Rhizosphere Environment Research Articles

The combined effects of climate, soil, and rhizospheric microorganisms determine the quality and suitable production zones of Stellaria dichotoma L. var. lanceolata Bge. in China

BackgroundStellaria dichotoma L. var. lanceolata Bge. (S. lanceolata) is a psammophytic plant endemic to the northwest region of China and has now developed into a cultivated economic crop. It is the original plant species used in traditional Chinese medicine as Yinchaihu. Recently, the lack of scientifically guided production zoning has exacerbated the arbitrary introduction and expansion of S. lanceolata cultivation, resulting in significant changes to its habitat and quality.MethodsThis study utilizes distribution data of wild S. lanceolata along with data from 33 environmental factors to analyze the primary habitat factors influencing the species' distribution using the Maxent model, simulating both current and future suitable production zones. Additionally, amplicon sequencing was employed to investigate changes in rhizospheric soil microorganisms across different cultivation sites and years. Furthermore, metabolomics, near-infrared spectroscopy, and the quantification of active ingredient content were used to assess the effects of various suitable zones on S. lanceolata.ResultsThe migration trends of S. lanceolata toward the central and eastern regions of Inner Mongolia revealed that elev, bio_4, bio_13, bio_11, and S_clay are the primary ecological and soil factors influencing suitability zoning, contributing a cumulative rate of 80.5%. The rhizosphere microbial environment shifted significantly from high to medium suitability habitats. As cultivation duration increased, the diversity of fungi and bacteria and the functional genera within the rhizosphere exhibited significant changes. Notably, there were substantial alterations in metabolic processes and substance accumulation during the transition from high to medium and low suitability zones, resulting in the identification of 281 and 370 differential metabolites, respectively. Additionally, the near-infrared spectral characteristics and active ingredient content of S. lanceolata in high suitability zones displayed distinct specificity. In particular, the contents of total flavonoids (2.772 mg·g−1), dichotomines B (0.057 mg·g−1), and quercetin-3-O-β-D-glucoside (0.312 mg·g−1) were notably higher, with the overall quality score surpassing that of other suitable zones. ConclusionThis study revealed the key climatic, soil, and rhizosphere microbial environmental factors influencing the quality formation of S. lanceolata and the selection of suitable production zones, offering guidance for sustainable development and production zone planning.Graphical

Streptomyces sp. 30702 composite chitosan alleviates continuous cropping obstacles in Chinese yam by improving rhizospheric soil microbial environment: A field study in Hainan

Yam is a vital medicinal plant, yet its cultivation faces increasing challenges, particularly due to pathogenic diseases linked to continuous cropping obstacles. This study examines the effects of Streptomyces sp. 30702 and Chitosan on anthracnose and soil microbial communities across four treatment groups: CK (control), SP (Streptomyces sp. 30702), CTS (chitosan), and SC (combined Streptomyces sp. 30702 and Chitosan) within a continuous yam cropping system. The yam was watered every 20 days with 0.25 g plant−1 of chitosan and 4.2 × 10⁵ CFU plant−1 of Streptomyces sp. 30702. Notably, the SC treatment significantly reduced the disease index by 41.31 %, cut root-knot nematode populations by 95.40 %, and boosted yield by 205.45 % compared to CK (P > 0.05). SC treatment also increased soil levels of available nitrogen, phosphorus, potassium, and urease activity. High-throughput sequencing highlighted the dominance of three bacterial phyla (Acidobacteriota, Proteobacteria, and Actinobacteriota) and three fungal phyla (Ascomycota, Basidiomycota, and unidentified Fungi) at harvest. At the bacterial genus level, Bacillus showed a significant increase in SC compared to CK, while LEfSe analysis identified five marker microorganisms in CTS (including Flavobacterium) and four in SC at the fungal genus level. Importantly, SC management reduced the relative abundance of Colletotrichum, the primary cause of anthracnose, by 42.27 % compared to CK. In the Hainan yam continuous cropping system, four Amplicon Sequence Variants (ASVs) were identified as bacterial connectors, two as module hubs, and two as fungal connectors, underscoring their roles in decomposition and environmental adaptability. The results of the Redundancy Analysis (RDA) indicate that available phosphorus in the soil significantly affects the composition of bacterial and fungal communities, with the greatest influence. Additionally, available potassium, available nitrogen, and root-knot nematodes significantly influence the bacterial community, while available nitrogen and root-knot nematodes significantly affect the fungal community (P < 0.05). Overall, the combination of Streptomyces sp. 30702 and chitosan proved to be an effective bio-agent duo, regulating soil microbial communities, reducing anthracnose, and providing a theoretical basis for addressing continuous cropping challenges in yam cultivation.

Investigating the genomic and metabolic abilities of PGPR Pseudomonas fluorescens in promoting plant growth and fire blight management.

Pseudomonas fluorescens is commonly found in diverse environments and is well known for its metabolic and antagonistic properties. Despite its remarkable attributes, its potential role in promoting plant growth remains unexplored. This study examines these traits across 14 strains residing in diverse rhizosphere environments through pangenome and comparative genome analysis, alongside molecular docking studies against Erwinia amylovora to combat fire blight. Whole genome analysis revealed circular chromosome (6.01-7.07Mb) with GC content averaging 59.95-63.39%. Predicted genes included 16S rRNA and protein-coding genes ranging from 4435 to 6393bp and 1527 to 1541bp, respectively. Pangenome analysis unveiled an open pangenome, shedding light on genetic factors influencing plant growth promotion and biocontrol, including nitrogen fixation, phosphorus solubilization, siderophore production, stress tolerance, flagella biosynthesis, and induced systemic resistance. Furthermore, pyrrolnitrin, phenazine-1-carboxylic acid, pyoluteorin, lokisin, 2,4-diacetylpholoroglucinol and pseudomonic acid were identified. Molecular docking against key proteins of E. amylovora highlighted the high binding affinities of 2,4-diacetylphloroglucinol, pseudomonic acid, and lokisin. These findings underscore the multifaceted role of P. fluorescens in plant growth promotion and biocontrol, with key biomolecules showing promising applications in plant growth and defense against pathogens.

Green manure plants enhance atrazine degradation in agriculture soil through modulating rhizosphere microbial communities

The widespread use of atrazine in agriculture threatens soil health and the safety of agricultural products. In this study, the removal and mechanism of green manure plants (GMPs) hairy vetch (Vicia villosa Roth, VV) and ryegrass (Lolium perenne L., LP) to atrazine were investigated. The results showed that VV and LP show a certain tolerance to 5–25 mg/kg atrazine contamination compared to VV and LP without atrazine (VV0 and LP0), with LP exhibiting higher tolerance. Moreover, compared to CK, VV and LP significantly promoted the removal of atrazine by 13.49%∼26.41% and 13.98%∼23.42%, respectively. VV was more effective at lower concentrations (5–10 mg/kg), while LP showed better results at 25 mg/kg. Soil enzyme activities (catalase and urease), as well as bacterial abundance and diversity, were significantly increased by VV and LP treatments. LP had a stronger effect. The function analysis revealed that VV enhances the Cell growth and death pathway in the rhizosphere soil, while LP primarily boosts the Replication and repair pathway to cope with atrazine stress. This difference likely results from the distinct root structures of the two plants, which create varying rhizosphere environments. Additionally, VV and LP upregulate the Atrazine degradation pathway by enriching atrazine-degrading bacteria, thereby promoting atrazine removal. VV growth was affected under 25 mg/kg atrazine treatment, which may lead to lower Atrazine degradation pathway abundance in the rhizosphere compared to LP. This study provides a theoretical basis for selecting plant species for the remediation of atrazine-contaminated soils.

Influences of Community Coalescence on the Assembly of Bacterial Communities of the Small-Scale Complex Aquatic System from the Perspective of Bacterial Transmission, Core Taxa, and Co-occurrence Patterns

Recirculating aquaculture and aquaponics are considered sustainable aquaculture models playing important roles in animal-derived protein supply. In these aquaculture systems, microorganisms are crucial for the system stability. The community coalescence by mixing substances and microorganisms from various microhabitats under hydraulic forces is important for shaping the bacterial communities in these small-scale complex systems. However, the influences of community coalescence on bacterial communities remain rarely revealed in these systems. In this study, aquaponics (APS) and recirculating aquaculture (RAS) systems were set up to explore the bacterial community coalescence across different microhabitats, including water, fish feces, biofilter biofilms, and plant rhizosphere environment. Our results showed that diversity and compositions varied across different microhabitats in both systems. However, bacterial transmissions across these microhabitats differed between systems. The core microbiome of the RAS and APS were formed under community coalescence with the highest contribution of bacterial taxa derived from the fish feces. Nevertheless, the plant rhizosphere bacterial community also contributed to the core microbiome of the APS. Furthermore, the core taxa showed a higher average degree than the other nodes in the bacterial community networks in all microhabitats except for the plant rhizosphere environment, implying the important roles of core taxa in maintaining these bacterial community networks. Our results provide new insights into the assembly of bacterial communities under community coalescence in the artificial aquatic ecosystems comprising complex microhabitats, which is vital for developing microbial solutions for regulating the microbial communities to improve system performance in the future.

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

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

Diurnal Rhythmicity in the Rhizosphere Microbiome—Mechanistic Insights and Significance for Rhizosphere Function

ABSTRACTThe rhizosphere is a key interface between plants, microbes and the soil which influences plant health and nutrition and modulates terrestrial biogeochemical cycling. Recent research has shown that the rhizosphere environment is far more dynamic than previously recognised, with evidence emerging for diurnal rhythmicity in rhizosphere chemistry and microbial community composition. This rhythmicity is in part linked to the host plant's circadian rhythm, although some heterotrophic rhizosphere bacteria and fungi may also possess intrinsic rhythmicity. We review the evidence for diurnal rhythmicity in rhizosphere microbial communities and its link to the plant circadian clock. Factors which may drive microbial rhythmicity are discussed, including diurnal change in root exudate flux and composition, rhizosphere physico‐chemical properties and plant immunity. Microbial processes which could contribute to community rhythmicity are considered, including self‐sustained microbial rhythms, bacterial movement into and out of the rhizosphere, and microbe‐microbe interactions. We also consider evidence that changes in microbial composition mediated by the plant circadian clock may affect microbial function and its significance for plant health and broader soil biogeochemical cycling processes. We identify key knowledge gaps and approaches which could help to resolve the spatial and temporal variation and functional significance of rhizosphere microbial rhythmicity. This includes unravelling the factors which determine the oscillation of microbial activity, growth and death, and cross‐talk with the host over diurnal time frames. We conclude that diurnal rhythmicity is an inherent characteristic of the rhizosphere and that temporal factors should be considered and reported in rhizosphere studies.

Isolation and characterization of phosphate solubilizing bacteria from the rhizosphere of lentil (Lens culinaris M.) collected from Hagere Mariam district, Central Ethiopia.

Phosphorus plays a crucial role in regulating many of the plant's metabolic activities by enhancing physiological functions and stimulating biological activities such as nodulation, nitrogen fixation, and nutrient uptake in the soil rhizosphere environment. Inoculants of phosphorus solubilizing bacteria serve as an eco-friendly alternative technology that positively influences both soil sustainability and plant growth. The majority of North Shewa highland areas are characterized by low available phosphorus, primarily acidic, and exhibit strong phosphorus absorption. The objective of this study was to isolate and identify phosphorus solubilizing bacteria from the rhizosphere of lentils and characterize their phosphate solubilizing activity. The cultural, biochemical, physiological microbial analysis was conducted in the microbiology laboratory, department of biology. Pikovskaya's medium was utilized for the isolation, screening, and maintenance of phosphate solubilizing bacteria. Phosphate Solubilizing Bacteria were isolated using tri-calcium phosphate as the sole source of phosphorus in indicator plates. Fifteen phosphate solubilizing bacteria were isolated from lentil rhizosphere soil samples, among which six were the most efficient phosphate solubilizers designated as PSBYE, PSBYR, PSBYM, PSBYL, PSBW, and PSBSW. All isolates notably solubilized tri-calcium phosphate compared to the uninoculated control. The highest phosphorous solubilization was observed from the isolate PSBYL, with a value of 10.61mg/50ml, followed by PSBW with a value of 9.08 mg/50ml. The decrease in pH value correlated with the levels of tri-phosphate solubilization in the PVK broth by the PSB isolates. The pH dropped to 4.64 from the initial pH of 7.2 when grown in the broth, which suggests that the production of organic acids is likely the primary mechanism for phosphate solubilization.

Effects of vertical forest stratification on precipitation material redistribution and ecosystem health of Pinus massoniana in the Three Gorges Reservoir area of China

Vertical stratification of forest plays important roles in the local material balance and in maintaining forest health by distributing and redistributing precipitation materials through adsorption, fixation, and release. Differences in runoff nutrient concentrations among vertical layers are closely related to vertical stratification (factors such as the trunk, canopy, forest litter, and soil physical and chemical properties). Long-term forest observations revealed significant spatial differences in Pinus massoniana (Pinus massoniana Lamb.) forests in the Three Gorges Reservoir area. Pinus massoniana forests on downslopes were characterized by a dense canopy, green needles, and rich forest vegetation, while those on upslopes were characterized by low vegetation cover, dead trees, and decreases in the tree height, diameter at breast height, and volume per plant with increasing slope. By analyzing the soil at different sites, we found that the pH of the forest land soil differed significantly among different slope positions. Soil on upper slopes was significantly more acidic than soil on lower slopes, indicating that acidic substances were intercepted by filtration through the broad litter layer and the soil surface layer. This filtration process resulted in a normal rhizosphere environment suitable for the absorption of nutrients by vegetation on the lower slopes. In this way, downhill sites provided a good microenvironment for the growth of Pinus massoniana and other vegetation. Our results show that direct contact between needles and acid rain was not the main cause of root death. Instead, the redistribution of rainfall substances by forest spatial stratification caused changes in the soil microenvironment, which inhibited the absorption of nutrients by the roots of Pinus massoniana and the growth of understory plants in Pinus massoniana forests on upper slopes. These findings emphasize that increasing land cover with forests with vertical structural stratification plays an important role in woodland material redistribution and forest conservation.

Ecological impacts of diversified agroforestry on soil nutrients and bacterial communities in Pinus massoniana plantations in the southern subtropics

Converting forests from single-species to mixed-species planting affects soil chemical and biological properties, yet its impacts within medicinal plant-based agroforestry systems remain largely unexamined. This research assessed the soil nutrient spectrum and bacterial community composition in a monoculture Pinus massoniana (CK) and various agroforestry models: (M1) Pinus massoniana and Alpina oxyphylla, (M2) Pinus massoniana and Ficus simplicissima, (M3) Pinus massoniana and Amomum villosum, and (M4) Pinus massoniana and Curcuma longa, within both field soil and rhizosphere environments. Results showed significant (p < 0.05) improvements in soil pH and cation exchange capacity (CEC) in agroforestry systems. Agroforestry models exhibited greater variability in soil macronutrient distribution, including nitrogen, potassium, calcium, magnesium, and sulfur (N, K, Ca, Mg, S), compared to monocultures. Specifically, Curcuma longa (M4C.RS) had 46.12 % higher total N content than monoculture Pinus massoniana. Micronutrients were higher in agroforestry rhizospheres, except for total zinc, which was higher in monoculture Pinus massoniana. Bacterial community analysis revealed dominant phyla including Acidobacteriota, Proteobacteria, Actinobacteria, and Chloroflexi. Agroforestry models had higher abundance of Proteobacteria, while monoculture had higher Acidobacteriota. Alpha diversity metrics, including Chao1 and Shannon indices, indicated higher species richness and evenness in agroforestry models, particularly in the rhizosphere of Amomum villosum (M3A.RS) and Curcuma longa (M4C.RS). Phylogenetic analysis indicated greater genetic diversity in agroforestry models, in terms of species richness and phylogenetic variation especially for Proteobacteria. Cluster analysis and NMDS revealed close grouping of agroforestry models, with dbRDA showing significant associations between environmental variables (pH, CEC, and nutrient profile), emphasizing their critical role in shaping bacterial community composition, supported by Spearman correlation. Functional prediction (PICRUSt2) indicated metabolism as the predominant functional category. Therefore, transition from monoculture to agroforestry, especially with Curcuma longa (M4), significantly enhanced soil fertility and ecosystem sustainability.

The Impact of Grafting with Different Rootstocks on Eggplant (Solanum melongena L.) Growth and Its Rhizosphere Soil Microecology

This study investigated the effects of grafting on eggplant growth, yield, and disease resistance, with a focus on microbial dynamics in the rhizosphere. Eggplant scions were grafted onto rootstocks of wild eggplant and tomato, with self-rooted eggplants serving as controls. Greenhouse experiments were conducted over an eight-month growing period, using standard field practices such as film mulching and integrated water–fertilizer management. High-throughput sequencing was used to analyze the biological properties and microbial community of the rhizosphere soil. Results showed that plants grafted onto ‘Huimei Zhenba’ and ‘Torvum’ rootstocks yielded up to 36.89% more than self-rooted controls, achieving yields of 4619.59 kg and 4399.73 kg per 667 m², respectively. The disease incidence of bacterial wilt was reduced to as low as 3.33% in the ‘Huimei Zhenba’ treatment, compared to 55.56% in non-grafted controls. Additionally, grafted plants exhibited increased stem diameter and chlorophyll content, with the TL/HM combination reaching 54.23 ± 3.17 SPAD units. The enhanced microbial biomass of carbon, nitrogen, and phosphorus, particularly in the TL/HM treatment (377.59 mg/kg, 28.31 mg/kg, and 36.30 mg/kg, respectively), supports a more nutrient-rich rhizosphere environment. Moreover, soil enzyme activities, such as β-glucosidase and phosphatase, were significantly higher in grafted plants, enhancing nutrient cycling and potentially increasing resistance to pathogens. Overall, grafted eggplants demonstrated enhanced soil microbial biomass, enzyme activity, and a more diverse microbial community, which are critical factors contributing to the improved yield and disease resistance observed in grafted crops.

Flue-cured tobacco intercropping with insectary floral plants improves rhizosphere soil microbial communities and chemical properties of flue-cured tobacco

BackgroundContinuous cropping of the same crop leads to land degradation. This is also called the continuous-cropping obstacle. Currently, intercropping tobacco with other crops can serve as an effective strategy to alleviate continuous cropping obstacles.ResultsIn this study, tobacco K326 and insectary floral plants were used as materials, and seven treatments of tobacco monoculture (CK), tobacco intercropped with Tagetes erecta, Vicia villosa, Fagopyrum esculentum, Lobularia maritima, Trifolium repens, and Argyranthemum frutescens respectively, were set up to study their effects on rhizosphere soil chemical properties and composition and structure of rhizosphere soil microbial community of tobacco. The 16 S rRNA gene and ITS amplicons were sequenced using Illumina high-throughput sequencing. tobacco/insectary floral plants intercropping can influence rhizosphere soil chemical properties, which also change rhizosphere microbial communities. The CK and treatment groups tobacco rhizosphere soil microorganisms had significantly different genera, such as tobacco intercropping with T. repens and A. frutescens significantly increased the number of Fusarium and intercropping T. erecta, V. villosa, L. maritima, T. repens, and A. frutescens significantly increased the number of Sphingomonas and unknown Gemmatimonadaceae. Additionally, intercropping T. erecta, V. villosa and L. maritima changed the rhizosphere fungal and bacteria community and composition of tobacco and the positive correlation between tobacco rhizosphere the genera of fungi and bacterial were greater than CK. The pathway of the carbohydrate metabolism, amino acid metabolism, and energy metabolism in rhizosphere bacteria were significantly decreased after continuous cropping. Fungal symbiotic trophic and saprophytic trophic were significantly increased after intercropping V. villosa, L. maritima and plant pathogen and animal pathogen were increased after intercropping T. repens and A. frutescens. Additionally, bacterial and fungal communities significantly correlated with soil chemical properties, respectively.ConclusionThis study reveals that intercropping tobacco with insectary floral plants, particularly T. erecta, V. villosa, L. maritima and A. frutescens significantly affects soil chemical properties and alters rhizosphere microbial communities, increasing the abundance of certain microbial genera. Additionally, intercropping enhances pathways related to carbohydrate, amino acid, and energy metabolism in rhizosphere bacteria. These findings suggest that intercropping could provide a promising strategy to overcome challenges associated with continuous tobacco cropping by regulating the rhizosphere environment.

Impacts of shifting from single-species pine forests to distinct agroforestry models on soil fertility, exchangeable cations, and microbial functions

The transition from monoculture to mixed-species agroforestry systems affects soil organic matter and microbial activity. However, the specific dynamics of these changes, particularly within medicinal plant-based agroforestry, remain underexplored. This study investigates the impact of monoculture Pine (Pinus massoniana) forests and four agroforestry models: (M1) Pinus massoniana and Alpina oxyphylla, (M2) Pinus massoniana and Ficus simplicissima, (M3) Pinus massoniana and Amomum villosum, and (M4) Pinus massoniana and Curcuma longa on soil properties and microbial activity in rhizosphere and non-rhizosphere environments. Our results showed significantly higher pH (4.80) and total nitrogen (N) content (1.77 g kg−1) in the rhizosphere of model (M4) compared to (CK). Total organic carbon (TOC) and carbon fractions (POC, DOC, and MBC) also differed significantly across monoculture and agroforestry models, with highest TOC concentrations (31.70 g kg⁻1) in rhizosphere of CK. Exchangeable cations, including Ca2⁺, and Mg2⁺ were significantly higher in the rhizosphere of agroforestry models compared to CK, particularly in M4, where Ca2⁺ was recorded at 12.03 cmol kg−1 with the highest percent base saturation (PBS) at 90.17%. Enzymes leucine aminopeptidase and polyphenol oxidase varied significantly, with higher activity in the rhizosphere of agroforestry models and greater activity in non-rhizosphere of monoculture. Soil microbial respiration (MRes) revealed substantial differences, with an average 17% decrease in rhizosphere soil for models M2 and M4 and a 20.83% reduction in non-rhizosphere soil for model M1 compared to CK. Generalized Linear Model (GLM) demonstrated a significant positive correlation between TOC and MRes (R2 = 0.885, p < 0.01), indicating that higher TOC levels are linked with increased MRes. In conclusion, model M4 most effectively enhanced soil fertility and nutrient availability followed by the other agroforestry models tested. This suggests that integrating medicinal plants into agroforestry systems is a viable strategy for improving ecosystem functioning compared to monoculture practices.

Streptomyces improves sugarcane drought tolerance by enhancing phenylalanine biosynthesis and optimizing the rhizosphere environment

Drought stress is a common hazard faced by sugarcane growth, and utilizing microorganisms to enhance plant tolerance to abiotic stress has become an important method for sustainable agricultural development. Several studies have demonstrated that Streptomyces chartreuses WZS021 improves sugarcane tolerance to drought stress. However, the molecular mechanisms underlying tolerance at the transcriptional and metabolomic levels remain unclear. We comprehensively evaluated the physiological and molecular mechanisms by which WZS021 enhances drought tolerance in sugarcane, by performing transcriptome sequencing and non-targeted metabolomics; and examining rhizosphere soil properties and plant tissue antioxidant capacity. WZS021 inoculation improved the rhizosphere nutritional environment (AP, ammonia, OM) of sugarcane and enhanced the antioxidant capacity of plant roots, stems, and leaves (POD, SOD, CAT). Comprehensive analyses of the transcriptome and metabolome revealed that WZS021 mainly affects plant drought tolerance through phenylalanine metabolism, plant hormone signal transduction, and flavonoid biosynthesis pathways. The drought tolerance signaling molecules mediated by WZS021 include petunidin, salicylic acid, α-Linoleic acid, auxin, geranylgeraniol and phenylalanine, as well as key genes related to plant hormone signaling transduction (YUCCA, amiE, AUX, CYPs, PAL, etc.). Interestingly, inoculation with WZS021 during regular watering induces a transcriptome-level response to biological stress in sugarcane plants. This study further elucidates a WZS021-dependent rhizosphere-mediated regulatory mechanism for improving sugarcane drought tolerance, providing a theoretical basis for increasing sugarcane production capacity.

Feeling hormonal? Insights into bacterial auxin sensing and its physiological effects.

Plant-microbe communication involves a rich language of chemical signals. Among these signals are plant hormones such as auxins, which are primarily recognized for their roles in plant development. However, they also function in modulating plant-microbe interactions. Interestingly, many bacteria are capable of producing auxins too. Yet, the mechanisms by which auxins affect bacteria and the regulatory processes controlling their production are largely unknown. Rico-Jiménez and colleagues present new insights into the effects of the auxin indole-3-acetic acid on the physiology of the rhizobacterium Serratia plymuthica (M. Rico-Jiménez, Z. Udaondo, T. Krell, and M. A. Matilla, mSystems 9:e00165-24, 2024, https://doi.org/10.1128/msystems.00165-24). Their work provides a deeper mechanistic understanding of bacterial transcriptional responses to plant hormones and the impact on bacterial fitness in the context of the rhizosphere environment.

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

None declared.Conflict of interestPlantation of Chinese fir, a popular woody tree species, faces sustainable issues such as nutrient deficiency and increasing disease threat. Rhizosphere and endophytic bacteria play important roles in plant' nutrient absorption and stress alleviation. Our understanding on the microbiome structure and functions are 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 P-solubilising functional isolates was enriched in fine root, while pathogen antagonism isolates was 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 bacteriome, 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 plantation and sustainable development.

Rhizosphere microbial community assembly as influenced by reductive soil disinfestation to resist successive cropping obstacle.

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.

Unveiling the Hidden Responses: Metagenomic Insights into Dwarf Bamboo (Fargesia denudata) Rhizosphere under Drought and Nitrogen Challenges.

Dwarf bamboo (Fargesia denudata) is a crucial food source for the giant pandas. With its shallow root system and rapid growth, dwarf bamboo is highly sensitive to drought stress and nitrogen deposition, both major concerns of global climate change affecting plant growth and rhizosphere environments. However, few reports address the response mechanisms of the dwarf bamboo rhizosphere environment to these two factors. Therefore, this study investigated the effects of drought stress and nitrogen deposition on the physicochemical properties and microbial community composition of the arrow bamboo rhizosphere soil, using metagenomic sequencing to analyze functional genes involved in carbon and nitrogen cycles. Both drought stress and nitrogen deposition significantly altered the soil nutrient content, but their combination had no significant impact on these indicators. Nitrogen deposition increased the relative abundance of the microbial functional gene nrfA, while decreasing the abundances of nirK, nosZ, norB, and nifH. Drought stress inhibited the functional genes of key microbial enzymes involved in starch and sucrose metabolism, but promoted those involved in galactose metabolism, inositol phosphate metabolism, and hemicellulose degradation. NO3--N showed the highest correlation with N-cycling functional genes (p < 0.01). Total C and total N had the greatest impact on the relative abundance of key enzyme functional genes involved in carbon degradation. This research provides theoretical and technical references for the sustainable management and conservation of dwarf bamboo forests in giant panda habitats under global climate change.

Dynamic in situ detection in iRhizo-Chip reveals diurnal fluctuations of Bacillus subtilis in the rhizosphere

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.

The Structural and Functional Responses of Rhizosphere Bacteria to Biodegradable Microplastics in the Presence of Biofertilizers.

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.