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"study-abstract": "The goal of the analyses was to investigate the structure of the bacterial rhizospheric microbiota able to colonize the tomato root-P. parasitica pathosystem. 16S rRNA gene sequencing was used to describe the composition of the rhizospheric sub-microbiota of Solanum lycopersicum able to colonize tomato roots either axenic or partly covered with P. parasitica biofilms. Sampling was performed the 31st of May 2014, on soil supporting tomato growth (Solanum lycopersicum cv. Marmande). The experimental site was an E-W-oriented greenhouse located at the INRA Pathologie Végétale research unit in Montfavet (43.9 N 4.8 E). Thirty rhizospheric samples were grouped by 10 into three biological replicates (R1, R2, R3) on the basis of the distribution of the three samples from each area in distinct replicates. Biosamples results from the incubation and then the adhesion of microbial suspensions from R1, R2 and R3 at the root surface of tomato seedlings. M1R1, M1R2 and M1R3 correspond to the sub-microbiota adhering to axenic roots. M2R1, M2R2 and M2R3 correspond to the sub-microbiota adhering to roots partly covered with P. parasitica biofilms. An amplicon library was constructed (V3-V5 primers) for the six biosamples and sequenced using Illumina MiSeq technology. Sequence data are cleaned according to the FastQC quality parameters.",
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"study-abstract": "Plants host at the contact zone with soil a distinctive root-associated bacterial microbiota believed to function in plant nutrition and health. We investigated the diversity of the root microbiota within a phylogenetic framework of hosts: three Arabidopsis thaliana ecotypes along with its sister species Arabidopsis halleri and Arabidopsis lyrata as well as Cardamine hirsuta, which diverged from the former ~35 myr ago. We surveyed their microbiota under controlled environmental conditions and of A. thaliana and C. hirsuta in two natural habitats. Deep 16S rRNA gene profiling of root and corresponding soil samples identified a total of 237 quantifiable bacterial ribotypes, of which an average of 73 community members were enriched in roots. The composition of this root microbiota depends more on interactions with the environment than with host species. Inter-host species microbiota diversity is largely quantitative and is greater between the 3 Arabidopsis species than the 3 A. thaliana ecotypes. Host species-specific microbiota were identified at the levels of individual community members, taxonomic groups and whole root communities. Most of these signatures were observed in the phylogenetically distant C. hirsuta. However, the branching order of host phylogeny is incongruent with inter-species root microbiota diversity, indicating that host phylogenetic distance alone cannot explain root microbiota diversification. Our work reveals within 35 myr of host divergence a largely conserved and taxonomically narrow root microbiota, which comprises stable community members belonging to the Actinomycetales, Burkholderiales and Flavobacteriales.",
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"study-abstract": "Ectomycorrhizal basidiomycetes and root-associated ascomycetes, including root-endophytic ascomycetes, are one of the most diverse and important belowground plant symbionts in dipterocarp rainforests. Our study aimed to compare the biodiversity, host association pattern, and community structure of ectomycorrhizal basidiomycetes with those of root-associated ascomycetes in a lowland dipterocarp rainforest in Southeast Asia. The host-plant chloroplast large-subunit of ribulose-1,5-bisphosphate caboxylase/oxygenase (rbcL) region, and fungal internal transcribed spacer 2 (ITS2) region were sequenced using a tag-encoded, massively parallel 454 pyrosequencing analysis to identify host plant and root-associated fungal taxa in root samples. In total, 1245 ascomycetous and 127 putative ectomycorrhizal basidiomycetous taxa were detected from 442 root samples. The putative ectomycorrhizal basidiomycetes were likely to be associated with phylogenetically closely related dipterocarp taxa to greater or lesser extents, whereas host association patterns of the root-associated ascomycetes were much less distinct. The community structure of the putative ectomycorrhizal basidiomycetes was possibly more influenced by the host genetic distances than that of the root-associated ascomycetes. This study also indicated that in dipterocarp rainforests, root-associated ascomycetes were characterized by high biodiversity and indistinct host association patterns, whereas ectomycorrhizal fungi showed less biodiversity and a strong host phylogenetic preference for dipterocarp trees. Our findings suggested that root-associated ascomycetes (e.g., root-endophytic ascomycetes, may have biodiversity hotspots in the tropics, whereas biodiversity of ectomycorrhizal basidiomycetes increased with host phylogenetic diversity.",
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"centre-name": "Toju Laboratory, Center for Ecological Research, Kyoto University",
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"study-abstract": "Based on high-throughput sequencing of root-associated fungi in forest ecosystems, we performed a comparative analysis of arbuscular mycorrhizal, ectomycorrhizal, and saprotrophic/endophytic associations across a latitudinal gradient from cool-temperate to subtropical regions.",
"study-name": "Community-scale properties of arbuscular mycorrhizal, ectomycorrhizal, and endophytic associations in temperate and subtropical forests",
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"last-update": "2022-03-16T23:49:46",
"secondary-accession": "ERP011833",
"centre-name": "UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL",
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"study-abstract": "Bacteria living on and in leaves and roots influence many aspects of their hosts’ health, so the extent of plant genetic control over their microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies may overestimate the influence of certain plant genes on the microbiome and fail to detect others, because they do a poor job simulating true environmental heterogeneity. We conducted a large-scale field experiment to disentangle the effects of genotype, environment, age, and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta, a wild perennial mustard. Genetic control of the microbiome varied substantially among sites, and bacterial community composition shifted as plants aged. Furthermore, a large proportion of leaf bacteria were shared with roots, suggesting inoculation from soil. Our results highlight the complexity of microbiome formation in natural environments.",
"study-name": "16S rRNA amplicons (V4 region) of bacteria living on and in roots and leaves of Boechera stricta from field experiments in the Rocky Mountains",
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"secondary-accession": "DRP005886",
"centre-name": "Department of Biology, Graduate School of Science, Kobe University",
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"study-abstract": "Study of mycorrhizal fungi community. DNA was extracted from root tips of mycoheterotrophic plants and references.",
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"study-abstract": "We monitored how the rice root microbiota changes over the course of the plant''s life cycle. We inspected how rhizocompartment, field geography, seasonal variation, and plant development rates affect this process.Using these data we formed a model to predict plant age and tested how abiotic factors affect microbiota development.",
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"last-update": "2020-06-21T08:24:05",
"secondary-accession": "ERP023912",
"centre-name": "Uppsala BioCenter",
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"study-abstract": "Plant roots select non-random communities of fungi and bacteria from the surrounding soil that have effects on their health and growth, but we know little about the factors influencing their composition. We profiled bacterial microbiomes associated with individual ectomycorrhizal Pinus sylvestris roots colonised by different fungi and analysed differences in microbiome structure related to soils from distinct podzol horizons and effects of short term additions of N, a growth-limiting nutrient commonly applied as a fertiliser, but known to influence patterns of carbon allocation to roots. Ectomycorrhizal roots growing in soil from different horizons harboured distinct bacterial communities. The fungi colonising individual roots had a strong effect on the associated bacterial communities. Even closely related species within the same ectomycorrhizal genus had distinct bacterial microbiomes in unfertilised soil, but fertilisation removed this specificity. Effects of N were rapid and context dependent, being influenced by both soil type and the particular ectomycorrhizal fungi involved. Fungal community composition changed in soil from all horizons, but bacteria only responded strongly to N in soil from the B horizon where community structure was different and bacterial diversity was significantly reduced, possibly reflecting changed carbon allocation patterns.",
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"secondary-accession": "SRP102519",
"centre-name": "UC Davis",
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"study-abstract": "Plant-associated microorganisms are essential for their hosts'' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial species sampled across relatively small spatial scales. We focus on the microbial communities associated with Zostera marina, a marine foundation species found throughout the Northern Hemisphere, by sampling microbial communities present on the leaf and root surfaces of 129 eelgrass individuals and sequencing amplified fragments of the V4 region of the 16S rRNA gene on an Illumina MiSeq. Additionally, we sampled microbial communities from adjacent water and sediments to highlight important differences in the communities compared to those associated with plants. This study will allow us to compare global differences and detect assembly mechanisms of the microbial communities associated with roots.",
"study-name": "Global patterns of microbial diversity associated with eelgrass, Zostera marina",
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"study-abstract": "Charachterization of the microbiome in the roots of Arabidopsis plants growing in agar plates. Plants were germinated in plates with one of two phosphate conditions (+Pi or -Pi), and then transfered to a new plate with one of two Pi concentrations (100uM or 30uM). The plate of the second phosphate treatment was also inoculated with one of 25 synthetic bacterial communities, or kept under axenic conditions. The bacterial synthetic communities were made from pairs of bacterial blocks, were each block is made of 8-9 individual bacterial strains.",
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"study-abstract": "Feedback between plant species and the soil mycorrhizal fungi (biotic agents) shapes interspecific plant interactions, but it remains uncertain whether its effects are an essential component of plant community development. Two most dominant mycorrhizal types in temperate forests, arbuscular mycorrhizal and ectomycorrhizal plant species, can drive distinct dynamics in which the composition of the fungal community changes due to associations with plant community composition, and these changes differentially feed back on plant growth through the effects of (i) plant-fungus compatibility and (ii) common fungal networks. Here we investigate how plant community development is linked with mycorrhizal types, contrasting the effects of arbuscular mycorrhizal (AM) versus ectomycorrhizal (EcM) associations on seedling establishment. By simulating the scenario where established tree community modifies the soil fungal component (i.e., AM versus EcM inocula) and alters the competitive environment for new seedlings, we found that competition for soil nutrients influenced seedling establishment. The results showed that compatible seedlings had significantly greater leaf and root biomasses than incompatible seedlings, a benefit from the presence of established competitors through enhancing positive nutrient feedbacks. While plant-soil feedback mediated tree-seedling interactions for both AM and EcM associations, the estimated compatibility effects were more positive for EcM relative to AM associations. Notably, this coincided with the more pronounced sharing of fungal species and more structured formation of common fungal network in EcM systems compared to AM systems. Together these results suggest the link between seedling establishment and mycorrhizal functional differentiation.",
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"study-abstract": "Amplicon-based sequencing was used to examine the bacteria, fungi, and oomycetes associated with soils collected from almond orchards throughout the central valley of California. Later, peach seedlings were grown in these soils in a greenhouse, and amplicon sequencing was used to examine the root-associated microbial community.",
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"study-abstract": "To investigate the effects of soil disinfection treatments on the bacterial community composition and diversity adhering to the apple roots",
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"study-abstract": "Using ITS amplicon sequencing, structure and diversity of the root-associated fungal community of Ilex paraguariensis St. Hil (Yerba Mate) was investigated in a pot experiment in Argentina.",
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"study-abstract": "Using ITS amplicon sequencing, structure and diversity of the root-associated fungal communities of Ilex paraguariensis St. Hil (Yerba Mate) was investigated in different plantations from Argentina.",
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"study-abstract": "As part of the European Space Agency MELiSSA project, the effects of Myco Madness, a commercial combination of plant growth-promoting organisms, on the microbial communities of four common four crops (durum wheat, bread wheat, potato, soybean) cultivated in hydroponics was assessed. Small relative amounts (<0.5%) of successful infestation of plant root zone microbiome by Myco Madness PGPOs resulted in important changes in the composition of these communities. The dynamics of root zone communities were also followed over time. These results suggest that the microbial communities associated with hydroponic nutrient solutions are affected by plant developmental stage-associated changes in root exudation patterns.",
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