

Introduction

At present, the use of beneficial microorganisms to control cucumber Fusarium wilt is a widely used method, and the rhizosphere microecological reset is one of the mechanisms involved. However, how biocontrol strains reshape cucumber rhizosphere microecology remains to be further studied.

Methods

The composition changes of cucumber root exudates induced by biocontrol strain 1JN2, the microbial ecology of cucumber rhizosphere and the colonization ability of biocontrol strain 1JN2 in cucumber rhizosphere were analyzed through UHPLC-MS/MS analysis, Illumina high-throughput sequencing and SEM, respectively.

Results

First, cucumber plants treated with biocontrol Bacillus 1JN2 reduced the disease severity of Fusarium wilt by 60%. Significant changes in cucumber root exudates were found after 1JN2 inoculation and the contents of four amino acids including glutamine, tryptophan, glycine and glutamic acid were significantly increased. Second, It was found that the bacterial diversity in the rhizosphere of cucumber was significantly increased in both the strain treatment group and the amino acid mixture treatment group, The number of Bacillus was the largest in all dominant populations, exceeded 20% in all treatment groups. The bacteria of Hydrogenispora and Vicinamibacteria were significantly increased after treatment.

Discussion

Overall, the results demonstrated that amino acid substances in cucumber root exudates induced by biocontrol strain 1JN2 can shift the cucumber root microenvironment and prevent the occurrence of Fusarium wilt disease.

The Dynamic Changes of Brassica napus Seed Microbiota across the Entire Seed Life in the Field

The seed microbiota is an important component given by nature to plants, protecting seeds from damage by other organisms and abiotic stress. However, little is known about the dynamic changes and potential functions of the seed microbiota during seed development. In this study, we investigated the composition and potential functions of the seed microbiota of rapeseed (Brassica napus). A total of 2496 amplicon sequence variants (ASVs) belonging to 504 genera in 25 phyla were identified, and the seed microbiota of all sampling stages were divided into three groups. The microbiota of flower buds, young pods, and seeds at 20 days after flowering (daf) formed the first group; that of seeds at 30 daf, 40 daf and 50 daf formed the second group; that of mature seeds and parental seeds were clustered into the third group. The functions of seed microbiota were identified by using PICRUSt2, and it was found that the substance metabolism of seed microbiota was correlated with those of the seeds. Finally, sixty-one core ASVs, including several potential human pathogens, were identified, and a member of the seed core microbiota, Sphingomonas endophytica, was isolated from seeds and found to promote seedling growth and enhance resistance against Sclerotinia sclerotiorum, a major pathogen in rapeseed. Our findings provide a novel perspective for understanding the composition and functions of microbiota during seed development and may enhance the efficiency of mining beneficial seed microbes.

MAPK Cascades in Plant Microbiota Structure and Functioning

Mitogen-activated protein kinase (MAPK) cascades are highly conserved signaling modules that coordinate diverse biological processes such as plant innate immunity and development. Recently, MAPK cascades have emerged as pivotal regulators of the plant holobiont, influencing the assembly of normal plant microbiota, essential for maintaining optimal plant growth and health. In this review, we provide an overview of current knowledge on MAPK cascades, from upstream perception of microbial stimuli to downstream host responses. Synthesizing recent findings, we explore the intricate connections between MAPK signaling and the assembly and functioning of plant microbiota. Additionally, the role of MAPK activation in orchestrating dynamic changes in root exudation to shape microbiota composition is discussed. Finally, our review concludes by emphasizing the necessity for more sophisticated techniques to accurately decipher the role of MAPK signaling in establishing the plant holobiont relationship.

Holistic Approaches to Plant Stress Alleviation: A Comprehensive Review of the Role of Organic Compounds and Beneficial Bacteria in Promoting Growth and Health

Plants select microorganisms from the surrounding bulk soil, which act as a reservoir of microbial diversity and enrich a rhizosphere microbiome that helps in growth and stress alleviation. Plants use organic compounds that are released through root exudates to shape the rhizosphere microbiome. These organic compounds are of various spectrums and technically gear the interplay between plants and the microbial world. Although plants naturally produce organic compounds that influence the microbial world, numerous efforts have been made to boost the efficiency of the microbiome through the addition of organic compounds. Despite further crucial investigations, synergistic effects from organic compounds and beneficial bacteria combinations have been reported. In this review, we examine the relationship between organic compounds and beneficial bacteria in determining plant growth and biotic and abiotic stress alleviation. We investigate the molecular mechanism and biochemical responses of bacteria to organic compounds, and we discuss the plant growth modifications and stress alleviation done with the help of beneficial bacteria. We then exhibit the synergistic effects of both components to highlight future research directions to dwell on how microbial engineering and metagenomic approaches could be utilized to enhance the use of beneficial microbes and organic compounds.

Phosphorus deficiency is the main limiting factor for re-vegetation and soil microorganisms in Mu Us Sandy Land, Northwest China

Long-term drought induced by low rainfall leads to environmental degradation of land in arid and semi-arid regions. In past decades, re-vegetation of degraded sandy soils to prevent soil erosion has been widely employed, including in Mu Us Sandy Land, which suffers from severe soil erosion. However, it remains unclear how re-vegetation affects soil properties and soil microbes after long restoration periods. In this study, typical plots planting Artemisia ordosica and Salix psammophila were selected to investigate the influence of plant types on soil properties; an area of bare sandy land was used as a control. The results show that re-vegetation increased soil organic carbon (C), total nitrogen (N), soil microbial carbon, microbial nitrogen and soil organic acid, while decreasing soil total phosphorous (TP) content significantly, resulting in increased C/P and N/P ratios. Correlation analysis showed that TP was negatively correlated with oxalic acid (OA) and acetic acid (AA), indicating that increased AA and OA content could accelerate the active utilization of phosphorus and induced low TP in soil. Re-vegetation with A. ordosica significantly decreased the microbial diversity of topsoil. The redundancy analysis showed that TP was main index in affecting microbes. These results that lower P content, higher C/P and N/P ratio and influence of TP on microbes suggest that phosphorus is the main limiting factor for re-vegetation and growth of soil microorganisms. In the future, strategies for the development of sustainable ecosystems in regions suffers from severe soil erosion should consider phosphorus supplementation.

Dynamic metabolites: A bridge between plants and microbes

Plant metabolites have a great influence on soil microbiomes. Although few studies provided insights into plant-microbe interactions, we still know very little about how plants recruit their microbiome. Here, we discuss the dynamic progress that typical metabolites shape microbes by a variety of factors, such as physiographic factors, cultivar factors, phylogeny factors, and environmental stress. Several kinds of metabolites have been reviewed, including plant primary metabolites (PPMs), phytohormones, and plant secondary metabolites (PSMs). The microbes assembled by plant metabolites in return exert beneficial effects on plants, which have been widely applied in agriculture. What's more, we point out existing problems and future research directions, such as unclear mechanisms, few species, simple parts, and ignorance of absolute abundance. This review may inspire readers to study plant-metabolite-microbe interactions in the future.

The Cultured Microbiome of Pollinated Maize Silks Shifts after Infection with Fusarium graminearum and Varies by Distance from the Site of Pathogen Inoculation

Styles transmit pollen-derived sperm nuclei from pollen to ovules, but also transmit environmental pathogens. The microbiomes of styles are likely important for reproduction/disease, yet few studies exist. Whether style microbiome compositions are spatially responsive to pathogens is unknown. The maize pathogen Fusarium graminearum enters developing grain through the style (silk). We hypothesized that F. graminearum treatment shifts the cultured transmitting silk microbiome (TSM) compared to healthy silks in a distance-dependent manner. Another objective of the study was to culture microbes for future application. Bacteria were cultured from husk-covered silks of 14 F. graminearum-treated diverse maize genotypes, proximal (tip) and distal (base) to the F. graminearum inoculation site. Long-read 16S sequences from 398 isolates spanned 35 genera, 71 species, and 238 OTUs. More bacteria were cultured from F. graminearum-inoculated tips (271 isolates) versus base (127 isolates); healthy silks were balanced. F. graminearum caused a collapse in diversity of ~20-25% across multiple taxonomic levels. Some species were cultured exclusively or, more often, from F. graminearum-treated silks (e.g., Delftia acidovorans, Klebsiella aerogenes, K. grimontii, Pantoea ananatis, Stenotrophomonas pavanii). Overall, the results suggest that F. graminearum alters the TSM in a distance-dependent manner. Many isolates matched taxa that were previously identified using V4-MiSeq (core and F. graminearum-induced), but long-read sequencing clarified the taxonomy and uncovered greater diversity than was initially predicted (e.g., within Pantoea). These isolates represent the first comprehensive cultured collection from pathogen-treated maize silks to facilitate biocontrol efforts and microbial marker-assisted breeding.

Analysis of the rhizosphere bacterial diversity of Angelica dahurica var. formosana from different experimental sites and varieties (strains)

Background

Rhizosphere bacteria play important roles in plant growth and secondary metabolite accumulation. Moreover, only with favorable production areas and desirable germplasm can high-yield and high-quality medicinal materials be produced. However, whether origin and germplasm indirectly affect the yield and quality of Angelica dahurica var. formosana through rhizosphere bacterial effects are not known.

Methods

In this study, a high-throughput sequencing strategy was used to explore the relationship between the rhizosphere bacterial community and the cultivation of A. dahurica var. formosana from different production areas and germplasm for the first time.

Results

(1) Proteobacteria was the dominant bacterial phylum in the rhizosphere soil of A. dahurica var. formosana, and these bacteria were stable and conserved to a certain extent. (2) High abundance of Proteobacteria was an important rhizospheric indicator of high yield, and high abundance of Firmicutes was an important indicator of high quality. Proteobacteria and Firmicutes might have an important relationship with the yield and quality of A. dahurica var. formosana, respectively. (3) PCoA cluster analysis demonstrated that both production area and germplasm affected the bacterial community structure in the rhizosphere of A. dahurica var. formosana to a certain extent, and production area had the greatest effect. In addition to available potassium, the rhizosphere soil nutrient levels of different production areas strongly affected the bacterial diversity and community. These findings provide a theoretical basis for the exploitation and utilization of rhizosphere microbial resources of A. dahurica var. formosana and offer a novel approach for increasing the yield and quality of this crop.

Tapping the rhizosphere metabolites for the prebiotic control of soil-borne bacterial wilt disease

Prebiotics are compounds that selectively stimulate the growth and activity of beneficial microorganisms. The use of prebiotics is a well-established strategy for managing human gut health. This concept can also be extended to plants where plant rhizosphere microbiomes can improve the nutrient acquisition and disease resistance. However, we lack effective strategies for choosing metabolites to elicit the desired impacts on plant health. In this study, we target the rhizosphere of tomato (Solanum lycopersicum) suffering from wilt disease (caused by Ralstonia solanacearum) as source for potential prebiotic metabolites. We identify metabolites (ribose, lactic acid, xylose, mannose, maltose, gluconolactone, and ribitol) exclusively used by soil commensal bacteria (not positively correlated with R. solanacearum) but not efficiently used by the pathogen in vitro. Metabolites application in the soil with 1 µmol g^-1 soil effectively protects tomato and other Solanaceae crops, pepper (Capsicum annuum) and eggplant (Solanum melongena), from pathogen invasion. After adding prebiotics, the rhizosphere soil microbiome exhibits enrichment of pathways related to carbon metabolism and autotoxin degradation, which were driven by commensal microbes. Collectively, we propose a novel pathway for mining metabolites from the rhizosphere soil and their use as prebiotics to help control soil-borne bacterial wilt diseases.

How does the pattern of root metabolites regulating beneficial microorganisms change with different grazing pressures?

Grazing disturbance can change the structure of plant rhizosphere microbial communities and thereby alter the feedback to promote plant growth or induce plant defenses. However, little is known about how such changes occur and vary under different grazing pressures or the roles of root metabolites in altering the composition of rhizosphere microbial communities. In this study, the effects of different grazing pressures on the composition of microbial communities were investigated, and the mechanisms by which different grazing pressures changed rhizosphere microbiomes were explored with metabolomics. Grazing changed composition, functions, and co-expression networks of microbial communities. Under light grazing (LG), some saprophytic fungi, such as Lentinus sp., Ramichloridium sp., Ascobolus sp. and Hyphoderma sp., were significantly enriched, whereas under heavy grazing (HG), potentially beneficial rhizobacteria, such as Stenotrophomonas sp., Microbacterium sp., and Lysobacter sp., were significantly enriched. The beneficial mycorrhizal fungus Schizothecium sp. was significantly enriched in both LG and HG. Moreover, all enriched beneficial microorganisms were positively correlated with root metabolites, including amino acids (AAs), short-chain organic acids (SCOAs), and alkaloids. This suggests that these significantly enriched rhizosphere microbial changes may be caused by these differential root metabolites. Under LG, it is inferred that root metabolites, especially AAs such as L-Histidine, may regulate specific saprophytic fungi to participate in material transformations and the energy cycle and promote plant growth. Furthermore, to help alleviate the stress of HG and improve plant defenses, it is inferred that the root system actively regulates the synthesis of these root metabolites such as AAs, SCOAs, and alkaloids under grazing interference, and then secretes them to promote the growth of some specific plant growth-promoting rhizobacteria and fungi. To summarize, grasses can regulate beneficial microorganisms by changing root metabolites composition, and the response strategies vary under different grazing pressure in typical grassland ecosystems.

Growth Increase in the Herbaceous Plant Centella asiatica by the Plant Growth-Promoting Rhizobacteria Priestia megaterium HyangYak-01

Centella asiatica is a traditional herbaceous plant with numerous beneficial effects, widely known for its medicinal and cosmetic applications. Maximizing its growth can lead to beneficial effects, by focusing on the use of its active compounds. The use of plant growth-promoting rhizobacteria (PGPR) is known to be an alternative to chemical fertilizers. In this study, we used the PGPR Priestia megaterium HY-01 to increase the yield of C. asiatica. In vitro assays showed that HY-01 exhibited plant growth-promoting activities (IAA production, denitrification, phosphate solubilization, and urease activity). Genomic analyses also showed that the strain has plant growth-promoting-related genes that corroborate with the different PGP activities found in the assays. This strain was subsequently used in field experiments to test its effectiveness on the growth of C. asiatica. After four months of application, leaf and root samples were collected to measure the plant growth rate. Moreover, we checked the rhizosphere microbiome between the treated and non-treated plots. Our results suggest that treatment with Hyang-yak-01 not only improved the growth of C. asiatica (leaf length, leaf weight, leaf width, root length, root width, and chlorophyll content) but also influenced the rhizosphere microbiome. Biodiversity was higher in the treated group, and the bacterial composition was also different from the control group.

Plant pathogen resistance is mediated by recruitment of specific rhizosphere fungi

Beneficial interactions between plants and rhizosphere microorganisms are key determinants of plant health with the potential to enhance the sustainability of agricultural practices. However, pinpointing the mechanisms that determine plant disease protection is often difficult due to the complexity of microbial and plant-microbe interactions and their links with the plant's own defense systems. Here, we found that the resistance level of different banana varieties was correlated with the plant's ability to stimulate specific fungal taxa in the rhizosphere that are able to inhibit the Foc TR4 pathogen. These fungal taxa included members of the genera Trichoderma and Penicillium, and their growth was stimulated by plant exudates such as shikimic acid, D-(-)-ribofuranose, and propylene glycol. Furthermore, amending soils with these metabolites enhanced the resistance of a susceptible variety to Foc TR4, with no effect observed for the resistant variety. In total, our findings suggest that the ability to recruit pathogen-suppressive fungal taxa may be an important component in determining the level of pathogen resistance exhibited by plant varieties. This perspective opens up new avenues for improving plant health, in which both plant and associated microbial properties are considered.

Coptischinensis Franch root rot infection disrupts microecological balance of rhizosphere soil and endophytic microbiomes

Introduction

The ecological balance of the plant microbiome, as a barrier against pathogens, is very important for host health. Coptis chinensis is one of the important medicinal plants in China. In recent years, Illumina Miseq high-throughput sequencing technology was frequently used to analyze root rot pathogens and the effects of root rot on rhizosphere microorganisms of C. chinensis. But the effects of root rot infection on rhizosphere microecological balance of C. chinensis have received little attention.

Methods

In this study, Illumina Miseq high-throughput sequencing technology was applied to analyze the impact on microbial composition and diversity of C. chinensis by root rot.

Results

The results showed that root rot infection had significant impact on bacterial α-diversity in rhizome samples, but had no significant effect on that in leaf samples and rhizosphere soil samples, while root rot infection exhibited significant impact on the fungal α-diversity in leaf samples and rhizosphere soil samples, and no significant impact on that in rhizome samples. PCoA analysis showed that the root rot infection had a greater impact on the fungal community structure in the rhizosphere soil, rhizome, and leaf samples of C. chinensis than on the bacterial community structure. Root rot infection destroyed the microecological balance of the original microbiomes in the rhizosphere soil, rhizome, and leaf samples of C. chinensis, which may also be one of the reasons for the serious root rot of C. chinensis.

Discussion

In conclusion, our findings suggested that root rot infection with C. chinensis disrupts microecological balance of rhizosphere soil and endophytic microbiomes. The results of this study can provide theoretical basis for the prevention and control of C. chinensis root rot by microecological regulation.

The dynamics and transmission of antibiotic resistance associated with plant microbiomes

Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.

Artificial Intelligence: A Promising Tool in Exploring the Phytomicrobiome in Managing Disease and Promoting Plant Health

There is increasing interest in harnessing the microbiome to improve cropping systems. With the availability of high-throughput and low-cost sequencing technologies, gathering microbiome data is becoming more routine. However, the analysis of microbiome data is challenged by the size and complexity of the data, and the incomplete nature of many microbiome databases. Further, to bring microbiome data value, it often needs to be analyzed in conjunction with other complex data that impact on crop health and disease management, such as plant genotype and environmental factors. Artificial intelligence (AI), boosted through deep learning (DL), has achieved significant breakthroughs and is a powerful tool for managing large complex datasets such as the interplay between the microbiome, crop plants, and their environment. In this review, we aim to provide readers with a brief introduction to AI techniques, and we introduce how AI has been applied to areas of microbiome sequencing taxonomy, the functional annotation for microbiome sequences, associating the microbiome community with host traits, designing synthetic communities, genomic selection, field phenotyping, and disease forecasting. At the end of this review, we proposed further efforts that are required to fully exploit the power of AI in studying phytomicrobiomes.

Deciphering the Synergies of Reductive Soil Disinfestation Combined with Biochar and Antagonistic Microbial Inoculation in Cucumber Fusarium Wilt Suppression Through Rhizosphere Microbiota Structure

Application of reductive soil disinfestation (RSD), biochar, and antagonistic microbes have become increasingly popular strategies in a microbiome-based approach to control soil-borne diseases. The combined effect of these remediation methods on the suppression of cucumber Fusarium wilt associated with microbiota reconstruction, however, is still unknown. In this study, we applied RSD treatment together with biochar and microbial application of Trichoderma and Bacillus spp. in Fusarium-diseased cucumbers to investigate their effects on wilt suppression, soil chemical changes, microbial abundances, and the rhizosphere communities. The results showed that initial RSD treatment followed by biochar amendment (RSD-BC) and combined applications of microbial inoculation and biochar (RSD-SQR-T37-BC) decreased nitrate concentration and raised soil pH, soil organic carbon (SOC), and ammonium in the treated soils. Under RSD, the applications of Bacillus (RSD-SQR), Trichoderma (RSD-T37), and biochar (RSD-BC) suppressed wilt incidence by 26.8%, 37.5%, and 32.5%, respectively, compared to non-RSD treatments. Moreover, RSD-SQR-T37-BC and RSD-T37 caused greater suppressiveness of Fusarium wilt and F. oxysporum by 57.0 and 33.5%, respectively. Rhizosphere beta diversity and alpha diversity revealed a difference between RSD-treated and non-RSD microbial groups. The significant increase in the abundance, richness, and diversity of bacteria, and the decrease in the abundance and diversity of fungi under RSD-induced treatments attributed to the general suppression. Identified bacterial (Bacillus, Pseudoxanthomonas, Flavobacterium, Flavisolibacter, and Arthrobacter) and fungal (Trichoderma, Chaetomium, Cladosporium, Psathyrella, and Westerdykella) genera were likely the potential antagonists of specific disease suppression for their significant increase of abundances under RSD-treated soils and high relative importance in linear models. This study infers that the RSD treatment induces potential synergies with biochar amendment and microbial applications, resulting in enhanced general-to-specific suppression mechanisms by changing the microbial community composition in the cucumber rhizosphere.

Plant Microbiome: An Ocean of Possibilities for Improving Disease Resistance in Plants

Plant diseases pose a serious threat to crop production and the agricultural economy across the globe. Currently, chemical pesticides are frequently employed to combat these infections, which cause environmental toxicity and the emergence of resistant pathogens. Moreover, the genetic manipulation of plant defense pathways and the breeding of resistant genes has attained limited success due to the rapid evolution of pathogen virulence and resistance, together with host range expansion. Additionally, due to climate change and global warming, the occurrence of multiple stresses during disease outbreak has further impacted overall crop growth and productivity, posing a serious threat to food security. In this regard, harnessing the plant beneficial microbiome and its products can provide novel avenues for disease resistance in addition to boosting agricultural output, soil fertility and environmental sustainability. In plant-beneficial microbiome interactions, induced systemic resistance (ISR) has emerged as a key mechanism by which a beneficial microbiome primes the entire plant system for better defense against a wide range of phytopathogens and pests. In this review, we provide the recent developments on the role of plant beneficial microbiomes in disease resistance. We also highlight knowledge gaps and discuss how the plant immune system distinguishes pathogens and beneficial microbiota. Furthermore, we provide an overview on how immune signature hormones, such as salicylic acid (SA), jasmonic acid (JA) and ethylene (ET), shape plant beneficial microbiome. We also discuss the importance of various high-throughput tools and their integration with synthetic biology to design tailored microbial communities for disease resistance. Finally, we conclude by highlighting important themes that need future attention in order to fill the knowledge gaps regarding the plant immune system and plant-beneficial-microbiome-mediated disease resistance.

The Co-Association of Enterobacteriaceae and Pseudomonas with Specific Resistant Cucumber against Fusarium Wilt Disease

The root microbiota contributes to the plant's defense against stresses and pathogens. However, the co-association pattern of functional bacteria that improves plant resistance has not been interpreted clearly. Using Illumina high-throughput sequencing technology, the root bacterial community profiles of six cucumber cultivars with different resistance in response to the causative agent of cucumber Fusarium wilt (CFW), Fusarium oxysporum f. sp. cucumerinum (Foc), were analyzed. The principal coordinate analysis indicated that the interactions of the cultivars and pathogens drove the cucumber root bacterial communities (p = 0.001). The resistance-specific differential genera across the cultivars were identified, including Massilia in the resistant cultivars, unclassified Enterobacteriaceae in resistant CL11 and JY409, Pseudomonas in JY409, Cronobacter in moderately resistant ZN106, and unclassified Rhizobiaceae and Streptomyces in susceptible ZN6. The predominant root bacterium Massilia accounted for the relative abundance of up to 28.08-61.55%, but dramatically declined to 9.36% in Foc-inoculated susceptible ZN6. Pseudomonas ASV103 and ASV48 of Pseudomonadaceae and Cronobacter ASV162 of Enterobacteriaceae were consistently differential across the cultivars at the phylum, genus, and ASV levels. Using the culture-based method, antagonistic strains of Enterobacteriaceae with a high proportion of 51% were isolated. Furthermore, the bacterial complexes of Pantoea dispersa E318 + Pseudomonas koreensis Ps213 and Cronobacter spp. C1 + C7 reduced the disease index of CFW by 77.2% and 60.0% in the pot experiment, respectively. This study reveals the co-association of specific root bacteria with host plants and reveals insight into the suppressing mechanism of resistant cultivars against CFW disease by regulating the root microbiota.

Pseudomonas sivasensis 2RO45 inoculation alters the taxonomic structure and functioning of the canola rhizosphere microbial community

Inoculation with plant growth-promoting rhizobacteria (PGPR) is an eco-friendly sustainable strategy for improving crop productivity in diverse environments under different conditions. Our earlier study demonstrated that Pseudomonas sivasensis 2RO45 significantly stimulated canola (Brassica napus L. var. napus) growth. The aim of the present study was to investigate the structural and functional dynamics in the canola rhizosphere microbiome after inoculation with PGPR P. sivasensis 2RO45. The results based on alpha diversity metrics showed that P. sivasensis 2RO45 did not significantly alter the diversity of the native soil microbiota. However, the introduced strain modified the taxonomic structure of microbial communities, increasing the abundance of plant beneficial microorganisms, e.g., bacteria affiliated with families Comamonadaceae, Vicinamibacteraceae, genus Streptomyces, and fungi assigned to Nectriaceae, Didymellaceae, Exophiala, Cyphellophora vermispora, and Mortierella minutissima. The analysis of community level physiological profiling (CLPP) revealed that microbial communities in the P. sivasensis 2RO45 treated canola rhizospheres were more metabolically active than those in the non-treated canola rhizosphere. Four carbon sources (phenols, polymers, carboxylic acids, and amino acids) were better metabolized by the microbial communities from the rhizosphere of plants inoculated with the P. sivasensis 2RO45 than non-inoculated canola rhizospheres. Based on the community-level physiological profiles, the functional diversity of the rhizosphere microbiome was altered by the P. sivasensis 2RO45 inoculation. Substrate utilization Shannon diversity (H) index and evenness (E) index were significantly increased in the treated canola plants. The study provides new insight into PGPR-canola interactions for sustainable agriculture development.

Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease

The role of rhizosphere microbiota in the resistance of tomato plant against soil-borne Fusarium wilt disease (FWD) remains unclear. Here, we showed that the FWD incidence was significantly negatively correlated with the diversity of both rhizosphere bacterial and fungal communities. Using the microbiological culturomic approach, we selected 205 unique strains to construct different synthetic communities (SynComs), which were inoculated into germ-free tomato seedlings, and their roles in suppressing FWD were monitored using omics approach. Cross-kingdom (fungi and bacteria) SynComs were most effective in suppressing FWD than those of Fungal or Bacterial SynComs alone. This effect was underpinned by a combination of molecular mechanisms related to plant immunity and microbial interactions contributed by the bacterial and fungal communities. This study provides new insight into the dynamics of microbiota in pathogen suppression and host immunity interactions. Also, the formulation and manipulation of SynComs for functional complementation constitute a beneficial strategy in controlling soil-borne disease.

Elevated CO2 and biochar differentially affect plant C:N:P stoichiometry and soil microbiota in the rhizosphere of white lupin (Lupinus albus L.)

Biochar application is a potent climate change mitigation strategy in agroecosystems. However, little is known about the interactive effects of elevated CO₂ (eCO₂) and biochar on plant nutrient uptake and soil microbial processes. A pot experiment was conducted to investigate the effects of eCO₂ and biochar addition on plant C:N:P stoichiometry and rhizobacterial community for better management of nutrient balance and use efficiency in a future climate scenario. White lupin (Lupinus albus L.) was grown for 30 days in topsoil and subsoil with or without 2% corn-stubble biochar under ambient CO₂ (aCO₂: 390 ppm) or eCO₂ (550 ppm). Elevated CO₂ increased, but biochar decreased, plant biomass and shoot N and P uptake, with no interactions in either soil layer. Elevated CO₂ decreased shoot N concentration by 16% and biochar decreased shoot P concentration by 11%. As a result, eCO₂ increased shoot C:N ratio by 20% and decreased the N:P ratio by 11%. Biochar decreased shoot C:N ratio by 8% in the subsoil under eCO₂. However, biochar increased shoot C:P ratio by an average of 13% and N:P ratio by 23% in the subsoil. Moreover, plants grown in the subsoil showed lower shoot N (35%) and P (70%) uptake compared to the topsoil. The results indicate that N and P are the more limiting factors that regulate plant growth under eCO₂ and biochar application, respectively. Elevated CO₂ and biochar oppositely affected dominant rhizobacterial community composition, with the eCO₂ effect being greater. The microbiota in the subsoil held a greater diversity of contrasting species than the topsoil, which were associated with nutrient cycling, hydrocarbon degradation and plant productivity. These results enrich our understanding of potential soil nutrient cycling and plant nutrient balance in future agroecosystems.

Specific metabolites drive the deterministic assembly of diseased rhizosphere microbiome through weakening microbial degradation of autotoxin

BACKGROUND

Process and function that underlie the assembly of a rhizosphere microbial community may be strongly linked to the maintenance of plant health. However, their assembly processes and functional changes in the deterioration of soilborne disease remain unclear. Here, we investigated features of rhizosphere microbiomes related to Fusarium wilt disease and assessed their assembly by comparison pair of diseased/healthy sequencing data. The untargeted metabolomics was employed to explore potential community assembly drivers, and shotgun metagenome sequencing was used to reveal the mechanisms of metabolite-mediated process after soil conditioning.

RESULTS

Results showed the deterministic assembly process associated with diseased rhizosphere microbiomes, and this process was significantly correlated to five metabolites (tocopherol acetate, citrulline, galactitol, octadecylglycerol, and behenic acid). Application of the metabolites resulted in a deterministic assembly of microbiome with the high morbidity of watermelon. Furthermore, metabolite conditioning was found to weaken the function of autotoxin degradation undertaken by specific bacterial group (Bradyrhizobium, Streptomyces, Variovorax, Pseudomonas, and Sphingomonas) while promoting the metabolism of small-molecule sugars and acids initiated from another bacterial group (Anaeromyxobacter, Bdellovibrio, Conexibacter, Flavobacterium, and Gemmatimonas). Video Abstract CONCLUSION: These findings strongly suggest that shifts in a metabolite-mediated microbial community assembly process underpin the deterministic establishment of soilborne Fusarium wilt disease and reveal avenues for future research focusing on ameliorating crop loss due to this pathogen.

Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops

Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.

Co-analysis of cucumber rhizosphere metabolites and microbial PLFAs under excessive fertilization in solar greenhouse

Fertilizer application is the most common measure in agricultural production, which can promote the productivity of crops such as cucumbers, but the problem of excessive fertilization occurs frequently in solar greenhouses. However, the effects of fertilization levels on cucumber rhizosphere soil microbes and metabolites and their relationships are still unclear. In order to determine how fertilization levels affect the rhizosphere microenvironment, we set up four treatments in the solar greenhouse: no-fertilization (N0P0K0), normal fertilization (N1P1K1), slight excessive fertilization (N2P2K2), and extreme excessive fertilization (N3P3K3). The results showed that fertilization treatments significantly increased cucumber yield compared to no-fertilization, but, the yield of N3P3K3 was significantly lower than that of N1P1K1 and N2P2K2. Fertilization levels had significant effects on rhizosphere microorganisms, and pH, NH₄ ⁺-N and AP were the main environmental factors that affected the changes in microbial communities. The total PLFAs, the percentages of fungi and arbuscular mycorrhizal fungi (AMF) were significantly reduced and bacteria percentage was significantly increased in N3P3K3 compared to other fertilization treatments. Differential metabolites under different fertilization levels were mainly organic acids, esters and sugars. Soil phenols with autotoxic effect under fertilization treatments were higher than that of N0P0K0. In addition, compared with soil organic acids and alkanes of N0P0K0, N2P2K2 was significantly increased, and N3P3K3 was not significantly different. This suggested that cucumber could maintain microbial communities by secreting beneficial metabolites under slight excessive fertilization (N2P2K2). But under extremely excessive fertilization (N3P3K3), the self-regulating ability of cucumber plants and rhizosphere soil was insufficient to cope with high salt stress. Furthermore, co-occurrence network showed that 16:1ω5c (AMF) was positively correlated with 2-palmitoylglycerol, hentriacontane, 11-octadecenoic acid, decane,4-methyl- and d-trehalose, and negatively correlated with 9-octadecenoic acid at different fertilization levels. This indicated that the beneficial microorganisms in the cucumber rhizosphere soil promoted with beneficial metabolites and antagonized with harmful metabolites. But with the deepening of overfertilization, the content of beneficial microorganisms and metabolites decreased. The study provided new insights into the interaction of plant rhizosphere soil metabolites and soil microbiomes under the different fertilization levels.