有机肥替代部分化肥是实现化肥减量增效的重要途径,对提高作物产量、改善土壤肥力等具有显著效果,但其对温室气体排放以及增加土壤环境中污染物负荷的贡献亦不容小觑。本文重点综述了施用有机肥对作物品质、土壤改良、温室气体排放、农业面源污染等的影响,分析了有机肥施用研究现状,并对有机肥施用的研究趋势提出建议,首先不断优化发酵工艺提升有机肥品质是根本;其次强化品质性状评价在有机肥施用效果评价中的地位,充分依托长期定位观测和现代化监测手段,不断提升肥力监测水平,加强生态环境效应综合评价是保障,以期为科学、合理、高效使用有机肥,保障土壤资源的可持续利用提供指导。

Silage maize is vital to livestock development in northern China, but intensive chemical fertilization has led to soil degradation and reduced productivity. Bio-organic fertilizers offer a sustainable alternative, though their effects on soil multifunctionality remain underexplored. This study evaluated the impact of combining decomposed cow manure, Bacillus amyloliquefaciens, and mineral potassium fulvic acid with chemical fertilizers (NPK) on silage maize yield, soil microbial diversity, and ecosystem multifunctionality (EMF). Field experiments showed that bio-organic fertilization increased silage maize yield by 10.23% compared to chemical fertilizers alone, primarily by boosting labile organic carbon and soil enzyme activity. It also enhanced bacterial richness and diversity, with little effect on fungal communities. Microbial network analysis revealed more complex and stable bacterial networks under bio-organic treatments, indicating strengthened microbial interactions. Random forest and structural equation modeling (SEM) identified soil carbon storage and bacterial diversity as key drivers of EMF, which integrates soil functions such as nutrient cycling, decomposition, enzyme activity, and microbial diversity. These findings suggest that soil bacterial diversity and its interactions with soil properties are critical to both crop productivity and soil health. The optimal fertilization strategy for silage maize in this region involves the combined use of cattle manure, Bacillus amyloliquefaciens, mineral potassium fulvic acid, and NPK fertilizers. This approach improves yield, microbial diversity, and soil multifunctionality. Future studies should consider environmental variables and crop varieties across diverse regions to support broader application.

This study analyzes the soil water infiltration characteristics under muddy water irrigation and bio-organic fertilizer conditions in the current context of muddy water irrigation rarely being used in agricultural production and in combination with the problems of water resource shortages and low soil fertility in arid and semi-arid regions. An indoor one-dimensional soil column infiltration device was used for studying the effects of four muddy water sediment concentration levels (ρ0: 0; ρ1: 4%; ρ2: 8%; ρ3: 12%) and four bio-organic fertilizer levels (FO0: 0; FO1: 2250 kg·hm−2; FO2: 4500 kg·hm−2; sFO3: 6750 kg·hm−2) on soil water infiltration, evaporation characteristics, and leaching loss. The results demonstrated that a higher muddy water sediment concentration and fertilization level resulted in a smaller wetting front distance and cumulative infiltration amount within the same time, but the infiltration reduction rate (η) gradually increased. The three infiltration models (Kostiakov, Philip, and Horton) were fitted, and it was discovered that all three had good fitting results (R2 > 0.8), with the Kostiakov model displaying the best fit and the Horton model exhibiting the worst fit. The cumulative evaporation amount and evaporation time in muddy water irrigation and fertilization conditions was consistent with the Black and Rose evaporation models (R2 > 0.9), the Black model was proved to be higher than the Rose model. In comparison to ρ0, muddy water irrigation increased conductivity and total dissolved solids (TDS) in the leaching solution, but it reduced cumulative evaporation, soil moisture content, the uniformity coefficient of soil water distribution, and leaching solution volume. Compared with FO0, the application of bio-organic fertilizer increased soil water content and reduced soil water evaporation while also reducing the leaching solution volume, conductivity, and TDS in the leaching solution. The results of this research can provide scientific reference for the efficient utilization of muddy water irrigation and the rational application of bio-organic fertilizer.

The aim of the paper is to give an overview on the chemistry of soil organic carbon (SOC) affecting nutrient availability, the emission of greenhouse gases and detoxifying harmful substances in soil. Humic substances represent the stable part of SOC, accounting for between 50 and more than 80% of organically bound carbon in soil. Humic substances strongly affect the soil solution concentration of several plant nutrients and may increase P-, Fe-, and Cu- solubility, thereby increasing their plant availability. Soil organic carbon, mainly humic substances, can detoxify monomeric Al in acid soils, can strongly bind toxic heavy metals, making them unavailable to the plant roots, and may strongly bind a vast variety of harmful organic pollutants. Increasing SOC is an important goal in agriculture. The inclusion of mixtures of semi-perennial plant species and cultivars may strongly increase SOC and humic substance content in soils. To increase SOC, farmyard manure and its rotted or composted forms are superior compared to the separate application of straw and slurry to soil. The storage of carbon, mainly in organic form, in soils is very important in the context of the emission of greenhouse gases. Worldwide, soils release about 10 times more greenhouse gases compared to fossil fuel combustion. Small increments in SOC worldwide will strongly affect the concentration of atmospheric CO2. The public discussion on soil fertility and greenhouse gas emissionshas been politically controlled in a way that leaves the important and positive contribution of soil organic carbon and mainly humic substances partly misinterpreted and partly underestimated.

\n Plant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms (\n i.e.\n bioorganic fertilizers) has been shown to improve resistance against plant pathogens at least in part due to impacts on the structure and function of the resident soil microbiome. However, it remains unclear whether such improvements are driven by the specific action of microbial inoculants, microbial populations naturally resident to the organic fertilizer or the physical-chemical properties of the compost substrate. The aim of this study was to seek the ecological mechanisms involved in the disease suppressive activity of bio-organic fertilizers.\n

Aluminium (Al) toxicity impedes crop growth in acidic soils and is considered the second largest abiotic stress after drought for crops worldwide. Despite remarkable progress in understanding Al resistance in plants, it is still unknown whether and how the soil microbiota confers Al resistance to crops. Here we found that a synthetic community composed of highly Al-resistant bacterial strains isolated from the rice rhizosphere increased rice yield by 26.36% in acidic fields. The synthetic community harvested rhizodeposited carbon for successful proliferation and mitigated soil acidification and Al toxicity through extracellular protonation. The functional coordination between plants and microbes offers a promising way to increase the usage of legacy phosphorus in topsoil. These findings highlight the potential of microbial tools for advancing sustainable agriculture in acidic soils.© 2023. The Author(s), under exclusive licence to Springer Nature Limited.

Synthetic microbial communities (SynComs) are a promising tool for making full use of the beneficial functions imparted by whole bacterial consortia. However, the complexity of reconstructed SynComs often limits their application in sustainable agriculture. Furthermore, inter-strain interactions are often neglected during SynCom construction. Here, we propose a strategy for constructing a simplified and functional SynCom (sfSynCom) by using elite helper strains that significantly improve the beneficial functions of the core symbiotic strain, here <em>Bradyrhizobium elkanii</em> BXYD3, to sustain the growth of soybean (<em>Glycine max</em>). We first identified helper strains that significantly promote nodulation and nitrogen fixation in soybean mediated by BXYD3. Two of these helper strains assigned to the <em>Pantoea</em> taxon produce acyl homoserine lactones, which significantly enhanced the colonization and infection of soybean by BXYD3. Finally, we constructed a sfSynCom from these core and helper strains. This sfSynCom based on the core-helper strategy was more effective at promoting nodulation than inoculation with BXYD3 alone and achieved effects comparable to those of a complex elite SynCom previously constructed on the basis of potential beneficial functions between microbes and plants alone. Our results suggest that considering interactions between strains as well as those between strains and the host plant might allow construction of sfSynComs.

Endophytes often have dramatic effects on their host plants. Characterizing the relationships among members of these communities has focused on identifying the effects of single microbes on their host, but has generally overlooked interactions among the myriad microbes in natural communities as well as potential higher-order interactions. Network analyses offer a powerful means for characterizing patterns of interaction among microbial members of the phytobiome that may be crucial to mediating its assembly and function. We sampled twelve endophytic communities, comparing patterns of niche overlap between coexisting bacteria and fungi to evaluate the effect of nutrient supplementation on local and global competitive network structure. We found that, despite differences in the degree distribution, there were few significant differences in the global network structure of niche-overlap networks following persistent nutrient amendment. Likewise, we found idiosyncratic and weak evidence for higher-order interactions regardless of nutrient treatment. This work provides a first-time characterization of niche-overlap network structure in endophytic communities and serves as a framework for higher-resolution analyses of microbial interaction networks as a consequence and a cause of ecological variation in microbiome function.

Microbial communities exhibit intricate interactions underpinned by metabolic dependencies. To elucidate these dependencies, we present a workflow utilizing random matrix theory on metagenome-assembled genomes to construct co-occurrence and metabolic complementarity networks. We apply this approach to a temperature gradient hot spring, unraveling the interplay between thermal stress and metabolic cooperation. Our analysis reveals an increase in the frequency of metabolic interactions with rising temperatures. Amino acids, coenzyme A derivatives, and carbohydrates emerge as key exchange metabolites, forming the foundation for syntrophic dependencies, in which commensalistic interactions take a greater proportion than mutualistic ones. These metabolic exchanges are most prevalent between phylogenetically distant species, especially archaea-bacteria collaborations, as a crucial adaptation to harsh environments. Furthermore, we identify a significant positive correlation between basal metabolite exchange and genome size disparity, potentially signifying a means for streamlined genomes to leverage cooperation with metabolically richer partners. This phenomenon is also confirmed by another composting system which has a similar wide range of temperature fluctuations. Our workflow provides a feasible way to decipher the metabolic complementarity mechanisms underlying microbial interactions, and our findings suggested environmental stress regulates the cooperative strategies of thermophiles, while these dependencies have been potentially hardwired into their genomes during co-evolutions.© 2024. The Author(s).

Chemical (synthetic) fertilizers used indiscriminately for improved production pose a major threat to long-term soil fertility, the soil environment, and its components. The soil microbial community, however, plays a major and important role in fostering soil health and plant growth. While the use of synthetic fertilizers has a profound impact on plant growth, it also significantly alters the makeup of the microbial community towards a detrimental low, especially N and P fertilizers. Sustainable farming practices can reduce the depletion of natural resources and maintain both productivity and soil fertility. The use of minerals that contain fertilizer nutrients in their native state is a very promising approach to reducing emissions associated with the processing chemical industries. Organic material from natural sources (food waste, manure from livestock, agricultural biomass, etc.) acts as a source of microbial culture and encourages the release of nutrients into the soil during mineral weathering. The combination of nutrient-bearing minerals and their biological weathering agents together with organic matter has the potential to remediate, restore, and sustain depleted agricultural soils. Therefore, in this review, we emphasize the significance of sustaining agricultural productivity and microbial diversity in the rhizosphere, the two vital aspects of modern agricultural systems, through bio-organic mineral fertilizers.

Current agricultural practices face numerous challenges, including declining soil fertility and heavy reliance on chemical inputs. Rhizosphere microbial metabolites have emerged as promising agents for enhancing crop health and yield in a sustainable manner. These metabolites, including phytohormones, antibiotics, and volatile organic compounds, play critical roles in promoting plant growth, boosting resistance to pathogens, and improving resilience to environmental stresses. This review comprehensively outlines the mechanisms through which rhizosphere microbial metabolites influence crop health, traits, functional components, and yield. It also discusses the potential applications of microbial secondary metabolites in biofertilizers and highlights the challenges associated with their production and practical use. Measures to overcome these challenges are proposed, alongside an exploration of the future development of the functional fertilizer industry. The findings presented here provide a scientific basis for utilizing rhizosphere microbial metabolites to enhance agricultural sustainability, offering new strategies for future crop management. Integrating these microbial strategies could lead to increased crop productivity, improved quality, and reduced dependence on synthetic chemical inputs, thereby supporting a more environmentally friendly and resilient agricultural system.

To secure phosphorus (P) from soil, most land plants use a direct phosphate uptake pathway via root hairs and epidermis and an indirect phosphate uptake pathway via mycorrhizal symbiosis. The interaction between these two pathways is unclear. Here, we mapped a network between transcription factors and mycorrhizal symbiosis-related genes using Y1H. Intriguingly, this gene regulatory network is governed by the conserved P-sensing pathway, centered on phosphate starvation response (PHR) transcription factors. PHRs are required for mycorrhizal symbiosis and regulate symbiosis-related genes via the P1BS motif. SPX-domain proteins suppress OsPHR2-mediated induction of symbiosis-related genes and inhibit mycorrhizal infection. In contrast, plants overexpressing OsPHR2 show improved mycorrhizal infection and are partially resistant to P-mediated inhibition of symbiosis. Functional analyses of network nodes revealed co-regulation of hormonal signaling and mycorrhizal symbiosis. This network deciphers extensive regulation of mycorrhizal symbiosis by endogenous and exogenous signals and highlights co-option of the P-sensing pathway for mycorrhizal symbiosis.Copyright © 2021 Elsevier Inc. All rights reserved.

Phosphorus (P) deficiency is a common challenge in crop production because of its poor mobility through the soil. The root system plays a significant role in P absorption from the soil and is the initial indicator of low P levels. However, the phenotypic dynamics and longevity of cotton roots under P stress remain unknown. In this study, RhizoPot, an improvised in situ root observation device, was used to monitor the dynamics of root phenotypes of cotton seedlings under P-deficient (PD) and P-replete (PR) conditions. Low P stress reduced P absorption and accumulation in the roots, leading to low dry weight accumulation. Cotton seedlings responded to low P stress by increasing the number of lateral roots, specific root length, branch density, root length density, and length of root hairs. Additionally, the life span of root hairs was prolonged. Low P stress also reduced the average diameter of roots, promoted root extension, expanded the root coverage area, and increased the range of P acquisition. Principal component analysis revealed that the net root growth rate, root length density, root dry weight, P absorption efficiency, average root hair length, and taproot daily growth significantly influenced the cotton root architecture. Collectively, these results show that low P stress reduces the net growth rate of cotton seedling roots and restricts plant growth. Plants respond to P deficiency by extending the life span of root hairs and increasing specific root length and lateral root branch density. This change in root system architecture improves the adaptability of plants to low P conditions. The findings of this study may guide the selection of cotton varieties with efficient P utilization.

Phosphorus (P) is an important nutrient for plants, and a lack of available P greatly limits plant growth and development. Phosphate-solubilizing microorganisms (PSMs) significantly enhance the ability of plants to absorb and utilize P, which is important for improving plant nutrient turnover and yield. This article summarizes and analyzes how PSMs promote the absorption and utilization of P nutrients by plants from four perspectives: the types and functions of PSMs, phosphate-solubilizing mechanisms, main functional genes, and the impact of complex inoculation of PSMs on plant P acquisition. This article reviews the physiological and molecular mechanisms of phosphorus solubilization and growth promotion by PSMs, with a focus on analyzing the impact of PSMs on soil microbial communities and its interaction with root exudates. In order to better understand the ability of PSMs and their role in soil P transformation and to provide prospects for research on PSMs promoting plant P absorption. PSMs mainly activate insoluble P through the secretion of organic acids, phosphatase production, and mycorrhizal symbiosis, mycorrhizal symbiosis indirectly activates P via carbon exchange. PSMs can secrete organic acids and produce phosphatase, which plays a crucial role in soil P cycling, and related genes are involved in regulating the P-solubilization ability. This article reviews the mechanisms by which microorganisms promote plant uptake of soil P, which is of great significance for a deeper understanding of PSM-mediated soil P cycling, plant P uptake and utilization, and for improving the efficiency of P utilization in agriculture.

Nitrogen fertilizer is widely used in agriculture to boost crop yields. Plant growth-promoting rhizobacteria (PGPRs) can increase plant nitrogen use efficiency through nitrogen fixation and organic nitrogen mineralization. However, it is not known whether they can activate plant nitrogen uptake. In this study, we investigated the effects of volatile compounds (VCs) emitted by the PGPR strain Bacillus velezensis SQR9 on plant nitrogen uptake. Strain SQR9 VCs promoted nitrogen accumulation in both rice and Arabidopsis. In addition, isotope labeling experiments showed that strain SQR9 VCs promoted the absorption of nitrate and ammonium. Several key nitrogen-uptake genes were up-regulated by strain SQR9 VCs, such as AtNRT2.1 in Arabidopsis and OsNAR2.1, OsNRT2.3a, and OsAMT1 family members in rice, and the deletion of these genes compromised the promoting effect of strain SQR9 VCs on plant nitrogen absorption. Furthermore, calcium and the transcription factor NIN-LIKE PROTEIN 7 play an important role in nitrate uptake promoted by strain SQR9 VCs. Taken together, our results indicate that PGPRs can promote nitrogen uptake through regulating plant endogenous signaling and nitrogen transport pathways.

Decomposed organic materials, in combination with plant growth-promoting bacteria (PGPB), are environmentally friendly and reduce synthetic fertilizer use in rice production. A bio-organic fertilizer (BoF) was prepared using kitchen waste (79%), chita-dhan (unfilled rice grain) biochar (15%), rock phosphate (5%), and a consortium of 10 PGPB (1%) to supplement 30% nitrogen and to replace triple superphosphate (TSP) fertilizer in rice production with an improvement of soil health. PGPB were local isolates and identified using 16S ribosomal RNA partial gene sequences asBacillus mycoides,Proteussp.,Bacillus cereus, Bacillus subtilis, Bacillus pumilus, Paenibacillus polymyxa, andPaenibacillusspp. Isolates could fix N2by 0.7–1.4 g kg–1, solubilize 0.1–1.2 g kg–1phosphate, and produce 0.1–40 g kg–1indoleacetic acid. The performance of BoF was evaluated by 16 field experiments and 18 farmers’ field demonstration trials during the year 2017–2020 in different parts of Bangladesh. Performances of BoF were evaluated based on control (T1), full synthetic fertilizer dose of N, P, and K (T2), BoF (2 t ha–1) + 70% N as urea + 100% K as muriate of potash (T3), 70% N as urea + 100% P as TSP + 100% K as muriate of potash (T4), and 2 t ha–1BoF (T5) treatments. At the research station, average grain yield improved by 10–13% in T3compared with T2treatment. Depending on seasons, higher agronomic N use efficiency (19–30%), physiological N use efficiency (8–18%), partial factor productivity (PFP)N(114–150%), recovery efficiency (RE)N(3–31%), N harvest index (HIN) (14–24%), agronomic P use efficiency (22–25%), partial factor productivity of P (9–12%), AREP(15–23%), and HIP(3–6%) were obtained in T3compared with T2treatment. Research results were reflected in farmers’ field, and significant (P&amp;lt; 0.05) higher plant height, tiller, panicle, grain yield, partial factor productivity of N and P were obtained in the same treatment. Application of BoF improved soil organic carbon by 6–13%, along with an increased number of PGPB as compared with full synthetic fertilizer dose. In conclusion, tested BoF can be considered as a green technology to reduce 30% synthetic N and 100% TSP requirements in rice production with improved soil health.

Process and function that underlie the assembly of a rhizosphere microbial community may be strongly linked to the maintenance of plant health. However, their assembly processes and functional changes in the deterioration of soilborne disease remain unclear. Here, we investigated features of rhizosphere microbiomes related to Fusarium wilt disease and assessed their assembly by comparison pair of diseased/healthy sequencing data. The untargeted metabolomics was employed to explore potential community assembly drivers, and shotgun metagenome sequencing was used to reveal the mechanisms of metabolite-mediated process after soil conditioning.Results showed the deterministic assembly process associated with diseased rhizosphere microbiomes, and this process was significantly correlated to five metabolites (tocopherol acetate, citrulline, galactitol, octadecylglycerol, and behenic acid). Application of the metabolites resulted in a deterministic assembly of microbiome with the high morbidity of watermelon. Furthermore, metabolite conditioning was found to weaken the function of autotoxin degradation undertaken by specific bacterial group (Bradyrhizobium, Streptomyces, Variovorax, Pseudomonas, and Sphingomonas) while promoting the metabolism of small-molecule sugars and acids initiated from another bacterial group (Anaeromyxobacter, Bdellovibrio, Conexibacter, Flavobacterium, and Gemmatimonas). Video Abstract CONCLUSION: These findings strongly suggest that shifts in a metabolite-mediated microbial community assembly process underpin the deterministic establishment of soilborne Fusarium wilt disease and reveal avenues for future research focusing on ameliorating crop loss due to this pathogen.© 2022. The Author(s).

Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth-promoting bacteria and fungi in the rhizosphere prime the whole plant body for enhanced defense against a broad range of pathogens and insect herbivores. A wide variety of root-associated mutualists, including Pseudomonas, Bacillus, Trichoderma, and mycorrhiza species sensitize the plant immune system for enhanced defense without directly activating costly defenses. This review focuses on molecular processes at the interface between plant roots and ISR-eliciting mutualists, and on the progress in our understanding of ISR signaling and systemic defense priming. The central role of the root-specific transcription factor MYB72 in the onset of ISR and the role of phytohormones and defense regulatory proteins in the expression of ISR in aboveground plant parts are highlighted. Finally, the ecological function of ISR-inducing microbes in the root microbiome is discussed.

Resistant cultivars have played important roles in controlling Fusarium wilt disease, but the roles of rhizosphere interactions among different levels of resistant cultivars are still unknown. Here, two phenotypes of cucumber, one resistant and one with increased susceptibility to Fusarium oxysporum f.sp. cucumerinum (Foc), were grown in the soil and hydroponically, and then 16S rRNA gene sequencing and nontargeted metabolomics techniques were used to investigate rhizosphere microflora and root exudate profiles. Relatively high microbial community evenness for the Foc-susceptible cultivar was detected, and the relative abundances of Comamonadaceae and Xanthomonadaceae were higher for the Foc-susceptible cultivar than for the other cultivar. FishTaco analysis revealed that specific functional traits, such as protein synthesis and secretion, bacterial chemotaxis, and small organic acid metabolism pathways, were significantly upregulated in the rhizobacterial community of the Foc-susceptible cultivar. A machine-learning approach in conjunction with FishTaco plus metabolic pathway analysis revealed that four organic acids (citric acid, pyruvate acid, succinic acid, and fumarate) were released at higher abundance by the Foc-susceptible cultivar compared with the resistant cultivar, which may be responsible for the recruitment of Comamonadaceae, a potential beneficial microbial group. Further validation demonstrated that Comamonadaceae can be "cultured" by these organic acids. Together, compared with the resistant cultivar, the susceptible cucumber tends to assemble beneficial microbes by secreting more organic acids.© 2020. The Author(s).

\n Reducing chemical fertilizers in combination with bio-organic fertilizers can limit the use of chemical fertilizers while maintaining soil fertility. However, the effects of combined fertilization on soil chemical properties, microbial community structure, and crop yield and quality are unknown. Using high-throughput sequencing, we conducted field experiments using lettuce plants subjected to five fertilization treatments: chemical fertilizer with conventional fertilization rate (CK), chemical fertilizer reduction by 30% + 6,000 kg ha\n –1\n bio-organic fertilizer (T1), chemical fertilizer reduction by 30% + 9,000 kg ha\n –1\n bio-organic fertilizer (T2), chemical fertilizer reduction by 40% + 6,000 kg ha\n –1\n bio-organic fertilizer (T3), and chemical fertilizer reduction by 40% + 9,000 kg ha\n –1\n bio-organic fertilizer (T4). Compared with CK, the T1–T4 had significantly higher soil pH and soil organic matter (SOM) and showed increased richness and diversity of the bacterial community, and decreased richness and diversity of the fungal community. Principal coordinate analysis evidenced that the bacterial and fungal communities of CK and T1–T4 were distinctly separated. The Kruskal-Wallis\n H\n -test demonstrated that the fungal community was more sensitive than the bacterial community to chemical fertilizer reduction combined with bio-organic fertilizer. Among the soil chemical parameters measured, only TN (total nitrogen) was significantly correlated with bacterial and fungal community composition. The T1 and T2 increased lettuce yield. Moreover, T1–T4 characterized reduced nitrate content and increased levels of soluble sugars and vitamin C in lettuce. Overall, the combined application of reduced chemical fertilizer and bio-organic fertilizer effectively improved soil fertility, microbial community structure, and lettuce yield and quality. These findings have valuable implications for vegetable safety and long-term environmental sustainability.\n

\n Fertilizers and microbial communities that determine fertilizer efficiency are key to sustainable agricultural development. Sugarcane is an important sugar cash crop in China, and using bio-fertilizers is important for the sustainable development of China’s sugar industry. However, information on the effects of bio-fertilizers on sugarcane soil microbiota has rarely been studied. In this study, the effects of bio-fertilizer application on rhizosphere soil physicochemical indicators, microbial community composition, function, and network patterns of sugarcane were discussed using a high-throughput sequencing approach. The experimental design is as follows: CK: urea application (57 kg/ha), CF: compound fertilizer (450 kg/ha), BF1: bio-fertilizer (1500 kg/ha of bio-fertilizer + 57 kg/ha of urea), and BF2: bio-fertilizer (2250 kg/ha of bio-fertilizer + 57 kg/ha of urea). The results showed that the bio-fertilizer was effective in increasing sugarcane yield by 3–12% compared to the CF treatment group, while reducing soil acidification, changing the diversity of fungi and bacteria, and greatly altering the composition and structure of the inter-root microbial community. Variance partitioning canonical correspondence (VPA) analysis showed that soil physicochemical variables explained 80.09% and 73.31% of the variation in bacteria and fungi, respectively. Redundancy analysis and correlation heatmap showed that soil pH, total nitrogen, and available potassium were the main factors influencing bacterial community composition, while total soil phosphorus, available phosphorus, pH, and available nitrogen were the main drivers of fungal communities. Volcano plots showed that using bio-fertilizers contributed to the accumulation of more beneficial bacteria in the sugarcane rhizosphere level and the decline of pathogenic bacteria (e.g.,\n Leifsonia\n ), which may slow down or suppress the occurrence of diseases. Linear discriminant analysis (LDA) and effect size analysis (LEfSe) searched for biomarkers under different fertilizer treatments. Meanwhile, support vector machine (SVM) assessed the importance of the microbial genera contributing to the variability between fertilizers, of interest were the bacteria\n Anaerolineace\n,\n Vulgatibacter\n, and\n Paenibacillus\n and the fungi\n Cochliobolus\n,\n Sordariales\n, and\n Dothideomycetes\n between CF and BF2, compared to the other genera contributing to the variability. Network analysis (co-occurrence network) showed that the network structure of bio-fertilizers was closer to the network characteristics of healthy soils, indicating that bio-fertilizers can improve soil health to some extent, and therefore if bio-fertilizers can be used as an alternative to chemical fertilizers in the future alternative, it is important to achieve green soil development and improve the climate.\n

为探究生物有机肥的施用对燕麦生长发育的影响,以‘林纳’为试验材料,设置5个施肥处理,对其进行不同时间处理的干旱胁迫。结果表明,干旱初期,施化肥处理的土壤含水量高于施有机肥的土壤含水量,但在干旱胁迫后期表现为施有机肥处理的土壤含水量高于施化肥处理的土壤含水量,说明施生物有机肥对土壤水分含量有一定的影响。不同施肥处理下,茎重和根重总体呈现出施有机肥处理大于施化肥处理,除W4处理,其他处理施有机肥的根茎比大于施化肥的根茎比。不同施肥处理下的根系性状和叶性状也表现出不同差异。施有机肥可以促进根系的分蘖,以及植物地上和地下部分的生长,有效增加生物量。综合分析发现,6000 kg/hm ²的生物有机肥施肥量对燕麦干旱具有最显著的响应。

One model of a disease-suppressive soil predicts that the confrontation of plant with a phytopathogen can lead to the recruitment and accumulation of beneficial microorganisms. However, more information is need to be deciphered regarding which beneficial microbes become enriched, and how the disease suppression is achieved. Here, we conditioned soil by continuously growing eight generations of cucumber inoculated with Fusarium oxysporum f.sp. cucumerinum in a split-root- system. Disease incidence was found to decrease gradually upon pathogen infection accompanied with higher quantity of reactive oxygen species (ROS mainly OH·) in roots and accumulation of Bacillus and Sphingomonas. These key microbes were proven to protect the cucumber from pathogen infection by inducing high ROS level in the roots through enrichment of pathways, including a two-component system, a bacterial secretion system and flagellar assembly revealed by metagenomics sequencing. Untargeted metabolomics analysis combined with in vitro application assays suggested that threonic acid and lysine were pivotal to recruit Bacillus and Sphingomonas. Collectively, our study deciphered a "cry for help" case wherein cucumber releases particular compounds to enrich beneficial microbes that raise the ROS level of host to prevent pathogen attack. More importantly, this may be one of the fundamental mechanisms underpinning disease-suppressive soil formation.This article is protected by copyright. All rights reserved.

Plant pathogenic bacteria cause high crop and economic losses to human societies. Infections by such pathogens are challenging to control as they often arise through complex interactions between plants, pathogens and the plant microbiome. Experimental studies of this natural ecosystem at the microbiome-wide scale are rare, and consequently we have a poor understanding of how the taxonomic and functional microbiome composition and the resulting ecological interactions affect pathogen growth and disease outbreak. Here, we combine DNA-based soil microbiome analysis with in vitro and in planta bioassays to show that competition for iron via secreted siderophore molecules is a good predictor of microbe-pathogen interactions and plant protection. We examined the ability of 2,150 individual bacterial members of 80 rhizosphere microbiomes, covering all major phylogenetic lineages, to suppress the bacterium Ralstonia solanacearum, a global phytopathogen capable of infecting various crops. We found that secreted siderophores altered microbiome-pathogen interactions from complete pathogen suppression to strong facilitation. Rhizosphere microbiome members with growth-inhibitory siderophores could often suppress the pathogen in vitro as well as in natural and greenhouse soils, and protect tomato plants from infection. Conversely, rhizosphere microbiome members with growth-promotive siderophores were often inferior in competition and facilitated plant infection by the pathogen. Because siderophores are a chemically diverse group of molecules, with each siderophore type relying on a compatible receptor for iron uptake, our results suggest that pathogen-suppressive microbiome members produce siderophores that the pathogen cannot use. Our study establishes a causal mechanistic link between microbiome-level competition for iron and plant protection and opens promising avenues to use siderophore-mediated interactions as a tool for microbiome engineering and pathogen control.

Bioorganic fertilizers can alleviate (a) biotic stresses and sustainably increase crop yields. The effect of bioorganic fertilizers on the rhizosphere bacterial community of Panax notoginseng and soil metabolism remains unknown. Here, we tracked the changes in the soil physicochemical properties, bacterial microbiota responses, and soil metabolic functions after the addition of a bioorganic fertilizer in a P. notoginseng field. The application of a bioorganic fertilizer reduced the soil acidification, improved the organic matter, and increased the contents of the total/available soil nutrients. Soil amendment with a bioorganic fertilizer significantly affected the structure of the rhizosphere bacterial community, leading to the enrichment of specific bacterial consortia such as Rhodanobacter, Arthrobacter, Sphingomonas, Devosia, Pseudolabrys, Luteimonas, Lysobacter, Nitrosospira, and Nakamurella. Previously, many of these genera have been associated with nutrient cycling, plant productivity, and disease suppression. Metabolome analysis further highlighted that the bioorganic fertilizer treatment significantly reduced phenolic acids and flavonoids and enhanced organic acids, saccharides and alcohols, and amino acids. This result indicates a high survival of bacterial microbiota in the rhizosphere and an availability of nutrients for P. notoginseng growth. This work showed that the application of bioorganic fertilizers significantly improves soil health status, alters soil metabolic functions, and stimulates a specific subset of rhizosphere microbiota for nutrient cycling and disease protection in P. notoginseng.

Although researchers have begun cataloging the incredible diversity of bacteria found in soil, we are largely unable to interpret this information in an ecological context, including which groups of bacteria are most abundant in different soils and why. With this study, we examined how the abundances of major soil bacterial phyla correspond to the biotic and abiotic characteristics of the soil environment to determine if they can be divided into ecologically meaningful categories. To do this, we collected 71 unique soil samples from a wide range of ecosystems across North America and looked for relationships between soil properties and the relative abundances of six dominant bacterial phyla (Acidobacteria, Bacteroidetes, Firmicutes, Actinobacteria, alpha-Proteobacteria, and the beta-Proteobacteria). Of the soil properties measured, net carbon (C) mineralization rate (an index of C availability) was the best predictor of phylum-level abundances. There was a negative correlation between Acidobacteria abundance and C mineralization rates (r2 = 0.26, P < 0.001), while the abundances of beta-Proteobacteria and Bacteroidetes were positively correlated with C mineralization rates (r2 = 0.35, P < 0.001 and r2 = 0.34, P < 0.001, respectively). These patterns were explored further using both experimental and meta-analytical approaches. We amended soil cores from a specific site with varying levels of sucrose over a 12-month period to maintain a gradient of elevated C availabilities. This experiment confirmed our survey results: there was a negative relationship between C amendment level and the abundance of Acidobacteria (r2 = 0.42, P < 0.01) and a positive relationship for both Bacteroidetes and beta-Proteobacteria (r2 = 0.38 and 0.70, respectively; P < 0.01 for each). Further support for a relationship between the relative abundances of these bacterial phyla and C availability was garnered from an analysis of published bacterial clone libraries from bulk and rhizosphere soils. Together our survey, experimental, and meta-analytical results suggest that certain bacterial phyla can be differentiated into copiotrophic and oligotrophic categories that correspond to the r- and K-selected categories used to describe the ecological attributes of plants and animals. By applying the copiotroph-oligotroph concept to soil microorganisms we can make specific predictions about the ecological attributes of various bacterial taxa and better understand the structure and function of soil bacterial communities.

Direct seeding of rice has emerged as a strategy for sustainable rice (Oryza sativa L.) production because of advantages, such as fewer production links, labor and farmland water-saving, easy mechanization, and high economic benefits. However, few studies have investigated the effects of different organic fertilizers on soil fungal community and rice yield in dry direct-seeded paddy fields. In order to select the best combination of organic fertilizer and chemical fertilizer, field experiments were used to evaluate the role of no fertilizer (F0); CF, conventional NPK fertilizer, OF1, biochar + conventional NPK fertilizer; OF2, seaweed bioorganic fertilizer + conventional NPK fertilizer; OF3, Jishiwang bioorganic fertilizer + conventional NPK fertilizer; and OF4, attapulgite organic fertilizer + conventional NPK fertilizer on microbial structure and diversity and rice yield. Under Jishiwang bioorganic fertilizer + conventional NPK fertilization, the number of fungal OTUs was 365 and ranged from 1 to 9. The Ascomycota relative abundance was increased by 28.25% under Jishiwang bioorganic fertilizer application compared with CF, but the Basidiomycota decreased. Sordariomycetes and Leotiomycetes relative abundances were increased under organic fertilization. The relative abundance of dung saprotrophs, fungal parasites, and leaf saprotrophs was increased under organic fertilizer compared to CF, and animal pathogens decreased, but organic fertilizers also increased plant pathogens. Rice yield was increased under Jishiwang bioorganic fertilizer + conventional NPK fertilizer and was positively correlated with Ascomycota and Sordariomycetes relative abundances. The use of Jishiwang bioorganic fertilizer + conventional NPK fertilizer improves fungal community diversity and rice yield.

Conventional water and fertilizer management practices have led to elevated greenhouse gas emissions from rice fields and decreased the efficiency of water and fertilizer utilization in agricultural land. The implementation of water-saving irrigation and the substitution of chemical fertilizers with organic alternatives can influence CH4 and N2O emissions in rice fields. However, it remains unclear how the simultaneous application of both methods will affect the CH4 and N2O emissions in rice fields. Therefore, two irrigation methods (F: flooded irrigation; C: controlled irrigation) and three fertilization modes (A: full chemical fertilizer; B: bio-organic fertilizer replacing 15% chemical nitrogen fertilizer; C: bio-organic fertilizer replacing 30% chemical nitrogen fertilizer) were set up through field experiments to explore the effect of greenhouse gas emission reduction in rice fields by combining controlled irrigation and bio-organic fertilizers. Substituting some chemical fertilizers with bio-organic fertilizers can lower the peak CH4 and N2O fluxes in rice fields, leading to a decrease in the cumulative CH4 and N2O emissions by 11.9~29.7% and 10.8~57.3%, respectively. The reductions led to a considerable decrease in the global warming potential (GWP) and the greenhouse gas emission intensity (GHGI) by 16.1~48.1% and 16.3~48.1%, respectively. Controlled irrigation significantly reduced CH4 emissions by 55.2~69.4% compared with flooded irrigation in rice fields. However, it also increased N2O emissions by 47.5~207.9%, considerably reducing their GWPs by 11.8~45.5%. Neither bio-organic fertilizer substitution nor controlled irrigation significantly affected rice yield. Replacing 15% of chemical nitrogen fertilizers with bio-organic fertilizers in controlled irrigation rice fields can minimize rice GWP and GHGI. The study’s results are of significant importance for enhancing the regulation of greenhouse gases in farmland and achieving sustainable agriculture through cleaner production.

为促进高效环保的化肥替代品研发及农业废弃物资源化利用，本文分析有机肥替代化肥技术的可利用性，就其在粮食作物、经济作物生产中的实际应用进行讨论，分析减量化肥、配施有机肥对作物产量和品质、土壤质量等的影响。可利用性方面，有机肥原料充足，可利用性大，其中，人畜粪尿制成有机肥是较合适的办法。实际应用方面，在水稻、小麦、玉米等粮食作物生产中，有机肥部分替代化肥，可保证水稻各生育期的养分供给，提高小麦籽粒对氮素的吸收利用效率，提高玉米生物量和蛋白质含量；在棉、油菜、柚等经济作物生产中，有机肥部分替代化肥，可提高棉花品质和产量，有效减少油菜病害发生，改善柚叶片和果实养分状况。影响方面，应用该技术有助于促进作物生长发育，提升作物产量和品质，提高果实可溶性蛋白、维生素C含量等；提高土壤质量，改良土壤结构，降低土壤污染风险，提高土壤氮素利用率。本文为发展绿色农业循环经济提供参考。

Rock powders are low-cost potential sources of most of the nutrients required by higher plants for growth and development. However, slow dissolution rates of minerals represent an obstacle to the widespread use of rock powders in agriculture. Rhizosphere processes and biological weathering may further enhance mineral dissolution since the interaction between minerals, plants, and bacteria results in the release of macro- and micronutrients into the soil solution. Plants are important agents in this process acting directly in the mineral dissolution or sustaining a wide diversity of weathering microorganisms in the root environment. Meanwhile, root microorganisms promote mineral dissolution by producing complexing ligands (siderophores and organic acids), affecting the pH (via organic or inorganic acid production), or performing redox reactions. Besides that, a wide variety of rhizosphere bacteria and fungi could also promote plant development directly, synergistically contributing to the weathering activity performed by plants. The inoculation of weathering bacteria in soil or plants, especially combined with the use of crushed rocks, can increase soil fertility and improve crop production. This approach is more sustainable than conventional fertilization practices, which may contribute to reducing climate change linked to agricultural activity. Besides, it could decrease the dependency of developing countries on imported fertilizers, thus improving local development.

Soil microorganisms play a crucial role in maintaining the structure and function of soil ecosystems. This study aims to explore the effects of microbial fertilizers on improving soil physicochemical properties and promoting plant growth. The results show that the application of microbial fertilizers significantly increases the richness of soil microorganisms, maintains soil microecological balance, and effectively improves the soil environment. Through various secondary metabolites, proteins, and mucilage secreted by the developing plant root system, microbial fertilizers recruit specific fungal microorganisms. These microorganisms, by binding soil particles with their extracellular polysaccharides and entwining them, fix the soil, enhance the stability of soil aggregates, and ameliorate soil compaction. Moreover, after the application of microbial fertilizers, the enriched soil microbial community not only promotes the plant’s absorption and utilization of key elements such as nitrogen (N), phosphorus (P), and potassium (K), thereby increasing fruit yield and quality, but also competes with pathogens and induces systemic resistance in plants, effectively warding off pathogenic invasions. This study highlights the potential and importance of microbial fertilizers in promoting sustainable agricultural development, offering new strategies and perspectives for future agricultural production.