Search Results (1,271)

Alpine treeline and shrubline ecotones are climatically sensitive transition zones where vegetation shifts strongly influence belowground microbial processes. Soil bacteria and fungi, as core component of the soil microbiome, play vital roles in nutrient cycling and plant–soil interactions within these fragile ecosystems. However, the structure and diversity of soil microbial communities across the treeline–shrubline transition remain poorly understood. Here, we investigated soil bacterial and fungal communities across treeline and shrubline ecotones in two mountain on the eastern Tibetan Plateau. We further examined how soil physicochemical properties shaped microbial community assembly. Our results demonstrated that the community composition of both bacteria and fungi differed significantly between the treeline and shrubline ecotones, while the Shannon index showed no significant variation. At the phylum level, Proteobacteria, Actinobacteriota, and Acidobacteriota dominated bacterial communities, while Ascomycota and Basidiomycota were the predominant fungal phyla. Both the network complexity of soil bacterial and fungal communities changed significantly across ecotones. Specifically, bacterial network complexity increased significantly toward the shrubline, whereas fungal network complexity declined. Bacterial community compositions were co-regulated by both environmental and vegetation factors, while fungal community compositions were only regulated by soil pH. Redundancy analysis revealed that soil organic carbon, pH, and moisture were the primary drivers of bacterial community (38.17%), whereas vegetation cover, soil organic carbon, and moisture explained the largest proportion of fungal community (44.79%). Our findings reveal the distribution patterns and underlying shift mechanisms of microbial communities between the treeline and shrubline ecotone. These insights are crucial for mountain biodiversity conservation and for improving predictions of forest responses to climate change. Full article

Intensive ornamental planting is increasingly prevalent in urban green spaces, yet its effects on soil microbial community assembly and interaction networks remain poorly understood. Here, we examined shifts in soil properties, microbial diversity, community composition, and interaction networks across successive planting cycles. Bacterial alpha-diversity remained relatively stable, whereas fungal communities showed pronounced sensitivity to early planting stages. Beta-diversity analyses revealed that bacterial community composition was jointly influenced by planting stage and site type, while fungal communities were primarily structured by site characteristics. Co-occurrence network analysis revealed contrasting reassembly trajectories between microbial groups. Bacterial networks exhibited increasing complexity and modularity, indicating enhanced interaction intensity and competitive structuring under intensive management. In contrast, fungal networks displayed reduced connectivity but maintained or recovered modular organization, suggesting structural buffering. Notably, keystone taxa remained taxonomically conserved, indicating that network reorganization was driven by interaction rewiring rather than species turnover. We propose a dual-speed reassembly framework in which bacteria function as fast-responding components with dynamic interaction networks, whereas fungi act as slow-buffering, structurally persistent elements. This decoupling of short-term functional responsiveness and long-term stability provides new insights into how intensive management reshapes soil microbiomes in botanical garden ecosystems. Full article

Invasion by Spartina alterniflora has detrimental effects on existing ecosystems. Studies have shown that microorganisms can control plant growth and development. However, the root-associated community structures of bacteria, archaea, and fungi of S. alterniflora have rarely been investigated. Here, we applied metagenomics to reveal the bacterial, archaeal, and fungal communities across four root compartments, including the bulk soil, rhizosphere, rhizoplane, and endosphere. Our findings revealed the variation in different community structures. The bacterial and fungal communities exhibited greater potential environmental flexibility than the archaeal community. The endosphere environment had the simplest microbial networks and highest stability. Additionally, we identified root-exuded metabolites from S. alterniflora, which may influence microbial community assembly. Our results indicate that the rhizoplane plays a crucial role in controlling microbial entry into the root, selectively recruiting beneficial microbes for plant growth and colonization, thereby impacting nutrient cycling and plant health. This study provides insights into microbial diversity and function within the S. alterniflora root zone and suggests potential microbial-based strategies for managing this invasive species. Full article

Soil- and plant-associated fungi and bacteria are an important part of many ecosystems as they can affect plant health, growth and stress tolerance. However, it remains poorly understood whether the microbiomes differ between conifer species growing in the same site conditions and between tree ecosystem compartments. The main aim of the study was to describe and compare the microbiomes of Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies (L.) H. Karst.), growing in a boreal forest common garden experiment on adjacent forest plots, to analyse the tree species effect on the composition of the needle and surface soil organic-mineral horizon microbiomes. The needle and surface soil organic-mineral horizon bacterial and fungal microbiomes were simultaneously analysed by full-length 16S and ITS sequencing on a long-read sequencing platform; however, the bacterial analysis was restricted to soil samples. The highly abundant bacterial phyla in both pine and spruce soil were Actinomycetota, Pseudomonadota, Planctomycetota and Acidobacteriota. The dominant fungal phyla in pine and spruce surface organic-mineral soil was Basidiomycota, while the needles were dominated by Ascomycota. The results showed an effect of tree species on the soil bacterial and fungal microbiomes and needle fungal microbiomes based on alpha diversity, which was higher for Norway spruce compared to Scots pine. The results indicated that Norway spruce might be able to support higher microbial diversity, which could potentially be due to differences in needle longevity, root exudates, litter input and its degradation, between pine and spruce. Furthermore, the results indicated distinct microbiomes between the soil and needle compartments. Full article

To analyze the effects of in situ vegetable residue return on soil properties and microorganisms, this study conducted a continuous three-season in situ residue return experiment with four treatments: no return (CK), residue return (HTJ), residue return + compound microbial inoculant (HTJS), and residue return + ammonia water (HTJN). This study compared the treatment effects on soil quality. The results showed that, after the third tillage, the HTJS treatment increased soil organic carbon, total nitrogen, and mineralizable organic carbon content, and significantly enhanced the activity of soil β-glucosidase and soil peroxidase, which are related to carbon cycling enzymes compared to other treatments. There were no significant differences in bacterial or fungal α-diversity among treatments. Differences in fungal community soil β-diversity among treatments were significant. The HTJS treatment enriched organic matter-degrading bacteria Flavisolibacter and Devosia. Although HTJS increased the relative abundance of Fusarium, the field disease incidence index did not increase. The soil quality index (SQI), based on the minimum dataset (MDS), showed that HTJS had the highest SQI after the third tillage. Further path model analysis revealed that soil carbon components index and soil physicochemical index were the main controlling factors influencing the SQI. In conclusion, in situ residue return with a compound microbial inoculant (HTJS) is an effective strategy to simultaneously enhance soil fertility and biological activity by regulating the microbial community structure and associated enzyme activities. Full article

Soil fumigation effectively mitigates replanting obstacles induced by intensive cultivation, yet its non-targeted biocidal effects can suppress beneficial microbial activity, potentially compromising agricultural sustainability. Microbial inoculation, as a strategy to supplement beneficial microorganisms, is often employed to restore soil microbial communities. However, in practice, commonly used exogenous microbial consortia exhibit poor adaptability in non-native environments, frequently resulting in limited efficacy. To address this limitation, we propose an ecological intervention based on the reintroduction of indigenous cultivable microorganisms: cultivable microbial communities were isolated from healthy adjacent soils and inoculated into fumigated soils affected by replanting obstacles. The experimental soil consisted of black soil under continuous cropping, collected from Northeast China. The three treatments were continuous cropping soil (control), fumigated continuous cropping soil and fumigated continuous cropping soil after inoculation of indigenous cultivable microorganisms. Using high-throughput sequencing and agronomic–chemical analyses, combined with cross-domain networks and procrustes analysis, we systematically assessed the ecological effects of this approach on microbial restoration and the alleviation of replanting obstacles. The results showed that indigenous cultivable microorganism inoculation significantly increased the richness of bacterial and fungal communities in fumigated soils within 21 days, extending microbial richness and diversity. Furthermore, inoculation accelerated the reconstruction of dominant microbial community structures, with the relative abundance of dominant species reaching up to 80%. Positive synergistic interactions between bacteria and fungi increased by approximately 10%, enhancing network stability. Key bacterial taxa, such as Paenibacillus and Mycobacterium, were significantly correlated with available potassium and phosphorus content, while Micromonospora, Massilia, and Flavisolibacter influenced plant fresh weight, total nitrogen, and potassium accumulation. Key fungal taxa, such as Cryptococcus and Phialemonium, were significantly associated with soil organic matter stability, maize photosynthetic efficiency, plant dry weight, and total phosphorus content. This study confirms the ecological adaptability and functionality of indigenous cultivable microorganisms in soil ecosystem restoration, offering a low-risk, highly effective localized intervention strategy for sustainable agriculture. Full article

Baby maize (Zea mays L.) is widely cultivated across Asia due to its short growth cycle and adaptability to diverse agroecological conditions. However, its production is frequently constrained by low soil fertility, leading to the excessive use of chemical fertilizers, which in turn contributes to environmental degradation. Endophytic bacteria with the ability to fix atmospheric nitrogen and solubilize inorganic phosphate represent a sustainable alternative for improving nutrient availability. This study aimed to isolate and characterize endophytic bacteria exhibiting dual nitrogen-fixing and phosphate-solubilizing capabilities from baby maize roots. A total of ten bacterial isolates were obtained and screened using nitrogen-free Burk medium and NBRIP medium. Among these, strain CMB2 demonstrated superior functional traits. Molecular identification based on 16S rRNA gene sequencing confirmed that the isolate belongs to Bacillus stercoris. In vitro assays revealed that B. stercoris CMB2 exhibited significant nitrogenase activity, as determined by the acetylene reduction assay, and strong phosphate-solubilizing ability, indicated by a clear halo zone and a high solubilization index. These findings suggest that B. stercoris CMB2 is a promising multifunctional endophytic bacterium for enhancing nutrient availability under controlled conditions. Further validation under greenhouse and field conditions is required to assess its potential for improving plant growth and nutrient uptake in baby maize. Full article

Microcystin (MC) contamination of surface waters threatens ecosystems and public health. Nature-based solutions such as Multi-Soil-Layering (MSL) systems have been used for MC remediation. However, the biological mechanisms controlling MC degradation remain unclear. The present study investigates microbial community responses in two MSL systems with different clay contents (8% and 54%) exposed to MC-contaminated inputs (well water and eutrophied lake water). Samples were analysed before and after treatment using quantitative PCR (qPCR) to quantify the mlrA gene (encoding microcystinase) and its bacterial hosts. Next-generation sequencing (NGS) was used to assess microbial diversity, while the FAPROTAX database was used to predict functional characteristics. Results showed that MC was mainly adsorbed in pozzolan layers, while mlrA gene abundance and MC-degrading bacteria were higher in soil mixture layers. The presence of mlrA and associated bacteria was most pronounced in lake inflow samples, indicating intrinsic MC Biodegradation potential. Taxonomic analysis revealed dominant phyla including Proteobacteria, Actinobacteriota, Firmicutes, Chloroflexi and Bacteroidota. Functional analysis identified dominant traits such as chemoheterotrophy and aerobic metabolism. These findings provide new insights into microbial interactions in MSL systems and contribute to the optimisation of water treatment strategies for MC-contaminated environments. Full article

Ecological restoration is increasingly applied as an effective strategy for mitigating environmental risks associated with tailings impoundments. However, plant establishment and ecological recovery in tailings substrates are often limited by unfavorable physicochemical properties and potential toxicity. This study investigated the changes in soil microbial community structure and diversity under the synergistic remediation of compound organic fertilizer and plants. Field plots subjected to combined organic fertilizer–plant remediation in a tailings impoundment in northern China were selected. The high-throughput sequencing of bacterial 16S rRNA genes and fungal ITS regions was performed alongside analyses of soil physicochemical properties. Compared to the untreated tailings soil, remediated soils showed pH values closer to neutrality, lower electrical conductivity, and significantly higher organic matter content, indicating an overall reduction in environmental stress and potential toxicity. The relative abundance of copiotrophic bacteria, such as Proteobacteria, increased, whereas that of stress-tolerant taxa adapted to extreme environments, such as Firmicutes, decreased. Although slight variations in dominant groups were observed among plots with different plant species, key microbial groups contributing to soil environmental improvement were largely consistent. These findings demonstrate that this combined remediation effectively improves the physicochemical properties and microbial community structure of tailings soil, providing a risk-oriented and ecologically sustainable strategy for the ecological restoration of similar sites. Full article

Drought is a major constraint on crop productivity, and microbial inoculants are increasingly explored to mitigate plant water stress. However, most inoculant discovery pipelines rely on trait-based screening performed outside the ecological context in which beneficial plant-microbe interactions naturally arise. In natural soils, drought-exposed plants can reshape the rhizosphere environment by altering carbon allocation and root exudation, thereby selectively recruiting microorganisms compatible with water-limited conditions and effectively performing an ecological pre-selection. Here, we captured this process during early seedling establishment and leveraged drought-driven rhizosphere recruitment as a nature-guided strategy to nominate bacterial inoculant candidates. Tomato seedlings were grown in natural agricultural soil microcosms under well-watered and drought-stressed regimes, and cultivable bacteria were comparatively isolated from rhizosphere and bulk soil fractions. Recruitment-prioritized isolates were subsequently characterized through biochemical assays and genome-informed analyses to provide functional and taxonomic context and were evaluated in early inoculation assays under water stress. Drought-recruited isolates displayed distinct plant-associated responses, and genome-scale taxonomy indicated that one drought-associated isolate represents a genomically distinct lineage within the genus Paracoccus. Together, these findings highlight drought-driven rhizosphere recruitment as an ecologically grounded framework for identifying stress-compatible bacterial candidates and uncovering previously undescribed rhizosphere diversity. Full article

Clubroot caused by Plasmodiophora brassicae is a devastating soil-borne disease of oilseed rape, and physiological race differentiation of the pathogen greatly hinders disease control. The differential regulatory mechanisms of different P. brassicae races on the rhizosphere microecology remain unclear. This study aimed to reveal the race-specific effects of P. brassicae on the rhizosphere microenvironment, microbial community and nitrogen cycling of oilseed rape. A pot inoculation experiment was conducted with two typical races from Sichuan Province (race 4 CZ and race 2 KD), combined with soil physicochemical determination, high-throughput sequencing and functional prediction. The results showed that CZ exhibited a higher infection rate but a lower disease index than KD. Both races significantly decreased soil pH and reshaped soil nutrient profiles. Notably, CZ treatment caused a more pronounced pH decrease and was characterized by NH₄⁺-N accumulation, whereas KD treatment was dominated by NO₃⁻-N enrichment. Bacterial alpha diversity was increased by both races, following the order KD > CZ > CK. In contrast, fungal alpha diversity was decreased by both races, showing the pattern CK > KD > CZ. Distinct rhizosphere microbial community structures were formed under different race infections, and both races reduced the abundance of nitrogen-fixing bacteria and related functional genes. These findings indicate that distinct P. brassicae races shape race-specific rhizosphere microenvironments by differentially regulating soil acidification, nutrient availability and nitrogen-cycling functional microorganisms, thereby driving divergent pathogenic outcomes. This study is the first to reveal differential regulation of the rhizosphere microecology by distinct physiological races of P. brassicae, offering new insights for region-specific management of clubroot disease. Full article

The artificially modified Bacillus thuringiensis (Bt) protein can target lepidopteran pests, and planting genetically modified crops with insect-resistant traits is environmentally friendly. However, it is still uncertain whether the exogenous insect-resistant proteins in genetically modified crops will affect the soil rhizosphere microorganisms. This study utilized 16S rDNA sequencing technology to analyze the rhizosphere soil of insect-resistant genetically modified corn LD05 and its control variety Zheng58 at five developmental stages: before sowing, seedling stage, jointing stage, silk emergence stage, and maturity stage. Each sample was taken with six biological replicates, resulting in a total of 60 sequencing samples, with an average of 4368 OTUs obtained per sample. Both alpha and beta analyses showed that LD05 and Zheng58 did not have a significant impact on the soil rhizosphere microbial community. The developmental stage rather than the variety was the main factor causing differences in the bacterial community. Overall, there was no significant difference in the bacterial diversity between the insect-resistant genetically modified corn LD05 and its control variety Zheng58. The results provide useful information for understanding the impact of genetically modified crops on soil microbial communities and also provide a theoretical basis for the safety evaluation of LD05. Full article

Lycium ruthenicum is a typical desert halophyte with strong stress resistance and high medicinal value in the Tarim Basin. Root endophytic microbes play critical roles in host adaptation, nutrient cycling, and secondary metabolite accumulation. To clarify the diversity patterns of root endophytic bacteria and fungi and their relationships with environmental factors and fruit quality, high-throughput sequencing was used to analyze microbial community characteristics of Lycium ruthenicum collected from different habitats in the Tarim Basin. The results showed that rarefaction curves of alpha diversity indices (Chao1, Shannon, Pielou_e) tended to be saturated, indicating sufficient sequencing depth. Principal coordinate analysis (PCoA) revealed significant habitat-driven differentiation in both bacterial and fungal community structures. Community composition analysis showed that the relative abundance of dominant taxa at the phylum and genus levels differed significantly among sampling sites. Co-occurrence network analysis indicated that bacterial and fungal networks exhibited high modularity and were dominated by positive synergistic interactions, with Pseudomonas, Bacillus, Sphingomonas, Alternaria, and Fusarium as key hub genera. Moreover, root endophytic communities were significantly correlated with climatic variables, soil physicochemical properties, and fruit quality traits, including anthocyanin (AC), proanthocyanidin (PA), total flavonoids (TF), and total polyphenols (TP). Several keystone microbial genera were closely associated with the accumulation of functional metabolites in fruits. This study reveals the biogeographic distribution and co-occurrence characteristics of root endophytes in Lycium ruthenicum and provides a theoretical basis for understanding microbe–host–environment interactions and the quality improvement of desert medicinal plants. Full article

Glycosphingolipids are amphiphilic compounds that feature sugar or glycan moieties installed onto a ceramide lipid. The synthesis of glycosphingolipids by members of the human gut microbiome, and their known immune stimulating activity, have made them of interest for potential pharmaceutical roles. However, the known diversity of glycosphingolipid glycans in bacteria remains limited, highlighting the need to isolate novel glycosphingolipid-producing organisms as a source of these compounds. The order Sphingomonadales, one of the major clades of sphingolipid producing bacteria, conserves a serine palmitoyltransferase (SPT) enzyme needed for the initial biosynthetic step in sphingolipid production which can be targeted as part of isolation efforts. With these bacteria known to live in diverse environments such as soil microbiomes, soap scum biofilms, and cyanobacterial microbiomes, there are many environments to target for the isolation of these bacteria. In this work, we designed a set of polymerase chain reaction (PCR) primers for the isolation of diverse Sphingomonadales strains by targeting the SPT gene (spt), which we used to isolate strains from the genera Sphingomonas and Novosphingobium in soil, soap scum biofilms, and xenic cyanobacterial cultures. In these efforts, streptomycin improved the encounter rate, as represented by the SPT assay true-positive rate. Our isolates represent novel genomic space: with genomes from both genera that have low similarity to known genomes, suggestive of novel species, while several novel plasmids were also missing known marker sequences. Full article

Excessive fertilizer application is a common practice in agricultural production in the North China Plain. To determine an optimal fertilization strategy for summer maize with nitrogen-fixing bacterial inoculation, we conducted a two-year field experiment (2022–2023) using the conventional fertilization rate (600 kg ha⁻¹ NPK; N:P₂O₅:K₂O = 28:8:10; 100F by default) as a control and examined the effects of fertilizer reduction (at 90%, 80%, 62.5%, and 50% of 100F) combined with Azotobacter chroococcum inoculation on maize plants and soil. Although fertilizer reduction increased free amino acid content, soluble sugars, proteins, and fatty acids contents were reduced. However, bacterial inoculation significantly enhanced all the above nutritional indices in maize leaves. Bacterial inoculation under fertilizer reduction conditions can enhance the activity of key nitrogen metabolism enzymes (i.e., GS and GOGAT), which further supports nitrogen, sugar, and lipid metabolism in maize plants. Additionally, bacterial inoculation promoted root development, biomass accumulation, and grain nutritional value while significantly increasing yield under reduced fertilizer conditions. The highest yield (11,454 kg ha⁻¹) was achieved with bacterial inoculation at approximately 87F (≈522 kg ha⁻¹ NPK), while the non-inoculated control reached a peak yield (11,032 kg ha⁻¹) only at around 90.5F (≈543 kg ha⁻¹). The complementary effects of bacterial inoculation with fertilizer reduction resulted in improved nutrient supply and modulation of soil microbial diversity. Inoculation of A. chroococcum increased soil ammonium and nitrate levels and decreased soil pH, though it was associated with a decline in overall bacterial richness, which may have persistent and adverse effects on the soil. Both fertilizer reduction and bacterial inoculation significantly altered microbial community structure, with notable interannual variation. Collectively, our findings suggest that moderate fertilizer reduction (9.5–13%) combined with nitrogen-fixing bacteria inoculation can support sustainable maize production by maintaining higher yield, enhancing nutrient use efficiency, and improving soil health. However, due to pH-lowering effects, long-term monitoring is necessary to assess the ecological impact of nitrogen-fixing bacteria inoculation on soil microbial balance. Full article