Integrated microbiology and metabolomics analysis reveal responses of soil microorganisms and metabolic functions to phosphorus fertilizer on semiarid farm

The discrepancy in amino acids within high-temperature Daqu: A novel metabolic marker for the quality evaluation of Daqu

Mechanical pressing in Daqu production has introduced quality-affecting variations. Up to now, clear elucidation has not yet been applied to the mechanisms behind this phenomenon, and the determinants of Daqu quality are not yet completely excavated. For this reason, the physicochemical factors, enzyme activity, metabolites, and microbial communities were compared between the mechanical Daqu (MDQ) and traditional Daqu (TDQ) in this paper. The results showed significant differences in amino acids between MDQ and TDQ, with arginine being the key differentiator. High temperature, high moisture, and low acidity were crucial to Daqu's amino acid richness. Additionally, mechanical pressing affected core community stability. Bacillus was the primary biological factor for the discrepancy in amino acids. Further investigation indicated that arginine contributed to the reduction of lactic acid and higher alcohols in Jiupei, confirming that amino acids were potential novel markers affecting the quality of Daqu.

Integrated enzyme activities and untargeted metabolome to reveal the mechanism that allow long-term biochar-based fertilizer substitution improves soil quality and maize yield

Biochar-based fertilizer has potential benefits in improving soil quality and crop yield, but the biological mechanisms of soil microbial enzymes interacting with related metabolisms still need to be further investigated. In this study, we combined enzymology and untargeted metabolomics to investigate how biochar-based fertilizer substitution affects soil quality and crop yield by regulating soil enzymes and metabolites in dry-crop farmland. Our findings showed that biochar-based fertilizer substitution enhanced the activities of enzymes related to carbon, nitrogen, and phosphorus cycling, as well as influenced metabolite composition. The identified differential metabolites were enriched into 10 metabolic pathways including linoleic acid metabolism, fatty acid biosynthesis, styrene degradation, ABC transporters, biosynthesis of unsaturated fatty acids, glutathione metabolism, glycine, serine and threonine metabolism, phenylalanine metabolism, pyrimidine metabolism, and arachidonic acid metabolism. Substantial soil quality index improvement was demonstrated, with at least 63.46% increased, under biochar-based fertilizer application, while maize yield was increased by at least 11.16%, compared to conventional fertilizer. Model analysis elucidated mechanisms underlying soil quality and maize yield enhancement, emphasizing the importance of intrinsic regulation through the release of carbon- and nitrogen-related enzymes (e.g., α-glucosidase (α-GC), N-acetyl-β-D-glucosidase (NAG), and leucine aminopeptidase (LAP)) and specific metabolites (e.g., stearic acid, arachidonic acid, and melibiose). Moreover, the key role of soil quality factors was highlighted, with soil organic carbon (SOC), microbial biomass, and available nutrients playing a fundamental role in contributing to the increase in maize yield. The above findings illustrated that biochar-based fertilizer is crucial in modulating soil microbial activity and their metabolites, and their interactions in the soil are essential for promoting improved soil quality and crop yield.

Dynamic impact of polyethylene terephthalate nanoplastics on antibiotic resistance and microplastics degradation genes in the rhizosphere of Oryza sativa L

This study examined the effects of polyethylene terephthalate (PET) nanoplastics on the rhizosphere of Oryza sativa L., focusing on dynamic changes and interactions among microbial communities, antibiotic resistance genes (ARGs) and microplastic degradation genes (MDGs). PET exposure altered the structure and function of soil microbial, enabling specific microbial groups to thrive in polluted environments. High-dose PET treatments markedly increased the abundance and dissemination of ARGs, primarily via resistance mechanisms such as antibiotic efflux and target alteration. By providing additional carbon sources and surfaces for microbial attachment, PET stimulated the growth of microorganisms harboring MDGs, resulting in an increase in MDGs abundance. The elevated expression of MDGs facilitated the propagation of ARGs, with overlapping host microorganisms suggesting that certain microbial groups exhibit dual metabolic capabilities, enabling them to endure both antibiotic and microplastic pressures. Toxic byproducts of microplastic degradation, such as mono-ethylhexyl phthalate, further promoted ARGs dissemination by increasing horizontal gene transfer frequency. Structural equation modeling revealed that PET indirectly influenced ARGs and MDGs expression by altering soil C/N ratio, available phosphorus, and enzyme activities. Thus, nanoscale PET exacerbates ecological risks to soil microbial communities by driving co-propagation of ARGs and MDGs, highlighting the persistent threat of composite pollution to agroecosystems.

The effect of intercropping with Pandanus amaryllifolius Roxb. on rhizospheric microorganism of Areca catechu L

The intercropping pattern promotes the sustainable development of efficient agriculture, especially cash crops, such as Areca catechu L. and Pandanus amaryllifolius Roxb. intercropping plantation in China. However, the mechanisms underlying intercropping pattern effects on soil microbial community diversity and composition are poorly understood. A monoculture and intercropping field experiment of the two crops was established to monitor the changes of soil physicochemical properties, enzyme activities, microbial (bacterial and fungal) diversity, and composition. Soil bacterial rather than fungal communities' diversity is more sensitive to intercropping pattern. The intercropping significantly decreased rhizospheric bacterial diversity of Areca catechu L. by 4.21%, and the decrease of soil nutrient content may be the main reason for the change of soil enzyme activity, bacterial community diversity, and composition structure under intercropping pattern. Supplementing nutrients to the soil of intercropping systems is conducive to maintain soil health and ecosystem functional stability in the tropical compound cultivation plantation.

Root-associated microbial diversity and metabolomics in maize resistance to stalk rot

As one of the three major food crops in the world, maize plays a significant role in alleviating the food crisis. Maize stalk rot can reduce maize yield and mechanical harvesting efficiency. In addition, mycotoxins such as Deoxynivalenol (DON) and Zearalenone (ZEN) produced by maize stalk rot pathogens can also harm livestock and human health. Maize stalk rot is an infection of the whole growth period, and there are no effective control measures at present. Therefore, it is of great significant to study the pathogenesis and control mechanism of stalk rot from multiple perspectives. In the present study, root and rhizosphere soil of disease-resistant inbred line Y853 and disease-susceptible inbred line Q478 were collected at the dough stage (R4) and maturity stage (R6) of maize, respectively. The effects of resistant/susceptible inbred line on soil microorganisms were analyzed by amplicon sequences and metabolomics. The results showed that there was different microbial community composition from different inbred lines in different growth stages. Specifically, the abundance of Arthrobacter, Streptomyces and Bacillus in R4 rhizosphere soil was higher than that of R6, while the rhizosphere fungal composition of LR853 was significantly different from that of the other three compartments. Co-occurrence network analysis showed that the pathogen Fusarium had the highest degree centrality and closeness centrality in the DR478. Moreover, metabolomics analysis showed that four main metabolic pathways were significantly enriched, and 15 metabolites were upgrade in resistant inbred line. Furthermore, microbes, especially fungi, also were related to these 15 metabolites. Our results revealed that maize resistance to stalk rot is closely related to root-associated microbiota and rhizospheric metabolites, which would be a new perspective of phytopathogenic biocontrol.

Biodegradable and conventional mulches inhibit nitrogen fixation by peanut root nodules - potentially related to microplastics in the soil

Mulching has been demonstrated to improve the soil environment and promote plant growth. However, the effects of mulching and mulch-derived microplastics (MPs) on nitrogen fixation by root nodules remain unclear. In this study, we investigated the effects of polyethylene (PE) and polylactic acid-polybutylene adipate-co-terephthalate (PLA-PBAT) film mulching on nitrogen fixation by root nodules after 4 years of continuous mulching using 15N tracer technology. Additionally, we examined the relationship between nitrogen fixation and MPs. We found a reduction in the proportion of nitrogen fixation by nodules (54.3 %-58.7 %) due to mulching. This decrease may be attributed to reduced dinitrogenase activity and flavonoid content at the seedling stage caused by mulching, and mulching with PLA-PBAT films significantly decreased the abundance of Bradyrhizobium at maturity. Furthermore, combined analysis of nitrogen-fixing bacteria (nifH) and metabolomes indicated that N-lauroylethanolamine may act as a regulatory signal influencing the root nodule nitrogen fixation process and that mulching resulted in significant changes in its content. The mantel test and PLS-PM suggest that microplastic from mulching may harm root nodule nitrogen fixation. This study reveals the influence of mulching on plant nitrogen uptake and the potential threat of mulch-derived microplastics, with a special focus on root nodule nitrogen fixation.

Co-application of sheep manure and commercial organic fertilizer enhances plant productivity and soil quality in alpine mining areas

Background and aims

The addition of organic fertilizers and sheep slat manure have important effects on soil quality in alpine mining areas, but how they affect soil physicochemical properties and microorganisms is not yet known.

Methods

The current study employed field-controlled experiments and high-throughput sequencing technology to investigate differences in soil physicochemical properties, microbial community structures, and diversity under four treatments: no fertilization (CK), 100% sheep manure (SM), a combination of 50% sheep manure and 50% commercial organic fertilizer (MF), and 100% commercial organic fertilizer (OF).

Results

Aboveground biomass increased by 191.93, 253.22, and 133.32% under SM, MF and OF treatments, respectively, when compared to CK treatment. The MF treatment resulted in significantly higher soil total nitrogen, total phosphorus, organic matter, and available nitrogen content compared to other treatments. Soil total nitrogen content, total phosphorus content, organic matter, available nitrogen content and available phosphorus content were 211, 120, 380, 557, and 271% higher, respectively, under the MF treatment than the CK treatment. Different nutrient additions significantly influenced soil microbial community composition. The SM and MF treatments notably increased soil bacterial and fungal community Operational Taxonomic Units (OTUs) indices and Chao 1 indices, while nutrient addition had no meaningful effect on the Simpson indices for microbial communities. There was a highly significant positive correlation between aboveground biomass and observed soil nutrient content.

Conclusion

The combined application of sheep manure and commercial organic fertilizer is more conducive to improving soil quality and enhancing plant productivity in alpine mining areas.

An ideal leaf spraying strategy of brown sugar for edible medicinal plants of Viola inconspicua

The typical edible medicinal plants of Viola inconspicua were compared with leaf-green, biomass, metabolomes, and bacterial communities, after leaf-spraying water (A), brown sugar water (B), brown sugar, urea, and KH2PO4 water (C), or KH2PO4 and urea water (D). The plants sprayed with C solution presented relatively normal leaf-green and the highest biomass. In contrast of A group, B, C, and D groups were found with 72, 94, and 104 leaf differently accumulated metabolites (DAMs) and 105, 88, and 92 root DAMs, respectively. Typically, relative abundances of amino acids were elevated in C and D groups, while those of leaf flavonoids were increased in B group. Noticeably, leaf DAMs of C group versus A group had strong correlations with one to more phylum- or/and genus-dominant bacteria of C group. Taken together, leaf-spraying brown sugar, urea, and KH2PO4 water are ideal for holding leaf-green and biomass in V. inconspicua plants.

Soil Microbial and Metabolomic Shifts Induced by Phosphate-Solubilizing Bacterial Inoculation in Torreya grandis Seedlings

Phosphorus is crucial for plant growth and development, but excess fertilizer not absorbed by plants often binds with metal ions like iron and manganese, forming insoluble compounds that contribute to soil environmental pollution. This study investigates the impact of Burkholderia sp., a phosphate-solubilizing bacterium utilized as a biofertilizer, on the fertility of T. grandis soil, alongside the associated shifts in soil metabolites and their relationship with microbial communities after inoculation. The soil microbial community structures and metabolite profiles were analyzed via amplicon sequencing and high-resolution untargeted metabolomics. The inoculation of phosphate-solubilizing bacteria led to a significant (p < 0.05) enhancement in total phosphorus, potassium, and nitrogen concentrations in the soil, with a marked increase in available phosphorus in bulk soil (p < 0.05). Moreover, the microbial community structure exhibited significant shifts, particularly in the abundance of bacterial phyla such as Acidobacteria, Chloroflexi, Proteobacteria, and the fungal phylum Ascomycota. Metabolomic analysis revealed distinct metabolites, including fatty acids, hormones, amino acids, and drug-related compounds. Key microbial taxa such as Chloroflexi, Proteobacteria, Acidobacteria, Verrucomicrobia, Mucoromycota, and Ascomycota indirectly contributed to soil phosphorus metabolism by influencing these differential metabolites. In conclusion, the application of phosphate-solubilizing bacteria offers an innovative approach to improving soil quality in T. grandis, promoting phosphorus utilization efficiency, and enhancing soil ecosystem health by optimizing microbial communities and metabolite compositions.

Insights into the effects of anilofos on direct-seeded rice production system through untargeted metabolomics

Weed infestation is the major biological threat in direct-seeded rice production and can cause significant yield losses. The effective use of herbicides is particularly important in direct-seeded rice production. Anilofos, a pre-emergence herbicide, has been shown to be effective against the weed barnyardgrass. However, its impacts on crop yield and the direct-seeded rice production ecosystem remain underexplored. In this study, we conducted field trials and used untargeted metabolomics to investigate systemic effects of two different treatments (40 g/acre and 60 g/acre) on rice shoot and root as well as the rhizosphere soil during the critical tillering stage. Here, a total of 400 metabolites were determined in the crop and soil, with differential metabolites primarily comprising lipids and lipid-like molecules as well as phenylpropanoids and polyketides. Spearman correlation network analysis and a Zi-Pi plot revealed 7 key differential metabolites with significant topological roles, including succinic acid semialdehyde and riboflavin. KEGG pathway analysis showed that anilofos downregulated the amino acid metabolism while mainly promoted carbohydrate metabolism and secondary metabolites biosynthesis of the crop, which made minimal disruption on soil metabolism. Notably, we found 40 g/acre anilofos application could significantly improve the rice yield, potentially linked to the improved activity of flavonoid biosynthesis and starch and sucrose metabolism. This research provides a comprehensive evaluation of anilofos effects in the direct-seeded rice production system, offering new insights into optimizing herbicide use to improve agricultural sustainability and productivity.

Different responses of soil bacterial community to plant-plant interactions under organic-inorganic fertilizers affect seedling establishment during subalpine forest succession

Introduction

Rhizosphere bacterial community as a valuable indicator of soil quality and function, has been widespread studied. However, little knowledge is about the response of bacterial communities to plant-plant interaction and different fertilizers during secondary forest succession.

Methods

We conducted a field pot experiment applying organic and inorganic fertilizers to monocultures and mixed cultures of dominant plant species from mid- to late-successional stages (Salix oritrepha, Betula albosinensis, and Picea asperata), and investigated the responses of plant growth and rhizosphere bacterial communities.

Results and discussion

Results indicated that growth rate of plant height varied among plant species, but no significant differences were observed in soil bacterial diversity and composition among plant species or inter-specific interactions under control. Compared to control, inorganic fertilizer resulted in increases in plant growth and the relative abundance of Proteobacteria, Patescibacteria, Bacteroidetes and Gemmatimonadetes, while simultaneously leading to decrease in the relative abundance of Acidobacteria, Actinobacteria, Chloroflexi, Rokubacteria and Planctomycetes. When grown with other species, the bacterial communities in the mixture resembled those of S. oritrepha in singular monoculture under inorganic fertilizer treatment, but plant growth was not affected by interspecific interaction. Unlike inorganic fertilizer, organic fertilizer significantly affected bacterial communities and increased bacterial diversity, but did not alter the effects of plant-plant interactions on bacterial communities. It was also observed that organic fertilizer facilitated later successional species' growth (P. asperata and B. albosinensis) by the mid-successional species (S. oritrepha), ultimately facilitating secondary forest succession. In addition, plants at different successional stages harbor specific bacterial communities to affect their growth, and the bacterial communities contributed more than soil properties to the variations in the plant growth of S. oritrepha and P. asperata though the bacterial communities were regulated by soil factors. This finding highlights the significance of the rhizosphere bacteria on plant growth and plant community succession. It also emphasize the importance of considering both plant-plant interactions and diverse fertilizer types in forest restoration efforts and provide valuable insights into optimizing agronomic practices for secondary forest succession.

Responses of CO2 and CH4 in the alpine wetlands of the Tibetan Plateau to warming and nitrogen and phosphorus additions

Wetland ecosystems store large amounts of carbon, and CO2 and CH4 fluxes from this ecosystem receive the double impact of climate change and human activities. Nonetheless, research on how multi-gradient warming and nitrogen and phosphorus additions affect these wetland greenhouse gas emissions is still limited, particularly in alpine wetland ecosystems. Therefore, we conducted a field experiment on the Tibetan Plateau wetlands, investigating the effects of warming and nitrogen and phosphorus additions on the CO2 and CH4 fluxes in alpine wetlands. Results indicated that warming enhanced the CO2 absorption and CH4 emission in the alpine meadow ecosystem, possibly related to changes in plant growth and microbial activity induced by warming, while we noticed that the promotion of CO2 uptake weakened with the increase in the magnitude of warming, suggesting that there may be a temperature threshold beyond which the ecosystem's capacity for carbon sequestration may be reduced. Nitrogen addition increased CH4 emission, with the effect on CO2 absorption shifting from inhibition to enhancement as the amount of applied nitrogen or phosphorus increased. The interaction between warming and nitrogen and phosphorus additions further influenced CH4 emission, exhibiting a synergistic enhancement effect. This study deepens our understanding of the greenhouse gas responses of alpine wetland ecosystems to warming and nitrogen and phosphorus additions, which is significant for predicting and managing ecosystem carbon balance under global change.

Response of soil fungal-community structure and function to land conversion to agriculture in desert grassland

Land conversion to agriculture is an important factor affecting soil ecological processes in the desert grasslands of northern China. However, soil fungal-community structure and function in response to Land conversion remain unclear. In this study, desert grassland, artificial shrubland, and land conversion were investigated in the western part of the Mu Us Sandland (Yanchi, Ningxia; Dingbian, Shaanxi). We found that land conversion significantly increased soil total carbon, nitrogen, and phosphorus, and available phosphorous and potassium contents. In the early stage of conversion to agricultural (April), soil fungal operational taxonomic units and abundance-based coverage estimator were lower than those of dessert grasslands and shrubland plots and had significant correlations with pH, electric conductivity, and available phosphorus and potassium. The dominant phyla strongly correlated with soil physicochemical properties. Concomitantly, the relative abundance of Glomeromycota was significantly lower, and the complexity of the network in the land conversion plots was lower than that in the shrubland plots. In the late stage of land conversion (September), soil fungal operational taxonomic units and abundance-based coverage estimator were lower in the conversion plots than in the desert grassland plots, with more complex network relationships compared to the desert grassland or shrubland plots. Symbiotrophic groups, a functional group of desert grassland soil fungi, can be used as a predictor of environmental change; in addition, land conversion decreases the relative abundance of arbuscular mycorrhizal functional groups. Our study highlights the response of soil fungal communities and functions to human disturbances in desert grasslands. Considering the potential of land conversion to agriculture to influence soil secondary salinization, there is a need for continued observation of soil ecological health over the time continuum of land conversion to agriculture.

Investigating the impact of long-term bristlegrass coverage on rhizosphere microbiota, soil metabolites, and carbon-nitrogen dynamics for pear agronomic traits in orchards

Background

Grass coverage (GC) under no-tillage systems in orchards signifcantly infuences underground carbon (C) and nitrogen (N) sequestration, primarily through promoting mineral nutrient utilization by rhizospheric microorganisms. However, the comprehensive impact of GC on microbial communities and plant responses using soil metabolomics remains inadequately recognized.

Methods

We investigated two rhizosphere types established since 2002: bristlegrass (Setaria viridis (L.) P. Beauv.) coverage (SC) and clean cultivation (CC) to assess their efects on soil parameters, enzyme activities, and key pear agronomic traits, including yield (single fruit weight (SFW)) and qualities (soluble solids content (SSC), and total soluble sugar (TSS)). We combined microbiological analysis (16S rRNA sequencing) and non-targeted metabolomics (UPLC-MS/MS and GC-MS) to explore how microbial communities infuence fruit agronomic traits and soil nutrient dynamics in pear orchards under SC conditions.

Results

Our fndings indicate that SC signifcantly enhances soil organic carbon (SOC), soil organic nitrogen (SON), the C:N ratio, and available nitrogen (AN). Moreover, SC leads to pronounced increases in soil enzyme activities involved in the C cycle and storage, including soil sucrase, β-glucosidase, polyphenol oxidase and cellulase. Microbiome analysis revealed substantial diferences in microbial community composition and diversity indices between SC and CC rhizosphere soils within the 0-40 cm depth. Metabolomic analysis demonstrated significant alterations in metabolite profiles across both the 0-20 cm and 20-40 cm layers under SC conditions. The identifed metabolites primarily involve sugar and amino acid-related metabolic pathways, refecting perturbations in C and N metabolism consistent with shifts in bacterial community structure. Several plant growth-promoting rhizobacteria (PGPRs) taxa (e.g., Haliangium, Bacteroides, mle1-7, Subgroup_22, Ellin6067, MND1, Flavobacterium, and Cellvibrio) were enriched under SC, associated with metabolites such as sucrose, N-acetyl-D-glucosamine, N-acetyl-L-glutamic acid, rhamnose, UDP-GlcNAc and D-maltose. These fndings suggest their roles in promoting C and N sequestration processes through sucrose synthesis and glycolytic pathways in the soil, which was signifcantly correlated with the formation of agronomic traits such as fruit yield, SFW SSC and TSS (p<0.05), and SC treatments signifcantly increased yields by 35.40-62.72% and sucrose content in TSS by 2.43-3.96 times than CC treatments.

Conclusion

This study provides valuable insights into the efects of SC on soil microbial communities and plant physiology, enhancing our understanding of their implications for sustainable orchard management.

Metagenomic analysis of soil microbial communities associated with Poa alpigena Lindm in Haixin Mountain, Qinghai Lake

To investigate the impact of Poa alpigena Lindm on rhizosphere and bulk soil microorganisms in Haixin Mountain, Qinghai Lake, this study employed metagenomics technology to analyze the microbial communities of the samples. Results showed that 65 phyla, 139 classes, 278 orders, 596 families, 2376 genera, and 5545 species of soil microorganisms were identified from rhizosphere and bulk soil samples. Additionally, a microbial gene library specific to Poa alpigena Lindm was established for Qinghai Lake. Through α-diversity analysis, the richness and diversity of bulk microorganisms both significantly had a higher value than that in rhizosphere soil. The indicator microorganisms of rhizosphere and bulk soil at class level were Actinobacteria and Alphaproteobacteria, respectively. KEGG pathway analysis indicated that Carotenoid biosynthesis, Starch and sucrose metabolism, Bacterial chemotaxis, MAPK signaling pathway, Terpenoid backbone biosynthesis, and vancomycin resistance were the key differential metabolic pathways of rhizosphere soil microorganisms; in contrast, in bulk soil, the key differential metabolic were Benzoate degradation, Glycolysis gluconeogenesis, Aminobenzoate degradation, ABC transporters, Glyoxylate and dicarboxylate metabolism, oxidative phosphorylation, Degradation of aromatic compounds, Methane metabolism, Pyruvate metabolism and Microbial metabolism diverse environments. Our results indicated that Poa alpigena Lindm rhizosphere soil possessed selectivity for microorganisms in Qinghai Lake Haixin Mountain, and the rhizosphere soil also provided a suitable survival environment for microorganisms.

Enhancing phosphorus transformation in typical reddish paddy soil from China: Insights on long-term straw return and pig manure application via microbial mechanisms

Effective utilization of organic resources to activate residual phosphorus (P) in soil and enhance its availability is crucial for mitigating P resource scarcity and assessing the sustainable use of P in agricultural practices. However, the mechanisms through which organic resources affect soil P conversion via microorganisms and functional genes remain unknown, particularly in long-term organic-inorganic agricultural systems. In this study, we examined the impact of combined organic-inorganic fertilizer application on P availability, carbon (C) and P cycling genes, and microbial communities (bacterial and fungal) in reddish paddy soil based on a 42-year field experiment. The results indicated that long-term straw returning and pig manure application significantly augmented soil organic carbon (SOC), Olsen-P, microbial biomass carbon (MBC), microbial biomass phosphorus (MBP), enzyme-P, and CaCl2-P levels in paddy soils. Furthermore, these practices increased the abundance of soil C degradation genes, reduced the abundance of soil P cycling genes, and altered microbial community structure and network complexity. Notably, Module #3 ecological clusters in the fungal ecological co-occurrence network were significantly correlated with P cycling genes. Finally, our study demonstrated that long-term straw returning and pig manure application in paddy fields facilitated two robust and contrasting predictive relationships between C degradation (negative relationship) and P cycling (positive relationship) genes, respectively, and enzyme-P and HCl-P changes to improve soil P availability. This study can enhance our understanding of the role of soil microbial communities and functional genes in mediating P transformation to decipher the enhancement in P application efficiency driven by organic resources in reddish paddy soils.

Assessing the efficacy of natural soil biotin on soil quality, microbial diversity, and Rhododendron simsii growth for sustainable landscape architecture

Fertilization significantly influences soil quality and its sustainable use in urban garden maintenance. The widespread application of inorganic fertilizers has raised ecological concerns due to their potential environmental impacts. Organic fertilizers, while beneficial, often have slow effects and are costly. Biofertilizers, with their eco-friendly nature and low carbon footprint, are gaining attention for their multifaceted role in supporting plant growth. Despite the focus on fruit trees, vegetables, and medicinal plants, ornamental plants have been understudied. This study aims to evaluate the efficacy of a novel microbial fertilizer, 'natural soil biotin', on Rhododendron plants, specifically the Azalea hybrid 'Carnation'. The study employed a comparative approach to assess the impact of different fertilization strategies on soil properties, microbial diversity, enzyme activity, plant morphology, and physiological parameters. The application of 'natural soil biotin' was compared with the use of inorganic and organic fertilizers. The combined application of 'natural soil biotin' was found to effectively enhance soil properties and mitigate the impact of other fertilizers on soil pH. It also improved the relative abundance of beneficial microbial groups such as Proteobacteria, Ascomycota, and Basidiomycota. Furthermore, the mixed application significantly increased the activities of urease and sucrase in Rhododendron plants, which promoted their growth, development, and stress resistance. The results indicate that the mixed application of 'natural soil biotin' with inorganic and organic fertilizers not only improved the soil quality but also enhanced the efficiency of fertilizer utilization. This approach led to increased economic and environmental benefits in Rhododendron cultivation. The findings contribute to the foundation for soil improvement and ecological restoration, suggesting that 'natural soil biotin' could be a promising alternative or supplement to traditional fertilization methods in sustainable landscape architecture.

Effects of humic acid fertilizer on the growth and microbial network stability of Panax notoginseng from the forest understorey

Humic acid (HA) can substantially enhance plant growth and improve soil health. Currently, the impacts of HA concentrations variation on the development and soil quality of Panax notoginseng (Sanqi) from the forest understorey are still unclear. In this study, exogenous HA was administered to the roots of Sanqi at varying concentrations (2, 4, and 6 ml/L). Subsequently, the diversity and community structure of bacteria and fungi were assessed through high-throughput sequencing technology. The investigation further involved analyzing the interplay among the growth of sanqi, soil edaphic factors, and the microbial network stability. Our finding revealed that moderate concentrations (4 ml/L) of HA improved the fresh/dry weight of Sanqi and NO3--N levels. Compared with control, the moderate concentrations of HA had a notable impact on the bacterial and fungal communities compositions. However, there was no significant difference in the α and β diversity of bacteria and fungi. Moreover, the abundance of beneficial bacteria (Bradyrhizobium) and harmful bacteria (Xanthobacteraceae) increased and decreased at 4 ml/L HA, respectively, while the bacterial and fungal network stability were enhanced. Structural equation model (SEM) revealed that the fresh weight of Sanqi and bacterial and fungal communities were the factors that directly affected the microbial network stability at moderate concentrations of HA. In conclusion, 4 ml/L of HA is beneficial for promoting Sanqi growth and soil quality. Our study provides a reference for increasing the yield of Sanqi and sustainable development of the Sanqi-pine agroforestry system.

Intercropping enhances maize growth and nutrient uptake by driving the link between rhizosphere metabolites and microbiomes

Intercropping leads to different plant roots directly influencing belowground processes and has gained interest for its promotion of increased crop yields and resource utilization. However, the precise mechanisms through which the interactions between rhizosphere metabolites and the microbiome contribute to plant production remain ambiguous, thus impeding the understanding of the yield-enhancing advantages of intercropping. This study conducted field experiments (initiated in 2013) and pot experiments, coupled with multi-omics analysis, to investigate plant-metabolite-microbiome interactions in the rhizosphere of maize. Field-based data revealed significant differences in metabolite and microbiome profiles between the rhizosphere soils of maize monoculture and intercropping. In particular, intercropping soils exhibited higher microbial diversity and metabolite chemodiversity. The chemodiversity and composition of rhizosphere metabolites were significantly related to the diversity, community composition, and network complexity of soil microbiomes, and this relationship further impacted plant nutrient uptake. Pot-based findings demonstrated that the exogenous application of a metabolic mixture comprising key components enriched by intercropping (soyasapogenol B, 6-hydroxynicotinic acid, lycorine, shikimic acid, and phosphocreatine) significantly enhanced root activity, nutrient content, and biomass of maize in natural soil, but not in sterilized soil. Overall, this study emphasized the significance of rhizosphere metabolite-microbe interactions in enhancing yields in intercropping systems. It can provide new insights into rhizosphere controls within intensive agroecosystems, aiming to enhance crop production and ecosystem services.

Melatonin promotes the recovery of apple plants after waterlogging by shaping the structure and function of the rhizosphere microbiome

The dynamics of the physiological adaptability of plants and the rhizosphere soil environment after waterlogging remain unclear. Here we investigated the mechanisms regulating plant condition and shaping of the rhizosphere microbiome in a pot experiment. In the experiment, we added melatonin to waterlogged plants, which promoted waterlogging relief. The treatment significantly enhanced photosynthesis and the antioxidant capacity of apple plants, and significantly promoted nitrogen (N) utilization efficiency by upregulating genes related to N transport and metabolism. Multiperiod soil microbiome analysis showed the dynamic effects of melatonin on the diversity of the microbial community during waterlogging recovery. Random forest and linear regression analyses were used to screen for potential beneficial bacteria (e.g., Azoarcus, Pseudomonas and Nocardioides) specifically regulated by melatonin and revealed a positive correlation with soil nutrient levels and plant growth. Furthermore, metagenomic analyses revealed the regulatory effects of melatonin on genes involved in N cycling in soil. Melatonin positively contributed to the accumulation of plant dry weight by upregulating the expression of nifD and nifK (N fixation). In summary, melatonin positively regulates physiological functions in plants and the structure and function of the microbial community; it promoted the recovery of apple plants after waterlogging stress.

Mechanisms underlying the interactions and adaptability of nitrogen removal microorganisms in freshwater sediments

Microorganisms in eutrophic water play a vital role in nitrogen (N) removal, which contributes significantly to the nutrient cycling and sustainability of eutrophic ecosystems. However, the mechanisms underlying the interactions and adaptation strategies of the N removal microorganisms in eutrophic ecosystems remain unclear. We thus analyzed field sediments collected from a eutrophic freshwater ecosystem, enriched the N removal microorganisms, examined their function and adaptability through amplicon, metagenome and metatranscriptome sequencing. We found that the N removal activities could be affected through potential competition and inhibition among microbial metabolic pathways. High-diversity microbial communities generally increased the abundance and expression of N removal functional genes. Further enrichment experiments showed that the enrichment of N removal microorganisms led to a development of simplified but more stable microbial communities, characterized by similar evolutionary patterns among N removal microorganisms, tighter interactions, and increased adaptability. Notably, the sustained provision of NH4+ and NO2- during the enrichment could potentially strengthen the interconnections among denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) processes. Moreover, the identification of shared metabolic traits among denitrification, anammox and DNRA implies important cooperative associations and adaptability of N removal microorganisms. Our findings highlight the microbial interactions affect the adaptive strategies of key microbial taxa involved in N removal.

Soil metabolomics: Deciphering underground metabolic webs in terrestrial ecosystems

Soil metabolomics is an emerging approach for profiling diverse small molecule metabolites, i.e., metabolomes, in the soil. Soil metabolites, including fatty acids, amino acids, lipids, organic acids, sugars, and volatile organic compounds, often contain essential nutrients such as nitrogen, phosphorus, and sulfur and are directly linked to soil biogeochemical cycles driven by soil microorganisms. This paper presents an overview of methods for analyzing soil metabolites and the state-of-the-art of soil metabolomics in relation to soil nutrient cycling. We describe important applications of metabolomics in studying soil carbon cycling and sequestration, and the response of soil organic pools to changing environmental conditions. This includes using metabolomics to provide new insights into the close relationships between soil microbiome and metabolome, as well as responses of soil metabolome to plant and environmental stresses such as soil contamination. We also highlight the advantage of using soil metabolomics to study the biogeochemical cycles of elements and suggest that future research needs to better understand factors driving soil function and health.

Using multi-omics to explore the effect of Bacillus velezensis SAAS-63 on resisting nutrient stress in lettuce

To avoid the unreasonable use of chemical fertilizer, an environmentally friendly means of improving soil fertility is required. This study explored the role of the plant growth-promoting rhizosphere bacteria (PGPR) strain Bacillus velezensis SAAS-63 in improving nutrient stress in lettuce. Compared with no inoculation, B. velezensis SAAS-63 inoculants exhibited significantly increased fresh weight, root length, and shoot height under nutrient deficiency, as well as improved antioxidant activities and proline contents. The exogenous addition of B. velezensis SAAS-63 also significantly increased the accumulation of macroelements and micronutrients in lettuce. To elucidate the resistance mechanisms induced by B. velezensis SAAS-63 under nutrient stress, high-throughput sequencing and multi-omics analysis were performed. Inoculation with B. velezensis SAAS-63 altered the microbial community of the rhizosphere and increased the relative abundances of Streptomyces, Actinoallomurus, Verrucomicrobia, and Chloroflexi. It is worth noting that the inoculant SAAS-63 can affect plant rhizosphere metabolism. The inoculant changed the metabolic flow of phenylpropanoid metabolic pathway under nutrient deficiency and promoted phenylalanine to participate more in the synthesis of lignin precursors and coumarin substances by inhibiting the synthesis of flavone and isoflavone, thus improving plant resistance. This study showed that the addition of inoculant SAAS-63 could help plants recruit microorganisms to decompose and utilize trehalose and re-established the carbon metabolism of the plant rhizosphere. Additionally, microbes were found to be closely related to the accumulation of metabolites based on correlation analysis. The results indicated that the addition of PGPRs has an important role in regulating soil rhizosphere microbes and metabolism, providing valuable information for understanding how PGPRs affect complex biological processes and enhance plant adaptation to nutrient deficiency. KEY POINTS: • Inoculation with SAAS-63 significantly promoted plant growth under nutrient-deficient conditions • Inoculation with SAAS-63 affected rhizosphere microbial diversity and community structure • Inoculation with SAAS-63 affected plant rhizosphere metabolism and induced plants to synthesize substances that resist stress.

A comparative analysis of soil physicochemical properties and microbial community structure among four shelterbelt species in the northeast China plain

Conducting studies that focus on the alterations occurring in the soil microbiome within protection forests in the northeast plain is of utmost importance in evaluating the ecological rehabilitation of agricultural lands in the Mollisols region. Nevertheless, the presence of geographic factors contributes to substantial disparities in the microbiomes, and thus, addressing this aspect of influence becomes pivotal in ensuring the credibility of the collected data. Consequently, the objective is to compare the variations in soil physicochemical properties and microbial community structure within the understory of diverse shelterbelt species. In this study, we analyzed the understory soils of Juglans mandshurica (Jm), Fraxinus mandschurica (Fm), Acer mono (Am), and Betula platyphylla (Bp) from the same locality. We employed high-throughput sequencing technology and soil physicochemical data to investigate the impact of these different tree species on soil microbial communities, chemical properties, and enzyme activities in Mollisols areas. Significant variations in soil nutrients and enzyme activities were observed among tree species, with soil organic matter content ranging from 49.1 to 67.7 g/kg and cellulase content ranging from 5.3 to 524.0 μg/d/g. The impact of tree species on microbial diversities was found to be more pronounced in the bacterial community (Adnoism: R = 0.605) compared to the fungal community (Adnoism: R = 0.433). The linear discriminant analysis effect size (LEfSe) analysis revealed a total of 5 (Jm), 3 (Bp), and 6 (Am) bacterial biomarkers, as well as 2 (Jm), 6 (Fm), 4 (Bp), and 1 (Am) fungal biomarker at the genus level (LDA3). The presence of various tree species was observed to significantly alter the relative abundance of specific microbial community structures, specifically in Gammaproteobacteria, Ascomycota, and Basidiomycota. Furthermore, environmental factors, such as pH, total potassium, and available phosphorus were important factors influencing changes in bacterial communities. We propose that Fm be utilized as the primary tree species for establishing farmland protection forests in the northeastern region, owing to its superior impact on enhancing soil quality.

IMPORTANCE

The focal point of this study lies in the implementation of a controlled experiment conducted under field conditions. In this experiment, we deliberately selected four shelterbelts within the same field, characterized by identical planting density, and planting year. This deliberate selection effectively mitigated the potential impact of extraneous factors on the three microbiomes, thereby enhancing the reliability and validity of our findings.

Effect of Biogas Slurry on the Soil Properties and Microbial Composition in an Annual Ryegrass-Silage Maize Rotation System over a Five-Year Period

Soil health is seriously threatened by the overuse of chemical fertilizers in agricultural management. Biogas slurry is often seen as an organic fertilizer resource that is rich in nutrients, and its use has the goal of lowering the amount of chemical fertilizers used while preserving crop yields and soil health. However, the application of continuous biogas slurry has not yet been studied for its long-term impact on soil nutrients and microbial communities in a rotation system of annual ryegrass-silage maize (Zea mays). This study aimed to investigate the impacts on the chemical properties and microbial community of farmland soils to which chemical fertilizer (NPK) (225 kg ha-1), biogas slurry (150 t ha-1), and a combination (49.5 t ha-1 biogas slurry + 150 kg ha-1 chemical fertilizer) were applied for five years. The results indicated that compared to the control group, the long-term application of biogas slurry significantly increased the SOC, TN, AP, and AK values by 45.93%, 39.52%, 174.73%, and 161.54%, respectively; it neutralized acidic soil and increased the soil pH. TN, SOC, pH, and AP are all important environmental factors that influence the structural composition of the soil's bacterial and fungal communities. Chemical fertilizer application significantly increased the diversity of the bacterial community. Variation was observed in the composition of soil bacterial and fungal communities among the different treatments. The structure and diversity of soil microbes are affected by different methods of fertilization; the application of biogas slurry not only increases the contents of soil nutrients but also regulates the soil's bacterial and fungal community structures. Therefore, biogas slurry can serve as a sustainable management measure and offers an alternative to the application of chemical fertilizers for sustainable intensification.

Kalidium cuspidatum colonization changes the structure and function of salt crust microbial communities

The changes of soil moisture, salinity, and nutrients by halophyte colonization in high-salinity environment profoundly affect the assembly and structure of microbial communities. However, salt marshes in arid region have received little attention. This study was conducted in Lianhuachi Lake, a typical inland salt marsh wetland in China, to determine the physicochemical characteristics of salt crusts in [Kalidium cuspidatum (Ung.-Sternb.) Grub.] colonization areas and bulk soil, respectively, and to analyze the microbial community structure of salt crusts by high-throughput sequencing. Kalidium cuspidatum colonization significantly decreased total salinity, soil water content, and water-soluble ions of salt crusts and increased total carbon, total nitrogen, and total phosphorus content. At the same time, changes in physicochemical properties caused by Kalidium cuspidatum colonization affect the ecological processes of bacterial, fungal, and archaeal community assemblies in salt crusts. In addition, cross-kingdom network analysis showed that Kalidium cuspidatum colonization increased the complexity and stability of microbial networks in salt crust soils. Functional projections further showed that bacterial diversity had a potential driving effect on the nitrogen cycle function of salt crust. Our study further demonstrated the different ecological strategies of microorganisms for halophyte colonization in extreme environments and contributed to the understanding of restoration and management of salt marsh wetlands in arid region.

Alterations in the composition and metabolite profiles of the saline-alkali soil microbial community through biochar application

Saline-alkali soil poses significant chanllenges to sustainable development of agriculture. Although biochar is commonly used as a soil organic amendment, its microbial remediation mechanism on saline-alkali soil requires further confirmation. To address this, we conducted a pot experiment using cotton seedlings to explore the potential remediation mechanism of rice straw biochar (BC) at three different levels on saline-alkaline soil. The results showed that adding of 2% biochar greatly improved the quality of saline-alkaline soil by reducing pH levels, electrical conductivity (EC), and water-soluble ions. Moreover, biochar increased the soil organic matter (SOM), nutrient availability and extracellular enzyme activity. Interestingly, it also reduced soil salinity and salt content in various cotton plant tissues. Additionally, biochar had a notable impact on the composition of the microbial community, causing changes in soil metabolic pathways. Notably, the addition of biochar promoted the growth and metabolism of dominant salt-tolerant bacteria, such as Proteobacteria, Bacteroidota, Acidobacteriota, and Actinobacteriota. By enhancing the positive correlation between microorganisms and metabolites, biochar alleviated the inhibitory effect of salt ions on microorganisms. In conclusion, the incorporation of biochar significantly improves the soil microenvironment, reduces soil salinity, and shows promise in ameliorating saline-alkaline soil conditions.

The response of nutrient cycle, microbial community abundance and metabolic function to nitrogen fertilizer in rhizosphere soil of Phellodendron chinense Schneid seedlings

Nitrogen (N) as an essential macronutrient affects the soil nutrient cycle, microbial community abundance, and metabolic function. However, the specific responses of microorganisms and metabolic functions in rhizosphere soil of Phellodendron chinense Schneid seedlings to N addition remain unclear. In this study, four treatments (CK, N5, N10 and N15) were conducted, and the soil physicochemical properties, enzyme activities, microbial community abundances and diversities, metabolism, and gene expressions were investigated in rhizosphere soil of P. chinense Schneid. The results showed that N addition significantly decreased rhizosphere soil pH, among which the effect of N10 treatment was better. N10 treatment significantly increased the contents of available phosphorus (AP), available potassium (AK), ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3--N) and sucrase (SU) activity, as well as fungal diversity and the relative expression abundances of amoA and phoD genes in rhizosphere soil, but observably decreased the total phosphorus (TP) content, urease (UR) activity and bacterial diversity, among which the pH, soil organic matter (SOM), AP, NH4+-N and NO3--N were the main environmental factors for affecting rhizosphere soil microbial community structure based on RDA and correlation analyses. Meanwhile, N10 treatment notably enhanced the absolute abundances of the uracil, guanine, indole, prostaglandin F2α and γ-glutamylalanine, while reduced the contents of D-phenylalanine and phenylacetylglycine in rhizosphere soil of P. chinense Schneid seedlings. Furthermore, the soil available nutrients represented a significant correlation with soil metabolites and dominant microorganisms, suggesting that N10 addition effectively regulated microbial community abundance and metabolic functions by enhancing nutrient cycle in the rhizosphere soil of P. chinense Schneid seedlings.

Effects of continuous cropping on fungal community diversity and soil metabolites in soybean roots

IMPORTANCE

Soybean yield can be affected by soybean soil fungal communities in different tillage patterns. Soybean is an important food crop with great significance worldwide. Continuous cultivation resulted in soil nutrient deficiencies, disordered metabolism of root exudates, fungal pathogen accumulation, and an altered microbial community, which brought a drop in soybean output. In this study, taking the soybean agroecosystem in northeast China, we revealed the microbial ecology and soil metabolites spectrum, especially the diversity and composition of soil fungi and the correlation of pathogenic fungi, and discussed the mechanisms and the measures of alleviating the obstacles.

Responses of Soil Microbial Survival Strategies and Functional Changes to Wet-Dry Cycle Events

Soil microbial taxa have different functional ecological characteristics that influence the direction and intensity of plant-soil feedback responses to changes in the soil environment. However, the responses of soil microbial survival strategies to wet and dry events are poorly understood. In this study, soil physicochemical properties, enzyme activity, and high-throughput sequencing results were comprehensively anal0079zed in the irrigated cropland ecological zone of the northern plains of the Yellow River floodplain of China, where Oryza sativa was grown for a long period of time, converted to Zea mays after a year, and then Glycine max was planted. The results showed that different plant cultivations in a paddy-dryland rotation system affected soil physicochemical properties and enzyme activity, and G. max field cultivation resulted in higher total carbon, total nitrogen, soil total organic carbon, and available nitrogen content while significantly increasing α-glucosidase, β-glucosidase, and alkaline phosphatase activities in the soil. In addition, crop rotation altered the r/K-strategist bacteria, and the soil environment was the main factor affecting the community structure of r/K-strategist bacteria. The co-occurrence network revealed the inter-relationship between r/K-strategist bacteria and fungi, and with the succession of land rotation, the G. max sample plot exhibited more stable network relationships. Random forest analysis further indicated the importance of soil electrical conductivity, total carbon, total nitrogen, soil total organic carbon, available nitrogen, and α-glucosidase in the composition of soil microbial communities under wet-dry events and revealed significant correlations with r/K-strategist bacteria. Based on the functional predictions of microorganisms, wet-dry conversion altered the functions of bacteria and fungi and led to a more significant correlation between soil nutrient cycling taxa and environmental changes. This study contributes to a deeper understanding of microbial functional groups while helping to further our understanding of the potential functions of soil microbial functional groups in soil ecosystems.

Integrating metagenomics and metabolomics to study the response of microbiota in black soil degradation

As the largest commercial food production base and ecological security barrier, land degradation in black soil areas seriously threatens the global food supply and natural ecosystems. Therefore, determining the response of soil microbiota is crucial to restoring degraded soils. This study combined metagenomics and metabolomics to investigate the effect of different degrees of soil degradation on microbial community composition and metabolic function in black soils. It was found that alpha diversity in degraded soils (Shannon: 22.3) was higher than in nondegraded soil (ND) (Shannon: 21.8), and the degree of degradation significantly altered the structure and composition of soil microbial communities. The results of LEfSe analysis obtained 9 (ND), 7 (lightly degraded, LD), 10 (moderately degraded, MD), and 1 (severely degraded, SD) biomarkers in four samples. Bradyrhizobium, Sphingomonas, and Ramlibacter were significantly affected by soil degradation and can be considered biomarkers of ND, MD, and SD, respectively. Soil nutrient and enzyme activities decreased significantly with increasing black soil degradation, soil organic matter (SOM) content decreased from 11.12 % to 1.97 %, and Sucrase decreased from 23.53 to 6.59 mg/g/d. In addition, C was the critical driver affecting microbial community structure, contributing 61.2 % to differences in microbial community distribution, and microbial altering relative abundance which participle in the carbon cycle to respond to soil degradation. Metabolomic analyses indicated that soil degradation significantly modified the soil metabolite spectrum, and the metabolic functions of most microorganisms responding to soil degradation were adversely affected. The combined multi-omics analysis further indicated that biomarkers dominate in accumulating metabolites. These findings confirmed that due to their role in the composition and functioning of these degraded soils, these biomarkers could be employed in strategies for managing and restoring degraded black soils.

Improving soil phosphorus availability in saline areas by marine bacterium Bacillus paramycoides

The utilization of phosphate-solubilizing bacteria (PSB) in agriculture has long been proposed as an eco-friendly method to enhance soil phosphorus (P) availability, thereby reducing reliance on chemical P fertilizers. However, their application in saline soils is challenged by salt-induced stress on common PSB strains. In this study, we sourced bacterial strains from marine environments, aiming to identify robust PSB strains adaptable to saline conditions and assess their potential as P bio-fertilizers through a microcosm experiment. Our findings indicate that the inoculation of a selected marine PSB, Bacillus paramycoides 3-1a, increased soil available P content by 12.5% when applied alone and by 61.2% when combined with organic amendments. This enhancement results from improved inorganic P solubilization and organic P mineralization in soils. Additionally, these treatments raised soil nitrogen levels, reshaped microbial community structures, and significantly enhanced wheat (Triticum aestivum L.) growth, with P accumulation increasing by 24.2-40.9%. Our results underscore the potential of marine PSB in conjunction with organic amendments for the amelioration of saline agricultural soils.

Longitudinal Plant Health Monitoring via High-Resolution Mass Spectrometry Screening Workflows: Application to a Fertilizer Mediated Tomato Growth Experiment

Significant efforts have been spent in the modern era towards implementing environmentally friendly procedures like composting to mitigate the negative effects of intensive agricultural practices. In this context, a novel fertilizer was produced via the hydrolysis of an onion-derived compost, and has been previously comprehensively chemically characterized. In order to characterize its efficacy, the product was applied to tomato plants at five time points to monitor plant health and growth. Control samples were also used at each time point to eliminate confounding parameters due to the plant's normal growth process. After harvesting, the plant leaves were extracted using aq. MeOH (70:30, v/v) and analyzed via UPLC-QToF-MS, using a C18 column in both ionization modes (±ESI). The data-independent (DIA/bbCID) acquisition mode was employed, and the data were analyzed by MS-DIAL. Statistical analysis, including multivariate and trend analysis for longitudinal monitoring, were employed to highlight the differentiated features among the controls and treated plants as well as the time-point sequence. Metabolites related to plant growth belonging to several chemical classes were identified, proving the efficacy of the fertilizer product. Furthermore, the efficiency of the analytical and statistical workflows utilized was demonstrated.

Integrated metagenomics and metabolomics analysis reveals changes in the microbiome and metabolites in the rhizosphere soil of Fritillaria unibracteata

Fritillaria unibracteata (FU) is a renowned herb in China that requires strict growth conditions in its cultivation process. During this process, the soil microorganisms and their metabolites may directly affect the growth and development of FU, for example, the pathogen infection and sipeimine production. However, few systematic studies have reported the changes in the microbiome and metabolites during FU cultivation thus far. In this work, we simultaneously used metagenomics and metabolomics technology to monitor the changes in microbial communities and metabolites in the rhizosphere of FU during its cultivation for one, two, and three years. Moreover, the interaction between microorganisms and metabolites was investigated by co-occurrence network analysis. The results showed that the microbial composition between the three cultivation-year groups was significantly different (2020-2022). The dominant genera changed from Pseudomonas and Botrytis in CC1 to Mycolicibacterium and Pseudogymnoascus in CC3. The relative abundances of beneficial microorganisms decreased, while the relative abundances of harmful microorganisms showed an increasing trend. The metabolomics results showed that significant changes of the of metabolite composition were observed in the rhizosphere soil, and the relative abundances of some beneficial metabolites showed a decreasing trend. In this study, we discussed the changes in the microbiome and metabolites during the three-year cultivation of FU and revealed the relationship between microorganisms and metabolites. This work provides a reference for the efficient and sustainable cultivation of FU.

Low-temperature corn straw-degrading bacterial agent and moisture effects on indigenous microbes

While the in situ return of corn straw can improve soil fertility and farmland ecology, additional bacterial agents are required in low-temperature areas of northern China to accelerate straw degradation. Moisture is an important factor affecting microbial activity; however, owing to a lack of bacterial agents adapted to low-temperature complex soil environments, the effects of soil moisture on the interaction between exogenous bacterial agents and indigenous soil microorganisms remain unclear. To this end, we explored the effect of the compound bacterial agent CFF constructed using Pseudomonas putida and Acinetobacter lwoffii, developed to degrade corn straw in low-temperature soils (15 °C), on indigenous bacterial and fungal communities under dry (10% moisture content), slightly wet (20%), and wet (30%) soil-moisture conditions. The results showed that CFF application significantly affected the α-diversity of bacterial communities and changed both bacterial and fungal community structures, enhancing the correlation between microbial communities and soil-moisture content. CFF application also changed the network structure and the species of key microbial taxa, promoting more linkages among microbial genera. Notably, with an increase in soil moisture, CFF enhanced the rate of corn straw degradation by inducing positive interactions between bacterial and fungal genera and enriching straw degradation-related microbial taxa. Overall, our study demonstrates the alteration of indigenous microbial communities using bacterial agents (CFF) to overcome the limitations of indigenous microorganisms for in situ straw-return agriculture in low-temperature areas. KEY POINTS: • Low-temperature and variable moisture conditions (10-30%) were compared • Soil microbial network structure and linkages between genera were altered • CFF improves straw degradation via positive interactions between soil microbes.

New insights into the occurrence of continuous cropping obstacles in pea (Pisum sativum L.) from soil bacterial communities, root metabolism and gene transcription

BACKGROUND

Continuous cropping is a significant obstacle to sustainable development in the pea (Pisum sativum L.) industry, but the underlying mechanisms of this remain unclear. In this study, we used 16 S rDNA sequencing, transcriptomics, and metabolomics to analyze the response mechanism of roots and soil bacteria to continuous cropping and the relationship between soil bacteria and root phenotypes of different pea genotypes (Ding wan 10 and Yun wan 8).

RESULTS

Continuous cropping inhibited pea growth, with a greater effect on Ding wan 10 than Yun wan 8. Metabolomics showed that the number of differentially accumulated metabolites (DAMs) in pea roots increased with the number of continuous cropping, and more metabolic pathways were involved. Transcriptomics revealed that the number of differentially expressed genes (DEGs) increased with the number of continuous cropping. Continuous cropping altered the expression of genes involved in plant-pathogen interaction, MAPK signal transduction, and lignin synthesis pathways in pea roots, with more DEGs in Ding wan 10 than in Yun wan 8. The up-regulated expression of genes in the ethylene signal transduction pathway was evident in Ding wan 10. Soil bacterial diversity did not change, but the relative abundance of bacteria significantly responded to continuous cropping. Integrative analysis showed that the bacteria with significant relative abundance in the soil were strongly associated with the antioxidant synthesis and linoleic acid metabolism pathway of pea roots under continuous cropping once. Under continuous cropping twice, the bacteria with significant relative abundance changes were strongly associated with cysteine and methionine metabolism, fatty acid metabolism, phenylpropanoid biosynthesis, terpenoid backbone biosynthesis, linoleic acid, and amino sugar and nucleotide sugar metabolism.

CONCLUSION

Ding wan 10 was more sensitive to continuous cropping than Yun wan 8. Continuous cropping times and pea genotypes determined the differences in root metabolic pathways. There were common metabolic pathways in the two pea genotypes in response to continuous cropping, and the DEGs and DAMs in these metabolic pathways were strongly associated with the bacteria with significant changes in relative abundance in the soil. This study provides new insights into obstacles to continuous cropping in peas.

Diversity and structural analysis of rhizosphere soil microbial communities in wild and cultivated Rhizoma Atractylodis Macrocephalae and their effects on the accumulation of active components

Rhizosphere microorganisms are the main factors affecting the formation of high quality medicinal materials and promoting the accumulation of secondary metabolites. However, the composition, diversity, and function of rhizosphere microbial communities in endangered wild and cultivated Rhizoma Atractylodis Macrocephalae (RAM) and their relationships with active component accumulation have remained unclear. In this study, high-throughput sequencing and correlation analysis were used to study the rhizosphere microbial community diversity (bacteria and fungi) of three RAM species and its correlation with the accumulation of polysaccharides, atractylone, and lactones (I, II, and III). A total of 24 phyla, 46 classes, and 110 genera were detected. The dominant taxa were Proteobacteria, Ascomycota, and Basidiomycota. The microbial communities in both wild and artificially cultivated soil samples were extremely species-rich, but there were some differences in their structure and the relative abundances of microorganism taxa. Meanwhile, the contents of effective components in wild RAM were significantly higher than those in cultivated RAM. Correlation analysis showed that 16 bacterial and 10 fungal genera were positively or negatively correlated with active ingredient accumulation. These results showed that rhizosphere microorganisms could play an important role in component accumulation and might lay a foundation for future research on endangered materials.

Environmental pseudotargeted metabolomics: A high throughput and wide coverage method for metabolic profiling of 1000-year paddy soil chronosequences

Pseudotargeted metabolomics is achieved by introducing an algorithm designed to choose ions for selected ion monitoring from identified metabolites. This method integrates the advantages of both untargeted and targeted metabolomics. In this study, environmental pseudotargeted metabolomics was established to analyze the soil metabolites, based on microwave assisted derivatization followed by gas chromatography-mass spectrometry analysis. The method development included the optimization of extraction factors and derivatization conditions, evaluation of silylation reagent types and matrix-dependent behaviors. Under the optimal conditions, the microwave oximation and silylation were completed in 5 min and 9 min. A total of 184 metabolites from 26 chemical classifications were identified in soil matrices. The method validation demonstrated excellent performance in terms of linearity (correlation coefficient > 0.99), repeatability (relative standard deviation (RSD) < 20 %), reproducibility (RSD < 25 %), stability (relative difference < 10 % within 18 h), and sensitivity (16-110 times higher signal-to-noise ratio). This developed method was applied to characterize the metabolite compositions and metabolic profiling in a 1000-year paddy soil chronosequence. The relative abundance of trehalose was highest in 6-(40.3 %), 60-(55.8 %), 300-(67.7 %)and 1000-(61.7 %)years paddy soil, respectively, but long-chain fatty acids were most abundant in marine sediment (57.4 %). Forty-two characteristic metabolites were considered as primarily responsible for discriminating and characterizing the paddy soil chronosequences development and seven major metabolic pathways were altered. In addition, GC-MS metabolite profile presented better discriminating power in paddy soil ecosystem changes than phospholipid fatty acids (PLFAs). Overall, environmental pseudotargeted metabolomics can provide a high throughout and wide coverage approach for performing metabolic profiling in the soil research.

Bio-organic fertilizers improve Dendrocalamus farinosus growth by remolding the soil microbiome and metabolome

Organic and microbial fertilizers have potential advantages over inorganic fertilizers in improving soil fertility and crop yield without harmful side-effects. However, the effects of these bio-organic fertilizers on the soil microbiome and metabolome remain largely unknown, especially in the context of bamboo cultivation. In this study, we cultivated Dendrocalamus farinosus (D. farinosus) plants under five different fertilization conditions: organic fertilizer (OF), Bacillus amyloliquefaciens bio-fertilizer (Ba), Bacillus mucilaginosus Krassilnikov bio-fertilizer (BmK), organic fertilizer plus Bacillus amyloliquefaciens bio-fertilizer (OFBa), and organic fertilizer plus Bacillus mucilaginosus Krassilnikov bio-fertilizer (OFBmK). We conducted 16S rRNA sequencing and liquid chromatography/mass spectrometry (LC-MS) to evaluate the soil bacterial composition and soil metabolic activity in the different treatment groups. The results demonstrate that all the fertilization conditions altered the soil bacterial community composition. Moreover, the combination of organic and microbial fertilizers (i.e., in the OFBa and OFBmK groups) significantly affected the relative abundance of soil bacterial species; the largest number of dominant microbial communities were found in the OFBa group, which were strongly correlated with each other. Additionally, non-targeted metabolomics revealed that the levels of soil lipids and lipid-like molecules, and organic acids and their derivatives, were greatly altered under all treatment conditions. The levels of galactitol, guanine, and deoxycytidine were also markedly decreased in the OFBa and OFBmK groups. Moreover, we constructed a regulatory network to delineated the relationships between bamboo phenotype, soil enzymatic activity, soil differential metabolites, and dominant microbial. The network revealed that bio-organic fertilizers promoted bamboo growth by modifying the soil microbiome and metabolome. Accordingly, we concluded that the use of organic fertilizers, microbial fertilizers, or their combination regulated bacterial composition and soil metabolic processes. These findings provide new insights into how D. farinosus-bacterial interactions are affected by different fertilization regiments, which are directly applicable to the agricultural cultivation of bamboo.

Combination of biochar and AMF promotes phosphorus utilization by stimulating rhizosphere microbial co-occurrence networks and lipid metabolites of Phragmites

Agricultural biochar and arbuscular mycorrhizal fungi were used to promote the growth of Phragmites in the structural damaged and nutritional imbalanced littoral zone soils. Wheat straw biochar played a significant role in improving soil porosity and supplementing available phosphorus to 79.20 ± 3.20 mg/kg, compared with CK at 17.50 ± 0.88 mg/kg. The addition of Diversispora versiformis improved the plant net photosynthetic rate reaching up to 25.66 ± 0.65 μmol·m^-2·s^-1, which was 36.60 % higher than CK. The combination of biochar and fungi contributed to the whole plant dry weight biomass of 32.30 % and 234.00 % higher than the single biochar or AMF amendment groups, respectively. Meanwhile, the analysis of microbial co-occurrence networks showed the most relevant networks node species were mainly Talaromyces, Chaetomiacea and Gemmatimonadetes etc. Root lipid metabolite of Glycerophospholines further proved that phosphorus utilization was also enhanced endogenously in the rhizosphere soil. These results indicate that the combination of biochar and arbuscular mycorrhizal fungi play synergic role in enhancing phosphorus utilization endogenously and exogenously.

Co-analysis of cucumber rhizosphere metabolites and microbial PLFAs under excessive fertilization in solar greenhouse

Fertilizer application is the most common measure in agricultural production, which can promote the productivity of crops such as cucumbers, but the problem of excessive fertilization occurs frequently in solar greenhouses. However, the effects of fertilization levels on cucumber rhizosphere soil microbes and metabolites and their relationships are still unclear. In order to determine how fertilization levels affect the rhizosphere microenvironment, we set up four treatments in the solar greenhouse: no-fertilization (N0P0K0), normal fertilization (N1P1K1), slight excessive fertilization (N2P2K2), and extreme excessive fertilization (N3P3K3). The results showed that fertilization treatments significantly increased cucumber yield compared to no-fertilization, but, the yield of N3P3K3 was significantly lower than that of N1P1K1 and N2P2K2. Fertilization levels had significant effects on rhizosphere microorganisms, and pH, NH₄ ⁺-N and AP were the main environmental factors that affected the changes in microbial communities. The total PLFAs, the percentages of fungi and arbuscular mycorrhizal fungi (AMF) were significantly reduced and bacteria percentage was significantly increased in N3P3K3 compared to other fertilization treatments. Differential metabolites under different fertilization levels were mainly organic acids, esters and sugars. Soil phenols with autotoxic effect under fertilization treatments were higher than that of N0P0K0. In addition, compared with soil organic acids and alkanes of N0P0K0, N2P2K2 was significantly increased, and N3P3K3 was not significantly different. This suggested that cucumber could maintain microbial communities by secreting beneficial metabolites under slight excessive fertilization (N2P2K2). But under extremely excessive fertilization (N3P3K3), the self-regulating ability of cucumber plants and rhizosphere soil was insufficient to cope with high salt stress. Furthermore, co-occurrence network showed that 16:1ω5c (AMF) was positively correlated with 2-palmitoylglycerol, hentriacontane, 11-octadecenoic acid, decane,4-methyl- and d-trehalose, and negatively correlated with 9-octadecenoic acid at different fertilization levels. This indicated that the beneficial microorganisms in the cucumber rhizosphere soil promoted with beneficial metabolites and antagonized with harmful metabolites. But with the deepening of overfertilization, the content of beneficial microorganisms and metabolites decreased. The study provided new insights into the interaction of plant rhizosphere soil metabolites and soil microbiomes under the different fertilization levels.