Search Results (24)

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

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

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

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

Every land plant exists in a close relationship with microbial communities of several niches: rhizosphere, endosphere, phyllosphere, etc. The growth and yield of potato—a critical food crop worldwide—highly depend on the diversity and structure of the bacterial and fungal communities with which the potato plant coexists. The potato plant has a specific part, tubers, and the soil near the tubers as a sub-compartment is usually called the “geocaulosphere”, which is associated with the storage process and tare soil microbiome. Specific microbes can help the plant to adapt to particular environmental conditions and resist pathogens. There are a number of approaches to modulate the microbiome that provide organisms with desired features during inoculation. The mechanisms of plant–bacterial communication remain understudied, and for further engineering of microbiomes with particular features, the knowledge on the potato microbiome should be summarized. The most recent approaches to microbiome engineering include the construction of a synthetic microbial community or management of the plant microbiome using genome engineering. In this review, the various factors that determine the microbiome of potato and approaches that allow us to mitigate the negative impact of drought and pathogens are surveyed. Full article

The salinization of soils is a growing agricultural concern worldwide. Irrigation practices, drought, and climate change are leading to elevated salinity levels in many regions, resulting in reduced crop yields. However, there is potential for a solution in the microbiome of halophytes, which are naturally salt-tolerant plants. These plants harbor a salt-tolerant microbiome in their rhizosphere (around roots) and endosphere (within plant tissue). These bacteria may play a significant role in conferring salt tolerance to the host plants. This leads to the possibility of transferring these beneficial bacteria, known as salt-tolerant plant-growth-promoting bacteria (ST-PGPB), to salt-sensitive plants, enabling them to grow in salt-affected areas to improve crop productivity. In this review, the background of salt-tolerant microbiomes is discussed and their potential use as ST-PGPB inocula is explored. We focus on two Gram-negative bacterial genera, Halomonas and Kushneria, which are commonly found in highly saline environments. These genera have been found to be associated with some halophytes, suggesting their potential for facilitating ST-PGPB activity. The study of salt-tolerant microbiomes and their use as PGPB holds promise for addressing the challenges posed by soil salinity in the context of efforts to improve crop growth in salt-affected areas. Full article

Antibiotics enter the soil with compost prepared from livestock manures and other sources. There is concern that they may influence plant growth and cause antibiotic resistance in soil and plant endospheric microbiomes. In the present work, lettuce plants were cultivated in soil and hydroponics spiked with oxytetracycline (0, 15, and 300 mg × kg⁻¹ and 0, 15, and 50 mg × L^–1, respectively) during a 28-day greenhouse experiment. It was revealed that the antibiotic reduced the chlorophyll content, the biomass, and the length of the roots and stems by 1.4–4.7, 1.8–39, 2.5–3.2, and 1.8–6.3 times in soil and in hydroponics. The copy numbers of the tet(A) and tet(X) genes were revealed to be 4.51 × 10³–1.58 × 10⁵ and 8.36 × 10⁶–1.07 × 10⁸ copies × g^–1, respectively, suggesting the potential migration of these genes from soil/hydroponics to plant roots and leaves. According to a non-metric multidimensional scaling (NMDS) analysis of the 16S rRNA amplicon sequencing data, endospheric bacterial communities were similar in leaves and roots independent of the growing substrate and antibiotic concentration. While soil bacterial communities were unaffected by the presence of antibiotics, hydroponic communities exhibited dependency, likely attributable to the absence of the mitigating effect of soil particle absorption. Full article

The plant microbiome is one of the most important environments for ecological interactions between bacteria that impact the plant and the ecosystem. However, studies on the diversity of mobile genetic elements (such as plasmids) associated with the plant microbiome are very scarce. Here, we determined the bacterial community composition and the occurrence of plasmids in the microbiota associated with sea fig, Carpobrotus aequilaterus (N.E. Br.), a succulent species widely used as an ornamental plant in Chile. The abundance and composition of the endophytic and rhizospheric bacterial communities were determined by quantitative PCR (qPCR) and DNA metabarcoding analysis. Plasmid diversity in the plant microbiome was determined by plasmid DNA extraction and screened by endpoint PCR of backbone genes for four different incompatibility groups (Inc). The results showed about 106 copies of the 16S rRNA gene in the endosphere and rhizosphere, showing significant differences according to the diversity index. Proteobacteria (Pseudomonadota; 43.4%), Actinobacteria (Actinomycetota; 25.7%), and Bacteroidetes (Bacteroidota; 17.4%) were the most dominant taxa in both plant compartments, and chemoheterotrophy (30%) was the main predicted function assigned to the microbiota. Plasmid diversity analysis showed the presence of transferable plasmids in the endosphere and rhizosphere of C. aequilaterus, particularly among environmental plasmids belonging to the IncP and IncN incompatibility groups. Full article

Huanglongbing (HLB), also known as citrus greening, is an insidious disease in citrus and has become a threat to the sustainability of the citrus industry worldwide. In the U.S., Candidatus Liberibacter asiaticus (CLas) is the pathogen that is associated with HLB, an unculturable, phloem-limited bacteria, vectored by the Asian Citrus Psyllid (ACP, Diaphorina citri). There is no known cure nor treatment to effectively control HLB, and current control methods are primarily based on the use of insecticides and antibiotics, where effectiveness is limited and may have negative impacts on beneficial and non-target organisms. Thus, there is an urgent need for the development of effective and sustainable treatment options to reduce or eliminate CLas from infected trees. In the present study, we screened citrus-derived endophytes, their cell-free culture supernatants (CFCS), and crude plant extracts for antimicrobial activity against two culturable surrogates of CLas, Sinorhizobium meliloti and Liberibacter crescens. Candidates considered high-potential antimicrobial agents were assessed directly against CLas in vitro, using a propidium monoazide–based assay. As compared to the negative controls, statistically significant reductions of viable CLas cells were observed for each of the five bacterial CFCS. Subsequent 16S rRNA gene sequencing revealed that each of the five bacterial isolates were most closely related to Bacillus amyloliquefaciens, a species dominating the market of biological control products. As such, the aboveground endosphere of asymptomatic survivor citrus trees, grown in an organic orchard, were found to host bacterial endophytes capable of effectively disrupting CLas cell membranes. These results concur with the theory that native members of the citrus microbiome play a role in the development of HLB. Here, we identify five strains of Bacillus amyloliquefaciens demonstrating notable potential to be used as sources of novel antimicrobials for the sustainable management of HLB. Full article

The wheat (Triticum aestivum) microbiome is essential to its growth and adaptation under the current climatic crisis. Wheat breeding programs are often mainly focused on obtaining more resistant cultivars; thus, plant genotype-by-microbiome interactions have gained attention. In this sense, local wheat cultivars represent a unique opportunity to examine how bacterial communities are recruited and support plant growth under field conditions. In this study, we explored the diversity, community structure, and potential functions of root-associated bacterial communities of four Chilean wheat (Triticum aestivum) cultivars under field conditions through Illumina MiSeq. Analyses showed that Proteobacteria was the most abundant phylum in root endosphere (51.1 to 74.4%) and rhizosphere samples (39.3 to 44.9%) across wheat cultivars. Significant differences (p ≤ 0.05) in alpha and beta diversity were observed in root endosphere and rhizosphere samples, independently of wheat genotypes. Potassium was identified as the main factor driving the rhizosphere microbiomes of wheat. A higher proportion of shared operational taxonomic units (OTUs) were found in rhizosphere (mainly Pseudomonas, Flavobacterium, and Janthinobacterium) compared with root endosphere (dominated by Delftia, Acinetobacter, Stenotrophomonas, Kaistobacter) samples across all cultivars. Analyses of larger predicted functional activities revealed that chemoheterotrophy and aerobic chemoheterotrophy were more observed in the root endosphere environment, whereas among the minor functions, nitrogen cycling was the more predicted trait, related to rhizosphere samples. A co-occurrence analysis revealed complex bacterial interactions in wheat cultivars’ niche microbiomes identifying three (Comamonadaceae, Enterobacteraceae, Micrococcaceae) and four (Corynebacteraceae, Dermabacteraceae, Xanthomonadaceae, Staphylococcaceae) families as keystone taxa for the root endosphere and rhizosphere, respectively. It is suggested that such findings on the differences in root microbiomes associated with wheat cultivars under field conditions would help to develop new cultivars with abilities to recruit specific bacterial communities. Full article

Mal secco is a severe vascular citrus disease (MSD) caused by the mitosporic fungus Plenodomus tracheiphilus (Pt). The pathogen enters through wounds on the above- and below-ground parts of the tree. The susceptible species sour orange (Citrus aurantium) is the most commonly used rootstock for lemon trees in Italy. In this study, sour orange seedlings were wound-inoculated with P. tracheiphilus in leaves or roots. Six months post-inoculation, the microbial communities of rhizosphere, endorhizosphere, and xylem endosphere samples from inoculated and healthy plants were analyzed by 16S rRNA and ITS (internal transcribed spacer) amplicon sequencing. The DNA of Pt was quantified by real-time PCR in the three compartments. According to our results, the endorhizosphere of root-inoculated plants showed the highest concentration of the pathogen DNA. Bacterial populations of potentially beneficial taxa (e.g., Pseudomonas and Burkholderia) were depleted in the rhizosphere of the inoculated plants. Infection through leaves and roots also produced a network-wide rewiring of microbial associations in sour orange roots. Overall, our findings revealed community-level changes induced by Pt infection in the sour orange root and xylem microbiome, providing further insights into the beneficial multispecies interactions in Citrus-associated microbial communities. Full article

Agricultural practices can affect root-associated microbiota, but the effect of fertilization is still poorly examined. The aim of this study was to obtain 16S and ITS metagenomic profiles of tomato rhizosphere and root endosphere under mineral (NPK) fertilization in the open field experiment in the south of West Siberia. We found 6 bacterial and 3 fungal phyla in the roots and 24 bacterial and 16 fungal phyla in the rhizosphere. Proteobacteria and Actinobacteria together contributed 90% of the total number of sequence reads in roots and 50% in the rhizosphere, whereas Ascomycota ultimately prevailed in OTUs’ richness and abundance in both biotopes. Fertilization changed the relative abundance of 32 bacterial and 14 fungal OTUs in the rhizosphere and of 7 bacterial and 3 fungal OTUs in roots. The revealed root bacteriobiome response to conventional mineral NPK fertilization by the dominant taxa at the high taxonomic level (class) illustrates well the role of NPK-changed plant metabolism in shaping endophytic microbiota and hence fertilization potential in enhancing plant growth-promoting microorganisms and mitigating plant pathogens. Using fertilization rate gradient in further research may bring a more detailed understanding of how to modify and even fine-tune root-associated microbiomes in order to enhance crops’ health and yields. Full article

Plant roots recruit most prokaryotic members of their root microbiota from the locally available inoculum, but knowledge on the contribution of native microorganisms to the root microbiota of crops in native versus non-native areas remains scarce. We grew common bean (Phaseolus vulgaris) at a field site in its centre of domestication to characterise rhizosphere and endosphere bacterial communities at the vegetative, flowering, and pod filling stage. 16S r RNA gene amplicon sequencing of ten samples yielded 9,401,757 reads, of which 8,344,070 were assigned to 17,352 operational taxonomic units (OTUs). Rhizosphere communities were four times more diverse than in the endosphere and dominated by Actinobacteria, Bacteroidetes, Crenarchaeota, and Proteobacteria (endosphere: 99% Proteobacteria). We also detected high abundances of Gemmatimonadetes (6%), Chloroflexi (4%), and the archaeal phylum Thaumarchaeota (Candidatus Nitrososphaera: 11.5%): taxa less frequently reported from common bean rhizosphere. Among 154 OTUs with different abundances between vegetative and flowering stage, we detected increased read numbers of Chryseobacterium in the endosphere and a 40-fold increase in the abundances of OTUs classified as Rhizobium and Aeromonas (equivalent to 1.5% and over 6% of all reads in the rhizosphere). Our results indicate that bean recruits specific taxa into its microbiome when growing ‘at home’. Full article

Roots hold complex microbial communities at the soil–root interface, which can affect plant nutrition, growth, and health. Although the composition of plant microbiomes has been extensively described for various plant species and environments, little is known about the effect of wheat straw return (WSR) on the soybean root microbiota. We used Illumina-based 16S rRNA and ITS amplicon sequencing to track changes in bacterial and fungal microbiota in bulk soil and soybean rhizosphere, rhizoplane, s1and endosphere during the third and fourth years after implementing WSR in a wheat–soybean rotation system. The results revealed that WSR had a greater impact on fungal communities than bacterial communities, particularly in bulk soil, rhizosphere, and rhizoplane. WSR enriched the relative abundance of cellulose-degrading fungi (e.g., Acremonium, Trichoderma, and Myrmecridium, among which Trichoderma also had antimicrobial activity), saprotroph (e.g., Exophiala), and nitrogen cycling bacteria (e.g., Chryseolinea). Furthermore, WSR depleted the relative abundance of pathogenic fungi (e.g., Fusarium and Alternaria). These data revealed for the first time that WSR had diverse effects on soybean root-associated microbial community composition, not only in soil but also in the rhizosphere, rhizoplane, and endosphere. Full article