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The emergence of antibiotic-resistant diseases and increases in plant disease outbreaks, that threaten global food security, present major growing public health crises. Since most antibiotics originate from soil microorganisms, soil microbial communities offer promising reservoirs for discovering new compounds. This study explores antibiotic-producing rhizobacteria in Sage Hill's soil, a recently restored environment at UCLA. Biochemical and functional assays were used to characterize soil microbial communities from rhizosphere samples taken from Sage Hill. Using these methods, we identified antibiotic-producing bacteria, and likely Pseudomonas and Bacillus. These results underscore the importance of investigating soil microbial communities for novel antibiotic discovery and agricultural sustainability.

Plants release a wealth of metabolites into the rhizosphere that can shape the composition and activity of microbial communities in response to environmental stress. The connection between rhizodeposition and rhizosphere microbiome succession has been suggested, particularly under environmental stress conditions, yet definitive evidence is scarce. In this study, we investigated the relationship between rhizosphere chemistry, microbiome dynamics, and abiotic stress in the bioenergy crop switchgrass grown in a marginal soil under nutrient-limited, moisture-limited, and nitrogen (N)-replete, phosphorus (P)-replete, and NP-replete conditions. We combined 16S rRNA amplicon sequencing and LC-MS/MS-based metabolomics to link rhizosphere microbial communities and metabolites. We identified significant changes in rhizosphere metabolite profiles in response to abiotic stress and linked them to changes in microbial communities using network analysis. N-limitation amplified the abundance of aromatic acids, pentoses, and their derivatives in the rhizosphere, and their enhanced availability was linked to the abundance of bacterial lineages from Acidobacteria, Verrucomicrobia, Planctomycetes, and Alphaproteobacteria. Conversely, N-amended conditions increased the availability of N-rich rhizosphere compounds, which coincided with proliferation of Actinobacteria. Treatments with contrasting N availability differed greatly in the abundance of potential keystone metabolites; serotonin and ectoine were particularly abundant in N-replete soils, while chlorogenic, cinnamic, and glucuronic acids were enriched in N-limited soils. Serotonin, the keystone metabolite we identified with the largest number of links to microbial taxa, significantly affected root architecture and growth of rhizosphere microorganisms, highlighting its potential to shape microbial community and mediate rhizosphere plant-microbe interactions.

Arsenic contamination of soils threatens the health of millions globally through accumulation in crops. While plants detoxify arsenic via phytochelatin (PC) complexation and efflux of arsenite from roots, arsenite efflux mechanisms are not fully understood. Here, white lupin (Lupinus albus) was grown in semi-hydroponics and exudation of glutathione (GSH) derivatives and PCs in response to arsenic was scrutinised using LC-MS/MS. Inhibiting synthesis of PC precursor GSH with L-buthionine sulfoximine (BSO) or ABC transporters with vanadate drastically reduced (>22%) GSH-derivative and PC2 exudation, but not PC3 exudation. This was accompanied by arsenic hypersensitivity in plants treated with BSO and moderate sensitivity with vanadate treatment. Investigating arsenic-phytochelatin (As-PC) complexation revealed two distinct As-PC complexes, As bound to GSH and PC2 (GS-As-PC2) and As bound to PC3 (As-PC3), in exudates of As-treated lupin. Vanadate inhibited As-PC exudation, while BSO inhibited both the synthesis and exudation of As-PC complexes. These results demonstrate a role of GSH-derivatives and PC exudation in lupin arsenic tolerance and reveal As-PC exudation as a new potential mechanism contributing to active arsenic efflux in plants. Overall, this study uncovers insight into rhizosphere arsenic detoxification with potential to help mitigate pollution and reduce arsenic accumulation in crops.

Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.

It remains unclear whether microbial carbon limitation exists in the rhizosphere, a microbial hotspot characterized by intensive labile carbon input. Here, we collected rhizosphere soils attached to absorptive and transport roots and bulk soils in three alpine coniferous forests and evaluated the limiting resources of microbes based on the responses of microbial growth (18O incorporation into DNA) and respiration to full-factorial amendments of carbon, nitrogen, and phosphorus. The results showed that adding carbon enhanced microbial growth and respiration rates in the rhizosphere soils by 1.2- and 10.3-fold, respectively, indicating the existence of carbon limitation for both anabolic and catabolic processes. In contrast, the promoting effects of nutrient addition were weak or manifested only after the alleviation of carbon limitation, suggesting that nutrients were co-limiting or secondarily limiting resources. Moreover, the category and extent of microbial resource limitations were comparable between the rhizosphere of absorptive and transport roots, and between the rhizosphere and bulk soils. Overall, our findings offer direct evidence for the presence of microbial carbon limitation in the rhizosphere. [ABSTRACT FROM AUTHOR]

Predicting soil water status remotely is appealing due to its low cost and large‐scale application. During drought, plants can disconnect from the soil, causing disequilibrium between soil and plant water potentials at pre‐dawn. The impact of this disequilibrium on plant drought response and recovery is not well understood, potentially complicating soil water status predictions from plant spectral reflectance. This study aimed to quantify drought‐induced disequilibrium, evaluate plant responses and recovery, and determine the potential for predicting soil water status from plant spectral reflectance. Two species were tested: sweet corn (Zea mays), which disconnected from the soil during intense drought, and peanut (Arachis hypogaea), which did not. Sweet corn's hydraulic disconnection led to an extended 'hydrated' phase, but its recovery was slower than peanut's, which remained connected to the soil even at lower water potentials (−5 MPa). Leaf hyperspectral reflectance successfully predicted the soil water status of peanut consistently, but only until disequilibrium occurred in sweet corn. Our results reveal different hydraulic strategies for plants coping with extreme drought and provide the first example of using spectral reflectance to quantify rhizosphere water status, emphasizing the need for species‐specific considerations in soil water status predictions from canopy reflectance. Summary Statement: We developed models to accurately predict rhizosphere water status from hyperspectral imaging of roots and soil. We found canopies cannot always accurately predict rhizosphere water status—as our experiment revealed soil–plant disequilibrium in one species (sweet corn) but not another (peanut). [ABSTRACT FROM AUTHOR]

The construction of a plant rhizosphere system enriched with beneficial microbes (BMs) can efficiently help plants defend against phytophagous insects. However, our comprehensive understanding of this approach is still incomplete. In this review, we methodically analyzed the progress made over the last decade, identifying both challenges and opportunities. The main methods for developing a BMs‐enriched rhizosphere system include inoculating exogenous BMs into plants, amending the existing soil microbiomes with amendments, and utilizing plants to shape the soil microbiomes. BMs can assist plants in suppressing phytophagous insects across many orders, including 13 Lepidoptera, seven Homoptera, five Hemiptera, five Coleoptera, four Diptera, and one Thysanoptera species by inducing plant systemic resistance, enhancing plant tolerance, augmenting plant secondary metabolite production, and directly suppressing herbivores. Context‐dependent factors such as abiotic and biotic conditions, as well as the response of insect herbivores, can affect the outcomes of BM‐assisted plant defense. Several challenges and opportunities have emerged, including the development of synthetic microbial communities for herbivore control, the integration of biosensors for effectiveness assessment, the confirmation of BM targets for phytophagous insect defense, and the regulation of outcomes via smart farming with artificial intelligence. This study offers valuable insights for developing a BM‐enriched rhizosphere system within an integrated pest management approach. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Molybdenum plays an important role as a nutrient for plants. It has an important role in the process of plant growth and fixing nitrogen for the plant. A field experiment conducted in the autumn of 2023 aimed to study how different fertilizer treatments affected the availability of molybdenum in maize (Zea mays L.) rhizosphere and nonrhizosphere soils. The treatments included sheep manure at a rate of 8 tons per hectare, urea at 400 kg per hectare, humic acid at 500 cm³ per liter per dunum, and a control group. The experiment followed a randomized complete block design (RCBD) with three replications, using local maize seeds planted in 3 m by 3 m plots. After applying the treatments, the concentration of available molybdenum was measured in both soil regions at 70 and 100 days after planting. Results indicated that adding fertilizers (sheep manure, humic acid, and nitrogen) increased the concentration of available molybdenum in both soil regions. Specifically, the humic acid treatment had the highest concentration of available molybdenum at both 70 and 100 days, while the nitrogen treatment had the lowest. This highlights the importance of humic acid and organic materials in improving molybdenum availability. Furthermore, molybdenum concentration increased at the 100-day mark for all treatments outside the rhizosphere, except for the control, showing that all treatments enhanced molybdenum content both within and beyond the rhizosphere. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Recurring use of chemical fertilizers (CFs) in agriculture has resulted the remarkable improvement in crop productivity but their ruinous effects on environment have made a serious issue. Biological entities (e.g., several microorganisms) showing fertilizer‐like activities have gained attention in this regard. Several soil resident microorganisms interact strongly with neighboring plants and promote the growth and development of those plants through various means. In exchange of this, microbes utilize different compounds released from plant roots for their own nutrition. This mutualistic mode of interrelation predominantly relies on the transmission of signals from microbes to plants and vice versa. However, climatic factors (e.g., CO2 level, temperature, and water availability) are also important for this association. These bacterial strains are literally known as plant growth promoting rhizobacteria (PGPR) which facilitate plant growth through nitrogen fixation, mineral solubilization, phytostimulation, stress resistance, etc. Responding to the external environmental stimuli, they often modulate the expression of genes responsible for the transport of nutrients. Reduction of the use of CFs through the application of PGPR strains in the cultivation of some economically important plants has been reported by several authors. Significant yield improvement compared to the control groups was found in all experimental studies. Commercial development of the PGPR inoculants with remarkable biostimulating activities and their successive application should be expanded through collaborative association with different sectors after the removal of existing lacunae. Reading more than 100 articles on various aspects of rhizobacteria, the plan of writing this article has been executed. In this review, we have discussed about the colonization and potency of PGPR strains and how their well‐planned application in agriculture could evidently reinforce the global economy. The main structure of this text is designed as an outline from the development of interrelation between plants and PGPR to the commercialization of PGPR based on their potential role in the field of agriculture. [ABSTRACT FROM AUTHOR]

Background: Volatile organic compounds (VOCs) released by plants can act as signaling molecules mediating ecological interactions. Therefore, the study of VOCs mediated intra- and interspecific interactions with downstream plant physiological responses is critical to advance our understanding of mechanisms underlying information exchange in plants. Here, we investigated how plant-emitted VOCs affect the performance of an interspecific neighboring plant via induced shifts in root exudate chemistry with implications for root-associated microbiota recruitment. Results: First, we showed that VOCs emitted by potato-onion plants stimulate the growth of adjacent tomato plants. Then, we demonstrated that this positive effect on tomato biomass was attributed to shifts in the tomato rhizosphere microbiota. Specifically, we found potato-onion VOCs to indirectly affect the recruitment of specific bacteria (e.g., Pseudomonas and Bacillus spp.) in the tomato rhizosphere. Second, we identified and validated the compound dipropyl disulfide as the active molecule within the blend of potato-onion VOCs mediating this interspecific plant communication. Third, we showed that the effect on the tomato rhizosphere microbiota occurs via induced changes in root exudates of tomato plants caused by exposure to dipropyl disulfide. Last, Pseudomonas and Bacillus spp. bacteria enriched in the tomato rhizosphere were shown to have plant growth-promoting activities. Conclusions: Potato-onion VOCs—specifically dipropyl disulfide—can induce shifts in the root exudate of adjacent tomato plants, which results in the recruitment of plant-beneficial bacteria in the rhizosphere. Taken together, this study elucidated a new mechanism of interspecific plant interaction mediated by VOCs resulting in alterations in the rhizosphere microbiota with beneficial outcomes for plant performance. 4wKeniGUxY9GPejLMpvDe9 Video Abstract [ABSTRACT FROM AUTHOR]

Background Aims Methods Results Conclusions Liquid organic fertilizer (LOF) and root exudates contain easily decomposable carbon that can stimulate microbial growth. It is unknown what role the amount of organic matter (OM) in the growing media, and potential interactions between root presence and LOF, might play in enhancing the breakdown of OM.The aim was to better understand how the decomposition rate of plant litter is affected by added fertilizer, plant presence, and growing media OM content.A container experiment was conducted with and without tomato plants (Solanum lycopersicum L.; Heinz 5608 variety) present to evaluate the effect of three one‐time fertilizer additions (no fertilizer, LOF, and synthetic fertilizer) on litter decomposition rate. The equivalent amount of nitrogen (N), phosphorus (P), and potassium(K) was added in both fertilizer treatments. The experiment was conducted using two growing media, one containing high OM and one with negligible OM.The presence of tomato roots stimulated litter decomposition in high OM media, but not in low OM media. Adding LOF did not affect decomposition in either growing medium. Adding synthetic fertilizer led to a negative priming effect in low OM media when roots were present. The rate of decomposition was not affected by root traits.When ample OM was available, the presence of plant roots had a strong positive impact on litter decomposition. In both low and high OM media, a one‐time addition of fertilizer had minimal or negative effects on litter decomposition. We speculate that the continuous nature of root exudation leads to sustained changes in the microbial population (both community composition and size). Boosting root length growth via the one‐time addition of inorganic fertilizer when OM was negligible allowed the plant to outcompete decomposing microbes for N, possibly leading to selection for microbes that primarily feed on exudates, which resulted in retarded litter decomposition rates. In conclusion, as adding inorganic fertilizer stimulated plant and root growth more than adding the equivalent nutrients in LOF, particularly in growth media with a high OM content, it is better to add inorganic nutrients than LOF to stimulate OM breakdown when plants are present. [ABSTRACT FROM AUTHOR]

Microbiota living in the rhizosphere influences plant growth and fitness, from the opposite perspective; whether host genotypes control its root microbiota is of great interest to forest breeders and microbiologists. To improve lowyield plantations and promote sustainable management of Camellia oleifera, high-throughput sequencing was used to study the chemical properties and microbiome in rhizosphere soil of Camellia forests under three genotypes (common C. oleifera, local C. gauchowensis, and C. chekiangoleosa) and three growth stages (sapling stage at 4-year-old, primary fruit stage at 7-year-old, and full fruiting stage at 11-year-old). The results showed that the rhizosphere soil organic matter (OM), nutrient concentrations, diversity, and community composition of the microbiome were significantly varied among different Camellia genotypes. The relative abundance of symbiotic and pathotrophic fungi in the rhizosphere soil of C. chekiangoleosa was significantly higher than that of C. gauchowensis. Concentrations of OM, available phosphorus (AP), and bacterial alpha diversity increased with tree age. Fungi of Saitozyma, Mortierella, and Glomeromycota and bacteria of Burkholderia-Caballeronia-Paraburkholderia and Vicinamibacterales had potential for fertilizer development for Camellia plantation. Camellia genotypes and growth stages were significantly correlated with the rhizosphere soil pH, OM, and available potassium (AK). Soil pH and OM were key factors that affected the microbiome in the Camellia rhizosphere soils. In conclusion, tree genotypes and growth stages shaped microbial communities in Camellia rhizosphere soils, and some plant growth-promoting rhizobacteria were identified as preliminary candidates for improving Camellia plantation growth. [ABSTRACT FROM AUTHOR]

During the course of development plants form tight interactions with microorganisms inhabiting their root zone. In turn, rhizosphere bacteria, in particular members of the phylum Actinomycetota, positively influence the host plant by increasing access to essential nutrients and controlling the pathogenic microorganism's population. Herein, we report the characterisation of the rhizosphere associated actinobacteria community of Phyllostachys viridiglaucescens growing in the Nikitsky Botanical Garden (Crimean Peninsula, Ukraine). The overall composition of the bacterial community was elucidated by 16S rRNA gene amplicon sequencing followed by isolation of culturable microorganisms with the focus on actinomycetes. The metagenomic approach revealed that the representatives of phylum Actinomycetota (57.1%), Pseudomonadota (20.0%), and Acidobacteriota (12.2%) were dominating in the studied microbiome with Ilumatobacter (phylum Actinomycetota) (13.1%) being the dominant genus. Furthermore, a total of 159 actinomycete isolates, belonging to eight genera of Streptomyces, Micromonospora, Nonomuraea, Arthrobacter, Actinomadura, Kribbella, Cellulosimicrobium, and Mumia, were recovered from P. viridiglaucescens rhizosphere. The isolated species were tested for antimicrobial activity. 64% of isolates were active against at least one bacterial test-culture and 7.5% against fungal test culture. In overall, the rhizosphere bacterial communities act as a great source of actinobacterial diversity with the high potential for production of new bioactive compounds. [ABSTRACT FROM AUTHOR]

A novel actinobacterial strain, SB3-54T was isolated from rhizosphere soil of Cynanchum wilfodill, Jaecheon, Chungcheongbuk-do, Republic of Korea. Cells of strain SB3-54T were Gram-stain-positive, aerobic, rod-shaped, and flagellated which formed pale yellow colonies on Reasoner's 2A (R2A) agar. Growth occurred at 15–30 °C (optimum 25 °C), pH 5–8 (optimum pH 7), and 0–2.5% NaCl (optimum 0%). Phylogenetic and phylogenomic analyses showed that strain SB3-54T formed a separate lineage in the genus Jatrophihabitans with Jatrophihabitans telluris N237T. Strain SB3-54T was positive for catalase activity. Genomic analysis showed that SB3-54T has plant-beneficial function contributing (referred to as PBFC) genes such as root colonization and plant protection from oxidative stress. Furthermore, genome of SB3-54T contained gene clusters related to cytokinin biosynthesis, auxin response, tryptophan biosynthesis, siderophore biosynthesis and bacterial toxin-antitoxin systems. Strain SB3-54T contained iso-C16:0 as the major fatty acid and MK-9(H4) and MK-9(H6) as the predominant quinones. The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan. The major polar lipids were diphosphatidylglycerol, phosphatidylinositol polymannosides, two unidentified aminoglycophospholipids and three unidentified phospholipids. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain SB3-54T represents a novel species of the genus Jatrophihabitans. The type strain is SB3-54T (= KCTC 49134T = NBRC 114108T). [ABSTRACT FROM AUTHOR]

Background: The rhizosphere microbiome is critical for promoting plant growth and mitigating soil-borne pathogens. However, its role in fighting soil-borne virus-induced diseases, such as wheat yellow mosaic virus (WYMV) transmitted by Polymyxa graminis zoospores, remains largely underexplored. In this study, we hypothesized that during viral infections, plant microbiomes engage in critical interactions with plants, with key microbes playing vital roles in maintaining plant health. Our research aimed to identify microbial taxa that not only suppress the disease but also boost wheat yield by using a blend of techniques, including field surveys, yield assessments, high-throughput sequencing of plant and soil microbiomes, microbial isolation, hydroponic experiments, and transcriptome sequencing. Results: We found that, compared with roots and leaves, the rhizosphere microbiome showed a better performance in predicting wheat yield and the prevalence of P. graminis and WYMV across the three WYMV-impacted regions in China. Using machine learning, we found that healthy rhizospheres were marked with potentially beneficial microorganisms, such as Sphingomonas and Allorhizobium-Neorhizobium-Parararhizobium-Rhizobium, whereas diseased rhizospheres were associated with a higher prevalence of potential pathogens, such as Bipolaris and Fusicolla. Structural equation modeling showed that these biomarkers both directly and indirectly impacted wheat yield by modulating the rhizosphere microbiome and P. graminis abundance. Upon re-introduction of two key healthy rhizosphere biomarkers, Sphingomonas azotifigens and Rhizobium deserti, into the rhizosphere, wheat growth and health were enhanced. This was attributed to the up-regulation of auxin and cytokinin signaling pathways and the regulation of jasmonic acid and salicylic acid pathways during infections. Conclusions: Overall, our study revealed the critical role of the rhizosphere microbiome in combating soil-borne viral diseases, with specific rhizosphere microbes playing key roles in this process. 9s7rr2_Gfui1KYKQgMf1m6 Video Abstract [ABSTRACT FROM AUTHOR]

The plant mycobiome plays a crucial role in the host life cycle, influencing both healthy and diseased states, and is essential for plant tolerance to drought. In this study, we used ITS metabarcoding to investigate the fungal community of the drought-resistant plant Malva sylvestris L. in Morocco along a gradient of precipitation, encompassing subhumid and semi-arid environments. We sampled three biotopes: rhizosphere, bulk soil, and root endosphere. Our findings revealed an absence of beta-diversity differences between bulk soil and rhizosphere, indicating that the plant does not selectively influence its rhizosphere mycobiome. Additionally, ASVs belonging to the genus Alternaria represented up to 30% of reads in the plant's roots and correlated with drought (p = 0.006), indicating a potential role for this fungal genus in mitigating drought, possibly as part of the dark septate endophyte group. Root staining and microscopic observation revealed extensive colonization by fungal hyphae and microsclerotia-like structures. Furthermore, ASVs identified as Fusarium equiseti were also correlated with low precipitation and recognized as a hub taxon in the roots. However, it remains uncertain whether this species is pathogenic or beneficial to the plant. These insights contribute to our understanding of the plant mycobiome's role in drought tolerance and highlight the importance of specific fungal taxa in supporting plant health under varying environmental conditions. Future research should focus on characterizing these taxa's functional roles and their interactions with the host plant to further elucidate their contributions to drought resistance. [ABSTRACT FROM AUTHOR]

Background Results Conclusion Reductive soil disinfestation (RSD), which involves creating anaerobic conditions and incorporating large amounts of organic materials into the soil, has been identified as a reliable strategy for reducing soilborne diseases in successive cropping systems. However, limited research exists on the connections between soil microorganism composition and plant diseases under various types of organic material applications. This study aimed to evaluate the effects of distinct RSD strategies (control without soil amendment; RSD with 1500 kg ha−1 molasses powder; RSD with 3000 kg ha−1 molasses powder; RSD with 3000 kg ha−1 molasses powder and 37.5–41.3 kg ha−1 microbial agent) on the plant disease index, bacterial community composition and network structure in rhizosphere soil.RSD treatments significantly reduced the occurrence of black shank disease in tobacco and increased soil bacterial diversity. High amounts of molasses powder in RSD treatments further enhanced disease inhibition and reduced fungal abundance and Shannon index. RSD also increased the relative abundance of bacterial phylum Firmicutes and fungal phylum Ascomycota, while decreasing the relative abundance of bacterial phyla Chloroflexi and Acidobacteriota and fungal phylum Basidiomycota in rhizosphere soil. A multiple regression model identified bacterial positive cohesion as the primary factor influencing the plant disease index, with a greater impact than bacterial negative cohesion and community stability. The competition among beneficial bacteria for creating a healthy rhizosphere environment is likely a key factor in the success of RSD in reducing plant disease risk.RSD, especially with higher rates of molasses powder, is a viable strategy for controlling black shank disease in tobacco and promoting soil health by fostering beneficial microbial communities. This study provides guidelines for soil management and plant disease prevention. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

AbstractThe Korean fir (Abies koreana), a native coniferous species of Korea, predominantly inhabits the subalpine zone. Recently, this species has experienced a significant population decline, primarily attributed to environmental changes in the subalpine zone driven by global warming. Efforts to prevent the extinction of the Korean fir are underway, with a predominant focus on abiotic factors contributing to its decline. However, there is a notable lack of research on the complex interactions between microbial communities and Korean fir, particularly concerning how these interactions vary with the health status of the trees and their impact on population sustainability. Therefore, this study aimed to elucidate the rhizosphere fungal community structure associated with Korean fir trees in Jirisan National Park. We examined different habitat types, including the rhizospheres of native, cultivated, and dead Korean fir and bulk soil. Our findings revealed that the rhizosphere fungal community in the natural habitat of Korean fir predominantly comprises Agaricomycetes. Furthermore, the fungal community structure was more responsive to habitat type variations than seasonal changes. These findings provide basic information for conserving this endangered species and developing alternative habitats for the Korean fir. [ABSTRACT FROM AUTHOR]

Background: The root-associated microbiomes are crucial in promoting plant growth and development through symbiotic interactions with their hosts. Plants may shape their microbiomes by secreting specific root exudates. However, the potential mechanisms how plant species determine root exudates and drive microbiome assembly have been little studied. In this study, three wild tobaccos and one cultivated tobacco were used to investigate the commonalities and differences of both root-associated microbiomes and root exudates. Results: Amplicon sequencing results suggested that tobacco species significantly affected microbial communities in both the rhizosphere and root endosphere, with the strongest impact on the fungal community in the root endosphere. The microbial networks of wild tobacco species were more stable than that of the cultivated tobacco, and fungal members played a more important role in the networks of wild tobacco species, while bacterial members did so in the cultivated tobacco. The rhizosphere bacteria of wild tobacco species showed a higher functional diversity than that of the cultivated tobacco, while the bacteria in the root endosphere presented a contrary pattern. Metabolomics analysis showed significant differences in the composition and abundance of root exudates among the four tobacco species, and the greatest difference was found between the three wild species and the cultivated one. Correlation analysis showed the strongest correlation between metabolites and rhizosphere bacteria, in which O-benzoic acid (2-methoxybenzoic acid) had the most positive correlations with rhizosphere bacteria, while β-ureidoisobutenoic acid had the most negative correlations with rhizosphere bacteria. The rhizosphere bacteria Streptomyces, Hydrophilus and Roseobacter had the strongest positive correlations with metabolites, and the rhizosphere bacterium Nitrobacter had the most negative correlations with metabolites. Conclusion: This study revealed the differences of microbial communities and root exudates in the rhizosphere and root endosphere of four tobacco species, which can further improve our understanding of plant–microbiome interactions during crop domestication. [ABSTRACT FROM AUTHOR]

Introduction: Root exudates act as the "language" of plant-soil communication, facilitating crucial interactions, information exchange, and energy transfer between plants and soil. The interactions facilitated by root exudates between plants and microorganisms in the rhizosphere are crucial for nutrient uptake and stress resilience in plants. However, the mechanism underlying the interaction between root exudates and rhizosphere microorganisms in desert plants under drought conditions remains unclear, especially among closely related species. Methods: To reveal the ecological strategies employed by the genus Haloxylon in different habitats. Using DNA extraction and sequencing and UPLC-Q-Tof/MS methods, we studied root exudates and soil microorganisms from two closely related species, Haloxylon ammodendron (HA) and Haloxylon persicum (HP), to assess differences in their root exudates, soil microbial composition, and interactions. Results: Significant differences were found in soil properties and root traits between the two species, among which soil water content (SWC) and soil organic carbon (SOC) in rhizosphere and bulk soils (P < 0.05). While the metabolite classification of root exudates was similar, their components varied, with terpenoids being the main differential metabolites. Soil microbial structure and diversity also exhibited significant differences, with distinct key species in the network and differential functional processes mainly related to nitrogen and carbon cycles. Strong correlations were observed between root exudatemediated root traits, soil microorganisms, and soil properties, although the complex interactions differed between the two closely relative species. The primary metabolites found in the network of HA include sugars and fatty acids, while HP relies on secondary metabolites, steroids and terpenoids. Discussion: These findings suggest that root exudates are key in shaping rhizosphere microbial communities, increasing microbial functionality, fostering symbiotic relationships with hosts, and bolstering the resilience of plants to environmental stress. [ABSTRACT FROM AUTHOR]

Anthracnose caused by Colletotrichum is an increasingly severe disease of common vetch that reduces plant yield and quality. In this study, the effects of anthracnose on the rhizosphere soil microbial community of common vetch were studied via high-throughput sequencing. The relationship among the rhizosphere soil microbes and soil properties were analyzed. Lower fungal diversity was observed in rhizosphere soils of diseased plants. Variations in relative abundance were observed in the fungal phyla Mortierellomycota and Glomeromycota and in the bacterial phyla Acidobacteria, Oxyphotobacteria, and Verrucomicrobia. Gammaproteobacteria and Deltaproteobacteria were significantly more abundant in the rhizosphere soil of healthy plant. The bacterial community in the rhizosphere soil of diseased plant was involved in the synthesis of amino acids (glycine, serine, threonine, alanine, aspartate, and glutamate). Results of a redundancy analysis showed that Colletotrichum was negatively correlated with soil available potassium (AK) and the content of soil organic matter (SOC); however, it was positively correlated with soil pH. The relative abundances of Bacillus showed a negative correlation with soil pH and a positive correlation with AK and SOC content. The present study demonstrated that anthracnose could affect the rhizosphere soil microbial communities in common vetch, and soil properties have a close relationship with the rhizosphere soil microbes of common vetch. [ABSTRACT FROM AUTHOR]

Effective colonization by microbe in the rhizosphere is critical for establishing a beneficial symbiotic relationship with the host plant. Bacillus subtilis, a soil-dwelling bacterium that is commonly found in association with plants and their rhizosphere, has garnered interest for its potential to enhance plant growth, suppress pathogens, and contribute to sustainable agricultural practices. However, research on the dynamic distribution of B. subtilis within the rhizosphere and its interaction mechanisms with plant roots remains insufficient due to limitations in existing in situ detection methodologies. To achieve dynamic in situ detection of the rhizosphere environment, we established iRhizo-Chip, a microfluidics-based platform. Using this device to investigate microbial behavior within the rhizosphere, we found obvious diurnal fluctuations in the growth of B. subtilis in the rhizosphere. Temporal dynamic analysis of rhizosphere dissolved oxygen (DO), pH, dissolved organic carbon, and reactive oxygen species showed that diurnal fluctuations in the growth of B. subtilis are potentially related to a variety of environmental factors. Spatial dynamic analysis also showed that the spatial distribution changes of B. subtilis and DO and pH were similar. Subsequently, through in vitro control experiments, we proved that rhizosphere DO and pH are the main driving forces for diurnal fluctuations in the growth of B. subtilis. Our results show that the growth of B. subtilis is driven by rhizosphere DO and pH, resulting in diurnal fluctuations, and iRhizo-Chip is a valuable tool for studying plant rhizosphere dynamics. [ABSTRACT FROM AUTHOR]

Switchgrass (Panicum virgatum L.) is a native, low-input North American perennial crop primarily grown for bioenergy, livestock forage, and industrial fiber. To achieve no-input switchgrass production that meets biomass needs, several switchgrass genotypes have been identified that have a low or negative response to nitrogen fertilizer, i.e., the biomass accumulation with added nitrogen is less than or equal to that when grown without nitrogen. In order to improve the viability of low-input switchgrass production, a more detailed understanding of the biogeochemical mechanisms active in these select genotypes is needed. 16S and ITS amplicon sequencing and qPCR of key functional genes were applied to switchgrass rhizospheres to elucidate microbial community structure in high-producing, no-input switchgrass families. Rhizosphere microbial community structure differed strongly between sites, and nitrogen responsiveness. [ABSTRACT FROM AUTHOR]

Military sites, both active and decommissioned, are rarely studied and may represent a source of fungal bioresources with potential applications for the remediation of co-contaminated soils. The aims of this study were both deepening the knowledge on fungal communities of a decommissioned military site and identifying indigenous bioresources showing potentialities for downstream mycoremediation applications. The culturable fractions of soil fungal communities of an Italian decommissioned military site were isolated from six representative sampling plots. In addition, the fungal community of the rhizosphere of Plantago lanceolata was also isolated. α and β diversity indices were used to analyze biodiversity data of the isolated fungal communities. A polycyclic aromatic hydrocarbons (PAHs) enrichment microplate experiment in the presence of Zn, Pb, and Zn-Pb co-contamination was conducted, followed by in vitro functional traits screenings, to select the isolates with the best potential for future mycoremediation applications. Globally 101 taxa, accounting for a total of 546 strains, were isolated from the samples. The enrichment results highlighted several fungal species showing the ability to use PAHs as nutritional source, even in the co-presence of potentially toxic elements. Finally, the analysis of their functional traits revealed their potential for biotechnological applications in soil detoxification. [ABSTRACT FROM AUTHOR]

Summary: The onset of stomatal closure reduces transpiration during drought. In seed plants, drought causes declines in plant water status which increases leaf endogenous abscisic acid (ABA) levels required for stomatal closure. There are multiple possible points of increased belowground resistance in the soil–plant atmospheric continuum that could decrease leaf water potential enough to trigger ABA production and the subsequent decreases in transpiration.We investigate the dynamic patterns of leaf ABA levels, plant hydraulic conductance and the point of failure in the soil–plant conductance in the highly embolism‐resistant species Callitris tuberculata using continuous dendrometer measurements of leaf water potential during drought.We show that decreases in transpiration and ABA biosynthesis begin before any permanent decreases in predawn water potential, collapse in soil–plant hydraulic pathway and xylem embolism spread.We find that a dynamic but recoverable increases in hydraulic resistance in the soil in close proximity to the roots is the most likely driver of declines in midday leaf water potential needed for ABA biosynthesis and the onset of decreases in transpiration. [ABSTRACT FROM AUTHOR]

Soil salinization during wheat cultivation considerably diminishes soil fertility and impedes wheat growth, primarily due to rhizosphere microbial community changes. Our study investigates the application of Bacillus subtilis YJ-15, a strain isolated from the rhizosphere of wheat cultivated in salinized soil, as a soil remediation agent. This strain has demonstrated significant salt tolerance, disease suppression capabilities, and growth-promoting attributes in previous studies. The wheat rhizosphere was examined to assess the impact of Bacillus subtilis YJ-15 on microbial community composition and soil fertility. Fertility of soil in saline soil was significantly increased by inoculating wheat with YJ-15. The microbial community structure within the wheat rhizosphere inoculated with Bacillus subtilis YJ-15 was analyzed through sequencing on the Illumina MiSeq platform. Phyla Proteobacteria and Acidobacteria were identified as the dominant bacteria. Basidiomycota, Mortierellomycota, and Ascomycota dominated the fungal phyla. Among the bacterial genera, Pseudomonas, Arthrobacter, and Bacillus were predominant. The predominant fungal genera included Alternaria, Cephalotrichum, Mortierella, and Chaetomium. A significant increase in Gaiella and Haliangium levels was observed in the YJ group compared to the control group. Additionally, the fungal genera Epicoccum, Sporidiobolus, and Lecythophora have significantly increased in YJ abundance. One of the potential benefits of Bacillus subtilis YJ-15 in the cultivation of wheat on salinized land is its ability to enhance the rhizosphere microbial community structure and improve soil fertility. [ABSTRACT FROM AUTHOR]

The objective of this study was to isolate and characterize actinobacteria from the rhizosphere of medicinal and aromatic plants, specifically lavender (Lavandula angustifolia Mill.), lemon balm (Melissa officinalis L.), and oregano (Origanum vulgare L.). Rhizospheric soil samples revealed a high abundance of culturable actinobacteria (6.97–7.23 log10 CFU/g). Six isolates were selected for their promising enzymatic activities (lignin peroxidase, carboxymethyl cellulase) and antimicrobial properties. Isolates M345 and M162 exhibited the highest cellulase activity indices (3.19 ± 0.71 and 2.54 ± 0.22, respectively), with five isolates producing lignin peroxidase. These actinobacteria also demonstrated plant growth-promoting traits such as phosphate solubilization and nitrogen fixation, along with strong antimicrobial activity against Gram-negative bacteria and phytopathogenic fungi. Additionally, they significantly enhanced maize seed germination, increasing the vigor index from 4283.33 ± 1264.37 to 6248.28 ± 1661.94 compared to that of the control. These results indicate that the isolated actinobacteria strains hold potential as microbial inoculants for sustainable agriculture, contributing to soil health, plant growth, and pathogen management. [ABSTRACT FROM AUTHOR]

The root zone is a vital part of the Earth system and a key element in hydrology, ecology, agronomy, and land surface processes. However, its definition varies across disciplines, creating barriers to interdisciplinary understanding. Moreover, characterizing the root zone is challenging due to a lack of consensus on definitions, estimation methods, and their merits and limitations. This opinion paper provides a holistic definition of the root zone from a hydrology perspective, including its moisture storage, deficit, and storage capacity. We demonstrate that the root zone plays a critical role in the biosphere, pedosphere, rhizosphere, lithosphere, atmosphere, and cryosphere of the Earth system. We underscore the limitations of the traditional reductionist approach in modelling this complex and dynamic zone and advocate for a shift towards a holistic, ecosystem-centred approach. We argue that a holistic approach offers a more systematic, simple, dynamic, scalable, and observable way to describe and predict the role of the root zone in Earth system science. [ABSTRACT FROM AUTHOR]

To address the issue of phosphorus limitation in agricultural and forestry production and to identify green and economical alternatives to chemical phosphorus fertilizers, this paper reviews the utilization of phosphorus in plant–soil systems and explores the considerable potential for exploiting endogenous phosphorus resources. The application of phosphate-solubilizing microorganisms (PSMs) is emphasized for their role in phosphorus activation and plant growth promotion. A focus is placed on microbial interactions as an entry point to regulate the functional rhizosphere microbiome, introducing the concept of synthetic communities. This approach aims to deepen the understanding of PSM interactions across plant root, soil, and microbial interfaces, providing a theoretical foundation for the development and application of biological regulation technologies to enhance phosphorus utilization efficiency. [ABSTRACT FROM AUTHOR]

An experiment of pakchoi after conventional fertilization was conducted with Chlorella emersonii inoculation. The yield, nitrogen use efficiency, and rhizosphere microbial community of pakchoi were investigated, and the relationship among them was also determined. The results showed that C. emersonii inoculation with half dose increased the fresh weight and nitrogen use efficiency of pakchoi by 6.5% and 28.1%, respectively. Rhizosphere microbial community structure after C. emersonii inoculation was distinctly affected, which reflected the higher bacterial alpha diversity and lower fungal alpha diversity, and had positive and negative correlations with pakchoi performance characteristics, respectively. The dominant phyla showed that C. emersonii inoculation significantly increased the abundance of Proteobacteria and decreased the abundance of Actinobacteria for bacteria, however, all fungal abundances also decreased. At a higher classification resolution, C. emersonii inoculation enriched the indigenous Sphingomonas and introduced the nonindigenous Pseudofulvimonas involved in the nitrogen cycle, which might be responsible for the improvement of pakchoi yield by enhancing nitrogen use efficiency. The higher bacterial alpha diversity with enriched Sphingomonas and Pseudofulvimonas might provide a driving force for the greater pakchoi yield and nitrogen use efficiency under the half dose of C. emersonii inoculation compared with the total dose. This study suggested that C. emersonii inoculation improved the yield and nitrogen use efficiency of pakchoi through the amendment of beneficial rhizosphere microflora, especially those related to the nitrogen cycle, and confirmed the positive effectiveness of conventional fertilization regimes together with C. emersonii inoculation on fertilization efficiency and agricultural production. [ABSTRACT FROM AUTHOR]

One of the most talked about issues of the 21st century is climate change, as it affects not just our health but also forestry, agriculture, biodiversity, the ecosystem, and the energy supply. Greenhouse gases are the primary cause of climate change, having dramatic effects on the environment. Climate change has an impact on the function and composition of the terrestrial microbial community both directly and indirectly. Changes in the prevailing climatic conditions brought about by climate change will lead to modifications in plant physiology, root exudation, signal alteration, and the quantity, makeup, and diversity of soil microbial communities. Microbiological activity is very crucial in organic production systems due to the organic origin of microorganisms. Microbes that benefit crop plants are known as plant growth‐promoting microorganisms. Thus, the effects of climate change on the environment also have an impact on the abilities of beneficial bacteria to support plant growth, health, and root colonization. In this review, we have covered the effects of temperature, precipitation, drought, and CO2 on plant–microbe interactions, as well as some physiological implications of these changes. Additionally, this paper highlights the ways in which bacteria in plants' rhizosphere react to the dominant climatic conditions in the soil environment. The goal of this study is to analyze the effects of climate change on plant–microbe interactions. [ABSTRACT FROM AUTHOR]

The rhizosphere is an important interface for soil–plant interaction and a significant zone for the uptake and removal of heavy metals from soils. This study assesses the level of heavy metals contamination in the rhizosphere of plants growing at a decommissioned tailings dam in Ghana. Concentrations of heavy metals [Arsenic, Cadmium, Copper, Iron, Manganese and Zinc] and physicochemical parameters [pH, conductivity, total dissolved solids, phosphate, nitrate, sulfate] of rhizospheric soils were determined. The assessment of the extent of rhizospheric contamination was conducted using the enrichment factor (EF), geo-accumulation index (Igeo), and pollution load index (PLI). Factor analysis unveiled the most relevant heavy metal contributors to rhizosphere contamination. Results indicate moderate to significant enrichment of Cd (1.72 – 8.28) and Mn (1.70 – 8.32) in the rhizosphere. The PLI showed that rhizospheres are heavily polluted (18.8 – 29.6) and thus require remediation. Principal component analysis revealed significant Cd, As, and Fe contamination in the rhizosphere accrues from anthropogenic or mining activities. The levels of heavy metal ions in the rhizosphere suggest that Mimosa pudica, Centrosema pubescens, Leucaena leucocephala, Pueraria phaseoloides, and Tridax procumbens could be investigated as candidates for phytostabilization of mine tailings. This study emphasizes the importance of effective remediation and continual tailing dam monitoring before and after decommissioning to avert the spread of heavy metal contaminants. [ABSTRACT FROM AUTHOR]

This study reports a biorestoration strategy of highly weathered tailings piles generating As-rich acid mine drainage, which consisted of a grass cover assisted with geochemical processes (neutralization, precipitation, and sorption) induced by native soil and limestone. Besides, sulfate-reducing bacteria (SRB) are raised as a possible adjuvant in the biorestoration strategy. Tailings, soil, and limestone were collected in Zimapán, Mexico. Fungi and bacteria were isolated from tailings and identified by biochemical tests and the BIOLOG® database. SRB was also isolated from tailings in the Postgate and Baar culture media, then the kinetic growth was determined. Biorestoration experiments were carried out in rhizotrons containing different mixtures of tailings, soil, and limestone; afterward, grass seeds and SRB were added. Arsenic was selected as an indicator of the biorestoration strategy, discussing its biogeochemical behavior. Microbiological results showed the presence in tailings of 4 fungi strains belonging to the Aspergillus sp genus, whose existence does not favor the treatments due to its possible bioleaching capacity. Different bacteria were found, including Bacillus subtilis, Bacillus cereus, Ralstonia solanacearum, and Sphingomonas paucimobilis, which could benefit the treatments. The grass grew in all the treatments, reaching As concentrations of up to 2.83 mg/kg and 5.06 mg/kg in the aerial part and root, respectively. SEM–EDS analysis showed As sorbed on Fe-oxo-hydroxides and some amorphous morphologies containing Fe–As–S associations, which could be related to SRB-induced biogenic sulfides. This biorestoration strategy could be implemented in the field and sites with similar environmental problems. [ABSTRACT FROM AUTHOR]

Background: Soil bacteria often form close associations with their host plants, particularly within the root compartment, playing a significant role in plant growth and stress resilience. Vachellia tortilis subsp. raddiana, (V. tortilis subsp. raddiana)a leguminous tree, naturally thrives in the harsh, arid climate of the Guelmim region in southern Morocco. This study aims to explore the diversity and potential plant growth-promoting (PGP) activities of bacteria associated with this tree. Results: A total of 152 bacterial isolates were obtained from the rhizosphere of V. tortilis subsp. raddiana. Rep-PCR fingerprinting revealed 25 distinct genomic groups, leading to the selection of 84 representative strains for further molecular identification via 16 S rRNA gene sequencing. Seventeen genera were identified, with Bacillus and Pseudomonas being predominant. Bacillus strains demonstrated significant tolerance to water stress (up to 30% PEG), while Pseudomonas strains showed high salinity tolerance (up to 14% NaCl). In vitro studies indicated variability in PGP activities among the strains, including mineral solubilization, biological nitrogen fixation, ACC deaminase activity, and production of auxin, siderophores, ammonia, lytic enzymes, and HCN. Three elite strains were selected for greenhouse inoculation trials with V. tortilis subsp. raddiana. Strain LMR725 notably enhanced various plant growth parameters compared to uninoculated control plants. Conclusions: The findings underscore the potential of Bacillus and Pseudomonas strains as biofertilizers, with strain LMR725 showing particular promise in enhancing the growth of V. tortilis subsp. raddiana. This strain emerges as a strong candidate for biofertilizer formulation aimed at improving plant growth and resilience in arid environments. [ABSTRACT FROM AUTHOR]

Summary Interactions between plants and microorganisms are pivotal for plant growth and productivity. Several plant molecular mechanisms that shape these microbial communities have been identified. However, the importance of nitric oxide (NO) produced by plants for the associated microbiota remains elusive. Using Arabidopsis thaliana isogenic mutants overproducing NO (nox1, NO overexpression) or down‐producing NO (i.e. nia1nia2 impaired in the expression of both nitrate reductases NR1/NIA1 and NR2/NIA2; the 35s::GSNOR1 line overexpressing nitrosoglutathione reductase (GSNOR) and 35s::AHB1 line overexpressing haemoglobin 1 (AHB1)), we investigated how altered NO homeostasis affects microbial communities in the rhizosphere and in the roots, soil microbial activity and soil metabolites. We show that the rhizosphere microbiome was affected by the mutant genotypes, with the nox1 and nia1nia2 mutants causing opposite shifts in bacterial and fungal communities compared with the wild‐type (WT) Col‐0 in the rhizosphere and roots, respectively. These mutants also exhibited distinctive soil metabolite profiles than those from the other genotypes while soil microbial activity did not differ between the mutants and the WT Col‐0. Our findings support our hypothesis that changes in NO production by plants can influence the plant microbiome composition with differential effects between fungal and bacterial communities. [ABSTRACT FROM AUTHOR]

For taxonomy based classification of metagenomics assembled contigs, current methods use sequence similarity to identify their most likely taxonomy. However, in the related field of metagenomic binning, contigs are routinely clustered using information from both the contig sequences and their abundance. We introduce Taxometer, a neural network based method that improves the annotations and estimates the quality of any taxonomic classifier using contig abundance profiles and tetra-nucleotide frequencies. We apply Taxometer to five short-read CAMI2 datasets and find that it increases the average share of correct species-level contig annotations of the MMSeqs2 tool from 66.6% to 86.2%. Additionally, it reduce the share of wrong species-level annotations in the CAMI2 Rhizosphere dataset by an average of two-fold for Metabuli, Centrifuge, and Kraken2. Futhermore, we use Taxometer for benchmarking taxonomic classifiers on two complex long-read metagenomics data sets where ground truth is not known. Taxometer is available as open-source software and can enhance any taxonomic annotation of metagenomic contigs. Taxonomic classification of DNA sequences is typically performed on each sequence individually. Here the authors present a deep learning-based method that utilizes information across a dataset to enhance taxonomic annotations of any microbiome. [ABSTRACT FROM AUTHOR]

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. 5_PfxzZNKyxgT3zPqUmUdg Video Abstract [ABSTRACT FROM AUTHOR]

Introduction: Corm rot in saffron (Crocus sativus L.) significantly impacts yield and quality. Non-toxic fungi, particularly Trichoderma species, are valuable for biological control due to their production of diverse and biologically active secondary metabolites. Methods: This study aimed to isolate an effective antagonistic fungus against the pathogenic fungi causing corm rot in saffron. Four pathogenic fungi (Fusarium oxysporum, Fusarium solani, Penicillium citreosulfuratum, and Penicillium citrinum) were isolated from diseased saffron bulbs in Chongming. Initial screening through dual culture with these pathogens re-screening from rhizosphere soil samples of C. sativus based on its inhibitory effects through volatile, nonvolatile, and fermentation broth metabolites. The inhibitory effect of biocontrol fungi on pathogenic fungi in vitro was evaluated by morphological observation and molecular biology methods. Results: Antagonistic fungi were identified as Trichoderma brevicompactum DTN19. F. oxysporum was identified as the most severe pathogen. SEM (scanning electron microscope) and TEM (transmission electron microscope) observations revealed that T. brevicompactum DTN19 significantly inhibited the growth and development of F. oxysporum mycelium, disrupting its physiological structure and spore formation. Additionally, T. brevicompactum DTN19 demonstrated nitrogen fixation and production of cellulase, IAA (Indole acetic acid), and siderophores. Whole-genome sequencing of strain DTN19 revealed genes encoding protease, cellulase, chitinase, ß-glucosidase, siderophore, nitrogen cycle, and sulfate transporter-related proteins. Discussion: T. brevicompactum DTN19 may inhibit the propagation of pathogenic fungi by destroying their cell walls or producing antibiotics. It can also produce IAA and iron carriers, which have the potential to promote plant growth. Overall, T. brevicompactum DTN19 showed the development prospect of biological agents. [ABSTRACT FROM AUTHOR]

Plant-growth-promoting rhizobacteria (PGPR) play an important role in plant growth and rhizosphere soil. In order to evaluate the effects of PGPR strains on tea plant growth and the rhizosphere soil microenvironment, 38 PGPR strains belonging to the phyla Proteobacteria with different growth-promoting properties were isolated from the rhizosphere soil of tea plants. Among them, two PGPR strains with the best growth-promoting properties were then selected for the root irrigation. The PGPR treatment groups had a higher Chlorophyll (Chl) concentration in the eighth leaf of tea plants and significantly promoted the plant height and major soil elements. There were significant differences in microbial diversity and metabolite profiles in the rhizosphere between different experimental groups. PGPR improved the diversity of beneficial rhizosphere microorganisms and enhanced the root metabolites through the interaction between PGPR and tea plants. The results of this research are helpful for understanding the relationship between PGPR strains, tea plant growing, and rhizosphere soil microenvironment improvement. Moreover, they could be used as guidance to develop environmentally friendly biofertilizers with the selected PGPR instead of chemical fertilizers for tea plants. [ABSTRACT FROM AUTHOR]

Biodegradable microplastics (Bio-MPs) are a hot topic in soil research due to their potential to replace conventional microplastics. Biofertilizers are viewed as an alternative to inorganic fertilizers in agriculture due to their potential to enhance crop yields and food safety. The use of both can have direct and indirect effects on rhizosphere microorganisms. However, the influence of the coexistence of "Bio-MPs and biofertilizers" on rhizosphere microbial characteristics remains unclear. We investigated the effects of coexisting biofertilizers and Bio-MPs on the structure, function, and especially the carbon metabolic properties of crop rhizosphere bacteria, using a pot experiment in which polyethylene microplastics (PE-MPs) were used as a reference. The results showed that the existence of both microplastics (MPs) changed the physicochemical properties of the rhizosphere soil. Exposure to MPs also remarkably changed the composition and diversity of rhizosphere bacteria. The network was more complex in the Bio-MPs group. Additionally, metagenomic analyses showed that PE-MPs mainly affected microbial vitamin metabolism. Bio-MPs primarily changed the pathways related to carbon metabolism, such as causing declined carbon fixation/degradation and inhibition of methanogenesis. After partial least squares path model (PLS-PM) analysis, we observed that both materials influenced the rhizosphere environment through the bacterial communities and functions. Despite the degradability of Bio-MPs, our findings confirmed that the coexistence of biofertilizers and Bio-MPs affected the fertility of the rhizosphere. Regardless of the type of plastic, its use in soil requires an objective and scientifically grounded approach. [ABSTRACT FROM AUTHOR]

The gut microbiome of worms from composting facilities potentially harbors organisms that are beneficial to plant growth and development. In this experiment, we sought to examine the potential impacts of rhizosphere microbiomes derived from Eisenia fetida worm castings (i.e. vermicompost) on tomato (Solanum lycopersicum, L.) plant growth and physiology. Our experiment consisted of a greenhouse trial lasting 17 weeks total in which tomato plants were grown with one of three inoculant treatments: a microbial inoculant created from vermicompost (V), a microbial inoculant created from sterilized vermicompost (SV), and a no-compost control inoculant (C). We hypothesized that living microbiomes from the vermicompost inoculant treatment would enhance host plant growth and gene expression profiles compared to plants grown in sterile and control treatments. Our data showed that bacterial community composition was significantly altered in tomato rhizospheres, but fungal community composition was highly variable in each treatment. Plant phenotypes that were significantly enhanced in the vermicompost and sterile vermicompost treatments, compared to the control, included aboveground biomass and foliar δ15N nitrogen. RNA sequencing revealed distinct gene expression changes in the vermicompost treatment, including upregulation of nutrient transporter genes such as Solyc06g074995 (high affinity nitrate transporter), which exhibited a 250.2-fold increase in expression in the vermicompost treatment compared to both the sterile vermicompost and control treatments. The plant transcriptome data suggest that rhizosphere microbiomes derived from vermicompost can influence tomato gene expression and growth-related regulatory pathways, which highlights the value of RNA sequencing in uncovering molecular responses in plant microbiome studies. [ABSTRACT FROM AUTHOR]

Introduction: Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) is one of the primary routes of antimicrobial resistance (AMR) dissemination. In the One Health context, tracking the spread of mobile genetic elements (MGEs) carrying ARGs in agri-food ecosystems is pivotal in understanding AMR diffusion and estimating potential risks for human health. So far, little attention has been devoted to plant niches; hence, this study aimed to evaluate the conjugal transfer of ARGs to the bacterial community associated with the plant rhizosphere, a hotspot for microbial abundance and activity in the soil. We simulated a source of AMR determinants that could enter the food chain via plants through irrigation. Methods: Among the bacterial strains isolated from treated wastewater, the strain Klebsiella variicola EEF15 was selected as an ARG donor because of the relevance of Enterobacteriaceae in the AMR context and the One Health framework. The strain ability to recolonize lettuce, chosen as a model for vegetables that were consumed raw, was assessed by a rifampicin resistant mutant. K. variicola EEF15 was genetically manipulated to track the conjugal transfer of the broad host range plasmid pKJK5 containing a fluorescent marker gene to the natural rhizosphere microbiome obtained from lettuce plants. Transconjugants were sorted by fluorescent protein expression and identified through 16S rRNA gene amplicon sequencing. Results and discussion: K. variicola EEF15 was able to colonize the lettuce rhizosphere and inhabit its leaf endosphere 7 days past bacterial administration. Fluorescence stereomicroscopy revealed plasmid transfer at a frequency of 10−3; cell sorting allowed the selection of the transconjugants. The conjugation rates and the strain’s ability to colonize the plant rhizosphere and leaf endosphere make strain EEF15::lacIq -pLpp-mCherry-gmR with pKJK5::Plac::gfp an interesting candidate to study ARG spread in the agri-food ecosystem. Future studies taking advantage of additional environmental donor strains could provide a comprehensive snapshot of AMR spread in the One Health context. [ABSTRACT FROM AUTHOR]

The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture. [ABSTRACT FROM AUTHOR]

Introduction: Despite their adverse environmental effects, modern agriculture relies heavily on agrochemicals to manage diseases and pests and enhance plant growth and productivity. Some of these functions could instead be fulfilled by endophytes from the plant microbiota, which have diverse activities beneficial for plant growth and health. Methods: We therefore used a microbiome-guided top-down approach to select ten bacterial strains from different taxa in the core microbiome of tomato plants in the production chain for evaluation as potential bioinoculants. High-quality genomes for each strain were obtained using Oxford Nanopore long-read and Illumina short-read sequencing, enabling the dissection of their genetic makeup to identify phyto-beneficial traits. Results: Bacterial strains included both taxa commonly used as biofertilizers and biocontrol agents (i.e. Pseudomonas and Bacillus) as well as the less studied genera Leclercia, Chryseobacterium, Glutamicibacter, and Paenarthorbacter. When inoculated in the tomato rhizosphere, these strains promoted plant growth and reduced the severity of Fusarium Crown and Root Rot and Bacterial Spot infections. Genome analysis yielded a comprehensive inventory of genes from each strain related to processes including colonization, biofertilization, phytohormones, and plant signaling. Traits directly relevant to fertilization including phosphate solubilization and acquisition of nitrogen and iron were also identified. Moreover, the strains carried several functional genes putatively involved in abiotic stress alleviation and biotic stress management, traits that indirectly foster plant health and growth. Discussion: This study employs a top-down approach to identify new plant growth-promoting rhizobacteria (PGPRs), offering an alternative to the conventional bottom-up strategy. This method goes beyond the traditional screening of the strains and thus can expand the range of potential bioinoculants available for market application, paving the way to the use of new still underexplored genera. [ABSTRACT FROM AUTHOR]

Capsaicinoids are produced uniquely in pepper fruits, and its level determines the commercial quality and health-promoting properties of pepper. So, it is particularly important to increase capsaicinoids content in pepper. Rhizosphere microbiota is critical to plant growth and performance, and affected by plant varieties. However, the impact of pepper varieties with different capsaicinoids yields on the rhizosphere microbiota is poorly understood. Using high-throughput sequencing of the 16S rRNA and internal transcribed spacer (ITS) region, we investigated the rhizosphere microbial community among five pepper varieties containing different capsaicinoids. Our results demonstrated that pepper variety significantly influenced the diversity and structure of rhizosphere microbial community. Bacterial diversity in varieties with high capsaicinoids content was significantly higher than in varieties with low capsaicinoids content, while fungal diversity was opposite to bacterial diversity. The correlation analysis revealed that 19 dominant bacterial genera (e.g., Chujaibacter, Rhodanobacter, and Gemmatimonas) were significantly correlated with capsaicinoids content, and nine of them were also significantly associated with soil nutrients, whereas only one fungal genus (Podospora) was significantly correlated with capsaicinoids content. Additionally, almost all genera which significantly correlated to capsaicinoids content were biomarkers of the five pepper varieties and the correlation was well corresponding to the capsaicinoids content. Overall, our results confirmed that the variety of pepper significantly affected the rhizosphere microbial community in the fields, and bacteria and fungi responded differently to capsaicinoids, which may affect the biosynthesis of capsaicinoids and contribute to further improvement of capsaicinoids production in pepper fruits. [ABSTRACT FROM AUTHOR]

This study aimed for a better understanding of the niche specification of bacteria carrying the tfd-genes for aerobic 2,4-dichlorphenoxyacetic acid (2,4-D) degradation in the rice paddy ecosystem. To achieve this, a dedicated microcosm experiment was set up to mimic the rice paddy system, with and without 2,4-D addition, allowing spatial sampling of the different rice paddy compartments and niches, i.e., the main anaerobic bulk soil and the aerobic surface water, surface soil, root surface and rhizosphere compartments. No effect of 2,4-D on the growth and morphology of the rice plant was noted. 2,4-D removal was faster in the upper soil layers compared to the deeper layers and was more rapid after the second 2,4-D addition compared to the first. Moreover, higher relative abundances of the 2,4-D catabolic gene tfdA and of the mobile genetic elements IncP-1 and IS1071 reported to carry the tfd-genes, were observed in surface water and surface soil when 2,4-D was added. tfdA was also detected in the root surface and rhizosphere compartment but without response to 2,4-D addition. While analysis of the bacterial community composition using high-throughput 16S rRNA gene amplicon sequencing did not reveal expected tfd-carrying taxa, subtle community changes linked with 2,4-D treatment and the presence of the plant were observed. These findings suggest (i) that the surface soil and surface water are the primary and most favorable compartements/niches for tfdmediated aerobic 2,4-D biodegradation and (ii) that the community structure in the 2,4-D treated rice paddy ecosystem is determined by a niche-dependent complex interplay between the effects of the plant and of 2,4-D. [ABSTRACT FROM AUTHOR]

Despite gaining significant attention in recent years, it remains unclear whether mycorrhizal fungi distribute meaningful amounts of resources among trees in ways that increase the fitness of the receiving trees. To investigate this, we used pairs of shaded and unshaded Pinus halepensis or Quercus calliprinos saplings, growing in both inter‐ and intra‐specific combinations outdoors in forest soil. We examined the combined effects of indirect and direct below‐ground connections on tree performance and Non‐Structural Carbohydrate (NSC) pools. Although we did not observe any growth benefits, shaded recipient oaks exhibited higher levels of root and branch NSC compared to their control counterparts, which were not connected below‐ground. This finding suggests a potential benefit of establishing below‐ground connections. However, no such benefits were observed among the unshaded pairs or in the other inter‐ and intra‐specific pairs of pines and oaks. We monitored the carbon (C) flow from a 13CO2‐labelled donor pine tree to a below‐ground connected oak tree and demonstrated C transfer from pines to shaded oaks. We also identified the main fungal symbionts interacting with pines and oaks. Our findings indicate that the effects of below‐ground C transfer are context‐dependent, manifesting in nuanced alterations in plant NSC that are not readily apparent through conventional growth metrics. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Gas exchange in the soil is determined by the size and connectivity of air‐filled pores. Root mucilage reduces air‐filled pore connectivity and thus gas diffusivity. It is unclear to what extent mucilage affects soil pore connectivity and tortuosity. The aim of this study was to gain a better understanding of gas diffusion processes in the rhizosphere by explaining the geometric alterations of the soil pore space induced by mucilage. We quantified the effect of a root mucilage analogue collected from chia seeds without intrinsic respiratory activity on oxygen diffusion at different water contents during drying–rewetting cycles in a diffusion chamber experiment. Quantification of oxygen diffusion showed that mucilage decreased the gas diffusion coefficient in dry soil without affecting air‐filled porosity. Without mucilage, a hysteresis in gas diffusion coefficient during a drying–rewetting cycle was observed. The effect depended on particle size and diminished with increasing mucilage content. X‐ray computed tomography imaging indicated a hysteresis in the connectivity of the gas phase during a drying–rewetting cycle for samples without mucilage. This effect was attenuated with increasing mucilage content. Furthermore, electron microscopy showed that mucilage structures formed in drying soil increase with mucilage content, thereby progressively reducing the connectivity of the gas phase. In conclusion, the effect of mucilage on soil gas diffusion highly depends on soil texture and mucilage content. The diminishing hysteresis with the addition of mucilage suggests that plant roots secrete mucilage to balance oxygen availability and water content, even under fluctuating moisture conditions. [ABSTRACT FROM AUTHOR]

Tree lines in high latitudes and high altitudes are considered sentinels of global change. This manifests in accelerated encroachment of trees and shrubs and enhanced plant productivity, with currently unknown implications for the carbon balance of these biomes. Given the large soil organic carbon stocks in many tree line soils, we here wondered whether introducing highly productive plants would accelerate carbon cycling through rhizosphere priming effects and if certain soils would be more vulnerable to carbon loss from positive priming than others.To test this, organic and mineral soils were sampled above and below tree lines in the Swedish sub‐arctic and the Peruvian Andes. A greenhouse experiment was then performed to quantify plant‐induced changes in soil mineralisation rates (rhizosphere priming effect) and new C formation using natural abundance labelling and the C4‐species Cynodon dactylon. Several environmental, plant, soil and microbial parameter were monitored during the experiment to complement the observations on soil C cycling.Priming was predominantly positive at the beginning of the experiment, then systematically decreased in all soils during the plant growth season to be mostly negative at the end of the experiment at plant senescence. Independent of direction of priming, the magnitude of priming was always greater in organic than in corresponding mineral soils, which was best explained by the higher C contents of these soils. Integrated over the entire study period, the overall impact of priming (positive and negative) on the soil C balance was mostly negligible. Though net soil C loss was observed in organic soils from the sub‐arctic tundra in Sweden.Most notably, positive and negative priming effects were not mutually exclusive, rather omnipresent across ecosystems, depending on sampling time. The direction of priming seems to be fluctuating with plant productivity, rhizosphere carbon inputs and nutrient uptake. This highlights the need for integrative long‐term studies if we aim to understand priming effects at ecosystem scale and greenhouse and laboratory studies must be validated in situ to enable reliable ecological upscaling. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]