Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

CABO-16S-a Combined Archaea, Bacteria, Organelle 16S rRNA database framework for amplicon analysis of prokaryotes and eukaryotes in environmental samples

Identification of both prokaryotic and eukaryotic microorganisms in environmental samples is currently challenged by the need for additional sequencing to obtain separate 16S and 18S ribosomal RNA (rRNA) amplicons or the constraints imposed by "universal" primers. Organellar 16S rRNA sequences are amplified and sequenced along with prokaryote 16S rRNA and provide an alternative method to identify eukaryotic microorganisms. CABO-16S combines bacterial and archaeal sequences from the SILVA database with 16S rRNA sequences of plastids and other organelles from the PR2 database to enable identification of all 16S rRNA sequences. Comparison of CABO-16S with SILVA 138.2 results in equivalent taxonomic classification of mock communities and increased classification of diverse environmental samples. In particular, identification of phototrophic eukaryotes in shallow seagrass environments, marine waters, and lake waters was increased. The CABO-16S framework allows users to add custom sequences for further classification of underrepresented clades and can be easily updated with future releases of reference databases. Addition of sequences obtained from Sanger sequencing of methane seep sediments and curated sequences of the polyphyletic SEEP-SRB1 clade resulted in differentiation of syntrophic and non-syntrophic SEEP-SRB1 in hydrothermal vent sediments. CABO-16S highlights the benefit of combining and amending existing training sets when studying microorganisms in diverse environments.

Integrating ecological and evolutionary frameworks for SynCom success

Use of synthetic microbial communities (SynComs) is a promising approach that harnesses nature-based solutions to support soil fertility and food security, mitigate climate change impacts, and restore terrestrial ecosystems. Several microbial products are in the market, and many others are at different stages of development and commercialization. Yet, we are still far from being able to fully harness the potential and successful applications of such biotechnological tools. The limited field efficiency and efficacy of SynComs have significantly constrained commercial opportunities, resulting in market growth falling below expectations. To overcome these challenges and manage expectations, it is critical to address current limitations, failures, and potential environmental consequences of SynComs. In this Viewpoint, we explore how using multiple eco-evolutionary theories can inform SynCom design and success. We further discuss the current status of SynComs and identify the next steps needed to develop and deploy the next generation of tools to boost their ability to support multiple ecosystem services, including food security and environmental sustainability.

Deciphering factors influencing planktonic and sedimentary microbial assembly processes in Midwest salinity lakes

The salt lake ecosystem, characterized by extreme environmental gradients, harbors microbes that uniquely adapt to high salt stress through natural selection. However, how abiotic and biotic factors shape the microbial community assembly in Yuncheng Salt Lakes remains unclear. Here, we investigated the assembly processes and meta co-occurrence patterns of microbiota in both water and sediment sampled from 14 distinct wide range of salinity lakes in the Shanxi Yuncheng area, Midwest of China, using 16S rRNA and 18S rRNA gene sequencing technology combined with multivariate ecological and statistical methods. Habitat differentiation led to the differences in microbial diversity, co-occurrence patterns, and community assembly between sedimentary and planktonic communities. Sedimentary prokaryotes were more shaped by deterministic processes than planktonic bacterial communities. Salinity was a major abiotic factor influencing the balance between stochastic and deterministic processes in both sediment and water. Enhanced microbial interactions within sediments exhibited a more prominent impact in shaping community assembly, as indicated by the stronger association between network-inferred species and prokaryotic βNTI. Moreover, we revealed significant differences in how core species concerning βNTI responded to biotic and abiotic factors. Our findings elucidated the ecological process underlying microbial communities in Yuncheng Salt Lakes and shed light on the mechanism of microorganisms to maintain community complexity and diversity in the extreme environment. KEY POINTS: • Sedimentary prokaryotes were more shaped by deterministic processes than planktonic prokaryotic communities. • Salinity was a major factor influencing the balance between stochastic and deterministic process. • Inter-domain and intra-domain symbiotic interactions within sedimentary communities represent key biotic factors influencing their community assembly.

Hub metabolites at the root-microbiome interface: unlocking plant drought resilience

Drought is one of the most devastating environmental challenges, severely affecting agriculture, ecosystems, and global food security. Effective strategies to predict and mitigate drought are limited. The root-soil-microbiome interface is pivotal in mediating plant resilience to drought. Recent studies highlight dynamics between plant root exudates and microbial communities, influencing stress tolerance through chemical signaling under drought. By integrating plant molecular biology, root chemistry, and microbiome research, we discuss insights into how these mechanisms can be harnessed to enhance crop resilience. Here, we focus on the interplay between plants and their microbiomes with metabolites as a central point of interactions. We synthesize recent developments, identify critical knowledge gaps, and propose future directions to leverage plant-microbe interactions to improve plant drought tolerance.

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.

Linking plant genes to arthropod community dynamics: current progress and future challenges

Plant genetic variation can play a key role in shaping ecological communities. Prior work investigated the effects of coarse-grain variation among plant genotypes on their diverse arthropod communities. Several recent studies, however, have leveraged the boom of genomic resources to study how genome-wide plant variation influences associated communities. These studies have demonstrated that the effects of plant genomic variation are not just detectable but can be important drivers of arthropod communities in natural ecosystems. Field common gardens and lab-based mesocosm experiments are also revealing candidate genes that have large effects on arthropod communities. While we highlight these exciting results, we also discuss key challenges to address in future research. We argue that a major hurdle lies in the integration of genomic tools with hierarchical models of species communities (HMSCs). HMSCs are generative models that provide the opportunity to not only better understand the processes underlying community change but to also predict community dynamics. We also advocate for future research to apply models of genomic prediction to explore the genetic architecture of arthropod community phenotypes. We hypothesize that this genetic architecture will follow an exponential distribution, where a few genes of large effect, but also many genes of small effect, contribute to variation in arthropod communities. The next generation of studies linking plant genes to community dynamics will require interdisciplinary collaborations to build truly predictive models of plant genetic and arthropod community change.

Consumption of only wild foods induces large scale, partially persistent alterations to the gut microbiome

The gut microbiome (GM) is implicated in human health and varies among lifestyles. So-called "traditional" diets have been suggested to promote health-associated taxa. However, most studies focused only on diets including domesticated foods. Historically, humans consumed only wild foods, which might uniquely shape GM composition. We explored the impact of a wild-food-only diet on GM, particularly whether it increases the presence of health-associated and/or "old friend" taxa, and if the alterations to GM are persistent or transient. One participant collected daily fecal samples and recorded daily food consumption over an eight-week period, the middle four weeks of which he consumed only wild foods. Samples were profiled by 16S rRNA sequencing, and oligotyping and network analysis were conducted to assess microbial co-occurrence patterns. A wild-food-only diet considerably alters the composition of the GM, and the magnitude of the changes is larger than that observed in other diet interventions. No new taxa, including "old friends" appeared; instead, the proportions of already-present taxa shifted. Network analysis revealed distinct microbial co-abundance groups restructuring across dietary phases. There is a clear successional shift from the pre-, during- and post-wild-food-only diet. This analysis highlighted structural and functional shifts in microbial interactions, underscoring diet's role in shaping the gut ecosystem.

Endophytic fungi of Cynodon dactylon: a treasure trove of bioactive compounds

Cynodon dactylon (L.) Pers., commonly known as Bermuda grass, is a medicinally significant plant recognized for its diverse pharmacological properties. Recent research highlights that its association with endophytic fungi contributes to the synthesis of bioactive secondary metabolites with immense therapeutic and agricultural potential. These fungal endophytes produce a wide spectrum of bioactive compounds, including antimicrobial, antioxidant, anticancer, immunosuppressive, and plant growth-promoting agents, positioning them as valuable resources for drug discovery and sustainable biotechnological applications. Despite their vast potential, the biodiversity, metabolic pathways, and functional significance of endophytic fungi in C. dactylon remain underexplored. This review consolidates the current knowledge on the isolation, identification, and characterization of endophytic fungi from C. dactylon, emphasizing their bioactive metabolites and pharmacological significance. Furthermore, it explores their biotechnological applications and the future scope of utilizing these fungi in pharmaceutical and agricultural advancements. Understanding the metabolic potential of these fungal endophytes can open new avenues for harnessing novel bioactive compounds, contributing to the development of innovative therapeutics and eco-friendly agricultural solutions.

Priority Colonization of Endophytic Fungal Strains Drives Litter Decomposition and Saprotroph Assembly via Functional Trait Selection in Karst Oak Forests

Litter decomposition dynamics are largely governed by microbial interactions. While the involvement of endophytic fungi in early-stage decomposition and microbial succession is well established, their species-specific contributions to decomposer community assembly remain insufficiently understood. This study investigated the effects of single-strain endophytic colonization using dominant species (Tubakia dryina, Tubakia dryinoides, Guignardia sp.) and rare species (Neofusicoccum parvum, Penicillium citrinum) on Quercus acutissima leaf decomposition through a controlled field experiment in a karst ecosystem. Endophytes accelerated decomposition rates across treatments but paradoxically reduced transient CO2 emissions, linked to intensified microbial carbon and phosphorus limitations in late stages. Contrary to expectations, decomposition efficiency was governed by endophytic fungal species traits rather than colonization abundance, with rare species outperforming dominant taxa. Endophytes induced significant fungal community restructuring, reducing Ascomycota while enriching lignin-degrading Basidiomycota, but minimally affected bacterial composition. Co-occurrence networks revealed endophyte-driven fragmentation of microbial connectivity, with only two keystone fungal hubs (Trechispora sp. and Russula carmesina) identified compared to natural communities. Endophytic colonization improved fungal community assembly, mediated by an increase in lignin-degrading Basidiomycota and the suppression of pathogenic Leotiomycetes lineages. Our findings demonstrate that endophytes hierarchically regulate decomposer communities through phylogenetically conserved fungal interactions, prioritizing functional trait selection over competitive dominance, thereby stabilizing decomposition under nutrient constraints. This mechanistic framework advances predictions of litter decay dynamics in forest ecosystems undergoing microbial community perturbations.

Temporal dynamics and tissue-specific variations of the blueberry phyllosphere mycobiome

Highbush blueberry (Vaccinium corymbosum) is an economically important fruit-bearing woody perennial. Despite the importance of microbial communities to plant health, the aboveground (phyllosphere) microbiome of blueberry is understudied. The phyllosphere is exposed to varying conditions throughout a growing season. The fruit undergoes extensive physiological change across a season from bud to fruit. This study aimed to provide a temporal characterization of the blueberry phyllosphere across a growing season and a characterization of specific tissues and phenological stages. Blueberry branches were harvested every other week across 2 years and two locations during the development process of the blueberry fruits. The internal transcribed spacer regions were amplified from DNA extracts and sequenced to perform amplicon-based characterization of the fungal microbiome across time and plant tissue. Fungal communities showed changes in α-diversity depending on the week of harvest and tissue type. Early in the season, α-diversity was high, but it decreased in midseason when flowers developed into fruit. Later in the season, as the fruit ripened, α-diversity increased again. The β-diversity of the community changed across time and tissue types during plant development. Notable members of the identified core microbiome were members of the genus Alternaria, Peltaster, and Taphrina, as well as the pathogenic taxa Aureobasidium pullulans and Botrytis cinerea. This research provides background for future experimentation of understanding the microbial composition in the blueberry phyllosphere in relation to the infection court of pathogens (e.g. Colletotrichum fioriniae and B. cinerea) and the temporal components of blueberry plant health and management.

Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems

BACKGROUND

Microbial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.

RESULTS

This study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r = 0.5, p = 0.039) between microbial diversity and seed yield.

CONCLUSION

This study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability. Video Abstract.

Deterministic colonization arises early during the transition of soil bacteria to the phyllosphere and is shaped by plant-microbe interactions

BACKGROUND

Upon seed germination, soil bacteria are activated to transition to the plant and eventually colonize mature tissues like leaves. These bacteria are poised to significantly influence plant health, but we know little about their colonization routes. We studied the mechanisms of the transition of soil bacteria to germinating plants and leaves using an in-planta isolation approach and by experimentally manipulating inoculation times. We then tested how plant-microbe-microbe interactions shape assembly mechanisms in natural soil communities by amending soil with a trackable, labeled strain of the opportunistic pathogen Pseudomonas viridiflava (Pv3D9).

RESULTS

We identified 27 diverse genera of leaf-associated bacteria that could transition alone from a few cells near a germinating plant to mature leaves, suggesting that the soil-to-leaf transition is probably important for them in nature. Indeed, when plants were only inoculated by soil after the emergence of true leaves, less diverse bacteria transitioned to mature leaves via different colonization mechanisms than when plants germinated in the presence of soil microorganisms. In particular, deterministic processes drove the colonization of phylogenetic bins dominated by Pedobacter, Enterobacter, Stenotrophomonas, Janthinobacterium, Pseudomonas, and Chryseobacterium only in the natural soil-to-leaf transition. Host genotype and soil amendments with Pv3D9, both of which affect host physiology, had strong effects on mainly deterministic colonization.

CONCLUSIONS

Diverse bacteria transition from soil to leaves during natural colonization, resulting in characteristic diversity in healthy leaf microbiomes. The mechanisms of colonization are a mix of stochastic processes, which will be largely shaped by competition, and deterministic processes which are more responsive to factors that shape host physiology. In the chase toward targeted manipulation of microbiomes, identifying these mechanisms for a given host and environment provides important information. Developing targeted treatments, however, will require further dissection of the pathways by which host factors drive stochastic and deterministic transitions from soil to leaves. Video Abstract.

A co-conserved gene pair supports Caulobacter iron homeostasis during chelation stress

Synthetic metal chelators are widely used in industrial, clinical, and agricultural settings, leading to their accumulation in the environment. We measured the growth of Caulobacter crescentus, a soil and aquatic bacterium, in the presence of the ubiquitous chelator ethylenediaminetetraacetic acid (EDTA) and found that it restricts growth by lowering intracellular iron levels. Using barcoded transposon sequencing, we identified an operonic gene pair, cciT-cciO, that is required to maintain iron homeostasis in laboratory media during EDTA challenge. cciT encodes one of four TonB-dependent transporters that are regulated by the ferric uptake repressor (Fur) and stands out among this group of genes in its ability to support Caulobacter growth across diverse media conditions. The function of CciT strictly requires cciO, which encodes a cytoplasmic FeII dioxygenase-family protein. Our results thus define a functional partnership between an outer membrane iron receptor and a cytoplasmic dioxygenase that are broadly co-conserved in Proteobacteria. We expanded our analysis to natural environments by examining the growth of mutant strains in freshwater from two lakes, each with biochemical and geochemical profiles that differ markedly from standard laboratory media. In lake water, Caulobacter growth did not require cciT or cciO and was less affected by EDTA treatment. This result aligns with our observation that EDTA toxicity is influenced by common forms of biologically chelated iron and the spectrum of free cations present in the medium. Our study defines a conserved iron acquisition system in Proteobacteria and bridges laboratory-based physiology studies with real-world conditions.IMPORTANCEMetal-chelating chemicals are widely used across industries, including as preservatives in the food sector, but their full impact on microbial physiology is not well understood. We identified two genes, cciT and cciO, that function together to support Caulobacter crescentus iron balance when cells are exposed to the common synthetic chelator, EDTA. CciT is an outer membrane transporter and CciO is a dioxygenase-family protein that are mutually conserved in many bacteria, including human pathogens where mutations in cciT homologs are linked to clinical resistance to the siderophore antibiotic cefiderocol. This study identifies a conserved genetic system that supports iron homeostasis during chelation stress and illuminates the iron acquisition versatility and stress resilience of Caulobacter in freshwater environments.

Impact of Ectropis grisescens Warren (Lepidoptera: Geometridae) Infestation on the Tea Plant Rhizosphere Microbiome and Its Potential for Enhanced Biocontrol and Plant Health Management

The root-associated microbiome significantly influences plant health and pest resistance, yet the temporal dynamics of its compositional and functional change in response to Ectropis grisescens Warren (Lepidoptera: Geometridae) infestation remain largely unexplored. The study took samples of leaves, roots, and rhizosphere soil at different times after the plants were attacked by E. grisescens. These samples were analyzed using transcriptomic and high-throughput sequencing of 16S rRNA techniques. The goal was to understand how the plant's defense mechanisms and the microbial community around the roots changed after the attack. Additionally, bacterial feedback assays were conducted to evaluate the effects of selected microbial strains on plant growth and pest defense responses. By conducting 16S rRNA sequencing on the collected soil samples, we found significant shifts in bacterial communities by the seventh day, suggesting a lag in community adaptation. Transcriptomic analysis revealed that E. grisescens attack induced reprogramming of the tea root transcriptome, upregulating genes related to defensive pathways such as phenylpropanoid and flavonoid biosynthesis. Metagenomic data indicated functional changes in the rhizosphere microbiome, with enrichment in genes linked to metabolic pathways and nitrogen cycling. Network analysis showed a reorganization of core microbial members, favoring nitrogen-fixing bacteria like Burkholderia species. Bacterial feedback assays confirmed that selected strains, notably Burkholderia cepacia strain ABC4 (T1) and a nine-strain consortium (T5), enhanced plant growth and defense responses, including elevated levels of flavonoids, polyphenols, caffeine, jasmonic acid, and increased peroxidase (POD) and superoxide dismutase (SOD) activities. This study emphasizes the potential of utilizing root-associated microbial communities for sustainable pest management in tea cultivation, thereby enhancing resilience in tea crops while maintaining ecosystem balance.

Amplicon sequencing and culture-dependent approaches reveal core bacterial endophytes aiding freezing stress tolerance in alpine Rosaceae plants

Wild plants growing in alpine regions are associated with endophytic microbial communities that may support plant growth and survival under cold conditions. The structure and function of endophytic bacterial communities were characterized in flowers, leaves, and roots of three alpine Rosaceae plants in Alpine areas using a combined amplicon sequencing and culture-dependent approaches to determine the role of core taxa on plant freezing stress tolerance. Amplicon sequencing analysis revealed that plant tissue, collection site, and host plant are the main factors affecting the richness, diversity, and taxonomic structure of endophytic bacterial communities in alpine Rosaceae plants. Core endophytic bacterial taxa were identified as 31 amplicon sequence variants highly prevalent across all plant tissues. Psychrotolerant bacterial endophytes belonging to the core taxa of Duganella, Erwinia, Pseudomonas, and Rhizobium genera mitigated freezing stress in strawberry plants, demonstrating the beneficial role of endophytic bacterial communities and their potential use for cold stress mitigation in agriculture.IMPORTANCEFreezing stress is one of the major abiotic stresses affecting fruit production in Rosaceae crops. Current strategies to reduce freezing damage include physical and chemical methods, which have several limitations in terms of costs, efficacy, feasibility, and environmental impacts. The use or manipulation of plant-associated microbial communities was proposed as a promising sustainable approach to alleviate cold stress in crops, but no information is available on the possible mitigation of freezing stress in Rosaceae plants. A combination of amplicon sequencing, culture-dependent, and plant bioassay approaches revealed the beneficial role of the endophytic bacterial communities in alpine Rosaceae plants. In particular, we showed that culturable psychrotolerant bacterial endophytes belonging to the core taxa of Duganella, Erwinia, Pseudomonas, and Rhizobium genera can mitigate freezing stress on strawberry seedlings. Overall, this study demonstrates the potential use of psychrotolerant bacterial endophytes for the development of biostimulants for cold stress mitigation in agriculture.

Creation of a functional duckweed holobiont to reduce nutrient competition with microalgae for high-yield biomass production

Duckweed has been highlighted as an appropriate biomass for low-carbon industries because of its significantly high production rate and multiple resource value. However, the outbreak of microalgae is a practical issue that decreases duckweed production yield. This study demonstrated that the growth of the duckweed Lemna aequinoctialis from factory wastewater was enhanced by colonization with indigenous plant growth-promoting bacteria (PGPB), whereas the growth of a duckweed competitor microalga, Coelastrella sp. KC10, from the same wastewater was reduced by indigenous microalgal growth-inhibiting bacteria (MGIB). Finally, a quadruple co-culture of a synthetic duckweed holobiont, L. aequinoctialis colonized by both KLaR20 (PGPB) and KLaR16 (MGIB), and Coelastrella sp. KC10 successfully recovered the duckweed production level by 117.5% in frond number and 84.5% in dry weight compared to those in the absence of microalgae. This case study demonstrates for the first time that duckweed holobionts can be reconstructed and enforced to antagonize growth competitor microalgae.

Temporal dynamics of walnut phyllosphere microbiota under synergistic pathogen exposure and environmental perturbation

Introduction

Phyllosphere-associated microbes directly influence plant-pathogen interactions, and the external environment and the plant shape the phyllosphere microbiome.

Methods

In this study, we integrated 16S rRNA and ITS high-throughput sequencing to systematically investigate changes in the phyllosphere microbiome between symptomatic and asymptomatic walnut leaves affected by spot disease, with consideration of phenological stage progression. Additionally, we explored how abiotic (AT, DT, SCTCC & LPDD) and biotic factors (Pn & Gs) impact microbial communities.

Results

Our findings revealed significant differences in the diversity of the phyllosphere microbiome between symptomatic and asymptomatic leaves at the same phenological stage. Furthermore, the structure and function of phyllosphere-associated microbiome changed as the phenological stage progressed. Fungal taxa that related to the function Plant_Pathogen and bacterial taxa that related to the KEGG pathway functions Fatty acid biosynthesis and Biotin metabolism were increased in the symptomatic group. The keystone species driving the walnut phyllosphere microbiome was Pseudomonas spp., which substantially influenced the microbiome of symptomatic vs. asymptomatic leaves. Notably, Pseudomonas spp. interacted with Xanthomonas spp. and Pantoea spp. Correlation analysis revealed that the dew point temperature constituted the primary abiotic factor of phyllosphere bacterial community composition, whereas liquid precipitation depth dimension was identified as the dominant factor shaping fungal taxa. Additionally, leaf net photosynthetic rate and stomatal conductance were closely linked to the phyllosphere microbiome.

Discussion

These results advance our understanding of community-level microbial responses to pathogen invasion and highlight the multifactorial drivers of phyllosphere microbiome assembly. Ultimately, they contribute to predicting and managing walnut leaf-related diseases.

Unlocking the potential of ecofriendly guardians for biological control of plant diseases, crop protection and production in sustainable agriculture

Several beneficial microbial strains inhibit the growth of different phytopathogens and commercialized worldwide as biocontrol agents (BCAs) for plant disease management. These BCAs employ different strategies for growth inhibition of pathogens, which includes production of antibiotics, siderophores, lytic enzymes, bacteriocins, hydrogen cyanide, volatile organic compounds, biosurfactants and induction of systemic resistance. The efficacy of antagonistic strains could be further improved through genetic engineering for better disease suppression in sustainable farming practices. Some antagonistic microbial strains also possess plant-growth-promoting activities and their inoculation improved plant growth in addition to disease suppression. This review discusses the characterization of antagonistic microbes and their antimicrobial metabolites, and the application of these BCAs for disease control. The present review also provides a comprehensive summary of the genetic organization and regulation of the biosynthesis of different antimicrobial metabolites in antagonistic strains. Use of molecular engineering to improve production of metabolites in BCAs and their efficacy in disease control is also discussed. The application of these biopesticides will reduce use of conventional pesticides in disease control and help in achieving sustainable and eco-friendly agricultural systems.

Keystone root bacteria in Ambrosia artemisiifolia promote invasive growth by increasing the colonization rate of Funneliformis mosseae

Higher arbuscular mycorrhizal fungi (AMF) colonization rates in the roots of invasive plants than in those of native plants are associated with invasion success. Keystone plant-root bacteria (or root-associated bacteria) can influence plant growth by interacting with other members of the microbial community (eg.AMF). We aimed to investigate the effects of keystone taxa on AMF colonization and their interactions on invasive plant growth. Here, the common key root-associated species from the roots of Ambrosia artemisiifolia among four geographical populations in China were identified, and the strains were subsequently isolated. Plate and pot experiments were conducted to examine the impact of keystone species on the colonization of Funneliformis mosseae and elucidate the mechanisms that enhance plant growth. Sphingomonas was identified as a common keystone root-associated genus of A. artemisiifolia. Sphingomonas sanxanigenens was found to facilitate AMF colonization in the roots of A. artemisiifolia by promoting flavonoid biosynthesis. A synergistic effect on the growth of A. artemisiifolia was observed when the plant was co-inoculated with S. sanxanigenens and F. mosseae. This study provides new insights into the mechanisms whereby root-associated microbes facilitate AMF colonization in invasive plants. These findings confirm the pivotal role of keystone microbes in weed invasion and enhance our understanding that microbial synergistic interactions promote weed invasiveness.

Microbiome selection and evolution within wild and domesticated plants

Microbes are ubiquitously found across plant surfaces and even within their cells, forming the plant microbiome. Many of these microbes contribute to the functioning of the host and consequently affect its fitness. Therefore, in many contexts, including microbiome effects enables a better understanding of the phenotype of the plant rather than considering the genome alone. Changes in the microbiome composition are also associated with changes in the functioning of the host, and there has been considerable focus on how environmental variables regulate plant microbiomes. More recently, studies suggest that the host genome also preconditions the microbiome to the environment of the plant, and the microbiome is therefore subject to evolutionary forces. Here, we outline how plant microbiomes are governed by both environmental variables and evolutionary processes and how they can regulate plant health together.

Salt stress alters the selectivity of mature pecan for the rhizosphere community and its associated functional traits

Introduction

Salt stress is a major global environmental factor limiting plant growth. Rhizosphere bacteria, recruited from bulk soil, play a pivotal role in enhancing salt stress resistance in herbaceous and crop species. However, whether the rhizosphere bacterial community of a mature tree can respond to salt stress, particularly in saline-alkalitolerant trees, remains unexplored. Pecan (Carya illinoinensis), an important commercially cultivated nut tree, is considered saline-alkali tolerant.

Methods

Pecan trees (12 years) were subjected to different NaCl concentrations for 12 weeks. Collected samples included bulk soil, rhizosphere soil, roots, leaves, and fruit. Amplicon sequencing data and shotgun metagenomic sequencing data obtained from the samples were investigated: 1) microbial communities in various ecological niches of mature pecan trees; 2) the characteristic of the rhizosphere bacteria community and the associated functional traits when pecan suffered from salt stress.

Results and discussion

We characterized the mature pecan-associated microbiome (i.e., fruit, leaf, root, and rhizosphere soil) for the first time. These findings suggest that niche-based processes, such as habitat selection, drive bacterial and fungal community assembly in pecan tissues. Salt stress reduced bacterial diversity, altered community composition, and shifted pecan's selective pressure on Proteobacteria and Actinobacteria. Shotgun metagenomic sequencing further revealed functional traits of the rhizosphere microbiome in response to salt stress. This study enhances our understanding of mature tree-associated microbiomes and supports the theory that shaping the rhizosphere microbiome may be a strategy for saline-alkali-tolerant mature trees to resist salt stress. These findings provide insights into salt tolerance in mature trees and suggest potential applications, such as the development of bio-inoculants, for managing saline environments in agricultural and ecological contexts.

Incorporating microbiome analyses can enhance conservation of threatened species and ecosystem functions

Conservation genomics is a rapidly growing subdiscipline of conservation biology that uses genome-wide information to inform management of biodiversity at all levels. Such efforts typically focus on species or systems of conservation interest, but rarely consider associated microbes. At least three major approaches have been used to study how microorganisms broadly contribute to conservation areas: (1) diversity surveys map out microbial species distribution patterns in a variety of hosts, natural environments or regions; (2) functional surveys associate microbial communities with factors of interest, such as host health, symbiotic interactions, environmental characteristics, ecosystem processes, and biological invasions; and (3) manipulative experiments examine the response of changes to microbial communities or determine the functional roles of specific microbes within hosts or communities by adding, removing, or genetically modifying microbes. In practice, multiple approaches are often applied simultaneously. The results from all three conservation genomics approaches can be used to help design practical interventions and improve management actions, some of which we highlight below. However, experimental manipulations allow for more robust causal inferences and should be the ultimate goal of future work. Here we discuss how further integration of microbial research of a host's microbiome and of free living microbes into conservation biology will be an essential advancement for conservation of charismatic organisms and ecosystem functions in light of ongoing global environmental change.

Phyllosphere mycobiome in two Lycopodiaceae plant species: unraveling potential HupA-producing fungi and fungal interactions

Huperzine A (HupA), a lycopodium alkaloid with therapeutic potential for neurodegenerative diseases such as Alzheimer's disease, is found exclusively in some species of the Huperzioideae subfamily of Lycopodiaceae. Fungi associated with Huperzioideae species are potential contributors to HupA biosynthesis, offering promising prospects for HupA production. Despite its medical significance, limited knowledge of fungal diversity in lycophytes and the variability of HupA production in fungal strains have impeded the discovery and applications of HupA-producing fungi. Here, we investigated HupA concentrations and the mycobiome across various tissues of two Lycopodiaceae species, Huperzia asiatica (a HupA producer) and Diphasiastrum complanatum (a non-HupA producer). We aim to unveil the distribution of potential HupA-producing fungi in different plant tissues and elucidate fungal interactions within the mycobiome, aiming to uncover the role of HupA-producing fungi and pinpoint their potential fungal facilitators. Among the tissues, H. asiatica exhibited the highest HupA concentration in apical shoots (360.27 μg/g fresh weight) whereas D. complanatum showed no HupA presence in any tissue. We obtained 441 amplicon sequence variants (ASVs) from H. asiatica and 497 ASVs from D. complanatum. The fungal communities in bulbils and apical shoots of H. asiatica were low in diversity and dominated by Sordariomycetes, a fungal class harboring the majority of reported HupA-producing fungi. Integrating bioinformatics with published experimental reports, we identified 27 potential HupA-producing fungal ASVs, primarily in H. asiatica, with 12 ASVs identified as hubs in the fungal interaction network, underscoring their pivotal roles in mycobiome stability. Members of certain fungal genera, such as Penicillium, Trichoderma, Dioszegia, Exobasidium, Lycoperdon, and Cladosporium, exhibited strong connections with the potential HupA producers in H. asiatica's network rather than in D. complanatum's. This study advances our knowledge of fungal diversity in Lycopodiaceae and provides insights into the search for potential HupA-producing fungi and fungal facilitators. It highlights the importance of exploring young tissues and emphasizes the ecological interactions that may promote the fungi-mediated production of complex bioactive compounds, offering new directions for research in fungal ecology and secondary metabolite production.

The Changes of the Endophytic Bacterial Community from Pepper Varieties with Different Capsaicinoids

Capsaicinoids, the key compounds responsible for pepper pungency, have significant commercial and health value, yet the role of endophytic bacteria in their biosynthesis remains unclear. This study investigated the relationship between endophytic bacterial communities and capsaicinoid content across 100 Capsicum annuum varieties. Two high-capsaicinoid (35.0 and 24.8 mg/g) and two low-capsaicinoid (0.8 and 0.9 mg/g) varieties were selected for 16S rRNA sequencing and microbial analysis. High-capsaicinoid varieties exhibited greater bacterial richness and diversity compared to low-capsaicinoid varieties. Taxonomic profiling revealed distinct community compositions: Enterobacter, Bacteroides, and Escherichia_Shigella were enriched in high-capsaicinoid fruits and positively correlated with capsaicinoid levels, while Chujaibacter and Brochothrix dominated the low-capsaicinoid varieties. Functional annotation highlighted nitrogen-fixing bacteria as more abundant in high-capsaicinoid varieties. Inoculating peppers with isolated Enterobacter strains significantly increased capsaicinoid content, confirming its role in biosynthesis. These findings demonstrate that the pepper genotype shapes endophytic bacterial communities, which in turn influence capsaicinoid production through metabolic- and nitrogen-associated pathways. This study provides foundational insights into microbiome-mediated enhancement of pepper pungency, offering potential strategies for agricultural and industrial applications.

Symbiosis vs pathogenesis in plants: Reflections and perspectives

Plant-microbe partnerships constitute a complex and intricately woven network of connections that have evolved over countless centuries, involving both cooperation and antagonism. In various contexts, plants and microorganisms engage in mutually beneficial partnerships that enhance crop health and maintain balance in ecosystems. However, these associations also render plants susceptible to a range of pathogens. Understanding the fundamental molecular mechanisms governing these associations is crucial, given the notable susceptibility of plants to external environmental influences. Based on quorum sensing signals, phytohormone, and volatile organic carbon (VOC) production and others molecules, microorganisms influence plant growth, health, and defense responses. This review explores the multifaceted relationships between plants and their associated microorganisms, encompassing mutualism, commensalism, and antagonism. The molecular mechanisms of symbiotic and pathogenic interactions share similarities but lead to different outcomes. While symbiosis benefits both parties, pathogenesis harms the host. Genetic adaptations optimize these interactions, involving coevolution driving process. Environmental factors influence outcomes, emphasizing the need for understanding and manipulation of microbial communities for beneficial results. Research directions include employing multi-omics techniques, functional studies, investigating environmental factors, understanding evolutionary trajectories, and harnessing knowledge to engineer synthetic microbial consortia for sustainable agriculture and disease management.

Root system architecture plasticity with beneficial rhizosphere microbes: Current findings and future perspectives

The rhizosphere microbiota, often referred to as the plant's "second genome" plays a critical role in modulating root system architecture (RSA). Despite this, existing methods to analyze root phenotypes in the context of root-microbe interactions remain limited, and the precise mechanisms affecting RSA by microbes are still not fully understood. This review comprehensively evaluates current root phenotyping techniques relevant to plant-microbe interactions, discusses their limitations, and explores future directions for integrating advanced technologies to elucidate microbial roles in altering RSA. Here, we summarized that microbial metabolite, primarily through auxin signaling pathways, drive root development changes. By harnessing advanced phenotyping tools, we aim to uncover more detailed mechanisms by which microbes modify RSA, providing valuable insights into strategies for optimizing nutrient uptake, bolstering food security, and enhancing resilience against climate-induced environmental stresses.

A co-conserved gene pair supports Caulobacter iron homeostasis during chelation stress

Synthetic metal chelators are widely used in industrial, clinical, and agricultural settings, leading to their accumulation in the environment. We measured the growth of Caulobacter crescentus, a soil and aquatic bacterium, in the presence of the ubiquitous chelator ethylenediaminetetraacetic acid (EDTA) and found that it restricts growth by lowering intracellular iron levels. Using barcoded transposon sequencing, we identified an operonic gene pair, cciT-cciO, that is required to maintain iron homeostasis in laboratory media during EDTA challenge. cciT encodes one of four TonB-dependent transporters that are regulated by the ferric uptake repressor (Fur) and stands out among this group of genes in its ability to support Caulobacter growth across diverse media conditions. The function of CciT strictly requires cciO, which encodes a cytoplasmic FeII dioxygenase-family protein. Our results thus define a functional partnership between an outer membrane iron receptor and a cytoplasmic dioxygenase that are broadly co-conserved in Proteobacteria. We expanded our analysis to natural environments by examining the growth of mutant strains in freshwater from two lakes, each with biochemical and geochemical profiles that differ markedly from standard laboratory media. In lake water, Caulobacter growth did not require cciT or cciO and was less affected by EDTA treatment. This result aligns with our observation that EDTA toxicity is influenced by common forms of biologically chelated iron and the spectrum of free cations present in the medium. Our study defines a conserved iron acquisition system in Proteobacteria and bridges laboratory-based physiology studies with real-world conditions.

IMPORTANCE

Metal-chelating chemicals are widely used across industries, including as preservatives in the food sector, but their full impact on microbial physiology is not well understood. We identified two genes, cciT and cciO, that function together to support Caulobacter crescentus iron balance when cells are exposed to the common synthetic chelator, EDTA. CciT is an outer membrane transporter and CciO is a dioxygenase-family protein that are mutually conserved in many bacteria, including several human pathogens, where mutations in cciT homologs are linked to clinical resistance to the siderophore antibiotic, cefiderocol. This study identifies a conserved genetic system that supports iron homeostasis during chelation stress and illuminates the iron acquisition versatility and stress resilience of Caulobacter in freshwater environments.

Comparison of Rhizosphere Microbiomes Between Domesticated and Wild Wheat in a Typical Agricultural Field: Insights into Microbial Community Structure and Functional Shifts

While the differences between domesticated crops and their wild relatives have been extensively studied, less is known about their rhizosphere microbiomes, which hold potential for breeding stress-resistant traits. We compared the rhizosphere microbiomes of domesticated wheat (Triticum aestivum L.) and its wild ancestor (Triticum turgidum ssp. dicoccoides) in a typical agricultural field using 16S rRNA and ITS gene sequencing. Our results revealed a high level of conservation in the rhizosphere microbiomes between wild and domesticated wheat, with minimal divergence in community composition and microbial network structure. However, domesticated wheat exhibited a higher prevalence of fungal pathogens and increased functional redundancy, with significant enrichment of genes involved in carbon and nitrogen cycling. The microbial community assemblies in both wheats were predominantly governed by deterministic processes. This suggests that long-term conventional agricultural practices have imposed minor effects on the compositional differences between the microbiomes of wild and domesticated wheat. Nonetheless, the lower abundance of apparent pathogens in the rhizosphere of the wild wheat suggests greater natural biota or innate host plant resistance against pathogenic fungi. This study may provide valuable insights into the host selection, assembly patterns, and functional potential of microbial communities in wild versus domesticated wheat, with implications for manipulating microbial communities in future crop breeding.

Screening of Antagonistic Trichoderma Strains to Enhance Soybean Growth

This study investigates the isolation and screening of Trichoderma strains that exhibit antagonistic properties against soybean root-infecting Fusarium species, particularly F. oxysporum. From soybean rhizosphere soil, 37 antagonistic Trichoderma strains were identified using the plate confrontation method, demonstrating inhibitory effects ranging from 47.57% to 72.86% against F. oxysporum. Strain 235T4 exhibited the highest inhibition rate at 72.86%. Molecular identification confirmed that the strains belonged to eight species within the Trichoderma genus, with notable strains promoting soybean growth in greenhouse tests. In pot experiments, the application of Trichoderma significantly reduced the disease index of soybean plants inoculated with F. oxysporum, particularly with strain 223H16, which achieved an 83.78% control efficiency. Field applications further indicated enhanced soybean growth metrics, including increased pod numbers and plant height, when treated with specific Trichoderma strains. Additionally, Trichoderma application enriched the fungal diversity in the soybean rhizosphere, resulting in a significant reduction of Fusarium populations by approximately 50%. This study highlights the potential of Trichoderma species as biological control agents to enhance soybean health and productivity while improving soil fungal diversity.

Exploring the Grapevine Microbiome: Insights into the Microbial Ecosystem of Grape Berries

Plant growth, health, and resilience to stress are intricately linked to their associated microbiomes. Grapevine, functioning as a holobiont, forms essential relationships with fungi and bacteria across both its belowground (roots) and aboveground (leaves and berries) compartments. The root microbiome exhibits a stable, site-specific structure, whereas the microbiomes of ephemeral tissues such as leaves and berries, which regenerate annually, display more stochastic assembly patterns across growing seasons. Among these, grape berries represent a critical component in viticulture due to their direct influence on wine quality and flavor complexity. Berries provide a unique ecological niche, hosting diverse microbial communities composed of yeasts, bacteria, and fungi that interact with the grapevine and its surrounding environment. These microorganisms are not only pivotal to berry development but also contribute significantly to the synthesis of secondary metabolites and fermentation processes, ultimately shaping the sensory and organoleptic properties of wine. This review consolidates current knowledge on the grapevine microbiome, with a particular emphasis on the microbial dynamics of grape berries.

Turning antagonists into allies: Bacterial-fungal interactions enhance the efficacy of controlling Fusarium wilt disease

Intense microbial competition in soil has driven the evolution of resistance mechanisms, yet the implications of such evolution on plant health remain unclear. Our study explored the conversion from antagonism to coexistence between Bacillus velezensis (Bv) and Trichoderma guizhouense (Tg) and its effects on Fusarium wilt disease (FWD) control. We found a bacilysin transmembrane transporter (TgMFS4) in Tg, critical during cross-kingdom dialogue with Bv. Deleting Tgmfs4 (ΔTgmfs4) mitigated Bv-Tg antagonism, reduced bacilysin import into Tg, and elevated its level in the coculture environment. This increase acted as a feedback regulator, limiting overproduction and enhancing Bv biomass. ΔTgmfs4 coinoculation with Bv demonstrated enhanced FWD control relative to wild-type Tg (Tg-WT). In addition, the Tg-WT+ Bv consortium up-regulated antimycotic secretion pathways, whereas the ΔTgmfs4+ Bv consortium enriched the CAZyme (carbohydrate-active enzyme) family gene expression in the rhizosphere, potentiating plant immune responses. This study elucidates the intricacies of bacterial-fungal interactions and their ramifications for plant health.

Enhancing remediation efficiency of cadmium-contaminated soil: integrating forage-microorganism systems with agronomic strategies

Soil contamination due to heavy metals, especially cadmium (Cd), poses a growing concern. This study seeks to develop an economical and non-polluting sustainable remediation program for Cd-contaminated soil to address this issue. This study pioneered the exploration of Cd accumulation patterns in three forage species: Lolium multiflorum Lamk (LMJS), Sorghum bicolor × sudanense (SSBJ), and Sorghum sudanense (Piper) Stapf (SUJS) to identify their optimal harvest periods in Cd-contaminated soils. Additionally, a consortium of beneficial microorganisms (combinations of C, F, and H; C: 10% Bacillus subtilis; F: 20% Bacillus subtilis + 10% Bacillus cereus + 20% Citrobacter; H: 20% Deinococcus radiodurans + 10% Bacillus cereus) was implemented, with a focus on developing an efficient forage-microbial co-remediation system. Subsequently, agronomic strategies (mowing or chelating agents) were employed to improve the Cd enrichment capacity of the combined forage-microbe remediation system, offering sustainable field remediation strategies. The results indicate that the SSBJ + F combined remediation system was mowed on the 60th day (stubble left at 35 cm, light mowing) and harvested on the 120th day as the optimal choice. The bioaccumulation quantity (BCQ) unit accumulation in Cd-contaminated soil at a concentration of 10 mg/kg reached 0.397 mg/kg, and the annual Cd removal rate was 9.23%, representing a 29.63% increase compared to the control group. The results of this study provide valuable insights into the development of practical, field-applicable remedial measures for cadmium-contaminated soils while minimizing environmental impacts.

The legacy of endophytes for the formation of bioactive agents, pigments, biofertilizers, nanoparticles and bioremediation of environment

Endophytes have significant prospects for applications beyond their existing utilization in agriculture and the natural sciences. They form an endosymbiotic relationship with plants by colonizing the root tissues without detrimental effects. These endophytes comprise several microorganisms, including bacteria and fungi. They act as repositories of compounds of medicinal importance. They are considered sources of pigments besides synthetic dyes and assist with soil fertility and plant growth as bio-fertilizers. They also have immense potential for advanced technology using endophyte-synthesized nanoparticles. In assisting bioremediation, they facilitate detoxification of pollutants in all spheres of the environment. Studies on the potential of endophytic microbes in drug discovery and biotic stress management are underway. In this review, published databases on endophytes and their diverse roles and applications in various fields, such as bio-fertilizers and nanoparticles, as well as bioremediation, are critically discussed while exploring unanswered questions. In addition, future perspectives on endosymbiotic microorganisms and their prospective use in plants, environmental management, and medicine are discussed in this review.

Ecological filters shape arbuscular mycorrhizal fungal communities in the rhizosphere of secondary vegetation species in a temperate forest

The community assembly of arbuscular mycorrhizal fungi (AMF) in the rhizosphere results from the recruitment and selection of different AMF species with different functional traits. The aim of this study was to analyze the relationship between biotic and abiotic factors and the AMF community assembly in the rhizosphere of four secondary vegetation (SV) plant species in a temperate forest. We selected four sites at two altitudes, and we marked five individuals per plant species at each site. Soil rhizosphere samples were collected from each SV plant species, during the rainy and dry seasons. Soil samples from the rhizosphere of each plant species were analyzed for AMF spores, organic matter (OM), pH, soil moisture, and available phosphorus, and nitrogen. Three ecological filters influenced the AMF community assembly: host plant identity, abiotic factors, and AMF species co-occurrence. This assembly consisted of 61 AMF species, with different β-diversity values among plant species across seasons and altitudes. Canonical correspondence analysis revealed that AMF community composition is linked to OM and available P and N, with only a few AMF species co-occurring, while most do not. Our study highlights how ecological filters shape AMF structure, which is essential for understanding how soil and environmental factors affect AMF in SV plant species across seasons and altitudes.

Diversity, connectivity and negative interactions define robust microbiome networks across land, stream, and sea

In this era of rapid global change, factors influencing the stability of ecosystems and their functions have come into the spotlight. For decades the relationship between stability and complexity has been investigated in modeled and empirical systems, yet results remain largely context dependent. To overcome this we leverage a multiscale inventory of fungi and bacteria ranging from single sites along an environmental gradient, to habitats inclusive of land, sea and stream, to an entire watershed. We use networks to assess the relationship between microbiome complexity and robustness and identify fundamental principles of stability. We demonstrate that while some facets of complexity are positively associated with robustness, others are not. Beyond positive biodiversity x robustness relationships we find that the number of "gatekeeper" species or those that are highly connected and central within their networks, and the proportion of predicted negative interactions are universal indicators of robust microbiomes. With the potential promise of microbiome engineering to address global challenges ranging from human to ecosystem health we identify properties of microbiomes for future experimental studies that may enhance their stability. We emphasize that features beyond biodiversity and additional characteristics beyond stability such as adaptability should be considered in these efforts.

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.

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).

Microbiome of honey bee corbicular pollen: Factors influencing its structure and potential for studying pathogen transmission

Honey bees are exposed to a diverse variety of microbes in the environment. Many studies have been carried out on the microbiome of bee gut, beebread, and flower pollen. However, little is known regarding the microbiome of fresh corbicular pollen, which can directly reflect microbes acquired from the environment. Moreover, although evidences have suggested that floral resources in general can affect the bee-acquired microbes, whether specific forage plants affect the composition of these microbes is still unclear. Here, we characterized both the microbiome and plant composition of corbicular pollen in collection seasons over two years from six hives using 16S rRNA gene and ITS2 metabarcoding. The results reveal temporal changes in the microbiome and plant composition in corbicular pollen, which was influenced by environmental factors and the choice of forage plants. We identified several co-occurrences between plant and bacterial genera, indicating specific plant-microbe interactions. Many Spiroplasma species with various insect hosts, including a honey bee pathogen Spiroplasma melliferum, were shown to positively correlate with Rubus, suggesting this plant genus as an important node for microbial transmission. Overall, we demonstrated the potential of corbicular pollen for studying the transmission of microbes, especially pathogens. This framework can be applied in future research to explore the complicated pollinator-microbe-plant network in different ecosystems.

Medicago truncatula genotype drives the plant nutritional strategy and its associated rhizosphere bacterial communities

Harnessing the plant microbiome through plant genetics is of increasing interest to those seeking to improve plant nutrition and health. While genome-wide association studies (GWAS) have been conducted to identify plant genes driving the plant microbiome, more multidisciplinary studies are required to assess the relationships among plant genetics, plant microbiome and plant fitness. Using a metabarcoding approach, we characterized the rhizosphere bacterial communities of a core collection of 155 Medicago truncatula genotypes along with the plant phenotype and investigated the plant genetic effects through GWAS. The different genotypes within the M. truncatula core collection showed contrasting growth and nutritional strategies but few loci were associated with these ecophysiological traits. To go further, we described its associated rhizosphere bacterial communities, dominated by Proteobacteria, Actinobacteria and Bacteroidetes, and defined a core rhizosphere bacterial community. Next, the occurrences of bacterial candidates predicting plant ecophysiological traits of interest were identified using random forest analyses. Some of them were heritable and plant loci were identified, pinpointing genes related to response to hormone stimulus, systemic acquired resistance, response to stress, nutrient starvation or transport, and root development. Together, these results suggest that plant genetics can affect plant growth and nutritional strategies by harnessing keystone bacteria in a well-connected interaction network.

Harnessing the plant microbiome for sustainable crop production

Global research on the plant microbiome has enhanced our understanding of the complex interactions between plants and microorganisms. The structure and functions of plant-associated microorganisms, as well as the genetic, biochemical, physical and metabolic factors that influence the beneficial traits of plant microbiota have also been intensively studied. Harnessing the plant microbiome has led to the development of various microbial applications to improve crop productivity in the face of a range of challenges, for example, climate change, abiotic and biotic stresses, and declining soil properties. Microorganisms, particularly nitrogen-fixing rhizobia as well as mycorrhizae and biocontrol agents, have been applied for decades to improve plant nutrition and health. Still, there are limitations regarding efficacy and consistency under field conditions. Also, the wealth of expanding knowledge on microbiome diversity, functions and interactions represents a huge source of information to exploit for new types of application. In this Review, we explore plant microbiome functions, mechanisms, assembly and types of interaction, and discuss current applications and their pitfalls. Furthermore, we elaborate on how the latest findings in plant microbiome research may lead to the development of new or more advanced applications. Finally, we discuss research gaps to fully leverage microbiome functions for sustainable plant production.

Central Taxa Are Keystone Microbes During Early Succession

Microorganisms underpin numerous ecosystem processes and support biodiversity globally. Yet, we understand surprisingly little about what structures environmental microbiomes, including how to efficiently identify key players. Microbiome network theory predicts that highly connected hubs act as keystones, but this has never been empirically tested in nature. Combining culturing, sequencing, networks and field experiments, we isolated 'central' (highly connected, hub taxa), 'intermediate' (moderately connected), and 'peripheral' (weakly/unconnected) microbes and experimentally evaluated their effects on soil microbiome assembly during early succession in nature. Central early colonisers significantly (1) enhanced biodiversity (35%-40% richer communities), (2) reshaped trajectories of microbiome assembly and (3) increased recruitment of additional influential microbes by > 60%. In contrast, peripheral microbes did not increase diversity and were transient taxa, minimally affected by the presence of other microbes. This work elucidates fundamental principles of network theory in microbial ecology and demonstrates for the first time in nature that central microbes act as keystone taxa.

From nature to urbanity: exploring phyllosphere microbiome and functional gene responses to the Anthropocene

The Anthropocene exerts various pressures and influences on the stability and function of the Earth's ecosystems. However, our understanding of how the microbiome responds in form and function to these disturbances is still limited, particularly when considering the phyllosphere, which represents one of the largest microbial reservoirs in the terrestrial ecosystem. In this study, we comprehensively characterized tree phyllosphere bacteria and associated nutrient-cycling genes in natural, rural, suburban, and urban habitats in China. Results revealed that phyllosphere bacterial community diversity, richness, stability, and composition heterogeneity were greatest at the most disturbed sites. Stochastic processes primarily governed the assembly of phyllosphere bacterial communities, although the role of deterministic processes (environmental selection) in shaping these communities gradually increased as we moved from rural to urban sites. Our findings also suggest that human disturbance is associated with the reduced influence of drift as increasingly layered environmental filters deterministically constrain phyllosphere bacterial communities. The intensification of human activity was mirrored in changes in functional gene expression within the phyllosphere microbiome, resulting in enhanced gene abundance, diversity, and compositional variation in highly human-driven disturbed environments. Furthermore, we found that while the relative proportion of core microbial taxa decreased in disturbed habitats, a core set of microbial taxa shaped the distributional characteristics of both microbiomes and functional genes at all levels of disturbance. In sum, this study offers valuable insights into how anthropogenic disturbance may influence phyllosphere microbial dynamics and improves our understanding of the intricate relationship between environmental stressors, microbial communities, and plant function within the Anthropocene.

From synthetic communities to synthetic ecosystems: exploring causalities in plant-microbe-environment interactions

The plant microbiota research field has rapidly shifted from efforts aimed at gaining a descriptive understanding of microbiota composition to a focus on acquiring mechanistic insights into microbiota functions and assembly rules. This evolution was driven by our ability to establish comprehensive collections of plant-associated microbes and to reconstruct meaningful microbial synthetic communities (SynComs). We argue that this powerful deconstruction-reconstruction strategy can be used to reconstitute increasingly complex synthetic ecosystems (SynEcos) and mechanistically understand high-level biological organization. The transitioning from simple to more advanced, fully tractable and programmable gnotobiotic SynEcos is ongoing and aims at rationally simplifying natural ecosystems by engineering them. Such reconstitution ecology approaches represent an untapped strategy for bridging the gap between ecology and functional biology and for unraveling plant-microbiota-environment mechanisms that modulate ecosystem health, assembly, and functioning.

Microbes in reconstructive restoration: Divergence in constructed and natural tree island soil fungi affects tree growth

As ecosystems face unprecedented change and habitat loss, pursuing comprehensive and resilient habitat restoration will be integral to protecting and maintaining natural areas and the services they provide. Microbiomes offer an important avenue for improving restoration efforts as they are integral to ecosystem health and functioning. Despite microbiomes' importance, unresolved knowledge gaps hinder their inclusion in restoration efforts. Here, we address two critical gaps in understanding microbial roles in restoration-fungal microbiomes' importance in "reconstructive" restoration efforts and how management and restoration decisions interactively impact fungal communities and their cascading effects on trees. We combined field surveys, microbiome sequencing, and greenhouse experiments to determine how reconstructing an iconic landscape feature-tree islands-in the highly imperiled Everglades impacts fungal microbiomes and fungal effects on native tree species compared with their natural counterparts under different proposed hydrological management regimes. Constructed islands used in this research were built from peat soil and limestone collected from deep sloughs and levees nearby the restoration sites in 2003, providing 18 years for microbiome assembly on constructed islands. We found that while fungal microbiomes from natural and constructed tree islands exhibited similar diversity and richness, they differed significantly in community composition. These compositional differences arose mainly from changes to which fungal taxa were present on the islands rather than changes in relative abundances. Surprisingly, ~50% of fungal hub taxa (putative keystone fungi) from natural islands were missing on constructed islands, suggesting that differences in community composition of constructed island could be important for microbiome stability and function. The differences in fungal composition between natural and constructed islands had important consequences for tree growth. Specifically, these compositional differences interacted with hydrological regime (treatments simulating management strategies) to affect woody growth across the four tree species in our experiment. Taken together, our results demonstrate that reconstructing a landscape feature without consideration of microbiomes can result in diverging fungal communities that are likely to interact with management decisions leading to meaningful consequences for foundational primary producers. Our results recommend cooperation between restoration practitioners and ecologists to evaluate opportunities for active management and restoration of microbiomes during future reconstructive restoration.

Taming of the microbial beasts: Plant immunity tethers potentially pathogenic microbiota members

Plants are in intimate association with taxonomically structured microbial communities called the plant microbiota. There is growing evidence that the plant microbiota contributes to the holistic performance and general health of plants, especially under unfavorable situations. Despite the attached benefits, surprisingly, the plant microbiota in nature also includes potentially pathogenic strains, signifying that the plant hosts have tight control over these microbes. Despite the conceivable role of plant immunity in regulating its microbiota, we lack a complete understanding of its role in governing the assembly, maintenance, and function of the plant microbiota. Here, we highlight the recent progress on the mechanistic relevance of host immunity in orchestrating plant-microbiota dialogues and discuss the pluses and perils of these microbial assemblies.

Effect of exogenous treatment with zaxinone and its mimics on rice root microbiota across different growth stages

Enhancing crops productivity to ensure food security is one of the major challenges encountering agriculture today. A promising solution is the use of biostimulants, which encompass molecules that enhance plant fitness, growth, and productivity. The regulatory metabolite zaxinone and its mimics (MiZax3 and MiZax5) showed promising results in improving the growth and yield of several crops. Here, the impact of their exogenous application on soil and rice root microbiota was investigated. Plants grown in native paddy soil were treated with zaxinone, MiZax3, and MiZax5 and the composition of bacterial and fungal communities in soil, rhizosphere, and endosphere at the tillering and the milky stage was assessed. Furthermore, shoot metabolome profile and nutrient content of the seeds were evaluated. Results show that treatment with zaxinone and its mimics predominantly influenced the root endosphere prokaryotic community, causing a partial depletion of plant-beneficial microbes at the tillering stage, followed by a recovery of the prokaryotic community structure during the milky stage. Our study provides new insights into the role of zaxinone and MiZax in the interplay between rice and its root-associated microbiota and paves the way for their practical application in the field as ecologically friendly biostimulants to enhance crop productivity.

New Species of Diaporthales (Ascomycota) from Diseased Leaves in Fujian Province, China

Fungal biota represents important constituents of phyllosphere microorganisms. It is taxonomically highly diverse and influences plant physiology, metabolism and health. Members of the order Diaporthales are distributed worldwide and include devastating plant pathogens as well as endophytes and saprophytes. However, many phyllosphere Diaporthales species remain uncharacterized, with studies examining their diversity needed. Here, we report on the identification of several diaporthalean taxa samples collected from diseased leaves of Cinnamomum camphora (Lauraceae), Castanopsis fordii (Fagaceae) and Schima superba (Theaceae) in Fujian province, China. Based on morphological features coupled to multigene phylogenetic analyses of the internal transcribed spacer (ITS) region, the large subunit of nuclear ribosomal RNA (LSU), the partial beta-tubulin (tub2), histone H3 (his3), DNA-directed RNA polymerase II subunit (rpb2), translation elongation factor 1-α (tef1) and calmodulin (cal) genes, three new species of Diaporthales are introduced, namely, Diaporthe wuyishanensis, Gnomoniopsis wuyishanensis and Paratubakia schimae. This study contributes to our understanding on the biodiversity of diaporthalean fungi that are inhabitants of the phyllosphere of trees native to Asia.

Impact of foliar application of phyllosphere yeast strains combined with soil fertilizer application on rice growth and yield

BACKGROUND

The application of beneficial microbes in agriculture is gaining increasing attention as a means to reduce reliance on chemical fertilizers. This approach can potentially mitigate negative impacts on soil, animal, and human health, as well as decrease climate-changing factors. Among these microbes, yeast has been the least explored, particularly within the phyllosphere compartment. This study addresses this knowledge gap by investigating the potential of phyllosphere yeast to improve rice yield while reducing fertilizer dosage.

RESULTS

From fifty-two rice yeast phyllosphere isolates, we identified three yeast strains-Rhodotorula paludigena Y1, Pseudozyma sp. Y71, and Cryptococcus sp. Y72-that could thrive at 36 °C and possessed significant multifarious plant growth-promoting traits, enhancing rice root and shoot length upon seed inoculation. These three strains demonstrated favorable compatibility, leading to the creation of a yeast consortium. We assessed the combined effect of foliar application of this yeast consortium and individual strains with two distinct recommended doses of chemical fertilizers (RDCFs) (75 and 100%), as well as RDCFs alone (75 and 100%), in rice maintained in pot-culture and field experiments. The pot-culture experiment investigated the leaf microbial community, plant biochemicals, root and shoot length during the stem elongation, flowering, and dough phases, and yield-related parameters at harvest. The field experiment determined the actual yield. Integrated results from both experiments revealed that the yeast consortium with 75% RDCFs was more effective than the yeast consortium with 100% RDCFs, single strain applications with RDCFs (75 and 100%), and RDCFs alone (75 and 100%). Additionally, this treatment improved leaf metabolite levels compared to control rice plants.

CONCLUSIONS

Overall, a 25% reduction in soil chemical fertilizers combined with yeast consortium foliar application improved rice growth, biochemicals, and yield. This study also advances the field of phyllosphere yeast research in agriculture.

Plant-microbe interactions: PGPM as microbial inoculants/biofertilizers for sustaining crop productivity and soil fertility

Plant-microbe interactions play pivotal roles in sustaining crop productivity and soil fertility, offering promising avenues for sustainable agricultural practices. This review paper explores the multifaceted interactions between plants and various microorganisms, highlighting their significance in enhancing crop productivity, combating pathogens, and promoting soil health. Understanding these interactions is crucial for harnessing their potential in agricultural systems to address challenges such as food security and environmental sustainability. Therefore, the introduction of beneficial microbes into agricultural ecosystems by bio-augmentation reduces the negative effects of intensive, non-sustainable agriculture on the environment, society, and economy, into the mechanisms underlying the application of plant growth promoting microbes as microbial inoculants/biofertilizers; their interactions, the factors influencing their dynamics, and the implications for agricultural practices, emerging technologies and strategies that leverage plant-microbe interactions for improving crop yields, soil fertility, and overall agricultural sustainability.

Medicinal Plant Microbiomes: Factors Affecting Bacterial and Fungal Community Composition

This exploratory study was designed to identify factors implicating microbial influence on medicinal plant metabolomes. Utilizing a whole-microbiome approach, amplicon sequencing was used to identify the makeup of fungal and bacterial assemblages from endophytic (interior) and epiphytic (external) environments in two different sets of congeneric host-plant pairs, with collection of multiple samples of two medicinal plant species (Actaea racemosa, Rhodiola rosea) and two generic analogs (Actaea rubra, Rhodiola integrifolia). Diversity analysis of microbial assemblages revealed the influence of three primary factors driving variance in microbial community composition: host-plant taxonomy, the compartmentalization of microbial communities within discrete plant parts, and the scale of distance (microhabitat heterogeneity) between sampling locations. These three factors accounted for ~ 60% of variance within and between investigated microbiomes. Across all our collections, bacterial populations were more diverse than fungi (per compartment), and microbial density in epiphytic compartments (aerial parts, rhizosphere) were higher than those of endophytes (leaf and root). These comparative data point to key loci associated with variation between congeneric pairs and plant genera, providing insight into the complex and contrasting relationships found within this multi-kingdom coevolutionary relationship. Although reflective of only a limited set of botanical source materials, these data document the richness of a relatively unexplored component of the plant world and highlight the relevance of a whole-microbiome ecology-driven approach to botanical research and directed natural product investigations.