Background Beneficial plant-associated microorganisms are key drivers of sustainable agriculture. However, their discovery and practical application remain insufficiently explored. Here, we present the first comprehensive comparative genomic analysis of a newly identified Sinomonas strain together with all publicly available genomes to assess its agronomic potential Results Our results demonstrate that Sinomonas has an open pangenome and harbors multiple pathways for IAA biosynthesis, including a rare pathway found in only a limited number of bacterial taxa. The genus also contains genes involved in the synthesis of cytokinin analogues. In addition, genomic annotation identified ten genes putatively associated with phosphorus solubilization. A total of sixteen distinct biosynthetic gene clusters were identified, covering pathways for the biosynthesis of stenothricin, dactylocycline, aborycin, reveromycin, michiganin A, ikarugamycin, and peucechelin, all of which are compounds with reported antibacterial activity. In addition, Sinomonas carries multiple genes potentially involved in improving plant stress tolerance, including genes related to the biosynthesis of spermidine, 2,3-butanediol, acetoin, betaine, proline, and trehalose. Conclusion Overall, these findings highlight the functional diversity of the Sinomonas genome and provide preliminary insights into its potential agricultural applications.

This study investigated the mechanisms of cadmium (Cd) tolerance and root exudate-mediated soil activation in mulberry (Morus alba L.), a promising species for phytoremediation. Hydroponic experiments with Cd-tolerant seedlings exposed to 5 and 50 mg/L Cd revealed a biphasic concentration-dependent response. Low Cd induced negligible biological effects, whereas high Cd triggered substantial disturbances across multiple biological levels, including morphological alterations, physiological dysregulation and disrupted elemental accumulation patterns. Metabolomic profiling indicated that Cd stress significantly altered the secretion patterns of 17 root exudate metabolites in mulberry, exemplified by the upregulation of sucrose, lactose and 4-acetylbutyric acid, and the downregulation of β-alanine and myo-inositol. Further pathway enrichment analysis linked these differential metabolites to 17 metabolic pathways, with carbohydrate and amino acid metabolism as the main Cd-responsive pathways, suggesting their core role in mediating mulberry's Cd resistance. Root exudates enhanced soil Cd mobilisation in a positive concentration-dependent yet negative time-dependent manner. Consequently, mulberry adapts to Cd stress via metabolic reprogramming of root exudates-a strategic trade-off that serves a dual role by enhancing plant tolerance while simultaneously increasing Cd bioavailability in the soil. This insight provides a foundational framework for phytoremediation, centred on exudate management and the selection of stress-tolerant varieties.

Hydrothermal carbonization (HTC) offers a sustainable pathway to convert agricultural wastes into multifunctional hydrochars, yet the stability of hydrochars and the biotoxicity of hydrocharderived dissolved organic matter (DOM) as amendments for contaminated farmland soils remained understudied. Herein, this study investigates feedstock-dependent (straw: HS, swine manure: HSM, and cattle manure: HCM) and time-resolved variations in hydrochar and the derived DOM characteristics for farmland remediation potentials. Feedstock type dominated hydrochars and DOM functionality that manure-based hydrochars exhibited superior metal adsorption capacity (100 % Pb removal by HSM and 51.7-76.2 % by HCM), more biologically suitable C/N ratios (HSM: 15.0-16.5, HCM: 21.4-23.5), and germination index (HSM: 51.1-76.7 %, HCM: 56.2-82.2 %), correlating with the reduced phytotoxicity. The DOM derived from manure-based hydrochar contained more macromolecular fluorescent humus contents and various organic functional groups, while HS released more phytotoxic DOM with 44.3-68.3 % germination inhibition. DOM removal enhanced Pb adsorption capacities by 56.1-97.3 % for lignocellulose-rich HS. With elemental analysis and 2D-FTIR-COS analysis, the prolonged hydrothermal duration enhanced structural stability, reducing DOM release by 19.6-40.5 % through dehydration and decarboxylation. In addition, the stability of hydrochar, alongside the N content and the degree of dehydration and decarboxylation, significantly affected their toxicity to seed germination. In conclusion, the type of feedstock has the most substantial impact on hydrochars and DOM properties that HCM emerged as the most viable candidate due to synergistic benefits, while optimizing hydrothermal time improved performance agricultural remediation.

A novel strain of the genus Sinomonas, designated G460-2 T, was isolated from rice paddy soil. The cells of strain G460-2 T were Gram-positive, aerobic, and non-motile rods. The optimal growth conditions for this strain were observed at 30 °C and a pH of 7.0. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain G460-2 T shared the highest sequence similarity (98.41

The prevalence of antibiotic resistance genes (ARGs) in agricultural soils has garnered significant attention. However, the long-term impacts of various nitroge (N)-substitution fertilization regimes on the distribution of soil ARGs and their dominant drivers in a subtropical triple-cropping system remain largely unexplored. This study employed a metagenomic approach to analyze soil ARGs, microbial communities, mobile genetic elements (MGEs), and viruses from a maize-maize-cabbage rotation field experiment with five different fertilization regimes. Soil samples were collected in 2012 and 2021. A total of 615 unique ARG subtypes were identified, with multidrug, bacitracin, and rifamycin resistance genes being the most abundant. Notably, ARG types. the continuous application of fresh chicken manure (CM) over 10 years significantly increased both the count of unique ARG subtypes and the total ARG abundance compared to other fertilization regimes, such as inorganic fertilizer and composted chicken manure. Specifically, the abundance of genes associated with antibiotic target replacement (e.g., sul1 and sul2) in the CM-treated soil rose by 8.83-fold from 2021 to 2012. Our random forest analysis revealed that the abundance of three MGEs (QacEdelta, plasmids, and IstB), two viral families (Myoviridae and Podoviridae), two bacterial phyla (Chloroflexi and Planctomycetes), and two environmental factors (pH and soil organic matter (SOM)) significantly influenced the distribution of ARGs. Furthermore, variance decomposition analysis underscored the critical roles of the three MGEs and the two viral families in the dissemination of ARGs, suggesting that horizontal gene transfer (HGT) may play a key role in ARG spread. These findings enhance our understanding of how different fertilization practices influence ARG dissemination in subtropical triple-cropping agroecosystems over the long term and provide valuable insights for optimizing fertilization management strategies.

Soil co-contamination with heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) represents a widespread and challenging environmental issue that is difficult to address using conventional remediation methods. This review systematically examines the molecular mechanisms by which plant root exudates mediate the remediation of co-contaminated soils through synergistic interactions with rhizosphere microorganisms. We detail how plants dynamically adjust the composition and secretion of root exudates—such as organic acids, amino acids, sugars, and secondary metabolites—in response to combined HM-PAH stress. These exudates play multifaceted roles in remediation, including chelating HMs, enhancing PAH solubility and bioavailability, and acting as chemoattractants and metabolic substrates for rhizosphere microbes. In return, the recruited microbial communities contribute to pollutant detoxification through various mechanisms, such as biosurfactant production, enzymatic degradation, and improved plant nutrient acquisition. This reciprocal interaction forms a synergistic plant-microbe feedback loop that effectively mitigates combined contamination stress. By integrating evidence from diverse plant–soil systems, this review provides a comprehensive mechanistic framework for understanding root exudate-microbe interactions, offering critical insights for developing enhanced phytoremediation strategies to address complex environmental pollution.

Biological control has gained increasing attention as a strategy to address biotic and abiotic stresses in crops. In this study, we identified the strain KRS009 as Bacillus mojavensis through morphological identification and multilocus sequence analysis. KRS009 exhibited broad-spectrum antifungal activity against various phytopathogenic fungi by secreting soluble and volatile compounds. Additionally, the physio-biochemical traits of strain KRS009 were characterized, including its growth-promoting capabilities and active enzymes. Notably, KRS009 demonstrated the capacity for biofilm formation and exhibited tolerance to saline-alkali conditions. The biological security evaluation confirmed the safety of KRS009 for both humans and plants. Furthermore, strain KRS009 was found to trigger plant immunity by inducing systemic resistance through salicylic acid- and jasmonic acid-dependent signaling pathways. Greenhouse experiments conducted on cotton plants proved that the treatment with strain KRS009 effectively protected cotton against Verticillium wilt caused by Verticillium dahliae and promoted the growth of cotton under salt stress. These findings highlight the potential of B. mojavensis KRS009 as a promising biocontrol and biofertilizer agent for promoting plant growth, combating fungal diseases and mitigating salt stress in plants.

Bacillus velezensis is well known as a plant growth-promoting rhizobacteria (PGPR) and biocontrol agent. Nevertheless, there are very few reports on the study of B. velezensis on tomato early blight, especially the biocontrol effects among different inoculation concentrations. In this study, an IAA-producing strain, Bacillus velezensis YXDHD1-7 was isolated from the tomato rhizosphere soil, which had the strongest inhibitory effect against Alternaria solani. Inoculation with bacterial suspensions of this strain promoted the growth of tomato seedlings effectively. Furthermore, inoculations at 106, 107, and 108 cfu/mL resulted in control efficacies of 100%, 83.15%, and 69.90%, respectively. Genome sequencing showed that it possesses 22 gene clusters associated with the synthesis of antimicrobial metabolites and genes that are involved in the production of IAA. Furthermore, it may be able to produce spermidine and volatile compounds that also enhance plant growth and defense responses. Our results suggest that strain YXDHD1-7 prevents early blight disease by promoting growth and enhancing the defense enzyme activities in tomato plants. This strain is a promising candidate for an excellent microbial inoculant that can be used to enhance tomato production.

Tomato cultivars with contrasting resistance to pathogens regulate root exudates differentially in response to Ralstonia solanacearum attacks. However, strategies using innate root exudates against infection remain unknown. This study analyzed the innate root exudates of two tomato cultivars and their functions in regulating R. solanacearum infection. The innate root exudates differed between the two cultivars. Astaxanthin released from resistant plants inhibited colonization by R. solanacearum but promoted motility, while neferine released from susceptible plants suppressed motility and colonization. The secretion of astaxanthin in resistant tomatoes promoted the growth of biocontrol fungi in soil and reduced the abundance of pathogenic fungi. Neferine secreted by the susceptible cultivar inhibited the relative abundance of the bacterial-biocontrol-related Bacillus genus, indirectly reducing the soil's immune capacity. This study revealed contrasting strategies using root exudates in resistant and susceptible tomato cultivars to cope with R. solanacearum infection, providing a basis for breeding disease-resistant cultivars.

Mulberry is an economically important plant in the sericulture industry and traditional medicine. However, the genetic and evolutionary history of mulberry remains largely unknown. Here, this work presents the chromosome-level genome assembly of Morus atropurpurea (M. atropurpurea), originating from south China. Population genomic analysis using 425 mulberry accessions reveal that cultivated mulberry is classified into two species, M. atropurpurea and M. alba, which may have originated from two different mulberry progenitors and have independent and parallel domestication in north and south China, respectively. Extensive gene flow is revealed between different mulberry populations, contributing to genetic diversity in modern hybrid cultivars. This work also identifies the genetic architecture of the flowering time and leaf size. In addition, the genomic structure and evolution of sex-determining regions are identified. This study significantly advances the understanding of the genetic basis and domestication history of mulberry in the north and south, and provides valuable molecular markers of desirable traits for mulberry breeding.

Our knowledge of the composition and functions of the soil and rhizospheric microbiomes is rapidly increasing, but it is based on a few observational and experimental studies. The assembly patterns of the rhizospheric microbiome under different fertilizing regimes and the ecological function difference of rhizosphere under uncomposted and composted fertilizations are still unclear. Hence, we conducted a 6-year field experiment with different fertilizing regimes (no fertilization, mineral fertilization, uncomposted chicken manure, composted organic fertilization and partial compost substituted fertilization) of maize-cabbage rotation, and tested the soil properties, enzymatic activities, and microbial community composition by amplicon sequencing and functional genes abundance by Geochip 5.0 of maize rhizosphere. The results showed that continuous mineral (NPK) fertilizing and organic fertilizing (both uncomposted and composted) formed different rhizospheric soil environments, resulting in converse microbial community structure and functions. Continuous mineral fertilization led to severe soil acidification, and thus reduced bacteria diversity and recruited substantial beneficial fungi Trichoderma to counteract the pathogenic bacteria (Xanthomonas and Fusarium). The microbial functions under continuous mineral fertilizaion concentrated on dealing with different environmental stress (antioxidant enzyme, cold shock, osmotic stress in sub-categories). On the contrary, continuous organic fertilization provided a more suitable environment for microbial living, resulting in higher bacterial diversity and the composted one presented more varied ecological functions (including C/N/P cycle, metal homeostasis, microbial defence, and plant growth promotion). Composting contributed to the colonization of the biocontrol agent Bacillus and aggregation of ammonia-oxidizing archaea Candidatus nitrososphaera. The environmental factors that affect microbial assembly were pH and soil organic matter (SOM) contents for bacteria, SOM and available phophorus (AP) for fungi and pH and available nitrogen (AN) for archaea. Besides environmental influences, microbial interaction could also be an important aspect when assessing the contributing factors to microbiome assembly. Overall, this study provides ecological impact evidence on crop rhizosphere under various fertilizing regimes via a 6-year continuous study and proposed that composted fertilizer could be a more sustainable choice for eco-agriculture than uncomposted manure and mineral fertilizer.

Soil sustainability is based on soil microbial communities’ abundance and composition. Straw returning (SR) and nitrogen (N) fertilization influence soil fertility, enzyme activities, and the soil microbial community and structure. However, it remains unclear due to heterogeneous composition and varying decomposition rates of added straw. Therefore, the current study aimed to determine the effect of SR and N fertilizer application on soil organic carbon (SOC), total nitrogen (TN), urease (S-UE) activity, sucrase (S-SC) activity, cellulose (S-CL) activity, and bacterial, fungal, and nematode community composition from March to December 2020 at Guangxi University, China. Treatments included two planting patterns, that is, SR and traditional planting (TP) and six N fertilizer with 0, 100, 150, 200, 250, and 300 kg N ha–1. Straw returning significantly increased soil fertility, enzymatic activities, community diversity, and composition of bacterial and fungal communities compared to TP. Nitrogen fertilizer application increased soil fertility and enzymes and decreased the richness of bacterial and fungal communities. In SR added plots, the dominated bacterial phyla were Proteobacteria, Acidobacterioia, Nitrospirae, Chloroflexi, and Actinobacteriota; whereas fungal phyla were Ascomycota and Mortierellomycota and nematode genera were Pratylenchus and Acrobeloides. Co-occurrence network and redundancy analysis (RDA) showed that TN, SOC, and S-SC were closely correlated with bacterial community composition. It was concluded that the continuous SR and N fertilizer improved soil fertility and improved soil bacterial, fungal, and nematode community composition.

Severe nitrogen (N) loss is a barrier for composting treatment. Since N transformation during composting is closely related to nitrogen loss, the impacts of adding sulphur and Thiobacillus thioparus 1904 to N transformation during composting were investigated in this work. Physicochemical properties and the expression of genes encoding N-related proteins were analysed to evaluate microbiological processes associated with N dynamics. The results indicated that (1) sulphur addition reduced the pH and cumulative NH3 emission, and decreased N losses by 44.23%, while no significant differences were observed in the expression of N cycle-associated genes compared with the control treatment; (2) the application of T. thioparus 1904 increased NO3--N content, reduced N loss by 28.20%, and significantly enhanced the expression of ammonia monooxygenase A (archaeal amoA; AOA) and nitrite oxidoreductase A (nxrA) during the mature phase; (3) the combined application of sulphur and T. thioparus 1904 significantly affected the expression of functional genes related to nitrification and denitrification, which contributed to a reduction in accumulated NH3 emission, an increase in NO4+-N content, and a decrease in N losses by 70.94%. Expression of ammonia monooxygenase A (bacterial amoA; AOB), nxrA and nitrous oxide reductase Z (nosZ) genes in the combined treatment was positively correlated with NO3--N, whereas expression of AOA and accumulation of NH3 were negatively correlated with NO3--N. These results indicate that the combined application of sulphur and T. thioparus 1904 had a significant regulatory effect on N cycle genes and effectively reduced the N loss during composting.

Nitrogen limitation represents a major bottleneck during the revegetation of mine tailings. However, controls over key nitrogen-cycling genes in rhizospheric soils under differential vegetation management remain poorly understood. The abundance and transcriptional activity of nitrogen-cycling genes and the enzymatic activity of nitrogen transformation are mediated differentially during revegetation of mine tailings by Imperata cylindrica and Chrysopogon zizanioides plants. Results showed that the highest total organic carbon (TOC), total nitrogen (TN), and NH4+-N contents were found in the rhizosphere of I. cylindrica. The nifH gene abundances differed between I. cylindrica and C. zizanioides, and were higher in I. cylindrica which demonstrated by 3.39-fold higher mRNA transcript abundance of the nifH gene and a 2.15-fold higher nitrogen fixation rate in the rhizosphere. In addition, C. zizanioides exhibited a 4.94-fold higher transcript abundance of the archaeal amoA gene and the highest nitrification rate (1.706 +/- 0.293 mu g N-NO2- g(-1) h(-1)) in the rhizosphere. In conclusion, I. cylindrica and C. zizanioides stimulated the abundances and activities of nifH gene and archaeal amoA gene, respectively. In addition, I. cylindrica appears to be capable of enhancing nitrogen fixation and exhibited accelerated nitrogen accumulation, which may be particularly useful for the rehabilitation of mine tailings.

Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0–30 cm soils and altered the bacterial communities at 0–20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30–60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0–20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.

Native soil amendment has been widely used to stabilize mine tailings and speed up the development of soil biogeochemical functions before revegetation; however, it remains poorly understood about the response of microbial communities to ecological restoration of mine tailings with soil-covered strategy. In this study, microbial communities along a 60-cm profile were investigated in mine tailings during ecological restoration of two revegetation strategies (directly revegetation and native soil covered) with different plant species. The mine tailings were covered by native soils as thick as 40 cm for more than 10 years, and the total nitrogen, total organic carbon, water content, and heavy metal (Fe, Cu, and Zn) contents in the 0–40 cm intervals of profiles were changed. In addition, increased microbial diversity and changed microbial community structure were also found in the 10–40 cm intervals of profiles in soil-covered area. Soil-covered strategy rather than plant species and soil depth was the main factor influencing the bacterial community, which explained the largest portion (29.96%) of the observed variation. Compared directly to revegetation, soil-covered strategy exhibited the higher relative abundance of Acidobacteria and Deltaproteobacteria and the lower relative abundance of Bacteroidetes, Gemmatimonadetes, Betaproteobacteria, and Gammaproteobacteria. PICRUSt analysis further demonstrated that soil-covered caused energy metabolic functional changes in carbon, nitrogen, and sulfur metabolism. Given all these, the soil-covered strategy may be used to fast-track the establishment of native microbial communities and is conducive to the rehabilitation of biogeochemical processes for establishing native plant species.

The oxidization of metal sulfide in tailings causes acid mine drainage. However, it remains unclear whether vegetation prevents the oxidization of metal sulfides. The oxidization characteristics and microbial indices of the tailings in the presence of various plant species were investigated to explore the effects of vegetation on the oxidization of sulfide minerals in tailings. The pH, reducing sulfur, free iron oxides (Fed), chemical oxygen consumption (COC) and biological oxygen consumption (BOC) were measured. Key iron- and sulfur-oxidizing bacteria (Acidithiobacillus spp., Leptospirillum spp. and Thiobacillus spp.) were quantified using real-time PCR. The results indicate that vegetation growing on tailings can effectively prevent the oxidization of sulfide minerals in tailings. A higher pH and reducing-sulfur content and lower Fed were observed in the 0-30 cm depth interval in the presence of vegetation compared to bare tailings (BT). The COC gradually decreased with depth in all of the soil profiles; specifically, the COC rapidly decreased in the 10-20 cm interval in the presence of vegetation but gradually decreased in the BT profiles. Imperata cylindrica (IC) and Chrysopogon zizanoides (CZ) profiles contained the highest BOC in the 10-20 cm interval. The abundance of key iron- and sulfur-oxidizing bacteria in the vegetated tailings were significantly lower than in the BT; in particular, IC was associated with the lowest iron- and sulfur-oxidizing bacterial abundance. In conclusion, vegetation successfully prevented the oxidization of sulfide minerals in the tailings, and Imperata cylindrica is the most effective in reducing the number of iron- and sulfur-oxidizing bacteria and helped to prevent the oxidization of sulfide minerals in the long term.

We previously demonstrated that providing potato plants with an optimum nitrogen supply (in the form of urea; 135 kg hm-2) produces high crop yields and increased resistance to late blight. However, the mechanisms underlying these responses have not been well characterized. In this study, we examined the effects of various levels of nitrogen fertilization (four levels: N1, 45 kg hm-2, N2: 90 kg hm-2, N3: 135 kg hm-2 and N4: 180 kg hm-2) on soil bacterial growth, community diversity and soil enzyme activity. We found that application of the optimum amount of nitrogen promoted maximum levels of bacterial growth and community diversity development compared with the other treatments. In addition, the highest activities were detected for soil enzymes such as urease, invertase and acid phosphatase (but not catalase) under N3 conditions but not under N1, N2 or N4 conditions. These results suggest that proper nitrogen application provides soil microbes with optimum conditions for development. Thus, the optimum growth of rhizobacteria conferred by N3 treatment appears to be responsible for achieving the highest yields and strongest pathogen resistance in potato plants exposed to Phytophthora infestans. Key words: Late blight, potato plant, rhizobacteria, soil enzyme, urea fertilizer.

The Aureobasidium pullulans F4 was isolated from the rhizosphere of Hippochaete ramosissimum in Tongguanshan mine wasteland in Tongling City, Anhui Province. Liquid culture was conducted with four kinds of phosphorus sources, calcium phosphate, aluminum phosphate, ferric phosphate and rock phosphate to determine the pH, dissolved phosphorus, phosphorus in the bacteria and organic acid in the solution. The results showed that the phosphate solubilization by A. pullulans F4 varied with phosphorus sources, which decreased in order of aluminum phosphate > ferric phosphate, calcium phosphate > rock phosphate. The amounts of dissolved phosphorus in the different treatments were all higher than 200 mg x L(-1). The pH of the medium dropped immediately in 48 h, and the aluminum phosphate and ferric phosphate treatments showed a greater decrease in pH than the calcium phosphate and rock phosphate treatments. The organic acid synthesized by A. pullulans F4 included oxalic acid, citric acid and tartaric acid, and oxalic acid, among which oxalic acid was the dominated component. The phosphate dissolving capacity of A. pullulans F4 showed no significant correlation with organic acid, but significantly correlated with the pH. The available phosphorus was significantly improved with the combined application of A. pullulans F4 and glucose, suggesting A. pullulans F4 was a potent candidate for remediation of copper mine wastelands.