Specific metabolites drive the deterministic assembly of diseased rhizosphere microbiome through weakening microbial degradation of autotoxin

Role of iturin from Bacillus velezensis DMW1 in suppressing growth and pathogenicity of Plectosphaerella cucumerina in tomato by reshaping the rhizosphere microbial communities

Plant-associated microbiomes play a crucial role in suppressing plant and soil pathogens. However, the mechanisms by which pathogen invasion influences the interaction between bacteria and fungi remain unknown and warrant further investigation. In this study, Bacillus spp. was found to be more abundant in diseased rhizosphere in the presence of the soil-borne fungus Plectosphaerella cucumerina. Most of the isolated Bacillus spp. exhibited a robust ability to balance reactive oxygen species (ROS) and demonstrated broad-spectrum antagonistic activity against P. cucumerina, Phytophthora capsica, Fusarium oxysporum, and Ralstonia solanacearum. The secondary metabolite iturin was identified as the key antifungal compound produced by the representative strain Bacillus velezensis DMW1, which effectively inhibits fungal growth and disrupts cell structures. Transcriptome analysis revealed that fungi treated with iturin (28.67 µg/mL) exhibited 4995 differentially expressed genes (DEGs), including 2611 upregulated genes and 2384 downregulated genes, compared to the control group. Furthermore, the application of DMW1 and return-deficient mutant (Δitu) significantly altered microbial diversity and enriched beneficial microorganisms in the rhizosphere soil. The overall findings highlight the potential of DMW1 as a promising biological agent for controlling soil-borne diseases. Its strong antimicrobial properties, ability to colonize host plants effectively, and capacity to reshape the soil microbiota make it a valuable resource for enhancing microbial ecosystems and providing long-term benefits to plants.

Changes in the assembly and functional adaptation of endophytic microbial communities in Amorphophallus species with different levels of resistance to necrotrophic bacterial pathogen stress

Pcc is one of the key pathogenic factors responsible for destructive soft rot in konjac. To date, the assembly and functional adaptation of the plant endophytic microbiome under Pcc stress remain poorly understood. Here, we found that Pcc stress leads to rapid reorganization of the endogenous microbiome in multiple organs of both susceptible and resistant konjac plants. Under Pcc stress, the negative interactions within the bacterial-fungal interdomain network intensified, suggesting an increase in ecological competition between bacterial and fungal taxa. We further discovered that the relative abundance dynamics of the classes Dothideomycetes and Sordariomycetes, as core fungal taxa, changed in response to Pcc stress. By isolating culturable microorganisms, we demonstrated that 46 fungal strains strongly inhibited the growth of Pcc. This implies that endophytic fungal taxa in konjac may protect the host plant through ecological competition or by inhibiting the growth of pathogenic bacteria. Metagenomic analysis demonstrated that microbial communities associated with resistant Amorphophallus muelleri exhibited unique advantages over susceptible Amorphophallus konjac in enhancing environmental adaptability, regulating plant immune signaling, strengthening cell walls, and inducing defense responses. Our work provides important evidence that endophytic fungal taxa play a key role in the host plant's defense against necrotizing bacterial pathogens.

Evaluating the potential of digestate-loaded biochar in improving soil biological health and plant nutrition with less greenhouse gas emissions

Digestate has a great potential as a carbon (C) and nitrogen (N) soil amendment. Loading digestate onto biochar can produce a C- and N- enriched biochar fertilizer (i.e., digestate-loaded biochar, DLB), and help to solve digestate-specific issues. This study aims to evaluate the potential of DLB at optimal application rates in keeping plant (annual ryegrass) nutrition level while mitigating greenhouse gas emissions and improving soil biological health compared to chemical fertilizers in an acidic soil under liming or not. Soil biological health index was assessed through quantitative PCR and amplicon sequencing. The results showed that increasing DLB addition to 150 kg N ha-1 resulted in a similar N uptake of ryegrass to that under urea despite lower mineral N provided by DLB. This application rate decreased greenhouse gas emissions relative to urea, through decreasing CO2 emission despite increased CH4 emission. Compared to urea, this DLB rate did not change N2O emission, corresponding to the specifically increased abundance of nirK gene (1.3-fold) (and enriched denitrifier Dokdonella) for N2O production and nosZ clade I and II genes (87%) for N2O consumption. The DLB at 150 kg N ha-1 enhanced soil biological health index by 1.4-fold relative to urea through increasing microbial abundances particularly fungi, enriching beneficial microbes (plant-growth-promoting bacteria, mycorrhiza and dark-septate-endophyte), and increasing fungal diversity; this effect was less pronounced under liming. This study concludes that DLB can serve as an organic-mineral fertilizer in maintaining plant nutrition while decreasing greenhouse gas emissions and enhancing soil biological health, offering a sustainable approach to managing organic waste.

Beneficial soil microbiome profiles assembled using tetramycin to alleviate root rot disease in Panax notoginseng

Background

Root rot disease is a major threat to the sustainable production of Panax notoginseng. Tetramycin has a broad-spectrum fungicidal efficacy, low toxicity, and high efficiency, However, the prevention and control of root rot disease of P. notoginseng and the specific mechanism of action are still unclear.

Methods

In this paper, a combination of indoor and pot experiments was used to assess the effectiveness of tetramycin at alleviating root rot disease challenges encountered by P. notoginseng. Amplicon sequencing, metagenomic analysis with microbial verification were used to investigate the microecological mechanisms underlying tetramycin's ability to reduce soil biological barriers.

Results

We found that tetramycin significantly inhibited mycelial growth and spore germination of pathogenic fungi. Tetramycin, T2 (1000×) and T3 (500×), applied to continuous cropping soil, increased the seedling survival rates of P. notoginseng. Additionally, tetramycin reduced fungal α-diversity and shifted the fungal community assembly from deterministic to stochastic process. The microbial functions influenced by tetramycin were primarily associated with antibiotic synthesis and siderophore synthesis. Antibiotic efflux and inactivation have also been identified as the main resistance mechanisms. Microbial verification results showed that the artificially assembled tetramycin-regulated microbial community could indeed alleviate the occurrence of diseases. Furthermore, the cross-kingdom synthetic community assembled by the three key strains (Pseudomonas aeruginosa, Variovorax boronicumulans, and Cladosporium cycadicola) significantly improved the control of root rot disease and promoted plant growth.

Discussion

This study provides novel insights into developing efficient biological control strategies and elucidates the role and mechanism of tetramycin in modulating soil microflora assembly to strengthen host disease resistance.

The Unseen Impacts of Human Footprints: How Land Use Reshapes Actinobacterial Communities in the Brazilian Cerrado

Evaluating microbial community changes in soils allows the understanding of ecoevolutionary dynamics, providing information on microbiome responses to anthropological interferences, reduced biodiversity, and climatic changes. The actinobacteria phylum plays crucial roles from an ecological point of view and is the focus of the present study, which tracked changes in the actinobacterial communities from Brazilian Cerrado soil in an environmental protection unit, based on different land uses. The evaluation of 16S rRNA and further taxonomical clustering of operational taxonomic units (OTUs) indicated Actinomycetales as the main order within all land uses, ranging from 45.4-70.1%, with Micrococales and Rubrobacterales being found only in agricultural soils. The evaluation of taxonomical classes revealed Actinobacteria as the main representative in all land uses (45.5-70.4%), with a paired coprevalence of Thermoleophilia (43.4%) in secondary soils, a taxon associated with phosphorus-deficient grounds. The unraveling of families and genera was most challenging due to the OTUs' dispersion given the volume of data, coupled with a high percentage of unidentified genera (71.6-86.1%), mainly in conserved and preserved areas. The reduced biodiversity, reduced undescribed taxa, and enhanced potentially pathogenic strains in anthropogenic affected sites, which suffer more from climatic changes, denote the harm that human activity causes to microbiological diversity.

Changes in the community composition and function of the rhizosphere microbiome in tobacco plants with Fusarium root rot

Introduction

Tobacco root rot caused by Fusarium spp. is a soil-borne vascular disease that severely affects tobacco production worldwide. To date, the community composition and functional shifts of the rhizosphere microbiome in tobacco plants infected with Fusarium root rot remain poorly understood.

Methods

In this study, we analyzed the differences in the compositions and functions of the bacterial and fungal communities in the rhizosphere and root endosphere of healthy tobacco plants and tobacco with Fusarium root rot using amplicon sequencing and metagenomic sequencing.

Results and discussion

Our results showed that Fusarium root rot disrupted the stability of bacteria-fungi interkingdom networks and reduced the network complexity. Compared to healthy tobacco plants, the Chao1 index of bacterial communities in the rhizosphere soil of diseased plants increased by 4.09% (P < 0.05), while the Shannon and Chao1 indices of fungal communities decreased by 13.87 and 8.17%, respectively (P < 0.05). In the root tissues of diseased plants, the Shannon index of bacterial and fungal communities decreased by 17.71-27.05% (P < 0.05). Additionally, we observed that the rhizosphere microbial community of diseased tobacco plants shifted toward a pathological combination, with a significant increase in the relative abundance of harmful microbes such as Alternaria, Fusarium, and Filobasidium (89.46-921.29%) and a notable decrease in the relative abundance of beneficial microbes such as Lysobacter, Streptomyces, Mortierella, and Penicillium (48.48-81.56%). Metagenomic analysis further revealed that the tobacco rhizosphere microbial communities of diseased plants played a significant role in basic biological metabolism, energy production and conversion, signal transduction, and N metabolism, but their functions involved in C metabolism were significantly weakened. Our findings provide new insights into the changes in and interactions within the rhizosphere and root endosphere microbiomes of tobacco plants under the stress of Fusarium soil-borne fungal pathogens, while laying the foundation for the exploration, development, and utilization of beneficial microbial resources in healthy tobacco plants in the future.

Microbial diversity and interactions: Synergistic effects and potential applications of Pseudomonas and Bacillus consortia

Microbial diversity and interactions in the rhizosphere play a crucial role in plant health and ecosystem functioning. Among the myriads of rhizosphere microbes, Pseudomonas and Bacillus are prominent players known for their multifaceted functionalities and beneficial effects on plant growth. The molecular mechanism of interspecies interactions between natural isolates of Bacillus and Pseudomonas in medium conditions is well understood, but the interaction between the two in vivo remains unclear. This paper focuses on the possible synergies between Pseudomonas and Bacillus associated in practical applications (such as recruiting beneficial microbes, cross-feeding and niche complementarity), and looks forward to the application prospects of the consortium in agriculture, human health and bioremediation. Through in-depth understanding of the interactions between Pseudomonas and Bacillus as well as their application prospects in various fields, this study is expected to provide a new theoretical basis and practical guidance for promoting the research and application of rhizosphere microbes.

Small molecule metabolites drive plant rhizosphere microbial community assembly patterns

The assembly of rhizosphere microbial communities is essential for maintaining plant health, yet it is influenced by a wide range of biotic and abiotic factors. The key drivers shaping the composition of these communities, however, remain poorly understood. In this study, we analyzed 108 plant samples and evaluated root traits, plant growth characteristics, soil enzyme activities, rhizosphere metabolites, and soil chemical properties to identify the primary determinants of rhizosphere community assembly. Across 36 soil samples, we obtained 969,634 high-quality sequences, clustering into 6,284 ASVs predominantly classified into Proteobacteria (57.99%), Actinobacteria (30%), and Bacteroidetes (5.13%). Our findings revealed that rhizosphere metabolites accounted for more variance in microbial community composition compared to chemical properties (ANOVA, F = 1.53, p = 0.04), enzyme activities, or root traits (ANOVA, F = 1.04, p = 0.001). Seven small molecule metabolites, including glycerol, sorbitol, phytol, and alpha-ketoglutaric acid, were significantly correlated with βNTI, underscoring their role as critical drivers of microbial community assembly. The genus Rhizobium, significantly associated with βNTI (R = 0.25, p = 0.009), emerged as a keystone taxon shaping community structure. Soil culture experiments further validated that small molecule metabolites can modulate microbial community assembly. The ST treatment, enriched with these metabolites, produced 1,032,205 high-quality sequences and exhibited significant shifts in community composition (Adonis, p = 0.001, R = 0.463), with Rhizobium showing higher abundance compared to the control (CK). Variable selection (βNTI >2) drove phylogenetic turnover in ST, while stochastic processes (|βNTI| < 2) dominated in CK. This study provides quantitative insights into the role of rhizosphere metabolites in shaping microbial community assembly and highlights their potential for targeted modulation of rhizosphere microbiomes.

Ecological features of microbial community linked to stochastic and deterministic assembly processes in acid mine drainage

Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature (r = -0.518, P = 0.007) and dissolved oxygen (r = 0.471, P = 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments.

IMPORTANCE

Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.

Intercropping with Robinia pseudoacacia reduces soft rot incidence in konjac by modulating the root bacterial community

BACKGROUND

Soft rot (Pectobacterium aroidearum and Dickeya) is a devastating soil-borne bacterial disease that threatens konjac production. Intercropping with false acacia has been shown to significantly reduce soft rot incidence in konjac by shifting the microbial community. However, how intercropping shapes the root bacterial community and affects soft rot incidence remains unclear. To address this, we investigated three konjac intercropping systems (false acacia, paulownia, and maize) to explore the relationships among intercropping, soft rot incidence, root bacterial community, soil enzyme activity, and soil properties.

RESULTS

Konjac intercropped with false acacia exhibited the lowest soft rot incidence and the lowest abundance of pathogenic taxa. Soft rot incidence was negatively correlated with total soil nitrogen and potassium but positively correlated with total and available soil phosphorus. The bacterial community structure and function in konjac roots differed among intercropping types, mainly driven by available soil phosphorus. Beneficial microorganisms such as Bradyrhizobium and Variovorax were enriched under a false acacia intercropping system and were negatively correlated with soil-available phosphorus. Additionally, the stable bacterial community in healthy konjac roots under false acacia may make konjac less susceptible to pathogen invasion.

CONCLUSION

The study showed that intercropping reduced the soft rot incidence by regulating the structure and stability of the konjac root bacterial community, and soil-available phosphorus was the main factor affecting the difference in the konjac root bacterial community, which provided a basis for the management of soil fertilization in konjac cultivation. © 2024 Society of Chemical Industry.

Rhizosphere microbiome regulation: Unlocking the potential for plant growth

Rhizosphere microbial communities are essential for plant growth and health maintenance, but their recruitment and functions are affected by their interactions with host plants. Finding ways to use the interaction to achieve specific production purposes, so as to reduce the use of chemical fertilizers and pesticides, is an important research approach in the development of green agriculture. To demonstrate the importance of rhizosphere microbial communities and guide practical production applications, this review summarizes the outstanding performance of rhizosphere microbial communities in promoting plant growth and stress tolerance. We also discuss the effect of host plants on their rhizosphere microbes, especially emphasizing the important role of host plant species and genes in the specific recruitment of beneficial microorganisms to improve the plants' own traits. The aim of this review is to provide valuable insights into developing plant varieties that can consistently recruit specific beneficial microorganisms to improve crop adaptability and productivity, and thus can be applied to green and sustainable agriculture in the future.

Functional dynamics analysis of endophytic microbial communities during Amorphophallus muelleri seed maturation

Konjac seeds of Amorphophallus muelleri are produced through a unique form of apomixis in triploid parthenogenesis, and typically require a longer maturation period (approximately 8 months). To date, the relevant functions of endophytic microbial taxa during A. muelleri seed development and maturation remain largely unexplored. In this study, we analyzed the functional adaptability and temporal dynamics of endophytic microbial communities during three stages of A. muelleri seed maturation. Through metagenomic sequencing, we determined that the functions of the endophytic microbiome in A. muelleri seeds were driven by the seed maturation status, and the functions of the microbial communities in the seed coats and seeds differed significantly. The species annotation results show that Proteobacteria, Actinobacteria, Ascomycota, and Basidiomycota were the dominant bacterial and fungal communities in A. muelleri seeds at different maturation stages. The KEGG and COG functional gene annotation results revealed that the seed samples during the three maturation stages had higher KO functional diversity than the seed coat samples, and the COG functional diversity of the green and red seed samples was also significantly higher than that of the seed coat samples. At different maturation stages, microbial functional genes involved in energy production and conversion as well as carbon fixation were enriched in the A. muelleri seed coats, while microbial functional genes involved in signal transduction mechanisms, amino acid transport and metabolism, carbohydrate metabolism, and lipid metabolism were more highly expressed in the seeds. Moreover, in the middle to late stages of seed maturation, the microbial functional genes involved in the biosynthesis of resistant compounds such as phenols, flavonoids, and alkaloids were significantly enriched to enhance the resistance and environmental adaptation of A. muelleri seeds. The results verified that the functions of the endophytic microbial communities change dynamically during A. muelleri seed maturation to adapt to the current needs of the host plant, which has significant implications for the exploration and utilization of functional microbial resources in A. muelleri seeds.

Litter Removal Counteracts the Effects of Warming on Soil Bacterial Communities in the Qinghai-Tibet Plateau

Climate warming and high-intensity human activities threaten the stability of alpine meadow ecosystems. The stability of the soil microbial community is crucial for maintaining ecological service function. However, the effects of warming and litter removal on microbial interactions, community-building processes, and species coexistence strategies remain unclear. In this study, we used a fiberglass open-top chamber to simulate global change, and moderate grazing in winter was simulated by removing above-ground litter from all plants in the Qinghai-Tibet Plateau, China, to investigate the effects of warming, litter removal, and interactions on soil microbial communities. The treatments included (1) warming treatment (W); (2) litter removal treatment (L); (3) the combined treatment (WL); and (4) control (CK). The results show that compared with the control treatment, warming, litter removal, and the combined treatments increased bacterial Shannon diversity but reduced fungal Shannon diversity, and warming treatment significantly changed the bacterial community composition. Warming, litter removal, and the combined treatments reduced the colinear network connectivity among microorganisms but increased the modularity of the network, and the average path distance and average clustering coefficient were higher than those in the control group. Stochastic processes played a more important role in shaping the microbial community composition, and soil-available phosphorus and soil ammonium contributed more to the βNTI of the bacterial community, while total phosphorus and NAG enzyme in the soil contributed more to the βNTI of the fungal community. Notably, litter removal counteracts the effects of warming on bacterial communities. These results suggest that litter removal may enhance bacterial community stability under warming conditions, providing insights for managing alpine meadow ecosystems in the context of climate change.

Effects of storage period and season on the microecological characteristics of Jiangxiangxing high-temperature Daqu

Metagenomics, non-targeted metabolomics, and metaproteomics were employed to analyze the microecological succession of high-temperature Daqu during storage, elucidate the adaptation mechanism of the microbial community of Daqu to storage environments, and clarify the microecological characteristics of Daqu during different seasons. During storage, the relative abundances of Bacillus, Oceanobacillus, Staphylococcus, and Aspergillus in Daqu had significantly increased, while those of Kroppenstedtia, Saccharopolyspora, Thermoascus, and Thermomyces had significantly decreased. During the first 3 months of storage, compound metabolism of Daqu was primarily dominated by generation of small molecular substances and then shifted to metabolism of amino sugars. During the storage process, homogeneous selection (15.57 %) and homogeneous diffusion (14.86 %) of the microbial communities of Daqu were much larger than during the fermentation process, while the variable selection assembly (29.43 %) was smaller than during the fermentation process. Among the 2509 proteins identified in the four-season Daqu, bacterial protein expression was 1.46-fold greater than that of fungi. Seasonal factors influenced the function of Daqu by alterations to Bacillus subtilis, Oceanobacillus iheyensis, and Aspergillus nidulans and other microbial functions. Carbon and benzoic acid metabolism of Daqu was relatively increased during the spring, while metabolism of alkaloids and tyrosine was upregulated during the summer, amino acid synthesis and starch metabolism were enriched during the autumn, and peptidoglycan synthesis was relatively greater during the winter. Adjusting the moisture content of Daqu during the storage period was shown to reduce microecological differentiation caused by seasonal temperature variations.

The structure and function of rhizosphere bacterial communities: impact of chemical vs. bio-organic fertilizers on root disease, quality, and yield of Codonopsis pilosula

Introduction

Long-term use of chemical fertilizers (CFs) can cause soil compaction and acidification. In recent years, bio-organic fertilizers (BOFs) have begun to replace CFs in some vegetables and cash crops, but the application of CFs or BOFs has resulted in crop quality and disease occurrence.

Methods

This study aimed to analyze the microbial mechanism of differences between CFs and BOFs in root disease, quality, and yield of tuber Chinese herbal medicine. We studied the effects of CFs, organic fertilizers, commercial BOFs, biocontrol bacteria BOFs, and biocontrol fungi BOFs on rhizosphere microbial community structure and function, root rot, quality, and yield of Codonopsis pilosula at different periods after application and analyzed the correlation.

Results and discussion

Compared to CFs, the emergence rate and yield in BOF treatments were increased by 21.12 and 33.65%, respectively, and the ash content, water content, and disease index in the BOF treatments were decreased by 17.87, 8.19, and 76.60%, respectively. The structural equation model showed that CFs promoted the quality and yield of C. pilosula by influencing soil environmental factors, while BOFs directly drove soil bacterial community to reduce disease index and improve the quality and yield of C. pilosula. There was a stronger interaction and stability of soil microbial networks after BOF treatments. Microlunatus, Rubrobacter, Luteitalea, Nakamurella, and Pedomicrobium were identified as effector bacteria, which were related to disease prevention and yield and quality increase of C. pilosula. Microbial functional analysis indicated that the signal transduction and amino acid metabolism of soil bacteria might play a major role in improving the quality and yield of C. pilosula in the early and middle growth stages. In conclusion, compared to CFs, BOFs obtained a lower disease index of root rot and a higher quality and yield of C. pilosula by changing the structure and function of the rhizosphere bacterial community.

Multi-omics analysis of excessive nitrogen fertilizer application: Assessing environmental damage and solutions in potato farming

Potatoes (Solanum tuberosum L.) are the third largest food crop globally and are pivotal for global food security. Widespread N fertilizer waste in potato cultivation has caused diverse environmental issues. This study employed microbial metagenomic sequencing to analyze the causes behind the declining N use efficiency (NUE) and escalating greenhouse gas emissions resulting from excessive N fertilizer application. Addressing N fertilizer inefficiency through breeding has emerged as a viable solution for mitigating overuse in potato cultivation. In this study, transcriptome and metabolome analyses were applied to identify N fertilizer-responsive genes. Metagenomic sequencing revealed that excessive N fertilizer application triggered alterations in the population dynamics of 11 major bacterial phyla, consequently affecting soil microbial functions, particularly N metabolism pathways and bacterial secretion systems. Notably, the enzyme levels associated with NO3- increased, and those associated with NO and N2O increased. Furthermore, excessive N fertilizer application enhanced soil virulence factors and increased potato susceptibility to diseases. Transcriptome and metabolome sequencing revealed significant impacts of excessive N fertilizer use on lipid and amino acid metabolism pathways. Weighted gene co‑expression network analysis (WGCNA) was adopted to identify two genes associated with N fertilizer response: PGSC0003DMG400021157 and PGSC0003DMG400009544.

Ralstonia solanacearum Infection Drives the Assembly and Functional Adaptation of Potato Rhizosphere Microbial Communities

Bacterial wilt caused by Ralstonia solanacearum is a destructive disease that affects potato production, leading to severe yield losses. Currently, little is known about the changes in the assembly and functional adaptation of potato rhizosphere microbial communities during different stages of R. solanacearum infection. In this study, using amplicon and metagenomic sequencing approaches, we analyzed the changes in the composition and functions of bacterial and fungal communities in the potato rhizosphere across four stages of R. solanacearum infection. The results showed that R. solanacearum infection led to significant changes in the composition and functions of bacterial and fungal communities in the potato rhizosphere, with various microbial properties (including α,β-diversity, species composition, and community ecological functions) all being driven by R. solanacearum infection. The relative abundance of some beneficial microorganisms in the potato rhizosphere, including Firmicutes, Bacillus, Pseudomonas, and Mortierella, decreased as the duration of infection increased. Moreover, the related microbial communities played a significant role in basic metabolism and signal transduction; however, the functions involved in soil C, N, and P transformation weakened. This study provides new insights into the dynamic changes in the composition and functions of potato rhizosphere microbial communities at different stages of R. solanacearum infection to adapt to the growth promotion or disease suppression strategies of host plants, which may provide guidance for formulating future strategies to regulate microbial communities for the integrated control of soil-borne plant diseases.

Differential responses of soil bacteria, fungi and protists to root exudates and temperature

The impact of climate warming on soil microbes has been well documented, with studies revealing its effects on diversity, community structure and network dynamics. However, the consistency of soil microbial community assembly, particularly in response to diverse plant root exudates under varying temperature conditions, remains an unresolved issue. To address this issue, we employed a growth chamber to integrate temperature and root exudates in a controlled experiment to examine the response of soil bacteria, fungi, and protists. Our findings revealed that temperature independently regulated microbial diversity, with distinct patterns observed among bacteria, fungi, and protists. Both root exudates and temperature significantly influenced microbial community composition, yet interpretations of these factors varied among prokaryotes and eukaryotes. In addition to phototrophic bacteria and protists, as well as protistan consumers, root exudates determined to varying degrees the enrichment of other microbial functional guilds at specific temperatures. The effects of temperature and root exudates on microbial co-occurrence patterns were interdependent; root exudates primarily simplified the network at low and high temperatures, while responses to temperature varied between single and mixed exudate treatments. Moreover, temperature altered the composition of keystone species within the microbial network, while root exudates led to a decrease in their number. These results emphasize the substantial impact of plant root exudates on soil microbial community responses to temperature, underscoring the necessity for future climate change research to incorporate additional environmental variables.

Regulation of Bacterial Growth and Behavior by Host Plant

Plants are associated with diverse bacteria in nature. Some bacteria are pathogens that decrease plant fitness, and others are beneficial bacteria that promote plant growth and stress resistance. Emerging evidence also suggests that plant-associated commensal bacteria collectively contribute to plant health and are essential for plant survival in nature. Bacteria with different characteristics simultaneously colonize plant tissues. Thus, plants need to accommodate bacteria that provide service to the host plants, but they need to defend against pathogens at the same time. How do plants achieve this? In this review, we summarize how plants use physical barriers, control common goods such as water and nutrients, and produce antibacterial molecules to regulate bacterial growth and behavior. Furthermore, we highlight that plants use specialized metabolites that support or inhibit specific bacteria, thereby selectively recruiting plant-associated bacterial communities and regulating their function. We also raise important questions that need to be addressed to improve our understanding of plant-bacteria interactions.

Pathogen-driven Pseudomonas reshaped the phyllosphere microbiome in combination with Pseudostellaria heterophylla foliar disease resistance via the release of volatile organic compounds

BACKGROUND

Continuous monocropping obstacles are common in plants, especially medicinal plants, resulting in disease outbreaks and productivity reductions. Foliar disease, mainly caused by Fusarium oxysporum, results in a severe decrease in the yield of Pseudostellaria heterophylla annually. Determining an effective biomethod to alleviate this disease is urgently needed to improve its productivity and quality.

RESULTS

This study screened thirty-two keystone bacterial genera induced by pathogens in P. heterophylla rhizosphere soil under continuous monocropping conditions. Pseudomonas, Chryseobacterium, and Flavobacterium, referred to as the beneficial microbiota, were significantly attracted by pathogen infection. The P. palleroniana strain B-BH16-1 can directly inhibit the growth and spore formation of seven primary pathogens of P. heterophylla foliar disease by disrupting fusaric acid production via the emission of volatile organic compounds (VOCs). In addition, strain B-BH16-1 enhances the disease resistance of P. heterophylla by obliterating the pathogen and assembling beneficial microbiota.

CONCLUSION

Pathogen-induced Pseudomonas reshaped phyllosphere microbial communities via direct antagonism of pathogens and indirect disruption of the pathogen virulence factor biosynthesis to enhance disease suppression and improve yields. These results show that inhibiting pathogen virulence biosynthesis to reshape the plant microbial community using disease-induing probiotics will be an innovative strategy for managing plant disease, especially under continuous monoculture conditions.

Bacillus species are core microbiota of resistant maize cultivars that induce host metabolic defense against corn stalk rot

BACKGROUND

Microbes colonizing each compartment of terrestrial plants are indispensable for maintaining crop health. Although corn stalk rot (CSR) is a severe disease affecting maize (Zea mays) worldwide, the mechanisms underlying host-microbe interactions across vertical compartments in maize plants, which exhibit heterogeneous CSR-resistance, remain largely uncharacterized.

RESULTS

Here, we investigated the microbial communities associated with CSR-resistant and CSR-susceptible maize cultivars using multi-omics analysis coupled with experimental verification. Maize cultivars resistant to CSR reshaped the microbiota and recruited Bacillus species with three phenotypes against Fusarium graminearum including niche pre-emption, potential secretion of antimicrobial compounds, and no inhibition to alleviate pathogen stress. By inducing the expression of Tyrosine decarboxylase 1 (TYDC1), encoding an enzyme that catalyzes the production of tyramine and dopamine, Bacillus isolates that do not directly suppress pathogen infection induced the synthesis of berberine, an isoquinoline alkaloid that inhibits pathogen growth. These beneficial bacteria were recruited from the rhizosphere and transferred to the stems but not grains of the CSR-resistant plants.

CONCLUSIONS

The current study offers insight into how maize plants respond to and interact with their microbiome and lays the foundation for preventing and treating soil-borne pathogens. Video Abstract.

Plant growth promotion and biocontrol properties of a synthetic community in the control of apple disease

BACKGROUND

Apple Replant Disease (ARD) is common in major apple-growing regions worldwide, but the role of rhizosphere microbiota in conferring ARD resistance and promoting plant growth remains unclear.

RESULTS

In this study, a synthetic microbial community (SynCom) was developed to enhance apple plant growth and combat apple pathogens. Eight unique bacteria selected via microbial culture were used to construct the antagonistic synthetic community, which was then inoculated into apple seedlings in greenhouse experiments. Changes in the rhizomicroflora and the growth of aboveground plants were monitored. The eight strains, belonging to the genera Bacillus and Streptomyces, have the ability to antagonize pathogens such as Fusarium oxysporum, Rhizoctonia solani, Botryosphaeria ribis, and Physalospora piricola. Additionally, these eight strains can stably colonize in apple rhizosphere and some of them can produce siderophores, ACC deaminase, and IAA. Greenhouse experiments with Malus hupehensis Rehd indicated that SynCom promotes plant growth (5.23%) and increases the nutrient content of the soil, including soil organic matter (9.25%) and available K (1.99%), P (7.89%), and N (0.19%), and increases bacterial richness and the relative abundance of potentially beneficial bacteria. SynCom also increased the stability of the rhizosphere microbial community, the assembly of which was dominated by deterministic processes (|β NTI| > 2).

CONCLUSIONS

Our results provide insights into the contribution of the microbiome to pathogen inhibition and host growth. The formulation and manipulation of similar SynComs may be a beneficial strategy for promoting plant growth and controlling soil-borne disease.

Dopamine Alleviates Phloridzin Toxicity in Apple by Modifying Rhizosphere Bacterial Community Structure and Function

Phloridzin significantly influences apple plant growth, development, and resistance to environmental stresses by engaging in various metabolic processes. Its excessive accumulation in soil, attributed to continuous monoculture practices, not only inhibits plant growth but also disrupts the rhizosphere microbial community. This study aims to explore the remedial effects of dopamine, a known antioxidant and stress resistance modulator in plants, on the adverse impacts of phloridzin stress in apple. Through hydroponic and pot experiments, it was demonstrated that dopamine significantly mitigates the growth inhibition caused by phloridzin stress in apple by reducing reactive oxygen species levels and enhancing photosynthesis and nitrogen transport. Additionally, dopamine reduced phloridzin concentrations in both the rhizosphere and roots. Furthermore, dopamine positively influences the structure of the rhizosphere microbial community, enriching beneficial microbes associated with nitrogen cycling. It increases the potential for soil nitrogen degradation and fixation by upregulating the abundance of ureC, GDH, and nifH, as revealed by metagenomic analysis. This aids in alleviating phloridzin stress. The study reveals dopamine's pivotal roles in modulating rhizosphere ecology under phloridzin stress and suggests its potential in sustainable apple cultivation practices to counter ARD and enhance productivity.

Synthetic community derived from grafted watermelon rhizosphere provides protection for ungrafted watermelon against Fusarium oxysporum via microbial synergistic effects

BACKGROUND

Plant microbiota contributes to plant growth and health, including enhancing plant resistance to various diseases. Despite remarkable progress in understanding diseases resistance in plants, the precise role of rhizosphere microbiota in enhancing watermelon resistance against soil-borne diseases remains unclear. Here, we constructed a synthetic community (SynCom) of 16 core bacterial strains obtained from the rhizosphere of grafted watermelon plants. We further simplified SynCom and investigated the role of bacteria with synergistic interactions in promoting plant growth through a simple synthetic community.

RESULTS

Our results demonstrated that the SynCom significantly enhanced the growth and disease resistance of ungrafted watermelon grown in non-sterile soil. Furthermore, analysis of the amplicon and metagenome data revealed the pivotal role of Pseudomonas in enhancing plant health, as evidenced by a significant increase in the relative abundance and biofilm-forming pathways of Pseudomonas post-SynCom inoculation. Based on in vitro co-culture experiments and bacterial metabolomic analysis, we selected Pseudomonas along with seven other members of the SynCom that exhibited synergistic effects with Pseudomonas. It enabled us to further refine the initially constructed SynCom into a simplified SynCom comprising the eight selected bacterial species. Notably, the plant-promoting effects of simplified SynCom were similar to those of the initial SynCom. Furthermore, the simplified SynCom protected plants through synergistic effects of bacteria.

CONCLUSIONS

Our findings suggest that the SynCom proliferate in the rhizosphere and mitigate soil-borne diseases through microbial synergistic interactions, highlighting the potential of synergistic effects between microorganisms in enhancing plant health. This study provides a novel insight into using the functional SynCom as a promising solution for sustainable agriculture. Video Abstract.

Long-term conservation tillage increase cotton rhizosphere sequestration of soil organic carbon by changing specific microbial CO2 fixation pathways in coastal saline soil

Coastal saline soil is an important reserve resource for arable land globally. Data from 10 years of continuous stubble return and subsoiling experiments have revealed that these two conservation tillage measures significantly improve cotton rhizosphere soil organic carbon sequestration in coastal saline soil. However, the contribution of microbial fixation of atmospheric carbon dioxide (CO2) has remained unclear. Here, metagenomics and metabolomics analyses were used to deeply explore the microbial CO2 fixation process in rhizosphere soil of coastal saline cotton fields under long-term stubble return and subsoiling. Metagenomics analysis showed that stubble return and subsoiling mainly optimized CO2 fixing microorganism (CFM) communities by increasing the abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi, and improving composition diversity. Conjoint metagenomics and metabolomics analyses investigated the effects of stubble return and subsoiling on the reverse tricarboxylic acid (rTCA) cycle. The conversion of citrate to oxaloacetate was inhibited in the citrate cleavage reaction of the rTCA cycle. More citrate was converted to acetyl-CoA, which enhanced the subsequent CO2 fixation process of acetyl-CoA conversion to pyruvate. In the rTCA cycle reductive carboxylation reaction from 2-oxoglutarate to isocitrate, synthesis of the oxalosuccinate intermediate product was inhibited, with strengthened CO2 fixation involving the direct conversion of 2-oxoglutarate to isocitrate. The collective results demonstrate that stubble return and subsoiling optimizes rhizosphere CFM communities by increasing microbial diversity, in turn increasing CO2 fixation by enhancing the utilization of rTCA and 3-hydroxypropionate/4-hydroxybutyrate cycles by CFMs. These events increase the microbial CO2 fixation in the cotton rhizosphere, thereby promoting the accumulation of microbial biomass, and ultimately improving rhizosphere soil organic carbon. This study clarifies the impact of conservation tillage measures on microbial CO2 fixation in cotton rhizosphere of coastal saline soil, and provides fundamental data for the improvement of carbon sequestration in saline soil in agricultural ecosystems.

Soil prokaryotic and fungal biome structures associated with crop disease status across the Japan Archipelago

Archaea, bacteria, and fungi in the soil are increasingly recognized as determinants of agricultural productivity and sustainability. A crucial step for exploring soil microbiomes with important ecosystem functions is to perform statistical analyses on the potential relationship between microbiome structure and functions based on comparisons of hundreds or thousands of environmental samples collected across broad geographic ranges. In this study, we integrated agricultural field metadata with microbial community analyses by targeting 2,903 bulk soil samples collected along a latitudinal gradient from cool-temperate to subtropical regions in Japan (26.1-42.8 °N). The data involving 632 archaeal, 26,868 bacterial, and 4,889 fungal operational taxonomic units detected across the fields of 19 crop plant species allowed us to conduct statistical analyses (permutational analyses of variance, generalized linear mixed models, randomization analyses, and network analyses) on the relationship among edaphic factors, microbiome compositions, and crop disease prevalence. We then examined whether the diverse microbes form species sets varying in potential ecological impacts on crop plants. A network analysis suggested that the observed prokaryotes and fungi were classified into several species sets (network modules), which differed substantially in association with crop disease prevalence. Within the network of microbe-to-microbe coexistence, ecologically diverse microbes, such as an ammonium-oxidizing archaeon, an antibiotics-producing bacterium, and a potentially mycoparasitic fungus, were inferred to play key roles in shifts between crop-disease-promotive and crop-disease-suppressive states of soil microbiomes. The bird's-eye view of soil microbiome structure will provide a basis for designing and managing agroecosystems with high disease-suppressive functions.IMPORTANCEUnderstanding how microbiome structure and functions are organized in soil ecosystems is one of the major challenges in both basic ecology and applied microbiology. Given the ongoing worldwide degradation of agroecosystems, building frameworks for exploring structural diversity and functional profiles of soil microbiomes is an essential task. Our study provides an overview of cropland microbiome states in light of potential crop-disease-suppressive functions. The large data set allowed us to explore highly functional species sets that may be stably managed in agroecosystems. Furthermore, an analysis of network architecture highlighted species that are potentially used to cause shifts from disease-prevalent states of agroecosystems to disease-suppressive states. By extending the approach of comparative analyses toward broader geographic ranges and diverse agricultural practices, agroecosystem with maximized biological functions will be further explored.

Comparison of bio-beads combined with Pseudomonas edaphica and three phosphate materials for lead immobilization: Performance, mechanism and plant growth

Phosphate materials (PMs) combine with phosphate solubilizing bacteria play an essential roles in lead (Pb) immobilization, but their resulting ability to reduce Pb bioavailability may vary depending on PMs used. In this study, Pseudomonas edaphica GAU-665 and three PMs: tricalcium phosphate, calcium phytate and nano-hydroxyapatite were respectively encapsulated into bio-beads by sodium alginate, which immobilization efficiency of Pb2+ were 99.11%, 97.76% and 99.02% at initial Pb2+ concentration of 200 mg L-1, respectively. The Pb2+ immobilization performance of bio-beads under different conditions and their organic acids secreted were examined. Most Pb2+ was immobilized by bio-beads through combined functions of adsorption, precipitation, ion exchange and biomineralization, accompanied by the formation of more stable compounds such as Pb3(PO4)2, Pb5(PO4)3OH and Pb5(PO4)3Cl. Meanwhile, pot experimental results indicated that the inoculation of CPhy (calcium phytate) bio-beads with PSB have highest biomass and root growth of oat (Avena sativa L.) in Pb-stressed compared with CK, which increased the content of chlorophyll b (167.51%) in shoot. In addition, the CPhy bio-beads enhance the peroxidase, catalase activities and reduce the malondialdehyde content to alleviating lead physiological toxicity in oat, which reductions the Pb accumulation in shoot (52.06%) and root (81.04%), and increased the residual fraction of Pb by 165.80% in soil. These findings suggest the bio-beads combined with P. edaphica GAU-665 and calcium phytate is an efficient Pb immobilization material and provided feasible way to improve safety agricultural production and Pb-contaminated soil remediation.

Facilitating Effects of Reductive Soil Disinfestation on Soil Health and Physiological Properties of Panax ginseng

Chemical soil fumigation (CSF) and reductive soil disinfestation (RSD) have been proven to be effective agricultural strategies to improve soil quality, restructure microbial communities, and promote plant growth in soil degradation remediation. However, it is still unclear how RSD and CSF ensure soil and plant health by altering fungal communities. Field experiments were conducted to investigate the effects of CSF with chloropicrin, and RSD with animal feces on soil properties, fungal communities and functional composition, and plant physiological characteristics were evaluated. Results showed that RSD and CSF treatment improved soil properties, restructured fungal community composition and structure, enhanced fungal interactions and functions, and facilitated plant growth. There was a significant increase in OM, AN, and AP contents in the soil with both CSF and RSD treatments compared to CK. Meanwhile, compared with CK and CSF, RSD treatment significantly increased biocontrol Chaetomium relative abundance while reducing pathogenic Neonectria relative abundance, indicating that RSD has strong inhibition potential. Furthermore, the microbial network of RSD treatment was more complex and interconnected, and the functions of plant pathogens, and animal pathogen were decreased. Importantly, RSD treatment significantly increased plant SOD, CAT, POD activity, SP, Ca, Zn content, and decreased MDA, ABA, Mg, K, and Fe content. In summary, RSD treatment is more effective than CSF treatment, by stimulating the proliferation of probiotic communities to further enhance soil health and plant disease resistance.

The endophytic fungal community plays a crucial role in the resistance of host plants to necrotic bacterial pathogens

Konjac species (Amorphophallus spp.) are the only plant species in the world that are rich in a large amount of konjac glucomannan (KGM). These plants are widely cultivated as cash crops in tropical and subtropical countries in Asia, including China. Pectobacterium carotovorum subsp. carotovorum (Pcc) is one of the most destructive bacterial pathogens of konjac. Here, we analyzed the interactions between Pcc and susceptible and resistant konjac species from multiple perspectives. At the transcriptional and metabolic levels, the susceptible species A. konjac and resistant species A. muelleri exhibit similar molecular responses, activating plant hormone signaling pathways and metabolizing defense compounds such as phenylpropanoids and flavonoids to resist infection. Interestingly, we found that Pcc stress can lead to rapid recombination of endophytic microbial communities within a very short period (96 h). Under conditions of bacterial pathogen infection, the relative abundance of most bacterial communities in konjac tissue decreased sharply compared with that in healthy plants, while the relative abundance of some beneficial fungal communities increased significantly. The relative abundance of Cladosporium increased significantly in both kinds of infected konjac compared to that in healthy plants, and the relative abundance in resistant A. muelleri plants was greater than that in susceptible A. konjac plants. Among the isolated cultivable microorganisms, all three strains of Cladosporium strongly inhibited Pcc growth. Our results further elucidate the potential mechanism underlying konjac resistance to Pcc infection, highlighting the important role of endophytic microbial communities in resisting bacterial pathogen infections, especially the more direct role of fungal communities in inhibiting pathogen growth.

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.

Host genetic variation and specialized metabolites from wheat leaves enriches for phyllosphere Pseudomonas spp. with enriched antibiotic resistomes

Antibiotic resistance in plant-associated microbiomes poses significant risks for agricultural ecosystems and human health. Although accumulating evidence suggests a role for plant genotypes in shaping their microbiome, almost nothing is known about how the changes of plant genetic information affect the co-evolved plant microbiome carrying antibiotic resistance genes (ARGs). Here, we selected 16 wheat cultivars and experimentally explored the impact of host genetic variation on phyllosphere microbiome, ARGs, and metabolites. Our results demonstrated that host genetic variation significantly influenced the phyllosphere resistomes. Wheat genotypes exhibiting high phyllosphere ARGs were linked to elevated Pseudomonas populations, along with increased abundances of Pseudomonas aeruginosa biofilm formation genes. Further analysis of 350 Pseudomonas spp. genomes from diverse habitats at a global scale revealed that nearly all strains possess multiple ARGs, virulence factor genes (VFGs), and mobile genetic elements (MGEs) on their genomes, albeit with lower nucleotide diversity compared to other species. These findings suggested that the proliferation of Pseudomonas spp. in the phyllosphere significantly contributed to antibiotic resistance. We further observed direct links between the upregulated leaf metabolite DIMBOA-Glc, Pseudomonas spp., and enrichment of phyllosphere ARGs, which were corroborated by microcosm experiments demonstrating that DIMBOA-Glc significantly enhanced the relative abundance of Pseudomonas spp. Overall, alterations in leaf metabolites resulting from genetic variation throughout plant evolution may drive the development of highly specialized microbial communities capable of enriching phyllosphere ARGs. This study enhances our understanding of how plants actively shape microbial communities and clarifies the impact of host genetic variation on the plant resistomes.

Coping with extremes: Alternations in diet, gut microbiota, and hepatic metabolic functions in a highland passerine

In wild animals, diet and gut microbiota interactions are critical moderators of metabolic functions and are highly contingent on habitat conditions. Challenged by the extreme conditions of high-altitude environments, the strategies implemented by highland animals to adjust their diet and gut microbial composition and modulate their metabolic substrates remain largely unexplored. By employing a typical human commensal species, the Eurasian tree sparrow (Passer montanus, ETS), as a model species, we studied the differences in diet, digestive tract morphology and enzyme activity, gut microbiota, and metabolic energy profiling between highland (the Qinghai-Tibet Plateau, QTP; 3230 m) and lowland (Shijiazhuang, Hebei; 80 m) populations. Our results showed that highland ETSs had enlarged digestive organs and longer small intestinal villi, while no differences in key digestive enzyme activities were observed between the two populations. The 18S rRNA sequencing results revealed that the dietary composition of highland ETSs were more animal-based and less plant-based than those of the lowland ones. Furthermore, 16S rRNA sequencing results suggested that the intestinal microbial communities were structurally segregated between populations. PICRUSt metagenome predictions further indicated that the expression patterns of microbial genes involved in material and energy metabolism, immune system and infection, and xenobiotic biodegradation were strikingly different between the two populations. Analysis of liver metabolomics revealed significant metabolic differences between highland and lowland ETSs in terms of substrate utilization, as well as distinct sex-specific alterations in glycerophospholipids. Furthermore, the interplay between diet, liver metabolism, and gut microbiota suggests a dietary shift resulting in corresponding changes in gut microbiota and metabolic functions. Our findings indicate that highland ETSs have evolved to optimize digestion and absorption, rely on more protein-rich foods, and possess gut microbiota tailored to their dietary composition, likely adaptive physiological and ecological strategies adopted to cope with extreme highland environments.

Rice bacterial leaf blight drives rhizosphere microbial assembly and function adaptation

IMPORTANCE

Our results suggest that rhizosphere bacteria are more sensitive to bacterial leaf blight (BLB) than fungi. BLB infection decreased the diversity of the rhizosphere bacterial community but increased the complexity and size of the rhizosphere microbial community co-occurrence networks. In addition, the relative abundance of the genera Streptomyces, Chitinophaga, Sphingomonas, and Bacillus increased significantly. Finally, these findings contribute to the understanding of plant-microbiome interactions by providing critical insight into the ecological mechanisms by which rhizosphere microbes respond to phyllosphere diseases. In addition, it also lays the foundation and provides data to support the use of plant microbes to promote plant health in sustainable agriculture, providing critical insight into ecological mechanisms.

Rhizosphere shapes the associations between protistan predators and bacteria within microbiomes through the deterministic selection on bacterial communities

The assembly of bacterial communities in the rhizosphere is well-documented and plays a crucial role in supporting plant performance. However, we have limited knowledge of how plant rhizosphere determines the assembly of protistan predators and whether the potential associations between protistan predators and bacterial communities shift due to rhizosphere selection. To address this, we examined bacterial and protistan taxa from 443 agricultural soil samples including bulk and rhizosphere soils. Our results presented distinct patterns of bacteria and protistan predators in rhizosphere microbiome assembly. Community assembly of protistan predators was determined by a stochastic process in the rhizosphere and the diversity of protistan predators was reduced in the rhizosphere compared to bulk soils, these may be attributed to the indirect impacts from the altered bacterial communities that showed deterministic process assembly in the rhizosphere. Interestingly, we observed that the plant rhizosphere facilitates more close interrelationships between protistan predators and bacterial communities, which might promote a healthy rhizosphere microbial community for plant growth. Overall, our findings indicate that the potential predator-prey relationships within the microbiome, mediated by plant rhizosphere, might contribute to plant performance in agricultural ecosystems.

The loss of microbial autotoxin degradation functions is associated with the decline of beneficial bacterial agents induced by phenolic acids

Continuous cultivation of medicinal plants can disrupt the rhizosphere's microbial community. There is still a need to know about the beneficial bacterial community, their putative drivers, and the potential functions they may have. This study used different growth years of Sanqi ginseng (Panax notoginseng) with root rot to look at the beneficial microbial community structure, the function of microbial carbon source utilization, and the function of rhizosphere soil metabolism. The beneficial bacterial community changed and the relative abundance of beneficial agents was suppressed significantly with the successive Sanqi ginseng plantings. The carbon source utilization capacity and diversity increased significantly, whereas three autotoxin degradation-related pathways (biosynthesis of other secondary metabolites, metabolism of terpenoids and polyketides, and xenobiotics biodegradation and metabolism) were downregulated considerably with planting year extended. The changes in the beneficial agents were driven by the shifts in phenolic acid profiles, and the decline of beneficial microbes led to the loss of microbial autotoxin degradation functions. Overall, these results provide insight into beneficial microbes, microbial functions, phenolic acids, and their interactions, and these findings are essential for maintaining healthy and sustainable cultivation of Sanqi ginseng. IMPORTANCE Sanqi ginseng is a valuable perennial Chinese herb with various benefits for human health. However, continuous cultivation causes a high incidence of root rot disease, which leads to decreased yield and serious economic losses and ultimately impedes the sustainable development of Chinese medicine production. The significance of this study is to reveal the pattern of changes in beneficial bacteria and their related functions in root rot diseased rhizosphere with the successive planting years of Sanqi ginseng. This study found that the decline of beneficial bacterial agents mediated by phenolic acid profiles appears to be associated with the loss of microbial autotoxin degradation functions. This result may have new implications for deciphering the causes of Sanqi ginseng's continuous cropping obstacles.

Tapping the rhizosphere metabolites for the prebiotic control of soil-borne bacterial wilt disease

Prebiotics are compounds that selectively stimulate the growth and activity of beneficial microorganisms. The use of prebiotics is a well-established strategy for managing human gut health. This concept can also be extended to plants where plant rhizosphere microbiomes can improve the nutrient acquisition and disease resistance. However, we lack effective strategies for choosing metabolites to elicit the desired impacts on plant health. In this study, we target the rhizosphere of tomato (Solanum lycopersicum) suffering from wilt disease (caused by Ralstonia solanacearum) as source for potential prebiotic metabolites. We identify metabolites (ribose, lactic acid, xylose, mannose, maltose, gluconolactone, and ribitol) exclusively used by soil commensal bacteria (not positively correlated with R. solanacearum) but not efficiently used by the pathogen in vitro. Metabolites application in the soil with 1 µmol g^-1 soil effectively protects tomato and other Solanaceae crops, pepper (Capsicum annuum) and eggplant (Solanum melongena), from pathogen invasion. After adding prebiotics, the rhizosphere soil microbiome exhibits enrichment of pathways related to carbon metabolism and autotoxin degradation, which were driven by commensal microbes. Collectively, we propose a novel pathway for mining metabolites from the rhizosphere soil and their use as prebiotics to help control soil-borne bacterial wilt diseases.

Dopamine alleviates cadmium stress in apple trees by recruiting beneficial microorganisms to enhance the physiological resilience revealed by high-throughput sequencing and soil metabolomics

Dopamine has demonstrated promise as a stress-relief substance. However, the function of dopamine in Cd tolerance and its mechanism remains largely unknown. The current study was performed to investigate the mechanism of dopamine on alleviating apple Cd stress through regular application of CdCl2 and dopamine solution to potting soil. The results indicated that dopamine significantly reduced reactive oxygen species (ROS) and Cd accumulation and alleviated the inhibitory effect of Cd stress on the growth of apple plants through activation of the antioxidant system, enhancement of photosynthetic capacity, and regulation of gene expression related to Cd absorption and detoxification. The richness of the rhizosphere microbial community increased, and community composition and assembly were affected by dopamine treatment. Network analysis of microbial communities showed that the numbers of nodes and total links increased significantly after dopamine treatment, while the keystone species shifted. Linear discriminant analysis effect size indicated that some biomarkers were significantly enriched after dopamine treatment, suggesting that dopamine induced plants to recruit potentially beneficial microorganisms (Pseudoxanthomonas, Aeromicrobium, Bradyrhizobium, Frankia, Saccharimonadales, Novosphingobium, and Streptomyces) to resist Cd stress. The co-occurrence network showed several metabolites that were positively correlated with relative growth rate and negatively correlated with Cd accumulation, suggesting that potentially beneficial microorganisms may be attracted by several metabolites (L-threonic acid, profenamine, juniperic acid and (3β,5ξ,9ξ)-3,6,19-trihydroxyurs-12-en-28-oic acid). Our results demonstrate that dopamine alleviates Cd stress in apple trees by recruiting beneficial microorganisms to enhance the physiological resilience revealed. This study provides an effective means to reduce the harm to agricultural production caused by heavy metals.

Plant pathogen resistance is mediated by recruitment of specific rhizosphere fungi

Beneficial interactions between plants and rhizosphere microorganisms are key determinants of plant health with the potential to enhance the sustainability of agricultural practices. However, pinpointing the mechanisms that determine plant disease protection is often difficult due to the complexity of microbial and plant-microbe interactions and their links with the plant's own defense systems. Here, we found that the resistance level of different banana varieties was correlated with the plant's ability to stimulate specific fungal taxa in the rhizosphere that are able to inhibit the Foc TR4 pathogen. These fungal taxa included members of the genera Trichoderma and Penicillium, and their growth was stimulated by plant exudates such as shikimic acid, D-(-)-ribofuranose, and propylene glycol. Furthermore, amending soils with these metabolites enhanced the resistance of a susceptible variety to Foc TR4, with no effect observed for the resistant variety. In total, our findings suggest that the ability to recruit pathogen-suppressive fungal taxa may be an important component in determining the level of pathogen resistance exhibited by plant varieties. This perspective opens up new avenues for improving plant health, in which both plant and associated microbial properties are considered.

Genome-Wide Tissue-Specific Genes Identification for Novel Tissue-Specific Promoters Discovery in Soybean

Promoters play a crucial role in controlling the spatial and temporal expression of genes at transcriptional levels in the process of higher plant growth and development. The spatial, efficient, and correct regulation of exogenous genes expression, as desired, is the key point in plant genetic engineering research. Constitutive promoters widely used in plant genetic transformation are limited because, sometimes, they may cause potential negative effects. This issue can be solved, to a certain extent, by using tissue-specific promoters. Compared with constitutive promoters, a few tissue-specific promoters have been isolated and applied. In this study, based on the transcriptome data, a total of 288 tissue-specific genes were collected, expressed in seven tissues, including the leaves, stems, flowers, pods, seeds, roots, and nodules of soybean (Glycine max). KEGG pathway enrichment analysis was carried out, and 52 metabolites were annotated. A total of 12 tissue-specific genes were selected via the transcription expression level and validated through real-time quantitative PCR, of which 10 genes showed tissue-specific expression. The 3-kb 5' upstream regions of ten genes were obtained as putative promoters. Further analysis showed that all the 10 promoters contained many tissue-specific cis-elements. These results demonstrate that high-throughput transcriptional data can be used as effective tools, providing a guide for high-throughput novel tissue-specific promoter discovery.

Synergistic analysis of performance, functional genes, and microbial community assembly in SNDPR process under Zn(II) stress

One of the most prevalent heavy metals found in rural sewage is Zn(II), while its effect on simultaneous nitrification, denitrification and phosphorus removal (SNDPR) remains unclear. In this work, the responses of SNDPR performance to long-term Zn(II) stress were investigated in a cross-flow honeycomb bionic carrier biofilm system. The results indicated that Zn(II) stress at 1 and 5 mg L^-1 could increase nitrogen removal. Maximum ammonia nitrogen, total nitrogen, and phosphorus removal efficiencies of up to 88.54%, 83.19%, and 83.65% were obtained at Zn(II) concentration of 5 mg L^-1. The functional genes, such as archaeal amoA, bacterial amoA, NarG, NirS, NapA, and NirK, also reached the highest value at 5 mg L^-1 Zn(II), with the absolute abundances of 7.73 × 10⁵, 1.57 × 10⁶, 6.68 × 10⁸, 1.05 × 10⁹, 1.79 × 10⁸, and 2.09 × 10⁸ copies·g^-1 dry weight, respectively. The neutral community model demonstrated that deterministic selection was responsible for the system's microbial community assembly. Additionally, response regimes with extracellular polymeric substances and cooperation among microorganisms facilitated the stability of the reactor effluent. Overall, the findings of this paper contribute to improving the efficiency of wastewater treatment.

Improving radish phosphorus utilization efficiency and inhibiting Cd and Pb uptake by using heavy metal-immobilizing and phosphate-solubilizing bacteria

Phosphate-solubilizing bacteria play a key role in increasing plant growth as potential suppliers of soluble phosphorus and have great potential for the remediation of heavy metal-polluted soils. However, the soil and microbiological mechanisms by which phosphate-solubilizing bacteria prevent heavy metal absorption in radish have not been adequately studied. Here, the mechanisms of phosphorus solubilization, Cd and Pb immobilization, and the inhibition of heavy metal absorption by phosphate-solubilizing bacteria were studied in radish through solution adsorption and pot experiments. Two phosphate-solubilizing bacteria with high Cd and Pb removal rates (46.9-97.12 %), Klebsiella sp. M2 and Kluyvera sp. M8, were isolated. The soluble phosphorus content released by strains M2 and M8 was 265-277 mg L^-1, achieved by secreting oxalic acid, ascorbic acid, citric acid, and succinic acid in an inorganic phosphorus medium containing 3 mg L^-1 Cd and 5 mg L^-1 Pb. Furthermore, these two functional strains induced the formation of Pb₂(PO₄)₂, Cd(PO₃)₂, Fe₂Pb₃(PO₄)₂, CdS, and PbS precipitates that immobilized Cd and Pb in the solution. In general, strains M2 and M8 inhibited the absorption of Cd and Pb by radish by the following mechanisms: i) bacterial cell wall adsorption, ii) induction of Pb₂(PO₄)₂, Cd(PO₃)₂, Fe₂Pb₃(PO₄)₂, CdS, and PbS precipitation in the solution/soil, iii) increases in the Ca₂P and FeP contents in the radish rhizosphere, and iv) the promotion of bacterial community enrichment toward phosphorus-solubilizing and plant growth-promoting properties (Ramlibacter, Enterobacter, Bacillus, Gemmatimonas, and Lysinibacillusin) in the radish rhizosphere. These results provide bacterial resources and technical approaches to heavy metal pollution amelioration and efficient phosphorus fertilizer use in farmland.

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.