Reduced chemodiversity suppresses rhizosphere microbiome functioning in the mono-cropped agroecosystems

Targeted manipulation of food webs in the plant rhizosphere

Trophic interactions between micro- and macro-organisms structure food webs in the plant rhizosphere. These interactions affect the plant-associated microbiota and nutrient dynamics, and influence plant health and performance. In this forum article we discuss the need for, and challenges associated with, targeted manipulation of soil food webs toward the development of multitrophic synthetic communities.

Plant Diversity Reduces the Risk of Antibiotic Resistance Genes in Agroecosystems

Despite advances in dispersal mechanisms and risk assessment of antibiotic resistance genes (ARGs), how plants influence ARG contamination in agricultural soils remains underexplored. Here, the impacts of plant species and diversity on ARGs and mobile genetic elements (MGEs) in three agricultural soils are comprehensively investigated in a pot experiment. The results indicate that increased plant diversity reduces ARGs and MGEs abundance by 19.2%-51.2%, whereas plant species exhibit inconsistent and soil-dependent effects. Potential bacterial hosts harboring abundant ARGs have greater relative abundance than nonhosts, and both their richness and cumulative relative abundance are reduced by plant diversity. Notably, hosts inhibited by plant diversity present a greater relative abundance than the other hosts. The enriched compounds in root exudates due to plant diversity play a more important role in the metabolic network and contribute to rebalancing of the abundance of potential hosts and nonhosts. An independent test using pure organics reveals that higher resource diversity, resulting from increased plant diversity, reduces the relative abundance and mobility of abundant and high-risk ARGs. This study highlights the resource-mediated mitigation of the risks posed by ARG contamination and indicates that ensuring plant and resource diversity is a promising strategy for controlling ARGs in agroecosystems.

Metabolomic insights into rhizosphere soil carbon component variations of Phragmites communis in the exposure of propranolol

Propranolol (PRO) has been detected in water bodies worldwide, attributed to the incomplete removal by wastewater treatment processes. Although reports exist on the removal of PRO by wetland plants such as Phragmites communis, research on the impact of PRO on soil organic carbon (SOC) components in these plants' rhizospheres remains scarce. This investigation examined the impacts of 0.5 μg/L and 50 μg/L concentrations of PRO on the rhizosphere of P. communis over a 21-day laboratory experiment. PRO exposure slightly promoted root growth, notably enhancing fine root development at a lower concentration. A notable decrease in SOC content was observed in the PRO-treated samples: specifically, the proportion of mineral-associated organic carbon (MAOC) rose (from 47.90 % to 33.17 %), whereas the proportion of particulate organic carbon (POC) significantly declined following PRO treatment (from 52.10 % to 66.83 %). Moreover, Proteobacteria and Nitrospirae experienced significant promotion in the high-concentration samples while Bacteroidetes and Verrucomicrobia were inhibited. The metabolomic analysis demonstrated that glycine, serine, and threonine metabolism was the principal differential metabolic pathway in varying concentrations of PRO exposure. Additionally, across varying PRO concentrations, plant influence emerged as the predominant factor affecting POC alterations, whereas MAOC changes resulted from the synergistic interaction of plants and associated bacteria. The outcomes of this study mark a critical advancement towards a thorough assessment of PRO's impact on the rhizosphere of wetland plants, bearing significant ramifications for evaluating PRO's environmental effects.

Plant growth-promoting fungi improve tobacco yield and chemical components by reassembling rhizosphere fungal microbiome and recruiting probiotic taxa

BACKGROUND

Tobacco production faces ongoing challenges due to soil degradation, leading to a persistent decline in yield. Plant growth-promoting fungi (PGPF) have been recognized as an environmentally friendly agricultural strategy. However, many commercial PGPF products exhibit instability due to insufficient environmental compatibility.

RESULTS

In this study, Penicillium sp. PQxj3 was isolated and assessed for its potential to enhance tobacco productivity under field conditions. The results demonstrated that Penicillium sp. PQxj3 treatment significantly promoted the tobacco growth and improved the crop yield. The height of tobacco in Penicillium sp. PQxj3 treatment group significantly increased by 50.19% and 24.05% compared with CK at exuberant and maturity period (P < 0.05). The average yield of tobacco significantly increased by 36.16% compared to CK (P < 0.05). Fungal microbiome analysis revealed that phylogenetically similar probiotic taxa were recruited by Penicillium sp. PQxj3 and reassembled tobacco rhizosphere fungal microbiome. The key chemical indicators of tobacco such as alkaloid, total sugar, and phosphorus were significantly enhanced in Penicillium sp. PQxj3 treatment. The recruited probiotic taxa (Penicillium brasilianum, Penicillium simplicissimum, Penicillium macrosclerotiorum and Penicillium senticosum) were significantly associated with alkaloid, total sugar etc. (P < 0.05), which were identified as the key drivers for improving the chemical components of tobacco. Transcriptome analysis indicated that Penicillium sp. PQxj3 promoted up-regulation of key functional genes involved in alkaloid, indoleacetic, and gibberellin biosynthesis pathways.

CONCLUSION

In summary, this study assessed the biopromotion mechanism of PGPF Penicillium sp. PQxj3 linking chemical traits, rhizosphere fungal microbiome, and transcriptome profiling. The findings provide a fundamental basis and a sustainable solution for developing fungal fertilizers to enhance agricultural sustainability.

Intercropping of tobacco and maize at seedling stage promotes crop growth through manipulating rhizosphere microenvironment

Introduction

Changes in the rhizosphere microbiome and metabolites resulting from crop intercropping can significantly enhance crop growth. While there has been an increasing number of studies on various crop combinations, research on the intercropping of tobacco and maize at seedling stage remains limited.

Methods

This study is the first to explore rhizosphere effects of intercropping between tobacco and maize seedling stages, we analyzed the nitrogen, phosphorus and potassium nutrients in the soil, and revealed the important effects on soil microbial community composition and metabolite profiles, thereby regulating crop growth and improving soil balance.

Results and discussion

Compared with mono-cropping, intercropping increased the biomass of the two crops and promoted the nutrient absorption of nitrogen, phosphorus and potassium. Under intercropping conditions, the activities of sucrase, catalase and nitrate reductase in tobacco rhizosphere soil and the content of available potassium, the activities of nitrate reductase and acid phosphatase in maize rhizosphere soil were significantly increasing. Rhizosphere soil bacterial and fungal communities such as Sphingomonas, Massilia, Humicola and Penicillium respond differently to crop planting patterns, and soil dominant microbial communities are regulated by environmental factors such as pH, Organic Matter, Available Potassium, Nitrate Reductase, and Urease Enzyme. Network analysis showed that soil microbial communities were more complex after intercropping, and the reciprocal relationship between bacteria and fungi was enhanced. The difference of metabolites in soil between intercropping and monocropping system was mainly concentrated in galactose metabolism, starch and sucrose metabolism pathway, and the content of carbohydrate metabolites was significantly higher than that of monocropping soil. Key metabolites such as D-Sucrose, D-Fructose-6-Phosphate, D-Glucose-1-Phosphatel significantly influence the composition of dominant microbial communities such as Sphingomonas and Penicillium. This study explained the effects of intercropping between flue-cured tobacco and maize on the content of soil metabolites and soil microbial composition in rhizosphere soil, and deepened the understanding that intercropping system can improve the growth of flue-cured crops seedlings through rhizosphere effects.

Exploiting microbial competition to promote plant health

The host-associated microbiota can promote colonization resistance against pathogens via a mechanism termed 'nutrient blocking', as highlighted in a recent article by Spragge et al. This implies that greater metabolic overlap between commensal taxa and pathogens leads to disease suppression. Here, we discuss future avenues for how this principle can be exploited in the rhizosphere microbiota to promote plant health.

The Structural and Functional Responses of Rhizosphere Bacteria to Biodegradable Microplastics in the Presence of Biofertilizers

Biodegradable microplastics (Bio-MPs) are a hot topic in soil research due to their potential to replace conventional microplastics. Biofertilizers are viewed as an alternative to inorganic fertilizers in agriculture due to their potential to enhance crop yields and food safety. The use of both can have direct and indirect effects on rhizosphere microorganisms. However, the influence of the coexistence of "Bio-MPs and biofertilizers" on rhizosphere microbial characteristics remains unclear. We investigated the effects of coexisting biofertilizers and Bio-MPs on the structure, function, and especially the carbon metabolic properties of crop rhizosphere bacteria, using a pot experiment in which polyethylene microplastics (PE-MPs) were used as a reference. The results showed that the existence of both microplastics (MPs) changed the physicochemical properties of the rhizosphere soil. Exposure to MPs also remarkably changed the composition and diversity of rhizosphere bacteria. The network was more complex in the Bio-MPs group. Additionally, metagenomic analyses showed that PE-MPs mainly affected microbial vitamin metabolism. Bio-MPs primarily changed the pathways related to carbon metabolism, such as causing declined carbon fixation/degradation and inhibition of methanogenesis. After partial least squares path model (PLS-PM) analysis, we observed that both materials influenced the rhizosphere environment through the bacterial communities and functions. Despite the degradability of Bio-MPs, our findings confirmed that the coexistence of biofertilizers and Bio-MPs affected the fertility of the rhizosphere. Regardless of the type of plastic, its use in soil requires an objective and scientifically grounded approach.

The vertical partitioning between denitrification and dissimilatory nitrate reduction to ammonium of coastal mangrove sediment microbiomes

Mangrove aquatic ecosystems receive substantial nitrogen (N) inputs from both land and sea, playing critical roles in modulating coastal N fluxes. The microbially-mediated competition between denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in mangrove sediments significantly impacts the N fate and transformation processes. Despite their recognized role in N loss or retention in surface sediments, how these two processes vary with sediment depths and their influential factors remain elusive. Here, we employed a comprehensive approach combining 15N isotope tracer, quantitative PCR (qPCR) and metagenomics to verify the vertical dynamics of denitrification and DNRA across five 100-cm mangrove sediment cores. Our results revealed a clear vertical partitioning, with denitrification dominated in 0-30 cm sediments, while DNRA played a greater role with increasing depths. Quantification of denitrification and DNRA functional genes further explained this phenomenon. Taxonomic analysis identified Pseudomonadota as the primary denitrification group, while Planctomycetota and Pseudomonadota exhibited high proportion in DNRA group. Furthermore, genome-resolved metagenomics revealed multiple salt-tolerance strategies and aromatic compound utilization potential in denitrification assemblages. This allowed denitrification to dominate in oxygen-fluctuating and higher-salinity surface sediments. However, the elevated C/N in anaerobic deep sediments favored DNRA, tending to generate biologically available NH4+. Together, our results uncover the depth-related variations in the microbially-mediated competition between denitrification and DNRA, regulating N dynamics in mangrove ecosystems.

Variation in Root-Associated Microbial Communities among Three Different Plant Species in Natural Desert Ecosystem

The process and function that underlie the assembly of root-associated microbiomes may be strongly linked to the survival strategy of plants. However, the assembly and functional changes of root-associated microbial communities in different desert plants in natural desert ecosystems are still unclear. Thus, we studied the microbial communities and diversity of root endosphere (RE), rhizosphere soil (RS), and bulk soil (BS) among three representative desert plants (Alhagi sparsifolia, Tamarix ramosissima, and Calligonum caput-medusae) in three Xinjiang desert regions {Taklimakan (CL), Gurbantünggüt (MSW), and Kumtag (TLF)} in China. This study found that the soil properties {electrical conductivity (EC), soil organic carbon (SOC), total nitrogen (TN) and phosphorus (TP), available nitrogen (AN) and phosphorus (AP)} of C. caput-medusae were significantly lower than those of A. sparsifolia and T. ramosissima, while the root nutrients (TN and TP) of A. sparsifolia were significantly higher compared to C. caput-medusae and T. ramosissima. The beta diversity of bacteria and fungi (RE) among the three desert plants was significantly different. The common OTU numbers of bacteria and fungi in three compartments (RE, RS, and BS) of the three desert plants were ranked as RS > BS > RE. The bacterial and fungal (RE) Shannon and Simpson indexes of C. caput-medusae were significantly lower as compared to those of A. sparsifolia and T. ramosissima. Additionally, bacterial and fungal (RE and RS) node numbers and average degree of C. caput-medusae were lower than those found in A. sparsifolia and T. ramosissima. Root and soil nutrients collectively contributed to the composition of root-associated bacterial (RE, 12.4%; RS, 10.6%; BS, 16.6%) and fungal communities (RE, 34.3%; RS, 1.5%; BS, 17.7%). These findings demonstrate variations in the bacterial and fungal populations across different plant species with distinct compartments (RE, RS, and BS) in arid environments. More importantly, the study highlights how much soil and plant nutrients contribute to root-associated microbial communities.

Soil metagenomics reveals the effect of nitrogen on soil microbial communities and nitrogen-cycle functional genes in the rhizosphere of Panax ginseng

Nitrogen (N) is the primary essential nutrient for ginseng growth, and a reasonable nitrogen application strategy is vital for maintaining the stability of soil microbial functional communities. However, how microbial-mediated functional genes involved in nitrogen cycling in the ginseng rhizosphere respond to nitrogen addition is largely unknown. In this study, metagenomic technology was used to study the effects of different nitrogen additions (N0: 0, N1: 20, N2: 40 N g/m2) on the microbial community and functional nitrogen cycling genes in the rhizosphere soil of ginseng, and soil properties related to the observed changes were evaluated. The results showed that N1 significantly increased the soil nutrient content compared to N0, and the N1 ginseng yield was the highest (29.90% and 38.05% higher than of N0 and N2, respectively). N2 significantly decreased the soil NO3 -N content (17.18 mg/kg lower than N0) and pH. This resulted in a decrease in the diversity of soil microorganisms, a decrease in beneficial bacteria, an increase in the number of pathogenic microorganisms, and an significant increase in the total abundance of denitrification, assimilatory nitrogen reduction, and dissimilatory nitrogen reduction genes, as well as the abundance of nxrA and napA genes (17.70% and 65.25% higher than N0, respectively), which are functional genes involved in nitrification that promote the soil nitrogen cycling process, and reduce the yield of ginseng. The results of the correlation analysis showed that pH was correlated with changes in the soil microbial community, and the contents of soil total nitrogen (TN), ammonium nitrogen (NH4 +-N), and alkaline-hydrolyzed nitrogen (AHN) were the main driving factors affecting the changes in nitrogen cycling functional genes in the rhizosphere soil of ginseng. In summary, nitrogen addition affects ginseng yield through changes in soil chemistry, nitrogen cycling processes, and functional microorganisms.

Diverse factors influence the amounts of carbon input to soils via rhizodeposition in plants: A review

Rhizodeposition encompasses the intricate processes through which plants generate organic compounds via photosynthesis, store these compounds within aboveground biomass and roots through top-down transport, and subsequently release this organic matter into the soil. Rhizodeposition represents one of the carbon (C) cycle in soils that can achieve long-term organic C sequestration. This function holds significant implications for mitigating the climate change that partly stems from the greenhouse effect associated with increased atmospheric carbon dioxide levels. Therefore, it is essential to further understand how the process of rhizodeposition allocates the photosynthetic C that plants create via photosynthesis. While many studies have explored the basic principles of rhizodeposition, along with the associated impact on soil C storage, there is a palpable absence of comprehensive reviews that summarize the various factors influencing this process. This paper compiles and analyzes the literature on plant rhizodeposition to describe how rhizodeposition influences soil C storage. Moreover, the review summarizes the impacts of soil physicochemical, microbial, and environmental characteristics on plant rhizodeposition and priming effects, and concludes with recommendations for future research.

Multigenerational Adaptation Can Enhance the Pathogen Resistance of Plants via Changes in Rhizosphere Microbial Community Assembly

Plants withstand pathogen attacks by recruiting beneficial bacteria to the rhizosphere and passing their legacy on to the next generation. However, the underlying mechanisms involved in this process remain unclear. In our study, we combined microbiomic and transcriptomic analyses to reveal how the rhizosphere microbiome assembled through multiple generations and defense-related genes expressed in Arabidopsis thaliana under pathogen attack stress. Our results showed that continuous exposure to the pathogen Pseudomonas syringae pv tomato DC3000 led to improved growth and increased disease resistance in a third generation of rps2 mutant Arabidopsis thaliana. It could be attributed to the enrichment of specific rhizosphere bacteria, such as Bacillus and Bacteroides. Pathways associated with plant immunity and growth in A. thaliana, such as MAPK signaling pathways, phytohormone signal transduction, ABC transporter proteins, and flavonoid biosynthesis, were activated under the influence of rhizosphere bacterial communities. Our findings provide a scientific basis for explaining the relationship between beneficial microbes and defense-related gene expression. Understanding microbial communities and the mechanisms involved in plant responses to disease can contribute to better plant management and reduction of pesticide use.

Biochar-bacteria-plant combined potential for remediation of oil-contaminated soil

Oil pollution is a common type of soil organic pollution that is harmful to the ecosystem. Bioremediation, particularly microbe-assisted phytoremediation of oil-contaminated soil, has become a research hotspot in recent years. In order to explore more appropriate bioremediation strategies for soil oil contamination and the mechanism of remediation, we compared the remediation effects of three plants when applied in combination with a microbial agent and biochar. The combined remediation approach of Tagetes erecta, microbial agent, and biochar exhibited the best plant growth and the highest total petroleum hydrocarbons degradation efficiency (76.60%). In addition, all of the remediation methods provided varying degrees of restoration of carbon and nitrogen contents of soils. High-throughput sequencing found that microbial community diversity and richness were enhanced in most restored soils. Some soil microorganisms associated with oil degradation and plant growth promotion such as Cavicella, C1_B045, Sphingomonas, MND1, Bacillus and Ramlibacter were identified in this study, among which Bacillus was the major component in the microbial agent. Bacillus was positively correlated with all soil remediation indicators tested and was substantially enriched in the rhizosphere of T. erecta. Functional gene prediction of the soil bacterial community based on the KEGG database revealed that pathways of carbohydrate metabolism and amino acid metabolism were up-regulated during remediation of oil-contaminated soils. This study provides a potential method for efficient remediation of oil-contaminated soils and thoroughly examines the biochar-bacteria-plant combined remediation mechanisms of oil-contaminated soil, as well as the combined effects from the perspective of soil bacterial communities.

Intercropping improves maize yield and nitrogen uptake by regulating nitrogen transformation and functional microbial abundance in rhizosphere soil

Intercropping-driven changes in nitrogen (N)-acquiring microbial genomes and functional expression regulate soil N availability and plant N uptake. However, present data seem to be limited to a specific community, obscuring the viewpoint of entire N-acquiring microbiomes and functions. Taking maize intercropped with legumes (peanut and soybean) and non-legumes (gingelly and sweet potato) as models, we studied the effects of intercropping on N transformations and N-acquiring microbiomes in rhizosphere soil across four maize growth stages. Meanwhile, we compiled promising strategies such as random forest analysis and structural equation model for the exploitation of the associations between microbe-driven N dynamics and soil-plant N trade-offs and maize productivity. Compared with monoculture, maize intercropping significantly increased the denitrification rate of rhizosphere soils across four maize growth stages, net N mineralization in the elongation and flowering stages, and the nitrification rate in the seedling and mature stages. The abundance of most N-acquiring microbial populations was influenced significantly by intercropping patterns and maize growth stages. Soil available N components (NH4+-N, NO3--N, and dissolved organic N content) showed a highly direct effect on plant N uptake, which mainly mediated by N transformations (denitrification rate) and N-acquiring populations (amoB, nirK3, and hzsB genes). Overall, the adaptation of N-acquiring microbiomes to changing rhizosphere micro-environments caused by intercropping patterns and maize development could promote soil N transformations and dynamics to meet demand of maize for N nutrient. This would offer another unique perspective to manage the benefits of the highly N-effective and production-effective intercropping ecosystems.

Plant Growth-Promoting Rhizobacteria Are Key to Promoting the Growth and Furanocoumarin Synthesis of Angelica dahurica var. formosana under Low-Nitrogen Conditions

Microbiomes are the most important members involved in the regulation of soil nitrogen metabolism. Beneficial interactions between plants and microbiomes contribute to improving the nitrogen utilization efficiency. In this study, we investigated the Apiaceae medicinal plant Angelica dahurica var. formosana. We found that under a low-nitrogen treatment, the abundance of carbon metabolites in the rhizosphere secretions of A. dahurica var. formosana significantly increased, thereby promoting the ratio of C to N in rhizosphere and nonrhizosphere soils, increasing carbon sequestration, and shaping the microbial community composition, thus promoting a higher yield and furanocoumarin synthesis. Confirmation through the construction of a synthetic microbial community and feedback experiments indicated that beneficial plant growth-promoting rhizobacteria play a crucial role in improving nitrogen utilization efficiency and selectively regulating the synthesis of target furanocoumarins under low nitrogen conditions. These findings may contribute additional theoretical evidence for understanding the mechanisms of interaction between medicinal plants and rhizosphere microorganisms.

Biodegradable microplastics reduce the effectiveness of biofertilizers by altering rhizospheric microecological functions

The effectiveness of biofertilizers as a cost-effective crop yield enhancer can be compromised by residual soil pollutants. However, the impact of accumulated polyadipate/butylene terephthalate microplastics (PBAT-MPs) from biodegradable mulch films on biofertilizer application and the consequent growth of crop plants remains unclear. Here, the effects of different levels of PBAT-MPs in soil treated with Bacillus amyloliquefaciens biofertilizer were assessed in a four-week potted experiment. PBAT-MPs significantly decreased the growth-promoting effect of the biofertilizer on Brassica chinensis L., resulting in a notable reduction in both above- and belowground biomass (up to 52.91% and 57.53%, respectively), as well as nitrate and crude fiber contents (up to 12.18% and 13.64%, respectively). In the rhizosphere microenvironment, PBAT-MPs increased soil organic carbon by 2.63-fold and organic matter by 2.68-fold, while enhancing sucrase (from 67.55% to 108.89%) and cellulase (from 31.26% to 49.10%) activities. PBAT-MPs also altered the rhizospheric bacterial community composition/diversity, resulting in more complex microbial networks. With regard to microbial function, PBAT-MPs impacted carbon metabolic function by inhibiting the 3-hydroxypropionate/4-hydroxybutyrate fixation pathway and influencing chitin and lignin degradation processes. Overall, the rhizospheric microbial profiles (composition, function, and network interactions) were the main contributors to plant growth inhibition. This study provides a practical case and theoretical basis for rational use of biodegradable mulch films and indicates that the residue of biodegradable films needs pay attention.

Effects of reductive soil disinfestation combined with different types of organic materials on the microbial community and functions

Reductive soil disinfestation (RSD) is an effective method to inhibit soilborne pathogens. However, it remains unclear how RSD combined with different types of organic materials affects the soil ecosystems of perennial plants. Pot experiments were conducted to investigate the effects of RSD incorporated with perilla (PF), alfalfa (MS), ethanol, and acetic acid on soil properties, enzyme activities, microbial communities and functions, and seedling growth. Results showed that RSD-related treatments improved soil properties and enzyme activities, changed microbial community composition and structure, enhanced microbial interactions and functions, and facilitated seedling growth. Compared with CK, RSD-related treatments increased soil pH, available nitrogen, and available potassium contents, sucrase and catalase activities, and decreased soil electric conductivity values. Meanwhile, RSD-related treatment also significantly reduced the relative abundance of Fusarium while increasing the relative abundance of Arthrobacter, Terrabacter, and Gemmatimonas. The reduction was more evident in PF and MS treatment, suggesting the potential for RSD combined with solid agricultural wastes to suppress pathogens. Furthermore, the microbial network of RSD-related treatment was more complex and interconnected, and the functions related to carbon, nitrogen, sulfur, and hydrogen cycling were significantly increased, while the functions of bacterial and fungal plant pathogens were decreased. Importantly, RSD-related treatments also significantly promoted seed germination and seedling growth. In summary, RSD combined with solid agricultural wastes is better than liquid easily degradable compounds by regulating the composition and function of microbial communities to improve soil quality and promote plant growth.IMPORTANCEReductive soil disinfestation (RSD) is an effective agricultural practice. We found that RSD combined with solid agricultural wastes is better than that of liquid easily degradable compounds, may improve soil quality and microbial community structure, inhibit the proliferation of pathogenic bacteria, and contribute to the growth of replanted crops. Thus, RSD combined with solid agricultural wastes is more effective than liquid easily degradable compounds.

Depletion of protective microbiota promotes the incidence of fruit disease

Plant-associated microbiomes play important roles in plant health and productivity. However, despite fruits being directly linked to plant productivity, little is known about the microbiomes of fruits and their potential association with fruit health. Here, by integrating 16S rRNA gene, ITS high-throughput sequencing data, and microbiological culturable approaches, we reported that roots and fruits (pods) of peanut, a typical plant that bears fruits underground, recruit different bacterial and fungal communities independently of cropping conditions and that the incidence of pod disease under monocropping conditions is attributed to the depletion of Bacillus genus and enrichment of Aspergillus genus in geocarposphere. On this basis, we constructed a synthetic community (SynCom) consisting of three Bacillus strains from geocarposphere soil under rotation conditions with high culturable abundance. Comparative transcriptome, microbiome profiling, and plant phytohormone signaling analysis reveal that the SynCom exhibited more effective Aspergillus growth inhibition and pod disease control than individual strain, which was underpinned by a combination of molecular mechanisms related to fungal cell proliferation interference, mycotoxins biosynthesis impairment, and jasmonic acid-mediated plant immunity activation. Overall, our results reveal the filter effect of plant organs on the microbiome and that depletion of key protective microbial community promotes the fruit disease incidence.

Fertilization Weakens the Ecological Succession of Dissolved Organic Matter in Paddy Rice Rhizosphere Soil at the Molecular Level

Dissolved organic matter (DOM) is involved in numerous biogeochemical processes, and understanding the ecological succession of DOM is crucial for predicting its response to farming (e.g., fertilization) practices. Although plentiful studies have examined how fertilization practice affects the content of soil DOM, it remains unknown how long-term fertilization drives the succession of soil DOM over temporal scales. Here, we investigated the succession of DOM in paddy rice rhizosphere soils subjected to different long-term fertilization treatments (CK: no fertilization; NPK: inorganic fertilization; OM: organic fertilization) along with plant growth. Our results demonstrated that long-term fertilization significantly promoted the molecular chemodiversity of DOM, but it weakened the correlation between DOM composition and plant development. Time-decay analysis indicated that the DOM composition had a shorter halving time under CK treatment (94.7 days), compared to NPK (337.4 days) and OM (223.8 days) treatments, reflecting a lower molecular turnover rate of DOM under fertilization. Moreover, plant development significantly affected the assembly process of DOM only under CK, not under NPK and OM treatments. Taken together, our results demonstrated that long-term fertilization, especially inorganic fertilization, greatly weakens the ecological succession of DOM in the plant rhizosphere, which has a profound implication for understanding the complex plant-DOM interactions.

Deciphering key factors in pathogen-suppressive microbiome assembly in the rhizosphere

In a plant-microbe symbiosis, the host plant plays a key role in promoting the association of beneficial microbes and maintaining microbiome homeostasis through microbe-associated molecular patterns (MAMPs). The associated microbes provide an additional layer of protection for plant immunity and help in nutrient acquisition. Despite identical MAMPs in pathogens and commensals, the plant distinguishes between them and promotes the enrichment of beneficial ones while defending against the pathogens. The rhizosphere is a narrow zone of soil surrounding living plant roots. Hence, various biotic and abiotic factors are involved in shaping the rhizosphere microbiome responsible for pathogen suppression. Efforts have been devoted to modifying the composition and structure of the rhizosphere microbiome. Nevertheless, systemic manipulation of the rhizosphere microbiome has been challenging, and predicting the resultant microbiome structure after an introduced change is difficult. This is due to the involvement of various factors that determine microbiome assembly and result in an increased complexity of microbial networks. Thus, a comprehensive analysis of critical factors that influence microbiome assembly in the rhizosphere will enable scientists to design intervention techniques to reshape the rhizosphere microbiome structure and functions systematically. In this review, we give highlights on fundamental concepts in soil suppressiveness and concisely explore studies on how plants monitor microbiome assembly and homeostasis. We then emphasize key factors that govern pathogen-suppressive microbiome assembly. We discuss how pathogen infection enhances plant immunity by employing a cry-for-help strategy and examine how domestication wipes out defensive genes in plants experiencing domestication syndrome. Additionally, we provide insights into how nutrient availability and pH determine pathogen suppression in the rhizosphere. We finally highlight up-to-date endeavors in rhizosphere microbiome manipulation to gain valuable insights into potential strategies by which microbiome structure could be reshaped to promote pathogen-suppressive soil development.

Sugarcane/soybean intercropping with reduced nitrogen addition promotes photosynthesized carbon sequestration in the soil

Introduction

Sugarcane/soybean intercropping with reduced nitrogen (N) addition has improved soil fertility and sustainable agricultural development in China. However, the effects of intercropping pattern and N fertilizer addition on the allocation of photosynthesized carbon (C) in plant-soil system were far less understood.

Methods

In this study, we performed an 13CO2 pulse labeling experiment to trace C footprints in plant-soil system under different cropping patterns [sugarcane monoculture (MS), sugarcane/soybean intercropping (SB)] and N addition levels [reduced N addition (N1) and conventional N addition (N2)].

Results and discussion

Our results showed that compared to sugarcane monoculture, sugarcane/soybean intercropping with N reduced addition increased sugarcane biomass and root/shoot ratio, which in turn led to 23.48% increase in total root biomass. The higher root biomass facilitated the flow of shoot fixed 13C to the soil in the form of rhizodeposits. More than 40% of the retained 13C in the soil was incorporated into the labile C pool [microbial biomass C (MBC) and dissolved organic C (DOC)] on day 1 after labeling. On day 27 after labeling, sugarcane/soybean intercropping with N reduced addition showed the highest 13C content in the MBC as well as in the soil, 1.89 and 1.14 times higher than the sugarcane monoculture, respectively. Moreover, intercropping pattern increased the content of labile C and labile N (alkaline N, ammonium N and nitrate N) in the soil. The structural equation model indicated that the cropping pattern regulated 13C sequestration in the soil mainly by driving changes in labile C, labile N content and root biomass in the soil. Our findings demonstrate that sugarcane/soybean intercropping with reduced N addition increases photosynthesized C sequestration in the soil, enhances the C sink capacity of agroecosystems.

Dynamics of organic acid exudation and rhizobacteria in maize rhizosphere respond to N-CDs

To sustainably feed the growing global population, it is essential to increase crop yields on limited land while reducing the use of fertilizers and agrochemicals. The rhizosphere regulation shows significant potential to address this challenge. Here, foliar applied doping of nitrogen in carbon dots (N-CDs) entered maize leaves, and were transported to the stems and roots. The internalized N-CDs significantly increased the biomass (26.4-93.8%) and photosynthesis (17.0-20.3 %) of maize seedling during the three-week application of N-CDs, providing the substrate for tricarboxylic acid cycle (TCA) in shoots and roots. Correspondingly, more organic acids involved in TCA cycle, such as citric acid (14.0-fold), succinic acid (4.4-fold) and malic acid (3.4-fold), were synthesized and then secreted into rhizosphere after exposed to N-CDs for one day. As the exposure time increased, greater secretion of above organic acids by the roots was induced. However, no significant change was observed in the relative abundance of rhizobacteria after foliar application with N-CDs for one day. After one week, the relative abundances of Azotobacter, Bacillus, Lysobacter, Mucilaginibacter, and Sphingomonas increased by 0.8-3.8 folds. The relative abundance of more beneficial rhizobacteria (Sphingomonas, Lysobacter, Rhizobium, Azotobacter, Pseudomonas, Mucilaginibacter and Bacillus) enriched by 0.3-6.0 folds after two weeks, and Sphingomonas, Flavisolibacter and Bacillus improved by 0.6-3.2 folds after three weeks. These dynamic changes suggested that N-CDs initiate the synthesis and secretion of organic acids and then recruited beneficial rhizobacteria. The hierarchical partitioning analysis further indicated that N-CDs-induced secretion of organic acids from the roots was the main drivers of rhizobacteria community dynamics. The differential microbes altered by N-CDs were mainly involved in nitrogen (N) and phosphorus (P) cycles, which are beneficial for N and P uptake, and maize growth. These results provide insights into understanding the rhizosphere regulation of nanomaterials to improve plant productivity and nutrient-use efficiency.

Different responses of the rhizosphere microbiome to Verticillium dahliae infection in two cotton cultivars

Verticillium wilt is a disastrous disease caused by Verticillium dahliae that severely damages the production of cotton in China. Even under homogeneous conditions, the same cotton cultivar facing V. dahliae tends to either stay healthy or become seriously ill and die. This binary outcome may be related to the interactions between microbiome assembly and plant health. Understanding how the rhizosphere microbiome responds to V. dahliae infection is vital to controlling Verticillium wilt through the manipulation of the microbiome. In this study, we evaluated the healthy and diseased rhizosphere microbiome of two upland cotton cultivars that are resistant to V. dahliae, Zhong 2 (resistant) and Xin 36 (susceptible), using 16S rRNA and ITS high-throughput sequencing. The results showed that the healthy rhizosphere of both resistant cultivar and susceptible cultivar had more unique bacterial ASVs than the diseased rhizosphere, whereas fewer unique fungal ASVs were found in the healthy rhizosphere of resistant cultivar. There were no significant differences in alpha diversity and beta diversity between the resistant cultivar and susceptible cultivar. In both resistant cultivar and susceptible cultivar, bacterial genera such as Pseudomonas and Acidobacteria bacterium LP6, and fungal genera such as Cephalotrichum and Mortierella were both highly enriched in the diseased rhizosphere, and Pseudomonas abundance in diseased rhizospheres was significantly higher than that in the healthy rhizosphere regardless of the cultivar type. However, cultivar and V. dahliae infection can cause composition changes in the rhizosphere bacterial and fungal communities, especially in the relative abundances of core microbiome members, which varied significantly, with different responses in the two cotton cultivars. Analysis of co-occurrence networks showed that resistant cultivar has a more complex network relationship than susceptible cultivar in the bacterial communities, and V. dahliae has a significant impact on the bacterial community structure. These findings will further broaden the understanding of plant-rhizosphere microbiome interactions and provide an integrative perspective on the cotton rhizosphere microbiome, which is beneficial to cotton health and production.

Functional immune boosters; the herb or its dead microbiome? Antigenic TLR4 agonist MAMPs found in 65 medicinal roots and algae's

Background

Humans have been consuming medicinal plants (as herbs/ spices) to combat illness for centuries while ascribing beneficial effects predominantly to the plant/phytochemical constituents, without recognizing the power of obligatory resident microorganism' communities (MOCs) (live/dead bacteria, fungus, yeast, molds etc.) which remain after industrial microbial reduction methods. Very little is known about the taxonomic identity of residual antigenic microbial associated molecular patterns (MAMPs) debris in our botanical over the counter (OTC) products, which if present would be recognized as foreign (non-self) antigenic matter by host pattern recognition receptors (PRRs) provoking a host immune response; this the basis of vaccine adjuvants. As of today, only few research groups have removed the herbal MAMP biomass from herbs, all suggesting that immune activation may not be from the plant but rather its microbial biomass; a hypothesis we corroborate.

Purpose

The purpose of this work was to conduct a high through put screening (HTPS) of over 2500 natural plants, OTC botanical supplements and phytochemicals to elucidate those with pro-inflammatory; toll like receptor 4 (TLR4) activating properties in macrophages.

Study Design

The HTPS was conducted on RAW 264.7 cells vs. lipopolysaccharide (LPS) E. coli 0111:B4, testing iNOS / nitric oxide production ( NO 2 - ) as a perimeter endpoint. The data show not a single drug/chemical/ phytochemical and approximately 98 % of botanicals to be immune idle (not effective) with only 65 pro-inflammatory (hits) in a potency range of LPS. Method validation studies eliminated the possibility of false artifact or contamination, and results were cross verified through multiple vendors/ manufacturers/lot numbers by botanical species. Lead botanicals were evaluated for plant concentration of LPS, 1,3:1,6-β-glucan, 1,3:1,4-β-D-glucan and α-glucans; where the former paralleled strength in vitro. LPS was then removed from plants using high-capacity endotoxin poly lysine columns, where bioactivity of LPS null "plant" extracts were lost. The stability of E.Coli 0111:B4 in an acid stomach mimetic model was confirmed. Last, we conducted a reverse culture on aerobic plate counts (APCs) from select hits, with subsequent isolation of gram-negative bacteria (MacConkey agar). Cultures were 1) heat destroyed (retested/ confirming bioactivity) and 2) subject to taxonomical identification by genetic sequencing 18S, ITS1, 5.8 s, ITS2 28S, and 16S.

Conclusion

The data show significant gram negative MAMP biomass dominance in A) roots (e.g. echinacea, yucca, burdock, stinging nettle, sarsaparilla, hydrangea, poke, madder, calamus, rhaponticum, pleurisy, aconite etc.) and B) oceanic plants / algae's (e.g. bladderwrack, chlorella, spirulina, kelp, and "OTC Seamoss-blends" (irish moss, bladderwrack, burdock root etc), as well as other random herbs (eg. corn silk, cleavers, watercress, cardamom seed, tribulus, duckweed, puffball, hordeum and pollen). The results show a dominance of gram negative microbes (e.g. Klebsilla aerogenes, Pantoae agglomerans, Cronobacter sakazakii), fungus (Glomeracaea, Ascomycota, Irpex lacteus, Aureobasidium pullulans, Fibroporia albicans, Chlorociboria clavula, Aspergillus_sp JUC-2), with black walnut hull, echinacea and burdock root also containing gram positive microbial strains (Fontibacillus, Paenibacillus, Enterococcus gallinarum, Bromate-reducing bacterium B6 and various strains of Clostridium).

Conclusion

This work brings attention to the existence of a functional immune bioactive herbal microbiome, independent from the plant. There is need to further this avenue of research, which should be carried out with consideration as to both positive or negative consequences arising from daily consumption of botanicals highly laden with bioactive MAMPS.

The Microbial Connection to Sustainable Agriculture

Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants' growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within the plant-soil microbiome is necessary to effectively deploy these organisms in sustainable agriculture. Although both the plant and soil microbiome have been studied over the decades, the efficiency of translating the laboratory and greenhouse findings to the field is largely dependent on the ability of the inoculants or beneficial microorganisms to colonize the soil and maintain stability in the ecosystem. Further, the plant and its environment are two variables that influence the plant and soil microbiome's diversity and structure. Thus, in recent years, researchers have looked into microbiome engineering that would enable them to modify the microbial communities in order to increase the efficiency and effectiveness of the inoculants. The engineering of environments is believed to support resistance to biotic and abiotic stressors, plant fitness, and productivity. Population characterization is crucial in microbiome manipulation, as well as in the identification of potential biofertilizers and biocontrol agents. Next-generation sequencing approaches that identify both culturable and non-culturable microbes associated with the soil and plant microbiome have expanded our knowledge in this area. Additionally, genome editing and multidisciplinary omics methods have provided scientists with a framework to engineer dependable and sustainable microbial communities that support high yield, disease resistance, nutrient cycling, and management of stressors. In this review, we present an overview of the role of beneficial microbes in sustainable agriculture, microbiome engineering, translation of this technology to the field, and the main approaches used by laboratories worldwide to study the plant-soil microbiome. These initiatives are important to the advancement of green technologies in agriculture.

Phototrophic Biofilms Transform Soil-Dissolved Organic Matter Similarly Despite Compositional and Environmental Differences

Dissolved organic matter (DOM) is the most reactive pool of organic carbon in soil and one of the most important components of the global carbon cycle. Phototrophic biofilms growing at the soil-water interface in periodically flooding-drying soils like paddy fields consume and produce DOM during their growth and decomposition. However, the effects of phototrophic biofilms on DOM remain poorly understood in these settings. Here, we found that phototrophic biofilms transformed DOM similarly despite differences in soil types and initial DOM compositions, with stronger effects on DOM molecular composition than soil organic carbon and nutrient contents. Specifically, growth of phototrophic biofilms, especially those genera belonging to Proteobacteria and Cyanobacteria, increased the abundance of labile DOM compounds and richness of molecular formulae, while biofilm decomposition decreased the relative abundance of labile components. After a growth and decomposition cycle, phototrophic biofilms universally drove the accumulation of persistent DOM compounds in soil. Our results revealed how phototrophic biofilms shape the richness and changes in soil DOM at the molecular level and provide a reference for using phototrophic biofilms to increase DOM bioactivity and soil fertility in agricultural settings.

Diseased-induced multifaceted variations in community assembly and functions of plant-associated microbiomes

Plant-associated microorganisms are believed to be part of the so-called extended plant phenotypes, affecting plant growth and health. Understanding how plant-associated microorganisms respond to pathogen invasion is crucial to controlling plant diseases through microbiome manipulation. In this study, healthy and diseased (bacterial wilt disease, BWD) tomato (Solanum lycopersicum L.) plants were harvested, and variations in the rhizosphere and root endosphere microbial communities were subsequently investigated using amplicon and shotgun metagenome sequencing. BWD led to a significant increase in rhizosphere bacterial diversity in the rhizosphere but reduced bacterial diversity in the root endosphere. The ecological null model indicated that BWD enhanced the bacterial deterministic processes in both the rhizosphere and root endosphere. Network analysis showed that microbial co-occurrence complexity was increased in BWD-infected plants. Moreover, higher universal ecological dynamics of microbial communities were observed in the diseased rhizosphere. Metagenomic analysis revealed the enrichment of more functional gene pathways in the infected rhizosphere. More importantly, when tomato plants were infected with BWD, some plant-harmful pathways such as quorum sensing were significantly enriched, while some plant-beneficial pathways such as streptomycin biosynthesis were depleted. These findings broaden the understanding of plant–microbiome interactions and provide new clues to the underlying mechanism behind the interaction between the plant microbiome and BWD.

Characterizing bacterial communities in Phragmites australis rhizosphere and non-rhizosphere sediments under pressure of antibiotics in a shallow lake

Introduction

Antibiotics are ubiquitous pollutants and widely found in aquatic ecosystems, which of rhizosphere sediment and rhizosphere bacterial communities had certain correlation. However, the response of bacterial communities in Phragmites australis rhizosphere and non-rhizosphere sediments to antibiotics stress is still poorly understood.

Methods

To address this knowledge gap, the samples of rhizosphere (R) and non-rhizosphere (NR) sediments of P. australis were collected to investigate the differences of bacterial communities under the influence of antibiotics and key bacterial species and dominate environmental factors in Baiyangdian (BYD) Lake.

Results

The results showed that the contents of norfloxacin (NOR), ciprofloxacin (CIP) and total antibiotics in rhizosphere sediments were significantly higher than that in non-rhizosphere sediments, meanwhile, bacterial communities in non-rhizosphere sediments had significantly higher diversity (Sobs, Shannon, Simpsoneven and PD) than those in rhizosphere sediments. Furthermore, total antibiotics and CIP were found to be the most important factors in bacterial diversity. The majority of the phyla in rhizosphere sediments were Firmicutes, Proteobacteria and Campilobacterota, while Proteobacteria, Chloroflexi was the most abundant phyla followed by Bacteroidota, Actinobacteriota in non-rhizosphere sediments. The dominate factors of shaping the bacterial communities in rhizosphere were total antibiotics, pH, sediment organic matter (SOM), and NH₄-N, while dissolved organic carbon (DOC), NO₃-N, pH, and water contents (WC) in non-rhizosphere sediments.

Discussion

It is suggested that antibiotics may have a substantial effect on bacterial communities in P. australis rhizosphere sediment, which showed potential risk for ARGs selection pressure and dissemination in shallow lake ecosystems.