Interactions between Plants and Soil Microbes in Natural Ecosystem

Aucklandia lappa Decne is a valuable medicinal herb highly susceptible to root rot, a disease that severely affects its yield and quality. This study provides a comprehensive characterization of the soil ecosystems in A. lappa habitats by integrating biogeochemical and microbial functional analyses. Rhizosphere soil samples were collected from healthy plants growing in loam soil (HLS), root-rot-affected plants growing in loam soil (RRLS), and healthy plants growing in clay soil (HCS) from habitats in the Kaizhou District of Chongqing, China. We analyzed soil physicochemical properties (pH, available nitrogen, potassium, phosphorus, organic matter content, and total carbon), enzyme activities (amylase, cellulase, saccharase, β-glucosidase, β-xylosidase, and laccase), and microbial community structure (using 16S/ITS sequencing). The results demonstrated significant differences in nutrient levels and enzyme activities between healthy and diseased soils, with root-rot-affected soils displaying higher nutrient content and distinct microbial diversity. Specific bacterial (Rahnella) and fungal genera (Trichosporiella, Cyberlindnera, Barnettozyma, and Ilyonectria) were enriched in root-rot-associated soils. This suggests that these microorganisms may participate in rhizosphere ecological responses associated with root rot occurrence, although their roles may include pathogen-associated processes or potential plant adaptation responses. The results demonstrate that root rot occurrence in A. lappa is associated with coordinated changes in rhizosphere nutrient status, enzyme activities, microbial community composition, and predicted functional profiles. However, the observational nature of this study does not allow causal relationships between these changes and root rot development to be established. Full article

Apple (Malus domestica Borkh.) is a major fruit crop of global economic importance, and China ranks first worldwide in both apple cultivation area and total production. With the large-scale renewal of aging orchards, apple replant disease (ARD) has become increasingly prevalent in major apple-producing regions. ARD is typically characterized by severe growth suppression, impaired root development, increased incidence of soil-borne diseases, and, in severe cases, seedling mortality. These symptoms substantially constrain orchard renewal, limit improvements in fruit yield and quality, and threaten the sustainable development of the apple industry. The etiology of ARD is complex and involves the synergistic interaction of three factors: soil microbial dysbiosis characterized by pathogen enrichment and the depletion of beneficial microorganisms; allelopathic autotoxicity caused by the accumulation of phenolic acids, especially phloridzin; and degraded soil physicochemical properties, including acidification, compaction, and nutrient imbalance. Current management strategies mainly include the use of ARD-tolerant rootstocks, microbial regulation, chemical and physical soil disinfection, and agronomic practices such as crop rotation and organic amendment application. Among these approaches, biological regulation mediated by beneficial rhizosphere and endophytic microorganisms has attracted increasing attention because of its environmental compatibility and sustainability. This review summarizes the occurrence patterns, regional characteristics, core pathogenic mechanisms, and integrated management strategies of ARD, with particular emphasis on the functional roles of rhizosphere and endophytic microbiomes in disease alleviation. The review provides a theoretical basis and practical reference for the development of green, efficient, and sustainable strategies for ARD control and apple orchard management. Full article

Plant-parasitic reniform nematodes of the genus Rotylenchulus are semi-endoparasites of herbaceous and woody plants occurring in regions with Mediterranean, tropical, and subtropical climates. In the present study, the occurrence of reniform nematodes in the rhizosphere of three olive orchards in Central Italy and six in Sicily (Italy) was investigated. Two Rotylenchulus species were recovered in olive groves in Central Italy, and no Rotylenchulus species were found in Sicily. Using the integrative taxonomy approach, combining morphological, molecular and multivariate morphological analyses, the two species were identified as R. borealis and R. macrodoratus. The D2-D3 sequencing of four individual specimens of Italian R. macrodoratus revealed the occurrence of unique haplotypes differing in nucleotide composition each other. Interestingly, the sequencing of different ITS clones from an individual specimen of the Italian R. borealis showed two ITS paralogs differing in length and nucleotide sequence compared with those of other specimens from the same population and showing higher similarity with those from other populations. Phylogenetic analyses, based on D2-D3 expansion domains of the 28S rRNA gene, ITS, and mitochondrial COI, confirmed the high level of ribosomal variability in both species and the occurrence of new mitochondrial haplotypes for the COI. The present study confirms the occurrence of high variability in Rotylenchulus genus and the existence of variant gene copies in the same specimen that could contribute to the survival of these species in different environments. Full article

Root exudates are key drivers of rhizosphere microbial assembly, yet their effects across coexisting plant species with different functional roles remain unclear. We examined the effects of root exudates from five desert steppe species in Inner Mongolia: one constructive species, two dominant species, and two accompanying species. Exudates were collected hydroponically and applied to bulk soil in a three-week incubation experiment. Microbial communities were analyzed using high-throughput sequencing, functional prediction, and co-occurrence network analysis. Exudate addition significantly altered bacterial community composition, reducing bacterial richness, while fungal communities showed weaker responses. Exudates from constructive and dominant species enriched Actinobacteria, including Rubrobacter, Arthrobacter, and Solirubrobacter, and increased functional groups linked to chemoheterotrophy and nitrogen transformation. In contrast, exudates from accompanying species induced distinct microbial assemblages without promoting Actinobacteria dominance. Exudate addition also increased bacterial network complexity, suggesting enhanced microbial interactions. Soil pH decreased and available nitrogen and phosphorus increased, strongly correlating with bacterial community shifts. Overall, root exudates mediate species-specific microbial assembly and functional reorganization in desert steppe soils, driven mainly by plant functional roles rather than taxonomic relatedness. This study provides new insights into how plant-derived substrates regulate microbial communities and nutrient cycling in arid ecosystems. Full article

Nitrogen addition significantly affects soil aggregate stability by altering the aggregate microenvironment. Although the ecological effects of nitrogen addition on soil aggregates have been extensively investigated, studies specifically focusing on the responses of soil aggregate stability in Larix olgensis forest understories remain scarce. The effects of different forms of nitrogen addition (urea (CO(NH₂)₂), ammonium chloride (NH₄Cl), and sodium nitrate (NaNO₃)) were investigated at 20 kg N·ha⁻¹·yr⁻¹ across all treatments, and the physicochemical properties, stability, and microbial community composition of soil aggregates were determined to analyze soil aggregate stability. NaNO₃ significantly increased soil nutrient contents, promoted the formation of macroaggregates, and significantly enhanced soil aggregate stability. NH₄Cl significantly decreased bacterial diversity in microaggregates, while NaNO₃ significantly elevated fungal diversity in macroaggregates. CO(NH₂)₂ and NH₄Cl increased the relative abundances of Ascomycota and Proteobacteria in microaggregates, whereas NaNO₃ elevated the relative abundances of Mortierellomycota and Gemmatimonadetes in soil aggregates of all particle sizes. These results indicated that NaNO₃ was more effective in improving soil aggregate stability and exerted regulatory effects on microbial community structure compared to the other nitrogen forms. These findings can provide a theoretical basis for an in-depth understanding of the microecological processes of forest soil aggregates under the context of nitrogen deposition. Full article

Pseudomonas has been revealed as an important member of plant probiotics, with its rich species diversity implying complementary plant growth-promoting (PGP) traits. However, information on Pseudomonas species in the microecology of Angelica sinensis and medicinal plants in general remains to be further investigated. This study examined the microecological characteristics, PGP traits, and their underlying molecular mechanisms of Pseudomonas. Filling this gap will provide an important reference for microbial community design centered on dominant functional bacterial genera. In this study, we characterized the microecological traits, PGP properties, and their underlying molecular mechanisms of Pseudomonas strains. Microbiome analysis identified Pseudomonas as the dominant genus in the rhizosphere and a core endophytic genus, exerting significant influences on both (path coefficients = 0.971, 0.872). Comparative phenomics suggested potential functional complementarity among different strains. Our observations revealed significant differentiation in PGP traits: P. umsongensis X08 showed exceptional performance in IAA and siderophore production (IAA: 1.24 mg/mL, siderophore halo diameter: 2.04 cm); P. frederiksbergensis X06 exhibited advantages in ACC deaminase activity and potassium solubilization; and P. allii X32 demonstrated high organic phosphorus solubilization capability (3.98 mg/L). Finally, genomic data revealed that P. allii X32 possesses a rich repertoire of PGP-related genes and metabolic pathways, providing a basis for establishing molecular mechanistic hypotheses for these traits. In summary, Pseudomonas strains from different species, which exhibit complementary probiotic functions without antagonism in the A. sinensis microecosystem, provide valuable microbial resources for the ecological cultivation of A. sinensis. Full article

Microorganisms are fundamental drivers of soil productivity, mediating nutrient cycling and pathogen suppression. In this study, we evaluated changes in the fungal community in the soil of barley (Hordeum vulgare L.) in a field experiment involving the application of a consortium of Paenibacillus pabuli, Priestia megaterium, Pseudomonas koreensis, and Pseudomonas orientalis. Seed pretreatment and seed pretreatment followed by rhizosphere drenching at different growth stages were implemented. Regarding fungal communities in bulk soil, the rhizospheres of untreated and treated plants were characterized based on full-length ribosomal RNA gene (18S-5.8S-28S) metabarcoding sequencing. Despite the compositional shifts, no statistical differences were observed among the alpha diversity metrics. Seed treatment resulted in long-term, targeted suppression of Fusarium graminearum, Fusarium fujikuroi, Fusarium musae, and Fusarium verticillioides from the booting through flowering and dough development stages, outperforming seed pretreatment followed by rhizosphere drenching. A low-modularity network was observed in the rhizosphere of untreated plants. Seed treatment fostered a highly interconnected and uniform network with low hub-betweenness scores. Rhizosphere drenching of pretreated seeds shifted the network topology toward higher hub-betweenness scores, reducing their connectivity by up to 10% in the rhizosphere and bulk soil. These findings provide a framework for optimizing the soil ecosystem for sustainable agriculture. Full article

Calocybe gambosa (Fr.) Donk is an edible mushroom, highly appreciated especially in Italy. It forms fairy rings (FRs) characterized by a zone of dead vegetation corresponding to the underground-extending mycelial front, followed by a “greener belt” where vegetation is thriving. To better understand this particular phenomenon, the effect of C. gambosa mycelium on plants were studied both in situ, across different zones of FRs (external area—EX, fungal front—FF, greener belt—GB, internal area—IN) of three fairy rings, and ex situ on Poa trivialis L. Plant community analysis revealed significant changes in plant species composition across the zones, characterized by a decline in diversity and a vegetation shift, from dicotyledons to monocotyledons, progressing from the EX toward the IN, where vegetation gradually begins to reestablish its original composition. Molecular and morphological analyses showed the endophytic colonization of C. gambosa mycelium within the herbaceous plants growing at the FF. Ex situ studies indicated pathogenic behavior of C. gambosa. After root colonization, it caused growth reduction in P. trivialis plants (79% reduction in root length, 76% reduction in leaf length), leaf yellowing, decreased photosynthetic pigments, and root necrosis. The cellulase (endo-1,4-β-glucanase), xylanase, polygalacturonase, and polymethylgalacturonase enzymatic activities of C. gambosa support its pathogenic effects. Conversely, volatile organic compounds (VOCs) produced by C. gambosa mycelium stimulated shoot development in P. trivialis (17% increase in shoot length), which accounts for the formation of the flourishing vegetation zone behind the FF. In contrast, soluble substances produced by C. gambosa mycelium did not affect the growth of P. trivialis. Our results suggest that C. gambosa plays a dual ecological role in regulating plant community dynamics within FRs: it acts as a pathogen by colonizing herbaceous plant roots and, at the same time, promotes vegetation growth through VOC production. Full article

Understanding root decomposition dynamics is essential to address declining carbon sequestration and nutrient imbalances in monoculture plantations. This study elucidates how forest gaps regulate Pinus massoniana root decomposition through comparative methodological analysis, providing theoretical foundations for near-natural forest management and carbon–nitrogen cycle optimization in plantations. The results showed the following: (1) Root decomposition was significantly accelerated by the in situ soil litterbag method (ISLM) versus the traditional litterbag method (LM) (decomposition rate (k) = 0.459 vs. 0.188), reducing the 95% decomposition time (T_0.95) by nearly nine years (6.53 years vs. 15.95 years). ISLM concurrently elevated the root potassium concentration and reconfigured the relationships between root decomposition and soil nutrients. (2) Lower-order roots (orders 1–3) decomposed significantly faster than higher-order roots (orders 4–5) (k = 0.455 vs. 0.193). This disparity was amplified under ISLM (lower-/higher-order root k ratio = 4.1) but diminished or reversed under LM (lower-/higher-order root k ratio = 0.8). (3) Forest gaps regulated decomposition through temporal phase interactions, accelerating decomposition initially (0–360 days) while inhibiting it later (360–720 days), particularly for higher-order roots. Notably, forest gap effects fundamentally reversed between methodologies (slight promotion under LM vs. significant inhibition under ISLM). Our study reveals that conventional LM may obscure genuine ecological interactions during root decomposition, confirms lower-order roots as rapid nutrient-cycling pathways, provides crucial methodological corrections for plantation nutrient models, and advances theoretical foundations for precision management of P. massoniana plantations. Full article

The long-term monocropping of red kidney beans in agricultural fields can lead to the occurrence of soil-borne diseases. Alterations in the composition of the soil microbial community are a primary cause of soil-borne diseases and a key factor in continuous cropping obstacles. Research exploring how different cultivation modes can modify the diversity and composition of the rhizosphere microbial community in red kidney beans, and thus mitigate the effects of continuous cropping obstacles, is ongoing. This study employed three cultivation modes: the continuous monocropping of red kidney beans, continuous monocropping of soybeans, and red kidney bean–soybean intercropping. To elucidate the composition and diversity of rhizosphere microbial communities, we conducted amplicon sequencing targeting the V3-V4 hypervariable regions of the bacterial 16S rRNA gene and the ITS1 region of fungal ribosomal DNA across distinct growth stages. The obtained sequencing data provide a robust basis for estimating soil microbial diversity. We observed that, under the intercropping mode, the composition of both bacteria and fungi more closely resembled that of soybean monocropping. The monocropping of red kidney beans increased the richness of rhizosphere bacteria and fungi and promoted the accumulation of pathogenic microorganisms. In contrast, intercropping cultivation and soybean monocropping favored the accumulation of beneficial bacteria such as Bacillus and Streptomyce, reduced pathogenic fungi including Alternaria and Mortierell, and exhibited less microbial variation across different growth stages. Compared to the monocropping of red kidney beans, these systems demonstrated more stable microbial structure and composition. The findings of this study will inform sustainable agricultural practices and soil management strategies. Full article

Potato early dying disease complex (PED) leads to premature senescence and rapid decline in potato plants. Unlike potato wilt caused solely by Verticillium species, PED symptoms are more severe due to the synergistic effects of multiple pathogens, including root-lesion nematodes, fungi such as Colletotrichum and Fusarium, and soft-rot bacteria. To investigate the microbiome responsible for PED, soil and stem samples from healthy-looking and symptomatic plants were analyzed using amplicon-targeted next-generation sequencing (Illumina MiSeq and PacBio technologies). Samples were collected from four locations in New Brunswick, Canada from fields previously rotated with barley or oat. Comparative analysis of the bacterial, fungal, and eukaryotic diversity in soil samples showed minimal differences, with only bacterial alpha diversity influenced by the plant health status. Verticillium dahliae was abundant in all soil samples, and its abundance was significantly higher in the stems of diseased plants. Additional fungal species implicated in PED, including Plectosphaerella cucumerina, Colletotrichum coccodes, Botrytis sp., and Alternaria alternata, were also identified in the stems. This study highlights the complex, plant-associated microbial interactions underlying PED and provides a foundation for microbiome-informed disease management strategies. Full article

The vegetation restoration of contaminated sites plays a critical role in ensuring the sustained stability and functional integrity of natural ecosystems. However, during the natural revegetation process, the variations in habitat conditions, bacterial community structure, and metabolic functions in aged, polluted soil are still unclear. In the present study, we investigated aged, polycyclic aromatic hydrocarbon (PAH)-polluted soils at closed, abandoned oil well sites from the Yellow River Delta. Using gene amplification and real-time qPCR methods, the abundance, taxonomy, and diversity characteristics of indigenous bacterial communities and functional bacteria carrying C12O genes in both vegetated soils and bare soils were investigated. The results show that natural revegetation significantly changes the physicochemical parameters, PAH content, and bacterial community structure of aged, PAH-polluted soils. When comparing the abundance and components of PAH-degrading bacterial communities in vegetated and bare soils, the PAH-degrading potential was revealed to be stimulated by vegetation communities. Through correlation analysis, dual stress from soil salinity and PAH contamination in bacterial communities was revealed to be mediated through alterations in the soil’s physicochemical properties by local vegetation. The network analysis revealed that bacterial communities in vegetated soils have higher network connectivity. These results elucidate the alterations in habitat conditions, bacterial components, and PAH-degrading communities following vegetation restoration, providing critical insights for optimizing ecological rehabilitation strategies in salinized and contaminated ecosystems. Full article

Biochar is an effective soil amendment for improving soil function; however, the effects of biochar produced at different pyrolysis temperatures on soil microbial community structure and enzyme activities remain insufficiently studied. A field experiment was conducted from 2023 to 2024 in the arid and semi-arid region of Northern China to investigate the effects of biochar produced at different pyrolysis temperatures (T1: 300 °C; T2: 500 °C; T3: 700 °C) and application rates (C1: 10 t ha⁻¹; C2: 20 t ha⁻¹; C3: 30 t ha⁻¹) on soil chemical properties, microbial community structure, enzyme activity, and potato nutrient use efficiency. The results indicated that the C2T2 treatment was most effective in enhancing soil fungal and actinomycete populations, increasing total microbial biomass, significantly improving soil enzyme activities, and ultimately promoting crop yield. Structural equation modeling indicated that biochar regulates soil nutrient supply, drives microbial community succession toward functional specialization, prolongs microbial regeneration cycles, and ultimately enhances potato nutrient use efficiency. The results of this research provide scientific evidence to support the sustainable development of potato farming in the North China region. Full article

Background/Objectives: Plant growth-promoting rhizobacteria (PGPR), particularly Bacillus spp., are pivotal in enhancing plant defense mechanisms against pathogens. This study aims to investigate the metabolic reprogramming of pine needles induced by Bacillus csuftcsp75 in response to the pathogen Diplodia pinea P9, evaluating its potential as a sustainable biocontrol agent. Methods: Using liquid chromatography–mass spectrometry (LC-MS/MS), we performed a principal component analysis and a cluster analysis to assess the metabolic alterations in treated versus control groups. This study focused on specific metabolites associated with plant defense. Results: Our findings indicate that treatment with Bacillus csuftcsp75 significantly modifies the metabolic profiles of pine needles, leading to notable increases in metabolites associated with flavonoid biosynthesis, particularly phenylpropanoid metabolism, as well as amino acid metabolism pathways. These metabolic changes indicate enhanced systemic acquired resistance (SAR) and induced systemic resistance (ISR), with treated plants exhibiting elevated levels of defense-related compounds such as 5-hydroxytryptophol and oleanolic acid. Conclusions: This study reveals that Bacillus csuftcsp75 enhances defense against pathogen P9 by modulating pine needle metabolism and activating key immune pathways, inducing systemic acquired resistance and induced systemic resistance, offering a natural alternative to chemical pesticides in sustainable agriculture. Full article

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