Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

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.

Rhizospheric crosstalk: A mechanistic overview of how plant secondary metabolites alleviate abiotic stresses

Plants often encounter incompatible growing conditions, such as drought, extreme temperatures, salinity, and heavy metals, which negatively impact their growth and development, resulting in reduced yield and, in severe cases, plant death. These stresses trigger the synthesis of plant secondary metabolites (PSMs), which help plants develop strategies to deter enemies, combat pathogens, outcompete competitors, and overcome environmental restraints. PSMs are released into the rhizosphere and play crucial roles in plant defense and communication. The multifunctionality of PSMs offers new insights into the plant intricate adaptive responses, which can refine our understanding of plant tolerance mechanisms in challenging environments. Thus, elucidating the chemical composition and functions of plant-derived specialized metabolites in the rhizosphere is the key to understanding interactions in this belowground environment. In this review, we aim to elucidate how PSMs exudation shapes the activities and abundance of the rhizosphere microbiome. We also highlight key environmental factors that regulate the structure and diversity of microbial communities. Finally, we discuss various preventive roles of PSMs, exploring how plants recruit microbes preemptively to mitigate diverse abiotic stresses. Additionally, we emphasize the significant contribution of phenolic compounds to the antioxidant defense response in plants, regulated through the shikimate pathway and is considered as a distinctive plant stress resilience component as compared to other PSMs under abiotic stress. Collectively, this study reveals the significance of understanding the multifaceted crosstalk between PSMs and the microbiome, which will facilitate the potential for developing methods to manipulate PSMs-microbiome interaction with predictive outcomes for sustainable crop production.

Insight into the composition and differentiation of endophytic microbial communities in kernels via 368 maize transcriptomes

INTRODUCTION

Kernels are important reproductive organs in maize, yet there is a lack of systematic investigation on the differences in the composition of endophytic microorganisms in plants from a population perspective.

OBJECTIVES

We aimed to elucidate the composition of endophytic microorganisms in developing maize kernels, emphasizing differences among various inbred lines.

METHODS

The transcriptomic data of 368 maize inbred lines were used to explore the composition and diversity of endophytic microorganisms.

RESULTS

The findings revealed a higher abundance of fungi than bacteria in developing maize kernels, followed by protozoa, while viruses were less abundant. There were significant differences in the composition and relative abundance of endophytic microorganisms among different maize lines. Diversity analysis revealed overall similarity in the community composition structure between tropical/subtropical (TST) and temperate (NSS) maize germplasm with apparent variations in community richness and abundance. The endophytic microorganisms network in the kernels from TST genotypes exhibited higher connectivity and stability compared to NSS kernels. Bacteria dominated the highly connected species in the networks, and different core species showed microbial phylum specificity. Some low-abundance species acted as core species, contributing to network stability. Beneficial bacteria were predominant in the core species of networks in TST kernels, while pathogenic bacteria were more abundant in the core species of networks in NSS kernels.

CONCLUSION

Tropical maize germplasm may have advantages in resisting the invasion of pathogenic microorganisms, providing excellent genetic resources for disease-resistant breeding.

Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns

Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of crop root microbiomes. By combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (68.9% from isolates) and 1,817 undefined species, expanding crop root bacterial diversity by 290.6%. The crop root viral genome collection (CRVC) contains 9,736 non-redundant viral genomes, with 1,572 previously unreported genus-level clusters in crop root microbiomes. From these, we identified conserved bacterial functions enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria-virus connections in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture.

Frateuria hangzhouensis sp. nov. Isolated from Soil of Moso Bamboo Forest in Hangzhou, China

A novel bacterium, designated STR12T, was isolated from the soil of a moso bamboo (Phyllostachys edulis) forest in Hangzhou, China. The strain was a Gram-stain-negative, rod-shaped, motile bacterium; the colonies of which were yellow, round, flat, sticky, and non-moist with a smooth margin after cultivation for 3 days at 28 °C. The strain grew at temperatures between 15 and 37 °C (optimum, 28 °C), pH values from 4.0 to 8.0 (optimum, pH 7.0), and salinities ranging from 0 to 5% (w/v) NaCl (optimum, 1%). Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the strain was grouped within a cluster of the genus Frateuria, showing the highest similarity with Frateuria flava MAH-13T (97.7%). The genome of strain STR12T was 3.74 Mb in length with a G+C content of 67.9%. Genome comparisons of strain STR12T with other species within the genus Frateuria revealed that the range of average nucleotide identity, DNA-DNA hybridization, and average amino acid identity values were 73.9-85.9%, 20.8-30.7%, and 62.7-86.7%, respectively, all of those were below the respective prokaryotic species delineation thresholds. The predominant quinone in strain STR12T was ubiquinone-8 and the major fatty acids were iso-C15:0, iso-C16:0, iso-C17:0, and Summed Feature 9. Polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, and one unidentified phosphoglycolipid. On basis of the finding of phylogenetic, physiological, and chemotaxonomic analyses, we proposed the name Frateuria hangzhouensis sp. nov. for the novel species in the genus Frateuria, of which the type strain was strain STR12T (= ACCC 61897T = GDMCC 1.2964T = JCM 35226T).

Endophytic Bacterial Communities Facilitate the Dissipation of Phthalates in Soil and Their Biodegradation in Oryza Sativa L

The role of endophytic bacterial communities in aiding the degradation of organic pollutants like phthalates (PAEs) in soil and in planta, as well as their effects on pollutant accumulation in plants, remains unclear. Herein, microcosm experiments were conducted with rice cultivated in agricultural soil polluted with di(2-ethylhexyl) phthalate (DEHP) and further verified with PAE-degrading endophytic consortia. Soil indigenous microbes, especially PAE-degrading bacteria, significantly contributed to DEHP dissipation in soil and diminished DEHP accumulation in rice. Endophytic bacterial communities participated in DEHP degradation in planta, as validated by efficient DEHP degradation by in vitro culturable endophytic consortia and abundant PAE-degrading genes. The inoculation of PAE-degrading endophytic consortia demonstrated their immigration between soil and roots (especially in low-PAE-accumulating cultivar), which enhanced DEHP degradation in soil and in planta and subsequently reduced rice PAE accumulation. This study underscores the facilitative role of endophytic bacterial communities in PAE degradation and in lowering PAE accumulation in crops.

Root microbiota regulates tiller number in rice

Rice tillering is an important agronomic trait regulated by plant genetic and environmental factors. However, the role and mechanism of the root microbiota in modulating rice tillering have not been explored. Here, we examined the root microbiota composition and tiller numbers of 182 genome-sequenced rice varieties grown under field conditions and uncovered a significant correlation between root microbiota composition and rice tiller number. Using cultivated bacterial isolates, we demonstrated that various members of the root microbiota can regulate rice tillering in both laboratory and field conditions. Genetic, biochemical, and structural analyses revealed that cyclo(Leu-Pro), produced by the tiller-inhibiting bacterium Exiguobacterium R2567, activates the rice strigolactone (SL) signaling pathway by binding to the SL receptor OsD14, thus regulating tillering. The present work provides insight into how the root microbiota regulates key agronomic traits and offers a promising strategy for optimizing crop growth by harnessing the root microbiota in sustainable agriculture.

DNA metabarcode analyses reveal similarities and differences in plant microbiomes of industrial hemp and medicinal Cannabis in China

Endophytic bacteria within plant tissues play crucial roles in plant health, stress tolerance, and contribute to the metabolite diversity of host plants. Cannabis sativa L. is an economically significant plant, with industrial hemp (IH) and medicinal Cannabis (MC) being the two main cultivars. However, the composition and functional traits of their endophytic bacterial communities in roots and leaves are not well understood. In this study, DNA metabarcode sequencing were employed to compare the bacterial communities between IH and MC. Significant differences were observed in the root and leaf niches. IH roots were enriched with stress-tolerant bacteria, while MC roots showed higher levels of biofilm-forming bacteria. In leaves, differences were even more pronounced, particularly in the abundance of Gram-negative bacteria, potential pathogens, stress-tolerant bacteria, and biofilm-forming bacteria. PICRUSt2 functional predictions revealed differences in nitrogen metabolism and secondary metabolite biosynthesis pathways in different cultivars and niches, while FAPROTAX analysis highlighted variations in carbon, nitrogen, and sulfur cycling functions. These findings underscore the distinct roles of bacterial communities in regulating plant health, stress responses, and metabolic processes in different niches and cultivars, providing insights for improving cultivation practices and plant resilience.

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.

Bacillus vallismortis acts against ginseng root rot by modifying the composition and microecological functions of ginseng root endophytes

Introduction

The endophytic microbiome serves a crucial function as a secondary line of defense against pathogen invasion in plants. This study aimed to clarify the mechanism of action of the ginseng plant growth-promoting rhizobacteria (PGPR) Bacillus vallismortis SZ-4 synergizing with endophytic microorganisms in the prevention and control of root rot.

Methods

Ginseng root samples from a susceptible group (CK) with a disease level of 0-2 and a biocontrol group (BIO) treated with strain SZ-4 were collected. We employed high-throughput sequencing to examine the microbial community structure of ginseng roots at different disease levels, explore beneficial endophytic bacteria, and evaluate the efficacy of strain SZ-4 in mitigating root rot through synergistic interactions with ginseng endophytic flora.

Results

The application of the PGPR B. vallismortis SZ-4 biocontrol fungicide has been found to help ginseng resist Fusarium solani by modulating the richness and structure of endophytic microbial populations. The endophytic bacteria HY-43 and HY-46 isolated from ginseng roots treated with B. vallismortis SZ-4 were identified as Bacillus velezensis based on morphological, physiological, and biochemical characteristics, as well as 16S rDNA and gyrB sequencing analyses. The endophytic bacteria HY-43 and HY-46 were combined with strain SZ-4 to generate the bacterial consortia CS4-43 and CS4-46, respectively. Both CS4-43 and CS4-46 significantly enhanced the inhibitory effects of the single strain SZ-4, as well as HY-43 and HY-46, against ginseng root rot, while also promoting plant growth.

Discussion

These findings offers a theoretical foundation for studying the microecological prevention and control of ginseng diseases as well as new insights for conducting research on the efficient and precise management of plant diseases.

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.

Improving Lunar Soil Simulant for Plant Cultivation: Earthworm-Mediated Organic Waste Integration and Plant-Microbe Interactions

Long-term human residence on the Moon is an inevitable trend in lunar exploration, necessitating the development of Bioregenerative Life Support Systems (BLSSs). In BLSSs, plant cultivation serves as the core functional unit, requiring substantial amounts of cultivation substrates. Lunar soil has potential as a cultivation substrate, but its suitability for plant growth must be improved to meet life-support requirements. As a fine-grained, organics-free, in situ resource, lunar soil's high compaction significantly restricts crops' root access to oxygen, water, and nutrients. While the addition of organic solid waste-a byproduct of BLSSs-could alleviate compaction, issues such as salinization, incomplete decomposition, and the presence of pathogens pose risks to crop health. In this study, we introduced earthworms into wheat cultivation systems to gradually digest, transfer (as vermicompost), and mix solid waste with a lunar soil simulant substrate. We set five experimental groups: a positive control group using vermiculite (named as V) as the optimal growth substrate, a negative control group using pure lunar soil simulant (LS), and three treatment groups using lunar soil simulant with solid waste and 15 (LS+15ew), 30 (LS+30ew), and 45 (LS+45ew) earthworms added. Our results demonstrated significant improvements in both compaction (e.g., bulk density, hydraulic conductivity) and salinization (e.g., salinity, electrical conductivity), likely due to the improved soil aggregate structures, which increased the porosity and ion adsorption capacity of the soil. Additionally, the microbial community within the substrate shifted toward a cooperative pattern dominated by significantly enriched plant probiotics. Consequently, the cultivated wheat achieved approximately 80% of the growth parameters (including production) compared to the control group grown in vermiculite with nutrient solution (representing ideal cultivation conditions), indicating sufficient nutrient supply from the mineralized waste. We can conclude that the earthworms "complementarily" improved the lunar soil simulant and organic waste by addressing compaction and salinization, respectively, leading to comprehensive improvements in key parameters, including the microbial environment. This study proposes a conceptual framework for improving lunar soil for crop cultivation, and it innovatively introduces earthworms as a preliminary yet effective solution. These findings provide a feasible and inspiring foundation for future lunar agriculture.

Uncovering the crucial metabolic pathways in the invasive plant Hydrocotyle verticillata for defence against copper exposure by integrative transcriptome and metabolome analysis

To throw light on the underlying strategies of Hydrocotyle verticillata coping with potentially toxic elements (PTEs) exposure. In this study, variations in the transcriptome and metabolomics of the leaves of plants exposed to various concentrations of copper ions (Cu2+) for 7 d were analyzed. Several crucial metabolic pathways involved in leaf defense against Cu2+ exposure were identified using integrative transcriptome and metabolome analysis. The pathways for plants coping with Cu2+ exposure were associated with carotenoid metabolism, amino acid metabolism, cutin, suberin, and wax biosynthesis, plant hormonal signal transduction, phenylpropanoid and terpenoid metabolisms. In the 90.0 μM Cu2+ treatment, abscisic acid 8'-hydroxylase was upregulated, reducing abscisic acid content, while downregulation of the BAK1 gene and pathogen-related protein genes triggered programmed cell death The positive role of antheraxanthin, γ-L-glutamylcysteine, γ-aminobutyric acid, and carnosine in the plant defense against 45.0 μM Cu2+ was observed. Lutein, 3,4-dihydrospheroidene, linoleic acid, glutamine, pyroglutamic acid, the gene encoding brassinosteroid resistant 1/2, and xyloglucan:xyloglucosyl transferase are involved in plant defense against 90.0 μM Cu2+. Compared to 0 mM, both Cu2+ treatments upregulated hexadecanedioic acid abundance and the gene encoding the auxin response protein. This study provides new insights into the underlying mechanisms through which invasive plants defend against PTE exposure.

Exploring the plant microbiome: A pathway to climate-smart crops

The advent of semi-dwarf crop varieties and fertilizers during the Green Revolution boosted yields and food security. However, unintended consequences such as environmental pollution and greenhouse gas emissions underscore the need for strategies to mitigate these impacts. Manipulating rhizosphere microbiomes, an aspect overlooked during crop domestication, offers a pathway for sustainable agriculture. We propose that modulating plant microbiomes can help establish "climate-smart crops" that improve yield and reduce negative impacts on the environment. Our proposed framework integrates plant genotype, root exudates, and microbes to optimize nutrient cycling, improve stress resilience, and expedite carbon sequestration. Integrating unselected ecological traits into crop breeding can promote agricultural sustainability, illuminating the nexus between plant genetics and ecosystem functioning.

The rhizosphere of Phaseolus vulgaris L. cultivars hosts a similar bacterial community in local agricultural soils

This study aimed to investigate the impact of various common beans (Phaseolus vulgaris L.) cultivars on the bacterial communities in the rhizosphere under local agricultural conditions. Even though the differences in cultivation history and physicochemical properties of nearby agriculture plots, the bacterial community in the bulk soil was quite similar and more diverse than that of the rhizosphere. The bacterial community of the rhizosphere was closely similar between Black and Bayo common bean cultivars but differs from Pinto Saltillo common beans collected in a different season. A shared bacterial group within the rhizosphere community across cultivars and specific taxa responding uniquely to each cultivar suggests a balance between responses to soil and plant cultivars. Nevertheless, rhizosphere composition was substantially influenced by the pre-existing soil bacterial community, whose diversity remained consistently similar under the studied field conditions. These findings provide a more comprehensive characterization of the rhizosphere across a limited range of domesticated common beans and agronomic soils that can be expanded to more common bean cultivars and soils to guide appropriate field interventions.

Root exudates and microbial metabolites: signals and nutrients in plant-microbe interactions

Plant roots meticulously select and attract particular microbial taxa from the surrounding bulk soil, thereby establishing a specialized and functionally diverse microbial community within the rhizosphere. Rhizosphere metabolites, including root exudates and microbial metabolites, function as both signals and nutrients that govern the assembly of the rhizosphere microbiome, playing crucial roles in mediating communications between plants and microbes. The environment and their feedback loops further influence these intricate interactions. However, whether and how specific metabolites shape plant-microbe interactions and facilitate diverse functions remains obscure. This review summarizes the current progress in plant-microbe communications mediated by chemical compounds and their functions in plant fitness and ecosystem functioning. Additionally, we raise some prospects on future directions for manipulating metabolite-mediated plant-microbe interactions to enhance crop productivity and health. Unveiling the biological roles of specific metabolites produced by plants and microbes will bridge the gap between fundamental research and practical applications.

Diversity and composition of soil microbial communities in the rhizospheres of late blight-resistant tomatoes after Phytophthora infestans inoculation

Late blight caused by the oomycete Phytophthora infestans poses a severe threat to global tomato (Solanum lycopersicum L.) production. While genetic resistance forms the cornerstone of disease control, the mechanisms underlying cultivar-specific resistance, particularly their interactions with rhizosphere microbiomes, remain poorly understood. To elucidate the mechanisms of tomato cultivar resistance to late blight and screen out antagonistic microorganisms against P. infestans, we investigated the microbial compositions in the rhizospheres of tomato cultivars with different late blight-resistance levels under both natural and P. infestans-inoculated conditions. Considerable differences in soil microbial diversity and composition of rhizospheres were found between late blight-resistant and -susceptible tomato cultivars. Under natural conditions, the resistant tomato cultivar exhibited higher bacterial diversity and lower fungal diversity than that of the susceptible cultivar. Additionally, after P. infestans inoculation, both the resistant and susceptible cultivars showed enrichment of microorganisms with potential antagonistic effects in the rhizospheres. Among them, bacterial genera, such as Pseudomonas, Azospirillum, and Acidovorax, and fungal genera, including Phoma, Arthrobotrys, Pseudallescheria, and Pseudolabrys, were enriched in the rhizospheres of the late blight-resistant tomato cultivar. In contrast, bacterial genera, including Flavobacterium, Pseudolabrys, and Burkholderia-Caballeronia-Paraburkholderia, and the Trichoderma fungal genus were enriched in the rhizospheres of the late blight-susceptible tomato cultivar. Simultaneously, the enrichment of pathogenic microorganisms, such as Neocosmospora and Plectosphaerella, was also detected in the rhizospheres of the susceptible tomato cultivar. Moreover, no enrichment of pathogenic microorganisms occurred in the late blight-resistant tomato cultivar after P. infestans inoculation. These findings suggest that these traits serve as effective defense mechanisms against pathogen invasion in resistant tomato cultivar. Overall, this study provides a comprehensive analysis of the rhizosphere microbial community structures in late blight-resistant and -susceptible tomato cultivars under natural conditions and their response following pathogen inoculation. Additionally, potential antagonistic microorganisms against late blight were also identified. The findings offer valuable insights for effective late blight management in tomatoes and contribute to the development of sustainable agricultural practices.

Conserved immunomodulation and variation in host association by Xanthomonadales commensals in Arabidopsis root microbiota

Suppression of chronic Arabidopsis immune responses is a widespread but typically strain-specific trait across the major bacterial lineages of the plant microbiota. We show by phylogenetic analysis and in planta associations with representative strains that immunomodulation is a highly conserved, ancestral trait across Xanthomonadales, and preceded specialization of some of these bacteria as host-adapted pathogens. Rhodanobacter R179 activates immune responses, yet root transcriptomics suggest this commensal evades host immune perception upon prolonged association. R179 camouflage likely results from combined activities of two transporter complexes (dssAB) and the selective elimination of immunogenic peptides derived from all partners. The ability of R179 to mask itself and other commensals from the plant immune system is consistent with a convergence of distinct root transcriptomes triggered by immunosuppressive or non-suppressive synthetic microbiota upon R179 co-inoculation. Immunomodulation through dssAB provided R179 with a competitive advantage in synthetic communities in the root compartment. We propose that extensive immunomodulation by Xanthomonadales is related to their adaptation to terrestrial habitats and might have contributed to variation in strain-specific root association, which together accounts for their prominent role in plant microbiota establishment.

From glycans to green biotechnology: exploring cell wall dynamics and phytobiota impact in plant glycopathology

Filamentous plant pathogens, including fungi and oomycetes, pose significant threats to cultivated crops, impacting agricultural productivity, quality and sustainability. Traditionally, disease control heavily relied on fungicides, but concerns about their negative impacts motivated stakeholders and government agencies to seek alternative solutions. Biocontrol agents (BCAs) have been developed as promising alternatives to minimize fungicide use. However, BCAs often exhibit inconsistent performances, undermining their efficacy as plant protection alternatives. The eukaryotic cell wall of plants and filamentous pathogens contributes significantly to their interaction with the environment and competitors. This highly adaptable and modular carbohydrate armor serves as the primary interface for communication, and the intricate interplay within this compartment is often mediated by carbohydrate-active enzymes (CAZymes) responsible for cell wall degradation and remodeling. These processes play a crucial role in the pathogenesis of plant diseases and contribute significantly to establishing both beneficial and detrimental microbiota. This review explores the interplay between cell wall dynamics and glycan interactions in the phytobiome scenario, providing holistic insights for efficiently exploiting microbial traits potentially involved in plant disease mitigation. Within this framework, the incorporation of glycobiology-related functional traits into the resident phytobiome can significantly enhance the plant's resilience to biotic stresses. Therefore, in the rational engineering of future beneficial consortia, it is imperative to recognize and leverage the understanding of cell wall interactions and the role of the glycome as an essential tool for the effective management of plant diseases.

Microbiome Analysis of Area in Proximity to White Spot Lesions Reveals More Harmful Plant Pathogens in Maize

Plant microbiomes play a major role in plant health, growth, and development, enhancing resistance to pathogen invasion. However, despite the extensive research on the phyllosphere microbiome, it remains unclear how the microbiome of leaves in proximity to diseased leaves responds to pathogen invasion. We investigate the response of the maize phyllosphere microbiome to maize white spot by assessing the microbiome dynamics associated with the white spot portion and the area in proximity using 16S and ITS high-throughput sequencing analysis. Our results showed that the bacterial diversities were higher in the diseased portion and area in proximity to the spot than those in healthy plants. At the same time, lower fungal diversity was recorded in the diseased portion compared to portions in proximity to it and healthy leaves. The spot portion had a significant influence on the microbial composition. The diseased portion, the area in proximity to it, and the healthy leaves were dominated by the bacterial genera Sphingomonas, Delftia, Chryseobacterium, Stenotrophomonas, Methylobacterium-methylorubrum, and Bacteroides. Still, the abundance of Sphingomonas decreased in the healthy leaves with a corresponding increase in Stenotrophomonas. Conversely, the fungal genus Setophoma dominated the diseased portion, while the fungal pathogens Cladosporium, Alternaria, and Exserohilum were highly abundant in the samples from the area in proximity to it. In addition, a co-occurrence network analysis revealed a complex fungal network in healthy leaves and those in proximity to leaves infected with white spot compared to the diseased portion. This study suggests that the area in proximity to the maize leaf infected with white spot disease is colonized by more harmful plant pathogenic fungi for disease progression.

Maize2035: A decadal vision for intelligent maize breeding

Maize, a cornerstone of global food security, has undergone remarkable transformations through breeding, yet further increase in global maize production faces mounting challenges in a changing world. In this Perspective paper, we overview the historical successes of maize breeding that laid the foundation for present opportunities. We examine both the specific and shared breeding goals related to diverse geographies and end-use demands. Achieving these coordinated breeding objectives requires a holistic approach to trait improvement for sustainable agriculture. We discuss cutting-edge solutions, including multi-omics approaches from single-cell analysis to holobionts, smart breeding with advanced technologies and algorithms, and the transformative potential of rational design with synthetic biology approaches. A transition toward a data-driven future is currently underway, with large-scale precision agriculture and autonomous systems poised to revolutionize farming practice. Realizing these futuristic opportunities hinges on collaborative efforts spanning scientific discoveries, technology translations, and socioeconomic considerations in maximizing human and environmental well-being.

Whole genome sequencing of Penicillium and Burkholderia strains antagonistic to the causal agent of kauri dieback disease (Phytophthora agathidicida) reveals biosynthetic gene clusters related to antimicrobial secondary metabolites

Phytophthora agathidicida is a virulent soil pathogen of Aotearoa New Zealand's iconic kauri tree species (Agathis australis (D. Don) Lindl.) and the primary causal agent of kauri dieback disease. To date, only a few control options are available to treat infected kauri that are expressing symptoms of dieback disease. Previous research has identified strains of Penicillium and Burkholderia that inhibited the mycelial growth of P. agathidicida in vitro. However, the mechanisms of inhibition remain unknown. By performing whole genome sequencing, we screened the genomes of four Penicillium and five Burkholderia strains to identify secondary metabolite encoding biosynthetic gene clusters (SM-BGCs) that may be implicated in the production of antimicrobial compounds. We identified various types of SM-BGCs in the genome of each strain, including polyketide synthases (PKSs), non-ribosomal peptide synthetases (NRPSs), and terpenes. Across all four of the Penicillium strains, five SM-BGCs were detected that encoded the biosynthesis of napthopyrone, clavaric acid, pyranonigrin E, dimethyl coprogen and asperlactone. Across all five of the Burkholderia strains, three SM-BGCs were detected that encoded the biosynthesis of ornibactin, pyochelin and pyrrolnitin. Our analysis detected numerous SM-BGCs which could not be characterised. Further efforts should be made to identify the compounds encoded by these SM-BGCs so that we can explore their antimicrobial potential. The potential inhibitory effects of the compounds encoded by the SM-BGCs identified in this study may be worthy of further investigation for their effect on the growth and virulence of P. agathidicida.

Seed microbiomes promote Astragalus mongholicus seed germination through pathogen suppression and cellulose degradation

BACKGROUND

Seed-associated microorganisms play crucial roles in maintaining plant health by providing nutrients and resistance to biotic and abiotic stresses. However, their functions in seed germination and disease resistance remain poorly understood. In this study, we investigated the microbial community assembly features and functional profiles of the spermosphere and endosphere microbiomes related to germinated and ungerminated seeds of Astragalus mongholicus by using amplicon and shotgun metagenome sequencing techniques. Additionally, we aimed to elucidate the relationship between beneficial microorganisms and seed germination through both in vitro and in vivo pot experiments.

RESULTS

Our findings revealed that germination significantly enhances the diversity of microbial communities associated with seeds. This increase in diversity is driven through environmental ecological niche differentiation, leading to the enrichment of potentially beneficial probiotic bacteria such as Pseudomonas and Pantoea. Conversely, Fusarium was consistently enriched in ungerminated seeds. The co-occurrence network patterns revealed that the microbial communities within germinated and ungerminated seeds presented distinct structures. Notably, germinated seeds exhibit more complex and interconnected networks, particularly for bacterial communities and their interactions with fungi. Metagenome analysis showed that germinated seed spermosphere soil had more functions related to pathogen inhibition and cellulose degradation. Through a combination of culture-dependent and germination experiments, we identified Fusarium solani as the pathogen. Consistent with the metagenome analysis, germination experiments further demonstrated that bacteria associated with pathogen inhibition and cellulose degradation could promote seed germination and vigor. Specifically, Paenibacillus sp. significantly enhanced A. mongholicus seed germination and plant growth.

CONCLUSIONS

Our study revealed the dynamics of seed-associated microorganisms during seed germination and confirmed their ecological role in promoting A. mongholicus seed germination by suppressing pathogens and degrading cellulose. This study offers a mechanistic understanding of how seed microorganisms facilitate successful seed germination, highlighting the potential for leveraging these microbial communities to increase plant health. Video Abstract.

Alternaria alternata JTF001 Metabolites Recruit Beneficial Microorganisms to Reduce the Parasitism of Orobanche aegyptiaca in Tomato

Orobanche aegyptiaca is a holoparasitic weed that extracts water, nutrients, and growth regulators from host plants, leading to significant yield and quality losses. Biocontrol microbial metabolites have been shown to enhance plant resistance against parasitic plants, yet the underlying microbial mechanisms remain poorly understood. In this study, we investigated the role of Alternaria alternata JTF001 (J1) microbial metabolites in recruiting beneficial microbes to the tomato rhizosphere and promoting the establishment of a disease-suppressive microbiome. Pot experiments revealed that J1 metabolite application significantly reduced O. aegyptiaca parasitism. High-throughput sequencing of full-length 16S rRNA genes and ITS regions, along with in vitro culture assays, demonstrated an increase in the abundance of plant-beneficial bacteria, particularly Pseudomonas spp. The three candidate beneficial strains (zOTU_388, zOTU_533, and zOTU_2335) showed an increase of 5.7-fold, 5.4-fold, and 4.7-fold, respectively. These results indicate that J1 metabolites induce the recruitment of a disease-suppressive microbiome in tomato seedlings, effectively inhibiting O. aegyptiaca parasitism. Our findings suggest that microbial metabolites represent a promising strategy for managing parasitic plant infestations through microbial community modulation, offering significant implications for sustainable agricultural practices.

Host Metabolic Alterations Mediate Phyllosphere Microbes Defense upon Xanthomonas oryzae pv oryzae Infection

Rice bacterial leaf blight, caused by Xanthomonas oryzae pv oryzae (Xoo), is a significant threat to global food security. Although the microbiome plays an important role in protecting plant health, how the phyllosphere microbiome is recruited and the underlying disease resistance mechanism remain unclear. This study investigates how rice phyllosphere microbiomes respond to pathogen invasion through a comprehensive multiomics approach, exploring the mechanisms of microbial defense and host resistance. We discovered that Xoo infection significantly reshapes the physicosphere microbial community. The bacterial network became more complex, with increased connectivity and interactions following infection. Metabolite profiling revealed that l-ornithine was a key compound to recruiting three keystone microbes, Brevundimonas (YB12), Pantoea (YN26), and Stenotrophomonas (YN10). These microbes reduced the disease index by up to 67.6%, and these microbes demonstrated distinct defense mechanisms. Brevundimonas directly antagonized Xoo by disrupting cell membrane structures, while Pantoea and Stenotrophomonas enhanced plant immune responses by significantly increasing salicylic acid and jasmonic acid levels and activating defense-related enzymes. Our findings provide novel insights into plant-microbe interactions, demonstrating how host metabolic changes recruit and activate beneficial phyllosphere microbes to combat pathogenic invasion. This research offers promising strategies for sustainable agricultural practices and disease management.

Two rice cultivars recruit different rhizospheric bacteria to promote aboveground regrowth after mechanical defoliation

Plants have evolved the ability to regrow after mechanical defoliation and environmental stresses. However, it is unclear whether and how defoliated plants exploit beneficial microbiota from the soil to promote aboveground regrowth. Here, we compared the defoliation-triggered changes in the root exudation and bacterial microbiome of two rice cultivars (Oryza sativa L ssp.), indica/xian cultivar Minghui63 and japonica/geng cultivar Nipponbare. The results show that reciprocal growth promotion existed between defoliated Minghui63 seedlings and soil bacteria. After the leaves were removed, the Minghui63 seedlings displayed approximately 1.5- and 2.1-fold higher root exudation and leaf regrowth rates, respectively, than did the Nipponbare seedlings. In field trials, Minghui63 and Nipponbare enriched taxonomically and functionally distinct bacteria in the rhizosphere and root. In particular, Minghui63 rhizosphere and root communities depleted bacteria whose functions are related to xenobiotics biodegradation and metabolism. The microbiome data implied that the bacterial family Rhodocyclaceae was specifically enriched during the regrowth of defoliated Minghui63 rice. We further isolated a Rhodocyclaceae strain, Uliginosibacterium gangwonense MDD1, from rice root. Compared with germ-free conditions, MDD1 inoculation promoted the aboveground regrowth of defoliated Minghui63 by 61% but had a weaker effect on Nipponbare plants, suggesting cultivar-specific associations between regrowth-promoting bacteria and rice. This study provides novel insight into microbiota‒root‒shoot communication, which is implicated in the belowground microbiome and aboveground regrowth in defoliated rice. These data will be helpful for microbiome engineering to increase rice resilience to defoliation and environmental stresses.IMPORTANCEAs sessile organisms, plants face a multitude of abiotic and biotic stresses which often result in defoliation. To survive, plants have evolved the ability to regrow leaves after stresses and wounding. Previous studies revealed that the rhizosphere microbiome affected plant growth and stress resilience; however, how belowground microbiota modulates the aboveground shoot regrowth is unclear. To address this question, we used rice, an important crop worldwide, to analyze the role of rhizosphere microbiota in leaf regrowth after defoliation. Our data indicate mutual growth promotion between defoliated rice and rhizosphere bacteria and such beneficial effect is cultivar specific. The microbiome analysis also led us to find a Uliginosibacterium gangwonense strain that promoted rice cv. MH63 leaf regrowth. Our findings therefore present a novel insight into plant-microbiome function and provide beneficial strains that potentially enhance rice stress resilience.

Metabolism of hemicelluloses by root-associated Bacteroidota species

Bacteroidota species are enriched in the plant microbiome and provide several beneficial functions for their host, including disease suppression. Determining the mechanisms that enable bacteroidota to colonise plant roots may therefore provide opportunities for enhancing crop production through microbiome engineering. By focusing on nutrient acquisition mechanisms, we discovered Bacteroidota species lack high affinity ATP-binding cassette transporters common in other plant-associated bacteria for capturing simple carbon exudates. Instead, bacteroidota possess TonB-dependent transporters predicted to import glycans produced by plant polysaccharide breakdown. Metatranscriptomics (oat rhizosphere) identified several TonB-dependent transporters genes that were highly expressed in Flavobacterium (phylum Bacteroidota). Using Flavobacterium johnsoniae as the model, we experimentally validated the function of one highly expressed TonB-dependent transporter, identifying a conserved Xyloglucan utilisation loci conferring the ability to import and degrade xyloglucan, the major hemicellulose secreted from plant roots. Xyloglucan utilisation loci harbour an endoxyloglucanase related to family 5 subfamily 4 subclade 2D glycoside hydrolases carrying a mutation that we demonstrate is required for full activity towards xyloglucan. Based on analysing 700 soil metagenomes, subclade 2D glycoside hydrolases have radiated in soil and are prevalent among plant-associated bacteroidota and certain taxa affiliated with Gammaproteobacteria. In bacteroidota, particularly Flavobacterium species, xyloglucan utilisation loci organisation was highly conserved, which may increase their competitive ability to utilise xyloglucan. Given bacteroidota lack high-affinity nutrient transporters for simple carbon, instead possessing xyloglucan utilisation loci and similar gene clusters, our data suggests hemicellulose exudates provide them with an important carbon source in the rhizosphere.

Identification of stress-alleviating strains from the core drought-responsive microbiome of Arabidopsis ecotypes

Plant genetic and metabolic cues are involved in assembling their "core microbiome" under normal growth conditions. However, whether there is a core "stress responsive microbiome" among natural plant ecotypes remains elusive. Drought is the most significant abiotic stress worldwide. Characterizing conserved core root microbiome changes upon drought stress has the potential to increase plant resistance and resilience in agriculture. We screened the drought tolerance of 130 worldwide Arabidopsis ecotypes and chose the extremely drought tolerant and sensitive ecotypes for comparative microbiome studies. We detected diverse shared differentially abundant ASVs, network driver taxa among ecotypes, suggesting the existence of core drought-responsive microbiome changes. We previously identified 1479 microorganisms through high-throughput culturing, and successfully matched diverse core drought responsive ASVs. Our phenotypic assays validated that only those core drought responsive ASVs with higher fold changes in drought tolerant ecotypes were more likely to protect plants from stress. Transcriptome analysis confirmed that a keystone strain, Massilia sp. 22G3, can broadly reshape osmotic stress responses in roots, such as enhancing the expression of water up-taking, ROS scavenging, and immune genes. Our work reveals the existence of a core drought-responsive microbiome and demonstrates its potential role in enhancing plant stress tolerance. This approach helps characterize keystone "core drought responsive" microbes, and we further provided potential mechanisms underlying Massilia sp. 22G3 mediated stress protection. This work also provided a research paradigm for guiding the discovery of core stress-alleviating microbiomes in crops using natural ecotypes (cultivars).

Effect of pathogen Globisporangium ultimum on plant growth and colonizing bacterial communities

Plants recruit plant-associated microbes from soil to enhance their growth and mitigate the adverse effects of pathogen invasion on plant health. How pathogens impact the interactions of the plant-associated microbes and plant growth is poorly understood. We established S-microsystems (sterile soil inoculated with 101 bacteria isolated from humus soil with Artemisia annua, Oryza sativa or Houttuynia cordata), and N-microsystems (natural soil with these plants) to evaluate the effects of the fungus Globisporangium ultimum on plant growth and their colonizing bacterial communities (CBCs). S-microsystems and N-microsystems were inoculated with and without G. ultimum, respectively. Their seedling growth and CBCs were investigated. Plant height and root numbers in A. annua, O. sativa and H. cordata S-microsystems with G. ultimum were 34.5 % and 52.8 %, 23.1 % and 31.3 %, 102.1 % and 45.0 % higher than those without G. ultimum, respectively. The CBCs were diverse among S-microsystems of A. annua, O. sativa and H. cordata, and the CBC abundances in the three S-microsystems without G. ultimum were higher than those with G. ultimum. The relative abundances of bacterial genera Rhizobium, Pseudomonas, Brevundimonas and Cupriavidus were significantly positively related to plant growth. We determined that the CBCs in A. annua, O. sativa and H. cordata were selective and related to the plant species, and can mitigate disadvantageous influences of G. ultimum on seedling growth. The plants and their CBCs' abundance and composition were differentially affected by G. ultimum. Our results provide evidence that CBCs promote plant growth due to dynamic changes in the composition and abundance of CBC members, which were affected by plant species and biotic factors.

Two new strains of Streptomyces with metabolic potential for biological control of pear black spot disease

BACKGROUND

Pear black spot is caused by Alternaria tenuissima. It is one of the diseases of concern limiting pear production worldwide. Existing cultivation methods and fungicides are not sufficient to control early blight. Therefore, the aim of this study was to isolate and characterize two strains of Streptomyces and evaluate their potential for biological control of crop diseases caused by Alternaria tenuissima while promoting plant growth. It enriches the resources of biocontrol strains.

METHODS

In this study, the genetic background of the strain was elucidated through 16S rRNA gene analysis and multiphase taxonomic identification methods. The metabolic potential of the strain was assessed using a variety of approaches, including antiSMASH, COG, and KEGG databases, RGI tools, as well as the scanning of CAZY and plant-promoting genes. The biocontrol potential of the strain was further substantiated through a combination of plate experiments, gene cluster biopathway resolution and mass spectrometry validation of metabolites. Finally, the biocontrol efficacy of the strain was confirmed through fruit control experiments.

RESULTS

The study identified the potential new species status of the strains. Strain TRM 76130 exhibited a gene size of 5.94 Mbp and a G + C content of 73.65%, while strain TRM 76172 had a gene size of 8.30 Mbp and a G + C content of 71.38%. Both strains contained genes related to amino acid transport and metabolism, along with several CAZY genes and 19 plant growth factors. The resistance genes of strain TRM 76172 were classified as macrolides, and genomic prediction revealed the biosynthetic pathway of the active compound Candidin. Mass spectrometry analysis indicated that strains TRM 76172 and TRM 76130 contained the active compounds amphotericin A and daptomycin, respectively. The pear assays demonstrated that both strains of Streptomyces were capable of reducing the symptoms of pear black spot.

CONCLUSION

The present study concludes that strains TRM76172 and TRM76130 possess significant potential to control Alternaria tenuissima and promote plant growth, thereby enriching the biocontrol fungal library.

Industrial hemp (Cannabis sativa L.) adapts to cadmium stress by reshaping rhizosphere fungal community

Increasing evidence indicates that plants under environmental stress can actively seek the help of microbes ('cry-for-help' hypothesis). However, empirical evidence underlying this strategy is limited under metal-stress conditions. Here, we employed integrated microbial community profiling in cadmium (Cd) polluted soil and culture-based methods to investigate the three-way interactions between the industrial hemp (Cannabis Sativa L.), rhizospheric microbes, and Cd stress. Results from the pot and three cycles of the successful hemp planting experiments showed that Cd stress significantly affected the composition of rhizosphere fungi in industrial hemp and induced enrichment of the fungal operational taxonomic unit (OTU)3 (Cladosporium). A representative of OTU3 (strain DM-2) was successfully isolated. In a hydroponic experiment, inoculation of DM-2 significantly increased the shoot length (by 25.84 %) and fresh weight (by 92.66 %) of hemp seedlings when compared to the absence of DM-2 under the Cd stress. The findings indicate that DM-2 inoculation could effectively alleviate the Cd stress in hemp seedlings. Metabolomic analysis of spent media with or without DM-2 revealed the association of DM-2 with the transformation of root exudates to melatonin, which may be a key chemical in plant-microbe interactions against abiotic stresses. The findings will inform efforts to manipulate the root microbiome to enhance plant growth in polluted environments.

Dynamic interaction of antibiotic resistance between plant microbiome and organic fertilizers: sources, dissemination, and health risks

Antibiotic resistance is a global health problem driven by the irrational use of antibiotics in different areas (such as agriculture, animal farming, and human healthcare). Sub-lethal concentrations of antibiotic residues impose selective pressure on environmental, plant-associated, and human microbiome leading to the emergence of antibiotic-resistant bacteria (ARB). This review summarizes all sources of antibiotic resistance in agricultural soils (including manure, sewage sludge, wastewater, hospitals/pharmaceutical industry, and bioinoculants). The factors (such as the physicochemical properties of soil, root exudates, concentration of antibiotic exposure, and heavy metals) that facilitate the transmission of resistance in plant microbiomes are discussed. Potential solutions for effective measures and control of antibiotic resistance in the environment are also hypothesized. Manure exhibits the highest antibiotics load, followed by hospital and municipal WW. Chlortetracycline, tetracycline, and sulfadiazine have the highest concentrations in the manure. Antibiotic resistance from organic fertilizers is transmitted to the plant microbiome via horizontal gene transfer (HGT). Plant microbiomes serve as transmission routes of ARB and ARGS to humans. The ingestion of ARB leads to human health risks (such as ineffectiveness of medication, increased morbidity, and mortality).

Enhancing the phytoextraction capacity of chromium-contaminated soil by co-addition of garbage enzymes and microelectrolytic iron-carbon fillers

Most improved strategies for phytoextraction do not achieve a synergistic enhancement of chromium (Cr) accumulation capacity and biomass. This study investigated the impacts of co-addition of garbage enzyme (GE) and microelectrolytic iron-carbon filler (MF) on soil physicochemical properties, as well as form and uptake of Cr during aging and phytoextraction process. The response of rhizosphere microbial community to co-addition and its role in enhancing the remediation performance of ryegrass was further analyzed. Co-addition of GE and MF during the 12-day aging process resulted in an increase of nutrients, a shift from an oxidising to a reducing soil environment, a decrease of Cr(VI) content, and an enhancement of soil microbial community diversity and richness, creating a suitable environment for subsequent phytoextraction. During the 40-day phytoextraction process, co-addition played a crucial role in facilitating the establishment of a complex, efficient and interdependent ecological network among soil microorganisms and contributed to the evolution of microbial community composition and functional pathways. An increase in the relative abundance of Trichococcus, Azospirillum and g_norank_f_JG30-KF-CM45 elevated soil nutrient levels, while a decrease in the relative abundance of TM7a and Brucella reduced pathogen harbouring. Meanwhile, co-addition increased the relative abundance of Bacillus, Arthrobacter and Exiguobacterium, attenuated Cr phytotoxicity and improved soil biochemical activity. These markedly diminished oxidative damage and improved ryegrass growth by reducing malondialdehyde accumulation. In addition, regular additions of GE and the increase in relative abundance of norank_fnorank_o_Microtrichales led to rhizosphere acidification, which inhibited short-term Cr immobilization and contributed to a notable increase in phytoextraction efficiency. This study presents a strategy to enhance phytoremediation efficiency and soil quality during phytoextraction of Cr-contaminated soils.

Root, Nodule and Soil Bacterial Communities Associated With the Invasive Nitrogen-Fixing Lupinus polyphyllus

Plants host microorganisms that can facilitate their success in becoming invasive. Established plant invasions might thus provide useful insights into potential changes in plant-associated microbiomes over the course of the invasion process. Here, we investigated the endophytic bacterial communities of the invasive herbaceous legume Lupinus polyphyllus, which is able to form mutualistic associations with N-fixing bacteria. More specifically, we examined the alpha diversity (observed bacterial taxa richness and Shannon diversity) and composition of bacterial communities in roots and nodules sampled from core and edge locations within 10 established invasion sites (> 10 years old) in southwestern Finland. Moreover, we compared the alpha diversity and structure of bacterial communities in the rhizosphere and bulk soil between core and edge locations within these invasion sites. We found that roots and nodules had distinctive endophytic bacterial communities, with roots having 24% higher bacterial alpha diversity (Shannon diversity) than nodules. In nodules, the dominant bacteria were assigned to the family Bradyrhizobiaceae, which includes N-fixing bacteria. Soil bacterial communities, instead, were shaped by soil type, with bulk soil hosting up to 27% higher alpha diversity (richness and Shannon diversity) than rhizosphere soil; however, there was no apparent difference in their community composition. Soil bacterial communities were only weakly associated with soil chemistry. Endophytic and soil bacterial communities did not differ between core and edge locations within the established invasions. Our findings suggest that L. polyphyllus may not induce dramatic changes in the bacterial communities with which it associates over the course of the local invasion process.

Phytoremediation of trichloroethylene in the soil/groundwater environment: Progress, problems, and potential

Trichloroethylene (TCE) poses a significant environmental threat in groundwater and soil, necessitating effective remediation strategies. Phytoremediation offers a cost-effective and environmentally friendly approach to remediation. However, the mechanisms governing plant uptake, volatilisation, and degradation of TCE remain poorly understood. This review explores the mechanisms of TCE phytoremediation, metabolic pathways, and influencing factors, emphasizing future research directions to improve the understanding of TCE phytoremediation. The results showed that although the proportion of TCE phytovolatilisation is limited, it is important at sites chronically contaminated with TCE. The rhizosphere is a key microzone for pollutant redox reactions that significantly enhance its effectiveness when its characteristics are fully utilised and manipulated through reinforcement. Future research should focus on manipulating microbial communities through methods such as the application of endophytic bacteria and genetic modification. However, practical applications are in their infancy and further investigation is needed. Furthermore, many findings are based on non-uniform parameters or unstandardised methods, making them difficult to compare. Therefore, future studies should provide more standardised experimental parameters and employ accurate and standardised methods to develop suitable prediction models, enhancing data comparability and deepening our understanding of plant detoxification mechanisms.

Melatonin alleviates apple replant disease by regulating the endophytic microbiome of roots and phloridzin accumulation

Melatonin administration is an environmentally effective strategy to mitigate apple replant disease (ARD), but its mechanism of action is unknown. This study investigated the protective effect of melatonin on ARD and the underlying mechanism. In field experiments, melatonin significantly reduced phloridzin levels in apple roots and rhizosphere soil. A correlation analysis indicated that a potential antagonistic interaction between melatonin and phloridzin was crucial for improving soil physicochemical properties, increasing the diversity of endophytic bacterial communities in roots of apple seedlings, and promoting mineral element absorption by the plants. Melatonin also reduced the abundance of Fusarium in roots. The ability of melatonin to reduce phloridzin levels both in soil and in plants was also demonstrated in a pot experiment. Azovibrio were specifically recruited in response to melatonin and their abundance was negatively correlated with phloridzin levels. Fusarium species that have a negative impact on plant growth were also inhibited by melatonin. Our results show that melatonin improves the rhizosphere environment as well as the structure of the endophytic microbiota community, by reducing phloridzin levels in rhizosphere soil and roots. These regulatory effects of melatonin support its use to improve the physiological state of plants under ARD conditions and thereby overcome the barriers of perennial cropping systems.

Microbiome diversity and variations in industrial hemp genotypes

Microbes like bacteria and fungi are crucial for host plant growth and development. However, environmental factors and host genotypes can influence microbiome composition and diversity in plants such as industrial hemp (Cannabis sativa L.). Herein, we evaluated the endophytic and rhizosphere microbial communities of two cannabidiol (CBD; Sweet Sensi and Cherry Wine) and two fibers (American Victory and Unknown). The four hemp varieties showed significant variations in microbiome diversity. The roots had significantly abundant fungal and bacterial endophyte diversity indices, whereas the stem had higher fungal than bacterial diversity. Interestingly, the soil system showed no significant diversity variation across CBD vs. fiber genotypes. In fungal phyla, Ascomycota and Basidiomycota were significantly more abundant in roots and stems than leaves in CBD-rich genotypes compared to fiber-rich genotypes. The highly abundant bacterial phyla were Proteobacteria, Acidobacteria, and Actinobacteria. We found 16 and 11 core-microbiome bacterial and fungal species across genotypes. Sphingomonas, Pseudomonas, and Bacillus were the core bacteria of fiber genotypes with high abundance compared to CBD genotypes. Contrarily, Microbacterium, and Rhizobium were significantly higher in CBD than fiber. The Alternaria and Gibberella formed a core-fungal microbiome of fiber-genotype than CBD. Contrarily, Penicillium, and Nigrospora were significantly more abundant in CBD than fiber genotypes. In conclusion, specific hemp genotypes recruit specialized microbial communities in the rhizosphere and phyllosphere. Utilizing the core-microbiome species can help to maintain and improve the growth of hemp plants and to target specialized traits of the genotype.

Lipidomics of Caco-2 Cells Under Simulated Microgravity Conditions

Microgravity may profoundly impact the cardiovascular system, skeletal muscle system, and immune system of astronauts. At the cellular level, microgravity may also affect cell proliferation, differentiation, and growth, as well as lipid metabolism. In this work, we investigated lipid changes in Caco-2 cells cultured in a clinostat for 24 h under simulated microgravity conditions (SMC). Complex lipids were measured using a UHPLC-QTOF/MS platform, and the data were subjected to multivariate analysis. Under SMC, levels of ceramides Cer 18:0;O2/16:0, Cer 18:1;O2/16:0, Cer 18:1; O2/22:0, Cer 18:1;O2/24:0, and Cer 18:2;O2/24:0 were found to be upregulated, while sphingomyelins SM 16:1;O2/16:0, SM 16:1;O2/18:1, SM 18:1;O2/24:0, and SM 18:2;O2/24:0 were found to be downregulated. On the other hand, considering that sphingolipids are involved in the process of inflammation, we also treated Caco-2 cells with dextran sodium sulfate (DSS) to induce cell inflammation and lipopolysaccharide (LPS) to induce cell immune responses. As a result, we observed similar lipid dysregulation, indicating that SMC may exert a condition similar to inflammation. Our lipidomics strategy provides new insights into the altered metabolic pathway of ceramides and sphingomyelins of Caco-2 cells under SMC.

Delayed Sowing Reduced Verticillium Wilt by Altering Soil Temperature and Humidity to Enhance Beneficial Rhizosphere Bacteria of Sunflower

Sunflower Verticillium Wilt (SVW) caused by Verticillium dahliae is a significant threat to sunflower production in China. This soilborne disease is difficult to control. It has been observed that delayed sowing reduces the severity of SVW on different varieties and across various locations. Soil was collected from multiple locations with different sowing dates to understand the underlying biological mechanisms driving this phenomenon. The soil bacterial community was characterized through 16S rRNA gene amplicon sequencing performed on the Illumina MiSeq platform, followed by comprehensive bioinformatics analysis. Microsclerotia numbers in soil were detected using both NP-10 selective medium and quantitative polymerase chain reaction (qPCR). By delaying the sowing date, the number of microsclerotia in soil and the biomass of V. dahliae colonized inside sunflower roots were reduced during the early developmental stages (V2-V6) of sunflowers. Amplicon sequencing revealed an increased abundance of bacterial genera, such as Pseudomonas, Azoarcus, and Bacillus in soil samples collected from delayed sowing plots. Five bacterial strains isolated from the delayed sowing plot exhibited strong antagonistic effects against V. dahliae. The result of the pot experiments indicated that supplying two different synthetic communities (SynComs) in the pot did increase the control efficiencies on SVW by 19.08% and 37.82% separately. Additionally, soil temperature and humidity across different sowing dates were also monitored, and a significant correlation between disease severity and environmental factors was observed. In conclusion, delayed sowing appears to decrease microsclerotia levels by recruiting beneficial rhizosphere bacteria, thereby reducing the severity of SVW.

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.

Fire-associated microbial shifts in soils of western conifer forests with Armillaria root disease

Fires in coniferous forests throughout the northern United States alter ecosystem processes and ecological communities, including the diversity and composition of microbial communities living in the soil. In addition to its influence on ecosystem processes and functions, the soil microbiome can interact with soilborne pathogens to facilitate or suppress plant disease development. Altering the microbiome composition to promote taxa that inhibit pathogenic activity has been suggested as a management strategy for forest diseases, including Armillaria root disease caused by Armillaria solidipes, which causes growth loss and mortality of conifers. These forest ecosystems are experiencing increased wildfire burn severity that could influence A. solidipes activity and interactions of the soil microbiome with Armillaria root disease. In this research, we examine changes to the soil microbiome following three levels of burn severity in a coniferous forest in northern Idaho, United States, where Armillaria root disease is prevalent. We further determine how these changes correspond to the soil microbiomes associated with the pathogen A. solidipes, and a putatively beneficial species, A. altimontana. At 15-months post-fire, we found significant differences in richness and diversity between bacterial communities associated with unburned and burned areas, yet no significant changes to these metrics were found in fungal communities following fire. However, both bacterial and fungal communities showed compositional changes associated with burn severity, including microbial taxa with altered relative abundance. Further, significant differences in the relative abundance of certain microbial taxa in communities associated with the three burn severity levels overlapped with taxa associated with various Armillaria spp. Following severe burn, we observed a decreased relative abundance of beneficial ectomycorrhizal fungi associated with the microbial communities of A. altimontana, which may contribute to the antagonistic activity of this soil microbial community. Additionally, A. solidipes and associated microbial taxa were found to dominate following high-severity burns, suggesting that severe fires provide suitable environmental conditions for these species. Overall, our results suggest that shifts in the soil microbiome and an associated increase in the activity of A. solidipes following high-severity burns in similar conifer forests may result in priority areas for monitoring and proactive management of Armillaria root disease.

IMPORTANCE

With its influence on ecosystem processes and functions, the soil microbiome can interact with soilborne pathogens to facilitate or suppress plant disease development. These forest ecosystems are experiencing increased wildfire frequency and burn severity that could influence the fungal root pathogen, Armillaria solidipes, and interactions with the soil microbiome. We examined changes to the soil microbiome following three levels of burn severity, and examined how these changes correspond with A. solidipes, and a putatively beneficial species, A. altimontana. Following severe burn, there was a decreased relative abundance of ectomycorrhizal fungi associated A. altimontana. A. solidipes and associated microbial taxa dominated following high-severity burns, suggesting that severe fires provide suitable environmental conditions for these species. Our results suggest that shifts in the soil microbiome and an associated increase in the activity of A. solidipes following high-severity burns in conifer forests may result in priority areas for monitoring and proactive management of Armillaria root disease.

Response of Yields, Soil Physiochemical Characteristics, and the Rhizosphere Microbiome to the Occurrence of Root Rot Caused by Fusarium solani in Ligusticum chuanxiong Hort

Ligusticum chuanxiong Hort. is considered an important medicinal herb with extremely high economic value and medicinal value due to its various effects, including anti-oxidation, sedative action, hepatoprotection, and invigorating blood circulation. However, L. chuanxiong cultivation is hampered by various plant diseases, especially the root rot caused by Fusarium solani, hindering the sustainable development of the L. chuanxiong industry. The occurrence of soil-borne diseases is closely linked to imbalances in the microbial community structure. Here, we studied the yields, rhizosphere microbiota, and soil physiochemical characteristics of healthy and diseased L. chuanxiong plants affected by root rot with high-throughput sequencing and microbial network analysis, aiming to explore the relationships between soil environmental factors, microbiomes, and plant health of L. chuanxiong. According to the results, L. chuanxiong root rot significantly decreased the yields, altered microbial community diversity and composition, enriched more pathogenic fungi, recruited some beneficial bacteria, and reduced microbial interaction network stability. The Mantel test showed that soil organic matter and pH were the major environmental factors modulating plant microbiome assembly. The root rot severity was significantly affected by soil physiochemical properties, including organic matter, cation exchange capacity, available nitrogen, phosphorus, potassium, and pH. Furthermore, two differential microbes that have great potential in the biocontrol of L. chuanxiong root rot were dug out in the obtained results, which were the genera Trichoderma and Bacillus. This study provided a theoretical basis for further studies revealing the microecological mechanism of L. chuanxiong root rot and the ecological prevention and control of L. chuanxiong root rot from a microbial ecology perspective.

Harnessing the plant microbiome for environmental sustainability: From ecological foundations to novel applications

In plant environments, there exist heterogeneous microbial communities, referred to as the plant microbiota, which are recruited by plants and play crucial roles in promoting plant growth, aiding in resistance against pathogens and environmental stresses, thereby maintaining plant health. These microorganisms, along with their genomes, collectively form the plant microbiome. Research on the plant microbiome can help unravel the intricate interactions between plants and microbes, providing a theoretical foundation to reduce pesticide use, enhance agricultural productivity, and promote environmental sustainability. Despite significant progress in the field of research, unresolved challenges persist due to ongoing technological limitations and the complexities inherent in studying microorganisms at small scales. Recently, synthetic community (SynCom) has emerged as a novel technique for microbiome research, showing promising prospects for applications in the plant microbiome field. This article systematically introduces the origin and distribution of plant microbiota, the processes of their recruitment and colonization, and the mechanisms underlying their beneficial functions for plants, from the aspects of composition, assembly, and function. Furthermore, we discuss the principles, applications, challenges, and prospects of SynCom for promoting plant health.

Microbial necromass contribution to soil carbon storage via community assembly processes

Soil organic matter has been well acknowledged as a natural solution to mitigate climate change and to maintain agricultural productivity. Microbial necromass is an important contributor to soil organic carbon (SOC) storage, and serves as a resource pool for microbial utilization. The trade-off between microbial births/deaths and resource acquisition might influence the fate of microbial necromass in the SOC pool, which remains poorly understood. We coupled soil microbial assembly with microbial necromass contribution to SOC on a long-term, no-till (NT) farm that received maize (Zea mays L.) stover mulching in amounts of 0 %, 33 %, 67 %, and 100 % for 8 y. We characterized soil microbial assembly using the Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP), and microbial necromass using its biomarker amino sugars. We found that 100 % maize stover mulching (NT100) was associated with significantly lower amino sugars (66.4 mg g-1 SOC) than the other treatments (>70 mg g-1 SOC). Bacterial and fungal communities responded divergently to maize stover mulching: bacterial communities were positive for phylogenetic diversity, while fungal communities were positive for taxonomic richness. Soil bacterial communities influenced microbial necromass contribution to SOC through determinism on certain phylogenetic groups and bacterial bin composition, while fungal communities impacted SOC accumulation through taxonomic richness, which is enhanced by the positive contribution of dispersal limitation-dominated saprotrophic guilds. The prevalence of homogeneous selection and dispersal limitation on microbial cell wall-degrading bacteria, specifically Chitinophagaceae, along with increased soil fungal richness and interactions, might induce the decreased microbial necromass contribution to SOC under NT100. Our findings shed new light on the role of microbial assembly in shaping the dynamics of microbial necromass and SOC storage. This advances our understanding of the biological mechanisms that underpin microbial necromass associated with SOC storage, with implications for sustainable agriculture and mitigation of climate change.

Shifts in bacterial community composition during symbiotic seed germination of a terrestrial orchid and effects on protocorm development

Fungi and bacteria often occupy very similar niches; they interact closely with each other, and bacteria can provide direct or indirect benefits to plants that form mutualistic interactions with fungi. In orchids, successful seed germination largely depends on compatible mycorrhizal fungi, but whether and how bacteria contribute to seed germination and protocorm development remains largely unknown. Here, we performed field and laboratory experiments to assess the potential role of bacteria in mediating seed germination and protocorm development in the terrestrial orchid Gymnadenia conopsea. Our results suggested that bacterial and fungal communities differ between developmental stages in the germination process. The diversity of bacterial and fungal communities and their interaction network in germinating seeds (Stage 1) differed significantly from those in later developmental stages (Stages 2-5). Pseudomonas gradually became the dominant bacterial group as the protocorms matured and showed a positive association with Ceratobasidiaceae fungi. Seed germination tests in vitro demonstrated that co-inoculation of Ceratobasidium sp. GS2 with Pseudomonas isolates significantly improved protocorm growth and development, suggesting that the observed increase in Pseudomonas abundance during protocorm development directly or indirectly improves the growth of germinating seeds. Overall, our findings indicate that bacteria may exert non-negligible effects on seed germination of orchids and, therefore, offer valuable perspectives for future strategies for conservation and cultivating orchid species.

IMPORTANCE

It is well known that orchid seeds depend on mycorrhizal fungi to supply the necessary nutrients that support germination in natural environments. Apart from fungi, bacteria may also be involved in the germination process of orchid seeds, but so far, their role has not been intensively studied. This research provides evidence that bacterial community composition changes during seed germination of the terrestrial orchid Gymnadenia conopsea. Interestingly, in vitro experiments showed that Pseudomonas spp., which were the most dominant bacteria in the later germination stages, improved protocorm growth. These results suggest that bacteria contribute to the germination of orchid seeds, which may open new perspectives to apply bacteria as a biofertilizer in the introduction and restoration of G. conopsea populations.

Characteristics of soil microbial community assembly patterns in fields with serious occurrence of tobacco Fusarium wilt disease

Introduction

Fusarium wilt disease (FWD) of tobacco is a destructive disease caused by Fusarium spp. in tobacco-growing regions worldwide. The Fusarium spp. infection may alter the composition and structure of the tobacco root microbial community; however, the relationship between these factors under large-scale geographical conditions in China remains underexplored.

Methods

In the context of this investigation, soil samples from the rhizosphere of tobacco plants were procured from fields afflicted with FWD and those devoid of the disease in the Hanzhong region of Shaanxi province, as well as in the Sanmenxia and Nanyang regions of Henan province. These regions are recognized for the commercial cultivation of tobacco. The examination focused on discerning the influence of tobacco FWD on the composition and configuration of the rhizosphere microbial community, along with their co-occurrence patterns. This scrutiny was underpinned by targeted PCR amplification and high-throughput sequencing (amplicon sequencing) of the 16S rRNA gene and the ITS1 region.

Results

The amplicon data analyses showed that FWD influenced the microbial structure and composition of the tobacco rhizosphere soil. FWD had a greater impact on the microbiome of the tobacco fungal community than on the microbiome of the bacterial community. Healthy plants had the ability to recruit potential beneficial bacteria. Diseased plants were more susceptible to colonization by other pathogenic fungi, but they still had the capacity to recruit potential beneficial bacteria. The analysis of microbial intra- and inter-kingdom networks further indicated that FWD destabilized microbial networks. In the overall microbial interaction, microorganisms primarily interacted within their boundaries, but FWD increased the proportion of interactions occurring across boundaries. In addition, FWD could disrupt the interactions within microbial network modules.

Discussion

This study provides evidence that FWD can cause changes in the composition and network of microbial communities, affecting the interactions among various microorganisms, including bacteria and fungi. These findings contribute to our understanding of how plant microbiomes change due to disease. Furthermore, they add to our knowledge of the mechanisms that govern the assembly and interactions of microbial communities under the influence of FWD.

Cross-niche protection of kiwi plant against above-ground canker disease by beneficial rhizosphere Flavobacterium

Beneficial rhizosphere microorganisms are widely employed to shield crops from underground pathogen infections. In this study, we challenge this conventional idea by employing rhizosphere soil bacteria to safeguard kiwi plants against the above-ground canker, caused by Pseudomonas syringae pv. actinidiae (Psa). Microbiome comparisons were conducted in different resistant cultivars Actinidia chinensis var. deliciosa 'Hayward' and A. chinensis var. chinensis 'Hongyang'. Our findings reveal the most notable disparity in the rhizosphere soil microbiome, with the Flavobacterium significantly enriched in the rhizosphere soil of more resistant cultivar, 'Hayward'. We isolated Flavobacterium isolates and observed their efficacy in preventing Psa infection, which is further confirmed in field trial by using a representative strain Flavobacterium soyae F55. Furthermore, undescribed gene clusters responsible for antimicrobial metabolite biosynthesis were identified in F. soyae F55, and F. soyae F55 growth was evidently promoted by the root exudates of 'Hayward'. The results underscore the potential of beneficial rhizosphere soil bacteria in protection against above-ground disease.

Distribution and characterization of endophytic and rhizosphere bacteriome of below-ground tissues in Chinese fir plantation

Plantations of Chinese fir, a popular woody tree species, face sustainable issues, such as nutrient deficiency and increasing disease threat. Rhizosphere and endophytic bacteria play important roles in plants' nutrient absorption and stress alleviation. Our understanding of the microbiome structure and functions is proceeding rapidly in model plants and some crop species. Yet, the spatial distribution and functional patterns of the bacteriome for the woody trees remain largely unexplored. In this study, we collected rhizosphere soil, non-rhizosphere soil, fine root, thick root and primary root samples of Chinese fir and investigated the structure and distribution of bacteriome, as well as the beneficial effects of endophytic bacterial isolates. We discovered that Burkholderia and Paraburkholderia genera were overwhelmingly enriched in rhizosphere soil, and the abundance of Pseudomonas genus was significantly enhanced in fine root. By isolating and testing the nutrient absorption and pathogen antagonism functions of representative endophytic bacteria species in Pseudomonas and Burkholderia, we noticed that phosphorus-solubilizing functional isolates were enriched in fine root, while pathogen antagonism isolates were enriched in thick root. As a conclusion, our study revealed that the endophytic and rhizosphere environments of Chinese fir hold distinct structure and abundance of bacteriomes, with potential specific functional enrichment of some bacterial clades. These findings assist us to further study the potential regulation mechanism of endophytic functional bacteria by the host tree, which will contribute to beneficial microbe application in forestry plantations and sustainable development.

Extensive genomic study characterizing three Paracoccaceae populations and revealing Pseudogemmobacter lacusdianii sp. nov. and Paracoccus broussonetiae sp. nov

Bacteria within the family Paracoccaceae show promising potential for applications in various fields, garnering significant research attention. Three Gram stain-negative bacteria, strains CPCC 101601T, CPCC 101403T, and CPCC 100767, were isolated from diverse environments: freshwater, rhizosphere soil of Broussonetia papyrifera, and the phycosphere, respectively. Analysis of their 16S rRNA gene sequences, compared with those in the GenBank database, indicated that they belong to the family Paracoccaceae, with nucleotide similarities of 92.5%-99.9% to all of the Paracoccaceae members with valid taxonomic names. Phylogenetic studies based on 16S rRNA gene and whole-genome sequences identified CPCC 101601T as a member of the genus Pseudogemmobacter, CPCC 101403T belonging to the genus Paracoccus, and CPCC 100767 as part of the genus Gemmobacter. Notably, genomic analysis using average nucleotide identity (ANI; <95%) and digital DNA-DNA hybridization (dDDH; <70%) with their closely related strains suggested that CPCC 101601T and CPCC 101403T represent new species within their respective genera. Conversely, CPCC 100767 exhibited high ANI (98.5%) and dDDH (87.4%) values with Gemmobacter fulvus con5T, indicating it belongs to this already recognized species. The in-depth genomic analysis revealed that strains CPCC 101601T, CPCC 101403T, and CPCC 100767 harbor key genes related to the pathways for denitrifying, MA utilization, and polyhydroxyalkanoate biosynthesis. Moreover, genotyping and phenotyping analysis confirmed that strain CPCC 100767 has the ability to convert atmospheric nitrogen into ammonia and produce 5-aminolevulinic acid, whereas CPCC 101601T can only perform the former bioprocess.IMPORTANCEBased on polyphasic taxonomic study, two new species, Pseudogemmobacter lacusdianii and Paracoccus broussonetiae, affiliated with the family Paracoccaceae were identified. This expands our understanding of the family Paracoccaceae and provides new microbial materials for further studies. Modern genomic techniques such as average nucleotide identity and digital DNA-DNA hybridization were utilized to determine species affiliations. These methods offer more precise results than traditional classification mainly based on 16S rRNA gene analysis. Beyond classification of these strains, the research delved into their genomes and discovered key genes related to denitrification, MA utilization, and polyhydroxyalkanoate biosynthesis. The identification of these genes provides a molecular basis for understanding the environmental roles of these strains. Particularly, strain CPCC 100767 demonstrated the ability to convert atmospheric nitrogen into ammonia and produce 5-aminolevulinic acid. These bioprocess capabilities are of significant practical value, such as in agricultural production for use as biofertilizers or biostimulants.