Endosphere Compartments Research Articles

Rhizosphere-xylem sap connections in the olive tree microbiome: implications for biostimulation approaches.

Climate change is endangering olive groves. Farmers are adapting by exploring new varieties of olive trees and examining the role of microbiomes in plant health.The main objectives of this work were to determine the primary factors that influence the microbiome of olive trees and to analyze the connection between the rhizosphere and endosphere compartments. The rhizosphere and xylem sap microbiomes of two olive tree varieties were characterized by next-generation 16S rRNA amplicon sequencing, and soil descriptors were analyzed. Bacterial communities in the rhizosphere of olive trees were more diverse than those found in the xylem sap. Pseudomonadota, Actinobacteriota, Acidobacteriota, and Bacillota were the dominant phyla in both compartments. At the genus level, only very few taxa were shared between soil and sap bacterial communities. The composition of the bacteriome was more affected by the plant compartment than by the olive cultivar or soil properties, and a direct route from the rhizosphere to the endosphere could not be confirmed. The large number of plant growth-promoting bacteria found in both compartments provides promising prospects for improving agricultural outcomes through microbiome engineering.

Endophytic bacteria in the periglacial plant Potentilla fruticosa var. albicans are influenced by habitat type

BackgroundMicrobial communities in different plant compartments are relatively independent entities. However, the influence of environmental factors on the microbial community in different compartments of periglacial plants remains unclear. In this study, we quantified the bacterial communities in the rhizosphere soil, as well as root and leaf endosphere compartments of a periglacial plant, Potentilla fruticosa var. albicans, using high-throughput DNA sequencing. Moreover, we evaluated the impacts of habitat types (glacier terminus zone, moraine ridge, and alpine meadow) on the bacterial community in different plant compartments of Potentilla fruticosa var. albicans.ResultsOur results showed that habitat type had a significant effect on the alpha diversity (Chao1 richness) of endophytic bacteria, but not on the rhizospheric bacteria. The community composition of rhizospheric and endophytic bacteria was significantly different across the three habitats, and habitat type had a greater effect on the endophytic bacteria than on rhizospheric bacteria. The contribution of rhizosphere soil to the root and leaf endophytes decreased with the transformation of habitats from glacier terminus zone to alpine meadow. In contrast, host selection pressure sequentially increased from the glacier terminus zone to the moraine ridge to the alpine meadow. Furthermore, we found that the bacterial co-occurrence network in the alpine meadow was more modular but had lower complexity and connectedness than that in the glacier terminus zone. The bacterial community was governed primarily by stochastic processes regardless of habitat type.ConclusionThis study reveals that the diversity and composition of endophytic bacteria associated with Potentilla fruticosa var. albicans are more affected by habitat types than that of rhizospheric bacteria. Our study also demonstrates that the assembly patterns and co-occurrence patterns of bacterial communities associated with Potentilla fruticosa var. albicans vary by habitat type. These results advance the current understanding of community assembly and ecological interactions of microbial communities associated with periglacial plants.

Variations in microbial assemblage between rhizosphere and root endosphere microbiomes contribute to host plant growth under cadmium stress.

In this study, we revealed that the variation in rhizosphere and root endosphere microbial assemblage between host plant ecotypes contribute to their differential abilities to withstand cadmium (Cd) stressors. Furthermore, our study found that phenolic compounds, such as benzenoids and flavonoids, could function as both essential carbon sources and semiochemicals, thereby contributing to the assemblage of rhizosphere microbiome to resist Cd stress. Our findings provide new insights into the mechanisms that drive the differential assemblage of rhizosphere and root endosphere microbiomes to enhance plant growth under abiotic stress.

Differed Growth Stage Dynamics of Root-Associated Bacterial and Fungal Community Structure Associated with Halophytic Plant Lycium ruthenicum.

Lycium ruthenicum, a halophytic shrub, has been used to remediate saline soils in northwest China. However, little is known about its root-associated microbial community and how it may be affected by the plant’s growth cycle. In this study, we investigate the microbial community structure of L. ruthenicum by examining three root compartments (rhizosphere, rhizoplane, and endosphere) during four growth stages (vegetative, flowering, fruiting, and senescence). The microbial community diversity and composition were determined by Illumina MiSeq sequencing of the 16S V3–V4 and 18S ITS regions. Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, and Acidobacteria were the dominant bacterial phyla, while Ascomycota, Basidiomycota, and Mortierellomycota were the most dominant fungal phyla. The alpha diversity of the bacterial communities was highest in the rhizosphere and decreased from the rhizosphere to the endosphere compartments; the fungal communities did not show a consistent trend. The rhizosphere, rhizoplane, and endosphere had distinct bacterial community structures among the three root compartments and from the bulk soil. Additionally, PERMANOVA indicated that the effect of rhizocompartments explained a large proportion of the total community variation. Differential and biomarker analysis not only revealed that each compartment had unique biomarkers and was enriched for specific bacteria, but also that the biomarkers changed with the plant growth cycle. Fungi were also affected by the rhizocompartment, but to a much less so than bacteria, with significant differences in the community composition along the root compartments observed only during the vegetative and flowering stages. Instead, the growth stages appear to account for most of the fungal community variation as demonstrated by PCoA and NMDS, and supported by differential and biomarker analysis, which revealed that the fungal community composition in the rhizosphere and endosphere were dynamic in response to the growth stage. Many enriched OTUs or biomarkers that were identified in the root compartments were potentially beneficial to the plant, meanwhile, some harmful OTUs were excluded from the root, implying that the host plant can select for beneficial bacteria and fungi, which can promote plant growth or increase salt tolerance. In conclusion, the root compartment and growth stage were both determinant factors in structuring the microbial communities of L. ruthenicum, but the effects were different in bacteria and fungi, suggesting that bacterial and fungal community structures respond differently to these growth factors.

Microbiomes of Antarctic pearlwort (Colobanthus quitensis) of the maritime Antarctic: distinct diversity and core microbes in rhizosphere and endosphere compartments of the plant

Microbiomes of Antarctic pearlwort (Colobanthus quitensis) of the maritime Antarctic: distinct diversity and core microbes in rhizosphere and endosphere compartments of the plant

Grazing Affects Bacterial and Fungal Diversities and Communities in the Rhizosphere and Endosphere Compartments of Leymus chinensis through Regulating Nutrient and Ion Distribution.

Plant-associated endophytic microorganisms are essential to developing successful strategies for sustainable agriculture. Grazing is an effective practice of grassland utilization through regulating multitrophic relationships in natural grasslands. This study was conducted for exploring the effects of grazing on the diversities and communities of bacteria and fungi presented in rhizosphere soils, roots, stems, and leaves of Leymus chinensis (L. chinensis), based on high-throughput sequencing. Grazing increased bacterial diversity but reduced fungal diversity in plant leaves. Further analysis confirmed that the abundance of Chloroflexi, Gemmatimonadota, Nitrospirota, Sordariales, and Pezizales in plant leaves was increased by grazing. The Bray–Curtis similarities of microbial communities in the endosphere were higher under grazing plots than non-grazing plots. Moreover, the bacterial communities were significantly correlated with ions, while the nutrient and negative ions exhibited strong influence on fungal communities. We concluded that grazing-induced changes of microbial diversities and communities in different compartments of a dominant perennial grass (L. chinensis) could be attributed to the nutrient and ion distribution in host plant. The current study highlights the importance of livestock in mediating diversities and communities of endophytic microbes, and will be useful for better understanding the complexity of multitrophic interactions in a grassland ecosystem.

Assembly and variation of root-associated microbiota of rice during their vegetative growth phase with and without lindane pollutant

Soil-derived microbiota associated with plant roots are conducive to plant growth and stress resistance. However, the spatio-temporal dynamics of microbiota in response to organochlorine pollution during the unstable vegetative growth phase of rice is not well understood. In this study, we focused on the rice (Oryza sativa L.) microbiota across the bulk soil, rhizosphere and endosphere compartments during the vegetative growth phase in two different soils with and without lindane pollutant. The results showed that the factors of growth time, soil types and rhizo-compartments had significant influence on the microbial communities of rice, while lindane mostly stimulated the construction of endosphere microbiota at the vegetative phase. Active rice root-soil-microbe interactions induced an inhibition effect on lindane removal at the later vegetative growth phase in rice-growth-dependent anaerobic condition, likely due to the root oxygen loss and microbial mediated co-occurring competitive electron-consuming redox processes in soils. Each rhizo-compartment owned distinct microbial communities, and therefore, presented specific ecologically functional categories, while the moderate functional differences were also affected by plants species and residual pollution stress. This work revealed the underground micro-ecological process of microbiota and especially their potential linkage to the natural attenuation of residual organochlorine such as lindane.

Effect of Inorganic N Top Dressing and Trichoderma harzianum Seed-Inoculation on Crop Yield and the Shaping of Root Microbial Communities of Wheat Plants Cultivated Under High Basal N Fertilization.

Wheat crop production needs nitrogen (N) for ensuring yield and quality. High doses of inorganic N fertilizer are applied to soil before sowing (basal dressing), with additional doses supplied along the cultivation (top dressing). Here, a long-term wheat field trial (12 plots), including four conditions (control, N top dressing, Trichoderma harzianum T34 seed-inoculation, and top dressing plus T34) in triplicate, was performed to assess, under high basal N fertilization, the influence of these treatments on crop yield and root microbial community shaping. Crop yield was not affected by top dressing and T. harzianum T34, but top dressing significantly increased grain protein and gluten contents. Twenty-seven-week old wheat plants were collected at 12 days after top dressing application and sampled as bulk soil, rhizosphere and root endosphere compartments in order to analyze their bacterial and fungal assemblies by 16S rDNA and ITS2 high-throughput sequencing, respectively. Significant differences for bacterial and fungal richness and diversity were detected among the three compartments with a microbial decline from bulk soil to root endosphere. The most abundant wheat root phyla were Proteobacteria and Actinobacteria for bacteria, and Ascomycota and Basidiomycota for fungi. An enrichment of genera commonly associated with soils subjected to chemical N fertilization was observed: Kaistobacter, Mortierella, and Solicoccozyma in bulk soil, Olpidium in rhizosphere, and Janthinobacterium and Pedobacter in root endosphere. Taxa whose abundance significantly differed among conditions within each compartment were identified. Results show that: (i) single or strain T34-combined application of N top dressing affected to a greater extent the bulk soil bacterial levels than the use of T34 alone; (ii) when N top dressing and T34 were applied in combination, the N fertilizer played a more decisive role in the bacterial microbiome than T34; (iii) many genera of plant beneficial bacteria, negatively affected by N top dressing, were increased by the application of T34 alone; (iv) bulk soil and rhizosphere fungal microbiomes were affected by any of the three treatments assayed; and (v) all treatments reduced Claroideoglomus in bulk soil but the single application of T34 raised the rhizosphere levels of this mycorrhizal fungus.

Growth of Arabidopsis thaliana in rhizobox culture system evaluated through the lens of root microbiome

The present study provides an insight on physiological parameters and root-associated microbiome of two complementary Arabidopsis thaliana culture systems suitable for physiological studies. Methods: A. thaliana plants were grown in rhizobox and in classic pot culture. An analysis of plant growth parameters along with the characterization of the bacterial communities of the compost and the rhizosphere, rhizoplane and endosphere compartments were performed. Results: A. thaliana plants grown in rhizobox exhibited a plant habitus similar to those grown in pots during the first month, but with a delayed leaf initiation and slower rate of growth over the experiment. No nutrient deficiency symptoms were observed in these plants. The rhizobox design permits the migration of bacteria from compost to plant roots and allowed root-bacteria interactions to be established as in traditional pot culture. Some differences into the composition of the rhizobiome were highlighted between the two culture systems. Nevertheless, key bacterial taxa that help to ensure plant growth and health colonized the rhizo- and endosphere compartments in both systems. Conclusions: This study gives some clues for future research programs and selection of efficient root systems with the use of such specific culture devices.

Endophytic Microbiome of Biofuel Plant Miscanthus sinensis (Poaceae) Interacts with Environmental Gradients.

Miscanthus in Taiwan occupies a cline along altitude and adapts to diverse environments, e.g., habitats of high salinity and volcanoes. Rhizospheric and endophytic bacteria may help Miscanthus acclimate to those stresses. The relative contributions of rhizosphere vs. endosphere compartments to the adaptation remain unknown. Here, we used targeted metagenomics to compare the microbial communities in the rhizosphere and endosphere among ecotypes of M. sinensis that dwell habitats under different stresses. Proteobacteria and Actinobacteria predominated in the endosphere. Diverse phyla constituted the rhizosphere microbiome, including a core microbiome found consistently across habitats. In endosphere, the predominance of the bacteria colonizing from the surrounding soil suggests that soil recruitment must have subsequently determined the endophytic microbiome in Miscanthus roots. In endosphere, the bacterial diversity decreased with the altitude, likely corresponding to rising limitation to microorganisms according to the species-energy theory. Specific endophytes were associated with different environmental stresses, e.g., Pseudomonas spp. for alpine and Agrobacterium spp. for coastal habitats. This suggests Miscanthus actively recruits an endosphere microbiome from the rhizosphere it influences.

Leaf and Root Endospheres Harbor Lower Fungal Diversity and Less Complex Fungal Co-occurrence Patterns Than Rhizosphere.

Plant-associated microbiomes are key determinants of host-plant fitness, productivity, and function. However, compared to bacterial community, we still lack fundamental knowledge concerning the variation in the fungal microbiome at the plant niche level. In this study, we quantified the fungal communities in the rhizosphere soil, as well as leaf and root endosphere compartments of a subtropical island shrub, Mussaenda kwangtungensis, using high-throughput DNA sequencing. We found that fungal microbiomes varied significantly across different plant compartments. Rhizosphere soil exhibited the highest level of fungal diversity, whereas the lowest level was found in the leaf endosphere. Further, the fungal communities inhabiting the root endosphere shared a greater proportion of fungal operational taxonomic units (OTUs) with rhizosphere communities than with leaf fungal endophyte communities, despite significant separation in community structure between the two belowground compartments. The fungal co-occurrence networks in the three compartments of M. kwangtungensis showed scale-free features and non-random co-occurrence patterns and matched the topological properties of small-world and evidently modular structure. Additionally, the rhizosphere network was more complex and showed higher centrality and connectedness than the leaf and root endosphere networks. Overall, our findings provide comprehensive insights into the structural variability, niche differentiation, and co-occurrence patterns in the plant associated fungal microbiome.

Plant compartment and genetic variation drive microbiome composition in switchgrass roots

SummarySwitchgrass (Panicum virgatum) is a promising biofuel crop native to the United States with genotypes that are adapted to a wide range of distinct ecosystems. Various plants have been shown to undergo symbioses with plant growth‐promoting bacteria and fungi, however, plant‐associated microbial communities of switchgrass have not been extensively studied to date. We present 16S ribosomal RNA gene and internal transcribed spacer (ITS) data of rhizosphere and root endosphere compartments of four switchgrass genotypes to test the hypothesis that host selection of its root microbiota prevails after transfer to non‐native soil. We show that differences in bacterial, archaeal and fungal community composition and diversity are strongly driven by plant compartment and switchgrass genotypes and ecotypes. Plant‐associated microbiota show an enrichment in Alphaproteobacteria and Actinobacteria as well as Sordariales and Pleosporales compared with the surrounding soil. Root associated compartments display low‐complexity communities dominated and enriched in Actinobacteria, in particular Streptomyces, in the lowland genotypes, and in Alphaproteobacteria, specifically Sphingobium, in the upland genotypes. Our comprehensive root analysis serves as a snapshot of host‐specific bacterial and fungal associations of switchgrass in the field and confirms that host‐selected microbiomes persist after transfer to non‐native soil.

Bacterial Root Microbiome of Plants Growing in Oil Sands Reclamation Covers.

Oil sands mining in northern Alberta impacts a large footprint, but the industry is committed to reclaim all disturbed land to an ecologically healthy state in response to environmental regulations. However, these newly reconstructed landscapes may be limited by several factors that include low soil nutrient levels and reduced microbial activity. Rhizosphere microorganisms colonize plant roots providing hosts with nutrients, stimulating growth, suppressing disease and increasing tolerance to abiotic stress. High-throughput sequencing techniques can be used to provide a detailed characterization of microbial community structure. This study used 16S rRNA amplicon sequencing to characterize the bacterial root microbiome associated with annual barley (Hordeum vulgare) and sweet clover (Melilotus albus) growing in an oil sands reclamation area. Our results indicate that Proteobacteria dominated the endosphere, whereas other phyla such as Acidobacteria and Gemmatimonadetes were restricted to the rhizosphere, suggesting that plants have the ability to select for certain soil bacterial consortia. The bacterial community in the endosphere compartments were less rich and diverse compared to the rhizosphere. Furthermore, it was apparent that sweet clover plants were more selective, as the community exhibited a lower richness and diversity compared to barley. Members of the family Rhizobiaceae, such as Sinorhizobium and Rhizobium were mainly associated with clover, whereas Acholeplasma (wall-less bacteria transmitted by insects) was unique to barley. Genera from the Enterobacteriaceae family, such as Yersinia and Lentzea were also mostly detected in barley, while other genera such Pseudomonas and Pantoea were able to successfully colonize both plants. Endophytic bacterial profiles varied within the same plant species at different sampling locations; however, these differences were driven by factors other than slope positions or cover management. Our results suggest that bacterial endophytic communities of plants growing in land reclamation systems are a subset of the rhizosphere community and selection is driven by plant factors.

Biocontrol and plant growth promoting properties of Streptomyces mutabilis strain IA1 isolated from a Saharan soil on wheat seedlings and visualization of its niches of colonization

In this study, the biocontrol ability and colonization behavior of a highly antagonistic Streptomyces mutabilis strain, named IA1, recently isolated from a Saharan soil, were assessed on wheat seedlings. In this study we showed that strain IA1 secretes IAA and GA3 and is able to enhance growth of wheat seedlings. Using DOPE-FISH coupled with confocal laser scanning microscopy (CLSM), we observed moreover that following caryopsis inoculation and plant growth the strain can colonize the rhizoplane, the surface of caryopsis as well as the endorhiza, crossing from the rhizodermis up to the vascular system. Interestingly, further visualizations revealed that the actinobacterial strain could also be endophytic inside the caryopsis up to the endocarp layer (the dried fruit part, not the seed part of grain). Disease caused by Fusariumculmorum was further evaluated on seedlings and results showed that coated seeds with strain IA1 can reduce both disease occurrence (64.7%) and decrease severity (79.6%). This study showed that strain IA1 derived from a Saharan soil could protect a temperate crop from F. culmorum seedling blight, promote growth and colonize various niches on the surfaces of the phytosphere (roots, seeds) as well as plant endosphere compartments.