Search Results (114)

Domestication reduced the genetic diversity in modern crops, often resulting in reduced resilience to biotic and abiotic stress. Evidence is now accumulating that domestication also altered the structure and function of root-associated microbiomes, creating new opportunities to harness beneficial microbes for breeding and crop improvement. Using multi-region 16S rRNA sequencing, we compared the rhizosphere and endosphere bacterial communities of cultivated tomato (Solanum lycopersicum cv. Moneymaker) with six wild relatives (S. pimpinellifolium, S. huaylasense, S. peruvianum, S. chilense, S. habrochaites, and S. pennellii) spanning the main wild lineages within Solanum sect. Lycopersicon. Bacterial community structure in the rhizosphere was broadly conserved across all seven hosts, and diversity remained comparable among genotypes. Despite this overall stability, the rhizosphere microbiomes were ordered along a gradient consistent with host phylogeny, with Moneymaker clustering near S. pimpinellifolium, the four green-fruited Eriopersicon species forming a cohesive block, and S. pennellii occupying the most distinct position. Within this hierarchy, individual hosts showed specific recruitment preferences, including enrichment of Streptomycetaceae in S. pimpinellifolium, Bacillaceae in S. chilense, and contrasting patterns of nitrifiers among Eriopersicon species and S. pennellii. Differential abundance testing in the endosphere revealed consistent reductions in several bacterial families in wild accessions, alongside the enrichment of Streptomycetaceae and Rhodobiaceae in multiple wild species. Overall, our study suggests that domestication exerted a modest effect on tomato root microbiomes, while wild relatives retained microbial association traits that could be harnessed in microbiome-informed breeding to improve resilience in cultivated tomato. Full article

This study investigates the bacterial community structure and diversity across different root compartments (non-rhizosphere soil, rhizosphere soil, rhizosphere, and endosphere) of Camellia oleifera and their associations with three cultivars (‘Huashuo’, ‘Huajin’, ‘Huaxin’). High-throughput sequencing and bioinformatics analyses were performed to characterize the bacterial communities. A total of 22 phyla, 59 classes, 155 orders, 268 families, 523 genera, 929 species, and 2045 operational taxonomic units (OTUs) were identified. Alpha diversity indices (Shannon, Simpson, Chao1) showed no statistically significant differences among the three cultivars, but varied significantly across root compartments. The rhizosphere exhibited the highest bacterial diversity and richness, which was significantly higher than that in the endosphere. At the phylum level, Proteobacteria, Chloroflexi, Actinobacteriota, Acidobacteriota, Firmicutes, and Bacteroidetes dominated the communities. Significant differences were observed in the relative abundance of dominant genera (e.g., Proteus, actinomycetes) among varieties and root compartments. PCoA analysis revealed that ‘Huaxin’ had a distinct bacterial community structure compared to ‘Huashuo’ and ‘Huajin’, while the endosphere was separated from other compartments. Interaction network analysis indicated that most bacterial interactions were positive, with Colidextribacter, Uliginosibacterium, and Aliidongia showing the highest centrality, suggesting their key roles in maintaining community stability. This study provides novel insights into the distribution patterns and driving factors of root-associated bacteria in C. oleifera, laying a theoretical foundation for future research on disease control and quality improvement of this crop. Full article

Peganum harmala (L.) Schrad., a perennial medicinal plant thriving in arid Moroccan soils, represents a natural reservoir of unexplored bacterial diversity. To uncover its hidden foliar endosphere microbiota, we isolated and characterized two Acinetobacter strains: a novel endophytic bacterium, AGC35, and another strain, AGC59, newly reported from this host. Both are non-halophilic, aerobic, Gram-negative bacteria exhibiting optimal growth at 30–35 °C, pH5, and with 1% NaCl. An integrative genomic, phylogenetic, functional, and phenotypic characterization classified both strains within the genus Acinetobacter (class Gamma-pseudomonadota). However, Average Nucleotide Identity (<96%) and digital DNA-DNA Hybridization (<70%) values distinguished the AGC35 strain as a novel species, for which the name Acinetobacter endophylla sp. nov. is proposed. A comparative genomic and phenotypic analysis with the co-isolated Acinetobacter pittii strain AGC59 revealed extensive genome rearrangements, reflecting distinct evolutionary lineage and ecological strategies. While both genomes share core metabolic pathways, A. endophylla harbors specialized genes for the degradation of plant-derived aromatic compounds (e.g., catechol) but shows reduced capacities in carbohydrate metabolism and osmotic stress tolerance, traits indicative of a metabolic specialist with plant-growth-promotion potential, including phosphorus, potassium, and silicon solubilization and indole-3-acetic acid production. In contrast, A. pittii exhibits a more generalist genome enriched in stress functions. Analysis using the Antibiotics and Secondary Metabolite Analysis Shell revealed multiple biosynthetic gene clusters in both strains, showing ≤26% similarity to known references, suggesting the potential for novel antimicrobial secondary metabolite biosynthesis, including antifungal lipopeptides and thiopeptide antibiotics. Altogether, functional specialization and ecological coherence of these findings support the recognition of A. endophylla sp. nov. as a genomically and functionally distinct species, highlighting niche partitioning and adaptive metabolism within the P. harmala holobiont. These results underscore the plant’s value as a reservoir of untapped microbial diversity with significant ecological and biotechnological relevance. Finally, future work will focus on elucidating the novel metabolites encoded by the biosynthetic gene clusters in both isolates and exploring their applications in crop-improvement strategies and natural-product discovery. Full article

Antarctica harbors some of the most extreme ecosystems on earth, where only two vascular plants persist. The native grass Deschampsia antarctica provides a model for plant–microbe interactions under intense abiotic stress. We present the first multi-compartmental and multi-kingdom characterization of bacterial and fungal communities associated with D. antarctica across three South Shetland Islands. Metabarcoding revealed strong compartmentalization: the rhizosphere displayed the highest richness and complex bacterial–fungal networks; the root endosphere showed intermediate diversity with keystone taxa such as Rhizobiales and Streptomyces; and the leaf endosphere was simplified, dominated by stress-tolerant taxa including Pseudomonas and Helotiales. Despite marked soil heterogeneity, phosphorus enrichment at Admiralty Bay, base cations at Coppermine Cove, and iron at Byers Peninsula, a conserved core (20 bacterial and 5 fungal genera) persisted, mainly cold-adapted saprotrophs and plant-associated taxa. Fungal assemblages were more responsive to soil chemistry, with site-specific enrichments such as Zymoseptoria and Herpotrichia. Overall, D. antarctica holobionts exhibited a dual strategy: conserved microbial backbones confer stability, while localized assemblages shaped by soil chemistry and geography enhance adaptability. Together, these findings provide one of the most integrative characterizations of the D. antarctica holobiont to date, revealing how conserved and adaptive microbial components support plant resilience under extreme Antarctic conditions and offering valuable insights for predicting biological responses to ongoing climate change. Full article

The intricate connections between plants and the microbial populations that surround them are crucial for plant development and resilience, but little is known about the evolutionary processes influencing these partnerships. Less is known about how pathogenic and beneficial microbes coevolve with their plant hosts over ecological and evolutionary timeframes, despite the fact that several studies identify rhizosphere and endophytic microbes that support nutrient acquisition, disease resistance, and stress tolerance. Using molecular, ecological, and evolutionary investigations from soil, rhizosphere, and endosphere habitats, this review summarizes current findings on microbial coevolution in plant–microbe systems. We look at the endosymbiotic processes that underlie the development of organelles, the mechanisms of mutualism and antagonism, and the eco-evolutionary feedbacks that affect plant health and agricultural output. The inadequate comprehension of intraspecific microbial diversity, the application of laboratory coevolution experiments to field settings, and the long-term effects of climate change on the evolutionary dynamics of plants and microbiomes are some of the major knowledge gaps. When pathogenic and beneficial microbes apply selective pressures to one another and their common host, coevolution takes place. This results in mutual genetic and physiological adaptations, such as modifications to host immunity, microbial virulence, or competitive tactics, which influence the way the two types interact over time. We conclude that understanding plants as holobiont-integrated units of hosts and their microbiomes offers fresh chances to develop microbiome-based approaches to sustainable agriculture, such as coevolutionary breeding programs, precision biofertilizers, and resilient cropping systems. Full article

The undefined microbial ecology of Aconitum carmichaelii root rot in western Yunnan constrains the advancement of eco-friendly control strategies. The identification of potential pathogenic determinants affecting A. carmichaelii growth is imperative for sustainable cultivation and ecosystem integrity. High-throughput sequencing was employed to profile microbial communities across four critical niches, namely rhizosphere soil, tuberous root epidermis, root endosphere, and fibrous roots of healthy and diseased A. carmichaelii. The physicochemical properties of corresponding rhizosphere soils were concurrently analyzed. Putative pathogens were isolated from diseased rhizospheres and tubers through culturing with Koch’s postulates validation, while beneficial microorganisms exhibiting antagonism against pathogens and plant growth-promoting (PGP) traits were isolated from healthy rhizospheres. Highly virulent strains (2F14, FZ1, L23) and their consortia were targeted for suppression. Strain DX3, demonstrating optimal PGP and antagonistic capacity in vitro, was selected for pot trials evaluating growth enhancement and disease control efficacy. Significant disparities in rhizosphere soil properties and bacterial/fungal community structures were evident between healthy and diseased cohorts. Fifteen putative pathogens spanning eight species across four genera were isolated: Fusarium solani, F. avenaceum, Clonostachys rosea, Mucor racemosus, M. irregularis, M. hiemalis, Serratia liquefaciens, and S. marcescens. Concurrently, eight PGP biocontrol strains were identified: Bacillus amyloliquefaciens, B. velezensis, B. subtilis, B. pumilus, and Paenibacillus polymyxa. Pot trials revealed that Bacillus spp. enhanced soil physiochemical properties through nitrogen fixation, phosphate solubilization, potassium mobilization, siderophore production, and cellulose degradation, significantly promoting plant growth. Critically, DX3 inoculation elevated defense-related enzyme activities in A. carmichaelii, enhanced host resistance to root rot, and achieved >50% disease suppression efficacy. This work delineates key pathogenic determinants of Yunnan A. carmichaelii root rot and identifies promising multifunctional microbial resources with dual PGP and biocontrol attributes. Our findings provide novel insights into rhizosphere microbiome-mediated plant health and establish a paradigm for sustainable disease management. Full article

Increasing demand for high-quality food is driving the development of biologized farming methods, which involve the use of microorganisms, including endophytes, to stimulate plant growth. However, research on the composition of endosphere microbiomes is limited. The study presents an analysis of the bacterial endophytic microbiome in lettuce seeds (Lactuca sativa L., cv. Ozornik) using high-throughput sequencing of 16S rRNA amplicons. It evaluates the taxonomic composition and putative functional properties of seed endophytic bacteria. The microbial community exhibited low diversity (Shannon index ranged from 1.1 to 1.84, Simpson index from 0.57 to 0.83). The bacterial endophytic community of lettuce seeds was dominated by Pseudomonadota (83%), Actinomycetota (14%), and Bacillota (3%). The genera identified within the microbiome included Pantoea (32%), Rhodococcus (13%), Candidatus Profftella (13%), Janthinobacterium (7%), Pseudomonas (9%), Enterococcus (3%), and Alcaligenes (2%), which exhibit a broad spectrum of beneficial properties: plant growth promotion (PGPB), suppression of phytopathogens, enhanced stress tolerance, participation in contaminant biodegradation, and heavy metal detoxification. The structure and functional potential of the microbiome vary between samples, potentially due to differences in source material and cultivation conditions. The obtained results expand our understanding of the composition and functions of endophytic bacteria in lettuce seeds, which is important for the development of novel biocontrol agents for plants consumed by humans in an unprocessed form. Full article

Desert plants host specialized microbiomes that contribute to their survival under extreme conditions; yet, niche and specific microbial dynamics remain poorly understood. In this study, we used 16S rRNA amplicon sequencing to characterize the bacterial communities associated with Leptadenia pyrotechnica, which is a desert-adapted shrub. Five representative sample types were analyzed: rhizospheric soil from a non-arid adjacent location (control; S1); rhizospheric soil from the arid site (S4); and stem endosphere from the arid site (S5, S6, and S7). For each sample type, three biological replicates were collected from different healthy plants to ensure independence. Sequencing yielded high-quality datasets (89,000–134,000 reads/sample) with ASV retention ratios of 68–80%, confirming their sufficient depth for diversity profiling. Alpha diversity indices revealed a markedly greater richness in rhizospheric samples (e.g., S1 Shannon: 3.04; 530 ASVs) than in endosphere samples (Shannon < 1.0; ASVs ≤ 33), consistent with known gradients in desert plant microbiomes. Rarefaction curves confirmed the completeness of sampling. Beta diversity analyses, including PCoA and hierarchical clustering, showed clear segregation between rhizospheric and endophytic communities, indicating strong compartment-specific structuring. The rhizosphere was dominated by Actinobacteria (48%), Proteobacteria (32%), and Firmicutes (10%), whereas the stem endosphere was enriched in Proteobacteria (45%) and Actinobacteria (40%). Taxonomic profiling revealed that Bacillota and Actinomycetota dominated rhizospheric soils, including Bacillus licheniformis, while stem tissues were enriched in Cyanobacteriota and Alphaproteobacteria, suggesting host-driven filtering. Genera such as Cupriavidus, Massilia, and Noviherbaspirillum were exclusive to the rhizosphere, while Paracholeplasma appeared uniquely in stem sample S6. Archaea and rare phyla were nearly absent. The current findings indicate that L. pyrotechnica harbors distinct microbial assemblages in rhizospheric and endophytic niches, reflecting microhabitat-driven selection. These microbial communities may contribute to host resilience by harboring taxa with potential stress-tolerance traits, offering insights for microbiome-informed strategies in arid land restoration. Full article

Plant-associated microbiomes play a critical role in plant health, nutrition, growth, and adaptation. This study aimed to investigate the formation pathways of the endospheric microbiome in lettuce (Lactuca sativa) through vertical (seed) and horizontal (substrate) transmission in hydroponic and soil environments. The bacterial microbiomes from the seeds, roots, leaves, and substrates were analyzed via 16S rRNA gene sequencing. The seed microbiome contained 236 OTUs dominated by Verrucomicrobia (31%) and Firmicutes (29%). Rhizospheric soil contained 1594 OTUs, while the hydroponic solution had 448 OTUs. The root endosphere from soil-grown lettuce contained 295 OTUs, compared with 177 in hydroponic conditions, and the leaf microbiome contained 43 OTUs in soil and 115 OTUs in hydroponics. In total, 30–51% of the leaf and root microbiomes originated from the seed microbiota, while 53–65% of the root microbiome originated from the substrate. Microbiome overlap was observed between the rhizospheric soil and the root microbiome. This study provides new insights into the microbiome of lettuce seeds and the pathways of formation of the endospheric microbiome in adult plants. These findings lay the groundwork for future research aimed at better understanding microbiome dynamics in leafy crops and plant protection. Full article

Cultivated pasture grasses contribute forage to more than 40% of cattle produced in 11 southern states in the USA. In recent years the increasing intoxication of cattle feeding on pasture grasses raised serious concerns about their palatability. While molecular and metagenomics techniques have revealed the great diversity of microbial composition and functional richness of the grass endosphere microbiome, meta-sequencing techniques enable us to gain a bird’s-eye view of all plant-associated microbiomes as a ‘holobiont’. Plant holobionts provide a more comprehensive approach where one can define the functions of microbial communities and feedback between the core and satellite microbiomes of a targeted host. In the near future we will be able to tailor our grasses and their endosphere microbiomes through the host-directed selection of a ‘modular microbiome’, leading to ‘plant enhanced holobionts’ as a microbiome-driven solution to managing the intoxication of pasture grasses in livestock. The present review aims to understand the potential co-relation between the endosphere microbiome community composition and mycotoxin production in forage grasses in the southern United States. Full article

Seagrass meadows play a critical role in biogeochemical cycling, especially in nitrogen and sulphur processes, driven by their associated microbiome. This study provides a novel functional analysis of microbial communities in seagrass (Zostera marina) rhizosphere and endosphere, comparing seedlings and mature plants. While nitrogen-fixing bacteria are more abundant in seedlings, mature plants exhibit greater microbial diversity and stability. Sediment samples show higher microbial diversity than roots, suggesting distinct niche environments in seagrass roots. Key microbial taxa (sulphur-oxidizing and nitrogen-cycling bacteria) were observed across developmental stages, with rapid establishment in seedlings aiding survival in sulphide-rich, anoxic sediments. Chromatiales, which oxidize sulphur, are hypothesized to support juvenile plant growth by mitigating sulphide toxicity, a key stressor in early development. Additionally, sulfate-reducing bacteria (SRB), though potentially harmful due to H₂S production, may also aid in nitrogen fixation by producing ammonium. The study underscores the dynamic relationship between seagrass and its microbiome, especially the differences in microbial community structure and function between juvenile and mature plants. The study emphasizes the need for a deeper understanding of microbial roles within the seagrass holobiont to aid with Blue Carbon stores and to improve restoration success, particularly for juvenile plants struggling to establish effective microbiomes. Full article

Plant microbiomes provide significant fitness advantages to their plant hosts, especially in the sub-nival belt. Studies to date have primarily focused on belowground communities in this region. Here, we utilized high-throughput DNA sequencing to quantify bacterial communities in the rhizosphere soil as well as in the root and leaf endosphere compartments of Silene nigrescens to uncover the differentiation and interconnections of these bacterial communities along the soil-to-plant continuum. Our findings reveal that the bacterial communities exhibit notable variation across different plant compartment niches: the rhizosphere soil, root endosphere, and leaf endosphere. There was a progressive decline in diversity, network complexity, network modularity, and niche breadth from the rhizosphere soil to the root endosphere, and further to the leaf endosphere. Conversely, both the host plant selection effect and the stability of these communities showed an increasing trend. Total nitrogen and total potassium emerged as crucial factors accounting for the observed differences in diversity and composition, respectively. Additionally, 3.6% of the total amplicon sequence variants (ASVs) were shared across the rhizosphere soil, root endosphere, and leaf endosphere. Source-tracking analysis further revealed bacterial community migration among these compartments. The genera Pseudomonas, IMCC26256, Mycobacterium, Phyllobacterium, and Sphingomonas constituted the core of the bacterial microbiome. These taxa are shared across all three compartment niches and function as key connector species. Notably, Pseudomonas stands out as the predominant taxon among these bacteria, with nitrogen being the most significant factor influencing its relative abundance. These findings deepen our understanding of the assembly principles and ecological dynamics of the plant microbiome in the sub-nival belt, offering an integrated framework for its study. Full article

Plant-associated microbes play a crucial role in plant adaptability by facilitating nutrient acquisition, growth, and stress resistance. However, the effects of herbicides on microbial communities in different root-associated niches and their impact on weed–microbe interactions are not well understood. Beckmannia syzigachne, a problematic weed, reduces crop yield and quality. In this study, we investigated bacterial and fungal community diversity in B. syzigachne using 16S and internal transcribed spacer (ITS) rRNA sequencing. Significant differences were observed in bacterial community structure across four root-associated niches, with diversity decreasing from bulk soil to endosphere. The sensitive genotype exhibited higher bacterial diversity compared to the resistant biotype, indicating that sample type is the primary factor influencing microbial community composition, with genotype playing a secondary role. Additionally, we examined fungal communities in sensitive and resistant populations, identifying 271 fungal operational taxonomic units (OTUs). Ascomycota, Basidiomycota, and Rozellomycota were dominant in the sensitive population, while the resistant population contained two unique OTUs, Saccharomyces sp. and Apiotrichum montevideense, which were absent in the sensitive population. This study provides insights into how bacterial and fungal communities in B. syzigachne populations respond to herbicide exposure, contributing to a deeper understanding of weed–microbe interactions. Full article

In the recent past, microbiome manipulation has emerged as a promising approach to improve plant growth performance by exploring the deep insight of plant–microbe interactions. The exploration of a plant microbiome either present on an ectosphere or endosphere can provide a far better understanding about the potential application of plant-associated microbes for the improvement of plant growth, protection from pathogen invasion, and tolerance to environmental stresses of a diverse nature. In this context, next-generation sequencing methods, omics approaches, and synthetic biology have made significant progress in plant microbiome research and are being frequently used to explore the intriguing role of plant-associated microorganisms. Despite the successfulness of conventional approaches, the incorporation of CRISPR/Cas9, RNA interference technology, rhizosphere engineering, microbiome engineering, and other manipulation techniques appear to be a promising approach to enhancing plant performance, and tolerance against biotic and abiotic stress factors. The present review presents the significance of plant microbe interaction, vital functional aspects, collaborative action, potential constraints, and finally the latest developments in bioengineering approaches destined for microbiome modulation with an objective to improve the performance of a host plant challenged with environmental stressors. Full article