Search Results (64)

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

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

The study aimed to investigate the effect of soil textural or soil mineral fraction substrates (loam and gravel) from karst desertification areas on the rhizospheric and root-associated bacterial community structure of Dalbergia odorifera (an N-fixing tree), using high-throughput sequencing techniques, based on treatment methods of whole-root and two-chambered split-root systems. Further, this study determined the relative importance of the plant and substrate properties on the rhizospheric, non-rhizospheric and endospheric bacteria composition. The type of substrate exerts a significant influence on both rhizospheric and non-rhizospheric bacterial communities, whereas endophytic communities within the root system are predominantly determined by plant species rather than substrate type. The analysis revealed that endospheric bacterial diversity was considerably lower than that of rhizospheric and non-rhizospheric communities. Cluster analysis indicated that endospheric bacterial samples formed a distinct cluster, while rhizospheric and non-rhizospheric bacteria in the soil substrate grouped into one branch, and those in the gravel substrate formed another branch. In comparison to the gravel treatments, a reduced bacterial abundance was observed in the rhizosphere and non-rhizosphere of nitrogen-fixing plants in soil, potentially due to the interplay of lower nutrient availability and increased porosity in gravel treatments. Proteobacteria, which are involved in the nitrogen cycle, exhibited the highest abundance. In contrast, Acidobacteria, Firmicutes and other bacterial phyla involved in nutrient cycling demonstrated higher abundance, with their presence being more pronounced in extreme environments, such as gravel treatments, compared to soil substrates. These results suggest that nitrogen-fixing plants can respond to extreme environments by increasing bacterial abundance. The findings of this study provide a theoretical basis for the use of D. odorifera for ecosystem recovery and vegetation restoration. Full article

The assembly of plant root microbiomes is a dynamic process. Understanding the roles of root-associated microbiomes in rice development requires dissecting their assembly throughout the rice life cycle under diverse environments and exploring correlations with soil properties and rice physiology. In this study, we performed amplicon sequencing targeting fungal ITS and the bacterial 16S rRNA gene to characterize and compare bacterial and fungal community dynamics of the rice root endosphere and soil in organic and conventional paddy fields. Our analysis revealed that root microbial diversity and composition was significantly influenced by agricultural practices and rice developmental stages (p < 0.05). The root microbiome in the organic paddy field showed greater temporal variability, with typical methane-oxidizing bacteria accumulating during the tillering stage and the amount of symbiotic nitrogen-fixing bacteria increasing dramatically at the early ripening stage. Redundancy analysis identified ammonium nitrogen, iron, and soil organic matter as key drivers of microbial composition. Furthermore, correlation analysis between developmental stage-enriched bacterial biomarkers in rice roots and leaf mineral nutrients showed that highly mobile macronutrient concentrations positively correlated with early-stage biomarkers and negatively correlated with later-stage biomarkers in both paddy fields. Notably, later-stage biomarkers in the conventional paddy field tended to show stronger correlations with low-mobility nutrients. These findings suggest potential strategies for optimizing microbiome management to enhance productivity and sustainability. Full article

This study aimed to investigate the impact of nitrogen (N) fertilizer on bacterial community composition and diversity in the rhizosphere and endosphere of rice at different growth stages. Two treatments, N0 (no N application) and N1 (270 kg N ha⁻¹), were implemented, with samples collected during the jointing, tasseling, and maturity stages. High-throughput sequencing was used to analyze the structure and composition of bacterial communities associated with Huaidao No. 5 (japonica conventional rice). The findings indicated that root zone location was the primary factor influencing the diversity and composition of rice root-associated bacterial communities. Further analysis revealed that nitrogen fertilizer primarily influenced rhizosphere bacterial diversity, while endosphere bacterial diversity was more significantly affected by growth stages. Rice recruited distinct beneficial bacteria in the rhizosphere and endosphere depending on the growth stage. Additionally, the relative abundance of functional genes related to nitrogen metabolism in root-associated bacteria was not significantly influenced by nitrogen application at 270 kg N ha⁻¹. These findings offer valuable insights into how nitrogen fertilizer affects plant root bacterial communities across different growth stages. Full article

Drought stress has a significant impact on agricultural productivity, affecting key crops such as soybeans, the second most widely cultivated crop in the United States. Endophytic and rhizospheric microbial diversity analyses were conducted with soybean plants cultivated during the 2023 growing season amid extreme weather conditions of prolonged high temperatures and drought in Louisiana. Specifically, surviving and non-surviving soybean plants were collected from two plots of a Louisiana soybean field severely damaged by extreme heat and drought conditions in 2023. Although no significant difference was observed between surviving and non-surviving plants in microbial diversity of the rhizosphere, obvious differences were found in the structure of the endophytic microbial community in root tissues between the two plant conditions. In particular, the bacterial genera belonging to Proteobacteria, Pseudomonas and Pantoea, were predominant in the surviving root tissues, while the bacterial genus Streptomyces was conspicuously dominant in the non-surviving (dead) root tissues. Co-occurrence patterns and network centrality analyses enabled us to discern the intricate characteristics of operational taxonomic units (OTUs) within endophytic and rhizospheric networks. Additionally, we isolated and identified bacterial strains that enhanced soybean tolerance to drought stresses, which were sourced from soybean plants under a drought field condition. The 16S rDNA sequence analysis revealed that the beneficial bacterial strains belong to the genera Acinetobacter, Pseudomonas, Enterobacter, and Stenotrophomonas. Specific bacterial strains, particularly those identified as Acinetobacter pittii and Pseudomonas sp., significantly enhanced plant growth metrics and reduced drought stress indices in soybean plants through seed treatment. Overall, this study advances our understanding of the soybean-associated microbiome structure under drought stress, paving the way for future research to develop innovative strategies and biological tools for enhancing soybean resilience to drought. Full article

Endophytic bacteria play crucial roles in plant pathogen protection and growth. Oryza eichingeri is a unique wild rice species rich with genetic resources. Studies have explored beneficial endophytic bacteria and investigated the synergistic interaction between microbes and wild rice. However, the endophytic bacterial community of Oryza eichingeri and their plant growth-promoting (PGP) abilities characteristics remain largely unknown. Here, endophytic bacteria in the root, stem, and leaf tissues of Oryza eichingeri were characterized using metagenomic Illumina 16S rRNA gene sequencing. Additionally, culturable endophytic bacteria were isolated. The metagenomic analysis showed that, compared to those in other tissue compartments, the endophytic bacterial community in the roots had a more complex structure and enhanced functions, and each compartment had its own specific endophytic bacterial biomarkers. A total of 94 endophytic bacteria were isolated from Oryza eichingeri, among which 80 strains possessed PGP traits including increasing phosphate solubilization, siderophore production, IAA production, and nitrogen fixation. These strains displayed good PGP effects on cultivated rice seedlings, promoting the formation of strong root systems, stimulating biomass accumulation, and increasing root length and plant height. These findings provide insights into the composition of the bacterial endosphere of Oryza eichingeri and potential applications of the dominant PGP bacteria in rice cultivation. Full article

Raising rice (Oryza sativa L.) seedlings under LED lighting reduces nursing space and labor while ensuring health and quality. This study compared rice seedlings grown under natural light (NL) and LED lighting (AL), with and without inoculation of the beneficial fungus Falciphora oryzae. The results showed that NL-grown seedlings had greater stem diameters and shoot and root weights. The AL treatment induced higher plant height in some cultivars and longer root lengths in others. Microbial inoculation minimally affected phenotypes but increased root length in one cultivar. Chlorophyll content was unchanged across the treatments, while malondialdehyde (MDA) levels rose under AL in one cultivar, and catalase (CAT) levels were elevated in two cultivars under AL. Microbial inoculation reduced CAT levels under AL. The AL + M treatment increased rhizosphere prokaryotic community evenness and altered prokaryotic compositions in the rhizosphere and root endosphere, with Burkholderia and Paraburkholderia taxa showing differential responses to the treatments. These findings underscore the role of microbial inoculation in enhancing rice seedling health and resilience under artificial lighting, contributing to sustainable agriculture and food security. Full article

Atractylodes macrocephala, a perennial herb widely used in traditional Chinese medicine, is highly prone to root rot, which significantly reduces its yield and quality. This study compared the physicochemical properties of soil from healthy and diseased A. macrocephala plants and analyzed the microbial diversity in the endophytic, rhizosphere, and root zone soils. The results showed that the diseased plants had higher levels of available potassium and electrical conductivity in the rhizosphere, both positively correlated with the severity of root rot, while soil pH was negatively correlated. The diversity and richness of endophytic bacterial and fungal communities were significantly reduced in diseased plants. Additionally, root rot led to major changes in the rhizosphere microbial community, with an increased abundance of Proteobacteria and Ascomycota, and a decrease in Firmicutes, Bacteroidetes, Actinobacteria, and Basidiomycota. Fusarium oxysporum, Fusarium solani, and Fusarium fujikuroi were identified as key pathogens associated with root rot. This study enhances our understanding of the microbial interactions in soils affected by root rot, offering a foundation for developing soil improvement and biological control strategies to mitigate this disease in A. macrocephala cultivation. Full article

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

The root microbiota plays a crucial role in assisting the plant host in combating various biotic and abiotic stresses, notably drought, which poses a significant threat to global food security. Despite extensive efforts to understand the shifts in rhizosphere and endosphere bacteriomes, there remains a gap in comprehending how drought stress influences the co-occurring network patterns within these compartments and their ecological functional potentials. To address this gap, a pot experiment was conducted with two treatments: continuous flooding as a control and drought treatment. Bulk soil, rhizosphere, and endosphere samples were collected and subjected to high-throughput sequencing and bioinformatics analysis. The results revealed that drought stress significantly reduced the rice biomass but increased the Shannon diversity index in both the rhizosphere and endosphere bacterial communities with no observable effect on richness across compartments. Additionally, drought treatment markedly altered the community structure and bacterial assemblages in these compartments, resulting in the specific enrichment of Actinobacteriota, Gemmatimonadetes, and Patescibacteria, while Bacteroidetes and Firmicutes were depleted in the rhizosphere and endosphere. Furthermore, drought heightened the complexity of the co-occurring networks and the proportions of positive links across all sampling compartments; this effect was accompanied by an increase in the number of connectors in the bulk soil and rhizosphere, as well as module hubs in the rhizosphere. Functional potential prediction indicated that drought stress significantly altered multiple potential ecological functions across all sampling compartments, particularly enriching functions related to the oxidation of sulfur, manganese, and hydrogen in the bulk soil, while functions associated with iron oxidation were significantly depleted in the rhizosphere. Overall, our results demonstrate that under drought stress, rice may specifically enrich certain bacterial taxa and enhance their positive interactions within its root system to improve adaptation. Full article

The search for new biodegradable fertilizers to increase the productivity of agricultural plants is an urgent task. In this study, a complex microfertilizer was developed based on a chelating agent—glutamic-N,N-diacetic acid (GLDA). The evaluation encompassed assessments of biodegradability and effectiveness in fostering lettuce plant growth in hydroponic and conventional soil settings. The impact on endospheric bacteria, a sensitive indicator, was also examined. Results indicated a 59.8% degradation rate of the GLDA complex on the 28th day. The most notable positive effects were observed in above-ground plant biomass, with a 4.6-fold increase for hydroponics and 1.5 to 1.8-fold increases for root and foliar treatments in soil. In hydroponics, GLDA-treated plants showed 24 and 45 operational taxonomic units (OTUs) for leaves and 272 and 258 for roots (GLDA-treated and control plants). In soil, the OTU counts were 270 and 101, 221 and 111, and 198 and 116 in the leaves and roots of GLDA-treated and control plants (under root and foliar treatments), respectively. Non-metric multidimensional scaling (NMDS) and Indicator Species Analysis (ISA) demonstrated significant distinctions in endospheric communities between substrates (hydroponics and soil) in the presence of GLDA. Importantly, GLDA use simplified the composition of endospheric bacterial communities. Full article

Microorganisms associated with plants play a crucial role in their growth, development, and overall health. However, much remains unclear regarding the relative significance of tree species identity and spatial variation in shaping the distribution of plant bacterial communities across large tropical regions, as well as how these communities respond to environmental changes. In this study, we aimed to elucidate the characteristics of bacterial community composition in association with two rare and endangered tropical tree species, Dacrydium pectinatum and Vatica mangachapoi, across various geographical locations on Hainan Island. Our findings can be summarized as follows: (1) Significant differences existed in the bacterial composition between D. pectinatum and V. mangachapoi, as observed in the diversity of bacterial populations within the root endosphere. Plant host-related variables, such as nitrogen content, emerged as key drivers influencing leaf bacterial community compositions, underscoring the substantial impact of plant identity on bacterial composition. (2) Environmental factors associated with geographical locations, including temperature and soil pH, predominantly drove changes in both leaf and root-associated bacterial community compositions. These findings underscored the influence of geographical locations on shaping plant-associated bacterial communities. (3) Further analysis revealed that geographical locations exerted a greater influence than tree species identity on bacterial community compositions and diversity. Overall, our study underscores that environmental variables tied to geographical location primarily dictate changes in plant bacterial community composition. These insights contribute to our understanding of microbial biogeography in tropical regions and carry significant implications for the conservation of rare and endangered tropical trees. Full article